Starting phenix.real_space_refine on Sun Sep 13 07:31:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9y90_72686/09_2026/9y90_72686.cif Found real_map, /net/cci-nas-00/data/ceres_data/9y90_72686/09_2026/9y90_72686.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9y90_72686/09_2026/9y90_72686.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9y90_72686/09_2026/9y90_72686.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9y90_72686/09_2026/9y90_72686.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9y90_72686/09_2026/9y90_72686.map" } resolution = 3.43 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.015 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 138 5.16 5 C 13194 2.51 5 N 3534 2.21 5 O 4296 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 53 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 21162 Number of models: 1 Model: "" Number of chains: 51 Chain: "F" Number of atoms: 995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 995 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "I" Number of atoms: 797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 797 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "J" Number of atoms: 1139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1139 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 2, 'TRANS': 140} Chain breaks: 1 Chain: "K" Number of atoms: 3551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3551 Classifications: {'peptide': 451} Link IDs: {'PTRANS': 22, 'TRANS': 428} Chain breaks: 2 Chain: "A" Number of atoms: 995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 995 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "B" Number of atoms: 797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 797 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "C" Number of atoms: 1139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1139 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 2, 'TRANS': 140} Chain breaks: 1 Chain: "D" Number of atoms: 3551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3551 Classifications: {'peptide': 451} Link IDs: {'PTRANS': 22, 'TRANS': 428} Chain breaks: 2 Chain: "E" Number of atoms: 995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 995 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "G" Number of atoms: 797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 797 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "H" Number of atoms: 1139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1139 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 2, 'TRANS': 140} Chain breaks: 1 Chain: "L" Number of atoms: 3551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3551 Classifications: {'peptide': 451} Link IDs: {'PTRANS': 22, 'TRANS': 428} Chain breaks: 2 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} 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: "Q" 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: "R" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 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: 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: "V" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "W" 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: "X" 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: "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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} 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: 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: "c" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "d" 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: "e" 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: "f" 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: "g" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "h" 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: "i" 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: "j" 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: "k" 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: "l" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} 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: "m" 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: "n" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "o" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "p" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "r" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "s" 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: "J" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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: "K" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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: "D" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "H" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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: "L" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 4.71, per 1000 atoms: 0.22 Number of scatterers: 21162 At special positions: 0 Unit cell: (151.62, 146.205, 123.462, 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 138 16.00 O 4296 8.00 N 3534 7.00 C 13194 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 92 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.03 Simple disulfide: pdb=" SG CYS J 598 " - pdb=" SG CYS J 604 " distance=2.03 Simple disulfide: pdb=" SG CYS J 605 " - pdb=" SG CYS K 501 " distance=2.03 Simple disulfide: pdb=" SG CYS K 54 " - pdb=" SG CYS K 74 " distance=2.03 Simple disulfide: pdb=" SG CYS K 119 " - pdb=" SG CYS K 205 " distance=2.03 Simple disulfide: pdb=" SG CYS K 126 " - pdb=" SG CYS K 196 " distance=2.03 Simple disulfide: pdb=" SG CYS K 131 " - pdb=" SG CYS K 157 " distance=2.03 Simple disulfide: pdb=" SG CYS K 201 " - pdb=" SG CYS K 433 " distance=2.04 Simple disulfide: pdb=" SG CYS K 218 " - pdb=" SG CYS K 247 " distance=2.04 Simple disulfide: pdb=" SG CYS K 228 " - pdb=" SG CYS K 239 " distance=2.03 Simple disulfide: pdb=" SG CYS K 296 " - pdb=" SG CYS K 331 " distance=2.05 Simple disulfide: pdb=" SG CYS K 296 " - pdb=" SG CYS K 445 " distance=2.05 Simple disulfide: pdb=" SG CYS K 378 " - pdb=" SG CYS K 445 " distance=2.04 Simple disulfide: pdb=" SG CYS K 385 " - pdb=" SG CYS K 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 92 " distance=2.04 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.02 Simple disulfide: pdb=" SG CYS C 598 " - pdb=" SG CYS C 604 " distance=2.02 Simple disulfide: pdb=" SG CYS C 605 " - pdb=" SG CYS D 501 " distance=2.03 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 74 " distance=2.03 Simple disulfide: pdb=" SG CYS D 119 " - pdb=" SG CYS D 205 " distance=2.03 Simple disulfide: pdb=" SG CYS D 126 " - pdb=" SG CYS D 196 " distance=2.04 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 157 " distance=2.03 Simple disulfide: pdb=" SG CYS D 201 " - pdb=" SG CYS D 433 " distance=2.03 Simple disulfide: pdb=" SG CYS D 218 " - pdb=" SG CYS D 247 " distance=2.03 Simple disulfide: pdb=" SG CYS D 228 " - pdb=" SG CYS D 239 " distance=2.03 Simple disulfide: pdb=" SG CYS D 296 " - pdb=" SG CYS D 331 " distance=2.05 Simple disulfide: pdb=" SG CYS D 296 " - pdb=" SG CYS D 445 " distance=2.05 Simple disulfide: pdb=" SG CYS D 378 " - pdb=" SG CYS D 445 " distance=2.04 Simple disulfide: pdb=" SG CYS D 385 " - pdb=" SG CYS D 418 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 92 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.02 Simple disulfide: pdb=" SG CYS H 598 " - pdb=" SG CYS H 604 " distance=2.03 Simple disulfide: pdb=" SG CYS H 605 " - pdb=" SG CYS L 501 " distance=2.03 Simple disulfide: pdb=" SG CYS L 54 " - pdb=" SG CYS L 74 " distance=2.03 Simple disulfide: pdb=" SG CYS L 119 " - pdb=" SG CYS L 205 " distance=2.03 Simple disulfide: pdb=" SG CYS L 126 " - pdb=" SG CYS L 196 " distance=2.03 Simple disulfide: pdb=" SG CYS L 131 " - pdb=" SG CYS L 157 " distance=2.03 Simple disulfide: pdb=" SG CYS L 201 " - pdb=" SG CYS L 433 " distance=2.03 Simple disulfide: pdb=" SG CYS L 218 " - pdb=" SG CYS L 247 " distance=2.03 Simple disulfide: pdb=" SG CYS L 228 " - pdb=" SG CYS L 239 " distance=2.03 Simple disulfide: pdb=" SG CYS L 296 " - pdb=" SG CYS L 331 " distance=2.05 Simple disulfide: pdb=" SG CYS L 296 " - pdb=" SG CYS L 445 " distance=2.05 Simple disulfide: pdb=" SG CYS L 378 " - pdb=" SG CYS L 445 " distance=2.04 Simple disulfide: pdb=" SG CYS L 385 " - pdb=" SG CYS L 418 " 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 ALPHA1-3 " BMA P 3 " - " MAN P 4 " " BMA R 3 " - " MAN R 4 " " BMA V 3 " - " MAN V 4 " " BMA a 3 " - " MAN a 4 " " BMA c 3 " - " MAN c 4 " " BMA g 3 " - " MAN g 4 " " BMA l 3 " - " MAN l 4 " " BMA n 3 " - " MAN n 4 " " BMA r 3 " - " MAN r 4 " ALPHA1-6 " BMA R 3 " - " MAN R 5 " " BMA V 3 " - " MAN V 5 " " BMA c 3 " - " MAN c 5 " " BMA g 3 " - " MAN g 5 " " BMA n 3 " - " MAN n 5 " " BMA r 3 " - " MAN r 5 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " 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 V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " 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 b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " " NAG h 1 " - " NAG h 2 " " NAG h 2 " - " BMA h 3 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG l 2 " - " BMA l 3 " " NAG m 1 " - " NAG m 2 " " NAG m 2 " - " BMA m 3 " " NAG n 1 " - " NAG n 2 " " NAG n 2 " - " BMA n 3 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 2 " " NAG q 1 " - " NAG q 2 " " NAG r 1 " - " NAG r 2 " " NAG r 2 " - " BMA r 3 " " NAG s 1 " - " NAG s 2 " " NAG s 2 " - " BMA s 3 " NAG-ASN " NAG C 701 " - " ASN C 611 " " NAG C 702 " - " ASN C 637 " " NAG C 703 " - " ASN C 618 " " NAG D 601 " - " ASN D 88 " " NAG D 602 " - " ASN D 133 " " NAG D 603 " - " ASN D 301 " " NAG D 604 " - " ASN D 339 " " NAG D 605 " - " ASN D 234 " " NAG D 606 " - " ASN D 355 " " NAG D 607 " - " ASN D 137 " " NAG D 608 " - " ASN D 462 " " NAG H 701 " - " ASN H 611 " " NAG H 702 " - " ASN H 637 " " NAG H 703 " - " ASN H 618 " " NAG J 701 " - " ASN J 611 " " NAG J 702 " - " ASN J 637 " " NAG J 703 " - " ASN J 618 " " NAG K 601 " - " ASN K 88 " " NAG K 602 " - " ASN K 133 " " NAG K 603 " - " ASN K 301 " " NAG K 604 " - " ASN K 339 " " NAG K 605 " - " ASN K 234 " " NAG K 606 " - " ASN K 355 " " NAG K 607 " - " ASN K 137 " " NAG K 608 " - " ASN K 462 " " NAG L 601 " - " ASN L 88 " " NAG L 602 " - " ASN L 133 " " NAG L 603 " - " ASN L 301 " " NAG L 604 " - " ASN L 339 " " NAG L 605 " - " ASN L 234 " " NAG L 606 " - " ASN L 355 " " NAG L 607 " - " ASN L 137 " " NAG L 608 " - " ASN L 462 " " NAG M 1 " - " ASN K 160 " " NAG N 1 " - " ASN K 197 " " NAG O 1 " - " ASN K 295 " " NAG P 1 " - " ASN K 363 " " NAG Q 1 " - " ASN K 386 " " NAG R 1 " - " ASN K 262 " " NAG S 1 " - " ASN K 448 " " NAG T 1 " - " ASN K 332 " " NAG U 1 " - " ASN K 392 " " NAG V 1 " - " ASN K 276 " " NAG W 1 " - " ASN K 156 " " NAG X 1 " - " ASN D 160 " " NAG Y 1 " - " ASN D 197 " " NAG Z 1 " - " ASN D 295 " " NAG a 1 " - " ASN D 363 " " NAG b 1 " - " ASN D 386 " " NAG c 1 " - " ASN D 262 " " NAG d 1 " - " ASN D 448 " " NAG e 1 " - " ASN D 332 " " NAG f 1 " - " ASN D 392 " " NAG g 1 " - " ASN D 276 " " NAG h 1 " - " ASN D 156 " " NAG i 1 " - " ASN L 160 " " NAG j 1 " - " ASN L 197 " " NAG k 1 " - " ASN L 295 " " NAG l 1 " - " ASN L 363 " " NAG m 1 " - " ASN L 386 " " NAG n 1 " - " ASN L 262 " " NAG o 1 " - " ASN L 448 " " NAG p 1 " - " ASN L 332 " " NAG q 1 " - " ASN L 392 " " NAG r 1 " - " ASN L 276 " " NAG s 1 " - " ASN L 156 " Time building additional restraints: 1.92 Conformation dependent library (CDL) restraints added in 786.6 milliseconds 4842 Ramachandran restraints generated. 2421 Oldfield, 0 Emsley, 2421 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4578 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 53 sheets defined 23.3% alpha, 28.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'F' and resid 28 through 30 No H-bonds generated for 'chain 'F' and resid 28 through 30' Processing helix chain 'F' and resid 61 through 64 removed outlier: 3.739A pdb=" N GLN F 64 " --> pdb=" O HIS F 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 61 through 64' Processing helix chain 'F' and resid 83 through 87 removed outlier: 3.640A pdb=" N THR F 87 " --> pdb=" O SER F 84 " (cutoff:3.500A) Processing helix chain 'F' and resid 98 through 100B removed outlier: 3.550A pdb=" N GLN F 100B" --> pdb=" O TYR F 99 " (cutoff:3.500A) Processing helix chain 'J' and resid 523 through 527 removed outlier: 4.537A pdb=" N GLY J 527 " --> pdb=" O GLY J 524 " (cutoff:3.500A) Processing helix chain 'J' and resid 529 through 534 Processing helix chain 'J' and resid 536 through 544 removed outlier: 4.392A pdb=" N GLN J 540 " --> pdb=" O THR J 536 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ASN J 543 " --> pdb=" O VAL J 539 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU J 544 " --> pdb=" O GLN J 540 " (cutoff:3.500A) Processing helix chain 'J' and resid 547 through 558 removed outlier: 3.950A pdb=" N SER J 553 " --> pdb=" O GLN J 550 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASN J 554 " --> pdb=" O GLN J 551 " (cutoff:3.500A) Processing helix chain 'J' and resid 569 through 596 removed outlier: 3.542A pdb=" N ILE J 573 " --> pdb=" O THR J 569 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ALA J 578 " --> pdb=" O LYS J 574 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASP J 589 " --> pdb=" O ARG J 585 " (cutoff:3.500A) Processing helix chain 'J' and resid 611 through 615 Processing helix chain 'J' and resid 627 through 636 removed outlier: 3.851A pdb=" N LYS J 633 " --> pdb=" O LEU J 629 " (cutoff:3.500A) Processing helix chain 'J' and resid 638 through 664 removed outlier: 3.533A pdb=" N SER J 649 " --> pdb=" O LEU J 645 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLN J 650 " --> pdb=" O LEU J 646 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ASN J 651 " --> pdb=" O GLU J 647 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ASN J 656 " --> pdb=" O GLN J 652 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU J 660 " --> pdb=" O ASN J 656 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N LEU J 663 " --> pdb=" O ASP J 659 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ASP J 664 " --> pdb=" O LEU J 660 " (cutoff:3.500A) Processing helix chain 'K' and resid 57 through 64 Processing helix chain 'K' and resid 70 through 74 Processing helix chain 'K' and resid 99 through 117 removed outlier: 3.550A pdb=" N LEU K 116 " --> pdb=" O TRP K 112 " (cutoff:3.500A) Processing helix chain 'K' and resid 123 through 126 Processing helix chain 'K' and resid 334 through 354 removed outlier: 3.537A pdb=" N GLU K 340 " --> pdb=" O ALA K 336 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLY K 343 " --> pdb=" O ASN K 339 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS K 347 " --> pdb=" O GLY K 343 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLN K 348 " --> pdb=" O LYS K 344 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYS K 351 " --> pdb=" O LYS K 347 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N HIS K 352 " --> pdb=" O GLN K 348 " (cutoff:3.500A) Processing helix chain 'K' and resid 368 through 373 removed outlier: 3.731A pdb=" N THR K 373 " --> pdb=" O LEU K 369 " (cutoff:3.500A) Processing helix chain 'K' and resid 387 through 390 Processing helix chain 'K' and resid 474 through 482 removed outlier: 4.404A pdb=" N TRP K 479 " --> pdb=" O ARG K 476 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ARG K 480 " --> pdb=" O ASP K 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 30 No H-bonds generated for 'chain 'A' and resid 28 through 30' Processing helix chain 'A' and resid 61 through 64 removed outlier: 3.733A pdb=" N GLN A 64 " --> pdb=" O HIS A 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 61 through 64' Processing helix chain 'A' and resid 83 through 87 removed outlier: 3.778A pdb=" N THR A 87 " --> pdb=" O SER A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 100B Processing helix chain 'C' and resid 529 through 534 Processing helix chain 'C' and resid 537 through 544 removed outlier: 4.211A pdb=" N ASN C 543 " --> pdb=" O VAL C 539 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU C 544 " --> pdb=" O GLN C 540 " (cutoff:3.500A) Processing helix chain 'C' and resid 547 through 557 removed outlier: 3.893A pdb=" N SER C 553 " --> pdb=" O GLN C 550 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ASN C 554 " --> pdb=" O GLN C 551 " (cutoff:3.500A) Processing helix chain 'C' and resid 569 through 595 removed outlier: 3.872A pdb=" N GLN C 577 " --> pdb=" O ILE C 573 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA C 578 " --> pdb=" O LYS C 574 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASP C 589 " --> pdb=" O ARG C 585 " (cutoff:3.500A) Processing helix chain 'C' and resid 611 through 615 removed outlier: 3.625A pdb=" N SER C 615 " --> pdb=" O SER C 612 " (cutoff:3.500A) Processing helix chain 'C' and resid 627 through 635 removed outlier: 3.626A pdb=" N LYS C 633 " --> pdb=" O LEU C 629 " (cutoff:3.500A) Processing helix chain 'C' and resid 638 through 662 removed outlier: 3.651A pdb=" N SER C 649 " --> pdb=" O LEU C 645 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ASN C 651 " --> pdb=" O GLU C 647 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLN C 658 " --> pdb=" O GLU C 654 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 64 removed outlier: 3.610A pdb=" N ALA D 60 " --> pdb=" O ASP D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 117 removed outlier: 4.259A pdb=" N GLU D 102 " --> pdb=" O ASN D 98 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU D 116 " --> pdb=" O TRP D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 126 Processing helix chain 'D' and resid 334 through 354 removed outlier: 3.583A pdb=" N GLU D 340 " --> pdb=" O ALA D 336 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LYS D 347 " --> pdb=" O GLY D 343 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLN D 348 " --> pdb=" O LYS D 344 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS D 351 " --> pdb=" O LYS D 347 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N HIS D 352 " --> pdb=" O GLN D 348 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 373 removed outlier: 3.728A pdb=" N THR D 373 " --> pdb=" O LEU D 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 381 Processing helix chain 'D' and resid 387 through 390 Processing helix chain 'D' and resid 475 through 480 Processing helix chain 'E' and resid 28 through 30 No H-bonds generated for 'chain 'E' and resid 28 through 30' Processing helix chain 'E' and resid 61 through 64 removed outlier: 3.705A pdb=" N GLN E 64 " --> pdb=" O HIS E 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 61 through 64' Processing helix chain 'E' and resid 83 through 87 removed outlier: 3.696A pdb=" N THR E 87 " --> pdb=" O SER E 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 100B Processing helix chain 'H' and resid 523 through 527 removed outlier: 4.467A pdb=" N GLY H 527 " --> pdb=" O GLY H 524 " (cutoff:3.500A) Processing helix chain 'H' and resid 529 through 534 Processing helix chain 'H' and resid 537 through 544 removed outlier: 4.242A pdb=" N ASN H 543 " --> pdb=" O VAL H 539 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU H 544 " --> pdb=" O GLN H 540 " (cutoff:3.500A) Processing helix chain 'H' and resid 547 through 558 removed outlier: 4.285A pdb=" N SER H 553 " --> pdb=" O GLN H 550 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ASN H 554 " --> pdb=" O GLN H 551 " (cutoff:3.500A) Processing helix chain 'H' and resid 569 through 596 removed outlier: 4.354A pdb=" N ALA H 578 " --> pdb=" O LYS H 574 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASP H 589 " --> pdb=" O ARG H 585 " (cutoff:3.500A) Processing helix chain 'H' and resid 611 through 615 Processing helix chain 'H' and resid 627 through 636 removed outlier: 3.997A pdb=" N LYS H 633 " --> pdb=" O LEU H 629 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLU H 634 " --> pdb=" O GLN H 630 " (cutoff:3.500A) Processing helix chain 'H' and resid 638 through 664 removed outlier: 3.553A pdb=" N ILE H 642 " --> pdb=" O TYR H 638 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLY H 644 " --> pdb=" O GLN H 640 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLN H 650 " --> pdb=" O LEU H 646 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ASN H 651 " --> pdb=" O GLU H 647 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU H 660 " --> pdb=" O ASN H 656 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N LEU H 663 " --> pdb=" O ASP H 659 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ASP H 664 " --> pdb=" O LEU H 660 " (cutoff:3.500A) Processing helix chain 'L' and resid 59 through 64 Processing helix chain 'L' and resid 70 through 74 Processing helix chain 'L' and resid 98 through 117 removed outlier: 4.225A pdb=" N GLU L 102 " --> pdb=" O ASN L 98 " (cutoff:3.500A) Processing helix chain 'L' and resid 123 through 126 Processing helix chain 'L' and resid 195 through 198 Processing helix chain 'L' and resid 334 through 354 removed outlier: 3.795A pdb=" N LYS L 347 " --> pdb=" O GLY L 343 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLN L 348 " --> pdb=" O LYS L 344 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LYS L 351 " --> pdb=" O LYS L 347 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N HIS L 352 " --> pdb=" O GLN L 348 " (cutoff:3.500A) Processing helix chain 'L' and resid 368 through 373 removed outlier: 3.583A pdb=" N THR L 373 " --> pdb=" O LEU L 369 " (cutoff:3.500A) Processing helix chain 'L' and resid 386 through 390 removed outlier: 4.538A pdb=" N GLY L 389 " --> pdb=" O ASN L 386 " (cutoff:3.500A) Processing helix chain 'L' and resid 474 through 482 removed outlier: 3.612A pdb=" N ASP L 477 " --> pdb=" O ASP L 474 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N TRP L 479 " --> pdb=" O ARG L 476 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARG L 480 " --> pdb=" O ASP L 477 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'F' and resid 3 through 6 removed outlier: 3.705A pdb=" N VAL F 18 " --> pdb=" O LEU F 82 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR F 70 " --> pdb=" O TYR F 79 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 10 through 12 removed outlier: 3.673A pdb=" N GLU F 10 " --> pdb=" O LEU F 108 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N VAL F 34 " --> pdb=" O TRP F 50 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N TRP F 50 " --> pdb=" O VAL F 34 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N TRP F 36 " --> pdb=" O MET F 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'I' and resid 5 through 6 Processing sheet with id=AA4, first strand: chain 'I' and resid 53 through 54 removed outlier: 6.523A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'I' and resid 53 through 54 removed outlier: 6.523A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'J' and resid 603 through 609 removed outlier: 7.907A pdb=" N CYS J 604 " --> pdb=" O TYR K 40 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N TYR K 40 " --> pdb=" O CYS J 604 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N THR J 606 " --> pdb=" O VAL K 38 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N VAL K 38 " --> pdb=" O THR J 606 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N VAL J 608 " --> pdb=" O VAL K 36 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N TRP K 35 " --> pdb=" O THR K 499 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N THR K 499 " --> pdb=" O TRP K 35 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'K' and resid 45 through 47 removed outlier: 3.989A pdb=" N ILE K 225 " --> pdb=" O VAL K 245 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N VAL K 242 " --> pdb=" O LEU K 86 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'K' and resid 53 through 55 Processing sheet with id=AA9, first strand: chain 'K' and resid 91 through 94 removed outlier: 3.686A pdb=" N GLU K 91 " --> pdb=" O CYS K 239 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N PHE K 93 " --> pdb=" O GLY K 237 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLY K 237 " --> pdb=" O PHE K 93 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'K' and resid 120 through 121 removed outlier: 4.132A pdb=" N VAL K 120 " --> pdb=" O GLN K 203 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N THR K 202 " --> pdb=" O TYR K 435 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 169 through 177 Processing sheet with id=AB3, first strand: chain 'K' and resid 259 through 261 removed outlier: 6.688A pdb=" N LEU K 260 " --> pdb=" O THR K 450 " (cutoff:3.500A) removed outlier: 9.302A pdb=" N VAL K 446 " --> pdb=" O VAL K 292 " (cutoff:3.500A) removed outlier: 10.360A pdb=" N VAL K 292 " --> pdb=" O VAL K 446 " (cutoff:3.500A) removed outlier: 8.831A pdb=" N ASN K 448 " --> pdb=" O THR K 290 " (cutoff:3.500A) removed outlier: 10.403A pdb=" N THR K 290 " --> pdb=" O ASN K 448 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N THR K 450 " --> pdb=" O PHE K 288 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'K' and resid 259 through 261 removed outlier: 6.688A pdb=" N LEU K 260 " --> pdb=" O THR K 450 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'K' and resid 298 through 302 removed outlier: 7.191A pdb=" N ASN K 300 " --> pdb=" O ILE K 443 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N ILE K 443 " --> pdb=" O ASN K 300 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'K' and resid 304 through 312 removed outlier: 6.900A pdb=" N GLN K 315 " --> pdb=" O ILE K 309 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'K' and resid 329 through 333 removed outlier: 4.194A pdb=" N ALA K 329 " --> pdb=" O CYS K 418 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N CYS K 331 " --> pdb=" O LEU K 416 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LYS K 421 " --> pdb=" O PHE K 382 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N PHE K 382 " --> pdb=" O LYS K 421 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'K' and resid 359 through 361 removed outlier: 3.817A pdb=" N SER K 393 " --> pdb=" O PHE K 361 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 3 through 6 removed outlier: 3.866A pdb=" N VAL A 18 " --> pdb=" O LEU A 82 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR A 70 " --> pdb=" O TYR A 79 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 10 through 12 removed outlier: 3.607A pdb=" N GLU A 10 " --> pdb=" O LEU A 108 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N VAL A 34 " --> pdb=" O TRP A 50 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N TRP A 50 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N TRP A 36 " --> pdb=" O MET A 48 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 19 through 22 Processing sheet with id=AC3, first strand: chain 'B' and resid 53 through 54 removed outlier: 6.464A pdb=" N TRP B 35 " --> pdb=" O LEU B 47 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 603 through 609 removed outlier: 7.876A pdb=" N CYS C 604 " --> pdb=" O TYR D 40 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N TYR D 40 " --> pdb=" O CYS C 604 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N THR C 606 " --> pdb=" O VAL D 38 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N VAL D 38 " --> pdb=" O THR C 606 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N VAL C 608 " --> pdb=" O VAL D 36 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 45 through 47 removed outlier: 3.542A pdb=" N ILE D 225 " --> pdb=" O VAL D 245 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 53 through 55 Processing sheet with id=AC7, first strand: chain 'D' and resid 66 through 67 removed outlier: 7.222A pdb=" N HIS D 66 " --> pdb=" O SER D 209 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'D' and resid 91 through 94 removed outlier: 3.745A pdb=" N GLU D 91 " --> pdb=" O CYS D 239 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N PHE D 93 " --> pdb=" O GLY D 237 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLY D 237 " --> pdb=" O PHE D 93 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 120 through 121 removed outlier: 4.129A pdb=" N VAL D 120 " --> pdb=" O GLN D 203 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N THR D 202 " --> pdb=" O TYR D 435 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 154 through 162 Processing sheet with id=AD2, first strand: chain 'D' and resid 181 through 183 Processing sheet with id=AD3, first strand: chain 'D' and resid 259 through 261 removed outlier: 6.648A pdb=" N LEU D 260 " --> pdb=" O THR D 450 " (cutoff:3.500A) removed outlier: 9.430A pdb=" N VAL D 446 " --> pdb=" O VAL D 292 " (cutoff:3.500A) removed outlier: 10.498A pdb=" N VAL D 292 " --> pdb=" O VAL D 446 " (cutoff:3.500A) removed outlier: 9.151A pdb=" N ASN D 448 " --> pdb=" O THR D 290 " (cutoff:3.500A) removed outlier: 10.600A pdb=" N THR D 290 " --> pdb=" O ASN D 448 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N THR D 450 " --> pdb=" O PHE D 288 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 259 through 261 removed outlier: 6.648A pdb=" N LEU D 260 " --> pdb=" O THR D 450 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 315 through 323 removed outlier: 6.920A pdb=" N GLN D 315 " --> pdb=" O ILE D 309 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N THR D 303 " --> pdb=" O GLY D 321 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N ILE D 322 " --> pdb=" O ASN D 301 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N ASN D 301 " --> pdb=" O ILE D 322 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N ASN D 300 " --> pdb=" O ILE D 443 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N ILE D 443 " --> pdb=" O ASN D 300 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 329 through 333 removed outlier: 4.210A pdb=" N ALA D 329 " --> pdb=" O CYS D 418 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N CYS D 331 " --> pdb=" O LEU D 416 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYS D 421 " --> pdb=" O PHE D 382 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N PHE D 382 " --> pdb=" O LYS D 421 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N PHE D 376 " --> pdb=" O PHE D 383 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 359 through 361 removed outlier: 3.573A pdb=" N ILE D 359 " --> pdb=" O TRP D 395 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N SER D 393 " --> pdb=" O PHE D 361 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 3 through 6 removed outlier: 3.875A pdb=" N VAL E 18 " --> pdb=" O LEU E 82 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR E 70 " --> pdb=" O TYR E 79 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.633A pdb=" N GLU E 10 " --> pdb=" O LEU E 108 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N VAL E 34 " --> pdb=" O TRP E 50 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N TRP E 50 " --> pdb=" O VAL E 34 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N TRP E 36 " --> pdb=" O MET E 48 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 19 through 22 Processing sheet with id=AE2, first strand: chain 'G' and resid 53 through 54 removed outlier: 6.404A pdb=" N TRP G 35 " --> pdb=" O LEU G 47 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 53 through 54 removed outlier: 6.404A pdb=" N TRP G 35 " --> pdb=" O LEU G 47 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 603 through 609 removed outlier: 5.134A pdb=" N VAL L 36 " --> pdb=" O THR H 606 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N TRP L 35 " --> pdb=" O THR L 499 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N THR L 499 " --> pdb=" O TRP L 35 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'L' and resid 45 through 47 removed outlier: 3.581A pdb=" N ILE L 225 " --> pdb=" O VAL L 245 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N VAL L 242 " --> pdb=" O LEU L 86 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'L' and resid 53 through 55 Processing sheet with id=AE7, first strand: chain 'L' and resid 91 through 94 removed outlier: 3.627A pdb=" N GLU L 91 " --> pdb=" O CYS L 239 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N PHE L 93 " --> pdb=" O GLY L 237 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLY L 237 " --> pdb=" O PHE L 93 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'L' and resid 120 through 121 removed outlier: 4.149A pdb=" N VAL L 120 " --> pdb=" O GLN L 203 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N THR L 202 " --> pdb=" O TYR L 435 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'L' and resid 129 through 130 Processing sheet with id=AF1, first strand: chain 'L' and resid 154 through 162 Processing sheet with id=AF2, first strand: chain 'L' and resid 259 through 261 removed outlier: 6.485A pdb=" N LEU L 260 " --> pdb=" O THR L 450 " (cutoff:3.500A) removed outlier: 9.319A pdb=" N VAL L 446 " --> pdb=" O VAL L 292 " (cutoff:3.500A) removed outlier: 10.510A pdb=" N VAL L 292 " --> pdb=" O VAL L 446 " (cutoff:3.500A) removed outlier: 9.097A pdb=" N ASN L 448 " --> pdb=" O THR L 290 " (cutoff:3.500A) removed outlier: 10.559A pdb=" N THR L 290 " --> pdb=" O ASN L 448 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N THR L 450 " --> pdb=" O PHE L 288 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'L' and resid 259 through 261 removed outlier: 6.485A pdb=" N LEU L 260 " --> pdb=" O THR L 450 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'L' and resid 298 through 302 removed outlier: 7.198A pdb=" N ASN L 300 " --> pdb=" O ILE L 443 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N ILE L 443 " --> pdb=" O ASN L 300 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'L' and resid 304 through 312 removed outlier: 6.939A pdb=" N GLN L 315 " --> pdb=" O ILE L 309 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'L' and resid 331 through 333 removed outlier: 3.627A pdb=" N CYS L 331 " --> pdb=" O LEU L 416 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'L' and resid 359 through 360 Processing sheet with id=AF8, first strand: chain 'L' and resid 374 through 377 removed outlier: 3.527A pdb=" N PHE L 376 " --> pdb=" O PHE L 383 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N PHE L 382 " --> pdb=" O LYS L 421 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS L 421 " --> pdb=" O PHE L 382 " (cutoff:3.500A) 679 hydrogen bonds defined for protein. 1638 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: 3.76 Time building geometry restraints manager: 2.44 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: 6545 1.35 - 1.47: 5748 1.47 - 1.60: 9097 1.60 - 1.73: 0 1.73 - 1.86: 192 Bond restraints: 21582 Sorted by residual: bond pdb=" C CYS K 218 " pdb=" N ALA K 219 " ideal model delta sigma weight residual 1.329 1.400 -0.072 1.86e-02 2.89e+03 1.49e+01 bond pdb=" CA ASN D 392 " pdb=" C ASN D 392 " ideal model delta sigma weight residual 1.533 1.511 0.022 9.60e-03 1.09e+04 5.11e+00 bond pdb=" CA ASN H 625 " pdb=" CB ASN H 625 " ideal model delta sigma weight residual 1.530 1.555 -0.025 1.39e-02 5.18e+03 3.33e+00 bond pdb=" CB CYS D 296 " pdb=" SG CYS D 296 " ideal model delta sigma weight residual 1.808 1.748 0.060 3.30e-02 9.18e+02 3.27e+00 bond pdb=" CB CYS K 296 " pdb=" SG CYS K 296 " ideal model delta sigma weight residual 1.808 1.749 0.059 3.30e-02 9.18e+02 3.20e+00 ... (remaining 21577 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.98: 28443 1.98 - 3.96: 721 3.96 - 5.94: 100 5.94 - 7.91: 8 7.91 - 9.89: 2 Bond angle restraints: 29274 Sorted by residual: angle pdb=" N ASN G 30 " pdb=" CA ASN G 30 " pdb=" C ASN G 30 " ideal model delta sigma weight residual 107.32 117.21 -9.89 1.65e+00 3.67e-01 3.59e+01 angle pdb=" N ASP G 31 " pdb=" CA ASP G 31 " pdb=" C ASP G 31 " ideal model delta sigma weight residual 110.80 120.24 -9.44 2.13e+00 2.20e-01 1.97e+01 angle pdb=" N ILE J 622 " pdb=" CA ILE J 622 " pdb=" C ILE J 622 " ideal model delta sigma weight residual 113.71 109.90 3.81 9.50e-01 1.11e+00 1.60e+01 angle pdb=" N ILE C 622 " pdb=" CA ILE C 622 " pdb=" C ILE C 622 " ideal model delta sigma weight residual 112.12 108.98 3.14 8.40e-01 1.42e+00 1.39e+01 angle pdb=" N GLU K 268 " pdb=" CA GLU K 268 " pdb=" CB GLU K 268 " ideal model delta sigma weight residual 114.17 109.96 4.21 1.14e+00 7.69e-01 1.36e+01 ... (remaining 29269 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 12934 17.95 - 35.89: 1206 35.89 - 53.84: 335 53.84 - 71.78: 99 71.78 - 89.73: 27 Dihedral angle restraints: 14601 sinusoidal: 7509 harmonic: 7092 Sorted by residual: dihedral pdb=" CB CYS L 119 " pdb=" SG CYS L 119 " pdb=" SG CYS L 205 " pdb=" CB CYS L 205 " ideal model delta sinusoidal sigma weight residual -86.00 -140.85 54.85 1 1.00e+01 1.00e-02 4.07e+01 dihedral pdb=" CA ASN G 30 " pdb=" C ASN G 30 " pdb=" N ASP G 31 " pdb=" CA ASP G 31 " ideal model delta harmonic sigma weight residual 180.00 148.45 31.55 0 5.00e+00 4.00e-02 3.98e+01 dihedral pdb=" CB CYS K 119 " pdb=" SG CYS K 119 " pdb=" SG CYS K 205 " pdb=" CB CYS K 205 " ideal model delta sinusoidal sigma weight residual -86.00 -139.69 53.69 1 1.00e+01 1.00e-02 3.92e+01 ... (remaining 14598 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 3202 0.069 - 0.138: 388 0.138 - 0.207: 35 0.207 - 0.276: 1 0.276 - 0.345: 1 Chirality restraints: 3627 Sorted by residual: chirality pdb=" C1 NAG f 2 " pdb=" O4 NAG f 1 " pdb=" C2 NAG f 2 " pdb=" O5 NAG f 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-02 2.50e+03 7.37e+01 chirality pdb=" C1 NAG f 1 " pdb=" ND2 ASN D 392 " pdb=" C2 NAG f 1 " pdb=" O5 NAG f 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.75 0.35 2.00e-01 2.50e+01 2.98e+00 chirality pdb=" C1 NAG L 604 " pdb=" ND2 ASN L 339 " pdb=" C2 NAG L 604 " pdb=" O5 NAG L 604 " both_signs ideal model delta sigma weight residual False -2.40 -2.19 -0.21 2.00e-01 2.50e+01 1.08e+00 ... (remaining 3624 not shown) Planarity restraints: 3636 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG f 2 " 0.318 2.00e-02 2.50e+03 2.73e-01 9.34e+02 pdb=" C7 NAG f 2 " -0.077 2.00e-02 2.50e+03 pdb=" C8 NAG f 2 " 0.019 2.00e-02 2.50e+03 pdb=" N2 NAG f 2 " -0.471 2.00e-02 2.50e+03 pdb=" O7 NAG f 2 " 0.212 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG f 1 " 0.296 2.00e-02 2.50e+03 2.53e-01 7.99e+02 pdb=" C7 NAG f 1 " -0.071 2.00e-02 2.50e+03 pdb=" C8 NAG f 1 " 0.169 2.00e-02 2.50e+03 pdb=" N2 NAG f 1 " -0.443 2.00e-02 2.50e+03 pdb=" O7 NAG f 1 " 0.049 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 53 " -0.180 9.50e-02 1.11e+02 8.09e-02 4.47e+00 pdb=" NE ARG E 53 " 0.015 2.00e-02 2.50e+03 pdb=" CZ ARG E 53 " -0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG E 53 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG E 53 " -0.003 2.00e-02 2.50e+03 ... (remaining 3633 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 245 2.63 - 3.20: 19062 3.20 - 3.76: 29247 3.76 - 4.33: 41938 4.33 - 4.90: 71031 Nonbonded interactions: 161523 Sorted by model distance: nonbonded pdb=" OD2 ASP E 72 " pdb=" OG SER E 74 " model vdw 2.059 3.040 nonbonded pdb=" OD1 ASP F 72 " pdb=" OG SER F 74 " model vdw 2.086 3.040 nonbonded pdb=" OD1 ASP E 98 " pdb=" N TYR E 99 " model vdw 2.141 3.120 nonbonded pdb=" OD1 ASP A 98 " pdb=" N TYR A 99 " model vdw 2.143 3.120 nonbonded pdb=" OD1 ASP F 98 " pdb=" N TYR F 99 " model vdw 2.175 3.120 ... (remaining 161518 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 'E' selection = chain 'F' } ncs_group { reference = chain 'B' selection = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'C' selection = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'D' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'o' selection = chain 'p' selection = chain 'q' } ncs_group { reference = chain 'P' selection = chain 'a' selection = chain 'l' } ncs_group { reference = chain 'Q' selection = chain 'W' selection = chain 'b' selection = chain 'h' selection = chain 'm' selection = chain 's' } ncs_group { reference = chain 'R' selection = chain 'V' selection = chain 'c' selection = chain 'g' selection = chain 'n' selection = chain 'r' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.090 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: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 18.890 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 21756 Z= 0.183 Angle : 0.841 18.872 29751 Z= 0.419 Chirality : 0.045 0.345 3627 Planarity : 0.008 0.273 3570 Dihedral : 15.214 89.727 9888 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.37 % Allowed : 6.53 % Favored : 93.10 % Rotamer: Outliers : 2.46 % Allowed : 16.18 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.26 (0.16), residues: 2421 helix: -1.33 (0.25), residues: 381 sheet: -1.45 (0.20), residues: 669 loop : -1.55 (0.16), residues: 1371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 53 TYR 0.019 0.001 TYR D 173 PHE 0.026 0.001 PHE L 53 TRP 0.036 0.001 TRP D 35 HIS 0.005 0.001 HIS D 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.18 (21582) covalent geometry : angle 0.74665 / 0.40 (29274) SS BOND : bond 0.00764 / 0.56 ( 45) SS BOND : angle 2.24003 / 1.37 ( 90) hydrogen bonds : bond 0.26335 / 17.65 ( 654) hydrogen bonds : angle 9.69342 / 6.75 ( 1638) link_ALPHA1-3 : bond 0.01813 / 0.88 ( 9) link_ALPHA1-3 : angle 1.61877 / 0.98 ( 27) link_ALPHA1-6 : bond 0.01489 / 0.75 ( 6) link_ALPHA1-6 : angle 1.44314 / 0.97 ( 18) link_BETA1-4 : bond 0.01017 / 0.72 ( 48) link_BETA1-4 : angle 3.77256 / 2.60 ( 144) link_NAG-ASN : bond 0.00726 / 0.52 ( 66) link_NAG-ASN : angle 3.26730 / 2.14 ( 198) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4842 Ramachandran restraints generated. 2421 Oldfield, 0 Emsley, 2421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4842 Ramachandran restraints generated. 2421 Oldfield, 0 Emsley, 2421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 568 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 515 time to evaluate : 0.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 5 THR cc_start: 0.8632 (OUTLIER) cc_final: 0.8419 (p) REVERT: J 574 LYS cc_start: 0.8975 (ttmt) cc_final: 0.8662 (tttt) REVERT: A 80 MET cc_start: 0.8150 (ttp) cc_final: 0.7748 (tmm) REVERT: A 94 ARG cc_start: 0.8325 (ttp-170) cc_final: 0.7887 (ttp-110) REVERT: A 100 TYR cc_start: 0.8553 (m-80) cc_final: 0.8274 (m-80) REVERT: A 100 GLN cc_start: 0.7845 (mm-40) cc_final: 0.7568 (mt0) REVERT: C 620 SER cc_start: 0.5889 (m) cc_final: 0.5126 (p) REVERT: C 626 MET cc_start: 0.6568 (ttm) cc_final: 0.6240 (ttm) REVERT: D 99 ASN cc_start: 0.8510 (t0) cc_final: 0.8223 (t0) REVERT: D 111 LEU cc_start: 0.9300 (mm) cc_final: 0.8995 (mt) REVERT: D 248 THR cc_start: 0.8493 (m) cc_final: 0.8236 (p) REVERT: H 574 LYS cc_start: 0.8930 (ttmt) cc_final: 0.8666 (tttt) REVERT: L 248 THR cc_start: 0.8415 (m) cc_final: 0.8091 (p) REVERT: L 377 ASN cc_start: 0.8415 (p0) cc_final: 0.8015 (p0) REVERT: L 426 MET cc_start: 0.8543 (tpp) cc_final: 0.8029 (tpt) outliers start: 53 outliers final: 28 residues processed: 554 average time/residue: 0.1817 time to fit residues: 148.2591 Evaluate side-chains 376 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 347 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 92 CYS Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 45 LYS Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain J residue 587 LEU Chi-restraints excluded: chain K residue 54 CYS Chi-restraints excluded: chain K residue 163 THR Chi-restraints excluded: chain K residue 465 THR Chi-restraints excluded: chain K residue 494 LEU Chi-restraints excluded: chain A residue 100 HIS Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain D residue 197 ASN Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 461 THR Chi-restraints excluded: chain D residue 464 THR Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain H residue 619 LEU Chi-restraints excluded: chain L residue 132 THR Chi-restraints excluded: chain L residue 296 CYS Chi-restraints excluded: chain L residue 330 HIS Chi-restraints excluded: chain L residue 340 GLU Chi-restraints excluded: chain L residue 393 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 216 optimal weight: 3.9990 chunk 98 optimal weight: 8.9990 chunk 194 optimal weight: 6.9990 chunk 227 optimal weight: 3.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 1.9990 chunk 235 optimal weight: 2.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 100BGLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 2 ASN I 6 GLN K 280 ASN K 352 HIS B 89 GLN B 90 HIS C 554 ASN D 99 ASN D 103 GLN D 328 GLN D 352 HIS D 374 HIS ** E 100BGLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 6 GLN H 540 GLN H 562 GLN H 575 GLN H 616 ASN L 85 HIS L 136 ASN L 249 HIS L 280 ASN L 352 HIS L 411 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.110910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.086082 restraints weight = 37824.768| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 3.16 r_work: 0.2994 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 21756 Z= 0.241 Angle : 0.855 11.205 29751 Z= 0.406 Chirality : 0.050 0.281 3627 Planarity : 0.005 0.050 3570 Dihedral : 9.479 60.741 5336 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.36 % Favored : 93.39 % Rotamer: Outliers : 4.97 % Allowed : 18.08 % Favored : 76.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.20 (0.16), residues: 2421 helix: -0.59 (0.26), residues: 405 sheet: -1.54 (0.19), residues: 672 loop : -1.67 (0.16), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 617 TYR 0.018 0.002 TYR F 32 PHE 0.022 0.002 PHE G 28 TRP 0.020 0.002 TRP F 47 HIS 0.005 0.001 HIS K 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00557 / 0.24 (21582) covalent geometry : angle 0.77913 / 0.39 (29274) SS BOND : bond 0.00972 / 0.69 ( 45) SS BOND : angle 2.36255 / 1.43 ( 90) hydrogen bonds : bond 0.05860 / 4.01 ( 654) hydrogen bonds : angle 6.36881 / 4.46 ( 1638) link_ALPHA1-3 : bond 0.00999 / 0.49 ( 9) link_ALPHA1-3 : angle 1.71442 / 1.03 ( 27) link_ALPHA1-6 : bond 0.00691 / 0.34 ( 6) link_ALPHA1-6 : angle 1.69403 / 1.18 ( 18) link_BETA1-4 : bond 0.00598 / 0.34 ( 48) link_BETA1-4 : angle 2.83780 / 1.96 ( 144) link_NAG-ASN : bond 0.00731 / 0.44 ( 66) link_NAG-ASN : angle 3.30506 / 2.21 ( 198) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4842 Ramachandran restraints generated. 2421 Oldfield, 0 Emsley, 2421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4842 Ramachandran restraints generated. 2421 Oldfield, 0 Emsley, 2421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 339 time to evaluate : 0.970 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 99 TYR cc_start: 0.8010 (t80) cc_final: 0.7429 (t80) REVERT: I 105 ASP cc_start: 0.7811 (t0) cc_final: 0.7514 (t0) REVERT: J 574 LYS cc_start: 0.9045 (ttmt) cc_final: 0.8738 (mttt) REVERT: J 622 ILE cc_start: 0.8914 (OUTLIER) cc_final: 0.8527 (mp) REVERT: K 66 HIS cc_start: 0.8212 (m-70) cc_final: 0.7981 (m-70) REVERT: A 12 LYS cc_start: 0.8597 (mptt) cc_final: 0.8301 (mptt) REVERT: B 49 PHE cc_start: 0.8281 (t80) cc_final: 0.7922 (t80) REVERT: B 105 ASP cc_start: 0.6207 (t0) cc_final: 0.5953 (t0) REVERT: C 620 SER cc_start: 0.6100 (m) cc_final: 0.5788 (p) REVERT: D 111 LEU cc_start: 0.9395 (mm) cc_final: 0.9136 (mt) REVERT: D 248 THR cc_start: 0.8856 (m) cc_final: 0.8472 (p) REVERT: D 426 MET cc_start: 0.8837 (tpp) cc_final: 0.8600 (tpt) REVERT: E 12 LYS cc_start: 0.8692 (mptt) cc_final: 0.8246 (mptt) REVERT: E 100 TYR cc_start: 0.8883 (t80) cc_final: 0.8046 (t80) REVERT: G 106 MET cc_start: 0.7012 (mmm) cc_final: 0.6417 (mmm) REVERT: H 621 GLU cc_start: 0.5758 (tm-30) cc_final: 0.5516 (tm-30) REVERT: H 632 ASP cc_start: 0.8757 (t0) cc_final: 0.8427 (t0) REVERT: H 656 ASN cc_start: 0.8001 (t0) cc_final: 0.7645 (m-40) REVERT: L 248 THR cc_start: 0.8859 (m) cc_final: 0.8469 (p) REVERT: L 327 ARG cc_start: 0.8574 (mtp85) cc_final: 0.8369 (mtm-85) REVERT: L 330 HIS cc_start: 0.8269 (OUTLIER) cc_final: 0.8009 (p90) REVERT: L 377 ASN cc_start: 0.8866 (p0) cc_final: 0.8526 (p0) REVERT: L 500 ARG cc_start: 0.7797 (mtp85) cc_final: 0.7546 (mtp180) outliers start: 107 outliers final: 63 residues processed: 425 average time/residue: 0.1621 time to fit residues: 105.9465 Evaluate side-chains 373 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 308 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 10 GLU Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 89 VAL Chi-restraints excluded: chain F residue 92 CYS Chi-restraints excluded: chain F residue 100 TYR Chi-restraints excluded: chain I residue 9 SER Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 23 CYS Chi-restraints excluded: chain I residue 27 GLN Chi-restraints excluded: chain I residue 32 GLU Chi-restraints excluded: chain I residue 45 LYS Chi-restraints excluded: chain I residue 91 LEU Chi-restraints excluded: chain J residue 544 LEU Chi-restraints excluded: chain J residue 568 LEU Chi-restraints excluded: chain J residue 569 THR Chi-restraints excluded: chain J residue 587 LEU Chi-restraints excluded: chain J residue 622 ILE Chi-restraints excluded: chain K residue 47 ASP Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 75 VAL Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 280 ASN Chi-restraints excluded: chain K residue 450 THR Chi-restraints excluded: chain K residue 465 THR Chi-restraints excluded: chain A residue 10 GLU Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 100 HIS Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain C residue 622 ILE Chi-restraints excluded: chain C residue 636 SER Chi-restraints excluded: chain D residue 197 ASN Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 388 SER Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain D residue 450 THR Chi-restraints excluded: chain D residue 465 THR Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 84 SER Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 54 LEU Chi-restraints excluded: chain G residue 83 PHE Chi-restraints excluded: chain H residue 534 SER Chi-restraints excluded: chain H residue 543 ASN Chi-restraints excluded: chain H residue 619 LEU Chi-restraints excluded: chain H residue 641 ILE Chi-restraints excluded: chain L residue 47 ASP Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain L residue 330 HIS Chi-restraints excluded: chain L residue 333 VAL Chi-restraints excluded: chain L residue 450 THR Chi-restraints excluded: chain L residue 464 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 85 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 133 optimal weight: 0.3980 chunk 144 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 chunk 174 optimal weight: 0.9990 chunk 86 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 chunk 184 optimal weight: 0.7980 chunk 169 optimal weight: 0.1980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 100BGLN F 100DHIS I 90 HIS K 280 ASN ** A 100BGLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 77 ASN B 90 HIS E 100BGLN E 100DHIS ** G 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 562 GLN H 563 GLN L 315 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.112485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.087478 restraints weight = 37970.210| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 3.16 r_work: 0.3008 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.2613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 21756 Z= 0.135 Angle : 0.741 11.694 29751 Z= 0.347 Chirality : 0.047 0.328 3627 Planarity : 0.004 0.047 3570 Dihedral : 8.351 58.309 5313 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.16 % Favored : 94.63 % Rotamer: Outliers : 4.28 % Allowed : 19.29 % Favored : 76.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.98 (0.16), residues: 2421 helix: -0.20 (0.26), residues: 411 sheet: -1.37 (0.19), residues: 672 loop : -1.64 (0.16), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG K 166 TYR 0.020 0.001 TYR E 100F PHE 0.019 0.001 PHE B 67 TRP 0.019 0.001 TRP L 479 HIS 0.004 0.001 HIS D 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (21582) covalent geometry : angle 0.66770 / 0.33 (29274) SS BOND : bond 0.00695 / 0.50 ( 45) SS BOND : angle 1.88624 / 1.15 ( 90) hydrogen bonds : bond 0.04743 / 3.24 ( 654) hydrogen bonds : angle 5.65632 / 3.97 ( 1638) link_ALPHA1-3 : bond 0.01143 / 0.56 ( 9) link_ALPHA1-3 : angle 1.32452 / 0.79 ( 27) link_ALPHA1-6 : bond 0.00929 / 0.44 ( 6) link_ALPHA1-6 : angle 1.52141 / 1.03 ( 18) link_BETA1-4 : bond 0.00602 / 0.37 ( 48) link_BETA1-4 : angle 2.38635 / 1.66 ( 144) link_NAG-ASN : bond 0.00653 / 0.40 ( 66) link_NAG-ASN : angle 3.23075 / 2.16 ( 198) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4842 Ramachandran restraints generated. 2421 Oldfield, 0 Emsley, 2421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4842 Ramachandran restraints generated. 2421 Oldfield, 0 Emsley, 2421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 343 time to evaluate : 0.824 Fit side-chains revert: symmetry clash REVERT: F 12 LYS cc_start: 0.8643 (mptt) cc_final: 0.8151 (mptt) REVERT: F 99 TYR cc_start: 0.7888 (t80) cc_final: 0.7199 (t80) REVERT: I 37 GLN cc_start: 0.9251 (OUTLIER) cc_final: 0.8975 (tt0) REVERT: I 105 ASP cc_start: 0.7382 (t0) cc_final: 0.7114 (t0) REVERT: I 106 MET cc_start: 0.7299 (mtp) cc_final: 0.6919 (mtp) REVERT: J 574 LYS cc_start: 0.8838 (OUTLIER) cc_final: 0.8614 (mmmt) REVERT: J 622 ILE cc_start: 0.8801 (OUTLIER) cc_final: 0.8532 (mp) REVERT: K 66 HIS cc_start: 0.8250 (m-70) cc_final: 0.8022 (m-70) REVERT: K 246 GLN cc_start: 0.8491 (OUTLIER) cc_final: 0.8254 (pm20) REVERT: A 5 VAL cc_start: 0.9281 (OUTLIER) cc_final: 0.9055 (m) REVERT: A 12 LYS cc_start: 0.8548 (mptt) cc_final: 0.8294 (mptt) REVERT: B 105 ASP cc_start: 0.6582 (t0) cc_final: 0.6189 (t0) REVERT: C 543 ASN cc_start: 0.8967 (OUTLIER) cc_final: 0.8758 (m110) REVERT: D 125 LEU cc_start: 0.9210 (OUTLIER) cc_final: 0.8935 (mm) REVERT: D 161 MET cc_start: 0.8256 (tpp) cc_final: 0.8020 (tpp) REVERT: D 248 THR cc_start: 0.8810 (m) cc_final: 0.8390 (p) REVERT: G 2 ASN cc_start: 0.7949 (m-40) cc_final: 0.7662 (m110) REVERT: L 248 THR cc_start: 0.8882 (m) cc_final: 0.8484 (p) REVERT: L 330 HIS cc_start: 0.8158 (OUTLIER) cc_final: 0.7821 (p90) REVERT: L 377 ASN cc_start: 0.8911 (p0) cc_final: 0.8546 (p0) outliers start: 92 outliers final: 53 residues processed: 405 average time/residue: 0.1583 time to fit residues: 98.6246 Evaluate side-chains 373 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 312 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 10 GLU Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 84 SER Chi-restraints excluded: chain F residue 100 TYR Chi-restraints excluded: chain I residue 10 SER Chi-restraints excluded: chain I residue 23 CYS Chi-restraints excluded: chain I residue 27 GLN Chi-restraints excluded: chain I residue 32 GLU Chi-restraints excluded: chain I residue 37 GLN Chi-restraints excluded: chain I residue 45 LYS Chi-restraints excluded: chain J residue 544 LEU Chi-restraints excluded: chain J residue 568 LEU Chi-restraints excluded: chain J residue 574 LYS Chi-restraints excluded: chain J residue 622 ILE Chi-restraints excluded: chain J residue 641 ILE Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 246 GLN Chi-restraints excluded: chain K residue 280 ASN Chi-restraints excluded: chain K residue 388 SER Chi-restraints excluded: chain K residue 465 THR Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 10 GLU Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 100 TYR Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 32 GLU Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain C residue 543 ASN Chi-restraints excluded: chain C residue 587 LEU Chi-restraints excluded: chain C residue 636 SER Chi-restraints excluded: chain C residue 641 ILE Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 126 CYS Chi-restraints excluded: chain D residue 197 ASN Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 296 CYS Chi-restraints excluded: chain D residue 388 SER Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain E residue 51 MET Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 100 TYR Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 37 GLN Chi-restraints excluded: chain G residue 83 PHE Chi-restraints excluded: chain H residue 542 ARG Chi-restraints excluded: chain H residue 576 LEU Chi-restraints excluded: chain H residue 619 LEU Chi-restraints excluded: chain H residue 641 ILE Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain L residue 125 LEU Chi-restraints excluded: chain L residue 138 ILE Chi-restraints excluded: chain L residue 330 HIS Chi-restraints excluded: chain L residue 333 VAL Chi-restraints excluded: chain L residue 450 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 9 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 107 optimal weight: 3.9990 chunk 141 optimal weight: 1.9990 chunk 146 optimal weight: 3.9990 chunk 39 optimal weight: 10.0000 chunk 40 optimal weight: 6.9990 chunk 168 optimal weight: 2.9990 chunk 131 optimal weight: 1.9990 chunk 158 optimal weight: 0.9990 chunk 145 optimal weight: 0.6980 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 90 HIS K 114 GLN K 280 ASN A 100BGLN B 30 ASN B 90 HIS D 114 GLN E 100BGLN G 90 HIS H 562 GLN L 183 GLN L 280 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.109885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.084671 restraints weight = 38559.929| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 3.19 r_work: 0.2961 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.2903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 21756 Z= 0.207 Angle : 0.762 12.337 29751 Z= 0.358 Chirality : 0.048 0.526 3627 Planarity : 0.004 0.053 3570 Dihedral : 7.951 56.918 5306 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.28 % Favored : 93.47 % Rotamer: Outliers : 5.11 % Allowed : 19.53 % Favored : 75.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.80 (0.16), residues: 2421 helix: 0.32 (0.27), residues: 387 sheet: -1.40 (0.20), residues: 645 loop : -1.54 (0.16), residues: 1389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 61 TYR 0.027 0.002 TYR E 100F PHE 0.013 0.001 PHE L 382 TRP 0.019 0.002 TRP F 47 HIS 0.004 0.001 HIS K 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00478 / 0.21 (21582) covalent geometry : angle 0.68901 / 0.34 (29274) SS BOND : bond 0.00791 / 0.57 ( 45) SS BOND : angle 2.04111 / 1.23 ( 90) hydrogen bonds : bond 0.04582 / 3.14 ( 654) hydrogen bonds : angle 5.54411 / 3.90 ( 1638) link_ALPHA1-3 : bond 0.01021 / 0.49 ( 9) link_ALPHA1-3 : angle 1.49079 / 0.88 ( 27) link_ALPHA1-6 : bond 0.00717 / 0.33 ( 6) link_ALPHA1-6 : angle 1.53205 / 1.02 ( 18) link_BETA1-4 : bond 0.00587 / 0.35 ( 48) link_BETA1-4 : angle 2.32444 / 1.63 ( 144) link_NAG-ASN : bond 0.00642 / 0.38 ( 66) link_NAG-ASN : angle 3.27759 / 2.21 ( 198) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4842 Ramachandran restraints generated. 2421 Oldfield, 0 Emsley, 2421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4842 Ramachandran restraints generated. 2421 Oldfield, 0 Emsley, 2421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 328 time to evaluate : 0.847 Fit side-chains revert: symmetry clash REVERT: F 12 LYS cc_start: 0.8722 (mptt) cc_final: 0.8228 (mptt) REVERT: F 99 TYR cc_start: 0.7942 (t80) cc_final: 0.7548 (t80) REVERT: I 105 ASP cc_start: 0.7316 (t0) cc_final: 0.7003 (t0) REVERT: I 106 MET cc_start: 0.7314 (mtp) cc_final: 0.6897 (mtp) REVERT: J 622 ILE cc_start: 0.8862 (OUTLIER) cc_final: 0.8508 (mp) REVERT: J 632 ASP cc_start: 0.8569 (t0) cc_final: 0.8321 (t0) REVERT: K 66 HIS cc_start: 0.8464 (m-70) cc_final: 0.8210 (m-70) REVERT: K 104 MET cc_start: 0.9081 (ttp) cc_final: 0.8687 (tmm) REVERT: K 246 GLN cc_start: 0.8450 (OUTLIER) cc_final: 0.8200 (pm20) REVERT: B 105 ASP cc_start: 0.6688 (t0) cc_final: 0.6245 (t0) REVERT: D 66 HIS cc_start: 0.8453 (OUTLIER) cc_final: 0.8206 (m-70) REVERT: D 104 MET cc_start: 0.9023 (ttp) cc_final: 0.8694 (ttt) REVERT: D 161 MET cc_start: 0.8343 (tpp) cc_final: 0.8050 (tpp) REVERT: D 248 THR cc_start: 0.8875 (m) cc_final: 0.8481 (p) REVERT: E 12 LYS cc_start: 0.8778 (mptt) cc_final: 0.8363 (mptt) REVERT: G 9 SER cc_start: 0.8429 (t) cc_final: 0.7844 (p) REVERT: G 49 PHE cc_start: 0.8272 (t80) cc_final: 0.7911 (t80) REVERT: H 632 ASP cc_start: 0.8735 (t0) cc_final: 0.8469 (t0) REVERT: H 654 GLU cc_start: 0.8113 (mm-30) cc_final: 0.7802 (mm-30) REVERT: L 248 THR cc_start: 0.8904 (m) cc_final: 0.8535 (p) REVERT: L 330 HIS cc_start: 0.8245 (OUTLIER) cc_final: 0.7879 (p90) REVERT: L 377 ASN cc_start: 0.8932 (p0) cc_final: 0.8558 (p0) outliers start: 110 outliers final: 83 residues processed: 399 average time/residue: 0.1615 time to fit residues: 99.4625 Evaluate side-chains 398 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 311 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 10 GLU Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 84 SER Chi-restraints excluded: chain F residue 100 TYR Chi-restraints excluded: chain I residue 10 SER Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 22 THR Chi-restraints excluded: chain I residue 23 CYS Chi-restraints excluded: chain I residue 27 GLN Chi-restraints excluded: chain I residue 32 GLU Chi-restraints excluded: chain I residue 45 LYS Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain J residue 529 THR Chi-restraints excluded: chain J residue 544 LEU Chi-restraints excluded: chain J residue 549 VAL Chi-restraints excluded: chain J residue 568 LEU Chi-restraints excluded: chain J residue 587 LEU Chi-restraints excluded: chain J residue 622 ILE Chi-restraints excluded: chain J residue 641 ILE Chi-restraints excluded: chain K residue 47 ASP Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 126 CYS Chi-restraints excluded: chain K residue 190 GLU Chi-restraints excluded: chain K residue 246 GLN Chi-restraints excluded: chain K residue 268 GLU Chi-restraints excluded: chain K residue 280 ASN Chi-restraints excluded: chain K residue 388 SER Chi-restraints excluded: chain K residue 450 THR Chi-restraints excluded: chain K residue 465 THR Chi-restraints excluded: chain A residue 10 GLU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 100 TYR Chi-restraints excluded: chain A residue 100 GLN Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 32 GLU Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 622 ILE Chi-restraints excluded: chain C residue 641 ILE Chi-restraints excluded: chain D residue 66 HIS Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 126 CYS Chi-restraints excluded: chain D residue 197 ASN Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 388 SER Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain D residue 450 THR Chi-restraints excluded: chain D residue 465 THR Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 51 MET Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 84 SER Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 100 TYR Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 32 GLU Chi-restraints excluded: chain G residue 37 GLN Chi-restraints excluded: chain G residue 83 PHE Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 91 LEU Chi-restraints excluded: chain H residue 542 ARG Chi-restraints excluded: chain H residue 619 LEU Chi-restraints excluded: chain H residue 641 ILE Chi-restraints excluded: chain L residue 47 ASP Chi-restraints excluded: chain L residue 51 THR Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain L residue 138 ILE Chi-restraints excluded: chain L residue 297 THR Chi-restraints excluded: chain L residue 330 HIS Chi-restraints excluded: chain L residue 333 VAL Chi-restraints excluded: chain L residue 450 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 133 optimal weight: 4.9990 chunk 215 optimal weight: 4.9990 chunk 82 optimal weight: 0.8980 chunk 120 optimal weight: 0.0050 chunk 46 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 199 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 190 optimal weight: 4.9990 chunk 173 optimal weight: 1.9990 overall best weight: 1.1800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 2 ASN I 90 HIS K 280 ASN B 30 ASN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 90 HIS H 562 GLN H 625 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.110817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.085165 restraints weight = 38152.899| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 3.33 r_work: 0.2970 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.3108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 21756 Z= 0.162 Angle : 0.739 15.545 29751 Z= 0.347 Chirality : 0.047 0.509 3627 Planarity : 0.004 0.046 3570 Dihedral : 7.842 59.470 5306 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.07 % Favored : 93.72 % Rotamer: Outliers : 5.35 % Allowed : 19.53 % Favored : 75.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.72 (0.16), residues: 2421 helix: 0.50 (0.27), residues: 387 sheet: -1.37 (0.20), residues: 663 loop : -1.50 (0.16), residues: 1371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 24 TYR 0.018 0.002 TYR E 100F PHE 0.010 0.001 PHE F 91 TRP 0.015 0.001 TRP F 47 HIS 0.003 0.001 HIS D 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 (21582) covalent geometry : angle 0.66031 / 0.33 (29274) SS BOND : bond 0.00714 / 0.52 ( 45) SS BOND : angle 1.85878 / 1.12 ( 90) hydrogen bonds : bond 0.04197 / 2.86 ( 654) hydrogen bonds : angle 5.36841 / 3.78 ( 1638) link_ALPHA1-3 : bond 0.01001 / 0.49 ( 9) link_ALPHA1-3 : angle 1.35457 / 0.80 ( 27) link_ALPHA1-6 : bond 0.00662 / 0.31 ( 6) link_ALPHA1-6 : angle 1.45347 / 0.94 ( 18) link_BETA1-4 : bond 0.00582 / 0.35 ( 48) link_BETA1-4 : angle 2.18453 / 1.53 ( 144) link_NAG-ASN : bond 0.00637 / 0.39 ( 66) link_NAG-ASN : angle 3.48900 / 2.42 ( 198) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4842 Ramachandran restraints generated. 2421 Oldfield, 0 Emsley, 2421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4842 Ramachandran restraints generated. 2421 Oldfield, 0 Emsley, 2421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 317 time to evaluate : 0.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 12 LYS cc_start: 0.8670 (mptt) cc_final: 0.8180 (mptt) REVERT: F 99 TYR cc_start: 0.7828 (t80) cc_final: 0.7505 (t80) REVERT: I 105 ASP cc_start: 0.7375 (t0) cc_final: 0.7001 (t0) REVERT: I 106 MET cc_start: 0.7264 (mtp) cc_final: 0.6844 (mtp) REVERT: J 619 LEU cc_start: 0.3500 (OUTLIER) cc_final: 0.2391 (pt) REVERT: J 622 ILE cc_start: 0.8837 (OUTLIER) cc_final: 0.8499 (mp) REVERT: K 66 HIS cc_start: 0.8425 (m-70) cc_final: 0.8178 (m-70) REVERT: K 104 MET cc_start: 0.9082 (OUTLIER) cc_final: 0.8650 (ttp) REVERT: K 161 MET cc_start: 0.8254 (tpp) cc_final: 0.7884 (tpp) REVERT: K 246 GLN cc_start: 0.8436 (OUTLIER) cc_final: 0.8186 (pm20) REVERT: B 18 ARG cc_start: 0.7599 (OUTLIER) cc_final: 0.6768 (mmm-85) REVERT: B 105 ASP cc_start: 0.6738 (t0) cc_final: 0.6290 (t0) REVERT: D 66 HIS cc_start: 0.8361 (OUTLIER) cc_final: 0.8084 (m-70) REVERT: D 161 MET cc_start: 0.8339 (tpp) cc_final: 0.8082 (tpp) REVERT: D 248 THR cc_start: 0.8826 (m) cc_final: 0.8413 (p) REVERT: E 12 LYS cc_start: 0.8771 (mptt) cc_final: 0.8340 (mptt) REVERT: G 18 ARG cc_start: 0.7437 (OUTLIER) cc_final: 0.6399 (mmm-85) REVERT: G 49 PHE cc_start: 0.8256 (t80) cc_final: 0.7998 (t80) REVERT: L 248 THR cc_start: 0.8862 (m) cc_final: 0.8507 (p) REVERT: L 330 HIS cc_start: 0.8238 (OUTLIER) cc_final: 0.7831 (p90) REVERT: L 377 ASN cc_start: 0.8960 (p0) cc_final: 0.8585 (p0) outliers start: 115 outliers final: 79 residues processed: 395 average time/residue: 0.1596 time to fit residues: 97.4052 Evaluate side-chains 393 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 306 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 10 GLU Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 84 SER Chi-restraints excluded: chain F residue 100 TYR Chi-restraints excluded: chain I residue 10 SER Chi-restraints excluded: chain I residue 22 THR Chi-restraints excluded: chain I residue 23 CYS Chi-restraints excluded: chain I residue 27 GLN Chi-restraints excluded: chain I residue 32 GLU Chi-restraints excluded: chain I residue 37 GLN Chi-restraints excluded: chain I residue 45 LYS Chi-restraints excluded: chain J residue 549 VAL Chi-restraints excluded: chain J residue 619 LEU Chi-restraints excluded: chain J residue 622 ILE Chi-restraints excluded: chain J residue 641 ILE Chi-restraints excluded: chain K residue 47 ASP Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 88 ASN Chi-restraints excluded: chain K residue 104 MET Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 126 CYS Chi-restraints excluded: chain K residue 190 GLU Chi-restraints excluded: chain K residue 246 GLN Chi-restraints excluded: chain K residue 247 CYS Chi-restraints excluded: chain K residue 268 GLU Chi-restraints excluded: chain K residue 280 ASN Chi-restraints excluded: chain K residue 388 SER Chi-restraints excluded: chain K residue 450 THR Chi-restraints excluded: chain K residue 465 THR Chi-restraints excluded: chain A residue 10 GLU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 61 HIS Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 100 TYR Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 18 ARG Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 32 GLU Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 615 SER Chi-restraints excluded: chain C residue 622 ILE Chi-restraints excluded: chain C residue 636 SER Chi-restraints excluded: chain C residue 641 ILE Chi-restraints excluded: chain D residue 66 HIS Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 126 CYS Chi-restraints excluded: chain D residue 197 ASN Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 388 SER Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain D residue 450 THR Chi-restraints excluded: chain D residue 465 THR Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 100 TYR Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 18 ARG Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 37 GLN Chi-restraints excluded: chain G residue 83 PHE Chi-restraints excluded: chain G residue 91 LEU Chi-restraints excluded: chain H residue 576 LEU Chi-restraints excluded: chain H residue 619 LEU Chi-restraints excluded: chain H residue 625 ASN Chi-restraints excluded: chain H residue 626 MET Chi-restraints excluded: chain H residue 641 ILE Chi-restraints excluded: chain L residue 47 ASP Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain L residue 125 LEU Chi-restraints excluded: chain L residue 138 ILE Chi-restraints excluded: chain L residue 330 HIS Chi-restraints excluded: chain L residue 333 VAL Chi-restraints excluded: chain L residue 450 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 56 optimal weight: 6.9990 chunk 236 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 197 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 205 optimal weight: 0.9980 chunk 183 optimal weight: 0.6980 chunk 216 optimal weight: 5.9990 chunk 232 optimal weight: 0.9980 chunk 226 optimal weight: 0.1980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 100BGLN I 90 HIS J 564 HIS K 280 ASN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 90 HIS H 562 GLN H 625 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.111838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.086315 restraints weight = 38087.818| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 3.29 r_work: 0.2992 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.3291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 21756 Z= 0.133 Angle : 0.712 13.962 29751 Z= 0.335 Chirality : 0.047 0.774 3627 Planarity : 0.004 0.042 3570 Dihedral : 7.597 58.186 5306 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.03 % Favored : 93.80 % Rotamer: Outliers : 5.30 % Allowed : 18.97 % Favored : 75.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.61 (0.17), residues: 2421 helix: 0.69 (0.27), residues: 387 sheet: -1.33 (0.19), residues: 678 loop : -1.45 (0.16), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 24 TYR 0.021 0.001 TYR H 638 PHE 0.009 0.001 PHE F 91 TRP 0.013 0.001 TRP J 610 HIS 0.003 0.001 HIS K 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (21582) covalent geometry : angle 0.63816 / 0.32 (29274) SS BOND : bond 0.00608 / 0.43 ( 45) SS BOND : angle 1.70728 / 1.05 ( 90) hydrogen bonds : bond 0.03867 / 2.63 ( 654) hydrogen bonds : angle 5.18986 / 3.66 ( 1638) link_ALPHA1-3 : bond 0.01040 / 0.51 ( 9) link_ALPHA1-3 : angle 1.31490 / 0.77 ( 27) link_ALPHA1-6 : bond 0.00602 / 0.28 ( 6) link_ALPHA1-6 : angle 1.44054 / 0.92 ( 18) link_BETA1-4 : bond 0.00590 / 0.36 ( 48) link_BETA1-4 : angle 2.09066 / 1.46 ( 144) link_NAG-ASN : bond 0.00605 / 0.36 ( 66) link_NAG-ASN : angle 3.33414 / 2.34 ( 198) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4842 Ramachandran restraints generated. 2421 Oldfield, 0 Emsley, 2421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4842 Ramachandran restraints generated. 2421 Oldfield, 0 Emsley, 2421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 324 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 105 ASP cc_start: 0.7387 (t0) cc_final: 0.6980 (t0) REVERT: I 106 MET cc_start: 0.7239 (mtp) cc_final: 0.6805 (mtp) REVERT: J 535 MET cc_start: 0.8486 (mpp) cc_final: 0.8252 (mtm) REVERT: J 619 LEU cc_start: 0.3552 (OUTLIER) cc_final: 0.2428 (pt) REVERT: J 622 ILE cc_start: 0.8810 (OUTLIER) cc_final: 0.8517 (mp) REVERT: K 66 HIS cc_start: 0.8396 (m-70) cc_final: 0.8121 (m-70) REVERT: K 104 MET cc_start: 0.9078 (OUTLIER) cc_final: 0.8632 (ttp) REVERT: K 161 MET cc_start: 0.8276 (tpp) cc_final: 0.7976 (tpp) REVERT: K 246 GLN cc_start: 0.8399 (OUTLIER) cc_final: 0.8164 (pm20) REVERT: A 12 LYS cc_start: 0.8604 (mptt) cc_final: 0.8068 (mptt) REVERT: B 18 ARG cc_start: 0.7588 (OUTLIER) cc_final: 0.6740 (mmm-85) REVERT: B 105 ASP cc_start: 0.6692 (t0) cc_final: 0.6225 (t0) REVERT: D 66 HIS cc_start: 0.8354 (OUTLIER) cc_final: 0.8071 (m-70) REVERT: D 161 MET cc_start: 0.8332 (tpp) cc_final: 0.8105 (tpp) REVERT: D 166 ARG cc_start: 0.7964 (ttp-110) cc_final: 0.7416 (ttp-110) REVERT: D 248 THR cc_start: 0.8838 (m) cc_final: 0.8423 (p) REVERT: E 12 LYS cc_start: 0.8784 (mptt) cc_final: 0.8333 (mptt) REVERT: G 18 ARG cc_start: 0.7553 (OUTLIER) cc_final: 0.6567 (mmm-85) REVERT: H 540 GLN cc_start: 0.8648 (OUTLIER) cc_final: 0.7306 (mp10) REVERT: H 632 ASP cc_start: 0.8710 (t0) cc_final: 0.8459 (t0) REVERT: L 248 THR cc_start: 0.8860 (m) cc_final: 0.8494 (p) REVERT: L 330 HIS cc_start: 0.8227 (OUTLIER) cc_final: 0.7794 (p90) REVERT: L 377 ASN cc_start: 0.8972 (p0) cc_final: 0.8599 (p0) outliers start: 114 outliers final: 78 residues processed: 402 average time/residue: 0.1557 time to fit residues: 96.2711 Evaluate side-chains 397 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 310 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 10 GLU Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 84 SER Chi-restraints excluded: chain F residue 100 TYR Chi-restraints excluded: chain I residue 10 SER Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 22 THR Chi-restraints excluded: chain I residue 23 CYS Chi-restraints excluded: chain I residue 32 GLU Chi-restraints excluded: chain I residue 37 GLN Chi-restraints excluded: chain I residue 45 LYS Chi-restraints excluded: chain I residue 63 SER Chi-restraints excluded: chain J residue 544 LEU Chi-restraints excluded: chain J residue 569 THR Chi-restraints excluded: chain J residue 619 LEU Chi-restraints excluded: chain J residue 622 ILE Chi-restraints excluded: chain J residue 641 ILE Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 88 ASN Chi-restraints excluded: chain K residue 104 MET Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 246 GLN Chi-restraints excluded: chain K residue 247 CYS Chi-restraints excluded: chain K residue 268 GLU Chi-restraints excluded: chain K residue 349 LEU Chi-restraints excluded: chain K residue 450 THR Chi-restraints excluded: chain K residue 465 THR Chi-restraints excluded: chain A residue 10 GLU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 100 TYR Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 18 ARG Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain C residue 569 THR Chi-restraints excluded: chain C residue 615 SER Chi-restraints excluded: chain C residue 622 ILE Chi-restraints excluded: chain C residue 636 SER Chi-restraints excluded: chain C residue 641 ILE Chi-restraints excluded: chain D residue 66 HIS Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 126 CYS Chi-restraints excluded: chain D residue 197 ASN Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 388 SER Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain D residue 450 THR Chi-restraints excluded: chain D residue 464 THR Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 51 MET Chi-restraints excluded: chain E residue 84 SER Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 100 TYR Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 18 ARG Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 32 GLU Chi-restraints excluded: chain G residue 83 PHE Chi-restraints excluded: chain G residue 91 LEU Chi-restraints excluded: chain H residue 540 GLN Chi-restraints excluded: chain H residue 542 ARG Chi-restraints excluded: chain H residue 619 LEU Chi-restraints excluded: chain H residue 626 MET Chi-restraints excluded: chain H residue 641 ILE Chi-restraints excluded: chain L residue 47 ASP Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain L residue 125 LEU Chi-restraints excluded: chain L residue 126 CYS Chi-restraints excluded: chain L residue 138 ILE Chi-restraints excluded: chain L residue 294 ILE Chi-restraints excluded: chain L residue 330 HIS Chi-restraints excluded: chain L residue 333 VAL Chi-restraints excluded: chain L residue 450 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 113 optimal weight: 5.9990 chunk 226 optimal weight: 7.9990 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 chunk 99 optimal weight: 10.0000 chunk 209 optimal weight: 2.9990 chunk 101 optimal weight: 0.9990 chunk 136 optimal weight: 6.9990 chunk 130 optimal weight: 0.0040 chunk 203 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 overall best weight: 1.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 61 HIS I 90 HIS B 30 ASN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 562 GLN H 651 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.109669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.084294 restraints weight = 38448.698| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 3.33 r_work: 0.2940 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.3376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 21756 Z= 0.212 Angle : 0.753 11.413 29751 Z= 0.356 Chirality : 0.047 0.584 3627 Planarity : 0.004 0.049 3570 Dihedral : 7.717 58.362 5306 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.57 % Favored : 93.27 % Rotamer: Outliers : 5.25 % Allowed : 19.43 % Favored : 75.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.66 (0.17), residues: 2421 helix: 0.77 (0.28), residues: 387 sheet: -1.47 (0.19), residues: 696 loop : -1.44 (0.16), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 24 TYR 0.027 0.002 TYR H 638 PHE 0.015 0.001 PHE F 91 TRP 0.020 0.002 TRP D 479 HIS 0.004 0.001 HIS K 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00494 / 0.21 (21582) covalent geometry : angle 0.68471 / 0.34 (29274) SS BOND : bond 0.00729 / 0.53 ( 45) SS BOND : angle 1.98640 / 1.19 ( 90) hydrogen bonds : bond 0.04145 / 2.83 ( 654) hydrogen bonds : angle 5.29197 / 3.73 ( 1638) link_ALPHA1-3 : bond 0.00843 / 0.40 ( 9) link_ALPHA1-3 : angle 1.37952 / 0.81 ( 27) link_ALPHA1-6 : bond 0.00490 / 0.22 ( 6) link_ALPHA1-6 : angle 1.48165 / 0.94 ( 18) link_BETA1-4 : bond 0.00566 / 0.34 ( 48) link_BETA1-4 : angle 2.13911 / 1.51 ( 144) link_NAG-ASN : bond 0.00624 / 0.38 ( 66) link_NAG-ASN : angle 3.19344 / 2.19 ( 198) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4842 Ramachandran restraints generated. 2421 Oldfield, 0 Emsley, 2421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4842 Ramachandran restraints generated. 2421 Oldfield, 0 Emsley, 2421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 316 time to evaluate : 1.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 12 LYS cc_start: 0.8687 (mptt) cc_final: 0.8185 (mptt) REVERT: I 105 ASP cc_start: 0.7403 (t0) cc_final: 0.7147 (t0) REVERT: I 106 MET cc_start: 0.7271 (mtp) cc_final: 0.6985 (mtp) REVERT: J 619 LEU cc_start: 0.3594 (OUTLIER) cc_final: 0.2452 (pt) REVERT: J 622 ILE cc_start: 0.8864 (OUTLIER) cc_final: 0.8425 (mp) REVERT: K 66 HIS cc_start: 0.8504 (m-70) cc_final: 0.8247 (m-70) REVERT: K 104 MET cc_start: 0.9146 (OUTLIER) cc_final: 0.8703 (ttp) REVERT: K 246 GLN cc_start: 0.8459 (OUTLIER) cc_final: 0.8213 (pm20) REVERT: B 18 ARG cc_start: 0.7649 (OUTLIER) cc_final: 0.6479 (mmm-85) REVERT: B 100 ARG cc_start: 0.8597 (tpt90) cc_final: 0.8313 (tpt90) REVERT: B 105 ASP cc_start: 0.6720 (t0) cc_final: 0.6247 (t0) REVERT: C 620 SER cc_start: 0.6471 (m) cc_final: 0.5998 (p) REVERT: D 66 HIS cc_start: 0.8424 (OUTLIER) cc_final: 0.8140 (m-70) REVERT: D 104 MET cc_start: 0.8766 (OUTLIER) cc_final: 0.8513 (ttp) REVERT: D 161 MET cc_start: 0.8322 (tpp) cc_final: 0.8031 (tpp) REVERT: D 248 THR cc_start: 0.8854 (m) cc_final: 0.8437 (p) REVERT: E 12 LYS cc_start: 0.8814 (mptt) cc_final: 0.8364 (mptt) REVERT: G 18 ARG cc_start: 0.7587 (OUTLIER) cc_final: 0.6495 (mmm-85) REVERT: H 540 GLN cc_start: 0.8755 (OUTLIER) cc_final: 0.7069 (mp10) REVERT: L 95 MET cc_start: 0.8848 (ttp) cc_final: 0.8642 (ttp) REVERT: L 248 THR cc_start: 0.8851 (m) cc_final: 0.8499 (p) REVERT: L 330 HIS cc_start: 0.8281 (OUTLIER) cc_final: 0.7818 (p90) REVERT: L 377 ASN cc_start: 0.8971 (p0) cc_final: 0.8586 (p0) outliers start: 113 outliers final: 88 residues processed: 391 average time/residue: 0.1624 time to fit residues: 97.2675 Evaluate side-chains 406 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 308 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 10 GLU Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 84 SER Chi-restraints excluded: chain F residue 100 TYR Chi-restraints excluded: chain I residue 10 SER Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 22 THR Chi-restraints excluded: chain I residue 23 CYS Chi-restraints excluded: chain I residue 32 GLU Chi-restraints excluded: chain I residue 37 GLN Chi-restraints excluded: chain I residue 45 LYS Chi-restraints excluded: chain J residue 529 THR Chi-restraints excluded: chain J residue 544 LEU Chi-restraints excluded: chain J residue 569 THR Chi-restraints excluded: chain J residue 619 LEU Chi-restraints excluded: chain J residue 622 ILE Chi-restraints excluded: chain J residue 626 MET Chi-restraints excluded: chain J residue 641 ILE Chi-restraints excluded: chain J residue 651 ASN Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 88 ASN Chi-restraints excluded: chain K residue 104 MET Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 126 CYS Chi-restraints excluded: chain K residue 246 GLN Chi-restraints excluded: chain K residue 247 CYS Chi-restraints excluded: chain K residue 268 GLU Chi-restraints excluded: chain K residue 388 SER Chi-restraints excluded: chain K residue 450 THR Chi-restraints excluded: chain K residue 465 THR Chi-restraints excluded: chain A residue 10 GLU Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 61 HIS Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 100 TYR Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 18 ARG Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 32 GLU Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain C residue 549 VAL Chi-restraints excluded: chain C residue 615 SER Chi-restraints excluded: chain C residue 622 ILE Chi-restraints excluded: chain C residue 636 SER Chi-restraints excluded: chain C residue 641 ILE Chi-restraints excluded: chain D residue 66 HIS Chi-restraints excluded: chain D residue 104 MET Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 126 CYS Chi-restraints excluded: chain D residue 197 ASN Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 215 ILE Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 388 SER Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain D residue 450 THR Chi-restraints excluded: chain D residue 464 THR Chi-restraints excluded: chain D residue 488 VAL Chi-restraints excluded: chain D residue 496 VAL Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 10 GLU Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 84 SER Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 100 TYR Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 18 ARG Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 32 GLU Chi-restraints excluded: chain G residue 37 GLN Chi-restraints excluded: chain G residue 91 LEU Chi-restraints excluded: chain H residue 540 GLN Chi-restraints excluded: chain H residue 542 ARG Chi-restraints excluded: chain H residue 576 LEU Chi-restraints excluded: chain H residue 619 LEU Chi-restraints excluded: chain H residue 641 ILE Chi-restraints excluded: chain H residue 651 ASN Chi-restraints excluded: chain L residue 47 ASP Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain L residue 125 LEU Chi-restraints excluded: chain L residue 126 CYS Chi-restraints excluded: chain L residue 138 ILE Chi-restraints excluded: chain L residue 294 ILE Chi-restraints excluded: chain L residue 330 HIS Chi-restraints excluded: chain L residue 333 VAL Chi-restraints excluded: chain L residue 450 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 63 optimal weight: 3.9990 chunk 203 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 chunk 134 optimal weight: 0.1980 chunk 70 optimal weight: 0.7980 chunk 138 optimal weight: 0.0170 chunk 21 optimal weight: 0.8980 chunk 44 optimal weight: 0.9990 chunk 124 optimal weight: 2.9990 chunk 74 optimal weight: 0.7980 chunk 174 optimal weight: 0.5980 overall best weight: 0.4818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 90 HIS B 30 ASN D 280 ASN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 562 GLN H 575 GLN ** H 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 280 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.112385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.087277 restraints weight = 38047.453| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 3.38 r_work: 0.2995 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.3597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 21756 Z= 0.126 Angle : 0.707 11.661 29751 Z= 0.334 Chirality : 0.047 0.743 3627 Planarity : 0.004 0.044 3570 Dihedral : 7.489 59.004 5306 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.58 % Favored : 94.26 % Rotamer: Outliers : 4.23 % Allowed : 20.97 % Favored : 74.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.54 (0.17), residues: 2421 helix: 0.89 (0.27), residues: 387 sheet: -1.34 (0.19), residues: 699 loop : -1.41 (0.16), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 24 TYR 0.024 0.001 TYR H 638 PHE 0.038 0.001 PHE G 28 TRP 0.029 0.001 TRP D 112 HIS 0.003 0.001 HIS K 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (21582) covalent geometry : angle 0.63729 / 0.32 (29274) SS BOND : bond 0.00551 / 0.39 ( 45) SS BOND : angle 1.57967 / 0.96 ( 90) hydrogen bonds : bond 0.03661 / 2.49 ( 654) hydrogen bonds : angle 5.09008 / 3.60 ( 1638) link_ALPHA1-3 : bond 0.00877 / 0.43 ( 9) link_ALPHA1-3 : angle 1.25066 / 0.72 ( 27) link_ALPHA1-6 : bond 0.00587 / 0.28 ( 6) link_ALPHA1-6 : angle 1.43455 / 0.90 ( 18) link_BETA1-4 : bond 0.00613 / 0.38 ( 48) link_BETA1-4 : angle 2.00815 / 1.41 ( 144) link_NAG-ASN : bond 0.00684 / 0.37 ( 66) link_NAG-ASN : angle 3.27060 / 2.24 ( 198) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4842 Ramachandran restraints generated. 2421 Oldfield, 0 Emsley, 2421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4842 Ramachandran restraints generated. 2421 Oldfield, 0 Emsley, 2421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 337 time to evaluate : 0.800 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: I 105 ASP cc_start: 0.7376 (t0) cc_final: 0.7125 (t0) REVERT: I 106 MET cc_start: 0.7291 (mtp) cc_final: 0.7047 (mtp) REVERT: J 619 LEU cc_start: 0.3582 (OUTLIER) cc_final: 0.2439 (pt) REVERT: J 622 ILE cc_start: 0.8855 (OUTLIER) cc_final: 0.8503 (mp) REVERT: K 66 HIS cc_start: 0.8465 (m-70) cc_final: 0.8237 (m-70) REVERT: K 104 MET cc_start: 0.9038 (OUTLIER) cc_final: 0.8680 (ttp) REVERT: K 161 MET cc_start: 0.8285 (tpp) cc_final: 0.7985 (tpp) REVERT: K 246 GLN cc_start: 0.8393 (OUTLIER) cc_final: 0.8172 (pm20) REVERT: B 105 ASP cc_start: 0.6719 (t0) cc_final: 0.6226 (t0) REVERT: C 632 ASP cc_start: 0.8417 (t0) cc_final: 0.8209 (t0) REVERT: D 66 HIS cc_start: 0.8310 (OUTLIER) cc_final: 0.8009 (m-70) REVERT: D 161 MET cc_start: 0.8264 (tpp) cc_final: 0.8005 (tpp) REVERT: D 166 ARG cc_start: 0.7951 (ttp-110) cc_final: 0.7428 (ttp-110) REVERT: D 248 THR cc_start: 0.8757 (m) cc_final: 0.8373 (p) REVERT: E 12 LYS cc_start: 0.8839 (mptt) cc_final: 0.8496 (mptt) REVERT: G 9 SER cc_start: 0.8302 (t) cc_final: 0.8043 (p) REVERT: G 18 ARG cc_start: 0.7641 (OUTLIER) cc_final: 0.6508 (mmm-85) REVERT: H 540 GLN cc_start: 0.8660 (OUTLIER) cc_final: 0.7162 (mp10) REVERT: H 587 LEU cc_start: 0.9158 (tp) cc_final: 0.8947 (tp) REVERT: L 166 ARG cc_start: 0.8063 (ttp-110) cc_final: 0.7843 (ttp-110) REVERT: L 248 THR cc_start: 0.8799 (m) cc_final: 0.8436 (p) REVERT: L 330 HIS cc_start: 0.8219 (OUTLIER) cc_final: 0.7711 (p90) REVERT: L 377 ASN cc_start: 0.8909 (p0) cc_final: 0.8561 (p0) outliers start: 91 outliers final: 70 residues processed: 392 average time/residue: 0.1592 time to fit residues: 95.3027 Evaluate side-chains 392 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 314 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 84 SER Chi-restraints excluded: chain F residue 100 TYR Chi-restraints excluded: chain I residue 10 SER Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 22 THR Chi-restraints excluded: chain I residue 23 CYS Chi-restraints excluded: chain I residue 32 GLU Chi-restraints excluded: chain I residue 37 GLN Chi-restraints excluded: chain I residue 45 LYS Chi-restraints excluded: chain J residue 569 THR Chi-restraints excluded: chain J residue 619 LEU Chi-restraints excluded: chain J residue 622 ILE Chi-restraints excluded: chain J residue 626 MET Chi-restraints excluded: chain J residue 641 ILE Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 88 ASN Chi-restraints excluded: chain K residue 104 MET Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 126 CYS Chi-restraints excluded: chain K residue 246 GLN Chi-restraints excluded: chain K residue 247 CYS Chi-restraints excluded: chain K residue 268 GLU Chi-restraints excluded: chain K residue 388 SER Chi-restraints excluded: chain K residue 465 THR Chi-restraints excluded: chain A residue 10 GLU Chi-restraints excluded: chain A residue 61 HIS Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 100 TYR Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 32 GLU Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 63 SER Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain C residue 529 THR Chi-restraints excluded: chain C residue 615 SER Chi-restraints excluded: chain C residue 622 ILE Chi-restraints excluded: chain C residue 641 ILE Chi-restraints excluded: chain D residue 66 HIS Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 126 CYS Chi-restraints excluded: chain D residue 197 ASN Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 388 SER Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain D residue 464 THR Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 97 ILE Chi-restraints excluded: chain E residue 100 TYR Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 18 ARG Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain H residue 540 GLN Chi-restraints excluded: chain H residue 542 ARG Chi-restraints excluded: chain H residue 575 GLN Chi-restraints excluded: chain H residue 619 LEU Chi-restraints excluded: chain H residue 626 MET Chi-restraints excluded: chain H residue 641 ILE Chi-restraints excluded: chain L residue 47 ASP Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain L residue 125 LEU Chi-restraints excluded: chain L residue 126 CYS Chi-restraints excluded: chain L residue 138 ILE Chi-restraints excluded: chain L residue 294 ILE Chi-restraints excluded: chain L residue 330 HIS Chi-restraints excluded: chain L residue 333 VAL Chi-restraints excluded: chain L residue 388 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 44 optimal weight: 4.9990 chunk 40 optimal weight: 0.0070 chunk 78 optimal weight: 0.6980 chunk 41 optimal weight: 4.9990 chunk 218 optimal weight: 4.9990 chunk 194 optimal weight: 2.9990 chunk 197 optimal weight: 7.9990 chunk 29 optimal weight: 0.3980 chunk 38 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 191 optimal weight: 0.0570 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 100BGLN I 90 HIS K 136 ASN B 6 GLN B 30 ASN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 562 GLN H 575 GLN H 651 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.112559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.087424 restraints weight = 38024.087| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 3.29 r_work: 0.3007 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.3718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 21756 Z= 0.128 Angle : 0.726 13.896 29751 Z= 0.342 Chirality : 0.047 0.823 3627 Planarity : 0.004 0.044 3570 Dihedral : 7.393 59.733 5306 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.20 % Favored : 93.64 % Rotamer: Outliers : 4.23 % Allowed : 21.01 % Favored : 74.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.45 (0.17), residues: 2421 helix: 0.98 (0.27), residues: 387 sheet: -1.28 (0.20), residues: 699 loop : -1.36 (0.16), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 24 TYR 0.020 0.001 TYR J 638 PHE 0.040 0.001 PHE G 28 TRP 0.028 0.001 TRP H 610 HIS 0.003 0.001 HIS K 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 (21582) covalent geometry : angle 0.65216 / 0.32 (29274) SS BOND : bond 0.00556 / 0.39 ( 45) SS BOND : angle 1.81986 / 1.07 ( 90) hydrogen bonds : bond 0.03569 / 2.45 ( 654) hydrogen bonds : angle 4.97411 / 3.51 ( 1638) link_ALPHA1-3 : bond 0.00814 / 0.40 ( 9) link_ALPHA1-3 : angle 1.27295 / 0.74 ( 27) link_ALPHA1-6 : bond 0.00495 / 0.23 ( 6) link_ALPHA1-6 : angle 1.45516 / 0.91 ( 18) link_BETA1-4 : bond 0.00581 / 0.35 ( 48) link_BETA1-4 : angle 1.96802 / 1.39 ( 144) link_NAG-ASN : bond 0.00615 / 0.34 ( 66) link_NAG-ASN : angle 3.39896 / 2.35 ( 198) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4842 Ramachandran restraints generated. 2421 Oldfield, 0 Emsley, 2421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4842 Ramachandran restraints generated. 2421 Oldfield, 0 Emsley, 2421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 328 time to evaluate : 0.774 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 105 ASP cc_start: 0.7377 (t0) cc_final: 0.7123 (t0) REVERT: I 106 MET cc_start: 0.7291 (mtp) cc_final: 0.7038 (mtp) REVERT: J 619 LEU cc_start: 0.3501 (OUTLIER) cc_final: 0.2401 (pt) REVERT: J 622 ILE cc_start: 0.8821 (OUTLIER) cc_final: 0.8451 (mp) REVERT: K 66 HIS cc_start: 0.8451 (m-70) cc_final: 0.8219 (m-70) REVERT: K 104 MET cc_start: 0.9059 (OUTLIER) cc_final: 0.8648 (ttp) REVERT: K 246 GLN cc_start: 0.8341 (OUTLIER) cc_final: 0.8138 (pm20) REVERT: A 99 TYR cc_start: 0.8326 (OUTLIER) cc_final: 0.7980 (t80) REVERT: B 105 ASP cc_start: 0.6710 (t0) cc_final: 0.6218 (t0) REVERT: C 620 SER cc_start: 0.6608 (m) cc_final: 0.6115 (p) REVERT: D 66 HIS cc_start: 0.8280 (OUTLIER) cc_final: 0.7949 (m-70) REVERT: D 161 MET cc_start: 0.8261 (tpp) cc_final: 0.8019 (tpp) REVERT: D 166 ARG cc_start: 0.7897 (ttp-110) cc_final: 0.7428 (ttp-110) REVERT: D 248 THR cc_start: 0.8769 (m) cc_final: 0.8394 (p) REVERT: E 12 LYS cc_start: 0.8868 (mptt) cc_final: 0.8528 (mptt) REVERT: G 18 ARG cc_start: 0.7591 (OUTLIER) cc_final: 0.6619 (mmm-85) REVERT: G 24 ARG cc_start: 0.8403 (ptm-80) cc_final: 0.8114 (ptt-90) REVERT: H 540 GLN cc_start: 0.8648 (OUTLIER) cc_final: 0.6985 (mp10) REVERT: H 587 LEU cc_start: 0.9125 (tp) cc_final: 0.8902 (tp) REVERT: H 611 ASN cc_start: 0.6525 (m-40) cc_final: 0.6210 (m-40) REVERT: L 248 THR cc_start: 0.8807 (m) cc_final: 0.8442 (p) REVERT: L 330 HIS cc_start: 0.8208 (OUTLIER) cc_final: 0.7704 (p90) REVERT: L 377 ASN cc_start: 0.8892 (p0) cc_final: 0.8523 (p0) outliers start: 91 outliers final: 72 residues processed: 382 average time/residue: 0.1591 time to fit residues: 93.7863 Evaluate side-chains 405 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 324 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 84 SER Chi-restraints excluded: chain F residue 100 TYR Chi-restraints excluded: chain I residue 10 SER Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 22 THR Chi-restraints excluded: chain I residue 23 CYS Chi-restraints excluded: chain I residue 32 GLU Chi-restraints excluded: chain I residue 37 GLN Chi-restraints excluded: chain I residue 45 LYS Chi-restraints excluded: chain I residue 63 SER Chi-restraints excluded: chain J residue 544 LEU Chi-restraints excluded: chain J residue 569 THR Chi-restraints excluded: chain J residue 619 LEU Chi-restraints excluded: chain J residue 622 ILE Chi-restraints excluded: chain J residue 635 ILE Chi-restraints excluded: chain J residue 641 ILE Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 61 TYR Chi-restraints excluded: chain K residue 88 ASN Chi-restraints excluded: chain K residue 104 MET Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 125 LEU Chi-restraints excluded: chain K residue 126 CYS Chi-restraints excluded: chain K residue 246 GLN Chi-restraints excluded: chain K residue 247 CYS Chi-restraints excluded: chain K residue 268 GLU Chi-restraints excluded: chain K residue 388 SER Chi-restraints excluded: chain K residue 465 THR Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 61 HIS Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 99 TYR Chi-restraints excluded: chain A residue 100 TYR Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain C residue 615 SER Chi-restraints excluded: chain C residue 622 ILE Chi-restraints excluded: chain C residue 641 ILE Chi-restraints excluded: chain D residue 66 HIS Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 126 CYS Chi-restraints excluded: chain D residue 197 ASN Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 388 SER Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain D residue 464 THR Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 51 MET Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 97 ILE Chi-restraints excluded: chain E residue 100 TYR Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 18 ARG Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 91 LEU Chi-restraints excluded: chain H residue 540 GLN Chi-restraints excluded: chain H residue 542 ARG Chi-restraints excluded: chain H residue 575 GLN Chi-restraints excluded: chain H residue 619 LEU Chi-restraints excluded: chain H residue 641 ILE Chi-restraints excluded: chain L residue 47 ASP Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain L residue 125 LEU Chi-restraints excluded: chain L residue 126 CYS Chi-restraints excluded: chain L residue 294 ILE Chi-restraints excluded: chain L residue 330 HIS Chi-restraints excluded: chain L residue 333 VAL Chi-restraints excluded: chain L residue 388 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 21 optimal weight: 4.9990 chunk 28 optimal weight: 0.7980 chunk 231 optimal weight: 0.7980 chunk 75 optimal weight: 1.9990 chunk 241 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 236 optimal weight: 3.9990 chunk 224 optimal weight: 0.8980 chunk 1 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 194 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 90 HIS B 30 ASN B 89 GLN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 562 GLN H 575 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.111838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.086621 restraints weight = 38325.762| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 3.38 r_work: 0.2983 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.3760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 21756 Z= 0.155 Angle : 0.732 11.187 29751 Z= 0.345 Chirality : 0.047 0.732 3627 Planarity : 0.004 0.046 3570 Dihedral : 7.413 59.589 5306 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.36 % Favored : 93.47 % Rotamer: Outliers : 4.00 % Allowed : 21.25 % Favored : 74.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.45 (0.17), residues: 2421 helix: 1.05 (0.27), residues: 387 sheet: -1.29 (0.20), residues: 699 loop : -1.38 (0.16), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 24 TYR 0.029 0.002 TYR F 32 PHE 0.016 0.001 PHE L 53 TRP 0.024 0.001 TRP H 610 HIS 0.003 0.001 HIS K 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 (21582) covalent geometry : angle 0.66614 / 0.33 (29274) SS BOND : bond 0.00633 / 0.44 ( 45) SS BOND : angle 1.68126 / 1.03 ( 90) hydrogen bonds : bond 0.03628 / 2.47 ( 654) hydrogen bonds : angle 5.01774 / 3.54 ( 1638) link_ALPHA1-3 : bond 0.00780 / 0.38 ( 9) link_ALPHA1-3 : angle 1.30024 / 0.76 ( 27) link_ALPHA1-6 : bond 0.00455 / 0.21 ( 6) link_ALPHA1-6 : angle 1.46587 / 0.92 ( 18) link_BETA1-4 : bond 0.00581 / 0.34 ( 48) link_BETA1-4 : angle 1.96670 / 1.40 ( 144) link_NAG-ASN : bond 0.00596 / 0.34 ( 66) link_NAG-ASN : angle 3.22017 / 2.21 ( 198) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4842 Ramachandran restraints generated. 2421 Oldfield, 0 Emsley, 2421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4842 Ramachandran restraints generated. 2421 Oldfield, 0 Emsley, 2421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 322 time to evaluate : 0.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 105 ASP cc_start: 0.7376 (t0) cc_final: 0.7122 (t0) REVERT: I 106 MET cc_start: 0.7302 (mtp) cc_final: 0.7044 (mtp) REVERT: J 619 LEU cc_start: 0.3517 (OUTLIER) cc_final: 0.2408 (pt) REVERT: K 66 HIS cc_start: 0.8494 (m-70) cc_final: 0.8259 (m-70) REVERT: K 104 MET cc_start: 0.9071 (OUTLIER) cc_final: 0.8705 (ttp) REVERT: K 161 MET cc_start: 0.8358 (tpp) cc_final: 0.8049 (tpp) REVERT: K 246 GLN cc_start: 0.8354 (OUTLIER) cc_final: 0.8147 (pm20) REVERT: B 105 ASP cc_start: 0.6649 (t0) cc_final: 0.6160 (t0) REVERT: C 620 SER cc_start: 0.6362 (m) cc_final: 0.5836 (p) REVERT: D 66 HIS cc_start: 0.8306 (OUTLIER) cc_final: 0.7978 (m-70) REVERT: D 161 MET cc_start: 0.8257 (tpp) cc_final: 0.7983 (tpp) REVERT: D 248 THR cc_start: 0.8785 (m) cc_final: 0.8403 (p) REVERT: E 12 LYS cc_start: 0.8888 (mptt) cc_final: 0.8518 (mptt) REVERT: G 18 ARG cc_start: 0.7616 (OUTLIER) cc_final: 0.6563 (mmm-85) REVERT: G 24 ARG cc_start: 0.8411 (ptm-80) cc_final: 0.8106 (ptt-90) REVERT: H 540 GLN cc_start: 0.8678 (OUTLIER) cc_final: 0.6916 (mp10) REVERT: H 587 LEU cc_start: 0.9191 (tp) cc_final: 0.8971 (tp) REVERT: H 611 ASN cc_start: 0.6739 (m-40) cc_final: 0.6375 (m-40) REVERT: L 248 THR cc_start: 0.8794 (m) cc_final: 0.8423 (p) REVERT: L 330 HIS cc_start: 0.8203 (OUTLIER) cc_final: 0.7696 (p90) REVERT: L 377 ASN cc_start: 0.8929 (p0) cc_final: 0.8577 (p0) outliers start: 86 outliers final: 74 residues processed: 376 average time/residue: 0.1572 time to fit residues: 90.9511 Evaluate side-chains 396 residues out of total 2151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 315 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 46 GLU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 84 SER Chi-restraints excluded: chain F residue 100 TYR Chi-restraints excluded: chain I residue 10 SER Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 22 THR Chi-restraints excluded: chain I residue 23 CYS Chi-restraints excluded: chain I residue 32 GLU Chi-restraints excluded: chain I residue 37 GLN Chi-restraints excluded: chain I residue 45 LYS Chi-restraints excluded: chain I residue 63 SER Chi-restraints excluded: chain J residue 544 LEU Chi-restraints excluded: chain J residue 569 THR Chi-restraints excluded: chain J residue 619 LEU Chi-restraints excluded: chain J residue 626 MET Chi-restraints excluded: chain J residue 635 ILE Chi-restraints excluded: chain J residue 641 ILE Chi-restraints excluded: chain K residue 51 THR Chi-restraints excluded: chain K residue 61 TYR Chi-restraints excluded: chain K residue 88 ASN Chi-restraints excluded: chain K residue 104 MET Chi-restraints excluded: chain K residue 120 VAL Chi-restraints excluded: chain K residue 125 LEU Chi-restraints excluded: chain K residue 126 CYS Chi-restraints excluded: chain K residue 246 GLN Chi-restraints excluded: chain K residue 247 CYS Chi-restraints excluded: chain K residue 268 GLU Chi-restraints excluded: chain K residue 388 SER Chi-restraints excluded: chain K residue 465 THR Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 61 HIS Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 100 TYR Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain C residue 615 SER Chi-restraints excluded: chain C residue 622 ILE Chi-restraints excluded: chain C residue 641 ILE Chi-restraints excluded: chain D residue 66 HIS Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 126 CYS Chi-restraints excluded: chain D residue 197 ASN Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 388 SER Chi-restraints excluded: chain D residue 443 ILE Chi-restraints excluded: chain D residue 464 THR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 51 MET Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 84 SER Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 97 ILE Chi-restraints excluded: chain E residue 100 TYR Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 18 ARG Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 22 THR Chi-restraints excluded: chain G residue 91 LEU Chi-restraints excluded: chain H residue 540 GLN Chi-restraints excluded: chain H residue 542 ARG Chi-restraints excluded: chain H residue 619 LEU Chi-restraints excluded: chain H residue 641 ILE Chi-restraints excluded: chain L residue 47 ASP Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain L residue 125 LEU Chi-restraints excluded: chain L residue 294 ILE Chi-restraints excluded: chain L residue 330 HIS Chi-restraints excluded: chain L residue 333 VAL Chi-restraints excluded: chain L residue 388 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 243 random chunks: chunk 234 optimal weight: 0.7980 chunk 198 optimal weight: 3.9990 chunk 25 optimal weight: 8.9990 chunk 19 optimal weight: 4.9990 chunk 214 optimal weight: 0.8980 chunk 225 optimal weight: 4.9990 chunk 159 optimal weight: 2.9990 chunk 126 optimal weight: 0.5980 chunk 202 optimal weight: 3.9990 chunk 154 optimal weight: 0.5980 chunk 185 optimal weight: 6.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 100BGLN I 90 HIS B 30 ASN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 562 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.111582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.086252 restraints weight = 38224.502| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 3.37 r_work: 0.2973 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.3803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 21756 Z= 0.159 Angle : 0.730 11.111 29751 Z= 0.345 Chirality : 0.047 0.653 3627 Planarity : 0.004 0.049 3570 Dihedral : 7.461 59.620 5306 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.32 % Favored : 93.52 % Rotamer: Outliers : 4.23 % Allowed : 21.01 % Favored : 74.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.42 (0.17), residues: 2421 helix: 1.12 (0.27), residues: 387 sheet: -1.28 (0.20), residues: 699 loop : -1.37 (0.16), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG L 166 TYR 0.028 0.002 TYR F 32 PHE 0.036 0.001 PHE G 28 TRP 0.026 0.001 TRP H 614 HIS 0.003 0.001 HIS K 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.16 (21582) covalent geometry : angle 0.66542 / 0.33 (29274) SS BOND : bond 0.00603 / 0.43 ( 45) SS BOND : angle 1.71411 / 1.04 ( 90) hydrogen bonds : bond 0.03704 / 2.52 ( 654) hydrogen bonds : angle 5.01829 / 3.55 ( 1638) link_ALPHA1-3 : bond 0.00760 / 0.37 ( 9) link_ALPHA1-3 : angle 1.30907 / 0.76 ( 27) link_ALPHA1-6 : bond 0.00443 / 0.21 ( 6) link_ALPHA1-6 : angle 1.47847 / 0.92 ( 18) link_BETA1-4 : bond 0.00580 / 0.34 ( 48) link_BETA1-4 : angle 1.97904 / 1.41 ( 144) link_NAG-ASN : bond 0.00575 / 0.33 ( 66) link_NAG-ASN : angle 3.14343 / 2.16 ( 198) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4605.99 seconds wall clock time: 80 minutes 23.58 seconds (4823.58 seconds total)