Starting phenix.real_space_refine on Sun Mar 24 05:28:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7llk_23424/03_2024/7llk_23424_trim.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7llk_23424/03_2024/7llk_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_23424/03_2024/7llk_23424.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7llk_23424/03_2024/7llk_23424.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7llk_23424/03_2024/7llk_23424_trim.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7llk_23424/03_2024/7llk_23424_trim.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= 0.004 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-dev-5265/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 dihedrals: 6 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 dihedrals: 9 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 dihedrals: 9 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 dihedrals: 9 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 dihedrals: 9 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 dihedrals: 9 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 dihedrals: 12 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 dihedrals: 9 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 dihedrals: 9 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 dihedrals: 6 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 dihedrals: 9 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 dihedrals: 12 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 dihedrals: 9 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 dihedrals: 9 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 dihedrals: 9 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 dihedrals: 9 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 dihedrals: 12 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 dihedrals: 9 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 dihedrals: 9 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 dihedrals: 6 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 dihedrals: 9 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 dihedrals: 12 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 dihedrals: 9 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 dihedrals: 9 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 dihedrals: 9 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 dihedrals: 9 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 dihedrals: 12 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 dihedrals: 9 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 dihedrals: 9 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 dihedrals: 6 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 dihedrals: 9 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 dihedrals: 12 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 dihedrals: 9 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 dihedrals: 12 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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 16.24, per 1000 atoms: 0.42 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: 32.93 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: 3.20 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: 15.82 Time building geometry restraints manager: 34.14 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 - 21.67: 17820 21.67 - 43.33: 1336 43.33 - 65.00: 584 65.00 - 86.67: 249 86.67 - 108.34: 121 Dihedral angle restraints: 20110 sinusoidal: 11986 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 20107 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: 1.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.580 Extract box with map and model: 8.980 Check model and map are aligned: 0.550 Set scattering table: 0.340 Process input model: 120.750 Find NCS groups from input model: 1.960 Set up NCS constraints: 0.620 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 138.660 ------------------------------------------------------------------------------- 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 : 21.774 108.337 9253 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 % Allowed : 10.14 % Favored : 85.33 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.166 0.031 TRP I 427 HIS 0.016 0.004 HIS A 72 PHE 0.080 0.018 PHE A 376 TYR 0.118 0.020 TYR A 316 ARG 0.010 0.001 ARG I 429 *********************** 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 : 3.282 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 REVERT: E 215 ILE cc_start: 0.8310 (OUTLIER) cc_final: 0.7927 (mp) REVERT: F 588 GLU cc_start: 0.8396 (tp30) cc_final: 0.8021 (tp30) REVERT: F 596 TRP cc_start: 0.7897 (m-10) cc_final: 0.7665 (m-10) REVERT: H 48 MET cc_start: 0.2008 (mtp) cc_final: 0.1644 (tmm) REVERT: B 588 GLU cc_start: 0.8528 (tp30) cc_final: 0.8320 (tp30) REVERT: I 164 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.7764 (pp20) REVERT: I 499 THR cc_start: 0.7661 (OUTLIER) cc_final: 0.7361 (m) REVERT: J 580 VAL cc_start: 0.9362 (t) cc_final: 0.9151 (p) outliers start: 95 outliers final: 56 residues processed: 302 average time/residue: 0.8289 time to fit residues: 363.1013 Evaluate side-chains 230 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 171 time to evaluate : 4.114 ------------------------------------------------------------------------------- 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: 1.9990 chunk 179 optimal weight: 5.9990 chunk 99 optimal weight: 7.9990 chunk 61 optimal weight: 3.9990 chunk 121 optimal weight: 5.9990 chunk 95 optimal weight: 5.9990 chunk 185 optimal weight: 5.9990 chunk 71 optimal weight: 5.9990 chunk 112 optimal weight: 5.9990 chunk 138 optimal weight: 7.9990 chunk 215 optimal weight: 30.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ** I 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 241 ASN I 302 ASN I 332 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.3092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 20751 Z= 0.364 Angle : 1.049 15.041 28151 Z= 0.530 Chirality : 0.060 0.760 3462 Planarity : 0.008 0.155 3422 Dihedral : 18.064 78.818 4783 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 15.90 Ramachandran Plot: Outliers : 0.73 % Allowed : 11.78 % Favored : 87.49 % Rotamer: Outliers : 0.24 % Allowed : 3.71 % Favored : 96.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: -3.50 (0.15), residues: 2343 helix: -2.01 (0.22), residues: 378 sheet: -1.99 (0.26), residues: 333 loop : -2.66 (0.13), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP I 427 HIS 0.011 0.003 HIS E 72 PHE 0.030 0.002 PHE C 91 TYR 0.021 0.002 TYR E 316 ARG 0.006 0.001 ARG K 64 *********************** 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 195 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 190 time to evaluate : 3.055 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: F 588 GLU cc_start: 0.8798 (tp30) cc_final: 0.8371 (tp30) REVERT: F 592 LEU cc_start: 0.9512 (mt) cc_final: 0.8961 (mt) REVERT: G 2 MET cc_start: 0.7065 (mtt) cc_final: 0.6611 (ttp) REVERT: B 580 VAL cc_start: 0.9502 (p) cc_final: 0.9124 (p) REVERT: I 161 MET cc_start: 0.7285 (tpt) cc_final: 0.6933 (tpp) REVERT: I 434 MET cc_start: 0.8614 (tpp) cc_final: 0.8326 (tpp) REVERT: L 48 MET cc_start: 0.5004 (ttp) cc_final: 0.4415 (tmm) outliers start: 5 outliers final: 4 residues processed: 195 average time/residue: 0.8855 time to fit residues: 246.5856 Evaluate side-chains 159 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 155 time to evaluate : 2.998 ------------------------------------------------------------------------------- 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: 6.9990 chunk 66 optimal weight: 9.9990 chunk 179 optimal weight: 20.0000 chunk 146 optimal weight: 9.9990 chunk 59 optimal weight: 9.9990 chunk 215 optimal weight: 4.9990 chunk 232 optimal weight: 6.9990 chunk 192 optimal weight: 5.9990 chunk 213 optimal weight: 8.9990 chunk 73 optimal weight: 9.9990 chunk 172 optimal weight: 9.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 398 ASN D 95 ASN ** I 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 95 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.3927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.098 20751 Z= 0.363 Angle : 0.957 13.942 28151 Z= 0.487 Chirality : 0.056 0.582 3462 Planarity : 0.007 0.153 3422 Dihedral : 13.580 59.969 4783 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 23.71 Ramachandran Plot: Outliers : 0.64 % Allowed : 14.08 % Favored : 85.28 % Rotamer: Outliers : 0.24 % Allowed : 3.81 % Favored : 95.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: -3.65 (0.15), residues: 2343 helix: -1.98 (0.23), residues: 381 sheet: -2.14 (0.23), residues: 456 loop : -2.78 (0.14), residues: 1506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.003 TRP K 32 HIS 0.009 0.002 HIS K 96 PHE 0.024 0.002 PHE G 67 TYR 0.023 0.002 TYR H 36 ARG 0.009 0.001 ARG G 64 *********************** REFINEMENT MACRO_CYCLE 3 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 179 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 174 time to evaluate : 2.984 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: F 588 GLU cc_start: 0.8860 (tp30) cc_final: 0.8657 (tp30) REVERT: H 48 MET cc_start: 0.6964 (tmm) cc_final: 0.6707 (tmm) REVERT: I 161 MET cc_start: 0.7345 (tpt) cc_final: 0.6956 (tpp) REVERT: J 530 MET cc_start: 0.7772 (mtp) cc_final: 0.6611 (mtm) outliers start: 5 outliers final: 4 residues processed: 179 average time/residue: 0.8752 time to fit residues: 224.3911 Evaluate side-chains 153 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 149 time to evaluate : 3.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 213 optimal weight: 7.9990 chunk 162 optimal weight: 10.0000 chunk 111 optimal weight: 8.9990 chunk 23 optimal weight: 8.9990 chunk 102 optimal weight: 1.9990 chunk 144 optimal weight: 20.0000 chunk 216 optimal weight: 5.9990 chunk 229 optimal weight: 8.9990 chunk 113 optimal weight: 9.9990 chunk 205 optimal weight: 10.0000 chunk 61 optimal weight: 0.0470 overall best weight: 5.0086 ------------------------------------------------------------------------------- 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** ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 96 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.4404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 20751 Z= 0.289 Angle : 0.850 10.147 28151 Z= 0.433 Chirality : 0.052 0.524 3462 Planarity : 0.006 0.126 3422 Dihedral : 11.191 59.466 4783 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 22.14 Ramachandran Plot: Outliers : 0.51 % Allowed : 13.70 % Favored : 85.79 % Rotamer: Outliers : 0.10 % Allowed : 2.67 % Favored : 97.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.15 % Twisted General : 0.13 % 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: -3.49 (0.16), residues: 2343 helix: -1.71 (0.24), residues: 381 sheet: -2.03 (0.25), residues: 405 loop : -2.73 (0.14), residues: 1557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP G 32 HIS 0.006 0.002 HIS E 72 PHE 0.015 0.002 PHE G 91 TYR 0.027 0.002 TYR F 638 ARG 0.005 0.000 ARG E 500 *********************** REFINEMENT MACRO_CYCLE 4 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 172 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 170 time to evaluate : 3.124 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: F 530 MET cc_start: 0.7663 (mtp) cc_final: 0.6482 (mtm) REVERT: H 48 MET cc_start: 0.7703 (tmm) cc_final: 0.7248 (tmm) REVERT: B 580 VAL cc_start: 0.9550 (p) cc_final: 0.9112 (p) REVERT: B 626 MET cc_start: 0.8122 (mmp) cc_final: 0.7880 (mmm) REVERT: I 161 MET cc_start: 0.7442 (tpt) cc_final: 0.6977 (tpp) REVERT: J 530 MET cc_start: 0.7735 (mtp) cc_final: 0.6316 (mtm) outliers start: 2 outliers final: 2 residues processed: 172 average time/residue: 0.8738 time to fit residues: 218.6405 Evaluate side-chains 148 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 146 time to evaluate : 3.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 190 optimal weight: 10.0000 chunk 130 optimal weight: 4.9990 chunk 3 optimal weight: 8.9990 chunk 170 optimal weight: 9.9990 chunk 94 optimal weight: 8.9990 chunk 195 optimal weight: 5.9990 chunk 158 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 116 optimal weight: 5.9990 chunk 205 optimal weight: 10.0000 chunk 57 optimal weight: 0.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- 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** ** A 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 216 HIS J 535 ASN L 51 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.4818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 20751 Z= 0.298 Angle : 0.821 7.091 28151 Z= 0.422 Chirality : 0.050 0.505 3462 Planarity : 0.006 0.109 3422 Dihedral : 10.324 59.275 4783 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 24.45 Ramachandran Plot: Outliers : 0.43 % Allowed : 15.32 % Favored : 84.25 % Rotamer: Outliers : 0.10 % Allowed : 2.24 % Favored : 97.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.15 % Twisted General : 0.13 % 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: -3.54 (0.16), residues: 2343 helix: -1.69 (0.24), residues: 381 sheet: -2.18 (0.26), residues: 390 loop : -2.74 (0.14), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP K 103 HIS 0.008 0.002 HIS E 72 PHE 0.022 0.002 PHE I 210 TYR 0.047 0.002 TYR K 56 ARG 0.006 0.000 ARG A 456 *********************** REFINEMENT MACRO_CYCLE 5 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 166 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 164 time to evaluate : 2.546 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: F 530 MET cc_start: 0.7678 (mtp) cc_final: 0.6455 (mtm) REVERT: H 48 MET cc_start: 0.7700 (tmm) cc_final: 0.7144 (tmm) REVERT: B 530 MET cc_start: 0.6650 (mtt) cc_final: 0.6380 (mtt) REVERT: B 626 MET cc_start: 0.8197 (mmp) cc_final: 0.7780 (mmm) REVERT: C 35 MET cc_start: 0.6897 (tpt) cc_final: 0.6561 (tpp) REVERT: I 161 MET cc_start: 0.7465 (tpt) cc_final: 0.7040 (tpp) REVERT: J 530 MET cc_start: 0.7851 (mtp) cc_final: 0.6378 (mtm) outliers start: 2 outliers final: 2 residues processed: 166 average time/residue: 0.8307 time to fit residues: 199.1654 Evaluate side-chains 143 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 141 time to evaluate : 3.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 77 optimal weight: 8.9990 chunk 206 optimal weight: 8.9990 chunk 45 optimal weight: 5.9990 chunk 134 optimal weight: 8.9990 chunk 56 optimal weight: 9.9990 chunk 229 optimal weight: 9.9990 chunk 190 optimal weight: 6.9990 chunk 106 optimal weight: 9.9990 chunk 19 optimal weight: 8.9990 chunk 75 optimal weight: 3.9990 chunk 120 optimal weight: 10.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- 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 ** A 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.5410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 20751 Z= 0.381 Angle : 0.876 8.294 28151 Z= 0.454 Chirality : 0.050 0.533 3462 Planarity : 0.006 0.139 3422 Dihedral : 10.153 59.011 4783 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 34.95 Ramachandran Plot: Outliers : 0.43 % Allowed : 16.01 % Favored : 83.57 % Rotamer: Outliers : 0.10 % Allowed : 2.81 % Favored : 97.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.26 % 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: -3.85 (0.15), residues: 2343 helix: -1.88 (0.24), residues: 381 sheet: -2.65 (0.23), residues: 429 loop : -2.86 (0.14), residues: 1533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP E 96 HIS 0.009 0.002 HIS A 85 PHE 0.024 0.003 PHE C 100A TYR 0.029 0.003 TYR K 56 ARG 0.031 0.001 ARG E 500 *********************** REFINEMENT MACRO_CYCLE 6 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 158 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 156 time to evaluate : 3.178 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: F 530 MET cc_start: 0.7917 (mtp) cc_final: 0.6676 (mtm) REVERT: H 48 MET cc_start: 0.7757 (tmm) cc_final: 0.7168 (tmm) REVERT: B 580 VAL cc_start: 0.9552 (p) cc_final: 0.9208 (p) REVERT: J 530 MET cc_start: 0.7973 (mtp) cc_final: 0.7013 (mtm) outliers start: 2 outliers final: 2 residues processed: 158 average time/residue: 0.8281 time to fit residues: 190.0738 Evaluate side-chains 135 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 133 time to evaluate : 3.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 221 optimal weight: 7.9990 chunk 25 optimal weight: 0.9980 chunk 130 optimal weight: 2.9990 chunk 167 optimal weight: 9.9990 chunk 129 optimal weight: 5.9990 chunk 193 optimal weight: 0.0570 chunk 128 optimal weight: 5.9990 chunk 228 optimal weight: 9.9990 chunk 142 optimal weight: 5.9990 chunk 139 optimal weight: 9.9990 chunk 105 optimal weight: 10.0000 overall best weight: 3.2104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 428 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.5475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 20751 Z= 0.227 Angle : 0.762 7.372 28151 Z= 0.391 Chirality : 0.048 0.501 3462 Planarity : 0.005 0.073 3422 Dihedral : 9.684 55.971 4783 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 24.50 Ramachandran Plot: Outliers : 0.38 % Allowed : 13.87 % Favored : 85.74 % Rotamer: Outliers : 0.10 % Allowed : 1.86 % Favored : 98.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.13 % 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: -3.66 (0.16), residues: 2343 helix: -1.79 (0.24), residues: 399 sheet: -2.57 (0.23), residues: 441 loop : -2.70 (0.15), residues: 1503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 479 HIS 0.006 0.001 HIS E 72 PHE 0.023 0.002 PHE C 67 TYR 0.050 0.002 TYR K 56 ARG 0.007 0.000 ARG C 64 *********************** REFINEMENT MACRO_CYCLE 7 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 159 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 157 time to evaluate : 3.233 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: F 530 MET cc_start: 0.7753 (mtp) cc_final: 0.6382 (mtm) REVERT: H 48 MET cc_start: 0.7503 (tmm) cc_final: 0.6856 (tmm) REVERT: B 530 MET cc_start: 0.6648 (mtt) cc_final: 0.6394 (mtt) REVERT: B 589 VAL cc_start: 0.9463 (m) cc_final: 0.8992 (m) REVERT: J 530 MET cc_start: 0.7782 (mtp) cc_final: 0.6733 (mtm) REVERT: K 82 MET cc_start: 0.9305 (mpp) cc_final: 0.8655 (mpp) REVERT: L 80 ASP cc_start: 0.7969 (p0) cc_final: 0.7749 (p0) outliers start: 2 outliers final: 2 residues processed: 159 average time/residue: 0.9149 time to fit residues: 211.6151 Evaluate side-chains 134 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 132 time to evaluate : 3.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 141 optimal weight: 8.9990 chunk 91 optimal weight: 1.9990 chunk 136 optimal weight: 20.0000 chunk 68 optimal weight: 9.9990 chunk 44 optimal weight: 20.0000 chunk 145 optimal weight: 10.0000 chunk 155 optimal weight: 9.9990 chunk 112 optimal weight: 9.9990 chunk 21 optimal weight: 10.0000 chunk 179 optimal weight: 9.9990 chunk 207 optimal weight: 0.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 535 ASN ** A 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 302 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.5814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 20751 Z= 0.343 Angle : 0.824 8.587 28151 Z= 0.426 Chirality : 0.048 0.494 3462 Planarity : 0.006 0.078 3422 Dihedral : 9.722 57.325 4783 Min Nonbonded Distance : 1.758 Molprobity Statistics. All-atom Clashscore : 32.96 Ramachandran Plot: Outliers : 0.38 % Allowed : 16.56 % Favored : 83.06 % Rotamer: Outliers : 0.10 % Allowed : 1.29 % Favored : 98.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.22 % 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: -3.83 (0.15), residues: 2343 helix: -1.91 (0.24), residues: 381 sheet: -2.86 (0.25), residues: 387 loop : -2.78 (0.14), residues: 1575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 479 HIS 0.008 0.002 HIS A 85 PHE 0.015 0.002 PHE K 91 TYR 0.047 0.002 TYR K 56 ARG 0.007 0.001 ARG B 585 *********************** REFINEMENT MACRO_CYCLE 8 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 153 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 151 time to evaluate : 3.309 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: H 48 MET cc_start: 0.7753 (tmm) cc_final: 0.7099 (tmm) REVERT: B 580 VAL cc_start: 0.9533 (p) cc_final: 0.9032 (p) REVERT: J 530 MET cc_start: 0.7990 (mtp) cc_final: 0.6940 (mtm) outliers start: 2 outliers final: 2 residues processed: 153 average time/residue: 0.8805 time to fit residues: 194.6281 Evaluate side-chains 130 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 128 time to evaluate : 3.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 218 optimal weight: 3.9990 chunk 199 optimal weight: 8.9990 chunk 212 optimal weight: 2.9990 chunk 128 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 167 optimal weight: 9.9990 chunk 65 optimal weight: 6.9990 chunk 192 optimal weight: 10.0000 chunk 201 optimal weight: 8.9990 chunk 139 optimal weight: 10.0000 chunk 225 optimal weight: 6.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.5869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 20751 Z= 0.233 Angle : 0.748 7.307 28151 Z= 0.385 Chirality : 0.047 0.463 3462 Planarity : 0.005 0.078 3422 Dihedral : 9.419 57.460 4783 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 26.54 Ramachandran Plot: Outliers : 0.38 % Allowed : 15.07 % Favored : 84.55 % Rotamer: Outliers : 0.10 % Allowed : 1.05 % Favored : 98.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.15 % Twisted General : 0.13 % 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: -3.69 (0.16), residues: 2343 helix: -1.87 (0.23), residues: 402 sheet: -2.65 (0.23), residues: 450 loop : -2.68 (0.15), residues: 1491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP E 96 HIS 0.006 0.001 HIS A 216 PHE 0.012 0.002 PHE A 210 TYR 0.021 0.002 TYR A 217 ARG 0.007 0.000 ARG L 54 *********************** REFINEMENT MACRO_CYCLE 9 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 151 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 149 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 48 MET cc_start: 0.7654 (tmm) cc_final: 0.6986 (tmm) REVERT: H 60 GLU cc_start: 0.7260 (tp30) cc_final: 0.7056 (tp30) REVERT: J 530 MET cc_start: 0.7849 (mtp) cc_final: 0.6775 (mtm) REVERT: L 80 ASP cc_start: 0.8006 (p0) cc_final: 0.7733 (p0) outliers start: 2 outliers final: 2 residues processed: 151 average time/residue: 0.9187 time to fit residues: 199.0678 Evaluate side-chains 130 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 128 time to evaluate : 3.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 137 optimal weight: 9.9990 chunk 106 optimal weight: 8.9990 chunk 156 optimal weight: 7.9990 chunk 236 optimal weight: 2.9990 chunk 217 optimal weight: 6.9990 chunk 188 optimal weight: 10.0000 chunk 19 optimal weight: 0.6980 chunk 145 optimal weight: 9.9990 chunk 115 optimal weight: 0.6980 chunk 149 optimal weight: 10.0000 chunk 200 optimal weight: 0.9980 overall best weight: 2.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.5926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 20751 Z= 0.203 Angle : 0.715 7.339 28151 Z= 0.367 Chirality : 0.047 0.445 3462 Planarity : 0.005 0.078 3422 Dihedral : 9.092 59.540 4783 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 24.35 Ramachandran Plot: Outliers : 0.38 % Allowed : 14.77 % Favored : 84.85 % Rotamer: Outliers : 0.10 % Allowed : 0.81 % Favored : 99.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.15 % Twisted General : 0.09 % 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: -3.56 (0.16), residues: 2343 helix: -1.72 (0.23), residues: 384 sheet: -2.56 (0.23), residues: 450 loop : -2.61 (0.15), residues: 1509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP A 479 HIS 0.007 0.001 HIS C 96 PHE 0.011 0.001 PHE H 62 TYR 0.021 0.002 TYR D 32 ARG 0.003 0.000 ARG D 61 ********************** REFINEMENT MACRO_CYCLE 10 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 155 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 153 time to evaluate : 3.072 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: H 48 MET cc_start: 0.7588 (tmm) cc_final: 0.6943 (tmm) REVERT: C 103 TRP cc_start: 0.8715 (t-100) cc_final: 0.8403 (t-100) REVERT: J 530 MET cc_start: 0.7810 (mtp) cc_final: 0.6726 (mtm) REVERT: J 589 VAL cc_start: 0.9542 (m) cc_final: 0.9020 (m) REVERT: L 48 MET cc_start: 0.7054 (ttp) cc_final: 0.5922 (tmm) REVERT: L 80 ASP cc_start: 0.7976 (p0) cc_final: 0.7685 (p0) outliers start: 2 outliers final: 2 residues processed: 155 average time/residue: 0.8936 time to fit residues: 197.6841 Evaluate side-chains 137 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 135 time to evaluate : 3.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 57 optimal weight: 6.9990 chunk 173 optimal weight: 9.9990 chunk 27 optimal weight: 10.0000 chunk 52 optimal weight: 10.0000 chunk 188 optimal weight: 10.0000 chunk 78 optimal weight: 0.7980 chunk 193 optimal weight: 9.9990 chunk 23 optimal weight: 10.0000 chunk 34 optimal weight: 2.9990 chunk 165 optimal weight: 8.9990 chunk 10 optimal weight: 9.9990 overall best weight: 5.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 332 ASN ** I 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.039662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.034088 restraints weight = 941270.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.035473 restraints weight = 421188.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.036304 restraints weight = 232524.230| |-----------------------------------------------------------------------------| r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.6158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 20751 Z= 0.309 Angle : 0.774 7.520 28151 Z= 0.401 Chirality : 0.047 0.464 3462 Planarity : 0.005 0.082 3422 Dihedral : 9.198 59.587 4783 Min Nonbonded Distance : 1.736 Molprobity Statistics. All-atom Clashscore : 31.07 Ramachandran Plot: Outliers : 0.43 % Allowed : 17.41 % Favored : 82.16 % Rotamer: Outliers : 0.10 % Allowed : 0.62 % Favored : 99.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.15 % Twisted General : 0.18 % 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: -3.66 (0.16), residues: 2343 helix: -1.64 (0.24), residues: 366 sheet: -2.56 (0.24), residues: 420 loop : -2.75 (0.14), residues: 1557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 479 HIS 0.007 0.002 HIS E 330 PHE 0.016 0.002 PHE K 91 TYR 0.017 0.002 TYR D 32 ARG 0.004 0.001 ARG B 585 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6423.71 seconds wall clock time: 123 minutes 28.53 seconds (7408.53 seconds total)