Starting phenix.real_space_refine on Tue Feb 20 18:12:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m5e_23674/02_2024/7m5e_23674_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m5e_23674/02_2024/7m5e_23674.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m5e_23674/02_2024/7m5e_23674.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m5e_23674/02_2024/7m5e_23674.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m5e_23674/02_2024/7m5e_23674_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m5e_23674/02_2024/7m5e_23674_updated.pdb" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.126 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 147 5.16 5 C 18048 2.51 5 N 4521 2.21 5 O 5850 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 TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 188": "OE1" <-> "OE2" Residue "A TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 301": "NH1" <-> "NH2" Residue "A PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 382": "OE1" <-> "OE2" Residue "A ASP 422": "OD1" <-> "OD2" Residue "A PHE 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 499": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 523": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 537": "OD1" <-> "OD2" Residue "A TYR 577": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 630": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 635": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 649": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 740": "OD1" <-> "OD2" Residue "A PHE 778": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 786": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 788": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 814": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 824": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 905": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 922": "OD1" <-> "OD2" Residue "A PHE 977": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 978": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1001": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1012": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1090": "OE1" <-> "OE2" Residue "A PHE 1126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 188": "OE1" <-> "OE2" Residue "C TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 301": "NH1" <-> "NH2" Residue "C PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 382": "OE1" <-> "OE2" Residue "C TYR 409": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 422": "OD1" <-> "OD2" Residue "C PHE 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 499": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 523": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 537": "OD1" <-> "OD2" Residue "C TYR 577": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 630": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 635": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 649": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 740": "OD1" <-> "OD2" Residue "C PHE 778": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 786": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 788": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 814": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 824": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 905": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 922": "OD1" <-> "OD2" Residue "C PHE 977": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 978": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1001": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1012": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1090": "OE1" <-> "OE2" Residue "C PHE 1126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 188": "OE1" <-> "OE2" Residue "E TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 301": "NH1" <-> "NH2" Residue "E PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 382": "OE1" <-> "OE2" Residue "E ASP 422": "OD1" <-> "OD2" Residue "E PHE 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 499": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 523": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 537": "OD1" <-> "OD2" Residue "E TYR 577": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 630": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 635": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 649": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 740": "OD1" <-> "OD2" Residue "E PHE 778": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 786": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 788": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 814": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 824": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 905": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 922": "OD1" <-> "OD2" Residue "E PHE 977": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 978": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1001": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1012": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 1090": "OE1" <-> "OE2" Residue "E PHE 1126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1204": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 28566 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 8915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1159, 8915 Classifications: {'peptide': 1159} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 58, 'TRANS': 1100} Chain breaks: 4 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 4, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 36 Chain: "C" Number of atoms: 8915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1159, 8915 Classifications: {'peptide': 1159} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 58, 'TRANS': 1100} Chain breaks: 4 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 4, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 36 Chain: "E" Number of atoms: 8915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1159, 8915 Classifications: {'peptide': 1159} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 58, 'TRANS': 1100} Chain breaks: 4 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 4, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 36 Chain: "B" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 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: "F" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "G" 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: "H" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "L" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 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: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "Q" 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: "R" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "V" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 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: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "a" 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: "b" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 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: 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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "f" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "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: "A" Number of atoms: 151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 151 Unusual residues: {'FOL': 1, 'NAG': 7, 'SIA': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "C" Number of atoms: 151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 151 Unusual residues: {'FOL': 1, 'NAG': 7, 'SIA': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "E" Number of atoms: 151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 151 Unusual residues: {'FOL': 1, 'NAG': 7, 'SIA': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 15.16, per 1000 atoms: 0.53 Number of scatterers: 28566 At special positions: 0 Unit cell: (150.15, 141.75, 160.65, 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 147 16.00 O 5850 8.00 N 4521 7.00 C 18048 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=51, symmetry=0 Simple disulfide: pdb=" SG CYS A 30 " - pdb=" SG CYS A 195 " distance=2.19 Simple disulfide: pdb=" SG CYS A 176 " - pdb=" SG CYS A 214 " distance=2.03 Simple disulfide: pdb=" SG CYS A 185 " - pdb=" SG CYS A 237 " distance=2.06 Simple disulfide: pdb=" SG CYS A 339 " - pdb=" SG CYS A 349 " distance=2.01 Simple disulfide: pdb=" SG CYS A 383 " - pdb=" SG CYS A 407 " distance=2.03 Simple disulfide: pdb=" SG CYS A 425 " - pdb=" SG CYS A 478 " distance=2.17 Simple disulfide: pdb=" SG CYS A 437 " - pdb=" SG CYS A 585 " distance=2.13 Simple disulfide: pdb=" SG CYS A 503 " - pdb=" SG CYS A 526 " distance=2.02 Simple disulfide: pdb=" SG CYS A 603 " - pdb=" SG CYS A 654 " distance=2.03 Simple disulfide: pdb=" SG CYS A 620 " - pdb=" SG CYS A 650 " distance=2.03 Simple disulfide: pdb=" SG CYS A 679 " - pdb=" SG CYS A 713 " distance=2.09 Simple disulfide: pdb=" SG CYS A 727 " - pdb=" SG CYS A 736 " distance=2.03 Simple disulfide: pdb=" SG CYS A 806 " - pdb=" SG CYS A 828 " distance=2.13 Simple disulfide: pdb=" SG CYS A 811 " - pdb=" SG CYS A 817 " distance=2.19 Simple disulfide: pdb=" SG CYS A 912 " - pdb=" SG CYS A 925 " distance=2.09 Simple disulfide: pdb=" SG CYS A1106 " - pdb=" SG CYS A1117 " distance=2.02 Simple disulfide: pdb=" SG CYS A1156 " - pdb=" SG CYS A1164 " distance=2.03 Simple disulfide: pdb=" SG CYS C 30 " - pdb=" SG CYS C 195 " distance=2.19 Simple disulfide: pdb=" SG CYS C 176 " - pdb=" SG CYS C 214 " distance=2.03 Simple disulfide: pdb=" SG CYS C 185 " - pdb=" SG CYS C 237 " distance=2.06 Simple disulfide: pdb=" SG CYS C 339 " - pdb=" SG CYS C 349 " distance=2.01 Simple disulfide: pdb=" SG CYS C 383 " - pdb=" SG CYS C 407 " distance=2.03 Simple disulfide: pdb=" SG CYS C 425 " - pdb=" SG CYS C 478 " distance=2.17 Simple disulfide: pdb=" SG CYS C 437 " - pdb=" SG CYS C 585 " distance=2.13 Simple disulfide: pdb=" SG CYS C 503 " - pdb=" SG CYS C 526 " distance=2.02 Simple disulfide: pdb=" SG CYS C 603 " - pdb=" SG CYS C 654 " distance=2.03 Simple disulfide: pdb=" SG CYS C 620 " - pdb=" SG CYS C 650 " distance=2.03 Simple disulfide: pdb=" SG CYS C 679 " - pdb=" SG CYS C 713 " distance=2.09 Simple disulfide: pdb=" SG CYS C 727 " - pdb=" SG CYS C 736 " distance=2.03 Simple disulfide: pdb=" SG CYS C 806 " - pdb=" SG CYS C 828 " distance=2.13 Simple disulfide: pdb=" SG CYS C 811 " - pdb=" SG CYS C 817 " distance=2.19 Simple disulfide: pdb=" SG CYS C 912 " - pdb=" SG CYS C 925 " distance=2.09 Simple disulfide: pdb=" SG CYS C1106 " - pdb=" SG CYS C1117 " distance=2.02 Simple disulfide: pdb=" SG CYS C1156 " - pdb=" SG CYS C1164 " distance=2.03 Simple disulfide: pdb=" SG CYS E 30 " - pdb=" SG CYS E 195 " distance=2.19 Simple disulfide: pdb=" SG CYS E 176 " - pdb=" SG CYS E 214 " distance=2.03 Simple disulfide: pdb=" SG CYS E 185 " - pdb=" SG CYS E 237 " distance=2.06 Simple disulfide: pdb=" SG CYS E 339 " - pdb=" SG CYS E 349 " distance=2.01 Simple disulfide: pdb=" SG CYS E 383 " - pdb=" SG CYS E 407 " distance=2.03 Simple disulfide: pdb=" SG CYS E 425 " - pdb=" SG CYS E 478 " distance=2.17 Simple disulfide: pdb=" SG CYS E 437 " - pdb=" SG CYS E 585 " distance=2.13 Simple disulfide: pdb=" SG CYS E 503 " - pdb=" SG CYS E 526 " distance=2.02 Simple disulfide: pdb=" SG CYS E 603 " - pdb=" SG CYS E 654 " distance=2.03 Simple disulfide: pdb=" SG CYS E 620 " - pdb=" SG CYS E 650 " distance=2.03 Simple disulfide: pdb=" SG CYS E 679 " - pdb=" SG CYS E 713 " distance=2.09 Simple disulfide: pdb=" SG CYS E 727 " - pdb=" SG CYS E 736 " distance=2.03 Simple disulfide: pdb=" SG CYS E 806 " - pdb=" SG CYS E 828 " distance=2.13 Simple disulfide: pdb=" SG CYS E 811 " - pdb=" SG CYS E 817 " distance=2.19 Simple disulfide: pdb=" SG CYS E 912 " - pdb=" SG CYS E 925 " distance=2.09 Simple disulfide: pdb=" SG CYS E1106 " - pdb=" SG CYS E1117 " distance=2.02 Simple disulfide: pdb=" SG CYS E1156 " - pdb=" SG CYS E1164 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN F 4 " - " MAN F 5 " " MAN F 6 " - " MAN F 7 " " MAN P 4 " - " MAN P 5 " " MAN P 6 " - " MAN P 7 " " MAN Z 4 " - " MAN Z 5 " " MAN Z 6 " - " MAN Z 7 " ALPHA1-3 " BMA B 3 " - " MAN B 4 " " BMA F 3 " - " MAN F 4 " " BMA H 3 " - " MAN H 4 " " BMA K 3 " - " MAN K 4 " " BMA L 3 " - " MAN L 4 " " BMA N 3 " - " MAN N 4 " " BMA P 3 " - " MAN P 4 " " BMA R 3 " - " MAN R 4 " " BMA U 3 " - " MAN U 4 " " BMA V 3 " - " MAN V 4 " " BMA X 3 " - " MAN X 4 " " BMA Z 3 " - " MAN Z 4 " " BMA b 3 " - " MAN b 4 " " BMA e 3 " - " MAN e 4 " " BMA f 3 " - " MAN f 4 " ALPHA1-6 " BMA F 3 " - " MAN F 6 " " BMA K 3 " - " MAN K 5 " " BMA L 3 " - " MAN L 5 " " BMA P 3 " - " MAN P 6 " " BMA U 3 " - " MAN U 5 " " BMA V 3 " - " MAN V 5 " " BMA Z 3 " - " MAN Z 6 " " BMA e 3 " - " MAN e 5 " " BMA f 3 " - " MAN f 5 " BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " " NAG D 1 " - " NAG D 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " 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 N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " 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 V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " 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 e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " NAG-ASN " NAG A1402 " - " ASN A 487 " " NAG A1403 " - " ASN A 592 " " NAG A1404 " - " ASN A 619 " " NAG A1405 " - " ASN A 719 " " NAG A1406 " - " ASN A 774 " " NAG A1407 " - " ASN A 785 " " NAG A1408 " - " ASN A 155 " " NAG B 1 " - " ASN A 222 " " NAG C1402 " - " ASN C 487 " " NAG C1403 " - " ASN C 592 " " NAG C1404 " - " ASN C 619 " " NAG C1405 " - " ASN C 719 " " NAG C1406 " - " ASN C 774 " " NAG C1407 " - " ASN C 785 " " NAG C1408 " - " ASN C 155 " " NAG D 1 " - " ASN A 236 " " NAG E1402 " - " ASN E 487 " " NAG E1403 " - " ASN E 592 " " NAG E1404 " - " ASN E 619 " " NAG E1405 " - " ASN E 719 " " NAG E1406 " - " ASN E 774 " " NAG E1407 " - " ASN E 785 " " NAG E1408 " - " ASN E 155 " " NAG F 1 " - " ASN A 410 " " NAG G 1 " - " ASN A 870 " " NAG H 1 " - " ASN A1213 " " NAG I 1 " - " ASN A 66 " " NAG J 1 " - " ASN A 104 " " NAG K 1 " - " ASN A 125 " " NAG L 1 " - " ASN A 166 " " NAG M 1 " - " ASN A 244 " " NAG N 1 " - " ASN C 222 " " NAG O 1 " - " ASN C 236 " " NAG P 1 " - " ASN C 410 " " NAG Q 1 " - " ASN C 870 " " NAG R 1 " - " ASN C1213 " " NAG S 1 " - " ASN C 66 " " NAG T 1 " - " ASN C 104 " " NAG U 1 " - " ASN C 125 " " NAG V 1 " - " ASN C 166 " " NAG W 1 " - " ASN C 244 " " NAG X 1 " - " ASN E 222 " " NAG Y 1 " - " ASN E 236 " " NAG Z 1 " - " ASN E 410 " " NAG a 1 " - " ASN E 870 " " NAG b 1 " - " ASN E1213 " " NAG c 1 " - " ASN E 66 " " NAG d 1 " - " ASN E 104 " " NAG e 1 " - " ASN E 125 " " NAG f 1 " - " ASN E 166 " " NAG g 1 " - " ASN E 244 " Time building additional restraints: 14.01 Conformation dependent library (CDL) restraints added in 5.1 seconds 6894 Ramachandran restraints generated. 3447 Oldfield, 0 Emsley, 3447 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input volumes are d-peptide like pdb=" CB FOL A1401 " pdb=" CB FOL C1401 " pdb=" CB FOL E1401 " Number of C-beta restraints generated: 6456 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 93 helices and 57 sheets defined 23.5% alpha, 24.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.29 Creating SS restraints... Processing helix chain 'A' and resid 37 through 40 Processing helix chain 'A' and resid 50 through 52 No H-bonds generated for 'chain 'A' and resid 50 through 52' Processing helix chain 'A' and resid 210 through 213 No H-bonds generated for 'chain 'A' and resid 210 through 213' Processing helix chain 'A' and resid 223 through 231 removed outlier: 3.907A pdb=" N TYR A 231 " --> pdb=" O SER A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 306 No H-bonds generated for 'chain 'A' and resid 304 through 306' Processing helix chain 'A' and resid 343 through 350 Processing helix chain 'A' and resid 387 through 389 No H-bonds generated for 'chain 'A' and resid 387 through 389' Processing helix chain 'A' and resid 396 through 398 No H-bonds generated for 'chain 'A' and resid 396 through 398' Processing helix chain 'A' and resid 412 through 417 removed outlier: 4.876A pdb=" N LEU A 417 " --> pdb=" O LYS A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 433 No H-bonds generated for 'chain 'A' and resid 430 through 433' Processing helix chain 'A' and resid 450 through 456 removed outlier: 5.366A pdb=" N SER A 454 " --> pdb=" O SER A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 467 Processing helix chain 'A' and resid 525 through 528 removed outlier: 3.893A pdb=" N SER A 528 " --> pdb=" O PRO A 525 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 525 through 528' Processing helix chain 'A' and resid 547 through 549 No H-bonds generated for 'chain 'A' and resid 547 through 549' Processing helix chain 'A' and resid 597 through 599 No H-bonds generated for 'chain 'A' and resid 597 through 599' Processing helix chain 'A' and resid 626 through 628 No H-bonds generated for 'chain 'A' and resid 626 through 628' Processing helix chain 'A' and resid 679 through 681 No H-bonds generated for 'chain 'A' and resid 679 through 681' Processing helix chain 'A' and resid 806 through 811 Processing helix chain 'A' and resid 815 through 824 removed outlier: 4.182A pdb=" N GLU A 823 " --> pdb=" O GLN A 819 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N TYR A 824 " --> pdb=" O LEU A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 827 through 853 Processing helix chain 'A' and resid 889 through 896 Processing helix chain 'A' and resid 908 through 914 removed outlier: 3.720A pdb=" N MET A 913 " --> pdb=" O TYR A 909 " (cutoff:3.500A) Processing helix chain 'A' and resid 925 through 930 removed outlier: 4.088A pdb=" N ALA A 930 " --> pdb=" O GLN A 927 " (cutoff:3.500A) Processing helix chain 'A' and resid 941 through 958 removed outlier: 4.814A pdb=" N ALA A 956 " --> pdb=" O LEU A 952 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N GLY A 957 " --> pdb=" O GLY A 953 " (cutoff:3.500A) Processing helix chain 'A' and resid 972 through 983 removed outlier: 3.656A pdb=" N VAL A 983 " --> pdb=" O ARG A 979 " (cutoff:3.500A) Processing helix chain 'A' and resid 987 through 992 Processing helix chain 'A' and resid 994 through 1008 removed outlier: 3.875A pdb=" N MET A1008 " --> pdb=" O ALA A1004 " (cutoff:3.500A) Processing helix chain 'A' and resid 1017 through 1041 removed outlier: 3.843A pdb=" N LEU A1036 " --> pdb=" O ALA A1032 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LEU A1040 " --> pdb=" O LEU A1036 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N SER A1041 " --> pdb=" O ALA A1037 " (cutoff:3.500A) Processing helix chain 'A' and resid 1051 through 1057 Processing helix chain 'A' and resid 1060 through 1106 removed outlier: 4.572A pdb=" N ALA A1065 " --> pdb=" O PRO A1061 " (cutoff:3.500A) Processing helix chain 'A' and resid 1220 through 1222 No H-bonds generated for 'chain 'A' and resid 1220 through 1222' Processing helix chain 'C' and resid 37 through 40 Processing helix chain 'C' and resid 50 through 52 No H-bonds generated for 'chain 'C' and resid 50 through 52' Processing helix chain 'C' and resid 210 through 213 No H-bonds generated for 'chain 'C' and resid 210 through 213' Processing helix chain 'C' and resid 223 through 231 removed outlier: 3.907A pdb=" N TYR C 231 " --> pdb=" O SER C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 304 through 306 No H-bonds generated for 'chain 'C' and resid 304 through 306' Processing helix chain 'C' and resid 343 through 350 Processing helix chain 'C' and resid 387 through 389 No H-bonds generated for 'chain 'C' and resid 387 through 389' Processing helix chain 'C' and resid 396 through 398 No H-bonds generated for 'chain 'C' and resid 396 through 398' Processing helix chain 'C' and resid 412 through 417 removed outlier: 4.876A pdb=" N LEU C 417 " --> pdb=" O LYS C 413 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 433 No H-bonds generated for 'chain 'C' and resid 430 through 433' Processing helix chain 'C' and resid 450 through 456 removed outlier: 5.366A pdb=" N SER C 454 " --> pdb=" O SER C 451 " (cutoff:3.500A) Processing helix chain 'C' and resid 463 through 467 Processing helix chain 'C' and resid 525 through 528 removed outlier: 3.894A pdb=" N SER C 528 " --> pdb=" O PRO C 525 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 525 through 528' Processing helix chain 'C' and resid 547 through 549 No H-bonds generated for 'chain 'C' and resid 547 through 549' Processing helix chain 'C' and resid 597 through 599 No H-bonds generated for 'chain 'C' and resid 597 through 599' Processing helix chain 'C' and resid 626 through 628 No H-bonds generated for 'chain 'C' and resid 626 through 628' Processing helix chain 'C' and resid 679 through 681 No H-bonds generated for 'chain 'C' and resid 679 through 681' Processing helix chain 'C' and resid 806 through 811 Processing helix chain 'C' and resid 815 through 824 removed outlier: 4.182A pdb=" N GLU C 823 " --> pdb=" O GLN C 819 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N TYR C 824 " --> pdb=" O LEU C 820 " (cutoff:3.500A) Processing helix chain 'C' and resid 827 through 853 Processing helix chain 'C' and resid 889 through 896 Processing helix chain 'C' and resid 908 through 914 removed outlier: 3.720A pdb=" N MET C 913 " --> pdb=" O TYR C 909 " (cutoff:3.500A) Processing helix chain 'C' and resid 925 through 930 removed outlier: 4.088A pdb=" N ALA C 930 " --> pdb=" O GLN C 927 " (cutoff:3.500A) Processing helix chain 'C' and resid 941 through 958 removed outlier: 4.813A pdb=" N ALA C 956 " --> pdb=" O LEU C 952 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N GLY C 957 " --> pdb=" O GLY C 953 " (cutoff:3.500A) Processing helix chain 'C' and resid 972 through 983 removed outlier: 3.656A pdb=" N VAL C 983 " --> pdb=" O ARG C 979 " (cutoff:3.500A) Processing helix chain 'C' and resid 987 through 992 Processing helix chain 'C' and resid 994 through 1008 removed outlier: 3.875A pdb=" N MET C1008 " --> pdb=" O ALA C1004 " (cutoff:3.500A) Processing helix chain 'C' and resid 1017 through 1041 removed outlier: 3.843A pdb=" N LEU C1036 " --> pdb=" O ALA C1032 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LEU C1040 " --> pdb=" O LEU C1036 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N SER C1041 " --> pdb=" O ALA C1037 " (cutoff:3.500A) Processing helix chain 'C' and resid 1051 through 1057 Processing helix chain 'C' and resid 1060 through 1106 removed outlier: 4.572A pdb=" N ALA C1065 " --> pdb=" O PRO C1061 " (cutoff:3.500A) Processing helix chain 'C' and resid 1220 through 1222 No H-bonds generated for 'chain 'C' and resid 1220 through 1222' Processing helix chain 'E' and resid 37 through 40 Processing helix chain 'E' and resid 50 through 52 No H-bonds generated for 'chain 'E' and resid 50 through 52' Processing helix chain 'E' and resid 210 through 213 No H-bonds generated for 'chain 'E' and resid 210 through 213' Processing helix chain 'E' and resid 223 through 231 removed outlier: 3.907A pdb=" N TYR E 231 " --> pdb=" O SER E 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 304 through 306 No H-bonds generated for 'chain 'E' and resid 304 through 306' Processing helix chain 'E' and resid 343 through 350 Processing helix chain 'E' and resid 387 through 389 No H-bonds generated for 'chain 'E' and resid 387 through 389' Processing helix chain 'E' and resid 396 through 398 No H-bonds generated for 'chain 'E' and resid 396 through 398' Processing helix chain 'E' and resid 412 through 417 removed outlier: 4.876A pdb=" N LEU E 417 " --> pdb=" O LYS E 413 " (cutoff:3.500A) Processing helix chain 'E' and resid 430 through 433 No H-bonds generated for 'chain 'E' and resid 430 through 433' Processing helix chain 'E' and resid 450 through 456 removed outlier: 5.366A pdb=" N SER E 454 " --> pdb=" O SER E 451 " (cutoff:3.500A) Processing helix chain 'E' and resid 463 through 467 Processing helix chain 'E' and resid 525 through 528 removed outlier: 3.893A pdb=" N SER E 528 " --> pdb=" O PRO E 525 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 525 through 528' Processing helix chain 'E' and resid 547 through 549 No H-bonds generated for 'chain 'E' and resid 547 through 549' Processing helix chain 'E' and resid 597 through 599 No H-bonds generated for 'chain 'E' and resid 597 through 599' Processing helix chain 'E' and resid 626 through 628 No H-bonds generated for 'chain 'E' and resid 626 through 628' Processing helix chain 'E' and resid 679 through 681 No H-bonds generated for 'chain 'E' and resid 679 through 681' Processing helix chain 'E' and resid 806 through 811 Processing helix chain 'E' and resid 815 through 824 removed outlier: 4.182A pdb=" N GLU E 823 " --> pdb=" O GLN E 819 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N TYR E 824 " --> pdb=" O LEU E 820 " (cutoff:3.500A) Processing helix chain 'E' and resid 827 through 853 Processing helix chain 'E' and resid 889 through 896 Processing helix chain 'E' and resid 908 through 914 removed outlier: 3.720A pdb=" N MET E 913 " --> pdb=" O TYR E 909 " (cutoff:3.500A) Processing helix chain 'E' and resid 925 through 930 removed outlier: 4.088A pdb=" N ALA E 930 " --> pdb=" O GLN E 927 " (cutoff:3.500A) Processing helix chain 'E' and resid 941 through 958 removed outlier: 4.814A pdb=" N ALA E 956 " --> pdb=" O LEU E 952 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N GLY E 957 " --> pdb=" O GLY E 953 " (cutoff:3.500A) Processing helix chain 'E' and resid 972 through 983 removed outlier: 3.656A pdb=" N VAL E 983 " --> pdb=" O ARG E 979 " (cutoff:3.500A) Processing helix chain 'E' and resid 987 through 992 Processing helix chain 'E' and resid 994 through 1008 removed outlier: 3.875A pdb=" N MET E1008 " --> pdb=" O ALA E1004 " (cutoff:3.500A) Processing helix chain 'E' and resid 1017 through 1041 removed outlier: 3.843A pdb=" N LEU E1036 " --> pdb=" O ALA E1032 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LEU E1040 " --> pdb=" O LEU E1036 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N SER E1041 " --> pdb=" O ALA E1037 " (cutoff:3.500A) Processing helix chain 'E' and resid 1051 through 1057 Processing helix chain 'E' and resid 1060 through 1106 removed outlier: 4.572A pdb=" N ALA E1065 " --> pdb=" O PRO E1061 " (cutoff:3.500A) Processing helix chain 'E' and resid 1220 through 1222 No H-bonds generated for 'chain 'E' and resid 1220 through 1222' Processing sheet with id= A, first strand: chain 'A' and resid 33 through 35 removed outlier: 6.359A pdb=" N LEU A 100 " --> pdb=" O ASP A 34 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 68 through 75 removed outlier: 4.185A pdb=" N ARG A 335 " --> pdb=" O ASP A 326 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 83 through 85 removed outlier: 6.092A pdb=" N SER A 267 " --> pdb=" O GLN A 280 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N GLN A 280 " --> pdb=" O SER A 267 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 127 through 129 Processing sheet with id= E, first strand: chain 'A' and resid 292 through 295 removed outlier: 4.008A pdb=" N PHE A 239 " --> pdb=" O TYR A 184 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 186 through 189 Processing sheet with id= G, first strand: chain 'A' and resid 206 through 208 removed outlier: 3.797A pdb=" N HIS A 208 " --> pdb=" O SER A 299 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 359 through 363 removed outlier: 4.714A pdb=" N VAL A 659 " --> pdb=" O VAL A 363 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 373 through 376 removed outlier: 7.804A pdb=" N VAL A 374 " --> pdb=" O CYS A 603 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N GLU A 605 " --> pdb=" O VAL A 374 " (cutoff:3.500A) removed outlier: 8.222A pdb=" N GLU A 376 " --> pdb=" O GLU A 605 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N SER A 607 " --> pdb=" O GLU A 376 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N VAL A 639 " --> pdb=" O LEU A 651 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N VAL A 631 " --> pdb=" O VAL A 639 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 400 through 404 removed outlier: 3.603A pdb=" N SER A 440 " --> pdb=" O GLN A 576 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N THR A 483 " --> pdb=" O VAL A 420 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N VAL A 420 " --> pdb=" O THR A 483 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 407 through 409 Processing sheet with id= L, first strand: chain 'A' and resid 513 through 515 removed outlier: 6.224A pdb=" N SER A 557 " --> pdb=" O ASN A 501 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N CYS A 503 " --> pdb=" O VAL A 555 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N VAL A 555 " --> pdb=" O CYS A 503 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ARG A 505 " --> pdb=" O TRP A 553 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N TRP A 553 " --> pdb=" O ARG A 505 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'A' and resid 735 through 738 removed outlier: 7.718A pdb=" N SER A 761 " --> pdb=" O SER A 720 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N LEU A 722 " --> pdb=" O SER A 761 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'A' and resid 778 through 783 Processing sheet with id= O, first strand: chain 'A' and resid 785 through 796 removed outlier: 5.908A pdb=" N TYR A1141 " --> pdb=" O HIS A1122 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N HIS A1122 " --> pdb=" O TYR A1141 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'A' and resid 801 through 804 removed outlier: 4.548A pdb=" N LYS A 801 " --> pdb=" O LEU A 935 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'A' and resid 1212 through 1214 removed outlier: 5.525A pdb=" N ASN A1163 " --> pdb=" O ASP A1157 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N CYS A1164 " --> pdb=" O VAL A1205 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'A' and resid 1170 through 1173 Processing sheet with id= S, first strand: chain 'A' and resid 153 through 155 Processing sheet with id= T, first strand: chain 'C' and resid 33 through 35 removed outlier: 6.359A pdb=" N LEU C 100 " --> pdb=" O ASP C 34 " (cutoff:3.500A) No H-bonds generated for sheet with id= T Processing sheet with id= U, first strand: chain 'C' and resid 68 through 75 removed outlier: 4.185A pdb=" N ARG C 335 " --> pdb=" O ASP C 326 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'C' and resid 83 through 85 removed outlier: 6.092A pdb=" N SER C 267 " --> pdb=" O GLN C 280 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N GLN C 280 " --> pdb=" O SER C 267 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'C' and resid 127 through 129 Processing sheet with id= X, first strand: chain 'C' and resid 292 through 295 removed outlier: 4.008A pdb=" N PHE C 239 " --> pdb=" O TYR C 184 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'C' and resid 186 through 189 Processing sheet with id= Z, first strand: chain 'C' and resid 206 through 208 removed outlier: 3.798A pdb=" N HIS C 208 " --> pdb=" O SER C 299 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'C' and resid 359 through 363 removed outlier: 4.713A pdb=" N VAL C 659 " --> pdb=" O VAL C 363 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'C' and resid 373 through 376 removed outlier: 7.804A pdb=" N VAL C 374 " --> pdb=" O CYS C 603 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N GLU C 605 " --> pdb=" O VAL C 374 " (cutoff:3.500A) removed outlier: 8.222A pdb=" N GLU C 376 " --> pdb=" O GLU C 605 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N SER C 607 " --> pdb=" O GLU C 376 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N VAL C 639 " --> pdb=" O LEU C 651 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N VAL C 631 " --> pdb=" O VAL C 639 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'C' and resid 400 through 404 removed outlier: 3.603A pdb=" N SER C 440 " --> pdb=" O GLN C 576 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N THR C 483 " --> pdb=" O VAL C 420 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N VAL C 420 " --> pdb=" O THR C 483 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'C' and resid 407 through 409 Processing sheet with id= AE, first strand: chain 'C' and resid 513 through 515 removed outlier: 6.225A pdb=" N SER C 557 " --> pdb=" O ASN C 501 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N CYS C 503 " --> pdb=" O VAL C 555 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N VAL C 555 " --> pdb=" O CYS C 503 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ARG C 505 " --> pdb=" O TRP C 553 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N TRP C 553 " --> pdb=" O ARG C 505 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'C' and resid 735 through 738 removed outlier: 7.717A pdb=" N SER C 761 " --> pdb=" O SER C 720 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LEU C 722 " --> pdb=" O SER C 761 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'C' and resid 778 through 783 Processing sheet with id= AH, first strand: chain 'C' and resid 785 through 796 removed outlier: 5.908A pdb=" N TYR C1141 " --> pdb=" O HIS C1122 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N HIS C1122 " --> pdb=" O TYR C1141 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'C' and resid 801 through 804 removed outlier: 4.547A pdb=" N LYS C 801 " --> pdb=" O LEU C 935 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'C' and resid 1212 through 1214 removed outlier: 5.525A pdb=" N ASN C1163 " --> pdb=" O ASP C1157 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N CYS C1164 " --> pdb=" O VAL C1205 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'C' and resid 1170 through 1173 Processing sheet with id= AL, first strand: chain 'C' and resid 153 through 155 Processing sheet with id= AM, first strand: chain 'E' and resid 33 through 35 removed outlier: 6.359A pdb=" N LEU E 100 " --> pdb=" O ASP E 34 " (cutoff:3.500A) No H-bonds generated for sheet with id= AM Processing sheet with id= AN, first strand: chain 'E' and resid 68 through 75 removed outlier: 4.185A pdb=" N ARG E 335 " --> pdb=" O ASP E 326 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'E' and resid 83 through 85 removed outlier: 6.093A pdb=" N SER E 267 " --> pdb=" O GLN E 280 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N GLN E 280 " --> pdb=" O SER E 267 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'E' and resid 127 through 129 Processing sheet with id= AQ, first strand: chain 'E' and resid 292 through 295 removed outlier: 4.009A pdb=" N PHE E 239 " --> pdb=" O TYR E 184 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'E' and resid 186 through 189 Processing sheet with id= AS, first strand: chain 'E' and resid 206 through 208 removed outlier: 3.797A pdb=" N HIS E 208 " --> pdb=" O SER E 299 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'E' and resid 359 through 363 removed outlier: 4.713A pdb=" N VAL E 659 " --> pdb=" O VAL E 363 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'E' and resid 373 through 376 removed outlier: 7.804A pdb=" N VAL E 374 " --> pdb=" O CYS E 603 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N GLU E 605 " --> pdb=" O VAL E 374 " (cutoff:3.500A) removed outlier: 8.222A pdb=" N GLU E 376 " --> pdb=" O GLU E 605 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N SER E 607 " --> pdb=" O GLU E 376 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N VAL E 639 " --> pdb=" O LEU E 651 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N VAL E 631 " --> pdb=" O VAL E 639 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'E' and resid 400 through 404 removed outlier: 3.604A pdb=" N SER E 440 " --> pdb=" O GLN E 576 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N THR E 483 " --> pdb=" O VAL E 420 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N VAL E 420 " --> pdb=" O THR E 483 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'E' and resid 407 through 409 Processing sheet with id= AX, first strand: chain 'E' and resid 513 through 515 removed outlier: 6.225A pdb=" N SER E 557 " --> pdb=" O ASN E 501 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N CYS E 503 " --> pdb=" O VAL E 555 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N VAL E 555 " --> pdb=" O CYS E 503 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ARG E 505 " --> pdb=" O TRP E 553 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N TRP E 553 " --> pdb=" O ARG E 505 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'E' and resid 735 through 738 removed outlier: 7.719A pdb=" N SER E 761 " --> pdb=" O SER E 720 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N LEU E 722 " --> pdb=" O SER E 761 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain 'E' and resid 778 through 783 Processing sheet with id= BA, first strand: chain 'E' and resid 785 through 796 removed outlier: 5.908A pdb=" N TYR E1141 " --> pdb=" O HIS E1122 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N HIS E1122 " --> pdb=" O TYR E1141 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain 'E' and resid 801 through 804 removed outlier: 4.547A pdb=" N LYS E 801 " --> pdb=" O LEU E 935 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'E' and resid 1212 through 1214 removed outlier: 5.524A pdb=" N ASN E1163 " --> pdb=" O ASP E1157 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N CYS E1164 " --> pdb=" O VAL E1205 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain 'E' and resid 1170 through 1173 Processing sheet with id= BE, first strand: chain 'E' and resid 153 through 155 990 hydrogen bonds defined for protein. 2727 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: 12.94 Time building geometry restraints manager: 14.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 4691 1.30 - 1.44: 8240 1.44 - 1.57: 16009 1.57 - 1.71: 70 1.71 - 1.84: 192 Bond restraints: 29202 Sorted by residual: bond pdb=" C GLN C1097 " pdb=" O GLN C1097 " ideal model delta sigma weight residual 1.237 1.174 0.063 1.17e-02 7.31e+03 2.90e+01 bond pdb=" C GLN A1097 " pdb=" O GLN A1097 " ideal model delta sigma weight residual 1.237 1.174 0.063 1.17e-02 7.31e+03 2.90e+01 bond pdb=" C GLN E1097 " pdb=" O GLN E1097 " ideal model delta sigma weight residual 1.237 1.174 0.063 1.17e-02 7.31e+03 2.89e+01 bond pdb=" C SER E1095 " pdb=" O SER E1095 " ideal model delta sigma weight residual 1.236 1.170 0.066 1.26e-02 6.30e+03 2.73e+01 bond pdb=" C SER A1095 " pdb=" O SER A1095 " ideal model delta sigma weight residual 1.236 1.171 0.066 1.26e-02 6.30e+03 2.73e+01 ... (remaining 29197 not shown) Histogram of bond angle deviations from ideal: 95.92 - 103.60: 405 103.60 - 111.28: 12448 111.28 - 118.97: 11039 118.97 - 126.65: 15699 126.65 - 134.33: 171 Bond angle restraints: 39762 Sorted by residual: angle pdb=" N TRP E 960 " pdb=" CA TRP E 960 " pdb=" C TRP E 960 " ideal model delta sigma weight residual 111.14 132.19 -21.05 1.08e+00 8.57e-01 3.80e+02 angle pdb=" N TRP A 960 " pdb=" CA TRP A 960 " pdb=" C TRP A 960 " ideal model delta sigma weight residual 111.14 132.14 -21.00 1.08e+00 8.57e-01 3.78e+02 angle pdb=" N TRP C 960 " pdb=" CA TRP C 960 " pdb=" C TRP C 960 " ideal model delta sigma weight residual 111.14 132.12 -20.98 1.08e+00 8.57e-01 3.78e+02 angle pdb=" N TRP E 960 " pdb=" CA TRP E 960 " pdb=" CB TRP E 960 " ideal model delta sigma weight residual 110.07 95.92 14.15 1.45e+00 4.76e-01 9.52e+01 angle pdb=" N TRP A 960 " pdb=" CA TRP A 960 " pdb=" CB TRP A 960 " ideal model delta sigma weight residual 110.07 95.94 14.13 1.45e+00 4.76e-01 9.49e+01 ... (remaining 39757 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.84: 18444 26.84 - 53.67: 327 53.67 - 80.51: 132 80.51 - 107.35: 153 107.35 - 134.18: 18 Dihedral angle restraints: 19074 sinusoidal: 8958 harmonic: 10116 Sorted by residual: dihedral pdb=" N FOL C1401 " pdb=" C FOL C1401 " pdb=" C11 FOL C1401 " pdb=" C16 FOL C1401 " ideal model delta sinusoidal sigma weight residual -0.09 -134.27 134.18 1 2.00e+01 2.50e-03 4.07e+01 dihedral pdb=" N FOL A1401 " pdb=" C FOL A1401 " pdb=" C11 FOL A1401 " pdb=" C16 FOL A1401 " ideal model delta sinusoidal sigma weight residual -0.09 -134.22 134.13 1 2.00e+01 2.50e-03 4.07e+01 dihedral pdb=" N FOL E1401 " pdb=" C FOL E1401 " pdb=" C11 FOL E1401 " pdb=" C16 FOL E1401 " ideal model delta sinusoidal sigma weight residual -0.09 -134.18 134.09 1 2.00e+01 2.50e-03 4.07e+01 ... (remaining 19071 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 3281 0.086 - 0.173: 1081 0.173 - 0.259: 284 0.259 - 0.346: 134 0.346 - 0.432: 68 Chirality restraints: 4848 Sorted by residual: chirality pdb=" C1 NAG W 2 " pdb=" O4 NAG W 1 " pdb=" C2 NAG W 2 " pdb=" O5 NAG W 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.54 0.14 2.00e-02 2.50e+03 4.62e+01 chirality pdb=" C1 NAG M 2 " pdb=" O4 NAG M 1 " pdb=" C2 NAG M 2 " pdb=" O5 NAG M 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.54 0.14 2.00e-02 2.50e+03 4.59e+01 chirality pdb=" C1 NAG g 2 " pdb=" O4 NAG g 1 " pdb=" C2 NAG g 2 " pdb=" O5 NAG g 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.54 0.14 2.00e-02 2.50e+03 4.58e+01 ... (remaining 4845 not shown) Planarity restraints: 4995 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN E 166 " 0.067 2.00e-02 2.50e+03 6.82e-02 5.81e+01 pdb=" CG ASN E 166 " -0.035 2.00e-02 2.50e+03 pdb=" OD1 ASN E 166 " -0.012 2.00e-02 2.50e+03 pdb=" ND2 ASN E 166 " -0.103 2.00e-02 2.50e+03 pdb=" C1 NAG f 1 " 0.083 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 166 " -0.067 2.00e-02 2.50e+03 6.81e-02 5.80e+01 pdb=" CG ASN A 166 " 0.035 2.00e-02 2.50e+03 pdb=" OD1 ASN A 166 " 0.012 2.00e-02 2.50e+03 pdb=" ND2 ASN A 166 " 0.103 2.00e-02 2.50e+03 pdb=" C1 NAG L 1 " -0.082 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 166 " -0.067 2.00e-02 2.50e+03 6.80e-02 5.77e+01 pdb=" CG ASN C 166 " 0.035 2.00e-02 2.50e+03 pdb=" OD1 ASN C 166 " 0.012 2.00e-02 2.50e+03 pdb=" ND2 ASN C 166 " 0.102 2.00e-02 2.50e+03 pdb=" C1 NAG V 1 " -0.082 2.00e-02 2.50e+03 ... (remaining 4992 not shown) Histogram of nonbonded interaction distances: 2.43 - 2.93: 12935 2.93 - 3.42: 26338 3.42 - 3.91: 51062 3.91 - 4.41: 59265 4.41 - 4.90: 93357 Nonbonded interactions: 242957 Sorted by model distance: nonbonded pdb=" N ASP E 343 " pdb=" OD1 ASP E 343 " model vdw 2.433 2.520 nonbonded pdb=" N ASP A 343 " pdb=" OD1 ASP A 343 " model vdw 2.433 2.520 nonbonded pdb=" N ASP C 343 " pdb=" OD1 ASP C 343 " model vdw 2.434 2.520 nonbonded pdb=" OH TYR C 219 " pdb=" OE2 GLU C 247 " model vdw 2.490 2.440 nonbonded pdb=" OH TYR A 219 " pdb=" OE2 GLU A 247 " model vdw 2.490 2.440 ... (remaining 242952 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'H' selection = chain 'N' selection = chain 'R' selection = chain 'X' selection = chain 'b' } ncs_group { reference = chain 'D' selection = chain 'I' selection = chain 'J' selection = chain 'M' selection = chain 'O' selection = chain 'S' selection = chain 'T' selection = chain 'W' selection = chain 'Y' selection = chain 'c' selection = chain 'd' selection = chain 'g' } ncs_group { reference = chain 'F' selection = chain 'P' selection = chain 'Z' } ncs_group { reference = chain 'G' selection = chain 'Q' selection = chain 'a' } ncs_group { reference = chain 'K' selection = chain 'L' selection = chain 'U' selection = chain 'V' selection = chain 'e' selection = chain 'f' } 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: 2.870 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: 14.960 Check model and map are aligned: 0.410 Set scattering table: 0.300 Process input model: 81.940 Find NCS groups from input model: 1.680 Set up NCS constraints: 0.450 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:10.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 113.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 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 : 0.018 0.116 29202 Z= 1.170 Angle : 1.466 21.048 39762 Z= 0.964 Chirality : 0.109 0.432 4848 Planarity : 0.006 0.027 4944 Dihedral : 15.699 134.184 12465 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 1.16 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.83 % Favored : 98.09 % Rotamer: Outliers : 0.20 % Allowed : 0.81 % Favored : 98.98 % Cbeta Deviations : 0.09 % 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 (0.13), residues: 3447 helix: -0.23 (0.17), residues: 702 sheet: 0.82 (0.18), residues: 750 loop : 0.62 (0.13), residues: 1995 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.004 TRP C1184 HIS 0.005 0.001 HIS C 91 PHE 0.024 0.004 PHE A 473 TYR 0.050 0.006 TYR C 184 ARG 0.005 0.001 ARG E 334 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6894 Ramachandran restraints generated. 3447 Oldfield, 0 Emsley, 3447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6894 Ramachandran restraints generated. 3447 Oldfield, 0 Emsley, 3447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 2976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 445 time to evaluate : 2.940 Fit side-chains REVERT: A 71 TYR cc_start: 0.8475 (t80) cc_final: 0.8070 (t80) REVERT: C 161 MET cc_start: 0.6815 (mmm) cc_final: 0.6390 (mmm) REVERT: E 452 MET cc_start: 0.8852 (mtp) cc_final: 0.8592 (mtp) outliers start: 6 outliers final: 2 residues processed: 450 average time/residue: 1.3429 time to fit residues: 708.6866 Evaluate side-chains 252 residues out of total 2976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 250 time to evaluate : 3.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain C residue 199 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 291 optimal weight: 0.6980 chunk 261 optimal weight: 2.9990 chunk 145 optimal weight: 0.9980 chunk 89 optimal weight: 0.7980 chunk 176 optimal weight: 0.7980 chunk 139 optimal weight: 0.6980 chunk 270 optimal weight: 0.7980 chunk 104 optimal weight: 0.6980 chunk 164 optimal weight: 1.9990 chunk 201 optimal weight: 0.5980 chunk 313 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 167 HIS A 280 GLN A 466 GLN ** A 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1009 GLN A1169 ASN C 280 GLN C 466 GLN C 521 ASN C 765 ASN C 812 ASN E 280 GLN E 521 ASN E1009 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.099 29202 Z= 0.245 Angle : 0.686 17.949 39762 Z= 0.351 Chirality : 0.050 0.351 4848 Planarity : 0.004 0.043 4944 Dihedral : 13.415 120.895 6511 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.76 % Allowed : 6.58 % Favored : 91.66 % Cbeta Deviations : 0.15 % 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: 0.76 (0.14), residues: 3447 helix: 1.02 (0.20), residues: 702 sheet: 0.45 (0.17), residues: 870 loop : 0.48 (0.14), residues: 1875 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 960 HIS 0.006 0.001 HIS C 348 PHE 0.012 0.002 PHE C 183 TYR 0.014 0.001 TYR E1141 ARG 0.006 0.000 ARG C1069 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6894 Ramachandran restraints generated. 3447 Oldfield, 0 Emsley, 3447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6894 Ramachandran restraints generated. 3447 Oldfield, 0 Emsley, 3447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 2976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 321 time to evaluate : 3.658 Fit side-chains revert: symmetry clash REVERT: A 71 TYR cc_start: 0.8409 (t80) cc_final: 0.8068 (t80) REVERT: A 261 GLN cc_start: 0.8046 (mt0) cc_final: 0.7773 (mt0) REVERT: C 725 GLU cc_start: 0.6062 (OUTLIER) cc_final: 0.5655 (mp0) REVERT: C 1105 GLU cc_start: 0.7131 (OUTLIER) cc_final: 0.6884 (tm-30) REVERT: E 1105 GLU cc_start: 0.7266 (OUTLIER) cc_final: 0.6683 (tm-30) outliers start: 52 outliers final: 16 residues processed: 345 average time/residue: 1.3373 time to fit residues: 545.7328 Evaluate side-chains 266 residues out of total 2976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 247 time to evaluate : 3.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 1009 GLN Chi-restraints excluded: chain A residue 1062 GLU Chi-restraints excluded: chain C residue 199 ASN Chi-restraints excluded: chain C residue 415 LEU Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain C residue 557 SER Chi-restraints excluded: chain C residue 725 GLU Chi-restraints excluded: chain C residue 943 MET Chi-restraints excluded: chain C residue 961 THR Chi-restraints excluded: chain C residue 1105 GLU Chi-restraints excluded: chain E residue 199 ASN Chi-restraints excluded: chain E residue 419 SER Chi-restraints excluded: chain E residue 943 MET Chi-restraints excluded: chain E residue 1105 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 174 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 chunk 260 optimal weight: 2.9990 chunk 213 optimal weight: 3.9990 chunk 86 optimal weight: 5.9990 chunk 313 optimal weight: 0.3980 chunk 339 optimal weight: 3.9990 chunk 279 optimal weight: 5.9990 chunk 311 optimal weight: 0.0670 chunk 107 optimal weight: 0.8980 chunk 251 optimal weight: 0.9980 overall best weight: 1.0720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 167 HIS A 848 ASN A 994 GLN A1097 GLN E 421 ASN E 466 GLN E 812 ASN E 987 GLN E1009 GLN E1084 GLN E1169 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 29202 Z= 0.284 Angle : 0.643 17.498 39762 Z= 0.324 Chirality : 0.049 0.625 4848 Planarity : 0.004 0.036 4944 Dihedral : 11.306 101.579 6511 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.44 % Allowed : 8.21 % Favored : 89.35 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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 (0.14), residues: 3447 helix: 1.16 (0.20), residues: 702 sheet: 0.44 (0.17), residues: 891 loop : 0.27 (0.14), residues: 1854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 310 HIS 0.005 0.001 HIS E 681 PHE 0.018 0.001 PHE A 239 TYR 0.017 0.001 TYR A 184 ARG 0.009 0.000 ARG C1069 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6894 Ramachandran restraints generated. 3447 Oldfield, 0 Emsley, 3447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6894 Ramachandran restraints generated. 3447 Oldfield, 0 Emsley, 3447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 270 time to evaluate : 3.225 Fit side-chains revert: symmetry clash REVERT: A 71 TYR cc_start: 0.8427 (t80) cc_final: 0.8161 (t80) REVERT: A 199 ASN cc_start: 0.6997 (p0) cc_final: 0.6602 (p0) REVERT: A 740 ASP cc_start: 0.7233 (OUTLIER) cc_final: 0.7021 (m-30) REVERT: C 141 ARG cc_start: 0.7559 (OUTLIER) cc_final: 0.7354 (mtm110) REVERT: C 251 LEU cc_start: 0.8390 (OUTLIER) cc_final: 0.8133 (tp) REVERT: C 291 LYS cc_start: 0.8621 (OUTLIER) cc_final: 0.8383 (mtpt) REVERT: E 1105 GLU cc_start: 0.7236 (OUTLIER) cc_final: 0.6654 (tm-30) outliers start: 72 outliers final: 26 residues processed: 310 average time/residue: 1.3686 time to fit residues: 500.9549 Evaluate side-chains 275 residues out of total 2976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 244 time to evaluate : 3.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 740 ASP Chi-restraints excluded: chain A residue 899 THR Chi-restraints excluded: chain A residue 958 VAL Chi-restraints excluded: chain A residue 1062 GLU Chi-restraints excluded: chain C residue 141 ARG Chi-restraints excluded: chain C residue 199 ASN Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 291 LYS Chi-restraints excluded: chain C residue 386 SER Chi-restraints excluded: chain C residue 457 SER Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain C residue 557 SER Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 943 MET Chi-restraints excluded: chain C residue 961 THR Chi-restraints excluded: chain C residue 1035 LYS Chi-restraints excluded: chain C residue 1068 ASP Chi-restraints excluded: chain E residue 199 ASN Chi-restraints excluded: chain E residue 386 SER Chi-restraints excluded: chain E residue 419 SER Chi-restraints excluded: chain E residue 457 SER Chi-restraints excluded: chain E residue 943 MET Chi-restraints excluded: chain E residue 1062 GLU Chi-restraints excluded: chain E residue 1105 GLU Chi-restraints excluded: chain E residue 1112 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 310 optimal weight: 0.0370 chunk 235 optimal weight: 1.9990 chunk 162 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 149 optimal weight: 0.6980 chunk 210 optimal weight: 6.9990 chunk 314 optimal weight: 5.9990 chunk 333 optimal weight: 0.6980 chunk 164 optimal weight: 0.6980 chunk 298 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 overall best weight: 0.6260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 167 HIS A 261 GLN A 427 GLN A 848 ASN A1020 GLN A1212 GLN C 812 ASN C 994 GLN C1020 GLN E 421 ASN E 647 ASN E 812 ASN E 987 GLN E1009 GLN E1020 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 29202 Z= 0.201 Angle : 0.575 16.594 39762 Z= 0.290 Chirality : 0.046 0.461 4848 Planarity : 0.004 0.038 4944 Dihedral : 8.664 82.394 6509 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.14 % Allowed : 9.12 % Favored : 88.74 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.60 (0.14), residues: 3447 helix: 1.51 (0.20), residues: 684 sheet: 0.39 (0.17), residues: 912 loop : 0.08 (0.14), residues: 1851 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 310 HIS 0.003 0.001 HIS E 681 PHE 0.016 0.001 PHE E 183 TYR 0.011 0.001 TYR E1141 ARG 0.005 0.000 ARG C1069 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6894 Ramachandran restraints generated. 3447 Oldfield, 0 Emsley, 3447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6894 Ramachandran restraints generated. 3447 Oldfield, 0 Emsley, 3447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 2976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 271 time to evaluate : 3.459 Fit side-chains revert: symmetry clash REVERT: A 71 TYR cc_start: 0.8403 (t80) cc_final: 0.8085 (t80) REVERT: A 199 ASN cc_start: 0.7009 (p0) cc_final: 0.6643 (p0) REVERT: A 740 ASP cc_start: 0.7316 (m-30) cc_final: 0.7054 (m-30) REVERT: C 240 MET cc_start: 0.8011 (ttm) cc_final: 0.7803 (ttm) REVERT: C 251 LEU cc_start: 0.8256 (OUTLIER) cc_final: 0.8025 (tp) REVERT: C 369 LYS cc_start: 0.7171 (mptt) cc_final: 0.6941 (mptt) REVERT: E 1105 GLU cc_start: 0.7229 (OUTLIER) cc_final: 0.6660 (tm-30) outliers start: 63 outliers final: 23 residues processed: 303 average time/residue: 1.3580 time to fit residues: 485.8130 Evaluate side-chains 268 residues out of total 2976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 243 time to evaluate : 3.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 473 PHE Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 943 MET Chi-restraints excluded: chain C residue 199 ASN Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 386 SER Chi-restraints excluded: chain C residue 413 LYS Chi-restraints excluded: chain C residue 473 PHE Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain C residue 557 SER Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 943 MET Chi-restraints excluded: chain E residue 199 ASN Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain E residue 386 SER Chi-restraints excluded: chain E residue 419 SER Chi-restraints excluded: chain E residue 718 VAL Chi-restraints excluded: chain E residue 943 MET Chi-restraints excluded: chain E residue 1062 GLU Chi-restraints excluded: chain E residue 1105 GLU Chi-restraints excluded: chain E residue 1112 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 277 optimal weight: 0.0050 chunk 189 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 248 optimal weight: 4.9990 chunk 137 optimal weight: 0.7980 chunk 284 optimal weight: 0.8980 chunk 230 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 170 optimal weight: 0.5980 chunk 299 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 overall best weight: 0.8596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 167 HIS A 427 GLN A 812 ASN A 848 ASN A 987 GLN A1003 GLN A1009 GLN C 280 GLN C 812 ASN E 60 GLN E 280 GLN E 812 ASN E1009 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 29202 Z= 0.235 Angle : 0.603 28.234 39762 Z= 0.301 Chirality : 0.046 0.519 4848 Planarity : 0.004 0.040 4944 Dihedral : 7.425 67.965 6509 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.20 % Allowed : 9.26 % Favored : 88.54 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.14), residues: 3447 helix: 1.35 (0.20), residues: 708 sheet: 0.30 (0.17), residues: 912 loop : -0.01 (0.14), residues: 1827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 310 HIS 0.004 0.001 HIS A 167 PHE 0.016 0.001 PHE E 183 TYR 0.015 0.001 TYR A 184 ARG 0.006 0.000 ARG C 542 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6894 Ramachandran restraints generated. 3447 Oldfield, 0 Emsley, 3447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6894 Ramachandran restraints generated. 3447 Oldfield, 0 Emsley, 3447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 2976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 258 time to evaluate : 3.092 Fit side-chains revert: symmetry clash REVERT: A 71 TYR cc_start: 0.8409 (t80) cc_final: 0.8022 (t80) REVERT: A 199 ASN cc_start: 0.7036 (OUTLIER) cc_final: 0.6650 (p0) REVERT: A 1008 MET cc_start: 0.7425 (OUTLIER) cc_final: 0.7113 (ptp) REVERT: C 141 ARG cc_start: 0.7526 (OUTLIER) cc_final: 0.7316 (mtm110) REVERT: C 251 LEU cc_start: 0.8323 (OUTLIER) cc_final: 0.8103 (tp) REVERT: E 1105 GLU cc_start: 0.7254 (OUTLIER) cc_final: 0.6678 (tm-30) outliers start: 65 outliers final: 35 residues processed: 297 average time/residue: 1.2665 time to fit residues: 446.9604 Evaluate side-chains 276 residues out of total 2976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 236 time to evaluate : 2.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 473 PHE Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 899 THR Chi-restraints excluded: chain A residue 943 MET Chi-restraints excluded: chain A residue 1008 MET Chi-restraints excluded: chain C residue 141 ARG Chi-restraints excluded: chain C residue 199 ASN Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 386 SER Chi-restraints excluded: chain C residue 413 LYS Chi-restraints excluded: chain C residue 450 LEU Chi-restraints excluded: chain C residue 457 SER Chi-restraints excluded: chain C residue 473 PHE Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain C residue 557 SER Chi-restraints excluded: chain C residue 661 VAL Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 943 MET Chi-restraints excluded: chain C residue 961 THR Chi-restraints excluded: chain E residue 199 ASN Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain E residue 386 SER Chi-restraints excluded: chain E residue 413 LYS Chi-restraints excluded: chain E residue 419 SER Chi-restraints excluded: chain E residue 457 SER Chi-restraints excluded: chain E residue 661 VAL Chi-restraints excluded: chain E residue 718 VAL Chi-restraints excluded: chain E residue 899 THR Chi-restraints excluded: chain E residue 938 LEU Chi-restraints excluded: chain E residue 943 MET Chi-restraints excluded: chain E residue 964 LEU Chi-restraints excluded: chain E residue 1062 GLU Chi-restraints excluded: chain E residue 1105 GLU Chi-restraints excluded: chain E residue 1112 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 112 optimal weight: 1.9990 chunk 300 optimal weight: 0.1980 chunk 65 optimal weight: 2.9990 chunk 195 optimal weight: 0.0470 chunk 82 optimal weight: 0.5980 chunk 333 optimal weight: 3.9990 chunk 277 optimal weight: 1.9990 chunk 154 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 110 optimal weight: 0.9980 chunk 175 optimal weight: 0.5980 overall best weight: 0.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 167 HIS A 319 GLN ** A 812 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 280 GLN C 319 GLN ** C 681 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 812 ASN E 280 GLN E 319 GLN E 812 ASN E 914 GLN E1031 GLN E1084 GLN E1212 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.2674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 29202 Z= 0.173 Angle : 0.569 23.683 39762 Z= 0.284 Chirality : 0.045 0.437 4848 Planarity : 0.004 0.051 4944 Dihedral : 6.540 56.169 6509 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.27 % Allowed : 10.00 % Favored : 87.72 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.49 (0.14), residues: 3447 helix: 1.38 (0.20), residues: 726 sheet: 0.30 (0.16), residues: 948 loop : -0.01 (0.14), residues: 1773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 310 HIS 0.003 0.001 HIS E 681 PHE 0.015 0.001 PHE A 239 TYR 0.011 0.001 TYR C1141 ARG 0.010 0.000 ARG C1069 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6894 Ramachandran restraints generated. 3447 Oldfield, 0 Emsley, 3447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6894 Ramachandran restraints generated. 3447 Oldfield, 0 Emsley, 3447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 250 time to evaluate : 3.301 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 71 TYR cc_start: 0.8409 (t80) cc_final: 0.8026 (t80) REVERT: A 199 ASN cc_start: 0.7032 (p0) cc_final: 0.6718 (p0) REVERT: C 251 LEU cc_start: 0.8238 (OUTLIER) cc_final: 0.7999 (tp) REVERT: C 620 CYS cc_start: 0.5635 (t) cc_final: 0.5249 (t) REVERT: E 261 GLN cc_start: 0.7910 (mt0) cc_final: 0.7708 (mt0) outliers start: 67 outliers final: 34 residues processed: 290 average time/residue: 1.3291 time to fit residues: 458.5331 Evaluate side-chains 266 residues out of total 2976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 231 time to evaluate : 3.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 473 PHE Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 899 THR Chi-restraints excluded: chain A residue 943 MET Chi-restraints excluded: chain C residue 199 ASN Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 386 SER Chi-restraints excluded: chain C residue 413 LYS Chi-restraints excluded: chain C residue 457 SER Chi-restraints excluded: chain C residue 473 PHE Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain C residue 557 SER Chi-restraints excluded: chain C residue 661 VAL Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 848 ASN Chi-restraints excluded: chain C residue 943 MET Chi-restraints excluded: chain C residue 1068 ASP Chi-restraints excluded: chain E residue 199 ASN Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain E residue 319 GLN Chi-restraints excluded: chain E residue 386 SER Chi-restraints excluded: chain E residue 413 LYS Chi-restraints excluded: chain E residue 419 SER Chi-restraints excluded: chain E residue 457 SER Chi-restraints excluded: chain E residue 661 VAL Chi-restraints excluded: chain E residue 718 VAL Chi-restraints excluded: chain E residue 938 LEU Chi-restraints excluded: chain E residue 943 MET Chi-restraints excluded: chain E residue 964 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 321 optimal weight: 0.7980 chunk 37 optimal weight: 3.9990 chunk 190 optimal weight: 2.9990 chunk 243 optimal weight: 2.9990 chunk 188 optimal weight: 1.9990 chunk 280 optimal weight: 3.9990 chunk 186 optimal weight: 0.4980 chunk 332 optimal weight: 2.9990 chunk 208 optimal weight: 2.9990 chunk 202 optimal weight: 0.8980 chunk 153 optimal weight: 0.9980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 GLN ** A 812 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 848 ASN A1003 GLN A1009 GLN C 280 GLN C 427 GLN ** C 681 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 812 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 812 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 914 GLN E1031 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.2673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 29202 Z= 0.261 Angle : 0.594 20.657 39762 Z= 0.297 Chirality : 0.046 0.466 4848 Planarity : 0.004 0.040 4944 Dihedral : 6.580 52.918 6509 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.97 % Allowed : 10.38 % Favored : 87.66 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.51 (0.14), residues: 3447 helix: 1.33 (0.20), residues: 723 sheet: 0.32 (0.17), residues: 927 loop : 0.04 (0.14), residues: 1797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 310 HIS 0.003 0.001 HIS C 681 PHE 0.015 0.001 PHE A 183 TYR 0.014 0.001 TYR E 77 ARG 0.011 0.000 ARG A1069 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6894 Ramachandran restraints generated. 3447 Oldfield, 0 Emsley, 3447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6894 Ramachandran restraints generated. 3447 Oldfield, 0 Emsley, 3447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 231 time to evaluate : 3.096 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 71 TYR cc_start: 0.8414 (t80) cc_final: 0.8020 (t80) REVERT: A 199 ASN cc_start: 0.7066 (OUTLIER) cc_final: 0.6702 (p0) REVERT: C 251 LEU cc_start: 0.8326 (OUTLIER) cc_final: 0.8104 (tp) REVERT: E 1105 GLU cc_start: 0.7275 (OUTLIER) cc_final: 0.6685 (tm-30) outliers start: 58 outliers final: 33 residues processed: 266 average time/residue: 1.2396 time to fit residues: 396.1758 Evaluate side-chains 264 residues out of total 2976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 228 time to evaluate : 3.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 473 PHE Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 899 THR Chi-restraints excluded: chain A residue 943 MET Chi-restraints excluded: chain A residue 1009 GLN Chi-restraints excluded: chain C residue 152 SER Chi-restraints excluded: chain C residue 199 ASN Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 386 SER Chi-restraints excluded: chain C residue 413 LYS Chi-restraints excluded: chain C residue 457 SER Chi-restraints excluded: chain C residue 473 PHE Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain C residue 557 SER Chi-restraints excluded: chain C residue 661 VAL Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 943 MET Chi-restraints excluded: chain C residue 961 THR Chi-restraints excluded: chain E residue 199 ASN Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain E residue 386 SER Chi-restraints excluded: chain E residue 413 LYS Chi-restraints excluded: chain E residue 419 SER Chi-restraints excluded: chain E residue 457 SER Chi-restraints excluded: chain E residue 661 VAL Chi-restraints excluded: chain E residue 718 VAL Chi-restraints excluded: chain E residue 938 LEU Chi-restraints excluded: chain E residue 943 MET Chi-restraints excluded: chain E residue 964 LEU Chi-restraints excluded: chain E residue 1105 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 205 optimal weight: 0.0370 chunk 132 optimal weight: 0.6980 chunk 198 optimal weight: 4.9990 chunk 100 optimal weight: 0.8980 chunk 65 optimal weight: 3.9990 chunk 64 optimal weight: 0.6980 chunk 211 optimal weight: 3.9990 chunk 226 optimal weight: 1.9990 chunk 164 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 261 optimal weight: 1.9990 overall best weight: 0.8660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 GLN ** A 812 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1009 GLN A1072 ASN C 280 GLN ** C 681 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 812 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 812 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.2726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 29202 Z= 0.232 Angle : 0.586 19.543 39762 Z= 0.292 Chirality : 0.045 0.471 4848 Planarity : 0.004 0.039 4944 Dihedral : 6.423 53.816 6509 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.66 % Allowed : 10.95 % Favored : 87.39 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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 (0.14), residues: 3447 helix: 1.34 (0.20), residues: 723 sheet: 0.35 (0.17), residues: 912 loop : -0.02 (0.14), residues: 1812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 310 HIS 0.004 0.001 HIS A 681 PHE 0.017 0.001 PHE C 183 TYR 0.012 0.001 TYR A 361 ARG 0.008 0.000 ARG A1069 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6894 Ramachandran restraints generated. 3447 Oldfield, 0 Emsley, 3447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6894 Ramachandran restraints generated. 3447 Oldfield, 0 Emsley, 3447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 234 time to evaluate : 3.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 TYR cc_start: 0.8414 (t80) cc_final: 0.8012 (t80) REVERT: A 199 ASN cc_start: 0.7034 (OUTLIER) cc_final: 0.6717 (p0) REVERT: A 914 GLN cc_start: 0.6298 (OUTLIER) cc_final: 0.6048 (mt0) REVERT: C 251 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.8087 (tp) REVERT: E 1105 GLU cc_start: 0.7271 (OUTLIER) cc_final: 0.6725 (tm-30) outliers start: 49 outliers final: 31 residues processed: 260 average time/residue: 1.2558 time to fit residues: 390.8414 Evaluate side-chains 266 residues out of total 2976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 231 time to evaluate : 3.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 473 PHE Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 899 THR Chi-restraints excluded: chain A residue 914 GLN Chi-restraints excluded: chain A residue 943 MET Chi-restraints excluded: chain C residue 199 ASN Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 386 SER Chi-restraints excluded: chain C residue 413 LYS Chi-restraints excluded: chain C residue 457 SER Chi-restraints excluded: chain C residue 473 PHE Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain C residue 557 SER Chi-restraints excluded: chain C residue 661 VAL Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 943 MET Chi-restraints excluded: chain C residue 961 THR Chi-restraints excluded: chain C residue 1068 ASP Chi-restraints excluded: chain E residue 199 ASN Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain E residue 386 SER Chi-restraints excluded: chain E residue 413 LYS Chi-restraints excluded: chain E residue 419 SER Chi-restraints excluded: chain E residue 457 SER Chi-restraints excluded: chain E residue 661 VAL Chi-restraints excluded: chain E residue 718 VAL Chi-restraints excluded: chain E residue 938 LEU Chi-restraints excluded: chain E residue 943 MET Chi-restraints excluded: chain E residue 964 LEU Chi-restraints excluded: chain E residue 1105 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 302 optimal weight: 0.5980 chunk 318 optimal weight: 3.9990 chunk 290 optimal weight: 2.9990 chunk 309 optimal weight: 0.7980 chunk 186 optimal weight: 0.4980 chunk 134 optimal weight: 0.0870 chunk 243 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 280 optimal weight: 3.9990 chunk 293 optimal weight: 0.8980 chunk 308 optimal weight: 1.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 GLN A 427 GLN ** A 812 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1009 GLN A1072 ASN C 280 GLN C 421 ASN C 647 ASN ** C 812 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 60 GLN ** E 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 280 GLN ** E 812 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.2825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 29202 Z= 0.185 Angle : 0.563 17.986 39762 Z= 0.281 Chirality : 0.044 0.461 4848 Planarity : 0.004 0.038 4944 Dihedral : 6.054 53.260 6509 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.59 % Allowed : 11.12 % Favored : 87.28 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.52 (0.14), residues: 3447 helix: 1.43 (0.20), residues: 723 sheet: 0.29 (0.17), residues: 927 loop : 0.03 (0.14), residues: 1797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 310 HIS 0.004 0.001 HIS C 681 PHE 0.016 0.001 PHE C 183 TYR 0.011 0.001 TYR E1141 ARG 0.008 0.000 ARG A1069 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6894 Ramachandran restraints generated. 3447 Oldfield, 0 Emsley, 3447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6894 Ramachandran restraints generated. 3447 Oldfield, 0 Emsley, 3447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 235 time to evaluate : 3.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 199 ASN cc_start: 0.6989 (OUTLIER) cc_final: 0.6687 (p0) REVERT: C 251 LEU cc_start: 0.8272 (OUTLIER) cc_final: 0.8044 (tp) outliers start: 47 outliers final: 31 residues processed: 262 average time/residue: 1.2655 time to fit residues: 398.7997 Evaluate side-chains 263 residues out of total 2976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 230 time to evaluate : 3.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 899 THR Chi-restraints excluded: chain A residue 943 MET Chi-restraints excluded: chain C residue 152 SER Chi-restraints excluded: chain C residue 199 ASN Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 386 SER Chi-restraints excluded: chain C residue 413 LYS Chi-restraints excluded: chain C residue 457 SER Chi-restraints excluded: chain C residue 473 PHE Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain C residue 557 SER Chi-restraints excluded: chain C residue 661 VAL Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 943 MET Chi-restraints excluded: chain C residue 961 THR Chi-restraints excluded: chain E residue 199 ASN Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain E residue 386 SER Chi-restraints excluded: chain E residue 413 LYS Chi-restraints excluded: chain E residue 419 SER Chi-restraints excluded: chain E residue 453 LYS Chi-restraints excluded: chain E residue 457 SER Chi-restraints excluded: chain E residue 661 VAL Chi-restraints excluded: chain E residue 718 VAL Chi-restraints excluded: chain E residue 938 LEU Chi-restraints excluded: chain E residue 943 MET Chi-restraints excluded: chain E residue 964 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 203 optimal weight: 4.9990 chunk 327 optimal weight: 3.9990 chunk 199 optimal weight: 0.9980 chunk 155 optimal weight: 0.8980 chunk 227 optimal weight: 2.9990 chunk 343 optimal weight: 1.9990 chunk 316 optimal weight: 0.9980 chunk 273 optimal weight: 0.1980 chunk 28 optimal weight: 0.9980 chunk 211 optimal weight: 0.9990 chunk 167 optimal weight: 0.0980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 167 HIS A 280 GLN ** A 812 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1031 GLN ** C 812 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 280 GLN ** E 812 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 29202 Z= 0.194 Angle : 0.573 21.952 39762 Z= 0.287 Chirality : 0.045 0.462 4848 Planarity : 0.004 0.038 4944 Dihedral : 5.947 52.717 6509 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.25 % Allowed : 11.43 % Favored : 87.32 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.53 (0.14), residues: 3447 helix: 1.44 (0.20), residues: 723 sheet: 0.27 (0.17), residues: 939 loop : 0.05 (0.14), residues: 1785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 310 HIS 0.004 0.001 HIS C 681 PHE 0.020 0.001 PHE A 239 TYR 0.011 0.001 TYR C1141 ARG 0.008 0.000 ARG A1069 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6894 Ramachandran restraints generated. 3447 Oldfield, 0 Emsley, 3447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6894 Ramachandran restraints generated. 3447 Oldfield, 0 Emsley, 3447 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 239 time to evaluate : 2.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 199 ASN cc_start: 0.6993 (OUTLIER) cc_final: 0.6709 (p0) REVERT: C 251 LEU cc_start: 0.8248 (OUTLIER) cc_final: 0.8038 (tp) REVERT: C 620 CYS cc_start: 0.5771 (t) cc_final: 0.5360 (t) REVERT: C 650 CYS cc_start: 0.5684 (m) cc_final: 0.5435 (m) outliers start: 37 outliers final: 31 residues processed: 261 average time/residue: 1.2158 time to fit residues: 380.0809 Evaluate side-chains 263 residues out of total 2976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 230 time to evaluate : 3.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 ASN Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 473 PHE Chi-restraints excluded: chain A residue 490 THR Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 899 THR Chi-restraints excluded: chain A residue 943 MET Chi-restraints excluded: chain C residue 152 SER Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 386 SER Chi-restraints excluded: chain C residue 413 LYS Chi-restraints excluded: chain C residue 457 SER Chi-restraints excluded: chain C residue 473 PHE Chi-restraints excluded: chain C residue 490 THR Chi-restraints excluded: chain C residue 661 VAL Chi-restraints excluded: chain C residue 718 VAL Chi-restraints excluded: chain C residue 943 MET Chi-restraints excluded: chain C residue 961 THR Chi-restraints excluded: chain E residue 199 ASN Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain E residue 386 SER Chi-restraints excluded: chain E residue 413 LYS Chi-restraints excluded: chain E residue 419 SER Chi-restraints excluded: chain E residue 453 LYS Chi-restraints excluded: chain E residue 457 SER Chi-restraints excluded: chain E residue 661 VAL Chi-restraints excluded: chain E residue 718 VAL Chi-restraints excluded: chain E residue 938 LEU Chi-restraints excluded: chain E residue 943 MET Chi-restraints excluded: chain E residue 964 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 217 optimal weight: 2.9990 chunk 291 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 chunk 252 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 76 optimal weight: 0.2980 chunk 274 optimal weight: 0.0470 chunk 114 optimal weight: 0.8980 chunk 281 optimal weight: 0.0030 chunk 34 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 overall best weight: 0.4490 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 GLN A1031 GLN A1084 GLN C 427 GLN C 521 ASN ** C 812 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 261 GLN E 280 GLN E 427 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.128953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.095428 restraints weight = 31316.936| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 2.43 r_work: 0.2911 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2758 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.2940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 29202 Z= 0.165 Angle : 0.558 21.533 39762 Z= 0.279 Chirality : 0.044 0.454 4848 Planarity : 0.004 0.039 4944 Dihedral : 5.650 53.441 6507 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.25 % Allowed : 11.70 % Favored : 87.05 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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 (0.14), residues: 3447 helix: 1.52 (0.20), residues: 723 sheet: 0.26 (0.16), residues: 960 loop : -0.03 (0.14), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 310 HIS 0.005 0.001 HIS C 681 PHE 0.016 0.001 PHE C 183 TYR 0.011 0.001 TYR C1141 ARG 0.008 0.000 ARG A1069 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8869.91 seconds wall clock time: 160 minutes 22.09 seconds (9622.09 seconds total)