Starting phenix.real_space_refine on Thu Feb 22 05:04:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w9k_8786/02_2024/5w9k_8786.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w9k_8786/02_2024/5w9k_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_8786/02_2024/5w9k_8786.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w9k_8786/02_2024/5w9k_8786.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w9k_8786/02_2024/5w9k_8786.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w9k_8786/02_2024/5w9k_8786.pdb" } resolution = 4.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 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. 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: 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 16.61, per 1000 atoms: 0.51 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: 12.40 Conformation dependent library (CDL) restraints added in 5.7 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: 4.12 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: 16.97 Time building geometry restraints manager: 13.40 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 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: 1.880 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: 8.020 Check model and map are aligned: 0.480 Set scattering table: 0.300 Process input model: 87.650 Find NCS groups from input model: 2.260 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 103.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 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 : 1.741 17.691 45746 Z= 1.191 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 : 4.66 Ramachandran Plot: Outliers : 0.62 % Allowed : 3.65 % Favored : 95.73 % Rotamer: Outliers : 0.14 % Allowed : 0.55 % Favored : 99.31 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.084 0.009 TRP B 47 HIS 0.007 0.002 HIS K 681 PHE 0.062 0.005 PHE F 98 TYR 0.076 0.007 TYR K 642 ARG 0.006 0.001 ARG E 94 *********************** 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 : 3.600 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 REVERT: A 794 TYR cc_start: 0.9172 (t80) cc_final: 0.8762 (t80) REVERT: A 805 ASP cc_start: 0.8360 (t0) cc_final: 0.7487 (m-30) REVERT: A 843 ASP cc_start: 0.8351 (m-30) cc_final: 0.8087 (m-30) REVERT: A 943 MET cc_start: 0.9244 (mtp) cc_final: 0.8656 (ttp) REVERT: A 978 TYR cc_start: 0.8576 (t80) cc_final: 0.8307 (t80) REVERT: A 980 LEU cc_start: 0.9556 (mt) cc_final: 0.9323 (mm) REVERT: A 1138 HIS cc_start: 0.9138 (m-70) cc_final: 0.8705 (m-70) REVERT: B 4 LEU cc_start: 0.7446 (mt) cc_final: 0.7219 (mt) REVERT: B 5 GLN cc_start: 0.8014 (tp40) cc_final: 0.7443 (mp10) REVERT: B 18 VAL cc_start: 0.6037 (p) cc_final: 0.5745 (t) REVERT: B 61 GLN cc_start: 0.9232 (mt0) cc_final: 0.8765 (pp30) REVERT: B 69 MET cc_start: 0.6274 (mtt) cc_final: 0.3993 (mtt) REVERT: B 81 GLU cc_start: 0.8374 (tt0) cc_final: 0.7905 (tm-30) REVERT: B 82 ARG cc_start: 0.7794 (mtt180) cc_final: 0.7445 (mtm180) REVERT: C 35 TRP cc_start: 0.6874 (m100) cc_final: 0.6470 (m100) REVERT: C 42 GLN cc_start: 0.8256 (pt0) cc_final: 0.7902 (mp10) REVERT: C 44 PRO cc_start: 0.8469 (Cg_endo) cc_final: 0.7949 (Cg_exo) REVERT: C 62 PHE cc_start: 0.8080 (m-80) cc_final: 0.7799 (m-80) REVERT: C 70 ASP cc_start: 0.9008 (t70) cc_final: 0.8690 (p0) REVERT: C 73 LEU cc_start: 0.7821 (tp) cc_final: 0.7217 (tp) REVERT: C 92 LYS cc_start: 0.8824 (tmtt) cc_final: 0.8590 (tttp) REVERT: D 821 LEU cc_start: 0.8926 (tp) cc_final: 0.8531 (tp) REVERT: D 843 ASP cc_start: 0.8607 (m-30) cc_final: 0.8296 (t0) REVERT: D 938 LEU cc_start: 0.8955 (tp) cc_final: 0.8573 (tp) REVERT: D 1033 LEU cc_start: 0.9565 (mt) cc_final: 0.9201 (tp) REVERT: D 1141 TYR cc_start: 0.7818 (t80) cc_final: 0.7477 (t80) REVERT: E 2 VAL cc_start: 0.6649 (t) cc_final: 0.5518 (t) REVERT: E 69 MET cc_start: 0.7600 (mtt) cc_final: 0.6560 (mtt) REVERT: E 85 GLU cc_start: 0.7908 (mt-10) cc_final: 0.7701 (pt0) REVERT: E 103 TRP cc_start: 0.5176 (m-90) cc_final: 0.3815 (m100) REVERT: F 2 ILE cc_start: 0.8826 (mp) cc_final: 0.8069 (mm) REVERT: F 11 LEU cc_start: 0.7633 (tp) cc_final: 0.7336 (pp) REVERT: F 27 GLU cc_start: 0.8455 (tt0) cc_final: 0.8162 (tm-30) REVERT: F 42 GLN cc_start: 0.7574 (pt0) cc_final: 0.7041 (mp10) REVERT: F 80 GLU cc_start: 0.6760 (pm20) cc_final: 0.6321 (tm-30) REVERT: F 89 GLN cc_start: 0.7649 (tt0) cc_final: 0.7050 (tm-30) REVERT: F 91 SER cc_start: 0.8059 (m) cc_final: 0.7835 (p) REVERT: F 98 PHE cc_start: 0.7011 (p90) cc_final: 0.6727 (p90) REVERT: G 816 LYS cc_start: 0.7779 (tptt) cc_final: 0.7572 (tttt) REVERT: G 906 MET cc_start: 0.5704 (mmp) cc_final: 0.4964 (mmm) REVERT: G 932 TYR cc_start: 0.6957 (m-10) cc_final: 0.6449 (m-10) REVERT: G 938 LEU cc_start: 0.9408 (tp) cc_final: 0.9037 (tp) REVERT: G 1027 ASN cc_start: 0.8657 (m-40) cc_final: 0.8282 (t0) REVERT: G 1104 ASN cc_start: 0.9343 (m-40) cc_final: 0.8843 (t0) REVERT: G 1191 PHE cc_start: 0.8309 (t80) cc_final: 0.7762 (t80) REVERT: H 18 VAL cc_start: 0.8764 (p) cc_final: 0.8466 (p) REVERT: H 23 LYS cc_start: 0.9222 (tttt) cc_final: 0.8683 (ptpp) REVERT: H 31 ASP cc_start: 0.8450 (m-30) cc_final: 0.7606 (t70) REVERT: H 35 HIS cc_start: 0.9049 (m-70) cc_final: 0.8421 (m170) REVERT: H 66 ARG cc_start: 0.7830 (mtp85) cc_final: 0.7430 (mmt90) REVERT: I 33 MET cc_start: 0.7328 (tpp) cc_final: 0.6582 (tpp) REVERT: I 35 TRP cc_start: 0.6640 (m100) cc_final: 0.6278 (m100) REVERT: I 36 PHE cc_start: 0.9295 (m-80) cc_final: 0.8574 (m-80) REVERT: I 47 LEU cc_start: 0.7735 (mt) cc_final: 0.7490 (mm) REVERT: I 73 LEU cc_start: 0.8526 (tp) cc_final: 0.8171 (tp) REVERT: I 102 THR cc_start: 0.7141 (p) cc_final: 0.6257 (t) REVERT: I 104 LEU cc_start: 0.8392 (tp) cc_final: 0.7917 (tp) REVERT: J 71 TYR cc_start: 0.8184 (t80) cc_final: 0.7614 (t80) REVERT: J 86 VAL cc_start: 0.8063 (t) cc_final: 0.6629 (t) REVERT: J 116 PHE cc_start: 0.9289 (p90) cc_final: 0.8725 (p90) REVERT: J 204 PHE cc_start: 0.6833 (t80) cc_final: 0.6379 (t80) REVERT: J 278 MET cc_start: 0.8477 (mtp) cc_final: 0.7773 (tpp) REVERT: J 293 TYR cc_start: 0.7871 (t80) cc_final: 0.7447 (t80) REVERT: J 296 ILE cc_start: 0.8646 (mt) cc_final: 0.8100 (mt) REVERT: J 389 LEU cc_start: 0.8260 (mt) cc_final: 0.7886 (pp) REVERT: J 651 LEU cc_start: 0.9391 (tp) cc_final: 0.9111 (tp) REVERT: J 717 LEU cc_start: 0.8589 (mm) cc_final: 0.8332 (mt) REVERT: J 726 ASP cc_start: 0.7859 (t0) cc_final: 0.7283 (p0) REVERT: J 731 LEU cc_start: 0.9045 (mt) cc_final: 0.8665 (mp) REVERT: K 52 LYS cc_start: 0.9289 (mmtt) cc_final: 0.8977 (mmmt) REVERT: K 120 ILE cc_start: 0.9472 (mt) cc_final: 0.9260 (tp) REVERT: K 126 SER cc_start: 0.8700 (t) cc_final: 0.8403 (p) REVERT: K 317 LYS cc_start: 0.9295 (mttt) cc_final: 0.8963 (mmmt) REVERT: K 318 LEU cc_start: 0.9183 (mt) cc_final: 0.8895 (mt) REVERT: K 323 PHE cc_start: 0.8990 (m-80) cc_final: 0.8695 (m-10) REVERT: K 337 ILE cc_start: 0.9183 (mt) cc_final: 0.8912 (mm) REVERT: K 452 MET cc_start: 0.5533 (mmm) cc_final: 0.5051 (ttt) REVERT: K 472 SER cc_start: 0.6980 (t) cc_final: 0.6748 (p) REVERT: K 618 GLN cc_start: 0.9023 (pt0) cc_final: 0.8699 (tm-30) REVERT: K 629 ARG cc_start: 0.7665 (mmt180) cc_final: 0.7309 (mtp180) REVERT: L 36 GLN cc_start: 0.7526 (mm-40) cc_final: 0.6889 (mp10) REVERT: L 149 LEU cc_start: 0.8909 (mp) cc_final: 0.8675 (mt) REVERT: L 180 LEU cc_start: 0.8649 (tp) cc_final: 0.8448 (tp) REVERT: L 218 ASN cc_start: 0.8789 (t0) cc_final: 0.8122 (p0) REVERT: L 587 LYS cc_start: 0.7655 (mmtt) cc_final: 0.7448 (mtpp) REVERT: L 605 GLU cc_start: 0.9033 (tt0) cc_final: 0.8764 (tp30) REVERT: L 637 ASN cc_start: 0.8339 (m-40) cc_final: 0.7895 (m110) REVERT: L 693 THR cc_start: 0.4019 (t) cc_final: 0.3470 (p) outliers start: 5 outliers final: 1 residues processed: 853 average time/residue: 0.4832 time to fit residues: 656.3077 Evaluate side-chains 425 residues out of total 3642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 424 time to evaluate : 3.637 ------------------------------------------------------------------------------- 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: 5.9990 chunk 170 optimal weight: 1.9990 chunk 329 optimal weight: 6.9990 chunk 127 optimal weight: 20.0000 chunk 200 optimal weight: 5.9990 chunk 245 optimal weight: 10.0000 chunk 381 optimal weight: 10.0000 overall best weight: 2.5988 ------------------------------------------------------------------------------- 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 ** C 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 76 HIS ** D 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 808 GLN D 812 ASN ** D 839 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27DASN F 42 GLN F 74 ASN ** G 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 974 GLN G 993 ASN ** G1027 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G1097 GLN G1129 ASN H 41 HIS I 34 ASN I 76 HIS I 90 GLN J 342 ASN K 98 GLN L 261 GLN L 377 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.2878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 33645 Z= 0.243 Angle : 0.712 10.678 45746 Z= 0.395 Chirality : 0.046 0.358 5075 Planarity : 0.007 0.099 5942 Dihedral : 5.652 27.760 4616 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.18 % Favored : 96.54 % Rotamer: Outliers : 0.05 % Allowed : 1.73 % Favored : 98.22 % 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: 1.35 (0.13), residues: 4214 helix: 1.08 (0.19), residues: 689 sheet: 0.60 (0.15), residues: 975 loop : 1.16 (0.13), residues: 2550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP H 36 HIS 0.007 0.001 HIS G1122 PHE 0.042 0.002 PHE J 101 TYR 0.032 0.002 TYR G 905 ARG 0.010 0.001 ARG L 614 *********************** 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 569 residues out of total 3642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 567 time to evaluate : 3.390 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: A 794 TYR cc_start: 0.8930 (t80) cc_final: 0.8575 (t80) REVERT: A 805 ASP cc_start: 0.8621 (t0) cc_final: 0.7747 (m-30) REVERT: A 875 GLU cc_start: 0.8245 (pm20) cc_final: 0.7775 (pm20) REVERT: A 943 MET cc_start: 0.9142 (mtp) cc_final: 0.8582 (ttp) REVERT: A 978 TYR cc_start: 0.8619 (t80) cc_final: 0.8385 (t80) REVERT: A 1058 LEU cc_start: 0.8112 (mt) cc_final: 0.7214 (mt) REVERT: A 1177 ASN cc_start: 0.8577 (t0) cc_final: 0.8199 (t0) REVERT: B 5 GLN cc_start: 0.8335 (tp40) cc_final: 0.7703 (mp10) REVERT: B 6 GLN cc_start: 0.5867 (tp-100) cc_final: 0.5369 (tp40) REVERT: B 48 ILE cc_start: 0.7916 (mm) cc_final: 0.7707 (mm) REVERT: B 72 ASP cc_start: 0.8465 (t0) cc_final: 0.8203 (t0) REVERT: B 76 SER cc_start: 0.9423 (m) cc_final: 0.9041 (p) REVERT: B 81 GLU cc_start: 0.8370 (tt0) cc_final: 0.7832 (tp30) REVERT: B 82 ARG cc_start: 0.7827 (mtt180) cc_final: 0.7441 (mtm180) REVERT: B 103 TRP cc_start: 0.6724 (m100) cc_final: 0.6514 (m100) REVERT: C 18 ARG cc_start: 0.7151 (ttt-90) cc_final: 0.6818 (ttt-90) REVERT: C 44 PRO cc_start: 0.8436 (Cg_endo) cc_final: 0.8101 (Cg_exo) REVERT: C 62 PHE cc_start: 0.8100 (m-80) cc_final: 0.7806 (m-80) REVERT: C 70 ASP cc_start: 0.8788 (t70) cc_final: 0.8577 (p0) REVERT: C 87 PHE cc_start: 0.7873 (m-80) cc_final: 0.7359 (m-80) REVERT: D 757 MET cc_start: 0.8518 (mmm) cc_final: 0.8237 (mmm) REVERT: D 843 ASP cc_start: 0.8680 (m-30) cc_final: 0.8427 (m-30) REVERT: D 906 MET cc_start: 0.5897 (ppp) cc_final: 0.4946 (mtt) REVERT: D 938 LEU cc_start: 0.8953 (tp) cc_final: 0.8458 (tp) REVERT: D 999 ASN cc_start: 0.8597 (m-40) cc_final: 0.8121 (t0) REVERT: D 1008 MET cc_start: 0.8925 (mtm) cc_final: 0.8594 (tpp) REVERT: D 1169 ASN cc_start: 0.7580 (t0) cc_final: 0.7293 (t0) REVERT: E 45 LEU cc_start: 0.8692 (tp) cc_final: 0.8360 (tp) REVERT: E 46 GLU cc_start: 0.9156 (mm-30) cc_final: 0.8675 (tp30) REVERT: E 63 PHE cc_start: 0.8412 (m-80) cc_final: 0.7752 (m-10) REVERT: E 69 MET cc_start: 0.7326 (mtt) cc_final: 0.6957 (mtt) REVERT: E 100 MET cc_start: 0.6443 (pmm) cc_final: 0.5872 (pmm) REVERT: E 107 THR cc_start: 0.5452 (t) cc_final: 0.5096 (m) REVERT: F 1 ASP cc_start: 0.7642 (p0) cc_final: 0.7420 (p0) REVERT: F 2 ILE cc_start: 0.8834 (mp) cc_final: 0.7768 (mm) REVERT: F 21 ILE cc_start: 0.8544 (mm) cc_final: 0.8245 (tp) REVERT: F 27 GLU cc_start: 0.8443 (tt0) cc_final: 0.8073 (tm-30) REVERT: F 38 GLN cc_start: 0.8096 (tt0) cc_final: 0.7673 (tt0) REVERT: F 80 GLU cc_start: 0.6815 (pm20) cc_final: 0.6435 (tm-30) REVERT: G 816 LYS cc_start: 0.7782 (tptt) cc_final: 0.7450 (tttt) REVERT: G 906 MET cc_start: 0.5202 (mmp) cc_final: 0.4330 (mmm) REVERT: G 932 TYR cc_start: 0.6361 (m-10) cc_final: 0.6064 (m-10) REVERT: G 1177 ASN cc_start: 0.9210 (t0) cc_final: 0.8896 (t0) REVERT: G 1182 ASP cc_start: 0.7756 (t70) cc_final: 0.7542 (t70) REVERT: G 1191 PHE cc_start: 0.8543 (t80) cc_final: 0.7756 (t80) REVERT: H 2 VAL cc_start: 0.5976 (t) cc_final: 0.5548 (t) REVERT: H 13 ARG cc_start: 0.7651 (tpm170) cc_final: 0.7387 (tpp-160) REVERT: H 23 LYS cc_start: 0.9043 (tttt) cc_final: 0.8757 (ptpt) REVERT: H 31 ASP cc_start: 0.8299 (m-30) cc_final: 0.7536 (t70) REVERT: H 34 ILE cc_start: 0.8982 (tp) cc_final: 0.8692 (tp) REVERT: H 35 HIS cc_start: 0.8662 (m-70) cc_final: 0.8030 (m-70) REVERT: H 64 LYS cc_start: 0.7536 (mttt) cc_final: 0.7294 (tppt) REVERT: H 66 ARG cc_start: 0.7943 (mtp85) cc_final: 0.7565 (mmt90) REVERT: H 68 THR cc_start: 0.9030 (t) cc_final: 0.8741 (p) REVERT: H 81 GLU cc_start: 0.9216 (mp0) cc_final: 0.8983 (mp0) REVERT: I 33 MET cc_start: 0.7880 (tpp) cc_final: 0.7081 (tpp) REVERT: I 36 PHE cc_start: 0.9128 (m-80) cc_final: 0.8400 (m-80) REVERT: I 73 LEU cc_start: 0.8576 (tp) cc_final: 0.8120 (tp) REVERT: I 96 ARG cc_start: 0.6675 (mmm-85) cc_final: 0.6384 (mmm-85) REVERT: J 69 ILE cc_start: 0.9302 (tp) cc_final: 0.9083 (mp) REVERT: J 71 TYR cc_start: 0.8194 (t80) cc_final: 0.7553 (t80) REVERT: J 75 PHE cc_start: 0.8679 (m-80) cc_final: 0.8137 (m-80) REVERT: J 171 LEU cc_start: 0.9345 (pp) cc_final: 0.9069 (pp) REVERT: J 278 MET cc_start: 0.8272 (mtp) cc_final: 0.7973 (tpp) REVERT: J 389 LEU cc_start: 0.8183 (mt) cc_final: 0.7893 (pp) REVERT: J 617 PHE cc_start: 0.7915 (m-80) cc_final: 0.7566 (m-10) REVERT: J 651 LEU cc_start: 0.9287 (tp) cc_final: 0.9043 (tp) REVERT: J 726 ASP cc_start: 0.7708 (t0) cc_final: 0.7184 (p0) REVERT: K 52 LYS cc_start: 0.9362 (mmtt) cc_final: 0.9027 (mmmt) REVERT: K 56 ILE cc_start: 0.9560 (mm) cc_final: 0.9351 (mm) REVERT: K 317 LYS cc_start: 0.9227 (mttt) cc_final: 0.9014 (mmmt) REVERT: K 452 MET cc_start: 0.4697 (mmm) cc_final: 0.4267 (ttt) REVERT: L 36 GLN cc_start: 0.7629 (mm-40) cc_final: 0.7105 (mp10) REVERT: L 56 ILE cc_start: 0.9533 (mm) cc_final: 0.9323 (pt) REVERT: L 169 LEU cc_start: 0.9577 (tt) cc_final: 0.9374 (tt) REVERT: L 277 ASN cc_start: 0.8794 (m-40) cc_final: 0.8499 (m110) REVERT: L 296 ILE cc_start: 0.8692 (mm) cc_final: 0.8337 (mm) REVERT: L 324 LEU cc_start: 0.9387 (mm) cc_final: 0.9148 (mm) REVERT: L 563 MET cc_start: 0.7448 (ptm) cc_final: 0.6961 (tmm) REVERT: L 637 ASN cc_start: 0.8129 (m-40) cc_final: 0.7722 (m110) REVERT: L 724 VAL cc_start: 0.8900 (m) cc_final: 0.8659 (p) REVERT: L 729 LEU cc_start: 0.9457 (mt) cc_final: 0.9255 (mt) outliers start: 2 outliers final: 0 residues processed: 569 average time/residue: 0.4305 time to fit residues: 400.4569 Evaluate side-chains 372 residues out of total 3642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 372 time to evaluate : 3.549 ------------------------------------------------------------------------------- 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: 20.0000 chunk 118 optimal weight: 20.0000 chunk 317 optimal weight: 7.9990 chunk 259 optimal weight: 40.0000 chunk 105 optimal weight: 4.9990 chunk 382 optimal weight: 5.9990 chunk 412 optimal weight: 6.9990 chunk 340 optimal weight: 6.9990 chunk 378 optimal weight: 9.9990 chunk 130 optimal weight: 8.9990 chunk 306 optimal weight: 10.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- 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 5 GLN C 37 GLN C 90 GLN D 792 GLN ** D 839 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 842 GLN E 5 GLN G 974 GLN G1104 ASN G1212 GLN ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 41 HIS ** I 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 236 ASN J 421 ASN J 619 ASN K 125 ASN K 406 ASN K 421 ASN K 471 GLN ** L 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 125 ASN L 236 ASN L 346 GLN L 637 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.4146 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= 0.357 Angle : 0.761 11.807 45746 Z= 0.416 Chirality : 0.046 0.217 5075 Planarity : 0.006 0.087 5942 Dihedral : 5.670 29.135 4616 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 14.98 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.49 % Favored : 95.25 % Rotamer: Outliers : 0.11 % Allowed : 2.64 % Favored : 97.25 % 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: 0.47 (0.13), residues: 4214 helix: 0.74 (0.19), residues: 698 sheet: 0.12 (0.15), residues: 1026 loop : 0.41 (0.13), residues: 2490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP B 36 HIS 0.009 0.002 HIS J 91 PHE 0.039 0.003 PHE J 101 TYR 0.038 0.002 TYR G 905 ARG 0.016 0.001 ARG L 119 *********************** 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 428 residues out of total 3642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 424 time to evaluate : 3.969 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: A 805 ASP cc_start: 0.8945 (t0) cc_final: 0.7966 (m-30) REVERT: A 978 TYR cc_start: 0.8772 (t80) cc_final: 0.8556 (t80) REVERT: B 5 GLN cc_start: 0.8373 (tp-100) cc_final: 0.7646 (mp10) REVERT: B 6 GLN cc_start: 0.6195 (tp-100) cc_final: 0.5567 (tp40) REVERT: B 72 ASP cc_start: 0.8443 (t0) cc_final: 0.8198 (t0) REVERT: B 76 SER cc_start: 0.9401 (m) cc_final: 0.9078 (p) REVERT: B 81 GLU cc_start: 0.8342 (tt0) cc_final: 0.7864 (tp30) REVERT: B 82 ARG cc_start: 0.7855 (mtt180) cc_final: 0.7470 (mtm180) REVERT: B 100 TYR cc_start: 0.7968 (m-80) cc_final: 0.7700 (m-80) REVERT: C 28 TYR cc_start: 0.8325 (m-80) cc_final: 0.7919 (m-80) REVERT: C 32 PHE cc_start: 0.7052 (m-10) cc_final: 0.6705 (m-10) REVERT: C 44 PRO cc_start: 0.8331 (Cg_endo) cc_final: 0.7951 (Cg_exo) REVERT: C 85 MET cc_start: 0.8317 (tpt) cc_final: 0.8086 (tpp) REVERT: C 87 PHE cc_start: 0.7665 (m-80) cc_final: 0.7319 (m-10) REVERT: C 92 LYS cc_start: 0.9122 (tmtt) cc_final: 0.8908 (tttp) REVERT: D 757 MET cc_start: 0.8480 (mmm) cc_final: 0.8192 (mmm) REVERT: D 777 TYR cc_start: 0.8968 (p90) cc_final: 0.8604 (p90) REVERT: D 913 MET cc_start: 0.6651 (mtt) cc_final: 0.6419 (mmm) REVERT: D 999 ASN cc_start: 0.8713 (m-40) cc_final: 0.8169 (t0) REVERT: D 1008 MET cc_start: 0.8987 (mtm) cc_final: 0.8764 (tpp) REVERT: E 85 GLU cc_start: 0.7995 (mt-10) cc_final: 0.7705 (pm20) REVERT: E 95 LYS cc_start: 0.7391 (tttt) cc_final: 0.7184 (tttp) REVERT: E 107 THR cc_start: 0.5777 (t) cc_final: 0.5464 (m) REVERT: F 2 ILE cc_start: 0.8881 (mp) cc_final: 0.8008 (mm) REVERT: F 27 GLU cc_start: 0.8384 (tt0) cc_final: 0.8012 (tm-30) REVERT: F 80 GLU cc_start: 0.6575 (pm20) cc_final: 0.6081 (tm-30) REVERT: G 816 LYS cc_start: 0.7772 (tptt) cc_final: 0.7485 (tttt) REVERT: G 906 MET cc_start: 0.5654 (mmp) cc_final: 0.4877 (mmm) REVERT: G 1104 ASN cc_start: 0.9615 (OUTLIER) cc_final: 0.8525 (t0) REVERT: H 23 LYS cc_start: 0.9143 (tttt) cc_final: 0.8795 (ttpp) REVERT: H 31 ASP cc_start: 0.8489 (m-30) cc_final: 0.8055 (t70) REVERT: H 34 ILE cc_start: 0.8939 (tp) cc_final: 0.8608 (tp) REVERT: H 35 HIS cc_start: 0.8526 (m-70) cc_final: 0.8151 (m-70) REVERT: H 62 LYS cc_start: 0.8087 (ptmm) cc_final: 0.7435 (ptpp) REVERT: H 66 ARG cc_start: 0.8139 (mtp85) cc_final: 0.7671 (mmt90) REVERT: H 68 THR cc_start: 0.9047 (t) cc_final: 0.8729 (p) REVERT: H 81 GLU cc_start: 0.9216 (mp0) cc_final: 0.8964 (mp0) REVERT: I 18 ARG cc_start: 0.8460 (ttp80) cc_final: 0.8221 (mpp-170) REVERT: I 33 MET cc_start: 0.7582 (tpp) cc_final: 0.7358 (tpp) REVERT: I 36 PHE cc_start: 0.9332 (m-80) cc_final: 0.8354 (m-80) REVERT: I 78 VAL cc_start: 0.7421 (t) cc_final: 0.6981 (p) REVERT: I 96 ARG cc_start: 0.6726 (mmm-85) cc_final: 0.6407 (mmm-85) REVERT: J 71 TYR cc_start: 0.8274 (t80) cc_final: 0.7759 (t80) REVERT: J 278 MET cc_start: 0.8288 (mtp) cc_final: 0.7977 (tpp) REVERT: J 389 LEU cc_start: 0.8190 (mt) cc_final: 0.7730 (pp) REVERT: J 726 ASP cc_start: 0.7916 (t0) cc_final: 0.7375 (p0) REVERT: K 56 ILE cc_start: 0.9588 (mm) cc_final: 0.9388 (mm) REVERT: K 75 PHE cc_start: 0.8721 (m-80) cc_final: 0.8484 (m-80) REVERT: K 278 MET cc_start: 0.8531 (mmp) cc_final: 0.8174 (mmm) REVERT: K 452 MET cc_start: 0.4945 (mmm) cc_final: 0.4399 (ttt) REVERT: K 637 ASN cc_start: 0.8900 (t0) cc_final: 0.8683 (t0) REVERT: K 673 LEU cc_start: 0.9409 (tp) cc_final: 0.9092 (mt) REVERT: L 148 MET cc_start: 0.8584 (tpt) cc_final: 0.7914 (tpp) REVERT: L 149 LEU cc_start: 0.9001 (mt) cc_final: 0.8680 (mt) REVERT: L 277 ASN cc_start: 0.8887 (m-40) cc_final: 0.8332 (m110) REVERT: L 351 TYR cc_start: 0.9059 (m-10) cc_final: 0.8856 (m-10) REVERT: L 563 MET cc_start: 0.7518 (ptm) cc_final: 0.7140 (tmm) REVERT: L 689 TYR cc_start: 0.5544 (p90) cc_final: 0.5116 (p90) REVERT: L 729 LEU cc_start: 0.9471 (mt) cc_final: 0.9247 (mt) outliers start: 4 outliers final: 1 residues processed: 428 average time/residue: 0.4358 time to fit residues: 307.1637 Evaluate side-chains 309 residues out of total 3642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 307 time to evaluate : 3.610 ------------------------------------------------------------------------------- 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: 6.9990 chunk 287 optimal weight: 0.9990 chunk 198 optimal weight: 30.0000 chunk 42 optimal weight: 9.9990 chunk 182 optimal weight: 4.9990 chunk 256 optimal weight: 7.9990 chunk 383 optimal weight: 10.0000 chunk 405 optimal weight: 8.9990 chunk 200 optimal weight: 30.0000 chunk 363 optimal weight: 6.9990 chunk 109 optimal weight: 10.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- 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** A1145 ASN B 39 GLN D 792 GLN F 89 GLN G 974 GLN ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 27DASN ** I 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 628 GLN ** L 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 628 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.4764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 33645 Z= 0.294 Angle : 0.681 10.302 45746 Z= 0.369 Chirality : 0.045 0.205 5075 Planarity : 0.006 0.080 5942 Dihedral : 5.539 28.564 4616 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 14.61 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.56 % Favored : 95.21 % Rotamer: Outliers : 0.03 % Allowed : 2.39 % Favored : 97.58 % 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: 0.18 (0.13), residues: 4214 helix: 0.77 (0.19), residues: 714 sheet: 0.03 (0.15), residues: 1052 loop : 0.08 (0.13), residues: 2448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 36 HIS 0.009 0.001 HIS G1122 PHE 0.039 0.002 PHE J 101 TYR 0.030 0.002 TYR G 905 ARG 0.007 0.001 ARG L 691 *********************** 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 403 residues out of total 3642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 402 time to evaluate : 4.065 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: A 804 VAL cc_start: 0.9436 (t) cc_final: 0.9132 (m) REVERT: A 805 ASP cc_start: 0.9037 (t0) cc_final: 0.8097 (m-30) REVERT: A 875 GLU cc_start: 0.8354 (pm20) cc_final: 0.7824 (pm20) REVERT: A 978 TYR cc_start: 0.8880 (t80) cc_final: 0.8624 (t80) REVERT: A 1058 LEU cc_start: 0.8296 (mt) cc_final: 0.7988 (mp) REVERT: A 1077 THR cc_start: 0.9276 (p) cc_final: 0.8940 (p) REVERT: B 39 GLN cc_start: 0.8565 (OUTLIER) cc_final: 0.8352 (tm-30) REVERT: B 60 ASN cc_start: 0.8424 (t0) cc_final: 0.8012 (t0) REVERT: B 72 ASP cc_start: 0.8407 (t0) cc_final: 0.8145 (t0) REVERT: B 76 SER cc_start: 0.9371 (m) cc_final: 0.9152 (t) REVERT: B 81 GLU cc_start: 0.8389 (tt0) cc_final: 0.7880 (tp30) REVERT: B 82 ARG cc_start: 0.7702 (mtt180) cc_final: 0.7242 (mtm180) REVERT: B 100 TYR cc_start: 0.7992 (m-80) cc_final: 0.7738 (m-80) REVERT: C 2 ILE cc_start: 0.8613 (mt) cc_final: 0.7335 (mt) REVERT: C 27 GLU cc_start: 0.8142 (tt0) cc_final: 0.7695 (mp0) REVERT: C 32 PHE cc_start: 0.7010 (m-10) cc_final: 0.6503 (m-10) REVERT: C 48 ILE cc_start: 0.7658 (pt) cc_final: 0.6546 (pt) REVERT: C 62 PHE cc_start: 0.8235 (m-80) cc_final: 0.7846 (p90) REVERT: C 85 MET cc_start: 0.8356 (tpt) cc_final: 0.8029 (tpp) REVERT: C 86 TYR cc_start: 0.7640 (m-80) cc_final: 0.7114 (m-80) REVERT: C 92 LYS cc_start: 0.9049 (tmtt) cc_final: 0.8798 (tttt) REVERT: D 757 MET cc_start: 0.8498 (mmm) cc_final: 0.8219 (mmm) REVERT: D 943 MET cc_start: 0.9070 (mmm) cc_final: 0.8830 (mmt) REVERT: D 999 ASN cc_start: 0.8693 (m-40) cc_final: 0.8124 (t0) REVERT: D 1001 PHE cc_start: 0.9255 (t80) cc_final: 0.8827 (t80) REVERT: D 1132 ASN cc_start: 0.9173 (m-40) cc_final: 0.8966 (m-40) REVERT: D 1169 ASN cc_start: 0.8717 (t0) cc_final: 0.8379 (t0) REVERT: E 53 TYR cc_start: 0.8347 (t80) cc_final: 0.8051 (t80) REVERT: E 80 MET cc_start: 0.8932 (mtm) cc_final: 0.8011 (ppp) REVERT: E 85 GLU cc_start: 0.8113 (mt-10) cc_final: 0.7859 (pm20) REVERT: E 100 MET cc_start: 0.6301 (pmm) cc_final: 0.6099 (pmm) REVERT: E 107 THR cc_start: 0.5953 (t) cc_final: 0.5666 (m) REVERT: F 2 ILE cc_start: 0.8525 (mp) cc_final: 0.7979 (mm) REVERT: F 27 GLU cc_start: 0.8346 (tt0) cc_final: 0.8002 (tm-30) REVERT: F 32 PHE cc_start: 0.8441 (m-80) cc_final: 0.8018 (m-80) REVERT: F 33 MET cc_start: 0.7637 (mmm) cc_final: 0.7393 (mmm) REVERT: F 34 ASN cc_start: 0.7691 (m110) cc_final: 0.7282 (m110) REVERT: F 80 GLU cc_start: 0.6764 (pm20) cc_final: 0.6279 (tm-30) REVERT: G 816 LYS cc_start: 0.7725 (tptt) cc_final: 0.7438 (tptt) REVERT: G 906 MET cc_start: 0.5530 (mmp) cc_final: 0.4875 (mmm) REVERT: G 1039 GLU cc_start: 0.9037 (mm-30) cc_final: 0.8670 (mm-30) REVERT: G 1182 ASP cc_start: 0.8313 (t0) cc_final: 0.8067 (t0) REVERT: H 23 LYS cc_start: 0.9166 (tttt) cc_final: 0.8827 (ttpp) REVERT: H 34 ILE cc_start: 0.8836 (tp) cc_final: 0.8552 (tp) REVERT: H 35 HIS cc_start: 0.8662 (m-70) cc_final: 0.8266 (m170) REVERT: H 45 LEU cc_start: 0.7584 (mp) cc_final: 0.7210 (mp) REVERT: H 66 ARG cc_start: 0.8227 (mtp85) cc_final: 0.7540 (mmt90) REVERT: H 68 THR cc_start: 0.8943 (t) cc_final: 0.8675 (p) REVERT: H 81 GLU cc_start: 0.9214 (mp0) cc_final: 0.8959 (mp0) REVERT: H 95 LYS cc_start: 0.7765 (ptmm) cc_final: 0.7548 (ptmt) REVERT: H 100 ASP cc_start: 0.8866 (t0) cc_final: 0.8532 (t0) REVERT: I 18 ARG cc_start: 0.8475 (ttp80) cc_final: 0.8254 (mpp-170) REVERT: I 27 VAL cc_start: 0.8278 (p) cc_final: 0.7508 (p) REVERT: I 33 MET cc_start: 0.7663 (tpp) cc_final: 0.7301 (tpp) REVERT: I 36 PHE cc_start: 0.9317 (m-80) cc_final: 0.8292 (m-80) REVERT: I 92 LYS cc_start: 0.9257 (tmtt) cc_final: 0.8585 (tptt) REVERT: J 71 TYR cc_start: 0.8399 (t80) cc_final: 0.7918 (t80) REVERT: J 278 MET cc_start: 0.8193 (mtp) cc_final: 0.7917 (tpp) REVERT: J 389 LEU cc_start: 0.8157 (mt) cc_final: 0.7692 (pp) REVERT: J 726 ASP cc_start: 0.8049 (t0) cc_final: 0.7317 (p0) REVERT: K 56 ILE cc_start: 0.9626 (mm) cc_final: 0.9384 (mm) REVERT: K 278 MET cc_start: 0.8569 (mmp) cc_final: 0.7687 (tpp) REVERT: K 452 MET cc_start: 0.5120 (mmm) cc_final: 0.4592 (ttt) REVERT: K 637 ASN cc_start: 0.8860 (t0) cc_final: 0.8597 (t0) REVERT: K 673 LEU cc_start: 0.9340 (tp) cc_final: 0.9112 (mt) REVERT: L 148 MET cc_start: 0.8441 (tpt) cc_final: 0.8051 (tpp) REVERT: L 149 LEU cc_start: 0.8935 (mt) cc_final: 0.8642 (mt) REVERT: L 277 ASN cc_start: 0.8984 (m-40) cc_final: 0.8374 (m110) REVERT: L 563 MET cc_start: 0.7571 (ptm) cc_final: 0.7313 (tmm) REVERT: L 648 TYR cc_start: 0.7712 (t80) cc_final: 0.7475 (t80) REVERT: L 729 LEU cc_start: 0.9484 (mt) cc_final: 0.9245 (mt) outliers start: 1 outliers final: 0 residues processed: 402 average time/residue: 0.4242 time to fit residues: 283.7956 Evaluate side-chains 303 residues out of total 3642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 302 time to evaluate : 3.867 ------------------------------------------------------------------------------- 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: 6.9990 chunk 230 optimal weight: 6.9990 chunk 5 optimal weight: 5.9990 chunk 302 optimal weight: 8.9990 chunk 167 optimal weight: 0.7980 chunk 346 optimal weight: 4.9990 chunk 280 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 207 optimal weight: 0.0470 chunk 364 optimal weight: 30.0000 chunk 102 optimal weight: 6.9990 overall best weight: 3.3684 ------------------------------------------------------------------------------- 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** ** B 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 3 GLN G1104 ASN I 42 GLN K 471 GLN L 78 GLN L 98 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.5021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 33645 Z= 0.214 Angle : 0.612 9.541 45746 Z= 0.331 Chirality : 0.043 0.216 5075 Planarity : 0.005 0.077 5942 Dihedral : 5.281 39.362 4616 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.79 % Favored : 95.02 % Rotamer: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % 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: 0.20 (0.13), residues: 4214 helix: 1.09 (0.20), residues: 707 sheet: -0.00 (0.15), residues: 1061 loop : 0.01 (0.13), residues: 2446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D1184 HIS 0.005 0.001 HIS J 681 PHE 0.030 0.002 PHE J 101 TYR 0.025 0.001 TYR G 905 ARG 0.006 0.000 ARG D1057 *********************** 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 401 residues out of total 3642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 401 time to evaluate : 3.703 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: A 804 VAL cc_start: 0.9410 (t) cc_final: 0.9130 (m) REVERT: A 805 ASP cc_start: 0.9043 (t0) cc_final: 0.8035 (m-30) REVERT: A 875 GLU cc_start: 0.8287 (pm20) cc_final: 0.7813 (pm20) REVERT: A 892 ASP cc_start: 0.8772 (t0) cc_final: 0.8325 (t0) REVERT: A 896 ASP cc_start: 0.8883 (m-30) cc_final: 0.8545 (m-30) REVERT: B 60 ASN cc_start: 0.8299 (t0) cc_final: 0.7875 (t0) REVERT: B 72 ASP cc_start: 0.8575 (t0) cc_final: 0.8339 (t0) REVERT: B 76 SER cc_start: 0.9318 (m) cc_final: 0.9100 (p) REVERT: B 81 GLU cc_start: 0.8359 (tt0) cc_final: 0.7849 (tp30) REVERT: B 82 ARG cc_start: 0.7667 (mtt180) cc_final: 0.7161 (mtm180) REVERT: C 32 PHE cc_start: 0.7173 (m-10) cc_final: 0.6772 (m-10) REVERT: C 62 PHE cc_start: 0.8304 (m-80) cc_final: 0.8072 (m-10) REVERT: C 85 MET cc_start: 0.8444 (tpt) cc_final: 0.8214 (tpp) REVERT: C 86 TYR cc_start: 0.7505 (m-80) cc_final: 0.6948 (m-80) REVERT: C 87 PHE cc_start: 0.7899 (m-10) cc_final: 0.7516 (m-10) REVERT: C 92 LYS cc_start: 0.9075 (tmtt) cc_final: 0.8830 (tttt) REVERT: D 757 MET cc_start: 0.8436 (mmm) cc_final: 0.8154 (mmm) REVERT: D 943 MET cc_start: 0.9087 (mmm) cc_final: 0.8851 (mmt) REVERT: D 999 ASN cc_start: 0.8786 (m-40) cc_final: 0.8177 (t0) REVERT: D 1001 PHE cc_start: 0.9187 (t80) cc_final: 0.8776 (t80) REVERT: D 1169 ASN cc_start: 0.8712 (t0) cc_final: 0.8463 (t0) REVERT: E 46 GLU cc_start: 0.9105 (mm-30) cc_final: 0.8870 (tp30) REVERT: E 53 TYR cc_start: 0.8263 (t80) cc_final: 0.7961 (t80) REVERT: E 69 MET cc_start: 0.6687 (mmt) cc_final: 0.6235 (mmt) REVERT: E 72 ASP cc_start: 0.5206 (t0) cc_final: 0.4863 (t0) REVERT: E 85 GLU cc_start: 0.8122 (mt-10) cc_final: 0.7877 (pm20) REVERT: E 100 MET cc_start: 0.6475 (pmm) cc_final: 0.5781 (pmm) REVERT: E 107 THR cc_start: 0.5935 (t) cc_final: 0.5603 (m) REVERT: F 2 ILE cc_start: 0.8559 (mp) cc_final: 0.8232 (mm) REVERT: F 27 GLU cc_start: 0.8340 (tt0) cc_final: 0.7973 (tm-30) REVERT: F 32 PHE cc_start: 0.8236 (m-80) cc_final: 0.7877 (m-80) REVERT: F 33 MET cc_start: 0.7886 (mmm) cc_final: 0.7557 (mmm) REVERT: F 36 PHE cc_start: 0.9033 (m-80) cc_final: 0.8566 (m-80) REVERT: F 80 GLU cc_start: 0.6871 (pm20) cc_final: 0.6426 (tm-30) REVERT: G 816 LYS cc_start: 0.7609 (tptt) cc_final: 0.7334 (tptm) REVERT: G 906 MET cc_start: 0.5498 (mmp) cc_final: 0.4880 (mmm) REVERT: G 1039 GLU cc_start: 0.8992 (mm-30) cc_final: 0.8658 (mm-30) REVERT: G 1182 ASP cc_start: 0.8279 (t0) cc_final: 0.8016 (t0) REVERT: H 23 LYS cc_start: 0.9163 (tttt) cc_final: 0.8780 (ttpp) REVERT: H 34 ILE cc_start: 0.8967 (tp) cc_final: 0.8677 (tp) REVERT: H 35 HIS cc_start: 0.8722 (m-70) cc_final: 0.8194 (m170) REVERT: H 66 ARG cc_start: 0.8162 (mtp85) cc_final: 0.7578 (mmt90) REVERT: H 68 THR cc_start: 0.8868 (t) cc_final: 0.8619 (p) REVERT: H 81 GLU cc_start: 0.9213 (mp0) cc_final: 0.8937 (mp0) REVERT: H 95 LYS cc_start: 0.7823 (ptmm) cc_final: 0.7389 (ptmt) REVERT: H 100 ASP cc_start: 0.8895 (t0) cc_final: 0.8642 (t0) REVERT: I 18 ARG cc_start: 0.8447 (ttp80) cc_final: 0.7774 (ttp80) REVERT: I 33 MET cc_start: 0.7705 (tpp) cc_final: 0.7453 (tpp) REVERT: I 36 PHE cc_start: 0.9290 (m-80) cc_final: 0.8250 (m-80) REVERT: J 71 TYR cc_start: 0.8400 (t80) cc_final: 0.7911 (t80) REVERT: J 148 MET cc_start: 0.8092 (mmm) cc_final: 0.7776 (tpp) REVERT: J 278 MET cc_start: 0.8109 (mtp) cc_final: 0.7787 (tpp) REVERT: J 389 LEU cc_start: 0.8132 (mt) cc_final: 0.7674 (pp) REVERT: J 726 ASP cc_start: 0.8067 (t0) cc_final: 0.7245 (p0) REVERT: K 56 ILE cc_start: 0.9638 (mm) cc_final: 0.9412 (mm) REVERT: K 452 MET cc_start: 0.5206 (mmm) cc_final: 0.4686 (ttt) REVERT: K 637 ASN cc_start: 0.8870 (t0) cc_final: 0.8610 (t0) REVERT: L 148 MET cc_start: 0.8570 (tpt) cc_final: 0.8146 (tpp) REVERT: L 149 LEU cc_start: 0.8978 (mt) cc_final: 0.8666 (mt) REVERT: L 277 ASN cc_start: 0.9027 (m-40) cc_final: 0.8394 (m110) REVERT: L 563 MET cc_start: 0.7631 (ptm) cc_final: 0.7399 (tmm) outliers start: 0 outliers final: 0 residues processed: 401 average time/residue: 0.4288 time to fit residues: 286.7073 Evaluate side-chains 301 residues out of total 3642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 301 time to evaluate : 3.590 ------------------------------------------------------------------------------- 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: 20.0000 chunk 80 optimal weight: 7.9990 chunk 238 optimal weight: 5.9990 chunk 100 optimal weight: 10.0000 chunk 406 optimal weight: 20.0000 chunk 337 optimal weight: 0.9990 chunk 188 optimal weight: 8.9990 chunk 33 optimal weight: 9.9990 chunk 134 optimal weight: 5.9990 chunk 213 optimal weight: 7.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- 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** ** 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 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 6 GLN D 792 GLN ** D1104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 3 GLN ** K 708 GLN ** 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: 0.7770 moved from start: 0.5482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 33645 Z= 0.312 Angle : 0.676 10.410 45746 Z= 0.364 Chirality : 0.044 0.206 5075 Planarity : 0.005 0.058 5942 Dihedral : 5.489 36.528 4616 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 16.83 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.55 % Favored : 94.26 % Rotamer: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.40 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.11 (0.13), residues: 4214 helix: 0.82 (0.20), residues: 707 sheet: -0.14 (0.15), residues: 1066 loop : -0.23 (0.13), residues: 2441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 36 HIS 0.006 0.001 HIS J 681 PHE 0.045 0.002 PHE E 29 TYR 0.028 0.002 TYR G 905 ARG 0.007 0.001 ARG L 691 *********************** 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 364 residues out of total 3642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 364 time to evaluate : 3.759 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: A 804 VAL cc_start: 0.9433 (t) cc_final: 0.9177 (m) REVERT: A 805 ASP cc_start: 0.9052 (t0) cc_final: 0.8036 (m-30) REVERT: A 875 GLU cc_start: 0.8467 (pm20) cc_final: 0.7962 (pm20) REVERT: A 1059 ASP cc_start: 0.8494 (t70) cc_final: 0.8280 (t70) REVERT: B 60 ASN cc_start: 0.8342 (t0) cc_final: 0.7829 (t0) REVERT: B 72 ASP cc_start: 0.8549 (t0) cc_final: 0.8292 (t0) REVERT: B 80 MET cc_start: 0.7467 (mtp) cc_final: 0.7158 (mtp) REVERT: B 81 GLU cc_start: 0.8506 (tt0) cc_final: 0.8027 (tp30) REVERT: B 82 ARG cc_start: 0.7733 (mtt180) cc_final: 0.7189 (mtm180) REVERT: C 2 ILE cc_start: 0.8440 (mm) cc_final: 0.8011 (tt) REVERT: C 27 GLU cc_start: 0.8154 (tt0) cc_final: 0.7738 (mp0) REVERT: C 32 PHE cc_start: 0.7146 (m-10) cc_final: 0.6801 (m-10) REVERT: C 62 PHE cc_start: 0.8298 (m-80) cc_final: 0.8068 (m-10) REVERT: C 86 TYR cc_start: 0.7598 (m-80) cc_final: 0.7127 (m-10) REVERT: C 87 PHE cc_start: 0.8105 (m-10) cc_final: 0.7554 (m-10) REVERT: C 92 LYS cc_start: 0.9039 (tmtt) cc_final: 0.8798 (tttp) REVERT: D 757 MET cc_start: 0.8413 (mmm) cc_final: 0.8129 (mmm) REVERT: D 943 MET cc_start: 0.9106 (mmm) cc_final: 0.8900 (mmt) REVERT: D 999 ASN cc_start: 0.8713 (m-40) cc_final: 0.7957 (t0) REVERT: D 1001 PHE cc_start: 0.9281 (t80) cc_final: 0.8857 (t80) REVERT: E 20 ILE cc_start: 0.8554 (pt) cc_final: 0.8309 (pt) REVERT: E 41 HIS cc_start: 0.7345 (m-70) cc_final: 0.7103 (m-70) REVERT: E 53 TYR cc_start: 0.8474 (t80) cc_final: 0.8170 (t80) REVERT: E 72 ASP cc_start: 0.4891 (t0) cc_final: 0.4560 (t0) REVERT: E 80 MET cc_start: 0.8799 (ttm) cc_final: 0.8490 (tmm) REVERT: E 95 LYS cc_start: 0.7835 (ptmm) cc_final: 0.7615 (ptmm) REVERT: E 107 THR cc_start: 0.5772 (t) cc_final: 0.5475 (m) REVERT: F 27 GLU cc_start: 0.8351 (tt0) cc_final: 0.7972 (tm-30) REVERT: F 32 PHE cc_start: 0.8249 (m-80) cc_final: 0.7899 (m-80) REVERT: F 33 MET cc_start: 0.7828 (mmm) cc_final: 0.7268 (mmm) REVERT: F 36 PHE cc_start: 0.8916 (m-80) cc_final: 0.8711 (m-80) REVERT: F 80 GLU cc_start: 0.6884 (pm20) cc_final: 0.6478 (tm-30) REVERT: F 97 THR cc_start: 0.9384 (t) cc_final: 0.9120 (p) REVERT: G 816 LYS cc_start: 0.7760 (tptt) cc_final: 0.7440 (tptt) REVERT: G 1039 GLU cc_start: 0.9063 (mm-30) cc_final: 0.8784 (mm-30) REVERT: G 1104 ASN cc_start: 0.9210 (m110) cc_final: 0.8585 (t0) REVERT: G 1182 ASP cc_start: 0.8398 (t0) cc_final: 0.8184 (t0) REVERT: H 23 LYS cc_start: 0.9183 (tttt) cc_final: 0.8921 (ttpt) REVERT: H 31 ASP cc_start: 0.8006 (t70) cc_final: 0.7747 (t70) REVERT: H 34 ILE cc_start: 0.8991 (tp) cc_final: 0.8722 (tp) REVERT: H 35 HIS cc_start: 0.8624 (m-70) cc_final: 0.8308 (m170) REVERT: H 68 THR cc_start: 0.8840 (t) cc_final: 0.8588 (p) REVERT: H 81 GLU cc_start: 0.9191 (mp0) cc_final: 0.8939 (mp0) REVERT: H 100 ASP cc_start: 0.8841 (t0) cc_final: 0.8531 (t0) REVERT: I 18 ARG cc_start: 0.8564 (ttp80) cc_final: 0.8362 (mpp-170) REVERT: I 33 MET cc_start: 0.7805 (tpp) cc_final: 0.7599 (tpp) REVERT: I 36 PHE cc_start: 0.9266 (m-80) cc_final: 0.8198 (m-80) REVERT: J 71 TYR cc_start: 0.8566 (t80) cc_final: 0.8126 (t80) REVERT: J 148 MET cc_start: 0.8116 (mmm) cc_final: 0.7815 (tpp) REVERT: J 278 MET cc_start: 0.8088 (mtp) cc_final: 0.7809 (tpp) REVERT: J 389 LEU cc_start: 0.8136 (mt) cc_final: 0.7646 (pp) REVERT: J 726 ASP cc_start: 0.8084 (t0) cc_final: 0.7222 (p0) REVERT: K 452 MET cc_start: 0.5294 (mmm) cc_final: 0.4740 (ttt) REVERT: K 637 ASN cc_start: 0.8918 (t0) cc_final: 0.8637 (t0) REVERT: L 148 MET cc_start: 0.8514 (tpt) cc_final: 0.8068 (tpp) REVERT: L 149 LEU cc_start: 0.8963 (mt) cc_final: 0.8601 (mt) REVERT: L 277 ASN cc_start: 0.9034 (m-40) cc_final: 0.8390 (m110) REVERT: L 648 TYR cc_start: 0.7726 (t80) cc_final: 0.7457 (t80) REVERT: L 729 LEU cc_start: 0.9494 (mt) cc_final: 0.9257 (mt) outliers start: 0 outliers final: 0 residues processed: 364 average time/residue: 0.4189 time to fit residues: 255.9213 Evaluate side-chains 287 residues out of total 3642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 287 time to evaluate : 4.058 ------------------------------------------------------------------------------- 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: 1.9990 chunk 231 optimal weight: 8.9990 chunk 296 optimal weight: 20.0000 chunk 229 optimal weight: 0.0870 chunk 342 optimal weight: 0.0020 chunk 226 optimal weight: 6.9990 chunk 404 optimal weight: 1.9990 chunk 253 optimal weight: 10.0000 chunk 246 optimal weight: 20.0000 chunk 186 optimal weight: 20.0000 overall best weight: 2.2172 ------------------------------------------------------------------------------- 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** ** B 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 792 GLN D1104 ASN ** G 800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.5564 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= 0.181 Angle : 0.591 9.681 45746 Z= 0.318 Chirality : 0.043 0.224 5075 Planarity : 0.004 0.063 5942 Dihedral : 5.135 37.612 4616 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.94 % Favored : 94.87 % Rotamer: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % 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: 0.08 (0.13), residues: 4214 helix: 1.17 (0.20), residues: 707 sheet: -0.05 (0.15), residues: 1069 loop : -0.15 (0.13), residues: 2438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP H 36 HIS 0.005 0.001 HIS L 348 PHE 0.035 0.002 PHE A 977 TYR 0.024 0.001 TYR A 905 ARG 0.007 0.000 ARG D1057 *********************** 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 390 residues out of total 3642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 390 time to evaluate : 3.642 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: A 804 VAL cc_start: 0.9436 (t) cc_final: 0.9173 (m) REVERT: A 805 ASP cc_start: 0.9113 (t0) cc_final: 0.8047 (m-30) REVERT: A 875 GLU cc_start: 0.8325 (pm20) cc_final: 0.7842 (pm20) REVERT: A 892 ASP cc_start: 0.8730 (t0) cc_final: 0.8309 (t0) REVERT: A 896 ASP cc_start: 0.8890 (m-30) cc_final: 0.8548 (m-30) REVERT: A 1036 LEU cc_start: 0.9223 (mp) cc_final: 0.8331 (tp) REVERT: A 1059 ASP cc_start: 0.8470 (t70) cc_final: 0.8162 (t70) REVERT: B 60 ASN cc_start: 0.8313 (t0) cc_final: 0.7808 (t0) REVERT: B 72 ASP cc_start: 0.8574 (t0) cc_final: 0.8314 (t0) REVERT: B 81 GLU cc_start: 0.8482 (tt0) cc_final: 0.7971 (tp30) REVERT: B 82 ARG cc_start: 0.7726 (mtt180) cc_final: 0.7237 (mpp80) REVERT: B 100 ASP cc_start: 0.8243 (m-30) cc_final: 0.8034 (m-30) REVERT: C 2 ILE cc_start: 0.8324 (mm) cc_final: 0.7942 (tt) REVERT: C 27 GLU cc_start: 0.8099 (tt0) cc_final: 0.7784 (mp0) REVERT: C 32 PHE cc_start: 0.7130 (m-10) cc_final: 0.6758 (m-10) REVERT: C 86 TYR cc_start: 0.7456 (m-80) cc_final: 0.7071 (m-10) REVERT: C 87 PHE cc_start: 0.8102 (m-10) cc_final: 0.7581 (m-10) REVERT: C 92 LYS cc_start: 0.9053 (tmtt) cc_final: 0.8734 (tttt) REVERT: D 757 MET cc_start: 0.8387 (mmm) cc_final: 0.8147 (mmm) REVERT: D 978 TYR cc_start: 0.8596 (t80) cc_final: 0.8355 (t80) REVERT: D 999 ASN cc_start: 0.8751 (m-40) cc_final: 0.7979 (t0) REVERT: D 1001 PHE cc_start: 0.9153 (t80) cc_final: 0.8669 (t80) REVERT: D 1169 ASN cc_start: 0.8617 (t0) cc_final: 0.8375 (t0) REVERT: E 20 ILE cc_start: 0.8549 (pt) cc_final: 0.8250 (pt) REVERT: E 41 HIS cc_start: 0.7313 (m-70) cc_final: 0.7048 (m-70) REVERT: E 46 GLU cc_start: 0.9072 (mm-30) cc_final: 0.8825 (tp30) REVERT: E 53 TYR cc_start: 0.8460 (t80) cc_final: 0.8110 (t80) REVERT: E 72 ASP cc_start: 0.5115 (t0) cc_final: 0.4780 (t0) REVERT: E 80 MET cc_start: 0.8744 (ttm) cc_final: 0.8439 (tmm) REVERT: E 107 THR cc_start: 0.5889 (t) cc_final: 0.5630 (m) REVERT: F 27 GLU cc_start: 0.8483 (tt0) cc_final: 0.7990 (tm-30) REVERT: F 32 PHE cc_start: 0.8188 (m-80) cc_final: 0.7863 (m-80) REVERT: F 36 PHE cc_start: 0.9071 (m-80) cc_final: 0.8816 (m-80) REVERT: F 80 GLU cc_start: 0.7015 (pm20) cc_final: 0.6517 (tm-30) REVERT: F 82 ASP cc_start: 0.6698 (m-30) cc_final: 0.6348 (p0) REVERT: F 97 THR cc_start: 0.9418 (t) cc_final: 0.9093 (p) REVERT: G 816 LYS cc_start: 0.7657 (tptt) cc_final: 0.7360 (tptm) REVERT: G 906 MET cc_start: 0.5413 (mmp) cc_final: 0.5096 (mmm) REVERT: G 1039 GLU cc_start: 0.8991 (mm-30) cc_final: 0.8720 (mm-30) REVERT: G 1182 ASP cc_start: 0.8336 (t0) cc_final: 0.8029 (t0) REVERT: H 23 LYS cc_start: 0.9174 (tttt) cc_final: 0.8884 (ttpt) REVERT: H 31 ASP cc_start: 0.8072 (t70) cc_final: 0.7795 (t70) REVERT: H 34 ILE cc_start: 0.8810 (tp) cc_final: 0.8463 (tp) REVERT: H 35 HIS cc_start: 0.8668 (m-70) cc_final: 0.8161 (m-70) REVERT: H 66 ARG cc_start: 0.8409 (mtp85) cc_final: 0.8111 (mtp85) REVERT: H 95 LYS cc_start: 0.7771 (ptmm) cc_final: 0.7495 (ptmt) REVERT: I 18 ARG cc_start: 0.8535 (ttp80) cc_final: 0.7894 (ttp80) REVERT: I 36 PHE cc_start: 0.9264 (m-80) cc_final: 0.8198 (m-80) REVERT: J 71 TYR cc_start: 0.8565 (t80) cc_final: 0.8074 (t80) REVERT: J 148 MET cc_start: 0.8137 (mmm) cc_final: 0.7680 (tpp) REVERT: J 326 ASP cc_start: 0.8865 (t0) cc_final: 0.8276 (p0) REVERT: J 389 LEU cc_start: 0.8091 (mt) cc_final: 0.7616 (pp) REVERT: J 617 PHE cc_start: 0.8256 (m-80) cc_final: 0.7767 (m-10) REVERT: J 726 ASP cc_start: 0.7965 (t0) cc_final: 0.7375 (p0) REVERT: K 56 ILE cc_start: 0.9652 (mm) cc_final: 0.9446 (mm) REVERT: K 172 LEU cc_start: 0.8998 (pt) cc_final: 0.8538 (tp) REVERT: K 452 MET cc_start: 0.5178 (mmm) cc_final: 0.4636 (ttt) REVERT: K 469 TYR cc_start: 0.5754 (t80) cc_final: 0.5553 (t80) REVERT: K 637 ASN cc_start: 0.8894 (t0) cc_final: 0.8675 (t0) REVERT: L 148 MET cc_start: 0.8576 (tpt) cc_final: 0.8155 (tpp) REVERT: L 149 LEU cc_start: 0.9009 (mt) cc_final: 0.8670 (mt) REVERT: L 277 ASN cc_start: 0.9070 (m-40) cc_final: 0.8400 (m110) outliers start: 0 outliers final: 0 residues processed: 390 average time/residue: 0.4192 time to fit residues: 275.0499 Evaluate side-chains 298 residues out of total 3642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 298 time to evaluate : 3.878 ------------------------------------------------------------------------------- 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: 10.0000 chunk 161 optimal weight: 10.0000 chunk 241 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 chunk 79 optimal weight: 5.9990 chunk 78 optimal weight: 6.9990 chunk 257 optimal weight: 2.9990 chunk 275 optimal weight: 10.0000 chunk 200 optimal weight: 7.9990 chunk 37 optimal weight: 10.0000 chunk 318 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 27DASN D 792 GLN ** D1104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1212 GLN G 800 GLN ** G 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.5801 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= 0.232 Angle : 0.617 9.487 45746 Z= 0.332 Chirality : 0.043 0.218 5075 Planarity : 0.005 0.106 5942 Dihedral : 5.156 35.913 4616 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 14.61 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.79 % Favored : 94.04 % Rotamer: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % 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: -0.04 (0.13), residues: 4214 helix: 1.06 (0.20), residues: 712 sheet: -0.10 (0.15), residues: 1070 loop : -0.24 (0.13), residues: 2432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP H 36 HIS 0.006 0.001 HIS L 348 PHE 0.028 0.002 PHE E 29 TYR 0.023 0.002 TYR G 905 ARG 0.005 0.000 ARG L 691 *********************** 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 370 residues out of total 3642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 370 time to evaluate : 3.632 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: A 804 VAL cc_start: 0.9445 (t) cc_final: 0.9196 (m) REVERT: A 805 ASP cc_start: 0.9092 (t0) cc_final: 0.8023 (m-30) REVERT: A 875 GLU cc_start: 0.8427 (pm20) cc_final: 0.7934 (pm20) REVERT: A 892 ASP cc_start: 0.8699 (t0) cc_final: 0.8283 (t0) REVERT: A 896 ASP cc_start: 0.8912 (m-30) cc_final: 0.8557 (m-30) REVERT: A 1059 ASP cc_start: 0.8528 (t70) cc_final: 0.8220 (t70) REVERT: A 1174 LYS cc_start: 0.9496 (tppp) cc_final: 0.9249 (tppt) REVERT: B 60 ASN cc_start: 0.8236 (t0) cc_final: 0.7784 (t0) REVERT: B 72 ASP cc_start: 0.8552 (t0) cc_final: 0.8278 (t0) REVERT: B 81 GLU cc_start: 0.8508 (tt0) cc_final: 0.7995 (tp30) REVERT: B 82 ARG cc_start: 0.7742 (mtt180) cc_final: 0.7256 (mpp80) REVERT: C 27 GLU cc_start: 0.8229 (tt0) cc_final: 0.7860 (mp0) REVERT: C 32 PHE cc_start: 0.7249 (m-10) cc_final: 0.6871 (m-10) REVERT: C 86 TYR cc_start: 0.7453 (m-80) cc_final: 0.7092 (m-10) REVERT: C 87 PHE cc_start: 0.8129 (m-10) cc_final: 0.7614 (m-10) REVERT: C 92 LYS cc_start: 0.9014 (tmtt) cc_final: 0.8703 (tttt) REVERT: D 757 MET cc_start: 0.8423 (mmm) cc_final: 0.8141 (mmm) REVERT: D 978 TYR cc_start: 0.8551 (t80) cc_final: 0.8343 (t80) REVERT: D 999 ASN cc_start: 0.8748 (m-40) cc_final: 0.7980 (t0) REVERT: D 1001 PHE cc_start: 0.9221 (t80) cc_final: 0.8706 (t80) REVERT: D 1169 ASN cc_start: 0.8730 (t0) cc_final: 0.8512 (t0) REVERT: E 41 HIS cc_start: 0.7346 (m-70) cc_final: 0.7066 (m-70) REVERT: E 53 TYR cc_start: 0.8538 (t80) cc_final: 0.8219 (t80) REVERT: E 69 MET cc_start: 0.6669 (mmt) cc_final: 0.6117 (mmt) REVERT: E 72 ASP cc_start: 0.5132 (t0) cc_final: 0.4802 (t0) REVERT: E 107 THR cc_start: 0.5898 (t) cc_final: 0.5630 (m) REVERT: F 27 GLU cc_start: 0.8491 (tt0) cc_final: 0.8054 (tm-30) REVERT: F 32 PHE cc_start: 0.8169 (m-80) cc_final: 0.7841 (m-80) REVERT: F 80 GLU cc_start: 0.6831 (pm20) cc_final: 0.6591 (tm-30) REVERT: G 816 LYS cc_start: 0.7744 (tptt) cc_final: 0.7399 (tptm) REVERT: G 906 MET cc_start: 0.5574 (mmp) cc_final: 0.5253 (mmm) REVERT: G 1039 GLU cc_start: 0.9009 (mm-30) cc_final: 0.8751 (mm-30) REVERT: H 23 LYS cc_start: 0.9171 (tttt) cc_final: 0.8873 (ttpt) REVERT: H 31 ASP cc_start: 0.8188 (t70) cc_final: 0.7881 (t70) REVERT: H 34 ILE cc_start: 0.8753 (tp) cc_final: 0.8507 (tp) REVERT: H 35 HIS cc_start: 0.8759 (m-70) cc_final: 0.8434 (m170) REVERT: H 66 ARG cc_start: 0.8351 (mtp85) cc_final: 0.8084 (mtp85) REVERT: H 95 LYS cc_start: 0.7852 (ptmm) cc_final: 0.7406 (ptmt) REVERT: I 18 ARG cc_start: 0.8558 (ttp80) cc_final: 0.8328 (mpp-170) REVERT: I 36 PHE cc_start: 0.9235 (m-80) cc_final: 0.8153 (m-80) REVERT: J 71 TYR cc_start: 0.8565 (t80) cc_final: 0.8105 (t80) REVERT: J 148 MET cc_start: 0.8211 (mmm) cc_final: 0.7859 (tpp) REVERT: J 326 ASP cc_start: 0.8890 (t0) cc_final: 0.8333 (p0) REVERT: J 389 LEU cc_start: 0.8087 (mt) cc_final: 0.7603 (pp) REVERT: J 617 PHE cc_start: 0.8310 (m-80) cc_final: 0.7803 (m-10) REVERT: J 726 ASP cc_start: 0.8105 (t0) cc_final: 0.7334 (p0) REVERT: K 172 LEU cc_start: 0.9013 (pt) cc_final: 0.8554 (tp) REVERT: K 278 MET cc_start: 0.8795 (mmp) cc_final: 0.7641 (mmp) REVERT: K 313 PHE cc_start: 0.7497 (t80) cc_final: 0.7281 (t80) REVERT: K 452 MET cc_start: 0.5265 (mmm) cc_final: 0.4712 (ttt) REVERT: K 469 TYR cc_start: 0.5799 (t80) cc_final: 0.5588 (t80) REVERT: K 629 ARG cc_start: 0.7594 (mmp80) cc_final: 0.6843 (mtp-110) REVERT: K 637 ASN cc_start: 0.8920 (t0) cc_final: 0.8686 (t0) REVERT: K 696 MET cc_start: 0.5958 (mmp) cc_final: 0.5595 (mmm) REVERT: L 148 MET cc_start: 0.8558 (tpt) cc_final: 0.8080 (tpp) REVERT: L 149 LEU cc_start: 0.8971 (mt) cc_final: 0.8616 (mt) REVERT: L 277 ASN cc_start: 0.9067 (m-40) cc_final: 0.8398 (m110) outliers start: 0 outliers final: 0 residues processed: 370 average time/residue: 0.4074 time to fit residues: 253.6228 Evaluate side-chains 279 residues out of total 3642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 279 time to evaluate : 3.633 ------------------------------------------------------------------------------- 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: 6.9990 chunk 353 optimal weight: 10.0000 chunk 377 optimal weight: 9.9990 chunk 227 optimal weight: 10.0000 chunk 164 optimal weight: 9.9990 chunk 296 optimal weight: 20.0000 chunk 115 optimal weight: 8.9990 chunk 340 optimal weight: 5.9990 chunk 356 optimal weight: 20.0000 chunk 375 optimal weight: 8.9990 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 842 GLN ** A1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1212 GLN ** B 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 800 GLN ** G 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 89 GLN J 98 GLN ** J 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 167 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.6334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 33645 Z= 0.391 Angle : 0.753 10.581 45746 Z= 0.407 Chirality : 0.046 0.204 5075 Planarity : 0.006 0.104 5942 Dihedral : 5.830 36.593 4616 Min Nonbonded Distance : 1.762 Molprobity Statistics. All-atom Clashscore : 20.47 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.17 % Favored : 92.67 % Rotamer: Outliers : 0.03 % Allowed : 0.66 % Favored : 99.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.40 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.13), residues: 4214 helix: 0.52 (0.19), residues: 705 sheet: -0.39 (0.15), residues: 1083 loop : -0.61 (0.13), residues: 2426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP D1184 HIS 0.010 0.002 HIS J 681 PHE 0.045 0.003 PHE G 895 TYR 0.032 0.003 TYR G 905 ARG 0.010 0.001 ARG L 691 *********************** 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 331 residues out of total 3642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 330 time to evaluate : 3.757 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: A 804 VAL cc_start: 0.9399 (t) cc_final: 0.9168 (m) REVERT: A 805 ASP cc_start: 0.9038 (t0) cc_final: 0.7900 (m-30) REVERT: A 875 GLU cc_start: 0.8640 (pm20) cc_final: 0.8169 (pm20) REVERT: A 892 ASP cc_start: 0.8861 (t0) cc_final: 0.8584 (t0) REVERT: A 896 ASP cc_start: 0.8868 (m-30) cc_final: 0.8439 (m-30) REVERT: B 60 ASN cc_start: 0.8194 (t0) cc_final: 0.7902 (t0) REVERT: B 72 ASP cc_start: 0.8447 (t0) cc_final: 0.8202 (t0) REVERT: B 81 GLU cc_start: 0.8517 (tt0) cc_final: 0.8016 (tp30) REVERT: B 82 ARG cc_start: 0.7716 (mtt180) cc_final: 0.7204 (mpp80) REVERT: C 27 GLU cc_start: 0.8118 (tt0) cc_final: 0.7762 (mp0) REVERT: C 32 PHE cc_start: 0.7287 (m-10) cc_final: 0.7054 (m-10) REVERT: C 86 TYR cc_start: 0.7280 (m-80) cc_final: 0.6940 (m-10) REVERT: C 87 PHE cc_start: 0.8122 (m-10) cc_final: 0.7596 (m-10) REVERT: C 92 LYS cc_start: 0.8982 (tmtt) cc_final: 0.8577 (ttpp) REVERT: D 757 MET cc_start: 0.8443 (mmm) cc_final: 0.8093 (mmm) REVERT: D 943 MET cc_start: 0.9124 (mmm) cc_final: 0.8793 (mmp) REVERT: D 978 TYR cc_start: 0.8449 (t80) cc_final: 0.8229 (t80) REVERT: D 999 ASN cc_start: 0.8740 (m-40) cc_final: 0.7865 (t0) REVERT: D 1001 PHE cc_start: 0.9225 (t80) cc_final: 0.8834 (t80) REVERT: D 1116 PHE cc_start: 0.7818 (m-80) cc_final: 0.7610 (m-80) REVERT: D 1132 ASN cc_start: 0.9177 (m-40) cc_final: 0.8884 (p0) REVERT: E 41 HIS cc_start: 0.7400 (m-70) cc_final: 0.7114 (m-70) REVERT: E 72 ASP cc_start: 0.5018 (t0) cc_final: 0.4688 (t0) REVERT: E 80 MET cc_start: 0.8584 (mtp) cc_final: 0.8239 (tmm) REVERT: E 107 THR cc_start: 0.5967 (t) cc_final: 0.5659 (m) REVERT: F 32 PHE cc_start: 0.8439 (m-80) cc_final: 0.8001 (m-80) REVERT: F 80 GLU cc_start: 0.6914 (pm20) cc_final: 0.6632 (tm-30) REVERT: G 816 LYS cc_start: 0.7772 (tptt) cc_final: 0.7496 (tptm) REVERT: G 906 MET cc_start: 0.6206 (mmp) cc_final: 0.5949 (mmt) REVERT: G 1039 GLU cc_start: 0.9088 (mm-30) cc_final: 0.8841 (mm-30) REVERT: H 23 LYS cc_start: 0.9208 (tttt) cc_final: 0.8920 (ttpt) REVERT: H 34 ILE cc_start: 0.8740 (tp) cc_final: 0.8466 (tp) REVERT: H 35 HIS cc_start: 0.8672 (m-70) cc_final: 0.8392 (m170) REVERT: I 18 ARG cc_start: 0.8603 (ttp80) cc_final: 0.8295 (ttp80) REVERT: I 36 PHE cc_start: 0.9256 (m-80) cc_final: 0.8163 (m-80) REVERT: J 71 TYR cc_start: 0.8740 (t80) cc_final: 0.8285 (t80) REVERT: J 148 MET cc_start: 0.8187 (mmm) cc_final: 0.7896 (tpp) REVERT: J 171 LEU cc_start: 0.9261 (pp) cc_final: 0.9007 (pp) REVERT: J 476 PRO cc_start: 0.6302 (Cg_endo) cc_final: 0.6088 (Cg_exo) REVERT: J 726 ASP cc_start: 0.8321 (t0) cc_final: 0.7404 (p0) REVERT: K 278 MET cc_start: 0.8966 (mmp) cc_final: 0.7956 (mmp) REVERT: K 452 MET cc_start: 0.5164 (mmm) cc_final: 0.4651 (ttt) REVERT: K 637 ASN cc_start: 0.9016 (t0) cc_final: 0.8742 (t0) REVERT: K 696 MET cc_start: 0.6453 (mmp) cc_final: 0.6089 (mmm) REVERT: L 148 MET cc_start: 0.8449 (tpt) cc_final: 0.8038 (tpp) REVERT: L 149 LEU cc_start: 0.9022 (mt) cc_final: 0.8678 (mt) REVERT: L 161 MET cc_start: 0.8517 (mpp) cc_final: 0.8240 (mpp) REVERT: L 648 TYR cc_start: 0.7687 (t80) cc_final: 0.7261 (t80) REVERT: L 696 MET cc_start: 0.6530 (pmm) cc_final: 0.6265 (pmm) outliers start: 1 outliers final: 0 residues processed: 331 average time/residue: 0.4165 time to fit residues: 231.7579 Evaluate side-chains 267 residues out of total 3642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 267 time to evaluate : 3.974 ------------------------------------------------------------------------------- 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: 20.0000 chunk 398 optimal weight: 0.8980 chunk 243 optimal weight: 5.9990 chunk 189 optimal weight: 7.9990 chunk 277 optimal weight: 4.9990 chunk 418 optimal weight: 2.9990 chunk 385 optimal weight: 10.0000 chunk 333 optimal weight: 9.9990 chunk 34 optimal weight: 8.9990 chunk 257 optimal weight: 8.9990 chunk 204 optimal weight: 4.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 842 GLN ** A1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1104 ASN ** B 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 89 GLN J 258 GLN ** K 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.6408 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= 0.230 Angle : 0.637 10.198 45746 Z= 0.342 Chirality : 0.044 0.227 5075 Planarity : 0.005 0.096 5942 Dihedral : 5.480 35.777 4616 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 15.81 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.17 % Favored : 93.66 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.40 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.47 (0.13), residues: 4214 helix: 0.86 (0.20), residues: 711 sheet: -0.38 (0.15), residues: 1057 loop : -0.58 (0.13), residues: 2446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP H 36 HIS 0.005 0.001 HIS L 348 PHE 0.037 0.002 PHE G 895 TYR 0.026 0.002 TYR A 905 ARG 0.005 0.000 ARG E 66 ********************** 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 347 residues out of total 3642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 347 time to evaluate : 4.690 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: A 804 VAL cc_start: 0.9385 (t) cc_final: 0.9125 (m) REVERT: A 805 ASP cc_start: 0.9027 (t0) cc_final: 0.7872 (m-30) REVERT: A 875 GLU cc_start: 0.8509 (pm20) cc_final: 0.7952 (pm20) REVERT: A 892 ASP cc_start: 0.8812 (t0) cc_final: 0.8530 (t0) REVERT: A 896 ASP cc_start: 0.8908 (m-30) cc_final: 0.8524 (m-30) REVERT: B 60 ASN cc_start: 0.8294 (t0) cc_final: 0.8013 (t0) REVERT: B 72 ASP cc_start: 0.8521 (t0) cc_final: 0.8274 (t0) REVERT: B 81 GLU cc_start: 0.8490 (tt0) cc_final: 0.7962 (tp30) REVERT: B 82 ARG cc_start: 0.7673 (mtt180) cc_final: 0.7092 (mtm-85) REVERT: C 27 GLU cc_start: 0.8036 (tt0) cc_final: 0.7740 (mp0) REVERT: C 32 PHE cc_start: 0.7018 (m-10) cc_final: 0.6785 (m-10) REVERT: C 86 TYR cc_start: 0.7412 (m-80) cc_final: 0.7065 (m-10) REVERT: C 87 PHE cc_start: 0.8115 (m-10) cc_final: 0.7580 (m-10) REVERT: C 92 LYS cc_start: 0.8964 (tmtt) cc_final: 0.8671 (tttt) REVERT: D 757 MET cc_start: 0.8424 (mmm) cc_final: 0.8172 (mmm) REVERT: D 978 TYR cc_start: 0.8447 (t80) cc_final: 0.8191 (t80) REVERT: D 999 ASN cc_start: 0.8676 (m-40) cc_final: 0.8021 (t0) REVERT: D 1001 PHE cc_start: 0.9168 (t80) cc_final: 0.8728 (t80) REVERT: D 1116 PHE cc_start: 0.8081 (m-80) cc_final: 0.7808 (m-80) REVERT: D 1132 ASN cc_start: 0.9172 (m-40) cc_final: 0.8867 (p0) REVERT: E 41 HIS cc_start: 0.7489 (m-70) cc_final: 0.7237 (m170) REVERT: E 53 TYR cc_start: 0.8791 (t80) cc_final: 0.8523 (t80) REVERT: E 72 ASP cc_start: 0.5134 (t0) cc_final: 0.4793 (t0) REVERT: E 80 MET cc_start: 0.8636 (mtp) cc_final: 0.8288 (tmm) REVERT: E 100 MET cc_start: 0.5392 (pmm) cc_final: 0.4864 (pmm) REVERT: E 107 THR cc_start: 0.5830 (t) cc_final: 0.5529 (m) REVERT: F 27 GLU cc_start: 0.8503 (tt0) cc_final: 0.8034 (tm-30) REVERT: F 32 PHE cc_start: 0.8337 (m-80) cc_final: 0.7989 (m-80) REVERT: F 80 GLU cc_start: 0.6991 (pm20) cc_final: 0.6724 (tm-30) REVERT: F 97 THR cc_start: 0.9465 (t) cc_final: 0.9253 (p) REVERT: G 816 LYS cc_start: 0.7886 (tptt) cc_final: 0.7667 (tttt) REVERT: G 906 MET cc_start: 0.6123 (mmp) cc_final: 0.5327 (mmt) REVERT: G 1039 GLU cc_start: 0.9008 (mm-30) cc_final: 0.8778 (mm-30) REVERT: H 23 LYS cc_start: 0.9205 (tttt) cc_final: 0.8893 (ttpt) REVERT: H 31 ASP cc_start: 0.8276 (t70) cc_final: 0.8019 (t70) REVERT: H 34 ILE cc_start: 0.8743 (tp) cc_final: 0.8504 (tp) REVERT: H 35 HIS cc_start: 0.8724 (m-70) cc_final: 0.8391 (m170) REVERT: H 68 THR cc_start: 0.8061 (p) cc_final: 0.7735 (p) REVERT: H 81 GLU cc_start: 0.9281 (mp0) cc_final: 0.9064 (mp0) REVERT: H 95 LYS cc_start: 0.7827 (ptmm) cc_final: 0.7494 (ptmt) REVERT: I 18 ARG cc_start: 0.8598 (ttp80) cc_final: 0.8271 (ttp80) REVERT: I 33 MET cc_start: 0.7139 (tpp) cc_final: 0.6887 (tpp) REVERT: I 36 PHE cc_start: 0.9244 (m-80) cc_final: 0.8154 (m-80) REVERT: J 71 TYR cc_start: 0.8680 (t80) cc_final: 0.8187 (t80) REVERT: J 148 MET cc_start: 0.8199 (mmm) cc_final: 0.7809 (tpp) REVERT: J 326 ASP cc_start: 0.8900 (t0) cc_final: 0.8297 (p0) REVERT: J 476 PRO cc_start: 0.6388 (Cg_endo) cc_final: 0.6179 (Cg_exo) REVERT: J 617 PHE cc_start: 0.8411 (m-80) cc_final: 0.7932 (m-10) REVERT: J 726 ASP cc_start: 0.8216 (t0) cc_final: 0.7279 (p0) REVERT: K 172 LEU cc_start: 0.9022 (pt) cc_final: 0.8603 (tp) REVERT: K 278 MET cc_start: 0.8984 (mmp) cc_final: 0.7887 (mmp) REVERT: K 452 MET cc_start: 0.5231 (mmm) cc_final: 0.4729 (ttt) REVERT: K 469 TYR cc_start: 0.5654 (t80) cc_final: 0.5441 (t80) REVERT: K 637 ASN cc_start: 0.8913 (t0) cc_final: 0.8710 (t0) REVERT: L 148 MET cc_start: 0.8529 (tpt) cc_final: 0.8128 (tpp) REVERT: L 149 LEU cc_start: 0.8986 (mt) cc_final: 0.8612 (mt) REVERT: L 161 MET cc_start: 0.8390 (mpp) cc_final: 0.8148 (mpp) REVERT: L 240 MET cc_start: 0.8351 (ttt) cc_final: 0.7976 (tpt) REVERT: L 277 ASN cc_start: 0.9157 (m-40) cc_final: 0.8623 (m110) REVERT: L 351 TYR cc_start: 0.9041 (m-10) cc_final: 0.8759 (m-10) REVERT: L 648 TYR cc_start: 0.7452 (t80) cc_final: 0.7175 (t80) REVERT: L 696 MET cc_start: 0.6322 (pmm) cc_final: 0.6121 (pmm) outliers start: 0 outliers final: 0 residues processed: 347 average time/residue: 0.4181 time to fit residues: 243.2774 Evaluate side-chains 280 residues out of total 3642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 280 time to evaluate : 3.669 ------------------------------------------------------------------------------- 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: 6.9990 chunk 354 optimal weight: 10.0000 chunk 102 optimal weight: 0.0980 chunk 307 optimal weight: 9.9990 chunk 49 optimal weight: 20.0000 chunk 92 optimal weight: 8.9990 chunk 333 optimal weight: 0.1980 chunk 139 optimal weight: 9.9990 chunk 342 optimal weight: 4.9990 chunk 42 optimal weight: 10.0000 chunk 61 optimal weight: 6.9990 overall best weight: 3.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 915 GLN ** A1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1063 GLN K 521 ASN ** K 708 GLN ** 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 = 0.3684 r_free = 0.3684 target = 0.083069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.064099 restraints weight = 192776.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.065446 restraints weight = 128471.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.066630 restraints weight = 89109.139| |-----------------------------------------------------------------------------| r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.6535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 33645 Z= 0.230 Angle : 0.627 10.546 45746 Z= 0.337 Chirality : 0.043 0.212 5075 Planarity : 0.005 0.090 5942 Dihedral : 5.320 34.307 4616 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 15.40 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.57 % Favored : 93.26 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.40 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.94 (0.20), residues: 711 sheet: -0.30 (0.15), residues: 1079 loop : -0.55 (0.13), residues: 2424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP H 36 HIS 0.005 0.001 HIS K 670 PHE 0.034 0.002 PHE G 895 TYR 0.025 0.002 TYR A 905 ARG 0.006 0.000 ARG H 66 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6972.97 seconds wall clock time: 128 minutes 25.47 seconds (7705.47 seconds total)