Starting phenix.real_space_refine on Sun Aug 11 04:16:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w9l_8787/08_2024/5w9l_8787.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w9l_8787/08_2024/5w9l_8787.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w9l_8787/08_2024/5w9l_8787.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w9l_8787/08_2024/5w9l_8787.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w9l_8787/08_2024/5w9l_8787.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w9l_8787/08_2024/5w9l_8787.cif" } resolution = 4.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 171 5.16 5 C 19747 2.51 5 N 5164 2.21 5 O 6036 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 PHE 778": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 786": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 788": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 793": "OE1" <-> "OE2" Residue "A PHE 814": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 824": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 850": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 869": "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 1001": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1012": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1019": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1044": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1171": "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 827": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 850": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 869": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 895": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 928": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 947": "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 1019": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1044": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1204": "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 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 GLU 27": "OE1" <-> "OE2" Residue "F PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 71": "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 GLU 793": "OE1" <-> "OE2" Residue "G TYR 809": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 814": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 824": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 850": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 869": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 895": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 928": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 932": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 947": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 977": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 1001": "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 1171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 1211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 46": "OE1" <-> "OE2" Residue "H PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 97": "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 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 79": "OE1" <-> "OE2" Residue "I TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 467": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 499": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 540": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 590": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 609": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 630": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 635": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 649": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 689": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 704": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 467": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 499": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 523": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 540": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 571": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 609": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 617": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 630": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 635": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 642": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 649": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 183": "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 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 332": "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 TYR 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 404": "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 PHE 446": "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 TYR 523": "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 GLU 549": "OE1" <-> "OE2" Residue "J PHE 571": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 577": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 590": "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 648": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 689": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 704": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 1.34s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 31118 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 3488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3488 Classifications: {'peptide': 456} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 430} Chain breaks: 2 Chain: "D" Number of atoms: 3545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3545 Classifications: {'peptide': 463} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 22, '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: 3545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3545 Classifications: {'peptide': 463} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 437} 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: "B" Number of atoms: 5658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 726, 5658 Classifications: {'peptide': 726} Link IDs: {'CIS': 3, 'PTRANS': 36, 'TRANS': 686} Chain: "C" Number of atoms: 5658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 726, 5658 Classifications: {'peptide': 726} Link IDs: {'CIS': 5, 'PTRANS': 36, 'TRANS': 684} Chain: "J" Number of atoms: 5658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 726, 5658 Classifications: {'peptide': 726} Link IDs: {'CIS': 5, 'PTRANS': 36, 'TRANS': 684} Time building chain proxies: 18.08, per 1000 atoms: 0.58 Number of scatterers: 31118 At special positions: 0 Unit cell: (155.04, 154.02, 222.36, 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 171 16.00 O 6036 8.00 N 5164 7.00 C 19747 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=55, symmetry=0 Simple disulfide: pdb=" SG CYS A 806 " - pdb=" SG CYS A 828 " distance=2.02 Simple disulfide: pdb=" SG CYS A 811 " - pdb=" SG CYS A 817 " distance=2.03 Simple disulfide: pdb=" SG CYS A 912 " - pdb=" SG CYS A 925 " distance=2.03 Simple disulfide: pdb=" SG CYS A1106 " - pdb=" SG CYS A1117 " distance=2.03 Simple disulfide: pdb=" SG CYS A1156 " - pdb=" SG CYS A1164 " distance=2.07 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=2.03 Simple disulfide: pdb=" SG CYS D 912 " - pdb=" SG CYS D 925 " distance=2.09 Simple disulfide: pdb=" SG CYS D1106 " - pdb=" SG CYS D1117 " distance=2.04 Simple disulfide: pdb=" SG CYS D1156 " - pdb=" SG CYS D1164 " distance=2.01 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 92 " distance=2.02 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.02 Simple disulfide: pdb=" SG CYS G 806 " - pdb=" SG CYS G 828 " distance=2.02 Simple disulfide: pdb=" SG CYS G 811 " - pdb=" SG CYS G 817 " distance=2.02 Simple disulfide: pdb=" SG CYS G 912 " - pdb=" SG CYS G 925 " distance=2.10 Simple disulfide: pdb=" SG CYS G1106 " - pdb=" SG CYS G1117 " distance=2.03 Simple disulfide: pdb=" SG CYS G1156 " - pdb=" SG CYS G1164 " distance=2.28 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=2.03 Simple disulfide: pdb=" SG CYS B 30 " - pdb=" SG CYS B 195 " distance=2.04 Simple disulfide: pdb=" SG CYS B 176 " - pdb=" SG CYS B 214 " distance=2.06 Simple disulfide: pdb=" SG CYS B 185 " - pdb=" SG CYS B 237 " distance=2.04 Simple disulfide: pdb=" SG CYS B 339 " - pdb=" SG CYS B 349 " distance=2.04 Simple disulfide: pdb=" SG CYS B 383 " - pdb=" SG CYS B 407 " distance=2.34 Simple disulfide: pdb=" SG CYS B 425 " - pdb=" SG CYS B 478 " distance=2.02 Simple disulfide: pdb=" SG CYS B 437 " - pdb=" SG CYS B 585 " distance=2.19 Simple disulfide: pdb=" SG CYS B 503 " - pdb=" SG CYS B 526 " distance=2.02 Simple disulfide: pdb=" SG CYS B 603 " - pdb=" SG CYS B 654 " distance=2.13 Simple disulfide: pdb=" SG CYS B 620 " - pdb=" SG CYS B 650 " distance=2.01 Simple disulfide: pdb=" SG CYS B 679 " - pdb=" SG CYS B 713 " distance=2.04 Simple disulfide: pdb=" SG CYS B 727 " - pdb=" SG CYS B 736 " distance=2.10 Simple disulfide: pdb=" SG CYS C 30 " - pdb=" SG CYS C 195 " distance=2.06 Simple disulfide: pdb=" SG CYS C 176 " - pdb=" SG CYS C 214 " distance=2.06 Simple disulfide: pdb=" SG CYS C 185 " - pdb=" SG CYS C 237 " distance=2.05 Simple disulfide: pdb=" SG CYS C 339 " - pdb=" SG CYS C 349 " distance=2.05 Simple disulfide: pdb=" SG CYS C 383 " - pdb=" SG CYS C 407 " distance=2.20 Simple disulfide: pdb=" SG CYS C 425 " - pdb=" SG CYS C 478 " distance=2.15 Simple disulfide: pdb=" SG CYS C 437 " - pdb=" SG CYS C 585 " distance=2.14 Simple disulfide: pdb=" SG CYS C 503 " - pdb=" SG CYS C 526 " distance=2.02 Simple disulfide: pdb=" SG CYS C 603 " - pdb=" SG CYS C 654 " distance=2.12 Simple disulfide: pdb=" SG CYS C 620 " - pdb=" SG CYS C 650 " distance=2.04 Simple disulfide: pdb=" SG CYS C 679 " - pdb=" SG CYS C 713 " distance=2.04 Simple disulfide: pdb=" SG CYS C 727 " - pdb=" SG CYS C 736 " distance=2.02 Simple disulfide: pdb=" SG CYS J 30 " - pdb=" SG CYS J 195 " distance=2.13 Simple disulfide: pdb=" SG CYS J 176 " - pdb=" SG CYS J 214 " distance=2.08 Simple disulfide: pdb=" SG CYS J 185 " - pdb=" SG CYS J 237 " distance=2.03 Simple disulfide: pdb=" SG CYS J 339 " - pdb=" SG CYS J 349 " distance=2.05 Simple disulfide: pdb=" SG CYS J 383 " - pdb=" SG CYS J 407 " distance=1.94 Simple disulfide: pdb=" SG CYS J 425 " - pdb=" SG CYS J 478 " distance=2.02 Simple disulfide: pdb=" SG CYS J 437 " - pdb=" SG CYS J 585 " distance=2.06 Simple disulfide: pdb=" SG CYS J 503 " - pdb=" SG CYS J 526 " distance=2.03 Simple disulfide: pdb=" SG CYS J 603 " - pdb=" SG CYS J 654 " distance=2.20 Simple disulfide: pdb=" SG CYS J 620 " - pdb=" SG CYS J 650 " distance=2.03 Simple disulfide: pdb=" SG CYS J 679 " - pdb=" SG CYS J 713 " distance=2.05 Simple disulfide: pdb=" SG CYS J 727 " - pdb=" SG CYS J 736 " distance=1.99 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: 11.37 Conformation dependent library (CDL) restraints added in 5.3 seconds 7984 Ramachandran restraints generated. 3992 Oldfield, 0 Emsley, 3992 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7468 Finding SS restraints... Secondary structure from input PDB file: 98 helices and 72 sheets defined 23.6% alpha, 27.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.53 Creating SS restraints... Processing helix chain 'A' and resid 814 through 823 removed outlier: 3.917A pdb=" N GLU A 823 " --> pdb=" O GLN A 819 " (cutoff:3.500A) Processing helix chain 'A' and resid 824 through 854 removed outlier: 3.992A pdb=" N CYS A 828 " --> pdb=" O TYR A 824 " (cutoff:3.500A) removed outlier: 3.560A 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: 3.557A pdb=" N ALA A 926 " --> pdb=" O ASP A 922 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N TYR A 928 " --> pdb=" O ILE A 924 " (cutoff:3.500A) removed outlier: 3.956A 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 1007 through 1012 removed outlier: 3.626A pdb=" N PHE A1012 " --> pdb=" O MET A1008 " (cutoff:3.500A) Processing helix chain 'A' and resid 1016 through 1040 removed outlier: 3.567A 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: 4.747A pdb=" N ALA A1065 " --> pdb=" O PRO A1061 " (cutoff:3.500A) Processing helix chain 'A' and resid 1198 through 1200 No H-bonds generated for 'chain 'A' and resid 1198 through 1200' Processing helix chain 'D' and resid 814 through 821 Processing helix chain 'D' and resid 824 through 854 removed outlier: 3.599A pdb=" N CYS D 828 " --> pdb=" O TYR D 824 " (cutoff:3.500A) removed outlier: 3.644A 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: 4.972A pdb=" N TYR D 928 " --> pdb=" O ILE D 924 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N VAL D 929 " --> pdb=" O CYS D 925 " (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 1008 removed outlier: 3.797A pdb=" N MET D1008 " --> pdb=" O ALA D1004 " (cutoff:3.500A) Processing helix chain 'D' and resid 1016 through 1039 Processing helix chain 'D' and resid 1040 through 1042 No H-bonds generated for 'chain 'D' and resid 1040 through 1042' Processing helix chain 'D' and resid 1050 through 1058 Processing helix chain 'D' and resid 1059 through 1104 removed outlier: 3.647A 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 31 Processing helix chain 'E' and resid 60 through 65 removed outlier: 4.021A pdb=" N GLY E 65 " --> pdb=" O GLN E 61 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 87 Processing helix chain 'F' and resid 79 through 83 Processing helix chain 'G' and resid 814 through 821 Processing helix chain 'G' and resid 824 through 854 removed outlier: 4.001A pdb=" N CYS G 828 " --> pdb=" O TYR G 824 " (cutoff:3.500A) removed outlier: 3.811A 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 908 through 912 Processing helix chain 'G' and resid 922 through 931 removed outlier: 5.006A pdb=" N TYR G 928 " --> pdb=" O ILE G 924 " (cutoff:3.500A) removed outlier: 4.142A 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: 3.563A 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: 4.917A pdb=" N ALA G1065 " --> pdb=" O PRO G1061 " (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 32 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 'B' and resid 37 through 41 removed outlier: 3.591A pdb=" N ASP B 41 " --> pdb=" O THR B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 53 Processing helix chain 'B' and resid 104 through 108 Processing helix chain 'B' and resid 133 through 137 Processing helix chain 'B' and resid 222 through 230 Processing helix chain 'B' and resid 303 through 307 removed outlier: 3.780A pdb=" N ARG B 307 " --> pdb=" O GLN B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 351 Processing helix chain 'B' and resid 385 through 390 removed outlier: 3.501A pdb=" N LEU B 388 " --> pdb=" O PHE B 385 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER B 390 " --> pdb=" O PRO B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 399 removed outlier: 3.657A pdb=" N PHE B 399 " --> pdb=" O VAL B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 415 Processing helix chain 'B' and resid 416 through 418 No H-bonds generated for 'chain 'B' and resid 416 through 418' Processing helix chain 'B' and resid 429 through 436 removed outlier: 3.898A pdb=" N ALA B 434 " --> pdb=" O PRO B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 456 removed outlier: 4.840A pdb=" N SER B 454 " --> pdb=" O SER B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 468 Processing helix chain 'B' and resid 524 through 529 Processing helix chain 'B' and resid 546 through 550 Processing helix chain 'B' and resid 676 through 678 No H-bonds generated for 'chain 'B' and resid 676 through 678' Processing helix chain 'B' and resid 694 through 702 removed outlier: 5.349A pdb=" N ARG B 700 " --> pdb=" O MET B 696 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 41 removed outlier: 4.076A pdb=" N ASP C 41 " --> pdb=" O THR C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 53 Processing helix chain 'C' and resid 104 through 108 Processing helix chain 'C' and resid 133 through 137 Processing helix chain 'C' and resid 222 through 230 Processing helix chain 'C' and resid 342 through 351 Processing helix chain 'C' and resid 385 through 390 removed outlier: 3.530A pdb=" N LEU C 388 " --> pdb=" O PHE C 385 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N SER C 390 " --> pdb=" O PRO C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 410 through 416 removed outlier: 3.611A pdb=" N LEU C 414 " --> pdb=" O ASN C 410 " (cutoff:3.500A) Processing helix chain 'C' and resid 431 through 436 Processing helix chain 'C' and resid 449 through 456 removed outlier: 4.898A pdb=" N SER C 454 " --> pdb=" O SER C 451 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 468 Processing helix chain 'C' and resid 524 through 529 Processing helix chain 'C' and resid 676 through 678 No H-bonds generated for 'chain 'C' and resid 676 through 678' Processing helix chain 'C' and resid 694 through 702 removed outlier: 4.914A pdb=" N ARG C 700 " --> pdb=" O MET C 696 " (cutoff:3.500A) Processing helix chain 'J' and resid 37 through 41 removed outlier: 3.624A 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 removed outlier: 4.008A pdb=" N ARG J 307 " --> pdb=" O GLN J 304 " (cutoff:3.500A) Processing helix chain 'J' and resid 342 through 351 Processing helix chain 'J' and resid 385 through 389 removed outlier: 3.504A pdb=" N LEU J 388 " --> pdb=" O PHE J 385 " (cutoff:3.500A) Processing helix chain 'J' and resid 410 through 416 removed outlier: 4.008A pdb=" N LEU J 414 " --> pdb=" O ASN J 410 " (cutoff:3.500A) Processing helix chain 'J' and resid 429 through 436 Processing helix chain 'J' and resid 449 through 456 removed outlier: 4.518A 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 676 through 678 No H-bonds generated for 'chain 'J' and resid 676 through 678' Processing helix chain 'J' and resid 694 through 702 removed outlier: 4.936A pdb=" N ARG J 700 " --> pdb=" O MET J 696 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 719 through 724 removed outlier: 7.259A pdb=" N LEU A 759 " --> pdb=" O SER B 720 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N LEU B 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: 5.684A 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 796 removed outlier: 6.931A pdb=" N TYR A 777 " --> pdb=" O ALA A1152 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ALA A1152 " --> pdb=" O TYR A 777 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N LYS A 779 " --> pdb=" O VAL A1150 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N VAL A1150 " --> pdb=" O LYS A 779 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N SER A 781 " --> pdb=" O GLU A1148 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N GLU A1148 " --> pdb=" O SER A 781 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N HIS A1146 " --> pdb=" O PRO A 783 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 802 through 804 Processing sheet with id=AA5, first strand: chain 'A' and resid 857 through 858 Processing sheet with id=AA6, first strand: chain 'A' and resid 1202 through 1204 removed outlier: 7.277A pdb=" N GLY A1154 " --> pdb=" O GLN A1212 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N ILE A1214 " --> pdb=" O GLY A1154 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N CYS A1156 " --> pdb=" O ILE A1214 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1171 through 1173 Processing sheet with id=AA8, first strand: chain 'C' and resid 719 through 724 removed outlier: 6.991A pdb=" N LEU D 759 " --> pdb=" O SER C 720 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N LEU C 722 " --> pdb=" O LEU D 759 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 768 through 769 removed outlier: 5.644A pdb=" N ILE D 768 " --> pdb=" O SER G 858 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'D' and resid 777 through 796 removed outlier: 6.922A pdb=" N TYR D 777 " --> pdb=" O ALA D1152 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ALA D1152 " --> pdb=" O TYR D 777 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N LYS D 779 " --> pdb=" O VAL D1150 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N VAL D1150 " --> pdb=" O LYS D 779 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N SER D 781 " --> pdb=" O GLU D1148 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N GLU D1148 " --> pdb=" O SER D 781 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N HIS D1146 " --> pdb=" O PRO D 783 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 777 through 796 removed outlier: 6.922A pdb=" N TYR D 777 " --> pdb=" O ALA D1152 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ALA D1152 " --> pdb=" O TYR D 777 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N LYS D 779 " --> pdb=" O VAL D1150 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N VAL D1150 " --> pdb=" O LYS D 779 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N SER D 781 " --> pdb=" O GLU D1148 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N GLU D1148 " --> pdb=" O SER D 781 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N HIS D1146 " --> pdb=" O PRO D 783 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N VAL D1150 " --> pdb=" O LYS D1174 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N PHE D1172 " --> pdb=" O ALA D1152 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 802 through 804 Processing sheet with id=AB4, first strand: chain 'D' and resid 1202 through 1205 removed outlier: 4.158A pdb=" N CYS D1164 " --> pdb=" O VAL D1205 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N CYS D1156 " --> pdb=" O ILE D1214 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 3 through 6 removed outlier: 3.897A pdb=" N ALA E 78 " --> pdb=" O CYS E 22 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 57 through 59 removed outlier: 6.289A pdb=" N SER E 44 " --> pdb=" O SER E 40 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N TRP E 36 " --> pdb=" O ILE E 48 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N VAL E 50 " --> pdb=" O ILE E 34 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ILE E 34 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N ALA E 33 " --> pdb=" O LYS E 95 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N CYS E 92 " --> pdb=" O TRP E 103 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N TRP E 103 " --> pdb=" O CYS E 92 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N ARG E 94 " --> pdb=" O ASP E 101 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N TYR E 98 " --> pdb=" O VAL E 100B" (cutoff:3.500A) removed outlier: 7.426A pdb=" N VAL E 100B" --> pdb=" O TYR E 98 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 57 through 59 removed outlier: 6.289A pdb=" N SER E 44 " --> pdb=" O SER E 40 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N TRP E 36 " --> pdb=" O ILE E 48 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N VAL E 50 " --> pdb=" O ILE E 34 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ILE E 34 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N ALA E 33 " --> pdb=" O LYS E 95 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.574A pdb=" N MET F 33 " --> pdb=" O SER F 49 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N SER F 49 " --> pdb=" O MET F 33 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 19 through 24 Processing sheet with id=AC1, first strand: chain 'J' and resid 719 through 724 removed outlier: 7.145A pdb=" N LEU G 759 " --> pdb=" O SER J 720 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N LEU J 722 " --> pdb=" O LEU G 759 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 777 through 796 removed outlier: 6.923A pdb=" N TYR G 777 " --> pdb=" O ALA G1152 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ALA G1152 " --> pdb=" O TYR G 777 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N LYS G 779 " --> pdb=" O VAL G1150 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N VAL G1150 " --> pdb=" O LYS G 779 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N SER G 781 " --> pdb=" O GLU G1148 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N GLU G1148 " --> pdb=" O SER G 781 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N HIS G1146 " --> pdb=" O PRO G 783 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 777 through 796 removed outlier: 6.923A pdb=" N TYR G 777 " --> pdb=" O ALA G1152 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ALA G1152 " --> pdb=" O TYR G 777 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N LYS G 779 " --> pdb=" O VAL G1150 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N VAL G1150 " --> pdb=" O LYS G 779 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N SER G 781 " --> pdb=" O GLU G1148 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N GLU G1148 " --> pdb=" O SER G 781 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N HIS G1146 " --> pdb=" O PRO G 783 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N VAL G1150 " --> pdb=" O LYS G1174 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N PHE G1172 " --> pdb=" O ALA G1152 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 802 through 804 Processing sheet with id=AC5, first strand: chain 'G' and resid 1155 through 1157 removed outlier: 3.839A pdb=" N ILE G1214 " --> pdb=" O CYS G1156 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 1164 through 1167 removed outlier: 3.899A pdb=" N CYS G1164 " --> pdb=" O VAL G1205 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.620A pdb=" N ALA H 78 " --> pdb=" O CYS H 22 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.345A pdb=" N SER H 44 " --> pdb=" O SER H 40 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N VAL H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ILE H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 96 through 99 removed outlier: 4.498A pdb=" N TYR H 98 " --> pdb=" O VAL H 100B" (cutoff:3.500A) removed outlier: 7.544A pdb=" N VAL H 100B" --> pdb=" O TYR H 98 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 10 through 13 removed outlier: 6.186A pdb=" N LEU I 11 " --> pdb=" O GLU I 105 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N MET I 33 " --> pdb=" O SER I 49 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N SER I 49 " --> pdb=" O MET I 33 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 17 through 24 removed outlier: 5.663A pdb=" N GLN I 17 " --> pdb=" O PRO I 77 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 33 through 35 removed outlier: 6.118A pdb=" N ASP B 34 " --> pdb=" O VAL B 102 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'B' and resid 63 through 64 removed outlier: 6.347A pdb=" N THR B 63 " --> pdb=" O TYR J 632 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N VAL J 639 " --> pdb=" O LEU J 651 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 69 through 75 removed outlier: 3.691A pdb=" N ARG B 335 " --> pdb=" O ASP B 326 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 83 through 85 removed outlier: 6.408A pdb=" N SER B 267 " --> pdb=" O GLN B 280 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N GLN B 280 " --> pdb=" O SER B 267 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 88 through 89 removed outlier: 7.713A pdb=" N SER B 88 " --> pdb=" O ILE B 300 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 92 through 93 Processing sheet with id=AD9, first strand: chain 'B' and resid 110 through 111 removed outlier: 4.532A pdb=" N ALA B 146 " --> pdb=" O ILE B 296 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N ILE B 186 " --> pdb=" O CYS B 237 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N CYS B 237 " --> pdb=" O ILE B 186 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N GLU B 188 " --> pdb=" O ARG B 235 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N ARG B 235 " --> pdb=" O GLU B 188 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 126 through 127 removed outlier: 4.481A pdb=" N SER B 126 " --> pdb=" O ILE B 140 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA B 309 " --> pdb=" O THR B 139 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 153 through 154 Processing sheet with id=AE3, first strand: chain 'B' and resid 359 through 366 removed outlier: 4.442A pdb=" N VAL B 659 " --> pdb=" O VAL B 363 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N SER B 365 " --> pdb=" O VAL B 657 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N VAL B 657 " --> pdb=" O SER B 365 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N GLY B 675 " --> pdb=" O PRO B 658 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N CYS B 713 " --> pdb=" O PHE B 674 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 374 through 376 Processing sheet with id=AE5, first strand: chain 'B' and resid 400 through 404 removed outlier: 6.790A pdb=" N THR B 483 " --> pdb=" O VAL B 420 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N VAL B 420 " --> pdb=" O THR B 483 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 513 through 515 removed outlier: 5.402A pdb=" N SER B 498 " --> pdb=" O VAL B 561 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N VAL B 561 " --> pdb=" O SER B 498 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N ILE B 500 " --> pdb=" O SER B 559 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N SER B 559 " --> pdb=" O ILE B 500 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B' and resid 617 through 619 removed outlier: 5.120A pdb=" N VAL B 639 " --> pdb=" O LEU B 651 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 33 through 35 Processing sheet with id=AE9, first strand: chain 'C' and resid 69 through 72 removed outlier: 3.702A pdb=" N ARG C 335 " --> pdb=" O ASP C 326 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 75 through 76 Processing sheet with id=AF2, first strand: chain 'C' and resid 75 through 76 removed outlier: 6.599A pdb=" N SER C 267 " --> pdb=" O GLN C 280 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N GLN C 280 " --> pdb=" O SER C 267 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 88 through 89 removed outlier: 7.482A pdb=" N SER C 88 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N THR C 206 " --> pdb=" O SER C 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF3 Processing sheet with id=AF4, first strand: chain 'C' and resid 92 through 93 Processing sheet with id=AF5, first strand: chain 'C' and resid 110 through 111 removed outlier: 4.526A pdb=" N ALA C 146 " --> pdb=" O ILE C 296 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LEU C 180 " --> pdb=" O THR C 242 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N THR C 242 " --> pdb=" O LEU C 180 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ALA C 182 " --> pdb=" O MET C 240 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N MET C 240 " --> pdb=" O ALA C 182 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N TYR C 184 " --> pdb=" O THR C 238 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ILE C 186 " --> pdb=" O ASN C 236 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N ASN C 236 " --> pdb=" O ILE C 186 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N GLU C 188 " --> pdb=" O LEU C 234 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N LEU C 234 " --> pdb=" O GLU C 188 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 126 through 127 removed outlier: 4.328A pdb=" N SER C 126 " --> pdb=" O ILE C 140 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA C 309 " --> pdb=" O THR C 139 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 153 through 154 Processing sheet with id=AF8, first strand: chain 'C' and resid 359 through 366 removed outlier: 4.230A pdb=" N VAL C 659 " --> pdb=" O VAL C 363 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N SER C 365 " --> pdb=" O VAL C 657 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N VAL C 657 " --> pdb=" O SER C 365 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N GLY C 675 " --> pdb=" O PRO C 658 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N CYS C 713 " --> pdb=" O PHE C 674 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 374 through 375 Processing sheet with id=AG1, first strand: chain 'C' and resid 381 through 382 removed outlier: 6.314A pdb=" N VAL C 381 " --> pdb=" O ASN C 408 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N CYS C 407 " --> pdb=" O CYS C 585 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG1 Processing sheet with id=AG2, first strand: chain 'C' and resid 400 through 404 removed outlier: 3.563A pdb=" N LYS C 400 " --> pdb=" O TYR C 445 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N THR C 483 " --> pdb=" O VAL C 420 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N VAL C 420 " --> pdb=" O THR C 483 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'C' and resid 513 through 515 removed outlier: 5.451A pdb=" N SER C 498 " --> pdb=" O VAL C 561 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N VAL C 561 " --> pdb=" O SER C 498 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N ILE C 500 " --> pdb=" O SER C 559 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N SER C 559 " --> pdb=" O ILE C 500 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'C' and resid 617 through 619 removed outlier: 5.519A pdb=" N VAL C 639 " --> pdb=" O LEU C 651 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N VAL C 631 " --> pdb=" O VAL C 639 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'J' and resid 33 through 35 Processing sheet with id=AG6, first strand: chain 'J' and resid 68 through 72 removed outlier: 3.633A pdb=" N ARG J 335 " --> pdb=" O ASP J 326 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'J' and resid 75 through 76 Processing sheet with id=AG8, first strand: chain 'J' and resid 75 through 76 removed outlier: 6.373A pdb=" N SER J 267 " --> pdb=" O GLN J 280 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N GLN J 280 " --> pdb=" O SER J 267 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'J' and resid 88 through 89 removed outlier: 7.462A pdb=" N SER J 88 " --> pdb=" O ILE J 300 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'J' and resid 92 through 93 Processing sheet with id=AH2, first strand: chain 'J' and resid 110 through 111 removed outlier: 4.554A pdb=" N ALA J 146 " --> pdb=" O ILE J 296 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N ILE J 186 " --> pdb=" O CYS J 237 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N CYS J 237 " --> pdb=" O ILE J 186 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N GLU J 188 " --> pdb=" O ARG J 235 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N ARG J 235 " --> pdb=" O GLU J 188 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'J' and resid 126 through 127 removed outlier: 4.355A pdb=" N SER J 126 " --> pdb=" O ILE J 140 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA J 309 " --> pdb=" O THR J 139 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'J' and resid 153 through 154 Processing sheet with id=AH5, first strand: chain 'J' and resid 359 through 366 removed outlier: 4.414A pdb=" N VAL J 659 " --> pdb=" O VAL J 363 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N SER J 365 " --> pdb=" O VAL J 657 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N VAL J 657 " --> pdb=" O SER J 365 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N GLY J 675 " --> pdb=" O PRO J 658 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N CYS J 713 " --> pdb=" O PHE J 674 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'J' and resid 371 through 375 removed outlier: 6.328A pdb=" N GLY J 372 " --> pdb=" O GLU J 605 " (cutoff:3.500A) removed outlier: 8.423A pdb=" N SER J 607 " --> pdb=" O GLY J 372 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N VAL J 374 " --> pdb=" O SER J 607 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'J' and resid 381 through 382 removed outlier: 6.476A pdb=" N VAL J 381 " --> pdb=" O ASN J 408 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N CYS J 407 " --> pdb=" O CYS J 585 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH7 Processing sheet with id=AH8, first strand: chain 'J' and resid 400 through 404 removed outlier: 3.537A pdb=" N LYS J 400 " --> pdb=" O TYR J 445 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N THR J 483 " --> pdb=" O VAL J 420 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N VAL J 420 " --> pdb=" O THR J 483 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'J' and resid 513 through 515 removed outlier: 5.437A pdb=" N SER J 498 " --> pdb=" O VAL J 561 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N VAL J 561 " --> pdb=" O SER J 498 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N ILE J 500 " --> pdb=" O SER J 559 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N SER J 559 " --> pdb=" O ILE J 500 " (cutoff:3.500A) 1208 hydrogen bonds defined for protein. 3141 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: 13.60 Time building geometry restraints manager: 12.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.34: 9457 1.34 - 1.48: 8966 1.48 - 1.61: 13197 1.61 - 1.75: 2 1.75 - 1.89: 231 Bond restraints: 31853 Sorted by residual: bond pdb=" N CYS J 585 " pdb=" CA CYS J 585 " ideal model delta sigma weight residual 1.456 1.372 0.084 8.70e-03 1.32e+04 9.25e+01 bond pdb=" CA VAL J 584 " pdb=" C VAL J 584 " ideal model delta sigma weight residual 1.524 1.424 0.099 1.23e-02 6.61e+03 6.52e+01 bond pdb=" CA CYS B 437 " pdb=" C CYS B 437 " ideal model delta sigma weight residual 1.523 1.619 -0.096 1.30e-02 5.92e+03 5.50e+01 bond pdb=" C CYS J 437 " pdb=" O CYS J 437 " ideal model delta sigma weight residual 1.235 1.314 -0.079 1.18e-02 7.18e+03 4.50e+01 bond pdb=" C CYS C 437 " pdb=" N TYR C 438 " ideal model delta sigma weight residual 1.331 1.400 -0.069 1.22e-02 6.72e+03 3.21e+01 ... (remaining 31848 not shown) Histogram of bond angle deviations from ideal: 95.26 - 103.20: 174 103.20 - 111.14: 12360 111.14 - 119.08: 13322 119.08 - 127.02: 17191 127.02 - 134.96: 278 Bond angle restraints: 43325 Sorted by residual: angle pdb=" C LEU D 935 " pdb=" N PRO D 936 " pdb=" CA PRO D 936 " ideal model delta sigma weight residual 119.66 127.46 -7.80 7.20e-01 1.93e+00 1.17e+02 angle pdb=" C GLN F 42 " pdb=" N PRO F 43 " pdb=" CA PRO F 43 " ideal model delta sigma weight residual 119.66 127.19 -7.53 7.20e-01 1.93e+00 1.09e+02 angle pdb=" C LEU A 935 " pdb=" N PRO A 936 " pdb=" CA PRO A 936 " ideal model delta sigma weight residual 119.66 127.14 -7.48 7.20e-01 1.93e+00 1.08e+02 angle pdb=" C GLY E 8 " pdb=" N PRO E 9 " pdb=" CA PRO E 9 " ideal model delta sigma weight residual 119.85 129.96 -10.11 1.01e+00 9.80e-01 1.00e+02 angle pdb=" O CYS J 437 " pdb=" C CYS J 437 " pdb=" N TYR J 438 " ideal model delta sigma weight residual 123.19 111.63 11.56 1.17e+00 7.31e-01 9.76e+01 ... (remaining 43320 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 18319 17.77 - 35.54: 440 35.54 - 53.32: 163 53.32 - 71.09: 67 71.09 - 88.86: 32 Dihedral angle restraints: 19021 sinusoidal: 7315 harmonic: 11706 Sorted by residual: dihedral pdb=" CB CYS B 727 " pdb=" SG CYS B 727 " pdb=" SG CYS B 736 " pdb=" CB CYS B 736 " ideal model delta sinusoidal sigma weight residual 93.00 175.48 -82.48 1 1.00e+01 1.00e-02 8.34e+01 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 93.00 172.84 -79.84 1 1.00e+01 1.00e-02 7.91e+01 dihedral pdb=" CB CYS D1106 " pdb=" SG CYS D1106 " pdb=" SG CYS D1117 " pdb=" CB CYS D1117 " ideal model delta sinusoidal sigma weight residual 93.00 165.53 -72.53 1 1.00e+01 1.00e-02 6.72e+01 ... (remaining 19018 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 3021 0.069 - 0.137: 1438 0.137 - 0.206: 304 0.206 - 0.275: 42 0.275 - 0.344: 10 Chirality restraints: 4815 Sorted by residual: chirality pdb=" CA ASN J 436 " pdb=" N ASN J 436 " pdb=" C ASN J 436 " pdb=" CB ASN J 436 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.95e+00 chirality pdb=" CA GLN J 688 " pdb=" N GLN J 688 " pdb=" C GLN J 688 " pdb=" CB GLN J 688 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.83e+00 chirality pdb=" CA THR C 63 " pdb=" N THR C 63 " pdb=" C THR C 63 " pdb=" CB THR C 63 " both_signs ideal model delta sigma weight residual False 2.53 2.19 0.33 2.00e-01 2.50e+01 2.78e+00 ... (remaining 4812 not shown) Planarity restraints: 5632 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU D1218 " 0.106 5.00e-02 4.00e+02 1.62e-01 4.20e+01 pdb=" N PRO D1219 " -0.280 5.00e-02 4.00e+02 pdb=" CA PRO D1219 " 0.091 5.00e-02 4.00e+02 pdb=" CD PRO D1219 " 0.083 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A1218 " 0.086 5.00e-02 4.00e+02 1.31e-01 2.74e+01 pdb=" N PRO A1219 " -0.226 5.00e-02 4.00e+02 pdb=" CA PRO A1219 " 0.073 5.00e-02 4.00e+02 pdb=" CD PRO A1219 " 0.067 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS I 76 " 0.083 5.00e-02 4.00e+02 1.24e-01 2.46e+01 pdb=" N PRO I 77 " -0.214 5.00e-02 4.00e+02 pdb=" CA PRO I 77 " 0.069 5.00e-02 4.00e+02 pdb=" CD PRO I 77 " 0.062 5.00e-02 4.00e+02 ... (remaining 5629 not shown) Histogram of nonbonded interaction distances: 1.52 - 2.20: 16 2.20 - 2.87: 12333 2.87 - 3.55: 43137 3.55 - 4.22: 77376 4.22 - 4.90: 125013 Nonbonded interactions: 257875 Sorted by model distance: nonbonded pdb=" OH TYR A 905 " pdb=" CA PRO A 936 " model vdw 1.520 3.470 nonbonded pdb=" CG2 VAL B 381 " pdb=" ND2 ASN B 408 " model vdw 1.572 3.540 nonbonded pdb=" CE2 PHE C 506 " pdb=" CG2 VAL C 555 " model vdw 1.574 3.760 nonbonded pdb=" O ASP B 384 " pdb=" CZ PHE B 404 " model vdw 1.808 3.340 nonbonded pdb=" CB VAL B 381 " pdb=" ND2 ASN B 408 " model vdw 1.930 3.550 ... (remaining 257870 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'D' and (resid 753 through 1175 or resid 1183 through 1223)) selection = (chain 'G' and (resid 753 through 1175 or resid 1183 through 1223)) } ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'J' } ncs_group { reference = chain 'E' selection = chain 'H' } ncs_group { reference = chain 'F' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.300 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: 1.060 Check model and map are aligned: 0.200 Set scattering table: 0.270 Process input model: 83.660 Find NCS groups from input model: 0.910 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 90.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 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 : 0.014 0.099 31853 Z= 0.880 Angle : 1.710 13.183 43325 Z= 1.181 Chirality : 0.078 0.344 4815 Planarity : 0.011 0.162 5632 Dihedral : 10.524 88.862 11388 Min Nonbonded Distance : 1.520 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.85 % Allowed : 4.48 % Favored : 94.66 % Rotamer: Outliers : 0.06 % Allowed : 0.46 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.59 % Cis-general : 0.50 % 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: 0.78 (0.13), residues: 3992 helix: -0.20 (0.18), residues: 703 sheet: 0.25 (0.16), residues: 898 loop : 1.08 (0.13), residues: 2391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.009 TRP H 47 HIS 0.015 0.002 HIS C 194 PHE 0.030 0.005 PHE I 32 TYR 0.056 0.007 TYR J 469 ARG 0.007 0.001 ARG G 841 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7984 Ramachandran restraints generated. 3992 Oldfield, 0 Emsley, 3992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7984 Ramachandran restraints generated. 3992 Oldfield, 0 Emsley, 3992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 652 residues out of total 3452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 650 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: 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 853 VAL cc_start: 0.9175 (t) cc_final: 0.8951 (m) REVERT: A 893 LEU cc_start: 0.8522 (mt) cc_final: 0.7874 (tt) REVERT: A 1104 ASN cc_start: 0.9237 (m-40) cc_final: 0.8891 (t0) REVERT: A 1126 PHE cc_start: 0.9233 (m-80) cc_final: 0.8652 (m-80) REVERT: A 1137 MET cc_start: 0.8941 (mtm) cc_final: 0.8530 (mpp) REVERT: D 779 LYS cc_start: 0.8748 (mttt) cc_final: 0.8392 (mmmt) REVERT: D 844 ASP cc_start: 0.8751 (m-30) cc_final: 0.8509 (m-30) REVERT: D 909 TYR cc_start: 0.7866 (t80) cc_final: 0.6964 (t80) REVERT: D 980 LEU cc_start: 0.9537 (mt) cc_final: 0.9278 (mt) REVERT: D 1012 PHE cc_start: 0.7570 (m-80) cc_final: 0.7315 (m-80) REVERT: D 1201 ASN cc_start: 0.8941 (m-40) cc_final: 0.8338 (p0) REVERT: E 12 VAL cc_start: 0.7718 (t) cc_final: 0.7279 (t) REVERT: E 69 MET cc_start: 0.7013 (mtt) cc_final: 0.6503 (mtt) REVERT: F 27 GLU cc_start: 0.9112 (tp30) cc_final: 0.8859 (tp30) REVERT: F 79 GLU cc_start: 0.6572 (mt-10) cc_final: 0.6339 (tm-30) REVERT: F 81 ASP cc_start: 0.7977 (m-30) cc_final: 0.6951 (m-30) REVERT: G 913 MET cc_start: 0.3610 (mtp) cc_final: 0.3181 (ttm) REVERT: G 940 ASP cc_start: 0.8594 (t0) cc_final: 0.8031 (t0) REVERT: G 977 PHE cc_start: 0.9470 (m-80) cc_final: 0.9204 (m-80) REVERT: G 990 LEU cc_start: 0.9609 (mt) cc_final: 0.9169 (tt) REVERT: G 1024 ASP cc_start: 0.8752 (m-30) cc_final: 0.8400 (t0) REVERT: G 1086 LEU cc_start: 0.9474 (mt) cc_final: 0.8748 (mt) REVERT: G 1182 ASP cc_start: 0.8878 (m-30) cc_final: 0.8398 (t70) REVERT: G 1190 SER cc_start: 0.7808 (t) cc_final: 0.7536 (t) REVERT: G 1201 ASN cc_start: 0.9427 (m-40) cc_final: 0.9219 (t0) REVERT: H 2 VAL cc_start: 0.7734 (t) cc_final: 0.7354 (t) REVERT: H 35 HIS cc_start: 0.9226 (m-70) cc_final: 0.8853 (m-70) REVERT: I 11 LEU cc_start: 0.8435 (tp) cc_final: 0.8229 (tp) REVERT: I 27 GLU cc_start: 0.7535 (tt0) cc_final: 0.6864 (tm-30) REVERT: I 27 ASP cc_start: 0.8354 (m-30) cc_final: 0.7562 (t0) REVERT: I 27 ASN cc_start: 0.8464 (t0) cc_final: 0.7879 (t0) REVERT: I 33 MET cc_start: 0.8645 (mmm) cc_final: 0.8367 (mmm) REVERT: I 47 LEU cc_start: 0.9583 (mt) cc_final: 0.9235 (mt) REVERT: B 239 PHE cc_start: 0.8786 (m-80) cc_final: 0.8522 (m-80) REVERT: B 278 MET cc_start: 0.9079 (mtp) cc_final: 0.8108 (mmm) REVERT: B 284 LEU cc_start: 0.9258 (mt) cc_final: 0.8972 (mp) REVERT: B 332 TYR cc_start: 0.9102 (m-80) cc_final: 0.8621 (m-10) REVERT: B 541 TYR cc_start: 0.6261 (m-80) cc_final: 0.5931 (m-80) REVERT: B 587 LYS cc_start: 0.7239 (mmtt) cc_final: 0.6595 (mtpt) REVERT: B 602 ASN cc_start: 0.7684 (m-40) cc_final: 0.6924 (p0) REVERT: B 638 LEU cc_start: 0.8825 (tp) cc_final: 0.8356 (pt) REVERT: B 651 LEU cc_start: 0.8802 (tp) cc_final: 0.8515 (tp) REVERT: B 656 SER cc_start: 0.8319 (m) cc_final: 0.7413 (p) REVERT: B 686 MET cc_start: 0.6586 (mmm) cc_final: 0.6321 (mmm) REVERT: C 216 ASP cc_start: 0.8801 (m-30) cc_final: 0.8543 (m-30) REVERT: C 321 LEU cc_start: 0.8618 (mt) cc_final: 0.8068 (mt) REVERT: C 400 LYS cc_start: 0.7396 (mttt) cc_final: 0.7056 (mttt) REVERT: C 406 ASN cc_start: 0.7795 (m-40) cc_final: 0.7571 (p0) REVERT: C 589 GLU cc_start: 0.7306 (mm-30) cc_final: 0.6966 (pm20) REVERT: C 635 TYR cc_start: 0.9146 (m-80) cc_final: 0.8658 (m-80) REVERT: J 75 PHE cc_start: 0.8397 (m-80) cc_final: 0.8049 (m-80) REVERT: J 161 MET cc_start: 0.7580 (tpp) cc_final: 0.7338 (ttp) REVERT: J 171 LEU cc_start: 0.9100 (tp) cc_final: 0.8649 (pp) REVERT: J 253 TRP cc_start: 0.8076 (m100) cc_final: 0.7830 (m100) REVERT: J 497 TYR cc_start: 0.1188 (m-80) cc_final: -0.1991 (m-80) REVERT: J 642 TYR cc_start: 0.7490 (t80) cc_final: 0.7170 (t80) REVERT: J 648 TYR cc_start: 0.7474 (t80) cc_final: 0.7033 (t80) outliers start: 2 outliers final: 1 residues processed: 651 average time/residue: 0.4277 time to fit residues: 446.6698 Evaluate side-chains 310 residues out of total 3452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 309 time to evaluate : 3.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 397 random chunks: chunk 335 optimal weight: 6.9990 chunk 300 optimal weight: 0.9990 chunk 166 optimal weight: 5.9990 chunk 102 optimal weight: 8.9990 chunk 202 optimal weight: 6.9990 chunk 160 optimal weight: 20.0000 chunk 311 optimal weight: 5.9990 chunk 120 optimal weight: 2.9990 chunk 189 optimal weight: 8.9990 chunk 231 optimal weight: 4.9990 chunk 360 optimal weight: 7.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1016 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 848 ASN D 927 GLN D1056 GLN D1146 HIS ** F 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 808 GLN G1104 ASN H 41 HIS B 521 ASN B 637 ASN ** C 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 167 HIS J 377 GLN J 637 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.2562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.112 31853 Z= 0.277 Angle : 0.739 10.715 43325 Z= 0.414 Chirality : 0.045 0.197 4815 Planarity : 0.007 0.107 5632 Dihedral : 5.567 26.686 4370 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.38 % Allowed : 4.01 % Favored : 95.62 % Rotamer: Outliers : 0.03 % Allowed : 1.22 % Favored : 98.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.59 % Cis-general : 0.50 % 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: 0.46 (0.13), residues: 3992 helix: 0.60 (0.19), residues: 670 sheet: 0.18 (0.16), residues: 929 loop : 0.42 (0.13), residues: 2393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP I 35 HIS 0.008 0.002 HIS B 681 PHE 0.039 0.002 PHE A 850 TYR 0.024 0.002 TYR G 978 ARG 0.004 0.001 ARG B 629 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7984 Ramachandran restraints generated. 3992 Oldfield, 0 Emsley, 3992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7984 Ramachandran restraints generated. 3992 Oldfield, 0 Emsley, 3992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 3452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 417 time to evaluate : 3.456 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: A 780 LEU cc_start: 0.9609 (tt) cc_final: 0.9255 (tt) REVERT: A 827 PHE cc_start: 0.9077 (m-10) cc_final: 0.8701 (m-80) REVERT: A 840 LEU cc_start: 0.9346 (mm) cc_final: 0.9007 (mm) REVERT: A 893 LEU cc_start: 0.8668 (mt) cc_final: 0.8107 (tp) REVERT: A 906 MET cc_start: 0.6862 (mmp) cc_final: 0.6287 (mpp) REVERT: A 933 LYS cc_start: 0.8673 (mttt) cc_final: 0.8202 (mmtt) REVERT: A 1126 PHE cc_start: 0.9311 (m-80) cc_final: 0.8830 (m-80) REVERT: A 1137 MET cc_start: 0.9059 (mtm) cc_final: 0.8723 (mpp) REVERT: D 779 LYS cc_start: 0.8836 (mttt) cc_final: 0.8203 (mmmt) REVERT: D 1180 ILE cc_start: 0.8774 (mp) cc_final: 0.8539 (mt) REVERT: D 1192 TYR cc_start: 0.8707 (t80) cc_final: 0.8461 (t80) REVERT: D 1201 ASN cc_start: 0.9089 (m-40) cc_final: 0.8480 (p0) REVERT: E 69 MET cc_start: 0.6716 (mtt) cc_final: 0.6470 (mtt) REVERT: F 27 GLU cc_start: 0.9106 (tp30) cc_final: 0.8887 (tm-30) REVERT: F 33 MET cc_start: 0.8418 (mmp) cc_final: 0.8124 (mmm) REVERT: F 81 ASP cc_start: 0.7890 (m-30) cc_final: 0.7499 (p0) REVERT: F 104 LEU cc_start: 0.9031 (tp) cc_final: 0.8805 (tp) REVERT: G 913 MET cc_start: 0.4065 (mtp) cc_final: 0.3487 (ttm) REVERT: G 940 ASP cc_start: 0.8775 (t0) cc_final: 0.7857 (t0) REVERT: G 943 MET cc_start: 0.8671 (tpp) cc_final: 0.8272 (mmt) REVERT: G 977 PHE cc_start: 0.9531 (m-80) cc_final: 0.9154 (m-80) REVERT: G 990 LEU cc_start: 0.9592 (mt) cc_final: 0.9285 (tt) REVERT: G 1024 ASP cc_start: 0.8693 (m-30) cc_final: 0.8390 (t0) REVERT: G 1036 LEU cc_start: 0.9318 (mt) cc_final: 0.9087 (mt) REVERT: G 1039 GLU cc_start: 0.8250 (mt-10) cc_final: 0.7990 (mt-10) REVERT: G 1040 LEU cc_start: 0.8821 (mm) cc_final: 0.8240 (tp) REVERT: G 1084 GLN cc_start: 0.9391 (tp40) cc_final: 0.9152 (tm-30) REVERT: G 1201 ASN cc_start: 0.9452 (m-40) cc_final: 0.9152 (m-40) REVERT: H 35 HIS cc_start: 0.9187 (m-70) cc_final: 0.8641 (m-70) REVERT: H 100 MET cc_start: 0.5482 (mmm) cc_final: 0.5105 (mmm) REVERT: I 27 GLU cc_start: 0.7440 (tt0) cc_final: 0.7080 (tm-30) REVERT: I 27 ASP cc_start: 0.8237 (m-30) cc_final: 0.7640 (t70) REVERT: I 33 MET cc_start: 0.8199 (mmm) cc_final: 0.7649 (mmm) REVERT: I 49 SER cc_start: 0.7765 (m) cc_final: 0.7337 (p) REVERT: I 73 LEU cc_start: 0.9074 (tp) cc_final: 0.8791 (tp) REVERT: B 49 ASP cc_start: 0.8744 (t0) cc_final: 0.6973 (t0) REVERT: B 230 GLU cc_start: 0.8940 (mt-10) cc_final: 0.8405 (tp30) REVERT: B 239 PHE cc_start: 0.8772 (m-80) cc_final: 0.8336 (m-80) REVERT: B 278 MET cc_start: 0.8898 (mtp) cc_final: 0.8058 (mmm) REVERT: B 287 TYR cc_start: 0.6455 (p90) cc_final: 0.6058 (p90) REVERT: B 313 PHE cc_start: 0.6015 (t80) cc_final: 0.5788 (t80) REVERT: B 332 TYR cc_start: 0.8921 (m-80) cc_final: 0.8375 (m-80) REVERT: B 343 ASP cc_start: 0.9051 (m-30) cc_final: 0.8710 (p0) REVERT: B 602 ASN cc_start: 0.7733 (m-40) cc_final: 0.6902 (p0) REVERT: C 49 ASP cc_start: 0.8185 (t0) cc_final: 0.7533 (m-30) REVERT: C 400 LYS cc_start: 0.7455 (mttt) cc_final: 0.7079 (mttt) REVERT: C 406 ASN cc_start: 0.8017 (m-40) cc_final: 0.7815 (p0) REVERT: C 589 GLU cc_start: 0.7242 (mm-30) cc_final: 0.6771 (pm20) REVERT: C 635 TYR cc_start: 0.9071 (m-80) cc_final: 0.8616 (m-80) REVERT: C 659 VAL cc_start: 0.9426 (m) cc_final: 0.9170 (p) REVERT: J 75 PHE cc_start: 0.8398 (m-80) cc_final: 0.8117 (m-80) REVERT: J 80 ASP cc_start: 0.8703 (t0) cc_final: 0.8487 (t0) REVERT: J 161 MET cc_start: 0.7546 (tpp) cc_final: 0.7172 (ttp) REVERT: J 240 MET cc_start: 0.8409 (ttt) cc_final: 0.8150 (ttt) REVERT: J 278 MET cc_start: 0.9489 (mmp) cc_final: 0.9181 (mmp) REVERT: J 321 LEU cc_start: 0.8363 (mt) cc_final: 0.7841 (mp) REVERT: J 377 GLN cc_start: 0.9029 (mt0) cc_final: 0.8812 (pm20) REVERT: J 497 TYR cc_start: 0.0368 (m-80) cc_final: -0.0239 (m-80) REVERT: J 689 TYR cc_start: 0.8217 (p90) cc_final: 0.7885 (p90) outliers start: 1 outliers final: 0 residues processed: 418 average time/residue: 0.4001 time to fit residues: 275.3131 Evaluate side-chains 268 residues out of total 3452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 268 time to evaluate : 3.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 61.019 > 50: distance: 62 - 83: 25.700 distance: 67 - 90: 29.803 distance: 74 - 77: 25.822 distance: 77 - 78: 48.237 distance: 78 - 79: 44.644 distance: 78 - 81: 31.546 distance: 79 - 83: 61.019 distance: 81 - 82: 44.533 distance: 83 - 84: 32.484 distance: 84 - 85: 35.680 distance: 84 - 87: 53.635 distance: 85 - 86: 31.454 distance: 85 - 90: 34.006 distance: 87 - 88: 32.580 distance: 87 - 89: 41.970 distance: 90 - 91: 26.419 distance: 91 - 92: 24.314 distance: 91 - 94: 24.781 distance: 92 - 93: 10.289 distance: 92 - 99: 15.075 distance: 94 - 95: 42.774 distance: 95 - 96: 8.796 distance: 96 - 97: 6.873 distance: 99 - 100: 12.689 distance: 100 - 101: 25.074 distance: 100 - 103: 25.523 distance: 101 - 102: 44.254 distance: 101 - 105: 39.768 distance: 103 - 104: 25.308 distance: 105 - 106: 11.313 distance: 106 - 107: 18.624 distance: 106 - 109: 31.697 distance: 107 - 108: 20.301 distance: 107 - 111: 41.896 distance: 109 - 110: 36.276 distance: 111 - 112: 8.512 distance: 112 - 113: 35.206 distance: 112 - 115: 29.851 distance: 113 - 114: 56.086 distance: 113 - 120: 49.325 distance: 115 - 116: 34.225 distance: 116 - 117: 24.948 distance: 117 - 118: 14.540 distance: 117 - 119: 20.032 distance: 120 - 121: 16.454 distance: 121 - 122: 30.354 distance: 121 - 124: 39.849 distance: 122 - 123: 40.013 distance: 122 - 126: 6.648 distance: 124 - 125: 37.818 distance: 126 - 127: 6.788 distance: 127 - 128: 41.263 distance: 127 - 130: 44.076 distance: 128 - 129: 55.474 distance: 128 - 132: 15.529 distance: 130 - 131: 56.955 distance: 132 - 133: 17.984 distance: 132 - 138: 25.528 distance: 133 - 134: 22.492 distance: 133 - 136: 25.860 distance: 134 - 135: 29.131 distance: 134 - 139: 20.320 distance: 136 - 137: 25.738 distance: 137 - 138: 38.478 distance: 139 - 140: 13.713 distance: 140 - 141: 10.251 distance: 140 - 143: 12.145 distance: 141 - 142: 8.702 distance: 141 - 147: 8.155 distance: 143 - 144: 8.819 distance: 143 - 145: 8.770 distance: 144 - 146: 11.844