Starting phenix.real_space_refine on Sun Aug 24 13:17:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8euw_28619/08_2025/8euw_28619.cif Found real_map, /net/cci-nas-00/data/ceres_data/8euw_28619/08_2025/8euw_28619.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8euw_28619/08_2025/8euw_28619.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8euw_28619/08_2025/8euw_28619.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8euw_28619/08_2025/8euw_28619.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8euw_28619/08_2025/8euw_28619.map" } resolution = 2.7 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= 0.038 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 129 5.16 5 C 12444 2.51 5 N 3336 2.21 5 O 4131 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20040 Number of models: 1 Model: "" Number of chains: 46 Chain: "A" Number of atoms: 3465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3465 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 22, 'TRANS': 418} Chain breaks: 3 Chain: "B" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1022 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 1, 'TRANS': 128} Chain breaks: 1 Chain: "C" Number of atoms: 3465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3465 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 22, 'TRANS': 418} Chain breaks: 3 Chain: "D" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1022 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 1, 'TRANS': 128} Chain breaks: 1 Chain: "E" Number of atoms: 3465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3465 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 22, 'TRANS': 418} Chain breaks: 3 Chain: "F" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1022 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 1, 'TRANS': 128} Chain breaks: 1 Chain: "G" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 950 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "H" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 817 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "I" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 950 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "J" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 817 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "K" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 950 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "L" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 817 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} 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: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 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: "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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "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: 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: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "h" Number of atoms: 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: 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: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "E" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "A" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 54 Classifications: {'water': 54} Link IDs: {None: 53} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 56 Classifications: {'water': 56} Link IDs: {None: 55} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 61 Classifications: {'water': 61} Link IDs: {None: 60} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 4.43, per 1000 atoms: 0.22 Number of scatterers: 20040 At special positions: 0 Unit cell: (153.55, 143.59, 121.18, 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 129 16.00 O 4131 8.00 N 3336 7.00 C 12444 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, 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=2.03 Simple disulfide: pdb=" SG CYS A 201 " - pdb=" SG CYS A 433 " distance=2.04 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C 201 " - pdb=" SG CYS C 433 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.04 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 D 605 " distance=2.03 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.03 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 201 " - pdb=" SG CYS E 433 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.04 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS F 605 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.05 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN P 4 " - " MAN P 5 " " MAN W 4 " - " MAN W 5 " " MAN g 4 " - " MAN g 5 " ALPHA1-3 " BMA P 3 " - " MAN P 4 " " BMA W 3 " - " MAN W 4 " " BMA g 3 " - " MAN g 4 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " NAG-ASN " NAG A 601 " - " ASN A 234 " " NAG A 602 " - " ASN A 392 " " NAG A 603 " - " ASN A 295 " " NAG A 604 " - " ASN A 301 " " NAG A 605 " - " ASN A 197 " " NAG A 606 " - " ASN A 276 " " NAG A 607 " - " ASN A 133 " " NAG C 601 " - " ASN C 234 " " NAG C 602 " - " ASN C 392 " " NAG C 603 " - " ASN C 295 " " NAG C 604 " - " ASN C 301 " " NAG C 605 " - " ASN C 197 " " NAG C 606 " - " ASN C 276 " " NAG C 607 " - " ASN C 133 " " NAG E 601 " - " ASN E 234 " " NAG E 602 " - " ASN E 392 " " NAG E 603 " - " ASN E 295 " " NAG E 604 " - " ASN E 301 " " NAG E 605 " - " ASN E 197 " " NAG E 606 " - " ASN E 276 " " NAG E 607 " - " ASN E 133 " " NAG M 1 " - " ASN A 160 " " NAG N 1 " - " ASN A 88 " " NAG O 1 " - " ASN A 386 " " NAG P 1 " - " ASN A 262 " " NAG Q 1 " - " ASN A 156 " " NAG R 1 " - " ASN A 332 " " NAG S 1 " - " ASN A 363 " " NAG T 1 " - " ASN C 160 " " NAG U 1 " - " ASN C 88 " " NAG V 1 " - " ASN C 386 " " NAG W 1 " - " ASN C 262 " " NAG X 1 " - " ASN C 156 " " NAG Y 1 " - " ASN C 332 " " NAG Z 1 " - " ASN C 363 " " NAG a 1 " - " ASN A 448 " " NAG b 1 " - " ASN E 160 " " NAG c 1 " - " ASN C 448 " " NAG d 1 " - " ASN E 88 " " NAG e 1 " - " ASN E 448 " " NAG f 1 " - " ASN E 386 " " NAG g 1 " - " ASN E 262 " " NAG h 1 " - " ASN E 156 " " NAG i 1 " - " ASN E 332 " " NAG j 1 " - " ASN E 363 " Time building additional restraints: 1.42 Conformation dependent library (CDL) restraints added in 683.8 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4434 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 44 sheets defined 21.5% alpha, 36.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'A' and resid 70 through 74 removed outlier: 3.878A pdb=" N ALA A 73 " --> pdb=" O ALA A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 117 removed outlier: 4.053A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 151 removed outlier: 4.010A pdb=" N ARG A 151 " --> pdb=" O ASP A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 198 Processing helix chain 'A' and resid 335 through 354 removed outlier: 3.943A pdb=" N LYS A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N HIS A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 475 through 484 removed outlier: 3.986A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 527 removed outlier: 4.309A pdb=" N GLY B 527 " --> pdb=" O GLY B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 543 removed outlier: 4.151A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 571 through 574 Processing helix chain 'B' and resid 575 through 595 Processing helix chain 'B' and resid 618 through 622 Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 663 removed outlier: 3.800A pdb=" N LEU B 663 " --> pdb=" O ASP B 659 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 74 removed outlier: 3.810A pdb=" N ALA C 73 " --> pdb=" O ALA C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 117 removed outlier: 4.047A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 151 removed outlier: 4.035A pdb=" N ARG C 151 " --> pdb=" O ASP C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 198 Processing helix chain 'C' and resid 335 through 354 removed outlier: 3.978A pdb=" N LYS C 351 " --> pdb=" O LYS C 347 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N HIS C 352 " --> pdb=" O GLN C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 475 through 484 removed outlier: 3.969A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 528 removed outlier: 4.209A pdb=" N GLY D 527 " --> pdb=" O GLY D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 534 Processing helix chain 'D' and resid 536 through 542 removed outlier: 3.647A pdb=" N GLN D 540 " --> pdb=" O THR D 536 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 595 removed outlier: 3.849A pdb=" N LEU D 576 " --> pdb=" O GLY D 572 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N GLN D 577 " --> pdb=" O ILE D 573 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N ALA D 578 " --> pdb=" O LYS D 574 " (cutoff:3.500A) Processing helix chain 'D' and resid 618 through 622 Processing helix chain 'D' and resid 627 through 635 Processing helix chain 'D' and resid 638 through 662 Processing helix chain 'E' and resid 70 through 74 removed outlier: 3.787A pdb=" N ALA E 73 " --> pdb=" O ALA E 70 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 117 removed outlier: 4.031A pdb=" N GLU E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 139 through 151 Processing helix chain 'E' and resid 195 through 198 Processing helix chain 'E' and resid 335 through 354 removed outlier: 4.299A pdb=" N LYS E 351 " --> pdb=" O LYS E 347 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N HIS E 352 " --> pdb=" O GLN E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 475 through 484 removed outlier: 3.965A pdb=" N GLU E 482 " --> pdb=" O ASN E 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 523 through 528 removed outlier: 4.186A pdb=" N GLY F 527 " --> pdb=" O GLY F 524 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 536 through 542 removed outlier: 3.677A pdb=" N GLN F 540 " --> pdb=" O THR F 536 " (cutoff:3.500A) Processing helix chain 'F' and resid 572 through 595 removed outlier: 4.182A pdb=" N LEU F 576 " --> pdb=" O GLY F 572 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N GLN F 577 " --> pdb=" O ILE F 573 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N ALA F 578 " --> pdb=" O LYS F 574 " (cutoff:3.500A) Processing helix chain 'F' and resid 619 through 624 removed outlier: 3.949A pdb=" N ASP F 624 " --> pdb=" O SER F 620 " (cutoff:3.500A) Processing helix chain 'F' and resid 627 through 635 Processing helix chain 'F' and resid 638 through 663 removed outlier: 3.810A pdb=" N LEU F 663 " --> pdb=" O ASP F 659 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 32 removed outlier: 3.923A pdb=" N ASN G 32 " --> pdb=" O PHE G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 87 removed outlier: 3.826A pdb=" N THR G 87 " --> pdb=" O SER G 84 " (cutoff:3.500A) Processing helix chain 'G' and resid 97 through 100A removed outlier: 3.609A pdb=" N ASN G 100 " --> pdb=" O TYR G 97 " (cutoff:3.500A) Processing helix chain 'H' and resid 79 through 83 removed outlier: 3.934A pdb=" N PHE H 83 " --> pdb=" O PRO H 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 32 removed outlier: 3.985A pdb=" N ASN I 32 " --> pdb=" O PHE I 29 " (cutoff:3.500A) Processing helix chain 'I' and resid 83 through 87 removed outlier: 3.782A pdb=" N THR I 87 " --> pdb=" O SER I 84 " (cutoff:3.500A) Processing helix chain 'J' and resid 79 through 83 removed outlier: 4.016A pdb=" N PHE J 83 " --> pdb=" O PRO J 80 " (cutoff:3.500A) Processing helix chain 'K' and resid 28 through 32 removed outlier: 3.873A pdb=" N ASN K 32 " --> pdb=" O PHE K 29 " (cutoff:3.500A) Processing helix chain 'K' and resid 83 through 87 removed outlier: 3.790A pdb=" N THR K 87 " --> pdb=" O SER K 84 " (cutoff:3.500A) Processing helix chain 'K' and resid 97 through 100A removed outlier: 3.649A pdb=" N ASN K 100 " --> pdb=" O TYR K 97 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.904A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 495 through 499 removed outlier: 5.646A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 8.118A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.778A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 75 through 76 removed outlier: 6.933A pdb=" N CYS A 54 " --> pdb=" O VAL A 75 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA5, first strand: chain 'A' and resid 120 through 121 removed outlier: 3.835A pdb=" N VAL A 120 " --> pdb=" O GLN A 203 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 169 through 177 Processing sheet with id=AA7, first strand: chain 'A' and resid 260 through 261 removed outlier: 6.444A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 9.986A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.401A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 9.498A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 10.411A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.197A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.094A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N THR A 450 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU A 381 " --> pdb=" O CYS A 378 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 271 through 273 removed outlier: 6.863A pdb=" N THR A 450 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 10.094A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 9.197A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.411A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.498A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 11.401A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 9.986A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N THR A 467 " --> pdb=" O ASP A 457 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N ILE A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N PHE A 468 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 304 through 312 removed outlier: 6.511A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 494 through 499 removed outlier: 5.886A pdb=" N VAL D 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 8.206A pdb=" N VAL C 38 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N THR D 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 8.174A pdb=" N TYR C 40 " --> pdb=" O CYS D 604 " (cutoff:3.500A) removed outlier: 8.346A pdb=" N CYS D 604 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.775A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 75 through 76 removed outlier: 6.954A pdb=" N CYS C 54 " --> pdb=" O VAL C 75 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AB5, first strand: chain 'C' and resid 169 through 177 Processing sheet with id=AB6, first strand: chain 'C' and resid 202 through 203 removed outlier: 6.409A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 260 through 261 removed outlier: 6.446A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) removed outlier: 9.919A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 11.342A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 9.518A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 10.424A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 9.210A pdb=" N ASN C 448 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 10.200A pdb=" N THR C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N THR C 450 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU C 381 " --> pdb=" O CYS C 378 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 271 through 273 removed outlier: 6.915A pdb=" N THR C 450 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 10.200A pdb=" N THR C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 9.210A pdb=" N ASN C 448 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 10.424A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 9.518A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 11.342A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 9.919A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N THR C 467 " --> pdb=" O ASP C 457 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N ILE C 358 " --> pdb=" O GLU C 466 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N PHE C 468 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 304 through 312 removed outlier: 6.511A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 494 through 499 removed outlier: 5.787A pdb=" N VAL F 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 8.311A pdb=" N VAL E 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N THR F 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 8.203A pdb=" N TYR E 40 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 8.415A pdb=" N CYS F 604 " --> pdb=" O TYR E 40 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.746A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N VAL E 242 " --> pdb=" O LEU E 86 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 75 through 76 removed outlier: 6.938A pdb=" N CYS E 54 " --> pdb=" O VAL E 75 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 91 through 94 Processing sheet with id=AC5, first strand: chain 'E' and resid 169 through 177 Processing sheet with id=AC6, first strand: chain 'E' and resid 202 through 203 removed outlier: 6.389A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 260 through 261 removed outlier: 6.446A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 9.969A pdb=" N ARG E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 11.379A pdb=" N ILE E 294 " --> pdb=" O ARG E 444 " (cutoff:3.500A) removed outlier: 9.516A pdb=" N VAL E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 10.442A pdb=" N VAL E 292 " --> pdb=" O VAL E 446 " (cutoff:3.500A) removed outlier: 9.237A pdb=" N ASN E 448 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 10.179A pdb=" N THR E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N THR E 450 " --> pdb=" O PHE E 288 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N GLN E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N SER E 334 " --> pdb=" O GLN E 293 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N PHE E 382 " --> pdb=" O LYS E 421 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 271 through 273 removed outlier: 7.020A pdb=" N THR E 450 " --> pdb=" O PHE E 288 " (cutoff:3.500A) removed outlier: 10.179A pdb=" N THR E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 9.237A pdb=" N ASN E 448 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 10.442A pdb=" N VAL E 292 " --> pdb=" O VAL E 446 " (cutoff:3.500A) removed outlier: 9.516A pdb=" N VAL E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 11.379A pdb=" N ILE E 294 " --> pdb=" O ARG E 444 " (cutoff:3.500A) removed outlier: 9.969A pdb=" N ARG E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N THR E 467 " --> pdb=" O ASP E 457 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N ILE E 358 " --> pdb=" O GLU E 466 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N PHE E 468 " --> pdb=" O ILE E 358 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ARG E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 304 through 312 removed outlier: 6.440A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 3 through 6 Processing sheet with id=AD2, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.377A pdb=" N LEU G 34 " --> pdb=" O TRP G 50 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N TRP G 50 " --> pdb=" O LEU G 34 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N TRP G 36 " --> pdb=" O LEU G 48 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 10 through 12 removed outlier: 3.807A pdb=" N VAL G 102 " --> pdb=" O ARG G 94 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 4 through 7 removed outlier: 11.870A pdb=" N CYS H 23 " --> pdb=" O THR H 74 " (cutoff:3.500A) removed outlier: 10.953A pdb=" N THR H 74 " --> pdb=" O CYS H 23 " (cutoff:3.500A) removed outlier: 11.911A pdb=" N ALA H 25 " --> pdb=" O THR H 72 " (cutoff:3.500A) removed outlier: 11.627A pdb=" N THR H 72 " --> pdb=" O ALA H 25 " (cutoff:3.500A) removed outlier: 11.214A pdb=" N GLN H 27 " --> pdb=" O HIS H 70 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N HIS H 70 " --> pdb=" O GLN H 27 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 10 through 13 removed outlier: 7.107A pdb=" N LEU H 33 " --> pdb=" O TYR H 49 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N TYR H 49 " --> pdb=" O LEU H 33 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N TRP H 35 " --> pdb=" O LEU H 47 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 3 through 6 Processing sheet with id=AD7, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.474A pdb=" N LEU I 34 " --> pdb=" O TRP I 50 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N TRP I 50 " --> pdb=" O LEU I 34 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N TRP I 36 " --> pdb=" O LEU I 48 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 10 through 12 removed outlier: 3.805A pdb=" N VAL I 102 " --> pdb=" O ARG I 94 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 4 through 7 removed outlier: 11.953A pdb=" N CYS J 23 " --> pdb=" O THR J 74 " (cutoff:3.500A) removed outlier: 11.011A pdb=" N THR J 74 " --> pdb=" O CYS J 23 " (cutoff:3.500A) removed outlier: 11.926A pdb=" N ALA J 25 " --> pdb=" O THR J 72 " (cutoff:3.500A) removed outlier: 11.603A pdb=" N THR J 72 " --> pdb=" O ALA J 25 " (cutoff:3.500A) removed outlier: 11.264A pdb=" N GLN J 27 " --> pdb=" O HIS J 70 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N HIS J 70 " --> pdb=" O GLN J 27 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 10 through 13 removed outlier: 7.200A pdb=" N LEU J 33 " --> pdb=" O TYR J 49 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N TYR J 49 " --> pdb=" O LEU J 33 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 10 through 13 removed outlier: 3.902A pdb=" N THR J 97 " --> pdb=" O HIS J 90 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'K' and resid 3 through 6 Processing sheet with id=AE4, first strand: chain 'K' and resid 10 through 12 removed outlier: 6.378A pdb=" N LEU K 34 " --> pdb=" O TRP K 50 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N TRP K 50 " --> pdb=" O LEU K 34 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N TRP K 36 " --> pdb=" O LEU K 48 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'K' and resid 10 through 12 removed outlier: 3.805A pdb=" N VAL K 102 " --> pdb=" O ARG K 94 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'L' and resid 4 through 7 removed outlier: 11.951A pdb=" N CYS L 23 " --> pdb=" O THR L 74 " (cutoff:3.500A) removed outlier: 10.897A pdb=" N THR L 74 " --> pdb=" O CYS L 23 " (cutoff:3.500A) removed outlier: 11.855A pdb=" N ALA L 25 " --> pdb=" O THR L 72 " (cutoff:3.500A) removed outlier: 11.523A pdb=" N THR L 72 " --> pdb=" O ALA L 25 " (cutoff:3.500A) removed outlier: 11.169A pdb=" N GLN L 27 " --> pdb=" O HIS L 70 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N HIS L 70 " --> pdb=" O GLN L 27 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'L' and resid 10 through 13 removed outlier: 7.112A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.933A pdb=" N THR L 97 " --> pdb=" O HIS L 90 " (cutoff:3.500A) 764 hydrogen bonds defined for protein. 1962 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: 4.06 Time building geometry restraints manager: 1.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.98 - 1.28: 3154 1.28 - 1.58: 16932 1.58 - 1.89: 175 1.89 - 2.19: 0 2.19 - 2.49: 1 Bond restraints: 20262 Sorted by residual: bond pdb=" CB PRO J 95 " pdb=" CG PRO J 95 " ideal model delta sigma weight residual 1.506 2.490 -0.984 3.90e-02 6.57e+02 6.37e+02 bond pdb=" CG PRO J 95 " pdb=" CD PRO J 95 " ideal model delta sigma weight residual 1.512 0.982 0.530 2.70e-02 1.37e+03 3.86e+02 bond pdb=" N PRO J 95 " pdb=" CA PRO J 95 " ideal model delta sigma weight residual 1.468 1.305 0.163 1.70e-02 3.46e+03 9.25e+01 bond pdb=" N PRO J 95 " pdb=" CD PRO J 95 " ideal model delta sigma weight residual 1.474 1.597 -0.123 1.40e-02 5.10e+03 7.69e+01 bond pdb=" CA PRO J 95 " pdb=" CB PRO J 95 " ideal model delta sigma weight residual 1.533 1.428 0.105 1.80e-02 3.09e+03 3.40e+01 ... (remaining 20257 not shown) Histogram of bond angle deviations from ideal: 0.00 - 18.10: 27503 18.10 - 36.20: 0 36.20 - 54.30: 0 54.30 - 72.40: 0 72.40 - 90.49: 1 Bond angle restraints: 27504 Sorted by residual: angle pdb=" CB PRO J 95 " pdb=" CG PRO J 95 " pdb=" CD PRO J 95 " ideal model delta sigma weight residual 105.40 14.91 90.49 2.30e+00 1.89e-01 1.55e+03 angle pdb=" N PRO J 95 " pdb=" CA PRO J 95 " pdb=" CB PRO J 95 " ideal model delta sigma weight residual 102.60 87.77 14.83 1.10e+00 8.26e-01 1.82e+02 angle pdb=" CA PRO J 95 " pdb=" N PRO J 95 " pdb=" CD PRO J 95 " ideal model delta sigma weight residual 111.50 95.16 16.34 1.40e+00 5.10e-01 1.36e+02 angle pdb=" N PRO J 95 " pdb=" CD PRO J 95 " pdb=" CG PRO J 95 " ideal model delta sigma weight residual 103.80 91.22 12.58 1.20e+00 6.94e-01 1.10e+02 angle pdb=" CA PRO J 95 " pdb=" CB PRO J 95 " pdb=" CG PRO J 95 " ideal model delta sigma weight residual 104.00 89.67 14.33 1.90e+00 2.77e-01 5.69e+01 ... (remaining 27499 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.71: 11947 21.71 - 43.42: 915 43.42 - 65.13: 216 65.13 - 86.84: 56 86.84 - 108.55: 27 Dihedral angle restraints: 13161 sinusoidal: 6276 harmonic: 6885 Sorted by residual: dihedral pdb=" CB CYS C 201 " pdb=" SG CYS C 201 " pdb=" SG CYS C 433 " pdb=" CB CYS C 433 " ideal model delta sinusoidal sigma weight residual -86.00 -147.90 61.90 1 1.00e+01 1.00e-02 5.08e+01 dihedral pdb=" CB CYS A 201 " pdb=" SG CYS A 201 " pdb=" SG CYS A 433 " pdb=" CB CYS A 433 " ideal model delta sinusoidal sigma weight residual -86.00 -145.66 59.66 1 1.00e+01 1.00e-02 4.75e+01 dihedral pdb=" CB CYS E 201 " pdb=" SG CYS E 201 " pdb=" SG CYS E 433 " pdb=" CB CYS E 433 " ideal model delta sinusoidal sigma weight residual -86.00 -145.08 59.08 1 1.00e+01 1.00e-02 4.67e+01 ... (remaining 13158 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.129: 3257 0.129 - 0.257: 54 0.257 - 0.386: 9 0.386 - 0.515: 0 0.515 - 0.643: 1 Chirality restraints: 3321 Sorted by residual: chirality pdb=" CA PRO J 95 " pdb=" N PRO J 95 " pdb=" C PRO J 95 " pdb=" CB PRO J 95 " both_signs ideal model delta sigma weight residual False 2.72 2.07 0.64 2.00e-01 2.50e+01 1.04e+01 chirality pdb=" C1 NAG E 601 " pdb=" ND2 ASN E 234 " pdb=" C2 NAG E 601 " pdb=" O5 NAG E 601 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.21e+00 chirality pdb=" C1 NAG A 601 " pdb=" ND2 ASN A 234 " pdb=" C2 NAG A 601 " pdb=" O5 NAG A 601 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.20e+00 ... (remaining 3318 not shown) Planarity restraints: 3444 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR J 94 " -0.103 5.00e-02 4.00e+02 1.45e-01 3.36e+01 pdb=" N PRO J 95 " 0.250 5.00e-02 4.00e+02 pdb=" CA PRO J 95 " -0.084 5.00e-02 4.00e+02 pdb=" CD PRO J 95 " -0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN E 136 " -0.014 2.00e-02 2.50e+03 2.77e-02 7.69e+00 pdb=" C ASN E 136 " 0.048 2.00e-02 2.50e+03 pdb=" O ASN E 136 " -0.018 2.00e-02 2.50e+03 pdb=" N ASN E 137 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN J 79 " 0.038 5.00e-02 4.00e+02 5.84e-02 5.45e+00 pdb=" N PRO J 80 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO J 80 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO J 80 " 0.033 5.00e-02 4.00e+02 ... (remaining 3441 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 232 2.64 - 3.20: 16996 3.20 - 3.77: 30714 3.77 - 4.33: 45236 4.33 - 4.90: 73383 Nonbonded interactions: 166561 Sorted by model distance: nonbonded pdb=" OG1 THR A 37 " pdb=" OG1 THR A 499 " model vdw 2.072 3.040 nonbonded pdb=" OG1 THR C 37 " pdb=" OG1 THR C 499 " model vdw 2.085 3.040 nonbonded pdb=" OG SER C 56 " pdb=" OG1 THR C 71 " model vdw 2.121 3.040 nonbonded pdb=" OG SER E 56 " pdb=" OG1 THR E 71 " model vdw 2.125 3.040 nonbonded pdb=" OG SER A 56 " pdb=" OG1 THR A 71 " model vdw 2.140 3.040 ... (remaining 166556 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'H' selection = chain 'J' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'O' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'V' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'e' selection = chain 'f' selection = chain 'h' selection = chain 'i' selection = chain 'j' } ncs_group { reference = chain 'N' selection = chain 'U' selection = chain 'd' } ncs_group { reference = chain 'P' selection = chain 'W' selection = chain 'g' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.030 Process input model: 17.680 Find NCS groups from input model: 0.470 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: 0.010 Load rotamer database and sin/cos tables:6.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 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 : 0.009 0.984 20385 Z= 0.322 Angle : 0.907 90.495 27831 Z= 0.428 Chirality : 0.051 0.643 3321 Planarity : 0.005 0.145 3399 Dihedral : 16.628 108.549 8601 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 1.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 0.48 % Allowed : 12.64 % Favored : 86.88 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 6.06 % 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 aren not related in a simple way. whole: 0.65 (0.18), residues: 2352 helix: 1.14 (0.29), residues: 411 sheet: 0.33 (0.18), residues: 780 loop : 0.40 (0.20), residues: 1161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 308 TYR 0.028 0.001 TYR A 173 PHE 0.009 0.001 PHE C 382 TRP 0.010 0.001 TRP I 47 HIS 0.005 0.001 HIS I 35 Details of bonding type rmsd covalent geometry : bond 0.00915 (20262) covalent geometry : angle 0.89166 (27504) SS BOND : bond 0.00361 ( 42) SS BOND : angle 1.54755 ( 84) hydrogen bonds : bond 0.13297 ( 718) hydrogen bonds : angle 5.98936 ( 1962) link_ALPHA1-2 : bond 0.00351 ( 3) link_ALPHA1-2 : angle 1.79999 ( 9) link_ALPHA1-3 : bond 0.00338 ( 3) link_ALPHA1-3 : angle 1.77237 ( 9) link_BETA1-4 : bond 0.00444 ( 30) link_BETA1-4 : angle 1.09229 ( 90) link_NAG-ASN : bond 0.00291 ( 45) link_NAG-ASN : angle 2.19097 ( 135) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 224 time to evaluate : 0.742 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 637 ASN cc_start: 0.7362 (m110) cc_final: 0.6809 (m110) REVERT: L 79 GLN cc_start: 0.6628 (OUTLIER) cc_final: 0.5775 (tm-30) outliers start: 10 outliers final: 7 residues processed: 234 average time/residue: 0.6258 time to fit residues: 164.8289 Evaluate side-chains 225 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 217 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain C residue 201 CYS Chi-restraints excluded: chain C residue 247 CYS Chi-restraints excluded: chain E residue 140 ASP Chi-restraints excluded: chain E residue 247 CYS Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain L residue 79 GLN Chi-restraints excluded: chain L residue 93 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 216 optimal weight: 9.9990 chunk 98 optimal weight: 0.5980 chunk 194 optimal weight: 5.9990 chunk 227 optimal weight: 20.0000 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 235 optimal weight: 5.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 GLN A 280 ASN B 591 GLN C 130 GLN E 130 GLN E 136 ASN E 422 GLN E 440 GLN F 591 GLN G 32 ASN G 76 ASN I 32 ASN I 76 ASN J 90 HIS K 32 ASN L 37 GLN L 90 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.196524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.139479 restraints weight = 19957.435| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 1.91 r_work: 0.3315 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.1446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 20385 Z= 0.186 Angle : 0.659 8.101 27831 Z= 0.326 Chirality : 0.047 0.290 3321 Planarity : 0.005 0.062 3399 Dihedral : 9.728 71.391 4241 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.78 % Allowed : 12.12 % Favored : 85.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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 aren not related in a simple way. whole: 0.69 (0.18), residues: 2352 helix: 0.94 (0.27), residues: 423 sheet: 0.31 (0.17), residues: 804 loop : 0.59 (0.20), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 298 TYR 0.015 0.002 TYR C 173 PHE 0.020 0.002 PHE E 383 TRP 0.013 0.002 TRP A 427 HIS 0.006 0.001 HIS E 352 Details of bonding type rmsd covalent geometry : bond 0.00435 (20262) covalent geometry : angle 0.61507 (27504) SS BOND : bond 0.00312 ( 42) SS BOND : angle 0.89320 ( 84) hydrogen bonds : bond 0.04515 ( 718) hydrogen bonds : angle 5.08318 ( 1962) link_ALPHA1-2 : bond 0.00380 ( 3) link_ALPHA1-2 : angle 2.10741 ( 9) link_ALPHA1-3 : bond 0.00817 ( 3) link_ALPHA1-3 : angle 2.02351 ( 9) link_BETA1-4 : bond 0.00455 ( 30) link_BETA1-4 : angle 1.65345 ( 90) link_NAG-ASN : bond 0.00481 ( 45) link_NAG-ASN : angle 3.07792 ( 135) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 230 time to evaluate : 0.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 GLU cc_start: 0.7565 (OUTLIER) cc_final: 0.7141 (tp30) REVERT: A 103 GLN cc_start: 0.8473 (mt0) cc_final: 0.8235 (mt0) REVERT: A 117 LYS cc_start: 0.8287 (mtpt) cc_final: 0.7898 (tptt) REVERT: A 325 ASP cc_start: 0.7757 (OUTLIER) cc_final: 0.7470 (t0) REVERT: C 92 GLU cc_start: 0.7629 (OUTLIER) cc_final: 0.7337 (tp30) REVERT: C 117 LYS cc_start: 0.8155 (OUTLIER) cc_final: 0.7791 (mmtt) REVERT: C 325 ASP cc_start: 0.7745 (OUTLIER) cc_final: 0.7285 (t0) REVERT: C 502 LYS cc_start: 0.8503 (tttm) cc_final: 0.8293 (tttm) REVERT: D 657 GLU cc_start: 0.6980 (OUTLIER) cc_final: 0.6717 (tt0) REVERT: E 91 GLU cc_start: 0.7744 (OUTLIER) cc_final: 0.6355 (tm-30) REVERT: E 92 GLU cc_start: 0.7340 (tm-30) cc_final: 0.7062 (tm-30) REVERT: E 335 LYS cc_start: 0.8340 (ttmt) cc_final: 0.8124 (ttpt) REVERT: E 502 LYS cc_start: 0.8494 (tttp) cc_final: 0.8288 (tttp) REVERT: H 48 ILE cc_start: 0.5982 (OUTLIER) cc_final: 0.5585 (pp) REVERT: H 54 LEU cc_start: 0.5880 (OUTLIER) cc_final: 0.5311 (mm) REVERT: J 48 ILE cc_start: 0.5977 (OUTLIER) cc_final: 0.5626 (pp) REVERT: J 91 MET cc_start: 0.5252 (ptt) cc_final: 0.4897 (ptp) REVERT: L 48 ILE cc_start: 0.5689 (OUTLIER) cc_final: 0.5083 (OUTLIER) REVERT: L 79 GLN cc_start: 0.5736 (OUTLIER) cc_final: 0.4762 (tm-30) REVERT: L 91 MET cc_start: 0.5170 (ptt) cc_final: 0.4639 (ptp) outliers start: 58 outliers final: 21 residues processed: 267 average time/residue: 0.5658 time to fit residues: 170.0570 Evaluate side-chains 253 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 221 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 117 LYS Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 444 ARG Chi-restraints excluded: chain D residue 636 SER Chi-restraints excluded: chain D residue 638 TYR Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 657 GLU Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain E residue 91 GLU Chi-restraints excluded: chain E residue 213 ILE Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 347 LYS Chi-restraints excluded: chain F residue 638 TYR Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 109 VAL Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 54 LEU Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 79 GLN Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 109 VAL Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 79 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 80 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 chunk 107 optimal weight: 0.5980 chunk 231 optimal weight: 6.9990 chunk 26 optimal weight: 1.9990 chunk 190 optimal weight: 30.0000 chunk 117 optimal weight: 3.9990 chunk 215 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 194 optimal weight: 6.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 GLN A 137 ASN C 130 GLN C 440 GLN E 130 GLN E 136 ASN E 440 GLN G 6 GLN I 32 ASN K 32 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.195536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.137630 restraints weight = 20083.829| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 1.97 r_work: 0.3301 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3180 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 20385 Z= 0.177 Angle : 0.620 9.215 27831 Z= 0.305 Chirality : 0.046 0.305 3321 Planarity : 0.004 0.061 3399 Dihedral : 8.177 59.469 4233 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.54 % Allowed : 13.46 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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 aren not related in a simple way. whole: 0.73 (0.18), residues: 2352 helix: 0.96 (0.27), residues: 429 sheet: 0.50 (0.17), residues: 801 loop : 0.46 (0.20), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 298 TYR 0.014 0.001 TYR E 384 PHE 0.018 0.002 PHE A 383 TRP 0.016 0.002 TRP E 427 HIS 0.006 0.001 HIS E 352 Details of bonding type rmsd covalent geometry : bond 0.00413 (20262) covalent geometry : angle 0.57546 (27504) SS BOND : bond 0.00297 ( 42) SS BOND : angle 0.69048 ( 84) hydrogen bonds : bond 0.04467 ( 718) hydrogen bonds : angle 5.03422 ( 1962) link_ALPHA1-2 : bond 0.00210 ( 3) link_ALPHA1-2 : angle 1.83228 ( 9) link_ALPHA1-3 : bond 0.00877 ( 3) link_ALPHA1-3 : angle 1.30634 ( 9) link_BETA1-4 : bond 0.00339 ( 30) link_BETA1-4 : angle 1.52878 ( 90) link_NAG-ASN : bond 0.00417 ( 45) link_NAG-ASN : angle 3.09713 ( 135) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 227 time to evaluate : 0.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 GLU cc_start: 0.7038 (mm-30) cc_final: 0.6810 (mm-30) REVERT: A 103 GLN cc_start: 0.8528 (mt0) cc_final: 0.8288 (mt0) REVERT: A 117 LYS cc_start: 0.8308 (mtpt) cc_final: 0.7936 (tptt) REVERT: A 130 GLN cc_start: 0.8821 (OUTLIER) cc_final: 0.8105 (mp-120) REVERT: B 588 ARG cc_start: 0.7812 (OUTLIER) cc_final: 0.7374 (tmm160) REVERT: B 637 ASN cc_start: 0.7537 (m110) cc_final: 0.6958 (m-40) REVERT: C 92 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.7301 (tm-30) REVERT: C 103 GLN cc_start: 0.8521 (mt0) cc_final: 0.8307 (mt0) REVERT: C 117 LYS cc_start: 0.8262 (OUTLIER) cc_final: 0.7869 (mmtt) REVERT: C 325 ASP cc_start: 0.7686 (OUTLIER) cc_final: 0.7303 (t0) REVERT: C 440 GLN cc_start: 0.8347 (OUTLIER) cc_final: 0.7957 (tp-100) REVERT: D 588 ARG cc_start: 0.7866 (OUTLIER) cc_final: 0.7475 (tmm160) REVERT: E 117 LYS cc_start: 0.8382 (mmmt) cc_final: 0.7939 (tppt) REVERT: E 335 LYS cc_start: 0.8337 (ttmt) cc_final: 0.8129 (ttpt) REVERT: G 75 ILE cc_start: 0.8142 (OUTLIER) cc_final: 0.7712 (pt) REVERT: H 54 LEU cc_start: 0.6014 (OUTLIER) cc_final: 0.5432 (mm) REVERT: H 79 GLN cc_start: 0.5429 (OUTLIER) cc_final: 0.4508 (tm-30) REVERT: J 42 LYS cc_start: 0.5672 (OUTLIER) cc_final: 0.4686 (ptpp) REVERT: J 48 ILE cc_start: 0.6061 (OUTLIER) cc_final: 0.5676 (pp) REVERT: L 48 ILE cc_start: 0.5741 (OUTLIER) cc_final: 0.5101 (pp) REVERT: L 79 GLN cc_start: 0.5681 (OUTLIER) cc_final: 0.4860 (tm-30) REVERT: L 91 MET cc_start: 0.5300 (ptt) cc_final: 0.4704 (ptp) outliers start: 53 outliers final: 20 residues processed: 260 average time/residue: 0.6549 time to fit residues: 190.3107 Evaluate side-chains 256 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 222 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 130 GLN Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain B residue 588 ARG Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 638 TYR Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 117 LYS Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 440 GLN Chi-restraints excluded: chain D residue 588 ARG Chi-restraints excluded: chain D residue 636 SER Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 440 GLN Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 75 ILE Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 109 VAL Chi-restraints excluded: chain H residue 54 LEU Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 79 GLN Chi-restraints excluded: chain J residue 42 LYS Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 79 GLN Chi-restraints excluded: chain J residue 91 MET Chi-restraints excluded: chain K residue 109 VAL Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 79 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 31 optimal weight: 3.9990 chunk 91 optimal weight: 0.0870 chunk 218 optimal weight: 6.9990 chunk 149 optimal weight: 0.7980 chunk 138 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 160 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 150 optimal weight: 0.0470 overall best weight: 0.9860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 ASN C 130 GLN C 440 GLN E 130 GLN E 440 GLN G 32 ASN I 6 GLN I 32 ASN K 6 GLN K 32 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.195712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.138055 restraints weight = 19999.118| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 1.95 r_work: 0.3306 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3185 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.1893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20385 Z= 0.152 Angle : 0.596 9.219 27831 Z= 0.293 Chirality : 0.045 0.310 3321 Planarity : 0.004 0.063 3399 Dihedral : 7.378 59.641 4233 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.83 % Allowed : 13.98 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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 aren not related in a simple way. whole: 0.75 (0.18), residues: 2352 helix: 1.05 (0.27), residues: 429 sheet: 0.50 (0.17), residues: 795 loop : 0.45 (0.20), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 178 TYR 0.011 0.001 TYR C 173 PHE 0.017 0.002 PHE E 383 TRP 0.017 0.002 TRP E 427 HIS 0.003 0.001 HIS E 352 Details of bonding type rmsd covalent geometry : bond 0.00348 (20262) covalent geometry : angle 0.55239 (27504) SS BOND : bond 0.00290 ( 42) SS BOND : angle 0.59508 ( 84) hydrogen bonds : bond 0.04130 ( 718) hydrogen bonds : angle 4.92422 ( 1962) link_ALPHA1-2 : bond 0.00259 ( 3) link_ALPHA1-2 : angle 1.83893 ( 9) link_ALPHA1-3 : bond 0.00957 ( 3) link_ALPHA1-3 : angle 1.44185 ( 9) link_BETA1-4 : bond 0.00307 ( 30) link_BETA1-4 : angle 1.51660 ( 90) link_NAG-ASN : bond 0.00383 ( 45) link_NAG-ASN : angle 2.99305 ( 135) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 225 time to evaluate : 0.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 GLU cc_start: 0.7050 (mm-30) cc_final: 0.6840 (mm-30) REVERT: A 92 GLU cc_start: 0.7611 (OUTLIER) cc_final: 0.7150 (tp30) REVERT: A 103 GLN cc_start: 0.8538 (mt0) cc_final: 0.8309 (mt0) REVERT: A 117 LYS cc_start: 0.8254 (mtpt) cc_final: 0.7930 (tptt) REVERT: B 588 ARG cc_start: 0.7811 (OUTLIER) cc_final: 0.7370 (tmm160) REVERT: B 637 ASN cc_start: 0.7529 (m110) cc_final: 0.6947 (m-40) REVERT: C 92 GLU cc_start: 0.7567 (OUTLIER) cc_final: 0.7293 (tm-30) REVERT: C 103 GLN cc_start: 0.8513 (mt0) cc_final: 0.8283 (mt0) REVERT: C 325 ASP cc_start: 0.7707 (OUTLIER) cc_final: 0.7328 (t0) REVERT: D 588 ARG cc_start: 0.7857 (OUTLIER) cc_final: 0.7463 (tmm160) REVERT: D 657 GLU cc_start: 0.6918 (OUTLIER) cc_final: 0.6671 (tt0) REVERT: E 117 LYS cc_start: 0.8351 (mmmt) cc_final: 0.7929 (tppt) REVERT: E 335 LYS cc_start: 0.8347 (ttmt) cc_final: 0.8135 (ttpt) REVERT: G 75 ILE cc_start: 0.8149 (OUTLIER) cc_final: 0.7684 (pt) REVERT: H 48 ILE cc_start: 0.6035 (OUTLIER) cc_final: 0.5635 (pp) REVERT: H 79 GLN cc_start: 0.5403 (OUTLIER) cc_final: 0.4476 (tm-30) REVERT: J 48 ILE cc_start: 0.6087 (OUTLIER) cc_final: 0.5701 (pp) REVERT: L 48 ILE cc_start: 0.5746 (OUTLIER) cc_final: 0.5110 (pp) REVERT: L 79 GLN cc_start: 0.5696 (OUTLIER) cc_final: 0.4928 (tm-30) REVERT: L 91 MET cc_start: 0.5412 (ptt) cc_final: 0.4887 (ptp) outliers start: 59 outliers final: 25 residues processed: 267 average time/residue: 0.6618 time to fit residues: 198.5624 Evaluate side-chains 258 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 221 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 588 ARG Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 638 TYR Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain D residue 588 ARG Chi-restraints excluded: chain D residue 636 SER Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 657 GLU Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 592 LEU Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain F residue 638 TYR Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 75 ILE Chi-restraints excluded: chain G residue 109 VAL Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 79 GLN Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 79 GLN Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 70 THR Chi-restraints excluded: chain K residue 109 VAL Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 79 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 187 optimal weight: 7.9990 chunk 23 optimal weight: 0.9980 chunk 159 optimal weight: 4.9990 chunk 120 optimal weight: 2.9990 chunk 236 optimal weight: 9.9990 chunk 214 optimal weight: 0.5980 chunk 27 optimal weight: 3.9990 chunk 188 optimal weight: 0.0770 chunk 160 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 185 optimal weight: 2.9990 overall best weight: 1.3342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 ASN A 130 GLN A 280 ASN C 130 GLN C 440 GLN D 630 GLN E 130 GLN E 136 ASN E 440 GLN G 32 ASN K 32 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.192776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.138658 restraints weight = 19912.552| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 1.83 r_work: 0.3234 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 20385 Z= 0.187 Angle : 0.630 10.606 27831 Z= 0.308 Chirality : 0.046 0.319 3321 Planarity : 0.004 0.062 3399 Dihedral : 6.891 59.389 4233 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 3.40 % Allowed : 13.94 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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 aren not related in a simple way. whole: 0.69 (0.18), residues: 2352 helix: 0.96 (0.27), residues: 429 sheet: 0.48 (0.18), residues: 795 loop : 0.41 (0.20), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 178 TYR 0.014 0.002 TYR E 384 PHE 0.020 0.002 PHE A 383 TRP 0.018 0.002 TRP E 427 HIS 0.005 0.001 HIS A 352 Details of bonding type rmsd covalent geometry : bond 0.00435 (20262) covalent geometry : angle 0.58475 (27504) SS BOND : bond 0.00344 ( 42) SS BOND : angle 0.65978 ( 84) hydrogen bonds : bond 0.04441 ( 718) hydrogen bonds : angle 4.98784 ( 1962) link_ALPHA1-2 : bond 0.00192 ( 3) link_ALPHA1-2 : angle 1.94156 ( 9) link_ALPHA1-3 : bond 0.00922 ( 3) link_ALPHA1-3 : angle 1.39660 ( 9) link_BETA1-4 : bond 0.00319 ( 30) link_BETA1-4 : angle 1.55200 ( 90) link_NAG-ASN : bond 0.00461 ( 45) link_NAG-ASN : angle 3.13992 ( 135) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 228 time to evaluate : 0.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.7874 (OUTLIER) cc_final: 0.7254 (mppt) REVERT: A 87 GLU cc_start: 0.7200 (mm-30) cc_final: 0.6999 (mm-30) REVERT: A 92 GLU cc_start: 0.7589 (OUTLIER) cc_final: 0.7117 (tp30) REVERT: A 103 GLN cc_start: 0.8582 (mt0) cc_final: 0.8339 (mt0) REVERT: A 117 LYS cc_start: 0.8283 (mtpt) cc_final: 0.7905 (tptt) REVERT: B 588 ARG cc_start: 0.7868 (OUTLIER) cc_final: 0.7436 (tmm160) REVERT: B 637 ASN cc_start: 0.7544 (m110) cc_final: 0.6955 (m-40) REVERT: C 92 GLU cc_start: 0.7599 (OUTLIER) cc_final: 0.7311 (tm-30) REVERT: C 103 GLN cc_start: 0.8595 (mt0) cc_final: 0.8358 (mt0) REVERT: C 117 LYS cc_start: 0.8366 (mmmt) cc_final: 0.7875 (mmtt) REVERT: C 325 ASP cc_start: 0.7778 (OUTLIER) cc_final: 0.7374 (t0) REVERT: C 440 GLN cc_start: 0.8396 (OUTLIER) cc_final: 0.8100 (tp-100) REVERT: D 588 ARG cc_start: 0.7912 (OUTLIER) cc_final: 0.7491 (tmm160) REVERT: D 657 GLU cc_start: 0.6946 (OUTLIER) cc_final: 0.6718 (tt0) REVERT: E 87 GLU cc_start: 0.7205 (mm-30) cc_final: 0.6988 (mm-30) REVERT: E 117 LYS cc_start: 0.8359 (mmmt) cc_final: 0.7921 (tppt) REVERT: E 335 LYS cc_start: 0.8380 (ttmt) cc_final: 0.8171 (ttpt) REVERT: G 75 ILE cc_start: 0.8112 (OUTLIER) cc_final: 0.7628 (pt) REVERT: H 48 ILE cc_start: 0.5916 (OUTLIER) cc_final: 0.5575 (pp) REVERT: H 54 LEU cc_start: 0.5947 (OUTLIER) cc_final: 0.5398 (mm) REVERT: H 79 GLN cc_start: 0.5308 (OUTLIER) cc_final: 0.4451 (tm-30) REVERT: J 42 LYS cc_start: 0.5941 (OUTLIER) cc_final: 0.4818 (ptpp) REVERT: J 48 ILE cc_start: 0.6059 (OUTLIER) cc_final: 0.5648 (pp) REVERT: L 48 ILE cc_start: 0.5738 (OUTLIER) cc_final: 0.5075 (pp) REVERT: L 54 LEU cc_start: 0.6073 (OUTLIER) cc_final: 0.5813 (mm) REVERT: L 79 GLN cc_start: 0.5587 (OUTLIER) cc_final: 0.4915 (tm-30) REVERT: L 91 MET cc_start: 0.5437 (ptt) cc_final: 0.4895 (ptp) outliers start: 71 outliers final: 34 residues processed: 274 average time/residue: 0.6689 time to fit residues: 205.9910 Evaluate side-chains 273 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 222 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 588 ARG Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 638 TYR Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 440 GLN Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 588 ARG Chi-restraints excluded: chain D residue 636 SER Chi-restraints excluded: chain D residue 638 TYR Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 657 GLU Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 347 LYS Chi-restraints excluded: chain E residue 440 GLN Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 592 LEU Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain F residue 638 TYR Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 75 ILE Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 109 VAL Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 54 LEU Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 79 GLN Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain J residue 42 LYS Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 79 GLN Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 109 VAL Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 79 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 212 optimal weight: 20.0000 chunk 17 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 210 optimal weight: 9.9990 chunk 2 optimal weight: 6.9990 chunk 121 optimal weight: 0.7980 chunk 162 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 143 optimal weight: 0.9990 chunk 95 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 GLN A 280 ASN C 130 GLN D 591 GLN E 130 GLN E 137 ASN F 543 ASN G 32 ASN I 32 ASN K 32 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.193846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.139518 restraints weight = 19927.895| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 1.77 r_work: 0.3250 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20385 Z= 0.141 Angle : 0.591 12.192 27831 Z= 0.290 Chirality : 0.045 0.313 3321 Planarity : 0.004 0.062 3399 Dihedral : 6.439 57.269 4233 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.87 % Allowed : 15.28 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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 aren not related in a simple way. whole: 0.76 (0.18), residues: 2352 helix: 1.13 (0.27), residues: 429 sheet: 0.49 (0.18), residues: 795 loop : 0.43 (0.20), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 178 TYR 0.011 0.001 TYR C 173 PHE 0.017 0.001 PHE E 383 TRP 0.019 0.001 TRP C 427 HIS 0.003 0.001 HIS I 35 Details of bonding type rmsd covalent geometry : bond 0.00322 (20262) covalent geometry : angle 0.54790 (27504) SS BOND : bond 0.00255 ( 42) SS BOND : angle 0.70353 ( 84) hydrogen bonds : bond 0.04023 ( 718) hydrogen bonds : angle 4.88821 ( 1962) link_ALPHA1-2 : bond 0.00235 ( 3) link_ALPHA1-2 : angle 1.90098 ( 9) link_ALPHA1-3 : bond 0.00989 ( 3) link_ALPHA1-3 : angle 1.40751 ( 9) link_BETA1-4 : bond 0.00320 ( 30) link_BETA1-4 : angle 1.47984 ( 90) link_NAG-ASN : bond 0.00361 ( 45) link_NAG-ASN : angle 2.95286 ( 135) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 229 time to evaluate : 0.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 GLU cc_start: 0.7172 (mm-30) cc_final: 0.6903 (mm-30) REVERT: A 92 GLU cc_start: 0.7505 (OUTLIER) cc_final: 0.7065 (tp30) REVERT: A 103 GLN cc_start: 0.8565 (mt0) cc_final: 0.8318 (mt0) REVERT: A 117 LYS cc_start: 0.8200 (OUTLIER) cc_final: 0.7837 (tptp) REVERT: B 588 ARG cc_start: 0.7804 (OUTLIER) cc_final: 0.7367 (tmm160) REVERT: B 637 ASN cc_start: 0.7448 (m110) cc_final: 0.6875 (m-40) REVERT: C 92 GLU cc_start: 0.7572 (OUTLIER) cc_final: 0.7289 (tm-30) REVERT: C 103 GLN cc_start: 0.8561 (mt0) cc_final: 0.8320 (mt0) REVERT: C 117 LYS cc_start: 0.8303 (mmmt) cc_final: 0.7819 (mmtt) REVERT: C 325 ASP cc_start: 0.7738 (OUTLIER) cc_final: 0.7330 (t0) REVERT: D 588 ARG cc_start: 0.7863 (OUTLIER) cc_final: 0.7437 (tmm160) REVERT: D 657 GLU cc_start: 0.6888 (OUTLIER) cc_final: 0.6644 (tt0) REVERT: E 117 LYS cc_start: 0.8283 (mmmt) cc_final: 0.7917 (tptp) REVERT: E 335 LYS cc_start: 0.8346 (ttmt) cc_final: 0.8052 (ttpt) REVERT: E 347 LYS cc_start: 0.7821 (OUTLIER) cc_final: 0.7523 (pttt) REVERT: G 75 ILE cc_start: 0.8107 (OUTLIER) cc_final: 0.7635 (pt) REVERT: H 32 GLU cc_start: 0.7226 (OUTLIER) cc_final: 0.6575 (mm-30) REVERT: H 48 ILE cc_start: 0.5957 (OUTLIER) cc_final: 0.5570 (pp) REVERT: H 79 GLN cc_start: 0.5400 (OUTLIER) cc_final: 0.4515 (tm-30) REVERT: J 42 LYS cc_start: 0.5934 (OUTLIER) cc_final: 0.4862 (ptpp) REVERT: J 48 ILE cc_start: 0.6079 (OUTLIER) cc_final: 0.5668 (pp) REVERT: J 54 LEU cc_start: 0.5809 (OUTLIER) cc_final: 0.5485 (mm) REVERT: L 12 SER cc_start: 0.7043 (OUTLIER) cc_final: 0.6509 (p) REVERT: L 48 ILE cc_start: 0.5712 (OUTLIER) cc_final: 0.5057 (pp) REVERT: L 54 LEU cc_start: 0.6077 (OUTLIER) cc_final: 0.5833 (mm) REVERT: L 79 GLN cc_start: 0.5683 (OUTLIER) cc_final: 0.5048 (tm-30) REVERT: L 91 MET cc_start: 0.5442 (ptt) cc_final: 0.4937 (ptp) outliers start: 60 outliers final: 29 residues processed: 271 average time/residue: 0.6086 time to fit residues: 185.4891 Evaluate side-chains 269 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 221 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 117 LYS Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 588 ARG Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 638 TYR Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain D residue 588 ARG Chi-restraints excluded: chain D residue 636 SER Chi-restraints excluded: chain D residue 638 TYR Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 657 GLU Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 347 LYS Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 592 LEU Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain F residue 638 TYR Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 75 ILE Chi-restraints excluded: chain G residue 109 VAL Chi-restraints excluded: chain H residue 32 GLU Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 79 GLN Chi-restraints excluded: chain J residue 42 LYS Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 54 LEU Chi-restraints excluded: chain J residue 79 GLN Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 67 VAL Chi-restraints excluded: chain K residue 109 VAL Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 79 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 109 optimal weight: 8.9990 chunk 203 optimal weight: 4.9990 chunk 180 optimal weight: 6.9990 chunk 210 optimal weight: 9.9990 chunk 102 optimal weight: 4.9990 chunk 181 optimal weight: 0.4980 chunk 95 optimal weight: 3.9990 chunk 67 optimal weight: 0.9990 chunk 173 optimal weight: 0.9980 chunk 221 optimal weight: 4.9990 chunk 120 optimal weight: 3.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 GLN A 280 ASN C 130 GLN C 355 ASN C 422 GLN C 440 GLN E 130 GLN E 440 GLN F 543 ASN G 32 ASN I 32 ASN K 32 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.190436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.136991 restraints weight = 20021.860| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 1.72 r_work: 0.3214 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 20385 Z= 0.269 Angle : 0.723 13.982 27831 Z= 0.352 Chirality : 0.049 0.339 3321 Planarity : 0.005 0.066 3399 Dihedral : 6.962 57.141 4233 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 3.21 % Allowed : 15.52 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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 aren not related in a simple way. whole: 0.48 (0.18), residues: 2352 helix: 0.51 (0.26), residues: 429 sheet: 0.42 (0.17), residues: 792 loop : 0.35 (0.20), residues: 1131 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 178 TYR 0.020 0.002 TYR E 384 PHE 0.022 0.002 PHE E 383 TRP 0.020 0.002 TRP C 427 HIS 0.007 0.001 HIS A 352 Details of bonding type rmsd covalent geometry : bond 0.00640 (20262) covalent geometry : angle 0.67482 (27504) SS BOND : bond 0.00458 ( 42) SS BOND : angle 0.92430 ( 84) hydrogen bonds : bond 0.05139 ( 718) hydrogen bonds : angle 5.18212 ( 1962) link_ALPHA1-2 : bond 0.00117 ( 3) link_ALPHA1-2 : angle 2.21259 ( 9) link_ALPHA1-3 : bond 0.00772 ( 3) link_ALPHA1-3 : angle 1.50712 ( 9) link_BETA1-4 : bond 0.00290 ( 30) link_BETA1-4 : angle 1.73467 ( 90) link_NAG-ASN : bond 0.00637 ( 45) link_NAG-ASN : angle 3.46884 ( 135) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 228 time to evaluate : 0.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.7905 (OUTLIER) cc_final: 0.7282 (mppt) REVERT: A 92 GLU cc_start: 0.7607 (OUTLIER) cc_final: 0.7101 (tp30) REVERT: A 103 GLN cc_start: 0.8611 (mt0) cc_final: 0.8360 (mt0) REVERT: A 117 LYS cc_start: 0.8346 (mttt) cc_final: 0.7932 (tptt) REVERT: B 588 ARG cc_start: 0.7920 (OUTLIER) cc_final: 0.7464 (tmm160) REVERT: B 637 ASN cc_start: 0.7511 (m110) cc_final: 0.6982 (m-40) REVERT: C 117 LYS cc_start: 0.8405 (mmmt) cc_final: 0.7904 (mmtt) REVERT: C 325 ASP cc_start: 0.7782 (OUTLIER) cc_final: 0.7338 (t0) REVERT: D 588 ARG cc_start: 0.7948 (OUTLIER) cc_final: 0.7433 (tmm160) REVERT: E 87 GLU cc_start: 0.7256 (mm-30) cc_final: 0.7036 (mm-30) REVERT: E 117 LYS cc_start: 0.8426 (mmmt) cc_final: 0.7966 (tppt) REVERT: E 269 GLU cc_start: 0.6851 (OUTLIER) cc_final: 0.6450 (mm-30) REVERT: E 335 LYS cc_start: 0.8412 (ttmt) cc_final: 0.8136 (ttpt) REVERT: E 440 GLN cc_start: 0.8308 (OUTLIER) cc_final: 0.7913 (tp-100) REVERT: G 75 ILE cc_start: 0.8129 (OUTLIER) cc_final: 0.7643 (pt) REVERT: H 32 GLU cc_start: 0.7219 (OUTLIER) cc_final: 0.6502 (mm-30) REVERT: H 48 ILE cc_start: 0.5880 (OUTLIER) cc_final: 0.5553 (pp) REVERT: H 54 LEU cc_start: 0.5984 (OUTLIER) cc_final: 0.5447 (mm) REVERT: H 79 GLN cc_start: 0.5419 (OUTLIER) cc_final: 0.4534 (tm-30) REVERT: J 42 LYS cc_start: 0.6002 (OUTLIER) cc_final: 0.4920 (ptpp) REVERT: J 48 ILE cc_start: 0.6103 (OUTLIER) cc_final: 0.5670 (pp) REVERT: J 54 LEU cc_start: 0.5939 (OUTLIER) cc_final: 0.5611 (mm) REVERT: L 12 SER cc_start: 0.7101 (OUTLIER) cc_final: 0.6521 (p) REVERT: L 48 ILE cc_start: 0.5866 (OUTLIER) cc_final: 0.5244 (pp) REVERT: L 54 LEU cc_start: 0.6154 (OUTLIER) cc_final: 0.5852 (mm) REVERT: L 79 GLN cc_start: 0.5622 (OUTLIER) cc_final: 0.5027 (tm-30) REVERT: L 91 MET cc_start: 0.5439 (ptt) cc_final: 0.4953 (ptp) outliers start: 67 outliers final: 32 residues processed: 272 average time/residue: 0.6032 time to fit residues: 184.7301 Evaluate side-chains 270 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 219 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 588 ARG Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 638 TYR Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 588 ARG Chi-restraints excluded: chain D residue 592 LEU Chi-restraints excluded: chain D residue 636 SER Chi-restraints excluded: chain D residue 638 TYR Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 269 GLU Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 440 GLN Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 592 LEU Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain F residue 638 TYR Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 75 ILE Chi-restraints excluded: chain G residue 109 VAL Chi-restraints excluded: chain H residue 32 GLU Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 54 LEU Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 79 GLN Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain J residue 42 LYS Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 54 LEU Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 67 VAL Chi-restraints excluded: chain K residue 109 VAL Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 79 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 19 optimal weight: 2.9990 chunk 152 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 134 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 231 optimal weight: 9.9990 chunk 146 optimal weight: 0.0980 chunk 224 optimal weight: 10.0000 chunk 90 optimal weight: 0.5980 chunk 108 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 GLN C 103 GLN C 130 GLN C 355 ASN C 440 GLN ** D 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 130 GLN E 137 ASN F 543 ASN G 32 ASN K 32 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.192756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.138501 restraints weight = 20105.778| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 1.79 r_work: 0.3253 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20385 Z= 0.147 Angle : 0.608 12.917 27831 Z= 0.298 Chirality : 0.045 0.320 3321 Planarity : 0.004 0.063 3399 Dihedral : 6.379 55.578 4233 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.68 % Allowed : 16.28 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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 aren not related in a simple way. whole: 0.65 (0.18), residues: 2352 helix: 0.96 (0.27), residues: 429 sheet: 0.47 (0.18), residues: 795 loop : 0.35 (0.20), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 308 TYR 0.011 0.001 TYR C 173 PHE 0.017 0.001 PHE E 383 TRP 0.024 0.002 TRP C 427 HIS 0.003 0.001 HIS I 35 Details of bonding type rmsd covalent geometry : bond 0.00334 (20262) covalent geometry : angle 0.56375 (27504) SS BOND : bond 0.00276 ( 42) SS BOND : angle 0.79127 ( 84) hydrogen bonds : bond 0.04134 ( 718) hydrogen bonds : angle 4.96777 ( 1962) link_ALPHA1-2 : bond 0.00169 ( 3) link_ALPHA1-2 : angle 1.99266 ( 9) link_ALPHA1-3 : bond 0.00950 ( 3) link_ALPHA1-3 : angle 1.37965 ( 9) link_BETA1-4 : bond 0.00301 ( 30) link_BETA1-4 : angle 1.54304 ( 90) link_NAG-ASN : bond 0.00371 ( 45) link_NAG-ASN : angle 3.03359 ( 135) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 224 time to evaluate : 0.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 GLU cc_start: 0.7463 (OUTLIER) cc_final: 0.7022 (tp30) REVERT: A 103 GLN cc_start: 0.8565 (mt0) cc_final: 0.8307 (mt0) REVERT: A 117 LYS cc_start: 0.8158 (OUTLIER) cc_final: 0.7773 (tptp) REVERT: B 588 ARG cc_start: 0.7797 (OUTLIER) cc_final: 0.7340 (tmm160) REVERT: B 637 ASN cc_start: 0.7407 (m110) cc_final: 0.6855 (m-40) REVERT: C 92 GLU cc_start: 0.7640 (tm-30) cc_final: 0.7435 (tm-30) REVERT: C 117 LYS cc_start: 0.8288 (mmmt) cc_final: 0.7810 (mmtt) REVERT: C 130 GLN cc_start: 0.8800 (OUTLIER) cc_final: 0.8072 (mp-120) REVERT: C 325 ASP cc_start: 0.7761 (OUTLIER) cc_final: 0.7326 (t0) REVERT: D 588 ARG cc_start: 0.7849 (OUTLIER) cc_final: 0.7365 (tmm160) REVERT: E 87 GLU cc_start: 0.7152 (mm-30) cc_final: 0.6939 (mm-30) REVERT: E 117 LYS cc_start: 0.8295 (mmmt) cc_final: 0.7844 (tppt) REVERT: G 75 ILE cc_start: 0.8025 (OUTLIER) cc_final: 0.7494 (pt) REVERT: H 32 GLU cc_start: 0.7182 (OUTLIER) cc_final: 0.6468 (mm-30) REVERT: H 48 ILE cc_start: 0.5815 (OUTLIER) cc_final: 0.5461 (pp) REVERT: H 79 GLN cc_start: 0.5480 (OUTLIER) cc_final: 0.4580 (tm-30) REVERT: J 42 LYS cc_start: 0.5984 (OUTLIER) cc_final: 0.4888 (ptpp) REVERT: J 48 ILE cc_start: 0.6155 (OUTLIER) cc_final: 0.5758 (pp) REVERT: J 54 LEU cc_start: 0.5853 (OUTLIER) cc_final: 0.5599 (mm) REVERT: L 12 SER cc_start: 0.7060 (OUTLIER) cc_final: 0.6492 (p) REVERT: L 48 ILE cc_start: 0.5805 (OUTLIER) cc_final: 0.5204 (OUTLIER) REVERT: L 54 LEU cc_start: 0.6094 (OUTLIER) cc_final: 0.5840 (mm) REVERT: L 91 MET cc_start: 0.5377 (ptt) cc_final: 0.4909 (ptp) outliers start: 56 outliers final: 31 residues processed: 262 average time/residue: 0.5617 time to fit residues: 165.8609 Evaluate side-chains 268 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 222 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 117 LYS Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 588 ARG Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 638 TYR Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 130 GLN Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 588 ARG Chi-restraints excluded: chain D residue 636 SER Chi-restraints excluded: chain D residue 638 TYR Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 592 LEU Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain F residue 638 TYR Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 75 ILE Chi-restraints excluded: chain G residue 109 VAL Chi-restraints excluded: chain H residue 32 GLU Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 79 GLN Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain J residue 42 LYS Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 54 LEU Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 67 VAL Chi-restraints excluded: chain K residue 109 VAL Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 79 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 50 optimal weight: 0.9990 chunk 99 optimal weight: 0.7980 chunk 222 optimal weight: 6.9990 chunk 115 optimal weight: 2.9990 chunk 177 optimal weight: 5.9990 chunk 135 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 202 optimal weight: 9.9990 chunk 217 optimal weight: 4.9990 chunk 232 optimal weight: 10.0000 chunk 145 optimal weight: 3.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 GLN A 280 ASN C 130 GLN C 137 ASN C 355 ASN C 440 GLN E 130 GLN E 137 ASN E 440 GLN G 32 ASN I 32 ASN K 32 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.190753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.135029 restraints weight = 19808.872| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 1.88 r_work: 0.3207 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 20385 Z= 0.293 Angle : 0.739 11.944 27831 Z= 0.360 Chirality : 0.050 0.340 3321 Planarity : 0.005 0.066 3399 Dihedral : 6.781 57.490 4233 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.68 % Allowed : 16.52 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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 aren not related in a simple way. whole: 0.38 (0.18), residues: 2352 helix: 0.45 (0.26), residues: 429 sheet: 0.43 (0.18), residues: 789 loop : 0.19 (0.20), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 178 TYR 0.022 0.002 TYR E 384 PHE 0.024 0.002 PHE A 383 TRP 0.020 0.002 TRP C 427 HIS 0.006 0.001 HIS A 352 Details of bonding type rmsd covalent geometry : bond 0.00693 (20262) covalent geometry : angle 0.69162 (27504) SS BOND : bond 0.00543 ( 42) SS BOND : angle 1.05829 ( 84) hydrogen bonds : bond 0.05209 ( 718) hydrogen bonds : angle 5.23984 ( 1962) link_ALPHA1-2 : bond 0.00097 ( 3) link_ALPHA1-2 : angle 2.25415 ( 9) link_ALPHA1-3 : bond 0.00751 ( 3) link_ALPHA1-3 : angle 1.47299 ( 9) link_BETA1-4 : bond 0.00283 ( 30) link_BETA1-4 : angle 1.78873 ( 90) link_NAG-ASN : bond 0.00654 ( 45) link_NAG-ASN : angle 3.44892 ( 135) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 228 time to evaluate : 0.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 GLU cc_start: 0.7592 (OUTLIER) cc_final: 0.7120 (tp30) REVERT: A 103 GLN cc_start: 0.8638 (mt0) cc_final: 0.8356 (mt0) REVERT: A 117 LYS cc_start: 0.8322 (OUTLIER) cc_final: 0.7901 (tptt) REVERT: A 430 ILE cc_start: 0.8936 (mm) cc_final: 0.8736 (mp) REVERT: B 588 ARG cc_start: 0.7902 (OUTLIER) cc_final: 0.7410 (tmm160) REVERT: B 589 ASP cc_start: 0.8392 (m-30) cc_final: 0.8180 (m-30) REVERT: B 637 ASN cc_start: 0.7425 (m110) cc_final: 0.6910 (m-40) REVERT: C 117 LYS cc_start: 0.8387 (mmmt) cc_final: 0.7889 (mmtt) REVERT: C 130 GLN cc_start: 0.8833 (OUTLIER) cc_final: 0.8498 (tp40) REVERT: C 325 ASP cc_start: 0.7775 (OUTLIER) cc_final: 0.7310 (t0) REVERT: D 588 ARG cc_start: 0.7932 (OUTLIER) cc_final: 0.7405 (tmm160) REVERT: D 589 ASP cc_start: 0.8193 (m-30) cc_final: 0.7953 (m-30) REVERT: E 87 GLU cc_start: 0.7268 (mm-30) cc_final: 0.7027 (mm-30) REVERT: E 117 LYS cc_start: 0.8421 (mmmt) cc_final: 0.7950 (tppt) REVERT: E 335 LYS cc_start: 0.8412 (ttmt) cc_final: 0.8130 (ttpt) REVERT: G 75 ILE cc_start: 0.8023 (OUTLIER) cc_final: 0.7567 (pt) REVERT: H 32 GLU cc_start: 0.7219 (OUTLIER) cc_final: 0.6513 (mm-30) REVERT: H 48 ILE cc_start: 0.5798 (OUTLIER) cc_final: 0.5402 (pp) REVERT: H 79 GLN cc_start: 0.5428 (OUTLIER) cc_final: 0.4538 (tm-30) REVERT: J 42 LYS cc_start: 0.6083 (OUTLIER) cc_final: 0.4929 (ptpp) REVERT: J 48 ILE cc_start: 0.6220 (OUTLIER) cc_final: 0.5793 (pp) REVERT: J 54 LEU cc_start: 0.5888 (OUTLIER) cc_final: 0.5638 (mm) REVERT: J 91 MET cc_start: 0.5353 (ptt) cc_final: 0.5024 (ptp) REVERT: L 12 SER cc_start: 0.7105 (OUTLIER) cc_final: 0.6521 (p) REVERT: L 48 ILE cc_start: 0.5830 (OUTLIER) cc_final: 0.5196 (pp) REVERT: L 54 LEU cc_start: 0.6124 (OUTLIER) cc_final: 0.5827 (mm) REVERT: L 91 MET cc_start: 0.5484 (ptt) cc_final: 0.5047 (ptp) outliers start: 56 outliers final: 34 residues processed: 267 average time/residue: 0.5943 time to fit residues: 177.7555 Evaluate side-chains 277 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 227 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 117 LYS Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 588 ARG Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 638 TYR Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 130 GLN Chi-restraints excluded: chain C residue 244 THR Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 588 ARG Chi-restraints excluded: chain D residue 636 SER Chi-restraints excluded: chain D residue 638 TYR Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain E residue 91 GLU Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 465 THR Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 592 LEU Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 67 VAL Chi-restraints excluded: chain G residue 75 ILE Chi-restraints excluded: chain G residue 109 VAL Chi-restraints excluded: chain H residue 32 GLU Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 79 GLN Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain J residue 42 LYS Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 54 LEU Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 67 VAL Chi-restraints excluded: chain K residue 109 VAL Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 79 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 175 optimal weight: 4.9990 chunk 196 optimal weight: 1.9990 chunk 152 optimal weight: 1.9990 chunk 215 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 chunk 153 optimal weight: 1.9990 chunk 95 optimal weight: 0.6980 chunk 223 optimal weight: 8.9990 chunk 40 optimal weight: 0.8980 chunk 140 optimal weight: 0.5980 chunk 213 optimal weight: 8.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 GLN C 130 GLN C 137 ASN C 355 ASN C 440 GLN ** D 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 130 GLN E 440 GLN G 32 ASN K 32 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.192341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.136660 restraints weight = 19882.723| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 1.88 r_work: 0.3235 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 20385 Z= 0.180 Angle : 0.646 13.174 27831 Z= 0.315 Chirality : 0.046 0.325 3321 Planarity : 0.004 0.066 3399 Dihedral : 6.459 57.155 4233 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.59 % Allowed : 16.62 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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 aren not related in a simple way. whole: 0.55 (0.18), residues: 2352 helix: 0.78 (0.27), residues: 429 sheet: 0.47 (0.18), residues: 795 loop : 0.29 (0.20), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 178 TYR 0.013 0.002 TYR E 384 PHE 0.019 0.002 PHE E 383 TRP 0.026 0.002 TRP C 427 HIS 0.003 0.001 HIS A 352 Details of bonding type rmsd covalent geometry : bond 0.00417 (20262) covalent geometry : angle 0.59996 (27504) SS BOND : bond 0.00319 ( 42) SS BOND : angle 0.81109 ( 84) hydrogen bonds : bond 0.04455 ( 718) hydrogen bonds : angle 5.06107 ( 1962) link_ALPHA1-2 : bond 0.00120 ( 3) link_ALPHA1-2 : angle 2.12236 ( 9) link_ALPHA1-3 : bond 0.00841 ( 3) link_ALPHA1-3 : angle 1.36714 ( 9) link_BETA1-4 : bond 0.00273 ( 30) link_BETA1-4 : angle 1.64083 ( 90) link_NAG-ASN : bond 0.00434 ( 45) link_NAG-ASN : angle 3.17561 ( 135) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 231 time to evaluate : 0.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 GLU cc_start: 0.7545 (OUTLIER) cc_final: 0.7087 (tp30) REVERT: A 103 GLN cc_start: 0.8599 (mt0) cc_final: 0.8326 (mt0) REVERT: A 117 LYS cc_start: 0.8201 (OUTLIER) cc_final: 0.7781 (tptt) REVERT: A 430 ILE cc_start: 0.8874 (mm) cc_final: 0.8667 (mp) REVERT: B 588 ARG cc_start: 0.7861 (OUTLIER) cc_final: 0.7400 (tmm160) REVERT: B 637 ASN cc_start: 0.7424 (m110) cc_final: 0.6913 (m-40) REVERT: C 117 LYS cc_start: 0.8336 (mmmt) cc_final: 0.7853 (mmtt) REVERT: C 325 ASP cc_start: 0.7768 (OUTLIER) cc_final: 0.7310 (t0) REVERT: D 588 ARG cc_start: 0.7914 (OUTLIER) cc_final: 0.7396 (tmm160) REVERT: D 589 ASP cc_start: 0.8175 (m-30) cc_final: 0.7947 (m-30) REVERT: E 117 LYS cc_start: 0.8347 (mmmt) cc_final: 0.7889 (tppt) REVERT: E 335 LYS cc_start: 0.8372 (ttmt) cc_final: 0.8101 (ttpt) REVERT: E 347 LYS cc_start: 0.7844 (pttt) cc_final: 0.7549 (pttm) REVERT: E 440 GLN cc_start: 0.8284 (OUTLIER) cc_final: 0.7869 (tp-100) REVERT: G 75 ILE cc_start: 0.8025 (OUTLIER) cc_final: 0.7526 (pt) REVERT: H 32 GLU cc_start: 0.7197 (OUTLIER) cc_final: 0.6491 (mm-30) REVERT: H 48 ILE cc_start: 0.5815 (OUTLIER) cc_final: 0.5430 (pp) REVERT: H 79 GLN cc_start: 0.5620 (OUTLIER) cc_final: 0.4697 (tm-30) REVERT: J 42 LYS cc_start: 0.6053 (OUTLIER) cc_final: 0.4920 (ptpp) REVERT: J 48 ILE cc_start: 0.6187 (OUTLIER) cc_final: 0.5772 (pp) REVERT: J 54 LEU cc_start: 0.5839 (OUTLIER) cc_final: 0.5624 (mm) REVERT: J 79 GLN cc_start: 0.5334 (OUTLIER) cc_final: 0.4611 (tm-30) REVERT: J 91 MET cc_start: 0.5421 (ptt) cc_final: 0.5054 (ptp) REVERT: L 12 SER cc_start: 0.7087 (OUTLIER) cc_final: 0.6504 (p) REVERT: L 48 ILE cc_start: 0.5829 (OUTLIER) cc_final: 0.5198 (pp) REVERT: L 54 LEU cc_start: 0.6082 (OUTLIER) cc_final: 0.5807 (mm) REVERT: L 91 MET cc_start: 0.5498 (ptt) cc_final: 0.5043 (ptp) outliers start: 54 outliers final: 32 residues processed: 266 average time/residue: 0.5982 time to fit residues: 178.3912 Evaluate side-chains 275 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 226 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 117 LYS Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 588 ARG Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 636 SER Chi-restraints excluded: chain B residue 638 TYR Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 46 LYS Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 588 ARG Chi-restraints excluded: chain D residue 636 SER Chi-restraints excluded: chain D residue 638 TYR Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain E residue 46 LYS Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 440 GLN Chi-restraints excluded: chain E residue 465 THR Chi-restraints excluded: chain F residue 538 THR Chi-restraints excluded: chain F residue 592 LEU Chi-restraints excluded: chain F residue 636 SER Chi-restraints excluded: chain F residue 638 TYR Chi-restraints excluded: chain G residue 20 VAL Chi-restraints excluded: chain G residue 75 ILE Chi-restraints excluded: chain G residue 109 VAL Chi-restraints excluded: chain H residue 32 GLU Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 79 GLN Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain J residue 42 LYS Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 54 LEU Chi-restraints excluded: chain J residue 79 GLN Chi-restraints excluded: chain K residue 11 VAL Chi-restraints excluded: chain K residue 67 VAL Chi-restraints excluded: chain K residue 109 VAL Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 79 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 181 optimal weight: 0.6980 chunk 111 optimal weight: 5.9990 chunk 23 optimal weight: 0.5980 chunk 44 optimal weight: 3.9990 chunk 97 optimal weight: 0.9980 chunk 108 optimal weight: 0.9990 chunk 165 optimal weight: 0.6980 chunk 157 optimal weight: 0.3980 chunk 96 optimal weight: 1.9990 chunk 89 optimal weight: 0.0870 chunk 214 optimal weight: 9.9990 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 GLN C 130 GLN C 355 ASN C 440 GLN ** D 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 130 GLN E 440 GLN G 32 ASN H 90 HIS K 32 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.194483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.139568 restraints weight = 19969.734| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 1.87 r_work: 0.3265 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 20385 Z= 0.112 Angle : 0.576 12.241 27831 Z= 0.283 Chirality : 0.044 0.310 3321 Planarity : 0.004 0.063 3399 Dihedral : 5.907 56.063 4233 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.30 % Allowed : 16.91 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % 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 aren not related in a simple way. whole: 0.76 (0.18), residues: 2352 helix: 1.13 (0.27), residues: 429 sheet: 0.53 (0.18), residues: 795 loop : 0.40 (0.20), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 178 TYR 0.013 0.001 TYR C 173 PHE 0.014 0.001 PHE E 383 TRP 0.028 0.001 TRP C 427 HIS 0.003 0.001 HIS K 35 Details of bonding type rmsd covalent geometry : bond 0.00247 (20262) covalent geometry : angle 0.53478 (27504) SS BOND : bond 0.00191 ( 42) SS BOND : angle 0.64692 ( 84) hydrogen bonds : bond 0.03743 ( 718) hydrogen bonds : angle 4.86374 ( 1962) link_ALPHA1-2 : bond 0.00184 ( 3) link_ALPHA1-2 : angle 1.90901 ( 9) link_ALPHA1-3 : bond 0.00937 ( 3) link_ALPHA1-3 : angle 1.20681 ( 9) link_BETA1-4 : bond 0.00308 ( 30) link_BETA1-4 : angle 1.50659 ( 90) link_NAG-ASN : bond 0.00291 ( 45) link_NAG-ASN : angle 2.81685 ( 135) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8234.15 seconds wall clock time: 140 minutes 40.91 seconds (8440.91 seconds total)