Starting phenix.real_space_refine on Sun Feb 25 12:46:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8io6_35609/02_2024/8io6_35609_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8io6_35609/02_2024/8io6_35609.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8io6_35609/02_2024/8io6_35609.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8io6_35609/02_2024/8io6_35609.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8io6_35609/02_2024/8io6_35609_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8io6_35609/02_2024/8io6_35609_updated.pdb" } resolution = 2.68 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.053 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: 6 Type Number sf(0) Gaussians P 16 5.49 5 Mg 8 5.21 5 S 160 5.16 5 C 32664 2.51 5 N 8776 2.21 5 O 9880 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 43": "NH1" <-> "NH2" Residue "A ARG 54": "NH1" <-> "NH2" Residue "A ARG 60": "NH1" <-> "NH2" Residue "A PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 146": "OE1" <-> "OE2" Residue "A ARG 203": "NH1" <-> "NH2" Residue "A GLU 273": "OE1" <-> "OE2" Residue "A ASP 276": "OD1" <-> "OD2" Residue "A ARG 328": "NH1" <-> "NH2" Residue "A GLU 348": "OE1" <-> "OE2" Residue "A PHE 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 368": "OE1" <-> "OE2" Residue "A ARG 383": "NH1" <-> "NH2" Residue "A GLU 392": "OE1" <-> "OE2" Residue "A TYR 394": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 428": "NH1" <-> "NH2" Residue "A ASP 461": "OD1" <-> "OD2" Residue "A GLU 520": "OE1" <-> "OE2" Residue "A ARG 524": "NH1" <-> "NH2" Residue "A ASP 580": "OD1" <-> "OD2" Residue "A GLU 639": "OE1" <-> "OE2" Residue "A GLU 685": "OE1" <-> "OE2" Residue "A GLU 694": "OE1" <-> "OE2" Residue "A GLU 735": "OE1" <-> "OE2" Residue "A ARG 748": "NH1" <-> "NH2" Residue "A ARG 754": "NH1" <-> "NH2" Residue "A ASP 766": "OD1" <-> "OD2" Residue "A GLU 778": "OE1" <-> "OE2" Residue "A PHE 780": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 783": "OE1" <-> "OE2" Residue "A TYR 798": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 43": "NH1" <-> "NH2" Residue "B ARG 54": "NH1" <-> "NH2" Residue "B ARG 60": "NH1" <-> "NH2" Residue "B PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 146": "OE1" <-> "OE2" Residue "B ARG 203": "NH1" <-> "NH2" Residue "B GLU 273": "OE1" <-> "OE2" Residue "B ASP 276": "OD1" <-> "OD2" Residue "B ARG 328": "NH1" <-> "NH2" Residue "B GLU 348": "OE1" <-> "OE2" Residue "B PHE 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 368": "OE1" <-> "OE2" Residue "B ARG 383": "NH1" <-> "NH2" Residue "B GLU 392": "OE1" <-> "OE2" Residue "B TYR 394": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 428": "NH1" <-> "NH2" Residue "B ASP 461": "OD1" <-> "OD2" Residue "B GLU 520": "OE1" <-> "OE2" Residue "B ARG 524": "NH1" <-> "NH2" Residue "B ASP 580": "OD1" <-> "OD2" Residue "B GLU 639": "OE1" <-> "OE2" Residue "B GLU 685": "OE1" <-> "OE2" Residue "B GLU 694": "OE1" <-> "OE2" Residue "B GLU 735": "OE1" <-> "OE2" Residue "B ARG 748": "NH1" <-> "NH2" Residue "B ARG 754": "NH1" <-> "NH2" Residue "B ASP 766": "OD1" <-> "OD2" Residue "B GLU 778": "OE1" <-> "OE2" Residue "B PHE 780": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 783": "OE1" <-> "OE2" Residue "B TYR 798": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 43": "NH1" <-> "NH2" Residue "C ARG 54": "NH1" <-> "NH2" Residue "C ARG 60": "NH1" <-> "NH2" Residue "C PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 146": "OE1" <-> "OE2" Residue "C ARG 203": "NH1" <-> "NH2" Residue "C GLU 273": "OE1" <-> "OE2" Residue "C ASP 276": "OD1" <-> "OD2" Residue "C ARG 328": "NH1" <-> "NH2" Residue "C GLU 348": "OE1" <-> "OE2" Residue "C PHE 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 368": "OE1" <-> "OE2" Residue "C ARG 383": "NH1" <-> "NH2" Residue "C GLU 392": "OE1" <-> "OE2" Residue "C TYR 394": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 428": "NH1" <-> "NH2" Residue "C ASP 461": "OD1" <-> "OD2" Residue "C GLU 520": "OE1" <-> "OE2" Residue "C ARG 524": "NH1" <-> "NH2" Residue "C ASP 580": "OD1" <-> "OD2" Residue "C GLU 639": "OE1" <-> "OE2" Residue "C GLU 685": "OE1" <-> "OE2" Residue "C GLU 694": "OE1" <-> "OE2" Residue "C GLU 735": "OE1" <-> "OE2" Residue "C ARG 748": "NH1" <-> "NH2" Residue "C ARG 754": "NH1" <-> "NH2" Residue "C ASP 766": "OD1" <-> "OD2" Residue "C GLU 778": "OE1" <-> "OE2" Residue "C PHE 780": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 783": "OE1" <-> "OE2" Residue "C TYR 798": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 43": "NH1" <-> "NH2" Residue "D ARG 54": "NH1" <-> "NH2" Residue "D ARG 60": "NH1" <-> "NH2" Residue "D PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 146": "OE1" <-> "OE2" Residue "D ARG 203": "NH1" <-> "NH2" Residue "D GLU 273": "OE1" <-> "OE2" Residue "D ASP 276": "OD1" <-> "OD2" Residue "D ARG 328": "NH1" <-> "NH2" Residue "D GLU 348": "OE1" <-> "OE2" Residue "D PHE 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 368": "OE1" <-> "OE2" Residue "D ARG 383": "NH1" <-> "NH2" Residue "D GLU 392": "OE1" <-> "OE2" Residue "D TYR 394": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 428": "NH1" <-> "NH2" Residue "D ASP 461": "OD1" <-> "OD2" Residue "D GLU 520": "OE1" <-> "OE2" Residue "D ARG 524": "NH1" <-> "NH2" Residue "D ASP 580": "OD1" <-> "OD2" Residue "D GLU 639": "OE1" <-> "OE2" Residue "D GLU 685": "OE1" <-> "OE2" Residue "D GLU 694": "OE1" <-> "OE2" Residue "D GLU 735": "OE1" <-> "OE2" Residue "D ARG 748": "NH1" <-> "NH2" Residue "D ARG 754": "NH1" <-> "NH2" Residue "D ASP 766": "OD1" <-> "OD2" Residue "D GLU 778": "OE1" <-> "OE2" Residue "D PHE 780": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 783": "OE1" <-> "OE2" Residue "D TYR 798": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 43": "NH1" <-> "NH2" Residue "E ARG 54": "NH1" <-> "NH2" Residue "E ARG 60": "NH1" <-> "NH2" Residue "E PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 146": "OE1" <-> "OE2" Residue "E ARG 203": "NH1" <-> "NH2" Residue "E GLU 273": "OE1" <-> "OE2" Residue "E ASP 276": "OD1" <-> "OD2" Residue "E ARG 328": "NH1" <-> "NH2" Residue "E GLU 348": "OE1" <-> "OE2" Residue "E PHE 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 368": "OE1" <-> "OE2" Residue "E ARG 383": "NH1" <-> "NH2" Residue "E GLU 392": "OE1" <-> "OE2" Residue "E TYR 394": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 428": "NH1" <-> "NH2" Residue "E ASP 461": "OD1" <-> "OD2" Residue "E GLU 520": "OE1" <-> "OE2" Residue "E ARG 524": "NH1" <-> "NH2" Residue "E ASP 580": "OD1" <-> "OD2" Residue "E GLU 639": "OE1" <-> "OE2" Residue "E GLU 685": "OE1" <-> "OE2" Residue "E GLU 694": "OE1" <-> "OE2" Residue "E GLU 735": "OE1" <-> "OE2" Residue "E ARG 748": "NH1" <-> "NH2" Residue "E ARG 754": "NH1" <-> "NH2" Residue "E ASP 766": "OD1" <-> "OD2" Residue "E GLU 778": "OE1" <-> "OE2" Residue "E PHE 780": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 783": "OE1" <-> "OE2" Residue "E TYR 798": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 43": "NH1" <-> "NH2" Residue "F ARG 54": "NH1" <-> "NH2" Residue "F ARG 60": "NH1" <-> "NH2" Residue "F PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 146": "OE1" <-> "OE2" Residue "F ARG 203": "NH1" <-> "NH2" Residue "F GLU 273": "OE1" <-> "OE2" Residue "F ASP 276": "OD1" <-> "OD2" Residue "F ARG 328": "NH1" <-> "NH2" Residue "F GLU 348": "OE1" <-> "OE2" Residue "F PHE 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 368": "OE1" <-> "OE2" Residue "F ARG 383": "NH1" <-> "NH2" Residue "F GLU 392": "OE1" <-> "OE2" Residue "F TYR 394": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 428": "NH1" <-> "NH2" Residue "F ASP 461": "OD1" <-> "OD2" Residue "F GLU 520": "OE1" <-> "OE2" Residue "F ARG 524": "NH1" <-> "NH2" Residue "F ASP 580": "OD1" <-> "OD2" Residue "F GLU 639": "OE1" <-> "OE2" Residue "F GLU 685": "OE1" <-> "OE2" Residue "F GLU 694": "OE1" <-> "OE2" Residue "F GLU 735": "OE1" <-> "OE2" Residue "F ARG 748": "NH1" <-> "NH2" Residue "F ARG 754": "NH1" <-> "NH2" Residue "F ASP 766": "OD1" <-> "OD2" Residue "F GLU 778": "OE1" <-> "OE2" Residue "F PHE 780": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 783": "OE1" <-> "OE2" Residue "F TYR 798": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 43": "NH1" <-> "NH2" Residue "G ARG 54": "NH1" <-> "NH2" Residue "G ARG 60": "NH1" <-> "NH2" Residue "G PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 146": "OE1" <-> "OE2" Residue "G ARG 203": "NH1" <-> "NH2" Residue "G GLU 273": "OE1" <-> "OE2" Residue "G ASP 276": "OD1" <-> "OD2" Residue "G ARG 328": "NH1" <-> "NH2" Residue "G GLU 348": "OE1" <-> "OE2" Residue "G PHE 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 368": "OE1" <-> "OE2" Residue "G ARG 383": "NH1" <-> "NH2" Residue "G GLU 392": "OE1" <-> "OE2" Residue "G TYR 394": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 428": "NH1" <-> "NH2" Residue "G ASP 461": "OD1" <-> "OD2" Residue "G GLU 520": "OE1" <-> "OE2" Residue "G ARG 524": "NH1" <-> "NH2" Residue "G ASP 580": "OD1" <-> "OD2" Residue "G GLU 639": "OE1" <-> "OE2" Residue "G GLU 685": "OE1" <-> "OE2" Residue "G GLU 694": "OE1" <-> "OE2" Residue "G GLU 735": "OE1" <-> "OE2" Residue "G ARG 748": "NH1" <-> "NH2" Residue "G ARG 754": "NH1" <-> "NH2" Residue "G ASP 766": "OD1" <-> "OD2" Residue "G GLU 778": "OE1" <-> "OE2" Residue "G PHE 780": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 783": "OE1" <-> "OE2" Residue "G TYR 798": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 43": "NH1" <-> "NH2" Residue "H ARG 54": "NH1" <-> "NH2" Residue "H ARG 60": "NH1" <-> "NH2" Residue "H PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 146": "OE1" <-> "OE2" Residue "H ARG 203": "NH1" <-> "NH2" Residue "H GLU 273": "OE1" <-> "OE2" Residue "H ASP 276": "OD1" <-> "OD2" Residue "H ARG 328": "NH1" <-> "NH2" Residue "H GLU 348": "OE1" <-> "OE2" Residue "H PHE 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 368": "OE1" <-> "OE2" Residue "H ARG 383": "NH1" <-> "NH2" Residue "H GLU 392": "OE1" <-> "OE2" Residue "H TYR 394": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 428": "NH1" <-> "NH2" Residue "H ASP 461": "OD1" <-> "OD2" Residue "H GLU 520": "OE1" <-> "OE2" Residue "H ARG 524": "NH1" <-> "NH2" Residue "H ASP 580": "OD1" <-> "OD2" Residue "H GLU 639": "OE1" <-> "OE2" Residue "H GLU 685": "OE1" <-> "OE2" Residue "H GLU 694": "OE1" <-> "OE2" Residue "H GLU 735": "OE1" <-> "OE2" Residue "H ARG 748": "NH1" <-> "NH2" Residue "H ARG 754": "NH1" <-> "NH2" Residue "H ASP 766": "OD1" <-> "OD2" Residue "H GLU 778": "OE1" <-> "OE2" Residue "H PHE 780": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 783": "OE1" <-> "OE2" Residue "H TYR 798": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 51504 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 6411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 806, 6411 Classifications: {'peptide': 806} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 765} Chain: "B" Number of atoms: 6411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 806, 6411 Classifications: {'peptide': 806} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 765} Chain: "C" Number of atoms: 6411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 806, 6411 Classifications: {'peptide': 806} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 765} Chain: "D" Number of atoms: 6411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 806, 6411 Classifications: {'peptide': 806} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 765} Chain: "E" Number of atoms: 6411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 806, 6411 Classifications: {'peptide': 806} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 765} Chain: "F" Number of atoms: 6411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 806, 6411 Classifications: {'peptide': 806} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 765} Chain: "G" Number of atoms: 6411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 806, 6411 Classifications: {'peptide': 806} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 765} Chain: "H" Number of atoms: 6411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 806, 6411 Classifications: {'peptide': 806} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 765} Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {' MG': 1, 'TPP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {' MG': 1, 'TPP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {' MG': 1, 'TPP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {' MG': 1, 'TPP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {' MG': 1, 'TPP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {' MG': 1, 'TPP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {' MG': 1, 'TPP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {' MG': 1, 'TPP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 25.13, per 1000 atoms: 0.49 Number of scatterers: 51504 At special positions: 0 Unit cell: (186.75, 186.75, 115.37, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 160 16.00 P 16 15.00 Mg 8 11.99 O 9880 8.00 N 8776 7.00 C 32664 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: 19.04 Conformation dependent library (CDL) restraints added in 8.9 seconds 12864 Ramachandran restraints generated. 6432 Oldfield, 0 Emsley, 6432 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11920 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 296 helices and 24 sheets defined 41.9% alpha, 8.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 11.78 Creating SS restraints... Processing helix chain 'A' and resid 19 through 41 removed outlier: 3.717A pdb=" N ILE A 40 " --> pdb=" O SER A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 56 No H-bonds generated for 'chain 'A' and resid 54 through 56' Processing helix chain 'A' and resid 68 through 85 Processing helix chain 'A' and resid 99 through 108 Processing helix chain 'A' and resid 111 through 115 Processing helix chain 'A' and resid 123 through 131 Processing helix chain 'A' and resid 160 through 167 Processing helix chain 'A' and resid 184 through 186 No H-bonds generated for 'chain 'A' and resid 184 through 186' Processing helix chain 'A' and resid 188 through 198 removed outlier: 4.480A pdb=" N GLN A 195 " --> pdb=" O ALA A 191 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N SER A 196 " --> pdb=" O THR A 192 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N ASN A 197 " --> pdb=" O GLY A 193 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N LYS A 198 " --> pdb=" O TRP A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 227 No H-bonds generated for 'chain 'A' and resid 225 through 227' Processing helix chain 'A' and resid 230 through 239 Processing helix chain 'A' and resid 256 through 283 removed outlier: 4.081A pdb=" N THR A 283 " --> pdb=" O ALA A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 319 No H-bonds generated for 'chain 'A' and resid 317 through 319' Processing helix chain 'A' and resid 331 through 344 removed outlier: 4.186A pdb=" N TYR A 344 " --> pdb=" O TRP A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 349 No H-bonds generated for 'chain 'A' and resid 346 through 349' Processing helix chain 'A' and resid 358 through 360 No H-bonds generated for 'chain 'A' and resid 358 through 360' Processing helix chain 'A' and resid 367 through 369 No H-bonds generated for 'chain 'A' and resid 367 through 369' Processing helix chain 'A' and resid 379 through 382 No H-bonds generated for 'chain 'A' and resid 379 through 382' Processing helix chain 'A' and resid 391 through 393 No H-bonds generated for 'chain 'A' and resid 391 through 393' Processing helix chain 'A' and resid 397 through 402 removed outlier: 4.095A pdb=" N TYR A 402 " --> pdb=" O VAL A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 425 removed outlier: 3.820A pdb=" N LEU A 415 " --> pdb=" O ALA A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 448 Processing helix chain 'A' and resid 479 through 491 Processing helix chain 'A' and resid 505 through 525 removed outlier: 5.000A pdb=" N SER A 510 " --> pdb=" O VAL A 507 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU A 512 " --> pdb=" O ASP A 509 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLU A 520 " --> pdb=" O LYS A 517 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ALA A 521 " --> pdb=" O TRP A 518 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL A 523 " --> pdb=" O GLU A 520 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG A 524 " --> pdb=" O ALA A 521 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N GLU A 525 " --> pdb=" O THR A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 545 No H-bonds generated for 'chain 'A' and resid 543 through 545' Processing helix chain 'A' and resid 551 through 553 No H-bonds generated for 'chain 'A' and resid 551 through 553' Processing helix chain 'A' and resid 558 through 565 removed outlier: 4.434A pdb=" N LYS A 565 " --> pdb=" O VAL A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 593 Processing helix chain 'A' and resid 614 through 623 removed outlier: 4.174A pdb=" N LYS A 623 " --> pdb=" O ALA A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 665 removed outlier: 3.505A pdb=" N GLU A 664 " --> pdb=" O ASP A 660 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU A 665 " --> pdb=" O LYS A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 677 through 680 Processing helix chain 'A' and resid 692 through 698 Processing helix chain 'A' and resid 713 through 717 Processing helix chain 'A' and resid 743 through 748 removed outlier: 3.609A pdb=" N VAL A 747 " --> pdb=" O PRO A 743 " (cutoff:3.500A) Processing helix chain 'A' and resid 754 through 765 Processing helix chain 'A' and resid 771 through 791 removed outlier: 3.596A pdb=" N ASP A 782 " --> pdb=" O GLU A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 796 through 799 No H-bonds generated for 'chain 'A' and resid 796 through 799' Processing helix chain 'B' and resid 19 through 41 removed outlier: 3.716A pdb=" N ILE B 40 " --> pdb=" O SER B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 54 through 56 No H-bonds generated for 'chain 'B' and resid 54 through 56' Processing helix chain 'B' and resid 68 through 85 Processing helix chain 'B' and resid 99 through 108 Processing helix chain 'B' and resid 111 through 115 Processing helix chain 'B' and resid 123 through 131 Processing helix chain 'B' and resid 160 through 167 Processing helix chain 'B' and resid 184 through 186 No H-bonds generated for 'chain 'B' and resid 184 through 186' Processing helix chain 'B' and resid 188 through 198 removed outlier: 4.479A pdb=" N GLN B 195 " --> pdb=" O ALA B 191 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N SER B 196 " --> pdb=" O THR B 192 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N ASN B 197 " --> pdb=" O GLY B 193 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N LYS B 198 " --> pdb=" O TRP B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 227 No H-bonds generated for 'chain 'B' and resid 225 through 227' Processing helix chain 'B' and resid 230 through 239 Processing helix chain 'B' and resid 256 through 283 removed outlier: 4.081A pdb=" N THR B 283 " --> pdb=" O ALA B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 319 No H-bonds generated for 'chain 'B' and resid 317 through 319' Processing helix chain 'B' and resid 331 through 344 removed outlier: 4.185A pdb=" N TYR B 344 " --> pdb=" O TRP B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 349 No H-bonds generated for 'chain 'B' and resid 346 through 349' Processing helix chain 'B' and resid 358 through 360 No H-bonds generated for 'chain 'B' and resid 358 through 360' Processing helix chain 'B' and resid 367 through 369 No H-bonds generated for 'chain 'B' and resid 367 through 369' Processing helix chain 'B' and resid 379 through 382 No H-bonds generated for 'chain 'B' and resid 379 through 382' Processing helix chain 'B' and resid 391 through 393 No H-bonds generated for 'chain 'B' and resid 391 through 393' Processing helix chain 'B' and resid 397 through 402 removed outlier: 4.095A pdb=" N TYR B 402 " --> pdb=" O VAL B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 425 removed outlier: 3.820A pdb=" N LEU B 415 " --> pdb=" O ALA B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 448 Processing helix chain 'B' and resid 479 through 491 Processing helix chain 'B' and resid 505 through 525 removed outlier: 4.999A pdb=" N SER B 510 " --> pdb=" O VAL B 507 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU B 512 " --> pdb=" O ASP B 509 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLU B 520 " --> pdb=" O LYS B 517 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ALA B 521 " --> pdb=" O TRP B 518 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL B 523 " --> pdb=" O GLU B 520 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG B 524 " --> pdb=" O ALA B 521 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N GLU B 525 " --> pdb=" O THR B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 545 No H-bonds generated for 'chain 'B' and resid 543 through 545' Processing helix chain 'B' and resid 551 through 553 No H-bonds generated for 'chain 'B' and resid 551 through 553' Processing helix chain 'B' and resid 558 through 565 removed outlier: 4.434A pdb=" N LYS B 565 " --> pdb=" O VAL B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 581 through 593 Processing helix chain 'B' and resid 614 through 623 removed outlier: 4.174A pdb=" N LYS B 623 " --> pdb=" O ALA B 619 " (cutoff:3.500A) Processing helix chain 'B' and resid 649 through 665 removed outlier: 3.506A pdb=" N GLU B 664 " --> pdb=" O ASP B 660 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU B 665 " --> pdb=" O LYS B 661 " (cutoff:3.500A) Processing helix chain 'B' and resid 677 through 680 Processing helix chain 'B' and resid 692 through 698 Processing helix chain 'B' and resid 713 through 717 Processing helix chain 'B' and resid 743 through 748 removed outlier: 3.609A pdb=" N VAL B 747 " --> pdb=" O PRO B 743 " (cutoff:3.500A) Processing helix chain 'B' and resid 754 through 765 Processing helix chain 'B' and resid 771 through 791 removed outlier: 3.597A pdb=" N ASP B 782 " --> pdb=" O GLU B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 796 through 799 No H-bonds generated for 'chain 'B' and resid 796 through 799' Processing helix chain 'C' and resid 19 through 41 removed outlier: 3.716A pdb=" N ILE C 40 " --> pdb=" O SER C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 56 No H-bonds generated for 'chain 'C' and resid 54 through 56' Processing helix chain 'C' and resid 68 through 85 Processing helix chain 'C' and resid 99 through 108 Processing helix chain 'C' and resid 111 through 115 Processing helix chain 'C' and resid 123 through 131 Processing helix chain 'C' and resid 160 through 167 Processing helix chain 'C' and resid 184 through 186 No H-bonds generated for 'chain 'C' and resid 184 through 186' Processing helix chain 'C' and resid 188 through 198 removed outlier: 4.479A pdb=" N GLN C 195 " --> pdb=" O ALA C 191 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N SER C 196 " --> pdb=" O THR C 192 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N ASN C 197 " --> pdb=" O GLY C 193 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N LYS C 198 " --> pdb=" O TRP C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 227 No H-bonds generated for 'chain 'C' and resid 225 through 227' Processing helix chain 'C' and resid 230 through 239 Processing helix chain 'C' and resid 256 through 283 removed outlier: 4.081A pdb=" N THR C 283 " --> pdb=" O ALA C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 319 No H-bonds generated for 'chain 'C' and resid 317 through 319' Processing helix chain 'C' and resid 331 through 344 removed outlier: 4.186A pdb=" N TYR C 344 " --> pdb=" O TRP C 340 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 349 No H-bonds generated for 'chain 'C' and resid 346 through 349' Processing helix chain 'C' and resid 358 through 360 No H-bonds generated for 'chain 'C' and resid 358 through 360' Processing helix chain 'C' and resid 367 through 369 No H-bonds generated for 'chain 'C' and resid 367 through 369' Processing helix chain 'C' and resid 379 through 382 No H-bonds generated for 'chain 'C' and resid 379 through 382' Processing helix chain 'C' and resid 391 through 393 No H-bonds generated for 'chain 'C' and resid 391 through 393' Processing helix chain 'C' and resid 397 through 402 removed outlier: 4.095A pdb=" N TYR C 402 " --> pdb=" O VAL C 399 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 425 removed outlier: 3.822A pdb=" N LEU C 415 " --> pdb=" O ALA C 411 " (cutoff:3.500A) Processing helix chain 'C' and resid 444 through 448 Processing helix chain 'C' and resid 479 through 491 Processing helix chain 'C' and resid 505 through 525 removed outlier: 4.999A pdb=" N SER C 510 " --> pdb=" O VAL C 507 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU C 512 " --> pdb=" O ASP C 509 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLU C 520 " --> pdb=" O LYS C 517 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ALA C 521 " --> pdb=" O TRP C 518 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL C 523 " --> pdb=" O GLU C 520 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG C 524 " --> pdb=" O ALA C 521 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N GLU C 525 " --> pdb=" O THR C 522 " (cutoff:3.500A) Processing helix chain 'C' and resid 543 through 545 No H-bonds generated for 'chain 'C' and resid 543 through 545' Processing helix chain 'C' and resid 551 through 553 No H-bonds generated for 'chain 'C' and resid 551 through 553' Processing helix chain 'C' and resid 558 through 565 removed outlier: 4.434A pdb=" N LYS C 565 " --> pdb=" O VAL C 561 " (cutoff:3.500A) Processing helix chain 'C' and resid 581 through 593 Processing helix chain 'C' and resid 614 through 623 removed outlier: 4.174A pdb=" N LYS C 623 " --> pdb=" O ALA C 619 " (cutoff:3.500A) Processing helix chain 'C' and resid 649 through 665 removed outlier: 3.506A pdb=" N GLU C 664 " --> pdb=" O ASP C 660 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU C 665 " --> pdb=" O LYS C 661 " (cutoff:3.500A) Processing helix chain 'C' and resid 677 through 680 Processing helix chain 'C' and resid 692 through 698 Processing helix chain 'C' and resid 713 through 717 Processing helix chain 'C' and resid 743 through 748 removed outlier: 3.609A pdb=" N VAL C 747 " --> pdb=" O PRO C 743 " (cutoff:3.500A) Processing helix chain 'C' and resid 754 through 765 Processing helix chain 'C' and resid 771 through 791 removed outlier: 3.596A pdb=" N ASP C 782 " --> pdb=" O GLU C 778 " (cutoff:3.500A) Processing helix chain 'C' and resid 796 through 799 No H-bonds generated for 'chain 'C' and resid 796 through 799' Processing helix chain 'D' and resid 19 through 41 removed outlier: 3.716A pdb=" N ILE D 40 " --> pdb=" O SER D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 54 through 56 No H-bonds generated for 'chain 'D' and resid 54 through 56' Processing helix chain 'D' and resid 68 through 85 Processing helix chain 'D' and resid 99 through 108 Processing helix chain 'D' and resid 111 through 115 Processing helix chain 'D' and resid 123 through 131 Processing helix chain 'D' and resid 160 through 167 Processing helix chain 'D' and resid 184 through 186 No H-bonds generated for 'chain 'D' and resid 184 through 186' Processing helix chain 'D' and resid 188 through 198 removed outlier: 4.479A pdb=" N GLN D 195 " --> pdb=" O ALA D 191 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N SER D 196 " --> pdb=" O THR D 192 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N ASN D 197 " --> pdb=" O GLY D 193 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N LYS D 198 " --> pdb=" O TRP D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 227 No H-bonds generated for 'chain 'D' and resid 225 through 227' Processing helix chain 'D' and resid 230 through 239 Processing helix chain 'D' and resid 256 through 283 removed outlier: 4.082A pdb=" N THR D 283 " --> pdb=" O ALA D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 319 No H-bonds generated for 'chain 'D' and resid 317 through 319' Processing helix chain 'D' and resid 331 through 344 removed outlier: 4.185A pdb=" N TYR D 344 " --> pdb=" O TRP D 340 " (cutoff:3.500A) Processing helix chain 'D' and resid 346 through 349 No H-bonds generated for 'chain 'D' and resid 346 through 349' Processing helix chain 'D' and resid 358 through 360 No H-bonds generated for 'chain 'D' and resid 358 through 360' Processing helix chain 'D' and resid 367 through 369 No H-bonds generated for 'chain 'D' and resid 367 through 369' Processing helix chain 'D' and resid 379 through 382 No H-bonds generated for 'chain 'D' and resid 379 through 382' Processing helix chain 'D' and resid 391 through 393 No H-bonds generated for 'chain 'D' and resid 391 through 393' Processing helix chain 'D' and resid 397 through 402 removed outlier: 4.095A pdb=" N TYR D 402 " --> pdb=" O VAL D 399 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 425 removed outlier: 3.821A pdb=" N LEU D 415 " --> pdb=" O ALA D 411 " (cutoff:3.500A) Processing helix chain 'D' and resid 444 through 448 Processing helix chain 'D' and resid 479 through 491 Processing helix chain 'D' and resid 505 through 525 removed outlier: 5.000A pdb=" N SER D 510 " --> pdb=" O VAL D 507 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU D 512 " --> pdb=" O ASP D 509 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLU D 520 " --> pdb=" O LYS D 517 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ALA D 521 " --> pdb=" O TRP D 518 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL D 523 " --> pdb=" O GLU D 520 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG D 524 " --> pdb=" O ALA D 521 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N GLU D 525 " --> pdb=" O THR D 522 " (cutoff:3.500A) Processing helix chain 'D' and resid 543 through 545 No H-bonds generated for 'chain 'D' and resid 543 through 545' Processing helix chain 'D' and resid 551 through 553 No H-bonds generated for 'chain 'D' and resid 551 through 553' Processing helix chain 'D' and resid 558 through 565 removed outlier: 4.434A pdb=" N LYS D 565 " --> pdb=" O VAL D 561 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 593 Processing helix chain 'D' and resid 614 through 623 removed outlier: 4.174A pdb=" N LYS D 623 " --> pdb=" O ALA D 619 " (cutoff:3.500A) Processing helix chain 'D' and resid 649 through 665 removed outlier: 3.506A pdb=" N GLU D 664 " --> pdb=" O ASP D 660 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU D 665 " --> pdb=" O LYS D 661 " (cutoff:3.500A) Processing helix chain 'D' and resid 677 through 680 Processing helix chain 'D' and resid 692 through 698 Processing helix chain 'D' and resid 713 through 717 Processing helix chain 'D' and resid 743 through 748 removed outlier: 3.609A pdb=" N VAL D 747 " --> pdb=" O PRO D 743 " (cutoff:3.500A) Processing helix chain 'D' and resid 754 through 765 Processing helix chain 'D' and resid 771 through 791 removed outlier: 3.597A pdb=" N ASP D 782 " --> pdb=" O GLU D 778 " (cutoff:3.500A) Processing helix chain 'D' and resid 796 through 799 No H-bonds generated for 'chain 'D' and resid 796 through 799' Processing helix chain 'E' and resid 19 through 41 removed outlier: 3.716A pdb=" N ILE E 40 " --> pdb=" O SER E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 54 through 56 No H-bonds generated for 'chain 'E' and resid 54 through 56' Processing helix chain 'E' and resid 68 through 85 Processing helix chain 'E' and resid 99 through 108 Processing helix chain 'E' and resid 111 through 115 Processing helix chain 'E' and resid 123 through 131 Processing helix chain 'E' and resid 160 through 167 Processing helix chain 'E' and resid 184 through 186 No H-bonds generated for 'chain 'E' and resid 184 through 186' Processing helix chain 'E' and resid 188 through 198 removed outlier: 4.479A pdb=" N GLN E 195 " --> pdb=" O ALA E 191 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N SER E 196 " --> pdb=" O THR E 192 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N ASN E 197 " --> pdb=" O GLY E 193 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N LYS E 198 " --> pdb=" O TRP E 194 " (cutoff:3.500A) Processing helix chain 'E' and resid 225 through 227 No H-bonds generated for 'chain 'E' and resid 225 through 227' Processing helix chain 'E' and resid 230 through 239 Processing helix chain 'E' and resid 256 through 283 removed outlier: 4.082A pdb=" N THR E 283 " --> pdb=" O ALA E 279 " (cutoff:3.500A) Processing helix chain 'E' and resid 317 through 319 No H-bonds generated for 'chain 'E' and resid 317 through 319' Processing helix chain 'E' and resid 331 through 344 removed outlier: 4.185A pdb=" N TYR E 344 " --> pdb=" O TRP E 340 " (cutoff:3.500A) Processing helix chain 'E' and resid 346 through 349 No H-bonds generated for 'chain 'E' and resid 346 through 349' Processing helix chain 'E' and resid 358 through 360 No H-bonds generated for 'chain 'E' and resid 358 through 360' Processing helix chain 'E' and resid 367 through 369 No H-bonds generated for 'chain 'E' and resid 367 through 369' Processing helix chain 'E' and resid 379 through 382 No H-bonds generated for 'chain 'E' and resid 379 through 382' Processing helix chain 'E' and resid 391 through 393 No H-bonds generated for 'chain 'E' and resid 391 through 393' Processing helix chain 'E' and resid 397 through 402 removed outlier: 4.095A pdb=" N TYR E 402 " --> pdb=" O VAL E 399 " (cutoff:3.500A) Processing helix chain 'E' and resid 411 through 425 removed outlier: 3.821A pdb=" N LEU E 415 " --> pdb=" O ALA E 411 " (cutoff:3.500A) Processing helix chain 'E' and resid 444 through 448 Processing helix chain 'E' and resid 479 through 491 Processing helix chain 'E' and resid 505 through 525 removed outlier: 4.999A pdb=" N SER E 510 " --> pdb=" O VAL E 507 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU E 512 " --> pdb=" O ASP E 509 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLU E 520 " --> pdb=" O LYS E 517 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ALA E 521 " --> pdb=" O TRP E 518 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL E 523 " --> pdb=" O GLU E 520 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG E 524 " --> pdb=" O ALA E 521 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N GLU E 525 " --> pdb=" O THR E 522 " (cutoff:3.500A) Processing helix chain 'E' and resid 543 through 545 No H-bonds generated for 'chain 'E' and resid 543 through 545' Processing helix chain 'E' and resid 551 through 553 No H-bonds generated for 'chain 'E' and resid 551 through 553' Processing helix chain 'E' and resid 558 through 565 removed outlier: 4.435A pdb=" N LYS E 565 " --> pdb=" O VAL E 561 " (cutoff:3.500A) Processing helix chain 'E' and resid 581 through 593 Processing helix chain 'E' and resid 614 through 623 removed outlier: 4.175A pdb=" N LYS E 623 " --> pdb=" O ALA E 619 " (cutoff:3.500A) Processing helix chain 'E' and resid 649 through 665 removed outlier: 3.507A pdb=" N GLU E 664 " --> pdb=" O ASP E 660 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU E 665 " --> pdb=" O LYS E 661 " (cutoff:3.500A) Processing helix chain 'E' and resid 677 through 680 Processing helix chain 'E' and resid 692 through 698 Processing helix chain 'E' and resid 713 through 717 Processing helix chain 'E' and resid 743 through 748 removed outlier: 3.609A pdb=" N VAL E 747 " --> pdb=" O PRO E 743 " (cutoff:3.500A) Processing helix chain 'E' and resid 754 through 765 Processing helix chain 'E' and resid 771 through 791 removed outlier: 3.596A pdb=" N ASP E 782 " --> pdb=" O GLU E 778 " (cutoff:3.500A) Processing helix chain 'E' and resid 796 through 799 No H-bonds generated for 'chain 'E' and resid 796 through 799' Processing helix chain 'F' and resid 19 through 41 removed outlier: 3.717A pdb=" N ILE F 40 " --> pdb=" O SER F 36 " (cutoff:3.500A) Processing helix chain 'F' and resid 54 through 56 No H-bonds generated for 'chain 'F' and resid 54 through 56' Processing helix chain 'F' and resid 68 through 85 Processing helix chain 'F' and resid 99 through 108 Processing helix chain 'F' and resid 111 through 115 Processing helix chain 'F' and resid 123 through 131 Processing helix chain 'F' and resid 160 through 167 Processing helix chain 'F' and resid 184 through 186 No H-bonds generated for 'chain 'F' and resid 184 through 186' Processing helix chain 'F' and resid 188 through 198 removed outlier: 4.479A pdb=" N GLN F 195 " --> pdb=" O ALA F 191 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N SER F 196 " --> pdb=" O THR F 192 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N ASN F 197 " --> pdb=" O GLY F 193 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N LYS F 198 " --> pdb=" O TRP F 194 " (cutoff:3.500A) Processing helix chain 'F' and resid 225 through 227 No H-bonds generated for 'chain 'F' and resid 225 through 227' Processing helix chain 'F' and resid 230 through 239 Processing helix chain 'F' and resid 256 through 283 removed outlier: 4.081A pdb=" N THR F 283 " --> pdb=" O ALA F 279 " (cutoff:3.500A) Processing helix chain 'F' and resid 317 through 319 No H-bonds generated for 'chain 'F' and resid 317 through 319' Processing helix chain 'F' and resid 331 through 344 removed outlier: 4.185A pdb=" N TYR F 344 " --> pdb=" O TRP F 340 " (cutoff:3.500A) Processing helix chain 'F' and resid 346 through 349 No H-bonds generated for 'chain 'F' and resid 346 through 349' Processing helix chain 'F' and resid 358 through 360 No H-bonds generated for 'chain 'F' and resid 358 through 360' Processing helix chain 'F' and resid 367 through 369 No H-bonds generated for 'chain 'F' and resid 367 through 369' Processing helix chain 'F' and resid 379 through 382 No H-bonds generated for 'chain 'F' and resid 379 through 382' Processing helix chain 'F' and resid 391 through 393 No H-bonds generated for 'chain 'F' and resid 391 through 393' Processing helix chain 'F' and resid 397 through 402 removed outlier: 4.095A pdb=" N TYR F 402 " --> pdb=" O VAL F 399 " (cutoff:3.500A) Processing helix chain 'F' and resid 411 through 425 removed outlier: 3.821A pdb=" N LEU F 415 " --> pdb=" O ALA F 411 " (cutoff:3.500A) Processing helix chain 'F' and resid 444 through 448 Processing helix chain 'F' and resid 479 through 491 Processing helix chain 'F' and resid 505 through 525 removed outlier: 5.000A pdb=" N SER F 510 " --> pdb=" O VAL F 507 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU F 512 " --> pdb=" O ASP F 509 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLU F 520 " --> pdb=" O LYS F 517 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ALA F 521 " --> pdb=" O TRP F 518 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL F 523 " --> pdb=" O GLU F 520 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG F 524 " --> pdb=" O ALA F 521 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N GLU F 525 " --> pdb=" O THR F 522 " (cutoff:3.500A) Processing helix chain 'F' and resid 543 through 545 No H-bonds generated for 'chain 'F' and resid 543 through 545' Processing helix chain 'F' and resid 551 through 553 No H-bonds generated for 'chain 'F' and resid 551 through 553' Processing helix chain 'F' and resid 558 through 565 removed outlier: 4.434A pdb=" N LYS F 565 " --> pdb=" O VAL F 561 " (cutoff:3.500A) Processing helix chain 'F' and resid 581 through 593 Processing helix chain 'F' and resid 614 through 623 removed outlier: 4.174A pdb=" N LYS F 623 " --> pdb=" O ALA F 619 " (cutoff:3.500A) Processing helix chain 'F' and resid 649 through 665 removed outlier: 3.505A pdb=" N GLU F 664 " --> pdb=" O ASP F 660 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU F 665 " --> pdb=" O LYS F 661 " (cutoff:3.500A) Processing helix chain 'F' and resid 677 through 680 Processing helix chain 'F' and resid 692 through 698 Processing helix chain 'F' and resid 713 through 717 Processing helix chain 'F' and resid 743 through 748 removed outlier: 3.609A pdb=" N VAL F 747 " --> pdb=" O PRO F 743 " (cutoff:3.500A) Processing helix chain 'F' and resid 754 through 765 Processing helix chain 'F' and resid 771 through 791 removed outlier: 3.596A pdb=" N ASP F 782 " --> pdb=" O GLU F 778 " (cutoff:3.500A) Processing helix chain 'F' and resid 796 through 799 No H-bonds generated for 'chain 'F' and resid 796 through 799' Processing helix chain 'G' and resid 19 through 41 removed outlier: 3.717A pdb=" N ILE G 40 " --> pdb=" O SER G 36 " (cutoff:3.500A) Processing helix chain 'G' and resid 54 through 56 No H-bonds generated for 'chain 'G' and resid 54 through 56' Processing helix chain 'G' and resid 68 through 85 Processing helix chain 'G' and resid 99 through 108 Processing helix chain 'G' and resid 111 through 115 Processing helix chain 'G' and resid 123 through 131 Processing helix chain 'G' and resid 160 through 167 Processing helix chain 'G' and resid 184 through 186 No H-bonds generated for 'chain 'G' and resid 184 through 186' Processing helix chain 'G' and resid 188 through 198 removed outlier: 4.479A pdb=" N GLN G 195 " --> pdb=" O ALA G 191 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N SER G 196 " --> pdb=" O THR G 192 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N ASN G 197 " --> pdb=" O GLY G 193 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N LYS G 198 " --> pdb=" O TRP G 194 " (cutoff:3.500A) Processing helix chain 'G' and resid 225 through 227 No H-bonds generated for 'chain 'G' and resid 225 through 227' Processing helix chain 'G' and resid 230 through 239 Processing helix chain 'G' and resid 256 through 283 removed outlier: 4.081A pdb=" N THR G 283 " --> pdb=" O ALA G 279 " (cutoff:3.500A) Processing helix chain 'G' and resid 317 through 319 No H-bonds generated for 'chain 'G' and resid 317 through 319' Processing helix chain 'G' and resid 331 through 344 removed outlier: 4.185A pdb=" N TYR G 344 " --> pdb=" O TRP G 340 " (cutoff:3.500A) Processing helix chain 'G' and resid 346 through 349 No H-bonds generated for 'chain 'G' and resid 346 through 349' Processing helix chain 'G' and resid 358 through 360 No H-bonds generated for 'chain 'G' and resid 358 through 360' Processing helix chain 'G' and resid 367 through 369 No H-bonds generated for 'chain 'G' and resid 367 through 369' Processing helix chain 'G' and resid 379 through 382 No H-bonds generated for 'chain 'G' and resid 379 through 382' Processing helix chain 'G' and resid 391 through 393 No H-bonds generated for 'chain 'G' and resid 391 through 393' Processing helix chain 'G' and resid 397 through 402 removed outlier: 4.094A pdb=" N TYR G 402 " --> pdb=" O VAL G 399 " (cutoff:3.500A) Processing helix chain 'G' and resid 411 through 425 removed outlier: 3.821A pdb=" N LEU G 415 " --> pdb=" O ALA G 411 " (cutoff:3.500A) Processing helix chain 'G' and resid 444 through 448 Processing helix chain 'G' and resid 479 through 491 Processing helix chain 'G' and resid 505 through 525 removed outlier: 5.000A pdb=" N SER G 510 " --> pdb=" O VAL G 507 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU G 512 " --> pdb=" O ASP G 509 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLU G 520 " --> pdb=" O LYS G 517 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ALA G 521 " --> pdb=" O TRP G 518 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL G 523 " --> pdb=" O GLU G 520 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG G 524 " --> pdb=" O ALA G 521 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N GLU G 525 " --> pdb=" O THR G 522 " (cutoff:3.500A) Processing helix chain 'G' and resid 543 through 545 No H-bonds generated for 'chain 'G' and resid 543 through 545' Processing helix chain 'G' and resid 551 through 553 No H-bonds generated for 'chain 'G' and resid 551 through 553' Processing helix chain 'G' and resid 558 through 565 removed outlier: 4.434A pdb=" N LYS G 565 " --> pdb=" O VAL G 561 " (cutoff:3.500A) Processing helix chain 'G' and resid 581 through 593 Processing helix chain 'G' and resid 614 through 623 removed outlier: 4.174A pdb=" N LYS G 623 " --> pdb=" O ALA G 619 " (cutoff:3.500A) Processing helix chain 'G' and resid 649 through 665 removed outlier: 3.507A pdb=" N GLU G 664 " --> pdb=" O ASP G 660 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU G 665 " --> pdb=" O LYS G 661 " (cutoff:3.500A) Processing helix chain 'G' and resid 677 through 680 Processing helix chain 'G' and resid 692 through 698 Processing helix chain 'G' and resid 713 through 717 Processing helix chain 'G' and resid 743 through 748 removed outlier: 3.609A pdb=" N VAL G 747 " --> pdb=" O PRO G 743 " (cutoff:3.500A) Processing helix chain 'G' and resid 754 through 765 Processing helix chain 'G' and resid 771 through 791 removed outlier: 3.596A pdb=" N ASP G 782 " --> pdb=" O GLU G 778 " (cutoff:3.500A) Processing helix chain 'G' and resid 796 through 799 No H-bonds generated for 'chain 'G' and resid 796 through 799' Processing helix chain 'H' and resid 19 through 41 removed outlier: 3.716A pdb=" N ILE H 40 " --> pdb=" O SER H 36 " (cutoff:3.500A) Processing helix chain 'H' and resid 54 through 56 No H-bonds generated for 'chain 'H' and resid 54 through 56' Processing helix chain 'H' and resid 68 through 85 Processing helix chain 'H' and resid 99 through 108 Processing helix chain 'H' and resid 111 through 115 Processing helix chain 'H' and resid 123 through 131 Processing helix chain 'H' and resid 160 through 167 Processing helix chain 'H' and resid 184 through 186 No H-bonds generated for 'chain 'H' and resid 184 through 186' Processing helix chain 'H' and resid 188 through 198 removed outlier: 4.479A pdb=" N GLN H 195 " --> pdb=" O ALA H 191 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N SER H 196 " --> pdb=" O THR H 192 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N ASN H 197 " --> pdb=" O GLY H 193 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N LYS H 198 " --> pdb=" O TRP H 194 " (cutoff:3.500A) Processing helix chain 'H' and resid 225 through 227 No H-bonds generated for 'chain 'H' and resid 225 through 227' Processing helix chain 'H' and resid 230 through 239 Processing helix chain 'H' and resid 256 through 283 removed outlier: 4.082A pdb=" N THR H 283 " --> pdb=" O ALA H 279 " (cutoff:3.500A) Processing helix chain 'H' and resid 317 through 319 No H-bonds generated for 'chain 'H' and resid 317 through 319' Processing helix chain 'H' and resid 331 through 344 removed outlier: 4.185A pdb=" N TYR H 344 " --> pdb=" O TRP H 340 " (cutoff:3.500A) Processing helix chain 'H' and resid 346 through 349 No H-bonds generated for 'chain 'H' and resid 346 through 349' Processing helix chain 'H' and resid 358 through 360 No H-bonds generated for 'chain 'H' and resid 358 through 360' Processing helix chain 'H' and resid 367 through 369 No H-bonds generated for 'chain 'H' and resid 367 through 369' Processing helix chain 'H' and resid 379 through 382 No H-bonds generated for 'chain 'H' and resid 379 through 382' Processing helix chain 'H' and resid 391 through 393 No H-bonds generated for 'chain 'H' and resid 391 through 393' Processing helix chain 'H' and resid 397 through 402 removed outlier: 4.095A pdb=" N TYR H 402 " --> pdb=" O VAL H 399 " (cutoff:3.500A) Processing helix chain 'H' and resid 411 through 425 removed outlier: 3.821A pdb=" N LEU H 415 " --> pdb=" O ALA H 411 " (cutoff:3.500A) Processing helix chain 'H' and resid 444 through 448 Processing helix chain 'H' and resid 479 through 491 Processing helix chain 'H' and resid 505 through 525 removed outlier: 5.000A pdb=" N SER H 510 " --> pdb=" O VAL H 507 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU H 512 " --> pdb=" O ASP H 509 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLU H 520 " --> pdb=" O LYS H 517 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ALA H 521 " --> pdb=" O TRP H 518 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL H 523 " --> pdb=" O GLU H 520 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG H 524 " --> pdb=" O ALA H 521 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N GLU H 525 " --> pdb=" O THR H 522 " (cutoff:3.500A) Processing helix chain 'H' and resid 543 through 545 No H-bonds generated for 'chain 'H' and resid 543 through 545' Processing helix chain 'H' and resid 551 through 553 No H-bonds generated for 'chain 'H' and resid 551 through 553' Processing helix chain 'H' and resid 558 through 565 removed outlier: 4.434A pdb=" N LYS H 565 " --> pdb=" O VAL H 561 " (cutoff:3.500A) Processing helix chain 'H' and resid 581 through 593 Processing helix chain 'H' and resid 614 through 623 removed outlier: 4.174A pdb=" N LYS H 623 " --> pdb=" O ALA H 619 " (cutoff:3.500A) Processing helix chain 'H' and resid 649 through 665 removed outlier: 3.506A pdb=" N GLU H 664 " --> pdb=" O ASP H 660 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU H 665 " --> pdb=" O LYS H 661 " (cutoff:3.500A) Processing helix chain 'H' and resid 677 through 680 Processing helix chain 'H' and resid 692 through 698 Processing helix chain 'H' and resid 713 through 717 Processing helix chain 'H' and resid 743 through 748 removed outlier: 3.609A pdb=" N VAL H 747 " --> pdb=" O PRO H 743 " (cutoff:3.500A) Processing helix chain 'H' and resid 754 through 765 Processing helix chain 'H' and resid 771 through 791 removed outlier: 3.596A pdb=" N ASP H 782 " --> pdb=" O GLU H 778 " (cutoff:3.500A) Processing helix chain 'H' and resid 796 through 799 No H-bonds generated for 'chain 'H' and resid 796 through 799' Processing sheet with id= A, first strand: chain 'A' and resid 175 through 181 removed outlier: 6.686A pdb=" N ILE A 207 " --> pdb=" O VAL A 176 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N ALA A 178 " --> pdb=" O ILE A 207 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LEU A 209 " --> pdb=" O ALA A 178 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N VAL A 180 " --> pdb=" O LEU A 209 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ILE A 211 " --> pdb=" O VAL A 180 " (cutoff:3.500A) removed outlier: 8.789A pdb=" N LEU A 212 " --> pdb=" O PRO A 292 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N LEU A 294 " --> pdb=" O LEU A 212 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N LEU A 214 " --> pdb=" O LEU A 294 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N PHE A 296 " --> pdb=" O LEU A 214 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 430 through 434 removed outlier: 6.847A pdb=" N HIS A 495 " --> pdb=" O ARG A 431 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N PHE A 433 " --> pdb=" O HIS A 495 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ILE A 497 " --> pdb=" O PHE A 433 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ASN A 536 " --> pdb=" O TRP A 498 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N SER A 500 " --> pdb=" O ASN A 536 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N LEU A 538 " --> pdb=" O SER A 500 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 625 through 627 removed outlier: 6.646A pdb=" N VAL A 642 " --> pdb=" O LYS A 670 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N VAL A 672 " --> pdb=" O VAL A 642 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N LEU A 644 " --> pdb=" O VAL A 672 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N VAL A 674 " --> pdb=" O LEU A 644 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ALA A 646 " --> pdb=" O VAL A 674 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 175 through 181 removed outlier: 6.687A pdb=" N ILE B 207 " --> pdb=" O VAL B 176 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N ALA B 178 " --> pdb=" O ILE B 207 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N LEU B 209 " --> pdb=" O ALA B 178 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N VAL B 180 " --> pdb=" O LEU B 209 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ILE B 211 " --> pdb=" O VAL B 180 " (cutoff:3.500A) removed outlier: 8.789A pdb=" N LEU B 212 " --> pdb=" O PRO B 292 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N LEU B 294 " --> pdb=" O LEU B 212 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N LEU B 214 " --> pdb=" O LEU B 294 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N PHE B 296 " --> pdb=" O LEU B 214 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 430 through 434 removed outlier: 6.846A pdb=" N HIS B 495 " --> pdb=" O ARG B 431 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N PHE B 433 " --> pdb=" O HIS B 495 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ILE B 497 " --> pdb=" O PHE B 433 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ASN B 536 " --> pdb=" O TRP B 498 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N SER B 500 " --> pdb=" O ASN B 536 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N LEU B 538 " --> pdb=" O SER B 500 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 625 through 627 removed outlier: 6.647A pdb=" N VAL B 642 " --> pdb=" O LYS B 670 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N VAL B 672 " --> pdb=" O VAL B 642 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N LEU B 644 " --> pdb=" O VAL B 672 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N VAL B 674 " --> pdb=" O LEU B 644 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ALA B 646 " --> pdb=" O VAL B 674 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 175 through 181 removed outlier: 6.687A pdb=" N ILE C 207 " --> pdb=" O VAL C 176 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N ALA C 178 " --> pdb=" O ILE C 207 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LEU C 209 " --> pdb=" O ALA C 178 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N VAL C 180 " --> pdb=" O LEU C 209 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ILE C 211 " --> pdb=" O VAL C 180 " (cutoff:3.500A) removed outlier: 8.789A pdb=" N LEU C 212 " --> pdb=" O PRO C 292 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N LEU C 294 " --> pdb=" O LEU C 212 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N LEU C 214 " --> pdb=" O LEU C 294 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N PHE C 296 " --> pdb=" O LEU C 214 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 430 through 434 removed outlier: 6.847A pdb=" N HIS C 495 " --> pdb=" O ARG C 431 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N PHE C 433 " --> pdb=" O HIS C 495 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ILE C 497 " --> pdb=" O PHE C 433 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ASN C 536 " --> pdb=" O TRP C 498 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N SER C 500 " --> pdb=" O ASN C 536 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N LEU C 538 " --> pdb=" O SER C 500 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 625 through 627 removed outlier: 6.646A pdb=" N VAL C 642 " --> pdb=" O LYS C 670 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N VAL C 672 " --> pdb=" O VAL C 642 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N LEU C 644 " --> pdb=" O VAL C 672 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N VAL C 674 " --> pdb=" O LEU C 644 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ALA C 646 " --> pdb=" O VAL C 674 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 175 through 181 removed outlier: 6.687A pdb=" N ILE D 207 " --> pdb=" O VAL D 176 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N ALA D 178 " --> pdb=" O ILE D 207 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N LEU D 209 " --> pdb=" O ALA D 178 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N VAL D 180 " --> pdb=" O LEU D 209 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ILE D 211 " --> pdb=" O VAL D 180 " (cutoff:3.500A) removed outlier: 8.789A pdb=" N LEU D 212 " --> pdb=" O PRO D 292 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N LEU D 294 " --> pdb=" O LEU D 212 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N LEU D 214 " --> pdb=" O LEU D 294 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N PHE D 296 " --> pdb=" O LEU D 214 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 430 through 434 removed outlier: 6.846A pdb=" N HIS D 495 " --> pdb=" O ARG D 431 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N PHE D 433 " --> pdb=" O HIS D 495 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ILE D 497 " --> pdb=" O PHE D 433 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ASN D 536 " --> pdb=" O TRP D 498 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N SER D 500 " --> pdb=" O ASN D 536 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N LEU D 538 " --> pdb=" O SER D 500 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 625 through 627 removed outlier: 6.647A pdb=" N VAL D 642 " --> pdb=" O LYS D 670 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N VAL D 672 " --> pdb=" O VAL D 642 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N LEU D 644 " --> pdb=" O VAL D 672 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N VAL D 674 " --> pdb=" O LEU D 644 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ALA D 646 " --> pdb=" O VAL D 674 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 175 through 181 removed outlier: 6.686A pdb=" N ILE E 207 " --> pdb=" O VAL E 176 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N ALA E 178 " --> pdb=" O ILE E 207 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N LEU E 209 " --> pdb=" O ALA E 178 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N VAL E 180 " --> pdb=" O LEU E 209 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ILE E 211 " --> pdb=" O VAL E 180 " (cutoff:3.500A) removed outlier: 8.789A pdb=" N LEU E 212 " --> pdb=" O PRO E 292 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N LEU E 294 " --> pdb=" O LEU E 212 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N LEU E 214 " --> pdb=" O LEU E 294 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N PHE E 296 " --> pdb=" O LEU E 214 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 430 through 434 removed outlier: 6.846A pdb=" N HIS E 495 " --> pdb=" O ARG E 431 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N PHE E 433 " --> pdb=" O HIS E 495 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ILE E 497 " --> pdb=" O PHE E 433 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ASN E 536 " --> pdb=" O TRP E 498 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N SER E 500 " --> pdb=" O ASN E 536 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N LEU E 538 " --> pdb=" O SER E 500 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 625 through 627 removed outlier: 6.647A pdb=" N VAL E 642 " --> pdb=" O LYS E 670 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N VAL E 672 " --> pdb=" O VAL E 642 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N LEU E 644 " --> pdb=" O VAL E 672 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N VAL E 674 " --> pdb=" O LEU E 644 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ALA E 646 " --> pdb=" O VAL E 674 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'F' and resid 175 through 181 removed outlier: 6.687A pdb=" N ILE F 207 " --> pdb=" O VAL F 176 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N ALA F 178 " --> pdb=" O ILE F 207 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LEU F 209 " --> pdb=" O ALA F 178 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N VAL F 180 " --> pdb=" O LEU F 209 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ILE F 211 " --> pdb=" O VAL F 180 " (cutoff:3.500A) removed outlier: 8.788A pdb=" N LEU F 212 " --> pdb=" O PRO F 292 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N LEU F 294 " --> pdb=" O LEU F 212 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N LEU F 214 " --> pdb=" O LEU F 294 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N PHE F 296 " --> pdb=" O LEU F 214 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'F' and resid 430 through 434 removed outlier: 6.846A pdb=" N HIS F 495 " --> pdb=" O ARG F 431 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N PHE F 433 " --> pdb=" O HIS F 495 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ILE F 497 " --> pdb=" O PHE F 433 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ASN F 536 " --> pdb=" O TRP F 498 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N SER F 500 " --> pdb=" O ASN F 536 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N LEU F 538 " --> pdb=" O SER F 500 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'F' and resid 625 through 627 removed outlier: 6.647A pdb=" N VAL F 642 " --> pdb=" O LYS F 670 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N VAL F 672 " --> pdb=" O VAL F 642 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N LEU F 644 " --> pdb=" O VAL F 672 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N VAL F 674 " --> pdb=" O LEU F 644 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ALA F 646 " --> pdb=" O VAL F 674 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'G' and resid 175 through 181 removed outlier: 6.687A pdb=" N ILE G 207 " --> pdb=" O VAL G 176 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N ALA G 178 " --> pdb=" O ILE G 207 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N LEU G 209 " --> pdb=" O ALA G 178 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N VAL G 180 " --> pdb=" O LEU G 209 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ILE G 211 " --> pdb=" O VAL G 180 " (cutoff:3.500A) removed outlier: 8.789A pdb=" N LEU G 212 " --> pdb=" O PRO G 292 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N LEU G 294 " --> pdb=" O LEU G 212 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N LEU G 214 " --> pdb=" O LEU G 294 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N PHE G 296 " --> pdb=" O LEU G 214 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'G' and resid 430 through 434 removed outlier: 6.846A pdb=" N HIS G 495 " --> pdb=" O ARG G 431 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N PHE G 433 " --> pdb=" O HIS G 495 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ILE G 497 " --> pdb=" O PHE G 433 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ASN G 536 " --> pdb=" O TRP G 498 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N SER G 500 " --> pdb=" O ASN G 536 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N LEU G 538 " --> pdb=" O SER G 500 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'G' and resid 625 through 627 removed outlier: 6.646A pdb=" N VAL G 642 " --> pdb=" O LYS G 670 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N VAL G 672 " --> pdb=" O VAL G 642 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N LEU G 644 " --> pdb=" O VAL G 672 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N VAL G 674 " --> pdb=" O LEU G 644 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ALA G 646 " --> pdb=" O VAL G 674 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'H' and resid 175 through 181 removed outlier: 6.686A pdb=" N ILE H 207 " --> pdb=" O VAL H 176 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N ALA H 178 " --> pdb=" O ILE H 207 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LEU H 209 " --> pdb=" O ALA H 178 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N VAL H 180 " --> pdb=" O LEU H 209 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ILE H 211 " --> pdb=" O VAL H 180 " (cutoff:3.500A) removed outlier: 8.790A pdb=" N LEU H 212 " --> pdb=" O PRO H 292 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N LEU H 294 " --> pdb=" O LEU H 212 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N LEU H 214 " --> pdb=" O LEU H 294 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N PHE H 296 " --> pdb=" O LEU H 214 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'H' and resid 430 through 434 removed outlier: 6.846A pdb=" N HIS H 495 " --> pdb=" O ARG H 431 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N PHE H 433 " --> pdb=" O HIS H 495 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ILE H 497 " --> pdb=" O PHE H 433 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ASN H 536 " --> pdb=" O TRP H 498 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N SER H 500 " --> pdb=" O ASN H 536 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N LEU H 538 " --> pdb=" O SER H 500 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'H' and resid 625 through 627 removed outlier: 6.646A pdb=" N VAL H 642 " --> pdb=" O LYS H 670 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N VAL H 672 " --> pdb=" O VAL H 642 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N LEU H 644 " --> pdb=" O VAL H 672 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N VAL H 674 " --> pdb=" O LEU H 644 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ALA H 646 " --> pdb=" O VAL H 674 " (cutoff:3.500A) 1640 hydrogen bonds defined for protein. 4536 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: 18.79 Time building geometry restraints manager: 20.56 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: 16834 1.34 - 1.45: 9167 1.45 - 1.57: 26623 1.57 - 1.69: 16 1.69 - 1.81: 280 Bond restraints: 52920 Sorted by residual: bond pdb=" O1A TPP D 900 " pdb=" PA TPP D 900 " ideal model delta sigma weight residual 1.479 1.509 -0.030 1.00e-02 1.00e+04 8.80e+00 bond pdb=" O1A TPP H 900 " pdb=" PA TPP H 900 " ideal model delta sigma weight residual 1.479 1.508 -0.029 1.00e-02 1.00e+04 8.49e+00 bond pdb=" O1A TPP F 900 " pdb=" PA TPP F 900 " ideal model delta sigma weight residual 1.479 1.508 -0.029 1.00e-02 1.00e+04 8.49e+00 bond pdb=" O1A TPP B 900 " pdb=" PA TPP B 900 " ideal model delta sigma weight residual 1.479 1.508 -0.029 1.00e-02 1.00e+04 8.13e+00 bond pdb=" O2A TPP H 900 " pdb=" PA TPP H 900 " ideal model delta sigma weight residual 1.527 1.475 0.052 2.30e-02 1.89e+03 5.05e+00 ... (remaining 52915 not shown) Histogram of bond angle deviations from ideal: 91.10 - 100.80: 56 100.80 - 110.49: 14587 110.49 - 120.19: 34486 120.19 - 129.88: 22271 129.88 - 139.57: 600 Bond angle restraints: 72000 Sorted by residual: angle pdb=" O2B TPP C 900 " pdb=" PB TPP C 900 " pdb=" O3A TPP C 900 " ideal model delta sigma weight residual 104.26 110.22 -5.96 1.33e+00 5.64e-01 2.00e+01 angle pdb=" O2B TPP A 900 " pdb=" PB TPP A 900 " pdb=" O3A TPP A 900 " ideal model delta sigma weight residual 104.26 110.21 -5.95 1.33e+00 5.64e-01 1.99e+01 angle pdb=" O2B TPP G 900 " pdb=" PB TPP G 900 " pdb=" O3A TPP G 900 " ideal model delta sigma weight residual 104.26 110.20 -5.94 1.33e+00 5.64e-01 1.99e+01 angle pdb=" O2B TPP E 900 " pdb=" PB TPP E 900 " pdb=" O3A TPP E 900 " ideal model delta sigma weight residual 104.26 110.20 -5.94 1.33e+00 5.64e-01 1.99e+01 angle pdb=" N GLU A 265 " pdb=" CA GLU A 265 " pdb=" CB GLU A 265 " ideal model delta sigma weight residual 110.12 116.00 -5.88 1.47e+00 4.63e-01 1.60e+01 ... (remaining 71995 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 28054 17.86 - 35.73: 2362 35.73 - 53.59: 375 53.59 - 71.46: 89 71.46 - 89.32: 64 Dihedral angle restraints: 30944 sinusoidal: 12320 harmonic: 18624 Sorted by residual: dihedral pdb=" CA VAL B 322 " pdb=" C VAL B 322 " pdb=" N PRO B 323 " pdb=" CA PRO B 323 " ideal model delta harmonic sigma weight residual 180.00 152.80 27.20 0 5.00e+00 4.00e-02 2.96e+01 dihedral pdb=" CA VAL D 322 " pdb=" C VAL D 322 " pdb=" N PRO D 323 " pdb=" CA PRO D 323 " ideal model delta harmonic sigma weight residual 180.00 152.80 27.20 0 5.00e+00 4.00e-02 2.96e+01 dihedral pdb=" CA VAL E 322 " pdb=" C VAL E 322 " pdb=" N PRO E 323 " pdb=" CA PRO E 323 " ideal model delta harmonic sigma weight residual 180.00 152.81 27.19 0 5.00e+00 4.00e-02 2.96e+01 ... (remaining 30941 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 5757 0.055 - 0.111: 1523 0.111 - 0.166: 255 0.166 - 0.221: 9 0.221 - 0.276: 8 Chirality restraints: 7552 Sorted by residual: chirality pdb=" CA TRP A 302 " pdb=" N TRP A 302 " pdb=" C TRP A 302 " pdb=" CB TRP A 302 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.91e+00 chirality pdb=" CA TRP F 302 " pdb=" N TRP F 302 " pdb=" C TRP F 302 " pdb=" CB TRP F 302 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.28 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" CA TRP E 302 " pdb=" N TRP E 302 " pdb=" C TRP E 302 " pdb=" CB TRP E 302 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.89e+00 ... (remaining 7549 not shown) Planarity restraints: 9456 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 302 " 0.026 2.00e-02 2.50e+03 3.98e-02 3.96e+01 pdb=" CG TRP A 302 " -0.098 2.00e-02 2.50e+03 pdb=" CD1 TRP A 302 " 0.071 2.00e-02 2.50e+03 pdb=" CD2 TRP A 302 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 302 " -0.013 2.00e-02 2.50e+03 pdb=" CE2 TRP A 302 " -0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP A 302 " 0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 302 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 302 " 0.018 2.00e-02 2.50e+03 pdb=" CH2 TRP A 302 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP G 302 " 0.026 2.00e-02 2.50e+03 3.98e-02 3.96e+01 pdb=" CG TRP G 302 " -0.097 2.00e-02 2.50e+03 pdb=" CD1 TRP G 302 " 0.071 2.00e-02 2.50e+03 pdb=" CD2 TRP G 302 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP G 302 " -0.013 2.00e-02 2.50e+03 pdb=" CE2 TRP G 302 " -0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP G 302 " 0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP G 302 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP G 302 " 0.018 2.00e-02 2.50e+03 pdb=" CH2 TRP G 302 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 302 " 0.026 2.00e-02 2.50e+03 3.97e-02 3.95e+01 pdb=" CG TRP E 302 " -0.097 2.00e-02 2.50e+03 pdb=" CD1 TRP E 302 " 0.071 2.00e-02 2.50e+03 pdb=" CD2 TRP E 302 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP E 302 " -0.013 2.00e-02 2.50e+03 pdb=" CE2 TRP E 302 " -0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP E 302 " 0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 302 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 302 " 0.018 2.00e-02 2.50e+03 pdb=" CH2 TRP E 302 " -0.001 2.00e-02 2.50e+03 ... (remaining 9453 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 358 2.50 - 3.10: 37978 3.10 - 3.70: 84119 3.70 - 4.30: 131033 4.30 - 4.90: 213613 Nonbonded interactions: 467101 Sorted by model distance: nonbonded pdb=" O1B TPP H 900 " pdb="MG MG H 901 " model vdw 1.898 2.170 nonbonded pdb=" O2B TPP G 900 " pdb="MG MG G 901 " model vdw 1.898 2.170 nonbonded pdb=" O2B TPP C 900 " pdb="MG MG C 901 " model vdw 1.898 2.170 nonbonded pdb=" O2B TPP E 900 " pdb="MG MG E 901 " model vdw 1.898 2.170 nonbonded pdb=" O1B TPP F 900 " pdb="MG MG F 901 " model vdw 1.898 2.170 ... (remaining 467096 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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: 2.800 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: 0.040 Extract box with map and model: 14.600 Check model and map are aligned: 0.690 Set scattering table: 0.420 Process input model: 125.790 Find NCS groups from input model: 3.330 Set up NCS constraints: 0.370 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:13.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 161.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 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 0.061 52920 Z= 0.465 Angle : 0.758 8.547 72000 Z= 0.450 Chirality : 0.049 0.276 7552 Planarity : 0.005 0.050 9456 Dihedral : 14.016 89.320 19024 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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 (0.10), residues: 6432 helix: -0.17 (0.09), residues: 2592 sheet: -0.52 (0.19), residues: 824 loop : -0.64 (0.11), residues: 3016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.098 0.003 TRP A 302 HIS 0.012 0.002 HIS H 213 PHE 0.030 0.003 PHE C 143 TYR 0.028 0.002 TYR G 402 ARG 0.007 0.001 ARG E 328 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12864 Ramachandran restraints generated. 6432 Oldfield, 0 Emsley, 6432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12864 Ramachandran restraints generated. 6432 Oldfield, 0 Emsley, 6432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 580 residues out of total 5400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 580 time to evaluate : 6.374 Fit side-chains outliers start: 0 outliers final: 8 residues processed: 580 average time/residue: 1.5545 time to fit residues: 1146.8334 Evaluate side-chains 310 residues out of total 5400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 302 time to evaluate : 5.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 782 ASP Chi-restraints excluded: chain B residue 782 ASP Chi-restraints excluded: chain C residue 782 ASP Chi-restraints excluded: chain D residue 782 ASP Chi-restraints excluded: chain E residue 782 ASP Chi-restraints excluded: chain F residue 782 ASP Chi-restraints excluded: chain G residue 782 ASP Chi-restraints excluded: chain H residue 782 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 640 random chunks: chunk 540 optimal weight: 4.9990 chunk 485 optimal weight: 5.9990 chunk 269 optimal weight: 0.9990 chunk 165 optimal weight: 4.9990 chunk 327 optimal weight: 1.9990 chunk 259 optimal weight: 0.7980 chunk 501 optimal weight: 0.9990 chunk 194 optimal weight: 3.9990 chunk 305 optimal weight: 9.9990 chunk 373 optimal weight: 3.9990 chunk 581 optimal weight: 0.8980 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 568 HIS ** A 710 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 568 HIS ** B 710 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 568 HIS ** C 710 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 568 HIS ** D 710 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 568 HIS ** E 710 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 256 HIS F 568 HIS ** F 710 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 568 HIS ** G 710 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 568 HIS ** H 710 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.1229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 52920 Z= 0.191 Angle : 0.539 10.293 72000 Z= 0.288 Chirality : 0.042 0.163 7552 Planarity : 0.004 0.047 9456 Dihedral : 5.903 44.344 7032 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.54 % Allowed : 5.13 % Favored : 93.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.01 (0.10), residues: 6432 helix: 0.60 (0.10), residues: 2624 sheet: -0.40 (0.19), residues: 856 loop : -0.28 (0.11), residues: 2952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP G 302 HIS 0.007 0.001 HIS B 320 PHE 0.014 0.001 PHE D 143 TYR 0.011 0.001 TYR B 165 ARG 0.006 0.000 ARG H 428 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12864 Ramachandran restraints generated. 6432 Oldfield, 0 Emsley, 6432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12864 Ramachandran restraints generated. 6432 Oldfield, 0 Emsley, 6432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 5400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 371 time to evaluate : 6.230 Fit side-chains outliers start: 83 outliers final: 8 residues processed: 417 average time/residue: 1.4829 time to fit residues: 805.5447 Evaluate side-chains 320 residues out of total 5400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 312 time to evaluate : 5.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain H residue 89 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 640 random chunks: chunk 322 optimal weight: 6.9990 chunk 180 optimal weight: 4.9990 chunk 483 optimal weight: 8.9990 chunk 395 optimal weight: 2.9990 chunk 160 optimal weight: 8.9990 chunk 582 optimal weight: 5.9990 chunk 628 optimal weight: 10.0000 chunk 518 optimal weight: 4.9990 chunk 577 optimal weight: 0.6980 chunk 198 optimal weight: 10.0000 chunk 467 optimal weight: 0.1980 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 710 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 710 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 710 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 710 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 710 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 710 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 710 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 710 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.1501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 52920 Z= 0.291 Angle : 0.536 6.295 72000 Z= 0.282 Chirality : 0.043 0.156 7552 Planarity : 0.004 0.047 9456 Dihedral : 5.330 40.309 7016 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.91 % Allowed : 6.76 % Favored : 91.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.40 (0.11), residues: 6432 helix: 0.93 (0.10), residues: 2608 sheet: -0.33 (0.19), residues: 856 loop : -0.01 (0.12), residues: 2968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 302 HIS 0.006 0.001 HIS E 506 PHE 0.013 0.001 PHE E 143 TYR 0.008 0.001 TYR F 709 ARG 0.004 0.000 ARG C 751 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12864 Ramachandran restraints generated. 6432 Oldfield, 0 Emsley, 6432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12864 Ramachandran restraints generated. 6432 Oldfield, 0 Emsley, 6432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 5400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 335 time to evaluate : 6.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 715 ASP cc_start: 0.6165 (OUTLIER) cc_final: 0.5908 (m-30) REVERT: B 715 ASP cc_start: 0.6122 (OUTLIER) cc_final: 0.5846 (m-30) REVERT: C 715 ASP cc_start: 0.6101 (OUTLIER) cc_final: 0.5839 (m-30) REVERT: D 715 ASP cc_start: 0.6116 (OUTLIER) cc_final: 0.5840 (m-30) REVERT: E 715 ASP cc_start: 0.6069 (OUTLIER) cc_final: 0.5797 (m-30) REVERT: F 715 ASP cc_start: 0.6166 (OUTLIER) cc_final: 0.5906 (m-30) REVERT: G 715 ASP cc_start: 0.6171 (OUTLIER) cc_final: 0.5913 (m-30) REVERT: H 715 ASP cc_start: 0.6151 (OUTLIER) cc_final: 0.5871 (m-30) outliers start: 103 outliers final: 28 residues processed: 398 average time/residue: 1.5419 time to fit residues: 792.5547 Evaluate side-chains 327 residues out of total 5400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 291 time to evaluate : 5.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 622 GLU Chi-restraints excluded: chain A residue 715 ASP Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 622 GLU Chi-restraints excluded: chain B residue 715 ASP Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 511 MET Chi-restraints excluded: chain C residue 622 GLU Chi-restraints excluded: chain C residue 715 ASP Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain D residue 622 GLU Chi-restraints excluded: chain D residue 715 ASP Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain E residue 622 GLU Chi-restraints excluded: chain E residue 715 ASP Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 322 VAL Chi-restraints excluded: chain F residue 511 MET Chi-restraints excluded: chain F residue 622 GLU Chi-restraints excluded: chain F residue 715 ASP Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 322 VAL Chi-restraints excluded: chain G residue 511 MET Chi-restraints excluded: chain G residue 622 GLU Chi-restraints excluded: chain G residue 715 ASP Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 322 VAL Chi-restraints excluded: chain H residue 461 ASP Chi-restraints excluded: chain H residue 622 GLU Chi-restraints excluded: chain H residue 715 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 640 random chunks: chunk 575 optimal weight: 4.9990 chunk 437 optimal weight: 1.9990 chunk 302 optimal weight: 10.0000 chunk 64 optimal weight: 9.9990 chunk 277 optimal weight: 0.6980 chunk 390 optimal weight: 6.9990 chunk 584 optimal weight: 2.9990 chunk 618 optimal weight: 9.9990 chunk 305 optimal weight: 10.0000 chunk 553 optimal weight: 0.0870 chunk 166 optimal weight: 6.9990 overall best weight: 2.1564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 710 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 710 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 710 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 710 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 710 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 710 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 710 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 710 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 52920 Z= 0.239 Angle : 0.503 6.293 72000 Z= 0.265 Chirality : 0.042 0.155 7552 Planarity : 0.004 0.047 9456 Dihedral : 5.113 39.547 7016 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.56 % Allowed : 8.70 % Favored : 89.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.57 (0.11), residues: 6432 helix: 1.12 (0.10), residues: 2608 sheet: -0.34 (0.19), residues: 856 loop : 0.08 (0.12), residues: 2968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP G 302 HIS 0.005 0.001 HIS F 506 PHE 0.010 0.001 PHE F 263 TYR 0.006 0.001 TYR F 709 ARG 0.003 0.000 ARG E 751 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12864 Ramachandran restraints generated. 6432 Oldfield, 0 Emsley, 6432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12864 Ramachandran restraints generated. 6432 Oldfield, 0 Emsley, 6432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 5400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 307 time to evaluate : 6.011 Fit side-chains REVERT: B 715 ASP cc_start: 0.5974 (OUTLIER) cc_final: 0.5726 (m-30) REVERT: D 715 ASP cc_start: 0.5967 (OUTLIER) cc_final: 0.5715 (m-30) REVERT: E 715 ASP cc_start: 0.5975 (OUTLIER) cc_final: 0.5728 (m-30) REVERT: H 715 ASP cc_start: 0.5973 (OUTLIER) cc_final: 0.5726 (m-30) outliers start: 84 outliers final: 20 residues processed: 355 average time/residue: 1.5362 time to fit residues: 699.6327 Evaluate side-chains 320 residues out of total 5400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 296 time to evaluate : 6.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 715 ASP Chi-restraints excluded: chain C residue 89 THR Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 511 MET Chi-restraints excluded: chain D residue 89 THR Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain D residue 715 ASP Chi-restraints excluded: chain E residue 89 THR Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain E residue 715 ASP Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 322 VAL Chi-restraints excluded: chain F residue 511 MET Chi-restraints excluded: chain G residue 89 THR Chi-restraints excluded: chain G residue 322 VAL Chi-restraints excluded: chain G residue 511 MET Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 322 VAL Chi-restraints excluded: chain H residue 461 ASP Chi-restraints excluded: chain H residue 715 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 640 random chunks: chunk 515 optimal weight: 2.9990 chunk 351 optimal weight: 9.9990 chunk 8 optimal weight: 5.9990 chunk 460 optimal weight: 0.7980 chunk 255 optimal weight: 5.9990 chunk 527 optimal weight: 2.9990 chunk 427 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 315 optimal weight: 0.8980 chunk 555 optimal weight: 0.8980 chunk 156 optimal weight: 9.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 710 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 710 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 710 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 710 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 710 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 710 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 710 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 710 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 52920 Z= 0.173 Angle : 0.481 7.759 72000 Z= 0.252 Chirality : 0.041 0.150 7552 Planarity : 0.004 0.047 9456 Dihedral : 4.874 38.872 7016 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.37 % Allowed : 9.02 % Favored : 89.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.71 (0.11), residues: 6432 helix: 1.19 (0.10), residues: 2616 sheet: -0.25 (0.19), residues: 856 loop : 0.20 (0.12), residues: 2960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F 302 HIS 0.005 0.001 HIS A 506 PHE 0.009 0.001 PHE C 263 TYR 0.007 0.001 TYR E 165 ARG 0.004 0.000 ARG C 751 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12864 Ramachandran restraints generated. 6432 Oldfield, 0 Emsley, 6432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12864 Ramachandran restraints generated. 6432 Oldfield, 0 Emsley, 6432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 5400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 308 time to evaluate : 5.866 Fit side-chains outliers start: 74 outliers final: 11 residues processed: 357 average time/residue: 1.4122 time to fit residues: 659.3426 Evaluate side-chains 310 residues out of total 5400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 299 time to evaluate : 5.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 511 MET Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain E residue 573 ILE Chi-restraints excluded: chain F residue 322 VAL Chi-restraints excluded: chain F residue 511 MET Chi-restraints excluded: chain G residue 322 VAL Chi-restraints excluded: chain H residue 322 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 640 random chunks: chunk 208 optimal weight: 5.9990 chunk 557 optimal weight: 10.0000 chunk 122 optimal weight: 4.9990 chunk 363 optimal weight: 6.9990 chunk 152 optimal weight: 10.0000 chunk 619 optimal weight: 0.0020 chunk 514 optimal weight: 0.9980 chunk 286 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 204 optimal weight: 9.9990 chunk 325 optimal weight: 9.9990 overall best weight: 1.7592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 142 HIS ** A 710 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 142 HIS B 468 HIS ** B 710 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 142 HIS ** C 710 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 142 HIS ** D 710 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 142 HIS ** E 710 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 468 HIS ** F 710 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 710 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 468 HIS ** H 710 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 52920 Z= 0.208 Angle : 0.480 7.420 72000 Z= 0.251 Chirality : 0.042 0.151 7552 Planarity : 0.004 0.047 9456 Dihedral : 4.796 40.045 7016 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.31 % Allowed : 9.46 % Favored : 89.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.77 (0.11), residues: 6432 helix: 1.23 (0.10), residues: 2624 sheet: -0.25 (0.19), residues: 856 loop : 0.25 (0.12), residues: 2952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP G 302 HIS 0.005 0.001 HIS A 506 PHE 0.010 0.001 PHE H 73 TYR 0.006 0.001 TYR F 165 ARG 0.005 0.000 ARG A 751 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12864 Ramachandran restraints generated. 6432 Oldfield, 0 Emsley, 6432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12864 Ramachandran restraints generated. 6432 Oldfield, 0 Emsley, 6432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 5400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 308 time to evaluate : 6.305 Fit side-chains outliers start: 71 outliers final: 14 residues processed: 355 average time/residue: 1.4667 time to fit residues: 675.9565 Evaluate side-chains 312 residues out of total 5400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 298 time to evaluate : 6.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 511 MET Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain E residue 422 ILE Chi-restraints excluded: chain E residue 511 MET Chi-restraints excluded: chain F residue 322 VAL Chi-restraints excluded: chain F residue 511 MET Chi-restraints excluded: chain G residue 322 VAL Chi-restraints excluded: chain G residue 511 MET Chi-restraints excluded: chain H residue 322 VAL Chi-restraints excluded: chain H residue 461 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 640 random chunks: chunk 597 optimal weight: 0.0010 chunk 69 optimal weight: 4.9990 chunk 352 optimal weight: 9.9990 chunk 452 optimal weight: 0.9980 chunk 350 optimal weight: 0.7980 chunk 521 optimal weight: 7.9990 chunk 345 optimal weight: 0.6980 chunk 616 optimal weight: 10.0000 chunk 386 optimal weight: 10.0000 chunk 376 optimal weight: 0.3980 chunk 284 optimal weight: 9.9990 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 710 HIS ** B 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 710 HIS ** C 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 710 HIS ** D 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 710 HIS ** E 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 710 HIS ** G 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 710 HIS ** H 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 142 HIS H 710 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 52920 Z= 0.139 Angle : 0.464 9.696 72000 Z= 0.243 Chirality : 0.041 0.143 7552 Planarity : 0.004 0.046 9456 Dihedral : 4.594 39.215 7016 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 0.81 % Allowed : 10.61 % Favored : 88.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.88 (0.11), residues: 6432 helix: 1.29 (0.10), residues: 2624 sheet: -0.21 (0.19), residues: 856 loop : 0.33 (0.12), residues: 2952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 302 HIS 0.010 0.001 HIS C 506 PHE 0.009 0.001 PHE D 296 TYR 0.008 0.001 TYR A 165 ARG 0.004 0.000 ARG C 751 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12864 Ramachandran restraints generated. 6432 Oldfield, 0 Emsley, 6432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12864 Ramachandran restraints generated. 6432 Oldfield, 0 Emsley, 6432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 5400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 332 time to evaluate : 5.847 Fit side-chains outliers start: 44 outliers final: 11 residues processed: 364 average time/residue: 1.4697 time to fit residues: 694.0882 Evaluate side-chains 311 residues out of total 5400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 300 time to evaluate : 6.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 511 MET Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain F residue 322 VAL Chi-restraints excluded: chain F residue 511 MET Chi-restraints excluded: chain G residue 322 VAL Chi-restraints excluded: chain G residue 511 MET Chi-restraints excluded: chain H residue 322 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 640 random chunks: chunk 381 optimal weight: 5.9990 chunk 246 optimal weight: 0.7980 chunk 368 optimal weight: 7.9990 chunk 185 optimal weight: 0.7980 chunk 121 optimal weight: 7.9990 chunk 119 optimal weight: 10.0000 chunk 392 optimal weight: 7.9990 chunk 420 optimal weight: 1.9990 chunk 304 optimal weight: 10.0000 chunk 57 optimal weight: 9.9990 chunk 484 optimal weight: 4.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 536 ASN ** B 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 536 ASN ** C 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 536 ASN ** D 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 468 HIS D 536 ASN ** E 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 536 ASN ** F 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 142 HIS F 536 ASN ** G 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 142 HIS G 468 HIS G 536 ASN ** H 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 536 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.2150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 52920 Z= 0.300 Angle : 0.529 9.442 72000 Z= 0.274 Chirality : 0.043 0.154 7552 Planarity : 0.004 0.045 9456 Dihedral : 4.748 40.965 7016 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 0.85 % Allowed : 11.39 % Favored : 87.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.79 (0.11), residues: 6432 helix: 1.26 (0.10), residues: 2624 sheet: -0.35 (0.19), residues: 880 loop : 0.28 (0.12), residues: 2928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 302 HIS 0.008 0.001 HIS H 506 PHE 0.012 0.001 PHE F 73 TYR 0.006 0.001 TYR H 709 ARG 0.003 0.000 ARG E 751 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12864 Ramachandran restraints generated. 6432 Oldfield, 0 Emsley, 6432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12864 Ramachandran restraints generated. 6432 Oldfield, 0 Emsley, 6432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 5400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 301 time to evaluate : 5.780 Fit side-chains outliers start: 46 outliers final: 21 residues processed: 334 average time/residue: 1.4833 time to fit residues: 638.9811 Evaluate side-chains 321 residues out of total 5400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 300 time to evaluate : 6.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 511 MET Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain D residue 412 THR Chi-restraints excluded: chain D residue 511 MET Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain E residue 511 MET Chi-restraints excluded: chain F residue 322 VAL Chi-restraints excluded: chain F residue 412 THR Chi-restraints excluded: chain F residue 511 MET Chi-restraints excluded: chain G residue 322 VAL Chi-restraints excluded: chain G residue 412 THR Chi-restraints excluded: chain G residue 511 MET Chi-restraints excluded: chain H residue 322 VAL Chi-restraints excluded: chain H residue 412 THR Chi-restraints excluded: chain H residue 461 ASP Chi-restraints excluded: chain H residue 511 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 640 random chunks: chunk 561 optimal weight: 10.0000 chunk 590 optimal weight: 8.9990 chunk 539 optimal weight: 7.9990 chunk 574 optimal weight: 6.9990 chunk 345 optimal weight: 8.9990 chunk 250 optimal weight: 0.0570 chunk 451 optimal weight: 0.8980 chunk 176 optimal weight: 3.9990 chunk 519 optimal weight: 9.9990 chunk 543 optimal weight: 9.9990 chunk 572 optimal weight: 1.9990 overall best weight: 2.7904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 468 HIS ** D 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 468 HIS ** F 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 52920 Z= 0.288 Angle : 0.531 10.091 72000 Z= 0.275 Chirality : 0.043 0.156 7552 Planarity : 0.004 0.044 9456 Dihedral : 4.771 40.244 7016 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.69 % Allowed : 11.80 % Favored : 87.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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 (0.11), residues: 6432 helix: 1.13 (0.10), residues: 2664 sheet: -0.34 (0.19), residues: 864 loop : 0.23 (0.12), residues: 2904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 302 HIS 0.007 0.001 HIS F 506 PHE 0.010 0.001 PHE B 73 TYR 0.006 0.001 TYR H 709 ARG 0.003 0.000 ARG B 751 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12864 Ramachandran restraints generated. 6432 Oldfield, 0 Emsley, 6432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12864 Ramachandran restraints generated. 6432 Oldfield, 0 Emsley, 6432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 5400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 312 time to evaluate : 5.895 Fit side-chains outliers start: 37 outliers final: 17 residues processed: 342 average time/residue: 1.5067 time to fit residues: 667.0554 Evaluate side-chains 312 residues out of total 5400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 295 time to evaluate : 5.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 412 THR Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain D residue 412 THR Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain E residue 412 THR Chi-restraints excluded: chain F residue 322 VAL Chi-restraints excluded: chain F residue 412 THR Chi-restraints excluded: chain G residue 322 VAL Chi-restraints excluded: chain G residue 412 THR Chi-restraints excluded: chain H residue 322 VAL Chi-restraints excluded: chain H residue 412 THR Chi-restraints excluded: chain H residue 461 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 640 random chunks: chunk 377 optimal weight: 8.9990 chunk 607 optimal weight: 6.9990 chunk 371 optimal weight: 1.9990 chunk 288 optimal weight: 4.9990 chunk 422 optimal weight: 5.9990 chunk 637 optimal weight: 7.9990 chunk 586 optimal weight: 4.9990 chunk 507 optimal weight: 0.9990 chunk 52 optimal weight: 0.0020 chunk 392 optimal weight: 0.0470 chunk 311 optimal weight: 7.9990 overall best weight: 1.6092 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 52920 Z= 0.211 Angle : 0.516 10.695 72000 Z= 0.268 Chirality : 0.042 0.153 7552 Planarity : 0.004 0.046 9456 Dihedral : 4.667 40.337 7016 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.33 % Allowed : 12.22 % Favored : 87.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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 (0.11), residues: 6432 helix: 1.16 (0.10), residues: 2672 sheet: -0.31 (0.19), residues: 864 loop : 0.30 (0.12), residues: 2896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 498 HIS 0.006 0.001 HIS G 506 PHE 0.009 0.001 PHE C 263 TYR 0.011 0.001 TYR C 159 ARG 0.003 0.000 ARG A 751 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12864 Ramachandran restraints generated. 6432 Oldfield, 0 Emsley, 6432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12864 Ramachandran restraints generated. 6432 Oldfield, 0 Emsley, 6432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 5400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 327 time to evaluate : 5.988 Fit side-chains outliers start: 18 outliers final: 11 residues processed: 345 average time/residue: 1.6070 time to fit residues: 714.5014 Evaluate side-chains 310 residues out of total 5400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 299 time to evaluate : 5.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain C residue 322 VAL Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain D residue 322 VAL Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain E residue 412 THR Chi-restraints excluded: chain E residue 573 ILE Chi-restraints excluded: chain F residue 322 VAL Chi-restraints excluded: chain G residue 322 VAL Chi-restraints excluded: chain H residue 322 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 640 random chunks: chunk 403 optimal weight: 5.9990 chunk 540 optimal weight: 9.9990 chunk 155 optimal weight: 5.9990 chunk 468 optimal weight: 8.9990 chunk 74 optimal weight: 6.9990 chunk 141 optimal weight: 1.9990 chunk 508 optimal weight: 2.9990 chunk 212 optimal weight: 0.2980 chunk 522 optimal weight: 0.9990 chunk 64 optimal weight: 9.9990 chunk 93 optimal weight: 0.5980 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.093841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.079404 restraints weight = 114513.180| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 2.89 r_work: 0.3120 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 52920 Z= 0.200 Angle : 0.526 10.744 72000 Z= 0.270 Chirality : 0.042 0.175 7552 Planarity : 0.004 0.046 9456 Dihedral : 4.593 41.152 7016 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.52 % Allowed : 12.06 % Favored : 87.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.79 (0.11), residues: 6432 helix: 1.19 (0.10), residues: 2664 sheet: -0.30 (0.19), residues: 864 loop : 0.33 (0.12), residues: 2904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 302 HIS 0.006 0.001 HIS H 506 PHE 0.009 0.001 PHE F 73 TYR 0.009 0.001 TYR G 159 ARG 0.003 0.000 ARG G 751 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13102.91 seconds wall clock time: 237 minutes 21.86 seconds (14241.86 seconds total)