Starting phenix.real_space_refine on Mon Feb 19 05:03:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dx2_30893/02_2024/7dx2_30893.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dx2_30893/02_2024/7dx2_30893.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dx2_30893/02_2024/7dx2_30893.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dx2_30893/02_2024/7dx2_30893.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dx2_30893/02_2024/7dx2_30893.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dx2_30893/02_2024/7dx2_30893.pdb" } resolution = 3.3 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= 0.004 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 102 5.16 5 C 15094 2.51 5 N 3858 2.21 5 O 4686 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 156": "OE1" <-> "OE2" Residue "A ARG 158": "NH1" <-> "NH2" Residue "A ARG 190": "NH1" <-> "NH2" Residue "A GLU 191": "OE1" <-> "OE2" Residue "A ARG 214": "NH1" <-> "NH2" Residue "A ARG 246": "NH1" <-> "NH2" Residue "A GLU 298": "OE1" <-> "OE2" Residue "A ARG 319": "NH1" <-> "NH2" Residue "A ARG 328": "NH1" <-> "NH2" Residue "A ARG 346": "NH1" <-> "NH2" Residue "A ARG 355": "NH1" <-> "NH2" Residue "A ARG 357": "NH1" <-> "NH2" Residue "A ARG 403": "NH1" <-> "NH2" Residue "A GLU 406": "OE1" <-> "OE2" Residue "A ARG 408": "NH1" <-> "NH2" Residue "A GLU 554": "OE1" <-> "OE2" Residue "A GLU 583": "OE1" <-> "OE2" Residue "A GLU 654": "OE1" <-> "OE2" Residue "A GLU 725": "OE1" <-> "OE2" Residue "A GLU 748": "OE1" <-> "OE2" Residue "A ARG 815": "NH1" <-> "NH2" Residue "A GLU 819": "OE1" <-> "OE2" Residue "A ARG 1107": "NH1" <-> "NH2" Residue "A GLU 1144": "OE1" <-> "OE2" Residue "B PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 156": "OE1" <-> "OE2" Residue "B ARG 158": "NH1" <-> "NH2" Residue "B ARG 190": "NH1" <-> "NH2" Residue "B GLU 191": "OE1" <-> "OE2" Residue "B ARG 214": "NH1" <-> "NH2" Residue "B ARG 246": "NH1" <-> "NH2" Residue "B GLU 298": "OE1" <-> "OE2" Residue "B ARG 319": "NH1" <-> "NH2" Residue "B ARG 328": "NH1" <-> "NH2" Residue "B ARG 346": "NH1" <-> "NH2" Residue "B ARG 355": "NH1" <-> "NH2" Residue "B ARG 357": "NH1" <-> "NH2" Residue "B ARG 403": "NH1" <-> "NH2" Residue "B GLU 406": "OE1" <-> "OE2" Residue "B ARG 408": "NH1" <-> "NH2" Residue "B GLU 554": "OE1" <-> "OE2" Residue "B GLU 583": "OE1" <-> "OE2" Residue "B GLU 654": "OE1" <-> "OE2" Residue "B GLU 725": "OE1" <-> "OE2" Residue "B GLU 748": "OE1" <-> "OE2" Residue "B ARG 815": "NH1" <-> "NH2" Residue "B GLU 918": "OE1" <-> "OE2" Residue "B GLU 1072": "OE1" <-> "OE2" Residue "B GLU 1144": "OE1" <-> "OE2" Residue "C PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 156": "OE1" <-> "OE2" Residue "C ARG 158": "NH1" <-> "NH2" Residue "C ARG 190": "NH1" <-> "NH2" Residue "C GLU 191": "OE1" <-> "OE2" Residue "C ARG 214": "NH1" <-> "NH2" Residue "C ARG 246": "NH1" <-> "NH2" Residue "C GLU 298": "OE1" <-> "OE2" Residue "C ARG 319": "NH1" <-> "NH2" Residue "C ARG 328": "NH1" <-> "NH2" Residue "C ARG 346": "NH1" <-> "NH2" Residue "C ARG 355": "NH1" <-> "NH2" Residue "C ARG 403": "NH1" <-> "NH2" Residue "C GLU 406": "OE1" <-> "OE2" Residue "C ARG 408": "NH1" <-> "NH2" Residue "C GLU 554": "OE1" <-> "OE2" Residue "C GLU 583": "OE1" <-> "OE2" Residue "C GLU 654": "OE1" <-> "OE2" Residue "C GLU 702": "OE1" <-> "OE2" Residue "C GLU 725": "OE1" <-> "OE2" Residue "C ARG 815": "NH1" <-> "NH2" Residue "C GLU 990": "OE1" <-> "OE2" Residue "C GLU 1031": "OE1" <-> "OE2" Residue "C GLU 1072": "OE1" <-> "OE2" Residue "C PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 23740 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 7586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 972, 7586 Classifications: {'peptide': 972} Link IDs: {'PTRANS': 48, 'TRANS': 923} Chain breaks: 9 Chain: "B" Number of atoms: 7580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 971, 7580 Classifications: {'peptide': 971} Link IDs: {'PTRANS': 48, 'TRANS': 922} Chain breaks: 9 Chain: "C" Number of atoms: 7580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 971, 7580 Classifications: {'peptide': 971} Link IDs: {'PTRANS': 48, 'TRANS': 922} Chain breaks: 9 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: 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: "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: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 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: 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: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 12.53, per 1000 atoms: 0.53 Number of scatterers: 23740 At special positions: 0 Unit cell: (139.136, 154.354, 169.572, 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 102 16.00 O 4686 8.00 N 3858 7.00 C 15094 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.17 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.11 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.16 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.05 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.04 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.04 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.55 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.12 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.05 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.05 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.04 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.12 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.17 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.51 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.34 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.05 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.04 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=1.98 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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 BETA1-4 " NAG B1409 " - " NAG B1410 " " 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 K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " 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 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-ASN " NAG A1401 " - " ASN A 61 " " NAG A1402 " - " ASN A 122 " " NAG A1403 " - " ASN A 165 " " NAG A1404 " - " ASN A 234 " " NAG A1405 " - " ASN A 282 " " NAG A1406 " - " ASN A 603 " " NAG A1407 " - " ASN A 616 " " NAG A1408 " - " ASN A 657 " " NAG A1409 " - " ASN A 709 " " NAG B1401 " - " ASN B 61 " " NAG B1402 " - " ASN B 122 " " NAG B1403 " - " ASN B 165 " " NAG B1404 " - " ASN B 234 " " NAG B1405 " - " ASN B 282 " " NAG B1406 " - " ASN B 603 " " NAG B1407 " - " ASN B 616 " " NAG B1408 " - " ASN B 657 " " NAG B1409 " - " ASN B1074 " " NAG C1401 " - " ASN C 61 " " NAG C1402 " - " ASN C 122 " " NAG C1403 " - " ASN C 165 " " NAG C1404 " - " ASN C 234 " " NAG C1405 " - " ASN C 282 " " NAG C1406 " - " ASN C 603 " " NAG C1407 " - " ASN C 616 " " NAG C1408 " - " ASN C 657 " " NAG D 1 " - " ASN A 331 " " NAG E 1 " - " ASN A 343 " " NAG F 1 " - " ASN A 717 " " NAG G 1 " - " ASN A 801 " " NAG H 1 " - " ASN A1074 " " NAG I 1 " - " ASN A1098 " " NAG J 1 " - " ASN A1134 " " NAG K 1 " - " ASN B 331 " " NAG L 1 " - " ASN B 343 " " NAG M 1 " - " ASN B 709 " " NAG N 1 " - " ASN B 717 " " NAG O 1 " - " ASN B 801 " " NAG P 1 " - " ASN B1098 " " NAG Q 1 " - " ASN B1134 " " NAG R 1 " - " ASN C 331 " " NAG S 1 " - " ASN C 343 " " NAG T 1 " - " ASN C 709 " " NAG U 1 " - " ASN C 717 " " NAG V 1 " - " ASN C 801 " " NAG W 1 " - " ASN C1074 " " NAG X 1 " - " ASN C1098 " " NAG Y 1 " - " ASN C1134 " Time building additional restraints: 9.35 Conformation dependent library (CDL) restraints added in 4.3 seconds 5708 Ramachandran restraints generated. 2854 Oldfield, 0 Emsley, 2854 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5462 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 41 sheets defined 24.8% alpha, 28.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.72 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 364 through 370 removed outlier: 4.074A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 390 removed outlier: 4.257A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASP A 389 " --> pdb=" O LYS A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 removed outlier: 3.624A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 removed outlier: 3.738A pdb=" N TYR A 421 " --> pdb=" O LYS A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.629A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.773A pdb=" N ASN A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU A 773 " --> pdb=" O GLY A 769 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN A 774 " --> pdb=" O ILE A 770 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 815 removed outlier: 3.635A pdb=" N LYS A 814 " --> pdb=" O LYS A 811 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG A 815 " --> pdb=" O PRO A 812 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 811 through 815' Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.647A pdb=" N LEU A 821 " --> pdb=" O PHE A 817 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.574A pdb=" N THR A 883 " --> pdb=" O ALA A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 918 removed outlier: 3.993A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 940 removed outlier: 3.626A pdb=" N LYS A 933 " --> pdb=" O SER A 929 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 964 removed outlier: 3.878A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 981 Processing helix chain 'A' and resid 987 through 1033 removed outlier: 4.061A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA A1020 " --> pdb=" O ALA A1016 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.648A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 364 through 370 removed outlier: 3.873A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 390 removed outlier: 4.257A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASP B 389 " --> pdb=" O LYS B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 removed outlier: 3.623A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 removed outlier: 3.737A pdb=" N TYR B 421 " --> pdb=" O LYS B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 747 through 754 removed outlier: 3.695A pdb=" N ASN B 751 " --> pdb=" O THR B 747 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.963A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS B 776 " --> pdb=" O VAL B 772 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 823 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.544A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 939 removed outlier: 3.605A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.009A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU B 962 " --> pdb=" O ALA B 958 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL B 963 " --> pdb=" O LEU B 959 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.245A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER B1021 " --> pdb=" O GLU B1017 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL B1033 " --> pdb=" O MET B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1145 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 364 through 370 removed outlier: 4.074A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 390 removed outlier: 4.258A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASP C 389 " --> pdb=" O LYS C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 removed outlier: 3.623A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.737A pdb=" N TYR C 421 " --> pdb=" O LYS C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.716A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.561A pdb=" N ILE C 770 " --> pdb=" O ALA C 766 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLN C 774 " --> pdb=" O ILE C 770 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS C 776 " --> pdb=" O VAL C 772 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.605A pdb=" N LEU C 821 " --> pdb=" O PHE C 817 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 919 through 939 removed outlier: 3.590A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.356A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR C 961 " --> pdb=" O GLN C 957 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 977 through 982 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.221A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA C1016 " --> pdb=" O LEU C1012 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.060A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 49 through 55 removed outlier: 3.857A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA4, first strand: chain 'A' and resid 116 through 121 removed outlier: 3.730A pdb=" N CYS A 131 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N ILE A 128 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N PHE A 168 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N VAL A 130 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N CYS A 166 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLN A 134 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N SER A 162 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 318 removed outlier: 3.946A pdb=" N GLY A 311 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N THR A 599 " --> pdb=" O GLY A 311 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.338A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 356 through 358 removed outlier: 3.543A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 448 through 453 removed outlier: 5.864A pdb=" N TYR A 449 " --> pdb=" O PHE A 497 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N PHE A 497 " --> pdb=" O TYR A 449 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N TYR A 451 " --> pdb=" O TYR A 495 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.790A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 9.182A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N SER A 673 " --> pdb=" O ILE A 693 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TYR A 695 " --> pdb=" O CYS A 671 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.588A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY A1059 " --> pdb=" O ALA A1056 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.588A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N GLN A1106 " --> pdb=" O GLU A1111 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N GLU A1111 " --> pdb=" O GLN A1106 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.506A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 788 through 790 Processing sheet with id=AB5, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.714A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.060A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 49 through 55 removed outlier: 3.856A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AB9, first strand: chain 'B' and resid 116 through 121 removed outlier: 3.730A pdb=" N CYS B 131 " --> pdb=" O SER B 116 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N ILE B 128 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N PHE B 168 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N VAL B 130 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N CYS B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLN B 134 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N SER B 162 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 309 through 319 removed outlier: 5.858A pdb=" N LYS B 310 " --> pdb=" O GLY B 601 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N GLY B 601 " --> pdb=" O LYS B 310 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLY B 593 " --> pdb=" O PHE B 318 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 376 through 379 Processing sheet with id=AC3, first strand: chain 'B' and resid 448 through 453 removed outlier: 5.864A pdb=" N TYR B 449 " --> pdb=" O PHE B 497 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N PHE B 497 " --> pdb=" O TYR B 449 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N TYR B 451 " --> pdb=" O TYR B 495 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 539 through 543 removed outlier: 5.337A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.332A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.703A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AC7, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.542A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.542A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.577A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD2, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.060A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 49 through 55 removed outlier: 3.857A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AD5, first strand: chain 'C' and resid 116 through 121 removed outlier: 3.730A pdb=" N CYS C 131 " --> pdb=" O SER C 116 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N ILE C 128 " --> pdb=" O PHE C 168 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N PHE C 168 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N VAL C 130 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N CYS C 166 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLN C 134 " --> pdb=" O SER C 162 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N SER C 162 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 311 through 319 removed outlier: 3.898A pdb=" N GLY C 311 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 376 through 379 Processing sheet with id=AD8, first strand: chain 'C' and resid 448 through 453 removed outlier: 5.864A pdb=" N TYR C 449 " --> pdb=" O PHE C 497 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N PHE C 497 " --> pdb=" O TYR C 449 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N TYR C 451 " --> pdb=" O TYR C 495 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 539 through 543 removed outlier: 3.887A pdb=" N VAL C 551 " --> pdb=" O THR C 588 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N THR C 588 " --> pdb=" O VAL C 551 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N THR C 553 " --> pdb=" O ASP C 586 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.801A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 9.251A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.590A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY C1059 " --> pdb=" O ALA C1056 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.590A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.568A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 1120 through 1122 882 hydrogen bonds defined for protein. 2388 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: 9.05 Time building geometry restraints manager: 10.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 5606 1.33 - 1.45: 5919 1.45 - 1.58: 12587 1.58 - 1.70: 0 1.70 - 1.83: 129 Bond restraints: 24241 Sorted by residual: bond pdb=" CA SER A 698 " pdb=" C SER A 698 " ideal model delta sigma weight residual 1.522 1.444 0.078 1.20e-02 6.94e+03 4.22e+01 bond pdb=" C THR A 588 " pdb=" N PRO A 589 " ideal model delta sigma weight residual 1.331 1.390 -0.059 1.20e-02 6.94e+03 2.42e+01 bond pdb=" C THR B 588 " pdb=" N PRO B 589 " ideal model delta sigma weight residual 1.330 1.389 -0.059 1.23e-02 6.61e+03 2.31e+01 bond pdb=" C HIS B1088 " pdb=" N PHE B1089 " ideal model delta sigma weight residual 1.331 1.262 0.069 1.59e-02 3.96e+03 1.87e+01 bond pdb=" N PRO A 589 " pdb=" CD PRO A 589 " ideal model delta sigma weight residual 1.473 1.531 -0.058 1.40e-02 5.10e+03 1.71e+01 ... (remaining 24236 not shown) Histogram of bond angle deviations from ideal: 97.60 - 105.81: 481 105.81 - 114.02: 14300 114.02 - 122.23: 14088 122.23 - 130.44: 4035 130.44 - 138.65: 67 Bond angle restraints: 32971 Sorted by residual: angle pdb=" N CYS B 538 " pdb=" CA CYS B 538 " pdb=" C CYS B 538 " ideal model delta sigma weight residual 110.10 100.89 9.21 1.49e+00 4.50e-01 3.82e+01 angle pdb=" N CYS A 538 " pdb=" CA CYS A 538 " pdb=" C CYS A 538 " ideal model delta sigma weight residual 110.10 100.92 9.18 1.49e+00 4.50e-01 3.80e+01 angle pdb=" C PHE C 86 " pdb=" N ASN C 87 " pdb=" CA ASN C 87 " ideal model delta sigma weight residual 121.54 132.81 -11.27 1.91e+00 2.74e-01 3.48e+01 angle pdb=" C PHE B 86 " pdb=" N ASN B 87 " pdb=" CA ASN B 87 " ideal model delta sigma weight residual 121.54 132.76 -11.22 1.91e+00 2.74e-01 3.45e+01 angle pdb=" C PHE A 86 " pdb=" N ASN A 87 " pdb=" CA ASN A 87 " ideal model delta sigma weight residual 121.54 132.74 -11.20 1.91e+00 2.74e-01 3.44e+01 ... (remaining 32966 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 13157 17.93 - 35.87: 1481 35.87 - 53.80: 511 53.80 - 71.74: 174 71.74 - 89.67: 44 Dihedral angle restraints: 15367 sinusoidal: 6895 harmonic: 8472 Sorted by residual: dihedral pdb=" CB CYS B 336 " pdb=" SG CYS B 336 " pdb=" SG CYS B 361 " pdb=" CB CYS B 361 " ideal model delta sinusoidal sigma weight residual 93.00 10.81 82.19 1 1.00e+01 1.00e-02 8.29e+01 dihedral pdb=" CB CYS A 617 " pdb=" SG CYS A 617 " pdb=" SG CYS A 649 " pdb=" CB CYS A 649 " ideal model delta sinusoidal sigma weight residual 93.00 21.10 71.90 1 1.00e+01 1.00e-02 6.62e+01 dihedral pdb=" CB CYS B 617 " pdb=" SG CYS B 617 " pdb=" SG CYS B 649 " pdb=" CB CYS B 649 " ideal model delta sinusoidal sigma weight residual 93.00 21.11 71.89 1 1.00e+01 1.00e-02 6.62e+01 ... (remaining 15364 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.329: 3965 0.329 - 0.658: 2 0.658 - 0.987: 4 0.987 - 1.316: 0 1.316 - 1.645: 3 Chirality restraints: 3974 Sorted by residual: chirality pdb=" C1 NAG R 2 " pdb=" O4 NAG R 1 " pdb=" C2 NAG R 2 " pdb=" O5 NAG R 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.72 -0.68 2.00e-02 2.50e+03 1.17e+03 chirality pdb=" C1 NAG B1410 " pdb=" O4 NAG B1409 " pdb=" C2 NAG B1410 " pdb=" O5 NAG B1410 " both_signs ideal model delta sigma weight residual False -2.40 -3.08 0.68 2.00e-02 2.50e+03 1.17e+03 chirality pdb=" C1 NAG Y 1 " pdb=" ND2 ASN C1134 " pdb=" C2 NAG Y 1 " pdb=" O5 NAG Y 1 " both_signs ideal model delta sigma weight residual False -2.40 -0.75 -1.65 2.00e-01 2.50e+01 6.77e+01 ... (remaining 3971 not shown) Planarity restraints: 4212 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 331 " -0.040 2.00e-02 2.50e+03 6.64e-02 5.52e+01 pdb=" CG ASN B 331 " 0.019 2.00e-02 2.50e+03 pdb=" OD1 ASN B 331 " -0.024 2.00e-02 2.50e+03 pdb=" ND2 ASN B 331 " 0.119 2.00e-02 2.50e+03 pdb=" C1 NAG K 1 " -0.074 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 709 " -0.047 2.00e-02 2.50e+03 5.85e-02 4.28e+01 pdb=" CG ASN A 709 " 0.019 2.00e-02 2.50e+03 pdb=" OD1 ASN A 709 " -0.003 2.00e-02 2.50e+03 pdb=" ND2 ASN A 709 " 0.100 2.00e-02 2.50e+03 pdb=" C1 NAG A1409 " -0.068 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 331 " -0.016 2.00e-02 2.50e+03 5.62e-02 3.95e+01 pdb=" CG ASN C 331 " 0.015 2.00e-02 2.50e+03 pdb=" OD1 ASN C 331 " -0.037 2.00e-02 2.50e+03 pdb=" ND2 ASN C 331 " 0.100 2.00e-02 2.50e+03 pdb=" C1 NAG R 1 " -0.063 2.00e-02 2.50e+03 ... (remaining 4209 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 207 2.50 - 3.10: 17097 3.10 - 3.70: 33275 3.70 - 4.30: 51224 4.30 - 4.90: 84969 Nonbonded interactions: 186772 Sorted by model distance: nonbonded pdb=" O SER B 316 " pdb=" ND2 ASN B 317 " model vdw 1.905 2.520 nonbonded pdb=" NH1 ARG A 346 " pdb=" O PHE A 347 " model vdw 1.982 2.520 nonbonded pdb=" NH1 ARG C 346 " pdb=" O PHE C 347 " model vdw 1.983 2.520 nonbonded pdb=" NH1 ARG B 346 " pdb=" O PHE B 347 " model vdw 1.983 2.520 nonbonded pdb=" O ARG C 328 " pdb=" CD1 PHE C 329 " model vdw 2.117 3.340 ... (remaining 186767 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 939 or resid 944 through 1146 or resid 1401 thr \ ough 1408)) selection = (chain 'B' and (resid 27 through 1146 or resid 1401 through 1408)) selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' } 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: 1.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 6.460 Check model and map are aligned: 0.410 Set scattering table: 0.260 Process input model: 62.780 Find NCS groups from input model: 1.750 Set up NCS constraints: 0.290 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 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 : 0.012 0.116 24241 Z= 0.783 Angle : 1.034 13.651 32971 Z= 0.596 Chirality : 0.081 1.645 3974 Planarity : 0.008 0.089 4164 Dihedral : 18.042 89.674 9797 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 22.56 Ramachandran Plot: Outliers : 3.12 % Allowed : 10.55 % Favored : 86.33 % Rotamer: Outliers : 12.95 % Allowed : 17.97 % Favored : 69.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -4.17 (0.13), residues: 2854 helix: -2.19 (0.16), residues: 651 sheet: -2.01 (0.17), residues: 708 loop : -3.51 (0.12), residues: 1495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.004 TRP B 104 HIS 0.009 0.002 HIS C1048 PHE 0.025 0.003 PHE A 898 TYR 0.027 0.003 TYR B1067 ARG 0.008 0.001 ARG A1039 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5708 Ramachandran restraints generated. 2854 Oldfield, 0 Emsley, 2854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5708 Ramachandran restraints generated. 2854 Oldfield, 0 Emsley, 2854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 660 residues out of total 2548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 330 poor density : 330 time to evaluate : 2.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 LEU cc_start: 0.7661 (tp) cc_final: 0.7255 (tp) REVERT: A 153 MET cc_start: 0.0857 (mpp) cc_final: -0.0123 (tmm) REVERT: A 324 GLU cc_start: 0.6114 (OUTLIER) cc_final: 0.4978 (pm20) REVERT: A 702 GLU cc_start: 0.6077 (OUTLIER) cc_final: 0.5759 (tp30) REVERT: A 883 THR cc_start: 0.9582 (OUTLIER) cc_final: 0.9267 (m) REVERT: A 1039 ARG cc_start: 0.9330 (OUTLIER) cc_final: 0.8215 (mtt180) REVERT: B 48 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8431 (mt) REVERT: B 153 MET cc_start: -0.0474 (mpp) cc_final: -0.0750 (pmm) REVERT: B 360 ASN cc_start: 0.5959 (OUTLIER) cc_final: 0.5739 (p0) REVERT: B 387 LEU cc_start: 0.8859 (mt) cc_final: 0.8496 (mt) REVERT: B 533 LEU cc_start: 0.7062 (OUTLIER) cc_final: 0.6741 (tp) REVERT: B 697 MET cc_start: 0.8237 (ptm) cc_final: 0.8032 (ptm) REVERT: B 1050 MET cc_start: 0.8958 (ptm) cc_final: 0.8756 (ptm) REVERT: C 66 HIS cc_start: 0.6725 (OUTLIER) cc_final: 0.6413 (m-70) REVERT: C 153 MET cc_start: -0.0803 (mpp) cc_final: -0.3514 (ttp) REVERT: C 158 ARG cc_start: 0.5138 (OUTLIER) cc_final: 0.4420 (mtp180) REVERT: C 389 ASP cc_start: 0.7974 (OUTLIER) cc_final: 0.7455 (m-30) REVERT: C 421 TYR cc_start: 0.7222 (OUTLIER) cc_final: 0.6355 (p90) REVERT: C 514 SER cc_start: 0.8821 (OUTLIER) cc_final: 0.8594 (p) REVERT: C 787 GLN cc_start: 0.7851 (OUTLIER) cc_final: 0.7624 (mm-40) outliers start: 330 outliers final: 71 residues processed: 608 average time/residue: 0.3510 time to fit residues: 330.7024 Evaluate side-chains 244 residues out of total 2548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 160 time to evaluate : 2.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASP Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 673 SER Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 704 SER Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 854 LYS Chi-restraints excluded: chain A residue 883 THR Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain A residue 1039 ARG Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 528 LYS Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 673 SER Chi-restraints excluded: chain B residue 748 GLU Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 158 ARG Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 357 ARG Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 403 ARG Chi-restraints excluded: chain C residue 421 TYR Chi-restraints excluded: chain C residue 438 SER Chi-restraints excluded: chain C residue 514 SER Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 814 LYS Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 245 optimal weight: 3.9990 chunk 220 optimal weight: 5.9990 chunk 122 optimal weight: 9.9990 chunk 75 optimal weight: 0.9990 chunk 148 optimal weight: 0.4980 chunk 117 optimal weight: 2.9990 chunk 228 optimal weight: 10.0000 chunk 88 optimal weight: 0.6980 chunk 138 optimal weight: 7.9990 chunk 169 optimal weight: 0.9990 chunk 264 optimal weight: 0.7980 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN A 137 ASN A 239 GLN A 317 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 440 ASN A 498 GLN A 644 GLN A 755 GLN A 762 GLN A 804 GLN A 901 GLN A 914 ASN A 919 ASN A 926 GLN A 955 ASN A 969 ASN ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1058 HIS A1101 HIS B 134 GLN B 137 ASN B 188 ASN B 239 GLN B 317 ASN B 422 ASN B 440 ASN B 498 GLN B 644 GLN B 703 ASN B 804 GLN B 901 GLN B 914 ASN B 919 ASN B 920 GLN B 926 GLN B 992 GLN B1054 GLN C 137 ASN C 164 ASN C 207 HIS C 422 ASN C 440 ASN C 498 GLN C 644 GLN C 703 ASN C 751 ASN C 784 GLN C 804 GLN C 901 GLN C 914 ASN C 926 GLN C 935 GLN C 969 ASN C 992 GLN C1010 GLN C1071 GLN C1101 HIS Total number of N/Q/H flips: 56 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.2582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 24241 Z= 0.217 Angle : 0.743 14.012 32971 Z= 0.368 Chirality : 0.050 0.451 3974 Planarity : 0.005 0.064 4164 Dihedral : 10.348 80.323 4746 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.85 % Favored : 91.84 % Rotamer: Outliers : 5.38 % Allowed : 19.94 % Favored : 74.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.53 (0.14), residues: 2854 helix: -0.08 (0.20), residues: 661 sheet: -1.02 (0.18), residues: 703 loop : -2.88 (0.13), residues: 1490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 436 HIS 0.005 0.001 HIS A1101 PHE 0.020 0.002 PHE C 329 TYR 0.018 0.001 TYR A1067 ARG 0.010 0.001 ARG B 403 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5708 Ramachandran restraints generated. 2854 Oldfield, 0 Emsley, 2854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5708 Ramachandran restraints generated. 2854 Oldfield, 0 Emsley, 2854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 196 time to evaluate : 2.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ILE cc_start: 0.8348 (pt) cc_final: 0.8122 (pt) REVERT: A 153 MET cc_start: 0.1100 (mpp) cc_final: -0.0015 (tmm) REVERT: A 883 THR cc_start: 0.9555 (OUTLIER) cc_final: 0.9141 (p) REVERT: B 48 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.8229 (mt) REVERT: B 315 THR cc_start: 0.9474 (OUTLIER) cc_final: 0.9232 (t) REVERT: B 360 ASN cc_start: 0.6307 (OUTLIER) cc_final: 0.5791 (p0) REVERT: B 518 LEU cc_start: -0.0287 (OUTLIER) cc_final: -0.1535 (mt) REVERT: C 153 MET cc_start: -0.0760 (mpp) cc_final: -0.3503 (ttp) REVERT: C 540 ASN cc_start: 0.7677 (OUTLIER) cc_final: 0.7402 (m110) REVERT: C 814 LYS cc_start: 0.7818 (OUTLIER) cc_final: 0.7506 (mptt) outliers start: 137 outliers final: 75 residues processed: 318 average time/residue: 0.3268 time to fit residues: 168.1336 Evaluate side-chains 234 residues out of total 2548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 152 time to evaluate : 2.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 704 SER Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 883 THR Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 814 LYS Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 146 optimal weight: 5.9990 chunk 82 optimal weight: 3.9990 chunk 219 optimal weight: 3.9990 chunk 179 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 264 optimal weight: 3.9990 chunk 285 optimal weight: 4.9990 chunk 235 optimal weight: 4.9990 chunk 262 optimal weight: 0.9980 chunk 90 optimal weight: 3.9990 chunk 212 optimal weight: 10.0000 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 ASN ** A 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 GLN B 450 ASN B 913 GLN C 207 HIS C 317 ASN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.3406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 24241 Z= 0.407 Angle : 0.747 11.438 32971 Z= 0.368 Chirality : 0.051 0.300 3974 Planarity : 0.005 0.050 4164 Dihedral : 9.125 59.977 4669 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.86 % Favored : 90.89 % Rotamer: Outliers : 5.18 % Allowed : 20.64 % Favored : 74.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.12 (0.15), residues: 2854 helix: 0.55 (0.21), residues: 661 sheet: -0.95 (0.18), residues: 712 loop : -2.67 (0.13), residues: 1481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 104 HIS 0.007 0.002 HIS A 207 PHE 0.026 0.002 PHE C 135 TYR 0.030 0.002 TYR A 453 ARG 0.006 0.001 ARG C 158 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5708 Ramachandran restraints generated. 2854 Oldfield, 0 Emsley, 2854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5708 Ramachandran restraints generated. 2854 Oldfield, 0 Emsley, 2854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 2548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 149 time to evaluate : 2.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ILE cc_start: 0.8256 (pt) cc_final: 0.7948 (pt) REVERT: A 153 MET cc_start: 0.1742 (mpp) cc_final: -0.0062 (mmt) REVERT: A 518 LEU cc_start: 0.4679 (OUTLIER) cc_final: 0.4449 (tt) REVERT: B 360 ASN cc_start: 0.6342 (OUTLIER) cc_final: 0.5921 (p0) REVERT: B 518 LEU cc_start: -0.0385 (OUTLIER) cc_final: -0.1399 (mt) REVERT: B 990 GLU cc_start: 0.6989 (OUTLIER) cc_final: 0.6674 (mp0) REVERT: C 421 TYR cc_start: 0.6872 (OUTLIER) cc_final: 0.5792 (p90) REVERT: C 540 ASN cc_start: 0.7716 (OUTLIER) cc_final: 0.7453 (m110) REVERT: C 565 PHE cc_start: 0.7208 (p90) cc_final: 0.6869 (p90) outliers start: 132 outliers final: 80 residues processed: 269 average time/residue: 0.3046 time to fit residues: 133.8841 Evaluate side-chains 216 residues out of total 2548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 130 time to evaluate : 2.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 883 THR Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 532 ASN Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 421 TYR Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 261 optimal weight: 3.9990 chunk 199 optimal weight: 3.9990 chunk 137 optimal weight: 0.0670 chunk 29 optimal weight: 0.0870 chunk 126 optimal weight: 9.9990 chunk 177 optimal weight: 7.9990 chunk 265 optimal weight: 0.9990 chunk 281 optimal weight: 2.9990 chunk 138 optimal weight: 6.9990 chunk 251 optimal weight: 1.9990 chunk 75 optimal weight: 0.6980 overall best weight: 0.7700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 115 GLN C 115 GLN C 207 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.3716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 24241 Z= 0.164 Angle : 0.627 11.071 32971 Z= 0.303 Chirality : 0.046 0.246 3974 Planarity : 0.004 0.042 4164 Dihedral : 8.105 59.998 4652 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.80 % Favored : 93.03 % Rotamer: Outliers : 4.12 % Allowed : 21.39 % Favored : 74.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.58 (0.15), residues: 2854 helix: 1.02 (0.21), residues: 659 sheet: -0.58 (0.18), residues: 698 loop : -2.35 (0.14), residues: 1497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 353 HIS 0.005 0.001 HIS A 207 PHE 0.020 0.001 PHE C 135 TYR 0.018 0.001 TYR A1067 ARG 0.004 0.000 ARG C 319 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5708 Ramachandran restraints generated. 2854 Oldfield, 0 Emsley, 2854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5708 Ramachandran restraints generated. 2854 Oldfield, 0 Emsley, 2854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 149 time to evaluate : 3.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ILE cc_start: 0.8106 (OUTLIER) cc_final: 0.7808 (pt) REVERT: A 153 MET cc_start: 0.1934 (mpp) cc_final: -0.0012 (mmt) REVERT: B 99 ASN cc_start: 0.6869 (OUTLIER) cc_final: 0.6564 (p0) REVERT: B 315 THR cc_start: 0.9530 (OUTLIER) cc_final: 0.9283 (m) REVERT: B 360 ASN cc_start: 0.6234 (OUTLIER) cc_final: 0.5809 (p0) REVERT: B 990 GLU cc_start: 0.6823 (OUTLIER) cc_final: 0.6499 (mp0) REVERT: C 102 ARG cc_start: 0.6290 (mmm-85) cc_final: 0.5873 (mmt180) REVERT: C 231 ILE cc_start: 0.7007 (OUTLIER) cc_final: 0.6576 (mt) REVERT: C 856 ASN cc_start: 0.9149 (OUTLIER) cc_final: 0.8647 (p0) outliers start: 105 outliers final: 60 residues processed: 244 average time/residue: 0.3190 time to fit residues: 128.2380 Evaluate side-chains 203 residues out of total 2548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 136 time to evaluate : 2.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 188 ASN Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 234 optimal weight: 7.9990 chunk 159 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 209 optimal weight: 0.9990 chunk 116 optimal weight: 5.9990 chunk 240 optimal weight: 9.9990 chunk 194 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 143 optimal weight: 9.9990 chunk 252 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 824 ASN A1071 GLN B 607 GLN C 207 HIS C 360 ASN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.4041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 24241 Z= 0.324 Angle : 0.683 11.669 32971 Z= 0.331 Chirality : 0.049 0.256 3974 Planarity : 0.004 0.043 4164 Dihedral : 7.941 59.857 4643 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.20 % Favored : 91.63 % Rotamer: Outliers : 4.16 % Allowed : 21.55 % Favored : 74.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.53 (0.15), residues: 2854 helix: 1.22 (0.22), residues: 641 sheet: -0.64 (0.18), residues: 715 loop : -2.31 (0.14), residues: 1498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 104 HIS 0.005 0.001 HIS C1058 PHE 0.017 0.002 PHE C 135 TYR 0.020 0.001 TYR B1067 ARG 0.004 0.000 ARG C 319 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5708 Ramachandran restraints generated. 2854 Oldfield, 0 Emsley, 2854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5708 Ramachandran restraints generated. 2854 Oldfield, 0 Emsley, 2854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 140 time to evaluate : 2.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ILE cc_start: 0.8189 (pt) cc_final: 0.7911 (pt) REVERT: A 153 MET cc_start: 0.2333 (mpp) cc_final: -0.0077 (mmt) REVERT: A 1106 GLN cc_start: 0.8941 (OUTLIER) cc_final: 0.8710 (pt0) REVERT: B 153 MET cc_start: -0.0507 (pmm) cc_final: -0.1829 (pmm) REVERT: B 315 THR cc_start: 0.9561 (OUTLIER) cc_final: 0.9344 (m) REVERT: C 102 ARG cc_start: 0.6342 (mmm-85) cc_final: 0.5950 (mmt180) REVERT: C 528 LYS cc_start: 0.7029 (tptt) cc_final: 0.6816 (tptt) REVERT: C 565 PHE cc_start: 0.7299 (p90) cc_final: 0.7046 (p90) outliers start: 106 outliers final: 76 residues processed: 238 average time/residue: 0.3244 time to fit residues: 127.8018 Evaluate side-chains 205 residues out of total 2548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 127 time to evaluate : 2.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 532 ASN Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 188 ASN Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 94 optimal weight: 2.9990 chunk 253 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 165 optimal weight: 7.9990 chunk 69 optimal weight: 0.9990 chunk 281 optimal weight: 1.9990 chunk 233 optimal weight: 20.0000 chunk 130 optimal weight: 0.0020 chunk 23 optimal weight: 0.3980 chunk 93 optimal weight: 0.9980 chunk 147 optimal weight: 7.9990 overall best weight: 0.8792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 207 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.4232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 24241 Z= 0.162 Angle : 0.609 11.425 32971 Z= 0.292 Chirality : 0.046 0.252 3974 Planarity : 0.004 0.041 4164 Dihedral : 7.313 59.137 4634 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.48 % Favored : 93.34 % Rotamer: Outliers : 3.34 % Allowed : 22.37 % Favored : 74.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.20 (0.15), residues: 2854 helix: 1.30 (0.21), residues: 659 sheet: -0.28 (0.18), residues: 705 loop : -2.13 (0.14), residues: 1490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 436 HIS 0.003 0.001 HIS B 519 PHE 0.020 0.001 PHE A 347 TYR 0.018 0.001 TYR A1067 ARG 0.011 0.000 ARG C 355 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5708 Ramachandran restraints generated. 2854 Oldfield, 0 Emsley, 2854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5708 Ramachandran restraints generated. 2854 Oldfield, 0 Emsley, 2854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 144 time to evaluate : 2.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ILE cc_start: 0.8203 (OUTLIER) cc_final: 0.7875 (pt) REVERT: A 153 MET cc_start: 0.2346 (mpp) cc_final: -0.0132 (mmt) REVERT: A 187 LYS cc_start: 0.6490 (OUTLIER) cc_final: 0.6199 (mtmm) REVERT: A 1106 GLN cc_start: 0.8749 (OUTLIER) cc_final: 0.8496 (pt0) REVERT: B 99 ASN cc_start: 0.6849 (OUTLIER) cc_final: 0.6557 (p0) REVERT: B 153 MET cc_start: -0.0421 (pmm) cc_final: -0.3298 (ptt) REVERT: C 102 ARG cc_start: 0.6328 (mmm-85) cc_final: 0.5911 (mmt180) REVERT: C 565 PHE cc_start: 0.7045 (p90) cc_final: 0.6794 (p90) outliers start: 85 outliers final: 70 residues processed: 218 average time/residue: 0.3193 time to fit residues: 115.5715 Evaluate side-chains 208 residues out of total 2548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 134 time to evaluate : 2.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 399 SER Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 188 ASN Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 271 optimal weight: 3.9990 chunk 31 optimal weight: 7.9990 chunk 160 optimal weight: 4.9990 chunk 205 optimal weight: 10.0000 chunk 159 optimal weight: 0.9980 chunk 237 optimal weight: 0.2980 chunk 157 optimal weight: 0.8980 chunk 280 optimal weight: 2.9990 chunk 175 optimal weight: 0.8980 chunk 170 optimal weight: 2.9990 chunk 129 optimal weight: 7.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 207 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.4391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 24241 Z= 0.185 Angle : 0.605 11.252 32971 Z= 0.289 Chirality : 0.046 0.247 3974 Planarity : 0.003 0.043 4164 Dihedral : 7.039 59.815 4633 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.15 % Favored : 92.68 % Rotamer: Outliers : 3.57 % Allowed : 22.49 % Favored : 73.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.06 (0.15), residues: 2854 helix: 1.53 (0.22), residues: 655 sheet: -0.27 (0.18), residues: 712 loop : -2.05 (0.14), residues: 1487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 436 HIS 0.004 0.001 HIS B 519 PHE 0.020 0.001 PHE C 92 TYR 0.019 0.001 TYR B1067 ARG 0.004 0.000 ARG C 355 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5708 Ramachandran restraints generated. 2854 Oldfield, 0 Emsley, 2854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5708 Ramachandran restraints generated. 2854 Oldfield, 0 Emsley, 2854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 140 time to evaluate : 2.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ILE cc_start: 0.8143 (pt) cc_final: 0.7845 (pt) REVERT: A 153 MET cc_start: 0.2646 (mpp) cc_final: -0.0022 (mmt) REVERT: A 187 LYS cc_start: 0.6490 (OUTLIER) cc_final: 0.6262 (mtmm) REVERT: A 1106 GLN cc_start: 0.8803 (OUTLIER) cc_final: 0.8519 (pt0) REVERT: B 153 MET cc_start: -0.0782 (pmm) cc_final: -0.3120 (ptt) REVERT: B 161 SER cc_start: 0.6882 (OUTLIER) cc_final: 0.6447 (p) REVERT: B 360 ASN cc_start: 0.6142 (OUTLIER) cc_final: 0.5807 (p0) REVERT: C 66 HIS cc_start: 0.6808 (OUTLIER) cc_final: 0.6262 (m-70) REVERT: C 565 PHE cc_start: 0.7148 (p90) cc_final: 0.6926 (p90) outliers start: 91 outliers final: 69 residues processed: 223 average time/residue: 0.3225 time to fit residues: 120.0872 Evaluate side-chains 200 residues out of total 2548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 126 time to evaluate : 2.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 188 ASN Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 173 optimal weight: 4.9990 chunk 112 optimal weight: 0.0870 chunk 167 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 55 optimal weight: 5.9990 chunk 54 optimal weight: 0.9980 chunk 178 optimal weight: 3.9990 chunk 191 optimal weight: 7.9990 chunk 138 optimal weight: 9.9990 chunk 26 optimal weight: 0.1980 chunk 220 optimal weight: 9.9990 overall best weight: 1.4562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 207 HIS ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.4531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 24241 Z= 0.202 Angle : 0.607 11.241 32971 Z= 0.289 Chirality : 0.046 0.249 3974 Planarity : 0.003 0.041 4164 Dihedral : 6.848 59.692 4623 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.41 % Favored : 93.41 % Rotamer: Outliers : 3.10 % Allowed : 22.92 % Favored : 73.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.01 (0.15), residues: 2854 helix: 1.48 (0.21), residues: 667 sheet: -0.14 (0.19), residues: 684 loop : -2.02 (0.14), residues: 1503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 436 HIS 0.004 0.001 HIS B 519 PHE 0.017 0.001 PHE C 92 TYR 0.019 0.001 TYR B1067 ARG 0.004 0.000 ARG C 355 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5708 Ramachandran restraints generated. 2854 Oldfield, 0 Emsley, 2854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5708 Ramachandran restraints generated. 2854 Oldfield, 0 Emsley, 2854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 2548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 131 time to evaluate : 2.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ILE cc_start: 0.8180 (pt) cc_final: 0.7889 (pt) REVERT: A 133 PHE cc_start: 0.5794 (m-80) cc_final: 0.5168 (m-80) REVERT: A 153 MET cc_start: 0.2800 (mpp) cc_final: -0.0005 (mmt) REVERT: A 187 LYS cc_start: 0.6393 (OUTLIER) cc_final: 0.6084 (mtmm) REVERT: A 1106 GLN cc_start: 0.8828 (OUTLIER) cc_final: 0.8558 (pt0) REVERT: B 153 MET cc_start: -0.0516 (pmm) cc_final: -0.2875 (ptt) REVERT: B 161 SER cc_start: 0.6521 (OUTLIER) cc_final: 0.6130 (p) REVERT: B 342 PHE cc_start: 0.6286 (m-80) cc_final: 0.6058 (m-80) REVERT: C 66 HIS cc_start: 0.6858 (OUTLIER) cc_final: 0.6274 (m-70) REVERT: C 565 PHE cc_start: 0.7257 (p90) cc_final: 0.6999 (p90) outliers start: 79 outliers final: 72 residues processed: 202 average time/residue: 0.3107 time to fit residues: 104.8057 Evaluate side-chains 206 residues out of total 2548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 130 time to evaluate : 2.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 188 ASN Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 255 optimal weight: 3.9990 chunk 268 optimal weight: 1.9990 chunk 245 optimal weight: 0.9980 chunk 261 optimal weight: 2.9990 chunk 157 optimal weight: 6.9990 chunk 113 optimal weight: 2.9990 chunk 205 optimal weight: 10.0000 chunk 80 optimal weight: 1.9990 chunk 236 optimal weight: 0.9980 chunk 247 optimal weight: 0.8980 chunk 260 optimal weight: 0.7980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 207 HIS C 394 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.4646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 24241 Z= 0.175 Angle : 0.595 11.221 32971 Z= 0.283 Chirality : 0.046 0.247 3974 Planarity : 0.003 0.043 4164 Dihedral : 6.693 58.458 4622 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.52 % Favored : 93.31 % Rotamer: Outliers : 3.41 % Allowed : 22.84 % Favored : 73.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.88 (0.15), residues: 2854 helix: 1.75 (0.22), residues: 645 sheet: -0.04 (0.19), residues: 682 loop : -1.98 (0.14), residues: 1527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 436 HIS 0.004 0.001 HIS B 519 PHE 0.031 0.001 PHE B 338 TYR 0.019 0.001 TYR B1067 ARG 0.007 0.000 ARG C 357 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5708 Ramachandran restraints generated. 2854 Oldfield, 0 Emsley, 2854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5708 Ramachandran restraints generated. 2854 Oldfield, 0 Emsley, 2854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 2548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 135 time to evaluate : 2.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.5954 (m-80) cc_final: 0.5166 (m-80) REVERT: A 153 MET cc_start: 0.2834 (mpp) cc_final: -0.0030 (mmt) REVERT: A 187 LYS cc_start: 0.6468 (OUTLIER) cc_final: 0.6178 (mtmm) REVERT: A 1106 GLN cc_start: 0.8804 (OUTLIER) cc_final: 0.8526 (pt0) REVERT: B 153 MET cc_start: -0.0652 (pmm) cc_final: -0.2876 (ptt) REVERT: B 161 SER cc_start: 0.6346 (OUTLIER) cc_final: 0.6090 (p) REVERT: B 342 PHE cc_start: 0.6297 (m-80) cc_final: 0.6071 (m-80) REVERT: B 990 GLU cc_start: 0.6786 (OUTLIER) cc_final: 0.6490 (mp0) REVERT: C 66 HIS cc_start: 0.6919 (OUTLIER) cc_final: 0.6329 (m-70) REVERT: C 565 PHE cc_start: 0.7299 (p90) cc_final: 0.7045 (p90) outliers start: 87 outliers final: 76 residues processed: 213 average time/residue: 0.2973 time to fit residues: 106.6222 Evaluate side-chains 207 residues out of total 2548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 126 time to evaluate : 2.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 188 ASN Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 171 optimal weight: 2.9990 chunk 276 optimal weight: 5.9990 chunk 168 optimal weight: 3.9990 chunk 131 optimal weight: 5.9990 chunk 192 optimal weight: 0.9990 chunk 289 optimal weight: 0.0270 chunk 266 optimal weight: 0.8980 chunk 230 optimal weight: 30.0000 chunk 23 optimal weight: 6.9990 chunk 178 optimal weight: 2.9990 chunk 141 optimal weight: 4.9990 overall best weight: 1.5844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 207 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.4704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 24241 Z= 0.215 Angle : 0.610 11.255 32971 Z= 0.292 Chirality : 0.046 0.245 3974 Planarity : 0.004 0.046 4164 Dihedral : 6.703 59.639 4620 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.76 % Favored : 93.06 % Rotamer: Outliers : 3.26 % Allowed : 22.84 % Favored : 73.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.88 (0.15), residues: 2854 helix: 1.80 (0.22), residues: 641 sheet: -0.03 (0.19), residues: 684 loop : -2.02 (0.14), residues: 1529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 436 HIS 0.004 0.001 HIS B 519 PHE 0.034 0.001 PHE B 338 TYR 0.019 0.001 TYR B1067 ARG 0.003 0.000 ARG B 567 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5708 Ramachandran restraints generated. 2854 Oldfield, 0 Emsley, 2854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5708 Ramachandran restraints generated. 2854 Oldfield, 0 Emsley, 2854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 2548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 131 time to evaluate : 2.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ILE cc_start: 0.8164 (pt) cc_final: 0.7875 (pt) REVERT: A 133 PHE cc_start: 0.5965 (m-80) cc_final: 0.5183 (m-80) REVERT: A 153 MET cc_start: 0.2636 (mpp) cc_final: -0.0079 (mmt) REVERT: A 1106 GLN cc_start: 0.8820 (OUTLIER) cc_final: 0.8538 (pt0) REVERT: B 153 MET cc_start: -0.0657 (pmm) cc_final: -0.2623 (ptt) REVERT: B 342 PHE cc_start: 0.6340 (m-80) cc_final: 0.6109 (m-80) REVERT: C 66 HIS cc_start: 0.6904 (OUTLIER) cc_final: 0.6260 (m-70) REVERT: C 565 PHE cc_start: 0.7411 (p90) cc_final: 0.7155 (p90) outliers start: 83 outliers final: 78 residues processed: 204 average time/residue: 0.3032 time to fit residues: 104.1028 Evaluate side-chains 207 residues out of total 2548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 127 time to evaluate : 2.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 104 TRP Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain B residue 990 GLU Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 188 ASN Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 503 VAL Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 540 ASN Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1145 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 183 optimal weight: 0.6980 chunk 245 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 212 optimal weight: 10.0000 chunk 34 optimal weight: 9.9990 chunk 64 optimal weight: 3.9990 chunk 231 optimal weight: 0.0370 chunk 96 optimal weight: 2.9990 chunk 237 optimal weight: 7.9990 chunk 29 optimal weight: 20.0000 chunk 42 optimal weight: 1.9990 overall best weight: 1.9464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 ASN B 703 ASN C 207 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.131519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.081608 restraints weight = 44140.857| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 2.82 r_work: 0.2791 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2658 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.4797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 24241 Z= 0.247 Angle : 0.627 11.263 32971 Z= 0.300 Chirality : 0.047 0.247 3974 Planarity : 0.004 0.048 4164 Dihedral : 6.802 59.955 4618 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.01 % Favored : 92.82 % Rotamer: Outliers : 3.41 % Allowed : 22.76 % Favored : 73.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.89 (0.15), residues: 2854 helix: 1.71 (0.22), residues: 647 sheet: 0.01 (0.19), residues: 690 loop : -2.02 (0.14), residues: 1517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 436 HIS 0.005 0.001 HIS B 519 PHE 0.032 0.001 PHE B 338 TYR 0.019 0.001 TYR B1067 ARG 0.010 0.000 ARG B 403 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4903.77 seconds wall clock time: 90 minutes 13.49 seconds (5413.49 seconds total)