Starting phenix.real_space_refine on Thu Mar 21 20:59:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w9l_8787/03_2024/5w9l_8787.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w9l_8787/03_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_8787/03_2024/5w9l_8787.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w9l_8787/03_2024/5w9l_8787.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w9l_8787/03_2024/5w9l_8787.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w9l_8787/03_2024/5w9l_8787.pdb" } 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: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 16.14, per 1000 atoms: 0.52 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: 12.32 Conformation dependent library (CDL) restraints added in 5.7 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: 3.96 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: 14.49 Time building geometry restraints manager: 13.35 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 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: 1.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 7.710 Check model and map are aligned: 0.460 Set scattering table: 0.270 Process input model: 85.310 Find NCS groups from input model: 1.990 Set up NCS constraints: 0.190 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 100.130 ------------------------------------------------------------------------------- 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 : 2.996 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: 0.4269 time to fit residues: 443.8100 Evaluate side-chains 310 residues out of total 3452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 309 time to evaluate : 3.580 ------------------------------------------------------------------------------- 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: 8.9990 chunk 166 optimal weight: 5.9990 chunk 102 optimal weight: 5.9990 chunk 202 optimal weight: 7.9990 chunk 160 optimal weight: 20.0000 chunk 311 optimal weight: 5.9990 chunk 120 optimal weight: 0.9980 chunk 189 optimal weight: 8.9990 chunk 231 optimal weight: 1.9990 chunk 360 optimal weight: 8.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 842 GLN ** A1016 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1146 HIS D 848 ASN ** D 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1056 GLN D1146 HIS D1212 GLN ** F 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 800 GLN G 808 GLN G1104 ASN G1132 ASN G1163 ASN H 41 HIS B 521 ASN C 98 GLN ** C 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 98 GLN J 167 HIS J 377 GLN J 637 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.2627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.129 31853 Z= 0.275 Angle : 0.734 10.908 43325 Z= 0.407 Chirality : 0.045 0.189 4815 Planarity : 0.007 0.107 5632 Dihedral : 5.552 27.078 4370 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.38 % Allowed : 4.21 % Favored : 95.42 % Rotamer: Outliers : 0.06 % Allowed : 1.25 % Favored : 98.70 % 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: 0.45 (0.13), residues: 3992 helix: 0.65 (0.19), residues: 670 sheet: 0.19 (0.16), residues: 938 loop : 0.38 (0.13), residues: 2384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP I 35 HIS 0.011 0.002 HIS B 681 PHE 0.040 0.002 PHE A 850 TYR 0.023 0.002 TYR G 932 ARG 0.004 0.001 ARG A 841 *********************** 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 426 residues out of total 3452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 424 time to evaluate : 3.549 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: A 780 LEU cc_start: 0.9567 (tt) cc_final: 0.9181 (tt) REVERT: A 803 THR cc_start: 0.9126 (p) cc_final: 0.8403 (p) REVERT: A 827 PHE cc_start: 0.9050 (m-10) cc_final: 0.8695 (m-80) REVERT: A 840 LEU cc_start: 0.9414 (mm) cc_final: 0.9182 (mm) REVERT: A 848 ASN cc_start: 0.8900 (m-40) cc_final: 0.8459 (t0) REVERT: A 893 LEU cc_start: 0.8672 (mt) cc_final: 0.8099 (tp) REVERT: A 906 MET cc_start: 0.6952 (mmp) cc_final: 0.6447 (mpp) REVERT: A 933 LYS cc_start: 0.8624 (mttt) cc_final: 0.8296 (mttp) REVERT: A 1126 PHE cc_start: 0.9301 (m-80) cc_final: 0.8819 (m-80) REVERT: A 1137 MET cc_start: 0.9064 (mtm) cc_final: 0.8735 (mpp) REVERT: D 779 LYS cc_start: 0.8852 (mttt) cc_final: 0.8259 (mmmt) REVERT: D 1180 ILE cc_start: 0.8809 (mp) cc_final: 0.8562 (mt) REVERT: D 1192 TYR cc_start: 0.8710 (t80) cc_final: 0.8471 (t80) REVERT: D 1201 ASN cc_start: 0.9060 (m-40) cc_final: 0.8450 (p0) REVERT: E 69 MET cc_start: 0.6711 (mtt) cc_final: 0.6470 (mtt) REVERT: F 33 MET cc_start: 0.8374 (mmp) cc_final: 0.8102 (mmm) REVERT: F 81 ASP cc_start: 0.7874 (m-30) cc_final: 0.7479 (p0) REVERT: F 104 LEU cc_start: 0.8988 (tp) cc_final: 0.8774 (tp) REVERT: G 940 ASP cc_start: 0.8771 (t0) cc_final: 0.7891 (t0) REVERT: G 943 MET cc_start: 0.8700 (tpp) cc_final: 0.8282 (mmt) REVERT: G 977 PHE cc_start: 0.9528 (m-80) cc_final: 0.9145 (m-80) REVERT: G 990 LEU cc_start: 0.9574 (mt) cc_final: 0.9280 (tt) REVERT: G 1024 ASP cc_start: 0.8683 (m-30) cc_final: 0.8395 (t0) REVERT: G 1036 LEU cc_start: 0.9301 (mt) cc_final: 0.9080 (mt) REVERT: G 1039 GLU cc_start: 0.8271 (mt-10) cc_final: 0.8010 (mt-10) REVERT: G 1040 LEU cc_start: 0.8932 (mm) cc_final: 0.8271 (tp) REVERT: G 1084 GLN cc_start: 0.9386 (tp40) cc_final: 0.9146 (tm-30) REVERT: G 1182 ASP cc_start: 0.8876 (m-30) cc_final: 0.8659 (t70) REVERT: G 1201 ASN cc_start: 0.9494 (m-40) cc_final: 0.9121 (m-40) REVERT: H 2 VAL cc_start: 0.7487 (t) cc_final: 0.7286 (t) REVERT: H 35 HIS cc_start: 0.9158 (m-70) cc_final: 0.8594 (m-70) REVERT: H 80 MET cc_start: 0.8632 (tmm) cc_final: 0.8325 (tmm) REVERT: H 100 MET cc_start: 0.5469 (mmm) cc_final: 0.5134 (mmm) REVERT: I 27 GLU cc_start: 0.7396 (tt0) cc_final: 0.7078 (tm-30) REVERT: I 27 ASP cc_start: 0.8007 (m-30) cc_final: 0.7535 (t70) REVERT: I 33 MET cc_start: 0.8155 (mmm) cc_final: 0.7565 (mmm) REVERT: B 49 ASP cc_start: 0.8661 (t0) cc_final: 0.7191 (t0) REVERT: B 230 GLU cc_start: 0.8904 (mt-10) cc_final: 0.8414 (tp30) REVERT: B 239 PHE cc_start: 0.8809 (m-80) cc_final: 0.8325 (m-80) REVERT: B 278 MET cc_start: 0.8893 (mtp) cc_final: 0.8009 (mmm) REVERT: B 284 LEU cc_start: 0.9182 (mt) cc_final: 0.8877 (mp) REVERT: B 287 TYR cc_start: 0.6416 (p90) cc_final: 0.6034 (p90) REVERT: B 313 PHE cc_start: 0.5998 (t80) cc_final: 0.5454 (t80) REVERT: B 332 TYR cc_start: 0.8958 (m-80) cc_final: 0.8641 (m-80) REVERT: B 343 ASP cc_start: 0.9003 (m-30) cc_final: 0.8674 (p0) REVERT: B 346 GLN cc_start: 0.8858 (tm-30) cc_final: 0.8536 (tm-30) REVERT: C 49 ASP cc_start: 0.8078 (t0) cc_final: 0.7569 (m-30) REVERT: C 321 LEU cc_start: 0.8431 (mt) cc_final: 0.8212 (mt) REVERT: C 400 LYS cc_start: 0.7440 (mttt) cc_final: 0.7109 (mttt) REVERT: C 406 ASN cc_start: 0.7982 (m-40) cc_final: 0.7747 (p0) REVERT: C 589 GLU cc_start: 0.7254 (mm-30) cc_final: 0.6782 (pm20) REVERT: C 635 TYR cc_start: 0.9080 (m-80) cc_final: 0.8594 (m-80) REVERT: C 637 ASN cc_start: 0.9291 (m110) cc_final: 0.8956 (m110) REVERT: C 659 VAL cc_start: 0.9410 (m) cc_final: 0.9155 (p) REVERT: J 75 PHE cc_start: 0.8390 (m-80) cc_final: 0.8107 (m-80) REVERT: J 80 ASP cc_start: 0.8754 (t0) cc_final: 0.8517 (t0) REVERT: J 161 MET cc_start: 0.7619 (tpp) cc_final: 0.7240 (ttp) REVERT: J 240 MET cc_start: 0.8432 (ttt) cc_final: 0.8188 (ttt) REVERT: J 278 MET cc_start: 0.9485 (mmp) cc_final: 0.9159 (mmp) REVERT: J 321 LEU cc_start: 0.8359 (mt) cc_final: 0.7847 (mp) REVERT: J 497 TYR cc_start: 0.0443 (m-80) cc_final: -0.0175 (m-80) REVERT: J 689 TYR cc_start: 0.8216 (p90) cc_final: 0.7929 (p90) outliers start: 2 outliers final: 1 residues processed: 425 average time/residue: 0.4192 time to fit residues: 292.1441 Evaluate side-chains 278 residues out of total 3452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 277 time to evaluate : 3.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 397 random chunks: chunk 200 optimal weight: 7.9990 chunk 111 optimal weight: 5.9990 chunk 300 optimal weight: 4.9990 chunk 245 optimal weight: 9.9990 chunk 99 optimal weight: 6.9990 chunk 361 optimal weight: 6.9990 chunk 390 optimal weight: 20.0000 chunk 321 optimal weight: 20.0000 chunk 358 optimal weight: 0.0770 chunk 123 optimal weight: 4.9990 chunk 289 optimal weight: 5.9990 overall best weight: 4.4146 ------------------------------------------------------------------------------- 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 915 GLN ** D 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1016 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 993 ASN G1104 ASN H 41 HIS B 167 HIS C 599 GLN ** C 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 708 GLN J 348 HIS J 421 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.3465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.131 31853 Z= 0.254 Angle : 0.664 9.881 43325 Z= 0.364 Chirality : 0.043 0.174 4815 Planarity : 0.006 0.096 5632 Dihedral : 5.263 28.925 4370 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.86 % Favored : 94.81 % Rotamer: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % 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: 0.28 (0.13), residues: 3992 helix: 0.78 (0.19), residues: 695 sheet: 0.21 (0.16), residues: 976 loop : 0.10 (0.13), residues: 2321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP J 553 HIS 0.008 0.002 HIS J 670 PHE 0.040 0.002 PHE A 850 TYR 0.030 0.002 TYR A 909 ARG 0.006 0.001 ARG H 82B *********************** REFINEMENT MACRO_CYCLE 3 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 353 residues out of total 3452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 353 time to evaluate : 3.441 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 840 LEU cc_start: 0.9610 (mm) cc_final: 0.9209 (mm) REVERT: A 893 LEU cc_start: 0.8796 (mt) cc_final: 0.8086 (tt) REVERT: A 906 MET cc_start: 0.6916 (mmp) cc_final: 0.6286 (mpp) REVERT: A 924 ILE cc_start: 0.7238 (pt) cc_final: 0.6755 (pt) REVERT: A 1126 PHE cc_start: 0.9282 (m-80) cc_final: 0.8796 (m-80) REVERT: A 1137 MET cc_start: 0.9045 (mtm) cc_final: 0.8669 (mpp) REVERT: D 779 LYS cc_start: 0.8759 (mttt) cc_final: 0.8306 (mmmt) REVERT: D 1201 ASN cc_start: 0.9224 (m-40) cc_final: 0.8583 (p0) REVERT: E 56 ASN cc_start: 0.8494 (m-40) cc_final: 0.7699 (p0) REVERT: E 63 PHE cc_start: 0.8822 (m-80) cc_final: 0.8604 (m-10) REVERT: E 69 MET cc_start: 0.6655 (mtt) cc_final: 0.5609 (mtt) REVERT: F 33 MET cc_start: 0.8506 (mmp) cc_final: 0.8214 (mmm) REVERT: F 81 ASP cc_start: 0.7904 (m-30) cc_final: 0.7484 (p0) REVERT: F 85 MET cc_start: 0.9228 (tpt) cc_final: 0.8909 (tpp) REVERT: F 104 LEU cc_start: 0.9025 (tp) cc_final: 0.8812 (tp) REVERT: G 854 LYS cc_start: 0.8664 (tmtt) cc_final: 0.8365 (tmtt) REVERT: G 940 ASP cc_start: 0.8814 (t0) cc_final: 0.8046 (t0) REVERT: G 954 SER cc_start: 0.8534 (p) cc_final: 0.8323 (p) REVERT: G 990 LEU cc_start: 0.9560 (mt) cc_final: 0.9360 (mt) REVERT: G 1040 LEU cc_start: 0.8931 (mm) cc_final: 0.8297 (tp) REVERT: G 1084 GLN cc_start: 0.9362 (tp40) cc_final: 0.9077 (tm-30) REVERT: G 1138 HIS cc_start: 0.8850 (m-70) cc_final: 0.8590 (m170) REVERT: G 1182 ASP cc_start: 0.8988 (m-30) cc_final: 0.8663 (t70) REVERT: G 1201 ASN cc_start: 0.9506 (m-40) cc_final: 0.9230 (m110) REVERT: H 2 VAL cc_start: 0.7726 (t) cc_final: 0.7494 (t) REVERT: H 35 HIS cc_start: 0.9209 (m-70) cc_final: 0.8600 (m-70) REVERT: I 27 GLU cc_start: 0.7801 (tt0) cc_final: 0.7138 (tm-30) REVERT: I 27 VAL cc_start: 0.6928 (p) cc_final: 0.5635 (p) REVERT: I 33 MET cc_start: 0.8690 (mmm) cc_final: 0.7569 (mmm) REVERT: B 56 ILE cc_start: 0.9164 (mm) cc_final: 0.8957 (mm) REVERT: B 239 PHE cc_start: 0.8820 (m-80) cc_final: 0.8320 (m-80) REVERT: B 278 MET cc_start: 0.8999 (mtp) cc_final: 0.8172 (mmm) REVERT: B 287 TYR cc_start: 0.6561 (p90) cc_final: 0.6201 (p90) REVERT: B 332 TYR cc_start: 0.8972 (m-80) cc_final: 0.8587 (m-10) REVERT: B 457 SER cc_start: 0.7901 (t) cc_final: 0.7675 (m) REVERT: C 49 ASP cc_start: 0.8268 (t0) cc_final: 0.7888 (t70) REVERT: C 388 LEU cc_start: 0.6101 (tp) cc_final: 0.5344 (tp) REVERT: C 406 ASN cc_start: 0.7923 (m-40) cc_final: 0.7580 (p0) REVERT: C 469 TYR cc_start: 0.5102 (t80) cc_final: 0.4628 (t80) REVERT: C 507 LEU cc_start: 0.7936 (tp) cc_final: 0.7699 (mp) REVERT: C 589 GLU cc_start: 0.7371 (mm-30) cc_final: 0.7000 (pm20) REVERT: C 635 TYR cc_start: 0.9058 (m-80) cc_final: 0.8627 (m-80) REVERT: C 637 ASN cc_start: 0.9260 (m110) cc_final: 0.8931 (m110) REVERT: J 75 PHE cc_start: 0.8555 (m-80) cc_final: 0.7374 (m-80) REVERT: J 161 MET cc_start: 0.7829 (tpp) cc_final: 0.7489 (ttm) REVERT: J 171 LEU cc_start: 0.9165 (tp) cc_final: 0.8698 (pp) REVERT: J 321 LEU cc_start: 0.8620 (mt) cc_final: 0.8346 (mp) REVERT: J 497 TYR cc_start: 0.2613 (m-80) cc_final: 0.1138 (m-80) outliers start: 0 outliers final: 0 residues processed: 353 average time/residue: 0.3793 time to fit residues: 223.6664 Evaluate side-chains 236 residues out of total 3452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 236 time to evaluate : 3.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 397 random chunks: chunk 356 optimal weight: 8.9990 chunk 271 optimal weight: 30.0000 chunk 187 optimal weight: 20.0000 chunk 39 optimal weight: 9.9990 chunk 172 optimal weight: 40.0000 chunk 242 optimal weight: 0.6980 chunk 362 optimal weight: 9.9990 chunk 383 optimal weight: 3.9990 chunk 189 optimal weight: 10.0000 chunk 343 optimal weight: 6.9990 chunk 103 optimal weight: 8.9990 overall best weight: 5.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 915 GLN ** A 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1016 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1023 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1129 ASN D 772 GLN D 993 ASN ** D1016 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1119 GLN F 34 ASN ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 836 HIS G 848 ASN G1119 GLN G1212 GLN H 41 HIS ** H 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 421 ASN ** B 637 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 280 GLN C 408 ASN ** C 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 627 GLN J 627 GLN J 681 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.4273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.102 31853 Z= 0.303 Angle : 0.692 10.393 43325 Z= 0.376 Chirality : 0.044 0.178 4815 Planarity : 0.006 0.083 5632 Dihedral : 5.387 31.019 4370 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 15.66 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.21 % Favored : 94.46 % Rotamer: Outliers : 0.03 % Allowed : 2.03 % Favored : 97.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.59 % Cis-general : 0.47 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.13), residues: 3992 helix: 0.53 (0.19), residues: 716 sheet: 0.09 (0.16), residues: 960 loop : -0.29 (0.13), residues: 2316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP J 310 HIS 0.009 0.002 HIS B 681 PHE 0.031 0.002 PHE A 850 TYR 0.030 0.002 TYR C 293 ARG 0.008 0.001 ARG B 62 *********************** REFINEMENT MACRO_CYCLE 4 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 301 residues out of total 3452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 300 time to evaluate : 3.228 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: A 840 LEU cc_start: 0.9656 (mm) cc_final: 0.9264 (mm) REVERT: A 893 LEU cc_start: 0.9057 (mt) cc_final: 0.8499 (tp) REVERT: A 906 MET cc_start: 0.7050 (mmp) cc_final: 0.6189 (mpp) REVERT: A 933 LYS cc_start: 0.8948 (mttt) cc_final: 0.8626 (mttp) REVERT: A 1126 PHE cc_start: 0.9239 (m-80) cc_final: 0.8730 (m-80) REVERT: A 1137 MET cc_start: 0.9171 (mtm) cc_final: 0.8752 (mpp) REVERT: D 779 LYS cc_start: 0.8772 (mttt) cc_final: 0.8334 (mmmt) REVERT: E 56 ASN cc_start: 0.8613 (m-40) cc_final: 0.8058 (p0) REVERT: F 33 MET cc_start: 0.8533 (mmp) cc_final: 0.8273 (mmm) REVERT: F 46 LEU cc_start: 0.8978 (tp) cc_final: 0.8676 (tp) REVERT: F 81 ASP cc_start: 0.8052 (m-30) cc_final: 0.7601 (p0) REVERT: F 85 MET cc_start: 0.9030 (tpt) cc_final: 0.8599 (tpt) REVERT: F 104 LEU cc_start: 0.9073 (tp) cc_final: 0.8861 (tp) REVERT: G 854 LYS cc_start: 0.8874 (tmtt) cc_final: 0.8551 (tmtt) REVERT: G 940 ASP cc_start: 0.8908 (t0) cc_final: 0.8224 (t0) REVERT: G 1039 GLU cc_start: 0.8144 (pt0) cc_final: 0.7892 (pt0) REVERT: G 1040 LEU cc_start: 0.8887 (mm) cc_final: 0.8027 (tp) REVERT: G 1084 GLN cc_start: 0.9474 (tp40) cc_final: 0.9091 (tm-30) REVERT: G 1138 HIS cc_start: 0.8699 (m-70) cc_final: 0.8348 (m170) REVERT: G 1182 ASP cc_start: 0.9146 (m-30) cc_final: 0.8777 (t70) REVERT: H 35 HIS cc_start: 0.9069 (m-70) cc_final: 0.8640 (m-70) REVERT: I 27 GLU cc_start: 0.7915 (tt0) cc_final: 0.7193 (tm-30) REVERT: I 27 VAL cc_start: 0.6814 (p) cc_final: 0.5441 (p) REVERT: I 33 MET cc_start: 0.8657 (mmm) cc_final: 0.7640 (mmm) REVERT: I 42 GLN cc_start: 0.9510 (mt0) cc_final: 0.8925 (mp-120) REVERT: I 47 LEU cc_start: 0.9532 (mt) cc_final: 0.9246 (mt) REVERT: B 49 ASP cc_start: 0.8527 (t0) cc_final: 0.8321 (t70) REVERT: B 56 ILE cc_start: 0.9269 (mm) cc_final: 0.9065 (mm) REVERT: B 278 MET cc_start: 0.9133 (mtp) cc_final: 0.8395 (mmm) REVERT: B 332 TYR cc_start: 0.8920 (m-80) cc_final: 0.8652 (m-80) REVERT: B 457 SER cc_start: 0.7799 (t) cc_final: 0.7585 (m) REVERT: B 686 MET cc_start: 0.5321 (mmt) cc_final: 0.5049 (mmp) REVERT: C 148 MET cc_start: 0.8515 (ttt) cc_final: 0.8271 (ttt) REVERT: C 149 LEU cc_start: 0.9529 (mm) cc_final: 0.9313 (mm) REVERT: C 367 GLU cc_start: 0.7815 (pt0) cc_final: 0.7568 (pt0) REVERT: C 388 LEU cc_start: 0.5235 (tp) cc_final: 0.4638 (tp) REVERT: C 406 ASN cc_start: 0.7909 (m-40) cc_final: 0.7567 (p0) REVERT: C 589 GLU cc_start: 0.7779 (mm-30) cc_final: 0.7197 (pm20) REVERT: C 635 TYR cc_start: 0.9034 (m-80) cc_final: 0.8669 (m-80) REVERT: C 637 ASN cc_start: 0.9238 (m110) cc_final: 0.8931 (m110) REVERT: J 75 PHE cc_start: 0.8885 (m-80) cc_final: 0.8624 (m-80) REVERT: J 149 LEU cc_start: 0.9125 (mp) cc_final: 0.8882 (mp) REVERT: J 278 MET cc_start: 0.9457 (mmp) cc_final: 0.9213 (mmp) REVERT: J 321 LEU cc_start: 0.8967 (mt) cc_final: 0.8512 (mp) outliers start: 1 outliers final: 0 residues processed: 301 average time/residue: 0.3867 time to fit residues: 193.6990 Evaluate side-chains 212 residues out of total 3452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 212 time to evaluate : 3.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 397 random chunks: chunk 319 optimal weight: 10.0000 chunk 217 optimal weight: 5.9990 chunk 5 optimal weight: 20.0000 chunk 285 optimal weight: 9.9990 chunk 158 optimal weight: 7.9990 chunk 327 optimal weight: 5.9990 chunk 265 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 195 optimal weight: 0.4980 chunk 344 optimal weight: 8.9990 chunk 96 optimal weight: 9.9990 overall best weight: 5.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 769 GLN ** A 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1016 ASN A1023 GLN ** A1163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 193 ASN B 280 GLN ** B 637 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 218 ASN ** C 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.4749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.095 31853 Z= 0.293 Angle : 0.664 11.123 43325 Z= 0.360 Chirality : 0.043 0.189 4815 Planarity : 0.005 0.075 5632 Dihedral : 5.349 31.231 4370 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 16.43 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.96 % Favored : 93.71 % Rotamer: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.59 % Cis-general : 0.47 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.35 (0.13), residues: 3992 helix: 0.65 (0.19), residues: 706 sheet: -0.06 (0.16), residues: 951 loop : -0.53 (0.13), residues: 2335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 44 HIS 0.007 0.001 HIS J 670 PHE 0.027 0.002 PHE A 850 TYR 0.025 0.002 TYR E 98 ARG 0.008 0.001 ARG B 691 *********************** REFINEMENT MACRO_CYCLE 5 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 295 residues out of total 3452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 295 time to evaluate : 3.612 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 840 LEU cc_start: 0.9647 (mm) cc_final: 0.9260 (mm) REVERT: A 906 MET cc_start: 0.7168 (mmp) cc_final: 0.6383 (mpp) REVERT: A 924 ILE cc_start: 0.7227 (pt) cc_final: 0.6692 (pt) REVERT: A 933 LYS cc_start: 0.8954 (mttt) cc_final: 0.8609 (mttp) REVERT: A 1039 GLU cc_start: 0.9227 (mm-30) cc_final: 0.8876 (mt-10) REVERT: A 1126 PHE cc_start: 0.9235 (m-80) cc_final: 0.8767 (m-80) REVERT: A 1137 MET cc_start: 0.9092 (mtm) cc_final: 0.8757 (mpp) REVERT: D 779 LYS cc_start: 0.8698 (mttt) cc_final: 0.8176 (mmmt) REVERT: D 1008 MET cc_start: 0.8554 (tpt) cc_final: 0.8267 (tpp) REVERT: E 56 ASN cc_start: 0.8715 (m-40) cc_final: 0.8150 (p0) REVERT: E 63 PHE cc_start: 0.8879 (m-80) cc_final: 0.8530 (m-80) REVERT: F 33 MET cc_start: 0.8383 (mmp) cc_final: 0.8177 (mmm) REVERT: F 81 ASP cc_start: 0.7901 (m-30) cc_final: 0.7442 (p0) REVERT: F 85 MET cc_start: 0.9089 (tpt) cc_final: 0.8572 (tpt) REVERT: F 104 LEU cc_start: 0.9030 (tp) cc_final: 0.8817 (tp) REVERT: G 940 ASP cc_start: 0.8674 (t0) cc_final: 0.7938 (t0) REVERT: G 978 TYR cc_start: 0.9028 (t80) cc_final: 0.8631 (t80) REVERT: G 1040 LEU cc_start: 0.8934 (mm) cc_final: 0.8055 (tt) REVERT: G 1084 GLN cc_start: 0.9504 (tp40) cc_final: 0.9093 (tm-30) REVERT: G 1138 HIS cc_start: 0.8759 (m-70) cc_final: 0.8355 (m170) REVERT: G 1182 ASP cc_start: 0.9194 (m-30) cc_final: 0.8862 (t70) REVERT: H 35 HIS cc_start: 0.9202 (m-70) cc_final: 0.8750 (m-70) REVERT: I 27 GLU cc_start: 0.7855 (tt0) cc_final: 0.7172 (tm-30) REVERT: I 27 VAL cc_start: 0.6684 (p) cc_final: 0.5339 (p) REVERT: I 33 MET cc_start: 0.8741 (mmm) cc_final: 0.7907 (mmm) REVERT: B 49 ASP cc_start: 0.8653 (t0) cc_final: 0.8433 (t70) REVERT: B 239 PHE cc_start: 0.8945 (m-80) cc_final: 0.8496 (m-80) REVERT: B 278 MET cc_start: 0.9077 (mtp) cc_final: 0.8298 (mmm) REVERT: B 332 TYR cc_start: 0.8897 (m-80) cc_final: 0.8506 (m-80) REVERT: B 523 TYR cc_start: 0.6892 (m-80) cc_final: 0.6276 (m-80) REVERT: C 388 LEU cc_start: 0.5005 (tp) cc_final: 0.4472 (tp) REVERT: C 589 GLU cc_start: 0.7801 (mm-30) cc_final: 0.7160 (pm20) REVERT: C 635 TYR cc_start: 0.8986 (m-80) cc_final: 0.8665 (m-80) REVERT: C 637 ASN cc_start: 0.9275 (m110) cc_final: 0.8976 (m110) REVERT: J 75 PHE cc_start: 0.8905 (m-80) cc_final: 0.8584 (m-80) REVERT: J 321 LEU cc_start: 0.8947 (mt) cc_final: 0.8484 (mp) outliers start: 0 outliers final: 0 residues processed: 295 average time/residue: 0.3905 time to fit residues: 193.2749 Evaluate side-chains 205 residues out of total 3452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 205 time to evaluate : 3.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 397 random chunks: chunk 129 optimal weight: 0.9990 chunk 345 optimal weight: 10.0000 chunk 75 optimal weight: 20.0000 chunk 225 optimal weight: 8.9990 chunk 94 optimal weight: 9.9990 chunk 384 optimal weight: 0.9980 chunk 318 optimal weight: 10.0000 chunk 177 optimal weight: 30.0000 chunk 31 optimal weight: 9.9990 chunk 127 optimal weight: 9.9990 chunk 201 optimal weight: 20.0000 overall best weight: 6.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 815 GLN ** A 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1145 ASN ** A1163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 41 HIS ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 637 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.5208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 31853 Z= 0.303 Angle : 0.676 10.859 43325 Z= 0.365 Chirality : 0.043 0.165 4815 Planarity : 0.005 0.070 5632 Dihedral : 5.453 31.779 4370 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 18.17 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.46 % Favored : 93.26 % Rotamer: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.59 % Cis-general : 0.47 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.13), residues: 3992 helix: 0.40 (0.19), residues: 729 sheet: -0.19 (0.17), residues: 903 loop : -0.78 (0.13), residues: 2360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP G 960 HIS 0.010 0.001 HIS J 670 PHE 0.027 0.002 PHE J 467 TYR 0.023 0.002 TYR E 98 ARG 0.008 0.001 ARG E 94 *********************** REFINEMENT MACRO_CYCLE 6 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 275 residues out of total 3452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 275 time to evaluate : 3.514 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 840 LEU cc_start: 0.9650 (mm) cc_final: 0.9213 (mm) REVERT: A 906 MET cc_start: 0.7040 (mmp) cc_final: 0.6342 (mpp) REVERT: A 913 MET cc_start: 0.6989 (mpp) cc_final: 0.6633 (mpp) REVERT: A 933 LYS cc_start: 0.8997 (mttt) cc_final: 0.8549 (mmtt) REVERT: A 1039 GLU cc_start: 0.9242 (mm-30) cc_final: 0.8955 (mt-10) REVERT: A 1126 PHE cc_start: 0.9216 (m-80) cc_final: 0.8688 (m-80) REVERT: A 1137 MET cc_start: 0.9115 (mtm) cc_final: 0.8762 (mpp) REVERT: D 1053 ASP cc_start: 0.9216 (t0) cc_final: 0.8986 (t70) REVERT: E 56 ASN cc_start: 0.8659 (m-40) cc_final: 0.8345 (p0) REVERT: E 63 PHE cc_start: 0.8940 (m-80) cc_final: 0.8549 (m-80) REVERT: E 72 ASP cc_start: 0.8880 (t0) cc_final: 0.8655 (t0) REVERT: E 100 MET cc_start: 0.6021 (tpp) cc_final: 0.5733 (tpp) REVERT: F 27 GLU cc_start: 0.8615 (pp20) cc_final: 0.8413 (pp20) REVERT: F 33 MET cc_start: 0.8409 (mmp) cc_final: 0.8193 (mmm) REVERT: F 81 ASP cc_start: 0.7863 (m-30) cc_final: 0.7360 (p0) REVERT: F 85 MET cc_start: 0.9082 (tpt) cc_final: 0.8827 (tpp) REVERT: F 104 LEU cc_start: 0.9060 (tp) cc_final: 0.8855 (tp) REVERT: G 1138 HIS cc_start: 0.8669 (m-70) cc_final: 0.8252 (m170) REVERT: G 1182 ASP cc_start: 0.9239 (m-30) cc_final: 0.8931 (t70) REVERT: H 35 HIS cc_start: 0.9229 (m-70) cc_final: 0.8857 (m-70) REVERT: I 27 GLU cc_start: 0.7934 (tt0) cc_final: 0.7192 (tm-30) REVERT: I 27 VAL cc_start: 0.6754 (p) cc_final: 0.5446 (p) REVERT: I 33 MET cc_start: 0.8782 (mmm) cc_final: 0.7954 (mmm) REVERT: B 49 ASP cc_start: 0.8643 (t0) cc_final: 0.7344 (t70) REVERT: B 52 LYS cc_start: 0.9288 (mptt) cc_final: 0.8876 (mptt) REVERT: B 239 PHE cc_start: 0.8941 (m-80) cc_final: 0.8578 (m-80) REVERT: B 278 MET cc_start: 0.9074 (mtp) cc_final: 0.8029 (tpp) REVERT: B 523 TYR cc_start: 0.6740 (m-80) cc_final: 0.6182 (m-80) REVERT: C 84 MET cc_start: 0.8341 (ppp) cc_final: 0.7984 (ttt) REVERT: C 180 LEU cc_start: 0.9538 (tp) cc_final: 0.9263 (pp) REVERT: C 388 LEU cc_start: 0.5447 (tp) cc_final: 0.4732 (tp) REVERT: C 466 GLN cc_start: 0.7248 (mm-40) cc_final: 0.6985 (mm-40) REVERT: C 589 GLU cc_start: 0.7918 (mm-30) cc_final: 0.7298 (pm20) REVERT: C 635 TYR cc_start: 0.8965 (m-80) cc_final: 0.8556 (m-80) REVERT: C 717 LEU cc_start: 0.8388 (mm) cc_final: 0.8160 (mm) REVERT: J 75 PHE cc_start: 0.8926 (m-80) cc_final: 0.8706 (m-80) REVERT: J 149 LEU cc_start: 0.9005 (mp) cc_final: 0.8766 (mp) REVERT: J 321 LEU cc_start: 0.8964 (mt) cc_final: 0.8422 (mp) REVERT: J 399 PHE cc_start: 0.6556 (m-10) cc_final: 0.6335 (m-10) REVERT: J 686 MET cc_start: 0.6889 (mpp) cc_final: 0.6684 (mpp) outliers start: 0 outliers final: 0 residues processed: 275 average time/residue: 0.3732 time to fit residues: 171.4910 Evaluate side-chains 203 residues out of total 3452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 203 time to evaluate : 3.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 397 random chunks: chunk 370 optimal weight: 7.9990 chunk 43 optimal weight: 8.9990 chunk 218 optimal weight: 0.0470 chunk 280 optimal weight: 8.9990 chunk 217 optimal weight: 40.0000 chunk 323 optimal weight: 6.9990 chunk 214 optimal weight: 8.9990 chunk 382 optimal weight: 5.9990 chunk 239 optimal weight: 20.0000 chunk 233 optimal weight: 40.0000 chunk 176 optimal weight: 20.0000 overall best weight: 6.0086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 815 GLN ** E 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 41 HIS ** B 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 346 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.5510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 31853 Z= 0.293 Angle : 0.668 11.728 43325 Z= 0.359 Chirality : 0.043 0.160 4815 Planarity : 0.005 0.079 5632 Dihedral : 5.468 31.619 4370 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 17.83 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.71 % Favored : 93.04 % Rotamer: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.59 % Cis-general : 0.47 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.13), residues: 3992 helix: 0.56 (0.19), residues: 712 sheet: -0.29 (0.17), residues: 905 loop : -0.89 (0.13), residues: 2375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 44 HIS 0.008 0.001 HIS H 41 PHE 0.039 0.002 PHE D 977 TYR 0.031 0.002 TYR A 928 ARG 0.006 0.001 ARG C 691 *********************** REFINEMENT MACRO_CYCLE 7 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 279 residues out of total 3452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 279 time to evaluate : 3.389 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 840 LEU cc_start: 0.9654 (mm) cc_final: 0.9213 (mm) REVERT: A 906 MET cc_start: 0.6993 (mmp) cc_final: 0.6308 (mpp) REVERT: A 933 LYS cc_start: 0.8997 (mttt) cc_final: 0.8611 (mttp) REVERT: A 1039 GLU cc_start: 0.9202 (mm-30) cc_final: 0.8946 (mt-10) REVERT: A 1126 PHE cc_start: 0.9213 (m-80) cc_final: 0.8702 (m-80) REVERT: A 1137 MET cc_start: 0.9105 (mtm) cc_final: 0.8728 (mpp) REVERT: D 818 GLU cc_start: 0.9173 (mm-30) cc_final: 0.8969 (mm-30) REVERT: D 913 MET cc_start: 0.6026 (mmt) cc_final: 0.5804 (mmp) REVERT: E 50 VAL cc_start: 0.8511 (p) cc_final: 0.8224 (p) REVERT: E 63 PHE cc_start: 0.8962 (m-80) cc_final: 0.8655 (m-80) REVERT: E 72 ASP cc_start: 0.8889 (t0) cc_final: 0.8651 (t0) REVERT: E 100 MET cc_start: 0.6420 (tpp) cc_final: 0.6077 (tpp) REVERT: F 27 GLU cc_start: 0.8625 (pp20) cc_final: 0.8347 (pp20) REVERT: F 33 MET cc_start: 0.8409 (mmp) cc_final: 0.8166 (mmm) REVERT: F 81 ASP cc_start: 0.8040 (m-30) cc_final: 0.7513 (p0) REVERT: F 85 MET cc_start: 0.9064 (tpt) cc_final: 0.8808 (tpp) REVERT: F 104 LEU cc_start: 0.9056 (tp) cc_final: 0.8850 (tp) REVERT: G 799 ILE cc_start: 0.9282 (pt) cc_final: 0.9068 (pt) REVERT: G 842 GLN cc_start: 0.9368 (mm-40) cc_final: 0.9168 (mm-40) REVERT: G 943 MET cc_start: 0.8615 (tpp) cc_final: 0.8353 (mmt) REVERT: G 1138 HIS cc_start: 0.8586 (m-70) cc_final: 0.8090 (m170) REVERT: G 1182 ASP cc_start: 0.9238 (m-30) cc_final: 0.8939 (t70) REVERT: H 2 VAL cc_start: 0.8144 (t) cc_final: 0.7891 (t) REVERT: H 35 HIS cc_start: 0.9235 (m-70) cc_final: 0.8788 (m-70) REVERT: I 27 GLU cc_start: 0.7982 (tt0) cc_final: 0.7302 (tm-30) REVERT: I 33 MET cc_start: 0.8819 (mmm) cc_final: 0.8066 (mmm) REVERT: B 49 ASP cc_start: 0.8628 (t0) cc_final: 0.7364 (t70) REVERT: B 52 LYS cc_start: 0.9298 (mptt) cc_final: 0.8881 (mptt) REVERT: B 239 PHE cc_start: 0.8962 (m-80) cc_final: 0.8524 (m-80) REVERT: B 278 MET cc_start: 0.9056 (mtp) cc_final: 0.7802 (tpp) REVERT: B 287 TYR cc_start: 0.6876 (p90) cc_final: 0.6247 (p90) REVERT: B 631 VAL cc_start: 0.8982 (t) cc_final: 0.8722 (t) REVERT: B 638 LEU cc_start: 0.9144 (tp) cc_final: 0.8493 (pp) REVERT: C 84 MET cc_start: 0.8327 (ppp) cc_final: 0.7982 (ttt) REVERT: C 180 LEU cc_start: 0.9533 (tp) cc_final: 0.9297 (pp) REVERT: C 466 GLN cc_start: 0.7222 (mm-40) cc_final: 0.6956 (mm-40) REVERT: C 589 GLU cc_start: 0.7929 (mm-30) cc_final: 0.7311 (pm20) REVERT: C 635 TYR cc_start: 0.8963 (m-80) cc_final: 0.8585 (m-80) REVERT: C 717 LEU cc_start: 0.8558 (mm) cc_final: 0.8196 (mm) REVERT: J 75 PHE cc_start: 0.8873 (m-80) cc_final: 0.8640 (m-80) REVERT: J 399 PHE cc_start: 0.6631 (m-10) cc_final: 0.5954 (m-10) REVERT: J 686 MET cc_start: 0.6994 (mpp) cc_final: 0.6777 (mpp) outliers start: 0 outliers final: 0 residues processed: 279 average time/residue: 0.3900 time to fit residues: 181.8688 Evaluate side-chains 207 residues out of total 3452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 207 time to evaluate : 3.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 397 random chunks: chunk 236 optimal weight: 50.0000 chunk 152 optimal weight: 8.9990 chunk 228 optimal weight: 30.0000 chunk 115 optimal weight: 0.9980 chunk 75 optimal weight: 5.9990 chunk 74 optimal weight: 3.9990 chunk 243 optimal weight: 7.9990 chunk 260 optimal weight: 40.0000 chunk 189 optimal weight: 6.9990 chunk 35 optimal weight: 6.9990 chunk 300 optimal weight: 9.9990 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1163 ASN ** E 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1023 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 41 HIS ** B 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 516 GLN ** C 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.5740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 31853 Z= 0.258 Angle : 0.641 11.622 43325 Z= 0.345 Chirality : 0.043 0.158 4815 Planarity : 0.005 0.075 5632 Dihedral : 5.401 31.188 4370 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 17.13 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.89 % Favored : 92.84 % Rotamer: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.59 % Cis-general : 0.47 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.13), residues: 3992 helix: 0.59 (0.19), residues: 725 sheet: -0.31 (0.17), residues: 915 loop : -0.94 (0.13), residues: 2352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J 553 HIS 0.006 0.001 HIS J 670 PHE 0.027 0.002 PHE J 467 TYR 0.027 0.002 TYR J 438 ARG 0.007 0.001 ARG D1057 *********************** REFINEMENT MACRO_CYCLE 8 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 265 residues out of total 3452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 265 time to evaluate : 3.212 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 840 LEU cc_start: 0.9652 (mm) cc_final: 0.9198 (mm) REVERT: A 906 MET cc_start: 0.6996 (mmp) cc_final: 0.6301 (mpp) REVERT: A 913 MET cc_start: 0.7174 (mpp) cc_final: 0.6970 (mpp) REVERT: A 924 ILE cc_start: 0.7243 (pt) cc_final: 0.6775 (pt) REVERT: A 933 LYS cc_start: 0.8985 (mttt) cc_final: 0.8608 (mttp) REVERT: A 1126 PHE cc_start: 0.9201 (m-80) cc_final: 0.8709 (m-80) REVERT: A 1137 MET cc_start: 0.9133 (mtm) cc_final: 0.8722 (mpp) REVERT: E 63 PHE cc_start: 0.9005 (m-80) cc_final: 0.8638 (m-80) REVERT: E 69 MET cc_start: 0.6914 (mtm) cc_final: 0.6680 (mtp) REVERT: E 72 ASP cc_start: 0.8881 (t0) cc_final: 0.8625 (t0) REVERT: E 100 MET cc_start: 0.6085 (tpp) cc_final: 0.5539 (tpp) REVERT: F 27 GLU cc_start: 0.8592 (pp20) cc_final: 0.8263 (pp20) REVERT: F 33 MET cc_start: 0.8380 (mmp) cc_final: 0.8147 (mmm) REVERT: F 81 ASP cc_start: 0.8013 (m-30) cc_final: 0.7446 (p0) REVERT: F 85 MET cc_start: 0.9030 (tpt) cc_final: 0.8777 (tpp) REVERT: F 104 LEU cc_start: 0.9066 (tp) cc_final: 0.8857 (tp) REVERT: G 799 ILE cc_start: 0.9269 (pt) cc_final: 0.9018 (pt) REVERT: G 943 MET cc_start: 0.8565 (tpp) cc_final: 0.8353 (mmt) REVERT: G 1138 HIS cc_start: 0.8714 (m-70) cc_final: 0.8219 (m170) REVERT: G 1182 ASP cc_start: 0.9236 (m-30) cc_final: 0.8955 (t70) REVERT: H 35 HIS cc_start: 0.9216 (m-70) cc_final: 0.8842 (m170) REVERT: I 27 GLU cc_start: 0.8061 (tt0) cc_final: 0.7346 (tm-30) REVERT: I 33 MET cc_start: 0.8841 (mmm) cc_final: 0.8084 (mmm) REVERT: B 49 ASP cc_start: 0.8587 (t0) cc_final: 0.7268 (t70) REVERT: B 52 LYS cc_start: 0.9271 (mptt) cc_final: 0.8828 (mptt) REVERT: B 84 MET cc_start: 0.9221 (tpt) cc_final: 0.9015 (tpt) REVERT: B 239 PHE cc_start: 0.8968 (m-80) cc_final: 0.8483 (m-80) REVERT: B 278 MET cc_start: 0.9083 (mtp) cc_final: 0.7821 (tpp) REVERT: B 287 TYR cc_start: 0.6866 (p90) cc_final: 0.6240 (p90) REVERT: B 631 VAL cc_start: 0.8989 (t) cc_final: 0.8757 (t) REVERT: B 638 LEU cc_start: 0.9093 (tp) cc_final: 0.8518 (pt) REVERT: B 651 LEU cc_start: 0.8702 (tp) cc_final: 0.8389 (tp) REVERT: C 84 MET cc_start: 0.8294 (ppp) cc_final: 0.7893 (ttt) REVERT: C 180 LEU cc_start: 0.9550 (tp) cc_final: 0.9301 (pp) REVERT: C 388 LEU cc_start: 0.5652 (tp) cc_final: 0.5420 (tp) REVERT: C 466 GLN cc_start: 0.7197 (mm-40) cc_final: 0.6924 (mm-40) REVERT: C 589 GLU cc_start: 0.8055 (mm-30) cc_final: 0.7461 (pm20) REVERT: C 635 TYR cc_start: 0.8954 (m-80) cc_final: 0.8576 (m-80) REVERT: C 717 LEU cc_start: 0.8577 (mm) cc_final: 0.8062 (mm) REVERT: J 75 PHE cc_start: 0.8823 (m-80) cc_final: 0.8570 (m-80) REVERT: J 161 MET cc_start: 0.8244 (ptt) cc_final: 0.7986 (tpt) REVERT: J 321 LEU cc_start: 0.9189 (tp) cc_final: 0.8778 (tp) outliers start: 0 outliers final: 0 residues processed: 265 average time/residue: 0.3858 time to fit residues: 171.5125 Evaluate side-chains 199 residues out of total 3452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 199 time to evaluate : 3.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 397 random chunks: chunk 348 optimal weight: 0.4980 chunk 366 optimal weight: 9.9990 chunk 334 optimal weight: 4.9990 chunk 356 optimal weight: 10.0000 chunk 214 optimal weight: 8.9990 chunk 155 optimal weight: 0.9980 chunk 279 optimal weight: 20.0000 chunk 109 optimal weight: 30.0000 chunk 322 optimal weight: 0.1980 chunk 337 optimal weight: 20.0000 chunk 355 optimal weight: 5.9990 overall best weight: 2.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1163 ASN ** E 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1023 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 41 HIS ** B 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 406 ASN ** J 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.5820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 31853 Z= 0.177 Angle : 0.588 10.953 43325 Z= 0.316 Chirality : 0.042 0.163 4815 Planarity : 0.005 0.066 5632 Dihedral : 5.044 28.688 4370 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 14.43 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.01 % Favored : 93.74 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % 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: -0.57 (0.13), residues: 3992 helix: 0.97 (0.20), residues: 725 sheet: -0.22 (0.16), residues: 931 loop : -0.87 (0.13), residues: 2336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP H 47 HIS 0.004 0.001 HIS B 681 PHE 0.041 0.002 PHE D 977 TYR 0.023 0.001 TYR C 293 ARG 0.005 0.000 ARG F 24 *********************** REFINEMENT MACRO_CYCLE 9 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 277 residues out of total 3452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 277 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 840 LEU cc_start: 0.9653 (mm) cc_final: 0.9270 (mm) REVERT: A 906 MET cc_start: 0.6866 (mmp) cc_final: 0.6159 (mpp) REVERT: A 913 MET cc_start: 0.7020 (mpp) cc_final: 0.6818 (mpp) REVERT: A 924 ILE cc_start: 0.7237 (pt) cc_final: 0.7022 (pt) REVERT: A 933 LYS cc_start: 0.8947 (mttt) cc_final: 0.8494 (mmtt) REVERT: A 1126 PHE cc_start: 0.9189 (m-80) cc_final: 0.8708 (m-80) REVERT: A 1137 MET cc_start: 0.9057 (mtm) cc_final: 0.8696 (mpp) REVERT: D 927 GLN cc_start: 0.8028 (tt0) cc_final: 0.7747 (tt0) REVERT: D 1137 MET cc_start: 0.9580 (mtt) cc_final: 0.9003 (mpp) REVERT: E 63 PHE cc_start: 0.8961 (m-80) cc_final: 0.8606 (m-80) REVERT: E 72 ASP cc_start: 0.8750 (t0) cc_final: 0.8493 (t0) REVERT: E 100 MET cc_start: 0.6239 (tpp) cc_final: 0.5947 (tpp) REVERT: F 27 GLU cc_start: 0.8548 (pp20) cc_final: 0.8177 (pp20) REVERT: F 81 ASP cc_start: 0.8003 (m-30) cc_final: 0.7454 (p0) REVERT: F 85 MET cc_start: 0.9026 (tpt) cc_final: 0.8746 (tpp) REVERT: F 104 LEU cc_start: 0.9062 (tp) cc_final: 0.8861 (tp) REVERT: G 1138 HIS cc_start: 0.8638 (m-70) cc_final: 0.8137 (m170) REVERT: G 1182 ASP cc_start: 0.9185 (m-30) cc_final: 0.8925 (t70) REVERT: H 35 HIS cc_start: 0.9187 (m-70) cc_final: 0.8854 (m170) REVERT: H 82 LEU cc_start: 0.8880 (tp) cc_final: 0.8537 (tt) REVERT: I 33 MET cc_start: 0.8700 (mmm) cc_final: 0.7931 (mmm) REVERT: I 42 GLN cc_start: 0.9462 (mt0) cc_final: 0.8774 (mp10) REVERT: B 49 ASP cc_start: 0.8634 (t0) cc_final: 0.7292 (t70) REVERT: B 52 LYS cc_start: 0.9249 (mptt) cc_final: 0.8789 (mptt) REVERT: B 239 PHE cc_start: 0.8942 (m-80) cc_final: 0.8458 (m-80) REVERT: B 278 MET cc_start: 0.9051 (mtp) cc_final: 0.7773 (tpp) REVERT: B 287 TYR cc_start: 0.6922 (p90) cc_final: 0.6289 (p90) REVERT: B 631 VAL cc_start: 0.8965 (t) cc_final: 0.8738 (t) REVERT: B 638 LEU cc_start: 0.9064 (tp) cc_final: 0.8454 (pt) REVERT: B 651 LEU cc_start: 0.8717 (tp) cc_final: 0.8397 (tp) REVERT: C 84 MET cc_start: 0.8239 (ppp) cc_final: 0.7685 (ttt) REVERT: C 180 LEU cc_start: 0.9580 (tp) cc_final: 0.9354 (pp) REVERT: C 466 GLN cc_start: 0.7304 (mm-40) cc_final: 0.7019 (mm-40) REVERT: C 589 GLU cc_start: 0.8101 (mm-30) cc_final: 0.7432 (pm20) REVERT: C 635 TYR cc_start: 0.9020 (m-80) cc_final: 0.8609 (m-80) REVERT: C 717 LEU cc_start: 0.8517 (mm) cc_final: 0.7988 (mm) REVERT: J 75 PHE cc_start: 0.8837 (m-80) cc_final: 0.8574 (m-80) REVERT: J 161 MET cc_start: 0.8308 (ptt) cc_final: 0.8089 (tpt) REVERT: J 321 LEU cc_start: 0.9204 (tp) cc_final: 0.8782 (tp) REVERT: J 399 PHE cc_start: 0.7487 (m-10) cc_final: 0.7219 (m-10) REVERT: J 469 TYR cc_start: 0.1313 (t80) cc_final: 0.0961 (t80) outliers start: 0 outliers final: 0 residues processed: 277 average time/residue: 0.4135 time to fit residues: 189.4838 Evaluate side-chains 207 residues out of total 3452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 207 time to evaluate : 3.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 397 random chunks: chunk 234 optimal weight: 7.9990 chunk 377 optimal weight: 20.0000 chunk 230 optimal weight: 9.9990 chunk 178 optimal weight: 6.9990 chunk 262 optimal weight: 20.0000 chunk 395 optimal weight: 0.6980 chunk 364 optimal weight: 9.9990 chunk 314 optimal weight: 9.9990 chunk 32 optimal weight: 6.9990 chunk 243 optimal weight: 10.0000 chunk 193 optimal weight: 3.9990 overall best weight: 5.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1163 ASN D1084 GLN D1119 GLN ** E 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 870 ASN ** G 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G1002 ASN ** G1023 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 41 HIS ** B 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 406 ASN ** C 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.6060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 31853 Z= 0.269 Angle : 0.651 12.603 43325 Z= 0.349 Chirality : 0.043 0.209 4815 Planarity : 0.005 0.076 5632 Dihedral : 5.277 29.869 4370 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 17.62 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.16 % Favored : 92.61 % Rotamer: Outliers : 0.03 % Allowed : 0.35 % Favored : 99.62 % 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: -0.73 (0.13), residues: 3992 helix: 0.63 (0.19), residues: 740 sheet: -0.18 (0.16), residues: 914 loop : -0.98 (0.13), residues: 2338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP J 553 HIS 0.011 0.001 HIS B 681 PHE 0.023 0.002 PHE J 467 TYR 0.024 0.002 TYR E 98 ARG 0.006 0.001 ARG G 847 ********************** REFINEMENT MACRO_CYCLE 10 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 274 residues out of total 3452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 273 time to evaluate : 3.451 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 840 LEU cc_start: 0.9668 (mm) cc_final: 0.9287 (mm) REVERT: A 906 MET cc_start: 0.6918 (mmp) cc_final: 0.6167 (mpp) REVERT: A 924 ILE cc_start: 0.7150 (pt) cc_final: 0.6816 (pt) REVERT: A 933 LYS cc_start: 0.9025 (mttt) cc_final: 0.8580 (mmtt) REVERT: A 1039 GLU cc_start: 0.9149 (mm-30) cc_final: 0.8877 (mt-10) REVERT: A 1126 PHE cc_start: 0.9153 (m-80) cc_final: 0.8667 (m-80) REVERT: A 1137 MET cc_start: 0.9118 (mtm) cc_final: 0.8652 (mpp) REVERT: D 757 MET cc_start: 0.9374 (tmm) cc_final: 0.9103 (tmm) REVERT: D 927 GLN cc_start: 0.8092 (tt0) cc_final: 0.7706 (tt0) REVERT: D 943 MET cc_start: 0.8937 (tpp) cc_final: 0.8420 (tpp) REVERT: D 1137 MET cc_start: 0.9612 (mtt) cc_final: 0.9029 (mpp) REVERT: D 1172 PHE cc_start: 0.8765 (m-10) cc_final: 0.8383 (m-10) REVERT: E 63 PHE cc_start: 0.8999 (m-80) cc_final: 0.8661 (m-80) REVERT: E 72 ASP cc_start: 0.8766 (t0) cc_final: 0.8523 (t0) REVERT: E 100 MET cc_start: 0.6263 (tpp) cc_final: 0.5924 (tpp) REVERT: F 27 GLU cc_start: 0.8602 (pp20) cc_final: 0.8184 (pp20) REVERT: F 33 MET cc_start: 0.8090 (mmp) cc_final: 0.7764 (mmm) REVERT: F 81 ASP cc_start: 0.7966 (m-30) cc_final: 0.7411 (p0) REVERT: F 85 MET cc_start: 0.9025 (tpt) cc_final: 0.8739 (tpp) REVERT: G 1138 HIS cc_start: 0.8659 (m-70) cc_final: 0.8235 (m170) REVERT: G 1182 ASP cc_start: 0.9207 (m-30) cc_final: 0.8904 (t70) REVERT: H 35 HIS cc_start: 0.9206 (m-70) cc_final: 0.8896 (m170) REVERT: H 43 LYS cc_start: 0.9084 (mttt) cc_final: 0.8571 (mtpt) REVERT: I 33 MET cc_start: 0.8746 (mmm) cc_final: 0.8030 (mmm) REVERT: I 42 GLN cc_start: 0.9462 (mt0) cc_final: 0.8767 (mp10) REVERT: B 49 ASP cc_start: 0.8616 (t0) cc_final: 0.7394 (t70) REVERT: B 52 LYS cc_start: 0.9219 (mptt) cc_final: 0.8765 (mptt) REVERT: B 278 MET cc_start: 0.9089 (mtp) cc_final: 0.8691 (mmm) REVERT: B 287 TYR cc_start: 0.6952 (p90) cc_final: 0.6341 (p90) REVERT: B 631 VAL cc_start: 0.8960 (t) cc_final: 0.8728 (t) REVERT: B 638 LEU cc_start: 0.9109 (tp) cc_final: 0.8491 (pt) REVERT: B 651 LEU cc_start: 0.8762 (tp) cc_final: 0.8459 (tp) REVERT: C 84 MET cc_start: 0.8286 (ppp) cc_final: 0.7785 (ttt) REVERT: C 180 LEU cc_start: 0.9576 (tp) cc_final: 0.9352 (pp) REVERT: C 466 GLN cc_start: 0.7298 (mm-40) cc_final: 0.7007 (mm-40) REVERT: C 497 TYR cc_start: 0.5470 (m-80) cc_final: 0.4839 (m-80) REVERT: C 589 GLU cc_start: 0.8125 (mm-30) cc_final: 0.7486 (pm20) REVERT: C 635 TYR cc_start: 0.9019 (m-80) cc_final: 0.8631 (m-80) REVERT: C 717 LEU cc_start: 0.8498 (mm) cc_final: 0.8037 (mm) REVERT: J 75 PHE cc_start: 0.8823 (m-80) cc_final: 0.8516 (m-80) REVERT: J 149 LEU cc_start: 0.8961 (mp) cc_final: 0.8742 (mp) REVERT: J 161 MET cc_start: 0.8386 (ptt) cc_final: 0.8144 (tpt) outliers start: 1 outliers final: 0 residues processed: 274 average time/residue: 0.3928 time to fit residues: 179.2025 Evaluate side-chains 196 residues out of total 3452 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 196 time to evaluate : 3.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 397 random chunks: chunk 250 optimal weight: 10.0000 chunk 335 optimal weight: 10.0000 chunk 96 optimal weight: 9.9990 chunk 290 optimal weight: 20.0000 chunk 46 optimal weight: 10.0000 chunk 87 optimal weight: 9.9990 chunk 315 optimal weight: 10.0000 chunk 132 optimal weight: 3.9990 chunk 323 optimal weight: 3.9990 chunk 39 optimal weight: 10.0000 chunk 58 optimal weight: 10.0000 overall best weight: 7.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1163 ASN A1217 ASN ** D 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 994 GLN ** E 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 981 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1023 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1028 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1176 ASN H 41 HIS ** B 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 522 GLN ** B 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 628 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.065386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.050977 restraints weight = 226694.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.052247 restraints weight = 154166.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.052761 restraints weight = 99173.002| |-----------------------------------------------------------------------------| r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.6465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.088 31853 Z= 0.359 Angle : 0.745 12.993 43325 Z= 0.401 Chirality : 0.045 0.204 4815 Planarity : 0.006 0.077 5632 Dihedral : 5.838 30.630 4370 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 22.26 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.34 % Favored : 91.43 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.59 % Cis-general : 0.47 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.25 (0.13), residues: 3992 helix: -0.01 (0.18), residues: 746 sheet: -0.51 (0.17), residues: 903 loop : -1.24 (0.13), residues: 2343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP J 553 HIS 0.010 0.002 HIS B 681 PHE 0.044 0.003 PHE D 977 TYR 0.033 0.002 TYR B 231 ARG 0.018 0.001 ARG G1113 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5547.20 seconds wall clock time: 102 minutes 26.15 seconds (6146.15 seconds total)