Starting phenix.real_space_refine on Fri Feb 23 02:24:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ilb_35532/02_2024/8ilb_35532_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ilb_35532/02_2024/8ilb_35532.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ilb_35532/02_2024/8ilb_35532.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ilb_35532/02_2024/8ilb_35532.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ilb_35532/02_2024/8ilb_35532_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ilb_35532/02_2024/8ilb_35532_neut.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 220 5.16 5 C 22990 2.51 5 N 6364 2.21 5 O 6748 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 16": "OD1" <-> "OD2" Residue "A TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 73": "OD1" <-> "OD2" Residue "A TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 107": "OE1" <-> "OE2" Residue "A PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 200": "OD1" <-> "OD2" Residue "A PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 422": "OE1" <-> "OE2" Residue "B TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 69": "OD1" <-> "OD2" Residue "B ASP 75": "OD1" <-> "OD2" Residue "B TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 91": "OE1" <-> "OE2" Residue "B TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 188": "OE1" <-> "OE2" Residue "B PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 335": "OD1" <-> "OD2" Residue "B PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 344": "OD1" <-> "OD2" Residue "B GLU 352": "OE1" <-> "OE2" Residue "B PHE 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 430": "OE1" <-> "OE2" Residue "B ASP 433": "OD1" <-> "OD2" Residue "B GLU 461": "OE1" <-> "OE2" Residue "C ASP 30": "OD1" <-> "OD2" Residue "C PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 73": "OD1" <-> "OD2" Residue "C TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 157": "OD1" <-> "OD2" Residue "C TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 245": "OE1" <-> "OE2" Residue "C GLU 246": "OE1" <-> "OE2" Residue "C GLU 252": "OE1" <-> "OE2" Residue "C PHE 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 283": "OD1" <-> "OD2" Residue "C ASP 299": "OD1" <-> "OD2" Residue "C PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 349": "OD1" <-> "OD2" Residue "C PHE 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 457": "OD1" <-> "OD2" Residue "C PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 465": "OE1" <-> "OE2" Residue "C PHE 466": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 16": "OD1" <-> "OD2" Residue "D TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 25": "OD1" <-> "OD2" Residue "D ASP 30": "OD1" <-> "OD2" Residue "D ASP 32": "OD1" <-> "OD2" Residue "D PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 73": "OD1" <-> "OD2" Residue "D TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 91": "OE1" <-> "OE2" Residue "D PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 157": "OD1" <-> "OD2" Residue "D GLU 188": "OE1" <-> "OE2" Residue "D PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 201": "OE1" <-> "OE2" Residue "D PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 252": "OE1" <-> "OE2" Residue "D GLU 256": "OE1" <-> "OE2" Residue "D ASP 265": "OD1" <-> "OD2" Residue "D PHE 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 393": "OD1" <-> "OD2" Residue "D PHE 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 422": "OE1" <-> "OE2" Residue "D PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 111": "OD1" <-> "OD2" Residue "E GLU 120": "OE1" <-> "OE2" Residue "E PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 95": "OD1" <-> "OD2" Residue "F PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 115": "OE1" <-> "OE2" Residue "H PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 135": "OD1" <-> "OD2" Residue "I PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 16": "OD1" <-> "OD2" Residue "J TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 73": "OD1" <-> "OD2" Residue "J TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 107": "OE1" <-> "OE2" Residue "J PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 155": "OE1" <-> "OE2" Residue "J TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 200": "OD1" <-> "OD2" Residue "J PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 422": "OE1" <-> "OE2" Residue "K TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 69": "OD1" <-> "OD2" Residue "K ASP 75": "OD1" <-> "OD2" Residue "K TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 91": "OE1" <-> "OE2" Residue "K TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 188": "OE1" <-> "OE2" Residue "K PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 335": "OD1" <-> "OD2" Residue "K PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 344": "OD1" <-> "OD2" Residue "K GLU 352": "OE1" <-> "OE2" Residue "K PHE 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 430": "OE1" <-> "OE2" Residue "K ASP 433": "OD1" <-> "OD2" Residue "K GLU 461": "OE1" <-> "OE2" Residue "L ASP 30": "OD1" <-> "OD2" Residue "L PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 157": "OD1" <-> "OD2" Residue "L TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 246": "OE1" <-> "OE2" Residue "L GLU 252": "OE1" <-> "OE2" Residue "L PHE 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 283": "OD1" <-> "OD2" Residue "L ASP 299": "OD1" <-> "OD2" Residue "L PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 349": "OD1" <-> "OD2" Residue "L PHE 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 457": "OD1" <-> "OD2" Residue "L PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 465": "OE1" <-> "OE2" Residue "L PHE 466": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 16": "OD1" <-> "OD2" Residue "M TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 25": "OD1" <-> "OD2" Residue "M ASP 30": "OD1" <-> "OD2" Residue "M ASP 32": "OD1" <-> "OD2" Residue "M PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 73": "OD1" <-> "OD2" Residue "M TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 91": "OE1" <-> "OE2" Residue "M PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 157": "OD1" <-> "OD2" Residue "M GLU 188": "OE1" <-> "OE2" Residue "M PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 200": "OD1" <-> "OD2" Residue "M GLU 201": "OE1" <-> "OE2" Residue "M PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 252": "OE1" <-> "OE2" Residue "M GLU 256": "OE1" <-> "OE2" Residue "M ASP 265": "OD1" <-> "OD2" Residue "M PHE 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 393": "OD1" <-> "OD2" Residue "M PHE 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 422": "OE1" <-> "OE2" Residue "M PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 111": "OD1" <-> "OD2" Residue "N GLU 120": "OE1" <-> "OE2" Residue "N PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 95": "OD1" <-> "OD2" Residue "O PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 115": "OE1" <-> "OE2" Residue "Q PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 135": "OD1" <-> "OD2" Residue "R PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 36322 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 3581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3581 Classifications: {'peptide': 456} Link IDs: {'PTRANS': 21, 'TRANS': 434} Chain: "B" Number of atoms: 3541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3541 Classifications: {'peptide': 451} Link IDs: {'PTRANS': 21, 'TRANS': 429} Chain: "C" Number of atoms: 3581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3581 Classifications: {'peptide': 456} Link IDs: {'PTRANS': 21, 'TRANS': 434} Chain: "D" Number of atoms: 3557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3557 Classifications: {'peptide': 453} Link IDs: {'PTRANS': 21, 'TRANS': 431} Chain: "E" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1640 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 12, 'TRANS': 194} Chain: "F" Number of atoms: 564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 564 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "G" Number of atoms: 564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 564 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "H" Number of atoms: 564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 564 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "I" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 569 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "J" Number of atoms: 3581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3581 Classifications: {'peptide': 456} Link IDs: {'PTRANS': 21, 'TRANS': 434} Chain: "K" Number of atoms: 3541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3541 Classifications: {'peptide': 451} Link IDs: {'PTRANS': 21, 'TRANS': 429} Chain: "L" Number of atoms: 3581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3581 Classifications: {'peptide': 456} Link IDs: {'PTRANS': 21, 'TRANS': 434} Chain: "M" Number of atoms: 3557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3557 Classifications: {'peptide': 453} Link IDs: {'PTRANS': 21, 'TRANS': 431} Chain: "N" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1640 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 12, 'TRANS': 194} Chain: "O" Number of atoms: 564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 564 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "P" Number of atoms: 564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 564 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "Q" Number of atoms: 564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 564 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "R" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 569 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 2, 'TRANS': 77} Time building chain proxies: 18.56, per 1000 atoms: 0.51 Number of scatterers: 36322 At special positions: 0 Unit cell: (151.716, 143.108, 136.652, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 220 16.00 O 6748 8.00 N 6364 7.00 C 22990 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 13.25 Conformation dependent library (CDL) restraints added in 6.9 seconds 9288 Ramachandran restraints generated. 4644 Oldfield, 0 Emsley, 4644 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8396 Finding SS restraints... Secondary structure from input PDB file: 170 helices and 32 sheets defined 40.6% alpha, 10.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.56 Creating SS restraints... Processing helix chain 'A' and resid 46 through 58 removed outlier: 3.779A pdb=" N ALA A 50 " --> pdb=" O PRO A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 118 removed outlier: 3.894A pdb=" N ILE A 113 " --> pdb=" O SER A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 143 Processing helix chain 'A' and resid 152 through 160 Processing helix chain 'A' and resid 178 through 193 removed outlier: 3.710A pdb=" N GLY A 193 " --> pdb=" O CYS A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 230 removed outlier: 3.642A pdb=" N ARG A 214 " --> pdb=" O ARG A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 257 Processing helix chain 'A' and resid 270 through 285 removed outlier: 3.760A pdb=" N ASN A 274 " --> pdb=" O GLY A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 319 removed outlier: 3.990A pdb=" N LEU A 311 " --> pdb=" O HIS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 345 removed outlier: 4.066A pdb=" N SER A 338 " --> pdb=" O GLY A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 358 Processing helix chain 'A' and resid 380 through 382 No H-bonds generated for 'chain 'A' and resid 380 through 382' Processing helix chain 'A' and resid 383 through 391 Processing helix chain 'A' and resid 400 through 405 removed outlier: 4.307A pdb=" N LEU A 404 " --> pdb=" O GLY A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 430 Processing helix chain 'A' and resid 437 through 446 Processing helix chain 'A' and resid 449 through 459 Processing helix chain 'B' and resid 46 through 58 removed outlier: 3.759A pdb=" N ALA B 50 " --> pdb=" O PRO B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 119 removed outlier: 3.934A pdb=" N ILE B 113 " --> pdb=" O SER B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 143 Processing helix chain 'B' and resid 152 through 160 removed outlier: 3.820A pdb=" N LEU B 159 " --> pdb=" O GLU B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 193 removed outlier: 3.833A pdb=" N GLY B 193 " --> pdb=" O CYS B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 230 removed outlier: 3.633A pdb=" N ARG B 214 " --> pdb=" O ARG B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 258 removed outlier: 3.646A pdb=" N GLY B 258 " --> pdb=" O ALA B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 285 removed outlier: 3.666A pdb=" N ASN B 274 " --> pdb=" O GLY B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 319 removed outlier: 3.890A pdb=" N LEU B 311 " --> pdb=" O HIS B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 348 removed outlier: 3.704A pdb=" N MET B 346 " --> pdb=" O PHE B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 358 removed outlier: 3.533A pdb=" N GLY B 358 " --> pdb=" O ARG B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 382 No H-bonds generated for 'chain 'B' and resid 380 through 382' Processing helix chain 'B' and resid 383 through 391 Processing helix chain 'B' and resid 400 through 405 removed outlier: 3.706A pdb=" N LEU B 404 " --> pdb=" O GLY B 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 430 Processing helix chain 'B' and resid 437 through 446 Processing helix chain 'B' and resid 449 through 459 Processing helix chain 'C' and resid 46 through 58 Processing helix chain 'C' and resid 109 through 118 removed outlier: 3.677A pdb=" N ILE C 113 " --> pdb=" O SER C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 124 Processing helix chain 'C' and resid 138 through 143 Processing helix chain 'C' and resid 152 through 160 removed outlier: 3.689A pdb=" N LEU C 159 " --> pdb=" O GLU C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 192 Processing helix chain 'C' and resid 210 through 230 removed outlier: 3.639A pdb=" N ARG C 214 " --> pdb=" O ARG C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 258 removed outlier: 3.543A pdb=" N GLY C 258 " --> pdb=" O ALA C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 285 removed outlier: 3.682A pdb=" N ASN C 274 " --> pdb=" O GLY C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 319 removed outlier: 3.855A pdb=" N LEU C 311 " --> pdb=" O HIS C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 345 Processing helix chain 'C' and resid 380 through 382 No H-bonds generated for 'chain 'C' and resid 380 through 382' Processing helix chain 'C' and resid 383 through 391 Processing helix chain 'C' and resid 400 through 405 removed outlier: 3.894A pdb=" N LEU C 404 " --> pdb=" O GLY C 400 " (cutoff:3.500A) Processing helix chain 'C' and resid 410 through 430 Processing helix chain 'C' and resid 437 through 446 Processing helix chain 'C' and resid 449 through 459 Processing helix chain 'D' and resid 46 through 58 removed outlier: 3.808A pdb=" N ALA D 50 " --> pdb=" O PRO D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 105 removed outlier: 3.976A pdb=" N LEU D 104 " --> pdb=" O PRO D 101 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N PHE D 105 " --> pdb=" O LEU D 102 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 101 through 105' Processing helix chain 'D' and resid 109 through 118 removed outlier: 3.930A pdb=" N ILE D 113 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 124 Processing helix chain 'D' and resid 138 through 143 Processing helix chain 'D' and resid 152 through 160 Processing helix chain 'D' and resid 178 through 193 removed outlier: 3.842A pdb=" N GLY D 193 " --> pdb=" O CYS D 189 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 230 removed outlier: 3.608A pdb=" N ARG D 214 " --> pdb=" O ARG D 210 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 257 Processing helix chain 'D' and resid 266 through 270 Processing helix chain 'D' and resid 270 through 285 removed outlier: 3.641A pdb=" N ASN D 274 " --> pdb=" O GLY D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 307 through 319 removed outlier: 3.869A pdb=" N LEU D 311 " --> pdb=" O HIS D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 346 removed outlier: 3.692A pdb=" N THR D 339 " --> pdb=" O ASP D 335 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N MET D 346 " --> pdb=" O PHE D 342 " (cutoff:3.500A) Processing helix chain 'D' and resid 354 through 358 Processing helix chain 'D' and resid 380 through 382 No H-bonds generated for 'chain 'D' and resid 380 through 382' Processing helix chain 'D' and resid 383 through 391 Processing helix chain 'D' and resid 400 through 405 removed outlier: 3.722A pdb=" N LEU D 404 " --> pdb=" O GLY D 400 " (cutoff:3.500A) Processing helix chain 'D' and resid 409 through 430 removed outlier: 3.572A pdb=" N GLU D 430 " --> pdb=" O GLN D 426 " (cutoff:3.500A) Processing helix chain 'D' and resid 437 through 447 Processing helix chain 'D' and resid 449 through 459 removed outlier: 3.624A pdb=" N TRP D 459 " --> pdb=" O ALA D 455 " (cutoff:3.500A) Processing helix chain 'E' and resid 76 through 80 removed outlier: 3.685A pdb=" N ARG E 80 " --> pdb=" O THR E 77 " (cutoff:3.500A) Processing helix chain 'E' and resid 83 through 93 Processing helix chain 'E' and resid 97 through 109 Proline residue: E 103 - end of helix Processing helix chain 'E' and resid 110 through 112 No H-bonds generated for 'chain 'E' and resid 110 through 112' Processing helix chain 'E' and resid 114 through 122 Processing helix chain 'E' and resid 125 through 144 removed outlier: 3.595A pdb=" N GLN E 144 " --> pdb=" O ASP E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 159 through 164 Processing helix chain 'E' and resid 165 through 169 removed outlier: 4.070A pdb=" N LEU E 168 " --> pdb=" O GLU E 165 " (cutoff:3.500A) Processing helix chain 'E' and resid 170 through 173 Processing helix chain 'E' and resid 174 through 184 removed outlier: 3.839A pdb=" N ARG E 184 " --> pdb=" O PHE E 180 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 200 Processing helix chain 'E' and resid 217 through 231 removed outlier: 3.709A pdb=" N CYS E 221 " --> pdb=" O LEU E 217 " (cutoff:3.500A) Processing helix chain 'E' and resid 239 through 249 removed outlier: 3.553A pdb=" N MET E 243 " --> pdb=" O GLN E 239 " (cutoff:3.500A) Processing helix chain 'E' and resid 253 through 265 Processing helix chain 'J' and resid 46 through 58 removed outlier: 3.779A pdb=" N ALA J 50 " --> pdb=" O PRO J 46 " (cutoff:3.500A) Processing helix chain 'J' and resid 109 through 118 removed outlier: 3.894A pdb=" N ILE J 113 " --> pdb=" O SER J 109 " (cutoff:3.500A) Processing helix chain 'J' and resid 138 through 143 Processing helix chain 'J' and resid 152 through 160 Processing helix chain 'J' and resid 178 through 193 removed outlier: 3.710A pdb=" N GLY J 193 " --> pdb=" O CYS J 189 " (cutoff:3.500A) Processing helix chain 'J' and resid 210 through 230 removed outlier: 3.641A pdb=" N ARG J 214 " --> pdb=" O ARG J 210 " (cutoff:3.500A) Processing helix chain 'J' and resid 243 through 257 Processing helix chain 'J' and resid 270 through 285 removed outlier: 3.759A pdb=" N ASN J 274 " --> pdb=" O GLY J 270 " (cutoff:3.500A) Processing helix chain 'J' and resid 307 through 319 removed outlier: 3.990A pdb=" N LEU J 311 " --> pdb=" O HIS J 307 " (cutoff:3.500A) Processing helix chain 'J' and resid 332 through 345 removed outlier: 4.066A pdb=" N SER J 338 " --> pdb=" O GLY J 334 " (cutoff:3.500A) Processing helix chain 'J' and resid 354 through 358 Processing helix chain 'J' and resid 380 through 382 No H-bonds generated for 'chain 'J' and resid 380 through 382' Processing helix chain 'J' and resid 383 through 391 Processing helix chain 'J' and resid 400 through 405 removed outlier: 4.307A pdb=" N LEU J 404 " --> pdb=" O GLY J 400 " (cutoff:3.500A) Processing helix chain 'J' and resid 410 through 430 Processing helix chain 'J' and resid 437 through 446 Processing helix chain 'J' and resid 449 through 459 Processing helix chain 'K' and resid 46 through 58 removed outlier: 3.759A pdb=" N ALA K 50 " --> pdb=" O PRO K 46 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N SER K 58 " --> pdb=" O ILE K 54 " (cutoff:3.500A) Processing helix chain 'K' and resid 109 through 119 removed outlier: 3.934A pdb=" N ILE K 113 " --> pdb=" O SER K 109 " (cutoff:3.500A) Processing helix chain 'K' and resid 138 through 143 Processing helix chain 'K' and resid 152 through 160 removed outlier: 3.821A pdb=" N LEU K 159 " --> pdb=" O GLU K 155 " (cutoff:3.500A) Processing helix chain 'K' and resid 178 through 193 removed outlier: 3.833A pdb=" N GLY K 193 " --> pdb=" O CYS K 189 " (cutoff:3.500A) Processing helix chain 'K' and resid 210 through 230 removed outlier: 3.633A pdb=" N ARG K 214 " --> pdb=" O ARG K 210 " (cutoff:3.500A) Processing helix chain 'K' and resid 243 through 258 removed outlier: 3.646A pdb=" N GLY K 258 " --> pdb=" O ALA K 254 " (cutoff:3.500A) Processing helix chain 'K' and resid 270 through 285 removed outlier: 3.666A pdb=" N ASN K 274 " --> pdb=" O GLY K 270 " (cutoff:3.500A) Processing helix chain 'K' and resid 307 through 319 removed outlier: 3.889A pdb=" N LEU K 311 " --> pdb=" O HIS K 307 " (cutoff:3.500A) Processing helix chain 'K' and resid 334 through 348 removed outlier: 3.704A pdb=" N MET K 346 " --> pdb=" O PHE K 342 " (cutoff:3.500A) Processing helix chain 'K' and resid 354 through 358 removed outlier: 3.533A pdb=" N GLY K 358 " --> pdb=" O ARG K 355 " (cutoff:3.500A) Processing helix chain 'K' and resid 380 through 382 No H-bonds generated for 'chain 'K' and resid 380 through 382' Processing helix chain 'K' and resid 383 through 391 Processing helix chain 'K' and resid 400 through 405 removed outlier: 3.706A pdb=" N LEU K 404 " --> pdb=" O GLY K 400 " (cutoff:3.500A) Processing helix chain 'K' and resid 410 through 430 Processing helix chain 'K' and resid 437 through 446 Processing helix chain 'K' and resid 449 through 459 Processing helix chain 'L' and resid 46 through 58 Processing helix chain 'L' and resid 109 through 118 removed outlier: 3.676A pdb=" N ILE L 113 " --> pdb=" O SER L 109 " (cutoff:3.500A) Processing helix chain 'L' and resid 120 through 124 Processing helix chain 'L' and resid 138 through 143 Processing helix chain 'L' and resid 152 through 160 removed outlier: 3.689A pdb=" N LEU L 159 " --> pdb=" O GLU L 155 " (cutoff:3.500A) Processing helix chain 'L' and resid 178 through 192 Processing helix chain 'L' and resid 210 through 230 removed outlier: 3.639A pdb=" N ARG L 214 " --> pdb=" O ARG L 210 " (cutoff:3.500A) Processing helix chain 'L' and resid 243 through 258 removed outlier: 3.543A pdb=" N GLY L 258 " --> pdb=" O ALA L 254 " (cutoff:3.500A) Processing helix chain 'L' and resid 270 through 285 removed outlier: 3.681A pdb=" N ASN L 274 " --> pdb=" O GLY L 270 " (cutoff:3.500A) Processing helix chain 'L' and resid 307 through 319 removed outlier: 3.855A pdb=" N LEU L 311 " --> pdb=" O HIS L 307 " (cutoff:3.500A) Processing helix chain 'L' and resid 332 through 345 Processing helix chain 'L' and resid 380 through 382 No H-bonds generated for 'chain 'L' and resid 380 through 382' Processing helix chain 'L' and resid 383 through 391 Processing helix chain 'L' and resid 400 through 405 removed outlier: 3.894A pdb=" N LEU L 404 " --> pdb=" O GLY L 400 " (cutoff:3.500A) Processing helix chain 'L' and resid 410 through 430 Processing helix chain 'L' and resid 437 through 446 Processing helix chain 'L' and resid 449 through 459 Processing helix chain 'M' and resid 46 through 58 removed outlier: 3.808A pdb=" N ALA M 50 " --> pdb=" O PRO M 46 " (cutoff:3.500A) Processing helix chain 'M' and resid 101 through 105 removed outlier: 3.976A pdb=" N LEU M 104 " --> pdb=" O PRO M 101 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N PHE M 105 " --> pdb=" O LEU M 102 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 101 through 105' Processing helix chain 'M' and resid 109 through 118 removed outlier: 3.930A pdb=" N ILE M 113 " --> pdb=" O SER M 109 " (cutoff:3.500A) Processing helix chain 'M' and resid 120 through 124 Processing helix chain 'M' and resid 138 through 143 Processing helix chain 'M' and resid 152 through 160 Processing helix chain 'M' and resid 178 through 193 removed outlier: 3.841A pdb=" N GLY M 193 " --> pdb=" O CYS M 189 " (cutoff:3.500A) Processing helix chain 'M' and resid 210 through 230 removed outlier: 3.608A pdb=" N ARG M 214 " --> pdb=" O ARG M 210 " (cutoff:3.500A) Processing helix chain 'M' and resid 243 through 257 Processing helix chain 'M' and resid 266 through 270 Processing helix chain 'M' and resid 270 through 285 removed outlier: 3.642A pdb=" N ASN M 274 " --> pdb=" O GLY M 270 " (cutoff:3.500A) Processing helix chain 'M' and resid 307 through 319 removed outlier: 3.870A pdb=" N LEU M 311 " --> pdb=" O HIS M 307 " (cutoff:3.500A) Processing helix chain 'M' and resid 335 through 346 removed outlier: 3.692A pdb=" N THR M 339 " --> pdb=" O ASP M 335 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N MET M 346 " --> pdb=" O PHE M 342 " (cutoff:3.500A) Processing helix chain 'M' and resid 354 through 358 Processing helix chain 'M' and resid 380 through 382 No H-bonds generated for 'chain 'M' and resid 380 through 382' Processing helix chain 'M' and resid 383 through 391 Processing helix chain 'M' and resid 400 through 405 removed outlier: 3.722A pdb=" N LEU M 404 " --> pdb=" O GLY M 400 " (cutoff:3.500A) Processing helix chain 'M' and resid 409 through 430 removed outlier: 3.572A pdb=" N GLU M 430 " --> pdb=" O GLN M 426 " (cutoff:3.500A) Processing helix chain 'M' and resid 437 through 447 Processing helix chain 'M' and resid 449 through 459 removed outlier: 3.625A pdb=" N TRP M 459 " --> pdb=" O ALA M 455 " (cutoff:3.500A) Processing helix chain 'N' and resid 76 through 80 removed outlier: 3.685A pdb=" N ARG N 80 " --> pdb=" O THR N 77 " (cutoff:3.500A) Processing helix chain 'N' and resid 83 through 93 Processing helix chain 'N' and resid 97 through 109 Proline residue: N 103 - end of helix Processing helix chain 'N' and resid 110 through 112 No H-bonds generated for 'chain 'N' and resid 110 through 112' Processing helix chain 'N' and resid 114 through 122 Processing helix chain 'N' and resid 125 through 144 removed outlier: 3.595A pdb=" N GLN N 144 " --> pdb=" O ASP N 140 " (cutoff:3.500A) Processing helix chain 'N' and resid 159 through 164 Processing helix chain 'N' and resid 165 through 169 removed outlier: 4.070A pdb=" N LEU N 168 " --> pdb=" O GLU N 165 " (cutoff:3.500A) Processing helix chain 'N' and resid 170 through 173 Processing helix chain 'N' and resid 174 through 184 removed outlier: 3.840A pdb=" N ARG N 184 " --> pdb=" O PHE N 180 " (cutoff:3.500A) Processing helix chain 'N' and resid 187 through 200 Processing helix chain 'N' and resid 217 through 231 removed outlier: 3.709A pdb=" N CYS N 221 " --> pdb=" O LEU N 217 " (cutoff:3.500A) Processing helix chain 'N' and resid 239 through 249 removed outlier: 3.554A pdb=" N MET N 243 " --> pdb=" O GLN N 239 " (cutoff:3.500A) Processing helix chain 'N' and resid 253 through 265 Processing sheet with id=AA1, first strand: chain 'A' and resid 80 through 86 removed outlier: 6.067A pdb=" N CYS A 81 " --> pdb=" O ALA A 99 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N ALA A 99 " --> pdb=" O CYS A 81 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N HIS A 83 " --> pdb=" O PHE A 97 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N LEU A 34 " --> pdb=" O ILE A 135 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N ILE A 135 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ALA A 36 " --> pdb=" O GLU A 133 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER A 129 " --> pdb=" O SER A 40 " (cutoff:3.500A) removed outlier: 9.007A pdb=" N GLY A 305 " --> pdb=" O ARG A 128 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N LEU A 130 " --> pdb=" O GLY A 305 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 166 through 170 removed outlier: 6.610A pdb=" N LEU A 167 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N LYS A 198 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N CYS A 169 " --> pdb=" O LYS A 198 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N THR A 197 " --> pdb=" O TYR A 236 " (cutoff:3.500A) removed outlier: 8.449A pdb=" N ASN A 238 " --> pdb=" O THR A 197 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N HIS A 235 " --> pdb=" O ILE A 261 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N MET A 263 " --> pdb=" O HIS A 235 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N LEU A 237 " --> pdb=" O MET A 263 " (cutoff:3.500A) removed outlier: 8.446A pdb=" N ASP A 265 " --> pdb=" O LEU A 237 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ILE A 262 " --> pdb=" O HIS A 289 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N HIS A 291 " --> pdb=" O ILE A 262 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N HIS A 264 " --> pdb=" O HIS A 291 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N HIS A 324 " --> pdb=" O ILE A 290 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N MET A 166 " --> pdb=" O LEU A 397 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N PHE A 399 " --> pdb=" O MET A 166 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N GLY A 168 " --> pdb=" O PHE A 399 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 350 through 351 Processing sheet with id=AA4, first strand: chain 'B' and resid 80 through 83 removed outlier: 5.911A pdb=" N CYS B 81 " --> pdb=" O ALA B 99 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ALA B 99 " --> pdb=" O CYS B 81 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N HIS B 83 " --> pdb=" O PHE B 97 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N LEU B 34 " --> pdb=" O ASP B 134 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N ASP B 134 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N ALA B 36 " --> pdb=" O LEU B 132 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N LEU B 132 " --> pdb=" O ALA B 36 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ARG B 38 " --> pdb=" O LEU B 130 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N LEU B 130 " --> pdb=" O ARG B 38 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N SER B 40 " --> pdb=" O ARG B 128 " (cutoff:3.500A) removed outlier: 9.073A pdb=" N GLY B 305 " --> pdb=" O ARG B 128 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N LEU B 130 " --> pdb=" O GLY B 305 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 166 through 170 removed outlier: 6.565A pdb=" N LEU B 167 " --> pdb=" O PHE B 196 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N LYS B 198 " --> pdb=" O LEU B 167 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N CYS B 169 " --> pdb=" O LYS B 198 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N THR B 197 " --> pdb=" O TYR B 236 " (cutoff:3.500A) removed outlier: 8.417A pdb=" N ASN B 238 " --> pdb=" O THR B 197 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N HIS B 235 " --> pdb=" O ILE B 261 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N MET B 263 " --> pdb=" O HIS B 235 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N LEU B 237 " --> pdb=" O MET B 263 " (cutoff:3.500A) removed outlier: 8.676A pdb=" N ASP B 265 " --> pdb=" O LEU B 237 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ILE B 262 " --> pdb=" O HIS B 289 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N HIS B 291 " --> pdb=" O ILE B 262 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N HIS B 264 " --> pdb=" O HIS B 291 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N HIS B 324 " --> pdb=" O ILE B 290 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N GLN B 398 " --> pdb=" O PRO B 373 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ALA B 375 " --> pdb=" O GLN B 398 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 350 through 351 Processing sheet with id=AA7, first strand: chain 'C' and resid 80 through 86 removed outlier: 5.899A pdb=" N CYS C 81 " --> pdb=" O ALA C 99 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ALA C 99 " --> pdb=" O CYS C 81 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N HIS C 83 " --> pdb=" O PHE C 97 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N LEU C 34 " --> pdb=" O ASP C 134 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N ASP C 134 " --> pdb=" O LEU C 34 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N ALA C 36 " --> pdb=" O LEU C 132 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N LEU C 132 " --> pdb=" O ALA C 36 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ARG C 38 " --> pdb=" O LEU C 130 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N LEU C 130 " --> pdb=" O ARG C 38 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N SER C 40 " --> pdb=" O ARG C 128 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLY C 305 " --> pdb=" O LEU C 130 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 166 through 170 removed outlier: 6.644A pdb=" N LEU C 167 " --> pdb=" O PHE C 196 " (cutoff:3.500A) removed outlier: 8.146A pdb=" N LYS C 198 " --> pdb=" O LEU C 167 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N CYS C 169 " --> pdb=" O LYS C 198 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N THR C 197 " --> pdb=" O TYR C 236 " (cutoff:3.500A) removed outlier: 8.387A pdb=" N ASN C 238 " --> pdb=" O THR C 197 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N HIS C 235 " --> pdb=" O ILE C 261 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N MET C 263 " --> pdb=" O HIS C 235 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N LEU C 237 " --> pdb=" O MET C 263 " (cutoff:3.500A) removed outlier: 8.492A pdb=" N ASP C 265 " --> pdb=" O LEU C 237 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ILE C 262 " --> pdb=" O HIS C 289 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N HIS C 291 " --> pdb=" O ILE C 262 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N HIS C 264 " --> pdb=" O HIS C 291 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N HIS C 324 " --> pdb=" O ILE C 290 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N GLN C 398 " --> pdb=" O PRO C 373 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ALA C 375 " --> pdb=" O GLN C 398 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 350 through 351 Processing sheet with id=AB1, first strand: chain 'D' and resid 80 through 83 removed outlier: 5.990A pdb=" N CYS D 81 " --> pdb=" O ALA D 99 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N ALA D 99 " --> pdb=" O CYS D 81 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N HIS D 83 " --> pdb=" O PHE D 97 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N LEU D 34 " --> pdb=" O ILE D 135 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N ILE D 135 " --> pdb=" O LEU D 34 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ALA D 36 " --> pdb=" O GLU D 133 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY D 305 " --> pdb=" O LEU D 130 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 234 through 236 removed outlier: 6.950A pdb=" N THR D 197 " --> pdb=" O TYR D 236 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N PHE D 196 " --> pdb=" O LEU D 167 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N GLN D 398 " --> pdb=" O PRO D 373 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ALA D 375 " --> pdb=" O GLN D 398 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N LEU D 323 " --> pdb=" O VAL D 374 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N HIS D 324 " --> pdb=" O ILE D 290 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ILE D 262 " --> pdb=" O HIS D 289 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N HIS D 291 " --> pdb=" O ILE D 262 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N HIS D 264 " --> pdb=" O HIS D 291 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 350 through 351 Processing sheet with id=AB4, first strand: chain 'F' and resid 80 through 82 Processing sheet with id=AB5, first strand: chain 'G' and resid 80 through 81 Processing sheet with id=AB6, first strand: chain 'H' and resid 80 through 82 Processing sheet with id=AB7, first strand: chain 'I' and resid 80 through 82 Processing sheet with id=AB8, first strand: chain 'J' and resid 80 through 86 removed outlier: 6.068A pdb=" N CYS J 81 " --> pdb=" O ALA J 99 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N ALA J 99 " --> pdb=" O CYS J 81 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N HIS J 83 " --> pdb=" O PHE J 97 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N LEU J 34 " --> pdb=" O ILE J 135 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N ILE J 135 " --> pdb=" O LEU J 34 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ALA J 36 " --> pdb=" O GLU J 133 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER J 129 " --> pdb=" O SER J 40 " (cutoff:3.500A) removed outlier: 9.007A pdb=" N GLY J 305 " --> pdb=" O ARG J 128 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N LEU J 130 " --> pdb=" O GLY J 305 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'J' and resid 166 through 170 removed outlier: 6.610A pdb=" N LEU J 167 " --> pdb=" O PHE J 196 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N LYS J 198 " --> pdb=" O LEU J 167 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N CYS J 169 " --> pdb=" O LYS J 198 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N THR J 197 " --> pdb=" O TYR J 236 " (cutoff:3.500A) removed outlier: 8.450A pdb=" N ASN J 238 " --> pdb=" O THR J 197 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N HIS J 235 " --> pdb=" O ILE J 261 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N MET J 263 " --> pdb=" O HIS J 235 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N LEU J 237 " --> pdb=" O MET J 263 " (cutoff:3.500A) removed outlier: 8.445A pdb=" N ASP J 265 " --> pdb=" O LEU J 237 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ILE J 262 " --> pdb=" O HIS J 289 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N HIS J 291 " --> pdb=" O ILE J 262 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N HIS J 264 " --> pdb=" O HIS J 291 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N HIS J 324 " --> pdb=" O ILE J 290 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N MET J 166 " --> pdb=" O LEU J 397 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N PHE J 399 " --> pdb=" O MET J 166 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N GLY J 168 " --> pdb=" O PHE J 399 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'J' and resid 350 through 351 Processing sheet with id=AC2, first strand: chain 'K' and resid 80 through 83 removed outlier: 5.912A pdb=" N CYS K 81 " --> pdb=" O ALA K 99 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ALA K 99 " --> pdb=" O CYS K 81 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N HIS K 83 " --> pdb=" O PHE K 97 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N LEU K 34 " --> pdb=" O ASP K 134 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N ASP K 134 " --> pdb=" O LEU K 34 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N ALA K 36 " --> pdb=" O LEU K 132 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N LEU K 132 " --> pdb=" O ALA K 36 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ARG K 38 " --> pdb=" O LEU K 130 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N LEU K 130 " --> pdb=" O ARG K 38 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N SER K 40 " --> pdb=" O ARG K 128 " (cutoff:3.500A) removed outlier: 9.073A pdb=" N GLY K 305 " --> pdb=" O ARG K 128 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N LEU K 130 " --> pdb=" O GLY K 305 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'K' and resid 166 through 170 removed outlier: 6.565A pdb=" N LEU K 167 " --> pdb=" O PHE K 196 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N LYS K 198 " --> pdb=" O LEU K 167 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N CYS K 169 " --> pdb=" O LYS K 198 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N THR K 197 " --> pdb=" O TYR K 236 " (cutoff:3.500A) removed outlier: 8.417A pdb=" N ASN K 238 " --> pdb=" O THR K 197 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N HIS K 235 " --> pdb=" O ILE K 261 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N MET K 263 " --> pdb=" O HIS K 235 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N LEU K 237 " --> pdb=" O MET K 263 " (cutoff:3.500A) removed outlier: 8.676A pdb=" N ASP K 265 " --> pdb=" O LEU K 237 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ILE K 262 " --> pdb=" O HIS K 289 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N HIS K 291 " --> pdb=" O ILE K 262 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N HIS K 264 " --> pdb=" O HIS K 291 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N HIS K 324 " --> pdb=" O ILE K 290 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N GLN K 398 " --> pdb=" O PRO K 373 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ALA K 375 " --> pdb=" O GLN K 398 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'K' and resid 350 through 351 Processing sheet with id=AC5, first strand: chain 'L' and resid 80 through 86 removed outlier: 5.899A pdb=" N CYS L 81 " --> pdb=" O ALA L 99 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ALA L 99 " --> pdb=" O CYS L 81 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N HIS L 83 " --> pdb=" O PHE L 97 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N LEU L 34 " --> pdb=" O ASP L 134 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N ASP L 134 " --> pdb=" O LEU L 34 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N ALA L 36 " --> pdb=" O LEU L 132 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N LEU L 132 " --> pdb=" O ALA L 36 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ARG L 38 " --> pdb=" O LEU L 130 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N LEU L 130 " --> pdb=" O ARG L 38 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N SER L 40 " --> pdb=" O ARG L 128 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLY L 305 " --> pdb=" O LEU L 130 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 234 through 236 removed outlier: 6.940A pdb=" N THR L 197 " --> pdb=" O TYR L 236 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N LEU L 167 " --> pdb=" O PHE L 196 " (cutoff:3.500A) removed outlier: 8.229A pdb=" N LYS L 198 " --> pdb=" O LEU L 167 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N CYS L 169 " --> pdb=" O LYS L 198 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N GLN L 398 " --> pdb=" O PRO L 373 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ALA L 375 " --> pdb=" O GLN L 398 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N HIS L 324 " --> pdb=" O ILE L 290 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ILE L 262 " --> pdb=" O HIS L 289 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N HIS L 291 " --> pdb=" O ILE L 262 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N HIS L 264 " --> pdb=" O HIS L 291 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'L' and resid 350 through 351 Processing sheet with id=AC8, first strand: chain 'M' and resid 80 through 83 removed outlier: 5.991A pdb=" N CYS M 81 " --> pdb=" O ALA M 99 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N ALA M 99 " --> pdb=" O CYS M 81 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N HIS M 83 " --> pdb=" O PHE M 97 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N LEU M 34 " --> pdb=" O ILE M 135 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N ILE M 135 " --> pdb=" O LEU M 34 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ALA M 36 " --> pdb=" O GLU M 133 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY M 305 " --> pdb=" O LEU M 130 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'M' and resid 234 through 236 removed outlier: 6.995A pdb=" N THR M 197 " --> pdb=" O TYR M 236 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE M 196 " --> pdb=" O LEU M 167 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N GLN M 398 " --> pdb=" O PRO M 373 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ALA M 375 " --> pdb=" O GLN M 398 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N LEU M 323 " --> pdb=" O VAL M 374 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N HIS M 324 " --> pdb=" O ILE M 290 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ILE M 262 " --> pdb=" O HIS M 289 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N HIS M 291 " --> pdb=" O ILE M 262 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N HIS M 264 " --> pdb=" O HIS M 291 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'M' and resid 350 through 351 Processing sheet with id=AD2, first strand: chain 'O' and resid 80 through 82 Processing sheet with id=AD3, first strand: chain 'P' and resid 80 through 81 Processing sheet with id=AD4, first strand: chain 'Q' and resid 80 through 82 Processing sheet with id=AD5, first strand: chain 'R' and resid 80 through 82 1351 hydrogen bonds defined for protein. 3873 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: 11.74 Time building geometry restraints manager: 14.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 11980 1.34 - 1.45: 5703 1.45 - 1.57: 19195 1.57 - 1.69: 0 1.69 - 1.81: 310 Bond restraints: 37188 Sorted by residual: bond pdb=" C LYS O 66 " pdb=" N PRO O 67 " ideal model delta sigma weight residual 1.332 1.383 -0.051 1.12e-02 7.97e+03 2.05e+01 bond pdb=" C ALA C 241 " pdb=" N PRO C 242 " ideal model delta sigma weight residual 1.336 1.379 -0.043 1.23e-02 6.61e+03 1.22e+01 bond pdb=" CA ALA G 124 " pdb=" C ALA G 124 " ideal model delta sigma weight residual 1.521 1.495 0.026 1.19e-02 7.06e+03 4.74e+00 bond pdb=" CA ASP K 299 " pdb=" CB ASP K 299 " ideal model delta sigma weight residual 1.539 1.434 0.106 4.88e-02 4.20e+02 4.68e+00 bond pdb=" CA ASP B 299 " pdb=" CB ASP B 299 " ideal model delta sigma weight residual 1.539 1.434 0.106 4.88e-02 4.20e+02 4.68e+00 ... (remaining 37183 not shown) Histogram of bond angle deviations from ideal: 99.69 - 107.02: 1192 107.02 - 114.35: 20987 114.35 - 121.68: 19783 121.68 - 129.01: 8040 129.01 - 136.34: 332 Bond angle restraints: 50334 Sorted by residual: angle pdb=" N GLY G 119 " pdb=" CA GLY G 119 " pdb=" C GLY G 119 " ideal model delta sigma weight residual 112.49 119.79 -7.30 1.21e+00 6.83e-01 3.64e+01 angle pdb=" N GLY H 119 " pdb=" CA GLY H 119 " pdb=" C GLY H 119 " ideal model delta sigma weight residual 112.73 119.95 -7.22 1.20e+00 6.94e-01 3.62e+01 angle pdb=" N LYS D 198 " pdb=" CA LYS D 198 " pdb=" C LYS D 198 " ideal model delta sigma weight residual 108.76 118.09 -9.33 1.69e+00 3.50e-01 3.04e+01 angle pdb=" N ILE F 127 " pdb=" CA ILE F 127 " pdb=" C ILE F 127 " ideal model delta sigma weight residual 111.58 117.33 -5.75 1.06e+00 8.90e-01 2.94e+01 angle pdb=" N GLY P 119 " pdb=" CA GLY P 119 " pdb=" C GLY P 119 " ideal model delta sigma weight residual 112.49 118.93 -6.44 1.21e+00 6.83e-01 2.84e+01 ... (remaining 50329 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.25: 19760 17.25 - 34.50: 1678 34.50 - 51.76: 307 51.76 - 69.01: 83 69.01 - 86.26: 30 Dihedral angle restraints: 21858 sinusoidal: 8678 harmonic: 13180 Sorted by residual: dihedral pdb=" CA ASN E 235 " pdb=" C ASN E 235 " pdb=" N PRO E 236 " pdb=" CA PRO E 236 " ideal model delta harmonic sigma weight residual -180.00 -146.52 -33.48 0 5.00e+00 4.00e-02 4.48e+01 dihedral pdb=" CA ASN N 235 " pdb=" C ASN N 235 " pdb=" N PRO N 236 " pdb=" CA PRO N 236 " ideal model delta harmonic sigma weight residual -180.00 -146.53 -33.47 0 5.00e+00 4.00e-02 4.48e+01 dihedral pdb=" CA ILE B 462 " pdb=" C ILE B 462 " pdb=" N LYS B 463 " pdb=" CA LYS B 463 " ideal model delta harmonic sigma weight residual -180.00 -151.64 -28.36 0 5.00e+00 4.00e-02 3.22e+01 ... (remaining 21855 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 4650 0.073 - 0.147: 666 0.147 - 0.220: 46 0.220 - 0.293: 4 0.293 - 0.367: 2 Chirality restraints: 5368 Sorted by residual: chirality pdb=" CA ASP L 69 " pdb=" N ASP L 69 " pdb=" C ASP L 69 " pdb=" CB ASP L 69 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.36e+00 chirality pdb=" CA LEU C 71 " pdb=" N LEU C 71 " pdb=" C LEU C 71 " pdb=" CB LEU C 71 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.43e+00 chirality pdb=" CA ILE F 127 " pdb=" N ILE F 127 " pdb=" C ILE F 127 " pdb=" CB ILE F 127 " both_signs ideal model delta sigma weight residual False 2.43 2.16 0.27 2.00e-01 2.50e+01 1.84e+00 ... (remaining 5365 not shown) Planarity restraints: 6622 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY F 128 " 0.010 2.00e-02 2.50e+03 2.07e-02 4.30e+00 pdb=" C GLY F 128 " -0.036 2.00e-02 2.50e+03 pdb=" O GLY F 128 " 0.013 2.00e-02 2.50e+03 pdb=" N GLY F 129 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA C 241 " 0.031 5.00e-02 4.00e+02 4.69e-02 3.52e+00 pdb=" N PRO C 242 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO C 242 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO C 242 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET J 259 " 0.030 5.00e-02 4.00e+02 4.62e-02 3.42e+00 pdb=" N PRO J 260 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO J 260 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO J 260 " 0.026 5.00e-02 4.00e+02 ... (remaining 6619 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 3222 2.73 - 3.27: 34643 3.27 - 3.82: 55803 3.82 - 4.36: 70189 4.36 - 4.90: 126041 Nonbonded interactions: 289898 Sorted by model distance: nonbonded pdb=" O LEU L 70 " pdb=" CG LEU L 71 " model vdw 2.190 3.470 nonbonded pdb=" OH TYR N 201 " pdb=" O PHE N 213 " model vdw 2.213 2.440 nonbonded pdb=" OH TYR E 201 " pdb=" O PHE E 213 " model vdw 2.213 2.440 nonbonded pdb=" N GLY K 330 " pdb=" O GLU O 136 " model vdw 2.219 2.520 nonbonded pdb=" N GLY B 330 " pdb=" O GLU F 136 " model vdw 2.219 2.520 ... (remaining 289893 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 16 through 466) selection = chain 'B' selection = (chain 'C' and resid 16 through 466) selection = (chain 'D' and resid 16 through 466) selection = (chain 'J' and resid 16 through 466) selection = chain 'K' selection = (chain 'L' and resid 16 through 466) selection = (chain 'M' and resid 16 through 466) } ncs_group { reference = chain 'E' selection = chain 'N' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = (chain 'I' and resid 58 through 136) selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = (chain 'R' and resid 58 through 136) } 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 individual isotropic 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: 1.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 7.370 Check model and map are aligned: 0.600 Set scattering table: 0.350 Process input model: 90.140 Find NCS groups from input model: 2.650 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 113.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 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 : 0.007 0.106 37188 Z= 0.450 Angle : 0.736 11.531 50334 Z= 0.423 Chirality : 0.051 0.367 5368 Planarity : 0.005 0.047 6622 Dihedral : 13.727 86.259 13462 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.94 % Favored : 91.02 % Rotamer: Outliers : 1.56 % Allowed : 4.44 % Favored : 94.01 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.96 % 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: -3.03 (0.11), residues: 4644 helix: -0.84 (0.12), residues: 1670 sheet: -0.98 (0.21), residues: 472 loop : -3.21 (0.10), residues: 2502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 67 HIS 0.005 0.001 HIS M 264 PHE 0.025 0.002 PHE K 342 TYR 0.011 0.001 TYR C 17 ARG 0.005 0.000 ARG L 212 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9288 Ramachandran restraints generated. 4644 Oldfield, 0 Emsley, 4644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9288 Ramachandran restraints generated. 4644 Oldfield, 0 Emsley, 4644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 3788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 459 time to evaluate : 4.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 426 GLN cc_start: 0.8408 (tp40) cc_final: 0.7580 (tp-100) REVERT: B 76 ARG cc_start: 0.8383 (mtp180) cc_final: 0.8152 (ttp80) REVERT: C 354 ASP cc_start: 0.7237 (t0) cc_final: 0.6867 (t0) REVERT: C 357 ARG cc_start: 0.7805 (mtt-85) cc_final: 0.7578 (mmm-85) REVERT: C 426 GLN cc_start: 0.8014 (tp40) cc_final: 0.7235 (tp-100) REVERT: D 342 PHE cc_start: 0.8725 (OUTLIER) cc_final: 0.8520 (t80) REVERT: D 354 ASP cc_start: 0.7714 (t0) cc_final: 0.7230 (t70) REVERT: D 426 GLN cc_start: 0.8306 (tt0) cc_final: 0.7834 (tp-100) REVERT: D 444 GLU cc_start: 0.8051 (mp0) cc_final: 0.7845 (mp0) REVERT: E 238 ASP cc_start: 0.6997 (m-30) cc_final: 0.6688 (m-30) REVERT: F 74 ASN cc_start: 0.7299 (OUTLIER) cc_final: 0.7054 (t160) REVERT: F 76 GLU cc_start: 0.7803 (OUTLIER) cc_final: 0.7538 (tm-30) REVERT: G 120 ASP cc_start: 0.8276 (OUTLIER) cc_final: 0.8015 (p0) REVERT: H 74 ASN cc_start: 0.7812 (t0) cc_final: 0.7327 (t0) REVERT: I 78 GLU cc_start: 0.7756 (pt0) cc_final: 0.7446 (pt0) REVERT: I 80 CYS cc_start: 0.7841 (m) cc_final: 0.7575 (p) REVERT: I 111 ARG cc_start: 0.8956 (mmt90) cc_final: 0.8630 (mmt-90) REVERT: J 426 GLN cc_start: 0.8408 (tp40) cc_final: 0.7587 (tp-100) REVERT: K 76 ARG cc_start: 0.8377 (mtp180) cc_final: 0.8144 (ttp80) REVERT: K 178 SER cc_start: 0.8217 (OUTLIER) cc_final: 0.7972 (p) REVERT: L 71 LEU cc_start: 0.7020 (OUTLIER) cc_final: 0.6806 (mm) REVERT: L 354 ASP cc_start: 0.7233 (t0) cc_final: 0.6865 (t0) REVERT: L 357 ARG cc_start: 0.7832 (mtt-85) cc_final: 0.7582 (mmm-85) REVERT: L 426 GLN cc_start: 0.8077 (tp40) cc_final: 0.7292 (tp-100) REVERT: M 342 PHE cc_start: 0.8699 (OUTLIER) cc_final: 0.8426 (t80) REVERT: M 354 ASP cc_start: 0.7725 (t0) cc_final: 0.7229 (t70) REVERT: M 426 GLN cc_start: 0.8314 (tt0) cc_final: 0.7760 (tp-100) REVERT: M 444 GLU cc_start: 0.8052 (mp0) cc_final: 0.7848 (mp0) REVERT: N 238 ASP cc_start: 0.7045 (m-30) cc_final: 0.6742 (m-30) REVERT: O 74 ASN cc_start: 0.7620 (OUTLIER) cc_final: 0.7373 (t160) REVERT: R 78 GLU cc_start: 0.7765 (pt0) cc_final: 0.7456 (pt0) REVERT: R 80 CYS cc_start: 0.7854 (m) cc_final: 0.7594 (p) REVERT: R 111 ARG cc_start: 0.8968 (mmt90) cc_final: 0.8647 (mmt-90) outliers start: 59 outliers final: 7 residues processed: 493 average time/residue: 1.7130 time to fit residues: 991.5719 Evaluate side-chains 332 residues out of total 3788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 317 time to evaluate : 4.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 457 ASP Chi-restraints excluded: chain C residue 178 SER Chi-restraints excluded: chain C residue 246 GLU Chi-restraints excluded: chain D residue 342 PHE Chi-restraints excluded: chain F residue 74 ASN Chi-restraints excluded: chain F residue 76 GLU Chi-restraints excluded: chain G residue 120 ASP Chi-restraints excluded: chain K residue 178 SER Chi-restraints excluded: chain K residue 457 ASP Chi-restraints excluded: chain L residue 70 LEU Chi-restraints excluded: chain L residue 71 LEU Chi-restraints excluded: chain L residue 178 SER Chi-restraints excluded: chain L residue 246 GLU Chi-restraints excluded: chain M residue 342 PHE Chi-restraints excluded: chain O residue 74 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 386 optimal weight: 2.9990 chunk 347 optimal weight: 0.3980 chunk 192 optimal weight: 20.0000 chunk 118 optimal weight: 1.9990 chunk 234 optimal weight: 7.9990 chunk 185 optimal weight: 5.9990 chunk 358 optimal weight: 0.7980 chunk 138 optimal weight: 20.0000 chunk 218 optimal weight: 20.0000 chunk 267 optimal weight: 3.9990 chunk 415 optimal weight: 9.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN A 150 HIS A 181 ASN A 209 GLN ** A 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 417 ASN ** B 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 350 HIS C 92 ASN C 209 GLN C 264 HIS C 417 ASN D 322 HIS D 426 GLN E 63 GLN E 130 ASN E 137 GLN E 233 ASN F 122 ASN G 68 ASN J 92 ASN J 150 HIS J 181 ASN J 209 GLN J 417 ASN ** K 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 350 HIS L 92 ASN L 209 GLN L 264 HIS L 417 ASN M 160 ASN M 322 HIS M 426 GLN N 63 GLN N 130 ASN N 137 GLN N 233 ASN O 68 ASN O 122 ASN P 68 ASN P 74 ASN P 122 ASN Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.1137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 37188 Z= 0.253 Angle : 0.585 8.564 50334 Z= 0.301 Chirality : 0.044 0.197 5368 Planarity : 0.005 0.048 6622 Dihedral : 5.556 72.903 5068 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 1.85 % Allowed : 10.19 % Favored : 87.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.96 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.12), residues: 4644 helix: 0.53 (0.13), residues: 1702 sheet: -0.64 (0.21), residues: 522 loop : -2.61 (0.11), residues: 2420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 408 HIS 0.004 0.001 HIS D 289 PHE 0.024 0.001 PHE B 342 TYR 0.019 0.001 TYR E 101 ARG 0.009 0.000 ARG J 302 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9288 Ramachandran restraints generated. 4644 Oldfield, 0 Emsley, 4644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9288 Ramachandran restraints generated. 4644 Oldfield, 0 Emsley, 4644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 3788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 366 time to evaluate : 4.080 Fit side-chains revert: symmetry clash REVERT: A 426 GLN cc_start: 0.8446 (tp40) cc_final: 0.7619 (tp-100) REVERT: B 76 ARG cc_start: 0.8399 (mtp180) cc_final: 0.8175 (ttp80) REVERT: B 283 ASP cc_start: 0.7429 (m-30) cc_final: 0.7219 (m-30) REVERT: C 209 GLN cc_start: 0.8387 (tt0) cc_final: 0.8110 (tt0) REVERT: C 354 ASP cc_start: 0.7116 (t0) cc_final: 0.6857 (t0) REVERT: C 357 ARG cc_start: 0.7879 (mtt-85) cc_final: 0.7634 (mmm-85) REVERT: C 426 GLN cc_start: 0.7976 (tp40) cc_final: 0.7207 (tp-100) REVERT: D 342 PHE cc_start: 0.8795 (OUTLIER) cc_final: 0.8576 (t80) REVERT: D 426 GLN cc_start: 0.8231 (tt0) cc_final: 0.7780 (tp-100) REVERT: F 74 ASN cc_start: 0.7642 (t0) cc_final: 0.7345 (t0) REVERT: F 76 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.7467 (tm-30) REVERT: F 78 GLU cc_start: 0.8048 (mm-30) cc_final: 0.7464 (tt0) REVERT: G 120 ASP cc_start: 0.8267 (OUTLIER) cc_final: 0.8062 (p0) REVERT: I 78 GLU cc_start: 0.7682 (pt0) cc_final: 0.7407 (pt0) REVERT: I 111 ARG cc_start: 0.8954 (mmt90) cc_final: 0.8654 (mmt-90) REVERT: J 74 MET cc_start: 0.6970 (tmm) cc_final: 0.6555 (tmm) REVERT: J 426 GLN cc_start: 0.8447 (tp40) cc_final: 0.7622 (tp-100) REVERT: K 76 ARG cc_start: 0.8397 (mtp180) cc_final: 0.8171 (ttp80) REVERT: L 209 GLN cc_start: 0.8394 (tt0) cc_final: 0.8115 (tt0) REVERT: L 357 ARG cc_start: 0.7879 (mtt-85) cc_final: 0.7676 (mmm-85) REVERT: L 426 GLN cc_start: 0.7976 (tp40) cc_final: 0.7213 (tp-100) REVERT: M 342 PHE cc_start: 0.8791 (OUTLIER) cc_final: 0.8583 (t80) REVERT: M 426 GLN cc_start: 0.8288 (tt0) cc_final: 0.7744 (tp-100) REVERT: Q 78 GLU cc_start: 0.8007 (OUTLIER) cc_final: 0.7801 (mm-30) REVERT: R 78 GLU cc_start: 0.7686 (pt0) cc_final: 0.7413 (pt0) REVERT: R 111 ARG cc_start: 0.8954 (mmt90) cc_final: 0.8658 (mmt-90) outliers start: 70 outliers final: 33 residues processed: 407 average time/residue: 1.6783 time to fit residues: 807.2588 Evaluate side-chains 341 residues out of total 3788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 303 time to evaluate : 4.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 342 PHE Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 213 ASP Chi-restraints excluded: chain B residue 457 ASP Chi-restraints excluded: chain C residue 178 SER Chi-restraints excluded: chain D residue 299 ASP Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain D residue 342 PHE Chi-restraints excluded: chain F residue 76 GLU Chi-restraints excluded: chain F residue 115 GLU Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 120 ASP Chi-restraints excluded: chain G residue 132 SER Chi-restraints excluded: chain I residue 65 THR Chi-restraints excluded: chain I residue 120 ASP Chi-restraints excluded: chain J residue 29 LYS Chi-restraints excluded: chain J residue 342 PHE Chi-restraints excluded: chain J residue 440 ASP Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 213 ASP Chi-restraints excluded: chain K residue 457 ASP Chi-restraints excluded: chain L residue 70 LEU Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 178 SER Chi-restraints excluded: chain L residue 246 GLU Chi-restraints excluded: chain L residue 256 GLU Chi-restraints excluded: chain M residue 299 ASP Chi-restraints excluded: chain M residue 335 ASP Chi-restraints excluded: chain M residue 342 PHE Chi-restraints excluded: chain O residue 115 GLU Chi-restraints excluded: chain P residue 84 SER Chi-restraints excluded: chain P residue 91 VAL Chi-restraints excluded: chain P residue 132 SER Chi-restraints excluded: chain Q residue 78 GLU Chi-restraints excluded: chain R residue 65 THR Chi-restraints excluded: chain R residue 120 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 231 optimal weight: 2.9990 chunk 129 optimal weight: 1.9990 chunk 346 optimal weight: 3.9990 chunk 283 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 416 optimal weight: 10.0000 chunk 450 optimal weight: 20.0000 chunk 371 optimal weight: 7.9990 chunk 413 optimal weight: 8.9990 chunk 142 optimal weight: 7.9990 chunk 334 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 324 HIS B 426 GLN C 226 GLN D 322 HIS G 122 ASN K 324 HIS K 426 GLN L 226 GLN M 322 HIS O 68 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.1371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 37188 Z= 0.301 Angle : 0.578 7.688 50334 Z= 0.298 Chirality : 0.044 0.176 5368 Planarity : 0.005 0.041 6622 Dihedral : 5.073 62.349 5058 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.26 % Favored : 92.70 % Rotamer: Outliers : 1.80 % Allowed : 12.96 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.96 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.12), residues: 4644 helix: 1.07 (0.13), residues: 1708 sheet: -0.41 (0.21), residues: 522 loop : -2.31 (0.12), residues: 2414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 408 HIS 0.005 0.001 HIS L 289 PHE 0.025 0.001 PHE B 342 TYR 0.016 0.001 TYR E 101 ARG 0.008 0.001 ARG C 302 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9288 Ramachandran restraints generated. 4644 Oldfield, 0 Emsley, 4644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9288 Ramachandran restraints generated. 4644 Oldfield, 0 Emsley, 4644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 3788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 338 time to evaluate : 4.246 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 302 ARG cc_start: 0.7844 (ttm110) cc_final: 0.7530 (mtp-110) REVERT: B 426 GLN cc_start: 0.8385 (OUTLIER) cc_final: 0.8089 (tp-100) REVERT: C 209 GLN cc_start: 0.8415 (tt0) cc_final: 0.8160 (tt0) REVERT: C 357 ARG cc_start: 0.7912 (mtt-85) cc_final: 0.7701 (mmm-85) REVERT: C 426 GLN cc_start: 0.7996 (tp40) cc_final: 0.7612 (tm-30) REVERT: D 354 ASP cc_start: 0.7570 (t0) cc_final: 0.7197 (t70) REVERT: D 426 GLN cc_start: 0.8232 (tt0) cc_final: 0.7757 (tp-100) REVERT: F 74 ASN cc_start: 0.7902 (t0) cc_final: 0.7615 (t0) REVERT: F 76 GLU cc_start: 0.7846 (mp0) cc_final: 0.7505 (tm-30) REVERT: F 78 GLU cc_start: 0.8078 (mm-30) cc_final: 0.7419 (tt0) REVERT: G 120 ASP cc_start: 0.8414 (OUTLIER) cc_final: 0.8135 (p0) REVERT: I 111 ARG cc_start: 0.8941 (mmt90) cc_final: 0.8637 (mmt-90) REVERT: J 302 ARG cc_start: 0.7845 (ttm110) cc_final: 0.7530 (mtp-110) REVERT: K 426 GLN cc_start: 0.8330 (OUTLIER) cc_final: 0.8063 (tp-100) REVERT: L 70 LEU cc_start: 0.6168 (OUTLIER) cc_final: 0.5661 (pp) REVERT: L 209 GLN cc_start: 0.8419 (tt0) cc_final: 0.8160 (tt0) REVERT: L 426 GLN cc_start: 0.7997 (tp40) cc_final: 0.7615 (tm-30) REVERT: M 354 ASP cc_start: 0.7609 (t0) cc_final: 0.7248 (t70) REVERT: M 426 GLN cc_start: 0.8191 (tt0) cc_final: 0.7717 (tp-100) REVERT: O 76 GLU cc_start: 0.7854 (mt-10) cc_final: 0.7587 (tm-30) REVERT: Q 113 LYS cc_start: 0.8825 (mtmm) cc_final: 0.8411 (mtpp) REVERT: R 111 ARG cc_start: 0.8943 (mmt90) cc_final: 0.8640 (mmt-90) outliers start: 68 outliers final: 35 residues processed: 375 average time/residue: 1.7181 time to fit residues: 760.5603 Evaluate side-chains 347 residues out of total 3788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 308 time to evaluate : 4.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 342 PHE Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 426 GLN Chi-restraints excluded: chain B residue 457 ASP Chi-restraints excluded: chain C residue 256 GLU Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain D residue 299 ASP Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain D residue 458 LEU Chi-restraints excluded: chain F residue 115 GLU Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 120 ASP Chi-restraints excluded: chain G residue 132 SER Chi-restraints excluded: chain I residue 65 THR Chi-restraints excluded: chain I residue 91 VAL Chi-restraints excluded: chain I residue 113 LYS Chi-restraints excluded: chain J residue 342 PHE Chi-restraints excluded: chain J residue 440 ASP Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 426 GLN Chi-restraints excluded: chain K residue 457 ASP Chi-restraints excluded: chain L residue 70 LEU Chi-restraints excluded: chain L residue 246 GLU Chi-restraints excluded: chain L residue 256 GLU Chi-restraints excluded: chain M residue 213 ASP Chi-restraints excluded: chain M residue 299 ASP Chi-restraints excluded: chain M residue 335 ASP Chi-restraints excluded: chain M residue 458 LEU Chi-restraints excluded: chain O residue 115 GLU Chi-restraints excluded: chain O residue 131 LEU Chi-restraints excluded: chain P residue 84 SER Chi-restraints excluded: chain P residue 91 VAL Chi-restraints excluded: chain P residue 132 SER Chi-restraints excluded: chain R residue 65 THR Chi-restraints excluded: chain R residue 91 VAL Chi-restraints excluded: chain R residue 113 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 411 optimal weight: 20.0000 chunk 313 optimal weight: 9.9990 chunk 216 optimal weight: 6.9990 chunk 46 optimal weight: 1.9990 chunk 198 optimal weight: 7.9990 chunk 279 optimal weight: 5.9990 chunk 418 optimal weight: 0.3980 chunk 442 optimal weight: 8.9990 chunk 218 optimal weight: 20.0000 chunk 396 optimal weight: 0.7980 chunk 119 optimal weight: 0.9980 overall best weight: 2.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 426 GLN B 426 GLN C 226 GLN D 181 ASN D 322 HIS J 426 GLN K 426 GLN L 226 GLN M 181 ASN M 322 HIS O 68 ASN Q 68 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 37188 Z= 0.247 Angle : 0.554 6.855 50334 Z= 0.285 Chirality : 0.043 0.165 5368 Planarity : 0.004 0.045 6622 Dihedral : 4.726 54.779 5049 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 2.48 % Allowed : 14.04 % Favored : 83.47 % Cbeta Deviations : 0.00 % 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: -0.75 (0.12), residues: 4644 helix: 1.43 (0.13), residues: 1708 sheet: -0.26 (0.21), residues: 526 loop : -2.10 (0.12), residues: 2410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP L 408 HIS 0.004 0.001 HIS K 289 PHE 0.022 0.001 PHE B 342 TYR 0.015 0.001 TYR N 101 ARG 0.008 0.000 ARG O 111 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9288 Ramachandran restraints generated. 4644 Oldfield, 0 Emsley, 4644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9288 Ramachandran restraints generated. 4644 Oldfield, 0 Emsley, 4644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 3788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 332 time to evaluate : 4.340 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 153 GLN cc_start: 0.8187 (OUTLIER) cc_final: 0.7546 (mm-40) REVERT: B 426 GLN cc_start: 0.8336 (OUTLIER) cc_final: 0.7530 (tm-30) REVERT: C 209 GLN cc_start: 0.8389 (tt0) cc_final: 0.8143 (tt0) REVERT: C 426 GLN cc_start: 0.7981 (tp40) cc_final: 0.7597 (tm-30) REVERT: D 342 PHE cc_start: 0.8820 (OUTLIER) cc_final: 0.8504 (OUTLIER) REVERT: D 426 GLN cc_start: 0.8130 (tt0) cc_final: 0.7700 (tp-100) REVERT: F 74 ASN cc_start: 0.8018 (t0) cc_final: 0.7729 (t0) REVERT: F 76 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.7479 (tm-30) REVERT: F 78 GLU cc_start: 0.8087 (mm-30) cc_final: 0.7485 (tt0) REVERT: G 111 ARG cc_start: 0.8708 (mpt-90) cc_final: 0.8389 (mmt-90) REVERT: H 113 LYS cc_start: 0.8853 (OUTLIER) cc_final: 0.8422 (mtpp) REVERT: I 111 ARG cc_start: 0.8924 (mmt90) cc_final: 0.8619 (mmt-90) REVERT: K 426 GLN cc_start: 0.8332 (OUTLIER) cc_final: 0.7532 (tm-30) REVERT: L 70 LEU cc_start: 0.6080 (OUTLIER) cc_final: 0.5500 (pp) REVERT: L 209 GLN cc_start: 0.8388 (tt0) cc_final: 0.8139 (tt0) REVERT: L 426 GLN cc_start: 0.7982 (tp40) cc_final: 0.7598 (tm-30) REVERT: M 342 PHE cc_start: 0.8816 (OUTLIER) cc_final: 0.8502 (OUTLIER) REVERT: M 426 GLN cc_start: 0.8123 (tt0) cc_final: 0.7696 (tp-100) REVERT: N 233 ASN cc_start: 0.6055 (OUTLIER) cc_final: 0.5799 (m110) REVERT: O 76 GLU cc_start: 0.7887 (mt-10) cc_final: 0.7614 (tm-30) REVERT: P 111 ARG cc_start: 0.8706 (mpt-90) cc_final: 0.8387 (mmt-90) REVERT: Q 78 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7828 (mm-30) REVERT: Q 113 LYS cc_start: 0.8852 (OUTLIER) cc_final: 0.8397 (mtpp) REVERT: R 111 ARG cc_start: 0.8926 (mmt90) cc_final: 0.8622 (mmt-90) outliers start: 94 outliers final: 47 residues processed: 392 average time/residue: 1.7081 time to fit residues: 790.6159 Evaluate side-chains 367 residues out of total 3788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 311 time to evaluate : 4.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 342 PHE Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 153 GLN Chi-restraints excluded: chain B residue 213 ASP Chi-restraints excluded: chain B residue 342 PHE Chi-restraints excluded: chain B residue 426 GLN Chi-restraints excluded: chain D residue 120 ASN Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 299 ASP Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain D residue 342 PHE Chi-restraints excluded: chain D residue 415 THR Chi-restraints excluded: chain F residue 76 GLU Chi-restraints excluded: chain F residue 94 ILE Chi-restraints excluded: chain F residue 115 GLU Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 132 SER Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain I residue 65 THR Chi-restraints excluded: chain I residue 91 VAL Chi-restraints excluded: chain J residue 29 LYS Chi-restraints excluded: chain J residue 31 THR Chi-restraints excluded: chain J residue 213 ASP Chi-restraints excluded: chain J residue 342 PHE Chi-restraints excluded: chain J residue 440 ASP Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 213 ASP Chi-restraints excluded: chain K residue 328 VAL Chi-restraints excluded: chain K residue 342 PHE Chi-restraints excluded: chain K residue 426 GLN Chi-restraints excluded: chain L residue 70 LEU Chi-restraints excluded: chain L residue 256 GLU Chi-restraints excluded: chain M residue 120 ASN Chi-restraints excluded: chain M residue 213 ASP Chi-restraints excluded: chain M residue 222 ILE Chi-restraints excluded: chain M residue 299 ASP Chi-restraints excluded: chain M residue 335 ASP Chi-restraints excluded: chain M residue 342 PHE Chi-restraints excluded: chain M residue 415 THR Chi-restraints excluded: chain N residue 233 ASN Chi-restraints excluded: chain O residue 94 ILE Chi-restraints excluded: chain O residue 115 GLU Chi-restraints excluded: chain P residue 84 SER Chi-restraints excluded: chain P residue 91 VAL Chi-restraints excluded: chain P residue 132 SER Chi-restraints excluded: chain Q residue 78 GLU Chi-restraints excluded: chain Q residue 113 LYS Chi-restraints excluded: chain R residue 65 THR Chi-restraints excluded: chain R residue 91 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 368 optimal weight: 7.9990 chunk 251 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 chunk 329 optimal weight: 3.9990 chunk 182 optimal weight: 20.0000 chunk 377 optimal weight: 0.7980 chunk 306 optimal weight: 6.9990 chunk 0 optimal weight: 8.9990 chunk 226 optimal weight: 7.9990 chunk 397 optimal weight: 7.9990 chunk 111 optimal weight: 4.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 324 HIS A 426 GLN B 426 GLN C 226 GLN D 322 HIS J 426 GLN K 426 GLN L 226 GLN M 322 HIS Q 68 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 37188 Z= 0.334 Angle : 0.592 8.510 50334 Z= 0.302 Chirality : 0.045 0.216 5368 Planarity : 0.005 0.048 6622 Dihedral : 4.500 41.831 5040 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer: Outliers : 2.56 % Allowed : 14.63 % Favored : 82.81 % Cbeta Deviations : 0.00 % 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: -0.69 (0.12), residues: 4644 helix: 1.53 (0.13), residues: 1698 sheet: -0.50 (0.20), residues: 566 loop : -2.05 (0.12), residues: 2380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP L 408 HIS 0.005 0.001 HIS B 289 PHE 0.024 0.001 PHE B 342 TYR 0.015 0.001 TYR N 101 ARG 0.010 0.001 ARG K 302 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9288 Ramachandran restraints generated. 4644 Oldfield, 0 Emsley, 4644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9288 Ramachandran restraints generated. 4644 Oldfield, 0 Emsley, 4644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 3788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 317 time to evaluate : 4.175 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 302 ARG cc_start: 0.7762 (ttm110) cc_final: 0.7441 (mtp-110) REVERT: B 155 GLU cc_start: 0.8324 (tt0) cc_final: 0.8012 (tt0) REVERT: B 426 GLN cc_start: 0.8378 (OUTLIER) cc_final: 0.7583 (tm-30) REVERT: C 209 GLN cc_start: 0.8427 (tt0) cc_final: 0.8191 (tt0) REVERT: C 426 GLN cc_start: 0.7993 (tp40) cc_final: 0.7609 (tm-30) REVERT: D 342 PHE cc_start: 0.8826 (OUTLIER) cc_final: 0.8558 (OUTLIER) REVERT: D 354 ASP cc_start: 0.7586 (t0) cc_final: 0.7250 (t70) REVERT: D 426 GLN cc_start: 0.8181 (tt0) cc_final: 0.7732 (tp-100) REVERT: F 74 ASN cc_start: 0.8000 (t0) cc_final: 0.7721 (t0) REVERT: F 76 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.7469 (tm-30) REVERT: F 78 GLU cc_start: 0.8072 (mm-30) cc_final: 0.7545 (tt0) REVERT: H 113 LYS cc_start: 0.8834 (OUTLIER) cc_final: 0.8399 (mtpp) REVERT: K 153 GLN cc_start: 0.8203 (OUTLIER) cc_final: 0.7559 (mm-40) REVERT: K 155 GLU cc_start: 0.8323 (tt0) cc_final: 0.8024 (tt0) REVERT: K 426 GLN cc_start: 0.8383 (OUTLIER) cc_final: 0.7588 (tm-30) REVERT: L 70 LEU cc_start: 0.6281 (OUTLIER) cc_final: 0.5662 (pp) REVERT: L 202 ASN cc_start: 0.8351 (OUTLIER) cc_final: 0.8145 (m-40) REVERT: L 209 GLN cc_start: 0.8427 (tt0) cc_final: 0.8187 (tt0) REVERT: L 426 GLN cc_start: 0.7995 (tp40) cc_final: 0.7609 (tm-30) REVERT: M 342 PHE cc_start: 0.8822 (OUTLIER) cc_final: 0.8562 (OUTLIER) REVERT: M 354 ASP cc_start: 0.7585 (t0) cc_final: 0.7127 (t70) REVERT: M 426 GLN cc_start: 0.8133 (tt0) cc_final: 0.7693 (tp-100) REVERT: N 233 ASN cc_start: 0.6029 (OUTLIER) cc_final: 0.5778 (m110) REVERT: O 76 GLU cc_start: 0.7938 (mt-10) cc_final: 0.7643 (tm-30) REVERT: Q 78 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7841 (mm-30) REVERT: Q 113 LYS cc_start: 0.8808 (OUTLIER) cc_final: 0.8345 (mtpp) outliers start: 97 outliers final: 55 residues processed: 376 average time/residue: 1.8560 time to fit residues: 830.4875 Evaluate side-chains 366 residues out of total 3788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 301 time to evaluate : 5.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 342 PHE Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 213 ASP Chi-restraints excluded: chain B residue 342 PHE Chi-restraints excluded: chain B residue 426 GLN Chi-restraints excluded: chain B residue 457 ASP Chi-restraints excluded: chain C residue 256 GLU Chi-restraints excluded: chain C residue 342 PHE Chi-restraints excluded: chain C residue 449 SER Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 120 ASN Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 299 ASP Chi-restraints excluded: chain D residue 335 ASP Chi-restraints excluded: chain D residue 342 PHE Chi-restraints excluded: chain D residue 415 THR Chi-restraints excluded: chain F residue 76 GLU Chi-restraints excluded: chain F residue 115 GLU Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 132 SER Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain I residue 65 THR Chi-restraints excluded: chain I residue 91 VAL Chi-restraints excluded: chain J residue 31 THR Chi-restraints excluded: chain J residue 213 ASP Chi-restraints excluded: chain J residue 342 PHE Chi-restraints excluded: chain J residue 440 ASP Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 48 ASP Chi-restraints excluded: chain K residue 87 VAL Chi-restraints excluded: chain K residue 153 GLN Chi-restraints excluded: chain K residue 213 ASP Chi-restraints excluded: chain K residue 342 PHE Chi-restraints excluded: chain K residue 426 GLN Chi-restraints excluded: chain K residue 457 ASP Chi-restraints excluded: chain L residue 70 LEU Chi-restraints excluded: chain L residue 202 ASN Chi-restraints excluded: chain L residue 256 GLU Chi-restraints excluded: chain L residue 342 PHE Chi-restraints excluded: chain L residue 449 SER Chi-restraints excluded: chain M residue 66 VAL Chi-restraints excluded: chain M residue 120 ASN Chi-restraints excluded: chain M residue 213 ASP Chi-restraints excluded: chain M residue 222 ILE Chi-restraints excluded: chain M residue 299 ASP Chi-restraints excluded: chain M residue 335 ASP Chi-restraints excluded: chain M residue 342 PHE Chi-restraints excluded: chain M residue 415 THR Chi-restraints excluded: chain N residue 233 ASN Chi-restraints excluded: chain O residue 115 GLU Chi-restraints excluded: chain O residue 131 LEU Chi-restraints excluded: chain P residue 84 SER Chi-restraints excluded: chain P residue 91 VAL Chi-restraints excluded: chain P residue 132 SER Chi-restraints excluded: chain Q residue 78 GLU Chi-restraints excluded: chain Q residue 113 LYS Chi-restraints excluded: chain R residue 65 THR Chi-restraints excluded: chain R residue 91 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 148 optimal weight: 1.9990 chunk 398 optimal weight: 4.9990 chunk 87 optimal weight: 1.9990 chunk 259 optimal weight: 0.9980 chunk 109 optimal weight: 0.9990 chunk 443 optimal weight: 20.0000 chunk 367 optimal weight: 5.9990 chunk 205 optimal weight: 4.9990 chunk 36 optimal weight: 4.9990 chunk 146 optimal weight: 4.9990 chunk 232 optimal weight: 0.0570 overall best weight: 1.2104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 426 GLN B 209 GLN B 426 GLN C 226 GLN D 322 HIS J 426 GLN K 426 GLN L 226 GLN M 322 HIS Q 68 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 37188 Z= 0.178 Angle : 0.533 9.768 50334 Z= 0.271 Chirality : 0.042 0.187 5368 Planarity : 0.004 0.052 6622 Dihedral : 4.260 41.293 5040 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 1.95 % Allowed : 15.58 % Favored : 82.47 % Cbeta Deviations : 0.00 % 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: -0.32 (0.13), residues: 4644 helix: 1.85 (0.13), residues: 1696 sheet: -0.24 (0.21), residues: 566 loop : -1.86 (0.12), residues: 2382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP J 211 HIS 0.005 0.001 HIS J 289 PHE 0.019 0.001 PHE O 130 TYR 0.015 0.001 TYR N 101 ARG 0.014 0.001 ARG K 302 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9288 Ramachandran restraints generated. 4644 Oldfield, 0 Emsley, 4644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9288 Ramachandran restraints generated. 4644 Oldfield, 0 Emsley, 4644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 3788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 333 time to evaluate : 4.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 408 TRP cc_start: 0.7536 (p90) cc_final: 0.7226 (p90) REVERT: B 153 GLN cc_start: 0.8176 (OUTLIER) cc_final: 0.7543 (mm-40) REVERT: B 155 GLU cc_start: 0.8297 (tt0) cc_final: 0.7951 (tt0) REVERT: B 426 GLN cc_start: 0.8374 (OUTLIER) cc_final: 0.7590 (tm-30) REVERT: C 426 GLN cc_start: 0.7987 (tp40) cc_final: 0.7617 (tm-30) REVERT: D 342 PHE cc_start: 0.8856 (OUTLIER) cc_final: 0.8547 (t80) REVERT: D 426 GLN cc_start: 0.8118 (tt0) cc_final: 0.7734 (tp-100) REVERT: F 74 ASN cc_start: 0.7978 (t0) cc_final: 0.7684 (t0) REVERT: F 76 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.7480 (tm-30) REVERT: F 78 GLU cc_start: 0.8068 (mm-30) cc_final: 0.7524 (tt0) REVERT: H 113 LYS cc_start: 0.8769 (OUTLIER) cc_final: 0.8320 (mtpm) REVERT: J 302 ARG cc_start: 0.7772 (ttm110) cc_final: 0.7478 (mtp-110) REVERT: J 408 TRP cc_start: 0.7633 (p90) cc_final: 0.7351 (p90) REVERT: K 153 GLN cc_start: 0.8179 (OUTLIER) cc_final: 0.7542 (mm-40) REVERT: K 155 GLU cc_start: 0.8300 (tt0) cc_final: 0.7955 (tt0) REVERT: K 426 GLN cc_start: 0.8361 (OUTLIER) cc_final: 0.7565 (tm-30) REVERT: L 426 GLN cc_start: 0.7988 (tp40) cc_final: 0.7618 (tm-30) REVERT: M 342 PHE cc_start: 0.8851 (OUTLIER) cc_final: 0.8548 (t80) REVERT: M 426 GLN cc_start: 0.8124 (tt0) cc_final: 0.7735 (tp-100) REVERT: N 233 ASN cc_start: 0.6015 (OUTLIER) cc_final: 0.5809 (m110) REVERT: Q 78 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7868 (mm-30) REVERT: Q 113 LYS cc_start: 0.8770 (OUTLIER) cc_final: 0.8323 (mtpm) outliers start: 74 outliers final: 42 residues processed: 379 average time/residue: 1.7142 time to fit residues: 767.2524 Evaluate side-chains 366 residues out of total 3788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 313 time to evaluate : 3.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 342 PHE Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 153 GLN Chi-restraints excluded: chain B residue 213 ASP Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 342 PHE Chi-restraints excluded: chain B residue 426 GLN Chi-restraints excluded: chain B residue 457 ASP Chi-restraints excluded: chain C residue 449 SER Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 120 ASN Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 342 PHE Chi-restraints excluded: chain F residue 76 GLU Chi-restraints excluded: chain F residue 115 GLU Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain G residue 65 THR Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain G residue 132 SER Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain I residue 65 THR Chi-restraints excluded: chain J residue 29 LYS Chi-restraints excluded: chain J residue 213 ASP Chi-restraints excluded: chain J residue 342 PHE Chi-restraints excluded: chain J residue 440 ASP Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 87 VAL Chi-restraints excluded: chain K residue 153 GLN Chi-restraints excluded: chain K residue 213 ASP Chi-restraints excluded: chain K residue 222 ILE Chi-restraints excluded: chain K residue 328 VAL Chi-restraints excluded: chain K residue 342 PHE Chi-restraints excluded: chain K residue 426 GLN Chi-restraints excluded: chain K residue 457 ASP Chi-restraints excluded: chain L residue 449 SER Chi-restraints excluded: chain M residue 27 THR Chi-restraints excluded: chain M residue 120 ASN Chi-restraints excluded: chain M residue 213 ASP Chi-restraints excluded: chain M residue 222 ILE Chi-restraints excluded: chain M residue 299 ASP Chi-restraints excluded: chain M residue 342 PHE Chi-restraints excluded: chain N residue 233 ASN Chi-restraints excluded: chain O residue 115 GLU Chi-restraints excluded: chain P residue 84 SER Chi-restraints excluded: chain P residue 132 SER Chi-restraints excluded: chain Q residue 78 GLU Chi-restraints excluded: chain Q residue 113 LYS Chi-restraints excluded: chain R residue 65 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 427 optimal weight: 20.0000 chunk 49 optimal weight: 9.9990 chunk 252 optimal weight: 3.9990 chunk 323 optimal weight: 9.9990 chunk 250 optimal weight: 8.9990 chunk 373 optimal weight: 0.9980 chunk 247 optimal weight: 5.9990 chunk 441 optimal weight: 10.0000 chunk 276 optimal weight: 0.5980 chunk 269 optimal weight: 7.9990 chunk 203 optimal weight: 10.0000 overall best weight: 3.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 GLN A 426 GLN B 426 GLN C 226 GLN D 322 HIS J 209 GLN J 426 GLN K 426 GLN L 226 GLN M 322 HIS Q 68 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 37188 Z= 0.432 Angle : 0.646 14.144 50334 Z= 0.327 Chirality : 0.047 0.285 5368 Planarity : 0.005 0.057 6622 Dihedral : 4.491 27.376 5038 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % Rotamer: Outliers : 2.75 % Allowed : 15.18 % Favored : 82.07 % Cbeta Deviations : 0.00 % 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: -0.55 (0.12), residues: 4644 helix: 1.62 (0.13), residues: 1698 sheet: -0.46 (0.20), residues: 548 loop : -1.92 (0.12), residues: 2398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 408 HIS 0.005 0.001 HIS K 289 PHE 0.027 0.002 PHE B 342 TYR 0.015 0.001 TYR N 101 ARG 0.014 0.001 ARG B 302 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9288 Ramachandran restraints generated. 4644 Oldfield, 0 Emsley, 4644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9288 Ramachandran restraints generated. 4644 Oldfield, 0 Emsley, 4644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 3788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 307 time to evaluate : 4.497 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 203 ILE cc_start: 0.8869 (OUTLIER) cc_final: 0.8411 (tt) REVERT: B 125 LYS cc_start: 0.8848 (OUTLIER) cc_final: 0.8588 (mmpt) REVERT: B 153 GLN cc_start: 0.8224 (OUTLIER) cc_final: 0.7613 (mm-40) REVERT: B 155 GLU cc_start: 0.8346 (tt0) cc_final: 0.8068 (tt0) REVERT: B 426 GLN cc_start: 0.8362 (OUTLIER) cc_final: 0.7619 (tm-30) REVERT: B 436 ARG cc_start: 0.8164 (OUTLIER) cc_final: 0.7947 (mtp85) REVERT: C 426 GLN cc_start: 0.8014 (tp40) cc_final: 0.7594 (tm-30) REVERT: D 342 PHE cc_start: 0.8732 (OUTLIER) cc_final: 0.8483 (OUTLIER) REVERT: D 354 ASP cc_start: 0.7568 (t0) cc_final: 0.7163 (t70) REVERT: D 426 GLN cc_start: 0.8190 (tt0) cc_final: 0.7721 (tp-100) REVERT: F 74 ASN cc_start: 0.8006 (t0) cc_final: 0.7715 (t0) REVERT: F 76 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7503 (tm-30) REVERT: F 78 GLU cc_start: 0.8034 (mm-30) cc_final: 0.7779 (tt0) REVERT: H 78 GLU cc_start: 0.8545 (tp30) cc_final: 0.8259 (mm-30) REVERT: H 113 LYS cc_start: 0.8791 (OUTLIER) cc_final: 0.8328 (mtpp) REVERT: J 203 ILE cc_start: 0.8869 (OUTLIER) cc_final: 0.8412 (tt) REVERT: J 436 ARG cc_start: 0.8075 (mtp85) cc_final: 0.7870 (mtp85) REVERT: K 153 GLN cc_start: 0.8229 (OUTLIER) cc_final: 0.7613 (mm-40) REVERT: K 155 GLU cc_start: 0.8343 (tt0) cc_final: 0.8076 (tt0) REVERT: K 426 GLN cc_start: 0.8368 (OUTLIER) cc_final: 0.7622 (tm-30) REVERT: L 202 ASN cc_start: 0.8436 (OUTLIER) cc_final: 0.8163 (m-40) REVERT: L 426 GLN cc_start: 0.8016 (tp40) cc_final: 0.7596 (tm-30) REVERT: M 342 PHE cc_start: 0.8729 (OUTLIER) cc_final: 0.8483 (OUTLIER) REVERT: M 354 ASP cc_start: 0.7557 (t0) cc_final: 0.7169 (t70) REVERT: M 426 GLN cc_start: 0.8217 (tt0) cc_final: 0.7747 (tp-100) REVERT: O 78 GLU cc_start: 0.7571 (tt0) cc_final: 0.7335 (tt0) REVERT: Q 74 ASN cc_start: 0.8416 (t0) cc_final: 0.8184 (t0) REVERT: Q 78 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7840 (mm-30) REVERT: Q 113 LYS cc_start: 0.8789 (OUTLIER) cc_final: 0.8312 (mtpp) outliers start: 104 outliers final: 56 residues processed: 377 average time/residue: 1.6534 time to fit residues: 739.3639 Evaluate side-chains 370 residues out of total 3788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 301 time to evaluate : 4.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 342 PHE Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 48 ASP Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 125 LYS Chi-restraints excluded: chain B residue 153 GLN Chi-restraints excluded: chain B residue 213 ASP Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 342 PHE Chi-restraints excluded: chain B residue 426 GLN Chi-restraints excluded: chain B residue 436 ARG Chi-restraints excluded: chain B residue 457 ASP Chi-restraints excluded: chain C residue 342 PHE Chi-restraints excluded: chain C residue 449 SER Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 120 ASN Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 342 PHE Chi-restraints excluded: chain F residue 76 GLU Chi-restraints excluded: chain F residue 115 GLU Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain G residue 65 THR Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain G residue 132 SER Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain I residue 65 THR Chi-restraints excluded: chain I residue 91 VAL Chi-restraints excluded: chain J residue 31 THR Chi-restraints excluded: chain J residue 203 ILE Chi-restraints excluded: chain J residue 213 ASP Chi-restraints excluded: chain J residue 342 PHE Chi-restraints excluded: chain J residue 440 ASP Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 48 ASP Chi-restraints excluded: chain K residue 87 VAL Chi-restraints excluded: chain K residue 153 GLN Chi-restraints excluded: chain K residue 213 ASP Chi-restraints excluded: chain K residue 222 ILE Chi-restraints excluded: chain K residue 328 VAL Chi-restraints excluded: chain K residue 342 PHE Chi-restraints excluded: chain K residue 426 GLN Chi-restraints excluded: chain K residue 457 ASP Chi-restraints excluded: chain L residue 202 ASN Chi-restraints excluded: chain L residue 342 PHE Chi-restraints excluded: chain L residue 449 SER Chi-restraints excluded: chain M residue 27 THR Chi-restraints excluded: chain M residue 66 VAL Chi-restraints excluded: chain M residue 87 VAL Chi-restraints excluded: chain M residue 120 ASN Chi-restraints excluded: chain M residue 213 ASP Chi-restraints excluded: chain M residue 222 ILE Chi-restraints excluded: chain M residue 299 ASP Chi-restraints excluded: chain M residue 342 PHE Chi-restraints excluded: chain O residue 115 GLU Chi-restraints excluded: chain O residue 131 LEU Chi-restraints excluded: chain P residue 65 THR Chi-restraints excluded: chain P residue 84 SER Chi-restraints excluded: chain P residue 132 SER Chi-restraints excluded: chain Q residue 78 GLU Chi-restraints excluded: chain Q residue 113 LYS Chi-restraints excluded: chain R residue 65 THR Chi-restraints excluded: chain R residue 91 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 273 optimal weight: 4.9990 chunk 176 optimal weight: 3.9990 chunk 263 optimal weight: 0.9990 chunk 132 optimal weight: 0.9980 chunk 86 optimal weight: 4.9990 chunk 85 optimal weight: 2.9990 chunk 280 optimal weight: 1.9990 chunk 300 optimal weight: 1.9990 chunk 218 optimal weight: 20.0000 chunk 41 optimal weight: 4.9990 chunk 346 optimal weight: 2.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 426 GLN B 426 GLN C 226 GLN C 295 HIS D 322 HIS J 426 GLN K 426 GLN L 226 GLN M 322 HIS Q 68 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.1879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 37188 Z= 0.228 Angle : 0.571 11.408 50334 Z= 0.288 Chirality : 0.043 0.266 5368 Planarity : 0.004 0.059 6622 Dihedral : 4.286 26.580 5038 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 2.24 % Allowed : 16.31 % Favored : 81.44 % Cbeta Deviations : 0.00 % 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: -0.29 (0.13), residues: 4644 helix: 1.84 (0.13), residues: 1700 sheet: -0.25 (0.20), residues: 566 loop : -1.81 (0.12), residues: 2378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 211 HIS 0.004 0.001 HIS L 289 PHE 0.022 0.001 PHE O 130 TYR 0.016 0.001 TYR K 435 ARG 0.014 0.001 ARG K 302 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9288 Ramachandran restraints generated. 4644 Oldfield, 0 Emsley, 4644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9288 Ramachandran restraints generated. 4644 Oldfield, 0 Emsley, 4644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 3788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 310 time to evaluate : 4.210 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 203 ILE cc_start: 0.8843 (OUTLIER) cc_final: 0.8383 (tt) REVERT: B 125 LYS cc_start: 0.8839 (OUTLIER) cc_final: 0.8583 (mmpt) REVERT: B 153 GLN cc_start: 0.8195 (OUTLIER) cc_final: 0.7583 (mm-40) REVERT: B 155 GLU cc_start: 0.8294 (tt0) cc_final: 0.7992 (tt0) REVERT: B 426 GLN cc_start: 0.8355 (OUTLIER) cc_final: 0.7561 (tm-30) REVERT: B 436 ARG cc_start: 0.8152 (OUTLIER) cc_final: 0.7941 (mtp85) REVERT: D 74 MET cc_start: 0.7268 (mmp) cc_final: 0.6943 (mpt) REVERT: D 342 PHE cc_start: 0.8778 (OUTLIER) cc_final: 0.8542 (t80) REVERT: D 426 GLN cc_start: 0.8147 (tt0) cc_final: 0.7725 (tp-100) REVERT: F 74 ASN cc_start: 0.8102 (t0) cc_final: 0.7769 (t0) REVERT: F 76 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7506 (tm-30) REVERT: H 78 GLU cc_start: 0.8512 (tp30) cc_final: 0.8182 (mm-30) REVERT: H 113 LYS cc_start: 0.8757 (OUTLIER) cc_final: 0.8310 (mtpm) REVERT: J 203 ILE cc_start: 0.8841 (OUTLIER) cc_final: 0.8380 (tt) REVERT: J 436 ARG cc_start: 0.8026 (OUTLIER) cc_final: 0.7811 (mtp85) REVERT: K 153 GLN cc_start: 0.8196 (OUTLIER) cc_final: 0.7582 (mm-40) REVERT: K 155 GLU cc_start: 0.8297 (tt0) cc_final: 0.7997 (tt0) REVERT: K 426 GLN cc_start: 0.8360 (OUTLIER) cc_final: 0.7563 (tm-30) REVERT: M 74 MET cc_start: 0.7271 (mmp) cc_final: 0.6959 (mpt) REVERT: M 342 PHE cc_start: 0.8775 (OUTLIER) cc_final: 0.8545 (t80) REVERT: M 426 GLN cc_start: 0.8152 (tt0) cc_final: 0.7724 (tp-100) REVERT: N 233 ASN cc_start: 0.5894 (OUTLIER) cc_final: 0.5663 (m110) REVERT: Q 113 LYS cc_start: 0.8734 (OUTLIER) cc_final: 0.8281 (mtpm) outliers start: 85 outliers final: 50 residues processed: 365 average time/residue: 1.7401 time to fit residues: 748.2726 Evaluate side-chains 361 residues out of total 3788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 296 time to evaluate : 3.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 342 PHE Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 125 LYS Chi-restraints excluded: chain B residue 153 GLN Chi-restraints excluded: chain B residue 213 ASP Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 342 PHE Chi-restraints excluded: chain B residue 426 GLN Chi-restraints excluded: chain B residue 436 ARG Chi-restraints excluded: chain B residue 457 ASP Chi-restraints excluded: chain C residue 342 PHE Chi-restraints excluded: chain C residue 449 SER Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 120 ASN Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 342 PHE Chi-restraints excluded: chain D residue 415 THR Chi-restraints excluded: chain F residue 76 GLU Chi-restraints excluded: chain F residue 115 GLU Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain G residue 65 THR Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain G residue 132 SER Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain I residue 65 THR Chi-restraints excluded: chain I residue 91 VAL Chi-restraints excluded: chain J residue 203 ILE Chi-restraints excluded: chain J residue 213 ASP Chi-restraints excluded: chain J residue 342 PHE Chi-restraints excluded: chain J residue 436 ARG Chi-restraints excluded: chain J residue 440 ASP Chi-restraints excluded: chain J residue 468 THR Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 87 VAL Chi-restraints excluded: chain K residue 153 GLN Chi-restraints excluded: chain K residue 213 ASP Chi-restraints excluded: chain K residue 222 ILE Chi-restraints excluded: chain K residue 328 VAL Chi-restraints excluded: chain K residue 342 PHE Chi-restraints excluded: chain K residue 426 GLN Chi-restraints excluded: chain K residue 457 ASP Chi-restraints excluded: chain L residue 70 LEU Chi-restraints excluded: chain L residue 342 PHE Chi-restraints excluded: chain L residue 449 SER Chi-restraints excluded: chain M residue 27 THR Chi-restraints excluded: chain M residue 120 ASN Chi-restraints excluded: chain M residue 213 ASP Chi-restraints excluded: chain M residue 222 ILE Chi-restraints excluded: chain M residue 299 ASP Chi-restraints excluded: chain M residue 342 PHE Chi-restraints excluded: chain M residue 415 THR Chi-restraints excluded: chain N residue 233 ASN Chi-restraints excluded: chain O residue 115 GLU Chi-restraints excluded: chain O residue 131 LEU Chi-restraints excluded: chain P residue 65 THR Chi-restraints excluded: chain P residue 84 SER Chi-restraints excluded: chain P residue 132 SER Chi-restraints excluded: chain Q residue 113 LYS Chi-restraints excluded: chain R residue 65 THR Chi-restraints excluded: chain R residue 91 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 401 optimal weight: 0.6980 chunk 422 optimal weight: 5.9990 chunk 385 optimal weight: 2.9990 chunk 411 optimal weight: 20.0000 chunk 247 optimal weight: 4.9990 chunk 179 optimal weight: 9.9990 chunk 323 optimal weight: 10.0000 chunk 126 optimal weight: 1.9990 chunk 371 optimal weight: 4.9990 chunk 389 optimal weight: 2.9990 chunk 409 optimal weight: 8.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 ASN A 426 GLN B 426 GLN C 209 GLN C 226 GLN D 322 HIS E 137 GLN J 410 ASN J 426 GLN K 426 GLN L 209 GLN L 226 GLN M 322 HIS N 137 GLN Q 68 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.1876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.100 37188 Z= 0.315 Angle : 0.608 11.686 50334 Z= 0.305 Chirality : 0.045 0.268 5368 Planarity : 0.005 0.064 6622 Dihedral : 4.336 26.412 5038 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 2.01 % Allowed : 16.74 % Favored : 81.26 % Cbeta Deviations : 0.00 % 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: -0.30 (0.13), residues: 4644 helix: 1.82 (0.13), residues: 1700 sheet: -0.30 (0.20), residues: 556 loop : -1.78 (0.12), residues: 2388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 408 HIS 0.005 0.001 HIS B 289 PHE 0.021 0.001 PHE F 130 TYR 0.015 0.001 TYR E 101 ARG 0.015 0.001 ARG B 302 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9288 Ramachandran restraints generated. 4644 Oldfield, 0 Emsley, 4644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9288 Ramachandran restraints generated. 4644 Oldfield, 0 Emsley, 4644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 3788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 303 time to evaluate : 4.151 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 203 ILE cc_start: 0.8852 (OUTLIER) cc_final: 0.8394 (tt) REVERT: A 436 ARG cc_start: 0.8021 (OUTLIER) cc_final: 0.7345 (mtt-85) REVERT: B 76 ARG cc_start: 0.8419 (mtp180) cc_final: 0.8173 (ttp80) REVERT: B 125 LYS cc_start: 0.8843 (OUTLIER) cc_final: 0.8585 (mmpt) REVERT: B 153 GLN cc_start: 0.8211 (OUTLIER) cc_final: 0.7608 (mm-40) REVERT: B 155 GLU cc_start: 0.8342 (tt0) cc_final: 0.8059 (tt0) REVERT: B 426 GLN cc_start: 0.8378 (OUTLIER) cc_final: 0.7600 (tm-30) REVERT: B 436 ARG cc_start: 0.8168 (OUTLIER) cc_final: 0.7929 (mtp85) REVERT: D 74 MET cc_start: 0.7275 (mmp) cc_final: 0.7014 (mpt) REVERT: D 342 PHE cc_start: 0.8756 (OUTLIER) cc_final: 0.8522 (t80) REVERT: D 426 GLN cc_start: 0.8158 (tt0) cc_final: 0.7715 (tp-100) REVERT: E 95 MET cc_start: 0.8381 (mtt) cc_final: 0.8054 (mpt) REVERT: F 74 ASN cc_start: 0.8157 (t0) cc_final: 0.7834 (t0) REVERT: F 76 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7514 (tm-30) REVERT: F 114 LYS cc_start: 0.9053 (OUTLIER) cc_final: 0.8779 (mmtp) REVERT: H 78 GLU cc_start: 0.8478 (tp30) cc_final: 0.8179 (mm-30) REVERT: H 113 LYS cc_start: 0.8758 (OUTLIER) cc_final: 0.8312 (mtpm) REVERT: J 203 ILE cc_start: 0.8853 (OUTLIER) cc_final: 0.8400 (tt) REVERT: J 436 ARG cc_start: 0.8024 (OUTLIER) cc_final: 0.7812 (mtp85) REVERT: K 76 ARG cc_start: 0.8414 (mtp180) cc_final: 0.8169 (ttp80) REVERT: K 153 GLN cc_start: 0.8211 (OUTLIER) cc_final: 0.7606 (mm-40) REVERT: K 155 GLU cc_start: 0.8344 (tt0) cc_final: 0.8059 (tt0) REVERT: K 426 GLN cc_start: 0.8378 (OUTLIER) cc_final: 0.7598 (tm-30) REVERT: M 74 MET cc_start: 0.7259 (mmp) cc_final: 0.7008 (mpt) REVERT: M 342 PHE cc_start: 0.8759 (OUTLIER) cc_final: 0.8521 (t80) REVERT: M 426 GLN cc_start: 0.8161 (tt0) cc_final: 0.7715 (tp-100) REVERT: N 95 MET cc_start: 0.8413 (mtt) cc_final: 0.8094 (mpt) REVERT: N 233 ASN cc_start: 0.6000 (OUTLIER) cc_final: 0.5764 (m110) REVERT: Q 113 LYS cc_start: 0.8750 (OUTLIER) cc_final: 0.8289 (mtpm) outliers start: 76 outliers final: 52 residues processed: 352 average time/residue: 1.6930 time to fit residues: 703.1274 Evaluate side-chains 363 residues out of total 3788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 294 time to evaluate : 3.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 342 PHE Chi-restraints excluded: chain A residue 436 ARG Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 468 THR Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 125 LYS Chi-restraints excluded: chain B residue 153 GLN Chi-restraints excluded: chain B residue 213 ASP Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 342 PHE Chi-restraints excluded: chain B residue 426 GLN Chi-restraints excluded: chain B residue 436 ARG Chi-restraints excluded: chain B residue 457 ASP Chi-restraints excluded: chain C residue 213 ASP Chi-restraints excluded: chain C residue 342 PHE Chi-restraints excluded: chain C residue 449 SER Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 120 ASN Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 342 PHE Chi-restraints excluded: chain F residue 76 GLU Chi-restraints excluded: chain F residue 114 LYS Chi-restraints excluded: chain F residue 115 GLU Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain G residue 65 THR Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain G residue 132 SER Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain I residue 65 THR Chi-restraints excluded: chain I residue 91 VAL Chi-restraints excluded: chain J residue 203 ILE Chi-restraints excluded: chain J residue 213 ASP Chi-restraints excluded: chain J residue 342 PHE Chi-restraints excluded: chain J residue 436 ARG Chi-restraints excluded: chain J residue 440 ASP Chi-restraints excluded: chain J residue 468 THR Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 87 VAL Chi-restraints excluded: chain K residue 153 GLN Chi-restraints excluded: chain K residue 213 ASP Chi-restraints excluded: chain K residue 222 ILE Chi-restraints excluded: chain K residue 328 VAL Chi-restraints excluded: chain K residue 342 PHE Chi-restraints excluded: chain K residue 426 GLN Chi-restraints excluded: chain K residue 457 ASP Chi-restraints excluded: chain L residue 64 THR Chi-restraints excluded: chain L residue 70 LEU Chi-restraints excluded: chain L residue 213 ASP Chi-restraints excluded: chain L residue 342 PHE Chi-restraints excluded: chain L residue 449 SER Chi-restraints excluded: chain M residue 27 THR Chi-restraints excluded: chain M residue 120 ASN Chi-restraints excluded: chain M residue 213 ASP Chi-restraints excluded: chain M residue 222 ILE Chi-restraints excluded: chain M residue 299 ASP Chi-restraints excluded: chain M residue 342 PHE Chi-restraints excluded: chain N residue 233 ASN Chi-restraints excluded: chain O residue 115 GLU Chi-restraints excluded: chain O residue 131 LEU Chi-restraints excluded: chain P residue 65 THR Chi-restraints excluded: chain P residue 84 SER Chi-restraints excluded: chain P residue 132 SER Chi-restraints excluded: chain Q residue 113 LYS Chi-restraints excluded: chain R residue 65 THR Chi-restraints excluded: chain R residue 91 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 270 optimal weight: 3.9990 chunk 434 optimal weight: 1.9990 chunk 265 optimal weight: 7.9990 chunk 206 optimal weight: 8.9990 chunk 302 optimal weight: 3.9990 chunk 456 optimal weight: 8.9990 chunk 419 optimal weight: 7.9990 chunk 363 optimal weight: 6.9990 chunk 37 optimal weight: 0.7980 chunk 280 optimal weight: 2.9990 chunk 222 optimal weight: 2.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 426 GLN B 426 GLN D 322 HIS G 74 ASN J 426 GLN K 426 GLN M 322 HIS Q 68 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.1917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 37188 Z= 0.297 Angle : 0.602 12.548 50334 Z= 0.303 Chirality : 0.044 0.266 5368 Planarity : 0.005 0.066 6622 Dihedral : 4.335 26.137 5038 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 1.98 % Allowed : 17.03 % Favored : 80.99 % Cbeta Deviations : 0.00 % 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: -0.27 (0.13), residues: 4644 helix: 1.84 (0.13), residues: 1700 sheet: -0.26 (0.20), residues: 556 loop : -1.75 (0.12), residues: 2388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 408 HIS 0.004 0.001 HIS B 289 PHE 0.023 0.001 PHE O 130 TYR 0.015 0.001 TYR E 101 ARG 0.015 0.001 ARG D 302 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9288 Ramachandran restraints generated. 4644 Oldfield, 0 Emsley, 4644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9288 Ramachandran restraints generated. 4644 Oldfield, 0 Emsley, 4644 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 3788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 297 time to evaluate : 4.526 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 203 ILE cc_start: 0.8859 (OUTLIER) cc_final: 0.8408 (tt) REVERT: A 436 ARG cc_start: 0.8027 (OUTLIER) cc_final: 0.7332 (mtt-85) REVERT: B 125 LYS cc_start: 0.8840 (OUTLIER) cc_final: 0.8634 (mmpt) REVERT: B 153 GLN cc_start: 0.8209 (OUTLIER) cc_final: 0.7606 (mm-40) REVERT: B 155 GLU cc_start: 0.8336 (tt0) cc_final: 0.8052 (tt0) REVERT: B 426 GLN cc_start: 0.8372 (OUTLIER) cc_final: 0.7615 (tm-30) REVERT: B 436 ARG cc_start: 0.8163 (OUTLIER) cc_final: 0.7923 (mtp85) REVERT: C 74 MET cc_start: 0.7831 (ttm) cc_final: 0.7585 (ttp) REVERT: D 74 MET cc_start: 0.7241 (mmp) cc_final: 0.6998 (mpt) REVERT: D 342 PHE cc_start: 0.8752 (OUTLIER) cc_final: 0.8523 (t80) REVERT: D 426 GLN cc_start: 0.8154 (tt0) cc_final: 0.7714 (tp-100) REVERT: F 74 ASN cc_start: 0.8182 (t0) cc_final: 0.7851 (t0) REVERT: F 76 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.7514 (tm-30) REVERT: H 78 GLU cc_start: 0.8468 (tp30) cc_final: 0.8231 (mm-30) REVERT: H 113 LYS cc_start: 0.8714 (OUTLIER) cc_final: 0.8255 (mtpm) REVERT: J 203 ILE cc_start: 0.8858 (OUTLIER) cc_final: 0.8396 (tt) REVERT: J 436 ARG cc_start: 0.8017 (OUTLIER) cc_final: 0.7804 (mtp85) REVERT: K 153 GLN cc_start: 0.8208 (OUTLIER) cc_final: 0.7606 (mm-40) REVERT: K 155 GLU cc_start: 0.8338 (tt0) cc_final: 0.8053 (tt0) REVERT: K 426 GLN cc_start: 0.8373 (OUTLIER) cc_final: 0.7615 (tm-30) REVERT: M 74 MET cc_start: 0.7246 (mmp) cc_final: 0.7012 (mpt) REVERT: M 342 PHE cc_start: 0.8751 (OUTLIER) cc_final: 0.8524 (t80) REVERT: M 426 GLN cc_start: 0.8156 (tt0) cc_final: 0.7712 (tp-100) REVERT: N 233 ASN cc_start: 0.5932 (OUTLIER) cc_final: 0.5697 (m110) REVERT: Q 113 LYS cc_start: 0.8747 (OUTLIER) cc_final: 0.8289 (mtpm) outliers start: 75 outliers final: 55 residues processed: 345 average time/residue: 1.6978 time to fit residues: 694.3641 Evaluate side-chains 364 residues out of total 3788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 293 time to evaluate : 4.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 342 PHE Chi-restraints excluded: chain A residue 436 ARG Chi-restraints excluded: chain A residue 440 ASP Chi-restraints excluded: chain A residue 468 THR Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 125 LYS Chi-restraints excluded: chain B residue 153 GLN Chi-restraints excluded: chain B residue 213 ASP Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 342 PHE Chi-restraints excluded: chain B residue 426 GLN Chi-restraints excluded: chain B residue 436 ARG Chi-restraints excluded: chain B residue 457 ASP Chi-restraints excluded: chain C residue 213 ASP Chi-restraints excluded: chain C residue 342 PHE Chi-restraints excluded: chain C residue 449 SER Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 120 ASN Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 342 PHE Chi-restraints excluded: chain F residue 76 GLU Chi-restraints excluded: chain F residue 115 GLU Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain G residue 65 THR Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain G residue 132 SER Chi-restraints excluded: chain H residue 113 LYS Chi-restraints excluded: chain I residue 65 THR Chi-restraints excluded: chain I residue 91 VAL Chi-restraints excluded: chain J residue 31 THR Chi-restraints excluded: chain J residue 203 ILE Chi-restraints excluded: chain J residue 213 ASP Chi-restraints excluded: chain J residue 342 PHE Chi-restraints excluded: chain J residue 436 ARG Chi-restraints excluded: chain J residue 440 ASP Chi-restraints excluded: chain J residue 457 ASP Chi-restraints excluded: chain J residue 468 THR Chi-restraints excluded: chain K residue 20 THR Chi-restraints excluded: chain K residue 48 ASP Chi-restraints excluded: chain K residue 87 VAL Chi-restraints excluded: chain K residue 153 GLN Chi-restraints excluded: chain K residue 213 ASP Chi-restraints excluded: chain K residue 222 ILE Chi-restraints excluded: chain K residue 328 VAL Chi-restraints excluded: chain K residue 342 PHE Chi-restraints excluded: chain K residue 426 GLN Chi-restraints excluded: chain K residue 457 ASP Chi-restraints excluded: chain L residue 64 THR Chi-restraints excluded: chain L residue 70 LEU Chi-restraints excluded: chain L residue 213 ASP Chi-restraints excluded: chain L residue 342 PHE Chi-restraints excluded: chain L residue 449 SER Chi-restraints excluded: chain M residue 27 THR Chi-restraints excluded: chain M residue 120 ASN Chi-restraints excluded: chain M residue 213 ASP Chi-restraints excluded: chain M residue 222 ILE Chi-restraints excluded: chain M residue 299 ASP Chi-restraints excluded: chain M residue 342 PHE Chi-restraints excluded: chain N residue 233 ASN Chi-restraints excluded: chain O residue 115 GLU Chi-restraints excluded: chain O residue 131 LEU Chi-restraints excluded: chain P residue 65 THR Chi-restraints excluded: chain P residue 84 SER Chi-restraints excluded: chain P residue 132 SER Chi-restraints excluded: chain Q residue 113 LYS Chi-restraints excluded: chain R residue 65 THR Chi-restraints excluded: chain R residue 91 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 458 random chunks: chunk 288 optimal weight: 2.9990 chunk 387 optimal weight: 3.9990 chunk 111 optimal weight: 3.9990 chunk 335 optimal weight: 4.9990 chunk 53 optimal weight: 0.7980 chunk 100 optimal weight: 0.6980 chunk 363 optimal weight: 8.9990 chunk 152 optimal weight: 3.9990 chunk 373 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 chunk 67 optimal weight: 3.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 426 GLN B 426 GLN D 322 HIS H 68 ASN J 426 GLN K 426 GLN M 322 HIS Q 68 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.129513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.081291 restraints weight = 49650.124| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 2.77 r_work: 0.2816 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.2636 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.122 37188 Z= 0.237 Angle : 0.588 15.833 50334 Z= 0.295 Chirality : 0.043 0.264 5368 Planarity : 0.005 0.065 6622 Dihedral : 4.240 25.739 5038 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 2.03 % Allowed : 16.92 % Favored : 81.05 % Cbeta Deviations : 0.00 % 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: -0.13 (0.13), residues: 4644 helix: 1.94 (0.13), residues: 1700 sheet: -0.13 (0.20), residues: 566 loop : -1.69 (0.13), residues: 2378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP L 211 HIS 0.004 0.001 HIS J 289 PHE 0.021 0.001 PHE F 130 TYR 0.015 0.001 TYR N 101 ARG 0.015 0.001 ARG B 302 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12553.27 seconds wall clock time: 224 minutes 11.86 seconds (13451.86 seconds total)