Starting phenix.real_space_refine on Wed Jul 24 02:03:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7usa_26730/07_2024/7usa_26730.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7usa_26730/07_2024/7usa_26730.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7usa_26730/07_2024/7usa_26730.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7usa_26730/07_2024/7usa_26730.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7usa_26730/07_2024/7usa_26730.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7usa_26730/07_2024/7usa_26730.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.085 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 126 5.16 5 C 15453 2.51 5 N 3973 2.21 5 O 4755 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 358": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 403": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 420": "OE1" <-> "OE2" Residue "A PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 437": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 482": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 573": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 576": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 590": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 622": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 655": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 658": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 691": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 711": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 712": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 722": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 727": "OD1" <-> "OD2" Residue "A TYR 731": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 773": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 780": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 840": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 901": "OD1" <-> "OD2" Residue "A PHE 905": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 929": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 965": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 978": "OE1" <-> "OE2" Residue "A TYR 980": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 987": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 991": "OD1" <-> "OD2" Residue "A TYR 998": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1078": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1133": "OD1" <-> "OD2" Residue "A TYR 1135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1171": "OE1" <-> "OE2" Residue "A PHE 1217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1260": "OD1" <-> "OD2" Residue "A PHE 1263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 358": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 403": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 420": "OE1" <-> "OE2" Residue "B PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 437": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 482": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 573": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 576": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 590": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 622": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 655": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 658": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 691": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 711": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 712": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 722": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 727": "OD1" <-> "OD2" Residue "B TYR 731": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 737": "OD1" <-> "OD2" Residue "B TYR 773": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 780": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 840": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 901": "OD1" <-> "OD2" Residue "B PHE 905": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 929": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 965": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 978": "OE1" <-> "OE2" Residue "B TYR 980": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 987": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 991": "OD1" <-> "OD2" Residue "B TYR 998": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1078": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 358": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 403": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 420": "OE1" <-> "OE2" Residue "C PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 437": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 467": "OE1" <-> "OE2" Residue "C TYR 482": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 573": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 576": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 590": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 622": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 655": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 658": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 691": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 711": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 712": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 722": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 727": "OD1" <-> "OD2" Residue "C TYR 731": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 737": "OD1" <-> "OD2" Residue "C TYR 773": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 780": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 840": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 901": "OD1" <-> "OD2" Residue "C PHE 905": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 929": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 965": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 978": "OE1" <-> "OE2" Residue "C TYR 980": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 987": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 991": "OD1" <-> "OD2" Residue "C TYR 998": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1078": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1281": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 24307 Number of models: 1 Model: "" Number of chains: 33 Chain: "A" Number of atoms: 7694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1061, 7694 Classifications: {'peptide': 1061} Incomplete info: {'truncation_to_alanine': 156} Link IDs: {'PTRANS': 40, 'TRANS': 1020} Chain breaks: 10 Unresolved non-hydrogen bonds: 509 Unresolved non-hydrogen angles: 652 Unresolved non-hydrogen dihedrals: 395 Unresolved non-hydrogen chiralities: 36 Planarities with less than four sites: {'GLN:plan1': 8, 'TYR:plan': 3, 'ASN:plan1': 18, 'TRP:plan': 2, 'ASP:plan': 31, 'PHE:plan': 3, 'GLU:plan': 18, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 343 Chain: "B" Number of atoms: 7678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1058, 7678 Classifications: {'peptide': 1058} Incomplete info: {'truncation_to_alanine': 150} Link IDs: {'PTRANS': 40, 'TRANS': 1017} Chain breaks: 10 Unresolved non-hydrogen bonds: 495 Unresolved non-hydrogen angles: 631 Unresolved non-hydrogen dihedrals: 379 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'GLN:plan1': 9, 'TYR:plan': 3, 'ASN:plan1': 12, 'TRP:plan': 1, 'ASP:plan': 29, 'PHE:plan': 2, 'GLU:plan': 19, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 317 Chain: "C" Number of atoms: 7693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1062, 7693 Classifications: {'peptide': 1062} Incomplete info: {'truncation_to_alanine': 155} Link IDs: {'PTRANS': 40, 'TRANS': 1021} Chain breaks: 10 Unresolved non-hydrogen bonds: 513 Unresolved non-hydrogen angles: 655 Unresolved non-hydrogen dihedrals: 394 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'GLN:plan1': 11, 'TYR:plan': 4, 'ASN:plan1': 16, 'TRP:plan': 1, 'ASP:plan': 27, 'PHE:plan': 2, 'GLU:plan': 19, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 333 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 14.69, per 1000 atoms: 0.60 Number of scatterers: 24307 At special positions: 0 Unit cell: (144.996, 153.426, 157.641, 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 126 16.00 O 4755 8.00 N 3973 7.00 C 15453 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 250 " - pdb=" SG CYS A 254 " distance=2.13 Simple disulfide: pdb=" SG CYS A 303 " - pdb=" SG CYS A 327 " distance=2.03 Simple disulfide: pdb=" SG CYS A 318 " - pdb=" SG CYS A 444 " distance=2.11 Simple disulfide: pdb=" SG CYS A 372 " - pdb=" SG CYS A 399 " distance=2.03 Simple disulfide: pdb=" SG CYS A 483 " - pdb=" SG CYS A 492 " distance=2.03 Simple disulfide: pdb=" SG CYS A 567 " - pdb=" SG CYS A 626 " distance=2.05 Simple disulfide: pdb=" SG CYS A 581 " - pdb=" SG CYS A 594 " distance=2.07 Simple disulfide: pdb=" SG CYS A 609 " - pdb=" SG CYS A 636 " distance=2.04 Simple disulfide: pdb=" SG CYS A 685 " - pdb=" SG CYS A 736 " distance=2.03 Simple disulfide: pdb=" SG CYS A 797 " - pdb=" SG CYS A 809 " distance=2.03 Simple disulfide: pdb=" SG CYS A 860 " - pdb=" SG CYS A 882 " distance=2.16 Simple disulfide: pdb=" SG CYS A 865 " - pdb=" SG CYS A 871 " distance=2.03 Simple disulfide: pdb=" SG CYS A 983 " - pdb=" SG CYS A 994 " distance=2.04 Simple disulfide: pdb=" SG CYS A1186 " - pdb=" SG CYS A1197 " distance=2.02 Simple disulfide: pdb=" SG CYS A1236 " - pdb=" SG CYS A1287 " distance=2.10 Simple disulfide: pdb=" SG CYS B 250 " - pdb=" SG CYS B 254 " distance=2.13 Simple disulfide: pdb=" SG CYS B 303 " - pdb=" SG CYS B 327 " distance=2.03 Simple disulfide: pdb=" SG CYS B 318 " - pdb=" SG CYS B 444 " distance=2.11 Simple disulfide: pdb=" SG CYS B 372 " - pdb=" SG CYS B 399 " distance=2.03 Simple disulfide: pdb=" SG CYS B 483 " - pdb=" SG CYS B 492 " distance=2.03 Simple disulfide: pdb=" SG CYS B 567 " - pdb=" SG CYS B 626 " distance=2.05 Simple disulfide: pdb=" SG CYS B 581 " - pdb=" SG CYS B 594 " distance=2.07 Simple disulfide: pdb=" SG CYS B 609 " - pdb=" SG CYS B 636 " distance=2.04 Simple disulfide: pdb=" SG CYS B 685 " - pdb=" SG CYS B 736 " distance=2.03 Simple disulfide: pdb=" SG CYS B 797 " - pdb=" SG CYS B 809 " distance=2.03 Simple disulfide: pdb=" SG CYS B 860 " - pdb=" SG CYS B 882 " distance=2.16 Simple disulfide: pdb=" SG CYS B 865 " - pdb=" SG CYS B 871 " distance=2.03 Simple disulfide: pdb=" SG CYS B 983 " - pdb=" SG CYS B 994 " distance=2.05 Simple disulfide: pdb=" SG CYS B1186 " - pdb=" SG CYS B1197 " distance=2.02 Simple disulfide: pdb=" SG CYS B1236 " - pdb=" SG CYS B1287 " distance=2.10 Simple disulfide: pdb=" SG CYS C 250 " - pdb=" SG CYS C 254 " distance=2.13 Simple disulfide: pdb=" SG CYS C 303 " - pdb=" SG CYS C 327 " distance=2.03 Simple disulfide: pdb=" SG CYS C 318 " - pdb=" SG CYS C 444 " distance=2.11 Simple disulfide: pdb=" SG CYS C 372 " - pdb=" SG CYS C 399 " distance=2.03 Simple disulfide: pdb=" SG CYS C 483 " - pdb=" SG CYS C 492 " distance=2.03 Simple disulfide: pdb=" SG CYS C 567 " - pdb=" SG CYS C 626 " distance=2.05 Simple disulfide: pdb=" SG CYS C 581 " - pdb=" SG CYS C 594 " distance=2.07 Simple disulfide: pdb=" SG CYS C 609 " - pdb=" SG CYS C 636 " distance=2.04 Simple disulfide: pdb=" SG CYS C 685 " - pdb=" SG CYS C 736 " distance=2.03 Simple disulfide: pdb=" SG CYS C 797 " - pdb=" SG CYS C 809 " distance=2.03 Simple disulfide: pdb=" SG CYS C 860 " - pdb=" SG CYS C 882 " distance=2.16 Simple disulfide: pdb=" SG CYS C 865 " - pdb=" SG CYS C 871 " distance=2.03 Simple disulfide: pdb=" SG CYS C 983 " - pdb=" SG CYS C 994 " distance=2.04 Simple disulfide: pdb=" SG CYS C1186 " - pdb=" SG CYS C1197 " distance=2.02 Simple disulfide: pdb=" SG CYS C1236 " - pdb=" SG CYS C1287 " distance=2.10 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 J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " NAG-ASN " NAG A1501 " - " ASN A 531 " " NAG A1502 " - " ASN A 553 " " NAG A1503 " - " ASN A 361 " " NAG A1504 " - " ASN A 515 " " NAG A1505 " - " ASN A1293 " " NAG A1506 " - " ASN A 703 " " NAG A1507 " - " ASN A 779 " " NAG A1508 " - " ASN A 561 " " NAG A1509 " - " ASN A 404 " " NAG A1510 " - " ASN A 818 " " NAG B1501 " - " ASN B 531 " " NAG B1502 " - " ASN B 553 " " NAG B1503 " - " ASN B 361 " " NAG B1504 " - " ASN B 515 " " NAG B1505 " - " ASN B1293 " " NAG B1506 " - " ASN B 703 " " NAG B1507 " - " ASN B 779 " " NAG B1508 " - " ASN B 561 " " NAG B1509 " - " ASN B 404 " " NAG B1510 " - " ASN B 818 " " NAG C1501 " - " ASN C 531 " " NAG C1502 " - " ASN C 553 " " NAG C1503 " - " ASN C 361 " " NAG C1504 " - " ASN C 515 " " NAG C1505 " - " ASN C1293 " " NAG C1506 " - " ASN C 703 " " NAG C1507 " - " ASN C 779 " " NAG C1508 " - " ASN C 561 " " NAG C1509 " - " ASN C 404 " " NAG C1510 " - " ASN C 818 " " NAG D 1 " - " ASN A 448 " " NAG E 1 " - " ASN A 920 " " NAG F 1 " - " ASN A1073 " " NAG G 1 " - " ASN A1199 " " NAG H 1 " - " ASN A 833 " " NAG I 1 " - " ASN A 839 " " NAG J 1 " - " ASN A 284 " " NAG K 1 " - " ASN A 724 " " NAG L 1 " - " ASN A 344 " " NAG M 1 " - " ASN B 448 " " NAG N 1 " - " ASN B 920 " " NAG O 1 " - " ASN B1073 " " NAG P 1 " - " ASN B1199 " " NAG Q 1 " - " ASN B 833 " " NAG R 1 " - " ASN B 839 " " NAG S 1 " - " ASN B 284 " " NAG T 1 " - " ASN B 724 " " NAG U 1 " - " ASN B 344 " " NAG V 1 " - " ASN C 448 " " NAG W 1 " - " ASN C 920 " " NAG X 1 " - " ASN C1073 " " NAG Y 1 " - " ASN C1199 " " NAG Z 1 " - " ASN C 833 " " NAG a 1 " - " ASN C 839 " " NAG b 1 " - " ASN C 284 " " NAG c 1 " - " ASN C 724 " " NAG d 1 " - " ASN C 344 " Time building additional restraints: 9.80 Conformation dependent library (CDL) restraints added in 4.4 seconds 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5954 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 39 sheets defined 26.5% alpha, 22.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.96 Creating SS restraints... Processing helix chain 'A' and resid 34 through 44 Processing helix chain 'A' and resid 45 through 47 No H-bonds generated for 'chain 'A' and resid 45 through 47' Processing helix chain 'A' and resid 254 through 259 removed outlier: 3.572A pdb=" N VAL A 258 " --> pdb=" O CYS A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 455 removed outlier: 3.506A pdb=" N GLY A 455 " --> pdb=" O GLY A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 494 removed outlier: 3.724A pdb=" N ILE A 490 " --> pdb=" O HIS A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 618 removed outlier: 4.027A pdb=" N ASN A 617 " --> pdb=" O ASP A 614 " (cutoff:3.500A) Processing helix chain 'A' and resid 859 through 865 Processing helix chain 'A' and resid 868 through 875 removed outlier: 3.556A pdb=" N LYS A 873 " --> pdb=" O PRO A 869 " (cutoff:3.500A) Processing helix chain 'A' and resid 878 through 902 Processing helix chain 'A' and resid 908 through 914 Processing helix chain 'A' and resid 915 through 920 Processing helix chain 'A' and resid 926 through 930 Processing helix chain 'A' and resid 939 through 944 Processing helix chain 'A' and resid 958 through 968 Processing helix chain 'A' and resid 980 through 985 Processing helix chain 'A' and resid 991 through 998 Processing helix chain 'A' and resid 1006 through 1023 Processing helix chain 'A' and resid 1024 through 1026 No H-bonds generated for 'chain 'A' and resid 1024 through 1026' Processing helix chain 'A' and resid 1037 through 1050 Processing helix chain 'A' and resid 1059 through 1079 Processing helix chain 'A' and resid 1093 through 1119 removed outlier: 3.768A pdb=" N LEU A1116 " --> pdb=" O ALA A1112 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR A1117 " --> pdb=" O LEU A1113 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLN A1119 " --> pdb=" O HIS A1115 " (cutoff:3.500A) Processing helix chain 'A' and resid 1120 through 1122 No H-bonds generated for 'chain 'A' and resid 1120 through 1122' Processing helix chain 'A' and resid 1130 through 1136 Processing helix chain 'A' and resid 1139 through 1187 removed outlier: 4.508A pdb=" N ALA A1145 " --> pdb=" O PRO A1141 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG A1149 " --> pdb=" O ALA A1145 " (cutoff:3.500A) Processing helix chain 'A' and resid 1277 through 1279 No H-bonds generated for 'chain 'A' and resid 1277 through 1279' Processing helix chain 'A' and resid 1298 through 1303 Processing helix chain 'B' and resid 35 through 44 Processing helix chain 'B' and resid 45 through 47 No H-bonds generated for 'chain 'B' and resid 45 through 47' Processing helix chain 'B' and resid 254 through 259 removed outlier: 3.572A pdb=" N VAL B 258 " --> pdb=" O CYS B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 455 removed outlier: 3.506A pdb=" N GLY B 455 " --> pdb=" O GLY B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 485 through 494 removed outlier: 3.724A pdb=" N ILE B 490 " --> pdb=" O HIS B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 618 removed outlier: 4.028A pdb=" N ASN B 617 " --> pdb=" O ASP B 614 " (cutoff:3.500A) Processing helix chain 'B' and resid 859 through 865 Processing helix chain 'B' and resid 868 through 875 removed outlier: 3.556A pdb=" N LYS B 873 " --> pdb=" O PRO B 869 " (cutoff:3.500A) Processing helix chain 'B' and resid 878 through 902 Processing helix chain 'B' and resid 908 through 914 Processing helix chain 'B' and resid 915 through 920 Processing helix chain 'B' and resid 926 through 930 Processing helix chain 'B' and resid 939 through 944 Processing helix chain 'B' and resid 958 through 968 Processing helix chain 'B' and resid 980 through 985 Processing helix chain 'B' and resid 991 through 998 Processing helix chain 'B' and resid 1006 through 1023 Processing helix chain 'B' and resid 1024 through 1026 No H-bonds generated for 'chain 'B' and resid 1024 through 1026' Processing helix chain 'B' and resid 1037 through 1050 Processing helix chain 'B' and resid 1059 through 1079 Processing helix chain 'B' and resid 1093 through 1119 removed outlier: 3.768A pdb=" N LEU B1116 " --> pdb=" O ALA B1112 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR B1117 " --> pdb=" O LEU B1113 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLN B1119 " --> pdb=" O HIS B1115 " (cutoff:3.500A) Processing helix chain 'B' and resid 1120 through 1122 No H-bonds generated for 'chain 'B' and resid 1120 through 1122' Processing helix chain 'B' and resid 1130 through 1136 Processing helix chain 'B' and resid 1139 through 1187 removed outlier: 4.508A pdb=" N ALA B1145 " --> pdb=" O PRO B1141 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG B1149 " --> pdb=" O ALA B1145 " (cutoff:3.500A) Processing helix chain 'B' and resid 1277 through 1279 No H-bonds generated for 'chain 'B' and resid 1277 through 1279' Processing helix chain 'B' and resid 1298 through 1303 Processing helix chain 'C' and resid 35 through 44 Processing helix chain 'C' and resid 45 through 47 No H-bonds generated for 'chain 'C' and resid 45 through 47' Processing helix chain 'C' and resid 254 through 259 removed outlier: 3.572A pdb=" N VAL C 258 " --> pdb=" O CYS C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 451 through 455 removed outlier: 3.506A pdb=" N GLY C 455 " --> pdb=" O GLY C 452 " (cutoff:3.500A) Processing helix chain 'C' and resid 485 through 494 removed outlier: 3.723A pdb=" N ILE C 490 " --> pdb=" O HIS C 486 " (cutoff:3.500A) Processing helix chain 'C' and resid 612 through 618 removed outlier: 4.028A pdb=" N ASN C 617 " --> pdb=" O ASP C 614 " (cutoff:3.500A) Processing helix chain 'C' and resid 859 through 865 Processing helix chain 'C' and resid 868 through 875 removed outlier: 3.556A pdb=" N LYS C 873 " --> pdb=" O PRO C 869 " (cutoff:3.500A) Processing helix chain 'C' and resid 878 through 902 Processing helix chain 'C' and resid 908 through 914 Processing helix chain 'C' and resid 915 through 920 Processing helix chain 'C' and resid 926 through 930 Processing helix chain 'C' and resid 939 through 944 Processing helix chain 'C' and resid 958 through 968 Processing helix chain 'C' and resid 980 through 985 Processing helix chain 'C' and resid 991 through 998 Processing helix chain 'C' and resid 1006 through 1023 Processing helix chain 'C' and resid 1024 through 1026 No H-bonds generated for 'chain 'C' and resid 1024 through 1026' Processing helix chain 'C' and resid 1037 through 1050 Processing helix chain 'C' and resid 1059 through 1079 Processing helix chain 'C' and resid 1093 through 1119 removed outlier: 3.768A pdb=" N LEU C1116 " --> pdb=" O ALA C1112 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR C1117 " --> pdb=" O LEU C1113 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLN C1119 " --> pdb=" O HIS C1115 " (cutoff:3.500A) Processing helix chain 'C' and resid 1120 through 1122 No H-bonds generated for 'chain 'C' and resid 1120 through 1122' Processing helix chain 'C' and resid 1130 through 1136 Processing helix chain 'C' and resid 1139 through 1187 removed outlier: 4.508A pdb=" N ALA C1145 " --> pdb=" O PRO C1141 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG C1149 " --> pdb=" O ALA C1145 " (cutoff:3.500A) Processing helix chain 'C' and resid 1277 through 1279 No H-bonds generated for 'chain 'C' and resid 1277 through 1279' Processing helix chain 'C' and resid 1298 through 1303 Processing sheet with id=AA1, first strand: chain 'A' and resid 52 through 57 Processing sheet with id=AA2, first strand: chain 'A' and resid 183 through 184 Processing sheet with id=AA3, first strand: chain 'A' and resid 290 through 307 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 290 through 307 current: chain 'A' and resid 421 through 424 removed outlier: 4.040A pdb=" N HIS A 428 " --> pdb=" O SER A 424 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N PHE A 437 " --> pdb=" O PHE A 429 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N ILE A 431 " --> pdb=" O ASN A 435 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N ASN A 435 " --> pdb=" O ILE A 431 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 434 through 438 current: chain 'A' and resid 477 through 482 Processing sheet with id=AA4, first strand: chain 'A' and resid 313 through 318 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 313 through 318 current: chain 'A' and resid 367 through 373 removed outlier: 7.686A pdb=" N CYS A 399 " --> pdb=" O TYR A 410 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N TYR A 410 " --> pdb=" O CYS A 399 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N VAL A 401 " --> pdb=" O LEU A 408 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 502 through 507 removed outlier: 3.812A pdb=" N GLY A 751 " --> pdb=" O ALA A 743 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 515 through 519 removed outlier: 4.399A pdb=" N ASN A 515 " --> pdb=" O CYS A 685 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N LEU A 720 " --> pdb=" O VAL A 733 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 527 through 540 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 546 through 548 current: chain 'A' and resid 592 through 593 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 592 through 593 current: chain 'A' and resid 648 through 666 Processing sheet with id=AA8, first strand: chain 'A' and resid 799 through 803 removed outlier: 6.753A pdb=" N VAL A 808 " --> pdb=" O ILE A 800 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N THR A 802 " --> pdb=" O ILE A 806 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ILE A 806 " --> pdb=" O THR A 802 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 820 through 822 removed outlier: 6.416A pdb=" N THR A 820 " --> pdb=" O VAL C 906 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 833 through 850 removed outlier: 6.493A pdb=" N ASN A 833 " --> pdb=" O THR A1230 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N THR A1230 " --> pdb=" O ASN A 833 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N THR A 835 " --> pdb=" O THR A1228 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N THR A1228 " --> pdb=" O THR A 835 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N TYR A1226 " --> pdb=" O PRO A 837 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ASN A 839 " --> pdb=" O THR A1224 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N GLY A1213 " --> pdb=" O ALA A1209 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N ALA A1209 " --> pdb=" O GLY A1213 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ILE A1215 " --> pdb=" O ALA A1207 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ALA A1207 " --> pdb=" O ILE A1215 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N PHE A1217 " --> pdb=" O SER A1205 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N SER A1205 " --> pdb=" O PHE A1217 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N THR A1219 " --> pdb=" O LEU A1203 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 856 through 858 Processing sheet with id=AB3, first strand: chain 'A' and resid 905 through 907 Processing sheet with id=AB4, first strand: chain 'A' and resid 1281 through 1284 Processing sheet with id=AB5, first strand: chain 'A' and resid 1253 through 1257 Processing sheet with id=AB6, first strand: chain 'B' and resid 52 through 57 Processing sheet with id=AB7, first strand: chain 'B' and resid 183 through 184 Processing sheet with id=AB8, first strand: chain 'B' and resid 290 through 307 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 290 through 307 current: chain 'B' and resid 421 through 424 removed outlier: 4.040A pdb=" N HIS B 428 " --> pdb=" O SER B 424 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N PHE B 437 " --> pdb=" O PHE B 429 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N ILE B 431 " --> pdb=" O ASN B 435 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N ASN B 435 " --> pdb=" O ILE B 431 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 434 through 438 current: chain 'B' and resid 477 through 482 Processing sheet with id=AB9, first strand: chain 'B' and resid 313 through 318 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 313 through 318 current: chain 'B' and resid 367 through 373 removed outlier: 7.686A pdb=" N CYS B 399 " --> pdb=" O TYR B 410 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N TYR B 410 " --> pdb=" O CYS B 399 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N VAL B 401 " --> pdb=" O LEU B 408 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 502 through 507 removed outlier: 3.813A pdb=" N GLY B 751 " --> pdb=" O ALA B 743 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 515 through 519 removed outlier: 4.399A pdb=" N ASN B 515 " --> pdb=" O CYS B 685 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N LEU B 720 " --> pdb=" O VAL B 733 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 527 through 540 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 546 through 548 current: chain 'B' and resid 592 through 593 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 592 through 593 current: chain 'B' and resid 648 through 666 Processing sheet with id=AC4, first strand: chain 'B' and resid 799 through 803 removed outlier: 6.753A pdb=" N VAL B 808 " --> pdb=" O ILE B 800 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N THR B 802 " --> pdb=" O ILE B 806 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ILE B 806 " --> pdb=" O THR B 802 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 833 through 850 removed outlier: 6.493A pdb=" N ASN B 833 " --> pdb=" O THR B1230 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N THR B1230 " --> pdb=" O ASN B 833 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N THR B 835 " --> pdb=" O THR B1228 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N THR B1228 " --> pdb=" O THR B 835 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N TYR B1226 " --> pdb=" O PRO B 837 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ASN B 839 " --> pdb=" O THR B1224 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N GLY B1213 " --> pdb=" O ALA B1209 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N ALA B1209 " --> pdb=" O GLY B1213 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ILE B1215 " --> pdb=" O ALA B1207 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ALA B1207 " --> pdb=" O ILE B1215 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N PHE B1217 " --> pdb=" O SER B1205 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N SER B1205 " --> pdb=" O PHE B1217 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N THR B1219 " --> pdb=" O LEU B1203 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 856 through 858 Processing sheet with id=AC7, first strand: chain 'B' and resid 905 through 907 Processing sheet with id=AC8, first strand: chain 'B' and resid 1281 through 1284 Processing sheet with id=AC9, first strand: chain 'B' and resid 1253 through 1257 Processing sheet with id=AD1, first strand: chain 'C' and resid 52 through 57 Processing sheet with id=AD2, first strand: chain 'C' and resid 183 through 185 Processing sheet with id=AD3, first strand: chain 'C' and resid 290 through 307 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 290 through 307 current: chain 'C' and resid 421 through 424 removed outlier: 4.040A pdb=" N HIS C 428 " --> pdb=" O SER C 424 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N PHE C 437 " --> pdb=" O PHE C 429 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N ILE C 431 " --> pdb=" O ASN C 435 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N ASN C 435 " --> pdb=" O ILE C 431 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 434 through 438 current: chain 'C' and resid 477 through 482 Processing sheet with id=AD4, first strand: chain 'C' and resid 313 through 318 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 313 through 318 current: chain 'C' and resid 367 through 373 removed outlier: 7.686A pdb=" N CYS C 399 " --> pdb=" O TYR C 410 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N TYR C 410 " --> pdb=" O CYS C 399 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N VAL C 401 " --> pdb=" O LEU C 408 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 502 through 507 removed outlier: 3.812A pdb=" N GLY C 751 " --> pdb=" O ALA C 743 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 515 through 519 removed outlier: 4.399A pdb=" N ASN C 515 " --> pdb=" O CYS C 685 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N LEU C 720 " --> pdb=" O VAL C 733 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 527 through 540 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 546 through 548 current: chain 'C' and resid 592 through 593 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 592 through 593 current: chain 'C' and resid 648 through 666 Processing sheet with id=AD8, first strand: chain 'C' and resid 799 through 803 removed outlier: 6.752A pdb=" N VAL C 808 " --> pdb=" O ILE C 800 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N THR C 802 " --> pdb=" O ILE C 806 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ILE C 806 " --> pdb=" O THR C 802 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 833 through 850 removed outlier: 6.493A pdb=" N ASN C 833 " --> pdb=" O THR C1230 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N THR C1230 " --> pdb=" O ASN C 833 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N THR C 835 " --> pdb=" O THR C1228 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N THR C1228 " --> pdb=" O THR C 835 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N TYR C1226 " --> pdb=" O PRO C 837 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ASN C 839 " --> pdb=" O THR C1224 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N GLY C1213 " --> pdb=" O ALA C1209 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N ALA C1209 " --> pdb=" O GLY C1213 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ILE C1215 " --> pdb=" O ALA C1207 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ALA C1207 " --> pdb=" O ILE C1215 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N PHE C1217 " --> pdb=" O SER C1205 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N SER C1205 " --> pdb=" O PHE C1217 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N THR C1219 " --> pdb=" O LEU C1203 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 856 through 858 Processing sheet with id=AE2, first strand: chain 'C' and resid 1281 through 1284 Processing sheet with id=AE3, first strand: chain 'C' and resid 1253 through 1257 821 hydrogen bonds defined for protein. 2277 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: 10.41 Time building geometry restraints manager: 10.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 6240 1.33 - 1.47: 7733 1.47 - 1.61: 10641 1.61 - 1.75: 9 1.75 - 1.89: 153 Bond restraints: 24776 Sorted by residual: bond pdb=" C CYS A 865 " pdb=" O CYS A 865 " ideal model delta sigma weight residual 1.234 1.345 -0.110 1.16e-02 7.43e+03 9.04e+01 bond pdb=" C CYS B 865 " pdb=" O CYS B 865 " ideal model delta sigma weight residual 1.234 1.344 -0.110 1.16e-02 7.43e+03 8.98e+01 bond pdb=" C CYS C 865 " pdb=" O CYS C 865 " ideal model delta sigma weight residual 1.234 1.344 -0.110 1.16e-02 7.43e+03 8.96e+01 bond pdb=" C CYS A 865 " pdb=" N ASN A 866 " ideal model delta sigma weight residual 1.334 1.266 0.068 1.25e-02 6.40e+03 2.95e+01 bond pdb=" C CYS B 865 " pdb=" N ASN B 866 " ideal model delta sigma weight residual 1.334 1.266 0.068 1.25e-02 6.40e+03 2.94e+01 ... (remaining 24771 not shown) Histogram of bond angle deviations from ideal: 92.50 - 103.39: 294 103.39 - 114.29: 14852 114.29 - 125.18: 18364 125.18 - 136.08: 379 136.08 - 146.97: 6 Bond angle restraints: 33895 Sorted by residual: angle pdb=" N SER C 584 " pdb=" CA SER C 584 " pdb=" C SER C 584 " ideal model delta sigma weight residual 114.56 146.97 -32.41 1.27e+00 6.20e-01 6.51e+02 angle pdb=" N SER B 584 " pdb=" CA SER B 584 " pdb=" C SER B 584 " ideal model delta sigma weight residual 114.56 146.96 -32.40 1.27e+00 6.20e-01 6.51e+02 angle pdb=" N SER A 584 " pdb=" CA SER A 584 " pdb=" C SER A 584 " ideal model delta sigma weight residual 114.56 146.93 -32.37 1.27e+00 6.20e-01 6.50e+02 angle pdb=" N LEU C 585 " pdb=" CA LEU C 585 " pdb=" CB LEU C 585 " ideal model delta sigma weight residual 110.49 140.89 -30.40 1.69e+00 3.50e-01 3.24e+02 angle pdb=" N LEU A 585 " pdb=" CA LEU A 585 " pdb=" CB LEU A 585 " ideal model delta sigma weight residual 110.49 140.86 -30.37 1.69e+00 3.50e-01 3.23e+02 ... (remaining 33890 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.62: 15131 21.62 - 43.25: 442 43.25 - 64.87: 73 64.87 - 86.49: 46 86.49 - 108.11: 24 Dihedral angle restraints: 15716 sinusoidal: 6475 harmonic: 9241 Sorted by residual: dihedral pdb=" N LEU C 585 " pdb=" C LEU C 585 " pdb=" CA LEU C 585 " pdb=" CB LEU C 585 " ideal model delta harmonic sigma weight residual 122.80 149.05 -26.25 0 2.50e+00 1.60e-01 1.10e+02 dihedral pdb=" N LEU A 585 " pdb=" C LEU A 585 " pdb=" CA LEU A 585 " pdb=" CB LEU A 585 " ideal model delta harmonic sigma weight residual 122.80 148.98 -26.18 0 2.50e+00 1.60e-01 1.10e+02 dihedral pdb=" N LEU B 585 " pdb=" C LEU B 585 " pdb=" CA LEU B 585 " pdb=" CB LEU B 585 " ideal model delta harmonic sigma weight residual 122.80 148.97 -26.17 0 2.50e+00 1.60e-01 1.10e+02 ... (remaining 15713 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.344: 4231 0.344 - 0.689: 96 0.689 - 1.033: 6 1.033 - 1.377: 3 1.377 - 1.722: 3 Chirality restraints: 4339 Sorted by residual: chirality pdb=" C1 NAG c 2 " pdb=" O4 NAG c 1 " pdb=" C2 NAG c 2 " pdb=" O5 NAG c 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-02 2.50e+03 1.19e+02 chirality pdb=" C1 NAG T 2 " pdb=" O4 NAG T 1 " pdb=" C2 NAG T 2 " pdb=" O5 NAG T 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-02 2.50e+03 1.19e+02 chirality pdb=" C1 NAG K 2 " pdb=" O4 NAG K 1 " pdb=" C2 NAG K 2 " pdb=" O5 NAG K 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-02 2.50e+03 1.18e+02 ... (remaining 4336 not shown) Planarity restraints: 4267 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG S 2 " 0.226 2.00e-02 2.50e+03 1.91e-01 4.55e+02 pdb=" C7 NAG S 2 " -0.049 2.00e-02 2.50e+03 pdb=" C8 NAG S 2 " -0.041 2.00e-02 2.50e+03 pdb=" N2 NAG S 2 " -0.310 2.00e-02 2.50e+03 pdb=" O7 NAG S 2 " 0.175 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG J 2 " 0.225 2.00e-02 2.50e+03 1.91e-01 4.55e+02 pdb=" C7 NAG J 2 " -0.049 2.00e-02 2.50e+03 pdb=" C8 NAG J 2 " -0.041 2.00e-02 2.50e+03 pdb=" N2 NAG J 2 " -0.310 2.00e-02 2.50e+03 pdb=" O7 NAG J 2 " 0.175 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG b 2 " 0.225 2.00e-02 2.50e+03 1.91e-01 4.54e+02 pdb=" C7 NAG b 2 " -0.049 2.00e-02 2.50e+03 pdb=" C8 NAG b 2 " -0.041 2.00e-02 2.50e+03 pdb=" N2 NAG b 2 " -0.310 2.00e-02 2.50e+03 pdb=" O7 NAG b 2 " 0.175 2.00e-02 2.50e+03 ... (remaining 4264 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.55: 52 2.55 - 3.14: 18892 3.14 - 3.73: 34829 3.73 - 4.31: 53829 4.31 - 4.90: 84693 Nonbonded interactions: 192295 Sorted by model distance: nonbonded pdb=" OG SER B 541 " pdb=" OD2 ASP C 560 " model vdw 1.968 2.440 nonbonded pdb=" CE2 TYR C 235 " pdb=" CZ PHE C 457 " model vdw 2.262 3.640 nonbonded pdb=" CE2 TYR A 235 " pdb=" CZ PHE A 457 " model vdw 2.263 3.640 nonbonded pdb=" CE2 TYR B 235 " pdb=" CZ PHE B 457 " model vdw 2.263 3.640 nonbonded pdb=" N SER B 541 " pdb=" O SER B 541 " model vdw 2.427 2.496 ... (remaining 192290 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 34 through 47 and (name N or name CA or name C or name O \ or name CB )) or resid 48 through 52 or (resid 53 through 55 and (name N or name \ CA or name C or name O or name CB )) or resid 56 through 180 or (resid 181 thro \ ugh 185 and (name N or name CA or name C or name O or name CB )) or resid 193 th \ rough 203 or resid 232 through 237 or (resid 238 through 249 and (name N or name \ CA or name C or name O or name CB )) or resid 250 through 272 or (resid 273 and \ (name N or name CA or name C or name O or name CB )) or resid 274 through 497 o \ r (resid 498 and (name N or name CA or name C or name O or name CB )) or resid 4 \ 99 through 546 or (resid 547 through 548 and (name N or name CA or name C or nam \ e O or name CB )) or resid 549 through 550 or (resid 551 and (name N or name CA \ or name C or name O or name CB )) or resid 552 through 648 or (resid 649 and (na \ me N or name CA or name C or name O or name CB )) or resid 650 through 869 or (r \ esid 870 and (name N or name CA or name C or name O or name CB )) or resid 871 t \ hrough 872 or (resid 873 and (name N or name CA or name C or name O or name CB ) \ ) or resid 874 through 876 or (resid 877 and (name N or name CA or name C or nam \ e O or name CB )) or resid 878 through 885 or (resid 886 and (name N or name CA \ or name C or name O or name CB )) or resid 887 through 922 or (resid 923 and (na \ me N or name CA or name C or name O or name CB )) or resid 924 through 987 or (r \ esid 988 and (name N or name CA or name C or name O or name CB )) or resid 989 t \ hrough 1055 or (resid 1056 through 1059 and (name N or name CA or name C or name \ O or name CB )) or resid 1060 through 1100 or (resid 1101 and (name N or name C \ A or name C or name O or name CB )) or resid 1102 or (resid 1103 and (name N or \ name CA or name C or name O or name CB )) or resid 1104 through 1110 or (resid 1 \ 111 through 1112 and (name N or name CA or name C or name O or name CB )) or res \ id 1113 through 1124 or (resid 1125 through 1126 and (name N or name CA or name \ C or name O or name CB )) or resid 1127 through 1132 or (resid 1133 and (name N \ or name CA or name C or name O or name CB )) or resid 1134 through 1138 or (resi \ d 1139 and (name N or name CA or name C or name O or name CB )) or resid 1140 th \ rough 1147 or (resid 1148 and (name N or name CA or name C or name O or name CB \ )) or resid 1149 through 1163 or (resid 1164 and (name N or name CA or name C or \ name O or name CB )) or resid 1165 through 1170 or (resid 1171 and (name N or n \ ame CA or name C or name O or name CB )) or resid 1172 through 1259 or (resid 12 \ 60 through 1262 and (name N or name CA or name C or name O or name CB )) or resi \ d 1263 through 1287 or (resid 1288 through 1290 and (name N or name CA or name C \ or name O or name CB )) or resid 1291 through 1294 or (resid 1295 through 1299 \ and (name N or name CA or name C or name O or name CB )) or resid 1300 through 1 \ 301 or (resid 1302 through 1303 and (name N or name CA or name C or name O or na \ me CB )) or resid 1501 through 1510)) selection = (chain 'B' and ((resid 34 through 47 and (name N or name CA or name C or name O \ or name CB )) or resid 48 through 200 or (resid 201 through 202 and (name N or n \ ame CA or name C or name O or name CB )) or (resid 203 through 234 and (name N o \ r name CA or name C or name O or name CB )) or resid 235 through 239 or (resid 2 \ 40 through 249 and (name N or name CA or name C or name O or name CB )) or resid \ 250 through 262 or (resid 263 and (name N or name CA or name C or name O or nam \ e CB )) or resid 264 through 272 or (resid 273 and (name N or name CA or name C \ or name O or name CB )) or resid 274 through 308 or (resid 309 and (name N or na \ me CA or name C or name O or name CB )) or resid 310 through 314 or (resid 315 a \ nd (name N or name CA or name C or name O or name CB )) or resid 316 through 325 \ or (resid 326 and (name N or name CA or name C or name O or name CB )) or resid \ 327 or (resid 328 through 330 and (name N or name CA or name C or name O or nam \ e CB )) or resid 331 through 332 or (resid 333 through 334 and (name N or name C \ A or name C or name O or name CB )) or resid 335 through 347 or (resid 348 and ( \ name N or name CA or name C or name O or name CB )) or resid 349 or (resid 350 a \ nd (name N or name CA or name C or name O or name CB )) or resid 351 through 362 \ or (resid 363 and (name N or name CA or name C or name O or name CB )) or resid \ 364 through 368 or (resid 369 and (name N or name CA or name C or name O or nam \ e CB )) or resid 370 through 538 or (resid 539 through 541 and (name N or name C \ A or name C or name O or name CB )) or resid 542 through 587 or (resid 588 throu \ gh 589 and (name N or name CA or name C or name O or name CB )) or resid 590 or \ (resid 591 through 593 and (name N or name CA or name C or name O or name CB )) \ or resid 594 through 596 or (resid 597 and (name N or name CA or name C or name \ O or name CB )) or resid 598 through 627 or (resid 628 and (name N or name CA or \ name C or name O or name CB )) or resid 629 through 631 or (resid 632 and (name \ N or name CA or name C or name O or name CB )) or resid 633 through 638 or (res \ id 639 and (name N or name CA or name C or name O or name CB )) or resid 640 thr \ ough 648 or (resid 649 and (name N or name CA or name C or name O or name CB )) \ or resid 650 through 662 or (resid 663 and (name N or name CA or name C or name \ O or name CB )) or resid 664 through 677 or (resid 678 and (name N or name CA or \ name C or name O or name CB )) or resid 679 through 682 or (resid 683 and (name \ N or name CA or name C or name O or name CB )) or resid 684 through 686 or (res \ id 687 and (name N or name CA or name C or name O or name CB )) or resid 688 thr \ ough 736 or (resid 737 and (name N or name CA or name C or name O or name CB )) \ or resid 738 through 745 or (resid 746 and (name N or name CA or name C or name \ O or name CB )) or resid 747 through 876 or (resid 877 and (name N or name CA or \ name C or name O or name CB )) or resid 878 through 885 or (resid 886 and (name \ N or name CA or name C or name O or name CB )) or resid 887 through 965 or (res \ id 966 and (name N or name CA or name C or name O or name CB )) or resid 967 thr \ ough 1009 or (resid 1010 and (name N or name CA or name C or name O or name CB ) \ ) or resid 1011 through 1055 or (resid 1056 through 1059 and (name N or name CA \ or name C or name O or name CB )) or resid 1060 through 1108 or (resid 1109 and \ (name N or name CA or name C or name O or name CB )) or resid 1110 through 1147 \ or (resid 1148 and (name N or name CA or name C or name O or name CB )) or resid \ 1149 through 1303 or resid 1501 through 1510)) selection = (chain 'C' and ((resid 34 through 47 and (name N or name CA or name C or name O \ or name CB )) or resid 48 through 185 or (resid 193 through 202 and (name N or n \ ame CA or name C or name O or name CB )) or resid 203 or resid 232 through 308 o \ r (resid 309 and (name N or name CA or name C or name O or name CB )) or resid 3 \ 10 through 314 or (resid 315 and (name N or name CA or name C or name O or name \ CB )) or resid 316 through 327 or (resid 328 through 330 and (name N or name CA \ or name C or name O or name CB )) or resid 331 through 332 or (resid 333 through \ 334 and (name N or name CA or name C or name O or name CB )) or resid 335 throu \ gh 347 or (resid 348 and (name N or name CA or name C or name O or name CB )) or \ resid 349 or (resid 350 and (name N or name CA or name C or name O or name CB ) \ ) or resid 351 through 362 or (resid 363 and (name N or name CA or name C or nam \ e O or name CB )) or resid 364 through 442 or (resid 443 and (name N or name CA \ or name C or name O or name CB )) or resid 444 through 466 or (resid 467 through \ 468 and (name N or name CA or name C or name O or name CB )) or resid 469 throu \ gh 534 or (resid 535 and (name N or name CA or name C or name O or name CB )) or \ resid 536 through 539 or (resid 540 through 541 and (name N or name CA or name \ C or name O or name CB )) or resid 542 through 546 or (resid 547 through 548 and \ (name N or name CA or name C or name O or name CB )) or resid 549 through 550 o \ r (resid 551 and (name N or name CA or name C or name O or name CB )) or resid 5 \ 52 through 559 or (resid 560 and (name N or name CA or name C or name O or name \ CB )) or resid 561 through 563 or (resid 564 and (name N or name CA or name C or \ name O or name CB )) or resid 565 through 578 or (resid 579 and (name N or name \ CA or name C or name O or name CB )) or resid 580 through 613 or (resid 614 and \ (name N or name CA or name C or name O or name CB )) or resid 615 through 627 o \ r (resid 628 and (name N or name CA or name C or name O or name CB )) or resid 6 \ 29 through 631 or (resid 632 and (name N or name CA or name C or name O or name \ CB )) or resid 633 through 662 or (resid 663 and (name N or name CA or name C or \ name O or name CB )) or resid 664 through 669 or (resid 677 through 678 and (na \ me N or name CA or name C or name O or name CB )) or resid 679 through 682 or (r \ esid 683 and (name N or name CA or name C or name O or name CB )) or resid 684 t \ hrough 686 or (resid 687 and (name N or name CA or name C or name O or name CB ) \ ) or resid 688 through 736 or (resid 737 and (name N or name CA or name C or nam \ e O or name CB )) or resid 738 through 745 or (resid 746 and (name N or name CA \ or name C or name O or name CB )) or resid 747 through 922 or (resid 923 and (na \ me N or name CA or name C or name O or name CB )) or resid 924 through 1102 or ( \ resid 1103 and (name N or name CA or name C or name O or name CB )) or resid 110 \ 4 through 1110 or (resid 1111 through 1112 and (name N or name CA or name C or n \ ame O or name CB )) or resid 1113 through 1287 or (resid 1288 through 1290 and ( \ name N or name CA or name C or name O or name CB )) or resid 1291 through 1294 o \ r (resid 1295 through 1299 and (name N or name CA or name C or name O or name CB \ )) or resid 1300 through 1303 or resid 1501 through 1510)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'T' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'c' } ncs_group { reference = chain 'J' selection = chain 'L' selection = chain 'S' selection = chain 'U' selection = chain 'b' selection = chain 'd' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.820 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: 0.930 Check model and map are aligned: 0.180 Set scattering table: 0.220 Process input model: 68.040 Find NCS groups from input model: 4.830 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 96.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 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 : 0.015 0.110 24776 Z= 0.963 Angle : 1.600 32.410 33895 Z= 1.035 Chirality : 0.130 1.722 4339 Planarity : 0.010 0.191 4210 Dihedral : 12.194 108.114 9627 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 1.95 Ramachandran Plot: Outliers : 0.29 % Allowed : 3.50 % Favored : 96.21 % Rotamer: Outliers : 0.04 % Allowed : 1.53 % Favored : 98.43 % Cbeta Deviations : 0.60 % 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 (0.14), residues: 3115 helix: 0.36 (0.17), residues: 705 sheet: 0.69 (0.17), residues: 783 loop : -0.31 (0.15), residues: 1627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.007 TRP C 458 HIS 0.005 0.001 HIS A1202 PHE 0.022 0.003 PHE C 524 TYR 0.046 0.006 TYR A1016 ARG 0.003 0.001 ARG C 397 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 391 time to evaluate : 2.434 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 392 average time/residue: 1.1170 time to fit residues: 515.5929 Evaluate side-chains 217 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 216 time to evaluate : 2.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 779 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 267 optimal weight: 0.9980 chunk 240 optimal weight: 0.5980 chunk 133 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 chunk 162 optimal weight: 0.9980 chunk 128 optimal weight: 0.7980 chunk 248 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 151 optimal weight: 0.8980 chunk 184 optimal weight: 0.8980 chunk 287 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 619 HIS A1076 GLN A1103 GLN A1107 ASN A1122 ASN B 578 HIS B 619 HIS B1076 GLN B1107 ASN B1109 GLN B1122 ASN B1208 ASN C 578 HIS C 619 HIS C1076 GLN C1103 GLN C1107 ASN C1122 ASN C1208 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 24776 Z= 0.223 Angle : 0.625 13.990 33895 Z= 0.321 Chirality : 0.049 0.497 4339 Planarity : 0.004 0.043 4210 Dihedral : 9.163 72.354 5241 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 2.12 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.18 % Favored : 97.69 % Rotamer: Outliers : 2.75 % Allowed : 6.59 % Favored : 90.67 % 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: 0.58 (0.15), residues: 3115 helix: 1.70 (0.19), residues: 711 sheet: 0.58 (0.18), residues: 756 loop : -0.24 (0.15), residues: 1648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 458 HIS 0.004 0.001 HIS B 821 PHE 0.016 0.002 PHE A 457 TYR 0.021 0.002 TYR B 398 ARG 0.004 0.000 ARG A1149 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 247 time to evaluate : 2.527 Fit side-chains revert: symmetry clash REVERT: A 471 GLN cc_start: 0.8380 (OUTLIER) cc_final: 0.7742 (tm-30) REVERT: A 576 TYR cc_start: 0.8750 (m-80) cc_final: 0.8494 (m-80) REVERT: A 956 TYR cc_start: 0.6252 (t80) cc_final: 0.6001 (t80) REVERT: A 1111 GLN cc_start: 0.8170 (mt0) cc_final: 0.7961 (mt0) REVERT: B 478 LYS cc_start: 0.8391 (OUTLIER) cc_final: 0.7926 (mtpp) REVERT: B 1104 ASP cc_start: 0.7872 (t0) cc_final: 0.7649 (t0) REVERT: B 1185 GLU cc_start: 0.8697 (OUTLIER) cc_final: 0.8181 (mt-10) REVERT: C 471 GLN cc_start: 0.8273 (OUTLIER) cc_final: 0.7896 (tm-30) REVERT: C 478 LYS cc_start: 0.8336 (OUTLIER) cc_final: 0.7822 (mtpp) outliers start: 63 outliers final: 24 residues processed: 282 average time/residue: 0.9549 time to fit residues: 327.1350 Evaluate side-chains 232 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 203 time to evaluate : 2.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain A residue 372 CYS Chi-restraints excluded: chain A residue 454 SER Chi-restraints excluded: chain A residue 471 GLN Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 922 THR Chi-restraints excluded: chain A residue 924 ASN Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 315 SER Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 454 SER Chi-restraints excluded: chain B residue 478 LYS Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 580 THR Chi-restraints excluded: chain B residue 628 SER Chi-restraints excluded: chain B residue 922 THR Chi-restraints excluded: chain B residue 924 ASN Chi-restraints excluded: chain B residue 1185 GLU Chi-restraints excluded: chain C residue 315 SER Chi-restraints excluded: chain C residue 371 SER Chi-restraints excluded: chain C residue 471 GLN Chi-restraints excluded: chain C residue 478 LYS Chi-restraints excluded: chain C residue 533 THR Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 628 SER Chi-restraints excluded: chain C residue 922 THR Chi-restraints excluded: chain C residue 924 ASN Chi-restraints excluded: chain C residue 992 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 159 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 239 optimal weight: 0.1980 chunk 196 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 288 optimal weight: 1.9990 chunk 311 optimal weight: 0.9990 chunk 256 optimal weight: 4.9990 chunk 285 optimal weight: 0.7980 chunk 98 optimal weight: 1.9990 chunk 231 optimal weight: 0.9990 overall best weight: 0.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 ASN A 527 HIS A1208 ASN B 527 HIS B 578 HIS B 883 GLN B 887 GLN C 302 ASN C 474 ASN C 527 HIS C 578 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 24776 Z= 0.201 Angle : 0.574 14.604 33895 Z= 0.291 Chirality : 0.048 0.397 4339 Planarity : 0.004 0.049 4210 Dihedral : 7.099 59.156 5239 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.38 % Favored : 97.53 % Rotamer: Outliers : 2.83 % Allowed : 7.68 % Favored : 89.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.15), residues: 3115 helix: 2.21 (0.19), residues: 717 sheet: 0.54 (0.18), residues: 727 loop : -0.25 (0.15), residues: 1671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 458 HIS 0.003 0.001 HIS A 765 PHE 0.015 0.001 PHE B 457 TYR 0.020 0.001 TYR A1016 ARG 0.003 0.000 ARG B1149 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 233 time to evaluate : 2.762 Fit side-chains revert: symmetry clash REVERT: A 471 GLN cc_start: 0.8386 (OUTLIER) cc_final: 0.7690 (tm-30) REVERT: A 576 TYR cc_start: 0.8811 (m-80) cc_final: 0.8534 (m-80) REVERT: A 956 TYR cc_start: 0.6275 (t80) cc_final: 0.6041 (t80) REVERT: A 1111 GLN cc_start: 0.8174 (mt0) cc_final: 0.7934 (mt0) REVERT: B 471 GLN cc_start: 0.8318 (OUTLIER) cc_final: 0.7858 (tm-30) REVERT: B 478 LYS cc_start: 0.8438 (OUTLIER) cc_final: 0.7969 (mtpp) REVERT: B 1104 ASP cc_start: 0.7736 (t0) cc_final: 0.7507 (t0) REVERT: B 1185 GLU cc_start: 0.8718 (OUTLIER) cc_final: 0.8208 (mt-10) REVERT: C 471 GLN cc_start: 0.8319 (OUTLIER) cc_final: 0.7829 (tm-30) REVERT: C 478 LYS cc_start: 0.8387 (OUTLIER) cc_final: 0.7912 (mtpp) outliers start: 65 outliers final: 30 residues processed: 270 average time/residue: 0.9143 time to fit residues: 304.0464 Evaluate side-chains 237 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 201 time to evaluate : 2.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain A residue 372 CYS Chi-restraints excluded: chain A residue 471 GLN Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 922 THR Chi-restraints excluded: chain A residue 1015 MET Chi-restraints excluded: chain A residue 1118 VAL Chi-restraints excluded: chain B residue 315 SER Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 471 GLN Chi-restraints excluded: chain B residue 478 LYS Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 580 THR Chi-restraints excluded: chain B residue 628 SER Chi-restraints excluded: chain B residue 922 THR Chi-restraints excluded: chain B residue 924 ASN Chi-restraints excluded: chain B residue 1007 VAL Chi-restraints excluded: chain B residue 1118 VAL Chi-restraints excluded: chain B residue 1185 GLU Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain C residue 315 SER Chi-restraints excluded: chain C residue 371 SER Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain C residue 471 GLN Chi-restraints excluded: chain C residue 478 LYS Chi-restraints excluded: chain C residue 533 THR Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 628 SER Chi-restraints excluded: chain C residue 736 CYS Chi-restraints excluded: chain C residue 922 THR Chi-restraints excluded: chain C residue 924 ASN Chi-restraints excluded: chain C residue 992 LEU Chi-restraints excluded: chain C residue 1007 VAL Chi-restraints excluded: chain C residue 1118 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 284 optimal weight: 0.4980 chunk 216 optimal weight: 9.9990 chunk 149 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 137 optimal weight: 3.9990 chunk 193 optimal weight: 0.9990 chunk 289 optimal weight: 0.7980 chunk 306 optimal weight: 2.9990 chunk 151 optimal weight: 2.9990 chunk 274 optimal weight: 0.9980 chunk 82 optimal weight: 4.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 ASN A 649 GLN A1122 ASN A1258 ASN B 302 ASN ** B 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 883 GLN B1122 ASN C1122 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 24776 Z= 0.261 Angle : 0.614 21.631 33895 Z= 0.311 Chirality : 0.049 0.384 4339 Planarity : 0.004 0.045 4210 Dihedral : 6.591 59.959 5239 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.44 % Favored : 97.46 % Rotamer: Outliers : 3.10 % Allowed : 8.63 % Favored : 88.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.65 (0.15), residues: 3115 helix: 2.36 (0.20), residues: 699 sheet: 0.56 (0.18), residues: 723 loop : -0.44 (0.15), residues: 1693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 426 HIS 0.004 0.001 HIS B 619 PHE 0.012 0.001 PHE A 457 TYR 0.023 0.001 TYR B 778 ARG 0.003 0.000 ARG C1149 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 225 time to evaluate : 2.526 Fit side-chains revert: symmetry clash REVERT: A 317 PHE cc_start: 0.7345 (OUTLIER) cc_final: 0.6928 (t80) REVERT: A 471 GLN cc_start: 0.8377 (OUTLIER) cc_final: 0.7645 (tm-30) REVERT: A 576 TYR cc_start: 0.8856 (m-80) cc_final: 0.8638 (m-80) REVERT: A 753 MET cc_start: 0.8332 (mpt) cc_final: 0.8015 (mpt) REVERT: A 1260 ASP cc_start: 0.6324 (OUTLIER) cc_final: 0.6099 (m-30) REVERT: B 471 GLN cc_start: 0.8347 (OUTLIER) cc_final: 0.7818 (tm-30) REVERT: B 478 LYS cc_start: 0.8479 (OUTLIER) cc_final: 0.8032 (mtpp) REVERT: B 1104 ASP cc_start: 0.7774 (t0) cc_final: 0.7539 (t0) REVERT: B 1185 GLU cc_start: 0.8760 (OUTLIER) cc_final: 0.8271 (mt-10) REVERT: C 317 PHE cc_start: 0.7536 (OUTLIER) cc_final: 0.7178 (t80) REVERT: C 471 GLN cc_start: 0.8316 (OUTLIER) cc_final: 0.7786 (tm-30) REVERT: C 478 LYS cc_start: 0.8404 (OUTLIER) cc_final: 0.7992 (mtpp) outliers start: 71 outliers final: 43 residues processed: 270 average time/residue: 0.9074 time to fit residues: 299.5775 Evaluate side-chains 263 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 211 time to evaluate : 2.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 317 PHE Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain A residue 372 CYS Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 454 SER Chi-restraints excluded: chain A residue 471 GLN Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 922 THR Chi-restraints excluded: chain A residue 924 ASN Chi-restraints excluded: chain A residue 1118 VAL Chi-restraints excluded: chain A residue 1260 ASP Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 315 SER Chi-restraints excluded: chain B residue 348 ASP Chi-restraints excluded: chain B residue 369 GLU Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 471 GLN Chi-restraints excluded: chain B residue 478 LYS Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 580 THR Chi-restraints excluded: chain B residue 628 SER Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 922 THR Chi-restraints excluded: chain B residue 924 ASN Chi-restraints excluded: chain B residue 1007 VAL Chi-restraints excluded: chain B residue 1118 VAL Chi-restraints excluded: chain B residue 1185 GLU Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain C residue 315 SER Chi-restraints excluded: chain C residue 317 PHE Chi-restraints excluded: chain C residue 348 ASP Chi-restraints excluded: chain C residue 371 SER Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain C residue 471 GLN Chi-restraints excluded: chain C residue 478 LYS Chi-restraints excluded: chain C residue 533 THR Chi-restraints excluded: chain C residue 577 VAL Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 628 SER Chi-restraints excluded: chain C residue 769 THR Chi-restraints excluded: chain C residue 922 THR Chi-restraints excluded: chain C residue 924 ASN Chi-restraints excluded: chain C residue 992 LEU Chi-restraints excluded: chain C residue 1007 VAL Chi-restraints excluded: chain C residue 1118 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 255 optimal weight: 5.9990 chunk 173 optimal weight: 1.9990 chunk 4 optimal weight: 30.0000 chunk 228 optimal weight: 2.9990 chunk 126 optimal weight: 0.8980 chunk 261 optimal weight: 2.9990 chunk 211 optimal weight: 1.9990 chunk 0 optimal weight: 40.0000 chunk 156 optimal weight: 1.9990 chunk 275 optimal weight: 0.9980 chunk 77 optimal weight: 4.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 ASN A 635 ASN A 866 ASN A1122 ASN ** B 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 866 ASN B1122 ASN C 866 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.2764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 24776 Z= 0.309 Angle : 0.610 18.289 33895 Z= 0.313 Chirality : 0.049 0.346 4339 Planarity : 0.004 0.047 4210 Dihedral : 6.294 59.546 5239 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.38 % Favored : 97.53 % Rotamer: Outliers : 3.45 % Allowed : 9.16 % Favored : 87.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.15), residues: 3115 helix: 2.18 (0.20), residues: 714 sheet: 0.61 (0.19), residues: 666 loop : -0.59 (0.14), residues: 1735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 426 HIS 0.005 0.001 HIS B 619 PHE 0.012 0.002 PHE A 457 TYR 0.022 0.002 TYR B1016 ARG 0.003 0.000 ARG A 982 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 218 time to evaluate : 2.533 Fit side-chains REVERT: A 317 PHE cc_start: 0.7280 (OUTLIER) cc_final: 0.6963 (t80) REVERT: A 471 GLN cc_start: 0.8366 (OUTLIER) cc_final: 0.7603 (tm-30) REVERT: A 576 TYR cc_start: 0.8885 (m-80) cc_final: 0.8625 (m-80) REVERT: A 753 MET cc_start: 0.8322 (mpt) cc_final: 0.8046 (mpt) REVERT: A 1260 ASP cc_start: 0.6431 (OUTLIER) cc_final: 0.6198 (m-30) REVERT: B 471 GLN cc_start: 0.8368 (OUTLIER) cc_final: 0.7814 (tm-30) REVERT: B 478 LYS cc_start: 0.8532 (OUTLIER) cc_final: 0.8056 (mtpp) REVERT: B 1104 ASP cc_start: 0.7783 (t0) cc_final: 0.7554 (t0) REVERT: B 1185 GLU cc_start: 0.8799 (OUTLIER) cc_final: 0.8367 (mt-10) REVERT: C 317 PHE cc_start: 0.7657 (OUTLIER) cc_final: 0.7358 (t80) REVERT: C 471 GLN cc_start: 0.8334 (OUTLIER) cc_final: 0.7786 (tm-30) REVERT: C 478 LYS cc_start: 0.8468 (OUTLIER) cc_final: 0.8059 (mtpp) REVERT: C 737 ASP cc_start: 0.7891 (p0) cc_final: 0.7531 (p0) outliers start: 79 outliers final: 49 residues processed: 268 average time/residue: 0.9187 time to fit residues: 302.3804 Evaluate side-chains 262 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 204 time to evaluate : 2.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 317 PHE Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 454 SER Chi-restraints excluded: chain A residue 471 GLN Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 922 THR Chi-restraints excluded: chain A residue 924 ASN Chi-restraints excluded: chain A residue 1015 MET Chi-restraints excluded: chain A residue 1118 VAL Chi-restraints excluded: chain A residue 1260 ASP Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 348 ASP Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 471 GLN Chi-restraints excluded: chain B residue 478 LYS Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 577 VAL Chi-restraints excluded: chain B residue 580 THR Chi-restraints excluded: chain B residue 628 SER Chi-restraints excluded: chain B residue 649 GLN Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 847 GLU Chi-restraints excluded: chain B residue 922 THR Chi-restraints excluded: chain B residue 924 ASN Chi-restraints excluded: chain B residue 1007 VAL Chi-restraints excluded: chain B residue 1118 VAL Chi-restraints excluded: chain B residue 1185 GLU Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain C residue 317 PHE Chi-restraints excluded: chain C residue 348 ASP Chi-restraints excluded: chain C residue 371 SER Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain C residue 471 GLN Chi-restraints excluded: chain C residue 478 LYS Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 533 THR Chi-restraints excluded: chain C residue 551 LEU Chi-restraints excluded: chain C residue 577 VAL Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 628 SER Chi-restraints excluded: chain C residue 769 THR Chi-restraints excluded: chain C residue 922 THR Chi-restraints excluded: chain C residue 924 ASN Chi-restraints excluded: chain C residue 992 LEU Chi-restraints excluded: chain C residue 1007 VAL Chi-restraints excluded: chain C residue 1118 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 103 optimal weight: 0.8980 chunk 275 optimal weight: 0.9980 chunk 60 optimal weight: 0.0070 chunk 179 optimal weight: 4.9990 chunk 75 optimal weight: 0.9980 chunk 306 optimal weight: 1.9990 chunk 254 optimal weight: 4.9990 chunk 142 optimal weight: 2.9990 chunk 25 optimal weight: 6.9990 chunk 101 optimal weight: 0.5980 chunk 161 optimal weight: 1.9990 overall best weight: 0.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 ASN A 649 GLN A 866 ASN ** B 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 866 ASN B1122 ASN C 866 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.2915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 24776 Z= 0.176 Angle : 0.545 16.668 33895 Z= 0.282 Chirality : 0.047 0.347 4339 Planarity : 0.004 0.046 4210 Dihedral : 6.089 58.169 5239 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.22 % Favored : 97.69 % Rotamer: Outliers : 2.53 % Allowed : 10.51 % Favored : 86.96 % 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: 0.59 (0.15), residues: 3115 helix: 2.31 (0.20), residues: 718 sheet: 0.62 (0.20), residues: 660 loop : -0.53 (0.14), residues: 1737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 458 HIS 0.004 0.001 HIS A 765 PHE 0.013 0.001 PHE A 457 TYR 0.021 0.001 TYR A 778 ARG 0.002 0.000 ARG B1149 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 211 time to evaluate : 2.529 Fit side-chains REVERT: A 471 GLN cc_start: 0.8325 (OUTLIER) cc_final: 0.7552 (tm-30) REVERT: A 576 TYR cc_start: 0.8859 (m-80) cc_final: 0.8603 (m-80) REVERT: A 753 MET cc_start: 0.8316 (mpt) cc_final: 0.8109 (mpt) REVERT: A 1260 ASP cc_start: 0.6401 (OUTLIER) cc_final: 0.6149 (m-30) REVERT: B 471 GLN cc_start: 0.8337 (OUTLIER) cc_final: 0.7765 (tm-30) REVERT: B 478 LYS cc_start: 0.8492 (OUTLIER) cc_final: 0.8016 (mtpp) REVERT: B 908 GLU cc_start: 0.7389 (OUTLIER) cc_final: 0.7185 (mm-30) REVERT: B 1104 ASP cc_start: 0.7707 (t0) cc_final: 0.7499 (t0) REVERT: B 1185 GLU cc_start: 0.8745 (OUTLIER) cc_final: 0.8255 (mt-10) REVERT: C 478 LYS cc_start: 0.8422 (OUTLIER) cc_final: 0.8044 (mtpp) REVERT: C 737 ASP cc_start: 0.7850 (p0) cc_final: 0.7505 (p0) outliers start: 58 outliers final: 34 residues processed: 246 average time/residue: 0.9436 time to fit residues: 281.7194 Evaluate side-chains 242 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 201 time to evaluate : 2.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 471 GLN Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 922 THR Chi-restraints excluded: chain A residue 924 ASN Chi-restraints excluded: chain A residue 1015 MET Chi-restraints excluded: chain A residue 1118 VAL Chi-restraints excluded: chain A residue 1260 ASP Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 317 PHE Chi-restraints excluded: chain B residue 348 ASP Chi-restraints excluded: chain B residue 369 GLU Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 471 GLN Chi-restraints excluded: chain B residue 478 LYS Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 580 THR Chi-restraints excluded: chain B residue 628 SER Chi-restraints excluded: chain B residue 649 GLN Chi-restraints excluded: chain B residue 908 GLU Chi-restraints excluded: chain B residue 922 THR Chi-restraints excluded: chain B residue 924 ASN Chi-restraints excluded: chain B residue 1109 GLN Chi-restraints excluded: chain B residue 1118 VAL Chi-restraints excluded: chain B residue 1185 GLU Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain C residue 371 SER Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain C residue 478 LYS Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 533 THR Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 628 SER Chi-restraints excluded: chain C residue 922 THR Chi-restraints excluded: chain C residue 924 ASN Chi-restraints excluded: chain C residue 992 LEU Chi-restraints excluded: chain C residue 1118 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 295 optimal weight: 0.7980 chunk 34 optimal weight: 0.8980 chunk 174 optimal weight: 2.9990 chunk 223 optimal weight: 3.9990 chunk 173 optimal weight: 2.9990 chunk 258 optimal weight: 6.9990 chunk 171 optimal weight: 1.9990 chunk 305 optimal weight: 1.9990 chunk 191 optimal weight: 3.9990 chunk 186 optimal weight: 2.9990 chunk 141 optimal weight: 0.9980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 ASN A1122 ASN ** B 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1122 ASN B1258 ASN C 635 ASN C 866 ASN C1122 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.3014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 24776 Z= 0.272 Angle : 0.604 16.827 33895 Z= 0.309 Chirality : 0.051 0.818 4339 Planarity : 0.004 0.047 4210 Dihedral : 6.867 116.034 5239 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.28 % Favored : 97.62 % Rotamer: Outliers : 2.79 % Allowed : 10.55 % Favored : 86.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 0.50 (0.15), residues: 3115 helix: 2.26 (0.20), residues: 714 sheet: 0.59 (0.20), residues: 664 loop : -0.61 (0.14), residues: 1737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 201 HIS 0.005 0.001 HIS B 765 PHE 0.016 0.001 PHE C 324 TYR 0.035 0.002 TYR B 778 ARG 0.002 0.000 ARG A 982 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 205 time to evaluate : 2.695 Fit side-chains revert: symmetry clash REVERT: A 471 GLN cc_start: 0.8359 (OUTLIER) cc_final: 0.7569 (tm-30) REVERT: A 576 TYR cc_start: 0.8881 (m-80) cc_final: 0.8640 (m-80) REVERT: A 753 MET cc_start: 0.8327 (mpt) cc_final: 0.8100 (mpt) REVERT: A 1257 ARG cc_start: 0.8161 (OUTLIER) cc_final: 0.7945 (ttt-90) REVERT: B 471 GLN cc_start: 0.8372 (OUTLIER) cc_final: 0.7777 (tm-30) REVERT: B 478 LYS cc_start: 0.8529 (OUTLIER) cc_final: 0.8083 (mtpp) REVERT: B 1104 ASP cc_start: 0.7757 (t0) cc_final: 0.7556 (t0) REVERT: B 1185 GLU cc_start: 0.8790 (OUTLIER) cc_final: 0.8329 (mt-10) REVERT: C 471 GLN cc_start: 0.8249 (OUTLIER) cc_final: 0.7755 (tm-30) REVERT: C 478 LYS cc_start: 0.8456 (OUTLIER) cc_final: 0.8030 (mtpp) REVERT: C 737 ASP cc_start: 0.7891 (p0) cc_final: 0.7601 (p0) outliers start: 64 outliers final: 46 residues processed: 249 average time/residue: 1.0055 time to fit residues: 303.6280 Evaluate side-chains 251 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 198 time to evaluate : 2.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 454 SER Chi-restraints excluded: chain A residue 471 GLN Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 580 THR Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 922 THR Chi-restraints excluded: chain A residue 924 ASN Chi-restraints excluded: chain A residue 1015 MET Chi-restraints excluded: chain A residue 1118 VAL Chi-restraints excluded: chain A residue 1257 ARG Chi-restraints excluded: chain A residue 1260 ASP Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 315 SER Chi-restraints excluded: chain B residue 317 PHE Chi-restraints excluded: chain B residue 348 ASP Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 425 LYS Chi-restraints excluded: chain B residue 471 GLN Chi-restraints excluded: chain B residue 478 LYS Chi-restraints excluded: chain B residue 533 THR Chi-restraints excluded: chain B residue 580 THR Chi-restraints excluded: chain B residue 628 SER Chi-restraints excluded: chain B residue 649 GLN Chi-restraints excluded: chain B residue 769 THR Chi-restraints excluded: chain B residue 922 THR Chi-restraints excluded: chain B residue 924 ASN Chi-restraints excluded: chain B residue 1109 GLN Chi-restraints excluded: chain B residue 1118 VAL Chi-restraints excluded: chain B residue 1185 GLU Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain C residue 315 SER Chi-restraints excluded: chain C residue 317 PHE Chi-restraints excluded: chain C residue 348 ASP Chi-restraints excluded: chain C residue 371 SER Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain C residue 471 GLN Chi-restraints excluded: chain C residue 478 LYS Chi-restraints excluded: chain C residue 533 THR Chi-restraints excluded: chain C residue 555 THR Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 628 SER Chi-restraints excluded: chain C residue 703 ASN Chi-restraints excluded: chain C residue 769 THR Chi-restraints excluded: chain C residue 922 THR Chi-restraints excluded: chain C residue 924 ASN Chi-restraints excluded: chain C residue 992 LEU Chi-restraints excluded: chain C residue 1118 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 189 optimal weight: 3.9990 chunk 122 optimal weight: 0.5980 chunk 182 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 chunk 60 optimal weight: 0.0060 chunk 59 optimal weight: 1.9990 chunk 194 optimal weight: 0.0980 chunk 208 optimal weight: 0.8980 chunk 151 optimal weight: 4.9990 chunk 28 optimal weight: 0.0980 chunk 240 optimal weight: 2.9990 overall best weight: 0.3396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 866 ASN ** B 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 866 ASN B1122 ASN B1258 ASN C 866 ASN C1122 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.3172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 24776 Z= 0.139 Angle : 0.532 17.879 33895 Z= 0.272 Chirality : 0.045 0.357 4339 Planarity : 0.004 0.046 4210 Dihedral : 6.632 112.785 5239 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.15 % Favored : 97.75 % Rotamer: Outliers : 2.05 % Allowed : 11.47 % Favored : 86.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.15), residues: 3115 helix: 2.58 (0.20), residues: 709 sheet: 0.67 (0.19), residues: 712 loop : -0.50 (0.15), residues: 1694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 201 HIS 0.008 0.001 HIS C 765 PHE 0.015 0.001 PHE C 324 TYR 0.026 0.001 TYR C 778 ARG 0.002 0.000 ARG B 982 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 206 time to evaluate : 2.279 Fit side-chains revert: symmetry clash REVERT: A 576 TYR cc_start: 0.8849 (m-80) cc_final: 0.8597 (m-80) REVERT: A 753 MET cc_start: 0.8331 (mpt) cc_final: 0.8121 (mpt) REVERT: A 847 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7800 (tt0) REVERT: A 1149 ARG cc_start: 0.7576 (mtt-85) cc_final: 0.7362 (mtt-85) REVERT: B 471 GLN cc_start: 0.8334 (OUTLIER) cc_final: 0.7734 (tm-30) REVERT: B 478 LYS cc_start: 0.8450 (OUTLIER) cc_final: 0.8007 (mtpp) REVERT: B 1185 GLU cc_start: 0.8708 (OUTLIER) cc_final: 0.8207 (mt-10) REVERT: C 478 LYS cc_start: 0.8425 (OUTLIER) cc_final: 0.8011 (mtpp) outliers start: 47 outliers final: 27 residues processed: 237 average time/residue: 0.9232 time to fit residues: 266.8380 Evaluate side-chains 231 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 199 time to evaluate : 2.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 922 THR Chi-restraints excluded: chain A residue 924 ASN Chi-restraints excluded: chain A residue 1118 VAL Chi-restraints excluded: chain A residue 1260 ASP Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 317 PHE Chi-restraints excluded: chain B residue 348 ASP Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 471 GLN Chi-restraints excluded: chain B residue 478 LYS Chi-restraints excluded: chain B residue 577 VAL Chi-restraints excluded: chain B residue 628 SER Chi-restraints excluded: chain B residue 922 THR Chi-restraints excluded: chain B residue 924 ASN Chi-restraints excluded: chain B residue 1109 GLN Chi-restraints excluded: chain B residue 1118 VAL Chi-restraints excluded: chain B residue 1185 GLU Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain C residue 317 PHE Chi-restraints excluded: chain C residue 478 LYS Chi-restraints excluded: chain C residue 555 THR Chi-restraints excluded: chain C residue 577 VAL Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 703 ASN Chi-restraints excluded: chain C residue 922 THR Chi-restraints excluded: chain C residue 924 ASN Chi-restraints excluded: chain C residue 1118 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 277 optimal weight: 0.5980 chunk 292 optimal weight: 1.9990 chunk 267 optimal weight: 2.9990 chunk 284 optimal weight: 8.9990 chunk 171 optimal weight: 1.9990 chunk 124 optimal weight: 0.5980 chunk 223 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 257 optimal weight: 4.9990 chunk 269 optimal weight: 2.9990 chunk 283 optimal weight: 0.7980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1122 ASN ** B 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1122 ASN C1122 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.3209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 24776 Z= 0.218 Angle : 0.572 17.386 33895 Z= 0.294 Chirality : 0.050 0.925 4339 Planarity : 0.004 0.047 4210 Dihedral : 6.833 109.838 5239 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.28 % Favored : 97.62 % Rotamer: Outliers : 2.09 % Allowed : 11.64 % Favored : 86.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: 0.62 (0.15), residues: 3115 helix: 2.44 (0.20), residues: 714 sheet: 0.53 (0.20), residues: 671 loop : -0.51 (0.15), residues: 1730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 201 HIS 0.004 0.001 HIS A 619 PHE 0.014 0.001 PHE C 324 TYR 0.029 0.002 TYR C 778 ARG 0.002 0.000 ARG A 569 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 197 time to evaluate : 3.185 Fit side-chains REVERT: A 495 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8833 (mt) REVERT: A 576 TYR cc_start: 0.8872 (m-80) cc_final: 0.8634 (m-80) REVERT: A 753 MET cc_start: 0.8333 (mpt) cc_final: 0.8125 (mpt) REVERT: A 847 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7876 (tt0) REVERT: B 471 GLN cc_start: 0.8362 (OUTLIER) cc_final: 0.7731 (tm-30) REVERT: B 478 LYS cc_start: 0.8487 (OUTLIER) cc_final: 0.8026 (mtpp) REVERT: B 1185 GLU cc_start: 0.8748 (OUTLIER) cc_final: 0.8279 (mt-10) REVERT: C 471 GLN cc_start: 0.8233 (OUTLIER) cc_final: 0.7653 (tm-30) REVERT: C 478 LYS cc_start: 0.8457 (OUTLIER) cc_final: 0.8030 (mtpp) REVERT: C 737 ASP cc_start: 0.7986 (p0) cc_final: 0.7729 (p0) outliers start: 48 outliers final: 32 residues processed: 236 average time/residue: 1.0294 time to fit residues: 294.2003 Evaluate side-chains 236 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 197 time to evaluate : 2.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 577 VAL Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 922 THR Chi-restraints excluded: chain A residue 924 ASN Chi-restraints excluded: chain A residue 1118 VAL Chi-restraints excluded: chain A residue 1260 ASP Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 315 SER Chi-restraints excluded: chain B residue 317 PHE Chi-restraints excluded: chain B residue 348 ASP Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 425 LYS Chi-restraints excluded: chain B residue 471 GLN Chi-restraints excluded: chain B residue 478 LYS Chi-restraints excluded: chain B residue 577 VAL Chi-restraints excluded: chain B residue 628 SER Chi-restraints excluded: chain B residue 649 GLN Chi-restraints excluded: chain B residue 922 THR Chi-restraints excluded: chain B residue 924 ASN Chi-restraints excluded: chain B residue 1109 GLN Chi-restraints excluded: chain B residue 1118 VAL Chi-restraints excluded: chain B residue 1185 GLU Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain C residue 317 PHE Chi-restraints excluded: chain C residue 348 ASP Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain C residue 471 GLN Chi-restraints excluded: chain C residue 478 LYS Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 922 THR Chi-restraints excluded: chain C residue 924 ASN Chi-restraints excluded: chain C residue 1118 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 186 optimal weight: 2.9990 chunk 301 optimal weight: 0.7980 chunk 183 optimal weight: 0.9990 chunk 142 optimal weight: 2.9990 chunk 209 optimal weight: 0.0020 chunk 315 optimal weight: 3.9990 chunk 290 optimal weight: 4.9990 chunk 251 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 194 optimal weight: 0.0570 chunk 154 optimal weight: 0.9980 overall best weight: 0.5106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 866 ASN A1122 ASN ** B 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 866 ASN B1122 ASN C 866 ASN C1122 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.3299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 24776 Z= 0.147 Angle : 0.524 15.815 33895 Z= 0.267 Chirality : 0.050 1.065 4339 Planarity : 0.004 0.046 4210 Dihedral : 6.750 119.917 5239 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.05 % Favored : 97.85 % Rotamer: Outliers : 1.74 % Allowed : 11.86 % Favored : 86.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.15), residues: 3115 helix: 2.63 (0.20), residues: 708 sheet: 0.54 (0.20), residues: 687 loop : -0.47 (0.15), residues: 1720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 201 HIS 0.003 0.000 HIS C 765 PHE 0.017 0.001 PHE C 324 TYR 0.023 0.001 TYR B 400 ARG 0.003 0.000 ARG C 700 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6230 Ramachandran restraints generated. 3115 Oldfield, 0 Emsley, 3115 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 201 time to evaluate : 2.529 Fit side-chains REVERT: A 495 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8788 (mt) REVERT: A 576 TYR cc_start: 0.8842 (m-80) cc_final: 0.8601 (m-80) REVERT: A 1149 ARG cc_start: 0.7576 (mtt-85) cc_final: 0.7364 (mtt-85) REVERT: B 471 GLN cc_start: 0.8336 (OUTLIER) cc_final: 0.7710 (tm-30) REVERT: B 478 LYS cc_start: 0.8452 (OUTLIER) cc_final: 0.8020 (mtpp) REVERT: B 1185 GLU cc_start: 0.8717 (OUTLIER) cc_final: 0.8223 (mt-10) REVERT: C 478 LYS cc_start: 0.8446 (OUTLIER) cc_final: 0.8054 (mtpp) REVERT: C 737 ASP cc_start: 0.7971 (p0) cc_final: 0.7700 (p0) outliers start: 40 outliers final: 28 residues processed: 229 average time/residue: 0.9959 time to fit residues: 274.9285 Evaluate side-chains 232 residues out of total 2754 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 199 time to evaluate : 2.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 SER Chi-restraints excluded: chain A residue 317 PHE Chi-restraints excluded: chain A residue 371 SER Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 922 THR Chi-restraints excluded: chain A residue 924 ASN Chi-restraints excluded: chain A residue 1118 VAL Chi-restraints excluded: chain A residue 1260 ASP Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain B residue 315 SER Chi-restraints excluded: chain B residue 317 PHE Chi-restraints excluded: chain B residue 348 ASP Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 471 GLN Chi-restraints excluded: chain B residue 478 LYS Chi-restraints excluded: chain B residue 628 SER Chi-restraints excluded: chain B residue 922 THR Chi-restraints excluded: chain B residue 924 ASN Chi-restraints excluded: chain B residue 1109 GLN Chi-restraints excluded: chain B residue 1118 VAL Chi-restraints excluded: chain B residue 1185 GLU Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain C residue 315 SER Chi-restraints excluded: chain C residue 317 PHE Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain C residue 478 LYS Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 580 THR Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 922 THR Chi-restraints excluded: chain C residue 924 ASN Chi-restraints excluded: chain C residue 1118 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 317 random chunks: chunk 199 optimal weight: 0.9990 chunk 267 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 231 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 chunk 69 optimal weight: 2.9990 chunk 251 optimal weight: 0.5980 chunk 105 optimal weight: 2.9990 chunk 258 optimal weight: 6.9990 chunk 31 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 635 ASN ** A 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1122 ASN B 635 ASN ** B 649 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1122 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.140922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.103249 restraints weight = 27059.673| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 2.30 r_work: 0.2875 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2738 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8830 moved from start: 0.3329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 24776 Z= 0.195 Angle : 0.534 15.509 33895 Z= 0.274 Chirality : 0.048 0.715 4339 Planarity : 0.004 0.047 4210 Dihedral : 6.699 116.347 5239 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.28 % Favored : 97.62 % Rotamer: Outliers : 1.92 % Allowed : 11.82 % Favored : 86.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.61 (0.15), residues: 3115 helix: 2.44 (0.20), residues: 720 sheet: 0.49 (0.20), residues: 675 loop : -0.51 (0.15), residues: 1720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 201 HIS 0.004 0.001 HIS A 619 PHE 0.017 0.001 PHE C 324 TYR 0.025 0.001 TYR A 403 ARG 0.002 0.000 ARG B 569 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7072.96 seconds wall clock time: 125 minutes 39.28 seconds (7539.28 seconds total)