Starting phenix.real_space_refine (version: 1.21rc1) on Tue May 16 10:29:59 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7llk_23424/05_2023/7llk_23424_trim.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7llk_23424/05_2023/7llk_23424.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/7llk_23424/05_2023/7llk_23424.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7llk_23424/05_2023/7llk_23424.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7llk_23424/05_2023/7llk_23424_trim.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7llk_23424/05_2023/7llk_23424_trim.pdb" } resolution = 4.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.111 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: 5 Type Number sf(0) Gaussians S 123 5.16 5 C 12739 2.51 5 N 3404 2.21 5 O 4089 1.98 5 H 18627 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E ARG 46": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 78": "OD1" <-> "OD2" Residue "E GLU 83": "OE1" <-> "OE2" Residue "E PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 164": "OE1" <-> "OE2" Residue "E ARG 169": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 185": "OE1" <-> "OE2" Residue "E GLU 190": "OE1" <-> "OE2" Residue "E ARG 308": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E TYR 316": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 335": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 337": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E GLU 344": "OE1" <-> "OE2" Residue "E TYR 352": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 381": "OE1" <-> "OE2" Residue "E PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 429": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E TYR 435": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 466": "OE1" <-> "OE2" Residue "E PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 469": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 500": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 504": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F PHE 522": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 584": "OE1" <-> "OE2" Residue "F ASP 620": "OD1" <-> "OD2" Residue "F GLU 621": "OE1" <-> "OE2" Residue "F ASP 632": "OD1" <-> "OD2" Residue "F ARG 644": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F GLU 647": "OE1" <-> "OE2" Residue "F GLU 648": "OE1" <-> "OE2" Residue "F GLU 654": "OE1" <-> "OE2" Residue "F ASP 664": "OD1" <-> "OD2" Residue "G PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G ASP 68": "OD1" <-> "OD2" Residue "G PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 85": "OE1" <-> "OE2" Residue "G PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ASP 80": "OD1" <-> "OD2" Residue "H GLU 83": "OE1" <-> "OE2" Residue "H GLU 85": "OE1" <-> "OE2" Residue "H TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ASP 92": "OD1" <-> "OD2" Residue "A ARG 46": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 62": "OE1" <-> "OE2" Residue "A ASP 78": "OD1" <-> "OD2" Residue "A GLU 83": "OE1" <-> "OE2" Residue "A PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 164": "OE1" <-> "OE2" Residue "A ARG 169": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 190": "OE1" <-> "OE2" Residue "A TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 308": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 316": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 335": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 337": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 344": "OE1" <-> "OE2" Residue "A TYR 352": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 429": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 435": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 466": "OE1" <-> "OE2" Residue "A PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 469": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 500": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 504": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 522": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 584": "OE1" <-> "OE2" Residue "B ASP 620": "OD1" <-> "OD2" Residue "B GLU 621": "OE1" <-> "OE2" Residue "B ARG 644": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 647": "OE1" <-> "OE2" Residue "B GLU 648": "OE1" <-> "OE2" Residue "B GLU 654": "OE1" <-> "OE2" Residue "B GLU 659": "OE1" <-> "OE2" Residue "B ASP 664": "OD1" <-> "OD2" Residue "C PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 68": "OD1" <-> "OD2" Residue "C PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 80": "OD1" <-> "OD2" Residue "D GLU 83": "OE1" <-> "OE2" Residue "D GLU 85": "OE1" <-> "OE2" Residue "D TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 92": "OD1" <-> "OD2" Residue "I ARG 46": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I ASP 78": "OD1" <-> "OD2" Residue "I PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I GLU 164": "OE1" <-> "OE2" Residue "I ARG 169": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I GLU 185": "OE1" <-> "OE2" Residue "I GLU 190": "OE1" <-> "OE2" Residue "I TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I ARG 308": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I TYR 316": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I ARG 335": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 337": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I GLU 344": "OE1" <-> "OE2" Residue "I TYR 352": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I GLU 381": "OE1" <-> "OE2" Residue "I PHE 391": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I ARG 429": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I TYR 435": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I ASP 461": "OD1" <-> "OD2" Residue "I GLU 466": "OE1" <-> "OE2" Residue "I PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I ARG 469": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 500": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 504": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J PHE 522": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J GLU 584": "OE1" <-> "OE2" Residue "J ASP 620": "OD1" <-> "OD2" Residue "J GLU 621": "OE1" <-> "OE2" Residue "J ASP 632": "OD1" <-> "OD2" Residue "J ARG 644": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J GLU 647": "OE1" <-> "OE2" Residue "J GLU 648": "OE1" <-> "OE2" Residue "J GLU 654": "OE1" <-> "OE2" Residue "J ASP 664": "OD1" <-> "OD2" Residue "K PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K ASP 68": "OD1" <-> "OD2" Residue "K PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L GLU 27": "OE1" <-> "OE2" Residue "L PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L ASP 80": "OD1" <-> "OD2" Residue "L GLU 83": "OE1" <-> "OE2" Residue "L GLU 85": "OE1" <-> "OE2" Residue "L ASP 92": "OD1" <-> "OD2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/chem_data/mon_lib" Total number of atoms: 38982 Number of models: 1 Model: "" Number of chains: 47 Chain: "E" Number of atoms: 6894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 6894 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 22, 'TRANS': 417} Chain breaks: 3 Chain: "F" Number of atoms: 2005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 2005 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 124} Chain breaks: 1 Chain: "G" Number of atoms: 2100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 2100 Classifications: {'peptide': 131} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 127} Chain: "H" Number of atoms: 1525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 1525 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 5, 'TRANS': 96} Chain breaks: 1 Chain: "A" Number of atoms: 6894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 6894 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 22, 'TRANS': 417} Chain breaks: 3 Chain: "B" Number of atoms: 2005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 2005 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 124} Chain breaks: 1 Chain: "C" Number of atoms: 2100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 2100 Classifications: {'peptide': 131} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 127} Chain: "D" Number of atoms: 1525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 1525 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 5, 'TRANS': 96} Chain breaks: 1 Chain: "I" Number of atoms: 6894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 6894 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 22, 'TRANS': 417} Chain breaks: 3 Chain: "J" Number of atoms: 2005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 2005 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 124} Chain breaks: 1 Chain: "K" Number of atoms: 2100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 2100 Classifications: {'peptide': 131} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 127} Chain: "L" Number of atoms: 1525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 1525 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 5, 'TRANS': 96} Chain breaks: 1 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "P" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "Q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "S" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "T" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "U" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "X" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "Y" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "Z" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "a" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "b" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "c" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "d" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "e" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "h" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "j" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "k" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "l" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "m" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "n" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "o" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "p" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "r" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "s" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "E" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "I" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 17.44, per 1000 atoms: 0.45 Number of scatterers: 38982 At special positions: 0 Unit cell: (159.104, 166.108, 121.079, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 123 16.00 O 4089 8.00 N 3404 7.00 C 12739 6.00 H 18627 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.11 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.04 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.02 Simple disulfide: pdb=" SG CYS E 201 " - pdb=" SG CYS E 433 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.02 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.04 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.02 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.04 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS F 605 " distance=2.04 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.05 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.08 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 201 " - pdb=" SG CYS A 433 " distance=2.02 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.01 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.04 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.02 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.01 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.04 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.02 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.04 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.05 Simple disulfide: pdb=" SG CYS I 54 " - pdb=" SG CYS I 74 " distance=2.03 Simple disulfide: pdb=" SG CYS I 119 " - pdb=" SG CYS I 205 " distance=2.08 Simple disulfide: pdb=" SG CYS I 126 " - pdb=" SG CYS I 196 " distance=2.02 Simple disulfide: pdb=" SG CYS I 131 " - pdb=" SG CYS I 157 " distance=2.03 Simple disulfide: pdb=" SG CYS I 201 " - pdb=" SG CYS I 433 " distance=2.03 Simple disulfide: pdb=" SG CYS I 218 " - pdb=" SG CYS I 247 " distance=2.02 Simple disulfide: pdb=" SG CYS I 228 " - pdb=" SG CYS I 239 " distance=2.04 Simple disulfide: pdb=" SG CYS I 296 " - pdb=" SG CYS I 331 " distance=2.02 Simple disulfide: pdb=" SG CYS I 378 " - pdb=" SG CYS I 445 " distance=2.03 Simple disulfide: pdb=" SG CYS I 385 " - pdb=" SG CYS I 418 " distance=2.05 Simple disulfide: pdb=" SG CYS I 501 " - pdb=" SG CYS J 605 " distance=2.03 Simple disulfide: pdb=" SG CYS J 598 " - pdb=" SG CYS J 604 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.07 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-6 " BMA S 3 " - " MAN S 4 " " BMA X 3 " - " MAN X 4 " " BMA c 3 " - " MAN c 4 " " BMA h 3 " - " MAN h 4 " " BMA n 3 " - " MAN n 4 " " BMA s 3 " - " MAN s 4 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " " NAG h 1 " - " NAG h 2 " " NAG h 2 " - " BMA h 3 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " BMA j 3 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " NAG l 2 " - " BMA l 3 " " NAG m 1 " - " NAG m 2 " " NAG m 2 " - " BMA m 3 " " NAG n 1 " - " NAG n 2 " " NAG n 2 " - " BMA n 3 " " NAG o 1 " - " NAG o 2 " " NAG o 2 " - " BMA o 3 " " NAG p 1 " - " NAG p 2 " " NAG p 2 " - " BMA p 3 " " NAG q 1 " - " NAG q 2 " " NAG r 1 " - " NAG r 2 " " NAG r 2 " - " BMA r 3 " " NAG s 1 " - " NAG s 2 " " NAG s 2 " - " BMA s 3 " NAG-ASN " NAG A 601 " - " ASN A 133 " " NAG A 602 " - " ASN A 363 " " NAG A 603 " - " ASN A 448 " " NAG A 604 " - " ASN A 88 " " NAG E 601 " - " ASN E 133 " " NAG E 602 " - " ASN E 363 " " NAG E 603 " - " ASN E 448 " " NAG I 601 " - " ASN I 133 " " NAG I 602 " - " ASN I 363 " " NAG I 603 " - " ASN I 448 " " NAG M 1 " - " ASN E 88 " " NAG N 1 " - " ASN I 88 " " NAG O 1 " - " ASN E 160 " " NAG Q 1 " - " ASN E 234 " " NAG R 1 " - " ASN E 392 " " NAG S 1 " - " ASN E 262 " " NAG T 1 " - " ASN E 301 " " NAG U 1 " - " ASN E 156 " " NAG V 1 " - " ASN E 197 " " NAG W 1 " - " ASN E 465 " " NAG Y 1 " - " ASN A 160 " " NAG a 1 " - " ASN A 234 " " NAG b 1 " - " ASN A 392 " " NAG c 1 " - " ASN A 262 " " NAG d 1 " - " ASN A 301 " " NAG e 1 " - " ASN A 156 " " NAG f 1 " - " ASN A 197 " " NAG g 1 " - " ASN A 465 " " NAG j 1 " - " ASN I 160 " " NAG l 1 " - " ASN I 234 " " NAG m 1 " - " ASN I 392 " " NAG n 1 " - " ASN I 262 " " NAG o 1 " - " ASN I 301 " " NAG p 1 " - " ASN I 156 " " NAG q 1 " - " ASN I 197 " " NAG r 1 " - " ASN I 465 " Time building additional restraints: 35.67 Conformation dependent library (CDL) restraints added in 3.3 seconds 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4458 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 49 sheets defined 21.3% alpha, 23.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.18 Creating SS restraints... Processing helix chain 'E' and resid 99 through 117 Processing helix chain 'E' and resid 334 through 354 removed outlier: 4.135A pdb=" N TRP E 338 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N THR E 351 " --> pdb=" O GLU E 347 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N TYR E 352 " --> pdb=" O LYS E 348 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N PHE E 353 " --> pdb=" O LEU E 349 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 387 through 391 Processing helix chain 'E' and resid 425 through 429 removed outlier: 3.854A pdb=" N ARG E 429 " --> pdb=" O MET E 426 " (cutoff:3.500A) Processing helix chain 'E' and resid 474 through 484 removed outlier: 5.355A pdb=" N GLU E 482 " --> pdb=" O ASN E 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 537 through 544 Processing helix chain 'F' and resid 569 through 596 removed outlier: 3.651A pdb=" N ILE F 573 " --> pdb=" O THR F 569 " (cutoff:3.500A) Processing helix chain 'F' and resid 618 through 625 Processing helix chain 'F' and resid 627 through 646 removed outlier: 6.298A pdb=" N ASN F 637 " --> pdb=" O LYS F 633 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N TYR F 638 " --> pdb=" O GLU F 634 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N GLN F 640 " --> pdb=" O ASN F 636 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N LEU F 641 " --> pdb=" O ASN F 637 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARG F 644 " --> pdb=" O GLN F 640 " (cutoff:3.500A) Processing helix chain 'F' and resid 648 through 653 Processing helix chain 'F' and resid 654 through 663 removed outlier: 4.840A pdb=" N LEU F 660 " --> pdb=" O ASN F 656 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU F 661 " --> pdb=" O GLU F 657 " (cutoff:3.500A) Processing helix chain 'G' and resid 62 through 67 removed outlier: 3.854A pdb=" N GLY G 65 " --> pdb=" O SER G 62 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N ARG G 66 " --> pdb=" O VAL G 63 " (cutoff:3.500A) Processing helix chain 'G' and resid 74 through 77 Processing helix chain 'G' and resid 83 through 87 Processing helix chain 'A' and resid 99 through 117 removed outlier: 3.567A pdb=" N ILE A 109 " --> pdb=" O HIS A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 209 removed outlier: 4.007A pdb=" N SER A 209 " --> pdb=" O PRO A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 354 removed outlier: 4.094A pdb=" N TRP A 338 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N TYR A 352 " --> pdb=" O LYS A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 387 through 391 Processing helix chain 'A' and resid 425 through 429 removed outlier: 3.797A pdb=" N ARG A 429 " --> pdb=" O MET A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 484 removed outlier: 5.214A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 537 through 546 removed outlier: 3.786A pdb=" N LEU B 545 " --> pdb=" O ALA B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 596 Processing helix chain 'B' and resid 618 through 625 Processing helix chain 'B' and resid 627 through 646 removed outlier: 5.938A pdb=" N ASN B 637 " --> pdb=" O LYS B 633 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N TYR B 638 " --> pdb=" O GLU B 634 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N GLN B 640 " --> pdb=" O ASN B 636 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N LEU B 641 " --> pdb=" O ASN B 637 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE B 642 " --> pdb=" O TYR B 638 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ARG B 644 " --> pdb=" O GLN B 640 " (cutoff:3.500A) Processing helix chain 'B' and resid 654 through 663 removed outlier: 4.910A pdb=" N LEU B 660 " --> pdb=" O ASN B 656 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU B 661 " --> pdb=" O GLU B 657 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 67 removed outlier: 4.481A pdb=" N ARG C 66 " --> pdb=" O VAL C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 77 Processing helix chain 'C' and resid 83 through 87 Processing helix chain 'I' and resid 99 through 117 Processing helix chain 'I' and resid 205 through 209 removed outlier: 3.517A pdb=" N SER I 209 " --> pdb=" O PRO I 206 " (cutoff:3.500A) Processing helix chain 'I' and resid 334 through 354 removed outlier: 4.155A pdb=" N TRP I 338 " --> pdb=" O SER I 334 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N TYR I 352 " --> pdb=" O LYS I 348 " (cutoff:3.500A) Processing helix chain 'I' and resid 368 through 373 Processing helix chain 'I' and resid 387 through 391 Processing helix chain 'I' and resid 425 through 429 removed outlier: 3.821A pdb=" N ARG I 429 " --> pdb=" O MET I 426 " (cutoff:3.500A) Processing helix chain 'I' and resid 474 through 484 removed outlier: 5.295A pdb=" N GLU I 482 " --> pdb=" O ASN I 478 " (cutoff:3.500A) Processing helix chain 'J' and resid 529 through 534 Processing helix chain 'J' and resid 537 through 546 removed outlier: 3.788A pdb=" N LEU J 545 " --> pdb=" O ALA J 541 " (cutoff:3.500A) Processing helix chain 'J' and resid 569 through 596 Processing helix chain 'J' and resid 618 through 625 Processing helix chain 'J' and resid 627 through 646 removed outlier: 3.509A pdb=" N GLU J 634 " --> pdb=" O GLN J 630 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ASN J 637 " --> pdb=" O LYS J 633 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N TYR J 638 " --> pdb=" O GLU J 634 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLN J 640 " --> pdb=" O ASN J 636 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N LEU J 641 " --> pdb=" O ASN J 637 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE J 642 " --> pdb=" O TYR J 638 " (cutoff:3.500A) Processing helix chain 'J' and resid 648 through 653 Processing helix chain 'J' and resid 654 through 663 removed outlier: 4.764A pdb=" N LEU J 660 " --> pdb=" O ASN J 656 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU J 661 " --> pdb=" O GLU J 657 " (cutoff:3.500A) Processing helix chain 'K' and resid 62 through 65 removed outlier: 3.803A pdb=" N GLY K 65 " --> pdb=" O SER K 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 62 through 65' Processing helix chain 'K' and resid 74 through 77 Processing helix chain 'K' and resid 83 through 87 Processing sheet with id=AA1, first strand: chain 'E' and resid 494 through 499 removed outlier: 3.736A pdb=" N VAL E 38 " --> pdb=" O CYS F 604 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 45 through 47 Processing sheet with id=AA3, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AA4, first strand: chain 'E' and resid 91 through 94 removed outlier: 4.209A pdb=" N GLU E 91 " --> pdb=" O CYS E 239 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N CYS E 239 " --> pdb=" O GLU E 91 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY E 237 " --> pdb=" O PHE E 93 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 120 through 121 Processing sheet with id=AA6, first strand: chain 'E' and resid 129 through 132 Processing sheet with id=AA7, first strand: chain 'E' and resid 181 through 183 Processing sheet with id=AA8, first strand: chain 'E' and resid 259 through 261 removed outlier: 6.576A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N GLY E 451 " --> pdb=" O GLN E 290 " (cutoff:3.500A) removed outlier: 10.797A pdb=" N GLN E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 12.231A pdb=" N LEU E 453 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 12.122A pdb=" N LEU E 288 " --> pdb=" O LEU E 453 " (cutoff:3.500A) removed outlier: 10.381A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 10.542A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 259 through 261 removed outlier: 6.576A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ILE E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 303 through 308 Processing sheet with id=AB2, first strand: chain 'E' and resid 329 through 330 removed outlier: 3.929A pdb=" N PHE E 382 " --> pdb=" O LYS E 421 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHE E 376 " --> pdb=" O PHE E 383 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 18 through 21 Processing sheet with id=AB4, first strand: chain 'G' and resid 88 through 95 removed outlier: 3.998A pdb=" N THR G 107 " --> pdb=" O TYR G 90 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N CYS G 92 " --> pdb=" O ARG G 105 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N ARG G 105 " --> pdb=" O CYS G 92 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N ARG G 94 " --> pdb=" O TRP G 103 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N TRP G 103 " --> pdb=" O ARG G 94 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 19 through 23 removed outlier: 3.931A pdb=" N ALA H 19 " --> pdb=" O ILE H 75 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 53 through 54 removed outlier: 6.916A pdb=" N TRP H 35 " --> pdb=" O VAL H 47 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER H 34 " --> pdb=" O GLN H 89 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU H 85 " --> pdb=" O GLN H 38 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N TYR H 86 " --> pdb=" O GLY H 101 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N GLY H 101 " --> pdb=" O TYR H 86 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ASP H 92 " --> pdb=" O TYR H 95A" (cutoff:3.500A) removed outlier: 6.039A pdb=" N TYR H 95A" --> pdb=" O ASP H 92 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 494 through 499 removed outlier: 4.697A pdb=" N VAL A 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N THR B 606 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL A 38 " --> pdb=" O CYS B 604 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AB9, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AC1, first strand: chain 'A' and resid 91 through 94 removed outlier: 3.700A pdb=" N GLU A 91 " --> pdb=" O CYS A 239 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLY A 237 " --> pdb=" O PHE A 93 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 130 through 132 Processing sheet with id=AC3, first strand: chain 'A' and resid 181 through 183 Processing sheet with id=AC4, first strand: chain 'A' and resid 201 through 202 Processing sheet with id=AC5, first strand: chain 'A' and resid 259 through 261 removed outlier: 6.267A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N GLY A 451 " --> pdb=" O GLN A 290 " (cutoff:3.500A) removed outlier: 10.732A pdb=" N GLN A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 12.153A pdb=" N LEU A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 12.209A pdb=" N LEU A 288 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 10.455A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 10.519A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 259 through 261 removed outlier: 6.267A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 303 through 308 Processing sheet with id=AC8, first strand: chain 'A' and resid 329 through 330 removed outlier: 3.810A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE A 376 " --> pdb=" O PHE A 383 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 359 through 361 Processing sheet with id=AD1, first strand: chain 'C' and resid 18 through 21 Processing sheet with id=AD2, first strand: chain 'C' and resid 88 through 89 Processing sheet with id=AD3, first strand: chain 'C' and resid 92 through 95 removed outlier: 4.524A pdb=" N LEU C 102 " --> pdb=" O ARG C 94 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 21 through 23 Processing sheet with id=AD5, first strand: chain 'D' and resid 53 through 54 removed outlier: 3.514A pdb=" N VAL D 47 " --> pdb=" O TRP D 35 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N TRP D 35 " --> pdb=" O VAL D 47 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N SER D 34 " --> pdb=" O GLN D 89 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLN D 89 " --> pdb=" O SER D 34 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU D 85 " --> pdb=" O GLN D 38 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N TYR D 86 " --> pdb=" O GLY D 101 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N GLY D 101 " --> pdb=" O TYR D 86 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ASP D 92 " --> pdb=" O TYR D 95A" (cutoff:3.500A) removed outlier: 6.168A pdb=" N TYR D 95A" --> pdb=" O ASP D 92 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 494 through 499 removed outlier: 4.610A pdb=" N VAL I 36 " --> pdb=" O THR J 606 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N THR J 606 " --> pdb=" O VAL I 36 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 45 through 47 Processing sheet with id=AD8, first strand: chain 'I' and resid 53 through 55 Processing sheet with id=AD9, first strand: chain 'I' and resid 91 through 94 removed outlier: 3.966A pdb=" N GLU I 91 " --> pdb=" O CYS I 239 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'I' and resid 120 through 121 Processing sheet with id=AE2, first strand: chain 'I' and resid 129 through 132 Processing sheet with id=AE3, first strand: chain 'I' and resid 181 through 183 Processing sheet with id=AE4, first strand: chain 'I' and resid 259 through 261 removed outlier: 6.492A pdb=" N LEU I 260 " --> pdb=" O THR I 450 " (cutoff:3.500A) removed outlier: 10.033A pdb=" N ASN I 448 " --> pdb=" O GLN I 290 " (cutoff:3.500A) removed outlier: 11.622A pdb=" N GLN I 290 " --> pdb=" O ASN I 448 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N THR I 450 " --> pdb=" O LEU I 288 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'I' and resid 259 through 261 removed outlier: 6.492A pdb=" N LEU I 260 " --> pdb=" O THR I 450 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'I' and resid 303 through 308 Processing sheet with id=AE7, first strand: chain 'I' and resid 329 through 330 removed outlier: 3.664A pdb=" N ALA I 329 " --> pdb=" O CYS I 418 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N PHE I 382 " --> pdb=" O LYS I 421 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'I' and resid 359 through 361 Processing sheet with id=AE9, first strand: chain 'K' and resid 18 through 21 Processing sheet with id=AF1, first strand: chain 'K' and resid 88 through 89 Processing sheet with id=AF2, first strand: chain 'K' and resid 92 through 95 removed outlier: 4.763A pdb=" N LEU K 102 " --> pdb=" O ARG K 94 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'L' and resid 19 through 23 removed outlier: 3.938A pdb=" N ALA L 19 " --> pdb=" O ILE L 75 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'L' and resid 53 through 54 removed outlier: 7.095A pdb=" N TRP L 35 " --> pdb=" O VAL L 47 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER L 34 " --> pdb=" O GLN L 89 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLU L 85 " --> pdb=" O GLN L 38 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N TYR L 86 " --> pdb=" O GLY L 101 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N GLY L 101 " --> pdb=" O TYR L 86 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ASP L 92 " --> pdb=" O TYR L 95A" (cutoff:3.500A) removed outlier: 5.960A pdb=" N TYR L 95A" --> pdb=" O ASP L 92 " (cutoff:3.500A) 603 hydrogen bonds defined for protein. 1563 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 16.98 Time building geometry restraints manager: 36.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 5281 1.03 - 1.23: 15611 1.23 - 1.43: 6339 1.43 - 1.63: 11985 1.63 - 1.83: 162 Bond restraints: 39378 Sorted by residual: bond pdb=" C ARG L 37 " pdb=" O ARG L 37 " ideal model delta sigma weight residual 1.233 1.136 0.097 1.28e-02 6.10e+03 5.72e+01 bond pdb=" CD1 TRP C 100C" pdb=" HD1 TRP C 100C" ideal model delta sigma weight residual 0.930 1.080 -0.150 2.00e-02 2.50e+03 5.59e+01 bond pdb=" CD2 PHE C 67 " pdb=" HD2 PHE C 67 " ideal model delta sigma weight residual 0.930 1.079 -0.149 2.00e-02 2.50e+03 5.58e+01 bond pdb=" CD2 PHE I 353 " pdb=" HD2 PHE I 353 " ideal model delta sigma weight residual 0.930 1.079 -0.149 2.00e-02 2.50e+03 5.58e+01 bond pdb=" N VAL A 292 " pdb=" H VAL A 292 " ideal model delta sigma weight residual 0.860 1.009 -0.149 2.00e-02 2.50e+03 5.58e+01 ... (remaining 39373 not shown) Histogram of bond angle deviations from ideal: 90.29 - 99.48: 31 99.48 - 108.67: 17786 108.67 - 117.87: 34213 117.87 - 127.06: 17834 127.06 - 136.25: 482 Bond angle restraints: 70346 Sorted by residual: angle pdb=" N PRO E 253 " pdb=" CA PRO E 253 " pdb=" C PRO E 253 " ideal model delta sigma weight residual 113.65 99.64 14.01 1.35e+00 5.49e-01 1.08e+02 angle pdb=" N PRO A 253 " pdb=" CA PRO A 253 " pdb=" C PRO A 253 " ideal model delta sigma weight residual 114.03 101.46 12.57 1.23e+00 6.61e-01 1.04e+02 angle pdb=" CA ASP C 101 " pdb=" CB ASP C 101 " pdb=" CG ASP C 101 " ideal model delta sigma weight residual 112.60 120.94 -8.34 1.00e+00 1.00e+00 6.96e+01 angle pdb=" N PRO A 206 " pdb=" CA PRO A 206 " pdb=" C PRO A 206 " ideal model delta sigma weight residual 114.03 103.99 10.04 1.23e+00 6.61e-01 6.66e+01 angle pdb=" N TYR F 586 " pdb=" CA TYR F 586 " pdb=" C TYR F 586 " ideal model delta sigma weight residual 111.28 102.39 8.89 1.09e+00 8.42e-01 6.65e+01 ... (remaining 70341 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.06: 13419 18.06 - 36.13: 1294 36.13 - 54.19: 284 54.19 - 72.25: 254 72.25 - 90.32: 43 Dihedral angle restraints: 15294 sinusoidal: 7170 harmonic: 8124 Sorted by residual: dihedral pdb=" C VAL L 26 " pdb=" N VAL L 26 " pdb=" CA VAL L 26 " pdb=" CB VAL L 26 " ideal model delta harmonic sigma weight residual -122.00 -136.71 14.71 0 2.50e+00 1.60e-01 3.46e+01 dihedral pdb=" CA ASN E 302 " pdb=" C ASN E 302 " pdb=" N THR E 303 " pdb=" CA THR E 303 " ideal model delta harmonic sigma weight residual 180.00 -150.71 -29.29 0 5.00e+00 4.00e-02 3.43e+01 dihedral pdb=" CA SER G 49 " pdb=" C SER G 49 " pdb=" N SER G 50 " pdb=" CA SER G 50 " ideal model delta harmonic sigma weight residual 180.00 150.86 29.14 0 5.00e+00 4.00e-02 3.40e+01 ... (remaining 15291 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.311: 3411 0.311 - 0.622: 47 0.622 - 0.933: 3 0.933 - 1.244: 0 1.244 - 1.554: 1 Chirality restraints: 3462 Sorted by residual: chirality pdb=" C1 NAG M 2 " pdb=" O4 NAG M 1 " pdb=" C2 NAG M 2 " pdb=" O5 NAG M 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-02 2.50e+03 2.39e+02 chirality pdb=" C1 BMA a 3 " pdb=" O4 NAG a 2 " pdb=" C2 BMA a 3 " pdb=" O5 BMA a 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.63 0.23 2.00e-02 2.50e+03 1.37e+02 chirality pdb=" C1 NAG m 2 " pdb=" O4 NAG m 1 " pdb=" C2 NAG m 2 " pdb=" O5 NAG m 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.63 0.23 2.00e-02 2.50e+03 1.27e+02 ... (remaining 3459 not shown) Planarity restraints: 5735 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN I 203 " -0.241 2.00e-02 2.50e+03 3.80e-01 2.17e+03 pdb=" CD GLN I 203 " 0.012 2.00e-02 2.50e+03 pdb=" OE1 GLN I 203 " 0.235 2.00e-02 2.50e+03 pdb=" NE2 GLN I 203 " -0.003 2.00e-02 2.50e+03 pdb="HE21 GLN I 203 " 0.612 2.00e-02 2.50e+03 pdb="HE22 GLN I 203 " -0.615 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN E 203 " -0.242 2.00e-02 2.50e+03 3.75e-01 2.10e+03 pdb=" CD GLN E 203 " 0.010 2.00e-02 2.50e+03 pdb=" OE1 GLN E 203 " 0.239 2.00e-02 2.50e+03 pdb=" NE2 GLN E 203 " -0.004 2.00e-02 2.50e+03 pdb="HE21 GLN E 203 " 0.601 2.00e-02 2.50e+03 pdb="HE22 GLN E 203 " -0.603 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN I 246 " -0.253 2.00e-02 2.50e+03 3.35e-01 1.68e+03 pdb=" CD GLN I 246 " 0.020 2.00e-02 2.50e+03 pdb=" OE1 GLN I 246 " 0.245 2.00e-02 2.50e+03 pdb=" NE2 GLN I 246 " -0.004 2.00e-02 2.50e+03 pdb="HE21 GLN I 246 " 0.519 2.00e-02 2.50e+03 pdb="HE22 GLN I 246 " -0.527 2.00e-02 2.50e+03 ... (remaining 5732 not shown) Histogram of nonbonded interaction distances: 1.37 - 2.01: 1137 2.01 - 2.66: 46837 2.66 - 3.31: 116842 3.31 - 3.95: 148719 3.95 - 4.60: 221386 Nonbonded interactions: 534921 Sorted by model distance: nonbonded pdb=" HG3 PRO I 212 " pdb="HG21 VAL I 254 " model vdw 1.366 2.440 nonbonded pdb=" HG SER H 67 " pdb=" OD1 ASP H 69 " model vdw 1.522 1.850 nonbonded pdb=" HG SER L 67 " pdb=" OD1 ASP L 69 " model vdw 1.562 1.850 nonbonded pdb=" HG1 THR I 138 " pdb=" OD1 ASP I 325 " model vdw 1.573 1.850 nonbonded pdb=" HG SER D 67 " pdb=" OD1 ASP D 69 " model vdw 1.588 1.850 ... (remaining 534916 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 32 through 504 or resid 601 through 603)) selection = chain 'E' selection = chain 'I' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'J' } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'K' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'V' selection = chain 'f' selection = chain 'q' } ncs_group { reference = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'T' selection = chain 'U' selection = chain 'W' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'd' selection = chain 'e' selection = chain 'g' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'o' selection = chain 'p' selection = chain 'r' } ncs_group { reference = chain 'S' selection = chain 'X' selection = chain 'c' selection = chain 'h' selection = chain 'n' selection = chain 's' } 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: 1.310 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: 0.490 Extract box with map and model: 9.630 Check model and map are aligned: 0.570 Set scattering table: 0.410 Process input model: 129.100 Find NCS groups from input model: 1.980 Set up NCS constraints: 0.630 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:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 146.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 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 : 0.015 0.097 20751 Z= 0.961 Angle : 2.147 20.396 28151 Z= 1.359 Chirality : 0.123 1.554 3462 Planarity : 0.020 0.290 3422 Dihedral : 16.378 90.315 7053 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 2.44 Ramachandran Plot: Outliers : 2.60 % Allowed : 12.59 % Favored : 84.81 % Rotamer Outliers : 4.52 % Cbeta Deviations : 0.63 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -3.42 (0.14), residues: 2343 helix: -2.28 (0.21), residues: 372 sheet: -1.51 (0.29), residues: 279 loop : -2.60 (0.13), residues: 1692 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 216 time to evaluate : 3.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 95 outliers final: 56 residues processed: 302 average time/residue: 0.7594 time to fit residues: 333.7419 Evaluate side-chains 226 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 170 time to evaluate : 2.467 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 56 outliers final: 14 residues processed: 56 average time/residue: 0.4848 time to fit residues: 46.4343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 200 optimal weight: 5.9990 chunk 179 optimal weight: 6.9990 chunk 99 optimal weight: 7.9990 chunk 61 optimal weight: 5.9990 chunk 121 optimal weight: 5.9990 chunk 95 optimal weight: 8.9990 chunk 185 optimal weight: 5.9990 chunk 71 optimal weight: 6.9990 chunk 112 optimal weight: 7.9990 chunk 138 optimal weight: 8.9990 chunk 215 optimal weight: 20.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 302 ASN E 478 ASN H 95 ASN ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 302 ASN B 652 GLN ** I 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 302 ASN I 332 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.3164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.089 20751 Z= 0.418 Angle : 1.039 14.071 28151 Z= 0.527 Chirality : 0.057 0.715 3462 Planarity : 0.008 0.153 3422 Dihedral : 9.991 32.768 2583 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 18.03 Ramachandran Plot: Outliers : 0.73 % Allowed : 12.51 % Favored : 86.77 % Rotamer Outliers : 0.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.48 % 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: -3.60 (0.15), residues: 2343 helix: -2.15 (0.22), residues: 375 sheet: -1.91 (0.26), residues: 333 loop : -2.74 (0.13), residues: 1635 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4686 Ramachandran restraints generated. 2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 179 time to evaluate : 2.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 7 residues processed: 187 average time/residue: 0.5964 time to fit residues: 159.2483 Evaluate side-chains 158 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 151 time to evaluate : 2.315 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 7 average time/residue: 0.3115 time to fit residues: 6.9432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 119 optimal weight: 7.9990 chunk 66 optimal weight: 0.9980 chunk 179 optimal weight: 9.9990 chunk 146 optimal weight: 6.9990 chunk 59 optimal weight: 20.0000 chunk 215 optimal weight: 3.9990 chunk 232 optimal weight: 10.0000 chunk 192 optimal weight: 9.9990 chunk 213 optimal weight: 9.9990 chunk 73 optimal weight: 7.9990 chunk 172 optimal weight: 9.9990 overall best weight: 5.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: