Starting phenix.real_space_refine on Tue May 20 20:47:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6dfg_7875/05_2025/6dfg_7875.cif Found real_map, /net/cci-nas-00/data/ceres_data/6dfg_7875/05_2025/6dfg_7875.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6dfg_7875/05_2025/6dfg_7875.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6dfg_7875/05_2025/6dfg_7875.map" model { file = "/net/cci-nas-00/data/ceres_data/6dfg_7875/05_2025/6dfg_7875.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6dfg_7875/05_2025/6dfg_7875.cif" } resolution = 4.42 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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 123 5.16 5 C 12570 2.51 5 N 3303 2.21 5 O 4194 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 20190 Number of models: 1 Model: "" Number of chains: 48 Chain: "A" Number of atoms: 3427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3427 Classifications: {'peptide': 435} Link IDs: {'PTRANS': 22, 'TRANS': 412} Chain breaks: 5 Chain: "B" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 917 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 1, 'TRANS': 113} Chain breaks: 1 Chain: "H" Number of atoms: 1007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1007 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 6, 'TRANS': 122} Chain: "L" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 806 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 6, 'TRANS': 99} Chain: "C" Number of atoms: 3427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3427 Classifications: {'peptide': 435} Link IDs: {'PTRANS': 22, 'TRANS': 412} Chain breaks: 5 Chain: "E" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 917 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 1, 'TRANS': 113} Chain breaks: 1 Chain: "G" Number of atoms: 1007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1007 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 6, 'TRANS': 122} Chain: "J" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 806 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 6, 'TRANS': 99} Chain: "D" Number of atoms: 3427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3427 Classifications: {'peptide': 435} Link IDs: {'PTRANS': 22, 'TRANS': 412} Chain breaks: 5 Chain: "F" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 917 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 1, 'TRANS': 113} Chain breaks: 1 Chain: "I" Number of atoms: 1007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1007 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 6, 'TRANS': 122} Chain: "K" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 806 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 6, 'TRANS': 99} Chain: "M" 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: "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: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "S" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 116 Unusual residues: {'BMA': 1, 'MAN': 7, 'NAG': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 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: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 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: "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: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "a" 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: "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: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 116 Unusual residues: {'BMA': 1, 'MAN': 7, 'NAG': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 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: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 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: 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: "h" 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: "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: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 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: 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: "m" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 116 Unusual residues: {'BMA': 1, 'MAN': 7, 'NAG': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 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: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 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: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} 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: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} 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: "G" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} 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: "I" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 12.49, per 1000 atoms: 0.62 Number of scatterers: 20190 At special positions: 0 Unit cell: (158.62, 166.86, 142.14, 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 123 16.00 O 4194 8.00 N 3303 7.00 C 12570 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.02 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.02 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=1.95 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.03 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.02 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.02 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS E 605 " distance=1.99 Simple disulfide: pdb=" SG CYS E 598 " - pdb=" SG CYS E 604 " distance=2.02 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " 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=2.03 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 157 " distance=2.02 Simple disulfide: pdb=" SG CYS D 218 " - pdb=" SG CYS D 247 " distance=2.02 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=2.03 Simple disulfide: pdb=" SG CYS D 378 " - pdb=" SG CYS D 445 " distance=2.03 Simple disulfide: pdb=" SG CYS D 385 " - pdb=" SG CYS D 418 " distance=2.03 Simple disulfide: pdb=" SG CYS D 501 " - pdb=" SG CYS F 605 " distance=2.14 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.02 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.04 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 ALPHA1-2 " MAN P 4 " - " MAN P 5 " " MAN S 4 " - " MAN S 5 " " MAN S 5 " - " MAN S 6 " " MAN S 8 " - " MAN S 9 " " MAN U 4 " - " MAN U 5 " " MAN U 5 " - " MAN U 6 " " MAN Z 4 " - " MAN Z 5 " " MAN c 4 " - " MAN c 5 " " MAN c 5 " - " MAN c 6 " " MAN c 8 " - " MAN c 9 " " MAN e 4 " - " MAN e 5 " " MAN e 5 " - " MAN e 6 " " MAN j 4 " - " MAN j 5 " " MAN m 4 " - " MAN m 5 " " MAN m 5 " - " MAN m 6 " " MAN m 8 " - " MAN m 9 " " MAN o 4 " - " MAN o 5 " " MAN o 5 " - " MAN o 6 " ALPHA1-3 " BMA M 3 " - " MAN M 4 " " BMA P 3 " - " MAN P 4 " " BMA S 3 " - " MAN S 4 " " MAN S 7 " - " MAN S 10 " " BMA U 3 " - " MAN U 4 " " BMA W 3 " - " MAN W 4 " " BMA Z 3 " - " MAN Z 4 " " BMA c 3 " - " MAN c 4 " " MAN c 7 " - " MAN c 10 " " BMA e 3 " - " MAN e 4 " " BMA g 3 " - " MAN g 4 " " BMA j 3 " - " MAN j 4 " " BMA m 3 " - " MAN m 4 " " MAN m 7 " - " MAN m 10 " " BMA o 3 " - " MAN o 4 " ALPHA1-6 " BMA P 3 " - " MAN P 6 " " BMA S 3 " - " MAN S 7 " " MAN S 7 " - " MAN S 8 " " BMA Z 3 " - " MAN Z 6 " " BMA c 3 " - " MAN c 7 " " MAN c 7 " - " MAN c 8 " " BMA j 3 " - " MAN j 6 " " BMA m 3 " - " MAN m 7 " " MAN m 7 " - " MAN m 8 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " 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 R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " 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 e 2 " - " BMA e 3 " " 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 i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " 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 o 1 " - " NAG o 2 " " NAG o 2 " - " BMA o 3 " " NAG p 1 " - " NAG p 2 " NAG-ASN " NAG A 605 " - " ASN A 137 " " NAG A 608 " - " ASN A 160 " " NAG A 611 " - " ASN A 234 " " NAG A 623 " - " ASN A 301 " " NAG A 634 " - " ASN A 339 " " NAG C 605 " - " ASN C 137 " " NAG C 608 " - " ASN C 160 " " NAG C 611 " - " ASN C 234 " " NAG C 623 " - " ASN C 301 " " NAG C 634 " - " ASN C 339 " " NAG D 605 " - " ASN D 137 " " NAG D 608 " - " ASN D 160 " " NAG D 611 " - " ASN D 234 " " NAG D 623 " - " ASN D 301 " " NAG D 634 " - " ASN D 339 " " NAG G 301 " - " ASN G 26 " " NAG H 301 " - " ASN H 26 " " NAG I 301 " - " ASN I 26 " " NAG M 1 " - " ASN A 133 " " NAG N 1 " - " ASN A 156 " " NAG O 1 " - " ASN A 197 " " NAG P 1 " - " ASN A 262 " " NAG Q 1 " - " ASN A 276 " " NAG R 1 " - " ASN A 295 " " NAG S 1 " - " ASN A 332 " " NAG T 1 " - " ASN A 386 " " NAG U 1 " - " ASN A 392 " " NAG V 1 " - " ASN A 448 " " NAG W 1 " - " ASN C 133 " " NAG X 1 " - " ASN C 156 " " NAG Y 1 " - " ASN C 197 " " NAG Z 1 " - " ASN C 262 " " NAG a 1 " - " ASN C 276 " " NAG b 1 " - " ASN C 295 " " NAG c 1 " - " ASN C 332 " " NAG d 1 " - " ASN C 386 " " NAG e 1 " - " ASN C 392 " " NAG f 1 " - " ASN C 448 " " NAG g 1 " - " ASN D 133 " " NAG h 1 " - " ASN D 156 " " NAG i 1 " - " ASN D 197 " " NAG j 1 " - " ASN D 262 " " NAG k 1 " - " ASN D 276 " " NAG l 1 " - " ASN D 295 " " NAG m 1 " - " ASN D 332 " " NAG n 1 " - " ASN D 386 " " NAG o 1 " - " ASN D 392 " " NAG p 1 " - " ASN D 448 " Time building additional restraints: 6.39 Conformation dependent library (CDL) restraints added in 2.5 seconds 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4386 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 51 sheets defined 16.1% alpha, 31.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.79 Creating SS restraints... Processing helix chain 'A' and resid 98 through 116 removed outlier: 4.009A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE A 108 " --> pdb=" O MET A 104 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ILE A 109 " --> pdb=" O HIS A 105 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU A 116 " --> pdb=" O TRP A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 354 removed outlier: 4.090A pdb=" N LYS A 344 " --> pdb=" O GLU A 340 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL A 345 " --> pdb=" O THR A 341 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N LYS A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 387 through 391 removed outlier: 3.517A pdb=" N LEU A 390 " --> pdb=" O THR A 387 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N PHE A 391 " --> pdb=" O SER A 388 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 387 through 391' Processing helix chain 'A' and resid 425 through 429 removed outlier: 3.647A pdb=" N GLN A 428 " --> pdb=" O ASN A 425 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG A 429 " --> pdb=" O MET A 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 425 through 429' Processing helix chain 'A' and resid 475 through 482 removed outlier: 3.697A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 531 through 537 removed outlier: 3.701A pdb=" N LEU B 537 " --> pdb=" O SER B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 543 removed outlier: 4.450A pdb=" N ARG B 542 " --> pdb=" O THR B 538 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 538 through 543' Processing helix chain 'B' and resid 580 through 585 Processing helix chain 'B' and resid 587 through 597 removed outlier: 3.557A pdb=" N LEU B 592 " --> pdb=" O ARG B 588 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ILE B 595 " --> pdb=" O GLN B 591 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLY B 597 " --> pdb=" O LEU B 593 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 635 Processing helix chain 'B' and resid 639 through 646 Processing helix chain 'B' and resid 648 through 653 removed outlier: 3.920A pdb=" N GLN B 653 " --> pdb=" O SER B 649 " (cutoff:3.500A) Processing helix chain 'B' and resid 654 through 657 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 27 through 30 Processing helix chain 'C' and resid 98 through 116 removed outlier: 4.009A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE C 108 " --> pdb=" O MET C 104 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE C 109 " --> pdb=" O HIS C 105 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU C 116 " --> pdb=" O TRP C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 354 removed outlier: 4.091A pdb=" N LYS C 344 " --> pdb=" O GLU C 340 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL C 345 " --> pdb=" O THR C 341 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N LYS C 351 " --> pdb=" O LYS C 347 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 387 through 391 removed outlier: 3.517A pdb=" N LEU C 390 " --> pdb=" O THR C 387 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N PHE C 391 " --> pdb=" O SER C 388 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 387 through 391' Processing helix chain 'C' and resid 425 through 429 removed outlier: 3.648A pdb=" N GLN C 428 " --> pdb=" O ASN C 425 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG C 429 " --> pdb=" O MET C 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 425 through 429' Processing helix chain 'C' and resid 475 through 482 removed outlier: 3.697A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'E' and resid 531 through 537 removed outlier: 3.700A pdb=" N LEU E 537 " --> pdb=" O SER E 534 " (cutoff:3.500A) Processing helix chain 'E' and resid 538 through 543 removed outlier: 4.450A pdb=" N ARG E 542 " --> pdb=" O THR E 538 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ASN E 543 " --> pdb=" O VAL E 539 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 538 through 543' Processing helix chain 'E' and resid 580 through 585 Processing helix chain 'E' and resid 587 through 597 removed outlier: 3.558A pdb=" N LEU E 592 " --> pdb=" O ARG E 588 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ILE E 595 " --> pdb=" O GLN E 591 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLY E 597 " --> pdb=" O LEU E 593 " (cutoff:3.500A) Processing helix chain 'E' and resid 630 through 635 Processing helix chain 'E' and resid 639 through 646 Processing helix chain 'E' and resid 648 through 653 removed outlier: 3.921A pdb=" N GLN E 653 " --> pdb=" O SER E 649 " (cutoff:3.500A) Processing helix chain 'E' and resid 654 through 657 Processing helix chain 'G' and resid 83 through 87 Processing helix chain 'J' and resid 27 through 30 Processing helix chain 'D' and resid 98 through 116 removed outlier: 4.009A pdb=" N GLU D 102 " --> pdb=" O ASN D 98 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE D 108 " --> pdb=" O MET D 104 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE D 109 " --> pdb=" O HIS D 105 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU D 116 " --> pdb=" O TRP D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 354 removed outlier: 4.090A pdb=" N LYS D 344 " --> pdb=" O GLU D 340 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL D 345 " --> pdb=" O THR D 341 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N LYS D 351 " --> pdb=" O LYS D 347 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 373 Processing helix chain 'D' and resid 387 through 391 removed outlier: 3.517A pdb=" N LEU D 390 " --> pdb=" O THR D 387 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N PHE D 391 " --> pdb=" O SER D 388 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 387 through 391' Processing helix chain 'D' and resid 425 through 429 removed outlier: 3.647A pdb=" N GLN D 428 " --> pdb=" O ASN D 425 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG D 429 " --> pdb=" O MET D 426 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 425 through 429' Processing helix chain 'D' and resid 475 through 482 removed outlier: 3.697A pdb=" N GLU D 482 " --> pdb=" O ASN D 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 531 through 537 removed outlier: 3.701A pdb=" N LEU F 537 " --> pdb=" O SER F 534 " (cutoff:3.500A) Processing helix chain 'F' and resid 538 through 543 removed outlier: 4.449A pdb=" N ARG F 542 " --> pdb=" O THR F 538 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ASN F 543 " --> pdb=" O VAL F 539 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 538 through 543' Processing helix chain 'F' and resid 580 through 585 Processing helix chain 'F' and resid 587 through 597 removed outlier: 3.558A pdb=" N LEU F 592 " --> pdb=" O ARG F 588 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ILE F 595 " --> pdb=" O GLN F 591 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLY F 597 " --> pdb=" O LEU F 593 " (cutoff:3.500A) Processing helix chain 'F' and resid 630 through 635 Processing helix chain 'F' and resid 639 through 646 Processing helix chain 'F' and resid 648 through 653 removed outlier: 3.920A pdb=" N GLN F 653 " --> pdb=" O SER F 649 " (cutoff:3.500A) Processing helix chain 'F' and resid 654 through 657 Processing helix chain 'I' and resid 83 through 87 Processing helix chain 'K' and resid 27 through 30 Processing sheet with id=AA1, first strand: chain 'A' and resid 498 through 499 removed outlier: 6.002A pdb=" N VAL A 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N THR B 606 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL A 38 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N CYS B 604 " --> pdb=" O VAL A 38 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 46 through 47 removed outlier: 4.060A pdb=" N LYS A 46 " --> pdb=" O LYS A 490 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA A 224 " --> pdb=" O VAL A 489 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 54 removed outlier: 3.726A pdb=" N PHE A 53 " --> pdb=" O CYS A 218 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 93 removed outlier: 3.625A pdb=" N GLU A 91 " --> pdb=" O CYS A 239 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N GLY A 237 " --> pdb=" O PHE A 93 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 130 through 133 removed outlier: 3.586A pdb=" N SER A 174 " --> pdb=" O CYS A 157 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 181 through 183 Processing sheet with id=AA7, first strand: chain 'A' and resid 200 through 203 removed outlier: 5.835A pdb=" N ALA A 200 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N TYR A 435 " --> pdb=" O ALA A 200 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N MET A 434 " --> pdb=" O ILE A 424 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 271 through 273 removed outlier: 3.584A pdb=" N ILE A 271 " --> pdb=" O GLN A 287 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 374 through 378 removed outlier: 3.519A pdb=" N CYS A 331 " --> pdb=" O LEU A 416 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASN A 295 " --> pdb=" O ASN A 332 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 302 through 308 removed outlier: 6.223A pdb=" N LYS A 305 " --> pdb=" O THR A 320 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N THR A 320 " --> pdb=" O LYS A 305 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ILE A 307 " --> pdb=" O TYR A 318 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N TYR A 318 " --> pdb=" O ILE A 307 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.557A pdb=" N SER H 21 " --> pdb=" O SER H 7 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.557A pdb=" N SER H 21 " --> pdb=" O SER H 7 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.711A pdb=" N TRP H 35 " --> pdb=" O ASP H 50 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ASP H 50 " --> pdb=" O TRP H 35 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.991A pdb=" N CYS H 92 " --> pdb=" O VAL H 102 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N VAL H 102 " --> pdb=" O CYS H 92 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ARG H 94 " --> pdb=" O MET H 100M" (cutoff:3.500A) removed outlier: 4.439A pdb=" N MET H 100M" --> pdb=" O ARG H 94 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ALA H 96 " --> pdb=" O TYR H 100K" (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 4 through 5 Processing sheet with id=AB7, first strand: chain 'L' and resid 9 through 13 removed outlier: 6.198A pdb=" N VAL L 11 " --> pdb=" O THR L 105 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASP L 85 " --> pdb=" O GLN L 38 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N TYR L 87 " --> pdb=" O TYR L 36 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N TRP L 35 " --> pdb=" O ILE L 47 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'L' and resid 9 through 13 removed outlier: 6.198A pdb=" N VAL L 11 " --> pdb=" O THR L 105 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER L 90 " --> pdb=" O MET L 97 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 498 through 499 removed outlier: 5.883A pdb=" N VAL C 36 " --> pdb=" O THR E 606 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR E 606 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N CYS E 604 " --> pdb=" O VAL C 38 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 46 through 47 removed outlier: 4.060A pdb=" N LYS C 46 " --> pdb=" O LYS C 490 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA C 224 " --> pdb=" O VAL C 489 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 53 through 54 removed outlier: 3.726A pdb=" N PHE C 53 " --> pdb=" O CYS C 218 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 91 through 93 removed outlier: 3.626A pdb=" N GLU C 91 " --> pdb=" O CYS C 239 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N GLY C 237 " --> pdb=" O PHE C 93 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 130 through 133 removed outlier: 3.586A pdb=" N SER C 174 " --> pdb=" O CYS C 157 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 181 through 183 Processing sheet with id=AC6, first strand: chain 'C' and resid 200 through 203 removed outlier: 5.835A pdb=" N ALA C 200 " --> pdb=" O ALA C 433 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N TYR C 435 " --> pdb=" O ALA C 200 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N MET C 434 " --> pdb=" O ILE C 424 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 271 through 273 removed outlier: 3.586A pdb=" N ILE C 271 " --> pdb=" O GLN C 287 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 374 through 378 removed outlier: 3.518A pdb=" N CYS C 331 " --> pdb=" O LEU C 416 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASN C 295 " --> pdb=" O ASN C 332 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 302 through 308 removed outlier: 6.222A pdb=" N LYS C 305 " --> pdb=" O THR C 320 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N THR C 320 " --> pdb=" O LYS C 305 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ILE C 307 " --> pdb=" O TYR C 318 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N TYR C 318 " --> pdb=" O ILE C 307 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 3 through 7 removed outlier: 3.556A pdb=" N SER G 21 " --> pdb=" O SER G 7 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 3 through 7 removed outlier: 3.556A pdb=" N SER G 21 " --> pdb=" O SER G 7 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 11 through 12 removed outlier: 6.711A pdb=" N TRP G 35 " --> pdb=" O ASP G 50 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ASP G 50 " --> pdb=" O TRP G 35 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N TRP G 36 " --> pdb=" O ILE G 48 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 11 through 12 removed outlier: 6.991A pdb=" N CYS G 92 " --> pdb=" O VAL G 102 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N VAL G 102 " --> pdb=" O CYS G 92 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ARG G 94 " --> pdb=" O MET G 100M" (cutoff:3.500A) removed outlier: 4.439A pdb=" N MET G 100M" --> pdb=" O ARG G 94 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ALA G 96 " --> pdb=" O TYR G 100K" (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'J' and resid 4 through 5 Processing sheet with id=AD6, first strand: chain 'J' and resid 9 through 13 removed outlier: 6.199A pdb=" N VAL J 11 " --> pdb=" O THR J 105 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASP J 85 " --> pdb=" O GLN J 38 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N TYR J 87 " --> pdb=" O TYR J 36 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N TRP J 35 " --> pdb=" O ILE J 47 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 9 through 13 removed outlier: 6.199A pdb=" N VAL J 11 " --> pdb=" O THR J 105 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER J 90 " --> pdb=" O MET J 97 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 498 through 499 removed outlier: 6.159A pdb=" N VAL D 36 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N THR F 606 " --> pdb=" O VAL D 36 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL D 38 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N CYS F 604 " --> pdb=" O VAL D 38 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 46 through 47 removed outlier: 4.060A pdb=" N LYS D 46 " --> pdb=" O LYS D 490 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA D 224 " --> pdb=" O VAL D 489 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N VAL D 242 " --> pdb=" O LEU D 86 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 53 through 54 removed outlier: 3.726A pdb=" N PHE D 53 " --> pdb=" O CYS D 218 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 91 through 93 removed outlier: 3.625A pdb=" N GLU D 91 " --> pdb=" O CYS D 239 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N GLY D 237 " --> pdb=" O PHE D 93 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 130 through 133 removed outlier: 3.586A pdb=" N SER D 174 " --> pdb=" O CYS D 157 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 181 through 183 Processing sheet with id=AE5, first strand: chain 'D' and resid 200 through 203 removed outlier: 5.835A pdb=" N ALA D 200 " --> pdb=" O ALA D 433 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N TYR D 435 " --> pdb=" O ALA D 200 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N THR D 202 " --> pdb=" O TYR D 435 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N MET D 434 " --> pdb=" O ILE D 424 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 271 through 273 removed outlier: 3.585A pdb=" N ILE D 271 " --> pdb=" O GLN D 287 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 374 through 378 removed outlier: 3.518A pdb=" N CYS D 331 " --> pdb=" O LEU D 416 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ALA D 329 " --> pdb=" O CYS D 418 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ASN D 295 " --> pdb=" O ASN D 332 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 302 through 308 removed outlier: 6.222A pdb=" N LYS D 305 " --> pdb=" O THR D 320 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N THR D 320 " --> pdb=" O LYS D 305 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ILE D 307 " --> pdb=" O TYR D 318 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N TYR D 318 " --> pdb=" O ILE D 307 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'I' and resid 3 through 7 removed outlier: 3.555A pdb=" N SER I 21 " --> pdb=" O SER I 7 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'I' and resid 3 through 7 removed outlier: 3.555A pdb=" N SER I 21 " --> pdb=" O SER I 7 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'I' and resid 11 through 12 removed outlier: 6.710A pdb=" N TRP I 35 " --> pdb=" O ASP I 50 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ASP I 50 " --> pdb=" O TRP I 35 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N TRP I 36 " --> pdb=" O ILE I 48 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'I' and resid 11 through 12 removed outlier: 6.991A pdb=" N CYS I 92 " --> pdb=" O VAL I 102 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N VAL I 102 " --> pdb=" O CYS I 92 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ARG I 94 " --> pdb=" O MET I 100M" (cutoff:3.500A) removed outlier: 4.438A pdb=" N MET I 100M" --> pdb=" O ARG I 94 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ALA I 96 " --> pdb=" O TYR I 100K" (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'K' and resid 4 through 5 Processing sheet with id=AF5, first strand: chain 'K' and resid 9 through 13 removed outlier: 6.198A pdb=" N VAL K 11 " --> pdb=" O THR K 105 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASP K 85 " --> pdb=" O GLN K 38 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N TYR K 87 " --> pdb=" O TYR K 36 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N TRP K 35 " --> pdb=" O ILE K 47 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'K' and resid 9 through 13 removed outlier: 6.198A pdb=" N VAL K 11 " --> pdb=" O THR K 105 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER K 90 " --> pdb=" O MET K 97 " (cutoff:3.500A) 577 hydrogen bonds defined for protein. 1461 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: 6.74 Time building geometry restraints manager: 7.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6156 1.34 - 1.46: 5223 1.46 - 1.58: 9033 1.58 - 1.70: 3 1.70 - 1.82: 168 Bond restraints: 20583 Sorted by residual: bond pdb=" C1 MAN S 10 " pdb=" O5 MAN S 10 " ideal model delta sigma weight residual 1.399 1.487 -0.088 2.00e-02 2.50e+03 1.93e+01 bond pdb=" C1 MAN m 10 " pdb=" O5 MAN m 10 " ideal model delta sigma weight residual 1.399 1.486 -0.087 2.00e-02 2.50e+03 1.91e+01 bond pdb=" C1 MAN c 10 " pdb=" O5 MAN c 10 " ideal model delta sigma weight residual 1.399 1.486 -0.087 2.00e-02 2.50e+03 1.89e+01 bond pdb=" C1 MAN c 10 " pdb=" C2 MAN c 10 " ideal model delta sigma weight residual 1.526 1.606 -0.080 2.00e-02 2.50e+03 1.60e+01 bond pdb=" C1 MAN m 10 " pdb=" C2 MAN m 10 " ideal model delta sigma weight residual 1.526 1.605 -0.079 2.00e-02 2.50e+03 1.58e+01 ... (remaining 20578 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.26: 26327 2.26 - 4.51: 1337 4.51 - 6.77: 206 6.77 - 9.02: 60 9.02 - 11.28: 33 Bond angle restraints: 27963 Sorted by residual: angle pdb=" C ASN D 136 " pdb=" N ASN D 137 " pdb=" CA ASN D 137 " ideal model delta sigma weight residual 121.54 132.82 -11.28 1.91e+00 2.74e-01 3.49e+01 angle pdb=" C ASN A 136 " pdb=" N ASN A 137 " pdb=" CA ASN A 137 " ideal model delta sigma weight residual 121.54 132.78 -11.24 1.91e+00 2.74e-01 3.46e+01 angle pdb=" C ASN C 136 " pdb=" N ASN C 137 " pdb=" CA ASN C 137 " ideal model delta sigma weight residual 121.54 132.78 -11.24 1.91e+00 2.74e-01 3.46e+01 angle pdb=" C ASN C 137 " pdb=" N ILE C 138 " pdb=" CA ILE C 138 " ideal model delta sigma weight residual 121.97 131.25 -9.28 1.80e+00 3.09e-01 2.66e+01 angle pdb=" C ASN D 137 " pdb=" N ILE D 138 " pdb=" CA ILE D 138 " ideal model delta sigma weight residual 121.97 131.23 -9.26 1.80e+00 3.09e-01 2.64e+01 ... (remaining 27958 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.50: 13315 22.50 - 45.00: 465 45.00 - 67.51: 133 67.51 - 90.01: 94 90.01 - 112.51: 60 Dihedral angle restraints: 14067 sinusoidal: 7278 harmonic: 6789 Sorted by residual: dihedral pdb=" CB CYS D 126 " pdb=" SG CYS D 126 " pdb=" SG CYS D 196 " pdb=" CB CYS D 196 " ideal model delta sinusoidal sigma weight residual 93.00 174.86 -81.86 1 1.00e+01 1.00e-02 8.24e+01 dihedral pdb=" CB CYS C 126 " pdb=" SG CYS C 126 " pdb=" SG CYS C 196 " pdb=" CB CYS C 196 " ideal model delta sinusoidal sigma weight residual 93.00 174.86 -81.86 1 1.00e+01 1.00e-02 8.24e+01 dihedral pdb=" CB CYS A 126 " pdb=" SG CYS A 126 " pdb=" SG CYS A 196 " pdb=" CB CYS A 196 " ideal model delta sinusoidal sigma weight residual 93.00 174.84 -81.84 1 1.00e+01 1.00e-02 8.24e+01 ... (remaining 14064 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 3140 0.099 - 0.198: 367 0.198 - 0.297: 30 0.297 - 0.396: 21 0.396 - 0.495: 3 Chirality restraints: 3561 Sorted by residual: chirality pdb=" C1 NAG Y 1 " pdb=" ND2 ASN C 197 " pdb=" C2 NAG Y 1 " pdb=" O5 NAG Y 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.91 -0.49 2.00e-01 2.50e+01 6.12e+00 chirality pdb=" C1 NAG O 1 " pdb=" ND2 ASN A 197 " pdb=" C2 NAG O 1 " pdb=" O5 NAG O 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.91 -0.49 2.00e-01 2.50e+01 5.88e+00 chirality pdb=" C1 NAG i 1 " pdb=" ND2 ASN D 197 " pdb=" C2 NAG i 1 " pdb=" O5 NAG i 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.92 -0.48 2.00e-01 2.50e+01 5.84e+00 ... (remaining 3558 not shown) Planarity restraints: 3393 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN H 26 " -0.035 2.00e-02 2.50e+03 3.62e-02 1.64e+01 pdb=" CG ASN H 26 " 0.015 2.00e-02 2.50e+03 pdb=" OD1 ASN H 26 " 0.013 2.00e-02 2.50e+03 pdb=" ND2 ASN H 26 " 0.053 2.00e-02 2.50e+03 pdb=" C1 NAG H 301 " -0.046 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 197 " 0.040 2.00e-02 2.50e+03 3.62e-02 1.64e+01 pdb=" CG ASN C 197 " -0.041 2.00e-02 2.50e+03 pdb=" OD1 ASN C 197 " -0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN C 197 " -0.039 2.00e-02 2.50e+03 pdb=" C1 NAG Y 1 " 0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 197 " 0.040 2.00e-02 2.50e+03 3.55e-02 1.58e+01 pdb=" CG ASN A 197 " -0.041 2.00e-02 2.50e+03 pdb=" OD1 ASN A 197 " -0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN A 197 " -0.038 2.00e-02 2.50e+03 pdb=" C1 NAG O 1 " 0.040 2.00e-02 2.50e+03 ... (remaining 3390 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 3928 2.77 - 3.30: 18011 3.30 - 3.84: 32493 3.84 - 4.37: 36517 4.37 - 4.90: 60722 Nonbonded interactions: 151671 Sorted by model distance: nonbonded pdb=" OD2 ASP H 50 " pdb=" O3 MAN U 6 " model vdw 2.240 3.040 nonbonded pdb=" NE2 HIS H 33 " pdb=" O2 MAN S 9 " model vdw 2.259 3.120 nonbonded pdb=" NH1 ARG H 29 " pdb=" O5 MAN S 7 " model vdw 2.263 3.120 nonbonded pdb=" O LEU F 646 " pdb=" ND2 ASN F 651 " model vdw 2.266 3.120 nonbonded pdb=" O LEU E 646 " pdb=" ND2 ASN E 651 " model vdw 2.267 3.120 ... (remaining 151666 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'W' selection = chain 'g' } ncs_group { reference = chain 'N' selection = chain 'O' selection = chain 'Q' selection = chain 'T' selection = chain 'V' selection = chain 'X' selection = chain 'Y' selection = chain 'a' selection = chain 'd' selection = chain 'f' selection = chain 'h' selection = chain 'i' selection = chain 'k' selection = chain 'n' selection = chain 'p' } ncs_group { reference = chain 'P' selection = chain 'U' selection = chain 'Z' selection = chain 'e' selection = chain 'j' selection = chain 'o' } ncs_group { reference = chain 'R' selection = chain 'b' selection = chain 'l' } ncs_group { reference = chain 'S' selection = chain 'c' selection = chain 'm' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.720 Check model and map are aligned: 0.130 Set scattering table: 0.180 Process input model: 45.570 Find NCS groups from input model: 1.010 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 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 : 0.008 0.113 20757 Z= 0.363 Angle : 1.247 11.579 28446 Z= 0.581 Chirality : 0.069 0.495 3561 Planarity : 0.007 0.060 3345 Dihedral : 16.006 112.510 9564 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.98 % Favored : 89.02 % Rotamer: Outliers : 0.29 % Allowed : 3.90 % Favored : 95.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.24 (0.15), residues: 2295 helix: -4.06 (0.14), residues: 324 sheet: -1.95 (0.18), residues: 693 loop : -3.05 (0.15), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.004 TRP B 614 HIS 0.007 0.002 HIS B 585 PHE 0.025 0.003 PHE I 78 TYR 0.031 0.004 TYR G 53 ARG 0.008 0.001 ARG H 29 Details of bonding type rmsd link_NAG-ASN : bond 0.01653 ( 48) link_NAG-ASN : angle 3.73170 ( 144) link_ALPHA1-6 : bond 0.00587 ( 9) link_ALPHA1-6 : angle 1.96880 ( 27) link_BETA1-4 : bond 0.00637 ( 45) link_BETA1-4 : angle 3.65174 ( 135) link_ALPHA1-2 : bond 0.00640 ( 18) link_ALPHA1-2 : angle 3.13979 ( 54) link_ALPHA1-3 : bond 0.01104 ( 15) link_ALPHA1-3 : angle 2.44953 ( 45) hydrogen bonds : bond 0.32048 ( 523) hydrogen bonds : angle 11.77462 ( 1461) SS BOND : bond 0.02346 ( 39) SS BOND : angle 1.88219 ( 78) covalent geometry : bond 0.00760 (20583) covalent geometry : angle 1.18416 (27963) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 286 time to evaluate : 2.070 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.8618 (ptm) cc_final: 0.7899 (ppp) REVERT: A 99 ASN cc_start: 0.8935 (m-40) cc_final: 0.8238 (t0) REVERT: A 195 ASN cc_start: 0.9061 (p0) cc_final: 0.8770 (p0) REVERT: B 606 THR cc_start: 0.8695 (p) cc_final: 0.8330 (t) REVERT: B 608 VAL cc_start: 0.9286 (p) cc_final: 0.9048 (p) REVERT: B 630 GLN cc_start: 0.9401 (mt0) cc_final: 0.9132 (mp10) REVERT: H 89 MET cc_start: 0.8723 (tpp) cc_final: 0.8368 (tpp) REVERT: L 97 MET cc_start: 0.8630 (pmm) cc_final: 0.8425 (pmm) REVERT: C 95 MET cc_start: 0.8539 (ptm) cc_final: 0.8027 (ppp) REVERT: C 195 ASN cc_start: 0.9091 (p0) cc_final: 0.8735 (p0) REVERT: E 574 LYS cc_start: 0.6968 (pttt) cc_final: 0.6638 (pttp) REVERT: E 606 THR cc_start: 0.8556 (p) cc_final: 0.8314 (t) REVERT: E 608 VAL cc_start: 0.9269 (p) cc_final: 0.9004 (p) REVERT: E 630 GLN cc_start: 0.9422 (mt0) cc_final: 0.9123 (mp10) REVERT: G 5 ARG cc_start: 0.8054 (ttt180) cc_final: 0.7818 (mtm-85) REVERT: G 32 ASP cc_start: 0.8282 (m-30) cc_final: 0.8065 (m-30) REVERT: G 89 MET cc_start: 0.8794 (tpp) cc_final: 0.8581 (tpp) REVERT: D 95 MET cc_start: 0.8695 (ptm) cc_final: 0.8137 (ppp) REVERT: D 99 ASN cc_start: 0.8838 (m-40) cc_final: 0.8248 (t0) REVERT: D 195 ASN cc_start: 0.9105 (p0) cc_final: 0.8515 (p0) REVERT: D 323 ILE cc_start: 0.9509 (OUTLIER) cc_final: 0.9243 (mp) REVERT: F 530 MET cc_start: 0.7685 (tpt) cc_final: 0.7281 (tpt) REVERT: F 542 ARG cc_start: 0.8449 (ptm-80) cc_final: 0.7769 (ttp80) REVERT: F 606 THR cc_start: 0.8600 (p) cc_final: 0.8288 (t) REVERT: F 608 VAL cc_start: 0.9153 (p) cc_final: 0.8881 (p) REVERT: F 648 GLU cc_start: 0.8644 (tt0) cc_final: 0.8364 (pt0) outliers start: 6 outliers final: 0 residues processed: 292 average time/residue: 0.3850 time to fit residues: 160.9480 Evaluate side-chains 144 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 143 time to evaluate : 2.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 192 optimal weight: 6.9990 chunk 172 optimal weight: 20.0000 chunk 95 optimal weight: 7.9990 chunk 59 optimal weight: 0.7980 chunk 116 optimal weight: 10.0000 chunk 92 optimal weight: 6.9990 chunk 178 optimal weight: 1.9990 chunk 69 optimal weight: 9.9990 chunk 108 optimal weight: 7.9990 chunk 133 optimal weight: 7.9990 chunk 207 optimal weight: 20.0000 overall best weight: 4.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 478 ASN ** B 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 GLN H 73 GLN C 103 GLN ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 478 ASN E 658 GLN G 73 GLN G 100JHIS D 103 GLN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 591 GLN F 658 GLN I 73 GLN I 100JHIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.041829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.034593 restraints weight = 176256.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.035562 restraints weight = 104172.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.036225 restraints weight = 72419.058| |-----------------------------------------------------------------------------| r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 20757 Z= 0.234 Angle : 0.927 10.430 28446 Z= 0.436 Chirality : 0.052 0.317 3561 Planarity : 0.006 0.063 3345 Dihedral : 14.643 73.812 5238 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.85 % Favored : 89.02 % Rotamer: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.56 (0.16), residues: 2295 helix: -3.00 (0.20), residues: 354 sheet: -1.69 (0.19), residues: 639 loop : -2.58 (0.16), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP F 596 HIS 0.008 0.002 HIS D 352 PHE 0.015 0.002 PHE G 78 TYR 0.016 0.002 TYR H 59 ARG 0.008 0.001 ARG G 66 Details of bonding type rmsd link_NAG-ASN : bond 0.00365 ( 48) link_NAG-ASN : angle 2.57232 ( 144) link_ALPHA1-6 : bond 0.00837 ( 9) link_ALPHA1-6 : angle 1.97185 ( 27) link_BETA1-4 : bond 0.00431 ( 45) link_BETA1-4 : angle 2.70983 ( 135) link_ALPHA1-2 : bond 0.00239 ( 18) link_ALPHA1-2 : angle 2.27995 ( 54) link_ALPHA1-3 : bond 0.01471 ( 15) link_ALPHA1-3 : angle 3.17183 ( 45) hydrogen bonds : bond 0.05496 ( 523) hydrogen bonds : angle 7.87856 ( 1461) SS BOND : bond 0.00296 ( 39) SS BOND : angle 1.03467 ( 78) covalent geometry : bond 0.00501 (20583) covalent geometry : angle 0.87811 (27963) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 196 time to evaluate : 2.208 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.8615 (ptm) cc_final: 0.8165 (ppp) REVERT: A 99 ASN cc_start: 0.8908 (m-40) cc_final: 0.8228 (t0) REVERT: B 607 ASN cc_start: 0.8989 (p0) cc_final: 0.8281 (m-40) REVERT: B 651 ASN cc_start: 0.8058 (m-40) cc_final: 0.7635 (m-40) REVERT: H 86 ASP cc_start: 0.7966 (m-30) cc_final: 0.7694 (m-30) REVERT: H 89 MET cc_start: 0.8600 (tpp) cc_final: 0.8392 (tpp) REVERT: L 4 LEU cc_start: 0.8358 (mt) cc_final: 0.7952 (mt) REVERT: C 95 MET cc_start: 0.8515 (ptm) cc_final: 0.8207 (ppp) REVERT: E 574 LYS cc_start: 0.6786 (pttt) cc_final: 0.6523 (pttp) REVERT: E 607 ASN cc_start: 0.8969 (p0) cc_final: 0.8313 (m-40) REVERT: E 630 GLN cc_start: 0.9331 (mt0) cc_final: 0.9084 (mt0) REVERT: E 651 ASN cc_start: 0.7937 (m-40) cc_final: 0.7473 (m-40) REVERT: G 5 ARG cc_start: 0.8084 (ttt180) cc_final: 0.7804 (mtm-85) REVERT: G 86 ASP cc_start: 0.8162 (m-30) cc_final: 0.7819 (m-30) REVERT: J 4 LEU cc_start: 0.8787 (mt) cc_final: 0.8584 (mp) REVERT: D 95 MET cc_start: 0.8695 (ptm) cc_final: 0.8276 (ppp) REVERT: D 99 ASN cc_start: 0.8897 (m-40) cc_final: 0.8169 (t0) REVERT: D 195 ASN cc_start: 0.9119 (p0) cc_final: 0.8686 (p0) REVERT: F 542 ARG cc_start: 0.8561 (ptm-80) cc_final: 0.7941 (ttp80) REVERT: F 607 ASN cc_start: 0.8899 (p0) cc_final: 0.8335 (m-40) REVERT: F 651 ASN cc_start: 0.8424 (m-40) cc_final: 0.8175 (m-40) REVERT: F 660 LEU cc_start: 0.8778 (mm) cc_final: 0.8525 (pp) outliers start: 0 outliers final: 0 residues processed: 196 average time/residue: 0.3378 time to fit residues: 100.2138 Evaluate side-chains 126 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 2.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 88 optimal weight: 6.9990 chunk 137 optimal weight: 0.1980 chunk 90 optimal weight: 2.9990 chunk 44 optimal weight: 0.0170 chunk 22 optimal weight: 6.9990 chunk 32 optimal weight: 5.9990 chunk 55 optimal weight: 30.0000 chunk 220 optimal weight: 10.0000 chunk 57 optimal weight: 20.0000 chunk 68 optimal weight: 5.9990 chunk 118 optimal weight: 6.9990 overall best weight: 3.0424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 136 ASN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 478 ASN ** F 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.041658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.034411 restraints weight = 175690.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.035389 restraints weight = 103066.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.036053 restraints weight = 71444.299| |-----------------------------------------------------------------------------| r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.2821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 20757 Z= 0.165 Angle : 0.825 9.371 28446 Z= 0.383 Chirality : 0.049 0.313 3561 Planarity : 0.004 0.046 3345 Dihedral : 12.218 73.962 5238 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.24 % Favored : 90.63 % Rotamer: Outliers : 0.05 % Allowed : 3.56 % Favored : 96.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.18 (0.16), residues: 2295 helix: -2.25 (0.24), residues: 372 sheet: -1.27 (0.19), residues: 639 loop : -2.58 (0.16), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP F 628 HIS 0.005 0.001 HIS A 352 PHE 0.015 0.002 PHE H 78 TYR 0.013 0.001 TYR F 586 ARG 0.006 0.000 ARG G 94 Details of bonding type rmsd link_NAG-ASN : bond 0.00232 ( 48) link_NAG-ASN : angle 2.31449 ( 144) link_ALPHA1-6 : bond 0.00751 ( 9) link_ALPHA1-6 : angle 2.03214 ( 27) link_BETA1-4 : bond 0.00391 ( 45) link_BETA1-4 : angle 2.29882 ( 135) link_ALPHA1-2 : bond 0.00372 ( 18) link_ALPHA1-2 : angle 2.26065 ( 54) link_ALPHA1-3 : bond 0.01658 ( 15) link_ALPHA1-3 : angle 2.72060 ( 45) hydrogen bonds : bond 0.04571 ( 523) hydrogen bonds : angle 7.02274 ( 1461) SS BOND : bond 0.00232 ( 39) SS BOND : angle 0.76056 ( 78) covalent geometry : bond 0.00357 (20583) covalent geometry : angle 0.78180 (27963) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 179 time to evaluate : 2.399 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.8545 (ptm) cc_final: 0.8286 (ppp) REVERT: A 99 ASN cc_start: 0.8892 (m-40) cc_final: 0.8211 (t0) REVERT: B 630 GLN cc_start: 0.8739 (pp30) cc_final: 0.7958 (pp30) REVERT: B 651 ASN cc_start: 0.7939 (m-40) cc_final: 0.6929 (m-40) REVERT: H 86 ASP cc_start: 0.7972 (m-30) cc_final: 0.7725 (m-30) REVERT: H 89 MET cc_start: 0.8572 (tpp) cc_final: 0.8286 (tpp) REVERT: L 4 LEU cc_start: 0.8411 (mt) cc_final: 0.8003 (mt) REVERT: C 95 MET cc_start: 0.8460 (ptm) cc_final: 0.8002 (ppp) REVERT: E 574 LYS cc_start: 0.6703 (pttt) cc_final: 0.6474 (pttp) REVERT: E 626 MET cc_start: 0.7684 (tmm) cc_final: 0.6909 (tmm) REVERT: E 630 GLN cc_start: 0.9361 (mt0) cc_final: 0.8998 (tm-30) REVERT: E 651 ASN cc_start: 0.8000 (m-40) cc_final: 0.7729 (m-40) REVERT: E 660 LEU cc_start: 0.8708 (mm) cc_final: 0.8467 (pp) REVERT: G 82 MET cc_start: 0.8822 (tmm) cc_final: 0.8607 (tmm) REVERT: G 86 ASP cc_start: 0.8010 (m-30) cc_final: 0.7792 (m-30) REVERT: G 100 GLU cc_start: 0.8669 (mm-30) cc_final: 0.7726 (mp0) REVERT: D 95 MET cc_start: 0.8629 (ptm) cc_final: 0.8408 (ppp) REVERT: D 99 ASN cc_start: 0.8870 (m-40) cc_final: 0.8201 (t0) REVERT: D 136 ASN cc_start: 0.5120 (OUTLIER) cc_final: 0.4733 (p0) REVERT: D 195 ASN cc_start: 0.9013 (p0) cc_final: 0.8613 (p0) REVERT: F 591 GLN cc_start: 0.8322 (pt0) cc_final: 0.7911 (tt0) REVERT: F 607 ASN cc_start: 0.8802 (p0) cc_final: 0.8266 (m-40) REVERT: F 651 ASN cc_start: 0.8120 (m-40) cc_final: 0.7453 (m-40) REVERT: F 660 LEU cc_start: 0.8822 (mm) cc_final: 0.8588 (pp) REVERT: I 63 LEU cc_start: 0.9155 (mt) cc_final: 0.8942 (mt) REVERT: I 81 LYS cc_start: 0.9004 (pttt) cc_final: 0.8744 (pttp) outliers start: 1 outliers final: 0 residues processed: 180 average time/residue: 0.3343 time to fit residues: 91.8008 Evaluate side-chains 123 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 122 time to evaluate : 2.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 49 optimal weight: 20.0000 chunk 224 optimal weight: 20.0000 chunk 209 optimal weight: 20.0000 chunk 19 optimal weight: 5.9990 chunk 117 optimal weight: 7.9990 chunk 218 optimal weight: 6.9990 chunk 161 optimal weight: 8.9990 chunk 168 optimal weight: 20.0000 chunk 208 optimal weight: 5.9990 chunk 191 optimal weight: 20.0000 chunk 130 optimal weight: 4.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 HIS ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 591 GLN ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 591 GLN D 105 HIS ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.039732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2714 r_free = 0.2714 target = 0.032535 restraints weight = 180466.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.033477 restraints weight = 106552.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.034132 restraints weight = 74203.459| |-----------------------------------------------------------------------------| r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.3549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 20757 Z= 0.274 Angle : 0.944 12.106 28446 Z= 0.435 Chirality : 0.050 0.285 3561 Planarity : 0.005 0.046 3345 Dihedral : 11.145 69.862 5238 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.13 % Allowed : 11.07 % Favored : 88.80 % Rotamer: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.07 (0.16), residues: 2295 helix: -2.10 (0.24), residues: 348 sheet: -1.15 (0.20), residues: 657 loop : -2.57 (0.16), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP F 596 HIS 0.006 0.002 HIS A 352 PHE 0.019 0.002 PHE H 78 TYR 0.019 0.002 TYR A 177 ARG 0.009 0.001 ARG D 350 Details of bonding type rmsd link_NAG-ASN : bond 0.00514 ( 48) link_NAG-ASN : angle 2.41786 ( 144) link_ALPHA1-6 : bond 0.00917 ( 9) link_ALPHA1-6 : angle 2.18618 ( 27) link_BETA1-4 : bond 0.00410 ( 45) link_BETA1-4 : angle 2.47020 ( 135) link_ALPHA1-2 : bond 0.00389 ( 18) link_ALPHA1-2 : angle 2.35339 ( 54) link_ALPHA1-3 : bond 0.01598 ( 15) link_ALPHA1-3 : angle 3.08625 ( 45) hydrogen bonds : bond 0.04401 ( 523) hydrogen bonds : angle 6.96255 ( 1461) SS BOND : bond 0.00366 ( 39) SS BOND : angle 1.10148 ( 78) covalent geometry : bond 0.00600 (20583) covalent geometry : angle 0.90129 (27963) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 2.296 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.8714 (ptm) cc_final: 0.8214 (ppp) REVERT: A 99 ASN cc_start: 0.8895 (m-40) cc_final: 0.8187 (t0) REVERT: B 607 ASN cc_start: 0.8973 (p0) cc_final: 0.8064 (m110) REVERT: B 651 ASN cc_start: 0.8176 (m-40) cc_final: 0.7967 (m-40) REVERT: L 4 LEU cc_start: 0.8511 (mt) cc_final: 0.8153 (mt) REVERT: C 95 MET cc_start: 0.8679 (ptm) cc_final: 0.8148 (ppp) REVERT: E 630 GLN cc_start: 0.9447 (mt0) cc_final: 0.9231 (mt0) REVERT: E 631 TRP cc_start: 0.8314 (t60) cc_final: 0.7622 (t60) REVERT: E 651 ASN cc_start: 0.8297 (m-40) cc_final: 0.8029 (m-40) REVERT: G 100 GLU cc_start: 0.8949 (mm-30) cc_final: 0.8084 (mp0) REVERT: D 95 MET cc_start: 0.8753 (ptm) cc_final: 0.8315 (ppp) REVERT: D 99 ASN cc_start: 0.8867 (m-40) cc_final: 0.8114 (t0) REVERT: D 195 ASN cc_start: 0.9181 (p0) cc_final: 0.8823 (p0) REVERT: D 350 ARG cc_start: 0.7845 (ttp80) cc_final: 0.7581 (ttt-90) REVERT: F 591 GLN cc_start: 0.8474 (pt0) cc_final: 0.8146 (tt0) REVERT: F 607 ASN cc_start: 0.8942 (p0) cc_final: 0.8008 (m-40) REVERT: F 651 ASN cc_start: 0.8311 (m-40) cc_final: 0.8087 (m-40) REVERT: F 660 LEU cc_start: 0.8889 (mm) cc_final: 0.8676 (pp) REVERT: I 63 LEU cc_start: 0.9247 (mt) cc_final: 0.9021 (mt) outliers start: 0 outliers final: 0 residues processed: 149 average time/residue: 0.3183 time to fit residues: 74.2406 Evaluate side-chains 112 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 2.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 124 optimal weight: 7.9990 chunk 75 optimal weight: 9.9990 chunk 171 optimal weight: 8.9990 chunk 4 optimal weight: 5.9990 chunk 189 optimal weight: 10.0000 chunk 103 optimal weight: 5.9990 chunk 72 optimal weight: 8.9990 chunk 19 optimal weight: 8.9990 chunk 64 optimal weight: 9.9990 chunk 148 optimal weight: 9.9990 chunk 13 optimal weight: 10.0000 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 105 HIS ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 591 GLN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.038530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2662 r_free = 0.2662 target = 0.031238 restraints weight = 178976.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2701 r_free = 0.2701 target = 0.032198 restraints weight = 103411.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.032848 restraints weight = 71095.340| |-----------------------------------------------------------------------------| r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.4232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.080 20757 Z= 0.302 Angle : 0.987 14.636 28446 Z= 0.454 Chirality : 0.051 0.326 3561 Planarity : 0.005 0.057 3345 Dihedral : 10.854 69.078 5238 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 15.72 Ramachandran Plot: Outliers : 0.09 % Allowed : 11.02 % Favored : 88.89 % Rotamer: Outliers : 0.10 % Allowed : 2.89 % Favored : 97.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.16 (0.16), residues: 2295 helix: -2.06 (0.24), residues: 348 sheet: -1.26 (0.19), residues: 720 loop : -2.69 (0.16), residues: 1227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP F 628 HIS 0.012 0.002 HIS E 585 PHE 0.020 0.003 PHE C 382 TYR 0.028 0.003 TYR A 217 ARG 0.010 0.001 ARG H 64 Details of bonding type rmsd link_NAG-ASN : bond 0.00603 ( 48) link_NAG-ASN : angle 2.65021 ( 144) link_ALPHA1-6 : bond 0.00873 ( 9) link_ALPHA1-6 : angle 2.30107 ( 27) link_BETA1-4 : bond 0.00436 ( 45) link_BETA1-4 : angle 2.38030 ( 135) link_ALPHA1-2 : bond 0.00487 ( 18) link_ALPHA1-2 : angle 2.43269 ( 54) link_ALPHA1-3 : bond 0.01618 ( 15) link_ALPHA1-3 : angle 2.98602 ( 45) hydrogen bonds : bond 0.04483 ( 523) hydrogen bonds : angle 7.01463 ( 1461) SS BOND : bond 0.00579 ( 39) SS BOND : angle 1.28940 ( 78) covalent geometry : bond 0.00652 (20583) covalent geometry : angle 0.94422 (27963) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4590 Ramachandran restraints generated. 2295 Oldfield, 0 Emsley, 2295 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 145 time to evaluate : 2.066 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: 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: A 99 ASN cc_start: 0.8859 (m-40) cc_final: 0.8209 (t0) REVERT: H 63 LEU cc_start: 0.8935 (mt) cc_final: 0.8704 (mt) REVERT: H 82 MET cc_start: 0.8958 (tmm) cc_final: 0.8687 (tmm) REVERT: H 89 MET cc_start: 0.8476 (tpt) cc_final: 0.7955 (tpp) REVERT: H 100 GLU cc_start: 0.8782 (mm-30) cc_final: 0.8252 (mp0) REVERT: C 95 MET cc_start: 0.8736 (ptm) cc_final: 0.8370 (ppp) REVERT: C 161 MET cc_start: 0.8696 (tpp) cc_final: 0.8434 (tpt) REVERT: E 626 MET cc_start: 0.7913 (tmm) cc_final: 0.7072 (tmm) REVERT: E 647 GLU cc_start: 0.9155 (pm20) cc_final: 0.8810 (pm20) REVERT: E 651 ASN cc_start: 0.8663 (m-40) cc_final: 0.8462 (m-40) REVERT: G 63 LEU cc_start: 0.9154 (mt) cc_final: 0.8948 (mt) REVERT: G 100 GLU cc_start: 0.8939 (mm-30) cc_final: 0.8292 (mm-30) REVERT: D 95 MET cc_start: 0.8835 (ptm) cc_final: 0.8453 (ppp) REVERT: D 99 ASN cc_start: 0.8876 (m-40) cc_final: 0.8174 (t0) REVERT: D 161 MET cc_start: 0.8670 (tpp) cc_final: 0.8466 (tpt) REVERT: D 195 ASN cc_start: 0.9117 (p0) cc_final: 0.8732 (p0) REVERT: F 651 ASN cc_start: 0.8600 (m-40) cc_final: 0.8355 (m-40) REVERT: F 660 LEU cc_start: 0.8740 (mm) cc_final: 0.8505 (pp) REVERT: I 63 LEU cc_start: 0.9180 (mt) cc_final: 0.8975 (mt) outliers start: 2 outliers final: 0 residues processed: 147 average time/residue: 0.3018 time to fit residues: 70.3913 Evaluate side-chains 108 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 2.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.1747 > 50: distance: 22 - 120: 34.825 distance: 25 - 117: 35.917 distance: 38 - 105: 31.259 distance: 41 - 102: 32.431 distance: 83 - 113: 36.734 distance: 86 - 110: 36.827 distance: 97 - 102: 35.902 distance: 102 - 103: 9.476 distance: 103 - 104: 39.958 distance: 103 - 106: 49.138 distance: 104 - 105: 49.400 distance: 104 - 110: 56.652 distance: 106 - 107: 51.068 distance: 107 - 108: 45.340 distance: 107 - 109: 10.274 distance: 111 - 112: 40.758 distance: 112 - 113: 40.176 distance: 112 - 117: 39.564 distance: 114 - 116: 41.366 distance: 117 - 118: 39.460 distance: 118 - 119: 44.855 distance: 118 - 121: 40.924 distance: 119 - 120: 42.562 distance: 119 - 125: 43.758 distance: 121 - 123: 39.217 distance: 122 - 124: 39.081 distance: 125 - 126: 40.448 distance: 126 - 127: 41.208 distance: 126 - 129: 39.597 distance: 127 - 128: 42.251 distance: 127 - 136: 63.369 distance: 130 - 131: 56.573 distance: 131 - 132: 6.043 distance: 132 - 133: 12.560 distance: 133 - 134: 29.821 distance: 133 - 135: 27.418 distance: 137 - 138: 40.264 distance: 138 - 140: 40.535 distance: 140 - 141: 52.695 distance: 141 - 142: 41.440 distance: 141 - 144: 39.880 distance: 142 - 147: 57.417 distance: 147 - 148: 38.777 distance: 149 - 150: 39.867 distance: 149 - 156: 19.167 distance: 151 - 152: 49.160 distance: 152 - 153: 29.676 distance: 156 - 157: 17.747 distance: 157 - 158: 19.391 distance: 157 - 160: 26.665 distance: 158 - 159: 46.184 distance: 158 - 161: 18.207 distance: 161 - 162: 54.319 distance: 162 - 163: 6.673 distance: 162 - 165: 40.910 distance: 163 - 164: 31.846 distance: 163 - 169: 40.440 distance: 165 - 166: 45.694 distance: 166 - 167: 15.013 distance: 166 - 168: 17.450 distance: 169 - 170: 56.783 distance: 170 - 173: 61.566 distance: 171 - 172: 38.968 distance: 171 - 177: 35.427 distance: 173 - 174: 34.279 distance: 174 - 175: 52.966 distance: 174 - 176: 54.240