Starting phenix.real_space_refine on Tue Jun 17 15:44:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8euw_28619/06_2025/8euw_28619.cif Found real_map, /net/cci-nas-00/data/ceres_data/8euw_28619/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8euw_28619/06_2025/8euw_28619.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8euw_28619/06_2025/8euw_28619.map" model { file = "/net/cci-nas-00/data/ceres_data/8euw_28619/06_2025/8euw_28619.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8euw_28619/06_2025/8euw_28619.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.038 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 12.76, per 1000 atoms: 0.64 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: 5.30 Conformation dependent library (CDL) restraints added in 2.4 seconds 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: 3.06 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: 7.70 Time building geometry restraints manager: 6.08 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: 0.00 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: 6.840 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: 0.760 Check model and map are aligned: 0.130 Set scattering table: 0.160 Process input model: 47.220 Find NCS groups from input model: 0.900 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.950 ------------------------------------------------------------------------------- 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 : 1.86 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (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 TRP 0.010 0.001 TRP I 47 HIS 0.005 0.001 HIS I 35 PHE 0.009 0.001 PHE C 382 TYR 0.028 0.001 TYR A 173 ARG 0.007 0.000 ARG C 308 Details of bonding type rmsd link_NAG-ASN : bond 0.00291 ( 45) link_NAG-ASN : angle 2.19097 ( 135) link_BETA1-4 : bond 0.00444 ( 30) link_BETA1-4 : angle 1.09229 ( 90) 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) hydrogen bonds : bond 0.13297 ( 718) hydrogen bonds : angle 5.98936 ( 1962) SS BOND : bond 0.00361 ( 42) SS BOND : angle 1.54755 ( 84) covalent geometry : bond 0.00915 (20262) covalent geometry : angle 0.89166 (27504) *********************** 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 : 1.981 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: 1.3618 time to fit residues: 360.4013 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 : 2.154 ------------------------------------------------------------------------------- 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 200 optimal weight: 5.9990 chunk 179 optimal weight: 9.9990 chunk 99 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 185 optimal weight: 8.9990 chunk 71 optimal weight: 0.5980 chunk 112 optimal weight: 5.9990 chunk 138 optimal weight: 0.8980 chunk 215 optimal weight: 0.6980 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 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: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.198213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.141827 restraints weight = 19967.960| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 1.89 r_work: 0.3348 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.1159 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= 0.159 Angle : 0.604 7.525 27831 Z= 0.301 Chirality : 0.045 0.278 3321 Planarity : 0.004 0.065 3399 Dihedral : 10.202 76.484 4241 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 1.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.35 % Allowed : 12.26 % Favored : 85.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.18), residues: 2352 helix: 1.10 (0.28), residues: 423 sheet: 0.43 (0.18), residues: 792 loop : 0.58 (0.20), residues: 1137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP G 47 HIS 0.004 0.001 HIS E 352 PHE 0.017 0.002 PHE E 383 TYR 0.016 0.001 TYR C 173 ARG 0.004 0.001 ARG E 298 Details of bonding type rmsd link_NAG-ASN : bond 0.00349 ( 45) link_NAG-ASN : angle 2.76276 ( 135) link_BETA1-4 : bond 0.00432 ( 30) link_BETA1-4 : angle 1.47314 ( 90) link_ALPHA1-2 : bond 0.00447 ( 3) link_ALPHA1-2 : angle 1.93697 ( 9) link_ALPHA1-3 : bond 0.01083 ( 3) link_ALPHA1-3 : angle 1.83767 ( 9) hydrogen bonds : bond 0.04405 ( 718) hydrogen bonds : angle 5.04691 ( 1962) SS BOND : bond 0.00248 ( 42) SS BOND : angle 0.74029 ( 84) covalent geometry : bond 0.00370 (20262) covalent geometry : angle 0.56603 (27504) *********************** 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 277 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 228 time to evaluate : 2.022 Fit side-chains revert: symmetry clash REVERT: A 46 LYS cc_start: 0.7896 (tppt) cc_final: 0.7593 (tppp) REVERT: A 92 GLU cc_start: 0.7620 (OUTLIER) cc_final: 0.7229 (tp30) REVERT: A 103 GLN cc_start: 0.8467 (mt0) cc_final: 0.8221 (mt0) REVERT: A 117 LYS cc_start: 0.8270 (mtpt) cc_final: 0.7888 (tptp) REVERT: A 325 ASP cc_start: 0.7662 (OUTLIER) cc_final: 0.7337 (t0) REVERT: C 92 GLU cc_start: 0.7691 (OUTLIER) cc_final: 0.7390 (tp30) REVERT: C 325 ASP cc_start: 0.7711 (OUTLIER) cc_final: 0.7268 (t0) REVERT: D 657 GLU cc_start: 0.6985 (OUTLIER) cc_final: 0.6722 (tt0) REVERT: E 103 GLN cc_start: 0.8395 (mt0) cc_final: 0.8090 (mt0) REVERT: E 335 LYS cc_start: 0.8380 (ttmt) cc_final: 0.8155 (ttpt) REVERT: F 588 ARG cc_start: 0.7837 (tmm160) cc_final: 0.7634 (tmm160) REVERT: H 48 ILE cc_start: 0.5904 (OUTLIER) cc_final: 0.5484 (pp) REVERT: H 54 LEU cc_start: 0.5945 (OUTLIER) cc_final: 0.5382 (mm) REVERT: J 48 ILE cc_start: 0.5932 (OUTLIER) cc_final: 0.5549 (pp) REVERT: J 91 MET cc_start: 0.5219 (ptt) cc_final: 0.4864 (ptp) REVERT: L 48 ILE cc_start: 0.5605 (OUTLIER) cc_final: 0.5027 (OUTLIER) REVERT: L 79 GLN cc_start: 0.5703 (OUTLIER) cc_final: 0.4731 (tm-30) REVERT: L 91 MET cc_start: 0.5158 (ptt) cc_final: 0.4556 (ptp) outliers start: 49 outliers final: 17 residues processed: 258 average time/residue: 1.4591 time to fit residues: 423.5815 Evaluate side-chains 244 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 218 time to evaluate : 2.251 ------------------------------------------------------------------------------- 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 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 213 ILE Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 347 LYS 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 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 82 optimal weight: 0.0040 chunk 154 optimal weight: 3.9990 chunk 189 optimal weight: 20.0000 chunk 63 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 chunk 188 optimal weight: 8.9990 chunk 53 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 30 optimal weight: 0.0270 chunk 202 optimal weight: 10.0000 chunk 119 optimal weight: 0.8980 overall best weight: 0.7852 ------------------------------------------------------------------------------- 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 440 GLN G 32 ASN I 32 ASN I 76 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 = 0.4134 r_free = 0.4134 target = 0.197884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.140603 restraints weight = 19863.149| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 1.93 r_work: 0.3331 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.1510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20385 Z= 0.130 Angle : 0.570 8.506 27831 Z= 0.281 Chirality : 0.044 0.285 3321 Planarity : 0.004 0.061 3399 Dihedral : 8.235 59.803 4233 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.44 % Allowed : 13.55 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.18), residues: 2352 helix: 1.24 (0.28), residues: 423 sheet: 0.49 (0.18), residues: 792 loop : 0.53 (0.20), residues: 1137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 47 HIS 0.003 0.001 HIS E 352 PHE 0.015 0.001 PHE E 383 TYR 0.013 0.001 TYR C 173 ARG 0.004 0.000 ARG E 298 Details of bonding type rmsd link_NAG-ASN : bond 0.00321 ( 45) link_NAG-ASN : angle 2.76969 ( 135) link_BETA1-4 : bond 0.00368 ( 30) link_BETA1-4 : angle 1.47988 ( 90) link_ALPHA1-2 : bond 0.00284 ( 3) link_ALPHA1-2 : angle 1.73275 ( 9) link_ALPHA1-3 : bond 0.00966 ( 3) link_ALPHA1-3 : angle 1.39585 ( 9) hydrogen bonds : bond 0.03913 ( 718) hydrogen bonds : angle 4.86596 ( 1962) SS BOND : bond 0.00237 ( 42) SS BOND : angle 0.88596 ( 84) covalent geometry : bond 0.00294 (20262) covalent geometry : angle 0.52937 (27504) *********************** 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 275 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 224 time to evaluate : 3.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 GLU cc_start: 0.6976 (mm-30) cc_final: 0.6717 (mm-30) REVERT: A 103 GLN cc_start: 0.8497 (mt0) cc_final: 0.8265 (mt0) REVERT: A 117 LYS cc_start: 0.8288 (mtpt) cc_final: 0.7956 (tptp) REVERT: A 325 ASP cc_start: 0.7730 (OUTLIER) cc_final: 0.7477 (t0) REVERT: B 637 ASN cc_start: 0.7583 (m110) cc_final: 0.6982 (m-40) REVERT: C 92 GLU cc_start: 0.7670 (OUTLIER) cc_final: 0.7421 (tp30) REVERT: C 117 LYS cc_start: 0.8223 (mmmt) cc_final: 0.7914 (mmtt) REVERT: C 130 GLN cc_start: 0.8815 (OUTLIER) cc_final: 0.8163 (mp-120) REVERT: C 325 ASP cc_start: 0.7757 (OUTLIER) cc_final: 0.7379 (t0) REVERT: C 440 GLN cc_start: 0.8352 (OUTLIER) cc_final: 0.7996 (tp-100) REVERT: E 91 GLU cc_start: 0.7788 (OUTLIER) cc_final: 0.6584 (tm-30) REVERT: E 117 LYS cc_start: 0.8308 (mmmt) cc_final: 0.7899 (tptt) REVERT: E 335 LYS cc_start: 0.8414 (ttmt) cc_final: 0.8211 (ttpt) REVERT: F 588 ARG cc_start: 0.7969 (tmm160) cc_final: 0.7727 (tmm160) REVERT: G 75 ILE cc_start: 0.8220 (OUTLIER) cc_final: 0.7796 (pt) REVERT: H 79 GLN cc_start: 0.5488 (OUTLIER) cc_final: 0.4546 (tm-30) REVERT: J 48 ILE cc_start: 0.6112 (OUTLIER) cc_final: 0.5745 (pp) REVERT: L 48 ILE cc_start: 0.5862 (OUTLIER) cc_final: 0.5225 (pp) REVERT: L 79 GLN cc_start: 0.5807 (OUTLIER) cc_final: 0.4928 (tm-30) REVERT: L 91 MET cc_start: 0.5213 (ptt) cc_final: 0.4688 (ptp) outliers start: 51 outliers final: 20 residues processed: 260 average time/residue: 1.7528 time to fit residues: 513.8226 Evaluate side-chains 255 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 224 time to evaluate : 2.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 130 GLN Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 440 GLN 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 E residue 46 LYS Chi-restraints excluded: chain E residue 91 GLU Chi-restraints excluded: chain E residue 325 ASP 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 82 VAL Chi-restraints excluded: chain G residue 109 VAL 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 209 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 226 optimal weight: 4.9990 chunk 232 optimal weight: 9.9990 chunk 22 optimal weight: 3.9990 chunk 115 optimal weight: 2.9990 chunk 201 optimal weight: 9.9990 chunk 49 optimal weight: 2.9990 chunk 167 optimal weight: 0.9980 chunk 173 optimal weight: 3.9990 chunk 235 optimal weight: 5.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- 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 E 130 GLN E 440 GLN G 6 GLN G 32 ASN I 6 GLN I 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 = 0.4095 r_free = 0.4095 target = 0.193855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.137022 restraints weight = 19945.239| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 2.02 r_work: 0.3267 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.1969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 20385 Z= 0.258 Angle : 0.719 10.724 27831 Z= 0.352 Chirality : 0.049 0.322 3321 Planarity : 0.005 0.067 3399 Dihedral : 7.983 58.038 4233 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.02 % Allowed : 13.98 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.17), residues: 2352 helix: 0.50 (0.26), residues: 441 sheet: 0.46 (0.18), residues: 780 loop : 0.37 (0.19), residues: 1131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 427 HIS 0.008 0.001 HIS E 352 PHE 0.022 0.002 PHE E 383 TYR 0.019 0.002 TYR E 384 ARG 0.006 0.001 ARG A 178 Details of bonding type rmsd link_NAG-ASN : bond 0.00601 ( 45) link_NAG-ASN : angle 3.43544 ( 135) link_BETA1-4 : bond 0.00300 ( 30) link_BETA1-4 : angle 1.67901 ( 90) link_ALPHA1-2 : bond 0.00210 ( 3) link_ALPHA1-2 : angle 1.99396 ( 9) link_ALPHA1-3 : bond 0.00787 ( 3) link_ALPHA1-3 : angle 1.54574 ( 9) hydrogen bonds : bond 0.05052 ( 718) hydrogen bonds : angle 5.14973 ( 1962) SS BOND : bond 0.00481 ( 42) SS BOND : angle 1.62120 ( 84) covalent geometry : bond 0.00609 (20262) covalent geometry : angle 0.66788 (27504) *********************** 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 281 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 218 time to evaluate : 3.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.7940 (OUTLIER) cc_final: 0.7313 (mppt) REVERT: A 87 GLU cc_start: 0.7091 (mm-30) cc_final: 0.6868 (mm-30) REVERT: A 92 GLU cc_start: 0.7660 (OUTLIER) cc_final: 0.7155 (tp30) REVERT: A 103 GLN cc_start: 0.8609 (mt0) cc_final: 0.8329 (mt0) REVERT: A 117 LYS cc_start: 0.8356 (mtpt) cc_final: 0.7947 (tptt) REVERT: B 637 ASN cc_start: 0.7561 (m110) cc_final: 0.6981 (m-40) REVERT: C 117 LYS cc_start: 0.8333 (mmmt) cc_final: 0.7954 (mmtt) REVERT: C 325 ASP cc_start: 0.7711 (OUTLIER) cc_final: 0.7320 (t0) REVERT: D 588 ARG cc_start: 0.7918 (OUTLIER) cc_final: 0.7464 (tmm160) REVERT: D 657 GLU cc_start: 0.6968 (OUTLIER) cc_final: 0.6716 (tt0) REVERT: E 91 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.6545 (tm-30) REVERT: E 335 LYS cc_start: 0.8389 (ttmt) cc_final: 0.8161 (ttpt) REVERT: H 48 ILE cc_start: 0.5929 (OUTLIER) cc_final: 0.5594 (pp) REVERT: H 54 LEU cc_start: 0.5989 (OUTLIER) cc_final: 0.5409 (mm) REVERT: H 79 GLN cc_start: 0.5199 (OUTLIER) cc_final: 0.4304 (tm-30) REVERT: J 42 LYS cc_start: 0.5675 (OUTLIER) cc_final: 0.4687 (ptpp) REVERT: J 48 ILE cc_start: 0.6076 (OUTLIER) cc_final: 0.5677 (pp) REVERT: L 48 ILE cc_start: 0.5707 (OUTLIER) cc_final: 0.5055 (pp) REVERT: L 79 GLN cc_start: 0.5593 (OUTLIER) cc_final: 0.4875 (tm-30) REVERT: L 91 MET cc_start: 0.5345 (ptt) cc_final: 0.4811 (ptp) outliers start: 63 outliers final: 31 residues processed: 261 average time/residue: 2.0812 time to fit residues: 616.9831 Evaluate side-chains 258 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 214 time to evaluate : 3.336 ------------------------------------------------------------------------------- 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 211 GLU Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain B residue 569 THR 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 247 CYS 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 91 GLU Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 247 CYS Chi-restraints excluded: chain E residue 325 ASP Chi-restraints excluded: chain E residue 440 GLN 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 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 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 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 166 optimal weight: 0.9990 chunk 219 optimal weight: 8.9990 chunk 54 optimal weight: 6.9990 chunk 122 optimal weight: 0.5980 chunk 120 optimal weight: 0.9990 chunk 74 optimal weight: 0.2980 chunk 209 optimal weight: 0.7980 chunk 132 optimal weight: 0.9980 chunk 206 optimal weight: 5.9990 chunk 101 optimal weight: 4.9990 chunk 195 optimal weight: 0.0040 overall best weight: 0.5392 ------------------------------------------------------------------------------- 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 440 GLN ** D 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 630 GLN ** D 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 130 GLN G 32 ASN K 6 GLN K 32 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.194697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.141298 restraints weight = 20036.733| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 1.81 r_work: 0.3281 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 20385 Z= 0.115 Angle : 0.566 8.801 27831 Z= 0.279 Chirality : 0.044 0.302 3321 Planarity : 0.004 0.064 3399 Dihedral : 6.717 58.765 4233 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.06 % Allowed : 15.47 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.18), residues: 2352 helix: 1.18 (0.28), residues: 429 sheet: 0.49 (0.18), residues: 795 loop : 0.49 (0.20), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 427 HIS 0.003 0.001 HIS I 35 PHE 0.016 0.001 PHE E 383 TYR 0.013 0.001 TYR C 173 ARG 0.004 0.000 ARG A 178 Details of bonding type rmsd link_NAG-ASN : bond 0.00306 ( 45) link_NAG-ASN : angle 2.80784 ( 135) link_BETA1-4 : bond 0.00355 ( 30) link_BETA1-4 : angle 1.41827 ( 90) link_ALPHA1-2 : bond 0.00238 ( 3) link_ALPHA1-2 : angle 1.78283 ( 9) link_ALPHA1-3 : bond 0.01052 ( 3) link_ALPHA1-3 : angle 1.36435 ( 9) hydrogen bonds : bond 0.03716 ( 718) hydrogen bonds : angle 4.81131 ( 1962) SS BOND : bond 0.00333 ( 42) SS BOND : angle 1.18751 ( 84) covalent geometry : bond 0.00254 (20262) covalent geometry : angle 0.52245 (27504) *********************** 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 275 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 232 time to evaluate : 2.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.7826 (tppt) cc_final: 0.7566 (tppp) REVERT: A 92 GLU cc_start: 0.7555 (OUTLIER) cc_final: 0.7128 (tp30) REVERT: A 103 GLN cc_start: 0.8499 (mt0) cc_final: 0.8235 (mt0) REVERT: A 117 LYS cc_start: 0.8084 (mtpt) cc_final: 0.7747 (tptp) REVERT: A 347 LYS cc_start: 0.7849 (ptpt) cc_final: 0.7403 (pttm) REVERT: B 637 ASN cc_start: 0.7336 (m110) cc_final: 0.6755 (m-40) REVERT: C 92 GLU cc_start: 0.7669 (tm-30) cc_final: 0.7456 (tm-30) REVERT: C 117 LYS cc_start: 0.8192 (mmmt) cc_final: 0.7818 (mmtt) REVERT: C 137 ASN cc_start: 0.7582 (m-40) cc_final: 0.7267 (m110) REVERT: C 325 ASP cc_start: 0.7739 (OUTLIER) cc_final: 0.7314 (t0) REVERT: D 588 ARG cc_start: 0.7900 (OUTLIER) cc_final: 0.7509 (tmm160) REVERT: D 589 ASP cc_start: 0.8058 (m-30) cc_final: 0.7715 (m-30) REVERT: E 117 LYS cc_start: 0.8224 (mmmt) cc_final: 0.7827 (tptt) REVERT: E 347 LYS cc_start: 0.7879 (pttt) cc_final: 0.7667 (pttt) REVERT: G 75 ILE cc_start: 0.8110 (OUTLIER) cc_final: 0.7630 (pt) REVERT: H 79 GLN cc_start: 0.5438 (OUTLIER) cc_final: 0.4553 (tm-30) REVERT: J 48 ILE cc_start: 0.6078 (OUTLIER) cc_final: 0.5679 (pp) REVERT: L 48 ILE cc_start: 0.5759 (OUTLIER) cc_final: 0.5125 (pp) REVERT: L 79 GLN cc_start: 0.5692 (OUTLIER) cc_final: 0.5002 (tm-30) REVERT: L 91 MET cc_start: 0.5416 (ptt) cc_final: 0.4907 (ptp) outliers start: 43 outliers final: 19 residues processed: 261 average time/residue: 1.4572 time to fit residues: 430.3610 Evaluate side-chains 248 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 221 time to evaluate : 2.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 211 GLU Chi-restraints excluded: chain B residue 569 THR 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 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 E residue 46 LYS 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 75 ILE Chi-restraints excluded: chain G residue 109 VAL 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 117 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 139 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 235 optimal weight: 0.8980 chunk 236 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 47 optimal weight: 8.9990 chunk 198 optimal weight: 6.9990 chunk 215 optimal weight: 2.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 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 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 = 0.4074 r_free = 0.4074 target = 0.192383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.137547 restraints weight = 19969.181| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 1.78 r_work: 0.3229 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.2119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 20385 Z= 0.212 Angle : 0.671 11.629 27831 Z= 0.328 Chirality : 0.047 0.323 3321 Planarity : 0.005 0.062 3399 Dihedral : 6.746 57.350 4233 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.97 % Allowed : 15.23 % Favored : 81.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.18), residues: 2352 helix: 0.90 (0.27), residues: 429 sheet: 0.43 (0.18), residues: 789 loop : 0.36 (0.20), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 427 HIS 0.005 0.001 HIS A 352 PHE 0.021 0.002 PHE E 383 TYR 0.016 0.002 TYR E 384 ARG 0.007 0.000 ARG A 178 Details of bonding type rmsd link_NAG-ASN : bond 0.00510 ( 45) link_NAG-ASN : angle 3.21001 ( 135) link_BETA1-4 : bond 0.00298 ( 30) link_BETA1-4 : angle 1.59451 ( 90) link_ALPHA1-2 : bond 0.00189 ( 3) link_ALPHA1-2 : angle 1.98827 ( 9) link_ALPHA1-3 : bond 0.00902 ( 3) link_ALPHA1-3 : angle 1.46425 ( 9) hydrogen bonds : bond 0.04632 ( 718) hydrogen bonds : angle 5.01722 ( 1962) SS BOND : bond 0.00439 ( 42) SS BOND : angle 1.54660 ( 84) covalent geometry : bond 0.00498 (20262) covalent geometry : angle 0.62255 (27504) *********************** 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 287 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 225 time to evaluate : 2.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 GLU cc_start: 0.7576 (OUTLIER) cc_final: 0.7081 (tp30) REVERT: A 103 GLN cc_start: 0.8578 (mt0) cc_final: 0.8310 (mt0) REVERT: A 117 LYS cc_start: 0.8302 (mttt) cc_final: 0.7923 (tptt) REVERT: B 588 ARG cc_start: 0.7896 (OUTLIER) cc_final: 0.7469 (tmm160) REVERT: B 637 ASN cc_start: 0.7409 (m110) cc_final: 0.6823 (m-40) REVERT: C 117 LYS cc_start: 0.8333 (mmmt) cc_final: 0.7966 (mmtt) REVERT: C 325 ASP cc_start: 0.7786 (OUTLIER) cc_final: 0.7371 (t0) REVERT: D 588 ARG cc_start: 0.7905 (OUTLIER) cc_final: 0.7434 (tmm160) REVERT: D 657 GLU cc_start: 0.6940 (OUTLIER) cc_final: 0.6700 (tt0) REVERT: E 87 GLU cc_start: 0.7193 (mm-30) cc_final: 0.6990 (mm-30) REVERT: E 117 LYS cc_start: 0.8360 (mmmt) cc_final: 0.7912 (tppt) REVERT: E 335 LYS cc_start: 0.8371 (ttmt) cc_final: 0.8083 (ttpt) REVERT: E 347 LYS cc_start: 0.7831 (pttt) cc_final: 0.7544 (pttt) REVERT: G 75 ILE cc_start: 0.8042 (OUTLIER) cc_final: 0.7563 (pt) REVERT: H 48 ILE cc_start: 0.5918 (OUTLIER) cc_final: 0.5544 (pp) REVERT: H 79 GLN cc_start: 0.5353 (OUTLIER) cc_final: 0.4486 (tm-30) REVERT: J 42 LYS cc_start: 0.5938 (OUTLIER) cc_final: 0.4855 (ptpp) REVERT: J 48 ILE cc_start: 0.6064 (OUTLIER) cc_final: 0.5660 (pp) REVERT: L 48 ILE cc_start: 0.5745 (OUTLIER) cc_final: 0.5078 (pp) REVERT: L 54 LEU cc_start: 0.6133 (OUTLIER) cc_final: 0.5859 (mm) REVERT: L 79 GLN cc_start: 0.5730 (OUTLIER) cc_final: 0.5084 (tm-30) REVERT: L 91 MET cc_start: 0.5436 (ptt) cc_final: 0.4916 (ptp) outliers start: 62 outliers final: 36 residues processed: 271 average time/residue: 1.4093 time to fit residues: 430.7121 Evaluate side-chains 268 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 219 time to evaluate : 2.099 ------------------------------------------------------------------------------- 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 A residue 244 THR Chi-restraints excluded: chain A residue 247 CYS 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 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 247 CYS 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 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 247 CYS 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 11 VAL 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 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 78 LEU 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 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 6 optimal weight: 0.6980 chunk 43 optimal weight: 0.8980 chunk 170 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 chunk 125 optimal weight: 0.6980 chunk 164 optimal weight: 0.8980 chunk 181 optimal weight: 5.9990 chunk 20 optimal weight: 0.7980 chunk 191 optimal weight: 6.9990 chunk 97 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 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 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 = 0.4086 r_free = 0.4086 target = 0.193739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.139912 restraints weight = 19907.347| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 1.81 r_work: 0.3259 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 20385 Z= 0.130 Angle : 0.590 12.390 27831 Z= 0.290 Chirality : 0.044 0.310 3321 Planarity : 0.004 0.062 3399 Dihedral : 6.191 54.685 4233 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.39 % Allowed : 16.09 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.18), residues: 2352 helix: 1.17 (0.28), residues: 429 sheet: 0.51 (0.18), residues: 789 loop : 0.42 (0.20), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 427 HIS 0.003 0.001 HIS I 35 PHE 0.016 0.001 PHE E 383 TYR 0.012 0.001 TYR C 173 ARG 0.007 0.000 ARG A 178 Details of bonding type rmsd link_NAG-ASN : bond 0.00326 ( 45) link_NAG-ASN : angle 2.88714 ( 135) link_BETA1-4 : bond 0.00326 ( 30) link_BETA1-4 : angle 1.45567 ( 90) link_ALPHA1-2 : bond 0.00208 ( 3) link_ALPHA1-2 : angle 1.87803 ( 9) link_ALPHA1-3 : bond 0.01007 ( 3) link_ALPHA1-3 : angle 1.36354 ( 9) hydrogen bonds : bond 0.03882 ( 718) hydrogen bonds : angle 4.84133 ( 1962) SS BOND : bond 0.00355 ( 42) SS BOND : angle 1.40552 ( 84) covalent geometry : bond 0.00295 (20262) covalent geometry : angle 0.54496 (27504) *********************** 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 280 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 230 time to evaluate : 1.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 GLU cc_start: 0.7466 (OUTLIER) cc_final: 0.7038 (tp30) REVERT: A 103 GLN cc_start: 0.8550 (mt0) cc_final: 0.8278 (mt0) REVERT: A 117 LYS cc_start: 0.8144 (OUTLIER) cc_final: 0.7763 (tptt) REVERT: B 588 ARG cc_start: 0.7811 (OUTLIER) cc_final: 0.7390 (tmm160) REVERT: B 637 ASN cc_start: 0.7296 (m110) cc_final: 0.6762 (m-40) REVERT: C 117 LYS cc_start: 0.8224 (mmmt) cc_final: 0.7846 (mmtt) REVERT: C 325 ASP cc_start: 0.7744 (OUTLIER) cc_final: 0.7367 (t0) REVERT: C 355 ASN cc_start: 0.7242 (OUTLIER) cc_final: 0.7021 (OUTLIER) REVERT: C 440 GLN cc_start: 0.8335 (OUTLIER) cc_final: 0.8000 (tp-100) REVERT: C 443 ILE cc_start: 0.8540 (pt) cc_final: 0.8334 (pt) REVERT: D 588 ARG cc_start: 0.7841 (OUTLIER) cc_final: 0.7407 (tmm160) REVERT: D 657 GLU cc_start: 0.6849 (OUTLIER) cc_final: 0.6615 (tt0) REVERT: E 117 LYS cc_start: 0.8251 (mmmt) cc_final: 0.7873 (tptp) REVERT: E 335 LYS cc_start: 0.8339 (ttmt) cc_final: 0.8047 (ttpt) REVERT: E 347 LYS cc_start: 0.7811 (pttt) cc_final: 0.7498 (pttt) REVERT: G 75 ILE cc_start: 0.8016 (OUTLIER) cc_final: 0.7463 (pt) REVERT: H 79 GLN cc_start: 0.5353 (OUTLIER) cc_final: 0.4479 (tm-30) REVERT: J 42 LYS cc_start: 0.6011 (OUTLIER) cc_final: 0.4932 (ptpp) REVERT: J 48 ILE cc_start: 0.6073 (OUTLIER) cc_final: 0.5666 (pp) REVERT: J 91 MET cc_start: 0.5284 (ptt) cc_final: 0.4954 (ptp) REVERT: L 12 SER cc_start: 0.7032 (OUTLIER) cc_final: 0.6511 (p) REVERT: L 48 ILE cc_start: 0.5727 (OUTLIER) cc_final: 0.5093 (pp) REVERT: L 79 GLN cc_start: 0.5685 (OUTLIER) cc_final: 0.5095 (tm-30) REVERT: L 91 MET cc_start: 0.5437 (ptt) cc_final: 0.4934 (ptp) outliers start: 50 outliers final: 30 residues processed: 265 average time/residue: 1.3723 time to fit residues: 408.6552 Evaluate side-chains 267 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 223 time to evaluate : 2.134 ------------------------------------------------------------------------------- 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 211 GLU Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain B residue 588 ARG 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 247 CYS Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 355 ASN 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 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 247 CYS 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 67 VAL Chi-restraints excluded: chain G residue 75 ILE Chi-restraints excluded: chain G residue 109 VAL 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 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 12 SER Chi-restraints excluded: chain L residue 48 ILE 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 164 optimal weight: 0.7980 chunk 223 optimal weight: 9.9990 chunk 203 optimal weight: 4.9990 chunk 50 optimal weight: 0.7980 chunk 38 optimal weight: 0.9980 chunk 158 optimal weight: 0.6980 chunk 55 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 227 optimal weight: 20.0000 chunk 219 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 130 GLN F 543 ASN G 32 ASN K 32 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.194172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.139311 restraints weight = 20058.960| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 1.88 r_work: 0.3259 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 20385 Z= 0.140 Angle : 0.596 13.266 27831 Z= 0.292 Chirality : 0.045 0.309 3321 Planarity : 0.004 0.062 3399 Dihedral : 5.976 53.107 4233 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.44 % Allowed : 16.14 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.18), residues: 2352 helix: 1.19 (0.27), residues: 429 sheet: 0.52 (0.18), residues: 789 loop : 0.42 (0.20), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 427 HIS 0.003 0.001 HIS I 35 PHE 0.016 0.001 PHE E 383 TYR 0.010 0.001 TYR C 173 ARG 0.008 0.000 ARG A 178 Details of bonding type rmsd link_NAG-ASN : bond 0.00347 ( 45) link_NAG-ASN : angle 2.86907 ( 135) link_BETA1-4 : bond 0.00315 ( 30) link_BETA1-4 : angle 1.46427 ( 90) link_ALPHA1-2 : bond 0.00212 ( 3) link_ALPHA1-2 : angle 1.87506 ( 9) link_ALPHA1-3 : bond 0.00972 ( 3) link_ALPHA1-3 : angle 1.29567 ( 9) hydrogen bonds : bond 0.03935 ( 718) hydrogen bonds : angle 4.82740 ( 1962) SS BOND : bond 0.00356 ( 42) SS BOND : angle 1.38545 ( 84) covalent geometry : bond 0.00322 (20262) covalent geometry : angle 0.55192 (27504) *********************** 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 275 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 224 time to evaluate : 2.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 GLU cc_start: 0.7503 (OUTLIER) cc_final: 0.7069 (tp30) REVERT: A 103 GLN cc_start: 0.8584 (mt0) cc_final: 0.8328 (mt0) REVERT: A 117 LYS cc_start: 0.8174 (OUTLIER) cc_final: 0.7805 (tptt) REVERT: B 588 ARG cc_start: 0.7835 (OUTLIER) cc_final: 0.7388 (tmm160) REVERT: B 637 ASN cc_start: 0.7292 (m110) cc_final: 0.6754 (m-40) REVERT: C 117 LYS cc_start: 0.8248 (mmmt) cc_final: 0.7879 (mmtt) REVERT: C 325 ASP cc_start: 0.7757 (OUTLIER) cc_final: 0.7361 (t0) REVERT: D 588 ARG cc_start: 0.7885 (OUTLIER) cc_final: 0.7465 (tmm160) REVERT: D 657 GLU cc_start: 0.6862 (OUTLIER) cc_final: 0.6629 (tt0) REVERT: E 117 LYS cc_start: 0.8259 (mmmt) cc_final: 0.7872 (tptp) REVERT: E 335 LYS cc_start: 0.8363 (ttmt) cc_final: 0.8075 (ttpt) REVERT: E 347 LYS cc_start: 0.7822 (OUTLIER) cc_final: 0.7500 (pttt) REVERT: G 75 ILE cc_start: 0.8058 (OUTLIER) cc_final: 0.7597 (pt) REVERT: H 79 GLN cc_start: 0.5557 (OUTLIER) cc_final: 0.4647 (tm-30) REVERT: H 91 MET cc_start: 0.5507 (ptp) cc_final: 0.5131 (ptt) REVERT: J 42 LYS cc_start: 0.6045 (OUTLIER) cc_final: 0.4962 (ptpp) REVERT: J 48 ILE cc_start: 0.6101 (OUTLIER) cc_final: 0.5703 (pp) REVERT: L 48 ILE cc_start: 0.5850 (OUTLIER) cc_final: 0.5257 (OUTLIER) REVERT: L 54 LEU cc_start: 0.6090 (OUTLIER) cc_final: 0.5869 (mm) REVERT: L 79 GLN cc_start: 0.5754 (OUTLIER) cc_final: 0.5136 (tm-30) REVERT: L 91 MET cc_start: 0.5486 (ptt) cc_final: 0.4988 (ptp) outliers start: 51 outliers final: 32 residues processed: 259 average time/residue: 1.3596 time to fit residues: 396.9030 Evaluate side-chains 269 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 224 time to evaluate : 1.965 ------------------------------------------------------------------------------- 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 A residue 247 CYS Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 588 ARG 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 247 CYS Chi-restraints excluded: chain C residue 325 ASP Chi-restraints excluded: chain C residue 355 ASN 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 247 CYS 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 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 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 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 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 34 optimal weight: 3.9990 chunk 134 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 234 optimal weight: 20.0000 chunk 212 optimal weight: 20.0000 chunk 30 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 177 optimal weight: 5.9990 chunk 103 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- 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 440 GLN ** D 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 130 GLN G 32 ASN I 32 ASN K 32 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.191696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.138894 restraints weight = 20056.605| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 1.72 r_work: 0.3238 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 20385 Z= 0.219 Angle : 0.681 13.406 27831 Z= 0.332 Chirality : 0.047 0.324 3321 Planarity : 0.005 0.063 3399 Dihedral : 6.292 54.538 4233 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.87 % Allowed : 15.85 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.18), residues: 2352 helix: 0.97 (0.27), residues: 423 sheet: 0.47 (0.18), residues: 783 loop : 0.31 (0.20), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 427 HIS 0.006 0.001 HIS C 352 PHE 0.021 0.002 PHE A 383 TYR 0.017 0.002 TYR E 384 ARG 0.010 0.001 ARG A 178 Details of bonding type rmsd link_NAG-ASN : bond 0.00507 ( 45) link_NAG-ASN : angle 3.22509 ( 135) link_BETA1-4 : bond 0.00271 ( 30) link_BETA1-4 : angle 1.61968 ( 90) link_ALPHA1-2 : bond 0.00162 ( 3) link_ALPHA1-2 : angle 2.05784 ( 9) link_ALPHA1-3 : bond 0.00846 ( 3) link_ALPHA1-3 : angle 1.36128 ( 9) hydrogen bonds : bond 0.04684 ( 718) hydrogen bonds : angle 5.03411 ( 1962) SS BOND : bond 0.00472 ( 42) SS BOND : angle 1.58447 ( 84) covalent geometry : bond 0.00516 (20262) covalent geometry : angle 0.63226 (27504) *********************** 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 282 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 222 time to evaluate : 2.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 GLU cc_start: 0.7583 (OUTLIER) cc_final: 0.7110 (tp30) REVERT: A 103 GLN cc_start: 0.8624 (mt0) cc_final: 0.8377 (mt0) REVERT: A 117 LYS cc_start: 0.8277 (OUTLIER) cc_final: 0.7898 (tptt) REVERT: B 588 ARG cc_start: 0.7861 (OUTLIER) cc_final: 0.7420 (tmm160) REVERT: B 637 ASN cc_start: 0.7400 (m110) cc_final: 0.6888 (m-40) REVERT: C 117 LYS cc_start: 0.8348 (mmmt) cc_final: 0.7956 (mmtt) REVERT: C 325 ASP cc_start: 0.7771 (OUTLIER) cc_final: 0.7356 (t0) REVERT: D 588 ARG cc_start: 0.7921 (OUTLIER) cc_final: 0.7432 (tmm160) REVERT: E 117 LYS cc_start: 0.8355 (mmmt) cc_final: 0.7903 (tppt) REVERT: E 335 LYS cc_start: 0.8391 (ttmt) cc_final: 0.8179 (ttpt) REVERT: E 347 LYS cc_start: 0.7839 (OUTLIER) cc_final: 0.7527 (pttt) REVERT: G 75 ILE cc_start: 0.8068 (OUTLIER) cc_final: 0.7527 (pt) REVERT: H 79 GLN cc_start: 0.5582 (OUTLIER) cc_final: 0.4666 (tm-30) REVERT: H 91 MET cc_start: 0.5423 (ptp) cc_final: 0.5044 (ptt) REVERT: J 42 LYS cc_start: 0.6058 (OUTLIER) cc_final: 0.4956 (ptpp) REVERT: J 48 ILE cc_start: 0.6111 (OUTLIER) cc_final: 0.5696 (pp) REVERT: J 54 LEU cc_start: 0.5926 (OUTLIER) cc_final: 0.5697 (mm) REVERT: J 91 MET cc_start: 0.5413 (ptt) cc_final: 0.5098 (ptp) REVERT: L 12 SER cc_start: 0.7092 (OUTLIER) cc_final: 0.6510 (p) REVERT: L 48 ILE cc_start: 0.5863 (OUTLIER) cc_final: 0.5260 (pp) REVERT: L 54 LEU cc_start: 0.6142 (OUTLIER) cc_final: 0.5915 (mm) REVERT: L 91 MET cc_start: 0.5438 (ptt) cc_final: 0.4977 (ptp) outliers start: 60 outliers final: 35 residues processed: 264 average time/residue: 1.3537 time to fit residues: 401.5744 Evaluate side-chains 269 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 220 time to evaluate : 2.049 ------------------------------------------------------------------------------- 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 A residue 244 THR Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 588 ARG Chi-restraints excluded: chain B residue 635 ILE 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 247 CYS 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 247 CYS 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 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 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 70 THR 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 143 optimal weight: 0.9980 chunk 61 optimal weight: 0.8980 chunk 162 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 151 optimal weight: 0.0020 chunk 217 optimal weight: 0.3980 chunk 100 optimal weight: 0.5980 chunk 226 optimal weight: 5.9990 chunk 52 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 chunk 36 optimal weight: 0.7980 overall best weight: 0.5388 ------------------------------------------------------------------------------- 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 440 GLN ** D 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 130 GLN G 32 ASN I 32 ASN K 32 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.194745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.140466 restraints weight = 20044.360| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 1.78 r_work: 0.3283 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.2234 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= 0.114 Angle : 0.570 12.099 27831 Z= 0.280 Chirality : 0.044 0.305 3321 Planarity : 0.004 0.063 3399 Dihedral : 5.590 52.976 4233 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.49 % Allowed : 16.33 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.18), residues: 2352 helix: 1.46 (0.28), residues: 411 sheet: 0.57 (0.18), residues: 789 loop : 0.35 (0.20), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 427 HIS 0.004 0.001 HIS I 35 PHE 0.013 0.001 PHE E 383 TYR 0.013 0.001 TYR C 173 ARG 0.009 0.000 ARG A 178 Details of bonding type rmsd link_NAG-ASN : bond 0.00287 ( 45) link_NAG-ASN : angle 2.71273 ( 135) link_BETA1-4 : bond 0.00351 ( 30) link_BETA1-4 : angle 1.43844 ( 90) link_ALPHA1-2 : bond 0.00194 ( 3) link_ALPHA1-2 : angle 1.82863 ( 9) link_ALPHA1-3 : bond 0.00959 ( 3) link_ALPHA1-3 : angle 1.18789 ( 9) hydrogen bonds : bond 0.03655 ( 718) hydrogen bonds : angle 4.76082 ( 1962) SS BOND : bond 0.00309 ( 42) SS BOND : angle 1.26949 ( 84) covalent geometry : bond 0.00253 (20262) covalent geometry : angle 0.52818 (27504) ********************** 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 278 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 226 time to evaluate : 2.050 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 GLU cc_start: 0.7442 (OUTLIER) cc_final: 0.7081 (tp30) REVERT: A 103 GLN cc_start: 0.8522 (mt0) cc_final: 0.8252 (mt0) REVERT: A 117 LYS cc_start: 0.8085 (OUTLIER) cc_final: 0.7744 (tptt) REVERT: B 588 ARG cc_start: 0.7799 (OUTLIER) cc_final: 0.7351 (tmm160) REVERT: B 637 ASN cc_start: 0.7228 (m110) cc_final: 0.6738 (m-40) REVERT: C 117 LYS cc_start: 0.8185 (mmmt) cc_final: 0.7829 (mmtt) REVERT: C 137 ASN cc_start: 0.7537 (m-40) cc_final: 0.7216 (m-40) REVERT: C 325 ASP cc_start: 0.7710 (OUTLIER) cc_final: 0.7322 (t0) REVERT: D 588 ARG cc_start: 0.7816 (OUTLIER) cc_final: 0.7391 (tmm160) REVERT: E 117 LYS cc_start: 0.8218 (mmmt) cc_final: 0.7835 (tptp) REVERT: E 347 LYS cc_start: 0.7779 (OUTLIER) cc_final: 0.7457 (pttt) REVERT: G 75 ILE cc_start: 0.8058 (OUTLIER) cc_final: 0.7591 (pt) REVERT: H 79 GLN cc_start: 0.5632 (OUTLIER) cc_final: 0.4701 (tm-30) REVERT: J 42 LYS cc_start: 0.6092 (OUTLIER) cc_final: 0.4994 (ptpp) REVERT: J 48 ILE cc_start: 0.6104 (OUTLIER) cc_final: 0.5715 (pp) REVERT: J 91 MET cc_start: 0.5426 (ptt) cc_final: 0.5106 (ptp) REVERT: K 69 MET cc_start: 0.7434 (mtt) cc_final: 0.7104 (mtp) REVERT: L 12 SER cc_start: 0.7037 (OUTLIER) cc_final: 0.6465 (p) REVERT: L 48 ILE cc_start: 0.5882 (OUTLIER) cc_final: 0.5325 (OUTLIER) REVERT: L 91 MET cc_start: 0.5481 (ptt) cc_final: 0.5003 (ptp) outliers start: 52 outliers final: 26 residues processed: 261 average time/residue: 1.3955 time to fit residues: 409.4276 Evaluate side-chains 259 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 222 time to evaluate : 2.170 ------------------------------------------------------------------------------- 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 A residue 247 CYS Chi-restraints excluded: chain B residue 588 ARG 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 247 CYS 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 247 CYS Chi-restraints excluded: chain E residue 347 LYS Chi-restraints excluded: chain F residue 538 THR 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 67 VAL Chi-restraints excluded: chain G residue 75 ILE Chi-restraints excluded: chain G residue 109 VAL 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 K residue 70 THR Chi-restraints excluded: chain K residue 109 VAL Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 48 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 215 optimal weight: 0.0670 chunk 5 optimal weight: 0.9990 chunk 125 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 177 optimal weight: 4.9990 chunk 150 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 225 optimal weight: 5.9990 chunk 164 optimal weight: 0.5980 chunk 162 optimal weight: 0.9980 chunk 191 optimal weight: 0.9980 overall best weight: 0.7320 ------------------------------------------------------------------------------- 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 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 130 GLN C 440 GLN ** D 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 130 GLN G 32 ASN I 32 ASN K 32 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.194295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.140374 restraints weight = 20036.097| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 1.81 r_work: 0.3258 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 20385 Z= 0.130 Angle : 0.586 12.080 27831 Z= 0.287 Chirality : 0.044 0.303 3321 Planarity : 0.004 0.063 3399 Dihedral : 5.292 42.268 4230 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.44 % Allowed : 16.62 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.18), residues: 2352 helix: 1.48 (0.28), residues: 408 sheet: 0.59 (0.18), residues: 789 loop : 0.37 (0.20), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 427 HIS 0.003 0.001 HIS I 35 PHE 0.015 0.001 PHE A 383 TYR 0.016 0.001 TYR I 27 ARG 0.009 0.000 ARG A 178 Details of bonding type rmsd link_NAG-ASN : bond 0.00320 ( 45) link_NAG-ASN : angle 2.74368 ( 135) link_BETA1-4 : bond 0.00309 ( 30) link_BETA1-4 : angle 1.44423 ( 90) link_ALPHA1-2 : bond 0.00226 ( 3) link_ALPHA1-2 : angle 1.83208 ( 9) link_ALPHA1-3 : bond 0.00900 ( 3) link_ALPHA1-3 : angle 1.12486 ( 9) hydrogen bonds : bond 0.03795 ( 718) hydrogen bonds : angle 4.75682 ( 1962) SS BOND : bond 0.00338 ( 42) SS BOND : angle 1.34601 ( 84) covalent geometry : bond 0.00296 (20262) covalent geometry : angle 0.54501 (27504) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19438.79 seconds wall clock time: 342 minutes 3.58 seconds (20523.58 seconds total)