Starting phenix.real_space_refine on Wed Nov 19 03:55:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6dfg_7875/11_2025/6dfg_7875.cif Found real_map, /net/cci-nas-00/data/ceres_data/6dfg_7875/11_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 { model { file = "/net/cci-nas-00/data/ceres_data/6dfg_7875/11_2025/6dfg_7875.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6dfg_7875/11_2025/6dfg_7875.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6dfg_7875/11_2025/6dfg_7875.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6dfg_7875/11_2025/6dfg_7875.map" } resolution = 4.42 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/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: 5.01, per 1000 atoms: 0.25 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: 2.31 Conformation dependent library (CDL) restraints added in 843.7 milliseconds 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: 0.99 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: 4.23 Time building geometry restraints manager: 2.87 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: 0.05 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: 1.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 20.520 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.070 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: 0.000 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.510 ------------------------------------------------------------------------------- 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 : 7.73 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -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 ARG 0.008 0.001 ARG H 29 TYR 0.031 0.004 TYR G 53 PHE 0.025 0.003 PHE I 78 TRP 0.034 0.004 TRP B 614 HIS 0.007 0.002 HIS B 585 Details of bonding type rmsd covalent geometry : bond 0.00760 (20583) covalent geometry : angle 1.18416 (27963) SS BOND : bond 0.02346 ( 39) SS BOND : angle 1.88219 ( 78) hydrogen bonds : bond 0.32048 ( 523) hydrogen bonds : angle 11.77462 ( 1461) 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) 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_NAG-ASN : bond 0.01653 ( 48) link_NAG-ASN : angle 3.73170 ( 144) *********************** 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 : 0.782 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.8618 (ptm) cc_final: 0.7896 (ppp) REVERT: A 99 ASN cc_start: 0.8935 (m-40) cc_final: 0.8230 (t0) REVERT: A 195 ASN cc_start: 0.9061 (p0) cc_final: 0.8773 (p0) REVERT: B 606 THR cc_start: 0.8695 (p) cc_final: 0.8311 (t) REVERT: B 608 VAL cc_start: 0.9286 (p) cc_final: 0.9044 (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: 0.8369 (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: 0.8022 (ppp) REVERT: C 195 ASN cc_start: 0.9091 (p0) cc_final: 0.8741 (p0) REVERT: E 574 LYS cc_start: 0.6968 (pttt) cc_final: 0.6612 (pttp) REVERT: E 606 THR cc_start: 0.8556 (p) cc_final: 0.8288 (t) REVERT: E 608 VAL cc_start: 0.9269 (p) cc_final: 0.9010 (p) REVERT: E 630 GLN cc_start: 0.9422 (mt0) cc_final: 0.9124 (mp10) REVERT: G 5 ARG cc_start: 0.8054 (ttt180) cc_final: 0.7814 (mtm-85) REVERT: G 32 ASP cc_start: 0.8282 (m-30) cc_final: 0.8067 (m-30) REVERT: G 89 MET cc_start: 0.8794 (tpp) cc_final: 0.8583 (tpp) REVERT: D 95 MET cc_start: 0.8695 (ptm) cc_final: 0.8131 (ppp) REVERT: D 99 ASN cc_start: 0.8838 (m-40) cc_final: 0.8228 (t0) REVERT: D 195 ASN cc_start: 0.9105 (p0) cc_final: 0.8623 (p0) REVERT: D 323 ILE cc_start: 0.9509 (OUTLIER) cc_final: 0.9244 (mp) REVERT: F 530 MET cc_start: 0.7685 (tpt) cc_final: 0.7285 (tpt) REVERT: F 542 ARG cc_start: 0.8449 (ptm-80) cc_final: 0.7757 (ttp80) REVERT: F 608 VAL cc_start: 0.9153 (p) cc_final: 0.8790 (p) REVERT: F 648 GLU cc_start: 0.8644 (tt0) cc_final: 0.8367 (pt0) outliers start: 6 outliers final: 0 residues processed: 292 average time/residue: 0.1889 time to fit residues: 78.9890 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 : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 216 optimal weight: 6.9990 chunk 98 optimal weight: 7.9990 chunk 194 optimal weight: 4.9990 chunk 227 optimal weight: 9.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 10.0000 chunk 200 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 103 GLN A 105 HIS ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 103 GLN ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 658 GLN G 100JHIS D 103 GLN D 105 HIS ** 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: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.041128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.033996 restraints weight = 176328.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.034946 restraints weight = 104197.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.035592 restraints weight = 72480.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.036041 restraints weight = 56094.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.036339 restraints weight = 46771.429| |-----------------------------------------------------------------------------| r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.091 20757 Z= 0.281 Angle : 0.987 10.640 28446 Z= 0.463 Chirality : 0.053 0.323 3561 Planarity : 0.006 0.060 3345 Dihedral : 14.688 73.732 5238 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 13.53 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.68 % Favored : 89.19 % Rotamer: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.62 (0.16), residues: 2295 helix: -3.06 (0.20), residues: 363 sheet: -1.77 (0.19), residues: 639 loop : -2.59 (0.16), residues: 1293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG L 61 TYR 0.032 0.003 TYR H 59 PHE 0.017 0.002 PHE G 78 TRP 0.037 0.003 TRP F 596 HIS 0.008 0.002 HIS H 52 Details of bonding type rmsd covalent geometry : bond 0.00606 (20583) covalent geometry : angle 0.93830 (27963) SS BOND : bond 0.00355 ( 39) SS BOND : angle 1.12356 ( 78) hydrogen bonds : bond 0.05591 ( 523) hydrogen bonds : angle 7.93840 ( 1461) link_ALPHA1-2 : bond 0.00300 ( 18) link_ALPHA1-2 : angle 2.37929 ( 54) link_ALPHA1-3 : bond 0.01378 ( 15) link_ALPHA1-3 : angle 3.36760 ( 45) link_ALPHA1-6 : bond 0.00858 ( 9) link_ALPHA1-6 : angle 2.18965 ( 27) link_BETA1-4 : bond 0.00387 ( 45) link_BETA1-4 : angle 2.76230 ( 135) link_NAG-ASN : bond 0.00469 ( 48) link_NAG-ASN : angle 2.64977 ( 144) *********************** 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 176 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 0.912 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: 0.8700 (ptm) cc_final: 0.8270 (ppp) REVERT: A 99 ASN cc_start: 0.8900 (m-40) cc_final: 0.8270 (t0) REVERT: A 104 MET cc_start: 0.8870 (tpt) cc_final: 0.8646 (tpt) REVERT: A 195 ASN cc_start: 0.9121 (p0) cc_final: 0.8781 (p0) REVERT: A 426 MET cc_start: 0.8319 (ttm) cc_final: 0.8089 (ttm) REVERT: B 606 THR cc_start: 0.8583 (p) cc_final: 0.8214 (t) REVERT: B 651 ASN cc_start: 0.8287 (m-40) cc_final: 0.8037 (m-40) REVERT: H 86 ASP cc_start: 0.7987 (m-30) cc_final: 0.7605 (m-30) REVERT: H 89 MET cc_start: 0.8486 (tpp) cc_final: 0.8252 (tpp) REVERT: L 4 LEU cc_start: 0.8517 (mt) cc_final: 0.8200 (mt) REVERT: C 95 MET cc_start: 0.8653 (ptm) cc_final: 0.8341 (ppp) REVERT: C 104 MET cc_start: 0.8824 (tpt) cc_final: 0.8612 (tpt) REVERT: C 426 MET cc_start: 0.8416 (ttm) cc_final: 0.8174 (ttm) REVERT: E 574 LYS cc_start: 0.6607 (pttt) cc_final: 0.6357 (pttp) REVERT: E 606 THR cc_start: 0.8519 (p) cc_final: 0.8254 (t) REVERT: E 607 ASN cc_start: 0.8552 (p0) cc_final: 0.8075 (m-40) REVERT: E 630 GLN cc_start: 0.9321 (mt0) cc_final: 0.9056 (mt0) REVERT: E 647 GLU cc_start: 0.8727 (pm20) cc_final: 0.8282 (pm20) REVERT: E 651 ASN cc_start: 0.8266 (m-40) cc_final: 0.8061 (m-40) REVERT: G 13 LYS cc_start: 0.8038 (mmtt) cc_final: 0.7478 (tppt) REVERT: G 86 ASP cc_start: 0.8199 (m-30) cc_final: 0.7867 (m-30) REVERT: G 100 GLU cc_start: 0.8611 (mm-30) cc_final: 0.7689 (mp0) REVERT: D 95 MET cc_start: 0.8770 (ptm) cc_final: 0.8375 (ppp) REVERT: D 99 ASN cc_start: 0.8857 (m-40) cc_final: 0.8203 (t0) REVERT: D 104 MET cc_start: 0.8755 (tpt) cc_final: 0.8500 (tpt) REVERT: D 195 ASN cc_start: 0.9087 (p0) cc_final: 0.8735 (p0) REVERT: F 542 ARG cc_start: 0.8593 (ptm-80) cc_final: 0.8030 (ttp80) REVERT: F 590 GLN cc_start: 0.8581 (tm-30) cc_final: 0.8371 (tm-30) REVERT: F 648 GLU cc_start: 0.9022 (tt0) cc_final: 0.8680 (pt0) REVERT: F 650 GLN cc_start: 0.7909 (tt0) cc_final: 0.7671 (mm110) REVERT: F 660 LEU cc_start: 0.8684 (mm) cc_final: 0.8478 (pp) REVERT: K 4 LEU cc_start: 0.8617 (mt) cc_final: 0.8315 (mt) outliers start: 0 outliers final: 0 residues processed: 176 average time/residue: 0.1706 time to fit residues: 45.3545 Evaluate side-chains 121 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 135 optimal weight: 7.9990 chunk 9 optimal weight: 7.9990 chunk 183 optimal weight: 9.9990 chunk 186 optimal weight: 30.0000 chunk 218 optimal weight: 0.7980 chunk 100 optimal weight: 6.9990 chunk 115 optimal weight: 30.0000 chunk 211 optimal weight: 6.9990 chunk 54 optimal weight: 1.9990 chunk 77 optimal weight: 0.3980 chunk 126 optimal weight: 9.9990 overall best weight: 3.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 ASN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 478 ASN ** B 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 73 GLN C 136 ASN ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 478 ASN D 136 ASN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 478 ASN ** F 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.041221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.033974 restraints weight = 175915.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.034952 restraints weight = 102712.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.035628 restraints weight = 70899.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.036083 restraints weight = 54558.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.036391 restraints weight = 45456.963| |-----------------------------------------------------------------------------| r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.2896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 20757 Z= 0.173 Angle : 0.837 9.506 28446 Z= 0.387 Chirality : 0.049 0.317 3561 Planarity : 0.004 0.047 3345 Dihedral : 12.349 73.750 5238 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.15 % Favored : 90.72 % Rotamer: Outliers : 0.14 % Allowed : 3.52 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.23 (0.16), residues: 2295 helix: -2.34 (0.23), residues: 375 sheet: -1.38 (0.19), residues: 636 loop : -2.55 (0.16), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 64 TYR 0.015 0.002 TYR F 586 PHE 0.015 0.002 PHE H 78 TRP 0.039 0.002 TRP B 596 HIS 0.005 0.001 HIS A 352 Details of bonding type rmsd covalent geometry : bond 0.00370 (20583) covalent geometry : angle 0.79510 (27963) SS BOND : bond 0.00208 ( 39) SS BOND : angle 0.76950 ( 78) hydrogen bonds : bond 0.04607 ( 523) hydrogen bonds : angle 7.09920 ( 1461) link_ALPHA1-2 : bond 0.00276 ( 18) link_ALPHA1-2 : angle 2.12632 ( 54) link_ALPHA1-3 : bond 0.01646 ( 15) link_ALPHA1-3 : angle 2.67104 ( 45) link_ALPHA1-6 : bond 0.00752 ( 9) link_ALPHA1-6 : angle 1.88419 ( 27) link_BETA1-4 : bond 0.00356 ( 45) link_BETA1-4 : angle 2.31206 ( 135) link_NAG-ASN : bond 0.00246 ( 48) link_NAG-ASN : angle 2.37469 ( 144) *********************** 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 179 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 176 time to evaluate : 0.701 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: 0.8612 (ptm) cc_final: 0.8409 (ppp) REVERT: A 99 ASN cc_start: 0.8843 (m-40) cc_final: 0.8268 (t0) REVERT: A 195 ASN cc_start: 0.8946 (p0) cc_final: 0.8735 (p0) REVERT: B 606 THR cc_start: 0.8410 (p) cc_final: 0.8130 (t) REVERT: B 630 GLN cc_start: 0.8670 (pp30) cc_final: 0.7963 (pp30) REVERT: H 13 LYS cc_start: 0.7724 (mmtt) cc_final: 0.7505 (tptt) REVERT: H 82 MET cc_start: 0.6615 (mpp) cc_final: 0.6363 (mpp) REVERT: H 86 ASP cc_start: 0.7982 (m-30) cc_final: 0.7754 (m-30) REVERT: H 100 GLU cc_start: 0.8496 (mm-30) cc_final: 0.8234 (mm-30) REVERT: L 4 LEU cc_start: 0.8399 (mt) cc_final: 0.8114 (mt) REVERT: C 95 MET cc_start: 0.8547 (ptm) cc_final: 0.8153 (ppp) REVERT: E 606 THR cc_start: 0.8524 (p) cc_final: 0.8317 (t) REVERT: E 626 MET cc_start: 0.7776 (tmm) cc_final: 0.5799 (tmm) REVERT: E 630 GLN cc_start: 0.9291 (mt0) cc_final: 0.8992 (tm-30) REVERT: E 651 ASN cc_start: 0.8313 (m-40) cc_final: 0.7797 (m-40) REVERT: G 82 MET cc_start: 0.7212 (mmp) cc_final: 0.6780 (mmm) REVERT: G 100 GLU cc_start: 0.8574 (mm-30) cc_final: 0.7653 (mp0) REVERT: D 99 ASN cc_start: 0.8841 (m-40) cc_final: 0.8232 (t0) REVERT: D 136 ASN cc_start: 0.5404 (OUTLIER) cc_final: 0.5033 (p0) REVERT: D 195 ASN cc_start: 0.8910 (p0) cc_final: 0.8548 (p0) REVERT: F 660 LEU cc_start: 0.8666 (mm) cc_final: 0.8448 (pp) REVERT: I 63 LEU cc_start: 0.9119 (mt) cc_final: 0.8912 (mt) outliers start: 3 outliers final: 0 residues processed: 179 average time/residue: 0.1532 time to fit residues: 42.0404 Evaluate side-chains 117 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 116 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 16 optimal weight: 4.9990 chunk 85 optimal weight: 8.9990 chunk 90 optimal weight: 8.9990 chunk 103 optimal weight: 5.9990 chunk 7 optimal weight: 0.7980 chunk 55 optimal weight: 8.9990 chunk 184 optimal weight: 6.9990 chunk 24 optimal weight: 5.9990 chunk 105 optimal weight: 9.9990 chunk 98 optimal weight: 7.9990 chunk 56 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 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 591 GLN ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 105 HIS ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 591 GLN G 73 GLN D 136 ASN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.039986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2726 r_free = 0.2726 target = 0.032742 restraints weight = 175914.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.033674 restraints weight = 104276.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.034338 restraints weight = 73392.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.034793 restraints weight = 56698.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.035123 restraints weight = 47195.889| |-----------------------------------------------------------------------------| r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.3514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 20757 Z= 0.225 Angle : 0.889 11.917 28446 Z= 0.409 Chirality : 0.050 0.292 3561 Planarity : 0.005 0.046 3345 Dihedral : 10.989 69.909 5238 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.13 % Allowed : 10.85 % Favored : 89.02 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.01 (0.16), residues: 2295 helix: -2.10 (0.24), residues: 342 sheet: -1.14 (0.20), residues: 657 loop : -2.51 (0.16), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 64 TYR 0.022 0.002 TYR F 586 PHE 0.018 0.002 PHE H 78 TRP 0.023 0.002 TRP B 631 HIS 0.006 0.002 HIS A 352 Details of bonding type rmsd covalent geometry : bond 0.00485 (20583) covalent geometry : angle 0.84635 (27963) SS BOND : bond 0.00810 ( 39) SS BOND : angle 1.07118 ( 78) hydrogen bonds : bond 0.04064 ( 523) hydrogen bonds : angle 6.83246 ( 1461) link_ALPHA1-2 : bond 0.00333 ( 18) link_ALPHA1-2 : angle 2.24301 ( 54) link_ALPHA1-3 : bond 0.01718 ( 15) link_ALPHA1-3 : angle 2.97047 ( 45) link_ALPHA1-6 : bond 0.00818 ( 9) link_ALPHA1-6 : angle 2.19784 ( 27) link_BETA1-4 : bond 0.00356 ( 45) link_BETA1-4 : angle 2.36763 ( 135) link_NAG-ASN : bond 0.00398 ( 48) link_NAG-ASN : angle 2.33704 ( 144) *********************** 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 158 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 157 time to evaluate : 0.773 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 99 ASN cc_start: 0.8911 (m-40) cc_final: 0.8244 (t0) REVERT: B 530 MET cc_start: 0.6917 (mmm) cc_final: 0.6527 (mmm) REVERT: B 647 GLU cc_start: 0.9051 (pm20) cc_final: 0.8678 (pm20) REVERT: B 651 ASN cc_start: 0.8236 (m-40) cc_final: 0.7953 (m-40) REVERT: H 82 MET cc_start: 0.6594 (mpp) cc_final: 0.6391 (mpp) REVERT: H 100 LEU cc_start: 0.9367 (tp) cc_final: 0.8657 (tp) REVERT: H 100 GLU cc_start: 0.8763 (mm-30) cc_final: 0.8192 (mm-30) REVERT: H 100 MET cc_start: 0.7294 (mmm) cc_final: 0.7030 (mmm) REVERT: L 4 LEU cc_start: 0.8509 (mt) cc_final: 0.8295 (mt) REVERT: C 95 MET cc_start: 0.8641 (ptm) cc_final: 0.8148 (ppp) REVERT: E 626 MET cc_start: 0.7715 (tmm) cc_final: 0.5798 (tmm) REVERT: E 630 GLN cc_start: 0.9393 (mt0) cc_final: 0.8927 (tm-30) REVERT: G 100 GLU cc_start: 0.8872 (mm-30) cc_final: 0.8024 (mp0) REVERT: D 95 MET cc_start: 0.8646 (ppp) cc_final: 0.8088 (ppp) REVERT: D 99 ASN cc_start: 0.8871 (m-40) cc_final: 0.8196 (t0) REVERT: D 195 ASN cc_start: 0.9075 (p0) cc_final: 0.8733 (p0) REVERT: F 651 ASN cc_start: 0.8133 (m-40) cc_final: 0.7523 (m-40) REVERT: F 660 LEU cc_start: 0.8785 (mm) cc_final: 0.8581 (pp) REVERT: I 43 LYS cc_start: 0.8591 (mmtt) cc_final: 0.8357 (mmtp) REVERT: I 63 LEU cc_start: 0.9219 (mt) cc_final: 0.8994 (mt) REVERT: I 82 MET cc_start: 0.7362 (mmp) cc_final: 0.7136 (mmp) outliers start: 1 outliers final: 0 residues processed: 158 average time/residue: 0.1493 time to fit residues: 36.8680 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 : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 210 optimal weight: 0.9980 chunk 29 optimal weight: 6.9990 chunk 132 optimal weight: 3.9990 chunk 13 optimal weight: 9.9990 chunk 124 optimal weight: 1.9990 chunk 84 optimal weight: 7.9990 chunk 91 optimal weight: 6.9990 chunk 157 optimal weight: 8.9990 chunk 96 optimal weight: 8.9990 chunk 60 optimal weight: 10.0000 chunk 150 optimal weight: 9.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- 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 ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.040193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.032953 restraints weight = 176761.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.033912 restraints weight = 104502.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.034563 restraints weight = 72846.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.035021 restraints weight = 56454.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.035330 restraints weight = 47041.147| |-----------------------------------------------------------------------------| r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.3832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 20757 Z= 0.190 Angle : 0.834 10.114 28446 Z= 0.386 Chirality : 0.049 0.290 3561 Planarity : 0.005 0.076 3345 Dihedral : 10.352 69.705 5238 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.15 % Favored : 90.72 % Rotamer: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.85 (0.16), residues: 2295 helix: -1.89 (0.25), residues: 348 sheet: -0.92 (0.21), residues: 642 loop : -2.49 (0.16), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 64 TYR 0.021 0.002 TYR F 586 PHE 0.017 0.002 PHE A 382 TRP 0.031 0.002 TRP B 596 HIS 0.007 0.001 HIS D 352 Details of bonding type rmsd covalent geometry : bond 0.00413 (20583) covalent geometry : angle 0.79384 (27963) SS BOND : bond 0.00353 ( 39) SS BOND : angle 1.06697 ( 78) hydrogen bonds : bond 0.03836 ( 523) hydrogen bonds : angle 6.54579 ( 1461) link_ALPHA1-2 : bond 0.00327 ( 18) link_ALPHA1-2 : angle 2.11729 ( 54) link_ALPHA1-3 : bond 0.01619 ( 15) link_ALPHA1-3 : angle 2.64209 ( 45) link_ALPHA1-6 : bond 0.00887 ( 9) link_ALPHA1-6 : angle 2.14959 ( 27) link_BETA1-4 : bond 0.00333 ( 45) link_BETA1-4 : angle 2.20364 ( 135) link_NAG-ASN : bond 0.00321 ( 48) link_NAG-ASN : angle 2.28368 ( 144) *********************** 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 149 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 0.856 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: A 95 MET cc_start: 0.8427 (ppp) cc_final: 0.7810 (ppp) REVERT: A 99 ASN cc_start: 0.8910 (m-40) cc_final: 0.8255 (t0) REVERT: B 606 THR cc_start: 0.8416 (p) cc_final: 0.8155 (t) REVERT: B 648 GLU cc_start: 0.8517 (pt0) cc_final: 0.7972 (pm20) REVERT: B 651 ASN cc_start: 0.8272 (m-40) cc_final: 0.8054 (m-40) REVERT: H 63 LEU cc_start: 0.8851 (mt) cc_final: 0.8649 (mt) REVERT: H 82 MET cc_start: 0.8980 (tmm) cc_final: 0.8720 (tmm) REVERT: H 82 MET cc_start: 0.6772 (mpp) cc_final: 0.6539 (mpp) REVERT: H 89 MET cc_start: 0.8384 (tpt) cc_final: 0.7762 (tpp) REVERT: H 100 LEU cc_start: 0.9427 (tp) cc_final: 0.8789 (tp) REVERT: H 100 GLU cc_start: 0.8727 (mm-30) cc_final: 0.8106 (mp0) REVERT: C 95 MET cc_start: 0.8548 (ptm) cc_final: 0.8154 (ppp) REVERT: E 606 THR cc_start: 0.8636 (p) cc_final: 0.8333 (t) REVERT: E 626 MET cc_start: 0.8035 (tmm) cc_final: 0.5744 (tmm) REVERT: E 630 GLN cc_start: 0.9399 (mt0) cc_final: 0.8291 (tm-30) REVERT: E 650 GLN cc_start: 0.7265 (mm110) cc_final: 0.7032 (mm110) REVERT: G 63 LEU cc_start: 0.9109 (mt) cc_final: 0.8898 (mt) REVERT: G 100 GLU cc_start: 0.8855 (mm-30) cc_final: 0.8002 (mp0) REVERT: J 28 LEU cc_start: 0.9110 (mm) cc_final: 0.8631 (tt) REVERT: D 95 MET cc_start: 0.8445 (ppp) cc_final: 0.7984 (ppp) REVERT: D 99 ASN cc_start: 0.8863 (m-40) cc_final: 0.8222 (t0) REVERT: D 195 ASN cc_start: 0.9043 (p0) cc_final: 0.8739 (p0) REVERT: F 530 MET cc_start: 0.6773 (tpt) cc_final: 0.6335 (tpt) REVERT: F 660 LEU cc_start: 0.8746 (mm) cc_final: 0.8513 (pp) REVERT: I 43 LYS cc_start: 0.8590 (mmtt) cc_final: 0.8347 (mmtp) REVERT: I 63 LEU cc_start: 0.9245 (mt) cc_final: 0.9010 (mt) REVERT: I 100 GLU cc_start: 0.8090 (mp0) cc_final: 0.7741 (mp0) outliers start: 0 outliers final: 0 residues processed: 149 average time/residue: 0.1507 time to fit residues: 35.4573 Evaluate side-chains 115 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 174 optimal weight: 5.9990 chunk 167 optimal weight: 10.0000 chunk 207 optimal weight: 3.9990 chunk 39 optimal weight: 30.0000 chunk 188 optimal weight: 6.9990 chunk 47 optimal weight: 1.9990 chunk 137 optimal weight: 0.5980 chunk 95 optimal weight: 8.9990 chunk 27 optimal weight: 3.9990 chunk 151 optimal weight: 6.9990 chunk 181 optimal weight: 0.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- 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 543 ASN ** 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 591 GLN ** E 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 543 ASN ** F 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.040739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.033360 restraints weight = 172391.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.034336 restraints weight = 101091.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.035019 restraints weight = 70490.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.035503 restraints weight = 54156.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.035845 restraints weight = 44788.574| |-----------------------------------------------------------------------------| r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.4022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 20757 Z= 0.142 Angle : 0.781 9.550 28446 Z= 0.362 Chirality : 0.048 0.287 3561 Planarity : 0.004 0.044 3345 Dihedral : 9.722 68.905 5238 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.37 % Favored : 90.54 % Rotamer: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.63 (0.17), residues: 2295 helix: -1.47 (0.26), residues: 330 sheet: -0.83 (0.20), residues: 678 loop : -2.41 (0.16), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 64 TYR 0.018 0.001 TYR F 586 PHE 0.016 0.002 PHE A 382 TRP 0.023 0.002 TRP D 112 HIS 0.003 0.001 HIS H 33 Details of bonding type rmsd covalent geometry : bond 0.00308 (20583) covalent geometry : angle 0.74212 (27963) SS BOND : bond 0.00205 ( 39) SS BOND : angle 0.91396 ( 78) hydrogen bonds : bond 0.03552 ( 523) hydrogen bonds : angle 6.38234 ( 1461) link_ALPHA1-2 : bond 0.00332 ( 18) link_ALPHA1-2 : angle 2.02568 ( 54) link_ALPHA1-3 : bond 0.01703 ( 15) link_ALPHA1-3 : angle 2.54669 ( 45) link_ALPHA1-6 : bond 0.00881 ( 9) link_ALPHA1-6 : angle 2.08677 ( 27) link_BETA1-4 : bond 0.00316 ( 45) link_BETA1-4 : angle 2.06270 ( 135) link_NAG-ASN : bond 0.00261 ( 48) link_NAG-ASN : angle 2.14140 ( 144) *********************** REFINEMENT MACRO_CYCLE 6 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 153 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 0.841 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: A 95 MET cc_start: 0.8334 (ppp) cc_final: 0.7878 (ppp) REVERT: A 99 ASN cc_start: 0.8891 (m-40) cc_final: 0.8257 (t0) REVERT: B 606 THR cc_start: 0.8465 (p) cc_final: 0.8217 (t) REVERT: B 626 MET cc_start: 0.8431 (mmp) cc_final: 0.8197 (mmm) REVERT: H 63 LEU cc_start: 0.8808 (mt) cc_final: 0.8602 (mt) REVERT: H 89 MET cc_start: 0.8406 (tpt) cc_final: 0.7833 (tpp) REVERT: H 100 GLU cc_start: 0.8696 (mm-30) cc_final: 0.8135 (mp0) REVERT: L 4 LEU cc_start: 0.8554 (mt) cc_final: 0.8193 (mt) REVERT: C 95 MET cc_start: 0.8511 (ptm) cc_final: 0.8161 (ppp) REVERT: E 606 THR cc_start: 0.8587 (p) cc_final: 0.8365 (t) REVERT: E 626 MET cc_start: 0.7917 (tmm) cc_final: 0.6097 (tmm) REVERT: E 630 GLN cc_start: 0.9304 (mt0) cc_final: 0.8906 (tm-30) REVERT: E 634 GLU cc_start: 0.8701 (pm20) cc_final: 0.8157 (pm20) REVERT: G 13 LYS cc_start: 0.7742 (mmtt) cc_final: 0.7353 (tppt) REVERT: G 63 LEU cc_start: 0.9090 (mt) cc_final: 0.8875 (mt) REVERT: G 100 GLU cc_start: 0.8823 (mm-30) cc_final: 0.8298 (mm-30) REVERT: J 17 GLN cc_start: 0.8834 (mp10) cc_final: 0.8521 (mp10) REVERT: D 95 MET cc_start: 0.8317 (ppp) cc_final: 0.7997 (ppp) REVERT: D 99 ASN cc_start: 0.8833 (m-40) cc_final: 0.8190 (t0) REVERT: D 195 ASN cc_start: 0.8978 (p0) cc_final: 0.8704 (p0) REVERT: F 530 MET cc_start: 0.6903 (tpt) cc_final: 0.6471 (tpt) REVERT: I 43 LYS cc_start: 0.8581 (mmtt) cc_final: 0.8376 (mmtp) REVERT: I 63 LEU cc_start: 0.9214 (mt) cc_final: 0.8981 (mt) REVERT: I 100 GLU cc_start: 0.8007 (mp0) cc_final: 0.7719 (mp0) outliers start: 0 outliers final: 0 residues processed: 153 average time/residue: 0.1446 time to fit residues: 35.2578 Evaluate side-chains 114 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 210 optimal weight: 0.1980 chunk 190 optimal weight: 8.9990 chunk 226 optimal weight: 9.9990 chunk 193 optimal weight: 2.9990 chunk 224 optimal weight: 9.9990 chunk 75 optimal weight: 10.0000 chunk 149 optimal weight: 2.9990 chunk 160 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 169 optimal weight: 5.9990 chunk 69 optimal weight: 6.9990 overall best weight: 2.4388 ------------------------------------------------------------------------------- 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 543 ASN ** 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 543 ASN E 591 GLN ** E 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 543 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.040692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.033436 restraints weight = 172216.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 19)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.034380 restraints weight = 102577.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.035054 restraints weight = 72154.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.035516 restraints weight = 55582.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.035844 restraints weight = 46242.823| |-----------------------------------------------------------------------------| r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.4187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 20757 Z= 0.142 Angle : 0.780 10.967 28446 Z= 0.360 Chirality : 0.048 0.356 3561 Planarity : 0.004 0.044 3345 Dihedral : 9.336 68.379 5238 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.19 % Favored : 90.72 % Rotamer: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.57 (0.17), residues: 2295 helix: -1.51 (0.26), residues: 345 sheet: -0.67 (0.20), residues: 675 loop : -2.44 (0.16), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 64 TYR 0.018 0.001 TYR F 586 PHE 0.015 0.001 PHE A 382 TRP 0.049 0.002 TRP B 596 HIS 0.003 0.001 HIS H 33 Details of bonding type rmsd covalent geometry : bond 0.00309 (20583) covalent geometry : angle 0.73722 (27963) SS BOND : bond 0.00194 ( 39) SS BOND : angle 0.85041 ( 78) hydrogen bonds : bond 0.03473 ( 523) hydrogen bonds : angle 6.19972 ( 1461) link_ALPHA1-2 : bond 0.00316 ( 18) link_ALPHA1-2 : angle 2.02382 ( 54) link_ALPHA1-3 : bond 0.01611 ( 15) link_ALPHA1-3 : angle 2.50657 ( 45) link_ALPHA1-6 : bond 0.00884 ( 9) link_ALPHA1-6 : angle 2.04918 ( 27) link_BETA1-4 : bond 0.00319 ( 45) link_BETA1-4 : angle 2.03178 ( 135) link_NAG-ASN : bond 0.00259 ( 48) link_NAG-ASN : angle 2.45248 ( 144) *********************** REFINEMENT MACRO_CYCLE 7 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 152 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 1.042 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: A 95 MET cc_start: 0.8232 (ppp) cc_final: 0.7819 (ppp) REVERT: A 99 ASN cc_start: 0.8880 (m-40) cc_final: 0.8193 (t0) REVERT: B 606 THR cc_start: 0.8440 (p) cc_final: 0.8182 (t) REVERT: H 63 LEU cc_start: 0.8746 (mt) cc_final: 0.8523 (mt) REVERT: H 82 MET cc_start: 0.8905 (tmm) cc_final: 0.8658 (tmm) REVERT: H 89 MET cc_start: 0.8562 (tpt) cc_final: 0.7938 (tpp) REVERT: H 100 GLU cc_start: 0.8875 (mm-30) cc_final: 0.8109 (mp0) REVERT: C 95 MET cc_start: 0.8448 (ptm) cc_final: 0.8035 (ppp) REVERT: E 606 THR cc_start: 0.8711 (p) cc_final: 0.8432 (t) REVERT: E 626 MET cc_start: 0.8016 (tmm) cc_final: 0.6133 (tmm) REVERT: E 630 GLN cc_start: 0.9387 (mt0) cc_final: 0.8859 (tm-30) REVERT: E 634 GLU cc_start: 0.8787 (pm20) cc_final: 0.8313 (pm20) REVERT: G 63 LEU cc_start: 0.9123 (mt) cc_final: 0.8894 (mt) REVERT: G 100 GLU cc_start: 0.8991 (mm-30) cc_final: 0.8426 (mm-30) REVERT: D 95 MET cc_start: 0.8205 (ppp) cc_final: 0.7868 (ppp) REVERT: D 99 ASN cc_start: 0.8850 (m-40) cc_final: 0.8165 (t0) REVERT: D 195 ASN cc_start: 0.9086 (p0) cc_final: 0.8831 (p0) REVERT: F 530 MET cc_start: 0.6875 (tpt) cc_final: 0.6435 (tpt) REVERT: I 43 LYS cc_start: 0.8620 (mmtt) cc_final: 0.8350 (mmtp) REVERT: I 63 LEU cc_start: 0.9230 (mt) cc_final: 0.8992 (mt) REVERT: I 89 MET cc_start: 0.8645 (tpt) cc_final: 0.8131 (tpp) REVERT: I 100 GLU cc_start: 0.8175 (mp0) cc_final: 0.7799 (mp0) outliers start: 0 outliers final: 0 residues processed: 152 average time/residue: 0.1465 time to fit residues: 35.5740 Evaluate side-chains 113 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 78 optimal weight: 6.9990 chunk 205 optimal weight: 6.9990 chunk 93 optimal weight: 0.0270 chunk 119 optimal weight: 20.0000 chunk 166 optimal weight: 8.9990 chunk 114 optimal weight: 10.0000 chunk 37 optimal weight: 6.9990 chunk 58 optimal weight: 0.0070 chunk 173 optimal weight: 0.0000 chunk 155 optimal weight: 20.0000 chunk 82 optimal weight: 8.9990 overall best weight: 2.8064 ------------------------------------------------------------------------------- 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 543 ASN ** 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 543 ASN E 591 GLN ** E 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 543 ASN ** K 89 GLN ** 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 = 0.3026 r_free = 0.3026 target = 0.040451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.033220 restraints weight = 172829.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.034189 restraints weight = 102764.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.034844 restraints weight = 71526.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.035316 restraints weight = 55363.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.035617 restraints weight = 45963.093| |-----------------------------------------------------------------------------| r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.4397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 20757 Z= 0.148 Angle : 0.780 11.278 28446 Z= 0.359 Chirality : 0.048 0.397 3561 Planarity : 0.004 0.044 3345 Dihedral : 8.979 67.298 5238 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.72 % Favored : 90.15 % Rotamer: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.40 (0.17), residues: 2295 helix: -0.91 (0.28), residues: 312 sheet: -0.60 (0.20), residues: 687 loop : -2.43 (0.16), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 64 TYR 0.018 0.001 TYR F 586 PHE 0.015 0.001 PHE A 382 TRP 0.016 0.002 TRP A 35 HIS 0.003 0.001 HIS A 352 Details of bonding type rmsd covalent geometry : bond 0.00320 (20583) covalent geometry : angle 0.73682 (27963) SS BOND : bond 0.00345 ( 39) SS BOND : angle 0.82514 ( 78) hydrogen bonds : bond 0.03337 ( 523) hydrogen bonds : angle 6.07316 ( 1461) link_ALPHA1-2 : bond 0.00292 ( 18) link_ALPHA1-2 : angle 2.02351 ( 54) link_ALPHA1-3 : bond 0.01659 ( 15) link_ALPHA1-3 : angle 2.53116 ( 45) link_ALPHA1-6 : bond 0.00908 ( 9) link_ALPHA1-6 : angle 2.03734 ( 27) link_BETA1-4 : bond 0.00309 ( 45) link_BETA1-4 : angle 1.99550 ( 135) link_NAG-ASN : bond 0.00336 ( 48) link_NAG-ASN : angle 2.49528 ( 144) *********************** REFINEMENT MACRO_CYCLE 8 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 : 0.787 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: A 95 MET cc_start: 0.8253 (ppp) cc_final: 0.7818 (ppp) REVERT: A 99 ASN cc_start: 0.8886 (m-40) cc_final: 0.8177 (t0) REVERT: B 530 MET cc_start: 0.6374 (mmm) cc_final: 0.6155 (mmm) REVERT: H 63 LEU cc_start: 0.8772 (mt) cc_final: 0.8549 (mt) REVERT: H 82 MET cc_start: 0.8869 (tmm) cc_final: 0.8486 (tmm) REVERT: H 89 MET cc_start: 0.8572 (tpt) cc_final: 0.8013 (tpp) REVERT: H 100 GLU cc_start: 0.8923 (mm-30) cc_final: 0.8226 (mp0) REVERT: H 100 MET cc_start: 0.7922 (mmm) cc_final: 0.7699 (mmm) REVERT: C 95 MET cc_start: 0.8439 (ptm) cc_final: 0.8035 (ppp) REVERT: C 434 MET cc_start: 0.8598 (tmm) cc_final: 0.8358 (tmm) REVERT: E 606 THR cc_start: 0.8732 (p) cc_final: 0.8458 (t) REVERT: G 13 LYS cc_start: 0.7661 (mmtt) cc_final: 0.7295 (tppt) REVERT: G 63 LEU cc_start: 0.9137 (mt) cc_final: 0.8914 (mt) REVERT: G 100 GLU cc_start: 0.9059 (mm-30) cc_final: 0.8446 (mm-30) REVERT: J 28 LEU cc_start: 0.9189 (mm) cc_final: 0.8851 (tt) REVERT: D 95 MET cc_start: 0.8191 (ppp) cc_final: 0.7828 (ppp) REVERT: D 99 ASN cc_start: 0.8859 (m-40) cc_final: 0.8179 (t0) REVERT: D 195 ASN cc_start: 0.9092 (p0) cc_final: 0.8806 (p0) REVERT: F 530 MET cc_start: 0.6980 (tpt) cc_final: 0.6491 (tpt) REVERT: I 43 LYS cc_start: 0.8666 (mmtt) cc_final: 0.8395 (mmtp) REVERT: I 63 LEU cc_start: 0.9200 (mt) cc_final: 0.8975 (mt) REVERT: I 82 MET cc_start: 0.7298 (mmp) cc_final: 0.6917 (mmp) REVERT: I 89 MET cc_start: 0.8674 (tpt) cc_final: 0.8229 (tpp) outliers start: 0 outliers final: 0 residues processed: 149 average time/residue: 0.1454 time to fit residues: 34.2391 Evaluate side-chains 110 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 79 optimal weight: 20.0000 chunk 80 optimal weight: 6.9990 chunk 123 optimal weight: 6.9990 chunk 145 optimal weight: 9.9990 chunk 204 optimal weight: 5.9990 chunk 100 optimal weight: 6.9990 chunk 56 optimal weight: 5.9990 chunk 75 optimal weight: 10.0000 chunk 41 optimal weight: 9.9990 chunk 183 optimal weight: 9.9990 chunk 104 optimal weight: 0.9980 overall best weight: 5.3988 ------------------------------------------------------------------------------- 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 543 ASN ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 543 ASN ** E 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 543 ASN ** F 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 656 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.039276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2702 r_free = 0.2702 target = 0.032116 restraints weight = 176182.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2738 r_free = 0.2738 target = 0.033028 restraints weight = 105448.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.033677 restraints weight = 74316.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.034132 restraints weight = 57530.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.034453 restraints weight = 47822.789| |-----------------------------------------------------------------------------| r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.4684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 20757 Z= 0.228 Angle : 0.870 10.791 28446 Z= 0.401 Chirality : 0.049 0.385 3561 Planarity : 0.004 0.045 3345 Dihedral : 9.288 65.718 5238 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.13 % Allowed : 11.02 % Favored : 88.85 % Rotamer: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.58 (0.17), residues: 2295 helix: -1.25 (0.27), residues: 330 sheet: -0.63 (0.20), residues: 681 loop : -2.56 (0.16), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 98 TYR 0.029 0.002 TYR A 217 PHE 0.020 0.002 PHE A 382 TRP 0.063 0.002 TRP B 596 HIS 0.005 0.002 HIS E 585 Details of bonding type rmsd covalent geometry : bond 0.00495 (20583) covalent geometry : angle 0.82727 (27963) SS BOND : bond 0.00370 ( 39) SS BOND : angle 1.16657 ( 78) hydrogen bonds : bond 0.03683 ( 523) hydrogen bonds : angle 6.38295 ( 1461) link_ALPHA1-2 : bond 0.00355 ( 18) link_ALPHA1-2 : angle 2.24061 ( 54) link_ALPHA1-3 : bond 0.01565 ( 15) link_ALPHA1-3 : angle 2.72887 ( 45) link_ALPHA1-6 : bond 0.00924 ( 9) link_ALPHA1-6 : angle 2.24513 ( 27) link_BETA1-4 : bond 0.00339 ( 45) link_BETA1-4 : angle 2.12384 ( 135) link_NAG-ASN : bond 0.00471 ( 48) link_NAG-ASN : angle 2.55928 ( 144) *********************** REFINEMENT MACRO_CYCLE 9 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 137 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.777 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: A 95 MET cc_start: 0.8451 (ppp) cc_final: 0.8164 (ppp) REVERT: A 99 ASN cc_start: 0.8892 (m-40) cc_final: 0.8198 (t0) REVERT: A 434 MET cc_start: 0.8498 (tmm) cc_final: 0.8258 (tmm) REVERT: B 651 ASN cc_start: 0.8533 (m-40) cc_final: 0.8324 (m-40) REVERT: H 63 LEU cc_start: 0.8853 (mt) cc_final: 0.8639 (mt) REVERT: H 82 MET cc_start: 0.8922 (tmm) cc_final: 0.8697 (tmm) REVERT: H 89 MET cc_start: 0.8590 (tpt) cc_final: 0.8130 (tpp) REVERT: H 100 GLU cc_start: 0.8958 (mm-30) cc_final: 0.8352 (mp0) REVERT: H 100 MET cc_start: 0.8382 (mmm) cc_final: 0.8175 (mmm) REVERT: C 95 MET cc_start: 0.8559 (ptm) cc_final: 0.8130 (ppp) REVERT: C 434 MET cc_start: 0.8604 (tmm) cc_final: 0.8294 (tmm) REVERT: E 542 ARG cc_start: 0.8543 (ptm-80) cc_final: 0.8212 (ttp80) REVERT: E 591 GLN cc_start: 0.9278 (tp40) cc_final: 0.8743 (tt0) REVERT: E 606 THR cc_start: 0.8763 (p) cc_final: 0.8377 (t) REVERT: E 630 GLN cc_start: 0.9479 (mt0) cc_final: 0.9240 (tm-30) REVERT: G 13 LYS cc_start: 0.7934 (mmtt) cc_final: 0.7284 (tppt) REVERT: G 63 LEU cc_start: 0.9154 (mt) cc_final: 0.8925 (mt) REVERT: G 100 GLU cc_start: 0.9073 (mm-30) cc_final: 0.8487 (mm-30) REVERT: J 28 LEU cc_start: 0.9279 (mm) cc_final: 0.8956 (tt) REVERT: D 95 MET cc_start: 0.8352 (ppp) cc_final: 0.7997 (ppp) REVERT: D 99 ASN cc_start: 0.8876 (m-40) cc_final: 0.8184 (t0) REVERT: D 104 MET cc_start: 0.8755 (tpt) cc_final: 0.8523 (tpt) REVERT: D 195 ASN cc_start: 0.9135 (p0) cc_final: 0.8884 (p0) REVERT: F 530 MET cc_start: 0.6944 (tpt) cc_final: 0.6486 (tpt) REVERT: I 43 LYS cc_start: 0.8754 (mmtt) cc_final: 0.8428 (mmtp) REVERT: I 82 MET cc_start: 0.7447 (mmp) cc_final: 0.7099 (mmp) REVERT: I 89 MET cc_start: 0.8745 (tpt) cc_final: 0.8373 (tpp) REVERT: I 100 GLU cc_start: 0.8210 (mp0) cc_final: 0.7918 (mp0) outliers start: 0 outliers final: 0 residues processed: 137 average time/residue: 0.1483 time to fit residues: 32.1694 Evaluate side-chains 106 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 48 optimal weight: 0.0670 chunk 74 optimal weight: 5.9990 chunk 132 optimal weight: 9.9990 chunk 73 optimal weight: 10.0000 chunk 136 optimal weight: 5.9990 chunk 22 optimal weight: 9.9990 chunk 208 optimal weight: 9.9990 chunk 31 optimal weight: 9.9990 chunk 170 optimal weight: 7.9990 chunk 83 optimal weight: 0.0030 chunk 36 optimal weight: 0.0770 overall best weight: 2.4290 ------------------------------------------------------------------------------- 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 543 ASN B 650 GLN ** B 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 543 ASN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 543 ASN F 656 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.040227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2737 r_free = 0.2737 target = 0.032997 restraints weight = 176887.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.033970 restraints weight = 103520.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.034647 restraints weight = 71629.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.035110 restraints weight = 55149.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.035424 restraints weight = 45876.820| |-----------------------------------------------------------------------------| r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.4787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 20757 Z= 0.145 Angle : 0.786 10.022 28446 Z= 0.364 Chirality : 0.049 0.370 3561 Planarity : 0.004 0.044 3345 Dihedral : 8.883 65.249 5238 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.19 % Favored : 90.68 % Rotamer: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.35 (0.17), residues: 2295 helix: -0.90 (0.29), residues: 312 sheet: -0.53 (0.20), residues: 705 loop : -2.44 (0.16), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG H 29 TYR 0.022 0.001 TYR A 217 PHE 0.016 0.001 PHE A 382 TRP 0.017 0.002 TRP A 35 HIS 0.003 0.001 HIS A 352 Details of bonding type rmsd covalent geometry : bond 0.00314 (20583) covalent geometry : angle 0.74543 (27963) SS BOND : bond 0.00203 ( 39) SS BOND : angle 1.16134 ( 78) hydrogen bonds : bond 0.03375 ( 523) hydrogen bonds : angle 6.11073 ( 1461) link_ALPHA1-2 : bond 0.00353 ( 18) link_ALPHA1-2 : angle 1.98724 ( 54) link_ALPHA1-3 : bond 0.01661 ( 15) link_ALPHA1-3 : angle 2.51386 ( 45) link_ALPHA1-6 : bond 0.00950 ( 9) link_ALPHA1-6 : angle 1.99683 ( 27) link_BETA1-4 : bond 0.00322 ( 45) link_BETA1-4 : angle 1.88813 ( 135) link_NAG-ASN : bond 0.00302 ( 48) link_NAG-ASN : angle 2.38987 ( 144) ********************** REFINEMENT MACRO_CYCLE 10 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 145 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 0.778 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: A 95 MET cc_start: 0.8441 (ppp) cc_final: 0.8120 (ppp) REVERT: A 99 ASN cc_start: 0.8902 (m-40) cc_final: 0.8324 (t0) REVERT: A 195 ASN cc_start: 0.8819 (p0) cc_final: 0.8603 (p0) REVERT: H 13 LYS cc_start: 0.7899 (mmtt) cc_final: 0.7287 (tppt) REVERT: H 63 LEU cc_start: 0.8785 (mt) cc_final: 0.8553 (mt) REVERT: H 82 MET cc_start: 0.8825 (tmm) cc_final: 0.8371 (tmm) REVERT: H 89 MET cc_start: 0.8368 (tpt) cc_final: 0.7996 (tpp) REVERT: H 100 GLU cc_start: 0.8729 (mm-30) cc_final: 0.8258 (mp0) REVERT: H 100 MET cc_start: 0.8358 (mmm) cc_final: 0.7899 (mmm) REVERT: C 95 MET cc_start: 0.8474 (ptm) cc_final: 0.8141 (ppp) REVERT: E 606 THR cc_start: 0.8670 (p) cc_final: 0.8439 (t) REVERT: E 630 GLN cc_start: 0.9344 (mt0) cc_final: 0.8992 (tm-30) REVERT: E 634 GLU cc_start: 0.8962 (pm20) cc_final: 0.8217 (pm20) REVERT: G 13 LYS cc_start: 0.7984 (mmtt) cc_final: 0.7425 (tppt) REVERT: G 63 LEU cc_start: 0.9055 (mt) cc_final: 0.8822 (mt) REVERT: G 100 GLU cc_start: 0.8868 (mm-30) cc_final: 0.8398 (mm-30) REVERT: J 28 LEU cc_start: 0.9247 (mm) cc_final: 0.8929 (tt) REVERT: D 95 MET cc_start: 0.8362 (ppp) cc_final: 0.7972 (ppp) REVERT: D 99 ASN cc_start: 0.8846 (m-40) cc_final: 0.8286 (t0) REVERT: F 530 MET cc_start: 0.7182 (tpt) cc_final: 0.6800 (tpt) REVERT: I 43 LYS cc_start: 0.8691 (mmtt) cc_final: 0.8459 (mmtp) REVERT: I 89 MET cc_start: 0.8429 (tpt) cc_final: 0.8131 (tpp) REVERT: I 100 GLU cc_start: 0.8058 (mp0) cc_final: 0.7817 (mp0) outliers start: 0 outliers final: 0 residues processed: 145 average time/residue: 0.1408 time to fit residues: 32.9596 Evaluate side-chains 110 residues out of total 2076 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 182 optimal weight: 20.0000 chunk 107 optimal weight: 5.9990 chunk 77 optimal weight: 0.8980 chunk 132 optimal weight: 6.9990 chunk 61 optimal weight: 0.0470 chunk 96 optimal weight: 6.9990 chunk 150 optimal weight: 9.9990 chunk 28 optimal weight: 0.9980 chunk 170 optimal weight: 6.9990 chunk 2 optimal weight: 10.0000 chunk 111 optimal weight: 4.9990 overall best weight: 2.5882 ------------------------------------------------------------------------------- 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 543 ASN ** B 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 136 ASN ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 543 ASN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 543 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.040217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2738 r_free = 0.2738 target = 0.033000 restraints weight = 176990.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.033967 restraints weight = 104015.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.034638 restraints weight = 72138.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.035103 restraints weight = 55636.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.035419 restraints weight = 46254.356| |-----------------------------------------------------------------------------| r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.4890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 20757 Z= 0.145 Angle : 0.781 10.860 28446 Z= 0.360 Chirality : 0.048 0.365 3561 Planarity : 0.004 0.044 3345 Dihedral : 8.710 64.703 5238 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.72 % Favored : 90.15 % Rotamer: Outliers : 0.05 % Allowed : 0.29 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.32 (0.17), residues: 2295 helix: -0.87 (0.29), residues: 312 sheet: -0.61 (0.20), residues: 717 loop : -2.36 (0.17), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 29 TYR 0.021 0.001 TYR C 217 PHE 0.016 0.001 PHE A 382 TRP 0.078 0.002 TRP E 596 HIS 0.003 0.001 HIS H 33 Details of bonding type rmsd covalent geometry : bond 0.00313 (20583) covalent geometry : angle 0.74098 (27963) SS BOND : bond 0.00227 ( 39) SS BOND : angle 1.21332 ( 78) hydrogen bonds : bond 0.03319 ( 523) hydrogen bonds : angle 6.08347 ( 1461) link_ALPHA1-2 : bond 0.00311 ( 18) link_ALPHA1-2 : angle 2.01657 ( 54) link_ALPHA1-3 : bond 0.01623 ( 15) link_ALPHA1-3 : angle 2.48853 ( 45) link_ALPHA1-6 : bond 0.00951 ( 9) link_ALPHA1-6 : angle 2.04788 ( 27) link_BETA1-4 : bond 0.00317 ( 45) link_BETA1-4 : angle 1.89691 ( 135) link_NAG-ASN : bond 0.00276 ( 48) link_NAG-ASN : angle 2.31621 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2619.74 seconds wall clock time: 46 minutes 54.23 seconds (2814.23 seconds total)