Starting phenix.real_space_refine on Tue Nov 19 18:34:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tl3_41360/11_2024/8tl3_41360.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tl3_41360/11_2024/8tl3_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tl3_41360/11_2024/8tl3_41360.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tl3_41360/11_2024/8tl3_41360.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tl3_41360/11_2024/8tl3_41360.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tl3_41360/11_2024/8tl3_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-5513/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: 13.29, per 1000 atoms: 0.66 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: 5.74 Conformation dependent library (CDL) restraints added in 2.3 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: 2.85 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: 8.04 Time building geometry restraints manager: 6.55 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'H' selection = chain 'J' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain '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: 8.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.780 Check model and map are aligned: 0.160 Set scattering table: 0.200 Process input model: 48.190 Find NCS groups from input model: 0.970 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.840 ------------------------------------------------------------------------------- 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 20478 Z= 0.273 Angle : 0.623 7.058 27831 Z= 0.296 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 *********************** 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 : 2.392 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: 0.3860 time to fit residues: 100.1471 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 : 3.811 ------------------------------------------------------------------------------- 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: 0.9990 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: 0.8242 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.0953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20478 Z= 0.209 Angle : 0.548 8.200 27831 Z= 0.278 Chirality : 0.044 0.268 3366 Planarity : 0.004 0.056 3447 Dihedral : 8.162 76.351 4268 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 0.96 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.77 % Favored : 98.19 % Rotamer: Outliers : 1.74 % Allowed : 10.20 % Favored : 88.06 % 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: 0.48 (0.17), residues: 2373 helix: 2.17 (0.29), residues: 408 sheet: 0.67 (0.18), residues: 747 loop : -0.53 (0.17), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 45 HIS 0.004 0.001 HIS C 374 PHE 0.017 0.001 PHE A 383 TYR 0.010 0.001 TYR L 49 ARG 0.006 0.000 ARG C 444 *********************** 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 221 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 184 time to evaluate : 1.611 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: 0.9051 (mttp) cc_final: 0.8676 (mtmt) REVERT: C 360 ARG cc_start: 0.8242 (mmm-85) cc_final: 0.8020 (ttp80) REVERT: C 502 LYS cc_start: 0.8139 (ptmm) cc_final: 0.7762 (tttm) REVERT: D 607 ASN cc_start: 0.8323 (t0) cc_final: 0.8024 (t0) REVERT: E 475 MET cc_start: 0.8631 (tpp) cc_final: 0.8371 (mmp) REVERT: F 633 LYS cc_start: 0.8553 (ttmm) cc_final: 0.8330 (mttt) REVERT: I 76 ASN cc_start: 0.5241 (OUTLIER) cc_final: 0.4849 (m110) REVERT: K 82 MET cc_start: 0.4266 (mmm) cc_final: 0.2793 (ptm) outliers start: 37 outliers final: 19 residues processed: 214 average time/residue: 0.2616 time to fit residues: 83.5431 Evaluate side-chains 196 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 176 time to evaluate : 1.574 ------------------------------------------------------------------------------- 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 184 ILE 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 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 121 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 181 optimal weight: 1.9990 chunk 148 optimal weight: 5.9990 chunk 60 optimal weight: 8.9990 chunk 218 optimal weight: 30.0000 chunk 235 optimal weight: 30.0000 chunk 194 optimal weight: 0.5980 chunk 216 optimal weight: 7.9990 chunk 74 optimal weight: 0.6980 chunk 175 optimal weight: 8.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- 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 85 HIS E 355 ASN F 652 GLN F 653 GLN F 658 GLN K 35AASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 20478 Z= 0.394 Angle : 0.707 14.142 27831 Z= 0.351 Chirality : 0.049 0.282 3366 Planarity : 0.005 0.056 3447 Dihedral : 7.261 62.044 4266 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 1.65 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.65 % Favored : 97.30 % Rotamer: Outliers : 2.30 % Allowed : 11.05 % Favored : 86.65 % 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: 0.08 (0.17), residues: 2373 helix: 1.55 (0.28), residues: 408 sheet: 0.58 (0.18), residues: 774 loop : -0.82 (0.17), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 45 HIS 0.006 0.001 HIS C 85 PHE 0.023 0.002 PHE A 383 TYR 0.011 0.002 TYR I 91 ARG 0.005 0.001 ARG C 444 *********************** 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 221 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 172 time to evaluate : 2.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 ARG cc_start: 0.8583 (OUTLIER) cc_final: 0.8297 (mtt90) REVERT: B 601 LYS cc_start: 0.9106 (mttp) cc_final: 0.8640 (mtmt) REVERT: D 654 GLU cc_start: 0.7714 (OUTLIER) cc_final: 0.7288 (mt-10) REVERT: I 76 ASN cc_start: 0.5520 (OUTLIER) cc_final: 0.5207 (m110) REVERT: K 82 MET cc_start: 0.4418 (mmm) cc_final: 0.2833 (ptm) outliers start: 49 outliers final: 24 residues processed: 208 average time/residue: 0.3757 time to fit residues: 116.1645 Evaluate side-chains 199 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 172 time to evaluate : 2.249 ------------------------------------------------------------------------------- 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 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 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 433 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 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 H residue 97 THR 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 215 optimal weight: 9.9990 chunk 164 optimal weight: 0.0010 chunk 113 optimal weight: 1.9990 chunk 24 optimal weight: 0.3980 chunk 104 optimal weight: 0.9980 chunk 146 optimal weight: 0.9980 chunk 219 optimal weight: 10.0000 chunk 231 optimal weight: 3.9990 chunk 114 optimal weight: 2.9990 chunk 207 optimal weight: 9.9990 chunk 62 optimal weight: 0.9980 overall best weight: 0.6786 ------------------------------------------------------------------------------- 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 355 ASN F 591 GLN F 653 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 20478 Z= 0.181 Angle : 0.534 9.232 27831 Z= 0.273 Chirality : 0.043 0.278 3366 Planarity : 0.004 0.055 3447 Dihedral : 6.283 57.625 4266 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 1.44 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.36 % Favored : 97.60 % Rotamer: Outliers : 2.26 % Allowed : 11.99 % Favored : 85.75 % 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: 0.19 (0.17), residues: 2373 helix: 1.73 (0.28), residues: 408 sheet: 0.60 (0.18), residues: 780 loop : -0.77 (0.17), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 427 HIS 0.003 0.001 HIS C 216 PHE 0.016 0.001 PHE A 383 TYR 0.010 0.001 TYR K 34 ARG 0.003 0.000 ARG C 444 *********************** 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 222 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 174 time to evaluate : 2.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 ARG cc_start: 0.8548 (OUTLIER) cc_final: 0.8241 (mtt90) REVERT: B 601 LYS cc_start: 0.9016 (mttp) cc_final: 0.8563 (mtmt) REVERT: C 492 GLU cc_start: 0.8722 (OUTLIER) cc_final: 0.8150 (mt-10) REVERT: C 502 LYS cc_start: 0.8810 (ptmm) cc_final: 0.8517 (tttm) REVERT: E 191 TYR cc_start: 0.9285 (m-80) cc_final: 0.9030 (m-80) REVERT: I 76 ASN cc_start: 0.5515 (OUTLIER) cc_final: 0.5198 (m110) REVERT: K 82 MET cc_start: 0.4373 (mmm) cc_final: 0.2826 (ptm) outliers start: 48 outliers final: 27 residues processed: 212 average time/residue: 0.3998 time to fit residues: 127.1715 Evaluate side-chains 202 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 172 time to evaluate : 2.170 ------------------------------------------------------------------------------- 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 B residue 612 SER Chi-restraints excluded: chain C residue 54 CYS 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 213 ILE 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 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 F residue 632 ASP Chi-restraints excluded: chain G residue 100 SER Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain I residue 63 LEU Chi-restraints excluded: chain I residue 76 ASN 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 193 optimal weight: 20.0000 chunk 131 optimal weight: 0.8980 chunk 3 optimal weight: 0.5980 chunk 172 optimal weight: 20.0000 chunk 95 optimal weight: 2.9990 chunk 197 optimal weight: 9.9990 chunk 160 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 118 optimal weight: 3.9990 chunk 208 optimal weight: 20.0000 chunk 58 optimal weight: 0.8980 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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 E 114 GLN E 355 ASN J 38 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 20478 Z= 0.312 Angle : 0.627 11.321 27831 Z= 0.312 Chirality : 0.046 0.292 3366 Planarity : 0.004 0.057 3447 Dihedral : 6.023 59.823 4266 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 1.70 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.49 % Favored : 97.39 % Rotamer: Outliers : 2.77 % Allowed : 12.36 % 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: 0.08 (0.17), residues: 2373 helix: 1.51 (0.28), residues: 408 sheet: 0.58 (0.18), residues: 780 loop : -0.82 (0.17), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 427 HIS 0.004 0.001 HIS C 85 PHE 0.021 0.002 PHE A 383 TYR 0.010 0.002 TYR I 91 ARG 0.002 0.000 ARG C 444 *********************** 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 227 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 168 time to evaluate : 2.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 ARG cc_start: 0.8590 (OUTLIER) cc_final: 0.8287 (mtt90) REVERT: B 601 LYS cc_start: 0.9066 (mttp) cc_final: 0.8605 (mtmt) REVERT: C 492 GLU cc_start: 0.8743 (OUTLIER) cc_final: 0.8159 (mt-10) REVERT: C 502 LYS cc_start: 0.8921 (ptmm) cc_final: 0.8679 (tttm) REVERT: E 168 LYS cc_start: 0.8651 (mmtt) cc_final: 0.8098 (mttt) REVERT: I 76 ASN cc_start: 0.5620 (OUTLIER) cc_final: 0.5342 (m110) REVERT: K 82 MET cc_start: 0.4363 (mmm) cc_final: 0.2790 (ptm) outliers start: 59 outliers final: 41 residues processed: 212 average time/residue: 0.3643 time to fit residues: 115.5342 Evaluate side-chains 212 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 168 time to evaluate : 2.243 ------------------------------------------------------------------------------- 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 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 202 THR Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 213 ILE 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 607 ASN 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 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 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 I residue 63 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 78 optimal weight: 1.9990 chunk 208 optimal weight: 10.0000 chunk 45 optimal weight: 1.9990 chunk 136 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 232 optimal weight: 4.9990 chunk 192 optimal weight: 6.9990 chunk 107 optimal weight: 0.0980 chunk 19 optimal weight: 0.0970 chunk 76 optimal weight: 3.9990 chunk 121 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 ASN A 355 ASN B 616 ASN C 355 ASN D 607 ASN E 114 GLN E 355 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 20478 Z= 0.271 Angle : 0.595 10.717 27831 Z= 0.299 Chirality : 0.045 0.291 3366 Planarity : 0.004 0.056 3447 Dihedral : 5.771 59.028 4266 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 1.80 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.49 % Favored : 97.39 % Rotamer: Outliers : 2.77 % Allowed : 12.93 % Favored : 84.30 % 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: 1.49 (0.28), residues: 408 sheet: 0.57 (0.18), residues: 780 loop : -0.85 (0.17), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 427 HIS 0.003 0.001 HIS A 216 PHE 0.019 0.001 PHE A 383 TYR 0.010 0.001 TYR I 91 ARG 0.002 0.000 ARG B 617 *********************** 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 225 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 166 time to evaluate : 2.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 ARG cc_start: 0.8580 (OUTLIER) cc_final: 0.8279 (mtt90) REVERT: B 601 LYS cc_start: 0.9049 (mttp) cc_final: 0.8595 (mtmt) REVERT: C 492 GLU cc_start: 0.8753 (OUTLIER) cc_final: 0.8174 (mt-10) REVERT: D 654 GLU cc_start: 0.7695 (OUTLIER) cc_final: 0.7311 (mt-10) REVERT: E 168 LYS cc_start: 0.8689 (mmtt) cc_final: 0.8114 (mttt) REVERT: I 76 ASN cc_start: 0.5597 (OUTLIER) cc_final: 0.5292 (m110) REVERT: K 82 MET cc_start: 0.4361 (mmm) cc_final: 0.2792 (ptm) outliers start: 59 outliers final: 38 residues processed: 212 average time/residue: 0.3636 time to fit residues: 115.1874 Evaluate side-chains 206 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 164 time to evaluate : 2.277 ------------------------------------------------------------------------------- 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 381 GLU Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain B residue 612 SER 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 202 THR Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 213 ILE 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 607 ASN 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 223 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 132 optimal weight: 4.9990 chunk 169 optimal weight: 1.9990 chunk 131 optimal weight: 0.7980 chunk 195 optimal weight: 10.0000 chunk 129 optimal weight: 1.9990 chunk 231 optimal weight: 5.9990 chunk 144 optimal weight: 4.9990 chunk 141 optimal weight: 4.9990 chunk 106 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- 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 D 607 ASN E 114 GLN E 355 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 20478 Z= 0.320 Angle : 0.628 11.763 27831 Z= 0.313 Chirality : 0.046 0.297 3366 Planarity : 0.004 0.057 3447 Dihedral : 5.654 56.788 4266 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 1.87 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.70 % Favored : 97.18 % Rotamer: Outliers : 2.82 % Allowed : 13.07 % Favored : 84.11 % 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: -0.02 (0.17), residues: 2373 helix: 1.39 (0.28), residues: 408 sheet: 0.55 (0.18), residues: 780 loop : -0.91 (0.17), residues: 1185 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 0.021 0.002 PHE A 383 TYR 0.010 0.002 TYR I 91 ARG 0.003 0.000 ARG B 617 *********************** 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 229 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 169 time to evaluate : 2.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 ARG cc_start: 0.8592 (OUTLIER) cc_final: 0.8299 (mtt90) REVERT: B 601 LYS cc_start: 0.9089 (mttp) cc_final: 0.8635 (mtmt) REVERT: B 619 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8360 (mp) REVERT: C 492 GLU cc_start: 0.8777 (OUTLIER) cc_final: 0.8187 (mt-10) REVERT: D 654 GLU cc_start: 0.7706 (OUTLIER) cc_final: 0.7333 (mt-10) REVERT: E 168 LYS cc_start: 0.8693 (mmtt) cc_final: 0.8094 (mttt) REVERT: I 76 ASN cc_start: 0.5744 (OUTLIER) cc_final: 0.5459 (m110) REVERT: K 82 MET cc_start: 0.4395 (mmm) cc_final: 0.2822 (ptm) outliers start: 60 outliers final: 39 residues processed: 215 average time/residue: 0.3672 time to fit residues: 117.2127 Evaluate side-chains 212 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 168 time to evaluate : 2.266 ------------------------------------------------------------------------------- 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 A residue 426 MET Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain B residue 619 LEU 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 213 ILE 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 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 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 I residue 76 ASN Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain L residue 72 THR 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 143 optimal weight: 0.6980 chunk 92 optimal weight: 0.6980 chunk 138 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 147 optimal weight: 1.9990 chunk 157 optimal weight: 0.2980 chunk 114 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 181 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 E 114 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 20478 Z= 0.184 Angle : 0.534 11.932 27831 Z= 0.272 Chirality : 0.043 0.287 3366 Planarity : 0.004 0.054 3447 Dihedral : 5.246 54.445 4266 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 1.75 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.40 % Favored : 97.47 % Rotamer: Outliers : 2.26 % Allowed : 13.96 % Favored : 83.78 % 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: 0.19 (0.17), residues: 2373 helix: 1.63 (0.28), residues: 408 sheet: 0.75 (0.18), residues: 780 loop : -0.85 (0.17), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 427 HIS 0.003 0.001 HIS A 216 PHE 0.016 0.001 PHE A 53 TYR 0.010 0.001 TYR K 34 ARG 0.002 0.000 ARG B 588 *********************** 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 215 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 167 time to evaluate : 2.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 ARG cc_start: 0.8561 (OUTLIER) cc_final: 0.8270 (mtt90) REVERT: A 426 MET cc_start: 0.7976 (OUTLIER) cc_final: 0.6490 (tmm) REVERT: B 601 LYS cc_start: 0.9047 (mttp) cc_final: 0.8607 (mtmt) REVERT: B 619 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8333 (mp) REVERT: C 492 GLU cc_start: 0.8744 (OUTLIER) cc_final: 0.8160 (mt-10) REVERT: D 654 GLU cc_start: 0.7696 (OUTLIER) cc_final: 0.7320 (mt-10) REVERT: E 168 LYS cc_start: 0.8689 (mmtt) cc_final: 0.8120 (mttt) REVERT: E 191 TYR cc_start: 0.9268 (m-80) cc_final: 0.9023 (m-80) REVERT: E 502 LYS cc_start: 0.8947 (ptmm) cc_final: 0.8460 (tttm) REVERT: I 76 ASN cc_start: 0.5778 (OUTLIER) cc_final: 0.5488 (m110) REVERT: K 82 MET cc_start: 0.4404 (mmm) cc_final: 0.2839 (ptm) outliers start: 48 outliers final: 36 residues processed: 205 average time/residue: 0.3696 time to fit residues: 114.2702 Evaluate side-chains 207 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 165 time to evaluate : 2.204 ------------------------------------------------------------------------------- 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 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 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 213 ILE 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 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 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 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 I residue 76 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 210 optimal weight: 2.9990 chunk 221 optimal weight: 3.9990 chunk 202 optimal weight: 0.0770 chunk 215 optimal weight: 8.9990 chunk 129 optimal weight: 2.9990 chunk 93 optimal weight: 0.5980 chunk 169 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 194 optimal weight: 5.9990 chunk 203 optimal weight: 10.0000 chunk 214 optimal weight: 5.9990 overall best weight: 1.9344 ------------------------------------------------------------------------------- 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 E 114 GLN F 653 GLN G 71 GLN H 100 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.2417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 20478 Z= 0.405 Angle : 0.711 12.974 27831 Z= 0.350 Chirality : 0.049 0.307 3366 Planarity : 0.005 0.057 3447 Dihedral : 5.502 50.764 4266 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 1.87 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.70 % Favored : 97.22 % Rotamer: Outliers : 2.49 % Allowed : 14.10 % 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: -0.12 (0.17), residues: 2373 helix: 1.23 (0.28), residues: 408 sheet: 0.52 (0.18), residues: 783 loop : -0.96 (0.17), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 427 HIS 0.004 0.001 HIS C 85 PHE 0.023 0.002 PHE A 383 TYR 0.012 0.002 TYR E 384 ARG 0.004 0.000 ARG E 298 *********************** 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 224 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 171 time to evaluate : 2.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 ARG cc_start: 0.8570 (OUTLIER) cc_final: 0.8249 (mtt90) REVERT: B 601 LYS cc_start: 0.9100 (mttp) cc_final: 0.8721 (mtmt) REVERT: B 619 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8361 (mp) REVERT: C 492 GLU cc_start: 0.8817 (OUTLIER) cc_final: 0.8216 (mt-10) REVERT: C 501 CYS cc_start: 0.7571 (OUTLIER) cc_final: 0.7138 (t) REVERT: D 654 GLU cc_start: 0.7736 (OUTLIER) cc_final: 0.7391 (mt-10) REVERT: F 601 LYS cc_start: 0.9071 (OUTLIER) cc_final: 0.8753 (mttm) REVERT: I 76 ASN cc_start: 0.5935 (OUTLIER) cc_final: 0.5647 (m-40) REVERT: K 82 MET cc_start: 0.4414 (mmm) cc_final: 0.2834 (ptm) outliers start: 53 outliers final: 37 residues processed: 212 average time/residue: 0.3661 time to fit residues: 116.5330 Evaluate side-chains 215 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 171 time to evaluate : 2.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 612 SER Chi-restraints excluded: chain B residue 619 LEU 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 213 ILE 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 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 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 F residue 601 LYS 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 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 I residue 76 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 141 optimal weight: 3.9990 chunk 227 optimal weight: 1.9990 chunk 139 optimal weight: 1.9990 chunk 108 optimal weight: 0.8980 chunk 158 optimal weight: 0.3980 chunk 239 optimal weight: 20.0000 chunk 220 optimal weight: 0.7980 chunk 190 optimal weight: 10.0000 chunk 19 optimal weight: 0.4980 chunk 147 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 E 114 GLN ** H 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 20478 Z= 0.220 Angle : 0.567 11.941 27831 Z= 0.288 Chirality : 0.044 0.293 3366 Planarity : 0.004 0.056 3447 Dihedral : 5.217 46.572 4266 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 2.18 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.70 % Favored : 97.22 % Rotamer: Outliers : 2.12 % Allowed : 14.57 % Favored : 83.31 % 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: 1.50 (0.28), residues: 408 sheet: 0.65 (0.18), residues: 774 loop : -0.94 (0.17), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 427 HIS 0.003 0.001 HIS A 216 PHE 0.017 0.001 PHE C 383 TYR 0.010 0.001 TYR G 91 ARG 0.002 0.000 ARG B 617 ********************** 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 211 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 166 time to evaluate : 2.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 ARG cc_start: 0.8566 (OUTLIER) cc_final: 0.8265 (mtt90) REVERT: A 426 MET cc_start: 0.8035 (OUTLIER) cc_final: 0.6497 (tmm) REVERT: B 601 LYS cc_start: 0.9046 (mttp) cc_final: 0.8598 (mtmt) REVERT: B 619 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8324 (mp) REVERT: C 492 GLU cc_start: 0.8778 (OUTLIER) cc_final: 0.8196 (mt-10) REVERT: C 501 CYS cc_start: 0.7482 (OUTLIER) cc_final: 0.7133 (t) REVERT: D 654 GLU cc_start: 0.7684 (OUTLIER) cc_final: 0.7340 (mt-10) REVERT: E 168 LYS cc_start: 0.8687 (mmtt) cc_final: 0.8108 (mttt) REVERT: E 191 TYR cc_start: 0.9290 (m-80) cc_final: 0.9039 (m-80) REVERT: I 76 ASN cc_start: 0.5899 (OUTLIER) cc_final: 0.5572 (m110) REVERT: K 82 MET cc_start: 0.4413 (mmm) cc_final: 0.2848 (ptm) outliers start: 45 outliers final: 34 residues processed: 201 average time/residue: 0.3679 time to fit residues: 110.8358 Evaluate side-chains 207 residues out of total 2127 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 166 time to evaluate : 2.255 ------------------------------------------------------------------------------- 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 612 SER Chi-restraints excluded: chain B residue 619 LEU 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 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 F residue 613 SER Chi-restraints excluded: chain F residue 626 MET Chi-restraints excluded: chain F residue 632 ASP 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 I residue 76 ASN Chi-restraints excluded: chain I residue 97 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 151 optimal weight: 1.9990 chunk 202 optimal weight: 20.0000 chunk 58 optimal weight: 0.5980 chunk 175 optimal weight: 20.0000 chunk 28 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 190 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 chunk 195 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 35 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 ASN B 616 ASN C 355 ASN E 114 GLN ** H 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.190013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.107512 restraints weight = 20093.234| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 2.56 r_work: 0.2740 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2581 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.2345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 20478 Z= 0.208 Angle : 0.556 12.355 27831 Z= 0.281 Chirality : 0.044 0.291 3366 Planarity : 0.004 0.055 3447 Dihedral : 4.994 41.890 4266 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 1.95 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.44 % Favored : 97.47 % Rotamer: Outliers : 1.93 % Allowed : 14.81 % Favored : 83.26 % 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: 0.15 (0.17), residues: 2373 helix: 1.59 (0.28), residues: 408 sheet: 0.72 (0.18), residues: 783 loop : -0.87 (0.17), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 427 HIS 0.003 0.001 HIS A 216 PHE 0.017 0.001 PHE C 383 TYR 0.010 0.001 TYR G 91 ARG 0.002 0.000 ARG B 617 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4440.46 seconds wall clock time: 149 minutes 3.19 seconds (8943.19 seconds total)