Starting phenix.real_space_refine on Tue Jun 17 12:36:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tl3_41360/06_2025/8tl3_41360.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tl3_41360/06_2025/8tl3_41360.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8tl3_41360/06_2025/8tl3_41360.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tl3_41360/06_2025/8tl3_41360.map" model { file = "/net/cci-nas-00/data/ceres_data/8tl3_41360/06_2025/8tl3_41360.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tl3_41360/06_2025/8tl3_41360.cif" } resolution = 3.1 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= 0.044 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 12555 2.51 5 N 3366 2.21 5 O 4020 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 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: 20070 Number of models: 1 Model: "" Number of chains: 42 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: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 973 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "H" Number of atoms: 861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 861 Classifications: {'peptide': 110} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 102} Chain: "I" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 973 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "J" Number of atoms: 861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 861 Classifications: {'peptide': 110} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 102} Chain: "K" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 973 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 4, 'TRANS': 121} Chain: "L" Number of atoms: 861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 861 Classifications: {'peptide': 110} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 102} 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 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: "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: "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: "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: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 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: 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: "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: 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: "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: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 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: "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: 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: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "l" Number of atoms: 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: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "E" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 14.34, per 1000 atoms: 0.71 Number of scatterers: 20070 At special positions: 0 Unit cell: (145.965, 153.739, 126.1, 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 4020 8.00 N 3366 7.00 C 12555 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=2.05 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.05 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=2.03 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=2.04 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=2.05 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS D 605 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.04 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=2.03 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=2.04 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=2.04 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=2.04 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 Q 4 " - " MAN Q 5 " " MAN Y 4 " - " MAN Y 5 " " MAN j 4 " - " MAN j 5 " ALPHA1-3 " BMA Q 3 " - " MAN Q 4 " " BMA Y 3 " - " MAN Y 4 " " BMA j 3 " - " MAN j 4 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " 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 V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " 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 e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " NAG-ASN " NAG A 601 " - " ASN A 234 " " NAG A 602 " - " ASN A 392 " " NAG A 603 " - " ASN A 301 " " NAG A 604 " - " ASN A 197 " " NAG A 605 " - " ASN A 88 " " NAG A 606 " - " ASN A 133 " " NAG C 601 " - " ASN C 234 " " NAG C 602 " - " ASN C 392 " " NAG C 603 " - " ASN C 301 " " NAG C 604 " - " ASN C 197 " " NAG C 605 " - " ASN C 88 " " NAG C 606 " - " ASN C 133 " " NAG E 601 " - " ASN E 234 " " NAG E 602 " - " ASN E 392 " " NAG E 603 " - " ASN E 301 " " NAG E 604 " - " ASN E 197 " " NAG E 605 " - " ASN E 88 " " NAG E 606 " - " ASN E 133 " " NAG M 1 " - " ASN A 448 " " NAG N 1 " - " ASN A 160 " " NAG O 1 " - " ASN A 276 " " NAG P 1 " - " ASN A 386 " " NAG Q 1 " - " ASN A 262 " " NAG R 1 " - " ASN A 156 " " NAG S 1 " - " ASN A 332 " " NAG T 1 " - " ASN A 363 " " NAG U 1 " - " ASN C 448 " " NAG V 1 " - " ASN C 160 " " NAG W 1 " - " ASN C 276 " " NAG X 1 " - " ASN C 386 " " NAG Y 1 " - " ASN C 262 " " NAG Z 1 " - " ASN C 156 " " NAG a 1 " - " ASN A 295 " " NAG b 1 " - " ASN C 332 " " NAG c 1 " - " ASN C 295 " " NAG d 1 " - " ASN C 363 " " NAG e 1 " - " ASN E 295 " " NAG f 1 " - " ASN E 448 " " NAG g 1 " - " ASN E 160 " " NAG h 1 " - " ASN E 276 " " NAG i 1 " - " ASN E 386 " " NAG j 1 " - " ASN E 262 " " NAG k 1 " - " ASN E 156 " " NAG l 1 " - " ASN E 332 " " NAG m 1 " - " ASN E 363 " Time building additional restraints: 5.67 Conformation dependent library (CDL) restraints added in 2.9 seconds 4746 Ramachandran restraints generated. 2373 Oldfield, 0 Emsley, 2373 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4494 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 44 sheets defined 19.0% alpha, 37.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.99 Creating SS restraints... Processing helix chain 'A' and resid 98 through 116 removed outlier: 4.156A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU A 116 " --> pdb=" O TRP A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 removed outlier: 3.671A pdb=" N LEU A 125 " --> pdb=" O LEU A 122 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N CYS A 126 " --> pdb=" O THR A 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 122 through 126' Processing helix chain 'A' and resid 195 through 198 Processing helix chain 'A' and resid 335 through 353 removed outlier: 3.813A pdb=" N LYS A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 4.053A 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 481 removed outlier: 3.534A pdb=" N TRP A 479 " --> pdb=" O MET A 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 546 removed outlier: 4.124A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU B 544 " --> pdb=" O GLN B 540 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LEU B 545 " --> pdb=" O ALA B 541 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N SER B 546 " --> pdb=" O ARG B 542 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 596 Processing helix chain 'B' and resid 619 through 624 removed outlier: 3.669A pdb=" N ASP B 624 " --> pdb=" O SER B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 662 removed outlier: 3.809A pdb=" N ILE B 642 " --> pdb=" O TYR B 638 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 116 removed outlier: 4.463A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU C 116 " --> pdb=" O TRP C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 removed outlier: 3.688A pdb=" N LEU C 125 " --> pdb=" O LEU C 122 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N CYS C 126 " --> pdb=" O THR C 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 122 through 126' Processing helix chain 'C' and resid 335 through 353 removed outlier: 3.780A pdb=" N LYS C 351 " --> pdb=" O LYS C 347 " (cutoff:3.500A) removed outlier: 4.043A 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 481 removed outlier: 3.584A pdb=" N TRP C 479 " --> pdb=" O MET C 475 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 534 Processing helix chain 'D' and resid 536 through 546 removed outlier: 4.032A pdb=" N GLN D 540 " --> pdb=" O THR D 536 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ASN D 543 " --> pdb=" O VAL D 539 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU D 544 " --> pdb=" O GLN D 540 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N LEU D 545 " --> pdb=" O ALA D 541 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N SER D 546 " --> pdb=" O ARG D 542 " (cutoff:3.500A) Processing helix chain 'D' and resid 570 through 596 removed outlier: 3.558A pdb=" N TRP D 596 " --> pdb=" O LEU D 592 " (cutoff:3.500A) Processing helix chain 'D' and resid 619 through 624 removed outlier: 3.749A pdb=" N ASP D 624 " --> pdb=" O SER D 620 " (cutoff:3.500A) Processing helix chain 'D' and resid 627 through 635 Processing helix chain 'D' and resid 638 through 662 removed outlier: 3.758A pdb=" N ILE D 642 " --> pdb=" O TYR D 638 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 116 removed outlier: 4.422A pdb=" N GLU E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU E 116 " --> pdb=" O TRP E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 139 through 151 removed outlier: 3.583A pdb=" N MET E 150 " --> pdb=" O THR E 139 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ARG E 151 " --> pdb=" O ASP E 140 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 139 through 151' Processing helix chain 'E' and resid 335 through 353 removed outlier: 3.787A pdb=" N LYS E 351 " --> pdb=" O LYS E 347 " (cutoff:3.500A) removed outlier: 4.035A 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 481 Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 536 through 546 removed outlier: 4.079A pdb=" N GLN F 540 " --> pdb=" O THR F 536 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASN F 543 " --> pdb=" O VAL F 539 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU F 544 " --> pdb=" O GLN F 540 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N LEU F 545 " --> pdb=" O ALA F 541 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N SER F 546 " --> pdb=" O ARG F 542 " (cutoff:3.500A) Processing helix chain 'F' and resid 570 through 596 removed outlier: 3.573A pdb=" N TRP F 596 " --> pdb=" O LEU F 592 " (cutoff:3.500A) Processing helix chain 'F' and resid 627 through 635 Processing helix chain 'F' and resid 638 through 662 removed outlier: 3.759A pdb=" N ILE F 642 " --> pdb=" O TYR F 638 " (cutoff:3.500A) Processing helix chain 'G' and resid 60 through 65 removed outlier: 4.442A pdb=" N SER G 65 " --> pdb=" O PRO G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 87 Processing helix chain 'H' and resid 79 through 83 removed outlier: 3.792A pdb=" N PHE H 83 " --> pdb=" O PRO H 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 83 through 87 Processing helix chain 'J' and resid 79 through 83 removed outlier: 3.767A pdb=" N PHE J 83 " --> pdb=" O PRO J 80 " (cutoff:3.500A) Processing helix chain 'K' and resid 60 through 65 removed outlier: 4.456A pdb=" N SER K 65 " --> pdb=" O PRO K 61 " (cutoff:3.500A) Processing helix chain 'K' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.784A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.520A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 8.415A pdb=" N TYR A 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.770A pdb=" N CYS B 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 4.040A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 55 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 169 through 177 Processing sheet with id=AA6, first strand: chain 'A' and resid 202 through 203 removed outlier: 6.648A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 260 through 261 removed outlier: 6.568A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 10.136A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.468A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 9.710A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 10.674A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.379A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.620A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N THR A 450 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 271 through 273 removed outlier: 7.190A pdb=" N THR A 450 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 10.620A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 9.379A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.674A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.710A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 11.468A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 10.136A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N THR A 467 " --> pdb=" O ASP A 457 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 304 through 312 removed outlier: 6.485A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 516 through 519 removed outlier: 6.497A pdb=" N GLY B 516 " --> pdb=" O ARG G 97 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N TYR G 99 " --> pdb=" O GLY B 516 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N VAL B 518 " --> pdb=" O TYR G 99 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLN G 95 " --> pdb=" O TYR G 34 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N TYR G 34 " --> pdb=" O GLN G 95 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N TRP G 35 " --> pdb=" O ASN G 50 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ASN G 50 " --> pdb=" O TRP G 35 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N TRP G 36 " --> pdb=" O ILE G 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 11 through 12 removed outlier: 3.687A pdb=" N SER G 100F" --> pdb=" O THR G 98 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N VAL G 100 " --> pdb=" O LEU G 100D" (cutoff:3.500A) removed outlier: 5.694A pdb=" N LEU G 100D" --> pdb=" O VAL G 100 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 494 through 499 removed outlier: 5.305A pdb=" N VAL D 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N VAL C 38 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N THR D 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 8.349A pdb=" N TYR C 40 " --> pdb=" O CYS D 604 " (cutoff:3.500A) removed outlier: 8.675A pdb=" N CYS D 604 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.880A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 53 through 55 Processing sheet with id=AB6, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AB7, first strand: chain 'C' and resid 169 through 177 Processing sheet with id=AB8, first strand: chain 'C' and resid 260 through 261 removed outlier: 6.574A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) removed outlier: 10.138A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 11.504A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 9.699A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 10.667A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 9.351A pdb=" N ASN C 448 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 10.527A pdb=" N THR C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N THR C 450 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 271 through 273 removed outlier: 7.140A pdb=" N THR C 450 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 10.527A pdb=" N THR C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 9.351A pdb=" N ASN C 448 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 10.667A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 9.699A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 11.504A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 10.138A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N THR C 467 " --> pdb=" O ASP C 457 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 304 through 312 removed outlier: 6.525A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 516 through 519 removed outlier: 6.410A pdb=" N GLY D 516 " --> pdb=" O ARG I 97 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N TYR I 99 " --> pdb=" O GLY D 516 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N VAL D 518 " --> pdb=" O TYR I 99 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLN I 95 " --> pdb=" O TYR I 34 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N TYR I 34 " --> pdb=" O GLN I 95 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N TRP I 35 " --> pdb=" O ASN I 50 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ASN I 50 " --> pdb=" O TRP I 35 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N TRP I 36 " --> pdb=" O ILE I 48 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 11 through 12 removed outlier: 3.697A pdb=" N SER I 100F" --> pdb=" O THR I 98 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N VAL I 100 " --> pdb=" O LEU I 100D" (cutoff:3.500A) removed outlier: 5.730A pdb=" N LEU I 100D" --> pdb=" O VAL I 100 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 494 through 499 removed outlier: 5.215A pdb=" N VAL F 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N VAL E 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N THR F 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 8.307A pdb=" N TYR E 40 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 8.614A pdb=" N CYS F 604 " --> pdb=" O TYR E 40 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.826A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N VAL E 242 " --> pdb=" O LEU E 86 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AC7, first strand: chain 'E' and resid 91 through 94 Processing sheet with id=AC8, first strand: chain 'E' and resid 169 through 177 Processing sheet with id=AC9, first strand: chain 'E' and resid 202 through 203 removed outlier: 6.706A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 260 through 261 removed outlier: 6.598A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 10.102A pdb=" N ARG E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 11.433A pdb=" N ILE E 294 " --> pdb=" O ARG E 444 " (cutoff:3.500A) removed outlier: 9.594A pdb=" N VAL E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 10.469A pdb=" N VAL E 292 " --> pdb=" O VAL E 446 " (cutoff:3.500A) removed outlier: 9.280A pdb=" N ASN E 448 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 10.405A pdb=" N THR E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N THR E 450 " --> pdb=" O PHE E 288 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N GLN E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N SER E 334 " --> pdb=" O GLN E 293 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N PHE E 382 " --> pdb=" O LYS E 421 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 271 through 273 removed outlier: 7.312A pdb=" N THR E 450 " --> pdb=" O PHE E 288 " (cutoff:3.500A) removed outlier: 10.405A pdb=" N THR E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 9.280A pdb=" N ASN E 448 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 10.469A pdb=" N VAL E 292 " --> pdb=" O VAL E 446 " (cutoff:3.500A) removed outlier: 9.594A pdb=" N VAL E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 11.433A pdb=" N ILE E 294 " --> pdb=" O ARG E 444 " (cutoff:3.500A) removed outlier: 10.102A pdb=" N ARG E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N THR E 467 " --> pdb=" O ASP E 457 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 304 through 312 removed outlier: 6.564A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 516 through 519 removed outlier: 3.969A pdb=" N GLY F 516 " --> pdb=" O GLN K 95 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N TRP K 35 " --> pdb=" O ASN K 50 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ASN K 50 " --> pdb=" O TRP K 35 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N TRP K 36 " --> pdb=" O ILE K 48 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'K' and resid 11 through 12 removed outlier: 3.754A pdb=" N SER K 100F" --> pdb=" O THR K 98 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N VAL K 100 " --> pdb=" O LEU K 100D" (cutoff:3.500A) removed outlier: 5.686A pdb=" N LEU K 100D" --> pdb=" O VAL K 100 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 3 through 7 Processing sheet with id=AD7, first strand: chain 'H' and resid 4 through 7 Processing sheet with id=AD8, first strand: chain 'H' and resid 10 through 13 removed outlier: 3.551A pdb=" N ASP H 105 " --> pdb=" O LEU H 11 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N LEU H 33 " --> pdb=" O TYR H 49 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N TYR H 49 " --> pdb=" O LEU H 33 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N TRP H 35 " --> pdb=" O LEU H 47 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'H' and resid 10 through 13 removed outlier: 3.551A pdb=" N ASP H 105 " --> pdb=" O LEU H 11 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLN H 90 " --> pdb=" O THR H 97 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N THR H 97 " --> pdb=" O GLN H 90 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'I' and resid 3 through 7 Processing sheet with id=AE2, first strand: chain 'J' and resid 4 through 7 Processing sheet with id=AE3, first strand: chain 'J' and resid 10 through 13 removed outlier: 3.531A pdb=" N ASP J 105 " --> pdb=" O LEU J 11 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N LEU J 33 " --> pdb=" O TYR J 49 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N TYR J 49 " --> pdb=" O LEU J 33 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 10 through 13 removed outlier: 3.531A pdb=" N ASP J 105 " --> pdb=" O LEU J 11 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLN J 90 " --> pdb=" O THR J 97 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N THR J 97 " --> pdb=" O GLN J 90 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'K' and resid 3 through 7 Processing sheet with id=AE6, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AE7, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.507A pdb=" N ASP L 105 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.547A 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: 3.507A pdb=" N ASP L 105 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLN L 90 " --> pdb=" O THR L 97 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) 766 hydrogen bonds defined for protein. 2034 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: 7.52 Time building geometry restraints manager: 6.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 6358 1.35 - 1.48: 5339 1.48 - 1.60: 8607 1.60 - 1.73: 0 1.73 - 1.85: 174 Bond restraints: 20478 Sorted by residual: bond pdb=" C ARG C 298 " pdb=" N PRO C 299 " ideal model delta sigma weight residual 1.336 1.357 -0.021 9.80e-03 1.04e+04 4.71e+00 bond pdb=" C1 NAG U 1 " pdb=" O5 NAG U 1 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.32e+00 bond pdb=" C1 NAG f 1 " pdb=" O5 NAG f 1 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.22e+00 bond pdb=" C1 NAG M 1 " pdb=" O5 NAG M 1 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.19e+00 bond pdb=" C1 NAG T 1 " pdb=" O5 NAG T 1 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.15e+00 ... (remaining 20473 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.41: 26762 1.41 - 2.82: 846 2.82 - 4.23: 172 4.23 - 5.65: 36 5.65 - 7.06: 15 Bond angle restraints: 27831 Sorted by residual: angle pdb=" CA ASN D 607 " pdb=" CB ASN D 607 " pdb=" CG ASN D 607 " ideal model delta sigma weight residual 112.60 115.81 -3.21 1.00e+00 1.00e+00 1.03e+01 angle pdb=" CA CYS A 247 " pdb=" CB CYS A 247 " pdb=" SG CYS A 247 " ideal model delta sigma weight residual 114.40 121.34 -6.94 2.30e+00 1.89e-01 9.12e+00 angle pdb=" CA CYS C 418 " pdb=" CB CYS C 418 " pdb=" SG CYS C 418 " ideal model delta sigma weight residual 114.40 120.86 -6.46 2.30e+00 1.89e-01 7.89e+00 angle pdb=" N CYS A 247 " pdb=" CA CYS A 247 " pdb=" C CYS A 247 " ideal model delta sigma weight residual 107.88 111.79 -3.91 1.41e+00 5.03e-01 7.71e+00 angle pdb=" CG LYS A 232 " pdb=" CD LYS A 232 " pdb=" CE LYS A 232 " ideal model delta sigma weight residual 111.30 117.46 -6.16 2.30e+00 1.89e-01 7.18e+00 ... (remaining 27826 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.70: 12105 21.70 - 43.39: 953 43.39 - 65.09: 177 65.09 - 86.79: 40 86.79 - 108.49: 15 Dihedral angle restraints: 13290 sinusoidal: 6318 harmonic: 6972 Sorted by residual: dihedral pdb=" CB CYS C 54 " pdb=" SG CYS C 54 " pdb=" SG CYS C 74 " pdb=" CB CYS C 74 " ideal model delta sinusoidal sigma weight residual -86.00 3.17 -89.17 1 1.00e+01 1.00e-02 9.46e+01 dihedral pdb=" CB CYS E 54 " pdb=" SG CYS E 54 " pdb=" SG CYS E 74 " pdb=" CB CYS E 74 " ideal model delta sinusoidal sigma weight residual 93.00 6.55 86.45 1 1.00e+01 1.00e-02 9.01e+01 dihedral pdb=" CB CYS A 54 " pdb=" SG CYS A 54 " pdb=" SG CYS A 74 " pdb=" CB CYS A 74 " ideal model delta sinusoidal sigma weight residual 93.00 9.31 83.69 1 1.00e+01 1.00e-02 8.55e+01 ... (remaining 13287 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 2857 0.059 - 0.117: 408 0.117 - 0.176: 95 0.176 - 0.235: 0 0.235 - 0.294: 6 Chirality restraints: 3366 Sorted by residual: chirality pdb=" C1 NAG Q 2 " pdb=" O4 NAG Q 1 " pdb=" C2 NAG Q 2 " pdb=" O5 NAG Q 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.37 -0.03 2.00e-02 2.50e+03 2.57e+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 -2.11 -0.29 2.00e-01 2.50e+01 2.15e+00 chirality pdb=" C1 NAG C 601 " pdb=" ND2 ASN C 234 " pdb=" C2 NAG C 601 " pdb=" O5 NAG C 601 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.08e+00 ... (remaining 3363 not shown) Planarity restraints: 3492 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS C 205 " 0.052 5.00e-02 4.00e+02 7.75e-02 9.60e+00 pdb=" N PRO C 206 " -0.134 5.00e-02 4.00e+02 pdb=" CA PRO C 206 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO C 206 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS A 205 " -0.047 5.00e-02 4.00e+02 7.01e-02 7.86e+00 pdb=" N PRO A 206 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO A 206 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 206 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS E 205 " -0.039 5.00e-02 4.00e+02 5.92e-02 5.60e+00 pdb=" N PRO E 206 " 0.102 5.00e-02 4.00e+02 pdb=" CA PRO E 206 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO E 206 " -0.033 5.00e-02 4.00e+02 ... (remaining 3489 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 138 2.62 - 3.19: 16140 3.19 - 3.76: 28216 3.76 - 4.33: 40347 4.33 - 4.90: 69332 Nonbonded interactions: 154173 Sorted by model distance: nonbonded pdb=" O LEU C 369 " pdb=" OG1 THR C 373 " model vdw 2.049 3.040 nonbonded pdb=" O LEU E 369 " pdb=" OG1 THR E 373 " model vdw 2.124 3.040 nonbonded pdb=" O LEU A 369 " pdb=" OG1 THR A 373 " model vdw 2.130 3.040 nonbonded pdb=" OG1 THR H 30 " pdb=" OD1 ASP H 32 " model vdw 2.263 3.040 nonbonded pdb=" O3 NAG l 1 " pdb=" O5 NAG l 2 " model vdw 2.279 3.040 ... (remaining 154168 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain '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 'N' selection = chain 'O' selection = chain 'P' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'k' selection = chain 'l' selection = chain 'm' } ncs_group { reference = chain 'Q' selection = chain 'Y' selection = chain 'j' } 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: 4.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.790 Check model and map are aligned: 0.150 Set scattering table: 0.170 Process input model: 50.310 Find NCS groups from input model: 1.020 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 20601 Z= 0.203 Angle : 0.645 7.058 28158 Z= 0.302 Chirality : 0.047 0.294 3366 Planarity : 0.004 0.077 3447 Dihedral : 15.470 108.486 8670 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 1.87 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.02 % Favored : 97.94 % Rotamer: Outliers : 0.19 % Allowed : 10.72 % Favored : 89.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 0.58 (0.18), residues: 2373 helix: 2.30 (0.28), residues: 408 sheet: 0.52 (0.18), residues: 795 loop : -0.36 (0.18), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP L 35 HIS 0.004 0.000 HIS A 216 PHE 0.010 0.001 PHE C 382 TYR 0.010 0.001 TYR A 191 ARG 0.006 0.000 ARG C 444 Details of bonding type rmsd link_NAG-ASN : bond 0.00269 ( 45) link_NAG-ASN : angle 1.96294 ( 135) link_BETA1-4 : bond 0.00434 ( 30) link_BETA1-4 : angle 0.89017 ( 90) link_ALPHA1-2 : bond 0.00350 ( 3) link_ALPHA1-2 : angle 1.61998 ( 9) link_ALPHA1-3 : bond 0.00508 ( 3) link_ALPHA1-3 : angle 1.43869 ( 9) hydrogen bonds : bond 0.09537 ( 739) hydrogen bonds : angle 5.42271 ( 2034) SS BOND : bond 0.00577 ( 42) SS BOND : angle 1.90278 ( 84) covalent geometry : bond 0.00421 (20478) covalent geometry : angle 0.62252 (27831) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4746 Ramachandran restraints generated. 2373 Oldfield, 0 Emsley, 2373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4746 Ramachandran restraints generated. 2373 Oldfield, 0 Emsley, 2373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 172 time to evaluate : 2.468 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 184 ILE cc_start: 0.8131 (tt) cc_final: 0.7889 (tt) REVERT: B 601 LYS cc_start: 0.8917 (mttp) cc_final: 0.8565 (mtmt) REVERT: F 653 GLN cc_start: 0.8017 (mt0) cc_final: 0.7700 (tt0) REVERT: K 82 MET cc_start: 0.4227 (mmm) cc_final: 0.2749 (ptm) outliers start: 4 outliers final: 1 residues processed: 175 average time/residue: 0.3818 time to fit residues: 98.9086 Evaluate side-chains 169 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 168 time to evaluate : 2.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 355 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 202 optimal weight: 6.9990 chunk 181 optimal weight: 0.0870 chunk 100 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 122 optimal weight: 0.0270 chunk 97 optimal weight: 5.9990 chunk 188 optimal weight: 9.9990 chunk 72 optimal weight: 0.0370 chunk 114 optimal weight: 2.9990 chunk 140 optimal weight: 2.9990 chunk 217 optimal weight: 9.9990 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 ASN B 616 ASN C 195 ASN C 246 GLN D 540 GLN D 616 ASN D 653 GLN D 658 GLN E 94 ASN E 355 ASN F 658 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.197917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.139093 restraints weight = 20277.082| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 1.88 r_work: 0.2894 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.0907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20601 Z= 0.118 Angle : 0.556 7.703 28158 Z= 0.275 Chirality : 0.043 0.263 3366 Planarity : 0.004 0.056 3447 Dihedral : 7.976 73.912 4268 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 0.94 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.73 % Favored : 98.23 % Rotamer: Outliers : 1.69 % Allowed : 10.30 % Favored : 88.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 0.56 (0.17), residues: 2373 helix: 2.26 (0.29), residues: 408 sheet: 0.71 (0.18), residues: 777 loop : -0.52 (0.17), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 96 HIS 0.004 0.001 HIS C 374 PHE 0.015 0.001 PHE A 383 TYR 0.010 0.001 TYR I 91 ARG 0.006 0.000 ARG C 444 Details of bonding type rmsd link_NAG-ASN : bond 0.00286 ( 45) link_NAG-ASN : angle 2.18348 ( 135) link_BETA1-4 : bond 0.00613 ( 30) link_BETA1-4 : angle 1.04678 ( 90) link_ALPHA1-2 : bond 0.00637 ( 3) link_ALPHA1-2 : angle 1.78735 ( 9) link_ALPHA1-3 : bond 0.01539 ( 3) link_ALPHA1-3 : angle 2.52330 ( 9) hydrogen bonds : bond 0.03847 ( 739) hydrogen bonds : angle 4.41897 ( 2034) SS BOND : bond 0.00454 ( 42) SS BOND : angle 1.35161 ( 84) covalent geometry : bond 0.00270 (20478) covalent geometry : angle 0.52625 (27831) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4746 Ramachandran restraints generated. 2373 Oldfield, 0 Emsley, 2373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4746 Ramachandran restraints generated. 2373 Oldfield, 0 Emsley, 2373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 184 time to evaluate : 2.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 601 LYS cc_start: 0.8925 (mttp) cc_final: 0.8619 (mtmt) REVERT: B 633 LYS cc_start: 0.8557 (ttmm) cc_final: 0.8113 (mttt) REVERT: C 117 LYS cc_start: 0.8005 (mttm) cc_final: 0.7794 (mttp) REVERT: C 360 ARG cc_start: 0.8450 (mmm-85) cc_final: 0.7947 (ttp80) REVERT: C 502 LYS cc_start: 0.7956 (ptmm) cc_final: 0.7579 (tttm) REVERT: D 607 ASN cc_start: 0.8470 (t0) cc_final: 0.8122 (t0) REVERT: I 76 ASN cc_start: 0.4857 (OUTLIER) cc_final: 0.4622 (m110) REVERT: K 82 MET cc_start: 0.4290 (mmm) cc_final: 0.2244 (ptm) outliers start: 36 outliers final: 19 residues processed: 214 average time/residue: 0.3734 time to fit residues: 120.8586 Evaluate side-chains 194 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 174 time to evaluate : 3.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 166 ARG Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain D residue 513 VAL Chi-restraints excluded: chain E residue 119 CYS Chi-restraints excluded: chain E residue 205 CYS Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain G residue 100 SER Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain I residue 76 ASN Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain K residue 57 THR Chi-restraints excluded: chain L residue 97 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 221 optimal weight: 9.9990 chunk 208 optimal weight: 10.0000 chunk 139 optimal weight: 0.9990 chunk 137 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 82 optimal weight: 0.6980 chunk 170 optimal weight: 5.9990 chunk 126 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 616 ASN C 246 GLN C 355 ASN D 616 ASN D 652 GLN E 355 ASN F 652 GLN F 653 GLN F 658 GLN K 35AASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.189840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.136710 restraints weight = 20108.686| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 1.79 r_work: 0.2846 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.1630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 20601 Z= 0.198 Angle : 0.688 12.520 28158 Z= 0.334 Chirality : 0.047 0.275 3366 Planarity : 0.005 0.054 3447 Dihedral : 7.043 59.842 4266 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 1.44 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.32 % Favored : 97.64 % Rotamer: Outliers : 1.88 % Allowed : 11.33 % Favored : 86.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.22 (0.17), residues: 2373 helix: 1.74 (0.28), residues: 408 sheet: 0.63 (0.18), residues: 774 loop : -0.75 (0.17), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 45 HIS 0.005 0.001 HIS C 85 PHE 0.022 0.002 PHE A 383 TYR 0.011 0.002 TYR A 486 ARG 0.004 0.001 ARG J 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00286 ( 45) link_NAG-ASN : angle 2.57236 ( 135) link_BETA1-4 : bond 0.00560 ( 30) link_BETA1-4 : angle 1.26912 ( 90) link_ALPHA1-2 : bond 0.00475 ( 3) link_ALPHA1-2 : angle 1.63561 ( 9) link_ALPHA1-3 : bond 0.01119 ( 3) link_ALPHA1-3 : angle 1.67434 ( 9) hydrogen bonds : bond 0.05874 ( 739) hydrogen bonds : angle 4.63980 ( 2034) SS BOND : bond 0.00720 ( 42) SS BOND : angle 1.98088 ( 84) covalent geometry : bond 0.00497 (20478) covalent geometry : angle 0.65424 (27831) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4746 Ramachandran restraints generated. 2373 Oldfield, 0 Emsley, 2373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4746 Ramachandran restraints generated. 2373 Oldfield, 0 Emsley, 2373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 178 time to evaluate : 3.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 ARG cc_start: 0.8653 (OUTLIER) cc_final: 0.8343 (mtt90) REVERT: B 601 LYS cc_start: 0.8965 (mttp) cc_final: 0.8513 (mtmt) REVERT: E 191 TYR cc_start: 0.9386 (m-80) cc_final: 0.9088 (m-80) REVERT: F 633 LYS cc_start: 0.8649 (ttmm) cc_final: 0.8385 (mttt) REVERT: G 82 MET cc_start: 0.3685 (mtp) cc_final: 0.3441 (mtp) REVERT: I 76 ASN cc_start: 0.5164 (OUTLIER) cc_final: 0.4932 (m110) REVERT: K 82 MET cc_start: 0.4516 (mmm) cc_final: 0.2405 (ptm) outliers start: 40 outliers final: 24 residues processed: 208 average time/residue: 0.5273 time to fit residues: 167.4862 Evaluate side-chains 202 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 176 time to evaluate : 3.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 381 GLU Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 166 ARG Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain D residue 513 VAL Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain D residue 655 LYS Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 205 CYS Chi-restraints excluded: chain E residue 243 SER Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 355 ASN Chi-restraints excluded: chain F residue 613 SER Chi-restraints excluded: chain G residue 100 SER Chi-restraints excluded: chain I residue 76 ASN Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain L residue 97 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 134 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 175 optimal weight: 10.0000 chunk 224 optimal weight: 20.0000 chunk 196 optimal weight: 9.9990 chunk 51 optimal weight: 0.0980 chunk 74 optimal weight: 0.9980 chunk 65 optimal weight: 0.2980 chunk 114 optimal weight: 2.9990 chunk 162 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 ASN B 616 ASN C 246 GLN C 355 ASN D 607 ASN D 616 ASN E 85 HIS E 355 ASN F 591 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.193748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.128724 restraints weight = 20304.108| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 2.03 r_work: 0.2721 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 20601 Z= 0.168 Angle : 0.637 11.027 28158 Z= 0.311 Chirality : 0.045 0.283 3366 Planarity : 0.004 0.055 3447 Dihedral : 6.286 56.824 4266 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 1.44 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.44 % Favored : 97.51 % Rotamer: Outliers : 2.44 % Allowed : 11.80 % Favored : 85.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.11 (0.17), residues: 2373 helix: 1.58 (0.28), residues: 408 sheet: 0.57 (0.18), residues: 780 loop : -0.81 (0.17), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 427 HIS 0.004 0.001 HIS C 216 PHE 0.020 0.002 PHE A 383 TYR 0.010 0.001 TYR I 91 ARG 0.003 0.000 ARG C 444 Details of bonding type rmsd link_NAG-ASN : bond 0.00257 ( 45) link_NAG-ASN : angle 2.55344 ( 135) link_BETA1-4 : bond 0.00553 ( 30) link_BETA1-4 : angle 1.26509 ( 90) link_ALPHA1-2 : bond 0.00396 ( 3) link_ALPHA1-2 : angle 1.64160 ( 9) link_ALPHA1-3 : bond 0.01081 ( 3) link_ALPHA1-3 : angle 1.84454 ( 9) hydrogen bonds : bond 0.05308 ( 739) hydrogen bonds : angle 4.52450 ( 2034) SS BOND : bond 0.00595 ( 42) SS BOND : angle 1.83986 ( 84) covalent geometry : bond 0.00416 (20478) covalent geometry : angle 0.60116 (27831) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4746 Ramachandran restraints generated. 2373 Oldfield, 0 Emsley, 2373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4746 Ramachandran restraints generated. 2373 Oldfield, 0 Emsley, 2373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 176 time to evaluate : 2.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 ARG cc_start: 0.8659 (OUTLIER) cc_final: 0.8331 (mtt90) REVERT: B 601 LYS cc_start: 0.8963 (mttp) cc_final: 0.8543 (mtmt) REVERT: C 492 GLU cc_start: 0.8818 (OUTLIER) cc_final: 0.8286 (mt-10) REVERT: D 654 GLU cc_start: 0.7543 (OUTLIER) cc_final: 0.7181 (mt-10) REVERT: K 82 MET cc_start: 0.4102 (mmm) cc_final: 0.2178 (ptm) outliers start: 52 outliers final: 28 residues processed: 216 average time/residue: 0.3658 time to fit residues: 117.5467 Evaluate side-chains 205 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 174 time to evaluate : 2.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 381 GLU Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 166 ARG Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 355 ASN Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain C residue 492 GLU Chi-restraints excluded: chain D residue 513 VAL Chi-restraints excluded: chain D residue 654 GLU Chi-restraints excluded: chain E residue 205 CYS Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain F residue 613 SER Chi-restraints excluded: chain G residue 100 SER Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain I residue 63 LEU Chi-restraints excluded: chain J residue 97 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 186 optimal weight: 20.0000 chunk 121 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 164 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 105 optimal weight: 0.9990 chunk 126 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 ASN B 616 ASN C 246 GLN C 355 ASN E 355 ASN F 653 GLN I 76 ASN J 38 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.191915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 85)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.125158 restraints weight = 20311.068| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 2.07 r_work: 0.2696 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 20601 Z= 0.182 Angle : 0.655 11.670 28158 Z= 0.319 Chirality : 0.046 0.289 3366 Planarity : 0.004 0.056 3447 Dihedral : 5.903 59.731 4266 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 1.59 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.57 % Favored : 97.30 % Rotamer: Outliers : 2.82 % Allowed : 12.32 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: 0.05 (0.17), residues: 2373 helix: 1.48 (0.28), residues: 408 sheet: 0.56 (0.18), residues: 780 loop : -0.84 (0.17), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 427 HIS 0.004 0.001 HIS C 85 PHE 0.020 0.002 PHE A 383 TYR 0.010 0.001 TYR I 91 ARG 0.003 0.000 ARG C 444 Details of bonding type rmsd link_NAG-ASN : bond 0.00269 ( 45) link_NAG-ASN : angle 2.57634 ( 135) link_BETA1-4 : bond 0.00559 ( 30) link_BETA1-4 : angle 1.30049 ( 90) link_ALPHA1-2 : bond 0.00350 ( 3) link_ALPHA1-2 : angle 1.70149 ( 9) link_ALPHA1-3 : bond 0.01039 ( 3) link_ALPHA1-3 : angle 1.80943 ( 9) hydrogen bonds : bond 0.05569 ( 739) hydrogen bonds : angle 4.52832 ( 2034) SS BOND : bond 0.00699 ( 42) SS BOND : angle 1.90801 ( 84) covalent geometry : bond 0.00455 (20478) covalent geometry : angle 0.61891 (27831) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4746 Ramachandran restraints generated. 2373 Oldfield, 0 Emsley, 2373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4746 Ramachandran restraints generated. 2373 Oldfield, 0 Emsley, 2373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 172 time to evaluate : 2.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 ARG cc_start: 0.8677 (OUTLIER) cc_final: 0.8346 (mtt90) REVERT: B 601 LYS cc_start: 0.8952 (mttp) cc_final: 0.8516 (mtmt) REVERT: C 492 GLU cc_start: 0.8847 (OUTLIER) cc_final: 0.8323 (mt-10) REVERT: C 500 ARG cc_start: 0.8004 (mtm-85) cc_final: 0.7696 (mtm-85) REVERT: C 502 LYS cc_start: 0.8895 (ptmm) cc_final: 0.8653 (tttm) REVERT: D 654 GLU cc_start: 0.7519 (OUTLIER) cc_final: 0.7155 (mt-10) REVERT: E 168 LYS cc_start: 0.8608 (mmtt) cc_final: 0.7871 (mttt) REVERT: K 82 MET cc_start: 0.4042 (mmm) cc_final: 0.2174 (ptm) outliers start: 60 outliers final: 37 residues processed: 217 average time/residue: 0.4445 time to fit residues: 144.9987 Evaluate side-chains 208 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 168 time to evaluate : 3.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 381 GLU Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 166 ARG Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain C residue 492 GLU Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain D residue 513 VAL Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain D residue 654 GLU Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 117 LYS Chi-restraints excluded: chain E residue 205 CYS Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 243 SER Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 333 VAL Chi-restraints excluded: chain F residue 613 SER Chi-restraints excluded: chain F residue 626 MET Chi-restraints excluded: chain F residue 632 ASP Chi-restraints excluded: chain G residue 100 SER Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain L residue 97 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 62 optimal weight: 0.6980 chunk 181 optimal weight: 0.9990 chunk 116 optimal weight: 4.9990 chunk 169 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 96 optimal weight: 0.6980 chunk 65 optimal weight: 0.3980 chunk 30 optimal weight: 2.9990 chunk 155 optimal weight: 1.9990 chunk 164 optimal weight: 0.5980 chunk 185 optimal weight: 20.0000 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 ASN A 355 ASN B 616 ASN C 355 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.190886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.109132 restraints weight = 20240.379| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 2.63 r_work: 0.2728 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work: 0.2569 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 20601 Z= 0.118 Angle : 0.571 11.071 28158 Z= 0.281 Chirality : 0.043 0.282 3366 Planarity : 0.004 0.054 3447 Dihedral : 5.472 59.593 4266 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 1.59 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.28 % Favored : 97.60 % Rotamer: Outliers : 2.40 % Allowed : 13.26 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: 0.18 (0.17), residues: 2373 helix: 1.68 (0.28), residues: 408 sheet: 0.68 (0.18), residues: 774 loop : -0.82 (0.17), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 427 HIS 0.003 0.001 HIS A 216 PHE 0.016 0.001 PHE C 383 TYR 0.010 0.001 TYR K 34 ARG 0.001 0.000 ARG C 192 Details of bonding type rmsd link_NAG-ASN : bond 0.00253 ( 45) link_NAG-ASN : angle 2.46892 ( 135) link_BETA1-4 : bond 0.00517 ( 30) link_BETA1-4 : angle 1.22617 ( 90) link_ALPHA1-2 : bond 0.00307 ( 3) link_ALPHA1-2 : angle 1.65229 ( 9) link_ALPHA1-3 : bond 0.01119 ( 3) link_ALPHA1-3 : angle 1.81255 ( 9) hydrogen bonds : bond 0.04519 ( 739) hydrogen bonds : angle 4.35653 ( 2034) SS BOND : bond 0.00591 ( 42) SS BOND : angle 1.78522 ( 84) covalent geometry : bond 0.00277 (20478) covalent geometry : angle 0.53268 (27831) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4746 Ramachandran restraints generated. 2373 Oldfield, 0 Emsley, 2373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4746 Ramachandran restraints generated. 2373 Oldfield, 0 Emsley, 2373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 169 time to evaluate : 2.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 ARG cc_start: 0.8576 (OUTLIER) cc_final: 0.8221 (mtt90) REVERT: A 426 MET cc_start: 0.8135 (OUTLIER) cc_final: 0.6579 (tmm) REVERT: B 601 LYS cc_start: 0.8784 (mttp) cc_final: 0.8396 (mtmt) REVERT: C 492 GLU cc_start: 0.8778 (OUTLIER) cc_final: 0.8353 (mt-10) REVERT: C 500 ARG cc_start: 0.7864 (mtm-85) cc_final: 0.7572 (mtm-85) REVERT: C 502 LYS cc_start: 0.8829 (ptmm) cc_final: 0.8560 (tttm) REVERT: D 654 GLU cc_start: 0.7355 (OUTLIER) cc_final: 0.7014 (mt-10) REVERT: E 117 LYS cc_start: 0.8159 (OUTLIER) cc_final: 0.7954 (mttp) REVERT: E 168 LYS cc_start: 0.8482 (mmtt) cc_final: 0.7641 (mttt) REVERT: E 191 TYR cc_start: 0.9440 (m-80) cc_final: 0.9135 (m-80) REVERT: G 100 SER cc_start: 0.7512 (OUTLIER) cc_final: 0.6757 (p) REVERT: K 82 MET cc_start: 0.3534 (mmm) cc_final: 0.2029 (ptm) outliers start: 51 outliers final: 32 residues processed: 208 average time/residue: 0.3636 time to fit residues: 113.1915 Evaluate side-chains 208 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 170 time to evaluate : 2.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 381 GLU Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain B residue 633 LYS Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 166 ARG Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 355 ASN Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain C residue 492 GLU Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain D residue 654 GLU Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 117 LYS Chi-restraints excluded: chain E residue 205 CYS Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 333 VAL Chi-restraints excluded: chain E residue 355 ASN Chi-restraints excluded: chain F residue 601 LYS Chi-restraints excluded: chain F residue 613 SER Chi-restraints excluded: chain F residue 626 MET Chi-restraints excluded: chain G residue 100 SER Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain I residue 63 LEU Chi-restraints excluded: chain L residue 97 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 34 optimal weight: 2.9990 chunk 213 optimal weight: 20.0000 chunk 166 optimal weight: 0.9990 chunk 130 optimal weight: 0.8980 chunk 128 optimal weight: 0.6980 chunk 88 optimal weight: 4.9990 chunk 172 optimal weight: 10.0000 chunk 51 optimal weight: 2.9990 chunk 145 optimal weight: 2.9990 chunk 228 optimal weight: 6.9990 chunk 4 optimal weight: 3.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 ASN A 377 ASN B 616 ASN C 355 ASN F 653 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.191525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.124517 restraints weight = 20120.912| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 2.17 r_work: 0.2644 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8731 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 20601 Z= 0.218 Angle : 0.699 12.723 28158 Z= 0.338 Chirality : 0.047 0.299 3366 Planarity : 0.005 0.056 3447 Dihedral : 5.536 56.627 4266 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 1.80 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.57 % Favored : 97.30 % Rotamer: Outliers : 2.91 % Allowed : 13.26 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -0.03 (0.17), residues: 2373 helix: 1.38 (0.28), residues: 408 sheet: 0.52 (0.18), residues: 783 loop : -0.89 (0.17), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 427 HIS 0.004 0.001 HIS A 216 PHE 0.022 0.002 PHE A 383 TYR 0.010 0.002 TYR A 318 ARG 0.003 0.000 ARG E 298 Details of bonding type rmsd link_NAG-ASN : bond 0.00309 ( 45) link_NAG-ASN : angle 2.63461 ( 135) link_BETA1-4 : bond 0.00567 ( 30) link_BETA1-4 : angle 1.33745 ( 90) link_ALPHA1-2 : bond 0.00346 ( 3) link_ALPHA1-2 : angle 1.79532 ( 9) link_ALPHA1-3 : bond 0.00984 ( 3) link_ALPHA1-3 : angle 1.78270 ( 9) hydrogen bonds : bond 0.06043 ( 739) hydrogen bonds : angle 4.54227 ( 2034) SS BOND : bond 0.00724 ( 42) SS BOND : angle 2.03885 ( 84) covalent geometry : bond 0.00554 (20478) covalent geometry : angle 0.66311 (27831) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4746 Ramachandran restraints generated. 2373 Oldfield, 0 Emsley, 2373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4746 Ramachandran restraints generated. 2373 Oldfield, 0 Emsley, 2373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 169 time to evaluate : 1.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 ARG cc_start: 0.8673 (OUTLIER) cc_final: 0.8335 (mtt90) REVERT: B 601 LYS cc_start: 0.8991 (mttp) cc_final: 0.8584 (mtmt) REVERT: B 619 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8124 (mp) REVERT: C 492 GLU cc_start: 0.8861 (OUTLIER) cc_final: 0.8328 (mt-10) REVERT: C 500 ARG cc_start: 0.8048 (mtm-85) cc_final: 0.7741 (mtm-85) REVERT: D 654 GLU cc_start: 0.7589 (OUTLIER) cc_final: 0.7250 (mt-10) REVERT: E 168 LYS cc_start: 0.8674 (mmtt) cc_final: 0.7938 (mttt) REVERT: K 82 MET cc_start: 0.4043 (mmm) cc_final: 0.2171 (ptm) outliers start: 62 outliers final: 42 residues processed: 215 average time/residue: 0.3558 time to fit residues: 114.6202 Evaluate side-chains 210 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 164 time to evaluate : 2.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 381 GLU Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 633 LYS Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 166 ARG Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain C residue 492 GLU Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain D residue 626 MET Chi-restraints excluded: chain D residue 654 GLU Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 117 LYS Chi-restraints excluded: chain E residue 205 CYS Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 243 SER Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 333 VAL Chi-restraints excluded: chain E residue 355 ASN Chi-restraints excluded: chain F residue 613 SER Chi-restraints excluded: chain F residue 626 MET Chi-restraints excluded: chain F residue 632 ASP Chi-restraints excluded: chain G residue 100 SER Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain I residue 63 LEU Chi-restraints excluded: chain L residue 97 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 64 optimal weight: 0.0980 chunk 121 optimal weight: 2.9990 chunk 156 optimal weight: 0.7980 chunk 54 optimal weight: 0.6980 chunk 161 optimal weight: 0.6980 chunk 209 optimal weight: 1.9990 chunk 148 optimal weight: 3.9990 chunk 154 optimal weight: 0.9990 chunk 50 optimal weight: 0.8980 chunk 56 optimal weight: 3.9990 chunk 233 optimal weight: 5.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 ASN B 575 GLN B 616 ASN C 355 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.192706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.113820 restraints weight = 20166.760| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 2.60 r_work: 0.2783 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.2623 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 20601 Z= 0.111 Angle : 0.560 11.280 28158 Z= 0.277 Chirality : 0.043 0.285 3366 Planarity : 0.004 0.055 3447 Dihedral : 5.123 54.209 4266 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 1.77 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.15 % Favored : 97.72 % Rotamer: Outliers : 1.93 % Allowed : 14.34 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: 0.20 (0.17), residues: 2373 helix: 1.65 (0.28), residues: 408 sheet: 0.79 (0.18), residues: 768 loop : -0.86 (0.17), residues: 1197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 427 HIS 0.003 0.001 HIS A 216 PHE 0.016 0.001 PHE A 353 TYR 0.010 0.001 TYR K 34 ARG 0.002 0.000 ARG B 617 Details of bonding type rmsd link_NAG-ASN : bond 0.00255 ( 45) link_NAG-ASN : angle 2.45312 ( 135) link_BETA1-4 : bond 0.00494 ( 30) link_BETA1-4 : angle 1.21756 ( 90) link_ALPHA1-2 : bond 0.00245 ( 3) link_ALPHA1-2 : angle 1.67756 ( 9) link_ALPHA1-3 : bond 0.01020 ( 3) link_ALPHA1-3 : angle 1.63966 ( 9) hydrogen bonds : bond 0.04337 ( 739) hydrogen bonds : angle 4.30135 ( 2034) SS BOND : bond 0.00485 ( 42) SS BOND : angle 1.72804 ( 84) covalent geometry : bond 0.00256 (20478) covalent geometry : angle 0.52229 (27831) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4746 Ramachandran restraints generated. 2373 Oldfield, 0 Emsley, 2373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4746 Ramachandran restraints generated. 2373 Oldfield, 0 Emsley, 2373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 169 time to evaluate : 2.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 426 MET cc_start: 0.8154 (OUTLIER) cc_final: 0.6631 (tmm) REVERT: B 601 LYS cc_start: 0.8878 (mttp) cc_final: 0.8498 (mtmt) REVERT: C 492 GLU cc_start: 0.8820 (OUTLIER) cc_final: 0.8374 (mt-10) REVERT: C 500 ARG cc_start: 0.7826 (mtm-85) cc_final: 0.7554 (mtm-85) REVERT: D 654 GLU cc_start: 0.7419 (OUTLIER) cc_final: 0.7084 (mt-10) REVERT: E 168 LYS cc_start: 0.8567 (mmtt) cc_final: 0.7768 (mttt) REVERT: E 191 TYR cc_start: 0.9419 (m-80) cc_final: 0.9135 (m-80) REVERT: E 502 LYS cc_start: 0.8712 (ptmm) cc_final: 0.8146 (tttm) REVERT: G 100 SER cc_start: 0.7637 (OUTLIER) cc_final: 0.6887 (p) REVERT: H 97 THR cc_start: 0.7648 (p) cc_final: 0.7384 (p) REVERT: K 82 MET cc_start: 0.3568 (mmm) cc_final: 0.2053 (ptm) outliers start: 41 outliers final: 29 residues processed: 203 average time/residue: 0.4601 time to fit residues: 141.7628 Evaluate side-chains 202 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 169 time to evaluate : 2.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 381 GLU Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain B residue 633 LYS Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 166 ARG Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 355 ASN Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain C residue 492 GLU Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain D residue 654 GLU Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 205 CYS Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 333 VAL Chi-restraints excluded: chain E residue 355 ASN Chi-restraints excluded: chain G residue 100 SER Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain I residue 63 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 101 optimal weight: 0.5980 chunk 30 optimal weight: 3.9990 chunk 133 optimal weight: 0.7980 chunk 162 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 175 optimal weight: 2.9990 chunk 166 optimal weight: 0.6980 chunk 117 optimal weight: 2.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 ASN B 616 ASN C 355 ASN F 653 GLN H 100 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.187430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.123460 restraints weight = 20280.723| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 1.96 r_work: 0.2739 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 20601 Z= 0.145 Angle : 0.609 12.432 28158 Z= 0.296 Chirality : 0.044 0.291 3366 Planarity : 0.004 0.054 3447 Dihedral : 5.036 51.727 4266 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 1.87 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.44 % Favored : 97.43 % Rotamer: Outliers : 2.02 % Allowed : 14.57 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: 0.17 (0.17), residues: 2373 helix: 1.60 (0.28), residues: 408 sheet: 0.72 (0.18), residues: 774 loop : -0.84 (0.17), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 427 HIS 0.003 0.001 HIS A 216 PHE 0.018 0.001 PHE A 383 TYR 0.010 0.001 TYR I 91 ARG 0.002 0.000 ARG B 617 Details of bonding type rmsd link_NAG-ASN : bond 0.00257 ( 45) link_NAG-ASN : angle 2.45424 ( 135) link_BETA1-4 : bond 0.00509 ( 30) link_BETA1-4 : angle 1.21708 ( 90) link_ALPHA1-2 : bond 0.00326 ( 3) link_ALPHA1-2 : angle 1.70559 ( 9) link_ALPHA1-3 : bond 0.00968 ( 3) link_ALPHA1-3 : angle 1.62779 ( 9) hydrogen bonds : bond 0.04888 ( 739) hydrogen bonds : angle 4.32422 ( 2034) SS BOND : bond 0.00602 ( 42) SS BOND : angle 1.82953 ( 84) covalent geometry : bond 0.00354 (20478) covalent geometry : angle 0.57357 (27831) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4746 Ramachandran restraints generated. 2373 Oldfield, 0 Emsley, 2373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4746 Ramachandran restraints generated. 2373 Oldfield, 0 Emsley, 2373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 165 time to evaluate : 4.092 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 601 LYS cc_start: 0.8915 (mttp) cc_final: 0.8500 (mtmt) REVERT: C 117 LYS cc_start: 0.8329 (mttm) cc_final: 0.8124 (mttp) REVERT: C 492 GLU cc_start: 0.8807 (OUTLIER) cc_final: 0.8265 (mt-10) REVERT: C 500 ARG cc_start: 0.7941 (mtm-85) cc_final: 0.7726 (mtm-85) REVERT: D 654 GLU cc_start: 0.7502 (OUTLIER) cc_final: 0.7161 (mt-10) REVERT: E 168 LYS cc_start: 0.8624 (mmtt) cc_final: 0.7913 (mttt) REVERT: E 191 TYR cc_start: 0.9395 (m-80) cc_final: 0.9104 (m-80) REVERT: E 502 LYS cc_start: 0.8803 (ptmm) cc_final: 0.8291 (tttm) REVERT: G 100 SER cc_start: 0.8107 (OUTLIER) cc_final: 0.7453 (p) REVERT: H 97 THR cc_start: 0.7903 (p) cc_final: 0.7695 (p) REVERT: K 82 MET cc_start: 0.4242 (mmm) cc_final: 0.2287 (ptm) outliers start: 43 outliers final: 31 residues processed: 202 average time/residue: 0.3923 time to fit residues: 119.2306 Evaluate side-chains 199 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 165 time to evaluate : 2.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 381 GLU Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain B residue 633 LYS Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 166 ARG Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain C residue 492 GLU Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain D residue 654 GLU Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 205 CYS Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 355 ASN Chi-restraints excluded: chain F residue 613 SER Chi-restraints excluded: chain G residue 100 SER Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain I residue 63 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 144 optimal weight: 5.9990 chunk 194 optimal weight: 2.9990 chunk 145 optimal weight: 2.9990 chunk 163 optimal weight: 0.6980 chunk 37 optimal weight: 0.7980 chunk 222 optimal weight: 5.9990 chunk 166 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 193 optimal weight: 5.9990 chunk 52 optimal weight: 4.9990 chunk 230 optimal weight: 40.0000 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 ASN B 616 ASN C 67 ASN C 355 ASN G 71 GLN ** H 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.187214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.116338 restraints weight = 20252.112| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 2.82 r_work: 0.2696 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 20601 Z= 0.211 Angle : 0.696 13.276 28158 Z= 0.337 Chirality : 0.047 0.304 3366 Planarity : 0.005 0.056 3447 Dihedral : 5.241 45.108 4266 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 2.08 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.82 % Favored : 97.09 % Rotamer: Outliers : 2.07 % Allowed : 14.53 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: 0.01 (0.17), residues: 2373 helix: 1.36 (0.28), residues: 408 sheet: 0.65 (0.18), residues: 774 loop : -0.92 (0.17), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 427 HIS 0.003 0.001 HIS C 216 PHE 0.020 0.002 PHE A 383 TYR 0.010 0.002 TYR A 318 ARG 0.003 0.000 ARG B 617 Details of bonding type rmsd link_NAG-ASN : bond 0.00297 ( 45) link_NAG-ASN : angle 2.63244 ( 135) link_BETA1-4 : bond 0.00534 ( 30) link_BETA1-4 : angle 1.31017 ( 90) link_ALPHA1-2 : bond 0.00263 ( 3) link_ALPHA1-2 : angle 1.83328 ( 9) link_ALPHA1-3 : bond 0.00925 ( 3) link_ALPHA1-3 : angle 1.56212 ( 9) hydrogen bonds : bond 0.06048 ( 739) hydrogen bonds : angle 4.51457 ( 2034) SS BOND : bond 0.00725 ( 42) SS BOND : angle 2.09565 ( 84) covalent geometry : bond 0.00533 (20478) covalent geometry : angle 0.66059 (27831) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4746 Ramachandran restraints generated. 2373 Oldfield, 0 Emsley, 2373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4746 Ramachandran restraints generated. 2373 Oldfield, 0 Emsley, 2373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 170 time to evaluate : 2.150 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 ARG cc_start: 0.8661 (OUTLIER) cc_final: 0.8320 (mtt90) REVERT: B 601 LYS cc_start: 0.8941 (mttp) cc_final: 0.8500 (mtmt) REVERT: C 492 GLU cc_start: 0.8847 (OUTLIER) cc_final: 0.8319 (mt-10) REVERT: C 500 ARG cc_start: 0.7980 (mtm-85) cc_final: 0.7638 (mtm180) REVERT: D 654 GLU cc_start: 0.7464 (OUTLIER) cc_final: 0.7125 (mt-10) REVERT: E 168 LYS cc_start: 0.8611 (mmtt) cc_final: 0.7858 (mttt) REVERT: G 100 SER cc_start: 0.7662 (OUTLIER) cc_final: 0.6894 (p) REVERT: K 82 MET cc_start: 0.3622 (mmm) cc_final: 0.2047 (ptm) outliers start: 44 outliers final: 36 residues processed: 204 average time/residue: 0.3743 time to fit residues: 113.7275 Evaluate side-chains 209 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 169 time to evaluate : 2.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 277 ILE Chi-restraints excluded: chain A residue 325 ASP Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 381 GLU Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain B residue 633 LYS Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 77 THR Chi-restraints excluded: chain C residue 166 ARG Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 333 VAL Chi-restraints excluded: chain C residue 433 CYS Chi-restraints excluded: chain C residue 492 GLU Chi-restraints excluded: chain C residue 501 CYS Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain D residue 654 GLU Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 205 CYS Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 243 SER Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 355 ASN Chi-restraints excluded: chain F residue 613 SER Chi-restraints excluded: chain F residue 632 ASP Chi-restraints excluded: chain G residue 100 SER Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain I residue 63 LEU Chi-restraints excluded: chain L residue 97 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 107 optimal weight: 0.3980 chunk 209 optimal weight: 3.9990 chunk 109 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 223 optimal weight: 6.9990 chunk 165 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 184 optimal weight: 30.0000 chunk 150 optimal weight: 0.7980 chunk 113 optimal weight: 2.9990 chunk 219 optimal weight: 6.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 616 ASN C 355 ASN G 100CHIS ** H 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.187906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.117059 restraints weight = 20265.650| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 2.88 r_work: 0.2789 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.120 20601 Z= 0.243 Angle : 0.857 59.196 28158 Z= 0.457 Chirality : 0.047 0.306 3366 Planarity : 0.005 0.057 3447 Dihedral : 5.258 45.075 4266 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 2.02 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.82 % Favored : 97.09 % Rotamer: Outliers : 2.16 % Allowed : 14.39 % Favored : 83.45 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -0.01 (0.17), residues: 2373 helix: 1.34 (0.28), residues: 408 sheet: 0.65 (0.18), residues: 774 loop : -0.93 (0.17), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 427 HIS 0.004 0.001 HIS C 374 PHE 0.021 0.002 PHE A 383 TYR 0.011 0.002 TYR E 384 ARG 0.003 0.000 ARG E 298 Details of bonding type rmsd link_NAG-ASN : bond 0.00295 ( 45) link_NAG-ASN : angle 2.62922 ( 135) link_BETA1-4 : bond 0.00561 ( 30) link_BETA1-4 : angle 1.31687 ( 90) link_ALPHA1-2 : bond 0.00188 ( 3) link_ALPHA1-2 : angle 1.82719 ( 9) link_ALPHA1-3 : bond 0.00933 ( 3) link_ALPHA1-3 : angle 1.56746 ( 9) hydrogen bonds : bond 0.06113 ( 739) hydrogen bonds : angle 4.51512 ( 2034) SS BOND : bond 0.00737 ( 42) SS BOND : angle 2.07501 ( 84) covalent geometry : bond 0.00586 (20478) covalent geometry : angle 0.82962 (27831) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11806.06 seconds wall clock time: 210 minutes 39.41 seconds (12639.41 seconds total)