Starting phenix.real_space_refine on Mon Nov 20 02:58:27 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pz8_20527/11_2023/6pz8_20527.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pz8_20527/11_2023/6pz8_20527.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pz8_20527/11_2023/6pz8_20527.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pz8_20527/11_2023/6pz8_20527.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pz8_20527/11_2023/6pz8_20527.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pz8_20527/11_2023/6pz8_20527.pdb" } resolution = 4.19 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.063 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 144 5.16 5 C 18096 2.51 5 N 4677 2.21 5 O 5766 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 777": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 778": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 788": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 824": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 850": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 895": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 905": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 928": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 932": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 940": "OD1" <-> "OD2" Residue "A TYR 947": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 977": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 978": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1012": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1044": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1053": "OD1" <-> "OD2" Residue "A PHE 1126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 609": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 617": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 635": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 642": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 649": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 689": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 704": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 27": "OE1" <-> "OE2" Residue "L PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 777": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 778": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 788": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 824": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 850": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 895": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 905": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 928": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 932": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 940": "OD1" <-> "OD2" Residue "E TYR 947": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 977": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 978": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1012": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1044": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 1053": "OD1" <-> "OD2" Residue "E PHE 1126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 609": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 617": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 635": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 642": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 649": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 689": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 704": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 27": "OE1" <-> "OE2" Residue "G PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 777": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 778": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 788": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 824": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 850": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 895": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 905": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 928": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 932": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 940": "OD1" <-> "OD2" Residue "I TYR 947": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 977": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 978": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 1012": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 1044": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 1053": "OD1" <-> "OD2" Residue "I PHE 1126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 1142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 609": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 617": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 635": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 642": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 649": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 689": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 704": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 27": "OE1" <-> "OE2" Residue "K PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 28683 Number of models: 1 Model: "" Number of chains: 42 Chain: "A" Number of atoms: 3546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3546 Classifications: {'peptide': 463} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 20, 'TRANS': 439} Chain breaks: 1 Chain: "B" Number of atoms: 4010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 513, 4010 Classifications: {'peptide': 513} Link IDs: {'CIS': 4, 'PTRANS': 22, 'TRANS': 486} Chain breaks: 1 Chain: "H" Number of atoms: 882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 882 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "L" Number of atoms: 771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 771 Classifications: {'peptide': 103} Link IDs: {'PCIS': 3, 'PTRANS': 4, 'TRANS': 95} Chain breaks: 1 Chain: "E" Number of atoms: 3546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3546 Classifications: {'peptide': 463} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 20, 'TRANS': 439} Chain breaks: 1 Chain: "J" Number of atoms: 4010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 513, 4010 Classifications: {'peptide': 513} Link IDs: {'CIS': 4, 'PTRANS': 22, 'TRANS': 486} Chain breaks: 1 Chain: "C" Number of atoms: 882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 882 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "G" Number of atoms: 771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 771 Classifications: {'peptide': 103} Link IDs: {'PCIS': 3, 'PTRANS': 4, 'TRANS': 95} Chain breaks: 1 Chain: "I" Number of atoms: 3546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3546 Classifications: {'peptide': 463} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 20, 'TRANS': 439} Chain breaks: 1 Chain: "F" Number of atoms: 4010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 513, 4010 Classifications: {'peptide': 513} Link IDs: {'CIS': 4, 'PTRANS': 22, 'TRANS': 486} Chain breaks: 1 Chain: "D" Number of atoms: 882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 882 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "K" Number of atoms: 771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 771 Classifications: {'peptide': 103} Link IDs: {'PCIS': 3, 'PTRANS': 4, 'TRANS': 95} Chain breaks: 1 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 chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 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 chiralities: 3 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "S" 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 chiralities: 5 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 chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Y" 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 chiralities: 3 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "a" 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 chiralities: 5 Chain: "b" 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 chiralities: 2 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 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 chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 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 chiralities: 3 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "i" 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 chiralities: 5 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 chiralities: 2 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "J" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "I" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 15.14, per 1000 atoms: 0.53 Number of scatterers: 28683 At special positions: 0 Unit cell: (173.4, 186.66, 185.64, 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 144 16.00 O 5766 8.00 N 4677 7.00 C 18096 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 806 " - pdb=" SG CYS A 828 " distance=2.02 Simple disulfide: pdb=" SG CYS A 811 " - pdb=" SG CYS A 817 " distance=1.76 Simple disulfide: pdb=" SG CYS A 912 " - pdb=" SG CYS A 925 " distance=2.03 Simple disulfide: pdb=" SG CYS A1156 " - pdb=" SG CYS A1164 " distance=2.04 Simple disulfide: pdb=" SG CYS B 30 " - pdb=" SG CYS B 195 " distance=2.04 Simple disulfide: pdb=" SG CYS B 176 " - pdb=" SG CYS B 214 " distance=2.04 Simple disulfide: pdb=" SG CYS B 185 " - pdb=" SG CYS B 237 " distance=2.03 Simple disulfide: pdb=" SG CYS B 339 " - pdb=" SG CYS B 349 " distance=2.03 Simple disulfide: pdb=" SG CYS B 603 " - pdb=" SG CYS B 654 " distance=2.08 Simple disulfide: pdb=" SG CYS B 620 " - pdb=" SG CYS B 650 " distance=2.03 Simple disulfide: pdb=" SG CYS B 679 " - pdb=" SG CYS B 713 " distance=2.04 Simple disulfide: pdb=" SG CYS B 727 " - pdb=" SG CYS B 736 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.02 Simple disulfide: pdb=" SG CYS E 806 " - pdb=" SG CYS E 828 " distance=2.02 Simple disulfide: pdb=" SG CYS E 811 " - pdb=" SG CYS E 817 " distance=1.76 Simple disulfide: pdb=" SG CYS E 912 " - pdb=" SG CYS E 925 " distance=2.03 Simple disulfide: pdb=" SG CYS E1156 " - pdb=" SG CYS E1164 " distance=2.04 Simple disulfide: pdb=" SG CYS J 30 " - pdb=" SG CYS J 195 " distance=2.04 Simple disulfide: pdb=" SG CYS J 176 " - pdb=" SG CYS J 214 " distance=2.04 Simple disulfide: pdb=" SG CYS J 185 " - pdb=" SG CYS J 237 " distance=2.03 Simple disulfide: pdb=" SG CYS J 339 " - pdb=" SG CYS J 349 " distance=2.03 Simple disulfide: pdb=" SG CYS J 603 " - pdb=" SG CYS J 654 " distance=2.08 Simple disulfide: pdb=" SG CYS J 620 " - pdb=" SG CYS J 650 " distance=2.03 Simple disulfide: pdb=" SG CYS J 679 " - pdb=" SG CYS J 713 " distance=2.04 Simple disulfide: pdb=" SG CYS J 727 " - pdb=" SG CYS J 736 " distance=2.02 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.02 Simple disulfide: pdb=" SG CYS I 806 " - pdb=" SG CYS I 828 " distance=2.02 Simple disulfide: pdb=" SG CYS I 811 " - pdb=" SG CYS I 817 " distance=1.76 Simple disulfide: pdb=" SG CYS I 912 " - pdb=" SG CYS I 925 " distance=2.03 Simple disulfide: pdb=" SG CYS I1156 " - pdb=" SG CYS I1164 " distance=2.04 Simple disulfide: pdb=" SG CYS F 30 " - pdb=" SG CYS F 195 " distance=2.04 Simple disulfide: pdb=" SG CYS F 176 " - pdb=" SG CYS F 214 " distance=2.04 Simple disulfide: pdb=" SG CYS F 185 " - pdb=" SG CYS F 237 " distance=2.03 Simple disulfide: pdb=" SG CYS F 339 " - pdb=" SG CYS F 349 " distance=2.03 Simple disulfide: pdb=" SG CYS F 603 " - pdb=" SG CYS F 654 " distance=2.08 Simple disulfide: pdb=" SG CYS F 620 " - pdb=" SG CYS F 650 " distance=2.03 Simple disulfide: pdb=" SG CYS F 679 " - pdb=" SG CYS F 713 " distance=2.04 Simple disulfide: pdb=" SG CYS F 727 " - pdb=" SG CYS F 736 " distance=2.02 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA S 3 " - " MAN S 4 " " BMA a 3 " - " MAN a 4 " " BMA i 3 " - " MAN i 4 " ALPHA1-6 " BMA S 3 " - " MAN S 5 " " BMA a 3 " - " MAN a 5 " " BMA i 3 " - " MAN i 5 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " NAG-ASN " NAG A1401 " - " ASN A 774 " " NAG B 801 " - " ASN B 719 " " NAG B 802 " - " ASN B 619 " " NAG B 803 " - " ASN B 66 " " NAG B 807 " - " ASN B 155 " " NAG B 817 " - " ASN B 244 " " NAG E1401 " - " ASN E 774 " " NAG F 801 " - " ASN F 719 " " NAG F 802 " - " ASN F 619 " " NAG F 803 " - " ASN F 66 " " NAG F 807 " - " ASN F 155 " " NAG F 817 " - " ASN F 244 " " NAG I1401 " - " ASN I 774 " " NAG J 801 " - " ASN J 719 " " NAG J 802 " - " ASN J 619 " " NAG J 803 " - " ASN J 66 " " NAG J 807 " - " ASN J 155 " " NAG J 817 " - " ASN J 244 " " NAG M 1 " - " ASN A 785 " " NAG N 1 " - " ASN A1176 " " NAG O 1 " - " ASN A 870 " " NAG P 1 " - " ASN A1213 " " NAG Q 1 " - " ASN B 125 " " NAG R 1 " - " ASN B 166 " " NAG S 1 " - " ASN B 222 " " NAG T 1 " - " ASN B 236 " " NAG U 1 " - " ASN E 785 " " NAG V 1 " - " ASN E1176 " " NAG W 1 " - " ASN E 870 " " NAG X 1 " - " ASN E1213 " " NAG Y 1 " - " ASN J 125 " " NAG Z 1 " - " ASN J 166 " " NAG a 1 " - " ASN J 222 " " NAG b 1 " - " ASN J 236 " " NAG c 1 " - " ASN I 785 " " NAG d 1 " - " ASN I1176 " " NAG e 1 " - " ASN I 870 " " NAG f 1 " - " ASN I1213 " " NAG g 1 " - " ASN F 125 " " NAG h 1 " - " ASN F 166 " " NAG i 1 " - " ASN F 222 " " NAG j 1 " - " ASN F 236 " Time building additional restraints: 12.49 Conformation dependent library (CDL) restraints added in 4.9 seconds 7086 Ramachandran restraints generated. 3543 Oldfield, 0 Emsley, 3543 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6612 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 69 sheets defined 24.3% alpha, 28.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.82 Creating SS restraints... Processing helix chain 'A' and resid 805 through 811 removed outlier: 3.847A pdb=" N CYS A 811 " --> pdb=" O LYS A 807 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 822 Processing helix chain 'A' and resid 824 through 854 removed outlier: 3.886A pdb=" N CYS A 828 " --> pdb=" O TYR A 824 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER A 852 " --> pdb=" O ASN A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 888 through 898 Processing helix chain 'A' and resid 908 through 913 removed outlier: 3.531A pdb=" N MET A 913 " --> pdb=" O ASP A 910 " (cutoff:3.500A) Processing helix chain 'A' and resid 926 through 931 Processing helix chain 'A' and resid 939 through 953 removed outlier: 4.040A pdb=" N MET A 943 " --> pdb=" O MET A 939 " (cutoff:3.500A) Processing helix chain 'A' and resid 971 through 982 Processing helix chain 'A' and resid 986 through 1007 removed outlier: 5.728A pdb=" N LYS A 995 " --> pdb=" O SER A 991 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N LEU A 996 " --> pdb=" O GLU A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1007 through 1012 removed outlier: 3.989A pdb=" N PHE A1012 " --> pdb=" O MET A1008 " (cutoff:3.500A) Processing helix chain 'A' and resid 1016 through 1039 Processing helix chain 'A' and resid 1040 through 1042 No H-bonds generated for 'chain 'A' and resid 1040 through 1042' Processing helix chain 'A' and resid 1050 through 1058 Processing helix chain 'A' and resid 1059 through 1106 removed outlier: 4.885A pdb=" N ALA A1065 " --> pdb=" O LEU A1061 " (cutoff:3.500A) Processing helix chain 'A' and resid 1198 through 1200 No H-bonds generated for 'chain 'A' and resid 1198 through 1200' Processing helix chain 'B' and resid 37 through 41 Processing helix chain 'B' and resid 49 through 53 Processing helix chain 'B' and resid 209 through 213 Processing helix chain 'B' and resid 222 through 231 removed outlier: 3.869A pdb=" N TYR B 231 " --> pdb=" O SER B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 307 Processing helix chain 'B' and resid 342 through 351 Processing helix chain 'B' and resid 675 through 682 removed outlier: 6.699A pdb=" N CYS B 679 " --> pdb=" O SER B 676 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N GLU B 680 " --> pdb=" O VAL B 677 " (cutoff:3.500A) Processing helix chain 'B' and resid 694 through 702 removed outlier: 5.047A pdb=" N ARG B 700 " --> pdb=" O MET B 696 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 31 Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 73 through 75 No H-bonds generated for 'chain 'H' and resid 73 through 75' Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'E' and resid 805 through 811 removed outlier: 3.847A pdb=" N CYS E 811 " --> pdb=" O LYS E 807 " (cutoff:3.500A) Processing helix chain 'E' and resid 814 through 822 Processing helix chain 'E' and resid 824 through 854 removed outlier: 3.886A pdb=" N CYS E 828 " --> pdb=" O TYR E 824 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER E 852 " --> pdb=" O ASN E 848 " (cutoff:3.500A) Processing helix chain 'E' and resid 888 through 898 Processing helix chain 'E' and resid 908 through 913 removed outlier: 3.531A pdb=" N MET E 913 " --> pdb=" O ASP E 910 " (cutoff:3.500A) Processing helix chain 'E' and resid 926 through 931 Processing helix chain 'E' and resid 939 through 953 removed outlier: 4.041A pdb=" N MET E 943 " --> pdb=" O MET E 939 " (cutoff:3.500A) Processing helix chain 'E' and resid 971 through 982 Processing helix chain 'E' and resid 986 through 1007 removed outlier: 5.728A pdb=" N LYS E 995 " --> pdb=" O SER E 991 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N LEU E 996 " --> pdb=" O GLU E 992 " (cutoff:3.500A) Processing helix chain 'E' and resid 1007 through 1012 removed outlier: 3.990A pdb=" N PHE E1012 " --> pdb=" O MET E1008 " (cutoff:3.500A) Processing helix chain 'E' and resid 1016 through 1039 Processing helix chain 'E' and resid 1040 through 1042 No H-bonds generated for 'chain 'E' and resid 1040 through 1042' Processing helix chain 'E' and resid 1050 through 1058 Processing helix chain 'E' and resid 1059 through 1106 removed outlier: 4.885A pdb=" N ALA E1065 " --> pdb=" O LEU E1061 " (cutoff:3.500A) Processing helix chain 'E' and resid 1198 through 1200 No H-bonds generated for 'chain 'E' and resid 1198 through 1200' Processing helix chain 'J' and resid 37 through 41 Processing helix chain 'J' and resid 49 through 53 Processing helix chain 'J' and resid 209 through 213 Processing helix chain 'J' and resid 222 through 231 removed outlier: 3.869A pdb=" N TYR J 231 " --> pdb=" O SER J 227 " (cutoff:3.500A) Processing helix chain 'J' and resid 303 through 307 Processing helix chain 'J' and resid 342 through 351 Processing helix chain 'J' and resid 675 through 682 removed outlier: 6.699A pdb=" N CYS J 679 " --> pdb=" O SER J 676 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N GLU J 680 " --> pdb=" O VAL J 677 " (cutoff:3.500A) Processing helix chain 'J' and resid 694 through 702 removed outlier: 5.047A pdb=" N ARG J 700 " --> pdb=" O MET J 696 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 31 Processing helix chain 'C' and resid 61 through 64 Processing helix chain 'C' and resid 73 through 75 No H-bonds generated for 'chain 'C' and resid 73 through 75' Processing helix chain 'C' and resid 83 through 87 Processing helix chain 'G' and resid 79 through 83 Processing helix chain 'I' and resid 805 through 811 removed outlier: 3.848A pdb=" N CYS I 811 " --> pdb=" O LYS I 807 " (cutoff:3.500A) Processing helix chain 'I' and resid 814 through 822 Processing helix chain 'I' and resid 824 through 854 removed outlier: 3.886A pdb=" N CYS I 828 " --> pdb=" O TYR I 824 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N SER I 852 " --> pdb=" O ASN I 848 " (cutoff:3.500A) Processing helix chain 'I' and resid 888 through 898 Processing helix chain 'I' and resid 908 through 913 removed outlier: 3.531A pdb=" N MET I 913 " --> pdb=" O ASP I 910 " (cutoff:3.500A) Processing helix chain 'I' and resid 926 through 931 Processing helix chain 'I' and resid 939 through 953 removed outlier: 4.041A pdb=" N MET I 943 " --> pdb=" O MET I 939 " (cutoff:3.500A) Processing helix chain 'I' and resid 971 through 982 Processing helix chain 'I' and resid 986 through 1007 removed outlier: 5.728A pdb=" N LYS I 995 " --> pdb=" O SER I 991 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N LEU I 996 " --> pdb=" O GLU I 992 " (cutoff:3.500A) Processing helix chain 'I' and resid 1007 through 1012 removed outlier: 3.989A pdb=" N PHE I1012 " --> pdb=" O MET I1008 " (cutoff:3.500A) Processing helix chain 'I' and resid 1016 through 1039 Processing helix chain 'I' and resid 1040 through 1042 No H-bonds generated for 'chain 'I' and resid 1040 through 1042' Processing helix chain 'I' and resid 1050 through 1058 Processing helix chain 'I' and resid 1059 through 1106 removed outlier: 4.885A pdb=" N ALA I1065 " --> pdb=" O LEU I1061 " (cutoff:3.500A) Processing helix chain 'I' and resid 1198 through 1200 No H-bonds generated for 'chain 'I' and resid 1198 through 1200' Processing helix chain 'F' and resid 37 through 41 Processing helix chain 'F' and resid 49 through 53 Processing helix chain 'F' and resid 209 through 213 Processing helix chain 'F' and resid 222 through 231 removed outlier: 3.869A pdb=" N TYR F 231 " --> pdb=" O SER F 227 " (cutoff:3.500A) Processing helix chain 'F' and resid 303 through 307 Processing helix chain 'F' and resid 342 through 351 Processing helix chain 'F' and resid 675 through 682 removed outlier: 6.699A pdb=" N CYS F 679 " --> pdb=" O SER F 676 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N GLU F 680 " --> pdb=" O VAL F 677 " (cutoff:3.500A) Processing helix chain 'F' and resid 694 through 702 removed outlier: 5.047A pdb=" N ARG F 700 " --> pdb=" O MET F 696 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 31 Processing helix chain 'D' and resid 61 through 64 Processing helix chain 'D' and resid 73 through 75 No H-bonds generated for 'chain 'D' and resid 73 through 75' Processing helix chain 'D' and resid 83 through 87 Processing helix chain 'K' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'B' and resid 719 through 724 removed outlier: 6.990A pdb=" N LEU A 759 " --> pdb=" O SER B 720 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU B 722 " --> pdb=" O LEU A 759 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N LEU B 735 " --> pdb=" O LEU B 731 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 768 through 769 removed outlier: 5.680A pdb=" N ILE A 768 " --> pdb=" O SER E 858 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 777 through 782 removed outlier: 5.623A pdb=" N VAL A1150 " --> pdb=" O LYS A1174 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N PHE A1172 " --> pdb=" O ALA A1152 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 785 through 796 removed outlier: 5.108A pdb=" N VAL A1124 " --> pdb=" O VAL A1139 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 802 through 804 Processing sheet with id=AA6, first strand: chain 'A' and resid 857 through 858 Processing sheet with id=AA7, first strand: chain 'A' and resid 1202 through 1204 removed outlier: 5.509A pdb=" N ASN A1163 " --> pdb=" O ASP A1157 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 33 through 35 removed outlier: 6.383A pdb=" N ASP B 34 " --> pdb=" O VAL B 102 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 63 through 64 removed outlier: 6.735A pdb=" N THR B 63 " --> pdb=" O TYR F 632 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N VAL F 631 " --> pdb=" O VAL F 639 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N VAL F 639 " --> pdb=" O LEU F 651 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 67 through 75 removed outlier: 3.964A pdb=" N ARG B 335 " --> pdb=" O ASP B 326 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 83 through 85 removed outlier: 5.884A pdb=" N SER B 267 " --> pdb=" O GLN B 280 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N GLN B 280 " --> pdb=" O SER B 267 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 88 through 89 removed outlier: 7.174A pdb=" N SER B 88 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N THR B 206 " --> pdb=" O SER B 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 110 through 111 removed outlier: 6.165A pdb=" N LEU B 180 " --> pdb=" O TYR B 241 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N TYR B 241 " --> pdb=" O LEU B 180 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N ALA B 182 " --> pdb=" O PHE B 239 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N PHE B 239 " --> pdb=" O ALA B 182 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N TYR B 184 " --> pdb=" O CYS B 237 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N CYS B 237 " --> pdb=" O TYR B 184 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 127 through 129 removed outlier: 3.661A pdb=" N ALA B 309 " --> pdb=" O THR B 139 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 153 through 154 Processing sheet with id=AB7, first strand: chain 'B' and resid 214 through 215 removed outlier: 4.011A pdb=" N SER B 215 " --> pdb=" O ASN B 218 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 361 through 366 removed outlier: 5.522A pdb=" N SER B 362 " --> pdb=" O VAL B 661 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N VAL B 661 " --> pdb=" O SER B 362 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N SER B 364 " --> pdb=" O VAL B 659 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N VAL B 659 " --> pdb=" O SER B 364 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 371 through 376 removed outlier: 4.147A pdb=" N GLU B 605 " --> pdb=" O GLY B 372 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 617 through 619 removed outlier: 5.208A pdb=" N VAL B 639 " --> pdb=" O LEU B 651 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N VAL B 631 " --> pdb=" O VAL B 639 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AC3, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.418A pdb=" N GLU H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N TYR H 33 " --> pdb=" O GLY H 95 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ILE H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N TRP H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.418A pdb=" N GLU H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N TYR H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N GLY H 96 " --> pdb=" O MET H 100A" (cutoff:3.500A) removed outlier: 6.842A pdb=" N MET H 100A" --> pdb=" O GLY H 96 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AC6, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.396A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N MET L 33 " --> pdb=" O HIS L 49 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N HIS L 49 " --> pdb=" O MET L 33 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.396A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'J' and resid 719 through 724 removed outlier: 6.990A pdb=" N LEU E 759 " --> pdb=" O SER J 720 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU J 722 " --> pdb=" O LEU E 759 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N LEU J 735 " --> pdb=" O LEU J 731 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 768 through 769 removed outlier: 5.680A pdb=" N ILE E 768 " --> pdb=" O SER I 858 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'E' and resid 777 through 782 removed outlier: 5.623A pdb=" N VAL E1150 " --> pdb=" O LYS E1174 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N PHE E1172 " --> pdb=" O ALA E1152 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 785 through 796 removed outlier: 5.108A pdb=" N VAL E1124 " --> pdb=" O VAL E1139 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 802 through 804 Processing sheet with id=AD4, first strand: chain 'E' and resid 1202 through 1204 removed outlier: 5.508A pdb=" N ASN E1163 " --> pdb=" O ASP E1157 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'J' and resid 33 through 35 removed outlier: 6.383A pdb=" N ASP J 34 " --> pdb=" O VAL J 102 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'J' and resid 67 through 75 removed outlier: 3.964A pdb=" N ARG J 335 " --> pdb=" O ASP J 326 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 83 through 85 removed outlier: 5.884A pdb=" N SER J 267 " --> pdb=" O GLN J 280 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N GLN J 280 " --> pdb=" O SER J 267 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'J' and resid 88 through 89 removed outlier: 7.174A pdb=" N SER J 88 " --> pdb=" O ILE J 300 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N THR J 206 " --> pdb=" O SER J 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'J' and resid 110 through 111 removed outlier: 6.165A pdb=" N LEU J 180 " --> pdb=" O TYR J 241 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N TYR J 241 " --> pdb=" O LEU J 180 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N ALA J 182 " --> pdb=" O PHE J 239 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N PHE J 239 " --> pdb=" O ALA J 182 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N TYR J 184 " --> pdb=" O CYS J 237 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N CYS J 237 " --> pdb=" O TYR J 184 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 127 through 129 removed outlier: 3.661A pdb=" N ALA J 309 " --> pdb=" O THR J 139 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 153 through 154 Processing sheet with id=AE3, first strand: chain 'J' and resid 214 through 215 removed outlier: 4.011A pdb=" N SER J 215 " --> pdb=" O ASN J 218 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 361 through 366 removed outlier: 5.522A pdb=" N SER J 362 " --> pdb=" O VAL J 661 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N VAL J 661 " --> pdb=" O SER J 362 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N SER J 364 " --> pdb=" O VAL J 659 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N VAL J 659 " --> pdb=" O SER J 364 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 371 through 376 removed outlier: 4.147A pdb=" N GLU J 605 " --> pdb=" O GLY J 372 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 617 through 619 removed outlier: 5.208A pdb=" N VAL J 639 " --> pdb=" O LEU J 651 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N VAL J 631 " --> pdb=" O VAL J 639 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 3 through 6 Processing sheet with id=AE8, first strand: chain 'C' and resid 10 through 11 removed outlier: 6.417A pdb=" N GLU C 10 " --> pdb=" O THR C 110 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N TYR C 33 " --> pdb=" O GLY C 95 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ILE C 34 " --> pdb=" O TRP C 50 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N TRP C 50 " --> pdb=" O ILE C 34 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N TRP C 36 " --> pdb=" O ILE C 48 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 10 through 11 removed outlier: 6.417A pdb=" N GLU C 10 " --> pdb=" O THR C 110 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N TYR C 102 " --> pdb=" O ARG C 94 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N GLY C 96 " --> pdb=" O MET C 100A" (cutoff:3.500A) removed outlier: 6.842A pdb=" N MET C 100A" --> pdb=" O GLY C 96 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'G' and resid 4 through 7 Processing sheet with id=AF2, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.396A pdb=" N LEU G 11 " --> pdb=" O GLU G 105 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N MET G 33 " --> pdb=" O HIS G 49 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N HIS G 49 " --> pdb=" O MET G 33 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N TRP G 35 " --> pdb=" O LEU G 47 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.396A pdb=" N LEU G 11 " --> pdb=" O GLU G 105 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N THR G 97 " --> pdb=" O GLN G 90 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'F' and resid 719 through 724 removed outlier: 6.990A pdb=" N LEU I 759 " --> pdb=" O SER F 720 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU F 722 " --> pdb=" O LEU I 759 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N LEU F 735 " --> pdb=" O LEU F 731 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'I' and resid 777 through 782 removed outlier: 5.623A pdb=" N VAL I1150 " --> pdb=" O LYS I1174 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N PHE I1172 " --> pdb=" O ALA I1152 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'I' and resid 785 through 796 removed outlier: 5.108A pdb=" N VAL I1124 " --> pdb=" O VAL I1139 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'I' and resid 802 through 804 Processing sheet with id=AF8, first strand: chain 'I' and resid 1202 through 1204 removed outlier: 5.509A pdb=" N ASN I1163 " --> pdb=" O ASP I1157 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'F' and resid 33 through 35 removed outlier: 6.383A pdb=" N ASP F 34 " --> pdb=" O VAL F 102 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF9 Processing sheet with id=AG1, first strand: chain 'F' and resid 67 through 75 removed outlier: 3.964A pdb=" N ARG F 335 " --> pdb=" O ASP F 326 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'F' and resid 83 through 85 removed outlier: 5.885A pdb=" N SER F 267 " --> pdb=" O GLN F 280 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N GLN F 280 " --> pdb=" O SER F 267 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'F' and resid 88 through 89 removed outlier: 7.174A pdb=" N SER F 88 " --> pdb=" O ILE F 300 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N THR F 206 " --> pdb=" O SER F 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG3 Processing sheet with id=AG4, first strand: chain 'F' and resid 110 through 111 removed outlier: 6.165A pdb=" N LEU F 180 " --> pdb=" O TYR F 241 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N TYR F 241 " --> pdb=" O LEU F 180 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N ALA F 182 " --> pdb=" O PHE F 239 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N PHE F 239 " --> pdb=" O ALA F 182 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N TYR F 184 " --> pdb=" O CYS F 237 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N CYS F 237 " --> pdb=" O TYR F 184 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'F' and resid 127 through 129 removed outlier: 3.661A pdb=" N ALA F 309 " --> pdb=" O THR F 139 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'F' and resid 153 through 154 Processing sheet with id=AG7, first strand: chain 'F' and resid 214 through 215 removed outlier: 4.011A pdb=" N SER F 215 " --> pdb=" O ASN F 218 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'F' and resid 361 through 366 removed outlier: 5.522A pdb=" N SER F 362 " --> pdb=" O VAL F 661 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N VAL F 661 " --> pdb=" O SER F 362 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N SER F 364 " --> pdb=" O VAL F 659 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N VAL F 659 " --> pdb=" O SER F 364 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'F' and resid 371 through 376 removed outlier: 4.147A pdb=" N GLU F 605 " --> pdb=" O GLY F 372 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'D' and resid 3 through 6 Processing sheet with id=AH2, first strand: chain 'D' and resid 10 through 11 removed outlier: 6.418A pdb=" N GLU D 10 " --> pdb=" O THR D 110 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N TYR D 33 " --> pdb=" O GLY D 95 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ILE D 34 " --> pdb=" O TRP D 50 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N TRP D 50 " --> pdb=" O ILE D 34 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N TRP D 36 " --> pdb=" O ILE D 48 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'D' and resid 10 through 11 removed outlier: 6.418A pdb=" N GLU D 10 " --> pdb=" O THR D 110 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N TYR D 102 " --> pdb=" O ARG D 94 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N GLY D 96 " --> pdb=" O MET D 100A" (cutoff:3.500A) removed outlier: 6.842A pdb=" N MET D 100A" --> pdb=" O GLY D 96 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'K' and resid 4 through 7 Processing sheet with id=AH5, first strand: chain 'K' and resid 10 through 12 removed outlier: 6.397A pdb=" N LEU K 11 " --> pdb=" O GLU K 105 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N MET K 33 " --> pdb=" O HIS K 49 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N HIS K 49 " --> pdb=" O MET K 33 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'K' and resid 10 through 12 removed outlier: 6.397A pdb=" N LEU K 11 " --> pdb=" O GLU K 105 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N THR K 97 " --> pdb=" O GLN K 90 " (cutoff:3.500A) 1178 hydrogen bonds defined for protein. 3024 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 14.54 Time building geometry restraints manager: 13.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 5741 1.32 - 1.46: 9910 1.46 - 1.59: 13437 1.59 - 1.73: 33 1.73 - 1.87: 192 Bond restraints: 29313 Sorted by residual: bond pdb=" CG GLN F 280 " pdb=" CD GLN F 280 " ideal model delta sigma weight residual 1.516 1.381 0.135 2.50e-02 1.60e+03 2.92e+01 bond pdb=" CG GLN J 280 " pdb=" CD GLN J 280 " ideal model delta sigma weight residual 1.516 1.381 0.135 2.50e-02 1.60e+03 2.90e+01 bond pdb=" CG GLN B 280 " pdb=" CD GLN B 280 " ideal model delta sigma weight residual 1.516 1.381 0.135 2.50e-02 1.60e+03 2.90e+01 bond pdb=" CB TYR J 58 " pdb=" CG TYR J 58 " ideal model delta sigma weight residual 1.512 1.403 0.109 2.20e-02 2.07e+03 2.45e+01 bond pdb=" CB TYR B 58 " pdb=" CG TYR B 58 " ideal model delta sigma weight residual 1.512 1.403 0.109 2.20e-02 2.07e+03 2.45e+01 ... (remaining 29308 not shown) Histogram of bond angle deviations from ideal: 97.32 - 104.66: 543 104.66 - 111.99: 13174 111.99 - 119.33: 10992 119.33 - 126.66: 14807 126.66 - 134.00: 309 Bond angle restraints: 39825 Sorted by residual: angle pdb=" N GLU F 367 " pdb=" CA GLU F 367 " pdb=" C GLU F 367 " ideal model delta sigma weight residual 111.07 121.18 -10.11 1.07e+00 8.73e-01 8.93e+01 angle pdb=" N GLU J 367 " pdb=" CA GLU J 367 " pdb=" C GLU J 367 " ideal model delta sigma weight residual 111.07 121.18 -10.11 1.07e+00 8.73e-01 8.93e+01 angle pdb=" N GLU B 367 " pdb=" CA GLU B 367 " pdb=" C GLU B 367 " ideal model delta sigma weight residual 111.07 121.17 -10.10 1.07e+00 8.73e-01 8.91e+01 angle pdb=" N VAL E 802 " pdb=" CA VAL E 802 " pdb=" C VAL E 802 " ideal model delta sigma weight residual 108.45 120.98 -12.53 1.48e+00 4.57e-01 7.17e+01 angle pdb=" N VAL A 802 " pdb=" CA VAL A 802 " pdb=" C VAL A 802 " ideal model delta sigma weight residual 108.45 120.97 -12.52 1.48e+00 4.57e-01 7.15e+01 ... (remaining 39820 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.91: 16085 16.91 - 33.82: 466 33.82 - 50.73: 110 50.73 - 67.64: 79 67.64 - 84.55: 42 Dihedral angle restraints: 16782 sinusoidal: 6414 harmonic: 10368 Sorted by residual: dihedral pdb=" CB CYS B 727 " pdb=" SG CYS B 727 " pdb=" SG CYS B 736 " pdb=" CB CYS B 736 " ideal model delta sinusoidal sigma weight residual 93.00 139.68 -46.68 1 1.00e+01 1.00e-02 3.01e+01 dihedral pdb=" CB CYS F 727 " pdb=" SG CYS F 727 " pdb=" SG CYS F 736 " pdb=" CB CYS F 736 " ideal model delta sinusoidal sigma weight residual 93.00 139.66 -46.66 1 1.00e+01 1.00e-02 3.01e+01 dihedral pdb=" CB CYS J 727 " pdb=" SG CYS J 727 " pdb=" SG CYS J 736 " pdb=" CB CYS J 736 " ideal model delta sinusoidal sigma weight residual 93.00 139.66 -46.66 1 1.00e+01 1.00e-02 3.01e+01 ... (remaining 16779 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 3078 0.093 - 0.185: 1200 0.185 - 0.278: 303 0.278 - 0.370: 56 0.370 - 0.463: 10 Chirality restraints: 4647 Sorted by residual: chirality pdb=" C1 NAG X 2 " pdb=" O4 NAG X 1 " pdb=" C2 NAG X 2 " pdb=" O5 NAG X 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.63 0.23 2.00e-02 2.50e+03 1.35e+02 chirality pdb=" C1 NAG f 2 " pdb=" O4 NAG f 1 " pdb=" C2 NAG f 2 " pdb=" O5 NAG f 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.63 0.23 2.00e-02 2.50e+03 1.33e+02 chirality pdb=" C1 NAG P 2 " pdb=" O4 NAG P 1 " pdb=" C2 NAG P 2 " pdb=" O5 NAG P 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.63 0.23 2.00e-02 2.50e+03 1.32e+02 ... (remaining 4644 not shown) Planarity restraints: 5103 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN F 66 " -0.061 2.00e-02 2.50e+03 6.35e-02 5.04e+01 pdb=" CG ASN F 66 " 0.027 2.00e-02 2.50e+03 pdb=" OD1 ASN F 66 " 0.010 2.00e-02 2.50e+03 pdb=" ND2 ASN F 66 " 0.100 2.00e-02 2.50e+03 pdb=" C1 NAG F 803 " -0.075 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN J 66 " 0.061 2.00e-02 2.50e+03 6.35e-02 5.03e+01 pdb=" CG ASN J 66 " -0.027 2.00e-02 2.50e+03 pdb=" OD1 ASN J 66 " -0.010 2.00e-02 2.50e+03 pdb=" ND2 ASN J 66 " -0.100 2.00e-02 2.50e+03 pdb=" C1 NAG J 803 " 0.075 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 66 " 0.061 2.00e-02 2.50e+03 6.34e-02 5.03e+01 pdb=" CG ASN B 66 " -0.027 2.00e-02 2.50e+03 pdb=" OD1 ASN B 66 " -0.010 2.00e-02 2.50e+03 pdb=" ND2 ASN B 66 " -0.100 2.00e-02 2.50e+03 pdb=" C1 NAG B 803 " 0.075 2.00e-02 2.50e+03 ... (remaining 5100 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 6388 2.78 - 3.31: 26777 3.31 - 3.84: 50574 3.84 - 4.37: 61300 4.37 - 4.90: 97567 Nonbonded interactions: 242606 Sorted by model distance: nonbonded pdb=" OG SER J 328 " pdb=" OD1 ASP J 330 " model vdw 2.247 2.440 nonbonded pdb=" OG SER F 328 " pdb=" OD1 ASP F 330 " model vdw 2.247 2.440 nonbonded pdb=" OG SER B 328 " pdb=" OD1 ASP B 330 " model vdw 2.247 2.440 nonbonded pdb=" O4 NAG e 2 " pdb=" O6 NAG e 2 " model vdw 2.267 2.440 nonbonded pdb=" O4 NAG O 2 " pdb=" O6 NAG O 2 " model vdw 2.268 2.440 ... (remaining 242601 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 'E' selection = chain 'I' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'J' } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'G' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'R' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Z' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'h' selection = chain 'j' } ncs_group { reference = chain 'Q' selection = chain 'Y' selection = chain 'g' } ncs_group { reference = chain 'S' selection = chain 'a' selection = chain 'i' } 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 group one per residue 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: 2.830 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: 10.620 Check model and map are aligned: 0.460 Set scattering table: 0.270 Process input model: 80.950 Find NCS groups from input model: 2.130 Set up NCS constraints: 0.490 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 100.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5861 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 0.135 29313 Z= 1.150 Angle : 1.820 12.531 39825 Z= 1.201 Chirality : 0.103 0.463 4647 Planarity : 0.010 0.056 5061 Dihedral : 11.123 84.546 10044 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 1.37 Ramachandran Plot: Outliers : 0.59 % Allowed : 3.22 % Favored : 96.19 % Rotamer: Outliers : 0.30 % Allowed : 1.02 % Favored : 98.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.53 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.13), residues: 3543 helix: -0.19 (0.17), residues: 666 sheet: 0.21 (0.17), residues: 867 loop : 0.55 (0.14), residues: 2010 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7086 Ramachandran restraints generated. 3543 Oldfield, 0 Emsley, 3543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7086 Ramachandran restraints generated. 3543 Oldfield, 0 Emsley, 3543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 636 residues out of total 3033 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 627 time to evaluate : 3.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 5 residues processed: 636 average time/residue: 0.4456 time to fit residues: 437.2315 Evaluate side-chains 312 residues out of total 3033 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 307 time to evaluate : 3.390 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2970 time to fit residues: 7.2901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 298 optimal weight: 7.9990 chunk 268 optimal weight: 1.9990 chunk 148 optimal weight: 4.9990 chunk 91 optimal weight: 6.9990 chunk 180 optimal weight: 9.9990 chunk 143 optimal weight: 0.9980 chunk 277 optimal weight: 1.9990 chunk 107 optimal weight: 7.9990 chunk 168 optimal weight: 0.9990 chunk 206 optimal weight: 30.0000 chunk 321 optimal weight: 7.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 832 ASN A 833 GLN A 839 ASN A 857 GLN ** A1084 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1138 HIS A1163 ASN ** A1177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 346 GLN B 637 ASN H 68 GLN E 812 ASN E 832 ASN E 833 GLN E 857 GLN ** E1084 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1129 ASN ** E1138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 346 GLN J 637 ASN ** C 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 6 GLN ** G 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 832 ASN I 833 GLN I 857 GLN ** I1084 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1129 ASN I1138 HIS I1163 ASN ** I1177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 346 GLN F 637 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6061 moved from start: 0.3069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 29313 Z= 0.253 Angle : 0.751 10.205 39825 Z= 0.404 Chirality : 0.048 0.306 4647 Planarity : 0.006 0.071 5061 Dihedral : 5.682 23.886 3873 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.25 % Allowed : 3.84 % Favored : 95.91 % Rotamer: Outliers : 0.33 % Allowed : 2.54 % Favored : 97.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.53 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.14), residues: 3543 helix: 0.74 (0.20), residues: 669 sheet: 0.10 (0.17), residues: 795 loop : -0.02 (0.13), residues: 2079 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7086 Ramachandran restraints generated. 3543 Oldfield, 0 Emsley, 3543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7086 Ramachandran restraints generated. 3543 Oldfield, 0 Emsley, 3543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 3033 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 408 time to evaluate : 2.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 3 residues processed: 418 average time/residue: 0.3897 time to fit residues: 260.6566 Evaluate side-chains 265 residues out of total 3033 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 262 time to evaluate : 3.198 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2746 time to fit residues: 5.7204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 178 optimal weight: 9.9990 chunk 99 optimal weight: 6.9990 chunk 267 optimal weight: 7.9990 chunk 218 optimal weight: 9.9990 chunk 88 optimal weight: 4.9990 chunk 322 optimal weight: 10.0000 chunk 347 optimal weight: 30.0000 chunk 286 optimal weight: 0.0870 chunk 319 optimal weight: 7.9990 chunk 109 optimal weight: 0.0050 chunk 258 optimal weight: 7.9990 overall best weight: 4.0178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1066 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1129 ASN A1132 ASN ** A1138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1212 GLN B 346 GLN ** B 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 5 GLN ** H 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 812 ASN E 833 GLN E1132 ASN ** E1138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1163 ASN ** E1177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1212 GLN ** J 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 5 GLN ** C 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1132 ASN ** I1138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I1212 GLN D 5 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6263 moved from start: 0.4218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 29313 Z= 0.279 Angle : 0.743 12.386 39825 Z= 0.392 Chirality : 0.047 0.318 4647 Planarity : 0.005 0.058 5061 Dihedral : 5.665 24.697 3873 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 20.67 Ramachandran Plot: Outliers : 0.34 % Allowed : 4.15 % Favored : 95.51 % Rotamer: Outliers : 0.16 % Allowed : 2.77 % Favored : 97.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.53 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.14), residues: 3543 helix: 0.25 (0.19), residues: 672 sheet: -0.19 (0.17), residues: 801 loop : -0.29 (0.14), residues: 2070 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7086 Ramachandran restraints generated. 3543 Oldfield, 0 Emsley, 3543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7086 Ramachandran restraints generated. 3543 Oldfield, 0 Emsley, 3543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 3033 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 375 time to evaluate : 3.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 0 residues processed: 379 average time/residue: 0.4453 time to fit residues: 270.8124 Evaluate side-chains 244 residues out of total 3033 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 244 time to evaluate : 3.121 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.1884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 318 optimal weight: 1.9990 chunk 242 optimal weight: 10.0000 chunk 167 optimal weight: 0.1980 chunk 35 optimal weight: 6.9990 chunk 153 optimal weight: 8.9990 chunk 216 optimal weight: 6.9990 chunk 323 optimal weight: 9.9990 chunk 342 optimal weight: 30.0000 chunk 168 optimal weight: 0.9980 chunk 306 optimal weight: 9.9990 chunk 92 optimal weight: 20.0000 overall best weight: 3.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 987 GLN ** A1066 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1177 ASN ** B 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 81 GLN E 772 GLN ** E 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 819 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 987 GLN ** E1138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 277 ASN J 346 GLN ** J 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 GLN ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 833 GLN I 987 GLN ** I1138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 277 ASN F 346 GLN ** F 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6305 moved from start: 0.4828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 29313 Z= 0.237 Angle : 0.680 14.629 39825 Z= 0.354 Chirality : 0.046 0.450 4647 Planarity : 0.005 0.058 5061 Dihedral : 5.550 26.269 3873 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 20.20 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.35 % Favored : 95.40 % Rotamer: Outliers : 0.03 % Allowed : 2.54 % Favored : 97.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.53 % 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: -0.60 (0.14), residues: 3543 helix: 0.25 (0.19), residues: 669 sheet: -0.40 (0.17), residues: 846 loop : -0.55 (0.14), residues: 2028 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7086 Ramachandran restraints generated. 3543 Oldfield, 0 Emsley, 3543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7086 Ramachandran restraints generated. 3543 Oldfield, 0 Emsley, 3543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 3033 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 336 time to evaluate : 3.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 337 average time/residue: 0.4123 time to fit residues: 225.4415 Evaluate side-chains 230 residues out of total 3033 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 230 time to evaluate : 3.197 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.2512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 284 optimal weight: 8.9990 chunk 194 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 254 optimal weight: 9.9990 chunk 141 optimal weight: 10.0000 chunk 291 optimal weight: 5.9990 chunk 236 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 174 optimal weight: 20.0000 chunk 307 optimal weight: 1.9990 chunk 86 optimal weight: 9.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1066 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 277 ASN ** B 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 43 GLN H 68 GLN H 81 GLN L 53 ASN ** E 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 815 GLN ** E 819 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1163 ASN ** J 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 GLN ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 53 ASN ** I 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 815 GLN ** I 819 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1129 ASN ** I1138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 53 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6462 moved from start: 0.5696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 29313 Z= 0.293 Angle : 0.760 10.739 39825 Z= 0.397 Chirality : 0.048 0.500 4647 Planarity : 0.005 0.047 5061 Dihedral : 5.928 27.188 3873 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 27.80 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.70 % Favored : 93.96 % Rotamer: Outliers : 0.07 % Allowed : 2.54 % Favored : 97.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.53 % 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: -0.96 (0.14), residues: 3543 helix: -0.18 (0.19), residues: 660 sheet: -0.46 (0.17), residues: 786 loop : -0.83 (0.14), residues: 2097 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7086 Ramachandran restraints generated. 3543 Oldfield, 0 Emsley, 3543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7086 Ramachandran restraints generated. 3543 Oldfield, 0 Emsley, 3543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 3033 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 320 time to evaluate : 4.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 322 average time/residue: 0.4034 time to fit residues: 213.4211 Evaluate side-chains 227 residues out of total 3033 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 225 time to evaluate : 3.022 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2711 time to fit residues: 5.1858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 115 optimal weight: 30.0000 chunk 308 optimal weight: 0.0570 chunk 67 optimal weight: 9.9990 chunk 200 optimal weight: 0.5980 chunk 84 optimal weight: 6.9990 chunk 342 optimal weight: 5.9990 chunk 284 optimal weight: 0.2980 chunk 158 optimal weight: 8.9990 chunk 28 optimal weight: 20.0000 chunk 113 optimal weight: 0.2980 chunk 179 optimal weight: 2.9990 overall best weight: 0.8500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1066 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 81 GLN L 90 GLN ** E 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 819 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 833 GLN J 346 GLN ** J 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 GLN G 90 GLN ** I 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 819 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 833 GLN ** I1138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 90 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6325 moved from start: 0.5696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 29313 Z= 0.177 Angle : 0.637 9.979 39825 Z= 0.330 Chirality : 0.046 0.441 4647 Planarity : 0.004 0.039 5061 Dihedral : 5.401 27.752 3873 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 18.91 Ramachandran Plot: Outliers : 0.34 % Allowed : 4.66 % Favored : 95.00 % Rotamer: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.53 % 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: -0.77 (0.14), residues: 3543 helix: 0.35 (0.19), residues: 663 sheet: -0.61 (0.17), residues: 801 loop : -0.71 (0.14), residues: 2079 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7086 Ramachandran restraints generated. 3543 Oldfield, 0 Emsley, 3543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7086 Ramachandran restraints generated. 3543 Oldfield, 0 Emsley, 3543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 3033 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 346 time to evaluate : 3.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 346 average time/residue: 0.4020 time to fit residues: 226.5323 Evaluate side-chains 233 residues out of total 3033 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 233 time to evaluate : 3.117 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.3134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 330 optimal weight: 20.0000 chunk 38 optimal weight: 7.9990 chunk 195 optimal weight: 9.9990 chunk 250 optimal weight: 0.2980 chunk 193 optimal weight: 8.9990 chunk 288 optimal weight: 0.0770 chunk 191 optimal weight: 9.9990 chunk 341 optimal weight: 8.9990 chunk 213 optimal weight: 0.7980 chunk 208 optimal weight: 6.9990 chunk 157 optimal weight: 20.0000 overall best weight: 3.2342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1066 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 819 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1163 ASN ** J 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 GLN ** I 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 819 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 833 GLN ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6418 moved from start: 0.6060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 29313 Z= 0.223 Angle : 0.661 9.908 39825 Z= 0.344 Chirality : 0.046 0.567 4647 Planarity : 0.005 0.042 5061 Dihedral : 5.483 26.484 3873 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 22.57 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.76 % Favored : 93.90 % Rotamer: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.53 % 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: -0.87 (0.14), residues: 3543 helix: 0.30 (0.19), residues: 660 sheet: -0.65 (0.17), residues: 813 loop : -0.79 (0.14), residues: 2070 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7086 Ramachandran restraints generated. 3543 Oldfield, 0 Emsley, 3543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7086 Ramachandran restraints generated. 3543 Oldfield, 0 Emsley, 3543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 3033 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 336 time to evaluate : 3.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 336 average time/residue: 0.3852 time to fit residues: 214.1947 Evaluate side-chains 235 residues out of total 3033 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 235 time to evaluate : 3.106 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.9837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 211 optimal weight: 20.0000 chunk 136 optimal weight: 3.9990 chunk 203 optimal weight: 7.9990 chunk 102 optimal weight: 9.9990 chunk 67 optimal weight: 9.9990 chunk 66 optimal weight: 9.9990 chunk 216 optimal weight: 0.0670 chunk 232 optimal weight: 30.0000 chunk 168 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 268 optimal weight: 0.6980 overall best weight: 2.5524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 833 GLN ** A1066 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 819 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 GLN ** I 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 819 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 833 GLN ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6407 moved from start: 0.6249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 29313 Z= 0.197 Angle : 0.649 9.604 39825 Z= 0.336 Chirality : 0.046 0.533 4647 Planarity : 0.005 0.059 5061 Dihedral : 5.410 26.634 3873 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 21.08 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.59 % Favored : 94.10 % Rotamer: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.53 % 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: 3543 helix: 0.43 (0.20), residues: 639 sheet: -0.55 (0.18), residues: 771 loop : -0.74 (0.14), residues: 2133 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7086 Ramachandran restraints generated. 3543 Oldfield, 0 Emsley, 3543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7086 Ramachandran restraints generated. 3543 Oldfield, 0 Emsley, 3543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 3033 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 335 time to evaluate : 3.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 335 average time/residue: 0.4057 time to fit residues: 225.3185 Evaluate side-chains 240 residues out of total 3033 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 240 time to evaluate : 3.263 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.3272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 310 optimal weight: 20.0000 chunk 326 optimal weight: 10.0000 chunk 298 optimal weight: 6.9990 chunk 317 optimal weight: 10.0000 chunk 191 optimal weight: 9.9990 chunk 138 optimal weight: 10.0000 chunk 249 optimal weight: 7.9990 chunk 97 optimal weight: 7.9990 chunk 287 optimal weight: 0.0020 chunk 300 optimal weight: 7.9990 chunk 316 optimal weight: 8.9990 overall best weight: 6.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 833 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 842 GLN ** A1066 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1104 ASN A1132 ASN ** B 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 819 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 819 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I1177 ASN ** F 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6609 moved from start: 0.7139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 29313 Z= 0.362 Angle : 0.864 10.766 39825 Z= 0.447 Chirality : 0.053 0.738 4647 Planarity : 0.006 0.048 5061 Dihedral : 6.404 28.521 3873 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 36.42 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.96 % Favored : 91.73 % Rotamer: Outliers : 0.03 % Allowed : 0.86 % Favored : 99.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.53 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.13), residues: 3543 helix: -0.67 (0.18), residues: 639 sheet: -0.77 (0.18), residues: 717 loop : -1.12 (0.13), residues: 2187 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7086 Ramachandran restraints generated. 3543 Oldfield, 0 Emsley, 3543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7086 Ramachandran restraints generated. 3543 Oldfield, 0 Emsley, 3543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 3033 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 306 time to evaluate : 3.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 307 average time/residue: 0.3956 time to fit residues: 201.2025 Evaluate side-chains 224 residues out of total 3033 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 224 time to evaluate : 3.128 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.2190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 208 optimal weight: 10.0000 chunk 336 optimal weight: 30.0000 chunk 205 optimal weight: 6.9990 chunk 159 optimal weight: 3.9990 chunk 233 optimal weight: 10.0000 chunk 352 optimal weight: 9.9990 chunk 324 optimal weight: 8.9990 chunk 280 optimal weight: 1.9990 chunk 29 optimal weight: 6.9990 chunk 216 optimal weight: 4.9990 chunk 172 optimal weight: 7.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 833 GLN ** A1066 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 819 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1104 ASN E1177 ASN ** J 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 599 GLN ** J 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 819 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 599 GLN ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 38 GLN ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6585 moved from start: 0.7389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 29313 Z= 0.291 Angle : 0.770 9.772 39825 Z= 0.401 Chirality : 0.050 0.651 4647 Planarity : 0.005 0.052 5061 Dihedral : 6.253 29.838 3873 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 30.91 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.28 % Favored : 92.41 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.53 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.14), residues: 3543 helix: -0.47 (0.19), residues: 624 sheet: -1.01 (0.18), residues: 750 loop : -1.14 (0.13), residues: 2169 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7086 Ramachandran restraints generated. 3543 Oldfield, 0 Emsley, 3543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7086 Ramachandran restraints generated. 3543 Oldfield, 0 Emsley, 3543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 3033 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 297 time to evaluate : 3.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 297 average time/residue: 0.3875 time to fit residues: 193.8505 Evaluate side-chains 227 residues out of total 3033 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 227 time to evaluate : 3.210 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.3836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 354 random chunks: chunk 223 optimal weight: 9.9990 chunk 299 optimal weight: 10.0000 chunk 86 optimal weight: 3.9990 chunk 258 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 78 optimal weight: 9.9990 chunk 281 optimal weight: 3.9990 chunk 117 optimal weight: 40.0000 chunk 288 optimal weight: 5.9990 chunk 35 optimal weight: 9.9990 chunk 51 optimal weight: 7.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1066 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 599 GLN ** H 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 819 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 277 ASN ** J 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 819 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1129 ASN ** I1138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.077287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.060177 restraints weight = 235131.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.060697 restraints weight = 209039.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.061292 restraints weight = 171237.801| |-----------------------------------------------------------------------------| r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6717 moved from start: 0.7732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 29313 Z= 0.282 Angle : 0.765 11.520 39825 Z= 0.398 Chirality : 0.049 0.610 4647 Planarity : 0.005 0.043 5061 Dihedral : 6.228 27.585 3873 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 30.72 Ramachandran Plot: Outliers : 0.31 % Allowed : 8.13 % Favored : 91.56 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.53 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.14), residues: 3543 helix: -0.42 (0.19), residues: 624 sheet: -0.99 (0.18), residues: 759 loop : -1.19 (0.13), residues: 2160 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5637.16 seconds wall clock time: 105 minutes 9.56 seconds (6309.56 seconds total)