Starting phenix.real_space_refine on Thu Apr 11 20:59:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kdg_22821/04_2024/7kdg_22821.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kdg_22821/04_2024/7kdg_22821.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kdg_22821/04_2024/7kdg_22821.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kdg_22821/04_2024/7kdg_22821.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kdg_22821/04_2024/7kdg_22821.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kdg_22821/04_2024/7kdg_22821.pdb" } resolution = 3.01 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= -0.001 sd= 0.067 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 99 5.16 5 C 15090 2.51 5 N 3852 2.21 5 O 4659 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 465": "OE1" <-> "OE2" Residue "A TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 490": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 578": "OD1" <-> "OD2" Residue "A TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 748": "OE1" <-> "OE2" Residue "A GLU 773": "OE1" <-> "OE2" Residue "A GLU 988": "OE1" <-> "OE2" Residue "A GLU 1111": "OE1" <-> "OE2" Residue "A PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1146": "OD1" <-> "OD2" Residue "B TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 169": "OE1" <-> "OE2" Residue "B TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 298": "OE1" <-> "OE2" Residue "B TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 465": "OE1" <-> "OE2" Residue "B TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 490": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 578": "OD1" <-> "OD2" Residue "B TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 619": "OE1" <-> "OE2" Residue "B TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 773": "OE1" <-> "OE2" Residue "B GLU 988": "OE1" <-> "OE2" Residue "B GLU 1092": "OE1" <-> "OE2" Residue "B PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1146": "OD1" <-> "OD2" Residue "C PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 169": "OE1" <-> "OE2" Residue "C TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 427": "OD1" <-> "OD2" Residue "C TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 465": "OE1" <-> "OE2" Residue "C TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 490": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 578": "OD1" <-> "OD2" Residue "C TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 773": "OE1" <-> "OE2" Residue "C GLU 988": "OE1" <-> "OE2" Residue "C GLU 1111": "OE1" <-> "OE2" Residue "C PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1146": "OD1" <-> "OD2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 23700 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 7606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 972, 7606 Classifications: {'peptide': 972} Link IDs: {'PTRANS': 46, 'TRANS': 925} Chain breaks: 11 Chain: "B" Number of atoms: 7606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 972, 7606 Classifications: {'peptide': 972} Link IDs: {'PTRANS': 46, 'TRANS': 925} Chain breaks: 11 Chain: "C" Number of atoms: 7606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 972, 7606 Classifications: {'peptide': 972} Link IDs: {'PTRANS': 46, 'TRANS': 925} Chain breaks: 11 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 12.51, per 1000 atoms: 0.53 Number of scatterers: 23700 At special positions: 0 Unit cell: (136.32, 127.8, 171.465, 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 99 16.00 O 4659 8.00 N 3852 7.00 C 15090 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.02 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=2.05 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.01 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.04 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.01 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.02 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.05 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.02 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.02 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=2.05 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.01 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=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.04 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.01 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.02 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=2.02 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.02 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.05 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.01 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=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.04 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.01 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.02 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 F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " NAG-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 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 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 D 1 " - " ASN A 234 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A 801 " " NAG G 1 " - " ASN A1098 " " NAG H 1 " - " ASN A1134 " " NAG I 1 " - " ASN B 234 " " NAG J 1 " - " ASN B 717 " " NAG K 1 " - " ASN B 801 " " NAG L 1 " - " ASN B1098 " " NAG M 1 " - " ASN B1134 " " NAG N 1 " - " ASN C 234 " " NAG O 1 " - " ASN C 717 " " NAG P 1 " - " ASN C 801 " " NAG Q 1 " - " ASN C1098 " " NAG R 1 " - " ASN C1134 " Time building additional restraints: 9.41 Conformation dependent library (CDL) restraints added in 4.0 seconds 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5484 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 47 sheets defined 27.2% alpha, 28.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.44 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 349 through 353 removed outlier: 3.953A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 370 removed outlier: 4.177A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 389 removed outlier: 4.559A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.171A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (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 removed outlier: 3.854A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.640A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 913 through 919 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 976 through 984 removed outlier: 3.529A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.152A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1127 through 1129 No H-bonds generated for 'chain 'A' and resid 1127 through 1129' Processing helix chain 'A' and resid 1140 through 1145 removed outlier: 4.305A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (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 349 through 353 removed outlier: 4.074A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 389 removed outlier: 3.544A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.154A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 421 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 755 removed outlier: 4.072A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.859A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.634A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.501A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 919 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 976 through 984 removed outlier: 3.546A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.229A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) Processing helix chain 'B' and resid 1127 through 1129 No H-bonds generated for 'chain 'B' and resid 1127 through 1129' Processing helix chain 'B' and resid 1141 through 1147 Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.941A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 383 through 389 removed outlier: 3.604A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.211A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 755 removed outlier: 4.055A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.823A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 825 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.618A 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 913 through 919 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 976 through 984 removed outlier: 3.523A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.109A pdb=" N VAL C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) Processing helix chain 'C' and resid 1127 through 1129 No H-bonds generated for 'chain 'C' and resid 1127 through 1129' Processing helix chain 'C' and resid 1141 through 1146 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.169A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.334A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.568A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.675A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.675A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.662A 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 Processing sheet with id=AA6, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.588A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.288A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 324 through 328 removed outlier: 4.293A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 324 through 328 removed outlier: 4.293A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AB2, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.886A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 452 through 453 Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.577A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 702 through 704 removed outlier: 6.691A pdb=" N ASN A 703 " --> pdb=" O LYS B 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: 3.623A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.292A 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: 7.208A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.903A 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: 4.441A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 788 through 790 removed outlier: 6.238A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.754A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.176A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.411A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.594A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.689A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC5, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.525A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.290A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.627A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC9, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.673A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 452 through 453 Processing sheet with id=AD2, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.604A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 701 through 704 Processing sheet with id=AD4, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.585A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 718 through 728 removed outlier: 5.694A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.463A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.754A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.126A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.309A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.494A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.624A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AE2, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.596A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.323A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.016A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.810A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AE7, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.604A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.514A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 718 through 728 removed outlier: 7.185A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.468A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.755A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 1058 hydrogen bonds defined for protein. 2892 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: 10.94 Time building geometry restraints manager: 10.18 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: 6182 1.33 - 1.46: 4733 1.46 - 1.58: 13160 1.58 - 1.71: 0 1.71 - 1.83: 123 Bond restraints: 24198 Sorted by residual: bond pdb=" C5 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.413 1.489 -0.076 2.00e-02 2.50e+03 1.45e+01 bond pdb=" C5 NAG M 2 " pdb=" O5 NAG M 2 " ideal model delta sigma weight residual 1.413 1.488 -0.075 2.00e-02 2.50e+03 1.42e+01 bond pdb=" C5 NAG I 2 " pdb=" O5 NAG I 2 " ideal model delta sigma weight residual 1.413 1.488 -0.075 2.00e-02 2.50e+03 1.42e+01 bond pdb=" C5 NAG N 2 " pdb=" O5 NAG N 2 " ideal model delta sigma weight residual 1.413 1.487 -0.074 2.00e-02 2.50e+03 1.38e+01 bond pdb=" C5 NAG B1305 " pdb=" O5 NAG B1305 " ideal model delta sigma weight residual 1.413 1.487 -0.074 2.00e-02 2.50e+03 1.37e+01 ... (remaining 24193 not shown) Histogram of bond angle deviations from ideal: 95.97 - 103.78: 240 103.78 - 111.58: 9377 111.58 - 119.38: 10188 119.38 - 127.18: 12910 127.18 - 134.98: 189 Bond angle restraints: 32904 Sorted by residual: angle pdb=" N CYS A 391 " pdb=" CA CYS A 391 " pdb=" C CYS A 391 " ideal model delta sigma weight residual 109.07 119.91 -10.84 1.52e+00 4.33e-01 5.09e+01 angle pdb=" N CYS C 391 " pdb=" CA CYS C 391 " pdb=" C CYS C 391 " ideal model delta sigma weight residual 109.07 119.48 -10.41 1.52e+00 4.33e-01 4.69e+01 angle pdb=" N CYS B 391 " pdb=" CA CYS B 391 " pdb=" C CYS B 391 " ideal model delta sigma weight residual 109.07 119.39 -10.32 1.52e+00 4.33e-01 4.61e+01 angle pdb=" CA ASP C 796 " pdb=" CB ASP C 796 " pdb=" CG ASP C 796 " ideal model delta sigma weight residual 112.60 118.63 -6.03 1.00e+00 1.00e+00 3.64e+01 angle pdb=" CA ASN A 422 " pdb=" CB ASN A 422 " pdb=" CG ASN A 422 " ideal model delta sigma weight residual 112.60 118.62 -6.02 1.00e+00 1.00e+00 3.63e+01 ... (remaining 32899 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.03: 14256 18.03 - 36.06: 794 36.06 - 54.09: 111 54.09 - 72.12: 32 72.12 - 90.15: 32 Dihedral angle restraints: 15225 sinusoidal: 6735 harmonic: 8490 Sorted by residual: dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual -86.00 -162.66 76.66 1 1.00e+01 1.00e-02 7.38e+01 dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -162.12 76.12 1 1.00e+01 1.00e-02 7.30e+01 dihedral pdb=" CB CYS C1082 " pdb=" SG CYS C1082 " pdb=" SG CYS C1126 " pdb=" CB CYS C1126 " ideal model delta sinusoidal sigma weight residual -86.00 -162.06 76.06 1 1.00e+01 1.00e-02 7.29e+01 ... (remaining 15222 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.105: 2802 0.105 - 0.210: 1023 0.210 - 0.316: 109 0.316 - 0.421: 14 0.421 - 0.526: 3 Chirality restraints: 3951 Sorted by residual: chirality pdb=" C1 NAG P 2 " pdb=" O4 NAG P 1 " pdb=" C2 NAG P 2 " pdb=" O5 NAG P 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.59 0.19 2.00e-02 2.50e+03 8.92e+01 chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.57 0.17 2.00e-02 2.50e+03 7.55e+01 chirality pdb=" C1 NAG N 2 " pdb=" O4 NAG N 1 " pdb=" C2 NAG N 2 " pdb=" O5 NAG N 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.57 0.17 2.00e-02 2.50e+03 7.34e+01 ... (remaining 3948 not shown) Planarity restraints: 4206 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 331 " 0.161 2.00e-02 2.50e+03 1.71e-01 3.67e+02 pdb=" CG ASN C 331 " -0.110 2.00e-02 2.50e+03 pdb=" OD1 ASN C 331 " 0.008 2.00e-02 2.50e+03 pdb=" ND2 ASN C 331 " -0.261 2.00e-02 2.50e+03 pdb=" C1 NAG C1304 " 0.201 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 657 " 0.155 2.00e-02 2.50e+03 1.68e-01 3.52e+02 pdb=" CG ASN A 657 " -0.087 2.00e-02 2.50e+03 pdb=" OD1 ASN A 657 " -0.008 2.00e-02 2.50e+03 pdb=" ND2 ASN A 657 " -0.262 2.00e-02 2.50e+03 pdb=" C1 NAG A1308 " 0.202 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 657 " -0.147 2.00e-02 2.50e+03 1.58e-01 3.11e+02 pdb=" CG ASN C 657 " 0.082 2.00e-02 2.50e+03 pdb=" OD1 ASN C 657 " 0.010 2.00e-02 2.50e+03 pdb=" ND2 ASN C 657 " 0.245 2.00e-02 2.50e+03 pdb=" C1 NAG C1308 " -0.190 2.00e-02 2.50e+03 ... (remaining 4203 not shown) Histogram of nonbonded interaction distances: 2.51 - 2.99: 11492 2.99 - 3.47: 22373 3.47 - 3.95: 39655 3.95 - 4.42: 43974 4.42 - 4.90: 74954 Nonbonded interactions: 192448 Sorted by model distance: nonbonded pdb=" OE2 GLU A 918 " pdb=" OG SER C1123 " model vdw 2.515 2.440 nonbonded pdb=" OG SER A1123 " pdb=" OE2 GLU B 918 " model vdw 2.515 2.440 nonbonded pdb=" OG SER B1123 " pdb=" OE2 GLU C 918 " model vdw 2.517 2.440 nonbonded pdb=" OD1 ASP C 364 " pdb=" OG SER C 366 " model vdw 2.529 2.440 nonbonded pdb=" OD1 ASP A 364 " pdb=" OG SER A 366 " model vdw 2.553 2.440 ... (remaining 192443 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 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } 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: 1.480 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: 7.590 Check model and map are aligned: 0.350 Set scattering table: 0.210 Process input model: 66.820 Find NCS groups from input model: 1.430 Set up NCS constraints: 0.260 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 80.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 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 : 0.014 0.076 24198 Z= 0.903 Angle : 1.758 13.796 32904 Z= 1.181 Chirality : 0.098 0.526 3951 Planarity : 0.013 0.176 4158 Dihedral : 12.134 90.155 9633 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 0.28 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.22 % Favored : 93.46 % Rotamer: Outliers : 0.31 % Allowed : 1.06 % Favored : 98.63 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.92 (0.14), residues: 2844 helix: -0.39 (0.18), residues: 627 sheet: 0.22 (0.20), residues: 552 loop : -0.98 (0.14), residues: 1665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.090 0.022 TRP B 64 HIS 0.009 0.002 HIS B 207 PHE 0.104 0.012 PHE B 718 TYR 0.142 0.020 TYR A 269 ARG 0.009 0.001 ARG B1019 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 2556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 376 time to evaluate : 2.614 Fit side-chains revert: symmetry clash REVERT: A 421 TYR cc_start: 0.7435 (m-80) cc_final: 0.6644 (m-80) REVERT: A 643 PHE cc_start: 0.7983 (t80) cc_final: 0.7712 (t80) REVERT: B 421 TYR cc_start: 0.7030 (m-80) cc_final: 0.5824 (m-80) REVERT: B 508 TYR cc_start: 0.7754 (m-80) cc_final: 0.7360 (m-80) REVERT: B 731 MET cc_start: 0.9143 (ptt) cc_final: 0.8843 (ptt) REVERT: B 855 PHE cc_start: 0.7609 (m-80) cc_final: 0.7333 (m-80) outliers start: 8 outliers final: 1 residues processed: 383 average time/residue: 0.3882 time to fit residues: 226.9187 Evaluate side-chains 199 residues out of total 2556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 198 time to evaluate : 2.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1004 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 245 optimal weight: 2.9990 chunk 220 optimal weight: 0.9990 chunk 122 optimal weight: 6.9990 chunk 75 optimal weight: 0.8980 chunk 148 optimal weight: 0.9990 chunk 117 optimal weight: 3.9990 chunk 228 optimal weight: 1.9990 chunk 88 optimal weight: 0.6980 chunk 138 optimal weight: 6.9990 chunk 169 optimal weight: 0.6980 chunk 264 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 314 GLN A 334 ASN B 437 ASN C 196 ASN C 207 HIS C 314 GLN C 422 ASN C 804 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.2163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 24198 Z= 0.209 Angle : 0.660 10.451 32904 Z= 0.342 Chirality : 0.046 0.215 3951 Planarity : 0.004 0.052 4158 Dihedral : 6.212 57.890 4424 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.41 % Allowed : 5.36 % Favored : 93.23 % 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: -0.04 (0.15), residues: 2844 helix: 1.30 (0.20), residues: 678 sheet: 0.20 (0.18), residues: 678 loop : -0.74 (0.15), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 64 HIS 0.005 0.001 HIS C 207 PHE 0.024 0.002 PHE B 400 TYR 0.020 0.002 TYR B 170 ARG 0.006 0.001 ARG B 237 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 226 time to evaluate : 2.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 508 TYR cc_start: 0.7817 (m-80) cc_final: 0.7374 (m-80) REVERT: B 421 TYR cc_start: 0.7225 (m-80) cc_final: 0.6797 (m-10) outliers start: 36 outliers final: 17 residues processed: 251 average time/residue: 0.3562 time to fit residues: 142.0617 Evaluate side-chains 187 residues out of total 2556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 170 time to evaluate : 2.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 987 VAL Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain B residue 1119 ASN Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1100 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 146 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 219 optimal weight: 7.9990 chunk 179 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 264 optimal weight: 3.9990 chunk 285 optimal weight: 2.9990 chunk 235 optimal weight: 10.0000 chunk 262 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 212 optimal weight: 8.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN A 334 ASN ** A 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS B 394 ASN B 613 GLN B 804 GLN ** B 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 334 ASN C 613 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.2575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.130 24198 Z= 0.363 Angle : 0.640 13.252 32904 Z= 0.332 Chirality : 0.048 0.487 3951 Planarity : 0.004 0.038 4158 Dihedral : 5.856 56.391 4424 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.56 % Allowed : 7.24 % Favored : 91.20 % 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: -0.09 (0.15), residues: 2844 helix: 1.39 (0.20), residues: 678 sheet: 0.12 (0.18), residues: 672 loop : -0.81 (0.15), residues: 1494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 353 HIS 0.008 0.001 HIS B1088 PHE 0.025 0.002 PHE B 168 TYR 0.024 0.002 TYR B 508 ARG 0.010 0.001 ARG C 403 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 2556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 187 time to evaluate : 2.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 731 MET cc_start: 0.9149 (ptt) cc_final: 0.8820 (ptt) outliers start: 40 outliers final: 23 residues processed: 221 average time/residue: 0.3519 time to fit residues: 126.1508 Evaluate side-chains 192 residues out of total 2556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 169 time to evaluate : 2.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1119 ASN Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1119 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 261 optimal weight: 3.9990 chunk 199 optimal weight: 6.9990 chunk 137 optimal weight: 6.9990 chunk 29 optimal weight: 7.9990 chunk 126 optimal weight: 0.9990 chunk 177 optimal weight: 0.8980 chunk 265 optimal weight: 0.9990 chunk 281 optimal weight: 0.9990 chunk 138 optimal weight: 4.9990 chunk 251 optimal weight: 0.9990 chunk 75 optimal weight: 0.9980 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 ASN A 506 GLN ** A 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN B 675 GLN ** B 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.2874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 24198 Z= 0.196 Angle : 0.540 8.272 32904 Z= 0.280 Chirality : 0.044 0.183 3951 Planarity : 0.004 0.037 4158 Dihedral : 5.389 55.205 4424 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.64 % Allowed : 7.98 % Favored : 90.38 % 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: 0.23 (0.15), residues: 2844 helix: 1.90 (0.20), residues: 660 sheet: 0.30 (0.18), residues: 642 loop : -0.69 (0.15), residues: 1542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 353 HIS 0.003 0.001 HIS B1088 PHE 0.022 0.001 PHE B 168 TYR 0.019 0.001 TYR C1067 ARG 0.004 0.000 ARG C 403 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 197 time to evaluate : 3.130 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 42 outliers final: 27 residues processed: 225 average time/residue: 0.3505 time to fit residues: 128.7610 Evaluate side-chains 198 residues out of total 2556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 171 time to evaluate : 2.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain B residue 1119 ASN Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1119 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 234 optimal weight: 4.9990 chunk 159 optimal weight: 2.9990 chunk 4 optimal weight: 0.0770 chunk 209 optimal weight: 2.9990 chunk 116 optimal weight: 3.9990 chunk 240 optimal weight: 0.8980 chunk 194 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 143 optimal weight: 2.9990 chunk 252 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 overall best weight: 1.7944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN A 334 ASN A 613 GLN ** A 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN ** B 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 437 ASN ** C 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.3009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 24198 Z= 0.301 Angle : 0.583 11.794 32904 Z= 0.302 Chirality : 0.047 0.582 3951 Planarity : 0.004 0.040 4158 Dihedral : 5.313 55.502 4424 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 1.96 % Allowed : 8.88 % Favored : 89.16 % 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: 0.09 (0.15), residues: 2844 helix: 1.77 (0.20), residues: 663 sheet: 0.26 (0.18), residues: 642 loop : -0.79 (0.15), residues: 1539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 353 HIS 0.005 0.001 HIS C1088 PHE 0.020 0.002 PHE B1121 TYR 0.021 0.002 TYR C1067 ARG 0.004 0.000 ARG B 190 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 175 time to evaluate : 2.601 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 731 MET cc_start: 0.9101 (ptt) cc_final: 0.8798 (ptt) REVERT: C 192 PHE cc_start: 0.7763 (m-80) cc_final: 0.7488 (m-10) outliers start: 50 outliers final: 32 residues processed: 211 average time/residue: 0.3431 time to fit residues: 117.3132 Evaluate side-chains 201 residues out of total 2556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 169 time to evaluate : 2.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 420 ASP Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 420 ASP Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1119 ASN Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 750 SER Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1119 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 94 optimal weight: 0.8980 chunk 253 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 165 optimal weight: 0.0770 chunk 69 optimal weight: 0.7980 chunk 281 optimal weight: 1.9990 chunk 233 optimal weight: 3.9990 chunk 130 optimal weight: 0.5980 chunk 23 optimal weight: 8.9990 chunk 93 optimal weight: 0.6980 chunk 147 optimal weight: 3.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 ASN ** A 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN ** B 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 334 ASN C 437 ASN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.3206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.063 24198 Z= 0.154 Angle : 0.506 8.069 32904 Z= 0.262 Chirality : 0.043 0.182 3951 Planarity : 0.003 0.040 4158 Dihedral : 4.855 54.440 4424 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.25 % Allowed : 9.86 % Favored : 88.89 % 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 (0.15), residues: 2844 helix: 2.10 (0.20), residues: 663 sheet: 0.35 (0.18), residues: 657 loop : -0.71 (0.15), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 353 HIS 0.002 0.000 HIS C 655 PHE 0.017 0.001 PHE B 347 TYR 0.022 0.001 TYR A 170 ARG 0.003 0.000 ARG B 190 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 200 time to evaluate : 2.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 731 MET cc_start: 0.8996 (ptt) cc_final: 0.8747 (ptt) REVERT: C 437 ASN cc_start: 0.7057 (OUTLIER) cc_final: 0.6740 (m-40) outliers start: 32 outliers final: 23 residues processed: 223 average time/residue: 0.3561 time to fit residues: 129.2995 Evaluate side-chains 197 residues out of total 2556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 173 time to evaluate : 2.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1119 ASN Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 437 ASN Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1119 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 271 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 chunk 160 optimal weight: 3.9990 chunk 205 optimal weight: 10.0000 chunk 159 optimal weight: 2.9990 chunk 237 optimal weight: 9.9990 chunk 157 optimal weight: 0.8980 chunk 280 optimal weight: 4.9990 chunk 175 optimal weight: 0.8980 chunk 170 optimal weight: 0.6980 chunk 129 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN A 613 GLN A 675 GLN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 334 ASN B 613 GLN ** B 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 437 ASN ** C 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.3291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 24198 Z= 0.208 Angle : 0.510 6.913 32904 Z= 0.265 Chirality : 0.043 0.188 3951 Planarity : 0.003 0.039 4158 Dihedral : 4.757 54.784 4424 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.68 % Allowed : 10.21 % Favored : 88.11 % 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: 0.30 (0.15), residues: 2844 helix: 2.05 (0.20), residues: 666 sheet: 0.32 (0.18), residues: 657 loop : -0.70 (0.15), residues: 1521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 353 HIS 0.004 0.001 HIS C 655 PHE 0.016 0.001 PHE B 347 TYR 0.019 0.001 TYR C1067 ARG 0.003 0.000 ARG B 237 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 2556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 185 time to evaluate : 3.013 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 731 MET cc_start: 0.9057 (ptt) cc_final: 0.8783 (ptt) REVERT: C 437 ASN cc_start: 0.7196 (OUTLIER) cc_final: 0.6846 (m-40) outliers start: 43 outliers final: 30 residues processed: 217 average time/residue: 0.3898 time to fit residues: 136.9625 Evaluate side-chains 206 residues out of total 2556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 175 time to evaluate : 2.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1119 ASN Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 437 ASN Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 750 SER Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1119 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 173 optimal weight: 7.9990 chunk 112 optimal weight: 5.9990 chunk 167 optimal weight: 3.9990 chunk 84 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 178 optimal weight: 2.9990 chunk 191 optimal weight: 0.8980 chunk 138 optimal weight: 4.9990 chunk 26 optimal weight: 10.0000 chunk 220 optimal weight: 8.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN A 613 GLN ** A 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 675 GLN ** C 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.3340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 24198 Z= 0.378 Angle : 0.581 7.102 32904 Z= 0.302 Chirality : 0.046 0.226 3951 Planarity : 0.004 0.040 4158 Dihedral : 5.047 56.851 4424 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.88 % Allowed : 10.41 % Favored : 87.72 % 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: 0.03 (0.15), residues: 2844 helix: 1.79 (0.20), residues: 663 sheet: 0.13 (0.18), residues: 663 loop : -0.84 (0.15), residues: 1518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 353 HIS 0.007 0.001 HIS C1088 PHE 0.024 0.002 PHE B1121 TYR 0.022 0.002 TYR C1067 ARG 0.006 0.001 ARG B 403 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 2556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 182 time to evaluate : 2.560 Fit side-chains revert: symmetry clash REVERT: A 314 GLN cc_start: 0.7775 (OUTLIER) cc_final: 0.7541 (mm-40) REVERT: A 731 MET cc_start: 0.9069 (ptt) cc_final: 0.8755 (ptt) outliers start: 48 outliers final: 36 residues processed: 215 average time/residue: 0.3403 time to fit residues: 118.6352 Evaluate side-chains 207 residues out of total 2556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 170 time to evaluate : 2.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 420 ASP Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1119 ASN Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 750 SER Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1119 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 255 optimal weight: 0.7980 chunk 268 optimal weight: 0.5980 chunk 245 optimal weight: 2.9990 chunk 261 optimal weight: 2.9990 chunk 157 optimal weight: 0.8980 chunk 113 optimal weight: 10.0000 chunk 205 optimal weight: 9.9990 chunk 80 optimal weight: 0.2980 chunk 236 optimal weight: 0.8980 chunk 247 optimal weight: 1.9990 chunk 260 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN A 613 GLN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS B 804 GLN ** B 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.3469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 24198 Z= 0.160 Angle : 0.494 7.257 32904 Z= 0.256 Chirality : 0.043 0.197 3951 Planarity : 0.003 0.039 4158 Dihedral : 4.703 55.600 4424 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.45 % Allowed : 10.84 % Favored : 87.72 % 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 (0.15), residues: 2844 helix: 2.17 (0.21), residues: 660 sheet: 0.21 (0.18), residues: 657 loop : -0.72 (0.15), residues: 1527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 353 HIS 0.002 0.000 HIS B 49 PHE 0.016 0.001 PHE B 192 TYR 0.021 0.001 TYR A 313 ARG 0.004 0.000 ARG B 237 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 180 time to evaluate : 2.722 Fit side-chains revert: symmetry clash REVERT: A 731 MET cc_start: 0.9001 (ptt) cc_final: 0.8692 (ptt) REVERT: A 1119 ASN cc_start: 0.7179 (OUTLIER) cc_final: 0.6461 (m110) REVERT: B 571 ASP cc_start: 0.7276 (OUTLIER) cc_final: 0.7010 (t0) REVERT: C 580 GLN cc_start: 0.6339 (mt0) cc_final: 0.6044 (mt0) outliers start: 37 outliers final: 27 residues processed: 207 average time/residue: 0.3417 time to fit residues: 114.9408 Evaluate side-chains 194 residues out of total 2556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 165 time to evaluate : 2.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1119 ASN Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1119 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 171 optimal weight: 0.8980 chunk 276 optimal weight: 3.9990 chunk 168 optimal weight: 3.9990 chunk 131 optimal weight: 0.7980 chunk 192 optimal weight: 2.9990 chunk 289 optimal weight: 0.9990 chunk 266 optimal weight: 0.9980 chunk 230 optimal weight: 7.9990 chunk 23 optimal weight: 10.0000 chunk 178 optimal weight: 3.9990 chunk 141 optimal weight: 0.0670 overall best weight: 0.7520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN A 613 GLN A 804 GLN ** A 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 804 GLN ** B 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.3569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 24198 Z= 0.165 Angle : 0.488 6.682 32904 Z= 0.253 Chirality : 0.043 0.193 3951 Planarity : 0.003 0.041 4158 Dihedral : 4.575 55.073 4424 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.29 % Allowed : 10.80 % Favored : 87.91 % 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: 0.38 (0.15), residues: 2844 helix: 2.29 (0.21), residues: 663 sheet: 0.27 (0.18), residues: 651 loop : -0.68 (0.15), residues: 1530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 353 HIS 0.003 0.001 HIS C 655 PHE 0.021 0.001 PHE C 168 TYR 0.018 0.001 TYR C1067 ARG 0.004 0.000 ARG B 237 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5688 Ramachandran restraints generated. 2844 Oldfield, 0 Emsley, 2844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 2556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 180 time to evaluate : 2.757 Fit side-chains revert: symmetry clash REVERT: A 731 MET cc_start: 0.9009 (ptt) cc_final: 0.8710 (ptt) REVERT: A 1119 ASN cc_start: 0.7111 (OUTLIER) cc_final: 0.6450 (m110) REVERT: B 571 ASP cc_start: 0.7332 (OUTLIER) cc_final: 0.7084 (t0) outliers start: 33 outliers final: 28 residues processed: 204 average time/residue: 0.3418 time to fit residues: 112.7590 Evaluate side-chains 199 residues out of total 2556 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 169 time to evaluate : 2.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 391 CYS Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 750 SER Chi-restraints excluded: chain A residue 1119 ASN Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 738 CYS Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1119 ASN Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 571 ASP Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1114 ILE Chi-restraints excluded: chain C residue 1119 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 183 optimal weight: 3.9990 chunk 245 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 212 optimal weight: 8.9990 chunk 34 optimal weight: 7.9990 chunk 64 optimal weight: 0.2980 chunk 231 optimal weight: 20.0000 chunk 96 optimal weight: 0.9990 chunk 237 optimal weight: 10.0000 chunk 29 optimal weight: 0.9990 chunk 42 optimal weight: 0.7980 overall best weight: 0.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 314 GLN ** A 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 804 GLN ** B 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 914 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.172618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.123807 restraints weight = 30443.195| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 2.77 r_work: 0.3333 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.3646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 24198 Z= 0.169 Angle : 0.483 6.637 32904 Z= 0.250 Chirality : 0.043 0.212 3951 Planarity : 0.003 0.040 4158 Dihedral : 4.508 55.340 4424 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.37 % Allowed : 10.92 % Favored : 87.72 % 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: 0.46 (0.15), residues: 2844 helix: 2.25 (0.21), residues: 666 sheet: 0.27 (0.19), residues: 636 loop : -0.53 (0.15), residues: 1542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 353 HIS 0.003 0.001 HIS A 519 PHE 0.014 0.001 PHE B 192 TYR 0.020 0.001 TYR B 904 ARG 0.004 0.000 ARG B 237 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4897.81 seconds wall clock time: 91 minutes 25.30 seconds (5485.30 seconds total)