Starting phenix.real_space_refine on Wed Mar 20 18:58:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oan_12777/03_2024/7oan_12777.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oan_12777/03_2024/7oan_12777.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oan_12777/03_2024/7oan_12777.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oan_12777/03_2024/7oan_12777.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oan_12777/03_2024/7oan_12777.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oan_12777/03_2024/7oan_12777.pdb" } resolution = 3.0 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= 0.002 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 132 5.16 5 C 17886 2.51 5 N 4638 2.21 5 O 5547 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 88": "OD1" <-> "OD2" Residue "A PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 215": "OD1" <-> "OD2" Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 281": "OE1" <-> "OE2" Residue "A TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 389": "OD1" <-> "OD2" Residue "A TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 578": "OD1" <-> "OD2" Residue "A GLU 661": "OE1" <-> "OE2" Residue "A PHE 817": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 990": "OE1" <-> "OE2" Residue "B PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 88": "OD1" <-> "OD2" Residue "B PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 215": "OD1" <-> "OD2" Residue "B TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 281": "OE1" <-> "OE2" Residue "B TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 389": "OD1" <-> "OD2" Residue "B TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 578": "OD1" <-> "OD2" Residue "B GLU 661": "OE1" <-> "OE2" Residue "B PHE 817": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 990": "OE1" <-> "OE2" Residue "C PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 88": "OD1" <-> "OD2" Residue "C PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 215": "OD1" <-> "OD2" Residue "C TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 281": "OE1" <-> "OE2" Residue "C TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 389": "OD1" <-> "OD2" Residue "C TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 578": "OD1" <-> "OD2" Residue "C GLU 661": "OE1" <-> "OE2" Residue "C PHE 817": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 990": "OE1" <-> "OE2" Residue "F TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 28203 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 8192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1049, 8192 Classifications: {'peptide': 1049} Incomplete info: {'backbone_only': 2} Link IDs: {'PTRANS': 53, 'TRANS': 995} Chain breaks: 7 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 8192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1049, 8192 Classifications: {'peptide': 1049} Incomplete info: {'backbone_only': 2} Link IDs: {'PTRANS': 53, 'TRANS': 995} Chain breaks: 7 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 8192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1049, 8192 Classifications: {'peptide': 1049} Incomplete info: {'backbone_only': 2} Link IDs: {'PTRANS': 53, 'TRANS': 995} Chain breaks: 7 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 901 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "G" Number of atoms: 901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 901 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "H" Number of atoms: 901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 901 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} 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: "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: "A" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "B" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "C" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Time building chain proxies: 14.94, per 1000 atoms: 0.53 Number of scatterers: 28203 At special positions: 0 Unit cell: (139.92, 149.46, 201.4, 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 132 16.00 O 5547 8.00 N 4638 7.00 C 17886 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.04 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 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=2.04 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=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.04 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.04 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 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=2.04 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=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.04 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 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=2.04 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=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.04 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 50 " - pdb=" SG CYS F 104 " distance=2.04 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 50 " - pdb=" SG CYS G 104 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 50 " - pdb=" SG CYS H 104 " distance=2.04 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 D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 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-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 331 " " NAG A1305 " - " ASN A 343 " " NAG A1306 " - " ASN A 603 " " NAG A1307 " - " ASN A 616 " " NAG A1308 " - " ASN A 657 " " NAG A1309 " - " ASN A 709 " " NAG A1310 " - " ASN A1074 " " NAG A1311 " - " ASN A 165 " " NAG A1312 " - " ASN A 17 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 331 " " NAG B1305 " - " ASN B 343 " " NAG B1306 " - " ASN B 603 " " NAG B1307 " - " ASN B 616 " " NAG B1308 " - " ASN B 657 " " NAG B1309 " - " ASN B 709 " " NAG B1310 " - " ASN B1074 " " NAG B1311 " - " ASN B 165 " " NAG B1312 " - " ASN B 17 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 282 " " NAG C1304 " - " ASN C 331 " " NAG C1305 " - " ASN C 343 " " NAG C1306 " - " ASN C 603 " " NAG C1307 " - " ASN C 616 " " NAG C1308 " - " ASN C 657 " " NAG C1309 " - " ASN C 709 " " NAG C1310 " - " ASN C1074 " " NAG C1311 " - " ASN C 165 " " NAG C1312 " - " ASN C 17 " " NAG D 1 " - " ASN A 234 " " NAG E 1 " - " ASN A 717 " " NAG I 1 " - " ASN A 801 " " NAG J 1 " - " ASN A1098 " " NAG K 1 " - " ASN A1134 " " NAG L 1 " - " ASN B 234 " " NAG M 1 " - " ASN B 717 " " NAG N 1 " - " ASN B 801 " " NAG O 1 " - " ASN B1098 " " NAG P 1 " - " ASN B1134 " " NAG Q 1 " - " ASN C 234 " " NAG R 1 " - " ASN C 717 " " NAG S 1 " - " ASN C 801 " " NAG T 1 " - " ASN C1098 " " NAG U 1 " - " ASN C1134 " Time building additional restraints: 11.98 Conformation dependent library (CDL) restraints added in 4.6 seconds 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6534 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 60 sheets defined 22.1% alpha, 32.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.74 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 365 through 371 Processing helix chain 'A' and resid 385 through 389 removed outlier: 4.147A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 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 Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.673A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 919 removed outlier: 3.955A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 977 through 982 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.410A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 4.591A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER A1147 " --> pdb=" O PRO A1143 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 365 through 371 Processing helix chain 'B' and resid 385 through 389 removed outlier: 4.148A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 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 Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.672A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 919 removed outlier: 3.956A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 977 through 982 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.410A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 4.590A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER B1147 " --> pdb=" O PRO B1143 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 365 through 371 Processing helix chain 'C' and resid 385 through 389 removed outlier: 4.148A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 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 Processing helix chain 'C' and resid 816 through 824 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.672A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 919 removed outlier: 3.955A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 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: 4.410A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.591A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER C1147 " --> pdb=" O PRO C1143 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 91 Processing helix chain 'G' and resid 87 through 91 Processing helix chain 'H' and resid 74 through 76 No H-bonds generated for 'chain 'H' and resid 74 through 76' Processing helix chain 'H' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 4.286A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N HIS A 207 " --> pdb=" O ALA A 222 " (cutoff:3.500A) removed outlier: 8.820A pdb=" N ALA A 222 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 27 through 30 removed outlier: 4.286A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.437A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.936A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.579A pdb=" N GLU A 132 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N SER A 162 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.620A pdb=" N SER A 172 " --> pdb=" O VAL A 126 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 141 through 143 Processing sheet with id=AA8, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.912A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.430A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 348 through 349 removed outlier: 7.302A pdb=" N ALA A 348 " --> pdb=" O VAL A 401 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 348 through 349 removed outlier: 7.302A pdb=" N ALA A 348 " --> pdb=" O VAL A 401 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.328A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.627A pdb=" N ALA A 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N LYS C 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N ASN A 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.648A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 718 through 728 removed outlier: 7.033A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.419A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 787 through 790 Processing sheet with id=AC1, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.434A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 27 through 30 removed outlier: 4.286A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 8.820A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 27 through 30 removed outlier: 4.286A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 42 through 43 removed outlier: 6.437A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.936A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.579A pdb=" N GLU B 132 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N SER B 162 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.621A pdb=" N SER B 172 " --> pdb=" O VAL B 126 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 141 through 143 Processing sheet with id=AC9, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.911A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 348 through 349 removed outlier: 7.301A pdb=" N ALA B 348 " --> pdb=" O VAL B 401 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 348 through 349 removed outlier: 7.301A pdb=" N ALA B 348 " --> pdb=" O VAL B 401 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD4, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.327A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.648A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 718 through 728 removed outlier: 7.033A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.420A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 787 through 790 Processing sheet with id=AD9, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.433A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 27 through 30 removed outlier: 4.287A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 8.821A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 27 through 30 removed outlier: 4.287A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.936A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.578A pdb=" N GLU C 132 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N SER C 162 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.621A pdb=" N SER C 172 " --> pdb=" O VAL C 126 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 141 through 143 Processing sheet with id=AE7, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.911A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 348 through 349 removed outlier: 7.301A pdb=" N ALA C 348 " --> pdb=" O VAL C 401 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 348 through 349 removed outlier: 7.301A pdb=" N ALA C 348 " --> pdb=" O VAL C 401 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF2, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.328A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.648A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 718 through 728 removed outlier: 7.033A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.420A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.434A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'F' and resid 3 through 8 Processing sheet with id=AF8, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.211A pdb=" N GLY F 10 " --> pdb=" O THR F 118 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N SER F 120 " --> pdb=" O GLY F 10 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N VAL F 12 " --> pdb=" O SER F 120 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N ARG F 38 " --> pdb=" O ARG F 47 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N ARG F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.211A pdb=" N GLY F 10 " --> pdb=" O THR F 118 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N SER F 120 " --> pdb=" O GLY F 10 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N VAL F 12 " --> pdb=" O SER F 120 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'G' and resid 3 through 8 Processing sheet with id=AG2, first strand: chain 'G' and resid 10 through 13 removed outlier: 6.210A pdb=" N GLY G 10 " --> pdb=" O THR G 118 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N SER G 120 " --> pdb=" O GLY G 10 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N VAL G 12 " --> pdb=" O SER G 120 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N ARG G 38 " --> pdb=" O ARG G 47 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N ARG G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'G' and resid 10 through 13 removed outlier: 6.210A pdb=" N GLY G 10 " --> pdb=" O THR G 118 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N SER G 120 " --> pdb=" O GLY G 10 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N VAL G 12 " --> pdb=" O SER G 120 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'H' and resid 3 through 8 Processing sheet with id=AG5, first strand: chain 'H' and resid 10 through 13 removed outlier: 6.210A pdb=" N GLY H 10 " --> pdb=" O THR H 118 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N SER H 120 " --> pdb=" O GLY H 10 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N VAL H 12 " --> pdb=" O SER H 120 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N ARG H 38 " --> pdb=" O ARG H 47 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N ARG H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'H' and resid 10 through 13 removed outlier: 6.210A pdb=" N GLY H 10 " --> pdb=" O THR H 118 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N SER H 120 " --> pdb=" O GLY H 10 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N VAL H 12 " --> pdb=" O SER H 120 " (cutoff:3.500A) 1243 hydrogen bonds defined for protein. 3342 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: 14.49 Time building geometry restraints manager: 12.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8423 1.33 - 1.45: 4267 1.45 - 1.57: 15954 1.57 - 1.70: 0 1.70 - 1.82: 168 Bond restraints: 28812 Sorted by residual: bond pdb=" N VAL C 213 " pdb=" CA VAL C 213 " ideal model delta sigma weight residual 1.456 1.489 -0.033 9.50e-03 1.11e+04 1.19e+01 bond pdb=" N VAL A 213 " pdb=" CA VAL A 213 " ideal model delta sigma weight residual 1.456 1.489 -0.033 9.50e-03 1.11e+04 1.18e+01 bond pdb=" N VAL B 213 " pdb=" CA VAL B 213 " ideal model delta sigma weight residual 1.456 1.489 -0.033 9.50e-03 1.11e+04 1.18e+01 bond pdb=" N VAL A1068 " pdb=" CA VAL A1068 " ideal model delta sigma weight residual 1.456 1.486 -0.029 8.70e-03 1.32e+04 1.13e+01 bond pdb=" N VAL C1068 " pdb=" CA VAL C1068 " ideal model delta sigma weight residual 1.456 1.486 -0.029 8.70e-03 1.32e+04 1.12e+01 ... (remaining 28807 not shown) Histogram of bond angle deviations from ideal: 98.52 - 105.69: 675 105.69 - 112.87: 15323 112.87 - 120.05: 11365 120.05 - 127.22: 11691 127.22 - 134.40: 132 Bond angle restraints: 39186 Sorted by residual: angle pdb=" CA ASP C 745 " pdb=" CB ASP C 745 " pdb=" CG ASP C 745 " ideal model delta sigma weight residual 112.60 117.99 -5.39 1.00e+00 1.00e+00 2.91e+01 angle pdb=" CA ASP A 745 " pdb=" CB ASP A 745 " pdb=" CG ASP A 745 " ideal model delta sigma weight residual 112.60 117.97 -5.37 1.00e+00 1.00e+00 2.88e+01 angle pdb=" CA ASP B 745 " pdb=" CB ASP B 745 " pdb=" CG ASP B 745 " ideal model delta sigma weight residual 112.60 117.96 -5.36 1.00e+00 1.00e+00 2.87e+01 angle pdb=" N THR C 618 " pdb=" CA THR C 618 " pdb=" C THR C 618 " ideal model delta sigma weight residual 113.18 106.56 6.62 1.33e+00 5.65e-01 2.48e+01 angle pdb=" N THR B 618 " pdb=" CA THR B 618 " pdb=" C THR B 618 " ideal model delta sigma weight residual 113.18 106.60 6.58 1.33e+00 5.65e-01 2.45e+01 ... (remaining 39181 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 16519 17.79 - 35.58: 1123 35.58 - 53.37: 277 53.37 - 71.16: 42 71.16 - 88.95: 48 Dihedral angle restraints: 18009 sinusoidal: 7845 harmonic: 10164 Sorted by residual: dihedral pdb=" CB CYS C1032 " pdb=" SG CYS C1032 " pdb=" SG CYS C1043 " pdb=" CB CYS C1043 " ideal model delta sinusoidal sigma weight residual 93.00 -178.05 -88.95 1 1.00e+01 1.00e-02 9.42e+01 dihedral pdb=" CB CYS B1032 " pdb=" SG CYS B1032 " pdb=" SG CYS B1043 " pdb=" CB CYS B1043 " ideal model delta sinusoidal sigma weight residual 93.00 -178.05 -88.95 1 1.00e+01 1.00e-02 9.42e+01 dihedral pdb=" CB CYS A1032 " pdb=" SG CYS A1032 " pdb=" SG CYS A1043 " pdb=" CB CYS A1043 " ideal model delta sinusoidal sigma weight residual 93.00 -178.09 -88.91 1 1.00e+01 1.00e-02 9.42e+01 ... (remaining 18006 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.204: 4623 0.204 - 0.408: 6 0.408 - 0.612: 3 0.612 - 0.816: 3 0.816 - 1.019: 3 Chirality restraints: 4638 Sorted by residual: chirality pdb=" C1 NAG C1303 " pdb=" ND2 ASN C 282 " pdb=" C2 NAG C1303 " pdb=" O5 NAG C1303 " both_signs ideal model delta sigma weight residual False -2.40 -1.38 -1.02 2.00e-01 2.50e+01 2.60e+01 chirality pdb=" C1 NAG A1303 " pdb=" ND2 ASN A 282 " pdb=" C2 NAG A1303 " pdb=" O5 NAG A1303 " both_signs ideal model delta sigma weight residual False -2.40 -1.38 -1.02 2.00e-01 2.50e+01 2.60e+01 chirality pdb=" C1 NAG B1303 " pdb=" ND2 ASN B 282 " pdb=" C2 NAG B1303 " pdb=" O5 NAG B1303 " both_signs ideal model delta sigma weight residual False -2.40 -1.38 -1.02 2.00e-01 2.50e+01 2.59e+01 ... (remaining 4635 not shown) Planarity restraints: 5043 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN B 506 " 0.035 5.00e-02 4.00e+02 5.37e-02 4.61e+00 pdb=" N PRO B 507 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO B 507 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 507 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN C 506 " 0.035 5.00e-02 4.00e+02 5.36e-02 4.59e+00 pdb=" N PRO C 507 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO C 507 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO C 507 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 506 " -0.035 5.00e-02 4.00e+02 5.35e-02 4.58e+00 pdb=" N PRO A 507 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO A 507 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 507 " -0.029 5.00e-02 4.00e+02 ... (remaining 5040 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 298 2.63 - 3.20: 25022 3.20 - 3.77: 43116 3.77 - 4.33: 62494 4.33 - 4.90: 100805 Nonbonded interactions: 231735 Sorted by model distance: nonbonded pdb=" OG1 THR A 108 " pdb=" O ASN A 234 " model vdw 2.066 2.440 nonbonded pdb=" OG1 THR B 108 " pdb=" O ASN B 234 " model vdw 2.067 2.440 nonbonded pdb=" OG1 THR C 108 " pdb=" O ASN C 234 " model vdw 2.068 2.440 nonbonded pdb=" OG1 THR C 393 " pdb=" O GLU C 516 " model vdw 2.130 2.440 nonbonded pdb=" OG1 THR B 393 " pdb=" O GLU B 516 " model vdw 2.130 2.440 ... (remaining 231730 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' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' 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' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' } 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: 1.700 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: 7.370 Check model and map are aligned: 0.460 Set scattering table: 0.280 Process input model: 77.390 Find NCS groups from input model: 2.060 Set up NCS constraints: 0.350 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 103.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 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 : 0.011 0.042 28812 Z= 0.746 Angle : 1.126 7.451 39186 Z= 0.794 Chirality : 0.076 1.019 4638 Planarity : 0.004 0.054 4992 Dihedral : 13.391 88.590 11331 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.02 % Favored : 95.80 % Rotamer: Outliers : 1.35 % Allowed : 1.35 % Favored : 97.30 % 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: -0.73 (0.13), residues: 3456 helix: 0.64 (0.20), residues: 693 sheet: -0.30 (0.16), residues: 837 loop : -0.97 (0.13), residues: 1926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP F 111 HIS 0.005 0.002 HIS A 519 PHE 0.019 0.003 PHE B 497 TYR 0.022 0.003 TYR C 265 ARG 0.019 0.001 ARG B 237 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 262 time to evaluate : 3.057 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: A 140 PHE cc_start: 0.9118 (p90) cc_final: 0.8826 (p90) REVERT: A 360 ASN cc_start: 0.9441 (m-40) cc_final: 0.8991 (t0) REVERT: A 370 ASN cc_start: 0.9215 (m-40) cc_final: 0.8939 (p0) REVERT: A 402 ILE cc_start: 0.9311 (pt) cc_final: 0.9036 (pp) REVERT: A 421 TYR cc_start: 0.8822 (m-80) cc_final: 0.8376 (m-10) REVERT: A 453 TYR cc_start: 0.7902 (OUTLIER) cc_final: 0.7654 (p90) REVERT: A 456 PHE cc_start: 0.8631 (m-80) cc_final: 0.8120 (m-10) REVERT: B 140 PHE cc_start: 0.9130 (p90) cc_final: 0.8891 (p90) REVERT: B 370 ASN cc_start: 0.9176 (m-40) cc_final: 0.8847 (p0) REVERT: B 402 ILE cc_start: 0.9353 (pt) cc_final: 0.9084 (pp) REVERT: B 408 ARG cc_start: 0.9182 (pmt-80) cc_final: 0.8971 (pmt-80) REVERT: B 421 TYR cc_start: 0.8788 (m-80) cc_final: 0.8312 (m-10) REVERT: B 453 TYR cc_start: 0.7840 (OUTLIER) cc_final: 0.7578 (p90) REVERT: B 456 PHE cc_start: 0.8695 (m-80) cc_final: 0.8136 (m-10) REVERT: B 492 LEU cc_start: 0.8874 (tp) cc_final: 0.8610 (tm) REVERT: C 140 PHE cc_start: 0.9078 (p90) cc_final: 0.8788 (p90) REVERT: C 360 ASN cc_start: 0.9457 (m-40) cc_final: 0.9059 (t0) REVERT: C 370 ASN cc_start: 0.9216 (m-40) cc_final: 0.8969 (p0) REVERT: C 402 ILE cc_start: 0.9288 (pt) cc_final: 0.9065 (pp) REVERT: C 408 ARG cc_start: 0.9141 (pmt-80) cc_final: 0.8894 (pmt-80) REVERT: C 453 TYR cc_start: 0.8070 (OUTLIER) cc_final: 0.7849 (p90) REVERT: C 456 PHE cc_start: 0.8731 (m-80) cc_final: 0.7899 (m-10) REVERT: F 54 PHE cc_start: 0.8699 (t80) cc_final: 0.8287 (t80) REVERT: G 54 PHE cc_start: 0.8656 (t80) cc_final: 0.7890 (t80) REVERT: H 29 LEU cc_start: 0.8913 (mt) cc_final: 0.8561 (tp) REVERT: H 54 PHE cc_start: 0.8831 (t80) cc_final: 0.8222 (t80) outliers start: 41 outliers final: 3 residues processed: 291 average time/residue: 1.4219 time to fit residues: 481.8837 Evaluate side-chains 156 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 150 time to evaluate : 3.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 453 TYR Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 814 LYS Chi-restraints excluded: chain C residue 453 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 293 optimal weight: 1.9990 chunk 263 optimal weight: 0.1980 chunk 146 optimal weight: 10.0000 chunk 90 optimal weight: 2.9990 chunk 177 optimal weight: 0.5980 chunk 140 optimal weight: 8.9990 chunk 272 optimal weight: 0.8980 chunk 105 optimal weight: 1.9990 chunk 165 optimal weight: 0.9980 chunk 203 optimal weight: 0.8980 chunk 316 optimal weight: 8.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 218 GLN C 957 GLN C1005 GLN ** H 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.1509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 28812 Z= 0.180 Angle : 0.577 7.229 39186 Z= 0.304 Chirality : 0.049 0.593 4638 Planarity : 0.004 0.047 4992 Dihedral : 6.926 56.377 5156 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 1.35 % Allowed : 6.41 % Favored : 92.24 % 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: -0.14 (0.14), residues: 3456 helix: 1.94 (0.20), residues: 663 sheet: -0.11 (0.16), residues: 885 loop : -0.82 (0.13), residues: 1908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP F 111 HIS 0.002 0.000 HIS A1064 PHE 0.023 0.001 PHE C 238 TYR 0.017 0.001 TYR C 495 ARG 0.010 0.001 ARG H 31 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 161 time to evaluate : 3.295 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: A 140 PHE cc_start: 0.9158 (p90) cc_final: 0.8945 (p90) REVERT: A 360 ASN cc_start: 0.9424 (m-40) cc_final: 0.8983 (t0) REVERT: A 370 ASN cc_start: 0.9249 (m-40) cc_final: 0.8954 (p0) REVERT: A 421 TYR cc_start: 0.8934 (m-80) cc_final: 0.8421 (m-10) REVERT: A 456 PHE cc_start: 0.8423 (m-80) cc_final: 0.8132 (m-10) REVERT: B 140 PHE cc_start: 0.9171 (p90) cc_final: 0.8890 (p90) REVERT: B 370 ASN cc_start: 0.9167 (m-40) cc_final: 0.8865 (p0) REVERT: B 408 ARG cc_start: 0.9200 (pmt-80) cc_final: 0.8956 (pmt-80) REVERT: B 421 TYR cc_start: 0.8898 (m-80) cc_final: 0.8354 (m-10) REVERT: B 456 PHE cc_start: 0.8509 (m-80) cc_final: 0.8137 (m-10) REVERT: B 950 ASP cc_start: 0.7987 (m-30) cc_final: 0.7711 (m-30) REVERT: B 1072 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7695 (mp0) REVERT: C 140 PHE cc_start: 0.9137 (p90) cc_final: 0.8822 (p90) REVERT: C 370 ASN cc_start: 0.9226 (m-40) cc_final: 0.8988 (p0) REVERT: C 408 ARG cc_start: 0.9162 (pmt-80) cc_final: 0.8872 (pmt-80) REVERT: C 421 TYR cc_start: 0.8886 (m-80) cc_final: 0.8430 (m-10) REVERT: C 456 PHE cc_start: 0.8473 (m-80) cc_final: 0.8124 (m-10) REVERT: C 950 ASP cc_start: 0.7843 (m-30) cc_final: 0.7600 (m-30) REVERT: F 2 VAL cc_start: 0.1234 (OUTLIER) cc_final: 0.1020 (m) REVERT: F 54 PHE cc_start: 0.8700 (t80) cc_final: 0.8177 (t80) REVERT: G 54 PHE cc_start: 0.8633 (t80) cc_final: 0.8192 (t80) REVERT: H 54 PHE cc_start: 0.8714 (t80) cc_final: 0.8165 (t80) outliers start: 41 outliers final: 13 residues processed: 187 average time/residue: 1.3510 time to fit residues: 297.6346 Evaluate side-chains 154 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 139 time to evaluate : 3.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 921 LYS Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain G residue 57 ILE Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 57 ILE Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 118 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 175 optimal weight: 3.9990 chunk 98 optimal weight: 4.9990 chunk 263 optimal weight: 1.9990 chunk 215 optimal weight: 0.7980 chunk 87 optimal weight: 7.9990 chunk 316 optimal weight: 20.0000 chunk 342 optimal weight: 6.9990 chunk 281 optimal weight: 3.9990 chunk 313 optimal weight: 50.0000 chunk 107 optimal weight: 0.0170 chunk 253 optimal weight: 9.9990 overall best weight: 2.1624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 675 GLN A 762 GLN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN B 675 GLN ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 125 ASN C 675 GLN C1005 GLN ** H 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.2033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 28812 Z= 0.283 Angle : 0.573 8.814 39186 Z= 0.300 Chirality : 0.048 0.538 4638 Planarity : 0.004 0.040 4992 Dihedral : 6.244 58.981 5142 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 1.78 % Allowed : 8.15 % Favored : 90.07 % 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: -0.02 (0.14), residues: 3456 helix: 2.12 (0.20), residues: 660 sheet: 0.12 (0.17), residues: 846 loop : -0.83 (0.13), residues: 1950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 258 HIS 0.003 0.001 HIS A1064 PHE 0.020 0.001 PHE B 238 TYR 0.028 0.001 TYR B 170 ARG 0.009 0.001 ARG C 214 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 144 time to evaluate : 3.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 PHE cc_start: 0.9200 (p90) cc_final: 0.8939 (p90) REVERT: A 360 ASN cc_start: 0.9418 (m-40) cc_final: 0.8973 (t0) REVERT: A 370 ASN cc_start: 0.9270 (m-40) cc_final: 0.8968 (p0) REVERT: A 421 TYR cc_start: 0.8985 (m-80) cc_final: 0.8389 (m-10) REVERT: B 140 PHE cc_start: 0.9228 (p90) cc_final: 0.8882 (p90) REVERT: B 153 MET cc_start: 0.7559 (OUTLIER) cc_final: 0.7214 (mmt) REVERT: B 370 ASN cc_start: 0.9188 (m-40) cc_final: 0.8878 (p0) REVERT: B 408 ARG cc_start: 0.9215 (pmt-80) cc_final: 0.8938 (pmt-80) REVERT: B 421 TYR cc_start: 0.8945 (m-80) cc_final: 0.8357 (m-10) REVERT: B 456 PHE cc_start: 0.8506 (m-80) cc_final: 0.8106 (m-10) REVERT: B 950 ASP cc_start: 0.8084 (m-30) cc_final: 0.7712 (m-30) REVERT: C 140 PHE cc_start: 0.9155 (p90) cc_final: 0.8753 (p90) REVERT: C 370 ASN cc_start: 0.9243 (m-40) cc_final: 0.8991 (p0) REVERT: C 408 ARG cc_start: 0.9217 (pmt-80) cc_final: 0.8979 (pmt-80) REVERT: C 421 TYR cc_start: 0.8929 (m-80) cc_final: 0.8440 (m-10) REVERT: C 456 PHE cc_start: 0.8495 (m-80) cc_final: 0.8133 (m-10) REVERT: C 603 ASN cc_start: 0.8768 (OUTLIER) cc_final: 0.8548 (t0) REVERT: F 54 PHE cc_start: 0.8830 (t80) cc_final: 0.8303 (t80) REVERT: F 76 MET cc_start: 0.4325 (OUTLIER) cc_final: 0.4075 (pmm) REVERT: F 100 VAL cc_start: 0.6521 (OUTLIER) cc_final: 0.6239 (t) REVERT: G 54 PHE cc_start: 0.9012 (t80) cc_final: 0.8529 (t80) REVERT: G 76 MET cc_start: 0.4378 (OUTLIER) cc_final: 0.4071 (pmm) REVERT: H 54 PHE cc_start: 0.8861 (t80) cc_final: 0.8224 (t80) outliers start: 54 outliers final: 20 residues processed: 185 average time/residue: 1.3589 time to fit residues: 296.1820 Evaluate side-chains 155 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 130 time to evaluate : 3.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 921 LYS Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 76 MET Chi-restraints excluded: chain F residue 100 VAL Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain G residue 57 ILE Chi-restraints excluded: chain G residue 76 MET Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain H residue 57 ILE Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 118 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 312 optimal weight: 20.0000 chunk 238 optimal weight: 20.0000 chunk 164 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 151 optimal weight: 8.9990 chunk 212 optimal weight: 5.9990 chunk 317 optimal weight: 6.9990 chunk 336 optimal weight: 9.9990 chunk 165 optimal weight: 3.9990 chunk 301 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 125 ASN A 675 GLN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 GLN ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN B1005 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 675 GLN C1002 GLN ** H 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 28812 Z= 0.281 Angle : 0.561 9.231 39186 Z= 0.292 Chirality : 0.049 0.528 4638 Planarity : 0.004 0.043 4992 Dihedral : 6.073 57.802 5142 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.87 % Allowed : 8.81 % Favored : 89.32 % 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: 0.02 (0.14), residues: 3456 helix: 1.97 (0.20), residues: 681 sheet: 0.17 (0.17), residues: 849 loop : -0.78 (0.13), residues: 1926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 258 HIS 0.002 0.001 HIS B1088 PHE 0.020 0.001 PHE B 168 TYR 0.022 0.001 TYR B 396 ARG 0.012 0.001 ARG C 214 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 141 time to evaluate : 3.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 PHE cc_start: 0.9209 (p90) cc_final: 0.8976 (p90) REVERT: A 153 MET cc_start: 0.7323 (OUTLIER) cc_final: 0.7118 (mmm) REVERT: A 360 ASN cc_start: 0.9414 (m-40) cc_final: 0.8980 (t0) REVERT: A 370 ASN cc_start: 0.9272 (m-40) cc_final: 0.8976 (p0) REVERT: A 900 MET cc_start: 0.8371 (OUTLIER) cc_final: 0.8116 (mtp) REVERT: B 140 PHE cc_start: 0.9201 (p90) cc_final: 0.8885 (p90) REVERT: B 153 MET cc_start: 0.7556 (OUTLIER) cc_final: 0.7240 (mmt) REVERT: B 370 ASN cc_start: 0.9204 (m-40) cc_final: 0.8954 (p0) REVERT: B 456 PHE cc_start: 0.8486 (m-80) cc_final: 0.7954 (m-10) REVERT: B 950 ASP cc_start: 0.8108 (m-30) cc_final: 0.7794 (m-30) REVERT: C 140 PHE cc_start: 0.9139 (p90) cc_final: 0.8725 (p90) REVERT: C 370 ASN cc_start: 0.9251 (m-40) cc_final: 0.8990 (p0) REVERT: C 408 ARG cc_start: 0.9220 (pmt-80) cc_final: 0.8958 (ppt170) REVERT: C 421 TYR cc_start: 0.8926 (m-80) cc_final: 0.8436 (m-10) REVERT: C 456 PHE cc_start: 0.8461 (m-80) cc_final: 0.8118 (m-10) REVERT: C 603 ASN cc_start: 0.8716 (OUTLIER) cc_final: 0.8491 (t0) REVERT: F 54 PHE cc_start: 0.8798 (t80) cc_final: 0.8279 (t80) REVERT: F 76 MET cc_start: 0.4278 (OUTLIER) cc_final: 0.3752 (pmm) REVERT: G 54 PHE cc_start: 0.8999 (t80) cc_final: 0.8553 (t80) REVERT: G 55 ASP cc_start: 0.8979 (t70) cc_final: 0.8734 (t0) REVERT: G 76 MET cc_start: 0.4787 (OUTLIER) cc_final: 0.4493 (pmm) REVERT: H 54 PHE cc_start: 0.8868 (t80) cc_final: 0.8344 (t80) REVERT: H 76 MET cc_start: 0.4350 (OUTLIER) cc_final: 0.3906 (pmm) REVERT: H 77 ASN cc_start: 0.7681 (t0) cc_final: 0.7427 (t0) outliers start: 57 outliers final: 21 residues processed: 177 average time/residue: 1.4309 time to fit residues: 297.9596 Evaluate side-chains 152 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 124 time to evaluate : 3.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain F residue 57 ILE Chi-restraints excluded: chain F residue 76 MET Chi-restraints excluded: chain F residue 80 TYR Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain G residue 57 ILE Chi-restraints excluded: chain G residue 76 MET Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain H residue 57 ILE Chi-restraints excluded: chain H residue 76 MET Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 118 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 280 optimal weight: 0.0370 chunk 190 optimal weight: 0.9980 chunk 4 optimal weight: 7.9990 chunk 250 optimal weight: 8.9990 chunk 138 optimal weight: 5.9990 chunk 287 optimal weight: 0.9980 chunk 232 optimal weight: 6.9990 chunk 0 optimal weight: 30.0000 chunk 171 optimal weight: 0.9980 chunk 301 optimal weight: 0.6980 chunk 84 optimal weight: 6.9990 overall best weight: 0.7458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 GLN ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN ** H 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 28812 Z= 0.154 Angle : 0.522 9.576 39186 Z= 0.273 Chirality : 0.047 0.499 4638 Planarity : 0.003 0.049 4992 Dihedral : 5.664 59.821 5142 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 1.84 % Allowed : 9.50 % Favored : 88.66 % 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: 0.17 (0.14), residues: 3456 helix: 2.18 (0.20), residues: 681 sheet: 0.27 (0.17), residues: 846 loop : -0.72 (0.13), residues: 1929 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP C 258 HIS 0.002 0.000 HIS B1048 PHE 0.015 0.001 PHE B 238 TYR 0.021 0.001 TYR H 109 ARG 0.014 0.001 ARG C 214 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 137 time to evaluate : 3.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 PHE cc_start: 0.9210 (p90) cc_final: 0.8979 (p90) REVERT: A 153 MET cc_start: 0.7202 (OUTLIER) cc_final: 0.6968 (mmm) REVERT: A 370 ASN cc_start: 0.9254 (m-40) cc_final: 0.9007 (p0) REVERT: B 140 PHE cc_start: 0.9185 (p90) cc_final: 0.8887 (p90) REVERT: B 153 MET cc_start: 0.7589 (mmm) cc_final: 0.7259 (mmt) REVERT: B 370 ASN cc_start: 0.9224 (m-40) cc_final: 0.8995 (p0) REVERT: B 456 PHE cc_start: 0.8443 (m-80) cc_final: 0.7930 (m-10) REVERT: B 950 ASP cc_start: 0.7994 (m-30) cc_final: 0.7716 (m-30) REVERT: C 24 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8534 (mm) REVERT: C 140 PHE cc_start: 0.9135 (p90) cc_final: 0.8835 (p90) REVERT: C 370 ASN cc_start: 0.9245 (m-40) cc_final: 0.8991 (p0) REVERT: C 408 ARG cc_start: 0.9229 (pmt-80) cc_final: 0.9006 (pmt-80) REVERT: C 456 PHE cc_start: 0.8405 (m-80) cc_final: 0.8173 (m-10) REVERT: F 54 PHE cc_start: 0.8840 (t80) cc_final: 0.8344 (t80) REVERT: F 55 ASP cc_start: 0.8956 (t70) cc_final: 0.8545 (t0) REVERT: F 76 MET cc_start: 0.4429 (OUTLIER) cc_final: 0.3885 (pmm) REVERT: G 54 PHE cc_start: 0.9060 (t80) cc_final: 0.8630 (t80) REVERT: G 76 MET cc_start: 0.4689 (OUTLIER) cc_final: 0.4252 (pmm) REVERT: H 54 PHE cc_start: 0.8921 (t80) cc_final: 0.8303 (t80) REVERT: H 76 MET cc_start: 0.4560 (OUTLIER) cc_final: 0.4059 (pmm) REVERT: H 77 ASN cc_start: 0.7621 (t0) cc_final: 0.7371 (t0) outliers start: 56 outliers final: 19 residues processed: 175 average time/residue: 1.3735 time to fit residues: 288.3469 Evaluate side-chains 147 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 123 time to evaluate : 3.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 76 MET Chi-restraints excluded: chain F residue 80 TYR Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain G residue 76 MET Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain H residue 76 MET Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 118 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 113 optimal weight: 10.0000 chunk 302 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 chunk 197 optimal weight: 0.0270 chunk 83 optimal weight: 6.9990 chunk 336 optimal weight: 0.9990 chunk 279 optimal weight: 4.9990 chunk 155 optimal weight: 5.9990 chunk 27 optimal weight: 0.0470 chunk 111 optimal weight: 3.9990 chunk 176 optimal weight: 5.9990 overall best weight: 2.0142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN A1002 GLN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN B1005 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 218 GLN C1002 GLN C1005 GLN ** H 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 28812 Z= 0.267 Angle : 0.548 9.436 39186 Z= 0.283 Chirality : 0.049 0.732 4638 Planarity : 0.003 0.050 4992 Dihedral : 5.522 59.289 5142 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 1.71 % Allowed : 10.26 % Favored : 88.03 % 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: 0.19 (0.14), residues: 3456 helix: 2.16 (0.20), residues: 681 sheet: 0.25 (0.17), residues: 849 loop : -0.68 (0.13), residues: 1926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP C 258 HIS 0.002 0.001 HIS A1064 PHE 0.022 0.001 PHE C 168 TYR 0.016 0.001 TYR B 265 ARG 0.015 0.001 ARG C 214 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 134 time to evaluate : 2.946 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 PHE cc_start: 0.9202 (p90) cc_final: 0.8980 (p90) REVERT: A 153 MET cc_start: 0.7145 (OUTLIER) cc_final: 0.6814 (mmm) REVERT: A 370 ASN cc_start: 0.9256 (m-40) cc_final: 0.8996 (p0) REVERT: A 900 MET cc_start: 0.8372 (OUTLIER) cc_final: 0.8110 (mtm) REVERT: B 140 PHE cc_start: 0.9224 (p90) cc_final: 0.8886 (p90) REVERT: B 153 MET cc_start: 0.7539 (OUTLIER) cc_final: 0.7154 (mmt) REVERT: B 370 ASN cc_start: 0.9234 (m-40) cc_final: 0.9001 (p0) REVERT: B 456 PHE cc_start: 0.8432 (m-80) cc_final: 0.8228 (m-10) REVERT: B 950 ASP cc_start: 0.8048 (m-30) cc_final: 0.7717 (m-30) REVERT: C 258 TRP cc_start: 0.7050 (p-90) cc_final: 0.6844 (p-90) REVERT: C 370 ASN cc_start: 0.9265 (m-40) cc_final: 0.8998 (p0) REVERT: C 408 ARG cc_start: 0.9247 (pmt-80) cc_final: 0.9011 (pmt-80) REVERT: C 456 PHE cc_start: 0.8671 (m-80) cc_final: 0.8225 (m-10) REVERT: F 54 PHE cc_start: 0.8857 (t80) cc_final: 0.8300 (t80) REVERT: F 76 MET cc_start: 0.4339 (OUTLIER) cc_final: 0.3791 (pmm) REVERT: G 54 PHE cc_start: 0.9069 (t80) cc_final: 0.8622 (t80) REVERT: G 76 MET cc_start: 0.4774 (OUTLIER) cc_final: 0.4514 (pmm) REVERT: H 54 PHE cc_start: 0.8918 (t80) cc_final: 0.8335 (t80) REVERT: H 76 MET cc_start: 0.4544 (OUTLIER) cc_final: 0.4063 (pmm) REVERT: H 77 ASN cc_start: 0.7625 (t0) cc_final: 0.7399 (t0) outliers start: 52 outliers final: 19 residues processed: 167 average time/residue: 1.3277 time to fit residues: 263.4283 Evaluate side-chains 145 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 120 time to evaluate : 2.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 76 MET Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain G residue 76 MET Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain H residue 57 ILE Chi-restraints excluded: chain H residue 76 MET Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 118 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 324 optimal weight: 0.0470 chunk 37 optimal weight: 10.0000 chunk 191 optimal weight: 0.9990 chunk 245 optimal weight: 9.9990 chunk 190 optimal weight: 2.9990 chunk 283 optimal weight: 7.9990 chunk 188 optimal weight: 2.9990 chunk 335 optimal weight: 0.8980 chunk 209 optimal weight: 8.9990 chunk 204 optimal weight: 0.2980 chunk 154 optimal weight: 4.9990 overall best weight: 1.0482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN C1005 GLN ** H 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.2839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 28812 Z= 0.175 Angle : 0.526 9.843 39186 Z= 0.272 Chirality : 0.047 0.477 4638 Planarity : 0.003 0.058 4992 Dihedral : 5.273 55.428 5142 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 1.55 % Allowed : 10.59 % Favored : 87.87 % 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: 0.28 (0.14), residues: 3456 helix: 2.20 (0.20), residues: 687 sheet: 0.33 (0.17), residues: 843 loop : -0.63 (0.14), residues: 1926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP B 258 HIS 0.003 0.000 HIS C 245 PHE 0.018 0.001 PHE B 565 TYR 0.015 0.001 TYR B 170 ARG 0.016 0.001 ARG A 214 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 131 time to evaluate : 2.815 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: A 370 ASN cc_start: 0.9263 (m-40) cc_final: 0.9031 (p0) REVERT: B 140 PHE cc_start: 0.9219 (p90) cc_final: 0.8894 (p90) REVERT: B 153 MET cc_start: 0.7503 (OUTLIER) cc_final: 0.7151 (mmt) REVERT: B 370 ASN cc_start: 0.9237 (m-40) cc_final: 0.9035 (p0) REVERT: B 456 PHE cc_start: 0.8723 (m-80) cc_final: 0.8240 (m-10) REVERT: C 24 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8560 (mm) REVERT: C 258 TRP cc_start: 0.7012 (p-90) cc_final: 0.6793 (p-90) REVERT: C 370 ASN cc_start: 0.9248 (m-40) cc_final: 0.8995 (p0) REVERT: C 408 ARG cc_start: 0.9254 (pmt-80) cc_final: 0.9002 (pmt-80) REVERT: C 456 PHE cc_start: 0.8683 (m-80) cc_final: 0.7953 (m-10) REVERT: F 54 PHE cc_start: 0.8886 (t80) cc_final: 0.8355 (t80) REVERT: F 76 MET cc_start: 0.4564 (OUTLIER) cc_final: 0.4053 (pmm) REVERT: G 54 PHE cc_start: 0.9145 (t80) cc_final: 0.8667 (t80) REVERT: G 76 MET cc_start: 0.4681 (OUTLIER) cc_final: 0.4455 (pmm) REVERT: H 54 PHE cc_start: 0.8928 (t80) cc_final: 0.8368 (t80) REVERT: H 76 MET cc_start: 0.4595 (OUTLIER) cc_final: 0.4122 (pmm) REVERT: H 77 ASN cc_start: 0.7609 (t0) cc_final: 0.7344 (t0) outliers start: 47 outliers final: 21 residues processed: 160 average time/residue: 1.3411 time to fit residues: 255.1373 Evaluate side-chains 147 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 121 time to evaluate : 3.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 603 ASN Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 1072 GLU Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 76 MET Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain G residue 76 MET Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain H residue 57 ILE Chi-restraints excluded: chain H residue 76 MET Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 118 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 207 optimal weight: 1.9990 chunk 133 optimal weight: 4.9990 chunk 200 optimal weight: 1.9990 chunk 101 optimal weight: 0.6980 chunk 65 optimal weight: 3.9990 chunk 64 optimal weight: 0.8980 chunk 213 optimal weight: 9.9990 chunk 228 optimal weight: 6.9990 chunk 165 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 263 optimal weight: 5.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN C1005 GLN ** H 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.2941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 28812 Z= 0.233 Angle : 0.531 9.843 39186 Z= 0.275 Chirality : 0.047 0.468 4638 Planarity : 0.003 0.056 4992 Dihedral : 5.105 51.309 5142 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 1.41 % Allowed : 10.95 % Favored : 87.64 % 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: 0.31 (0.14), residues: 3456 helix: 2.14 (0.20), residues: 690 sheet: 0.32 (0.16), residues: 879 loop : -0.58 (0.14), residues: 1887 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP B 258 HIS 0.004 0.000 HIS A 245 PHE 0.024 0.001 PHE B 168 TYR 0.016 0.001 TYR C 265 ARG 0.017 0.001 ARG C 214 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 127 time to evaluate : 3.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 370 ASN cc_start: 0.9270 (m-40) cc_final: 0.9036 (p0) REVERT: B 140 PHE cc_start: 0.9211 (p90) cc_final: 0.8898 (p90) REVERT: B 153 MET cc_start: 0.7496 (OUTLIER) cc_final: 0.7148 (mmt) REVERT: B 370 ASN cc_start: 0.9238 (m-40) cc_final: 0.9006 (p0) REVERT: B 456 PHE cc_start: 0.8713 (m-80) cc_final: 0.7929 (m-10) REVERT: C 24 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8622 (mm) REVERT: C 258 TRP cc_start: 0.6992 (p-90) cc_final: 0.6597 (p-90) REVERT: C 370 ASN cc_start: 0.9262 (m-40) cc_final: 0.9000 (p0) REVERT: C 408 ARG cc_start: 0.9266 (pmt-80) cc_final: 0.8934 (pmt-80) REVERT: C 456 PHE cc_start: 0.8487 (m-80) cc_final: 0.8262 (m-10) REVERT: F 54 PHE cc_start: 0.8957 (t80) cc_final: 0.8467 (t80) REVERT: F 76 MET cc_start: 0.4477 (OUTLIER) cc_final: 0.3951 (pmm) REVERT: G 54 PHE cc_start: 0.9160 (t80) cc_final: 0.8673 (t80) REVERT: G 76 MET cc_start: 0.4765 (OUTLIER) cc_final: 0.4349 (pmm) REVERT: H 54 PHE cc_start: 0.8983 (t80) cc_final: 0.8408 (t80) REVERT: H 76 MET cc_start: 0.4600 (OUTLIER) cc_final: 0.4164 (pmm) outliers start: 43 outliers final: 21 residues processed: 156 average time/residue: 1.3372 time to fit residues: 247.7217 Evaluate side-chains 148 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 122 time to evaluate : 3.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 76 MET Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain G residue 76 MET Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain H residue 57 ILE Chi-restraints excluded: chain H residue 76 MET Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 118 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 305 optimal weight: 5.9990 chunk 321 optimal weight: 30.0000 chunk 293 optimal weight: 0.9980 chunk 312 optimal weight: 8.9990 chunk 188 optimal weight: 0.8980 chunk 136 optimal weight: 7.9990 chunk 245 optimal weight: 10.0000 chunk 95 optimal weight: 2.9990 chunk 282 optimal weight: 4.9990 chunk 295 optimal weight: 6.9990 chunk 311 optimal weight: 1.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN B1005 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN C1005 GLN ** H 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.3043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 28812 Z= 0.302 Angle : 0.562 9.806 39186 Z= 0.289 Chirality : 0.047 0.466 4638 Planarity : 0.003 0.057 4992 Dihedral : 5.076 51.960 5142 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 1.38 % Allowed : 11.24 % Favored : 87.38 % 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: 0.33 (0.14), residues: 3456 helix: 2.14 (0.20), residues: 684 sheet: 0.20 (0.16), residues: 909 loop : -0.47 (0.14), residues: 1863 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP B 258 HIS 0.003 0.001 HIS A 245 PHE 0.022 0.001 PHE B 565 TYR 0.017 0.001 TYR B 265 ARG 0.016 0.001 ARG C 214 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 125 time to evaluate : 3.342 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: A 370 ASN cc_start: 0.9242 (m-40) cc_final: 0.8977 (p0) REVERT: B 140 PHE cc_start: 0.9224 (p90) cc_final: 0.8878 (p90) REVERT: B 153 MET cc_start: 0.7390 (OUTLIER) cc_final: 0.7015 (mmt) REVERT: B 370 ASN cc_start: 0.9245 (m-40) cc_final: 0.9010 (p0) REVERT: B 456 PHE cc_start: 0.8381 (m-80) cc_final: 0.8126 (m-10) REVERT: C 24 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8667 (mm) REVERT: C 258 TRP cc_start: 0.6970 (p-90) cc_final: 0.6541 (p-90) REVERT: C 370 ASN cc_start: 0.9269 (m-40) cc_final: 0.8987 (p0) REVERT: C 408 ARG cc_start: 0.9252 (pmt-80) cc_final: 0.8831 (ppt170) REVERT: C 456 PHE cc_start: 0.8725 (m-80) cc_final: 0.8219 (m-10) REVERT: F 54 PHE cc_start: 0.9059 (t80) cc_final: 0.8570 (t80) REVERT: F 76 MET cc_start: 0.4285 (OUTLIER) cc_final: 0.3834 (pmm) REVERT: G 54 PHE cc_start: 0.9204 (t80) cc_final: 0.8732 (t80) REVERT: G 76 MET cc_start: 0.4907 (OUTLIER) cc_final: 0.4463 (pmm) REVERT: H 54 PHE cc_start: 0.9002 (t80) cc_final: 0.8428 (t80) REVERT: H 76 MET cc_start: 0.4694 (OUTLIER) cc_final: 0.4215 (pmm) outliers start: 42 outliers final: 20 residues processed: 156 average time/residue: 1.3165 time to fit residues: 245.6942 Evaluate side-chains 148 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 123 time to evaluate : 3.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 76 MET Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain G residue 76 MET Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain H residue 57 ILE Chi-restraints excluded: chain H residue 76 MET Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 118 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 205 optimal weight: 0.9990 chunk 330 optimal weight: 5.9990 chunk 201 optimal weight: 0.9980 chunk 156 optimal weight: 8.9990 chunk 229 optimal weight: 7.9990 chunk 346 optimal weight: 6.9990 chunk 319 optimal weight: 8.9990 chunk 276 optimal weight: 4.9990 chunk 28 optimal weight: 5.9990 chunk 213 optimal weight: 0.3980 chunk 169 optimal weight: 2.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 481 ASN C1002 GLN C1005 GLN ** H 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.3142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 28812 Z= 0.270 Angle : 0.551 9.960 39186 Z= 0.284 Chirality : 0.047 0.464 4638 Planarity : 0.003 0.059 4992 Dihedral : 4.952 51.732 5142 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.35 % Allowed : 11.18 % Favored : 87.48 % 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: 0.32 (0.14), residues: 3456 helix: 2.15 (0.20), residues: 684 sheet: 0.18 (0.16), residues: 924 loop : -0.49 (0.14), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP B 258 HIS 0.002 0.001 HIS B1088 PHE 0.027 0.001 PHE B 168 TYR 0.017 0.001 TYR B 265 ARG 0.016 0.001 ARG B 214 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6912 Ramachandran restraints generated. 3456 Oldfield, 0 Emsley, 3456 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 126 time to evaluate : 2.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 370 ASN cc_start: 0.9249 (m-40) cc_final: 0.8999 (p0) REVERT: B 140 PHE cc_start: 0.9217 (p90) cc_final: 0.8870 (p90) REVERT: B 153 MET cc_start: 0.7391 (OUTLIER) cc_final: 0.7007 (mmt) REVERT: B 370 ASN cc_start: 0.9247 (m-40) cc_final: 0.9001 (p0) REVERT: B 456 PHE cc_start: 0.8657 (m-80) cc_final: 0.8139 (m-10) REVERT: C 24 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8621 (mm) REVERT: C 258 TRP cc_start: 0.7009 (p-90) cc_final: 0.6568 (p-90) REVERT: C 370 ASN cc_start: 0.9269 (m-40) cc_final: 0.8990 (p0) REVERT: C 378 LYS cc_start: 0.8735 (mptt) cc_final: 0.8535 (mmtt) REVERT: C 408 ARG cc_start: 0.9248 (pmt-80) cc_final: 0.8823 (ppt170) REVERT: C 456 PHE cc_start: 0.8619 (m-80) cc_final: 0.8122 (m-80) REVERT: F 54 PHE cc_start: 0.9084 (t80) cc_final: 0.8586 (t80) REVERT: F 76 MET cc_start: 0.4373 (OUTLIER) cc_final: 0.3907 (pmm) REVERT: G 54 PHE cc_start: 0.9238 (t80) cc_final: 0.8803 (t80) REVERT: G 76 MET cc_start: 0.4966 (OUTLIER) cc_final: 0.4543 (pmm) REVERT: H 54 PHE cc_start: 0.9027 (t80) cc_final: 0.8344 (t80) REVERT: H 76 MET cc_start: 0.4482 (OUTLIER) cc_final: 0.3998 (pmm) outliers start: 41 outliers final: 21 residues processed: 154 average time/residue: 1.3020 time to fit residues: 239.3240 Evaluate side-chains 145 residues out of total 3048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 119 time to evaluate : 3.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 603 ASN Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 76 MET Chi-restraints excluded: chain F residue 115 THR Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain G residue 76 MET Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain H residue 57 ILE Chi-restraints excluded: chain H residue 76 MET Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 118 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 219 optimal weight: 10.0000 chunk 294 optimal weight: 0.8980 chunk 84 optimal weight: 6.9990 chunk 254 optimal weight: 9.9990 chunk 40 optimal weight: 20.0000 chunk 76 optimal weight: 0.2980 chunk 276 optimal weight: 5.9990 chunk 115 optimal weight: 9.9990 chunk 283 optimal weight: 1.9990 chunk 35 optimal weight: 6.9990 chunk 50 optimal weight: 0.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 481 ASN ** B 675 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN B1005 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN C1005 GLN ** H 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.099402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.057069 restraints weight = 70863.176| |-----------------------------------------------------------------------------| r_work (start): 0.2894 rms_B_bonded: 3.37 r_work: 0.2721 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.3220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 28812 Z= 0.268 Angle : 0.554 10.013 39186 Z= 0.286 Chirality : 0.047 0.458 4638 Planarity : 0.003 0.057 4992 Dihedral : 4.920 51.880 5142 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 1.18 % Allowed : 11.60 % Favored : 87.21 % 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: 0.34 (0.14), residues: 3456 helix: 2.18 (0.20), residues: 684 sheet: 0.20 (0.16), residues: 924 loop : -0.47 (0.14), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP B 258 HIS 0.002 0.001 HIS A1064 PHE 0.026 0.001 PHE G 110 TYR 0.017 0.001 TYR C 265 ARG 0.016 0.001 ARG C 214 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6745.98 seconds wall clock time: 122 minutes 50.74 seconds (7370.74 seconds total)