Starting phenix.real_space_refine (version: dev) on Sun Dec 18 15:22:36 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w9k_8786/12_2022/5w9k_8786.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w9k_8786/12_2022/5w9k_8786.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w9k_8786/12_2022/5w9k_8786.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w9k_8786/12_2022/5w9k_8786.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w9k_8786/12_2022/5w9k_8786.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w9k_8786/12_2022/5w9k_8786.pdb" } resolution = 4.6 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.004 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A PHE 764": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 777": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 778": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 786": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 788": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 814": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 824": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 869": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 895": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 909": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 928": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 1001": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1012": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1044": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 764": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 777": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 778": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 786": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 788": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 809": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 814": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 824": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 869": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 895": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 909": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 928": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 947": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 977": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 978": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1001": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1012": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1044": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 764": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 777": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 778": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 786": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 788": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 814": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 824": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 869": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 909": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 928": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 947": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 977": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 978": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 1001": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 1012": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 1044": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 1116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 1126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 1141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 1153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 1171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 1204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 409": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 448": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 467": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 499": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 537": "OD1" <-> "OD2" Residue "J TYR 540": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 571": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 590": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 609": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 617": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 630": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 632": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 635": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 649": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 704": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 188": "OE1" <-> "OE2" Residue "K PHE 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 467": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 499": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 540": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 630": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 635": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 642": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 649": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 704": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 376": "OE1" <-> "OE2" Residue "L PHE 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 409": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 467": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 499": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 537": "OD1" <-> "OD2" Residue "L TYR 540": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 571": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 590": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 609": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 617": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 630": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 632": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 635": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 642": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 649": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 704": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 32873 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 461, 3531 Classifications: {'peptide': 461} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 21, 'TRANS': 436} Chain breaks: 1 Chain: "B" Number of atoms: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 948 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 2, 'TRANS': 116} Chain: "C" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 835 Classifications: {'peptide': 111} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 103} Chain: "D" Number of atoms: 3538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3538 Classifications: {'peptide': 462} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 21, 'TRANS': 437} Chain breaks: 1 Chain: "E" Number of atoms: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 948 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 2, 'TRANS': 116} Chain: "F" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 835 Classifications: {'peptide': 111} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 103} Chain: "G" Number of atoms: 3527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3527 Classifications: {'peptide': 460} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 21, 'TRANS': 435} Chain breaks: 1 Chain: "H" Number of atoms: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 948 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 2, 'TRANS': 116} Chain: "I" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 835 Classifications: {'peptide': 111} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 103} Chain: "J" Number of atoms: 5645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 724, 5645 Classifications: {'peptide': 724} Link IDs: {'CIS': 3, 'PTRANS': 35, 'TRANS': 685} Chain: "K" Number of atoms: 5645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 724, 5645 Classifications: {'peptide': 724} Link IDs: {'CIS': 5, 'PTRANS': 35, 'TRANS': 683} Chain: "L" Number of atoms: 5638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 723, 5638 Classifications: {'peptide': 723} Link IDs: {'CIS': 3, 'PTRANS': 35, 'TRANS': 684} Time building chain proxies: 17.72, per 1000 atoms: 0.54 Number of scatterers: 32873 At special positions: 0 Unit cell: (166.26, 154.02, 223.38, 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 180 16.00 O 6382 8.00 N 5462 7.00 C 20849 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=57, symmetry=0 Simple disulfide: pdb=" SG CYS A 806 " - pdb=" SG CYS A 828 " distance=2.03 Simple disulfide: pdb=" SG CYS A 811 " - pdb=" SG CYS A 817 " distance=1.99 Simple disulfide: pdb=" SG CYS A 912 " - pdb=" SG CYS A 925 " distance=2.08 Simple disulfide: pdb=" SG CYS A1106 " - pdb=" SG CYS A1117 " distance=2.03 Simple disulfide: pdb=" SG CYS A1156 " - pdb=" SG CYS A1164 " distance=2.19 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 92 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 88 " distance=2.04 Simple disulfide: pdb=" SG CYS D 806 " - pdb=" SG CYS D 828 " distance=2.03 Simple disulfide: pdb=" SG CYS D 811 " - pdb=" SG CYS D 817 " distance=2.02 Simple disulfide: pdb=" SG CYS D 912 " - pdb=" SG CYS D 925 " distance=2.07 Simple disulfide: pdb=" SG CYS D1106 " - pdb=" SG CYS D1117 " distance=2.17 Simple disulfide: pdb=" SG CYS D1156 " - pdb=" SG CYS D1164 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 92 " distance=2.11 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.03 Simple disulfide: pdb=" SG CYS G 806 " - pdb=" SG CYS G 828 " distance=2.03 Simple disulfide: pdb=" SG CYS G 811 " - pdb=" SG CYS G 817 " distance=2.07 Simple disulfide: pdb=" SG CYS G 912 " - pdb=" SG CYS G 925 " distance=2.87 Simple disulfide: pdb=" SG CYS G1106 " - pdb=" SG CYS G1117 " distance=2.03 Simple disulfide: pdb=" SG CYS G1156 " - pdb=" SG CYS G1164 " distance=2.01 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.04 Simple disulfide: pdb=" SG CYS J 30 " - pdb=" SG CYS J 195 " distance=2.09 Simple disulfide: pdb=" SG CYS J 176 " - pdb=" SG CYS J 214 " distance=2.07 Simple disulfide: pdb=" SG CYS J 185 " - pdb=" SG CYS J 237 " distance=2.65 Simple disulfide: pdb=" SG CYS J 339 " - pdb=" SG CYS J 349 " distance=2.03 Simple disulfide: pdb=" SG CYS J 383 " - pdb=" SG CYS J 407 " distance=2.04 Simple disulfide: pdb=" SG CYS J 425 " - pdb=" SG CYS J 478 " distance=2.08 Simple disulfide: pdb=" SG CYS J 437 " - pdb=" SG CYS J 585 " distance=1.78 Simple disulfide: pdb=" SG CYS J 503 " - pdb=" SG CYS J 526 " distance=2.04 Simple disulfide: pdb=" SG CYS J 603 " - pdb=" SG CYS J 654 " distance=1.63 Simple disulfide: pdb=" SG CYS J 620 " - pdb=" SG CYS J 650 " distance=1.80 Simple disulfide: pdb=" SG CYS J 679 " - pdb=" SG CYS J 713 " distance=2.03 Simple disulfide: pdb=" SG CYS J 727 " - pdb=" SG CYS J 736 " distance=2.02 Simple disulfide: pdb=" SG CYS K 30 " - pdb=" SG CYS K 195 " distance=2.05 Simple disulfide: pdb=" SG CYS K 176 " - pdb=" SG CYS K 214 " distance=2.05 Simple disulfide: pdb=" SG CYS K 185 " - pdb=" SG CYS K 237 " distance=2.03 Simple disulfide: pdb=" SG CYS K 339 " - pdb=" SG CYS K 349 " distance=2.04 Simple disulfide: pdb=" SG CYS K 383 " - pdb=" SG CYS K 407 " distance=2.83 Simple disulfide: pdb=" SG CYS K 425 " - pdb=" SG CYS K 478 " distance=2.01 Simple disulfide: pdb=" SG CYS K 437 " - pdb=" SG CYS K 585 " distance=2.13 Simple disulfide: pdb=" SG CYS K 503 " - pdb=" SG CYS K 526 " distance=2.03 Simple disulfide: pdb=" SG CYS K 603 " - pdb=" SG CYS K 654 " distance=2.09 Simple disulfide: pdb=" SG CYS K 620 " - pdb=" SG CYS K 650 " distance=1.77 Simple disulfide: pdb=" SG CYS K 679 " - pdb=" SG CYS K 713 " distance=2.03 Simple disulfide: pdb=" SG CYS K 727 " - pdb=" SG CYS K 736 " distance=1.98 Simple disulfide: pdb=" SG CYS L 30 " - pdb=" SG CYS L 195 " distance=2.04 Simple disulfide: pdb=" SG CYS L 176 " - pdb=" SG CYS L 214 " distance=2.07 Simple disulfide: pdb=" SG CYS L 185 " - pdb=" SG CYS L 237 " distance=2.14 Simple disulfide: pdb=" SG CYS L 339 " - pdb=" SG CYS L 349 " distance=2.04 Simple disulfide: pdb=" SG CYS L 383 " - pdb=" SG CYS L 407 " distance=2.43 Simple disulfide: pdb=" SG CYS L 425 " - pdb=" SG CYS L 478 " distance=2.33 Simple disulfide: pdb=" SG CYS L 437 " - pdb=" SG CYS L 585 " distance=1.90 Simple disulfide: pdb=" SG CYS L 503 " - pdb=" SG CYS L 526 " distance=2.02 Simple disulfide: pdb=" SG CYS L 603 " - pdb=" SG CYS L 654 " distance=1.68 Simple disulfide: pdb=" SG CYS L 620 " - pdb=" SG CYS L 650 " distance=1.79 Simple disulfide: pdb=" SG CYS L 679 " - pdb=" SG CYS L 713 " distance=2.03 Simple disulfide: pdb=" SG CYS L 727 " - pdb=" SG CYS L 736 " distance=2.06 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 Time building additional restraints: 12.66 Conformation dependent library (CDL) restraints added in 5.1 seconds 8428 Ramachandran restraints generated. 4214 Oldfield, 0 Emsley, 4214 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7878 Finding SS restraints... Secondary structure from input PDB file: 106 helices and 77 sheets defined 23.3% alpha, 26.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.80 Creating SS restraints... Processing helix chain 'A' and resid 814 through 823 removed outlier: 4.154A pdb=" N GLU A 823 " --> pdb=" O GLN A 819 " (cutoff:3.500A) Processing helix chain 'A' and resid 824 through 854 removed outlier: 3.893A pdb=" N CYS A 828 " --> pdb=" O TYR A 824 " (cutoff:3.500A) removed outlier: 3.812A 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 907 through 912 Processing helix chain 'A' and resid 922 through 931 removed outlier: 3.640A pdb=" N ALA A 926 " --> pdb=" O ASP A 922 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N TYR A 928 " --> pdb=" O ILE A 924 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N VAL A 929 " --> pdb=" O CYS A 925 " (cutoff:3.500A) Processing helix chain 'A' and resid 940 through 953 Processing helix chain 'A' and resid 971 through 982 Processing helix chain 'A' and resid 986 through 993 Processing helix chain 'A' and resid 993 through 1007 Processing helix chain 'A' and resid 1008 through 1010 No H-bonds generated for 'chain 'A' and resid 1008 through 1010' Processing helix chain 'A' and resid 1016 through 1040 removed outlier: 3.797A pdb=" N LEU A1040 " --> pdb=" O LEU A1036 " (cutoff:3.500A) Processing helix chain 'A' and resid 1050 through 1058 Processing helix chain 'A' and resid 1059 through 1104 removed outlier: 4.764A pdb=" N ALA A1065 " --> pdb=" O PRO A1061 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLN A1066 " --> pdb=" O GLU A1062 " (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 28 through 31 Processing helix chain 'B' and resid 61 through 64 Processing helix chain 'B' and resid 83 through 87 Processing helix chain 'C' and resid 79 through 83 Processing helix chain 'D' and resid 814 through 822 removed outlier: 3.790A pdb=" N ARG D 822 " --> pdb=" O GLU D 818 " (cutoff:3.500A) Processing helix chain 'D' and resid 824 through 854 removed outlier: 3.851A pdb=" N CYS D 828 " --> pdb=" O TYR D 824 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N SER D 852 " --> pdb=" O ASN D 848 " (cutoff:3.500A) Processing helix chain 'D' and resid 888 through 898 Processing helix chain 'D' and resid 907 through 912 Processing helix chain 'D' and resid 922 through 931 removed outlier: 4.756A pdb=" N TYR D 928 " --> pdb=" O ILE D 924 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N VAL D 929 " --> pdb=" O CYS D 925 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLY D 931 " --> pdb=" O GLN D 927 " (cutoff:3.500A) Processing helix chain 'D' and resid 940 through 953 Processing helix chain 'D' and resid 971 through 982 Processing helix chain 'D' and resid 986 through 993 Processing helix chain 'D' and resid 993 through 1007 Processing helix chain 'D' and resid 1008 through 1010 No H-bonds generated for 'chain 'D' and resid 1008 through 1010' Processing helix chain 'D' and resid 1016 through 1040 removed outlier: 3.525A pdb=" N ASN D1029 " --> pdb=" O ALA D1025 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LEU D1036 " --> pdb=" O ALA D1032 " (cutoff:3.500A) Processing helix chain 'D' and resid 1050 through 1058 Processing helix chain 'D' and resid 1059 through 1104 removed outlier: 4.051A pdb=" N ALA D1065 " --> pdb=" O PRO D1061 " (cutoff:3.500A) Processing helix chain 'D' and resid 1198 through 1200 No H-bonds generated for 'chain 'D' and resid 1198 through 1200' Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.669A pdb=" N TYR E 32 " --> pdb=" O PHE E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 61 through 64 Processing helix chain 'E' and resid 73 through 76 Processing helix chain 'E' and resid 83 through 87 Processing helix chain 'F' and resid 79 through 83 removed outlier: 3.513A pdb=" N THR F 83 " --> pdb=" O GLU F 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 814 through 822 Processing helix chain 'G' and resid 824 through 854 removed outlier: 3.847A pdb=" N CYS G 828 " --> pdb=" O TYR G 824 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N SER G 852 " --> pdb=" O ASN G 848 " (cutoff:3.500A) Processing helix chain 'G' and resid 888 through 898 Processing helix chain 'G' and resid 907 through 912 removed outlier: 3.502A pdb=" N ASP G 910 " --> pdb=" O GLN G 907 " (cutoff:3.500A) Processing helix chain 'G' and resid 922 through 931 removed outlier: 3.762A pdb=" N ALA G 926 " --> pdb=" O ASP G 922 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N TYR G 928 " --> pdb=" O ILE G 924 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N VAL G 929 " --> pdb=" O CYS G 925 " (cutoff:3.500A) Processing helix chain 'G' and resid 940 through 953 Processing helix chain 'G' and resid 971 through 982 Processing helix chain 'G' and resid 986 through 993 Processing helix chain 'G' and resid 993 through 1007 Processing helix chain 'G' and resid 1008 through 1010 No H-bonds generated for 'chain 'G' and resid 1008 through 1010' Processing helix chain 'G' and resid 1016 through 1040 removed outlier: 3.716A pdb=" N LEU G1040 " --> pdb=" O LEU G1036 " (cutoff:3.500A) Processing helix chain 'G' and resid 1050 through 1058 Processing helix chain 'G' and resid 1059 through 1104 removed outlier: 4.734A pdb=" N ALA G1065 " --> pdb=" O PRO G1061 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLN G1066 " --> pdb=" O GLU G1062 " (cutoff:3.500A) Processing helix chain 'G' and resid 1198 through 1200 No H-bonds generated for 'chain 'G' and resid 1198 through 1200' Processing helix chain 'H' and resid 28 through 31 Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'I' and resid 79 through 83 Processing helix chain 'J' and resid 37 through 41 removed outlier: 3.517A pdb=" N ASP J 41 " --> pdb=" O THR J 38 " (cutoff:3.500A) Processing helix chain 'J' and resid 49 through 53 Processing helix chain 'J' and resid 104 through 108 Processing helix chain 'J' and resid 133 through 137 Processing helix chain 'J' and resid 222 through 230 Processing helix chain 'J' and resid 303 through 307 Processing helix chain 'J' and resid 342 through 351 Processing helix chain 'J' and resid 385 through 390 removed outlier: 3.573A pdb=" N SER J 390 " --> pdb=" O PRO J 387 " (cutoff:3.500A) Processing helix chain 'J' and resid 395 through 399 removed outlier: 3.735A pdb=" N PHE J 399 " --> pdb=" O VAL J 396 " (cutoff:3.500A) Processing helix chain 'J' and resid 410 through 415 Processing helix chain 'J' and resid 416 through 418 No H-bonds generated for 'chain 'J' and resid 416 through 418' Processing helix chain 'J' and resid 429 through 436 removed outlier: 4.114A pdb=" N ALA J 434 " --> pdb=" O PRO J 430 " (cutoff:3.500A) Processing helix chain 'J' and resid 449 through 456 removed outlier: 4.872A pdb=" N SER J 454 " --> pdb=" O SER J 451 " (cutoff:3.500A) Processing helix chain 'J' and resid 462 through 468 Processing helix chain 'J' and resid 524 through 529 Processing helix chain 'J' and resid 546 through 550 Processing helix chain 'J' and resid 675 through 678 removed outlier: 3.645A pdb=" N ALA J 678 " --> pdb=" O GLY J 675 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 675 through 678' Processing helix chain 'J' and resid 694 through 702 removed outlier: 3.518A pdb=" N LYS J 698 " --> pdb=" O ARG J 694 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N ARG J 700 " --> pdb=" O MET J 696 " (cutoff:3.500A) Processing helix chain 'K' and resid 37 through 41 removed outlier: 4.069A pdb=" N ASP K 41 " --> pdb=" O THR K 38 " (cutoff:3.500A) Processing helix chain 'K' and resid 49 through 53 Processing helix chain 'K' and resid 104 through 108 Processing helix chain 'K' and resid 133 through 137 Processing helix chain 'K' and resid 222 through 230 Processing helix chain 'K' and resid 303 through 307 removed outlier: 3.975A pdb=" N ARG K 307 " --> pdb=" O GLN K 304 " (cutoff:3.500A) Processing helix chain 'K' and resid 342 through 351 Processing helix chain 'K' and resid 385 through 390 removed outlier: 3.572A pdb=" N SER K 390 " --> pdb=" O PRO K 387 " (cutoff:3.500A) Processing helix chain 'K' and resid 410 through 416 removed outlier: 3.577A pdb=" N LEU K 414 " --> pdb=" O ASN K 410 " (cutoff:3.500A) Processing helix chain 'K' and resid 431 through 436 Processing helix chain 'K' and resid 449 through 456 removed outlier: 5.232A pdb=" N SER K 454 " --> pdb=" O SER K 451 " (cutoff:3.500A) Processing helix chain 'K' and resid 462 through 468 Processing helix chain 'K' and resid 524 through 529 Processing helix chain 'K' and resid 675 through 682 removed outlier: 3.619A pdb=" N ALA K 678 " --> pdb=" O GLY K 675 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N CYS K 679 " --> pdb=" O SER K 676 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N GLU K 680 " --> pdb=" O VAL K 677 " (cutoff:3.500A) Processing helix chain 'K' and resid 694 through 702 removed outlier: 3.590A pdb=" N LYS K 698 " --> pdb=" O ARG K 694 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N ARG K 700 " --> pdb=" O MET K 696 " (cutoff:3.500A) Processing helix chain 'L' and resid 37 through 41 removed outlier: 3.529A pdb=" N ASP L 41 " --> pdb=" O THR L 38 " (cutoff:3.500A) Processing helix chain 'L' and resid 49 through 53 Processing helix chain 'L' and resid 104 through 108 Processing helix chain 'L' and resid 133 through 137 Processing helix chain 'L' and resid 222 through 230 Processing helix chain 'L' and resid 303 through 307 removed outlier: 3.751A pdb=" N ARG L 307 " --> pdb=" O GLN L 304 " (cutoff:3.500A) Processing helix chain 'L' and resid 342 through 351 Processing helix chain 'L' and resid 385 through 390 removed outlier: 3.546A pdb=" N SER L 390 " --> pdb=" O PRO L 387 " (cutoff:3.500A) Processing helix chain 'L' and resid 395 through 399 removed outlier: 3.763A pdb=" N PHE L 399 " --> pdb=" O VAL L 396 " (cutoff:3.500A) Processing helix chain 'L' and resid 410 through 415 Processing helix chain 'L' and resid 416 through 418 No H-bonds generated for 'chain 'L' and resid 416 through 418' Processing helix chain 'L' and resid 429 through 436 removed outlier: 4.026A pdb=" N ALA L 434 " --> pdb=" O PRO L 430 " (cutoff:3.500A) Processing helix chain 'L' and resid 449 through 456 removed outlier: 5.001A pdb=" N SER L 454 " --> pdb=" O SER L 451 " (cutoff:3.500A) Processing helix chain 'L' and resid 462 through 468 Processing helix chain 'L' and resid 524 through 529 Processing helix chain 'L' and resid 546 through 550 Processing helix chain 'L' and resid 675 through 678 removed outlier: 3.649A pdb=" N ALA L 678 " --> pdb=" O GLY L 675 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 675 through 678' Processing helix chain 'L' and resid 694 through 702 removed outlier: 3.572A pdb=" N LYS L 698 " --> pdb=" O ARG L 694 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N ARG L 700 " --> pdb=" O MET L 696 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'J' and resid 719 through 724 removed outlier: 7.373A pdb=" N LEU A 759 " --> pdb=" O SER J 720 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N LEU J 722 " --> pdb=" O LEU A 759 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 768 through 769 removed outlier: 5.810A pdb=" N ILE A 768 " --> pdb=" O SER D 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: 5.913A pdb=" N VAL A1150 " --> pdb=" O LYS A1174 " (cutoff:3.500A) removed outlier: 4.429A 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 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: 6.278A pdb=" N CYS A1156 " --> pdb=" O ILE A1214 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 3 through 6 Processing sheet with id=AA9, first strand: chain 'B' and resid 57 through 59 removed outlier: 6.462A pdb=" N SER B 44 " --> pdb=" O SER B 40 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N TRP B 36 " --> pdb=" O ILE B 48 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N VAL B 50 " --> pdb=" O ILE B 34 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ILE B 34 " --> pdb=" O VAL B 50 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 96 through 99 removed outlier: 4.481A pdb=" N TYR B 98 " --> pdb=" O VAL B 100B" (cutoff:3.500A) removed outlier: 7.543A pdb=" N VAL B 100B" --> pdb=" O TYR B 98 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 4 through 7 Processing sheet with id=AB3, first strand: chain 'C' and resid 10 through 13 removed outlier: 6.912A pdb=" N MET C 33 " --> pdb=" O SER C 49 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N SER C 49 " --> pdb=" O MET C 33 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N TRP C 35 " --> pdb=" O LEU C 47 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'K' and resid 719 through 724 removed outlier: 7.360A pdb=" N LEU D 759 " --> pdb=" O SER K 720 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N LEU K 722 " --> pdb=" O LEU D 759 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N GLY K 732 " --> pdb=" O LEU K 735 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N ALA K 737 " --> pdb=" O PRO K 730 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 768 through 769 removed outlier: 5.720A pdb=" N ILE D 768 " --> pdb=" O SER G 858 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'D' and resid 777 through 782 removed outlier: 5.824A pdb=" N VAL D1150 " --> pdb=" O LYS D1174 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N PHE D1172 " --> pdb=" O ALA D1152 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 785 through 796 Processing sheet with id=AB8, first strand: chain 'D' and resid 802 through 804 Processing sheet with id=AB9, first strand: chain 'D' and resid 1202 through 1204 removed outlier: 6.343A pdb=" N CYS D1156 " --> pdb=" O ILE D1214 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 3 through 6 removed outlier: 3.782A pdb=" N ALA E 78 " --> pdb=" O CYS E 22 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 57 through 59 removed outlier: 6.356A pdb=" N SER E 44 " --> pdb=" O SER E 40 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N TRP E 36 " --> pdb=" O ILE E 48 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N VAL E 50 " --> pdb=" O ILE E 34 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ILE E 34 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N CYS E 92 " --> pdb=" O TRP E 103 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N TRP E 103 " --> pdb=" O CYS E 92 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ARG E 94 " --> pdb=" O ASP E 101 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N TYR E 98 " --> pdb=" O VAL E 100B" (cutoff:3.500A) removed outlier: 7.578A pdb=" N VAL E 100B" --> pdb=" O TYR E 98 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 57 through 59 removed outlier: 6.356A pdb=" N SER E 44 " --> pdb=" O SER E 40 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N TRP E 36 " --> pdb=" O ILE E 48 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N VAL E 50 " --> pdb=" O ILE E 34 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ILE E 34 " --> pdb=" O VAL E 50 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 4 through 7 Processing sheet with id=AC5, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.850A pdb=" N MET F 33 " --> pdb=" O SER F 49 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N SER F 49 " --> pdb=" O MET F 33 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 719 through 724 removed outlier: 7.327A pdb=" N LEU G 759 " --> pdb=" O SER L 720 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N LEU L 722 " --> pdb=" O LEU G 759 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 777 through 782 removed outlier: 5.862A pdb=" N VAL G1150 " --> pdb=" O LYS G1174 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N PHE G1172 " --> pdb=" O ALA G1152 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 785 through 796 Processing sheet with id=AC9, first strand: chain 'G' and resid 802 through 804 Processing sheet with id=AD1, first strand: chain 'G' and resid 1202 through 1204 removed outlier: 6.431A pdb=" N CYS G1156 " --> pdb=" O ILE G1214 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AD3, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.522A pdb=" N SER H 44 " --> pdb=" O SER H 40 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N VAL H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ILE H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 96 through 99 removed outlier: 4.576A pdb=" N TYR H 98 " --> pdb=" O VAL H 100B" (cutoff:3.500A) removed outlier: 7.596A pdb=" N VAL H 100B" --> pdb=" O TYR H 98 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 4 through 7 Processing sheet with id=AD6, first strand: chain 'I' and resid 10 through 13 removed outlier: 6.891A pdb=" N MET I 33 " --> pdb=" O SER I 49 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N SER I 49 " --> pdb=" O MET I 33 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 33 through 35 Processing sheet with id=AD8, first strand: chain 'J' and resid 63 through 64 removed outlier: 6.301A pdb=" N THR J 63 " --> pdb=" O TYR L 632 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N VAL L 631 " --> pdb=" O VAL L 639 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N VAL L 639 " --> pdb=" O LEU L 651 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 68 through 72 removed outlier: 3.552A pdb=" N ARG J 335 " --> pdb=" O ASP J 326 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 75 through 76 Processing sheet with id=AE2, first strand: chain 'J' and resid 75 through 76 removed outlier: 6.490A pdb=" N SER J 267 " --> pdb=" O GLN J 280 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N GLN J 280 " --> pdb=" O SER J 267 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 88 through 89 removed outlier: 7.527A pdb=" N SER J 88 " --> pdb=" O ILE J 300 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 92 through 93 Processing sheet with id=AE5, first strand: chain 'J' and resid 110 through 111 removed outlier: 4.443A pdb=" N ALA J 146 " --> pdb=" O ILE J 296 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N CYS J 185 " --> pdb=" O THR J 168 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 110 through 111 removed outlier: 4.443A pdb=" N ALA J 146 " --> pdb=" O ILE J 296 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N CYS J 185 " --> pdb=" O THR J 168 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 126 through 127 removed outlier: 4.376A pdb=" N SER J 126 " --> pdb=" O ILE J 140 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA J 309 " --> pdb=" O THR J 139 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'J' and resid 153 through 154 Processing sheet with id=AE9, first strand: chain 'J' and resid 359 through 366 removed outlier: 4.131A pdb=" N VAL J 659 " --> pdb=" O VAL J 363 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N SER J 365 " --> pdb=" O VAL J 657 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N VAL J 657 " --> pdb=" O SER J 365 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'J' and resid 371 through 376 removed outlier: 4.596A pdb=" N GLU J 605 " --> pdb=" O GLY J 372 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLY J 615 " --> pdb=" O VAL J 604 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'J' and resid 400 through 404 removed outlier: 3.574A pdb=" N THR J 477 " --> pdb=" O SER J 426 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N THR J 483 " --> pdb=" O VAL J 420 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N VAL J 420 " --> pdb=" O THR J 483 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'J' and resid 513 through 515 removed outlier: 5.444A pdb=" N SER J 498 " --> pdb=" O VAL J 561 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N VAL J 561 " --> pdb=" O SER J 498 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N ILE J 500 " --> pdb=" O SER J 559 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N SER J 559 " --> pdb=" O ILE J 500 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'J' and resid 617 through 619 removed outlier: 5.038A pdb=" N VAL J 639 " --> pdb=" O LEU J 651 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N VAL J 631 " --> pdb=" O VAL J 639 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'K' and resid 33 through 35 Processing sheet with id=AF6, first strand: chain 'K' and resid 69 through 72 removed outlier: 3.620A pdb=" N ARG K 335 " --> pdb=" O ASP K 326 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'K' and resid 75 through 76 Processing sheet with id=AF8, first strand: chain 'K' and resid 75 through 76 removed outlier: 6.535A pdb=" N SER K 267 " --> pdb=" O GLN K 280 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N GLN K 280 " --> pdb=" O SER K 267 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'K' and resid 88 through 89 removed outlier: 7.626A pdb=" N SER K 88 " --> pdb=" O ILE K 300 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'K' and resid 92 through 93 Processing sheet with id=AG2, first strand: chain 'K' and resid 110 through 111 removed outlier: 4.425A pdb=" N ALA K 146 " --> pdb=" O ILE K 296 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N LEU K 180 " --> pdb=" O THR K 242 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N THR K 242 " --> pdb=" O LEU K 180 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ALA K 182 " --> pdb=" O MET K 240 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N MET K 240 " --> pdb=" O ALA K 182 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N TYR K 184 " --> pdb=" O THR K 238 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ILE K 186 " --> pdb=" O ASN K 236 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N ASN K 236 " --> pdb=" O ILE K 186 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N GLU K 188 " --> pdb=" O LEU K 234 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N LEU K 234 " --> pdb=" O GLU K 188 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'K' and resid 126 through 127 removed outlier: 4.422A pdb=" N SER K 126 " --> pdb=" O ILE K 140 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA K 309 " --> pdb=" O THR K 139 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'K' and resid 153 through 154 Processing sheet with id=AG5, first strand: chain 'K' and resid 359 through 366 removed outlier: 4.185A pdb=" N VAL K 659 " --> pdb=" O VAL K 363 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N SER K 365 " --> pdb=" O VAL K 657 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N VAL K 657 " --> pdb=" O SER K 365 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'K' and resid 374 through 375 Processing sheet with id=AG7, first strand: chain 'K' and resid 381 through 382 removed outlier: 6.209A pdb=" N VAL K 381 " --> pdb=" O ASN K 408 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N CYS K 407 " --> pdb=" O CYS K 585 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG7 Processing sheet with id=AG8, first strand: chain 'K' and resid 400 through 404 removed outlier: 3.537A pdb=" N LYS K 400 " --> pdb=" O TYR K 445 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE K 573 " --> pdb=" O CYS K 478 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N LEU K 479 " --> pdb=" O PHE K 423 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N PHE K 423 " --> pdb=" O LEU K 479 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N LEU K 481 " --> pdb=" O ASN K 421 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'K' and resid 513 through 515 removed outlier: 5.500A pdb=" N SER K 498 " --> pdb=" O VAL K 561 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N VAL K 561 " --> pdb=" O SER K 498 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N ILE K 500 " --> pdb=" O SER K 559 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N SER K 559 " --> pdb=" O ILE K 500 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'K' and resid 617 through 618 removed outlier: 5.634A pdb=" N VAL K 639 " --> pdb=" O LEU K 651 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N VAL K 631 " --> pdb=" O VAL K 639 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'L' and resid 33 through 35 Processing sheet with id=AH3, first strand: chain 'L' and resid 68 through 72 removed outlier: 3.602A pdb=" N ARG L 335 " --> pdb=" O ASP L 326 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'L' and resid 75 through 76 Processing sheet with id=AH5, first strand: chain 'L' and resid 75 through 76 removed outlier: 6.254A pdb=" N SER L 267 " --> pdb=" O GLN L 280 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N GLN L 280 " --> pdb=" O SER L 267 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'L' and resid 88 through 89 removed outlier: 3.974A pdb=" N SER L 88 " --> pdb=" O HIS L 298 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'L' and resid 92 through 93 Processing sheet with id=AH8, first strand: chain 'L' and resid 110 through 111 removed outlier: 4.594A pdb=" N ALA L 146 " --> pdb=" O ILE L 296 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N LEU L 180 " --> pdb=" O TYR L 241 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N TYR L 241 " --> pdb=" O LEU L 180 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ALA L 182 " --> pdb=" O PHE L 239 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N PHE L 239 " --> pdb=" O ALA L 182 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N TYR L 184 " --> pdb=" O CYS L 237 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N CYS L 237 " --> pdb=" O TYR L 184 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'L' and resid 126 through 127 removed outlier: 4.623A pdb=" N SER L 126 " --> pdb=" O ILE L 140 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA L 309 " --> pdb=" O THR L 139 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'L' and resid 153 through 154 Processing sheet with id=AI2, first strand: chain 'L' and resid 359 through 366 removed outlier: 4.334A pdb=" N VAL L 659 " --> pdb=" O VAL L 363 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N SER L 365 " --> pdb=" O VAL L 657 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N VAL L 657 " --> pdb=" O SER L 365 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'L' and resid 374 through 376 removed outlier: 3.844A pdb=" N GLY L 615 " --> pdb=" O VAL L 604 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'L' and resid 400 through 404 removed outlier: 7.257A pdb=" N LEU L 479 " --> pdb=" O PHE L 423 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N PHE L 423 " --> pdb=" O LEU L 479 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N LEU L 481 " --> pdb=" O ASN L 421 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'L' and resid 513 through 515 removed outlier: 5.401A pdb=" N SER L 498 " --> pdb=" O VAL L 561 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N VAL L 561 " --> pdb=" O SER L 498 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N ILE L 500 " --> pdb=" O SER L 559 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N SER L 559 " --> pdb=" O ILE L 500 " (cutoff:3.500A) 1291 hydrogen bonds defined for protein. 3276 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: 16.68 Time building geometry restraints manager: 13.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 6859 1.32 - 1.46: 10752 1.46 - 1.59: 15786 1.59 - 1.72: 2 1.72 - 1.85: 246 Bond restraints: 33645 Sorted by residual: bond pdb=" N ILE L 186 " pdb=" CA ILE L 186 " ideal model delta sigma weight residual 1.459 1.557 -0.098 1.19e-02 7.06e+03 6.74e+01 bond pdb=" CA CYS J 425 " pdb=" C CYS J 425 " ideal model delta sigma weight residual 1.522 1.426 0.096 1.24e-02 6.50e+03 5.96e+01 bond pdb=" CA CYS K 185 " pdb=" C CYS K 185 " ideal model delta sigma weight residual 1.522 1.616 -0.094 1.24e-02 6.50e+03 5.78e+01 bond pdb=" C CYS K 437 " pdb=" N TYR K 438 " ideal model delta sigma weight residual 1.331 1.429 -0.098 1.33e-02 5.65e+03 5.43e+01 bond pdb=" C ASN L 236 " pdb=" N CYS L 237 " ideal model delta sigma weight residual 1.330 1.413 -0.083 1.38e-02 5.25e+03 3.60e+01 ... (remaining 33640 not shown) Histogram of bond angle deviations from ideal: 91.27 - 100.82: 42 100.82 - 110.37: 9827 110.37 - 119.93: 21271 119.93 - 129.48: 14449 129.48 - 139.03: 157 Bond angle restraints: 45746 Sorted by residual: angle pdb=" N CYS L 736 " pdb=" CA CYS L 736 " pdb=" C CYS L 736 " ideal model delta sigma weight residual 108.96 91.27 17.69 1.49e+00 4.50e-01 1.41e+02 angle pdb=" O CYS L 185 " pdb=" C CYS L 185 " pdb=" N ILE L 186 " ideal model delta sigma weight residual 123.10 110.99 12.11 1.15e+00 7.56e-01 1.11e+02 angle pdb=" C GLN C 42 " pdb=" N PRO C 43 " pdb=" CA PRO C 43 " ideal model delta sigma weight residual 119.66 126.97 -7.31 7.20e-01 1.93e+00 1.03e+02 angle pdb=" C VAL I 58 " pdb=" N PRO I 59 " pdb=" CA PRO I 59 " ideal model delta sigma weight residual 119.92 130.56 -10.64 1.07e+00 8.73e-01 9.88e+01 angle pdb=" C VAL C 58 " pdb=" N PRO C 59 " pdb=" CA PRO C 59 " ideal model delta sigma weight residual 119.92 130.50 -10.58 1.07e+00 8.73e-01 9.78e+01 ... (remaining 45741 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.55: 19293 17.55 - 35.10: 519 35.10 - 52.64: 165 52.64 - 70.19: 86 70.19 - 87.74: 17 Dihedral angle restraints: 20080 sinusoidal: 7727 harmonic: 12353 Sorted by residual: dihedral pdb=" CB CYS F 23 " pdb=" SG CYS F 23 " pdb=" SG CYS F 88 " pdb=" CB CYS F 88 " ideal model delta sinusoidal sigma weight residual 93.00 177.87 -84.87 1 1.00e+01 1.00e-02 8.74e+01 dihedral pdb=" CB CYS C 23 " pdb=" SG CYS C 23 " pdb=" SG CYS C 88 " pdb=" CB CYS C 88 " ideal model delta sinusoidal sigma weight residual 93.00 167.99 -74.99 1 1.00e+01 1.00e-02 7.11e+01 dihedral pdb=" CB CYS I 23 " pdb=" SG CYS I 23 " pdb=" SG CYS I 88 " pdb=" CB CYS I 88 " ideal model delta sinusoidal sigma weight residual 93.00 165.24 -72.24 1 1.00e+01 1.00e-02 6.67e+01 ... (remaining 20077 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 4091 0.104 - 0.208: 917 0.208 - 0.312: 60 0.312 - 0.416: 4 0.416 - 0.520: 3 Chirality restraints: 5075 Sorted by residual: chirality pdb=" CA CYS J 736 " pdb=" N CYS J 736 " pdb=" C CYS J 736 " pdb=" CB CYS J 736 " both_signs ideal model delta sigma weight residual False 2.51 3.03 -0.52 2.00e-01 2.50e+01 6.77e+00 chirality pdb=" CA CYS J 383 " pdb=" N CYS J 383 " pdb=" C CYS J 383 " pdb=" CB CYS J 383 " both_signs ideal model delta sigma weight residual False 2.51 2.99 -0.48 2.00e-01 2.50e+01 5.71e+00 chirality pdb=" CA CYS L 736 " pdb=" N CYS L 736 " pdb=" C CYS L 736 " pdb=" CB CYS L 736 " both_signs ideal model delta sigma weight residual False 2.51 2.96 -0.45 2.00e-01 2.50e+01 5.04e+00 ... (remaining 5072 not shown) Planarity restraints: 5942 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 47 " -0.084 2.00e-02 2.50e+03 4.14e-02 4.28e+01 pdb=" CG TRP B 47 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 TRP B 47 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 TRP B 47 " 0.044 2.00e-02 2.50e+03 pdb=" NE1 TRP B 47 " 0.015 2.00e-02 2.50e+03 pdb=" CE2 TRP B 47 " 0.006 2.00e-02 2.50e+03 pdb=" CE3 TRP B 47 " 0.056 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 47 " -0.043 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 47 " 0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP B 47 " -0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP H 47 " -0.079 2.00e-02 2.50e+03 3.92e-02 3.85e+01 pdb=" CG TRP H 47 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 TRP H 47 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP H 47 " 0.044 2.00e-02 2.50e+03 pdb=" NE1 TRP H 47 " 0.013 2.00e-02 2.50e+03 pdb=" CE2 TRP H 47 " 0.007 2.00e-02 2.50e+03 pdb=" CE3 TRP H 47 " 0.053 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 47 " -0.039 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 47 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP H 47 " -0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR K 642 " -0.076 2.00e-02 2.50e+03 4.13e-02 3.41e+01 pdb=" CG TYR K 642 " 0.022 2.00e-02 2.50e+03 pdb=" CD1 TYR K 642 " 0.036 2.00e-02 2.50e+03 pdb=" CD2 TYR K 642 " 0.037 2.00e-02 2.50e+03 pdb=" CE1 TYR K 642 " 0.022 2.00e-02 2.50e+03 pdb=" CE2 TYR K 642 " 0.019 2.00e-02 2.50e+03 pdb=" CZ TYR K 642 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR K 642 " -0.062 2.00e-02 2.50e+03 ... (remaining 5939 not shown) Histogram of nonbonded interaction distances: 1.34 - 2.05: 20 2.05 - 2.77: 6298 2.77 - 3.48: 44263 3.48 - 4.19: 79715 4.19 - 4.90: 134222 Nonbonded interactions: 264518 Sorted by model distance: nonbonded pdb=" OH TYR G 905 " pdb=" CA PRO G 936 " model vdw 1.342 3.470 nonbonded pdb=" OH TYR A 905 " pdb=" CA PRO A 936 " model vdw 1.458 3.470 nonbonded pdb=" CE2 PHE K 506 " pdb=" CG2 VAL K 555 " model vdw 1.523 3.760 nonbonded pdb=" OH TYR A 905 " pdb=" CB PRO A 936 " model vdw 1.544 3.440 nonbonded pdb=" OH TYR G 905 " pdb=" CB PRO G 936 " model vdw 1.557 3.440 ... (remaining 264513 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 756 through 1223) selection = (chain 'D' and resid 756 through 1223) selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'H' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'I' } ncs_group { reference = (chain 'J' and resid 18 through 740) selection = (chain 'K' and resid 18 through 740) selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 180 5.16 5 C 20849 2.51 5 N 5462 2.21 5 O 6382 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 1.460 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: 0.030 Extract box with map and model: 9.130 Check model and map are aligned: 0.440 Convert atoms to be neutral: 0.290 Process input model: 87.550 Find NCS groups from input model: 2.210 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Set scattering table: 0.020 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 104.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 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 : 0.013 0.104 33645 Z= 0.877 Angle : 1.739 17.691 45746 Z= 1.189 Chirality : 0.083 0.520 5075 Planarity : 0.012 0.133 5942 Dihedral : 10.395 87.738 12031 Min Nonbonded Distance : 1.342 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.62 % Allowed : 3.65 % Favored : 95.73 % Rotamer Outliers : 0.14 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.42 % 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: 1.72 (0.13), residues: 4214 helix: -0.35 (0.16), residues: 657 sheet: 0.85 (0.16), residues: 940 loop : 1.95 (0.13), residues: 2617 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8428 Ramachandran restraints generated. 4214 Oldfield, 0 Emsley, 4214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8428 Ramachandran restraints generated. 4214 Oldfield, 0 Emsley, 4214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 853 residues out of total 3642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 848 time to evaluate : 3.763 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 853 average time/residue: 0.4408 time to fit residues: 598.5067 Evaluate side-chains 375 residues out of total 3642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 374 time to evaluate : 3.707 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.2738 time to fit residues: 5.5079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 354 optimal weight: 1.9990 chunk 318 optimal weight: 5.9990 chunk 176 optimal weight: 0.9980 chunk 108 optimal weight: 1.9990 chunk 214 optimal weight: 3.9990 chunk 170 optimal weight: 0.0670 chunk 329 optimal weight: 6.9990 chunk 127 optimal weight: 10.0000 chunk 200 optimal weight: 9.9990 chunk 245 optimal weight: 10.0000 chunk 381 optimal weight: 10.0000 overall best weight: 1.8124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 GLN A1023 GLN A1104 ASN A1129 ASN B 41 HIS ** B 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 37 GLN C 76 HIS C 89 GLN ** D 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 808 GLN D 812 ASN ** D 839 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1016 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27DASN F 74 ASN ** G 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 974 GLN G 993 ASN G1129 ASN H 41 HIS I 34 ASN I 76 HIS I 90 GLN J 342 ASN K 98 GLN ** K 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 261 GLN L 377 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.3016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 33645 Z= 0.227 Angle : 0.724 18.677 45746 Z= 0.395 Chirality : 0.046 0.300 5075 Planarity : 0.007 0.099 5942 Dihedral : 5.622 27.234 4616 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.31 % Allowed : 3.27 % Favored : 96.42 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.42 % 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: 1.36 (0.13), residues: 4214 helix: 1.05 (0.19), residues: 689 sheet: 0.67 (0.15), residues: 981 loop : 1.16 (0.13), residues: 2544 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8428 Ramachandran restraints generated. 4214 Oldfield, 0 Emsley, 4214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8428 Ramachandran restraints generated. 4214 Oldfield, 0 Emsley, 4214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 563 residues out of total 3642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 561 time to evaluate : 3.939 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 outliers start: 2 outliers final: 0 residues processed: 563 average time/residue: 0.4242 time to fit residues: 393.8302 Evaluate side-chains 339 residues out of total 3642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 339 time to evaluate : 3.808 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.7205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 211 optimal weight: 30.0000 chunk 118 optimal weight: 20.0000 chunk 317 optimal weight: 10.0000 chunk 259 optimal weight: 40.0000 chunk 105 optimal weight: 5.9990 chunk 382 optimal weight: 10.0000 chunk 412 optimal weight: 4.9990 chunk 340 optimal weight: 6.9990 chunk 378 optimal weight: 10.0000 chunk 130 optimal weight: 0.8980 chunk 306 optimal weight: 7.9990 overall best weight: 5.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 815 GLN A 839 ASN ** A 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 76 HIS ** C 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 839 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 842 GLN E 5 GLN F 34 ASN F 37 GLN G 974 GLN G1097 GLN G1212 GLN ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 41 HIS I 42 GLN J 236 ASN J 619 ASN K 125 ASN K 319 GLN ** K 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 406 ASN K 421 ASN ** L 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 125 ASN L 236 ASN L 277 ASN L 346 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.4008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.074 33645 Z= 0.305 Angle : 0.716 16.292 45746 Z= 0.387 Chirality : 0.045 0.213 5075 Planarity : 0.006 0.087 5942 Dihedral : 5.451 27.299 4616 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.15 % Favored : 95.59 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.42 % 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: 0.74 (0.13), residues: 4214 helix: 1.03 (0.19), residues: 702 sheet: 0.27 (0.14), residues: 1056 loop : 0.60 (0.13), residues: 2456 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8428 Ramachandran restraints generated. 4214 Oldfield, 0 Emsley, 4214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8428 Ramachandran restraints generated. 4214 Oldfield, 0 Emsley, 4214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 3642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 429 time to evaluate : 3.904 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: 2 outliers final: 1 residues processed: 431 average time/residue: 0.4376 time to fit residues: 310.6198 Evaluate side-chains 286 residues out of total 3642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 285 time to evaluate : 3.465 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2882 time to fit residues: 5.2777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 377 optimal weight: 7.9990 chunk 287 optimal weight: 50.0000 chunk 198 optimal weight: 40.0000 chunk 42 optimal weight: 10.0000 chunk 182 optimal weight: 20.0000 chunk 256 optimal weight: 30.0000 chunk 383 optimal weight: 9.9990 chunk 405 optimal weight: 0.3980 chunk 200 optimal weight: 30.0000 chunk 363 optimal weight: 6.9990 chunk 109 optimal weight: 9.9990 overall best weight: 7.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 839 ASN ** A 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 90 GLN D1129 ASN E 3 GLN F 37 GLN G 974 GLN I 27DASN J 277 ASN J 421 ASN J 628 GLN ** K 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 475 ASN K 516 GLN ** L 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 628 GLN L 688 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.5058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.060 33645 Z= 0.365 Angle : 0.771 16.306 45746 Z= 0.410 Chirality : 0.047 0.208 5075 Planarity : 0.006 0.081 5942 Dihedral : 5.821 28.498 4616 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 17.75 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.91 % Favored : 94.85 % Rotamer Outliers : 0.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.42 % 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: -0.00 (0.13), residues: 4214 helix: 0.52 (0.19), residues: 710 sheet: -0.01 (0.15), residues: 1054 loop : -0.05 (0.13), residues: 2450 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8428 Ramachandran restraints generated. 4214 Oldfield, 0 Emsley, 4214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8428 Ramachandran restraints generated. 4214 Oldfield, 0 Emsley, 4214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 3642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 367 time to evaluate : 3.843 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: 3 outliers final: 0 residues processed: 369 average time/residue: 0.4238 time to fit residues: 260.5594 Evaluate side-chains 267 residues out of total 3642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 267 time to evaluate : 3.753 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.1055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 338 optimal weight: 3.9990 chunk 230 optimal weight: 1.9990 chunk 5 optimal weight: 8.9990 chunk 302 optimal weight: 20.0000 chunk 167 optimal weight: 1.9990 chunk 346 optimal weight: 3.9990 chunk 280 optimal weight: 0.3980 chunk 0 optimal weight: 20.0000 chunk 207 optimal weight: 1.9990 chunk 364 optimal weight: 7.9990 chunk 102 optimal weight: 0.9980 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1129 ASN ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 39 GLN C 42 GLN D1132 ASN F 37 GLN K 319 GLN ** K 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 78 GLN L 98 GLN L 688 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.5125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.054 33645 Z= 0.175 Angle : 0.614 16.261 45746 Z= 0.323 Chirality : 0.044 0.208 5075 Planarity : 0.005 0.082 5942 Dihedral : 5.208 39.059 4616 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.41 % Favored : 95.37 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.42 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 0.26 (0.13), residues: 4214 helix: 1.12 (0.20), residues: 716 sheet: 0.12 (0.15), residues: 1042 loop : 0.01 (0.13), residues: 2456 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8428 Ramachandran restraints generated. 4214 Oldfield, 0 Emsley, 4214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8428 Ramachandran restraints generated. 4214 Oldfield, 0 Emsley, 4214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 3642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 415 time to evaluate : 3.721 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: 2 outliers final: 0 residues processed: 416 average time/residue: 0.4213 time to fit residues: 293.8465 Evaluate side-chains 284 residues out of total 3642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 284 time to evaluate : 3.870 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.1199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 136 optimal weight: 20.0000 chunk 365 optimal weight: 8.9990 chunk 80 optimal weight: 10.0000 chunk 238 optimal weight: 0.7980 chunk 100 optimal weight: 10.0000 chunk 406 optimal weight: 20.0000 chunk 337 optimal weight: 9.9990 chunk 188 optimal weight: 20.0000 chunk 33 optimal weight: 9.9990 chunk 134 optimal weight: 20.0000 chunk 213 optimal weight: 8.9990 overall best weight: 7.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1145 ASN ** B 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 39 GLN B 41 HIS ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 89 GLN ** K 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 167 HIS L 277 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.5739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.077 33645 Z= 0.391 Angle : 0.775 16.336 45746 Z= 0.410 Chirality : 0.046 0.193 5075 Planarity : 0.006 0.067 5942 Dihedral : 5.769 36.432 4616 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 19.93 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.15 % Favored : 93.66 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.42 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.39 (0.13), residues: 4214 helix: 0.27 (0.19), residues: 722 sheet: -0.14 (0.15), residues: 1058 loop : -0.40 (0.13), residues: 2434 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8428 Ramachandran restraints generated. 4214 Oldfield, 0 Emsley, 4214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8428 Ramachandran restraints generated. 4214 Oldfield, 0 Emsley, 4214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 3642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 345 time to evaluate : 4.017 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 outliers start: 0 outliers final: 0 residues processed: 345 average time/residue: 0.4398 time to fit residues: 256.8939 Evaluate side-chains 260 residues out of total 3642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 260 time to evaluate : 4.042 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.5364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 391 optimal weight: 7.9990 chunk 45 optimal weight: 3.9990 chunk 231 optimal weight: 10.0000 chunk 296 optimal weight: 5.9990 chunk 229 optimal weight: 9.9990 chunk 342 optimal weight: 2.9990 chunk 226 optimal weight: 5.9990 chunk 404 optimal weight: 20.0000 chunk 253 optimal weight: 20.0000 chunk 246 optimal weight: 30.0000 chunk 186 optimal weight: 20.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 839 ASN ** A 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 6 GLN ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1132 ASN ** G 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 688 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.5995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 33645 Z= 0.278 Angle : 0.679 16.951 45746 Z= 0.359 Chirality : 0.044 0.191 5075 Planarity : 0.005 0.063 5942 Dihedral : 5.567 37.536 4616 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 16.60 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.77 % Favored : 94.04 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.42 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.45 (0.13), residues: 4214 helix: 0.53 (0.19), residues: 723 sheet: -0.27 (0.15), residues: 1038 loop : -0.51 (0.13), residues: 2453 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8428 Ramachandran restraints generated. 4214 Oldfield, 0 Emsley, 4214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8428 Ramachandran restraints generated. 4214 Oldfield, 0 Emsley, 4214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 3642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 358 time to evaluate : 3.862 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 outliers start: 0 outliers final: 0 residues processed: 358 average time/residue: 0.4197 time to fit residues: 254.3008 Evaluate side-chains 268 residues out of total 3642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 268 time to evaluate : 3.779 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.1706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 250 optimal weight: 3.9990 chunk 161 optimal weight: 6.9990 chunk 241 optimal weight: 1.9990 chunk 121 optimal weight: 10.0000 chunk 79 optimal weight: 6.9990 chunk 78 optimal weight: 10.0000 chunk 257 optimal weight: 20.0000 chunk 275 optimal weight: 0.9990 chunk 200 optimal weight: 9.9990 chunk 37 optimal weight: 10.0000 chunk 318 optimal weight: 7.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 39 GLN ** C 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 98 GLN ** J 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 319 GLN ** K 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.6205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 33645 Z= 0.240 Angle : 0.655 16.427 45746 Z= 0.345 Chirality : 0.044 0.181 5075 Planarity : 0.005 0.106 5942 Dihedral : 5.427 29.644 4616 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 15.60 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.26 % Favored : 93.57 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.42 % 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: -0.42 (0.13), residues: 4214 helix: 0.73 (0.19), residues: 723 sheet: -0.22 (0.15), residues: 1031 loop : -0.56 (0.13), residues: 2460 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8428 Ramachandran restraints generated. 4214 Oldfield, 0 Emsley, 4214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8428 Ramachandran restraints generated. 4214 Oldfield, 0 Emsley, 4214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 3642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 354 time to evaluate : 4.417 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 outliers start: 0 outliers final: 0 residues processed: 354 average time/residue: 0.4064 time to fit residues: 244.8070 Evaluate side-chains 265 residues out of total 3642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 265 time to evaluate : 3.666 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.2721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 368 optimal weight: 20.0000 chunk 387 optimal weight: 10.0000 chunk 353 optimal weight: 3.9990 chunk 377 optimal weight: 3.9990 chunk 227 optimal weight: 9.9990 chunk 164 optimal weight: 10.0000 chunk 296 optimal weight: 20.0000 chunk 115 optimal weight: 20.0000 chunk 340 optimal weight: 8.9990 chunk 356 optimal weight: 20.0000 chunk 375 optimal weight: 6.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 915 GLN ** A1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1212 GLN ** B 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 GLN ** F 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 708 GLN ** K 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 471 GLN ** K 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.6534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.052 33645 Z= 0.345 Angle : 0.735 16.554 45746 Z= 0.388 Chirality : 0.045 0.215 5075 Planarity : 0.006 0.101 5942 Dihedral : 5.742 33.884 4616 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 19.39 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.24 % Favored : 92.60 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.42 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.13), residues: 4214 helix: 0.50 (0.19), residues: 710 sheet: -0.47 (0.15), residues: 1053 loop : -0.75 (0.13), residues: 2451 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8428 Ramachandran restraints generated. 4214 Oldfield, 0 Emsley, 4214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8428 Ramachandran restraints generated. 4214 Oldfield, 0 Emsley, 4214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 3642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 328 time to evaluate : 3.926 Fit side-chains 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: 329 average time/residue: 0.4221 time to fit residues: 235.9464 Evaluate side-chains 245 residues out of total 3642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 245 time to evaluate : 4.167 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.5669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 247 optimal weight: 5.9990 chunk 398 optimal weight: 30.0000 chunk 243 optimal weight: 9.9990 chunk 189 optimal weight: 5.9990 chunk 277 optimal weight: 6.9990 chunk 418 optimal weight: 6.9990 chunk 385 optimal weight: 6.9990 chunk 333 optimal weight: 20.0000 chunk 34 optimal weight: 1.9990 chunk 257 optimal weight: 10.0000 chunk 204 optimal weight: 5.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 839 ASN ** A 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 39 GLN ** F 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 258 GLN ** J 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 319 GLN ** K 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.6695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 33645 Z= 0.283 Angle : 0.695 16.657 45746 Z= 0.366 Chirality : 0.045 0.219 5075 Planarity : 0.005 0.093 5942 Dihedral : 5.640 33.673 4616 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 17.52 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.98 % Favored : 92.86 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.42 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.70 (0.13), residues: 4214 helix: 0.61 (0.20), residues: 711 sheet: -0.40 (0.15), residues: 1031 loop : -0.79 (0.13), residues: 2472 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8428 Ramachandran restraints generated. 4214 Oldfield, 0 Emsley, 4214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8428 Ramachandran restraints generated. 4214 Oldfield, 0 Emsley, 4214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 3642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 322 time to evaluate : 4.053 Fit side-chains 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: 322 average time/residue: 0.4288 time to fit residues: 236.3262 Evaluate side-chains 246 residues out of total 3642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 246 time to evaluate : 3.826 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.0741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 264 optimal weight: 10.0000 chunk 354 optimal weight: 10.0000 chunk 102 optimal weight: 2.9990 chunk 307 optimal weight: 10.0000 chunk 49 optimal weight: 20.0000 chunk 92 optimal weight: 5.9990 chunk 333 optimal weight: 20.0000 chunk 139 optimal weight: 9.9990 chunk 342 optimal weight: 10.0000 chunk 42 optimal weight: 0.9990 chunk 61 optimal weight: 0.0060 overall best weight: 4.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 39 GLN ** B 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 34 ASN ** G 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 319 GLN ** K 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 681 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.082797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.065108 restraints weight = 194598.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.065706 restraints weight = 128980.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.065587 restraints weight = 89299.208| |-----------------------------------------------------------------------------| r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.6801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 33645 Z= 0.231 Angle : 0.662 16.261 45746 Z= 0.347 Chirality : 0.044 0.231 5075 Planarity : 0.005 0.090 5942 Dihedral : 5.443 32.580 4616 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 16.26 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.93 % Favored : 92.90 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.42 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.13), residues: 4214 helix: 0.74 (0.20), residues: 718 sheet: -0.31 (0.15), residues: 1026 loop : -0.76 (0.13), residues: 2470 =============================================================================== Job complete usr+sys time: 6374.29 seconds wall clock time: 116 minutes 44.19 seconds (7004.19 seconds total)