Starting phenix.real_space_refine on Fri Feb 23 09:21:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uom_26650/02_2024/7uom_26650.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uom_26650/02_2024/7uom_26650.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uom_26650/02_2024/7uom_26650.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uom_26650/02_2024/7uom_26650.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uom_26650/02_2024/7uom_26650.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uom_26650/02_2024/7uom_26650.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 660 5.16 5 C 66720 2.51 5 N 17940 2.21 5 O 19320 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "01 TYR 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "01 GLU 469": "OE1" <-> "OE2" Residue "01 PHE 571": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "01 GLU 594": "OE1" <-> "OE2" Residue "02 PHE 571": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "02 PHE 606": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "03 GLU 469": "OE1" <-> "OE2" Residue "03 GLU 557": "OE1" <-> "OE2" Residue "04 GLU 535": "OE1" <-> "OE2" Residue "04 PHE 558": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "04 PHE 571": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "05 PHE 479": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "05 PHE 527": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "05 GLU 535": "OE1" <-> "OE2" Residue "05 GLU 550": "OE1" <-> "OE2" Residue "05 GLU 640": "OE1" <-> "OE2" Residue "0z TYR 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0z GLU 469": "OE1" <-> "OE2" Residue "0z PHE 571": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1a PHE 558": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1b GLU 456": "OE1" <-> "OE2" Residue "1b GLU 469": "OE1" <-> "OE2" Residue "1b PHE 479": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1b GLU 550": "OE1" <-> "OE2" Residue "1b PHE 558": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1b PHE 571": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1c GLU 469": "OE1" <-> "OE2" Residue "1c GLU 535": "OE1" <-> "OE2" Residue "1c GLU 640": "OE1" <-> "OE2" Residue "1d PHE 479": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1d GLU 640": "OE1" <-> "OE2" Residue "1e PHE 479": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1e PHE 606": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1f GLU 469": "OE1" <-> "OE2" Residue "1f PHE 479": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1f GLU 535": "OE1" <-> "OE2" Residue "1g GLU 469": "OE1" <-> "OE2" Residue "1g GLU 535": "OE1" <-> "OE2" Residue "1g PHE 571": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1h TYR 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1h PHE 527": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1h GLU 535": "OE1" <-> "OE2" Residue "1h GLU 550": "OE1" <-> "OE2" Residue "1h PHE 558": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1h GLU 640": "OE1" <-> "OE2" Residue "1i PHE 558": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1i PHE 606": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1j GLU 456": "OE1" <-> "OE2" Residue "1j PHE 479": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1j GLU 535": "OE1" <-> "OE2" Residue "1j GLU 550": "OE1" <-> "OE2" Residue "1j PHE 635": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1j GLU 640": "OE1" <-> "OE2" Residue "1k GLU 469": "OE1" <-> "OE2" Residue "1l GLU 469": "OE1" <-> "OE2" Residue "1l PHE 479": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1l GLU 535": "OE1" <-> "OE2" Residue "1l PHE 558": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1l PHE 563": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1l PHE 571": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1m GLU 469": "OE1" <-> "OE2" Residue "1m GLU 535": "OE1" <-> "OE2" Residue "1m PHE 558": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1n PHE 479": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1n GLU 535": "OE1" <-> "OE2" Residue "1n GLU 550": "OE1" <-> "OE2" Residue "1n PHE 558": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1n GLU 640": "OE1" <-> "OE2" Residue "1o PHE 479": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1o GLU 535": "OE1" <-> "OE2" Residue "1o GLU 550": "OE1" <-> "OE2" Residue "1o PHE 558": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1o PHE 571": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1p PHE 558": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1p PHE 606": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1q GLU 469": "OE1" <-> "OE2" Residue "1q GLU 550": "OE1" <-> "OE2" Residue "1q PHE 635": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1s GLU 469": "OE1" <-> "OE2" Residue "1s PHE 479": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1s GLU 535": "OE1" <-> "OE2" Residue "1s PHE 558": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1t GLU 535": "OE1" <-> "OE2" Residue "1t PHE 571": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1u GLU 469": "OE1" <-> "OE2" Residue "1u PHE 479": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1u GLU 535": "OE1" <-> "OE2" Residue "1u GLU 550": "OE1" <-> "OE2" Residue "1v GLU 469": "OE1" <-> "OE2" Residue "1v GLU 550": "OE1" <-> "OE2" Residue "1v PHE 558": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1v GLU 640": "OE1" <-> "OE2" Residue "1x GLU 469": "OE1" <-> "OE2" Residue "1x PHE 527": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1x PHE 558": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1x GLU 640": "OE1" <-> "OE2" Residue "1z PHE 558": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2a GLU 535": "OE1" <-> "OE2" Residue "2a PHE 558": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2b GLU 594": "OE1" <-> "OE2" Residue "2b PHE 606": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2c GLU 469": "OE1" <-> "OE2" Residue "2c GLU 535": "OE1" <-> "OE2" Residue "2d GLU 469": "OE1" <-> "OE2" Residue "2d PHE 479": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2d GLU 535": "OE1" <-> "OE2" Residue "2e PHE 479": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2f GLU 469": "OE1" <-> "OE2" Residue "2f PHE 527": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2f GLU 535": "OE1" <-> "OE2" Residue "2f GLU 550": "OE1" <-> "OE2" Residue "2f GLU 557": "OE1" <-> "OE2" Residue "2g PHE 479": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2h GLU 594": "OE1" <-> "OE2" Residue "2j GLU 535": "OE1" <-> "OE2" Residue "2k GLU 469": "OE1" <-> "OE2" Residue "2k PHE 479": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2k PHE 527": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2k GLU 550": "OE1" <-> "OE2" Residue "2k GLU 640": "OE1" <-> "OE2" Residue "2l GLU 550": "OE1" <-> "OE2" Residue "2m PHE 479": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2m PHE 558": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2n GLU 469": "OE1" <-> "OE2" Residue "2n PHE 479": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2n PHE 558": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2o TYR 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2o PHE 479": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2q GLU 469": "OE1" <-> "OE2" Residue "2q PHE 479": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2q GLU 535": "OE1" <-> "OE2" Residue "2s PHE 479": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2s PHE 558": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2t GLU 535": "OE1" <-> "OE2" Residue "2t GLU 550": "OE1" <-> "OE2" Residue "2t GLU 640": "OE1" <-> "OE2" Residue "2v GLU 594": "OE1" <-> "OE2" Residue "2w GLU 469": "OE1" <-> "OE2" Residue "2w PHE 558": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2y GLU 456": "OE1" <-> "OE2" Residue "2y GLU 469": "OE1" <-> "OE2" Residue "2y PHE 479": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2y GLU 535": "OE1" <-> "OE2" Residue "2z GLU 469": "OE1" <-> "OE2" Residue "2z PHE 479": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2z GLU 535": "OE1" <-> "OE2" Residue "3a GLU 535": "OE1" <-> "OE2" Residue "3a PHE 558": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3b TYR 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3b PHE 527": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3b GLU 535": "OE1" <-> "OE2" Residue "3b GLU 550": "OE1" <-> "OE2" Residue "3b PHE 558": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3b PHE 606": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3c GLU 469": "OE1" <-> "OE2" Time to flip residues: 0.24s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 104640 Number of models: 1 Model: "" Number of chains: 60 Chain: "01" Number of atoms: 1744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1744 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 215} Chain breaks: 1 Chain: "02" Number of atoms: 1744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1744 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 215} Chain breaks: 1 Chain: "03" Number of atoms: 1744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1744 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 215} Chain breaks: 1 Chain: "04" Number of atoms: 1744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1744 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 215} Chain breaks: 1 Chain: "05" Number of atoms: 1744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1744 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 215} Chain breaks: 1 Chain: "0z" Number of atoms: 1744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1744 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 215} Chain breaks: 1 Chain: "1a" Number of atoms: 1744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1744 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 215} Chain breaks: 1 Chain: "1b" Number of atoms: 1744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1744 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 215} Chain breaks: 1 Chain: "1c" Number of atoms: 1744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1744 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 215} Chain breaks: 1 Chain: "1d" Number of atoms: 1744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1744 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 215} Chain breaks: 1 Chain: "1e" Number of atoms: 1744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1744 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 215} Chain breaks: 1 Chain: "1f" Number of atoms: 1744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1744 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 215} Chain breaks: 1 Chain: "1g" Number of atoms: 1744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1744 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 215} Chain breaks: 1 Chain: "1h" Number of atoms: 1744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1744 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 215} Chain breaks: 1 Chain: "1i" Number of atoms: 1744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1744 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 215} Chain breaks: 1 Chain: "1j" Number of atoms: 1744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1744 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 215} Chain breaks: 1 Chain: "1k" Number of atoms: 1744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1744 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 215} Chain breaks: 1 Chain: "1l" Number of atoms: 1744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1744 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 215} Chain breaks: 1 Chain: "1m" Number of atoms: 1744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1744 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 215} Chain breaks: 1 Chain: "1n" Number of atoms: 1744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1744 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 215} Chain breaks: 1 Chain: "1o" Number of atoms: 1744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1744 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 215} Chain breaks: 1 Chain: "1p" Number of atoms: 1744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1744 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 215} Chain breaks: 1 Chain: "1q" Number of atoms: 1744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1744 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 215} Chain breaks: 1 Chain: "1r" Number of atoms: 1744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1744 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 215} Chain breaks: 1 Chain: "1s" Number of atoms: 1744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1744 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 215} Chain breaks: 1 Chain: "1t" Number of atoms: 1744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1744 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 215} Chain breaks: 1 Chain: "1u" Number of atoms: 1744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1744 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 215} Chain breaks: 1 Chain: "1v" Number of atoms: 1744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1744 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 215} Chain breaks: 1 Chain: "1w" Number of atoms: 1744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1744 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 215} Chain breaks: 1 Chain: "1x" Number of atoms: 1744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1744 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 215} Chain breaks: 1 Chain: "1z" Number of atoms: 1744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1744 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 215} Chain breaks: 1 Chain: "2a" Number of atoms: 1744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1744 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 215} Chain breaks: 1 Chain: "2b" Number of atoms: 1744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1744 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 215} Chain breaks: 1 Chain: "2c" Number of atoms: 1744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1744 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 215} Chain breaks: 1 Chain: "2d" Number of atoms: 1744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1744 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 215} Chain breaks: 1 Chain: "2e" Number of atoms: 1744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1744 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 215} Chain breaks: 1 Chain: "2f" Number of atoms: 1744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1744 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 215} Chain breaks: 1 Chain: "2g" Number of atoms: 1744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1744 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 215} Chain breaks: 1 Chain: "2h" Number of atoms: 1744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1744 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 215} Chain breaks: 1 Chain: "2i" Number of atoms: 1744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1744 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 215} Chain breaks: 1 Chain: "2j" Number of atoms: 1744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1744 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 215} Chain breaks: 1 Chain: "2k" Number of atoms: 1744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1744 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 215} Chain breaks: 1 Chain: "2l" Number of atoms: 1744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1744 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 215} Chain breaks: 1 Chain: "2m" Number of atoms: 1744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1744 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 215} Chain breaks: 1 Chain: "2n" Number of atoms: 1744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1744 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 215} Chain breaks: 1 Chain: "2o" Number of atoms: 1744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1744 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 215} Chain breaks: 1 Chain: "2p" Number of atoms: 1744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1744 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 215} Chain breaks: 1 Chain: "2q" Number of atoms: 1744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1744 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 215} Chain breaks: 1 Chain: "2r" Number of atoms: 1744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1744 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 215} Chain breaks: 1 Chain: "2s" Number of atoms: 1744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1744 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 215} Chain breaks: 1 Chain: "2t" Number of atoms: 1744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1744 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 215} Chain breaks: 1 Chain: "2u" Number of atoms: 1744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1744 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 215} Chain breaks: 1 Chain: "2v" Number of atoms: 1744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1744 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 215} Chain breaks: 1 Chain: "2w" Number of atoms: 1744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1744 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 215} Chain breaks: 1 Chain: "2x" Number of atoms: 1744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1744 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 215} Chain breaks: 1 Chain: "2y" Number of atoms: 1744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1744 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 215} Chain breaks: 1 Chain: "2z" Number of atoms: 1744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1744 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 215} Chain breaks: 1 Chain: "3a" Number of atoms: 1744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1744 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 215} Chain breaks: 1 Chain: "3b" Number of atoms: 1744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1744 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 215} Chain breaks: 1 Chain: "3c" Number of atoms: 1744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1744 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 215} Chain breaks: 1 Time building chain proxies: 45.92, per 1000 atoms: 0.44 Number of scatterers: 104640 At special positions: 0 Unit cell: (248.88, 248.88, 248.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 660 16.00 O 19320 8.00 N 17940 7.00 C 66720 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: 32.63 Conformation dependent library (CDL) restraints added in 14.3 seconds 26640 Ramachandran restraints generated. 13320 Oldfield, 0 Emsley, 13320 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 25680 Finding SS restraints... Secondary structure from input PDB file: 515 helices and 170 sheets defined 47.2% alpha, 25.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 10.13 Creating SS restraints... Processing helix chain '01' and resid 426 through 443 Processing helix chain '01' and resid 454 through 469 removed outlier: 3.543A pdb=" N LEU01 458 " --> pdb=" O MET01 454 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU01 459 " --> pdb=" O GLY01 455 " (cutoff:3.500A) Processing helix chain '01' and resid 475 through 491 removed outlier: 3.747A pdb=" N PHE01 479 " --> pdb=" O SER01 475 " (cutoff:3.500A) Processing helix chain '01' and resid 492 through 496 Processing helix chain '01' and resid 533 through 551 Processing helix chain '01' and resid 554 through 559 removed outlier: 3.598A pdb=" N PHE01 558 " --> pdb=" O PRO01 555 " (cutoff:3.500A) Processing helix chain '01' and resid 624 through 641 removed outlier: 3.556A pdb=" N LYS01 641 " --> pdb=" O LYS01 637 " (cutoff:3.500A) Processing helix chain '01' and resid 642 through 647 Processing helix chain '02' and resid 426 through 443 Processing helix chain '02' and resid 454 through 469 removed outlier: 3.586A pdb=" N LEU02 458 " --> pdb=" O MET02 454 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU02 459 " --> pdb=" O GLY02 455 " (cutoff:3.500A) Processing helix chain '02' and resid 475 through 491 removed outlier: 3.756A pdb=" N PHE02 479 " --> pdb=" O SER02 475 " (cutoff:3.500A) Processing helix chain '02' and resid 492 through 496 Processing helix chain '02' and resid 533 through 551 Processing helix chain '02' and resid 554 through 559 Processing helix chain '02' and resid 624 through 641 removed outlier: 3.573A pdb=" N LYS02 641 " --> pdb=" O LYS02 637 " (cutoff:3.500A) Processing helix chain '02' and resid 642 through 647 Processing helix chain '03' and resid 426 through 443 Processing helix chain '03' and resid 454 through 469 removed outlier: 3.649A pdb=" N LEU03 459 " --> pdb=" O GLY03 455 " (cutoff:3.500A) Processing helix chain '03' and resid 475 through 491 removed outlier: 3.629A pdb=" N PHE03 479 " --> pdb=" O SER03 475 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LYS03 482 " --> pdb=" O ASP03 478 " (cutoff:3.500A) Processing helix chain '03' and resid 491 through 496 removed outlier: 4.049A pdb=" N ASN03 495 " --> pdb=" O VAL03 491 " (cutoff:3.500A) Processing helix chain '03' and resid 533 through 551 Processing helix chain '03' and resid 554 through 559 Processing helix chain '03' and resid 569 through 572 Processing helix chain '03' and resid 624 through 641 removed outlier: 3.548A pdb=" N LYS03 641 " --> pdb=" O LYS03 637 " (cutoff:3.500A) Processing helix chain '03' and resid 642 through 647 Processing helix chain '04' and resid 426 through 443 removed outlier: 3.604A pdb=" N LYS04 440 " --> pdb=" O LEU04 436 " (cutoff:3.500A) Processing helix chain '04' and resid 454 through 469 removed outlier: 3.574A pdb=" N LEU04 459 " --> pdb=" O GLY04 455 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU04 463 " --> pdb=" O LEU04 459 " (cutoff:3.500A) Processing helix chain '04' and resid 475 through 491 removed outlier: 3.728A pdb=" N PHE04 479 " --> pdb=" O SER04 475 " (cutoff:3.500A) Processing helix chain '04' and resid 491 through 496 removed outlier: 4.080A pdb=" N ASN04 495 " --> pdb=" O VAL04 491 " (cutoff:3.500A) Processing helix chain '04' and resid 533 through 550 Processing helix chain '04' and resid 554 through 559 Processing helix chain '04' and resid 569 through 572 Processing helix chain '04' and resid 624 through 640 Processing helix chain '04' and resid 641 through 647 Processing helix chain '05' and resid 426 through 443 removed outlier: 3.573A pdb=" N GLN05 434 " --> pdb=" O ARG05 430 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ARG05 435 " --> pdb=" O VAL05 431 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS05 440 " --> pdb=" O LEU05 436 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLN05 441 " --> pdb=" O MET05 437 " (cutoff:3.500A) Processing helix chain '05' and resid 454 through 469 removed outlier: 3.504A pdb=" N GLU05 469 " --> pdb=" O ASN05 465 " (cutoff:3.500A) Processing helix chain '05' and resid 475 through 491 removed outlier: 3.587A pdb=" N PHE05 479 " --> pdb=" O SER05 475 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE05 480 " --> pdb=" O VAL05 476 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS05 482 " --> pdb=" O ASP05 478 " (cutoff:3.500A) Processing helix chain '05' and resid 533 through 550 Processing helix chain '05' and resid 554 through 559 Processing helix chain '05' and resid 569 through 572 Processing helix chain '05' and resid 624 through 640 Processing helix chain '05' and resid 641 through 647 Processing helix chain '0z' and resid 426 through 443 Processing helix chain '0z' and resid 454 through 469 removed outlier: 3.606A pdb=" N LEU0z 458 " --> pdb=" O MET0z 454 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU0z 459 " --> pdb=" O GLY0z 455 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLU0z 469 " --> pdb=" O ASN0z 465 " (cutoff:3.500A) Processing helix chain '0z' and resid 475 through 491 removed outlier: 3.742A pdb=" N PHE0z 479 " --> pdb=" O SER0z 475 " (cutoff:3.500A) Processing helix chain '0z' and resid 492 through 496 Processing helix chain '0z' and resid 533 through 551 Processing helix chain '0z' and resid 554 through 559 removed outlier: 3.585A pdb=" N PHE0z 558 " --> pdb=" O PRO0z 555 " (cutoff:3.500A) Processing helix chain '0z' and resid 569 through 572 Processing helix chain '0z' and resid 624 through 641 removed outlier: 3.518A pdb=" N LYS0z 641 " --> pdb=" O LYS0z 637 " (cutoff:3.500A) Processing helix chain '0z' and resid 642 through 647 Processing helix chain '1a' and resid 426 through 443 Processing helix chain '1a' and resid 454 through 469 removed outlier: 3.695A pdb=" N LEU1a 459 " --> pdb=" O GLY1a 455 " (cutoff:3.500A) Processing helix chain '1a' and resid 475 through 491 removed outlier: 3.596A pdb=" N PHE1a 479 " --> pdb=" O SER1a 475 " (cutoff:3.500A) Processing helix chain '1a' and resid 491 through 496 removed outlier: 4.031A pdb=" N ASN1a 495 " --> pdb=" O VAL1a 491 " (cutoff:3.500A) Processing helix chain '1a' and resid 533 through 551 Processing helix chain '1a' and resid 554 through 559 Processing helix chain '1a' and resid 569 through 572 Processing helix chain '1a' and resid 624 through 641 removed outlier: 3.584A pdb=" N LYS1a 641 " --> pdb=" O LYS1a 637 " (cutoff:3.500A) Processing helix chain '1a' and resid 642 through 647 Processing helix chain '1b' and resid 426 through 443 removed outlier: 3.608A pdb=" N ILE1b 443 " --> pdb=" O SER1b 439 " (cutoff:3.500A) Processing helix chain '1b' and resid 454 through 469 removed outlier: 3.530A pdb=" N LEU1b 458 " --> pdb=" O MET1b 454 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU1b 459 " --> pdb=" O GLY1b 455 " (cutoff:3.500A) Processing helix chain '1b' and resid 475 through 491 removed outlier: 3.665A pdb=" N PHE1b 479 " --> pdb=" O SER1b 475 " (cutoff:3.500A) Processing helix chain '1b' and resid 492 through 496 Processing helix chain '1b' and resid 533 through 551 Processing helix chain '1b' and resid 554 through 559 Processing helix chain '1b' and resid 569 through 572 Processing helix chain '1b' and resid 624 through 641 removed outlier: 3.964A pdb=" N LYS1b 641 " --> pdb=" O LYS1b 637 " (cutoff:3.500A) Processing helix chain '1b' and resid 642 through 647 Processing helix chain '1c' and resid 426 through 443 removed outlier: 3.596A pdb=" N GLN1c 434 " --> pdb=" O ARG1c 430 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ARG1c 435 " --> pdb=" O VAL1c 431 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS1c 440 " --> pdb=" O LEU1c 436 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN1c 441 " --> pdb=" O MET1c 437 " (cutoff:3.500A) Processing helix chain '1c' and resid 454 through 469 removed outlier: 3.596A pdb=" N LEU1c 458 " --> pdb=" O MET1c 454 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU1c 459 " --> pdb=" O GLY1c 455 " (cutoff:3.500A) Processing helix chain '1c' and resid 475 through 491 removed outlier: 3.585A pdb=" N PHE1c 479 " --> pdb=" O SER1c 475 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS1c 482 " --> pdb=" O ASP1c 478 " (cutoff:3.500A) Processing helix chain '1c' and resid 533 through 551 Processing helix chain '1c' and resid 554 through 559 removed outlier: 3.648A pdb=" N GLN1c 559 " --> pdb=" O HIS1c 556 " (cutoff:3.500A) Processing helix chain '1c' and resid 569 through 572 Processing helix chain '1c' and resid 624 through 641 Processing helix chain '1c' and resid 642 through 647 Processing helix chain '1d' and resid 426 through 443 Processing helix chain '1d' and resid 454 through 468 removed outlier: 3.693A pdb=" N LEU1d 459 " --> pdb=" O GLY1d 455 " (cutoff:3.500A) Processing helix chain '1d' and resid 475 through 491 removed outlier: 3.629A pdb=" N PHE1d 479 " --> pdb=" O SER1d 475 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS1d 482 " --> pdb=" O ASP1d 478 " (cutoff:3.500A) Processing helix chain '1d' and resid 492 through 496 Processing helix chain '1d' and resid 533 through 550 Processing helix chain '1d' and resid 554 through 559 removed outlier: 3.793A pdb=" N PHE1d 558 " --> pdb=" O PRO1d 555 " (cutoff:3.500A) Processing helix chain '1d' and resid 569 through 572 Processing helix chain '1d' and resid 624 through 641 removed outlier: 3.776A pdb=" N LYS1d 641 " --> pdb=" O LYS1d 637 " (cutoff:3.500A) Processing helix chain '1d' and resid 642 through 647 Processing helix chain '1e' and resid 426 through 443 removed outlier: 3.524A pdb=" N ILE1e 432 " --> pdb=" O ILE1e 428 " (cutoff:3.500A) Processing helix chain '1e' and resid 454 through 469 removed outlier: 3.681A pdb=" N LEU1e 459 " --> pdb=" O GLY1e 455 " (cutoff:3.500A) Processing helix chain '1e' and resid 475 through 491 removed outlier: 3.615A pdb=" N PHE1e 479 " --> pdb=" O SER1e 475 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS1e 482 " --> pdb=" O ASP1e 478 " (cutoff:3.500A) Processing helix chain '1e' and resid 533 through 551 Processing helix chain '1e' and resid 554 through 559 removed outlier: 3.558A pdb=" N PHE1e 558 " --> pdb=" O PRO1e 555 " (cutoff:3.500A) Processing helix chain '1e' and resid 569 through 572 Processing helix chain '1e' and resid 624 through 641 removed outlier: 3.551A pdb=" N LYS1e 641 " --> pdb=" O LYS1e 637 " (cutoff:3.500A) Processing helix chain '1e' and resid 642 through 647 Processing helix chain '1f' and resid 426 through 443 Processing helix chain '1f' and resid 454 through 469 removed outlier: 3.696A pdb=" N LEU1f 459 " --> pdb=" O GLY1f 455 " (cutoff:3.500A) Processing helix chain '1f' and resid 475 through 491 removed outlier: 3.616A pdb=" N PHE1f 479 " --> pdb=" O SER1f 475 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE1f 480 " --> pdb=" O VAL1f 476 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS1f 482 " --> pdb=" O ASP1f 478 " (cutoff:3.500A) Processing helix chain '1f' and resid 533 through 550 Processing helix chain '1f' and resid 554 through 559 removed outlier: 3.507A pdb=" N PHE1f 558 " --> pdb=" O PRO1f 555 " (cutoff:3.500A) Processing helix chain '1f' and resid 569 through 572 Processing helix chain '1f' and resid 624 through 640 Processing helix chain '1f' and resid 641 through 647 Processing helix chain '1g' and resid 426 through 443 Processing helix chain '1g' and resid 454 through 469 removed outlier: 3.564A pdb=" N LEU1g 459 " --> pdb=" O GLY1g 455 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU1g 463 " --> pdb=" O LEU1g 459 " (cutoff:3.500A) Processing helix chain '1g' and resid 475 through 491 removed outlier: 3.730A pdb=" N PHE1g 479 " --> pdb=" O SER1g 475 " (cutoff:3.500A) Processing helix chain '1g' and resid 492 through 496 Processing helix chain '1g' and resid 533 through 550 removed outlier: 3.501A pdb=" N ALA1g 538 " --> pdb=" O LEU1g 534 " (cutoff:3.500A) Processing helix chain '1g' and resid 554 through 559 Processing helix chain '1g' and resid 624 through 640 Processing helix chain '1g' and resid 641 through 647 Processing helix chain '1h' and resid 426 through 443 removed outlier: 3.541A pdb=" N ILE1h 432 " --> pdb=" O ILE1h 428 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLN1h 441 " --> pdb=" O MET1h 437 " (cutoff:3.500A) Processing helix chain '1h' and resid 454 through 468 removed outlier: 3.610A pdb=" N LEU1h 458 " --> pdb=" O MET1h 454 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU1h 459 " --> pdb=" O GLY1h 455 " (cutoff:3.500A) Processing helix chain '1h' and resid 475 through 491 removed outlier: 3.601A pdb=" N PHE1h 479 " --> pdb=" O SER1h 475 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE1h 480 " --> pdb=" O VAL1h 476 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS1h 482 " --> pdb=" O ASP1h 478 " (cutoff:3.500A) Processing helix chain '1h' and resid 533 through 550 Processing helix chain '1h' and resid 554 through 559 Processing helix chain '1h' and resid 569 through 572 Processing helix chain '1h' and resid 624 through 641 removed outlier: 3.590A pdb=" N LYS1h 641 " --> pdb=" O LYS1h 637 " (cutoff:3.500A) Processing helix chain '1h' and resid 642 through 647 Processing helix chain '1i' and resid 426 through 443 Processing helix chain '1i' and resid 454 through 469 removed outlier: 3.698A pdb=" N LEU1i 459 " --> pdb=" O GLY1i 455 " (cutoff:3.500A) Processing helix chain '1i' and resid 475 through 491 removed outlier: 3.615A pdb=" N PHE1i 479 " --> pdb=" O SER1i 475 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE1i 480 " --> pdb=" O VAL1i 476 " (cutoff:3.500A) Processing helix chain '1i' and resid 491 through 496 removed outlier: 4.051A pdb=" N ASN1i 495 " --> pdb=" O VAL1i 491 " (cutoff:3.500A) Processing helix chain '1i' and resid 533 through 550 Processing helix chain '1i' and resid 554 through 559 Processing helix chain '1i' and resid 569 through 572 Processing helix chain '1i' and resid 624 through 641 removed outlier: 3.527A pdb=" N LYS1i 641 " --> pdb=" O LYS1i 637 " (cutoff:3.500A) Processing helix chain '1i' and resid 642 through 647 Processing helix chain '1j' and resid 426 through 443 removed outlier: 3.527A pdb=" N LYS1j 440 " --> pdb=" O LEU1j 436 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLN1j 441 " --> pdb=" O MET1j 437 " (cutoff:3.500A) Processing helix chain '1j' and resid 454 through 469 removed outlier: 3.532A pdb=" N LEU1j 458 " --> pdb=" O MET1j 454 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU1j 459 " --> pdb=" O GLY1j 455 " (cutoff:3.500A) Processing helix chain '1j' and resid 475 through 491 removed outlier: 3.730A pdb=" N PHE1j 479 " --> pdb=" O SER1j 475 " (cutoff:3.500A) Processing helix chain '1j' and resid 491 through 496 removed outlier: 4.047A pdb=" N ASN1j 495 " --> pdb=" O VAL1j 491 " (cutoff:3.500A) Processing helix chain '1j' and resid 533 through 550 removed outlier: 3.516A pdb=" N ALA1j 538 " --> pdb=" O LEU1j 534 " (cutoff:3.500A) Processing helix chain '1j' and resid 554 through 559 removed outlier: 3.601A pdb=" N GLN1j 559 " --> pdb=" O HIS1j 556 " (cutoff:3.500A) Processing helix chain '1j' and resid 624 through 641 removed outlier: 3.675A pdb=" N LYS1j 641 " --> pdb=" O LYS1j 637 " (cutoff:3.500A) Processing helix chain '1j' and resid 642 through 647 Processing helix chain '1k' and resid 426 through 443 removed outlier: 3.777A pdb=" N ARG1k 435 " --> pdb=" O VAL1k 431 " (cutoff:3.500A) Processing helix chain '1k' and resid 454 through 468 removed outlier: 3.539A pdb=" N LEU1k 459 " --> pdb=" O GLY1k 455 " (cutoff:3.500A) Processing helix chain '1k' and resid 475 through 491 removed outlier: 3.581A pdb=" N PHE1k 479 " --> pdb=" O SER1k 475 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS1k 482 " --> pdb=" O ASP1k 478 " (cutoff:3.500A) Processing helix chain '1k' and resid 533 through 551 Processing helix chain '1k' and resid 554 through 559 removed outlier: 3.522A pdb=" N PHE1k 558 " --> pdb=" O GLN1k 554 " (cutoff:3.500A) Processing helix chain '1k' and resid 569 through 572 Processing helix chain '1k' and resid 624 through 641 Processing helix chain '1k' and resid 642 through 647 Processing helix chain '1l' and resid 426 through 441 Processing helix chain '1l' and resid 454 through 468 removed outlier: 3.516A pdb=" N LEU1l 459 " --> pdb=" O GLY1l 455 " (cutoff:3.500A) Processing helix chain '1l' and resid 475 through 491 removed outlier: 3.553A pdb=" N PHE1l 479 " --> pdb=" O SER1l 475 " (cutoff:3.500A) Processing helix chain '1l' and resid 491 through 496 removed outlier: 4.113A pdb=" N ASN1l 495 " --> pdb=" O VAL1l 491 " (cutoff:3.500A) Processing helix chain '1l' and resid 533 through 551 Processing helix chain '1l' and resid 554 through 559 Processing helix chain '1l' and resid 569 through 572 Processing helix chain '1l' and resid 624 through 641 removed outlier: 3.575A pdb=" N LYS1l 641 " --> pdb=" O LYS1l 637 " (cutoff:3.500A) Processing helix chain '1l' and resid 642 through 647 Processing helix chain '1m' and resid 426 through 443 Processing helix chain '1m' and resid 454 through 469 removed outlier: 3.565A pdb=" N LEU1m 459 " --> pdb=" O GLY1m 455 " (cutoff:3.500A) Processing helix chain '1m' and resid 475 through 491 Processing helix chain '1m' and resid 491 through 496 removed outlier: 4.092A pdb=" N ASN1m 495 " --> pdb=" O VAL1m 491 " (cutoff:3.500A) Processing helix chain '1m' and resid 533 through 550 removed outlier: 3.515A pdb=" N ALA1m 538 " --> pdb=" O LEU1m 534 " (cutoff:3.500A) Processing helix chain '1m' and resid 554 through 559 Processing helix chain '1m' and resid 569 through 572 Processing helix chain '1m' and resid 624 through 640 Processing helix chain '1m' and resid 641 through 647 Processing helix chain '1n' and resid 426 through 443 Processing helix chain '1n' and resid 454 through 469 removed outlier: 3.584A pdb=" N LEU1n 458 " --> pdb=" O MET1n 454 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU1n 459 " --> pdb=" O GLY1n 455 " (cutoff:3.500A) Processing helix chain '1n' and resid 475 through 491 removed outlier: 3.610A pdb=" N PHE1n 479 " --> pdb=" O SER1n 475 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE1n 480 " --> pdb=" O VAL1n 476 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS1n 482 " --> pdb=" O ASP1n 478 " (cutoff:3.500A) Processing helix chain '1n' and resid 533 through 551 Processing helix chain '1n' and resid 554 through 559 Processing helix chain '1n' and resid 569 through 572 Processing helix chain '1n' and resid 624 through 641 removed outlier: 3.822A pdb=" N LYS1n 641 " --> pdb=" O LYS1n 637 " (cutoff:3.500A) Processing helix chain '1n' and resid 642 through 647 Processing helix chain '1o' and resid 426 through 443 removed outlier: 3.513A pdb=" N LYS1o 440 " --> pdb=" O LEU1o 436 " (cutoff:3.500A) Processing helix chain '1o' and resid 454 through 469 removed outlier: 3.643A pdb=" N LEU1o 458 " --> pdb=" O MET1o 454 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU1o 459 " --> pdb=" O GLY1o 455 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU1o 463 " --> pdb=" O LEU1o 459 " (cutoff:3.500A) Processing helix chain '1o' and resid 475 through 491 Processing helix chain '1o' and resid 491 through 496 removed outlier: 4.086A pdb=" N ASN1o 495 " --> pdb=" O VAL1o 491 " (cutoff:3.500A) Processing helix chain '1o' and resid 533 through 550 Processing helix chain '1o' and resid 554 through 559 removed outlier: 3.505A pdb=" N PHE1o 558 " --> pdb=" O PRO1o 555 " (cutoff:3.500A) Processing helix chain '1o' and resid 624 through 641 removed outlier: 3.730A pdb=" N LYS1o 641 " --> pdb=" O LYS1o 637 " (cutoff:3.500A) Processing helix chain '1o' and resid 642 through 647 Processing helix chain '1p' and resid 426 through 441 Processing helix chain '1p' and resid 454 through 468 removed outlier: 3.560A pdb=" N LEU1p 458 " --> pdb=" O MET1p 454 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU1p 459 " --> pdb=" O GLY1p 455 " (cutoff:3.500A) Processing helix chain '1p' and resid 475 through 491 removed outlier: 3.674A pdb=" N PHE1p 479 " --> pdb=" O SER1p 475 " (cutoff:3.500A) Processing helix chain '1p' and resid 533 through 551 Processing helix chain '1p' and resid 554 through 559 Processing helix chain '1p' and resid 569 through 572 Processing helix chain '1p' and resid 624 through 640 Processing helix chain '1p' and resid 641 through 647 Processing helix chain '1q' and resid 426 through 443 removed outlier: 3.526A pdb=" N GLN1q 434 " --> pdb=" O ARG1q 430 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ARG1q 435 " --> pdb=" O VAL1q 431 " (cutoff:3.500A) Processing helix chain '1q' and resid 454 through 469 removed outlier: 3.600A pdb=" N LEU1q 459 " --> pdb=" O GLY1q 455 " (cutoff:3.500A) Processing helix chain '1q' and resid 475 through 491 removed outlier: 3.612A pdb=" N PHE1q 479 " --> pdb=" O SER1q 475 " (cutoff:3.500A) Processing helix chain '1q' and resid 533 through 550 Processing helix chain '1q' and resid 554 through 559 removed outlier: 3.845A pdb=" N PHE1q 558 " --> pdb=" O GLN1q 554 " (cutoff:3.500A) Processing helix chain '1q' and resid 569 through 572 Processing helix chain '1q' and resid 624 through 641 removed outlier: 3.553A pdb=" N LYS1q 641 " --> pdb=" O LYS1q 637 " (cutoff:3.500A) Processing helix chain '1q' and resid 642 through 647 Processing helix chain '1r' and resid 426 through 443 Processing helix chain '1r' and resid 454 through 469 removed outlier: 3.520A pdb=" N LEU1r 458 " --> pdb=" O MET1r 454 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU1r 459 " --> pdb=" O GLY1r 455 " (cutoff:3.500A) Processing helix chain '1r' and resid 475 through 491 removed outlier: 3.663A pdb=" N PHE1r 479 " --> pdb=" O SER1r 475 " (cutoff:3.500A) Processing helix chain '1r' and resid 491 through 496 removed outlier: 4.042A pdb=" N ASN1r 495 " --> pdb=" O VAL1r 491 " (cutoff:3.500A) Processing helix chain '1r' and resid 533 through 551 Processing helix chain '1r' and resid 554 through 559 Processing helix chain '1r' and resid 569 through 572 Processing helix chain '1r' and resid 624 through 641 removed outlier: 3.539A pdb=" N LYS1r 641 " --> pdb=" O LYS1r 637 " (cutoff:3.500A) Processing helix chain '1r' and resid 642 through 647 Processing helix chain '1s' and resid 426 through 443 removed outlier: 3.648A pdb=" N ILE1s 432 " --> pdb=" O ILE1s 428 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ARG1s 435 " --> pdb=" O VAL1s 431 " (cutoff:3.500A) Processing helix chain '1s' and resid 454 through 469 removed outlier: 3.648A pdb=" N LEU1s 459 " --> pdb=" O GLY1s 455 " (cutoff:3.500A) Processing helix chain '1s' and resid 475 through 491 removed outlier: 3.613A pdb=" N PHE1s 479 " --> pdb=" O SER1s 475 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS1s 482 " --> pdb=" O ASP1s 478 " (cutoff:3.500A) Processing helix chain '1s' and resid 533 through 550 Processing helix chain '1s' and resid 554 through 559 Processing helix chain '1s' and resid 569 through 572 Processing helix chain '1s' and resid 624 through 641 removed outlier: 3.749A pdb=" N LYS1s 641 " --> pdb=" O LYS1s 637 " (cutoff:3.500A) Processing helix chain '1s' and resid 642 through 647 Processing helix chain '1t' and resid 426 through 443 removed outlier: 3.650A pdb=" N ARG1t 435 " --> pdb=" O VAL1t 431 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN1t 441 " --> pdb=" O MET1t 437 " (cutoff:3.500A) Processing helix chain '1t' and resid 454 through 469 removed outlier: 3.688A pdb=" N LEU1t 459 " --> pdb=" O GLY1t 455 " (cutoff:3.500A) Processing helix chain '1t' and resid 475 through 491 removed outlier: 3.615A pdb=" N PHE1t 479 " --> pdb=" O SER1t 475 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LYS1t 482 " --> pdb=" O ASP1t 478 " (cutoff:3.500A) Processing helix chain '1t' and resid 491 through 496 removed outlier: 4.132A pdb=" N ASN1t 495 " --> pdb=" O VAL1t 491 " (cutoff:3.500A) Processing helix chain '1t' and resid 533 through 550 Processing helix chain '1t' and resid 554 through 559 Processing helix chain '1t' and resid 569 through 572 Processing helix chain '1t' and resid 624 through 641 removed outlier: 3.769A pdb=" N LYS1t 641 " --> pdb=" O LYS1t 637 " (cutoff:3.500A) Processing helix chain '1t' and resid 642 through 647 Processing helix chain '1u' and resid 426 through 443 removed outlier: 3.504A pdb=" N LYS1u 440 " --> pdb=" O LEU1u 436 " (cutoff:3.500A) Processing helix chain '1u' and resid 454 through 469 removed outlier: 3.678A pdb=" N LEU1u 459 " --> pdb=" O GLY1u 455 " (cutoff:3.500A) Processing helix chain '1u' and resid 475 through 491 removed outlier: 3.675A pdb=" N PHE1u 479 " --> pdb=" O SER1u 475 " (cutoff:3.500A) Processing helix chain '1u' and resid 491 through 496 removed outlier: 4.134A pdb=" N ASN1u 495 " --> pdb=" O VAL1u 491 " (cutoff:3.500A) Processing helix chain '1u' and resid 533 through 550 Processing helix chain '1u' and resid 554 through 559 removed outlier: 3.535A pdb=" N PHE1u 558 " --> pdb=" O PRO1u 555 " (cutoff:3.500A) Processing helix chain '1u' and resid 569 through 572 Processing helix chain '1u' and resid 624 through 641 removed outlier: 3.727A pdb=" N LYS1u 641 " --> pdb=" O LYS1u 637 " (cutoff:3.500A) Processing helix chain '1u' and resid 642 through 647 Processing helix chain '1v' and resid 426 through 443 removed outlier: 3.686A pdb=" N ILE1v 432 " --> pdb=" O ILE1v 428 " (cutoff:3.500A) Processing helix chain '1v' and resid 454 through 469 removed outlier: 3.580A pdb=" N LEU1v 458 " --> pdb=" O MET1v 454 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU1v 459 " --> pdb=" O GLY1v 455 " (cutoff:3.500A) Processing helix chain '1v' and resid 475 through 491 removed outlier: 3.595A pdb=" N PHE1v 479 " --> pdb=" O SER1v 475 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS1v 482 " --> pdb=" O ASP1v 478 " (cutoff:3.500A) Processing helix chain '1v' and resid 533 through 550 Processing helix chain '1v' and resid 554 through 559 Processing helix chain '1v' and resid 569 through 572 Processing helix chain '1v' and resid 624 through 640 Processing helix chain '1v' and resid 641 through 647 Processing helix chain '1w' and resid 426 through 443 Processing helix chain '1w' and resid 454 through 469 removed outlier: 3.697A pdb=" N LEU1w 459 " --> pdb=" O GLY1w 455 " (cutoff:3.500A) Processing helix chain '1w' and resid 475 through 491 removed outlier: 3.658A pdb=" N PHE1w 479 " --> pdb=" O SER1w 475 " (cutoff:3.500A) Processing helix chain '1w' and resid 491 through 496 removed outlier: 4.070A pdb=" N ASN1w 495 " --> pdb=" O VAL1w 491 " (cutoff:3.500A) Processing helix chain '1w' and resid 533 through 550 Processing helix chain '1w' and resid 554 through 559 Processing helix chain '1w' and resid 569 through 572 Processing helix chain '1w' and resid 624 through 641 removed outlier: 3.554A pdb=" N LYS1w 641 " --> pdb=" O LYS1w 637 " (cutoff:3.500A) Processing helix chain '1w' and resid 642 through 647 Processing helix chain '1x' and resid 426 through 443 removed outlier: 3.775A pdb=" N GLN1x 434 " --> pdb=" O ARG1x 430 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ARG1x 435 " --> pdb=" O VAL1x 431 " (cutoff:3.500A) Processing helix chain '1x' and resid 454 through 469 Processing helix chain '1x' and resid 475 through 491 removed outlier: 3.616A pdb=" N PHE1x 479 " --> pdb=" O SER1x 475 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS1x 482 " --> pdb=" O ASP1x 478 " (cutoff:3.500A) Processing helix chain '1x' and resid 491 through 496 removed outlier: 4.087A pdb=" N ASN1x 495 " --> pdb=" O VAL1x 491 " (cutoff:3.500A) Processing helix chain '1x' and resid 533 through 551 Processing helix chain '1x' and resid 554 through 559 Processing helix chain '1x' and resid 569 through 572 Processing helix chain '1x' and resid 624 through 641 removed outlier: 3.615A pdb=" N LYS1x 641 " --> pdb=" O LYS1x 637 " (cutoff:3.500A) Processing helix chain '1x' and resid 642 through 647 Processing helix chain '1z' and resid 426 through 443 Processing helix chain '1z' and resid 454 through 469 removed outlier: 3.584A pdb=" N LEU1z 459 " --> pdb=" O GLY1z 455 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLU1z 469 " --> pdb=" O ASN1z 465 " (cutoff:3.500A) Processing helix chain '1z' and resid 475 through 491 removed outlier: 3.671A pdb=" N PHE1z 479 " --> pdb=" O SER1z 475 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE1z 480 " --> pdb=" O VAL1z 476 " (cutoff:3.500A) Processing helix chain '1z' and resid 491 through 496 removed outlier: 4.065A pdb=" N ASN1z 495 " --> pdb=" O VAL1z 491 " (cutoff:3.500A) Processing helix chain '1z' and resid 533 through 551 Processing helix chain '1z' and resid 554 through 559 Processing helix chain '1z' and resid 569 through 572 Processing helix chain '1z' and resid 624 through 641 removed outlier: 3.571A pdb=" N LYS1z 641 " --> pdb=" O LYS1z 637 " (cutoff:3.500A) Processing helix chain '1z' and resid 642 through 647 Processing helix chain '2a' and resid 426 through 443 removed outlier: 3.628A pdb=" N LYS2a 440 " --> pdb=" O LEU2a 436 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLN2a 441 " --> pdb=" O MET2a 437 " (cutoff:3.500A) Processing helix chain '2a' and resid 454 through 469 removed outlier: 3.566A pdb=" N LEU2a 459 " --> pdb=" O GLY2a 455 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLU2a 463 " --> pdb=" O LEU2a 459 " (cutoff:3.500A) Processing helix chain '2a' and resid 475 through 491 removed outlier: 3.576A pdb=" N PHE2a 479 " --> pdb=" O SER2a 475 " (cutoff:3.500A) Processing helix chain '2a' and resid 491 through 496 removed outlier: 4.075A pdb=" N ASN2a 495 " --> pdb=" O VAL2a 491 " (cutoff:3.500A) Processing helix chain '2a' and resid 533 through 551 Processing helix chain '2a' and resid 554 through 559 Processing helix chain '2a' and resid 569 through 572 Processing helix chain '2a' and resid 624 through 641 removed outlier: 3.701A pdb=" N LYS2a 641 " --> pdb=" O LYS2a 637 " (cutoff:3.500A) Processing helix chain '2a' and resid 642 through 647 Processing helix chain '2b' and resid 426 through 443 removed outlier: 3.615A pdb=" N ARG2b 435 " --> pdb=" O VAL2b 431 " (cutoff:3.500A) Processing helix chain '2b' and resid 454 through 469 removed outlier: 3.536A pdb=" N LEU2b 458 " --> pdb=" O MET2b 454 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU2b 459 " --> pdb=" O GLY2b 455 " (cutoff:3.500A) Processing helix chain '2b' and resid 475 through 491 removed outlier: 3.687A pdb=" N PHE2b 479 " --> pdb=" O SER2b 475 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS2b 482 " --> pdb=" O ASP2b 478 " (cutoff:3.500A) Processing helix chain '2b' and resid 533 through 551 Processing helix chain '2b' and resid 554 through 559 Processing helix chain '2b' and resid 569 through 572 Processing helix chain '2b' and resid 624 through 641 removed outlier: 3.523A pdb=" N LYS2b 641 " --> pdb=" O LYS2b 637 " (cutoff:3.500A) Processing helix chain '2b' and resid 642 through 647 Processing helix chain '2c' and resid 426 through 443 removed outlier: 3.747A pdb=" N ARG2c 435 " --> pdb=" O VAL2c 431 " (cutoff:3.500A) Processing helix chain '2c' and resid 454 through 469 removed outlier: 3.767A pdb=" N LEU2c 459 " --> pdb=" O GLY2c 455 " (cutoff:3.500A) Processing helix chain '2c' and resid 475 through 491 removed outlier: 3.662A pdb=" N PHE2c 479 " --> pdb=" O SER2c 475 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS2c 482 " --> pdb=" O ASP2c 478 " (cutoff:3.500A) Processing helix chain '2c' and resid 491 through 496 removed outlier: 4.142A pdb=" N ASN2c 495 " --> pdb=" O VAL2c 491 " (cutoff:3.500A) Processing helix chain '2c' and resid 533 through 550 Processing helix chain '2c' and resid 554 through 559 removed outlier: 3.520A pdb=" N PHE2c 558 " --> pdb=" O PRO2c 555 " (cutoff:3.500A) Processing helix chain '2c' and resid 569 through 572 Processing helix chain '2c' and resid 624 through 641 removed outlier: 3.535A pdb=" N LYS2c 641 " --> pdb=" O LYS2c 637 " (cutoff:3.500A) Processing helix chain '2c' and resid 642 through 647 Processing helix chain '2d' and resid 426 through 443 removed outlier: 3.537A pdb=" N ILE2d 432 " --> pdb=" O ILE2d 428 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG2d 435 " --> pdb=" O VAL2d 431 " (cutoff:3.500A) Processing helix chain '2d' and resid 454 through 469 removed outlier: 3.579A pdb=" N LEU2d 458 " --> pdb=" O MET2d 454 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU2d 459 " --> pdb=" O GLY2d 455 " (cutoff:3.500A) Processing helix chain '2d' and resid 475 through 491 removed outlier: 3.645A pdb=" N PHE2d 479 " --> pdb=" O SER2d 475 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS2d 482 " --> pdb=" O ASP2d 478 " (cutoff:3.500A) Processing helix chain '2d' and resid 533 through 550 Processing helix chain '2d' and resid 554 through 559 Processing helix chain '2d' and resid 569 through 572 Processing helix chain '2d' and resid 624 through 641 removed outlier: 3.744A pdb=" N LYS2d 641 " --> pdb=" O LYS2d 637 " (cutoff:3.500A) Processing helix chain '2d' and resid 642 through 647 Processing helix chain '2e' and resid 426 through 443 removed outlier: 3.517A pdb=" N VAL2e 431 " --> pdb=" O ASN2e 427 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE2e 432 " --> pdb=" O ILE2e 428 " (cutoff:3.500A) Processing helix chain '2e' and resid 454 through 469 removed outlier: 3.519A pdb=" N LEU2e 458 " --> pdb=" O MET2e 454 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU2e 459 " --> pdb=" O GLY2e 455 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU2e 469 " --> pdb=" O ASN2e 465 " (cutoff:3.500A) Processing helix chain '2e' and resid 475 through 491 removed outlier: 3.718A pdb=" N PHE2e 479 " --> pdb=" O SER2e 475 " (cutoff:3.500A) Processing helix chain '2e' and resid 491 through 496 removed outlier: 4.099A pdb=" N ASN2e 495 " --> pdb=" O VAL2e 491 " (cutoff:3.500A) Processing helix chain '2e' and resid 533 through 551 Processing helix chain '2e' and resid 554 through 559 Processing helix chain '2e' and resid 569 through 572 Processing helix chain '2e' and resid 624 through 641 removed outlier: 3.557A pdb=" N LYS2e 641 " --> pdb=" O LYS2e 637 " (cutoff:3.500A) Processing helix chain '2e' and resid 642 through 647 Processing helix chain '2f' and resid 426 through 443 removed outlier: 3.621A pdb=" N ARG2f 435 " --> pdb=" O VAL2f 431 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS2f 440 " --> pdb=" O LEU2f 436 " (cutoff:3.500A) Processing helix chain '2f' and resid 454 through 469 removed outlier: 3.576A pdb=" N LEU2f 459 " --> pdb=" O GLY2f 455 " (cutoff:3.500A) Processing helix chain '2f' and resid 475 through 491 removed outlier: 3.597A pdb=" N PHE2f 479 " --> pdb=" O SER2f 475 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE2f 480 " --> pdb=" O VAL2f 476 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS2f 482 " --> pdb=" O ASP2f 478 " (cutoff:3.500A) Processing helix chain '2f' and resid 533 through 551 Processing helix chain '2f' and resid 555 through 559 Processing helix chain '2f' and resid 569 through 572 Processing helix chain '2f' and resid 624 through 641 removed outlier: 3.892A pdb=" N LYS2f 641 " --> pdb=" O LYS2f 637 " (cutoff:3.500A) Processing helix chain '2f' and resid 642 through 647 Processing helix chain '2g' and resid 426 through 443 Processing helix chain '2g' and resid 454 through 469 removed outlier: 3.675A pdb=" N LEU2g 459 " --> pdb=" O GLY2g 455 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU2g 469 " --> pdb=" O ASN2g 465 " (cutoff:3.500A) Processing helix chain '2g' and resid 475 through 491 removed outlier: 3.590A pdb=" N PHE2g 479 " --> pdb=" O SER2g 475 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS2g 482 " --> pdb=" O ASP2g 478 " (cutoff:3.500A) Processing helix chain '2g' and resid 491 through 496 removed outlier: 4.056A pdb=" N ASN2g 495 " --> pdb=" O VAL2g 491 " (cutoff:3.500A) Processing helix chain '2g' and resid 533 through 551 Processing helix chain '2g' and resid 554 through 559 Processing helix chain '2g' and resid 569 through 572 Processing helix chain '2g' and resid 624 through 641 removed outlier: 3.575A pdb=" N LYS2g 641 " --> pdb=" O LYS2g 637 " (cutoff:3.500A) Processing helix chain '2g' and resid 642 through 647 Processing helix chain '2h' and resid 426 through 443 Processing helix chain '2h' and resid 454 through 469 removed outlier: 3.565A pdb=" N LEU2h 458 " --> pdb=" O MET2h 454 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU2h 459 " --> pdb=" O GLY2h 455 " (cutoff:3.500A) Processing helix chain '2h' and resid 475 through 491 removed outlier: 3.774A pdb=" N PHE2h 479 " --> pdb=" O SER2h 475 " (cutoff:3.500A) Processing helix chain '2h' and resid 492 through 496 Processing helix chain '2h' and resid 533 through 551 Processing helix chain '2h' and resid 554 through 559 removed outlier: 3.526A pdb=" N PHE2h 558 " --> pdb=" O PRO2h 555 " (cutoff:3.500A) Processing helix chain '2h' and resid 569 through 572 Processing helix chain '2h' and resid 624 through 641 removed outlier: 3.611A pdb=" N LYS2h 641 " --> pdb=" O LYS2h 637 " (cutoff:3.500A) Processing helix chain '2h' and resid 642 through 647 Processing helix chain '2i' and resid 426 through 443 Processing helix chain '2i' and resid 454 through 469 removed outlier: 3.609A pdb=" N LEU2i 458 " --> pdb=" O MET2i 454 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU2i 459 " --> pdb=" O GLY2i 455 " (cutoff:3.500A) Processing helix chain '2i' and resid 475 through 491 removed outlier: 3.713A pdb=" N PHE2i 479 " --> pdb=" O SER2i 475 " (cutoff:3.500A) Processing helix chain '2i' and resid 492 through 496 Processing helix chain '2i' and resid 533 through 551 Processing helix chain '2i' and resid 554 through 559 removed outlier: 3.581A pdb=" N PHE2i 558 " --> pdb=" O PRO2i 555 " (cutoff:3.500A) Processing helix chain '2i' and resid 569 through 572 Processing helix chain '2i' and resid 624 through 641 removed outlier: 3.589A pdb=" N LYS2i 641 " --> pdb=" O LYS2i 637 " (cutoff:3.500A) Processing helix chain '2i' and resid 642 through 647 Processing helix chain '2j' and resid 426 through 443 Processing helix chain '2j' and resid 454 through 469 removed outlier: 3.580A pdb=" N LEU2j 458 " --> pdb=" O MET2j 454 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU2j 459 " --> pdb=" O GLY2j 455 " (cutoff:3.500A) Processing helix chain '2j' and resid 475 through 491 removed outlier: 3.739A pdb=" N PHE2j 479 " --> pdb=" O SER2j 475 " (cutoff:3.500A) Processing helix chain '2j' and resid 492 through 496 Processing helix chain '2j' and resid 533 through 551 removed outlier: 3.606A pdb=" N GLU2j 550 " --> pdb=" O THR2j 546 " (cutoff:3.500A) Processing helix chain '2j' and resid 554 through 559 Processing helix chain '2j' and resid 569 through 572 Processing helix chain '2j' and resid 624 through 640 Processing helix chain '2j' and resid 641 through 647 Processing helix chain '2k' and resid 426 through 443 Processing helix chain '2k' and resid 454 through 468 removed outlier: 3.586A pdb=" N LEU2k 458 " --> pdb=" O MET2k 454 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU2k 459 " --> pdb=" O GLY2k 455 " (cutoff:3.500A) Processing helix chain '2k' and resid 475 through 491 removed outlier: 3.601A pdb=" N PHE2k 479 " --> pdb=" O SER2k 475 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE2k 480 " --> pdb=" O VAL2k 476 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS2k 482 " --> pdb=" O ASP2k 478 " (cutoff:3.500A) Processing helix chain '2k' and resid 533 through 550 Processing helix chain '2k' and resid 554 through 558 Processing helix chain '2k' and resid 569 through 572 Processing helix chain '2k' and resid 624 through 640 Processing helix chain '2k' and resid 641 through 647 Processing helix chain '2l' and resid 426 through 443 Processing helix chain '2l' and resid 454 through 469 removed outlier: 3.537A pdb=" N LEU2l 459 " --> pdb=" O GLY2l 455 " (cutoff:3.500A) Processing helix chain '2l' and resid 475 through 491 removed outlier: 3.672A pdb=" N PHE2l 479 " --> pdb=" O SER2l 475 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE2l 480 " --> pdb=" O VAL2l 476 " (cutoff:3.500A) Processing helix chain '2l' and resid 491 through 496 removed outlier: 4.034A pdb=" N ASN2l 495 " --> pdb=" O VAL2l 491 " (cutoff:3.500A) Processing helix chain '2l' and resid 533 through 550 Processing helix chain '2l' and resid 554 through 559 removed outlier: 3.502A pdb=" N PHE2l 558 " --> pdb=" O PRO2l 555 " (cutoff:3.500A) Processing helix chain '2l' and resid 569 through 572 Processing helix chain '2l' and resid 624 through 640 Processing helix chain '2l' and resid 641 through 647 Processing helix chain '2m' and resid 426 through 443 Processing helix chain '2m' and resid 454 through 469 removed outlier: 3.634A pdb=" N LEU2m 459 " --> pdb=" O GLY2m 455 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLU2m 469 " --> pdb=" O ASN2m 465 " (cutoff:3.500A) Processing helix chain '2m' and resid 475 through 491 removed outlier: 3.732A pdb=" N PHE2m 479 " --> pdb=" O SER2m 475 " (cutoff:3.500A) Processing helix chain '2m' and resid 533 through 551 Processing helix chain '2m' and resid 554 through 559 Processing helix chain '2m' and resid 569 through 572 Processing helix chain '2m' and resid 624 through 641 removed outlier: 3.563A pdb=" N LYS2m 641 " --> pdb=" O LYS2m 637 " (cutoff:3.500A) Processing helix chain '2m' and resid 642 through 647 Processing helix chain '2n' and resid 426 through 443 removed outlier: 3.544A pdb=" N LYS2n 440 " --> pdb=" O LEU2n 436 " (cutoff:3.500A) Processing helix chain '2n' and resid 454 through 468 removed outlier: 3.587A pdb=" N LEU2n 458 " --> pdb=" O MET2n 454 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU2n 459 " --> pdb=" O GLY2n 455 " (cutoff:3.500A) Processing helix chain '2n' and resid 475 through 491 removed outlier: 3.724A pdb=" N PHE2n 479 " --> pdb=" O SER2n 475 " (cutoff:3.500A) Processing helix chain '2n' and resid 492 through 496 Processing helix chain '2n' and resid 533 through 551 Processing helix chain '2n' and resid 554 through 559 Processing helix chain '2n' and resid 569 through 572 Processing helix chain '2n' and resid 624 through 640 Processing helix chain '2n' and resid 641 through 647 Processing helix chain '2o' and resid 426 through 443 removed outlier: 3.521A pdb=" N LYS2o 440 " --> pdb=" O LEU2o 436 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN2o 441 " --> pdb=" O MET2o 437 " (cutoff:3.500A) Processing helix chain '2o' and resid 454 through 469 removed outlier: 3.554A pdb=" N LEU2o 458 " --> pdb=" O MET2o 454 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU2o 459 " --> pdb=" O GLY2o 455 " (cutoff:3.500A) Processing helix chain '2o' and resid 475 through 491 removed outlier: 3.640A pdb=" N PHE2o 479 " --> pdb=" O SER2o 475 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE2o 480 " --> pdb=" O VAL2o 476 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS2o 482 " --> pdb=" O ASP2o 478 " (cutoff:3.500A) Processing helix chain '2o' and resid 491 through 496 removed outlier: 4.092A pdb=" N ASN2o 495 " --> pdb=" O VAL2o 491 " (cutoff:3.500A) Processing helix chain '2o' and resid 533 through 551 Processing helix chain '2o' and resid 554 through 559 removed outlier: 3.568A pdb=" N PHE2o 558 " --> pdb=" O PRO2o 555 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLN2o 559 " --> pdb=" O HIS2o 556 " (cutoff:3.500A) Processing helix chain '2o' and resid 569 through 572 Processing helix chain '2o' and resid 624 through 641 removed outlier: 3.534A pdb=" N LYS2o 641 " --> pdb=" O LYS2o 637 " (cutoff:3.500A) Processing helix chain '2o' and resid 642 through 647 Processing helix chain '2p' and resid 426 through 443 Processing helix chain '2p' and resid 454 through 469 removed outlier: 3.632A pdb=" N LEU2p 459 " --> pdb=" O GLY2p 455 " (cutoff:3.500A) Processing helix chain '2p' and resid 475 through 491 removed outlier: 3.640A pdb=" N PHE2p 479 " --> pdb=" O SER2p 475 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE2p 480 " --> pdb=" O VAL2p 476 " (cutoff:3.500A) Processing helix chain '2p' and resid 491 through 496 removed outlier: 4.028A pdb=" N ASN2p 495 " --> pdb=" O VAL2p 491 " (cutoff:3.500A) Processing helix chain '2p' and resid 533 through 551 Processing helix chain '2p' and resid 554 through 559 removed outlier: 3.742A pdb=" N GLN2p 559 " --> pdb=" O HIS2p 556 " (cutoff:3.500A) Processing helix chain '2p' and resid 569 through 572 Processing helix chain '2p' and resid 624 through 641 removed outlier: 3.582A pdb=" N LYS2p 641 " --> pdb=" O LYS2p 637 " (cutoff:3.500A) Processing helix chain '2p' and resid 642 through 647 Processing helix chain '2q' and resid 426 through 443 Processing helix chain '2q' and resid 454 through 469 removed outlier: 3.544A pdb=" N LEU2q 458 " --> pdb=" O MET2q 454 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU2q 459 " --> pdb=" O GLY2q 455 " (cutoff:3.500A) Processing helix chain '2q' and resid 475 through 491 removed outlier: 3.671A pdb=" N PHE2q 479 " --> pdb=" O SER2q 475 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS2q 482 " --> pdb=" O ASP2q 478 " (cutoff:3.500A) Processing helix chain '2q' and resid 492 through 496 Processing helix chain '2q' and resid 533 through 551 Processing helix chain '2q' and resid 554 through 559 Processing helix chain '2q' and resid 569 through 572 Processing helix chain '2q' and resid 624 through 641 removed outlier: 3.771A pdb=" N LYS2q 641 " --> pdb=" O LYS2q 637 " (cutoff:3.500A) Processing helix chain '2q' and resid 642 through 647 Processing helix chain '2r' and resid 426 through 443 Processing helix chain '2r' and resid 454 through 469 removed outlier: 3.657A pdb=" N LEU2r 459 " --> pdb=" O GLY2r 455 " (cutoff:3.500A) Processing helix chain '2r' and resid 475 through 491 removed outlier: 3.693A pdb=" N PHE2r 479 " --> pdb=" O SER2r 475 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE2r 480 " --> pdb=" O VAL2r 476 " (cutoff:3.500A) Processing helix chain '2r' and resid 533 through 551 Processing helix chain '2r' and resid 554 through 559 removed outlier: 3.560A pdb=" N PHE2r 558 " --> pdb=" O PRO2r 555 " (cutoff:3.500A) Processing helix chain '2r' and resid 569 through 572 Processing helix chain '2r' and resid 624 through 641 removed outlier: 3.507A pdb=" N LYS2r 641 " --> pdb=" O LYS2r 637 " (cutoff:3.500A) Processing helix chain '2r' and resid 642 through 647 Processing helix chain '2s' and resid 426 through 443 Processing helix chain '2s' and resid 454 through 468 removed outlier: 3.596A pdb=" N LEU2s 459 " --> pdb=" O GLY2s 455 " (cutoff:3.500A) Processing helix chain '2s' and resid 475 through 491 removed outlier: 3.696A pdb=" N PHE2s 479 " --> pdb=" O SER2s 475 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE2s 480 " --> pdb=" O VAL2s 476 " (cutoff:3.500A) Processing helix chain '2s' and resid 491 through 496 removed outlier: 4.062A pdb=" N ASN2s 495 " --> pdb=" O VAL2s 491 " (cutoff:3.500A) Processing helix chain '2s' and resid 533 through 551 Processing helix chain '2s' and resid 554 through 559 removed outlier: 3.502A pdb=" N PHE2s 558 " --> pdb=" O PRO2s 555 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLN2s 559 " --> pdb=" O HIS2s 556 " (cutoff:3.500A) Processing helix chain '2s' and resid 569 through 572 Processing helix chain '2s' and resid 624 through 641 removed outlier: 3.531A pdb=" N LYS2s 641 " --> pdb=" O LYS2s 637 " (cutoff:3.500A) Processing helix chain '2s' and resid 642 through 647 Processing helix chain '2t' and resid 426 through 443 removed outlier: 3.582A pdb=" N GLN2t 441 " --> pdb=" O MET2t 437 " (cutoff:3.500A) Processing helix chain '2t' and resid 454 through 468 removed outlier: 3.944A pdb=" N LEU2t 458 " --> pdb=" O MET2t 454 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU2t 459 " --> pdb=" O GLY2t 455 " (cutoff:3.500A) Processing helix chain '2t' and resid 475 through 491 removed outlier: 3.601A pdb=" N PHE2t 479 " --> pdb=" O SER2t 475 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE2t 480 " --> pdb=" O VAL2t 476 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS2t 482 " --> pdb=" O ASP2t 478 " (cutoff:3.500A) Processing helix chain '2t' and resid 533 through 551 Processing helix chain '2t' and resid 554 through 559 Processing helix chain '2t' and resid 569 through 572 Processing helix chain '2t' and resid 624 through 640 Processing helix chain '2t' and resid 641 through 647 Processing helix chain '2u' and resid 426 through 443 removed outlier: 3.526A pdb=" N GLN2u 441 " --> pdb=" O MET2u 437 " (cutoff:3.500A) Processing helix chain '2u' and resid 454 through 469 removed outlier: 3.594A pdb=" N LEU2u 459 " --> pdb=" O GLY2u 455 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU2u 469 " --> pdb=" O ASN2u 465 " (cutoff:3.500A) Processing helix chain '2u' and resid 475 through 491 removed outlier: 3.675A pdb=" N PHE2u 479 " --> pdb=" O SER2u 475 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE2u 480 " --> pdb=" O VAL2u 476 " (cutoff:3.500A) Processing helix chain '2u' and resid 491 through 496 removed outlier: 4.041A pdb=" N ASN2u 495 " --> pdb=" O VAL2u 491 " (cutoff:3.500A) Processing helix chain '2u' and resid 533 through 551 Processing helix chain '2u' and resid 554 through 558 Processing helix chain '2u' and resid 569 through 572 Processing helix chain '2u' and resid 624 through 641 removed outlier: 3.531A pdb=" N LYS2u 641 " --> pdb=" O LYS2u 637 " (cutoff:3.500A) Processing helix chain '2u' and resid 642 through 647 Processing helix chain '2v' and resid 426 through 443 Processing helix chain '2v' and resid 454 through 469 removed outlier: 3.695A pdb=" N LEU2v 459 " --> pdb=" O GLY2v 455 " (cutoff:3.500A) Processing helix chain '2v' and resid 475 through 491 removed outlier: 3.720A pdb=" N PHE2v 479 " --> pdb=" O SER2v 475 " (cutoff:3.500A) Processing helix chain '2v' and resid 492 through 496 Processing helix chain '2v' and resid 533 through 551 Processing helix chain '2v' and resid 554 through 559 removed outlier: 3.520A pdb=" N PHE2v 558 " --> pdb=" O PRO2v 555 " (cutoff:3.500A) Processing helix chain '2v' and resid 569 through 572 Processing helix chain '2v' and resid 624 through 641 removed outlier: 3.629A pdb=" N LYS2v 641 " --> pdb=" O LYS2v 637 " (cutoff:3.500A) Processing helix chain '2v' and resid 642 through 647 Processing helix chain '2w' and resid 426 through 443 Processing helix chain '2w' and resid 454 through 469 removed outlier: 3.647A pdb=" N LEU2w 458 " --> pdb=" O MET2w 454 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU2w 459 " --> pdb=" O GLY2w 455 " (cutoff:3.500A) Processing helix chain '2w' and resid 475 through 491 removed outlier: 3.690A pdb=" N PHE2w 479 " --> pdb=" O SER2w 475 " (cutoff:3.500A) Processing helix chain '2w' and resid 533 through 551 Processing helix chain '2w' and resid 554 through 559 removed outlier: 3.519A pdb=" N PHE2w 558 " --> pdb=" O PRO2w 555 " (cutoff:3.500A) Processing helix chain '2w' and resid 569 through 572 Processing helix chain '2w' and resid 624 through 641 removed outlier: 3.615A pdb=" N LYS2w 641 " --> pdb=" O LYS2w 637 " (cutoff:3.500A) Processing helix chain '2w' and resid 642 through 647 Processing helix chain '2x' and resid 426 through 443 removed outlier: 3.610A pdb=" N ILE2x 432 " --> pdb=" O ILE2x 428 " (cutoff:3.500A) Processing helix chain '2x' and resid 454 through 468 removed outlier: 3.550A pdb=" N LEU2x 458 " --> pdb=" O MET2x 454 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU2x 459 " --> pdb=" O GLY2x 455 " (cutoff:3.500A) Processing helix chain '2x' and resid 475 through 491 removed outlier: 3.694A pdb=" N PHE2x 479 " --> pdb=" O SER2x 475 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS2x 482 " --> pdb=" O ASP2x 478 " (cutoff:3.500A) Processing helix chain '2x' and resid 492 through 496 Processing helix chain '2x' and resid 533 through 551 Processing helix chain '2x' and resid 554 through 559 removed outlier: 3.590A pdb=" N GLN2x 559 " --> pdb=" O HIS2x 556 " (cutoff:3.500A) Processing helix chain '2x' and resid 569 through 572 Processing helix chain '2x' and resid 624 through 640 Processing helix chain '2x' and resid 641 through 647 Processing helix chain '2y' and resid 426 through 443 removed outlier: 3.516A pdb=" N LYS2y 440 " --> pdb=" O LEU2y 436 " (cutoff:3.500A) Processing helix chain '2y' and resid 454 through 469 removed outlier: 3.516A pdb=" N LEU2y 458 " --> pdb=" O MET2y 454 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU2y 459 " --> pdb=" O GLY2y 455 " (cutoff:3.500A) Processing helix chain '2y' and resid 475 through 491 removed outlier: 3.706A pdb=" N PHE2y 479 " --> pdb=" O SER2y 475 " (cutoff:3.500A) Processing helix chain '2y' and resid 491 through 496 removed outlier: 4.095A pdb=" N ASN2y 495 " --> pdb=" O VAL2y 491 " (cutoff:3.500A) Processing helix chain '2y' and resid 533 through 551 Processing helix chain '2y' and resid 554 through 559 Processing helix chain '2y' and resid 569 through 572 Processing helix chain '2y' and resid 624 through 641 removed outlier: 3.600A pdb=" N LYS2y 641 " --> pdb=" O LYS2y 637 " (cutoff:3.500A) Processing helix chain '2y' and resid 642 through 647 removed outlier: 3.949A pdb=" N MET2y 645 " --> pdb=" O PRO2y 642 " (cutoff:3.500A) Processing helix chain '2z' and resid 426 through 443 Processing helix chain '2z' and resid 454 through 468 removed outlier: 3.641A pdb=" N LEU2z 459 " --> pdb=" O GLY2z 455 " (cutoff:3.500A) Processing helix chain '2z' and resid 475 through 491 removed outlier: 3.693A pdb=" N PHE2z 479 " --> pdb=" O SER2z 475 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE2z 480 " --> pdb=" O VAL2z 476 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS2z 482 " --> pdb=" O ASP2z 478 " (cutoff:3.500A) Processing helix chain '2z' and resid 533 through 551 Processing helix chain '2z' and resid 554 through 559 Processing helix chain '2z' and resid 569 through 572 Processing helix chain '2z' and resid 624 through 641 removed outlier: 3.787A pdb=" N LYS2z 641 " --> pdb=" O LYS2z 637 " (cutoff:3.500A) Processing helix chain '2z' and resid 642 through 647 Processing helix chain '3a' and resid 426 through 443 Processing helix chain '3a' and resid 454 through 468 removed outlier: 3.547A pdb=" N LEU3a 458 " --> pdb=" O MET3a 454 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU3a 459 " --> pdb=" O GLY3a 455 " (cutoff:3.500A) Processing helix chain '3a' and resid 475 through 491 removed outlier: 3.769A pdb=" N PHE3a 479 " --> pdb=" O SER3a 475 " (cutoff:3.500A) Processing helix chain '3a' and resid 492 through 496 Processing helix chain '3a' and resid 533 through 550 Processing helix chain '3a' and resid 554 through 559 removed outlier: 3.549A pdb=" N PHE3a 558 " --> pdb=" O PRO3a 555 " (cutoff:3.500A) Processing helix chain '3a' and resid 569 through 572 Processing helix chain '3a' and resid 624 through 641 removed outlier: 3.589A pdb=" N LYS3a 641 " --> pdb=" O LYS3a 637 " (cutoff:3.500A) Processing helix chain '3a' and resid 642 through 647 Processing helix chain '3b' and resid 426 through 443 removed outlier: 3.522A pdb=" N ILE3b 432 " --> pdb=" O ILE3b 428 " (cutoff:3.500A) Processing helix chain '3b' and resid 454 through 468 removed outlier: 3.585A pdb=" N LEU3b 458 " --> pdb=" O MET3b 454 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU3b 459 " --> pdb=" O GLY3b 455 " (cutoff:3.500A) Processing helix chain '3b' and resid 475 through 491 removed outlier: 3.777A pdb=" N PHE3b 479 " --> pdb=" O SER3b 475 " (cutoff:3.500A) Processing helix chain '3b' and resid 492 through 496 Processing helix chain '3b' and resid 533 through 551 removed outlier: 3.625A pdb=" N GLU3b 550 " --> pdb=" O THR3b 546 " (cutoff:3.500A) Processing helix chain '3b' and resid 554 through 559 Processing helix chain '3b' and resid 569 through 572 Processing helix chain '3b' and resid 624 through 640 Processing helix chain '3b' and resid 641 through 647 Processing helix chain '3c' and resid 426 through 443 Processing helix chain '3c' and resid 454 through 469 removed outlier: 3.576A pdb=" N LEU3c 458 " --> pdb=" O MET3c 454 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU3c 459 " --> pdb=" O GLY3c 455 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU3c 469 " --> pdb=" O ASN3c 465 " (cutoff:3.500A) Processing helix chain '3c' and resid 475 through 491 removed outlier: 3.758A pdb=" N PHE3c 479 " --> pdb=" O SER3c 475 " (cutoff:3.500A) Processing helix chain '3c' and resid 492 through 496 Processing helix chain '3c' and resid 533 through 551 Processing helix chain '3c' and resid 554 through 559 removed outlier: 3.529A pdb=" N PHE3c 558 " --> pdb=" O PRO3c 555 " (cutoff:3.500A) Processing helix chain '3c' and resid 569 through 572 Processing helix chain '3c' and resid 624 through 641 removed outlier: 3.580A pdb=" N LYS3c 641 " --> pdb=" O LYS3c 637 " (cutoff:3.500A) Processing helix chain '3c' and resid 642 through 647 Processing sheet with id=AA1, first strand: chain '01' and resid 422 through 424 Processing sheet with id=AA2, first strand: chain '01' and resid 525 through 526 removed outlier: 7.153A pdb=" N THR01 564 " --> pdb=" O LEU01 588 " (cutoff:3.500A) removed outlier: 8.401A pdb=" N ILE01 590 " --> pdb=" O THR01 564 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N SER01 566 " --> pdb=" O ILE01 590 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N TYR01 447 " --> pdb=" O SER0z 577 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '01' and resid 497 through 499 Processing sheet with id=AA4, first strand: chain '01' and resid 575 through 577 removed outlier: 3.697A pdb=" N TYR02 447 " --> pdb=" O SER01 577 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ASP02 607 " --> pdb=" O LEU02 597 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N LEU02 597 " --> pdb=" O ASP02 607 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ALA02 609 " --> pdb=" O ASP02 595 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N ASP02 595 " --> pdb=" O ALA02 609 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N MET02 611 " --> pdb=" O SER02 593 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N SER02 593 " --> pdb=" O MET02 611 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N SER02 613 " --> pdb=" O GLY02 591 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N THR02 564 " --> pdb=" O LEU02 588 " (cutoff:3.500A) removed outlier: 8.307A pdb=" N ILE02 590 " --> pdb=" O THR02 564 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N SER02 566 " --> pdb=" O ILE02 590 " (cutoff:3.500A) removed outlier: 8.838A pdb=" N ALA02 592 " --> pdb=" O SER02 566 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N ASN02 567 " --> pdb=" O ALA02 514 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain '01' and resid 594 through 599 Processing sheet with id=AA6, first strand: chain '02' and resid 422 through 424 Processing sheet with id=AA7, first strand: chain '02' and resid 575 through 577 removed outlier: 3.531A pdb=" N TYR0z 447 " --> pdb=" O SER02 577 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N THR0z 564 " --> pdb=" O LEU0z 588 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N ILE0z 590 " --> pdb=" O THR0z 564 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N SER0z 566 " --> pdb=" O ILE0z 590 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain '02' and resid 575 through 577 removed outlier: 3.531A pdb=" N TYR0z 447 " --> pdb=" O SER02 577 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain '03' and resid 422 through 424 Processing sheet with id=AB1, first strand: chain '03' and resid 525 through 526 removed outlier: 4.682A pdb=" N ASN03 567 " --> pdb=" O ALA03 514 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N THR03 564 " --> pdb=" O LEU03 588 " (cutoff:3.500A) removed outlier: 8.343A pdb=" N ILE03 590 " --> pdb=" O THR03 564 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N SER03 566 " --> pdb=" O ILE03 590 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain '03' and resid 525 through 526 removed outlier: 4.682A pdb=" N ASN03 567 " --> pdb=" O ALA03 514 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N THR03 564 " --> pdb=" O LEU03 588 " (cutoff:3.500A) removed outlier: 8.343A pdb=" N ILE03 590 " --> pdb=" O THR03 564 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N SER03 566 " --> pdb=" O ILE03 590 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain '03' and resid 497 through 499 Processing sheet with id=AB4, first strand: chain '03' and resid 575 through 577 removed outlier: 7.038A pdb=" N THR04 564 " --> pdb=" O LEU04 588 " (cutoff:3.500A) removed outlier: 8.272A pdb=" N ILE04 590 " --> pdb=" O THR04 564 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N SER04 566 " --> pdb=" O ILE04 590 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N ASN04 567 " --> pdb=" O ALA04 514 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain '03' and resid 575 through 577 Processing sheet with id=AB6, first strand: chain '04' and resid 422 through 424 Processing sheet with id=AB7, first strand: chain '04' and resid 575 through 576 removed outlier: 7.144A pdb=" N THR05 564 " --> pdb=" O LEU05 588 " (cutoff:3.500A) removed outlier: 8.519A pdb=" N ILE05 590 " --> pdb=" O THR05 564 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N SER05 566 " --> pdb=" O ILE05 590 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N ASN05 567 " --> pdb=" O ALA05 514 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain '05' and resid 594 through 599 Processing sheet with id=AB9, first strand: chain '1a' and resid 422 through 424 Processing sheet with id=AC1, first strand: chain '1a' and resid 525 through 526 removed outlier: 4.684A pdb=" N ASN1a 567 " --> pdb=" O ALA1a 514 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N THR1a 564 " --> pdb=" O LEU1a 588 " (cutoff:3.500A) removed outlier: 8.360A pdb=" N ILE1a 590 " --> pdb=" O THR1a 564 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N SER1a 566 " --> pdb=" O ILE1a 590 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA1a 609 " --> pdb=" O ARG1a 596 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain '1a' and resid 525 through 526 removed outlier: 4.684A pdb=" N ASN1a 567 " --> pdb=" O ALA1a 514 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N THR1a 564 " --> pdb=" O LEU1a 588 " (cutoff:3.500A) removed outlier: 8.360A pdb=" N ILE1a 590 " --> pdb=" O THR1a 564 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N SER1a 566 " --> pdb=" O ILE1a 590 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain '1a' and resid 497 through 499 Processing sheet with id=AC4, first strand: chain '1a' and resid 575 through 577 removed outlier: 7.084A pdb=" N THR1b 564 " --> pdb=" O LEU1b 588 " (cutoff:3.500A) removed outlier: 8.348A pdb=" N ILE1b 590 " --> pdb=" O THR1b 564 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N SER1b 566 " --> pdb=" O ILE1b 590 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N ASN1b 567 " --> pdb=" O ALA1b 514 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain '1a' and resid 575 through 577 Processing sheet with id=AC6, first strand: chain '1b' and resid 422 through 424 Processing sheet with id=AC7, first strand: chain '1b' and resid 575 through 577 removed outlier: 3.633A pdb=" N TYR1c 447 " --> pdb=" O SER1b 577 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ASP1c 607 " --> pdb=" O LEU1c 597 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N LEU1c 597 " --> pdb=" O ASP1c 607 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ALA1c 609 " --> pdb=" O ASP1c 595 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N ASP1c 595 " --> pdb=" O ALA1c 609 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N MET1c 611 " --> pdb=" O SER1c 593 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N SER1c 593 " --> pdb=" O MET1c 611 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N SER1c 613 " --> pdb=" O GLY1c 591 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N THR1c 564 " --> pdb=" O LEU1c 588 " (cutoff:3.500A) removed outlier: 8.490A pdb=" N ILE1c 590 " --> pdb=" O THR1c 564 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N SER1c 566 " --> pdb=" O ILE1c 590 " (cutoff:3.500A) removed outlier: 9.050A pdb=" N ALA1c 592 " --> pdb=" O SER1c 566 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N ASN1c 567 " --> pdb=" O ALA1c 514 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain '1d' and resid 422 through 424 Processing sheet with id=AC9, first strand: chain '1d' and resid 525 through 526 removed outlier: 4.667A pdb=" N ASN1d 567 " --> pdb=" O ALA1d 514 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N THR1d 564 " --> pdb=" O LEU1d 588 " (cutoff:3.500A) removed outlier: 8.468A pdb=" N ILE1d 590 " --> pdb=" O THR1d 564 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N SER1d 566 " --> pdb=" O ILE1d 590 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain '1d' and resid 525 through 526 removed outlier: 4.667A pdb=" N ASN1d 567 " --> pdb=" O ALA1d 514 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N THR1d 564 " --> pdb=" O LEU1d 588 " (cutoff:3.500A) removed outlier: 8.468A pdb=" N ILE1d 590 " --> pdb=" O THR1d 564 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N SER1d 566 " --> pdb=" O ILE1d 590 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain '1d' and resid 497 through 499 Processing sheet with id=AD3, first strand: chain '1d' and resid 575 through 576 removed outlier: 7.084A pdb=" N THR1e 564 " --> pdb=" O LEU1e 588 " (cutoff:3.500A) removed outlier: 8.466A pdb=" N ILE1e 590 " --> pdb=" O THR1e 564 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N SER1e 566 " --> pdb=" O ILE1e 590 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N ASN1e 567 " --> pdb=" O ALA1e 514 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain '1d' and resid 575 through 576 Processing sheet with id=AD5, first strand: chain '1e' and resid 422 through 424 Processing sheet with id=AD6, first strand: chain '1e' and resid 575 through 576 removed outlier: 7.089A pdb=" N THR1f 564 " --> pdb=" O LEU1f 588 " (cutoff:3.500A) removed outlier: 8.486A pdb=" N ILE1f 590 " --> pdb=" O THR1f 564 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N SER1f 566 " --> pdb=" O ILE1f 590 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N ASN1f 567 " --> pdb=" O ALA1f 514 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain '1e' and resid 575 through 576 Processing sheet with id=AD8, first strand: chain '1g' and resid 422 through 424 Processing sheet with id=AD9, first strand: chain '1g' and resid 525 through 526 removed outlier: 6.338A pdb=" N SER1g 512 " --> pdb=" O ILE1g 565 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N ASN1g 567 " --> pdb=" O SER1g 512 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N ALA1g 514 " --> pdb=" O ASN1g 567 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N THR1g 564 " --> pdb=" O LEU1g 588 " (cutoff:3.500A) removed outlier: 8.341A pdb=" N ILE1g 590 " --> pdb=" O THR1g 564 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N SER1g 566 " --> pdb=" O ILE1g 590 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain '1g' and resid 525 through 526 removed outlier: 6.338A pdb=" N SER1g 512 " --> pdb=" O ILE1g 565 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N ASN1g 567 " --> pdb=" O SER1g 512 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N ALA1g 514 " --> pdb=" O ASN1g 567 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N THR1g 564 " --> pdb=" O LEU1g 588 " (cutoff:3.500A) removed outlier: 8.341A pdb=" N ILE1g 590 " --> pdb=" O THR1g 564 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N SER1g 566 " --> pdb=" O ILE1g 590 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain '1g' and resid 497 through 498 removed outlier: 3.568A pdb=" N THR1i 421 " --> pdb=" O GLN1g 505 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain '1g' and resid 575 through 576 removed outlier: 4.225A pdb=" N THR1h 564 " --> pdb=" O CYS1h 586 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N SER1h 512 " --> pdb=" O ILE1h 565 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N ASN1h 567 " --> pdb=" O SER1h 512 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain '1g' and resid 575 through 576 Processing sheet with id=AE5, first strand: chain '1h' and resid 422 through 424 Processing sheet with id=AE6, first strand: chain '1h' and resid 575 through 576 removed outlier: 7.043A pdb=" N THR1i 564 " --> pdb=" O LEU1i 588 " (cutoff:3.500A) removed outlier: 8.339A pdb=" N ILE1i 590 " --> pdb=" O THR1i 564 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N SER1i 566 " --> pdb=" O ILE1i 590 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N ASN1i 567 " --> pdb=" O ALA1i 514 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain '1h' and resid 575 through 576 Processing sheet with id=AE8, first strand: chain '1j' and resid 422 through 424 Processing sheet with id=AE9, first strand: chain '1j' and resid 525 through 526 removed outlier: 4.740A pdb=" N ASN1j 567 " --> pdb=" O ALA1j 514 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N THR1j 564 " --> pdb=" O LEU1j 588 " (cutoff:3.500A) removed outlier: 8.337A pdb=" N ILE1j 590 " --> pdb=" O THR1j 564 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N SER1j 566 " --> pdb=" O ILE1j 590 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain '1j' and resid 525 through 526 removed outlier: 4.740A pdb=" N ASN1j 567 " --> pdb=" O ALA1j 514 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N THR1j 564 " --> pdb=" O LEU1j 588 " (cutoff:3.500A) removed outlier: 8.337A pdb=" N ILE1j 590 " --> pdb=" O THR1j 564 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N SER1j 566 " --> pdb=" O ILE1j 590 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain '1j' and resid 497 through 499 Processing sheet with id=AF3, first strand: chain '1j' and resid 575 through 576 removed outlier: 6.735A pdb=" N ASP1k 607 " --> pdb=" O LEU1k 597 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N LEU1k 597 " --> pdb=" O ASP1k 607 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ALA1k 609 " --> pdb=" O ASP1k 595 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N ASP1k 595 " --> pdb=" O ALA1k 609 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N MET1k 611 " --> pdb=" O SER1k 593 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N SER1k 593 " --> pdb=" O MET1k 611 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N SER1k 613 " --> pdb=" O GLY1k 591 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N THR1k 564 " --> pdb=" O CYS1k 586 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ASN1k 567 " --> pdb=" O ALA1k 514 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain '1k' and resid 422 through 424 Processing sheet with id=AF5, first strand: chain '1k' and resid 575 through 576 removed outlier: 7.013A pdb=" N THR1l 564 " --> pdb=" O LEU1l 588 " (cutoff:3.500A) removed outlier: 8.291A pdb=" N ILE1l 590 " --> pdb=" O THR1l 564 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N SER1l 566 " --> pdb=" O ILE1l 590 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N ASN1l 567 " --> pdb=" O ALA1l 514 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain '1k' and resid 575 through 576 Processing sheet with id=AF7, first strand: chain '1m' and resid 422 through 424 Processing sheet with id=AF8, first strand: chain '1m' and resid 525 through 526 removed outlier: 4.704A pdb=" N ASN1m 567 " --> pdb=" O ALA1m 514 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N THR1m 564 " --> pdb=" O LEU1m 588 " (cutoff:3.500A) removed outlier: 8.338A pdb=" N ILE1m 590 " --> pdb=" O THR1m 564 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N SER1m 566 " --> pdb=" O ILE1m 590 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain '1m' and resid 525 through 526 removed outlier: 4.704A pdb=" N ASN1m 567 " --> pdb=" O ALA1m 514 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N THR1m 564 " --> pdb=" O LEU1m 588 " (cutoff:3.500A) removed outlier: 8.338A pdb=" N ILE1m 590 " --> pdb=" O THR1m 564 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N SER1m 566 " --> pdb=" O ILE1m 590 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TYR1m 446 " --> pdb=" O CYS1m 618 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain '1m' and resid 502 through 504 Processing sheet with id=AG2, first strand: chain '1m' and resid 575 through 576 removed outlier: 4.163A pdb=" N THR1n 564 " --> pdb=" O CYS1n 586 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N ASN1n 567 " --> pdb=" O ALA1n 514 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain '1m' and resid 575 through 576 Processing sheet with id=AG4, first strand: chain '1n' and resid 422 through 424 Processing sheet with id=AG5, first strand: chain '1n' and resid 575 through 576 removed outlier: 7.091A pdb=" N THR2s 564 " --> pdb=" O LEU2s 588 " (cutoff:3.500A) removed outlier: 8.374A pdb=" N ILE2s 590 " --> pdb=" O THR2s 564 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N SER2s 566 " --> pdb=" O ILE2s 590 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N ASN2s 567 " --> pdb=" O ALA2s 514 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain '1n' and resid 575 through 576 Processing sheet with id=AG7, first strand: chain '1o' and resid 422 through 424 Processing sheet with id=AG8, first strand: chain '1o' and resid 525 through 526 removed outlier: 4.746A pdb=" N ASN1o 567 " --> pdb=" O ALA1o 514 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N THR1o 564 " --> pdb=" O LEU1o 588 " (cutoff:3.500A) removed outlier: 8.341A pdb=" N ILE1o 590 " --> pdb=" O THR1o 564 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N SER1o 566 " --> pdb=" O ILE1o 590 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain '1o' and resid 525 through 526 removed outlier: 4.746A pdb=" N ASN1o 567 " --> pdb=" O ALA1o 514 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N THR1o 564 " --> pdb=" O LEU1o 588 " (cutoff:3.500A) removed outlier: 8.341A pdb=" N ILE1o 590 " --> pdb=" O THR1o 564 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N SER1o 566 " --> pdb=" O ILE1o 590 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N TYR1o 447 " --> pdb=" O SER2u 577 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain '1o' and resid 497 through 498 Processing sheet with id=AH2, first strand: chain '1o' and resid 575 through 576 removed outlier: 6.807A pdb=" N ASP2t 607 " --> pdb=" O LEU2t 597 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N LEU2t 597 " --> pdb=" O ASP2t 607 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ALA2t 609 " --> pdb=" O ASP2t 595 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N ASP2t 595 " --> pdb=" O ALA2t 609 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N MET2t 611 " --> pdb=" O SER2t 593 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N SER2t 593 " --> pdb=" O MET2t 611 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N SER2t 613 " --> pdb=" O GLY2t 591 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N THR2t 564 " --> pdb=" O LEU2t 588 " (cutoff:3.500A) removed outlier: 8.535A pdb=" N ILE2t 590 " --> pdb=" O THR2t 564 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N SER2t 566 " --> pdb=" O ILE2t 590 " (cutoff:3.500A) removed outlier: 9.081A pdb=" N ALA2t 592 " --> pdb=" O SER2t 566 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N ASN2t 567 " --> pdb=" O ALA2t 514 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain '1p' and resid 422 through 424 Processing sheet with id=AH4, first strand: chain '1p' and resid 525 through 526 removed outlier: 4.705A pdb=" N ASN1p 567 " --> pdb=" O ALA1p 514 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N THR1p 564 " --> pdb=" O CYS1p 586 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N SER1p 613 " --> pdb=" O GLY1p 591 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N SER1p 593 " --> pdb=" O MET1p 611 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N MET1p 611 " --> pdb=" O SER1p 593 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N ASP1p 595 " --> pdb=" O ALA1p 609 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ALA1p 609 " --> pdb=" O ASP1p 595 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N LEU1p 597 " --> pdb=" O ASP1p 607 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ASP1p 607 " --> pdb=" O LEU1p 597 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain '1p' and resid 497 through 499 Processing sheet with id=AH6, first strand: chain '1p' and resid 575 through 576 removed outlier: 4.124A pdb=" N THR1q 564 " --> pdb=" O CYS1q 586 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE1q 590 " --> pdb=" O SER1q 566 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain '1p' and resid 575 through 576 Processing sheet with id=AH8, first strand: chain '1q' and resid 422 through 424 Processing sheet with id=AH9, first strand: chain '1q' and resid 575 through 577 removed outlier: 7.114A pdb=" N THR1r 564 " --> pdb=" O LEU1r 588 " (cutoff:3.500A) removed outlier: 8.340A pdb=" N ILE1r 590 " --> pdb=" O THR1r 564 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N SER1r 566 " --> pdb=" O ILE1r 590 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N ASN1r 567 " --> pdb=" O ALA1r 514 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain '1q' and resid 575 through 577 Processing sheet with id=AI2, first strand: chain '1s' and resid 422 through 424 Processing sheet with id=AI3, first strand: chain '1s' and resid 525 through 526 removed outlier: 4.744A pdb=" N ASN1s 567 " --> pdb=" O ALA1s 514 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N THR1s 564 " --> pdb=" O LEU1s 588 " (cutoff:3.500A) removed outlier: 8.478A pdb=" N ILE1s 590 " --> pdb=" O THR1s 564 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N SER1s 566 " --> pdb=" O ILE1s 590 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N TYR1s 447 " --> pdb=" O SER1u 577 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain '1s' and resid 497 through 499 Processing sheet with id=AI5, first strand: chain '1s' and resid 575 through 576 removed outlier: 7.088A pdb=" N THR1t 564 " --> pdb=" O LEU1t 588 " (cutoff:3.500A) removed outlier: 8.494A pdb=" N ILE1t 590 " --> pdb=" O THR1t 564 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N SER1t 566 " --> pdb=" O ILE1t 590 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N ASN1t 567 " --> pdb=" O ALA1t 514 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain '1s' and resid 596 through 599 Processing sheet with id=AI7, first strand: chain '1t' and resid 422 through 424 Processing sheet with id=AI8, first strand: chain '1t' and resid 575 through 577 removed outlier: 3.560A pdb=" N TYR1u 447 " --> pdb=" O SER1t 577 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N THR1u 564 " --> pdb=" O LEU1u 588 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N ILE1u 590 " --> pdb=" O THR1u 564 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N SER1u 566 " --> pdb=" O ILE1u 590 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N ASN1u 567 " --> pdb=" O ALA1u 514 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain '1t' and resid 575 through 577 removed outlier: 3.560A pdb=" N TYR1u 447 " --> pdb=" O SER1t 577 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain '1t' and resid 596 through 599 Processing sheet with id=AJ2, first strand: chain '1v' and resid 422 through 424 Processing sheet with id=AJ3, first strand: chain '1v' and resid 525 through 526 removed outlier: 4.714A pdb=" N ASN1v 567 " --> pdb=" O ALA1v 514 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N THR1v 564 " --> pdb=" O LEU1v 588 " (cutoff:3.500A) removed outlier: 8.498A pdb=" N ILE1v 590 " --> pdb=" O THR1v 564 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N SER1v 566 " --> pdb=" O ILE1v 590 " (cutoff:3.500A) removed outlier: 8.991A pdb=" N ALA1v 592 " --> pdb=" O SER1v 566 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N SER1v 613 " --> pdb=" O GLY1v 591 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N SER1v 593 " --> pdb=" O MET1v 611 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N MET1v 611 " --> pdb=" O SER1v 593 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N ASP1v 595 " --> pdb=" O ALA1v 609 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ALA1v 609 " --> pdb=" O ASP1v 595 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N LEU1v 597 " --> pdb=" O ASP1v 607 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ASP1v 607 " --> pdb=" O LEU1v 597 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N TYR1v 447 " --> pdb=" O SER2y 577 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain '1v' and resid 497 through 499 Processing sheet with id=AJ5, first strand: chain '1v' and resid 575 through 576 removed outlier: 7.090A pdb=" N THR1w 564 " --> pdb=" O LEU1w 588 " (cutoff:3.500A) removed outlier: 8.405A pdb=" N ILE1w 590 " --> pdb=" O THR1w 564 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N SER1w 566 " --> pdb=" O ILE1w 590 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ASN1w 567 " --> pdb=" O ALA1w 514 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain '1v' and resid 575 through 576 Processing sheet with id=AJ7, first strand: chain '1w' and resid 422 through 424 Processing sheet with id=AJ8, first strand: chain '1w' and resid 575 through 577 removed outlier: 6.236A pdb=" N MET2y 611 " --> pdb=" O SER2y 593 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N SER2y 593 " --> pdb=" O MET2y 611 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N SER2y 613 " --> pdb=" O GLY2y 591 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N THR2y 564 " --> pdb=" O LEU2y 588 " (cutoff:3.500A) removed outlier: 8.402A pdb=" N ILE2y 590 " --> pdb=" O THR2y 564 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N SER2y 566 " --> pdb=" O ILE2y 590 " (cutoff:3.500A) removed outlier: 8.981A pdb=" N ALA2y 592 " --> pdb=" O SER2y 566 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N ASN2y 567 " --> pdb=" O ALA2y 514 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain '1x' and resid 422 through 424 Processing sheet with id=AK1, first strand: chain '1x' and resid 525 through 526 removed outlier: 4.676A pdb=" N ASN1x 567 " --> pdb=" O ALA1x 514 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N THR1x 564 " --> pdb=" O CYS1x 586 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain '1x' and resid 497 through 499 Processing sheet with id=AK3, first strand: chain '1x' and resid 575 through 576 removed outlier: 7.012A pdb=" N THR1z 564 " --> pdb=" O LEU1z 588 " (cutoff:3.500A) removed outlier: 8.356A pdb=" N ILE1z 590 " --> pdb=" O THR1z 564 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N SER1z 566 " --> pdb=" O ILE1z 590 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N ASN1z 567 " --> pdb=" O ALA1z 514 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain '1x' and resid 575 through 576 Processing sheet with id=AK5, first strand: chain '1x' and resid 594 through 599 Processing sheet with id=AK6, first strand: chain '1z' and resid 421 through 424 Processing sheet with id=AK7, first strand: chain '1z' and resid 575 through 577 removed outlier: 3.613A pdb=" N TYR2a 447 " --> pdb=" O SER1z 577 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N THR2a 564 " --> pdb=" O LEU2a 588 " (cutoff:3.500A) removed outlier: 8.363A pdb=" N ILE2a 590 " --> pdb=" O THR2a 564 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N SER2a 566 " --> pdb=" O ILE2a 590 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N ASN2a 567 " --> pdb=" O ALA2a 514 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain '1z' and resid 575 through 577 removed outlier: 3.613A pdb=" N TYR2a 447 " --> pdb=" O SER1z 577 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain '2b' and resid 422 through 424 Processing sheet with id=AL1, first strand: chain '2b' and resid 525 through 526 removed outlier: 4.694A pdb=" N ASN2b 567 " --> pdb=" O ALA2b 514 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N THR2b 564 " --> pdb=" O LEU2b 588 " (cutoff:3.500A) removed outlier: 8.450A pdb=" N ILE2b 590 " --> pdb=" O THR2b 564 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N SER2b 566 " --> pdb=" O ILE2b 590 " (cutoff:3.500A) Processing sheet with id=AL2, first strand: chain '2b' and resid 497 through 499 Processing sheet with id=AL3, first strand: chain '2b' and resid 575 through 576 removed outlier: 7.015A pdb=" N THR2c 564 " --> pdb=" O LEU2c 588 " (cutoff:3.500A) removed outlier: 8.410A pdb=" N ILE2c 590 " --> pdb=" O THR2c 564 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N SER2c 566 " --> pdb=" O ILE2c 590 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N ASN2c 567 " --> pdb=" O ALA2c 514 " (cutoff:3.500A) Processing sheet with id=AL4, first strand: chain '2b' and resid 575 through 576 Processing sheet with id=AL5, first strand: chain '2b' and resid 594 through 599 Processing sheet with id=AL6, first strand: chain '2c' and resid 422 through 424 Processing sheet with id=AL7, first strand: chain '2c' and resid 575 through 576 removed outlier: 7.024A pdb=" N THR2d 564 " --> pdb=" O LEU2d 588 " (cutoff:3.500A) removed outlier: 8.426A pdb=" N ILE2d 590 " --> pdb=" O THR2d 564 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N SER2d 566 " --> pdb=" O ILE2d 590 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N SER2d 512 " --> pdb=" O ILE2d 565 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N ASN2d 567 " --> pdb=" O SER2d 512 " (cutoff:3.500A) Processing sheet with id=AL8, first strand: chain '2d' and resid 594 through 599 Processing sheet with id=AL9, first strand: chain '2e' and resid 422 through 424 Processing sheet with id=AM1, first strand: chain '2e' and resid 525 through 526 removed outlier: 4.733A pdb=" N ASN2e 567 " --> pdb=" O ALA2e 514 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N THR2e 564 " --> pdb=" O LEU2e 588 " (cutoff:3.500A) removed outlier: 8.361A pdb=" N ILE2e 590 " --> pdb=" O THR2e 564 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N SER2e 566 " --> pdb=" O ILE2e 590 " (cutoff:3.500A) Processing sheet with id=AM2, first strand: chain '2e' and resid 497 through 499 removed outlier: 3.566A pdb=" N VAL2e 502 " --> pdb=" O MET2e 499 " (cutoff:3.500A) Processing sheet with id=AM3, first strand: chain '2e' and resid 575 through 576 removed outlier: 6.798A pdb=" N ASP2f 607 " --> pdb=" O LEU2f 597 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N LEU2f 597 " --> pdb=" O ASP2f 607 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ALA2f 609 " --> pdb=" O ASP2f 595 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N ASP2f 595 " --> pdb=" O ALA2f 609 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N MET2f 611 " --> pdb=" O SER2f 593 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N SER2f 593 " --> pdb=" O MET2f 611 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N SER2f 613 " --> pdb=" O GLY2f 591 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N THR2f 564 " --> pdb=" O LEU2f 588 " (cutoff:3.500A) removed outlier: 8.552A pdb=" N ILE2f 590 " --> pdb=" O THR2f 564 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N SER2f 566 " --> pdb=" O ILE2f 590 " (cutoff:3.500A) removed outlier: 9.083A pdb=" N ALA2f 592 " --> pdb=" O SER2f 566 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N ASN2f 567 " --> pdb=" O ALA2f 514 " (cutoff:3.500A) Processing sheet with id=AM4, first strand: chain '2e' and resid 596 through 599 Processing sheet with id=AM5, first strand: chain '2f' and resid 422 through 424 Processing sheet with id=AM6, first strand: chain '2f' and resid 575 through 576 removed outlier: 7.038A pdb=" N THR2g 564 " --> pdb=" O LEU2g 588 " (cutoff:3.500A) removed outlier: 8.335A pdb=" N ILE2g 590 " --> pdb=" O THR2g 564 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N SER2g 566 " --> pdb=" O ILE2g 590 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ASN2g 567 " --> pdb=" O ALA2g 514 " (cutoff:3.500A) Processing sheet with id=AM7, first strand: chain '2f' and resid 575 through 576 Processing sheet with id=AM8, first strand: chain '2h' and resid 422 through 424 Processing sheet with id=AM9, first strand: chain '2h' and resid 525 through 526 removed outlier: 4.717A pdb=" N ASN2h 567 " --> pdb=" O ALA2h 514 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N THR2h 564 " --> pdb=" O LEU2h 588 " (cutoff:3.500A) removed outlier: 8.354A pdb=" N ILE2h 590 " --> pdb=" O THR2h 564 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N SER2h 566 " --> pdb=" O ILE2h 590 " (cutoff:3.500A) Processing sheet with id=AN1, first strand: chain '2h' and resid 497 through 499 Processing sheet with id=AN2, first strand: chain '2h' and resid 575 through 576 removed outlier: 7.091A pdb=" N THR2i 564 " --> pdb=" O LEU2i 588 " (cutoff:3.500A) removed outlier: 8.309A pdb=" N ILE2i 590 " --> pdb=" O THR2i 564 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N SER2i 566 " --> pdb=" O ILE2i 590 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ASP2i 510 " --> pdb=" O PHE2i 563 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N ILE2i 565 " --> pdb=" O ASP2i 510 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N SER2i 512 " --> pdb=" O ILE2i 565 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N ASN2i 567 " --> pdb=" O SER2i 512 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N ALA2i 514 " --> pdb=" O ASN2i 567 " (cutoff:3.500A) Processing sheet with id=AN3, first strand: chain '2h' and resid 575 through 576 Processing sheet with id=AN4, first strand: chain '2h' and resid 594 through 599 Processing sheet with id=AN5, first strand: chain '2i' and resid 422 through 424 Processing sheet with id=AN6, first strand: chain '2i' and resid 575 through 577 removed outlier: 3.541A pdb=" N TYR2j 447 " --> pdb=" O SER2i 577 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N THR2j 564 " --> pdb=" O LEU2j 588 " (cutoff:3.500A) removed outlier: 8.317A pdb=" N ILE2j 590 " --> pdb=" O THR2j 564 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N SER2j 566 " --> pdb=" O ILE2j 590 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N ASN2j 567 " --> pdb=" O ALA2j 514 " (cutoff:3.500A) Processing sheet with id=AN7, first strand: chain '2i' and resid 575 through 577 removed outlier: 3.541A pdb=" N TYR2j 447 " --> pdb=" O SER2i 577 " (cutoff:3.500A) Processing sheet with id=AN8, first strand: chain '2k' and resid 422 through 424 Processing sheet with id=AN9, first strand: chain '2k' and resid 525 through 526 removed outlier: 6.547A pdb=" N SER2k 512 " --> pdb=" O ILE2k 565 " (cutoff:3.500A) removed outlier: 8.122A pdb=" N ASN2k 567 " --> pdb=" O SER2k 512 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N THR2k 564 " --> pdb=" O CYS2k 586 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N SER2k 613 " --> pdb=" O GLY2k 591 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N SER2k 593 " --> pdb=" O MET2k 611 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N MET2k 611 " --> pdb=" O SER2k 593 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N ASP2k 595 " --> pdb=" O ALA2k 609 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ALA2k 609 " --> pdb=" O ASP2k 595 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N LEU2k 597 " --> pdb=" O ASP2k 607 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ASP2k 607 " --> pdb=" O LEU2k 597 " (cutoff:3.500A) Processing sheet with id=AO1, first strand: chain '2k' and resid 497 through 499 Processing sheet with id=AO2, first strand: chain '2k' and resid 575 through 576 removed outlier: 7.007A pdb=" N THR2l 564 " --> pdb=" O LEU2l 588 " (cutoff:3.500A) removed outlier: 8.341A pdb=" N ILE2l 590 " --> pdb=" O THR2l 564 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N SER2l 566 " --> pdb=" O ILE2l 590 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N ASN2l 567 " --> pdb=" O ALA2l 514 " (cutoff:3.500A) Processing sheet with id=AO3, first strand: chain '2k' and resid 575 through 576 Processing sheet with id=AO4, first strand: chain '2l' and resid 422 through 424 Processing sheet with id=AO5, first strand: chain '2l' and resid 575 through 577 removed outlier: 3.567A pdb=" N TYR2m 447 " --> pdb=" O SER2l 577 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N THR2m 564 " --> pdb=" O LEU2m 588 " (cutoff:3.500A) removed outlier: 8.347A pdb=" N ILE2m 590 " --> pdb=" O THR2m 564 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N SER2m 566 " --> pdb=" O ILE2m 590 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N ASN2m 567 " --> pdb=" O ALA2m 514 " (cutoff:3.500A) Processing sheet with id=AO6, first strand: chain '2m' and resid 596 through 599 Processing sheet with id=AO7, first strand: chain '2n' and resid 422 through 424 Processing sheet with id=AO8, first strand: chain '2n' and resid 525 through 526 removed outlier: 4.725A pdb=" N ASN2n 567 " --> pdb=" O ALA2n 514 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N THR2n 564 " --> pdb=" O LEU2n 588 " (cutoff:3.500A) removed outlier: 8.358A pdb=" N ILE2n 590 " --> pdb=" O THR2n 564 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N SER2n 566 " --> pdb=" O ILE2n 590 " (cutoff:3.500A) Processing sheet with id=AO9, first strand: chain '2n' and resid 525 through 526 removed outlier: 4.725A pdb=" N ASN2n 567 " --> pdb=" O ALA2n 514 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N THR2n 564 " --> pdb=" O LEU2n 588 " (cutoff:3.500A) removed outlier: 8.358A pdb=" N ILE2n 590 " --> pdb=" O THR2n 564 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N SER2n 566 " --> pdb=" O ILE2n 590 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N TYR2n 447 " --> pdb=" O SER2p 577 " (cutoff:3.500A) Processing sheet with id=AP1, first strand: chain '2n' and resid 497 through 498 Processing sheet with id=AP2, first strand: chain '2n' and resid 575 through 576 removed outlier: 4.212A pdb=" N THR2o 564 " --> pdb=" O CYS2o 586 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ASN2o 567 " --> pdb=" O ALA2o 514 " (cutoff:3.500A) Processing sheet with id=AP3, first strand: chain '2n' and resid 575 through 576 Processing sheet with id=AP4, first strand: chain '2o' and resid 422 through 424 Processing sheet with id=AP5, first strand: chain '2o' and resid 575 through 577 removed outlier: 3.536A pdb=" N TYR2p 447 " --> pdb=" O SER2o 577 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N THR2p 564 " --> pdb=" O LEU2p 588 " (cutoff:3.500A) removed outlier: 8.342A pdb=" N ILE2p 590 " --> pdb=" O THR2p 564 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N SER2p 566 " --> pdb=" O ILE2p 590 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N ASN2p 567 " --> pdb=" O ALA2p 514 " (cutoff:3.500A) Processing sheet with id=AP6, first strand: chain '2o' and resid 575 through 577 removed outlier: 3.536A pdb=" N TYR2p 447 " --> pdb=" O SER2o 577 " (cutoff:3.500A) Processing sheet with id=AP7, first strand: chain '2q' and resid 422 through 424 Processing sheet with id=AP8, first strand: chain '2q' and resid 525 through 526 removed outlier: 4.719A pdb=" N ASN2q 567 " --> pdb=" O ALA2q 514 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N THR2q 564 " --> pdb=" O LEU2q 588 " (cutoff:3.500A) removed outlier: 8.397A pdb=" N ILE2q 590 " --> pdb=" O THR2q 564 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N SER2q 566 " --> pdb=" O ILE2q 590 " (cutoff:3.500A) Processing sheet with id=AP9, first strand: chain '2q' and resid 525 through 526 removed outlier: 4.719A pdb=" N ASN2q 567 " --> pdb=" O ALA2q 514 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N THR2q 564 " --> pdb=" O LEU2q 588 " (cutoff:3.500A) removed outlier: 8.397A pdb=" N ILE2q 590 " --> pdb=" O THR2q 564 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N SER2q 566 " --> pdb=" O ILE2q 590 " (cutoff:3.500A) Processing sheet with id=AQ1, first strand: chain '2q' and resid 497 through 499 Processing sheet with id=AQ2, first strand: chain '2q' and resid 575 through 576 removed outlier: 7.080A pdb=" N THR2z 564 " --> pdb=" O LEU2z 588 " (cutoff:3.500A) removed outlier: 8.460A pdb=" N ILE2z 590 " --> pdb=" O THR2z 564 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N SER2z 566 " --> pdb=" O ILE2z 590 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N ASN2z 567 " --> pdb=" O ALA2z 514 " (cutoff:3.500A) Processing sheet with id=AQ3, first strand: chain '2q' and resid 575 through 576 Processing sheet with id=AQ4, first strand: chain '2r' and resid 525 through 526 removed outlier: 4.714A pdb=" N ASN2r 567 " --> pdb=" O ALA2r 514 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N THR2r 564 " --> pdb=" O LEU2r 588 " (cutoff:3.500A) removed outlier: 8.430A pdb=" N ILE2r 590 " --> pdb=" O THR2r 564 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N SER2r 566 " --> pdb=" O ILE2r 590 " (cutoff:3.500A) Processing sheet with id=AQ5, first strand: chain '2r' and resid 525 through 526 removed outlier: 4.714A pdb=" N ASN2r 567 " --> pdb=" O ALA2r 514 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N THR2r 564 " --> pdb=" O LEU2r 588 " (cutoff:3.500A) removed outlier: 8.430A pdb=" N ILE2r 590 " --> pdb=" O THR2r 564 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N SER2r 566 " --> pdb=" O ILE2r 590 " (cutoff:3.500A) Processing sheet with id=AQ6, first strand: chain '2r' and resid 497 through 499 Processing sheet with id=AQ7, first strand: chain '2t' and resid 422 through 424 Processing sheet with id=AQ8, first strand: chain '2t' and resid 575 through 576 removed outlier: 7.071A pdb=" N THR2u 564 " --> pdb=" O LEU2u 588 " (cutoff:3.500A) removed outlier: 8.375A pdb=" N ILE2u 590 " --> pdb=" O THR2u 564 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N SER2u 566 " --> pdb=" O ILE2u 590 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ASN2u 567 " --> pdb=" O ALA2u 514 " (cutoff:3.500A) Processing sheet with id=AQ9, first strand: chain '2t' and resid 575 through 576 Processing sheet with id=AR1, first strand: chain '2v' and resid 422 through 424 Processing sheet with id=AR2, first strand: chain '2v' and resid 525 through 526 removed outlier: 7.097A pdb=" N THR2v 564 " --> pdb=" O LEU2v 588 " (cutoff:3.500A) removed outlier: 8.333A pdb=" N ILE2v 590 " --> pdb=" O THR2v 564 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N SER2v 566 " --> pdb=" O ILE2v 590 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N TYR2v 447 " --> pdb=" O SER2x 577 " (cutoff:3.500A) Processing sheet with id=AR3, first strand: chain '2v' and resid 497 through 499 Processing sheet with id=AR4, first strand: chain '2v' and resid 575 through 577 removed outlier: 3.680A pdb=" N TYR2w 447 " --> pdb=" O SER2v 577 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ASP2w 607 " --> pdb=" O LEU2w 597 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N LEU2w 597 " --> pdb=" O ASP2w 607 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ALA2w 609 " --> pdb=" O ASP2w 595 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N ASP2w 595 " --> pdb=" O ALA2w 609 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N MET2w 611 " --> pdb=" O SER2w 593 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N SER2w 593 " --> pdb=" O MET2w 611 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N SER2w 613 " --> pdb=" O GLY2w 591 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N THR2w 564 " --> pdb=" O LEU2w 588 " (cutoff:3.500A) removed outlier: 8.436A pdb=" N ILE2w 590 " --> pdb=" O THR2w 564 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N SER2w 566 " --> pdb=" O ILE2w 590 " (cutoff:3.500A) removed outlier: 8.980A pdb=" N ALA2w 592 " --> pdb=" O SER2w 566 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N SER2w 512 " --> pdb=" O ILE2w 565 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N ASN2w 567 " --> pdb=" O SER2w 512 " (cutoff:3.500A) Processing sheet with id=AR5, first strand: chain '2v' and resid 594 through 599 Processing sheet with id=AR6, first strand: chain '2w' and resid 422 through 424 Processing sheet with id=AR7, first strand: chain '2w' and resid 575 through 577 removed outlier: 3.525A pdb=" N TYR2x 447 " --> pdb=" O SER2w 577 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ASP2x 607 " --> pdb=" O LEU2x 597 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N LEU2x 597 " --> pdb=" O ASP2x 607 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ALA2x 609 " --> pdb=" O ASP2x 595 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N ASP2x 595 " --> pdb=" O ALA2x 609 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N MET2x 611 " --> pdb=" O SER2x 593 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N SER2x 593 " --> pdb=" O MET2x 611 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N SER2x 613 " --> pdb=" O GLY2x 591 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N THR2x 564 " --> pdb=" O LEU2x 588 " (cutoff:3.500A) removed outlier: 8.427A pdb=" N ILE2x 590 " --> pdb=" O THR2x 564 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N SER2x 566 " --> pdb=" O ILE2x 590 " (cutoff:3.500A) removed outlier: 8.982A pdb=" N ALA2x 592 " --> pdb=" O SER2x 566 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N SER2x 512 " --> pdb=" O ILE2x 565 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N ASN2x 567 " --> pdb=" O SER2x 512 " (cutoff:3.500A) Processing sheet with id=AR8, first strand: chain '2y' and resid 596 through 599 Processing sheet with id=AR9, first strand: chain '3a' and resid 422 through 424 Processing sheet with id=AS1, first strand: chain '3a' and resid 525 through 526 removed outlier: 6.368A pdb=" N SER3a 512 " --> pdb=" O ILE3a 565 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N ASN3a 567 " --> pdb=" O SER3a 512 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N THR3a 564 " --> pdb=" O LEU3a 588 " (cutoff:3.500A) removed outlier: 8.384A pdb=" N ILE3a 590 " --> pdb=" O THR3a 564 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N SER3a 566 " --> pdb=" O ILE3a 590 " (cutoff:3.500A) removed outlier: 8.876A pdb=" N ALA3a 592 " --> pdb=" O SER3a 566 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N SER3a 613 " --> pdb=" O GLY3a 591 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N SER3a 593 " --> pdb=" O MET3a 611 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N MET3a 611 " --> pdb=" O SER3a 593 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N TYR3a 447 " --> pdb=" O SER3c 577 " (cutoff:3.500A) Processing sheet with id=AS2, first strand: chain '3a' and resid 497 through 499 Processing sheet with id=AS3, first strand: chain '3a' and resid 575 through 577 removed outlier: 3.572A pdb=" N TYR3b 447 " --> pdb=" O SER3a 577 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N THR3b 564 " --> pdb=" O LEU3b 588 " (cutoff:3.500A) removed outlier: 8.325A pdb=" N ILE3b 590 " --> pdb=" O THR3b 564 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N SER3b 566 " --> pdb=" O ILE3b 590 " (cutoff:3.500A) Processing sheet with id=AS4, first strand: chain '3a' and resid 596 through 599 Processing sheet with id=AS5, first strand: chain '3b' and resid 422 through 424 Processing sheet with id=AS6, first strand: chain '3b' and resid 575 through 577 removed outlier: 3.568A pdb=" N TYR3c 447 " --> pdb=" O SER3b 577 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N THR3c 564 " --> pdb=" O LEU3c 588 " (cutoff:3.500A) removed outlier: 8.362A pdb=" N ILE3c 590 " --> pdb=" O THR3c 564 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N SER3c 566 " --> pdb=" O ILE3c 590 " (cutoff:3.500A) Processing sheet with id=AS7, first strand: chain '3b' and resid 594 through 599 Processing sheet with id=AS8, first strand: chain '3c' and resid 594 through 599 6319 hydrogen bonds defined for protein. 16740 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: 78.74 Time building geometry restraints manager: 35.97 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: 34260 1.34 - 1.46: 21003 1.46 - 1.58: 49977 1.58 - 1.70: 0 1.70 - 1.82: 1140 Bond restraints: 106380 Sorted by residual: bond pdb=" C PRO2o 582 " pdb=" N PRO2o 583 " ideal model delta sigma weight residual 1.337 1.360 -0.023 1.24e-02 6.50e+03 3.33e+00 bond pdb=" C PRO2p 582 " pdb=" N PRO2p 583 " ideal model delta sigma weight residual 1.337 1.360 -0.023 1.24e-02 6.50e+03 3.33e+00 bond pdb=" C PRO2g 582 " pdb=" N PRO2g 583 " ideal model delta sigma weight residual 1.337 1.359 -0.022 1.24e-02 6.50e+03 3.22e+00 bond pdb=" C PRO2k 582 " pdb=" N PRO2k 583 " ideal model delta sigma weight residual 1.337 1.359 -0.021 1.24e-02 6.50e+03 3.00e+00 bond pdb=" C PRO1c 582 " pdb=" N PRO1c 583 " ideal model delta sigma weight residual 1.337 1.358 -0.021 1.24e-02 6.50e+03 2.98e+00 ... (remaining 106375 not shown) Histogram of bond angle deviations from ideal: 99.03 - 106.03: 2729 106.03 - 113.03: 60638 113.03 - 120.04: 33634 120.04 - 127.04: 46035 127.04 - 134.04: 1024 Bond angle restraints: 144060 Sorted by residual: angle pdb=" N ILE2b 531 " pdb=" CA ILE2b 531 " pdb=" C ILE2b 531 " ideal model delta sigma weight residual 113.71 108.45 5.26 9.50e-01 1.11e+00 3.06e+01 angle pdb=" N TYR2w 447 " pdb=" CA TYR2w 447 " pdb=" C TYR2w 447 " ideal model delta sigma weight residual 109.50 117.70 -8.20 1.58e+00 4.01e-01 2.69e+01 angle pdb=" N TYR3b 447 " pdb=" CA TYR3b 447 " pdb=" C TYR3b 447 " ideal model delta sigma weight residual 109.50 117.39 -7.89 1.58e+00 4.01e-01 2.49e+01 angle pdb=" N TYR3c 447 " pdb=" CA TYR3c 447 " pdb=" C TYR3c 447 " ideal model delta sigma weight residual 109.50 117.39 -7.89 1.58e+00 4.01e-01 2.49e+01 angle pdb=" N TYR2q 447 " pdb=" CA TYR2q 447 " pdb=" C TYR2q 447 " ideal model delta sigma weight residual 109.50 117.30 -7.80 1.58e+00 4.01e-01 2.44e+01 ... (remaining 144055 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.10: 60050 18.10 - 36.20: 4025 36.20 - 54.31: 886 54.31 - 72.41: 229 72.41 - 90.51: 30 Dihedral angle restraints: 65220 sinusoidal: 25920 harmonic: 39300 Sorted by residual: dihedral pdb=" CA HIS1i 445 " pdb=" C HIS1i 445 " pdb=" N TYR1i 446 " pdb=" CA TYR1i 446 " ideal model delta harmonic sigma weight residual 180.00 161.78 18.22 0 5.00e+00 4.00e-02 1.33e+01 dihedral pdb=" CA MET2y 645 " pdb=" C MET2y 645 " pdb=" N LEU2y 646 " pdb=" CA LEU2y 646 " ideal model delta harmonic sigma weight residual 180.00 162.51 17.49 0 5.00e+00 4.00e-02 1.22e+01 dihedral pdb=" CA TYR2c 446 " pdb=" C TYR2c 446 " pdb=" N TYR2c 447 " pdb=" CA TYR2c 447 " ideal model delta harmonic sigma weight residual -180.00 -162.63 -17.37 0 5.00e+00 4.00e-02 1.21e+01 ... (remaining 65217 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 11019 0.031 - 0.061: 3545 0.061 - 0.092: 1221 0.092 - 0.123: 1405 0.123 - 0.153: 30 Chirality restraints: 17220 Sorted by residual: chirality pdb=" CA ILE2b 531 " pdb=" N ILE2b 531 " pdb=" C ILE2b 531 " pdb=" CB ILE2b 531 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.88e-01 chirality pdb=" CA ILE1w 428 " pdb=" N ILE1w 428 " pdb=" C ILE1w 428 " pdb=" CB ILE1w 428 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.28e-01 chirality pdb=" CA ILE1f 531 " pdb=" N ILE1f 531 " pdb=" C ILE1f 531 " pdb=" CB ILE1f 531 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.22e-01 ... (remaining 17217 not shown) Planarity restraints: 18300 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE2a 423 " -0.045 5.00e-02 4.00e+02 6.68e-02 7.15e+00 pdb=" N PRO2a 424 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO2a 424 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO2a 424 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA MET2u 467 " -0.009 2.00e-02 2.50e+03 1.74e-02 3.03e+00 pdb=" C MET2u 467 " 0.030 2.00e-02 2.50e+03 pdb=" O MET2u 467 " -0.011 2.00e-02 2.50e+03 pdb=" N LEU2u 468 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN2a 581 " -0.027 5.00e-02 4.00e+02 4.04e-02 2.61e+00 pdb=" N PRO2a 582 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO2a 582 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO2a 582 " -0.022 5.00e-02 4.00e+02 ... (remaining 18297 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 21957 2.79 - 3.31: 104539 3.31 - 3.84: 170266 3.84 - 4.37: 193837 4.37 - 4.90: 336226 Nonbonded interactions: 826825 Sorted by model distance: nonbonded pdb=" OG SER1u 439 " pdb=" O ILE1u 580 " model vdw 2.256 2.440 nonbonded pdb=" OD1 ASN1q 575 " pdb=" OG1 THR1q 615 " model vdw 2.273 2.440 nonbonded pdb=" OG1 THR2p 564 " pdb=" OE1 GLN2p 584 " model vdw 2.280 2.440 nonbonded pdb=" OG SER2f 439 " pdb=" O ILE2f 580 " model vdw 2.284 2.440 nonbonded pdb=" OD1 ASN1w 575 " pdb=" OG1 THR1w 615 " model vdw 2.285 2.440 ... (remaining 826820 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 '01' selection = chain '02' selection = chain '03' selection = chain '04' selection = chain '05' selection = chain '0z' selection = chain '1a' selection = chain '1b' selection = chain '1c' selection = chain '1d' selection = chain '1e' selection = chain '1f' selection = chain '1g' selection = chain '1h' selection = chain '1i' selection = chain '1j' selection = chain '1k' selection = chain '1l' selection = chain '1m' selection = chain '1n' selection = chain '1o' selection = chain '1p' selection = chain '1q' selection = chain '1r' selection = chain '1s' selection = chain '1t' selection = chain '1u' selection = chain '1v' selection = chain '1w' selection = chain '1x' selection = chain '1z' selection = chain '2a' selection = chain '2b' selection = chain '2c' selection = chain '2d' selection = chain '2e' selection = chain '2f' selection = chain '2g' selection = chain '2h' selection = chain '2i' selection = chain '2j' selection = chain '2k' selection = chain '2l' selection = chain '2m' selection = chain '2n' selection = chain '2o' selection = chain '2p' selection = chain '2q' selection = chain '2r' selection = chain '2s' selection = chain '2t' selection = chain '2u' selection = chain '2v' selection = chain '2w' selection = chain '2x' selection = chain '2y' selection = chain '2z' selection = chain '3a' selection = chain '3b' selection = chain '3c' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 18.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.110 Extract box with map and model: 43.580 Check model and map are aligned: 1.160 Set scattering table: 0.730 Process input model: 260.660 Find NCS groups from input model: 5.580 Set up NCS constraints: 1.400 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: 0.020 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 334.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 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 : 0.002 0.065 106380 Z= 0.157 Angle : 0.648 10.807 144060 Z= 0.376 Chirality : 0.043 0.153 17220 Planarity : 0.004 0.067 18300 Dihedral : 13.351 90.512 39540 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 0.09 % Allowed : 6.79 % Favored : 93.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.08), residues: 13320 helix: 1.09 (0.07), residues: 4860 sheet: 0.10 (0.09), residues: 2940 loop : 0.93 (0.10), residues: 5520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP1m 498 HIS 0.006 0.001 HIS2t 445 PHE 0.009 0.001 PHE2o 558 TYR 0.015 0.001 TYR2o 446 ARG 0.006 0.000 ARG1b 636 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26640 Ramachandran restraints generated. 13320 Oldfield, 0 Emsley, 13320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26640 Ramachandran restraints generated. 13320 Oldfield, 0 Emsley, 13320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 901 residues out of total 11700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 890 time to evaluate : 9.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 04 437 MET cc_start: 0.9451 (tpp) cc_final: 0.8917 (tpt) REVERT: 04 445 HIS cc_start: 0.7285 (m-70) cc_final: 0.6996 (m90) REVERT: 1a 437 MET cc_start: 0.9106 (tmm) cc_final: 0.8741 (tmm) REVERT: 1b 437 MET cc_start: 0.8769 (tpt) cc_final: 0.8327 (tpt) REVERT: 1b 454 MET cc_start: 0.8425 (tpp) cc_final: 0.8101 (mmt) REVERT: 1j 454 MET cc_start: 0.9280 (mmm) cc_final: 0.8383 (mmm) REVERT: 1j 535 GLU cc_start: 0.8488 (tm-30) cc_final: 0.8128 (tm-30) REVERT: 1l 535 GLU cc_start: 0.8452 (tm-30) cc_final: 0.8176 (tm-30) REVERT: 1m 535 GLU cc_start: 0.8460 (tm-30) cc_final: 0.8072 (tm-30) REVERT: 1n 550 GLU cc_start: 0.6923 (mp0) cc_final: 0.6646 (mp0) REVERT: 1o 535 GLU cc_start: 0.8570 (tm-30) cc_final: 0.8155 (tm-30) REVERT: 1p 554 GLN cc_start: 0.8244 (mp10) cc_final: 0.8016 (mp10) REVERT: 1q 556 HIS cc_start: 0.7775 (t70) cc_final: 0.7568 (t70) REVERT: 1r 454 MET cc_start: 0.8457 (tpp) cc_final: 0.8027 (mmt) REVERT: 1s 550 GLU cc_start: 0.7540 (mp0) cc_final: 0.7323 (mp0) REVERT: 1t 434 GLN cc_start: 0.8289 (mp10) cc_final: 0.7949 (mp10) REVERT: 1t 535 GLU cc_start: 0.8632 (tm-30) cc_final: 0.8360 (tm-30) REVERT: 1t 611 MET cc_start: 0.8938 (mmp) cc_final: 0.8701 (mmm) REVERT: 1t 634 GLU cc_start: 0.8483 (tp30) cc_final: 0.8132 (tp30) REVERT: 1w 437 MET cc_start: 0.9188 (tmm) cc_final: 0.8727 (tmm) REVERT: 1z 437 MET cc_start: 0.9174 (tmm) cc_final: 0.8776 (tmm) REVERT: 2b 456 GLU cc_start: 0.8399 (mm-30) cc_final: 0.8133 (mp0) REVERT: 2c 535 GLU cc_start: 0.8755 (tm-30) cc_final: 0.8317 (tm-30) REVERT: 2e 454 MET cc_start: 0.9207 (mmm) cc_final: 0.8465 (mmm) REVERT: 2k 437 MET cc_start: 0.8435 (tpp) cc_final: 0.8134 (tpt) REVERT: 2p 437 MET cc_start: 0.9169 (tmm) cc_final: 0.8600 (tmm) REVERT: 2r 467 MET cc_start: 0.8285 (tpp) cc_final: 0.8029 (tpp) REVERT: 2s 611 MET cc_start: 0.8678 (mmm) cc_final: 0.8413 (mmm) REVERT: 2t 456 GLU cc_start: 0.8374 (mm-30) cc_final: 0.8152 (mm-30) REVERT: 2t 535 GLU cc_start: 0.8529 (tm-30) cc_final: 0.8299 (tm-30) REVERT: 2y 535 GLU cc_start: 0.8422 (tm-30) cc_final: 0.8162 (tm-30) REVERT: 3a 535 GLU cc_start: 0.8432 (tm-30) cc_final: 0.8081 (tm-30) outliers start: 11 outliers final: 3 residues processed: 894 average time/residue: 0.8982 time to fit residues: 1403.0930 Evaluate side-chains 717 residues out of total 11700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 714 time to evaluate : 9.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1s residue 469 GLU Chi-restraints excluded: chain 2g residue 612 MET Chi-restraints excluded: chain 2y residue 502 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1320 random chunks: chunk 1114 optimal weight: 4.9990 chunk 1000 optimal weight: 0.5980 chunk 555 optimal weight: 1.9990 chunk 341 optimal weight: 0.9980 chunk 674 optimal weight: 0.8980 chunk 534 optimal weight: 3.9990 chunk 1034 optimal weight: 10.0000 chunk 400 optimal weight: 1.9990 chunk 629 optimal weight: 2.9990 chunk 770 optimal weight: 10.0000 chunk 1198 optimal weight: 0.9980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 02 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 04 445 HIS 05 438 GLN ** 05 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0z 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1b 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1c 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1c 556 HIS 1d 434 GLN 1d 556 HIS 1e 434 GLN 1e 445 HIS ** 1j 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1j 495 ASN ** 1l 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1n 556 HIS 1q 445 HIS 1r 495 ASN 1u 445 HIS 1u 581 ASN 1u 584 GLN 1v 434 GLN 1v 438 GLN 1v 445 HIS 1w 427 ASN 1z 581 ASN 1z 584 GLN 2e 445 HIS 2f 445 HIS 2j 556 HIS ** 2l 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2o 581 ASN 2o 584 GLN 2s 581 ASN 2s 584 GLN ** 2t 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2u 556 HIS ** 2w 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3a 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.1505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 106380 Z= 0.203 Angle : 0.572 8.831 144060 Z= 0.301 Chirality : 0.045 0.138 17220 Planarity : 0.004 0.042 18300 Dihedral : 5.223 73.536 14227 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 1.24 % Allowed : 7.85 % Favored : 90.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.07), residues: 13320 helix: 1.46 (0.07), residues: 5340 sheet: 0.62 (0.10), residues: 2340 loop : 0.09 (0.09), residues: 5640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP2c 498 HIS 0.007 0.001 HIS1c 445 PHE 0.014 0.001 PHE2s 576 TYR 0.028 0.002 TYR1q 446 ARG 0.005 0.000 ARG1w 429 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26640 Ramachandran restraints generated. 13320 Oldfield, 0 Emsley, 13320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26640 Ramachandran restraints generated. 13320 Oldfield, 0 Emsley, 13320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 908 residues out of total 11700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 763 time to evaluate : 10.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 01 437 MET cc_start: 0.8734 (tmm) cc_final: 0.8321 (tmm) REVERT: 02 437 MET cc_start: 0.8658 (tmm) cc_final: 0.8325 (tmm) REVERT: 03 467 MET cc_start: 0.8465 (tmm) cc_final: 0.8135 (tmm) REVERT: 04 445 HIS cc_start: 0.7716 (m90) cc_final: 0.7316 (m90) REVERT: 05 434 GLN cc_start: 0.8039 (mp10) cc_final: 0.7468 (mp10) REVERT: 05 454 MET cc_start: 0.8293 (mmm) cc_final: 0.7881 (mmm) REVERT: 0z 467 MET cc_start: 0.8318 (tpp) cc_final: 0.8094 (tpp) REVERT: 1a 570 MET cc_start: 0.8092 (OUTLIER) cc_final: 0.7827 (mtp) REVERT: 1b 437 MET cc_start: 0.8845 (tpt) cc_final: 0.8439 (tpt) REVERT: 1b 454 MET cc_start: 0.8651 (tpp) cc_final: 0.8048 (mmt) REVERT: 1b 535 GLU cc_start: 0.8199 (tm-30) cc_final: 0.7626 (tm-30) REVERT: 1b 645 MET cc_start: 0.9003 (mtm) cc_final: 0.8478 (mtp) REVERT: 1c 445 HIS cc_start: 0.7697 (m-70) cc_final: 0.7449 (m90) REVERT: 1d 434 GLN cc_start: 0.7997 (mt0) cc_final: 0.7725 (mt0) REVERT: 1e 434 GLN cc_start: 0.8021 (mt0) cc_final: 0.7781 (mt0) REVERT: 1f 636 ARG cc_start: 0.8622 (OUTLIER) cc_final: 0.8408 (ttm-80) REVERT: 1g 437 MET cc_start: 0.9272 (tpt) cc_final: 0.8923 (tpt) REVERT: 1g 645 MET cc_start: 0.9101 (mtm) cc_final: 0.8732 (mtp) REVERT: 1h 437 MET cc_start: 0.9198 (tpt) cc_final: 0.8953 (tpt) REVERT: 1h 645 MET cc_start: 0.8666 (mtp) cc_final: 0.8451 (mtp) REVERT: 1j 437 MET cc_start: 0.9532 (tpp) cc_final: 0.9299 (tpt) REVERT: 1j 535 GLU cc_start: 0.8323 (tm-30) cc_final: 0.7921 (tm-30) REVERT: 1k 454 MET cc_start: 0.8774 (mmm) cc_final: 0.8185 (mmm) REVERT: 1k 535 GLU cc_start: 0.8370 (tm-30) cc_final: 0.8102 (tm-30) REVERT: 1l 467 MET cc_start: 0.8473 (tmm) cc_final: 0.8239 (tmm) REVERT: 1l 535 GLU cc_start: 0.8152 (tm-30) cc_final: 0.7744 (tm-30) REVERT: 1o 467 MET cc_start: 0.8113 (tpp) cc_final: 0.7908 (tpp) REVERT: 1o 535 GLU cc_start: 0.8296 (tm-30) cc_final: 0.7673 (tm-30) REVERT: 1s 434 GLN cc_start: 0.7715 (mp10) cc_final: 0.7333 (mp10) REVERT: 1s 467 MET cc_start: 0.8445 (tpp) cc_final: 0.8212 (tpp) REVERT: 1s 611 MET cc_start: 0.8995 (mmm) cc_final: 0.8691 (mmp) REVERT: 1t 535 GLU cc_start: 0.8409 (tm-30) cc_final: 0.8075 (tm-30) REVERT: 1u 535 GLU cc_start: 0.7999 (tm-30) cc_final: 0.7692 (tm-30) REVERT: 1v 645 MET cc_start: 0.8682 (mtp) cc_final: 0.8393 (mtp) REVERT: 1x 454 MET cc_start: 0.8429 (mmm) cc_final: 0.8229 (mmm) REVERT: 2a 467 MET cc_start: 0.8503 (mmp) cc_final: 0.8269 (mmm) REVERT: 2d 434 GLN cc_start: 0.7710 (mp10) cc_final: 0.7190 (mp10) REVERT: 2e 454 MET cc_start: 0.9214 (mmm) cc_final: 0.8379 (mmm) REVERT: 2f 645 MET cc_start: 0.8737 (mtp) cc_final: 0.8448 (mtp) REVERT: 2h 437 MET cc_start: 0.8712 (tmm) cc_final: 0.8187 (tmm) REVERT: 2i 437 MET cc_start: 0.8712 (tmm) cc_final: 0.8374 (tmm) REVERT: 2j 437 MET cc_start: 0.8601 (tmm) cc_final: 0.8215 (tmm) REVERT: 2k 437 MET cc_start: 0.8607 (tpp) cc_final: 0.8233 (tpt) REVERT: 2k 645 MET cc_start: 0.8689 (mtp) cc_final: 0.8347 (mtp) REVERT: 2l 535 GLU cc_start: 0.8223 (tm-30) cc_final: 0.7817 (tm-30) REVERT: 2n 467 MET cc_start: 0.8365 (mmm) cc_final: 0.8163 (tpp) REVERT: 2q 437 MET cc_start: 0.9234 (tpt) cc_final: 0.9015 (tpt) REVERT: 2s 554 GLN cc_start: 0.8089 (tm-30) cc_final: 0.7800 (tm-30) REVERT: 2v 437 MET cc_start: 0.8602 (tmm) cc_final: 0.8175 (tmm) REVERT: 2w 437 MET cc_start: 0.8602 (tmm) cc_final: 0.8292 (tmm) REVERT: 2x 437 MET cc_start: 0.8716 (tmm) cc_final: 0.8299 (tmm) REVERT: 2y 454 MET cc_start: 0.9071 (mmm) cc_final: 0.8188 (mmm) REVERT: 2y 535 GLU cc_start: 0.8169 (tm-30) cc_final: 0.7850 (tm-30) REVERT: 2z 535 GLU cc_start: 0.8474 (tm-30) cc_final: 0.8040 (tm-30) REVERT: 3a 437 MET cc_start: 0.8738 (tmm) cc_final: 0.8323 (tmm) REVERT: 3a 467 MET cc_start: 0.8215 (tpp) cc_final: 0.7850 (tpp) REVERT: 3a 535 GLU cc_start: 0.8155 (tm-30) cc_final: 0.7773 (tm-30) REVERT: 3b 437 MET cc_start: 0.8742 (tmm) cc_final: 0.8274 (tmm) REVERT: 3b 467 MET cc_start: 0.8355 (tpp) cc_final: 0.8137 (tpp) REVERT: 3c 437 MET cc_start: 0.8756 (tmm) cc_final: 0.8477 (tmm) outliers start: 145 outliers final: 74 residues processed: 824 average time/residue: 0.8835 time to fit residues: 1294.4662 Evaluate side-chains 783 residues out of total 11700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 707 time to evaluate : 9.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 01 residue 446 TYR Chi-restraints excluded: chain 02 residue 446 TYR Chi-restraints excluded: chain 05 residue 556 HIS Chi-restraints excluded: chain 05 residue 570 MET Chi-restraints excluded: chain 0z residue 446 TYR Chi-restraints excluded: chain 1a residue 570 MET Chi-restraints excluded: chain 1a residue 612 MET Chi-restraints excluded: chain 1b residue 499 MET Chi-restraints excluded: chain 1c residue 645 MET Chi-restraints excluded: chain 1d residue 556 HIS Chi-restraints excluded: chain 1e residue 446 TYR Chi-restraints excluded: chain 1f residue 612 MET Chi-restraints excluded: chain 1f residue 636 ARG Chi-restraints excluded: chain 1g residue 570 MET Chi-restraints excluded: chain 1h residue 445 HIS Chi-restraints excluded: chain 1i residue 570 MET Chi-restraints excluded: chain 1k residue 645 MET Chi-restraints excluded: chain 1l residue 570 MET Chi-restraints excluded: chain 1m residue 446 TYR Chi-restraints excluded: chain 1n residue 556 HIS Chi-restraints excluded: chain 1n residue 645 MET Chi-restraints excluded: chain 1o residue 570 MET Chi-restraints excluded: chain 1p residue 431 VAL Chi-restraints excluded: chain 1p residue 645 MET Chi-restraints excluded: chain 1q residue 456 GLU Chi-restraints excluded: chain 1q residue 612 MET Chi-restraints excluded: chain 1s residue 469 GLU Chi-restraints excluded: chain 1s residue 612 MET Chi-restraints excluded: chain 1t residue 612 MET Chi-restraints excluded: chain 1u residue 446 TYR Chi-restraints excluded: chain 1v residue 436 LEU Chi-restraints excluded: chain 1x residue 445 HIS Chi-restraints excluded: chain 1x residue 645 MET Chi-restraints excluded: chain 2b residue 446 TYR Chi-restraints excluded: chain 2b residue 556 HIS Chi-restraints excluded: chain 2c residue 612 MET Chi-restraints excluded: chain 2d residue 556 HIS Chi-restraints excluded: chain 2f residue 446 TYR Chi-restraints excluded: chain 2h residue 446 TYR Chi-restraints excluded: chain 2h residue 570 MET Chi-restraints excluded: chain 2i residue 446 TYR Chi-restraints excluded: chain 2i residue 570 MET Chi-restraints excluded: chain 2j residue 446 TYR Chi-restraints excluded: chain 2j residue 556 HIS Chi-restraints excluded: chain 2j residue 570 MET Chi-restraints excluded: chain 2k residue 431 VAL Chi-restraints excluded: chain 2k residue 445 HIS Chi-restraints excluded: chain 2k residue 556 HIS Chi-restraints excluded: chain 2l residue 570 MET Chi-restraints excluded: chain 2l residue 612 MET Chi-restraints excluded: chain 2o residue 445 HIS Chi-restraints excluded: chain 2o residue 645 MET Chi-restraints excluded: chain 2p residue 445 HIS Chi-restraints excluded: chain 2p residue 556 HIS Chi-restraints excluded: chain 2q residue 446 TYR Chi-restraints excluded: chain 2r residue 612 MET Chi-restraints excluded: chain 2s residue 445 HIS Chi-restraints excluded: chain 2t residue 445 HIS Chi-restraints excluded: chain 2t residue 645 MET Chi-restraints excluded: chain 2u residue 570 MET Chi-restraints excluded: chain 2u residue 612 MET Chi-restraints excluded: chain 2v residue 446 TYR Chi-restraints excluded: chain 2v residue 570 MET Chi-restraints excluded: chain 2w residue 446 TYR Chi-restraints excluded: chain 2w residue 570 MET Chi-restraints excluded: chain 2x residue 446 TYR Chi-restraints excluded: chain 2x residue 570 MET Chi-restraints excluded: chain 2y residue 570 MET Chi-restraints excluded: chain 2z residue 469 GLU Chi-restraints excluded: chain 2z residue 612 MET Chi-restraints excluded: chain 3a residue 446 TYR Chi-restraints excluded: chain 3a residue 570 MET Chi-restraints excluded: chain 3b residue 446 TYR Chi-restraints excluded: chain 3b residue 570 MET Chi-restraints excluded: chain 3c residue 446 TYR Chi-restraints excluded: chain 3c residue 570 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1320 random chunks: chunk 666 optimal weight: 0.9990 chunk 372 optimal weight: 0.9990 chunk 997 optimal weight: 0.9990 chunk 816 optimal weight: 3.9990 chunk 330 optimal weight: 10.0000 chunk 1200 optimal weight: 7.9990 chunk 1297 optimal weight: 3.9990 chunk 1069 optimal weight: 1.9990 chunk 1190 optimal weight: 3.9990 chunk 409 optimal weight: 5.9990 chunk 963 optimal weight: 4.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 05 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0z 438 GLN 1b 495 ASN ** 1c 556 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1d 556 HIS 1e 445 HIS ** 1g 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1j 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1k 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1k 581 ASN 1k 584 GLN ** 1l 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1l 495 ASN ** 1m 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1n 556 HIS 1q 556 HIS 1q 581 ASN 1q 584 GLN 1r 445 HIS 1t 434 GLN 2a 495 ASN ** 2c 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2f 445 HIS 2k 434 GLN ** 2l 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2s 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2t 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2u 556 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2z 445 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 106380 Z= 0.276 Angle : 0.563 8.505 144060 Z= 0.297 Chirality : 0.045 0.138 17220 Planarity : 0.004 0.043 18300 Dihedral : 5.091 52.911 14223 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 1.45 % Allowed : 8.87 % Favored : 89.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.07), residues: 13320 helix: 1.66 (0.07), residues: 5280 sheet: 0.11 (0.09), residues: 2880 loop : 0.23 (0.10), residues: 5160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP1t 498 HIS 0.021 0.001 HIS2j 556 PHE 0.014 0.001 PHE1n 558 TYR 0.027 0.002 TYR1q 446 ARG 0.006 0.000 ARG1w 429 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26640 Ramachandran restraints generated. 13320 Oldfield, 0 Emsley, 13320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26640 Ramachandran restraints generated. 13320 Oldfield, 0 Emsley, 13320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 889 residues out of total 11700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 719 time to evaluate : 9.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 01 437 MET cc_start: 0.8968 (tmm) cc_final: 0.8302 (tmm) REVERT: 02 437 MET cc_start: 0.8949 (tmm) cc_final: 0.8322 (tmm) REVERT: 03 467 MET cc_start: 0.8513 (tmm) cc_final: 0.8302 (tmm) REVERT: 04 467 MET cc_start: 0.8552 (mmm) cc_final: 0.8331 (tpp) REVERT: 05 434 GLN cc_start: 0.8182 (mp10) cc_final: 0.7650 (mp10) REVERT: 05 454 MET cc_start: 0.8401 (mmm) cc_final: 0.8036 (mmm) REVERT: 05 645 MET cc_start: 0.9015 (OUTLIER) cc_final: 0.8738 (mtp) REVERT: 0z 437 MET cc_start: 0.8662 (tmm) cc_final: 0.8284 (tmm) REVERT: 0z 467 MET cc_start: 0.8413 (tpp) cc_final: 0.8143 (tpp) REVERT: 1a 570 MET cc_start: 0.8107 (OUTLIER) cc_final: 0.7887 (mtp) REVERT: 1b 437 MET cc_start: 0.8829 (tpt) cc_final: 0.8421 (tpt) REVERT: 1b 535 GLU cc_start: 0.8137 (tm-30) cc_final: 0.7604 (tm-30) REVERT: 1b 645 MET cc_start: 0.9028 (mtm) cc_final: 0.8487 (mtp) REVERT: 1c 434 GLN cc_start: 0.7920 (mp10) cc_final: 0.7480 (mp10) REVERT: 1d 434 GLN cc_start: 0.7948 (mt0) cc_final: 0.7630 (mt0) REVERT: 1e 434 GLN cc_start: 0.8107 (mt0) cc_final: 0.7881 (mt0) REVERT: 1f 636 ARG cc_start: 0.8659 (OUTLIER) cc_final: 0.8451 (ttm-80) REVERT: 1g 645 MET cc_start: 0.9144 (mtm) cc_final: 0.8796 (mtp) REVERT: 1h 645 MET cc_start: 0.8695 (mtp) cc_final: 0.8405 (mtp) REVERT: 1j 570 MET cc_start: 0.7793 (ppp) cc_final: 0.7466 (ptp) REVERT: 1k 535 GLU cc_start: 0.8476 (tm-30) cc_final: 0.8205 (tm-30) REVERT: 1l 535 GLU cc_start: 0.8228 (tm-30) cc_final: 0.7820 (tm-30) REVERT: 1m 499 MET cc_start: 0.7972 (tpp) cc_final: 0.7685 (tpt) REVERT: 1o 467 MET cc_start: 0.8192 (tpp) cc_final: 0.7980 (tpp) REVERT: 1o 535 GLU cc_start: 0.8194 (tm-30) cc_final: 0.7708 (tm-30) REVERT: 1r 437 MET cc_start: 0.9009 (tmm) cc_final: 0.8134 (tmm) REVERT: 1s 467 MET cc_start: 0.8371 (tpp) cc_final: 0.8122 (tpp) REVERT: 1t 434 GLN cc_start: 0.8001 (mt0) cc_final: 0.7769 (mt0) REVERT: 1u 467 MET cc_start: 0.8436 (mmm) cc_final: 0.8165 (tpp) REVERT: 1v 437 MET cc_start: 0.9081 (tpt) cc_final: 0.8163 (tpt) REVERT: 1v 645 MET cc_start: 0.8715 (mtp) cc_final: 0.8435 (mtp) REVERT: 1x 454 MET cc_start: 0.8757 (mmm) cc_final: 0.8222 (mmm) REVERT: 1z 446 TYR cc_start: 0.8036 (p90) cc_final: 0.7831 (p90) REVERT: 2a 437 MET cc_start: 0.9396 (tpt) cc_final: 0.9164 (tpt) REVERT: 2b 467 MET cc_start: 0.8416 (tpp) cc_final: 0.8153 (tpp) REVERT: 2c 437 MET cc_start: 0.9271 (tpp) cc_final: 0.8874 (tpt) REVERT: 2c 467 MET cc_start: 0.8350 (tpp) cc_final: 0.8146 (tpp) REVERT: 2f 454 MET cc_start: 0.8751 (mmm) cc_final: 0.8199 (mmm) REVERT: 2f 645 MET cc_start: 0.8755 (mtp) cc_final: 0.8402 (mtp) REVERT: 2h 437 MET cc_start: 0.8838 (tmm) cc_final: 0.8374 (tmm) REVERT: 2i 437 MET cc_start: 0.8986 (tmm) cc_final: 0.8355 (tmm) REVERT: 2j 437 MET cc_start: 0.8802 (tmm) cc_final: 0.8392 (tmm) REVERT: 2k 645 MET cc_start: 0.8737 (mtp) cc_final: 0.8414 (mtp) REVERT: 2l 535 GLU cc_start: 0.8228 (tm-30) cc_final: 0.7694 (tm-30) REVERT: 2p 437 MET cc_start: 0.9020 (tmm) cc_final: 0.8128 (tmm) REVERT: 2p 611 MET cc_start: 0.8835 (mmt) cc_final: 0.8604 (mmt) REVERT: 2s 554 GLN cc_start: 0.8139 (tm-30) cc_final: 0.7855 (tm-30) REVERT: 2v 437 MET cc_start: 0.8766 (tmm) cc_final: 0.8322 (tmm) REVERT: 2w 437 MET cc_start: 0.8951 (tmm) cc_final: 0.8349 (tmm) REVERT: 2x 437 MET cc_start: 0.8832 (tmm) cc_final: 0.8378 (tmm) REVERT: 2y 467 MET cc_start: 0.8392 (mmm) cc_final: 0.8169 (tpp) REVERT: 2y 535 GLU cc_start: 0.8179 (tm-30) cc_final: 0.7710 (tm-30) REVERT: 2y 645 MET cc_start: 0.8755 (mtm) cc_final: 0.8494 (mtm) REVERT: 2z 535 GLU cc_start: 0.8511 (tm-30) cc_final: 0.8022 (tm-30) REVERT: 3a 437 MET cc_start: 0.8979 (tmm) cc_final: 0.8315 (tmm) REVERT: 3a 535 GLU cc_start: 0.7957 (tm-30) cc_final: 0.7454 (tm-30) REVERT: 3b 437 MET cc_start: 0.8962 (tmm) cc_final: 0.8305 (tmm) REVERT: 3b 467 MET cc_start: 0.8381 (tpp) cc_final: 0.7995 (tpp) REVERT: 3c 437 MET cc_start: 0.9029 (tmm) cc_final: 0.8419 (tmm) outliers start: 170 outliers final: 89 residues processed: 805 average time/residue: 0.8878 time to fit residues: 1268.2308 Evaluate side-chains 779 residues out of total 11700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 687 time to evaluate : 9.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 01 residue 446 TYR Chi-restraints excluded: chain 02 residue 446 TYR Chi-restraints excluded: chain 03 residue 445 HIS Chi-restraints excluded: chain 05 residue 556 HIS Chi-restraints excluded: chain 05 residue 570 MET Chi-restraints excluded: chain 05 residue 645 MET Chi-restraints excluded: chain 0z residue 446 TYR Chi-restraints excluded: chain 1a residue 570 MET Chi-restraints excluded: chain 1a residue 612 MET Chi-restraints excluded: chain 1b residue 499 MET Chi-restraints excluded: chain 1c residue 645 MET Chi-restraints excluded: chain 1e residue 446 TYR Chi-restraints excluded: chain 1f residue 446 TYR Chi-restraints excluded: chain 1f residue 570 MET Chi-restraints excluded: chain 1f residue 612 MET Chi-restraints excluded: chain 1f residue 636 ARG Chi-restraints excluded: chain 1h residue 445 HIS Chi-restraints excluded: chain 1i residue 541 VAL Chi-restraints excluded: chain 1k residue 445 HIS Chi-restraints excluded: chain 1k residue 645 MET Chi-restraints excluded: chain 1l residue 468 LEU Chi-restraints excluded: chain 1m residue 446 TYR Chi-restraints excluded: chain 1m residue 502 VAL Chi-restraints excluded: chain 1n residue 445 HIS Chi-restraints excluded: chain 1n residue 556 HIS Chi-restraints excluded: chain 1n residue 645 MET Chi-restraints excluded: chain 1o residue 570 MET Chi-restraints excluded: chain 1p residue 570 MET Chi-restraints excluded: chain 1p residue 645 MET Chi-restraints excluded: chain 1q residue 612 MET Chi-restraints excluded: chain 1s residue 469 GLU Chi-restraints excluded: chain 1s residue 612 MET Chi-restraints excluded: chain 1s residue 636 ARG Chi-restraints excluded: chain 1t residue 446 TYR Chi-restraints excluded: chain 1t residue 468 LEU Chi-restraints excluded: chain 1t residue 570 MET Chi-restraints excluded: chain 1t residue 612 MET Chi-restraints excluded: chain 1u residue 446 TYR Chi-restraints excluded: chain 1u residue 468 LEU Chi-restraints excluded: chain 1u residue 636 ARG Chi-restraints excluded: chain 1w residue 570 MET Chi-restraints excluded: chain 1x residue 445 HIS Chi-restraints excluded: chain 1x residue 645 MET Chi-restraints excluded: chain 1z residue 468 LEU Chi-restraints excluded: chain 1z residue 570 MET Chi-restraints excluded: chain 1z residue 612 MET Chi-restraints excluded: chain 2a residue 445 HIS Chi-restraints excluded: chain 2b residue 446 TYR Chi-restraints excluded: chain 2b residue 556 HIS Chi-restraints excluded: chain 2c residue 612 MET Chi-restraints excluded: chain 2c residue 636 ARG Chi-restraints excluded: chain 2d residue 499 MET Chi-restraints excluded: chain 2d residue 636 ARG Chi-restraints excluded: chain 2h residue 446 TYR Chi-restraints excluded: chain 2h residue 570 MET Chi-restraints excluded: chain 2i residue 446 TYR Chi-restraints excluded: chain 2i residue 570 MET Chi-restraints excluded: chain 2j residue 446 TYR Chi-restraints excluded: chain 2j residue 570 MET Chi-restraints excluded: chain 2k residue 445 HIS Chi-restraints excluded: chain 2k residue 636 ARG Chi-restraints excluded: chain 2l residue 570 MET Chi-restraints excluded: chain 2l residue 612 MET Chi-restraints excluded: chain 2m residue 446 TYR Chi-restraints excluded: chain 2n residue 446 TYR Chi-restraints excluded: chain 2o residue 445 HIS Chi-restraints excluded: chain 2o residue 570 MET Chi-restraints excluded: chain 2o residue 645 MET Chi-restraints excluded: chain 2p residue 445 HIS Chi-restraints excluded: chain 2q residue 446 TYR Chi-restraints excluded: chain 2r residue 612 MET Chi-restraints excluded: chain 2s residue 445 HIS Chi-restraints excluded: chain 2s residue 612 MET Chi-restraints excluded: chain 2t residue 445 HIS Chi-restraints excluded: chain 2t residue 645 MET Chi-restraints excluded: chain 2u residue 570 MET Chi-restraints excluded: chain 2u residue 612 MET Chi-restraints excluded: chain 2v residue 446 TYR Chi-restraints excluded: chain 2v residue 570 MET Chi-restraints excluded: chain 2w residue 446 TYR Chi-restraints excluded: chain 2w residue 570 MET Chi-restraints excluded: chain 2x residue 446 TYR Chi-restraints excluded: chain 2x residue 468 LEU Chi-restraints excluded: chain 2x residue 570 MET Chi-restraints excluded: chain 2y residue 446 TYR Chi-restraints excluded: chain 2y residue 570 MET Chi-restraints excluded: chain 2z residue 612 MET Chi-restraints excluded: chain 2z residue 636 ARG Chi-restraints excluded: chain 3a residue 446 TYR Chi-restraints excluded: chain 3a residue 570 MET Chi-restraints excluded: chain 3b residue 446 TYR Chi-restraints excluded: chain 3c residue 446 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1320 random chunks: chunk 1186 optimal weight: 4.9990 chunk 902 optimal weight: 10.0000 chunk 623 optimal weight: 4.9990 chunk 132 optimal weight: 10.0000 chunk 573 optimal weight: 10.0000 chunk 806 optimal weight: 2.9990 chunk 1205 optimal weight: 3.9990 chunk 1275 optimal weight: 3.9990 chunk 629 optimal weight: 0.4980 chunk 1142 optimal weight: 0.8980 chunk 343 optimal weight: 6.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 05 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1c 556 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1e 445 HIS ** 1g 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1i 581 ASN 1i 584 GLN ** 1j 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1k 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1l 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1m 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1n 556 HIS 1o 495 ASN ** 1q 556 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1w 581 ASN 1w 584 GLN 1w 620 HIS ** 2c 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2c 602 ASN 2e 495 ASN 2j 554 GLN ** 2l 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2l 581 ASN 2l 584 GLN 2m 495 ASN 2n 495 ASN 2r 581 ASN 2r 584 GLN ** 2s 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2t 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2u 556 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2w 434 GLN 2x 495 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 106380 Z= 0.364 Angle : 0.619 10.400 144060 Z= 0.319 Chirality : 0.046 0.146 17220 Planarity : 0.004 0.045 18300 Dihedral : 5.237 42.257 14223 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 1.70 % Allowed : 10.09 % Favored : 88.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.07), residues: 13320 helix: 1.62 (0.07), residues: 5280 sheet: -0.09 (0.09), residues: 2880 loop : 0.08 (0.09), residues: 5160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP2l 498 HIS 0.008 0.001 HIS1n 556 PHE 0.014 0.002 PHE2o 576 TYR 0.032 0.002 TYR2l 446 ARG 0.005 0.000 ARG1w 429 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26640 Ramachandran restraints generated. 13320 Oldfield, 0 Emsley, 13320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26640 Ramachandran restraints generated. 13320 Oldfield, 0 Emsley, 13320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 888 residues out of total 11700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 199 poor density : 689 time to evaluate : 9.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 01 437 MET cc_start: 0.8904 (tmm) cc_final: 0.8281 (tmm) REVERT: 01 467 MET cc_start: 0.8326 (tpp) cc_final: 0.8106 (tpp) REVERT: 02 437 MET cc_start: 0.8920 (tmm) cc_final: 0.8321 (tmm) REVERT: 03 446 TYR cc_start: 0.8367 (p90) cc_final: 0.8158 (p90) REVERT: 03 467 MET cc_start: 0.8468 (tmm) cc_final: 0.8221 (tmm) REVERT: 04 467 MET cc_start: 0.8419 (mmm) cc_final: 0.8149 (tpp) REVERT: 05 434 GLN cc_start: 0.8242 (mp10) cc_final: 0.7768 (mp10) REVERT: 05 454 MET cc_start: 0.8590 (mmm) cc_final: 0.8155 (mmm) REVERT: 05 645 MET cc_start: 0.9045 (OUTLIER) cc_final: 0.8673 (mtp) REVERT: 0z 437 MET cc_start: 0.8723 (tmm) cc_final: 0.8392 (tmm) REVERT: 0z 467 MET cc_start: 0.8419 (tpp) cc_final: 0.8158 (tpp) REVERT: 1b 437 MET cc_start: 0.8867 (tpt) cc_final: 0.8460 (tpt) REVERT: 1b 445 HIS cc_start: 0.7787 (m90) cc_final: 0.7429 (m90) REVERT: 1b 535 GLU cc_start: 0.8214 (tm-30) cc_final: 0.7689 (tm-30) REVERT: 1b 645 MET cc_start: 0.9031 (mtm) cc_final: 0.8528 (mtp) REVERT: 1c 434 GLN cc_start: 0.7976 (mp10) cc_final: 0.7540 (mp10) REVERT: 1d 434 GLN cc_start: 0.8056 (mt0) cc_final: 0.7784 (mt0) REVERT: 1e 434 GLN cc_start: 0.8143 (mt0) cc_final: 0.7895 (mt0) REVERT: 1f 636 ARG cc_start: 0.8686 (OUTLIER) cc_final: 0.8405 (ttm-80) REVERT: 1g 645 MET cc_start: 0.9165 (mtm) cc_final: 0.8807 (mtp) REVERT: 1h 570 MET cc_start: 0.7595 (OUTLIER) cc_final: 0.7289 (ptp) REVERT: 1h 645 MET cc_start: 0.8739 (mtp) cc_final: 0.8407 (mtp) REVERT: 1j 445 HIS cc_start: 0.8161 (m90) cc_final: 0.7631 (m90) REVERT: 1j 570 MET cc_start: 0.7700 (ppp) cc_final: 0.7489 (ptp) REVERT: 1k 535 GLU cc_start: 0.8469 (tm-30) cc_final: 0.8196 (tm-30) REVERT: 1k 595 ASP cc_start: 0.8686 (OUTLIER) cc_final: 0.8379 (p0) REVERT: 1l 535 GLU cc_start: 0.8343 (tm-30) cc_final: 0.7908 (tm-30) REVERT: 1m 499 MET cc_start: 0.7995 (tpp) cc_final: 0.7750 (tpt) REVERT: 1n 467 MET cc_start: 0.8295 (tpp) cc_final: 0.8078 (tpp) REVERT: 1n 570 MET cc_start: 0.7536 (OUTLIER) cc_final: 0.7224 (ptp) REVERT: 1o 467 MET cc_start: 0.8269 (tpp) cc_final: 0.7949 (tpp) REVERT: 1o 535 GLU cc_start: 0.8289 (tm-30) cc_final: 0.7790 (tm-30) REVERT: 1r 437 MET cc_start: 0.8993 (tmm) cc_final: 0.8145 (tmm) REVERT: 1s 467 MET cc_start: 0.8425 (tpp) cc_final: 0.8120 (tpp) REVERT: 1u 437 MET cc_start: 0.9240 (tpt) cc_final: 0.8828 (tpt) REVERT: 1u 467 MET cc_start: 0.8418 (mmm) cc_final: 0.7959 (tpp) REVERT: 1v 437 MET cc_start: 0.9194 (tpt) cc_final: 0.8168 (tpt) REVERT: 1v 645 MET cc_start: 0.8761 (mtp) cc_final: 0.8473 (mtp) REVERT: 1x 454 MET cc_start: 0.8854 (mmm) cc_final: 0.8276 (mmm) REVERT: 1z 446 TYR cc_start: 0.8316 (p90) cc_final: 0.8033 (p90) REVERT: 2a 437 MET cc_start: 0.9383 (tpt) cc_final: 0.9140 (tpt) REVERT: 2b 467 MET cc_start: 0.8393 (tpp) cc_final: 0.8042 (tpp) REVERT: 2c 437 MET cc_start: 0.9309 (tpp) cc_final: 0.8896 (tpt) REVERT: 2c 467 MET cc_start: 0.8387 (tpp) cc_final: 0.8137 (tpp) REVERT: 2e 467 MET cc_start: 0.8755 (tmm) cc_final: 0.8499 (tmm) REVERT: 2f 454 MET cc_start: 0.8918 (mmm) cc_final: 0.8419 (mmm) REVERT: 2f 645 MET cc_start: 0.8792 (mtp) cc_final: 0.8423 (mtp) REVERT: 2h 437 MET cc_start: 0.8995 (tmm) cc_final: 0.8364 (tmm) REVERT: 2i 437 MET cc_start: 0.8931 (tmm) cc_final: 0.8337 (tmm) REVERT: 2j 437 MET cc_start: 0.8952 (tmm) cc_final: 0.8367 (tmm) REVERT: 2k 645 MET cc_start: 0.8787 (mtp) cc_final: 0.8440 (mtp) REVERT: 2l 535 GLU cc_start: 0.8198 (tm-30) cc_final: 0.7689 (tm-30) REVERT: 2l 611 MET cc_start: 0.8871 (mmm) cc_final: 0.8494 (mmm) REVERT: 2m 467 MET cc_start: 0.8752 (tmm) cc_final: 0.8487 (tmm) REVERT: 2n 467 MET cc_start: 0.8063 (tpp) cc_final: 0.7788 (tpp) REVERT: 2p 437 MET cc_start: 0.9077 (tmm) cc_final: 0.8294 (tmm) REVERT: 2p 611 MET cc_start: 0.8867 (mmt) cc_final: 0.8539 (mmt) REVERT: 2s 554 GLN cc_start: 0.8193 (tm-30) cc_final: 0.7889 (tm-30) REVERT: 2u 467 MET cc_start: 0.8786 (tmm) cc_final: 0.8509 (tmm) REVERT: 2v 437 MET cc_start: 0.8989 (tmm) cc_final: 0.8372 (tmm) REVERT: 2w 437 MET cc_start: 0.8973 (tmm) cc_final: 0.8348 (tmm) REVERT: 2x 437 MET cc_start: 0.8968 (tmm) cc_final: 0.8296 (tmm) REVERT: 2y 467 MET cc_start: 0.8235 (mmm) cc_final: 0.7962 (tpp) REVERT: 2y 468 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8433 (mm) REVERT: 2y 645 MET cc_start: 0.8854 (mtm) cc_final: 0.8419 (mtm) REVERT: 2z 535 GLU cc_start: 0.8514 (tm-30) cc_final: 0.8053 (tm-30) REVERT: 2z 550 GLU cc_start: 0.7392 (mp0) cc_final: 0.7108 (mp0) REVERT: 3a 437 MET cc_start: 0.8913 (tmm) cc_final: 0.8296 (tmm) REVERT: 3b 437 MET cc_start: 0.8918 (tmm) cc_final: 0.8324 (tmm) REVERT: 3c 437 MET cc_start: 0.8919 (tmm) cc_final: 0.8284 (tmm) outliers start: 199 outliers final: 110 residues processed: 796 average time/residue: 0.8663 time to fit residues: 1220.9298 Evaluate side-chains 776 residues out of total 11700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 660 time to evaluate : 9.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 01 residue 446 TYR Chi-restraints excluded: chain 02 residue 446 TYR Chi-restraints excluded: chain 03 residue 445 HIS Chi-restraints excluded: chain 03 residue 541 VAL Chi-restraints excluded: chain 05 residue 468 LEU Chi-restraints excluded: chain 05 residue 556 HIS Chi-restraints excluded: chain 05 residue 570 MET Chi-restraints excluded: chain 05 residue 645 MET Chi-restraints excluded: chain 0z residue 446 TYR Chi-restraints excluded: chain 0z residue 594 GLU Chi-restraints excluded: chain 1a residue 468 LEU Chi-restraints excluded: chain 1a residue 541 VAL Chi-restraints excluded: chain 1a residue 612 MET Chi-restraints excluded: chain 1c residue 645 MET Chi-restraints excluded: chain 1d residue 468 LEU Chi-restraints excluded: chain 1d residue 556 HIS Chi-restraints excluded: chain 1e residue 446 TYR Chi-restraints excluded: chain 1f residue 446 TYR Chi-restraints excluded: chain 1f residue 570 MET Chi-restraints excluded: chain 1f residue 612 MET Chi-restraints excluded: chain 1f residue 636 ARG Chi-restraints excluded: chain 1h residue 445 HIS Chi-restraints excluded: chain 1h residue 468 LEU Chi-restraints excluded: chain 1h residue 570 MET Chi-restraints excluded: chain 1h residue 636 ARG Chi-restraints excluded: chain 1i residue 468 LEU Chi-restraints excluded: chain 1i residue 541 VAL Chi-restraints excluded: chain 1k residue 445 HIS Chi-restraints excluded: chain 1k residue 595 ASP Chi-restraints excluded: chain 1k residue 645 MET Chi-restraints excluded: chain 1l residue 570 MET Chi-restraints excluded: chain 1l residue 612 MET Chi-restraints excluded: chain 1m residue 446 TYR Chi-restraints excluded: chain 1n residue 445 HIS Chi-restraints excluded: chain 1n residue 556 HIS Chi-restraints excluded: chain 1n residue 570 MET Chi-restraints excluded: chain 1n residue 636 ARG Chi-restraints excluded: chain 1n residue 645 MET Chi-restraints excluded: chain 1o residue 570 MET Chi-restraints excluded: chain 1p residue 431 VAL Chi-restraints excluded: chain 1p residue 445 HIS Chi-restraints excluded: chain 1p residue 570 MET Chi-restraints excluded: chain 1p residue 588 LEU Chi-restraints excluded: chain 1p residue 645 MET Chi-restraints excluded: chain 1q residue 456 GLU Chi-restraints excluded: chain 1q residue 541 VAL Chi-restraints excluded: chain 1q residue 612 MET Chi-restraints excluded: chain 1r residue 427 ASN Chi-restraints excluded: chain 1r residue 446 TYR Chi-restraints excluded: chain 1s residue 469 GLU Chi-restraints excluded: chain 1s residue 612 MET Chi-restraints excluded: chain 1t residue 446 TYR Chi-restraints excluded: chain 1t residue 468 LEU Chi-restraints excluded: chain 1t residue 570 MET Chi-restraints excluded: chain 1t residue 612 MET Chi-restraints excluded: chain 1u residue 446 TYR Chi-restraints excluded: chain 1u residue 468 LEU Chi-restraints excluded: chain 1u residue 499 MET Chi-restraints excluded: chain 1u residue 636 ARG Chi-restraints excluded: chain 1v residue 556 HIS Chi-restraints excluded: chain 1v residue 570 MET Chi-restraints excluded: chain 1x residue 445 HIS Chi-restraints excluded: chain 1x residue 645 MET Chi-restraints excluded: chain 1z residue 612 MET Chi-restraints excluded: chain 2a residue 445 HIS Chi-restraints excluded: chain 2a residue 468 LEU Chi-restraints excluded: chain 2a residue 502 VAL Chi-restraints excluded: chain 2b residue 446 TYR Chi-restraints excluded: chain 2c residue 446 TYR Chi-restraints excluded: chain 2c residue 612 MET Chi-restraints excluded: chain 2c residue 636 ARG Chi-restraints excluded: chain 2d residue 499 MET Chi-restraints excluded: chain 2e residue 468 LEU Chi-restraints excluded: chain 2h residue 446 TYR Chi-restraints excluded: chain 2i residue 446 TYR Chi-restraints excluded: chain 2i residue 570 MET Chi-restraints excluded: chain 2j residue 446 TYR Chi-restraints excluded: chain 2j residue 570 MET Chi-restraints excluded: chain 2j residue 594 GLU Chi-restraints excluded: chain 2k residue 431 VAL Chi-restraints excluded: chain 2k residue 445 HIS Chi-restraints excluded: chain 2k residue 556 HIS Chi-restraints excluded: chain 2l residue 570 MET Chi-restraints excluded: chain 2l residue 612 MET Chi-restraints excluded: chain 2m residue 446 TYR Chi-restraints excluded: chain 2m residue 612 MET Chi-restraints excluded: chain 2n residue 446 TYR Chi-restraints excluded: chain 2o residue 445 HIS Chi-restraints excluded: chain 2o residue 570 MET Chi-restraints excluded: chain 2o residue 612 MET Chi-restraints excluded: chain 2o residue 645 MET Chi-restraints excluded: chain 2p residue 445 HIS Chi-restraints excluded: chain 2q residue 446 TYR Chi-restraints excluded: chain 2r residue 612 MET Chi-restraints excluded: chain 2s residue 445 HIS Chi-restraints excluded: chain 2s residue 541 VAL Chi-restraints excluded: chain 2s residue 612 MET Chi-restraints excluded: chain 2t residue 645 MET Chi-restraints excluded: chain 2u residue 446 TYR Chi-restraints excluded: chain 2u residue 612 MET Chi-restraints excluded: chain 2v residue 446 TYR Chi-restraints excluded: chain 2v residue 570 MET Chi-restraints excluded: chain 2w residue 446 TYR Chi-restraints excluded: chain 2w residue 570 MET Chi-restraints excluded: chain 2x residue 446 TYR Chi-restraints excluded: chain 2x residue 468 LEU Chi-restraints excluded: chain 2x residue 570 MET Chi-restraints excluded: chain 2y residue 446 TYR Chi-restraints excluded: chain 2y residue 468 LEU Chi-restraints excluded: chain 2y residue 570 MET Chi-restraints excluded: chain 2z residue 612 MET Chi-restraints excluded: chain 3a residue 446 TYR Chi-restraints excluded: chain 3a residue 570 MET Chi-restraints excluded: chain 3b residue 446 TYR Chi-restraints excluded: chain 3b residue 570 MET Chi-restraints excluded: chain 3c residue 446 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1320 random chunks: chunk 1062 optimal weight: 0.9980 chunk 724 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 950 optimal weight: 2.9990 chunk 526 optimal weight: 0.9980 chunk 1088 optimal weight: 0.4980 chunk 881 optimal weight: 9.9990 chunk 1 optimal weight: 0.9990 chunk 651 optimal weight: 1.9990 chunk 1145 optimal weight: 0.9990 chunk 321 optimal weight: 2.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 05 581 ASN 05 584 GLN ** 1c 556 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1e 445 HIS 1e 581 ASN 1e 584 GLN ** 1g 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1l 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1l 581 ASN 1l 584 GLN 1n 556 HIS 1n 581 ASN 1n 584 GLN ** 1q 556 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1t 581 ASN 1t 584 GLN 1v 581 ASN 1v 584 GLN ** 1x 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2f 445 HIS 2g 581 ASN 2g 584 GLN ** 2i 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2j 445 HIS ** 2j 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2k 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2l 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2m 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2s 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2u 556 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2u 581 ASN 2u 584 GLN 2z 581 ASN 2z 584 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.2232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 106380 Z= 0.171 Angle : 0.531 10.850 144060 Z= 0.272 Chirality : 0.044 0.143 17220 Planarity : 0.004 0.047 18300 Dihedral : 4.819 42.090 14223 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 1.60 % Allowed : 11.15 % Favored : 87.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.07), residues: 13320 helix: 1.88 (0.07), residues: 5280 sheet: 0.26 (0.09), residues: 2700 loop : -0.03 (0.09), residues: 5340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP2l 498 HIS 0.011 0.000 HIS1n 556 PHE 0.016 0.001 PHE1h 558 TYR 0.030 0.001 TYR2l 446 ARG 0.003 0.000 ARG1w 429 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26640 Ramachandran restraints generated. 13320 Oldfield, 0 Emsley, 13320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26640 Ramachandran restraints generated. 13320 Oldfield, 0 Emsley, 13320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 903 residues out of total 11700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 187 poor density : 716 time to evaluate : 9.443 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 01 437 MET cc_start: 0.8933 (tmm) cc_final: 0.8264 (tmm) REVERT: 02 437 MET cc_start: 0.8925 (tmm) cc_final: 0.8271 (tmm) REVERT: 04 467 MET cc_start: 0.8268 (mmm) cc_final: 0.8049 (tpp) REVERT: 05 434 GLN cc_start: 0.8316 (mp10) cc_final: 0.8010 (mp10) REVERT: 05 454 MET cc_start: 0.8466 (mmm) cc_final: 0.8025 (mmm) REVERT: 05 645 MET cc_start: 0.8957 (OUTLIER) cc_final: 0.8647 (mtp) REVERT: 0z 437 MET cc_start: 0.8951 (tmm) cc_final: 0.8306 (tmm) REVERT: 1a 467 MET cc_start: 0.8571 (tmm) cc_final: 0.8344 (tmm) REVERT: 1b 437 MET cc_start: 0.8841 (tpt) cc_final: 0.8471 (tpt) REVERT: 1b 454 MET cc_start: 0.9041 (mmm) cc_final: 0.8053 (mmm) REVERT: 1b 645 MET cc_start: 0.9017 (mtm) cc_final: 0.8509 (mtp) REVERT: 1c 434 GLN cc_start: 0.8154 (mt0) cc_final: 0.7737 (mp10) REVERT: 1d 434 GLN cc_start: 0.7906 (mt0) cc_final: 0.7632 (mt0) REVERT: 1e 434 GLN cc_start: 0.7983 (mt0) cc_final: 0.7645 (mt0) REVERT: 1g 645 MET cc_start: 0.9131 (mtm) cc_final: 0.8758 (mtp) REVERT: 1h 558 PHE cc_start: 0.7689 (t80) cc_final: 0.7305 (t80) REVERT: 1i 437 MET cc_start: 0.8951 (tmm) cc_final: 0.8122 (tmm) REVERT: 1i 467 MET cc_start: 0.8599 (tmm) cc_final: 0.8315 (tmm) REVERT: 1j 445 HIS cc_start: 0.8058 (m90) cc_final: 0.7629 (m90) REVERT: 1j 570 MET cc_start: 0.7810 (ppp) cc_final: 0.7591 (ptp) REVERT: 1k 434 GLN cc_start: 0.7771 (mp10) cc_final: 0.7353 (mp10) REVERT: 1k 454 MET cc_start: 0.8877 (mmm) cc_final: 0.8414 (mmm) REVERT: 1l 535 GLU cc_start: 0.8301 (tm-30) cc_final: 0.8022 (tm-30) REVERT: 1m 437 MET cc_start: 0.9338 (tpp) cc_final: 0.9035 (tpp) REVERT: 1n 570 MET cc_start: 0.7676 (OUTLIER) cc_final: 0.7350 (ptp) REVERT: 1n 611 MET cc_start: 0.8910 (mmm) cc_final: 0.8682 (mmt) REVERT: 1o 535 GLU cc_start: 0.8164 (tm-30) cc_final: 0.7670 (tm-30) REVERT: 1q 434 GLN cc_start: 0.8101 (mp10) cc_final: 0.7891 (mp10) REVERT: 1r 437 MET cc_start: 0.8945 (tmm) cc_final: 0.8108 (tmm) REVERT: 1s 467 MET cc_start: 0.8378 (tpp) cc_final: 0.8076 (tpp) REVERT: 1u 467 MET cc_start: 0.8385 (mmm) cc_final: 0.7987 (tpp) REVERT: 1v 437 MET cc_start: 0.9198 (tpt) cc_final: 0.8192 (tpt) REVERT: 1x 588 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8688 (tt) REVERT: 1z 467 MET cc_start: 0.8715 (tmm) cc_final: 0.8467 (tmm) REVERT: 2a 437 MET cc_start: 0.9411 (tpt) cc_final: 0.9196 (tpt) REVERT: 2a 467 MET cc_start: 0.8486 (mmm) cc_final: 0.8098 (tpp) REVERT: 2b 467 MET cc_start: 0.8398 (tpp) cc_final: 0.8042 (tpp) REVERT: 2c 437 MET cc_start: 0.9409 (tpp) cc_final: 0.8896 (tpt) REVERT: 2c 467 MET cc_start: 0.8411 (tpp) cc_final: 0.8137 (tpp) REVERT: 2e 467 MET cc_start: 0.8750 (tmm) cc_final: 0.8483 (tmm) REVERT: 2f 454 MET cc_start: 0.8790 (mmm) cc_final: 0.8348 (mmm) REVERT: 2g 437 MET cc_start: 0.9066 (tmm) cc_final: 0.8587 (tmm) REVERT: 2h 437 MET cc_start: 0.8990 (tmm) cc_final: 0.8314 (tmm) REVERT: 2i 437 MET cc_start: 0.8921 (tmm) cc_final: 0.8281 (tmm) REVERT: 2j 437 MET cc_start: 0.8947 (tmm) cc_final: 0.8320 (tmm) REVERT: 2l 437 MET cc_start: 0.8884 (tmm) cc_final: 0.7998 (tmm) REVERT: 2l 535 GLU cc_start: 0.8060 (tm-30) cc_final: 0.7580 (tm-30) REVERT: 2l 611 MET cc_start: 0.8679 (mmm) cc_final: 0.8463 (mmm) REVERT: 2m 467 MET cc_start: 0.8747 (tmm) cc_final: 0.8383 (tmm) REVERT: 2n 467 MET cc_start: 0.8168 (tpp) cc_final: 0.7918 (tpp) REVERT: 2o 467 MET cc_start: 0.8596 (tpp) cc_final: 0.8257 (tpp) REVERT: 2s 554 GLN cc_start: 0.8182 (tm-30) cc_final: 0.7870 (tm-30) REVERT: 2s 611 MET cc_start: 0.8675 (mmm) cc_final: 0.8391 (mmm) REVERT: 2u 467 MET cc_start: 0.8743 (tmm) cc_final: 0.8436 (tmm) REVERT: 2v 437 MET cc_start: 0.8990 (tmm) cc_final: 0.8330 (tmm) REVERT: 2w 437 MET cc_start: 0.8975 (tmm) cc_final: 0.8314 (tmm) REVERT: 2x 437 MET cc_start: 0.8949 (tmm) cc_final: 0.8218 (tmm) REVERT: 2y 467 MET cc_start: 0.8307 (mmm) cc_final: 0.7905 (tpp) REVERT: 2y 645 MET cc_start: 0.8789 (mtm) cc_final: 0.8462 (mtm) REVERT: 3a 437 MET cc_start: 0.8917 (tmm) cc_final: 0.8247 (tmm) REVERT: 3a 467 MET cc_start: 0.8107 (tpp) cc_final: 0.7885 (tpp) REVERT: 3b 437 MET cc_start: 0.8947 (tmm) cc_final: 0.8280 (tmm) REVERT: 3c 437 MET cc_start: 0.8997 (tmm) cc_final: 0.8358 (tmm) outliers start: 187 outliers final: 116 residues processed: 817 average time/residue: 0.8738 time to fit residues: 1265.8362 Evaluate side-chains 787 residues out of total 11700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 668 time to evaluate : 9.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 01 residue 446 TYR Chi-restraints excluded: chain 02 residue 446 TYR Chi-restraints excluded: chain 03 residue 445 HIS Chi-restraints excluded: chain 03 residue 541 VAL Chi-restraints excluded: chain 03 residue 612 MET Chi-restraints excluded: chain 05 residue 556 HIS Chi-restraints excluded: chain 05 residue 570 MET Chi-restraints excluded: chain 05 residue 636 ARG Chi-restraints excluded: chain 05 residue 645 MET Chi-restraints excluded: chain 0z residue 446 TYR Chi-restraints excluded: chain 0z residue 478 ASP Chi-restraints excluded: chain 0z residue 594 GLU Chi-restraints excluded: chain 1a residue 570 MET Chi-restraints excluded: chain 1a residue 612 MET Chi-restraints excluded: chain 1b residue 499 MET Chi-restraints excluded: chain 1c residue 645 MET Chi-restraints excluded: chain 1d residue 468 LEU Chi-restraints excluded: chain 1e residue 446 TYR Chi-restraints excluded: chain 1e residue 636 ARG Chi-restraints excluded: chain 1f residue 570 MET Chi-restraints excluded: chain 1f residue 612 MET Chi-restraints excluded: chain 1g residue 570 MET Chi-restraints excluded: chain 1h residue 445 HIS Chi-restraints excluded: chain 1h residue 468 LEU Chi-restraints excluded: chain 1h residue 636 ARG Chi-restraints excluded: chain 1i residue 570 MET Chi-restraints excluded: chain 1k residue 445 HIS Chi-restraints excluded: chain 1k residue 645 MET Chi-restraints excluded: chain 1l residue 478 ASP Chi-restraints excluded: chain 1l residue 570 MET Chi-restraints excluded: chain 1m residue 446 TYR Chi-restraints excluded: chain 1m residue 502 VAL Chi-restraints excluded: chain 1n residue 445 HIS Chi-restraints excluded: chain 1n residue 556 HIS Chi-restraints excluded: chain 1n residue 570 MET Chi-restraints excluded: chain 1n residue 636 ARG Chi-restraints excluded: chain 1n residue 645 MET Chi-restraints excluded: chain 1o residue 570 MET Chi-restraints excluded: chain 1p residue 445 HIS Chi-restraints excluded: chain 1p residue 570 MET Chi-restraints excluded: chain 1p residue 588 LEU Chi-restraints excluded: chain 1p residue 645 MET Chi-restraints excluded: chain 1q residue 541 VAL Chi-restraints excluded: chain 1q residue 612 MET Chi-restraints excluded: chain 1s residue 469 GLU Chi-restraints excluded: chain 1s residue 612 MET Chi-restraints excluded: chain 1s residue 636 ARG Chi-restraints excluded: chain 1t residue 570 MET Chi-restraints excluded: chain 1t residue 612 MET Chi-restraints excluded: chain 1t residue 636 ARG Chi-restraints excluded: chain 1u residue 446 TYR Chi-restraints excluded: chain 1u residue 468 LEU Chi-restraints excluded: chain 1u residue 499 MET Chi-restraints excluded: chain 1u residue 636 ARG Chi-restraints excluded: chain 1v residue 556 HIS Chi-restraints excluded: chain 1v residue 570 MET Chi-restraints excluded: chain 1v residue 636 ARG Chi-restraints excluded: chain 1w residue 541 VAL Chi-restraints excluded: chain 1w residue 570 MET Chi-restraints excluded: chain 1x residue 445 HIS Chi-restraints excluded: chain 1x residue 588 LEU Chi-restraints excluded: chain 1x residue 645 MET Chi-restraints excluded: chain 1z residue 445 HIS Chi-restraints excluded: chain 1z residue 570 MET Chi-restraints excluded: chain 1z residue 612 MET Chi-restraints excluded: chain 2a residue 445 HIS Chi-restraints excluded: chain 2b residue 636 ARG Chi-restraints excluded: chain 2c residue 446 TYR Chi-restraints excluded: chain 2c residue 612 MET Chi-restraints excluded: chain 2c residue 636 ARG Chi-restraints excluded: chain 2d residue 636 ARG Chi-restraints excluded: chain 2h residue 446 TYR Chi-restraints excluded: chain 2i residue 446 TYR Chi-restraints excluded: chain 2i residue 570 MET Chi-restraints excluded: chain 2j residue 446 TYR Chi-restraints excluded: chain 2j residue 478 ASP Chi-restraints excluded: chain 2j residue 570 MET Chi-restraints excluded: chain 2j residue 594 GLU Chi-restraints excluded: chain 2k residue 445 HIS Chi-restraints excluded: chain 2k residue 556 HIS Chi-restraints excluded: chain 2k residue 570 MET Chi-restraints excluded: chain 2l residue 541 VAL Chi-restraints excluded: chain 2l residue 570 MET Chi-restraints excluded: chain 2l residue 612 MET Chi-restraints excluded: chain 2m residue 446 TYR Chi-restraints excluded: chain 2n residue 446 TYR Chi-restraints excluded: chain 2o residue 445 HIS Chi-restraints excluded: chain 2o residue 570 MET Chi-restraints excluded: chain 2o residue 636 ARG Chi-restraints excluded: chain 2o residue 645 MET Chi-restraints excluded: chain 2p residue 445 HIS Chi-restraints excluded: chain 2q residue 446 TYR Chi-restraints excluded: chain 2q residue 636 ARG Chi-restraints excluded: chain 2r residue 612 MET Chi-restraints excluded: chain 2r residue 636 ARG Chi-restraints excluded: chain 2s residue 445 HIS Chi-restraints excluded: chain 2s residue 612 MET Chi-restraints excluded: chain 2t residue 645 MET Chi-restraints excluded: chain 2u residue 570 MET Chi-restraints excluded: chain 2u residue 612 MET Chi-restraints excluded: chain 2v residue 446 TYR Chi-restraints excluded: chain 2v residue 468 LEU Chi-restraints excluded: chain 2v residue 570 MET Chi-restraints excluded: chain 2w residue 446 TYR Chi-restraints excluded: chain 2w residue 478 ASP Chi-restraints excluded: chain 2w residue 570 MET Chi-restraints excluded: chain 2w residue 594 GLU Chi-restraints excluded: chain 2x residue 446 TYR Chi-restraints excluded: chain 2x residue 468 LEU Chi-restraints excluded: chain 2x residue 570 MET Chi-restraints excluded: chain 2y residue 570 MET Chi-restraints excluded: chain 2z residue 468 LEU Chi-restraints excluded: chain 2z residue 612 MET Chi-restraints excluded: chain 2z residue 636 ARG Chi-restraints excluded: chain 3a residue 446 TYR Chi-restraints excluded: chain 3a residue 478 ASP Chi-restraints excluded: chain 3a residue 570 MET Chi-restraints excluded: chain 3b residue 446 TYR Chi-restraints excluded: chain 3c residue 446 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1320 random chunks: chunk 429 optimal weight: 0.7980 chunk 1149 optimal weight: 4.9990 chunk 252 optimal weight: 6.9990 chunk 749 optimal weight: 10.0000 chunk 314 optimal weight: 3.9990 chunk 1277 optimal weight: 5.9990 chunk 1060 optimal weight: 0.7980 chunk 591 optimal weight: 6.9990 chunk 106 optimal weight: 6.9990 chunk 422 optimal weight: 1.9990 chunk 670 optimal weight: 0.0770 overall best weight: 1.5342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1c 556 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1e 445 HIS ** 1g 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1l 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1n 556 HIS ** 1q 556 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1v 445 HIS ** 2f 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2i 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2j 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2m 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2u 556 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2x 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.2318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 106380 Z= 0.244 Angle : 0.561 11.420 144060 Z= 0.284 Chirality : 0.045 0.142 17220 Planarity : 0.004 0.051 18300 Dihedral : 4.861 42.638 14223 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 1.77 % Allowed : 11.81 % Favored : 86.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.07), residues: 13320 helix: 1.90 (0.07), residues: 5280 sheet: 0.21 (0.09), residues: 2700 loop : -0.06 (0.09), residues: 5340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP2l 498 HIS 0.008 0.001 HIS1n 556 PHE 0.014 0.001 PHE1h 558 TYR 0.032 0.002 TYR03 446 ARG 0.003 0.000 ARG1w 429 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26640 Ramachandran restraints generated. 13320 Oldfield, 0 Emsley, 13320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26640 Ramachandran restraints generated. 13320 Oldfield, 0 Emsley, 13320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 881 residues out of total 11700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 207 poor density : 674 time to evaluate : 9.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 01 434 GLN cc_start: 0.8170 (OUTLIER) cc_final: 0.7915 (mp10) REVERT: 01 437 MET cc_start: 0.8925 (tmm) cc_final: 0.8269 (tmm) REVERT: 02 437 MET cc_start: 0.8893 (tmm) cc_final: 0.8259 (tmm) REVERT: 03 636 ARG cc_start: 0.8790 (OUTLIER) cc_final: 0.7883 (ttm-80) REVERT: 04 467 MET cc_start: 0.8243 (mmm) cc_final: 0.8036 (tpp) REVERT: 05 454 MET cc_start: 0.8655 (mmm) cc_final: 0.8162 (mmm) REVERT: 05 645 MET cc_start: 0.9001 (OUTLIER) cc_final: 0.8645 (mtp) REVERT: 0z 437 MET cc_start: 0.8951 (tmm) cc_final: 0.8316 (tmm) REVERT: 1b 437 MET cc_start: 0.8811 (tpt) cc_final: 0.8380 (tpt) REVERT: 1b 445 HIS cc_start: 0.7753 (m90) cc_final: 0.7401 (m90) REVERT: 1b 454 MET cc_start: 0.9097 (mmm) cc_final: 0.8027 (mmm) REVERT: 1b 645 MET cc_start: 0.9029 (mtm) cc_final: 0.8532 (mtp) REVERT: 1d 434 GLN cc_start: 0.7976 (mt0) cc_final: 0.7681 (mt0) REVERT: 1e 434 GLN cc_start: 0.7971 (mt0) cc_final: 0.7629 (mt0) REVERT: 1g 645 MET cc_start: 0.9151 (mtm) cc_final: 0.8782 (mtp) REVERT: 1h 558 PHE cc_start: 0.7698 (t80) cc_final: 0.7247 (t80) REVERT: 1h 645 MET cc_start: 0.8652 (mtp) cc_final: 0.8313 (mtp) REVERT: 1i 636 ARG cc_start: 0.8792 (OUTLIER) cc_final: 0.7890 (ttm-80) REVERT: 1j 445 HIS cc_start: 0.8060 (m90) cc_final: 0.7621 (m90) REVERT: 1j 570 MET cc_start: 0.7951 (ppp) cc_final: 0.7689 (ptp) REVERT: 1k 434 GLN cc_start: 0.7526 (mp10) cc_final: 0.7182 (mp10) REVERT: 1k 454 MET cc_start: 0.8927 (mmm) cc_final: 0.8472 (mmm) REVERT: 1k 595 ASP cc_start: 0.8614 (OUTLIER) cc_final: 0.8279 (p0) REVERT: 1l 535 GLU cc_start: 0.8321 (tm-30) cc_final: 0.8024 (tm-30) REVERT: 1m 437 MET cc_start: 0.9350 (tpp) cc_final: 0.9010 (tpp) REVERT: 1n 570 MET cc_start: 0.7722 (OUTLIER) cc_final: 0.7385 (ptp) REVERT: 1r 437 MET cc_start: 0.8964 (tmm) cc_final: 0.8133 (tmm) REVERT: 1s 467 MET cc_start: 0.8363 (tpp) cc_final: 0.8093 (tpp) REVERT: 1t 434 GLN cc_start: 0.8018 (mt0) cc_final: 0.7801 (mt0) REVERT: 1u 467 MET cc_start: 0.8397 (mmm) cc_final: 0.8035 (tpp) REVERT: 1v 437 MET cc_start: 0.9237 (tpt) cc_final: 0.8195 (tmm) REVERT: 1v 645 MET cc_start: 0.8681 (mtp) cc_final: 0.8404 (mtp) REVERT: 1x 434 GLN cc_start: 0.8213 (mp10) cc_final: 0.7717 (mp10) REVERT: 1x 454 MET cc_start: 0.8979 (mmm) cc_final: 0.8434 (mmm) REVERT: 2a 437 MET cc_start: 0.9406 (tpt) cc_final: 0.9152 (tpt) REVERT: 2a 467 MET cc_start: 0.8441 (mmm) cc_final: 0.8103 (tpp) REVERT: 2b 467 MET cc_start: 0.8382 (tpp) cc_final: 0.8047 (tpp) REVERT: 2c 467 MET cc_start: 0.8411 (tpp) cc_final: 0.8123 (tpp) REVERT: 2d 454 MET cc_start: 0.9112 (mmm) cc_final: 0.8763 (mmm) REVERT: 2f 454 MET cc_start: 0.8907 (mmm) cc_final: 0.8449 (mmm) REVERT: 2g 437 MET cc_start: 0.9075 (tmm) cc_final: 0.8645 (tmm) REVERT: 2h 437 MET cc_start: 0.8978 (tmm) cc_final: 0.8300 (tmm) REVERT: 2h 509 VAL cc_start: 0.9296 (OUTLIER) cc_final: 0.8987 (m) REVERT: 2i 437 MET cc_start: 0.8897 (tmm) cc_final: 0.8323 (tmm) REVERT: 2j 437 MET cc_start: 0.8941 (tmm) cc_final: 0.8338 (tmm) REVERT: 2k 645 MET cc_start: 0.8698 (mtp) cc_final: 0.8384 (mtp) REVERT: 2l 437 MET cc_start: 0.8891 (tmm) cc_final: 0.8050 (tmm) REVERT: 2l 535 GLU cc_start: 0.8123 (tm-30) cc_final: 0.7588 (tm-30) REVERT: 2l 611 MET cc_start: 0.8677 (mmm) cc_final: 0.8427 (mmm) REVERT: 2m 467 MET cc_start: 0.8794 (tmm) cc_final: 0.8487 (tmm) REVERT: 2n 467 MET cc_start: 0.8229 (tpp) cc_final: 0.7813 (tpp) REVERT: 2o 570 MET cc_start: 0.7791 (OUTLIER) cc_final: 0.7545 (ptp) REVERT: 2q 454 MET cc_start: 0.9101 (mmm) cc_final: 0.8821 (mmm) REVERT: 2s 554 GLN cc_start: 0.8155 (tm-30) cc_final: 0.7853 (tm-30) REVERT: 2s 611 MET cc_start: 0.8691 (mmm) cc_final: 0.8385 (mmm) REVERT: 2u 467 MET cc_start: 0.8722 (tmm) cc_final: 0.8437 (tmm) REVERT: 2v 437 MET cc_start: 0.8981 (tmm) cc_final: 0.8281 (tmm) REVERT: 2w 437 MET cc_start: 0.8956 (tmm) cc_final: 0.8295 (tmm) REVERT: 2x 437 MET cc_start: 0.8953 (tmm) cc_final: 0.8233 (tmm) REVERT: 2y 467 MET cc_start: 0.8234 (mmm) cc_final: 0.7835 (tpp) REVERT: 2y 645 MET cc_start: 0.8772 (mtm) cc_final: 0.8373 (mtm) REVERT: 3a 437 MET cc_start: 0.8913 (tmm) cc_final: 0.8261 (tmm) REVERT: 3a 467 MET cc_start: 0.8167 (tpp) cc_final: 0.7911 (tpp) REVERT: 3b 437 MET cc_start: 0.8959 (tmm) cc_final: 0.8319 (tmm) REVERT: 3c 437 MET cc_start: 0.9006 (tmm) cc_final: 0.8367 (tmm) outliers start: 207 outliers final: 131 residues processed: 785 average time/residue: 0.8766 time to fit residues: 1207.2838 Evaluate side-chains 802 residues out of total 11700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 663 time to evaluate : 9.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 01 residue 434 GLN Chi-restraints excluded: chain 01 residue 446 TYR Chi-restraints excluded: chain 02 residue 446 TYR Chi-restraints excluded: chain 03 residue 445 HIS Chi-restraints excluded: chain 03 residue 541 VAL Chi-restraints excluded: chain 03 residue 612 MET Chi-restraints excluded: chain 03 residue 636 ARG Chi-restraints excluded: chain 05 residue 468 LEU Chi-restraints excluded: chain 05 residue 556 HIS Chi-restraints excluded: chain 05 residue 570 MET Chi-restraints excluded: chain 05 residue 636 ARG Chi-restraints excluded: chain 05 residue 645 MET Chi-restraints excluded: chain 0z residue 446 TYR Chi-restraints excluded: chain 0z residue 468 LEU Chi-restraints excluded: chain 0z residue 478 ASP Chi-restraints excluded: chain 0z residue 594 GLU Chi-restraints excluded: chain 1a residue 612 MET Chi-restraints excluded: chain 1b residue 499 MET Chi-restraints excluded: chain 1c residue 636 ARG Chi-restraints excluded: chain 1c residue 645 MET Chi-restraints excluded: chain 1d residue 446 TYR Chi-restraints excluded: chain 1e residue 446 TYR Chi-restraints excluded: chain 1f residue 570 MET Chi-restraints excluded: chain 1f residue 612 MET Chi-restraints excluded: chain 1h residue 445 HIS Chi-restraints excluded: chain 1h residue 468 LEU Chi-restraints excluded: chain 1h residue 636 ARG Chi-restraints excluded: chain 1i residue 612 MET Chi-restraints excluded: chain 1i residue 636 ARG Chi-restraints excluded: chain 1j residue 499 MET Chi-restraints excluded: chain 1k residue 445 HIS Chi-restraints excluded: chain 1k residue 468 LEU Chi-restraints excluded: chain 1k residue 556 HIS Chi-restraints excluded: chain 1k residue 595 ASP Chi-restraints excluded: chain 1k residue 645 MET Chi-restraints excluded: chain 1l residue 478 ASP Chi-restraints excluded: chain 1l residue 541 VAL Chi-restraints excluded: chain 1m residue 446 TYR Chi-restraints excluded: chain 1m residue 502 VAL Chi-restraints excluded: chain 1n residue 445 HIS Chi-restraints excluded: chain 1n residue 556 HIS Chi-restraints excluded: chain 1n residue 570 MET Chi-restraints excluded: chain 1n residue 636 ARG Chi-restraints excluded: chain 1n residue 645 MET Chi-restraints excluded: chain 1o residue 446 TYR Chi-restraints excluded: chain 1o residue 570 MET Chi-restraints excluded: chain 1p residue 445 HIS Chi-restraints excluded: chain 1p residue 570 MET Chi-restraints excluded: chain 1p residue 588 LEU Chi-restraints excluded: chain 1p residue 612 MET Chi-restraints excluded: chain 1p residue 645 MET Chi-restraints excluded: chain 1q residue 541 VAL Chi-restraints excluded: chain 1q residue 612 MET Chi-restraints excluded: chain 1r residue 427 ASN Chi-restraints excluded: chain 1s residue 612 MET Chi-restraints excluded: chain 1s residue 636 ARG Chi-restraints excluded: chain 1t residue 468 LEU Chi-restraints excluded: chain 1t residue 570 MET Chi-restraints excluded: chain 1t residue 612 MET Chi-restraints excluded: chain 1t residue 636 ARG Chi-restraints excluded: chain 1u residue 446 TYR Chi-restraints excluded: chain 1u residue 468 LEU Chi-restraints excluded: chain 1u residue 499 MET Chi-restraints excluded: chain 1u residue 636 ARG Chi-restraints excluded: chain 1v residue 556 HIS Chi-restraints excluded: chain 1v residue 636 ARG Chi-restraints excluded: chain 1w residue 541 VAL Chi-restraints excluded: chain 1w residue 570 MET Chi-restraints excluded: chain 1x residue 445 HIS Chi-restraints excluded: chain 1x residue 556 HIS Chi-restraints excluded: chain 1x residue 645 MET Chi-restraints excluded: chain 1z residue 445 HIS Chi-restraints excluded: chain 1z residue 612 MET Chi-restraints excluded: chain 2a residue 445 HIS Chi-restraints excluded: chain 2a residue 499 MET Chi-restraints excluded: chain 2a residue 502 VAL Chi-restraints excluded: chain 2b residue 636 ARG Chi-restraints excluded: chain 2c residue 446 TYR Chi-restraints excluded: chain 2c residue 612 MET Chi-restraints excluded: chain 2c residue 636 ARG Chi-restraints excluded: chain 2d residue 499 MET Chi-restraints excluded: chain 2e residue 468 LEU Chi-restraints excluded: chain 2g residue 612 MET Chi-restraints excluded: chain 2h residue 446 TYR Chi-restraints excluded: chain 2h residue 509 VAL Chi-restraints excluded: chain 2i residue 446 TYR Chi-restraints excluded: chain 2j residue 446 TYR Chi-restraints excluded: chain 2j residue 570 MET Chi-restraints excluded: chain 2j residue 594 GLU Chi-restraints excluded: chain 2k residue 445 HIS Chi-restraints excluded: chain 2k residue 556 HIS Chi-restraints excluded: chain 2k residue 570 MET Chi-restraints excluded: chain 2k residue 636 ARG Chi-restraints excluded: chain 2l residue 541 VAL Chi-restraints excluded: chain 2l residue 570 MET Chi-restraints excluded: chain 2l residue 612 MET Chi-restraints excluded: chain 2m residue 446 TYR Chi-restraints excluded: chain 2m residue 468 LEU Chi-restraints excluded: chain 2m residue 612 MET Chi-restraints excluded: chain 2n residue 446 TYR Chi-restraints excluded: chain 2o residue 445 HIS Chi-restraints excluded: chain 2o residue 570 MET Chi-restraints excluded: chain 2o residue 636 ARG Chi-restraints excluded: chain 2o residue 645 MET Chi-restraints excluded: chain 2p residue 445 HIS Chi-restraints excluded: chain 2p residue 612 MET Chi-restraints excluded: chain 2q residue 446 TYR Chi-restraints excluded: chain 2r residue 612 MET Chi-restraints excluded: chain 2r residue 636 ARG Chi-restraints excluded: chain 2s residue 445 HIS Chi-restraints excluded: chain 2s residue 612 MET Chi-restraints excluded: chain 2t residue 468 LEU Chi-restraints excluded: chain 2t residue 612 MET Chi-restraints excluded: chain 2t residue 645 MET Chi-restraints excluded: chain 2u residue 446 TYR Chi-restraints excluded: chain 2u residue 541 VAL Chi-restraints excluded: chain 2u residue 570 MET Chi-restraints excluded: chain 2u residue 612 MET Chi-restraints excluded: chain 2v residue 446 TYR Chi-restraints excluded: chain 2v residue 468 LEU Chi-restraints excluded: chain 2v residue 570 MET Chi-restraints excluded: chain 2w residue 446 TYR Chi-restraints excluded: chain 2w residue 478 ASP Chi-restraints excluded: chain 2w residue 570 MET Chi-restraints excluded: chain 2w residue 594 GLU Chi-restraints excluded: chain 2x residue 446 TYR Chi-restraints excluded: chain 2x residue 468 LEU Chi-restraints excluded: chain 2x residue 570 MET Chi-restraints excluded: chain 2x residue 594 GLU Chi-restraints excluded: chain 2y residue 570 MET Chi-restraints excluded: chain 2y residue 594 GLU Chi-restraints excluded: chain 2z residue 468 LEU Chi-restraints excluded: chain 2z residue 612 MET Chi-restraints excluded: chain 2z residue 636 ARG Chi-restraints excluded: chain 3a residue 446 TYR Chi-restraints excluded: chain 3b residue 446 TYR Chi-restraints excluded: chain 3b residue 570 MET Chi-restraints excluded: chain 3c residue 446 TYR Chi-restraints excluded: chain 3c residue 468 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1320 random chunks: chunk 1231 optimal weight: 0.6980 chunk 143 optimal weight: 0.8980 chunk 727 optimal weight: 4.9990 chunk 932 optimal weight: 6.9990 chunk 722 optimal weight: 4.9990 chunk 1075 optimal weight: 6.9990 chunk 713 optimal weight: 0.7980 chunk 1272 optimal weight: 4.9990 chunk 796 optimal weight: 0.9980 chunk 775 optimal weight: 5.9990 chunk 587 optimal weight: 4.9990 overall best weight: 1.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1c 445 HIS ** 1c 556 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1e 445 HIS ** 1g 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1l 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1q 556 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2f 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2j 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2k 434 GLN ** 2m 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2u 556 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2x 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 106380 Z= 0.260 Angle : 0.571 12.108 144060 Z= 0.289 Chirality : 0.045 0.156 17220 Planarity : 0.004 0.053 18300 Dihedral : 4.883 34.703 14220 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 1.74 % Allowed : 12.15 % Favored : 86.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.07), residues: 13320 helix: 1.90 (0.07), residues: 5280 sheet: 0.14 (0.10), residues: 2700 loop : -0.07 (0.09), residues: 5340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP2l 498 HIS 0.007 0.001 HIS1n 556 PHE 0.017 0.001 PHE1h 558 TYR 0.031 0.002 TYR03 446 ARG 0.003 0.000 ARG1w 429 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26640 Ramachandran restraints generated. 13320 Oldfield, 0 Emsley, 13320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26640 Ramachandran restraints generated. 13320 Oldfield, 0 Emsley, 13320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 870 residues out of total 11700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 203 poor density : 667 time to evaluate : 9.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 01 437 MET cc_start: 0.8907 (tmm) cc_final: 0.8259 (tmm) REVERT: 02 437 MET cc_start: 0.8876 (tmm) cc_final: 0.8268 (tmm) REVERT: 05 454 MET cc_start: 0.8719 (mmm) cc_final: 0.8173 (mmm) REVERT: 05 645 MET cc_start: 0.8999 (OUTLIER) cc_final: 0.8672 (mtp) REVERT: 0z 437 MET cc_start: 0.8965 (tmm) cc_final: 0.8344 (tmm) REVERT: 1b 437 MET cc_start: 0.8816 (tpt) cc_final: 0.8388 (tpt) REVERT: 1b 445 HIS cc_start: 0.7786 (m90) cc_final: 0.7427 (m90) REVERT: 1b 645 MET cc_start: 0.9035 (mtm) cc_final: 0.8527 (mtp) REVERT: 1d 434 GLN cc_start: 0.7989 (mt0) cc_final: 0.7683 (mt0) REVERT: 1e 434 GLN cc_start: 0.8029 (mt0) cc_final: 0.7678 (mt0) REVERT: 1g 636 ARG cc_start: 0.8761 (OUTLIER) cc_final: 0.7690 (ttm-80) REVERT: 1g 645 MET cc_start: 0.9151 (mtm) cc_final: 0.8777 (mtp) REVERT: 1h 645 MET cc_start: 0.8657 (mtp) cc_final: 0.8316 (mtp) REVERT: 1i 636 ARG cc_start: 0.8802 (OUTLIER) cc_final: 0.7870 (ttm-80) REVERT: 1j 445 HIS cc_start: 0.8137 (m90) cc_final: 0.7698 (m90) REVERT: 1j 570 MET cc_start: 0.8038 (ppp) cc_final: 0.7706 (ptp) REVERT: 1k 434 GLN cc_start: 0.7841 (mt0) cc_final: 0.7547 (mp10) REVERT: 1k 595 ASP cc_start: 0.8626 (OUTLIER) cc_final: 0.8286 (p0) REVERT: 1l 535 GLU cc_start: 0.8309 (tm-30) cc_final: 0.8098 (tm-30) REVERT: 1m 437 MET cc_start: 0.9344 (tpp) cc_final: 0.8990 (tpp) REVERT: 1n 570 MET cc_start: 0.7733 (OUTLIER) cc_final: 0.7409 (ptp) REVERT: 1q 636 ARG cc_start: 0.8836 (OUTLIER) cc_final: 0.7892 (ttm-80) REVERT: 1r 437 MET cc_start: 0.8955 (tmm) cc_final: 0.8185 (tmm) REVERT: 1r 454 MET cc_start: 0.9087 (mmm) cc_final: 0.8225 (mmm) REVERT: 1s 434 GLN cc_start: 0.8011 (mt0) cc_final: 0.7567 (mp10) REVERT: 1s 467 MET cc_start: 0.8342 (tpp) cc_final: 0.8099 (tpp) REVERT: 1t 434 GLN cc_start: 0.8004 (mt0) cc_final: 0.7755 (mt0) REVERT: 1u 467 MET cc_start: 0.8388 (mmm) cc_final: 0.8054 (tpp) REVERT: 1v 437 MET cc_start: 0.9232 (tpt) cc_final: 0.8251 (tmm) REVERT: 1v 645 MET cc_start: 0.8688 (mtp) cc_final: 0.8404 (mtp) REVERT: 1x 434 GLN cc_start: 0.8221 (mp10) cc_final: 0.7695 (mp10) REVERT: 1x 454 MET cc_start: 0.8975 (mmm) cc_final: 0.8331 (mmm) REVERT: 2a 467 MET cc_start: 0.8427 (mmm) cc_final: 0.8125 (tpp) REVERT: 2b 454 MET cc_start: 0.9080 (mmm) cc_final: 0.8831 (mmm) REVERT: 2b 467 MET cc_start: 0.8391 (tpp) cc_final: 0.8055 (tpp) REVERT: 2c 437 MET cc_start: 0.9297 (tpp) cc_final: 0.8788 (tpt) REVERT: 2c 467 MET cc_start: 0.8418 (tpp) cc_final: 0.8123 (tpp) REVERT: 2d 454 MET cc_start: 0.9120 (mmm) cc_final: 0.8833 (mmm) REVERT: 2h 437 MET cc_start: 0.8960 (tmm) cc_final: 0.8313 (tmm) REVERT: 2h 509 VAL cc_start: 0.9309 (OUTLIER) cc_final: 0.8993 (m) REVERT: 2i 437 MET cc_start: 0.8811 (tmm) cc_final: 0.8218 (tmm) REVERT: 2j 437 MET cc_start: 0.8904 (tmm) cc_final: 0.8304 (tmm) REVERT: 2k 645 MET cc_start: 0.8698 (mtp) cc_final: 0.8385 (mtp) REVERT: 2l 535 GLU cc_start: 0.8083 (tm-30) cc_final: 0.7519 (tm-30) REVERT: 2l 611 MET cc_start: 0.8698 (mmm) cc_final: 0.8439 (mmm) REVERT: 2m 467 MET cc_start: 0.8708 (tmm) cc_final: 0.8452 (tmm) REVERT: 2n 467 MET cc_start: 0.8129 (tpp) cc_final: 0.7758 (tpp) REVERT: 2o 570 MET cc_start: 0.7799 (OUTLIER) cc_final: 0.7545 (ptp) REVERT: 2q 454 MET cc_start: 0.9107 (mmm) cc_final: 0.8883 (mmm) REVERT: 2s 554 GLN cc_start: 0.8166 (tm-30) cc_final: 0.7859 (tm-30) REVERT: 2s 611 MET cc_start: 0.8677 (mmm) cc_final: 0.8368 (mmm) REVERT: 2v 437 MET cc_start: 0.8957 (tmm) cc_final: 0.8336 (tmm) REVERT: 2w 437 MET cc_start: 0.8941 (tmm) cc_final: 0.8293 (tmm) REVERT: 2x 437 MET cc_start: 0.8952 (tmm) cc_final: 0.8204 (tmm) REVERT: 2y 467 MET cc_start: 0.8211 (mmm) cc_final: 0.7854 (tpp) REVERT: 2y 645 MET cc_start: 0.8800 (mtm) cc_final: 0.8380 (mtm) REVERT: 3a 437 MET cc_start: 0.8904 (tmm) cc_final: 0.8270 (tmm) REVERT: 3a 467 MET cc_start: 0.8119 (tpp) cc_final: 0.7871 (tpp) REVERT: 3a 611 MET cc_start: 0.9201 (mmt) cc_final: 0.8996 (mmp) REVERT: 3b 437 MET cc_start: 0.8932 (tmm) cc_final: 0.8277 (tmm) REVERT: 3c 437 MET cc_start: 0.8994 (tmm) cc_final: 0.8361 (tmm) outliers start: 203 outliers final: 146 residues processed: 774 average time/residue: 0.8758 time to fit residues: 1204.0102 Evaluate side-chains 811 residues out of total 11700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 657 time to evaluate : 9.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 01 residue 446 TYR Chi-restraints excluded: chain 02 residue 446 TYR Chi-restraints excluded: chain 03 residue 445 HIS Chi-restraints excluded: chain 03 residue 541 VAL Chi-restraints excluded: chain 03 residue 612 MET Chi-restraints excluded: chain 05 residue 468 LEU Chi-restraints excluded: chain 05 residue 556 HIS Chi-restraints excluded: chain 05 residue 570 MET Chi-restraints excluded: chain 05 residue 636 ARG Chi-restraints excluded: chain 05 residue 645 MET Chi-restraints excluded: chain 0z residue 446 TYR Chi-restraints excluded: chain 0z residue 468 LEU Chi-restraints excluded: chain 0z residue 478 ASP Chi-restraints excluded: chain 0z residue 570 MET Chi-restraints excluded: chain 0z residue 594 GLU Chi-restraints excluded: chain 1a residue 478 ASP Chi-restraints excluded: chain 1a residue 612 MET Chi-restraints excluded: chain 1b residue 499 MET Chi-restraints excluded: chain 1b residue 570 MET Chi-restraints excluded: chain 1c residue 469 GLU Chi-restraints excluded: chain 1c residue 645 MET Chi-restraints excluded: chain 1d residue 446 TYR Chi-restraints excluded: chain 1e residue 446 TYR Chi-restraints excluded: chain 1f residue 570 MET Chi-restraints excluded: chain 1f residue 612 MET Chi-restraints excluded: chain 1f residue 636 ARG Chi-restraints excluded: chain 1g residue 446 TYR Chi-restraints excluded: chain 1g residue 636 ARG Chi-restraints excluded: chain 1h residue 445 HIS Chi-restraints excluded: chain 1h residue 468 LEU Chi-restraints excluded: chain 1h residue 636 ARG Chi-restraints excluded: chain 1i residue 468 LEU Chi-restraints excluded: chain 1i residue 541 VAL Chi-restraints excluded: chain 1i residue 570 MET Chi-restraints excluded: chain 1i residue 612 MET Chi-restraints excluded: chain 1i residue 636 ARG Chi-restraints excluded: chain 1j residue 499 MET Chi-restraints excluded: chain 1k residue 445 HIS Chi-restraints excluded: chain 1k residue 595 ASP Chi-restraints excluded: chain 1k residue 645 MET Chi-restraints excluded: chain 1l residue 478 ASP Chi-restraints excluded: chain 1l residue 541 VAL Chi-restraints excluded: chain 1m residue 446 TYR Chi-restraints excluded: chain 1m residue 502 VAL Chi-restraints excluded: chain 1n residue 445 HIS Chi-restraints excluded: chain 1n residue 556 HIS Chi-restraints excluded: chain 1n residue 570 MET Chi-restraints excluded: chain 1n residue 588 LEU Chi-restraints excluded: chain 1n residue 636 ARG Chi-restraints excluded: chain 1n residue 645 MET Chi-restraints excluded: chain 1o residue 446 TYR Chi-restraints excluded: chain 1o residue 570 MET Chi-restraints excluded: chain 1p residue 445 HIS Chi-restraints excluded: chain 1p residue 570 MET Chi-restraints excluded: chain 1p residue 588 LEU Chi-restraints excluded: chain 1p residue 645 MET Chi-restraints excluded: chain 1q residue 541 VAL Chi-restraints excluded: chain 1q residue 612 MET Chi-restraints excluded: chain 1q residue 636 ARG Chi-restraints excluded: chain 1r residue 427 ASN Chi-restraints excluded: chain 1s residue 612 MET Chi-restraints excluded: chain 1s residue 636 ARG Chi-restraints excluded: chain 1t residue 570 MET Chi-restraints excluded: chain 1t residue 612 MET Chi-restraints excluded: chain 1t residue 636 ARG Chi-restraints excluded: chain 1u residue 446 TYR Chi-restraints excluded: chain 1u residue 499 MET Chi-restraints excluded: chain 1u residue 636 ARG Chi-restraints excluded: chain 1v residue 556 HIS Chi-restraints excluded: chain 1v residue 636 ARG Chi-restraints excluded: chain 1w residue 478 ASP Chi-restraints excluded: chain 1w residue 541 VAL Chi-restraints excluded: chain 1w residue 570 MET Chi-restraints excluded: chain 1x residue 445 HIS Chi-restraints excluded: chain 1x residue 556 HIS Chi-restraints excluded: chain 1x residue 636 ARG Chi-restraints excluded: chain 1x residue 645 MET Chi-restraints excluded: chain 1z residue 445 HIS Chi-restraints excluded: chain 1z residue 612 MET Chi-restraints excluded: chain 2a residue 445 HIS Chi-restraints excluded: chain 2a residue 499 MET Chi-restraints excluded: chain 2a residue 502 VAL Chi-restraints excluded: chain 2b residue 636 ARG Chi-restraints excluded: chain 2c residue 446 TYR Chi-restraints excluded: chain 2c residue 499 MET Chi-restraints excluded: chain 2c residue 612 MET Chi-restraints excluded: chain 2c residue 636 ARG Chi-restraints excluded: chain 2d residue 446 TYR Chi-restraints excluded: chain 2d residue 499 MET Chi-restraints excluded: chain 2d residue 636 ARG Chi-restraints excluded: chain 2e residue 446 TYR Chi-restraints excluded: chain 2g residue 612 MET Chi-restraints excluded: chain 2h residue 446 TYR Chi-restraints excluded: chain 2h residue 509 VAL Chi-restraints excluded: chain 2i residue 446 TYR Chi-restraints excluded: chain 2i residue 570 MET Chi-restraints excluded: chain 2j residue 446 TYR Chi-restraints excluded: chain 2j residue 478 ASP Chi-restraints excluded: chain 2j residue 570 MET Chi-restraints excluded: chain 2j residue 594 GLU Chi-restraints excluded: chain 2k residue 445 HIS Chi-restraints excluded: chain 2k residue 556 HIS Chi-restraints excluded: chain 2k residue 570 MET Chi-restraints excluded: chain 2k residue 636 ARG Chi-restraints excluded: chain 2l residue 541 VAL Chi-restraints excluded: chain 2l residue 612 MET Chi-restraints excluded: chain 2m residue 446 TYR Chi-restraints excluded: chain 2m residue 468 LEU Chi-restraints excluded: chain 2m residue 612 MET Chi-restraints excluded: chain 2n residue 446 TYR Chi-restraints excluded: chain 2o residue 445 HIS Chi-restraints excluded: chain 2o residue 468 LEU Chi-restraints excluded: chain 2o residue 570 MET Chi-restraints excluded: chain 2o residue 636 ARG Chi-restraints excluded: chain 2o residue 645 MET Chi-restraints excluded: chain 2p residue 445 HIS Chi-restraints excluded: chain 2p residue 612 MET Chi-restraints excluded: chain 2q residue 446 TYR Chi-restraints excluded: chain 2q residue 469 GLU Chi-restraints excluded: chain 2r residue 468 LEU Chi-restraints excluded: chain 2r residue 612 MET Chi-restraints excluded: chain 2s residue 445 HIS Chi-restraints excluded: chain 2s residue 468 LEU Chi-restraints excluded: chain 2s residue 541 VAL Chi-restraints excluded: chain 2s residue 612 MET Chi-restraints excluded: chain 2t residue 468 LEU Chi-restraints excluded: chain 2t residue 612 MET Chi-restraints excluded: chain 2t residue 645 MET Chi-restraints excluded: chain 2u residue 446 TYR Chi-restraints excluded: chain 2u residue 541 VAL Chi-restraints excluded: chain 2u residue 570 MET Chi-restraints excluded: chain 2u residue 612 MET Chi-restraints excluded: chain 2v residue 446 TYR Chi-restraints excluded: chain 2v residue 468 LEU Chi-restraints excluded: chain 2v residue 570 MET Chi-restraints excluded: chain 2w residue 446 TYR Chi-restraints excluded: chain 2w residue 478 ASP Chi-restraints excluded: chain 2w residue 570 MET Chi-restraints excluded: chain 2w residue 594 GLU Chi-restraints excluded: chain 2x residue 446 TYR Chi-restraints excluded: chain 2x residue 468 LEU Chi-restraints excluded: chain 2x residue 570 MET Chi-restraints excluded: chain 2x residue 594 GLU Chi-restraints excluded: chain 2y residue 570 MET Chi-restraints excluded: chain 2y residue 594 GLU Chi-restraints excluded: chain 2z residue 468 LEU Chi-restraints excluded: chain 2z residue 612 MET Chi-restraints excluded: chain 2z residue 636 ARG Chi-restraints excluded: chain 3a residue 446 TYR Chi-restraints excluded: chain 3a residue 594 GLU Chi-restraints excluded: chain 3b residue 446 TYR Chi-restraints excluded: chain 3b residue 570 MET Chi-restraints excluded: chain 3c residue 446 TYR Chi-restraints excluded: chain 3c residue 468 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1320 random chunks: chunk 787 optimal weight: 4.9990 chunk 508 optimal weight: 3.9990 chunk 759 optimal weight: 0.9980 chunk 383 optimal weight: 2.9990 chunk 249 optimal weight: 3.9990 chunk 246 optimal weight: 0.6980 chunk 808 optimal weight: 2.9990 chunk 866 optimal weight: 2.9990 chunk 629 optimal weight: 5.9990 chunk 118 optimal weight: 0.9990 chunk 1000 optimal weight: 0.1980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1a 581 ASN 1a 584 GLN ** 1c 556 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1c 581 ASN 1c 584 GLN 1e 445 HIS ** 1g 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1l 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1q 556 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1s 434 GLN 1u 434 GLN 1v 445 HIS ** 2f 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2j 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2k 434 GLN ** 2m 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2q 581 ASN 2q 584 GLN ** 2s 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2u 556 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2x 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 106380 Z= 0.199 Angle : 0.558 12.497 144060 Z= 0.279 Chirality : 0.044 0.160 17220 Planarity : 0.004 0.054 18300 Dihedral : 4.741 32.411 14220 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 1.50 % Allowed : 12.56 % Favored : 85.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.07), residues: 13320 helix: 1.96 (0.07), residues: 5280 sheet: 0.16 (0.09), residues: 3000 loop : 0.20 (0.10), residues: 5040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP2t 498 HIS 0.003 0.000 HIS2s 445 PHE 0.012 0.001 PHE1h 558 TYR 0.030 0.002 TYR2l 446 ARG 0.003 0.000 ARG05 430 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26640 Ramachandran restraints generated. 13320 Oldfield, 0 Emsley, 13320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26640 Ramachandran restraints generated. 13320 Oldfield, 0 Emsley, 13320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 860 residues out of total 11700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 684 time to evaluate : 9.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 01 437 MET cc_start: 0.8915 (tmm) cc_final: 0.8267 (tmm) REVERT: 02 434 GLN cc_start: 0.8077 (mp10) cc_final: 0.7837 (mp10) REVERT: 02 437 MET cc_start: 0.8888 (tmm) cc_final: 0.8264 (tmm) REVERT: 03 467 MET cc_start: 0.8353 (tmm) cc_final: 0.7988 (tmm) REVERT: 03 636 ARG cc_start: 0.8777 (OUTLIER) cc_final: 0.7908 (ttm-80) REVERT: 05 454 MET cc_start: 0.8739 (mmm) cc_final: 0.8205 (mmm) REVERT: 05 645 MET cc_start: 0.8945 (OUTLIER) cc_final: 0.8679 (mtp) REVERT: 0z 437 MET cc_start: 0.8983 (tmm) cc_final: 0.8344 (tmm) REVERT: 1a 467 MET cc_start: 0.8544 (tmm) cc_final: 0.8321 (tmm) REVERT: 1b 437 MET cc_start: 0.8815 (tpt) cc_final: 0.8362 (tpt) REVERT: 1b 445 HIS cc_start: 0.7691 (m90) cc_final: 0.7370 (m90) REVERT: 1b 454 MET cc_start: 0.9031 (mmm) cc_final: 0.8094 (mmm) REVERT: 1b 645 MET cc_start: 0.9018 (mtm) cc_final: 0.8511 (mtp) REVERT: 1d 434 GLN cc_start: 0.7966 (mt0) cc_final: 0.7663 (mt0) REVERT: 1d 437 MET cc_start: 0.9323 (tpt) cc_final: 0.9120 (tpt) REVERT: 1e 434 GLN cc_start: 0.7996 (mt0) cc_final: 0.7652 (mt0) REVERT: 1f 437 MET cc_start: 0.9370 (tpt) cc_final: 0.9130 (tpt) REVERT: 1g 636 ARG cc_start: 0.8737 (OUTLIER) cc_final: 0.7674 (ttm-80) REVERT: 1g 645 MET cc_start: 0.9135 (mtm) cc_final: 0.8755 (mtp) REVERT: 1h 645 MET cc_start: 0.8600 (mtp) cc_final: 0.8238 (mtp) REVERT: 1i 467 MET cc_start: 0.8485 (tmm) cc_final: 0.8267 (tmm) REVERT: 1i 636 ARG cc_start: 0.8779 (OUTLIER) cc_final: 0.7893 (ttm-80) REVERT: 1j 445 HIS cc_start: 0.8077 (m90) cc_final: 0.7634 (m90) REVERT: 1j 570 MET cc_start: 0.8095 (ppp) cc_final: 0.7734 (ptp) REVERT: 1k 434 GLN cc_start: 0.7877 (mt0) cc_final: 0.7630 (mp10) REVERT: 1k 595 ASP cc_start: 0.8589 (OUTLIER) cc_final: 0.8245 (p0) REVERT: 1l 535 GLU cc_start: 0.8309 (tm-30) cc_final: 0.8023 (tm-30) REVERT: 1m 437 MET cc_start: 0.9326 (tpp) cc_final: 0.8995 (tpp) REVERT: 1n 570 MET cc_start: 0.7607 (OUTLIER) cc_final: 0.7325 (ptp) REVERT: 1q 636 ARG cc_start: 0.8812 (OUTLIER) cc_final: 0.7871 (ttm-80) REVERT: 1r 437 MET cc_start: 0.9175 (tmm) cc_final: 0.8907 (tmm) REVERT: 1r 454 MET cc_start: 0.8985 (mmm) cc_final: 0.8227 (mmm) REVERT: 1s 437 MET cc_start: 0.9440 (tpt) cc_final: 0.9230 (tpt) REVERT: 1s 467 MET cc_start: 0.8275 (tpp) cc_final: 0.8070 (tpp) REVERT: 1u 467 MET cc_start: 0.8308 (mmm) cc_final: 0.8005 (tpp) REVERT: 1v 437 MET cc_start: 0.9250 (tpt) cc_final: 0.8346 (tmm) REVERT: 1v 535 GLU cc_start: 0.8070 (tm-30) cc_final: 0.7728 (tm-30) REVERT: 1v 645 MET cc_start: 0.8661 (mtp) cc_final: 0.8326 (mtp) REVERT: 1x 434 GLN cc_start: 0.8303 (mp10) cc_final: 0.7940 (mp10) REVERT: 1z 467 MET cc_start: 0.8683 (tmm) cc_final: 0.8401 (tmm) REVERT: 2a 467 MET cc_start: 0.8376 (mmm) cc_final: 0.8131 (tpp) REVERT: 2b 437 MET cc_start: 0.9346 (tpt) cc_final: 0.9133 (tpt) REVERT: 2b 454 MET cc_start: 0.9088 (mmm) cc_final: 0.8844 (mmm) REVERT: 2b 467 MET cc_start: 0.8366 (tpp) cc_final: 0.8122 (tpp) REVERT: 2c 437 MET cc_start: 0.9278 (tpp) cc_final: 0.8723 (tpt) REVERT: 2c 467 MET cc_start: 0.8405 (tpp) cc_final: 0.8194 (tpp) REVERT: 2d 437 MET cc_start: 0.9520 (tpt) cc_final: 0.9263 (tpt) REVERT: 2e 437 MET cc_start: 0.8484 (ttm) cc_final: 0.8097 (tmm) REVERT: 2e 467 MET cc_start: 0.8739 (tmm) cc_final: 0.8504 (tmm) REVERT: 2h 437 MET cc_start: 0.8958 (tmm) cc_final: 0.8292 (tmm) REVERT: 2h 509 VAL cc_start: 0.9289 (OUTLIER) cc_final: 0.8960 (m) REVERT: 2i 437 MET cc_start: 0.8796 (tmm) cc_final: 0.8221 (tmm) REVERT: 2j 437 MET cc_start: 0.8873 (tmm) cc_final: 0.8271 (tmm) REVERT: 2l 535 GLU cc_start: 0.8037 (tm-30) cc_final: 0.7397 (tm-30) REVERT: 2l 611 MET cc_start: 0.8623 (mmm) cc_final: 0.8363 (mmm) REVERT: 2l 636 ARG cc_start: 0.8772 (OUTLIER) cc_final: 0.7754 (ttm-80) REVERT: 2m 467 MET cc_start: 0.8679 (tmm) cc_final: 0.8436 (tmm) REVERT: 2n 467 MET cc_start: 0.8171 (tpp) cc_final: 0.7806 (tpp) REVERT: 2o 570 MET cc_start: 0.7771 (OUTLIER) cc_final: 0.7526 (ptp) REVERT: 2r 437 MET cc_start: 0.9341 (tpt) cc_final: 0.9114 (tpt) REVERT: 2s 554 GLN cc_start: 0.8194 (tm-30) cc_final: 0.7877 (tm-30) REVERT: 2s 611 MET cc_start: 0.8651 (mmm) cc_final: 0.8354 (mmm) REVERT: 2v 437 MET cc_start: 0.8992 (tmm) cc_final: 0.8356 (tmm) REVERT: 2w 437 MET cc_start: 0.8943 (tmm) cc_final: 0.8302 (tmm) REVERT: 2x 437 MET cc_start: 0.8955 (tmm) cc_final: 0.8212 (tmm) REVERT: 2y 467 MET cc_start: 0.8183 (mmm) cc_final: 0.7852 (tpp) REVERT: 2y 645 MET cc_start: 0.8792 (mtm) cc_final: 0.8351 (mtm) REVERT: 3a 437 MET cc_start: 0.8890 (tmm) cc_final: 0.8253 (tmm) REVERT: 3a 467 MET cc_start: 0.8120 (tpp) cc_final: 0.7875 (tpp) REVERT: 3a 611 MET cc_start: 0.9194 (mmt) cc_final: 0.8981 (mmp) REVERT: 3b 437 MET cc_start: 0.8943 (tmm) cc_final: 0.8286 (tmm) REVERT: 3c 437 MET cc_start: 0.8989 (tmm) cc_final: 0.8339 (tmm) outliers start: 176 outliers final: 138 residues processed: 773 average time/residue: 0.8685 time to fit residues: 1177.6979 Evaluate side-chains 813 residues out of total 11700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 665 time to evaluate : 8.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 01 residue 446 TYR Chi-restraints excluded: chain 02 residue 446 TYR Chi-restraints excluded: chain 03 residue 445 HIS Chi-restraints excluded: chain 03 residue 541 VAL Chi-restraints excluded: chain 03 residue 612 MET Chi-restraints excluded: chain 03 residue 636 ARG Chi-restraints excluded: chain 05 residue 468 LEU Chi-restraints excluded: chain 05 residue 556 HIS Chi-restraints excluded: chain 05 residue 570 MET Chi-restraints excluded: chain 05 residue 636 ARG Chi-restraints excluded: chain 05 residue 645 MET Chi-restraints excluded: chain 0z residue 446 TYR Chi-restraints excluded: chain 0z residue 468 LEU Chi-restraints excluded: chain 0z residue 478 ASP Chi-restraints excluded: chain 0z residue 594 GLU Chi-restraints excluded: chain 1a residue 478 ASP Chi-restraints excluded: chain 1a residue 570 MET Chi-restraints excluded: chain 1a residue 612 MET Chi-restraints excluded: chain 1c residue 636 ARG Chi-restraints excluded: chain 1c residue 645 MET Chi-restraints excluded: chain 1d residue 446 TYR Chi-restraints excluded: chain 1d residue 636 ARG Chi-restraints excluded: chain 1e residue 446 TYR Chi-restraints excluded: chain 1f residue 570 MET Chi-restraints excluded: chain 1f residue 612 MET Chi-restraints excluded: chain 1f residue 636 ARG Chi-restraints excluded: chain 1g residue 446 TYR Chi-restraints excluded: chain 1g residue 636 ARG Chi-restraints excluded: chain 1h residue 445 HIS Chi-restraints excluded: chain 1h residue 468 LEU Chi-restraints excluded: chain 1h residue 636 ARG Chi-restraints excluded: chain 1i residue 541 VAL Chi-restraints excluded: chain 1i residue 570 MET Chi-restraints excluded: chain 1i residue 612 MET Chi-restraints excluded: chain 1i residue 636 ARG Chi-restraints excluded: chain 1k residue 445 HIS Chi-restraints excluded: chain 1k residue 595 ASP Chi-restraints excluded: chain 1k residue 645 MET Chi-restraints excluded: chain 1l residue 478 ASP Chi-restraints excluded: chain 1l residue 541 VAL Chi-restraints excluded: chain 1m residue 502 VAL Chi-restraints excluded: chain 1n residue 445 HIS Chi-restraints excluded: chain 1n residue 556 HIS Chi-restraints excluded: chain 1n residue 570 MET Chi-restraints excluded: chain 1n residue 588 LEU Chi-restraints excluded: chain 1n residue 636 ARG Chi-restraints excluded: chain 1n residue 645 MET Chi-restraints excluded: chain 1o residue 446 TYR Chi-restraints excluded: chain 1o residue 570 MET Chi-restraints excluded: chain 1p residue 445 HIS Chi-restraints excluded: chain 1p residue 570 MET Chi-restraints excluded: chain 1p residue 588 LEU Chi-restraints excluded: chain 1p residue 645 MET Chi-restraints excluded: chain 1q residue 612 MET Chi-restraints excluded: chain 1q residue 636 ARG Chi-restraints excluded: chain 1s residue 612 MET Chi-restraints excluded: chain 1s residue 636 ARG Chi-restraints excluded: chain 1t residue 570 MET Chi-restraints excluded: chain 1t residue 612 MET Chi-restraints excluded: chain 1t residue 636 ARG Chi-restraints excluded: chain 1u residue 446 TYR Chi-restraints excluded: chain 1u residue 499 MET Chi-restraints excluded: chain 1u residue 636 ARG Chi-restraints excluded: chain 1v residue 556 HIS Chi-restraints excluded: chain 1v residue 636 ARG Chi-restraints excluded: chain 1w residue 478 ASP Chi-restraints excluded: chain 1w residue 541 VAL Chi-restraints excluded: chain 1w residue 570 MET Chi-restraints excluded: chain 1x residue 445 HIS Chi-restraints excluded: chain 1x residue 556 HIS Chi-restraints excluded: chain 1x residue 636 ARG Chi-restraints excluded: chain 1x residue 645 MET Chi-restraints excluded: chain 1z residue 445 HIS Chi-restraints excluded: chain 1z residue 570 MET Chi-restraints excluded: chain 1z residue 612 MET Chi-restraints excluded: chain 2a residue 445 HIS Chi-restraints excluded: chain 2a residue 499 MET Chi-restraints excluded: chain 2b residue 636 ARG Chi-restraints excluded: chain 2c residue 446 TYR Chi-restraints excluded: chain 2c residue 499 MET Chi-restraints excluded: chain 2c residue 612 MET Chi-restraints excluded: chain 2c residue 636 ARG Chi-restraints excluded: chain 2d residue 446 TYR Chi-restraints excluded: chain 2d residue 499 MET Chi-restraints excluded: chain 2d residue 636 ARG Chi-restraints excluded: chain 2e residue 446 TYR Chi-restraints excluded: chain 2g residue 612 MET Chi-restraints excluded: chain 2h residue 446 TYR Chi-restraints excluded: chain 2h residue 509 VAL Chi-restraints excluded: chain 2i residue 446 TYR Chi-restraints excluded: chain 2i residue 570 MET Chi-restraints excluded: chain 2j residue 446 TYR Chi-restraints excluded: chain 2j residue 478 ASP Chi-restraints excluded: chain 2j residue 556 HIS Chi-restraints excluded: chain 2j residue 570 MET Chi-restraints excluded: chain 2j residue 594 GLU Chi-restraints excluded: chain 2k residue 445 HIS Chi-restraints excluded: chain 2k residue 556 HIS Chi-restraints excluded: chain 2k residue 570 MET Chi-restraints excluded: chain 2l residue 541 VAL Chi-restraints excluded: chain 2l residue 570 MET Chi-restraints excluded: chain 2l residue 612 MET Chi-restraints excluded: chain 2l residue 636 ARG Chi-restraints excluded: chain 2m residue 446 TYR Chi-restraints excluded: chain 2n residue 446 TYR Chi-restraints excluded: chain 2o residue 445 HIS Chi-restraints excluded: chain 2o residue 570 MET Chi-restraints excluded: chain 2o residue 636 ARG Chi-restraints excluded: chain 2o residue 645 MET Chi-restraints excluded: chain 2p residue 445 HIS Chi-restraints excluded: chain 2p residue 612 MET Chi-restraints excluded: chain 2q residue 446 TYR Chi-restraints excluded: chain 2q residue 469 GLU Chi-restraints excluded: chain 2q residue 636 ARG Chi-restraints excluded: chain 2r residue 612 MET Chi-restraints excluded: chain 2s residue 445 HIS Chi-restraints excluded: chain 2s residue 468 LEU Chi-restraints excluded: chain 2s residue 541 VAL Chi-restraints excluded: chain 2s residue 612 MET Chi-restraints excluded: chain 2t residue 468 LEU Chi-restraints excluded: chain 2t residue 612 MET Chi-restraints excluded: chain 2t residue 636 ARG Chi-restraints excluded: chain 2t residue 645 MET Chi-restraints excluded: chain 2u residue 541 VAL Chi-restraints excluded: chain 2u residue 570 MET Chi-restraints excluded: chain 2u residue 612 MET Chi-restraints excluded: chain 2v residue 446 TYR Chi-restraints excluded: chain 2v residue 468 LEU Chi-restraints excluded: chain 2w residue 446 TYR Chi-restraints excluded: chain 2w residue 478 ASP Chi-restraints excluded: chain 2w residue 570 MET Chi-restraints excluded: chain 2w residue 594 GLU Chi-restraints excluded: chain 2x residue 446 TYR Chi-restraints excluded: chain 2x residue 468 LEU Chi-restraints excluded: chain 2x residue 570 MET Chi-restraints excluded: chain 2x residue 594 GLU Chi-restraints excluded: chain 2y residue 431 VAL Chi-restraints excluded: chain 2y residue 570 MET Chi-restraints excluded: chain 2z residue 612 MET Chi-restraints excluded: chain 2z residue 636 ARG Chi-restraints excluded: chain 3a residue 446 TYR Chi-restraints excluded: chain 3a residue 468 LEU Chi-restraints excluded: chain 3a residue 478 ASP Chi-restraints excluded: chain 3a residue 594 GLU Chi-restraints excluded: chain 3b residue 446 TYR Chi-restraints excluded: chain 3b residue 570 MET Chi-restraints excluded: chain 3c residue 446 TYR Chi-restraints excluded: chain 3c residue 468 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1320 random chunks: chunk 1157 optimal weight: 0.3980 chunk 1218 optimal weight: 9.9990 chunk 1112 optimal weight: 0.8980 chunk 1185 optimal weight: 6.9990 chunk 713 optimal weight: 2.9990 chunk 516 optimal weight: 0.7980 chunk 930 optimal weight: 1.9990 chunk 363 optimal weight: 1.9990 chunk 1071 optimal weight: 3.9990 chunk 1121 optimal weight: 3.9990 chunk 1181 optimal weight: 0.6980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0z 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1c 556 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1e 445 HIS ** 1g 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1l 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1q 556 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1x 581 ASN 1x 584 GLN ** 2f 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2j 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2m 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2u 556 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.2559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 106380 Z= 0.176 Angle : 0.554 12.990 144060 Z= 0.274 Chirality : 0.044 0.173 17220 Planarity : 0.004 0.055 18300 Dihedral : 4.611 30.612 14220 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 1.40 % Allowed : 12.75 % Favored : 85.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.07), residues: 13320 helix: 2.45 (0.07), residues: 4980 sheet: 0.22 (0.09), residues: 3000 loop : 0.62 (0.09), residues: 5340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP0z 498 HIS 0.004 0.000 HIS2s 445 PHE 0.014 0.001 PHE1h 558 TYR 0.030 0.001 TYR2l 446 ARG 0.005 0.000 ARG1t 549 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26640 Ramachandran restraints generated. 13320 Oldfield, 0 Emsley, 13320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26640 Ramachandran restraints generated. 13320 Oldfield, 0 Emsley, 13320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 858 residues out of total 11700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 694 time to evaluate : 9.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 01 437 MET cc_start: 0.8907 (tmm) cc_final: 0.8261 (tmm) REVERT: 02 437 MET cc_start: 0.8849 (tmm) cc_final: 0.8210 (tmm) REVERT: 03 467 MET cc_start: 0.8361 (tmm) cc_final: 0.8001 (tmm) REVERT: 03 636 ARG cc_start: 0.8767 (OUTLIER) cc_final: 0.7909 (ttm-80) REVERT: 05 454 MET cc_start: 0.8733 (mmm) cc_final: 0.8192 (mmm) REVERT: 0z 434 GLN cc_start: 0.8144 (OUTLIER) cc_final: 0.7831 (mp10) REVERT: 0z 437 MET cc_start: 0.8980 (tmm) cc_final: 0.8327 (tmm) REVERT: 1b 437 MET cc_start: 0.8796 (tpt) cc_final: 0.8350 (tpt) REVERT: 1b 445 HIS cc_start: 0.7727 (m90) cc_final: 0.7391 (m90) REVERT: 1b 454 MET cc_start: 0.8990 (mmm) cc_final: 0.8062 (mmm) REVERT: 1b 645 MET cc_start: 0.9000 (mtm) cc_final: 0.8489 (mtp) REVERT: 1d 434 GLN cc_start: 0.7942 (mt0) cc_final: 0.7635 (mt0) REVERT: 1e 434 GLN cc_start: 0.7925 (mt0) cc_final: 0.7573 (mt0) REVERT: 1e 437 MET cc_start: 0.9478 (tpt) cc_final: 0.9269 (tpt) REVERT: 1f 437 MET cc_start: 0.9377 (tpt) cc_final: 0.9162 (tpt) REVERT: 1g 636 ARG cc_start: 0.8719 (OUTLIER) cc_final: 0.7668 (ttm-80) REVERT: 1g 645 MET cc_start: 0.9116 (mtm) cc_final: 0.8732 (mtp) REVERT: 1i 636 ARG cc_start: 0.8769 (OUTLIER) cc_final: 0.7913 (ttm-80) REVERT: 1j 445 HIS cc_start: 0.8035 (m90) cc_final: 0.7644 (m90) REVERT: 1j 570 MET cc_start: 0.8100 (ppp) cc_final: 0.7684 (ptp) REVERT: 1k 434 GLN cc_start: 0.7809 (mt0) cc_final: 0.7530 (mp10) REVERT: 1k 454 MET cc_start: 0.8916 (mmm) cc_final: 0.8355 (mmm) REVERT: 1k 595 ASP cc_start: 0.8606 (OUTLIER) cc_final: 0.8292 (p0) REVERT: 1l 535 GLU cc_start: 0.8268 (tm-30) cc_final: 0.7844 (tm-30) REVERT: 1m 437 MET cc_start: 0.9311 (tpp) cc_final: 0.8994 (tpp) REVERT: 1n 570 MET cc_start: 0.7606 (OUTLIER) cc_final: 0.7339 (ptp) REVERT: 1q 636 ARG cc_start: 0.8797 (OUTLIER) cc_final: 0.7890 (ttm-80) REVERT: 1r 437 MET cc_start: 0.9157 (tmm) cc_final: 0.8887 (tmm) REVERT: 1r 454 MET cc_start: 0.8933 (mmm) cc_final: 0.8201 (mmm) REVERT: 1u 437 MET cc_start: 0.9439 (tpt) cc_final: 0.9222 (tpt) REVERT: 1u 467 MET cc_start: 0.8296 (mmm) cc_final: 0.8015 (tpp) REVERT: 1v 437 MET cc_start: 0.9261 (tpt) cc_final: 0.8357 (tmm) REVERT: 1v 535 GLU cc_start: 0.8056 (tm-30) cc_final: 0.7738 (tm-30) REVERT: 1v 645 MET cc_start: 0.8633 (mtp) cc_final: 0.8291 (mtp) REVERT: 1x 434 GLN cc_start: 0.8426 (mp10) cc_final: 0.8089 (mp10) REVERT: 1x 454 MET cc_start: 0.8926 (mmm) cc_final: 0.8117 (mmm) REVERT: 1z 467 MET cc_start: 0.8747 (tmm) cc_final: 0.8467 (tmm) REVERT: 2a 467 MET cc_start: 0.8394 (mmm) cc_final: 0.8188 (tpp) REVERT: 2b 467 MET cc_start: 0.8354 (tpp) cc_final: 0.8124 (tpp) REVERT: 2c 437 MET cc_start: 0.9286 (tpp) cc_final: 0.8744 (tpt) REVERT: 2d 434 GLN cc_start: 0.8270 (mt0) cc_final: 0.8003 (mt0) REVERT: 2d 467 MET cc_start: 0.7972 (tpp) cc_final: 0.7672 (tpp) REVERT: 2e 437 MET cc_start: 0.8480 (ttm) cc_final: 0.8108 (tmm) REVERT: 2e 467 MET cc_start: 0.8706 (tmm) cc_final: 0.8462 (tmm) REVERT: 2h 437 MET cc_start: 0.8959 (tmm) cc_final: 0.8313 (tmm) REVERT: 2h 509 VAL cc_start: 0.9279 (OUTLIER) cc_final: 0.8950 (m) REVERT: 2i 437 MET cc_start: 0.8795 (tmm) cc_final: 0.8212 (tmm) REVERT: 2j 437 MET cc_start: 0.8847 (tmm) cc_final: 0.8201 (tmm) REVERT: 2k 645 MET cc_start: 0.8680 (mtp) cc_final: 0.8388 (mtp) REVERT: 2l 535 GLU cc_start: 0.8017 (tm-30) cc_final: 0.7365 (tm-30) REVERT: 2l 611 MET cc_start: 0.8586 (mmm) cc_final: 0.8333 (mmm) REVERT: 2l 636 ARG cc_start: 0.8753 (OUTLIER) cc_final: 0.7755 (ttm-80) REVERT: 2m 467 MET cc_start: 0.8704 (tmm) cc_final: 0.8399 (tmm) REVERT: 2n 467 MET cc_start: 0.8162 (tpp) cc_final: 0.7809 (tpp) REVERT: 2o 570 MET cc_start: 0.7779 (OUTLIER) cc_final: 0.7541 (ptp) REVERT: 2q 434 GLN cc_start: 0.8052 (mt0) cc_final: 0.7846 (mt0) REVERT: 2s 554 GLN cc_start: 0.8175 (tm-30) cc_final: 0.7859 (tm-30) REVERT: 2s 611 MET cc_start: 0.8622 (mmm) cc_final: 0.8341 (mmm) REVERT: 2u 467 MET cc_start: 0.8715 (tmm) cc_final: 0.8371 (tmm) REVERT: 2v 437 MET cc_start: 0.8983 (tmm) cc_final: 0.8218 (tmm) REVERT: 2w 437 MET cc_start: 0.8934 (tmm) cc_final: 0.8249 (tmm) REVERT: 2x 437 MET cc_start: 0.8989 (tmm) cc_final: 0.8226 (tmm) REVERT: 2y 467 MET cc_start: 0.8251 (mmm) cc_final: 0.7846 (tpp) REVERT: 2y 645 MET cc_start: 0.8789 (mtm) cc_final: 0.8302 (mtm) REVERT: 3a 437 MET cc_start: 0.8892 (tmm) cc_final: 0.8246 (tmm) REVERT: 3a 467 MET cc_start: 0.8173 (tpp) cc_final: 0.7964 (tpp) REVERT: 3a 611 MET cc_start: 0.9187 (mmt) cc_final: 0.8966 (mmp) REVERT: 3b 437 MET cc_start: 0.8952 (tmm) cc_final: 0.8286 (tmm) REVERT: 3c 437 MET cc_start: 0.9015 (tmm) cc_final: 0.8354 (tmm) outliers start: 164 outliers final: 137 residues processed: 770 average time/residue: 0.8606 time to fit residues: 1163.7968 Evaluate side-chains 827 residues out of total 11700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 680 time to evaluate : 8.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 01 residue 446 TYR Chi-restraints excluded: chain 02 residue 446 TYR Chi-restraints excluded: chain 03 residue 445 HIS Chi-restraints excluded: chain 03 residue 541 VAL Chi-restraints excluded: chain 03 residue 612 MET Chi-restraints excluded: chain 03 residue 636 ARG Chi-restraints excluded: chain 05 residue 468 LEU Chi-restraints excluded: chain 05 residue 556 HIS Chi-restraints excluded: chain 05 residue 570 MET Chi-restraints excluded: chain 05 residue 636 ARG Chi-restraints excluded: chain 0z residue 434 GLN Chi-restraints excluded: chain 0z residue 446 TYR Chi-restraints excluded: chain 0z residue 468 LEU Chi-restraints excluded: chain 0z residue 478 ASP Chi-restraints excluded: chain 0z residue 594 GLU Chi-restraints excluded: chain 1a residue 478 ASP Chi-restraints excluded: chain 1a residue 570 MET Chi-restraints excluded: chain 1a residue 612 MET Chi-restraints excluded: chain 1b residue 570 MET Chi-restraints excluded: chain 1c residue 636 ARG Chi-restraints excluded: chain 1c residue 645 MET Chi-restraints excluded: chain 1d residue 636 ARG Chi-restraints excluded: chain 1e residue 446 TYR Chi-restraints excluded: chain 1f residue 570 MET Chi-restraints excluded: chain 1f residue 612 MET Chi-restraints excluded: chain 1f residue 636 ARG Chi-restraints excluded: chain 1g residue 446 TYR Chi-restraints excluded: chain 1g residue 636 ARG Chi-restraints excluded: chain 1h residue 445 HIS Chi-restraints excluded: chain 1h residue 468 LEU Chi-restraints excluded: chain 1h residue 636 ARG Chi-restraints excluded: chain 1i residue 541 VAL Chi-restraints excluded: chain 1i residue 612 MET Chi-restraints excluded: chain 1i residue 636 ARG Chi-restraints excluded: chain 1k residue 445 HIS Chi-restraints excluded: chain 1k residue 595 ASP Chi-restraints excluded: chain 1k residue 645 MET Chi-restraints excluded: chain 1l residue 478 ASP Chi-restraints excluded: chain 1l residue 541 VAL Chi-restraints excluded: chain 1m residue 502 VAL Chi-restraints excluded: chain 1n residue 445 HIS Chi-restraints excluded: chain 1n residue 556 HIS Chi-restraints excluded: chain 1n residue 570 MET Chi-restraints excluded: chain 1n residue 588 LEU Chi-restraints excluded: chain 1n residue 636 ARG Chi-restraints excluded: chain 1o residue 446 TYR Chi-restraints excluded: chain 1o residue 570 MET Chi-restraints excluded: chain 1p residue 445 HIS Chi-restraints excluded: chain 1p residue 570 MET Chi-restraints excluded: chain 1p residue 588 LEU Chi-restraints excluded: chain 1p residue 645 MET Chi-restraints excluded: chain 1q residue 478 ASP Chi-restraints excluded: chain 1q residue 541 VAL Chi-restraints excluded: chain 1q residue 612 MET Chi-restraints excluded: chain 1q residue 636 ARG Chi-restraints excluded: chain 1s residue 612 MET Chi-restraints excluded: chain 1s residue 636 ARG Chi-restraints excluded: chain 1t residue 437 MET Chi-restraints excluded: chain 1t residue 570 MET Chi-restraints excluded: chain 1t residue 612 MET Chi-restraints excluded: chain 1t residue 636 ARG Chi-restraints excluded: chain 1u residue 446 TYR Chi-restraints excluded: chain 1u residue 499 MET Chi-restraints excluded: chain 1u residue 636 ARG Chi-restraints excluded: chain 1v residue 556 HIS Chi-restraints excluded: chain 1w residue 478 ASP Chi-restraints excluded: chain 1w residue 541 VAL Chi-restraints excluded: chain 1w residue 570 MET Chi-restraints excluded: chain 1x residue 445 HIS Chi-restraints excluded: chain 1x residue 636 ARG Chi-restraints excluded: chain 1x residue 645 MET Chi-restraints excluded: chain 1z residue 445 HIS Chi-restraints excluded: chain 1z residue 570 MET Chi-restraints excluded: chain 1z residue 612 MET Chi-restraints excluded: chain 2a residue 445 HIS Chi-restraints excluded: chain 2a residue 499 MET Chi-restraints excluded: chain 2b residue 636 ARG Chi-restraints excluded: chain 2c residue 446 TYR Chi-restraints excluded: chain 2c residue 499 MET Chi-restraints excluded: chain 2c residue 612 MET Chi-restraints excluded: chain 2c residue 636 ARG Chi-restraints excluded: chain 2d residue 499 MET Chi-restraints excluded: chain 2d residue 636 ARG Chi-restraints excluded: chain 2e residue 446 TYR Chi-restraints excluded: chain 2g residue 612 MET Chi-restraints excluded: chain 2h residue 446 TYR Chi-restraints excluded: chain 2h residue 509 VAL Chi-restraints excluded: chain 2h residue 570 MET Chi-restraints excluded: chain 2i residue 446 TYR Chi-restraints excluded: chain 2i residue 570 MET Chi-restraints excluded: chain 2j residue 446 TYR Chi-restraints excluded: chain 2j residue 478 ASP Chi-restraints excluded: chain 2j residue 556 HIS Chi-restraints excluded: chain 2j residue 570 MET Chi-restraints excluded: chain 2j residue 594 GLU Chi-restraints excluded: chain 2k residue 445 HIS Chi-restraints excluded: chain 2k residue 556 HIS Chi-restraints excluded: chain 2k residue 570 MET Chi-restraints excluded: chain 2l residue 570 MET Chi-restraints excluded: chain 2l residue 612 MET Chi-restraints excluded: chain 2l residue 636 ARG Chi-restraints excluded: chain 2m residue 446 TYR Chi-restraints excluded: chain 2m residue 468 LEU Chi-restraints excluded: chain 2o residue 445 HIS Chi-restraints excluded: chain 2o residue 570 MET Chi-restraints excluded: chain 2o residue 636 ARG Chi-restraints excluded: chain 2o residue 645 MET Chi-restraints excluded: chain 2p residue 445 HIS Chi-restraints excluded: chain 2p residue 612 MET Chi-restraints excluded: chain 2q residue 446 TYR Chi-restraints excluded: chain 2q residue 469 GLU Chi-restraints excluded: chain 2q residue 636 ARG Chi-restraints excluded: chain 2r residue 612 MET Chi-restraints excluded: chain 2s residue 445 HIS Chi-restraints excluded: chain 2s residue 468 LEU Chi-restraints excluded: chain 2s residue 541 VAL Chi-restraints excluded: chain 2s residue 612 MET Chi-restraints excluded: chain 2t residue 468 LEU Chi-restraints excluded: chain 2t residue 612 MET Chi-restraints excluded: chain 2t residue 636 ARG Chi-restraints excluded: chain 2t residue 645 MET Chi-restraints excluded: chain 2u residue 541 VAL Chi-restraints excluded: chain 2u residue 570 MET Chi-restraints excluded: chain 2u residue 612 MET Chi-restraints excluded: chain 2v residue 446 TYR Chi-restraints excluded: chain 2v residue 468 LEU Chi-restraints excluded: chain 2v residue 570 MET Chi-restraints excluded: chain 2w residue 446 TYR Chi-restraints excluded: chain 2w residue 478 ASP Chi-restraints excluded: chain 2w residue 570 MET Chi-restraints excluded: chain 2w residue 594 GLU Chi-restraints excluded: chain 2x residue 446 TYR Chi-restraints excluded: chain 2x residue 468 LEU Chi-restraints excluded: chain 2x residue 570 MET Chi-restraints excluded: chain 2x residue 594 GLU Chi-restraints excluded: chain 2y residue 431 VAL Chi-restraints excluded: chain 2y residue 570 MET Chi-restraints excluded: chain 2z residue 612 MET Chi-restraints excluded: chain 2z residue 636 ARG Chi-restraints excluded: chain 3a residue 446 TYR Chi-restraints excluded: chain 3a residue 468 LEU Chi-restraints excluded: chain 3a residue 478 ASP Chi-restraints excluded: chain 3a residue 594 GLU Chi-restraints excluded: chain 3b residue 446 TYR Chi-restraints excluded: chain 3b residue 570 MET Chi-restraints excluded: chain 3c residue 446 TYR Chi-restraints excluded: chain 3c residue 468 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1320 random chunks: chunk 778 optimal weight: 0.7980 chunk 1253 optimal weight: 2.9990 chunk 765 optimal weight: 0.7980 chunk 594 optimal weight: 10.0000 chunk 871 optimal weight: 3.9990 chunk 1315 optimal weight: 4.9990 chunk 1210 optimal weight: 7.9990 chunk 1047 optimal weight: 0.4980 chunk 108 optimal weight: 4.9990 chunk 808 optimal weight: 0.9990 chunk 642 optimal weight: 3.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 02 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0z 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1c 556 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1e 445 HIS ** 1g 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1l 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1q 556 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1t 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1u 434 GLN 1z 495 ASN ** 2f 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2g 495 ASN ** 2j 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2m 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2u 445 HIS ** 2u 556 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.2589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 106380 Z= 0.205 Angle : 0.574 12.484 144060 Z= 0.282 Chirality : 0.044 0.167 17220 Planarity : 0.004 0.053 18300 Dihedral : 4.647 31.549 14220 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 1.32 % Allowed : 12.97 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.07), residues: 13320 helix: 2.37 (0.07), residues: 5040 sheet: 0.21 (0.09), residues: 3000 loop : 0.54 (0.09), residues: 5280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP2t 498 HIS 0.004 0.001 HIS2s 445 PHE 0.012 0.001 PHE1h 558 TYR 0.029 0.002 TYR2l 446 ARG 0.006 0.000 ARG1t 549 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26640 Ramachandran restraints generated. 13320 Oldfield, 0 Emsley, 13320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26640 Ramachandran restraints generated. 13320 Oldfield, 0 Emsley, 13320 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 837 residues out of total 11700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 683 time to evaluate : 8.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 01 437 MET cc_start: 0.8896 (tmm) cc_final: 0.8270 (tmm) REVERT: 02 437 MET cc_start: 0.8848 (tmm) cc_final: 0.8233 (tmm) REVERT: 03 467 MET cc_start: 0.8388 (tmm) cc_final: 0.8026 (tmm) REVERT: 03 636 ARG cc_start: 0.8766 (OUTLIER) cc_final: 0.7911 (ttm-80) REVERT: 05 454 MET cc_start: 0.8776 (mmm) cc_final: 0.8152 (mmm) REVERT: 0z 437 MET cc_start: 0.8966 (tmm) cc_final: 0.8431 (tmm) REVERT: 1b 437 MET cc_start: 0.8807 (tpt) cc_final: 0.8361 (tpt) REVERT: 1b 445 HIS cc_start: 0.7782 (m90) cc_final: 0.7424 (m90) REVERT: 1b 454 MET cc_start: 0.9008 (mmm) cc_final: 0.8082 (mmm) REVERT: 1b 645 MET cc_start: 0.8999 (mtm) cc_final: 0.8475 (mtp) REVERT: 1d 434 GLN cc_start: 0.7963 (mt0) cc_final: 0.7653 (mt0) REVERT: 1d 437 MET cc_start: 0.9345 (tpt) cc_final: 0.9129 (tpt) REVERT: 1e 434 GLN cc_start: 0.7989 (mt0) cc_final: 0.7647 (mt0) REVERT: 1e 437 MET cc_start: 0.9499 (tpt) cc_final: 0.9261 (tpt) REVERT: 1g 636 ARG cc_start: 0.8732 (OUTLIER) cc_final: 0.7679 (ttm-80) REVERT: 1g 645 MET cc_start: 0.9114 (mtm) cc_final: 0.8724 (mtp) REVERT: 1h 645 MET cc_start: 0.8601 (mtp) cc_final: 0.8385 (mtp) REVERT: 1i 636 ARG cc_start: 0.8767 (OUTLIER) cc_final: 0.7886 (ttm-80) REVERT: 1j 445 HIS cc_start: 0.8092 (m90) cc_final: 0.7673 (m90) REVERT: 1j 570 MET cc_start: 0.8143 (ppp) cc_final: 0.7712 (ptp) REVERT: 1k 434 GLN cc_start: 0.7805 (mt0) cc_final: 0.7526 (mp10) REVERT: 1k 454 MET cc_start: 0.8972 (mmm) cc_final: 0.8526 (mmm) REVERT: 1k 595 ASP cc_start: 0.8600 (OUTLIER) cc_final: 0.8265 (p0) REVERT: 1l 535 GLU cc_start: 0.8274 (tm-30) cc_final: 0.7856 (tm-30) REVERT: 1m 437 MET cc_start: 0.9324 (tpp) cc_final: 0.8996 (tpp) REVERT: 1n 570 MET cc_start: 0.7623 (OUTLIER) cc_final: 0.7358 (ptp) REVERT: 1q 636 ARG cc_start: 0.8811 (OUTLIER) cc_final: 0.7877 (ttm-80) REVERT: 1r 437 MET cc_start: 0.9163 (tmm) cc_final: 0.8899 (tmm) REVERT: 1r 454 MET cc_start: 0.8957 (mmm) cc_final: 0.8220 (mmm) REVERT: 1s 437 MET cc_start: 0.9408 (tpt) cc_final: 0.9186 (tpt) REVERT: 1u 437 MET cc_start: 0.9396 (tpt) cc_final: 0.9181 (tpt) REVERT: 1u 467 MET cc_start: 0.8302 (mmm) cc_final: 0.8033 (tpp) REVERT: 1v 437 MET cc_start: 0.9279 (tpt) cc_final: 0.8432 (tpt) REVERT: 1v 535 GLU cc_start: 0.8083 (tm-30) cc_final: 0.7774 (tm-30) REVERT: 1v 645 MET cc_start: 0.8641 (mtp) cc_final: 0.8301 (mtp) REVERT: 1x 434 GLN cc_start: 0.8422 (mp10) cc_final: 0.8090 (mp10) REVERT: 1x 454 MET cc_start: 0.8930 (mmm) cc_final: 0.8262 (mmm) REVERT: 1z 467 MET cc_start: 0.8761 (tmm) cc_final: 0.8482 (tmm) REVERT: 2c 437 MET cc_start: 0.9284 (tpp) cc_final: 0.8711 (tpt) REVERT: 2d 434 GLN cc_start: 0.8261 (mt0) cc_final: 0.8007 (mt0) REVERT: 2d 467 MET cc_start: 0.7974 (tpp) cc_final: 0.7674 (tpp) REVERT: 2d 535 GLU cc_start: 0.8460 (tm-30) cc_final: 0.8079 (tm-30) REVERT: 2e 437 MET cc_start: 0.8583 (ttm) cc_final: 0.8224 (tmm) REVERT: 2e 467 MET cc_start: 0.8670 (tmm) cc_final: 0.8423 (tmm) REVERT: 2g 636 ARG cc_start: 0.8801 (OUTLIER) cc_final: 0.7866 (ttm-80) REVERT: 2h 437 MET cc_start: 0.8952 (tmm) cc_final: 0.8308 (tmm) REVERT: 2h 509 VAL cc_start: 0.9291 (OUTLIER) cc_final: 0.8961 (m) REVERT: 2i 437 MET cc_start: 0.8788 (tmm) cc_final: 0.8218 (tmm) REVERT: 2j 437 MET cc_start: 0.8840 (tmm) cc_final: 0.8212 (tmm) REVERT: 2l 611 MET cc_start: 0.8605 (mmm) cc_final: 0.8343 (mmm) REVERT: 2l 636 ARG cc_start: 0.8717 (OUTLIER) cc_final: 0.7727 (ttm-80) REVERT: 2m 467 MET cc_start: 0.8717 (tmm) cc_final: 0.8412 (tmm) REVERT: 2n 467 MET cc_start: 0.8167 (tpp) cc_final: 0.7814 (tpp) REVERT: 2o 570 MET cc_start: 0.7786 (OUTLIER) cc_final: 0.7562 (ptp) REVERT: 2q 434 GLN cc_start: 0.7959 (mt0) cc_final: 0.7752 (mt0) REVERT: 2s 437 MET cc_start: 0.9190 (tmm) cc_final: 0.8177 (tmm) REVERT: 2s 554 GLN cc_start: 0.8175 (tm-30) cc_final: 0.7863 (tm-30) REVERT: 2s 611 MET cc_start: 0.8626 (mmm) cc_final: 0.8349 (mmm) REVERT: 2u 467 MET cc_start: 0.8714 (tmm) cc_final: 0.8377 (tmm) REVERT: 2v 437 MET cc_start: 0.8989 (tmm) cc_final: 0.8313 (tmm) REVERT: 2w 437 MET cc_start: 0.8933 (tmm) cc_final: 0.8267 (tmm) REVERT: 2x 437 MET cc_start: 0.9000 (tmm) cc_final: 0.8249 (tmm) REVERT: 2y 467 MET cc_start: 0.8143 (mmm) cc_final: 0.7706 (tpp) REVERT: 2y 645 MET cc_start: 0.8793 (mtm) cc_final: 0.8316 (mtm) REVERT: 3a 437 MET cc_start: 0.8886 (tmm) cc_final: 0.8254 (tmm) REVERT: 3a 467 MET cc_start: 0.8171 (tpp) cc_final: 0.7961 (tpp) REVERT: 3b 437 MET cc_start: 0.8946 (tmm) cc_final: 0.8300 (tmm) REVERT: 3c 437 MET cc_start: 0.8996 (tmm) cc_final: 0.8337 (tmm) outliers start: 154 outliers final: 132 residues processed: 755 average time/residue: 0.8650 time to fit residues: 1145.7104 Evaluate side-chains 813 residues out of total 11700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 671 time to evaluate : 8.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 01 residue 446 TYR Chi-restraints excluded: chain 02 residue 446 TYR Chi-restraints excluded: chain 03 residue 445 HIS Chi-restraints excluded: chain 03 residue 541 VAL Chi-restraints excluded: chain 03 residue 612 MET Chi-restraints excluded: chain 03 residue 636 ARG Chi-restraints excluded: chain 05 residue 468 LEU Chi-restraints excluded: chain 05 residue 556 HIS Chi-restraints excluded: chain 05 residue 636 ARG Chi-restraints excluded: chain 0z residue 446 TYR Chi-restraints excluded: chain 0z residue 468 LEU Chi-restraints excluded: chain 0z residue 478 ASP Chi-restraints excluded: chain 0z residue 594 GLU Chi-restraints excluded: chain 1a residue 478 ASP Chi-restraints excluded: chain 1a residue 612 MET Chi-restraints excluded: chain 1b residue 570 MET Chi-restraints excluded: chain 1c residue 636 ARG Chi-restraints excluded: chain 1c residue 645 MET Chi-restraints excluded: chain 1d residue 636 ARG Chi-restraints excluded: chain 1e residue 446 TYR Chi-restraints excluded: chain 1f residue 570 MET Chi-restraints excluded: chain 1f residue 612 MET Chi-restraints excluded: chain 1f residue 636 ARG Chi-restraints excluded: chain 1g residue 446 TYR Chi-restraints excluded: chain 1g residue 570 MET Chi-restraints excluded: chain 1g residue 636 ARG Chi-restraints excluded: chain 1h residue 445 HIS Chi-restraints excluded: chain 1h residue 468 LEU Chi-restraints excluded: chain 1h residue 636 ARG Chi-restraints excluded: chain 1i residue 541 VAL Chi-restraints excluded: chain 1i residue 612 MET Chi-restraints excluded: chain 1i residue 636 ARG Chi-restraints excluded: chain 1k residue 445 HIS Chi-restraints excluded: chain 1k residue 595 ASP Chi-restraints excluded: chain 1k residue 645 MET Chi-restraints excluded: chain 1l residue 478 ASP Chi-restraints excluded: chain 1l residue 541 VAL Chi-restraints excluded: chain 1m residue 502 VAL Chi-restraints excluded: chain 1n residue 445 HIS Chi-restraints excluded: chain 1n residue 556 HIS Chi-restraints excluded: chain 1n residue 570 MET Chi-restraints excluded: chain 1n residue 588 LEU Chi-restraints excluded: chain 1n residue 636 ARG Chi-restraints excluded: chain 1o residue 446 TYR Chi-restraints excluded: chain 1o residue 570 MET Chi-restraints excluded: chain 1p residue 445 HIS Chi-restraints excluded: chain 1p residue 570 MET Chi-restraints excluded: chain 1p residue 588 LEU Chi-restraints excluded: chain 1p residue 645 MET Chi-restraints excluded: chain 1q residue 541 VAL Chi-restraints excluded: chain 1q residue 612 MET Chi-restraints excluded: chain 1q residue 636 ARG Chi-restraints excluded: chain 1s residue 612 MET Chi-restraints excluded: chain 1s residue 636 ARG Chi-restraints excluded: chain 1t residue 570 MET Chi-restraints excluded: chain 1t residue 612 MET Chi-restraints excluded: chain 1t residue 636 ARG Chi-restraints excluded: chain 1u residue 446 TYR Chi-restraints excluded: chain 1u residue 499 MET Chi-restraints excluded: chain 1u residue 636 ARG Chi-restraints excluded: chain 1v residue 556 HIS Chi-restraints excluded: chain 1w residue 478 ASP Chi-restraints excluded: chain 1w residue 541 VAL Chi-restraints excluded: chain 1w residue 570 MET Chi-restraints excluded: chain 1x residue 445 HIS Chi-restraints excluded: chain 1x residue 636 ARG Chi-restraints excluded: chain 1x residue 645 MET Chi-restraints excluded: chain 1z residue 445 HIS Chi-restraints excluded: chain 1z residue 570 MET Chi-restraints excluded: chain 1z residue 612 MET Chi-restraints excluded: chain 2a residue 445 HIS Chi-restraints excluded: chain 2a residue 499 MET Chi-restraints excluded: chain 2b residue 636 ARG Chi-restraints excluded: chain 2c residue 446 TYR Chi-restraints excluded: chain 2c residue 499 MET Chi-restraints excluded: chain 2c residue 612 MET Chi-restraints excluded: chain 2c residue 636 ARG Chi-restraints excluded: chain 2d residue 499 MET Chi-restraints excluded: chain 2d residue 636 ARG Chi-restraints excluded: chain 2e residue 446 TYR Chi-restraints excluded: chain 2g residue 612 MET Chi-restraints excluded: chain 2g residue 636 ARG Chi-restraints excluded: chain 2h residue 446 TYR Chi-restraints excluded: chain 2h residue 509 VAL Chi-restraints excluded: chain 2h residue 570 MET Chi-restraints excluded: chain 2i residue 446 TYR Chi-restraints excluded: chain 2i residue 570 MET Chi-restraints excluded: chain 2j residue 446 TYR Chi-restraints excluded: chain 2j residue 478 ASP Chi-restraints excluded: chain 2j residue 556 HIS Chi-restraints excluded: chain 2j residue 570 MET Chi-restraints excluded: chain 2j residue 594 GLU Chi-restraints excluded: chain 2k residue 445 HIS Chi-restraints excluded: chain 2k residue 556 HIS Chi-restraints excluded: chain 2k residue 570 MET Chi-restraints excluded: chain 2k residue 636 ARG Chi-restraints excluded: chain 2l residue 541 VAL Chi-restraints excluded: chain 2l residue 570 MET Chi-restraints excluded: chain 2l residue 612 MET Chi-restraints excluded: chain 2l residue 636 ARG Chi-restraints excluded: chain 2m residue 446 TYR Chi-restraints excluded: chain 2o residue 445 HIS Chi-restraints excluded: chain 2o residue 570 MET Chi-restraints excluded: chain 2o residue 636 ARG Chi-restraints excluded: chain 2o residue 645 MET Chi-restraints excluded: chain 2p residue 445 HIS Chi-restraints excluded: chain 2q residue 446 TYR Chi-restraints excluded: chain 2q residue 636 ARG Chi-restraints excluded: chain 2r residue 612 MET Chi-restraints excluded: chain 2s residue 445 HIS Chi-restraints excluded: chain 2s residue 468 LEU Chi-restraints excluded: chain 2s residue 541 VAL Chi-restraints excluded: chain 2s residue 612 MET Chi-restraints excluded: chain 2t residue 468 LEU Chi-restraints excluded: chain 2t residue 612 MET Chi-restraints excluded: chain 2t residue 636 ARG Chi-restraints excluded: chain 2t residue 645 MET Chi-restraints excluded: chain 2u residue 541 VAL Chi-restraints excluded: chain 2u residue 570 MET Chi-restraints excluded: chain 2u residue 612 MET Chi-restraints excluded: chain 2v residue 446 TYR Chi-restraints excluded: chain 2v residue 570 MET Chi-restraints excluded: chain 2w residue 446 TYR Chi-restraints excluded: chain 2w residue 478 ASP Chi-restraints excluded: chain 2w residue 570 MET Chi-restraints excluded: chain 2w residue 594 GLU Chi-restraints excluded: chain 2x residue 446 TYR Chi-restraints excluded: chain 2x residue 468 LEU Chi-restraints excluded: chain 2x residue 570 MET Chi-restraints excluded: chain 2x residue 594 GLU Chi-restraints excluded: chain 2y residue 431 VAL Chi-restraints excluded: chain 2y residue 570 MET Chi-restraints excluded: chain 2z residue 612 MET Chi-restraints excluded: chain 2z residue 636 ARG Chi-restraints excluded: chain 3a residue 446 TYR Chi-restraints excluded: chain 3a residue 468 LEU Chi-restraints excluded: chain 3a residue 478 ASP Chi-restraints excluded: chain 3a residue 594 GLU Chi-restraints excluded: chain 3b residue 446 TYR Chi-restraints excluded: chain 3b residue 570 MET Chi-restraints excluded: chain 3c residue 446 TYR Chi-restraints excluded: chain 3c residue 468 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1320 random chunks: chunk 831 optimal weight: 6.9990 chunk 1115 optimal weight: 0.9980 chunk 320 optimal weight: 4.9990 chunk 965 optimal weight: 7.9990 chunk 154 optimal weight: 10.0000 chunk 291 optimal weight: 0.7980 chunk 1048 optimal weight: 0.0770 chunk 438 optimal weight: 3.9990 chunk 1077 optimal weight: 0.6980 chunk 132 optimal weight: 10.0000 chunk 193 optimal weight: 0.8980 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 02 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1c 556 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1e 445 HIS ** 1f 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1g 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1g 581 ASN 1g 584 GLN 1j 581 ASN 1j 584 GLN ** 1k 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1l 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1q 556 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1s 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1t 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2b 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2f 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2f 441 GLN ** 2h 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2j 554 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2m 445 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2o 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2r 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2u 556 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2z 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.069197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.056264 restraints weight = 371816.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.058214 restraints weight = 186988.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.059474 restraints weight = 124556.425| |-----------------------------------------------------------------------------| r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 106380 Z= 0.153 Angle : 0.560 12.384 144060 Z= 0.274 Chirality : 0.044 0.199 17220 Planarity : 0.004 0.051 18300 Dihedral : 4.492 29.563 14220 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.01 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 1.21 % Allowed : 13.19 % Favored : 85.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.08), residues: 13320 helix: 2.53 (0.07), residues: 4980 sheet: 0.29 (0.09), residues: 3000 loop : 0.69 (0.09), residues: 5340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP2l 498 HIS 0.005 0.000 HIS1k 556 PHE 0.015 0.001 PHE1h 558 TYR 0.029 0.001 TYR2l 446 ARG 0.008 0.000 ARG2d 549 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19712.10 seconds wall clock time: 351 minutes 5.75 seconds (21065.75 seconds total)