Starting phenix.real_space_refine on Thu Mar 21 03:11:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbj_27286/03_2024/8dbj_27286_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbj_27286/03_2024/8dbj_27286.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbj_27286/03_2024/8dbj_27286_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbj_27286/03_2024/8dbj_27286_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbj_27286/03_2024/8dbj_27286_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbj_27286/03_2024/8dbj_27286.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbj_27286/03_2024/8dbj_27286.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbj_27286/03_2024/8dbj_27286_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbj_27286/03_2024/8dbj_27286_updated.pdb" } resolution = 2.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.401 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 60 5.49 5 Mg 24 5.21 5 S 204 5.16 5 C 17964 2.51 5 N 5040 2.21 5 O 5700 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 22": "NH1" <-> "NH2" Residue "A GLU 39": "OE1" <-> "OE2" Residue "A ARG 49": "NH1" <-> "NH2" Residue "A GLU 69": "OE1" <-> "OE2" Residue "A ARG 84": "NH1" <-> "NH2" Residue "A GLU 148": "OE1" <-> "OE2" Residue "A ARG 156": "NH1" <-> "NH2" Residue "A ARG 163": "NH1" <-> "NH2" Residue "A ARG 177": "NH1" <-> "NH2" Residue "A ARG 184": "NH1" <-> "NH2" Residue "A ARG 204": "NH1" <-> "NH2" Residue "A ARG 214": "NH1" <-> "NH2" Residue "A ARG 243": "NH1" <-> "NH2" Residue "A ARG 260": "NH1" <-> "NH2" Residue "A GLU 267": "OE1" <-> "OE2" Residue "A GLU 298": "OE1" <-> "OE2" Residue "A ARG 301": "NH1" <-> "NH2" Residue "A ARG 302": "NH1" <-> "NH2" Residue "A GLU 307": "OE1" <-> "OE2" Residue "B ARG 22": "NH1" <-> "NH2" Residue "B GLU 39": "OE1" <-> "OE2" Residue "B ARG 49": "NH1" <-> "NH2" Residue "B GLU 69": "OE1" <-> "OE2" Residue "B ARG 84": "NH1" <-> "NH2" Residue "B GLU 148": "OE1" <-> "OE2" Residue "B ARG 156": "NH1" <-> "NH2" Residue "B ARG 163": "NH1" <-> "NH2" Residue "B ARG 177": "NH1" <-> "NH2" Residue "B ARG 184": "NH1" <-> "NH2" Residue "B ARG 204": "NH1" <-> "NH2" Residue "B ARG 214": "NH1" <-> "NH2" Residue "B ARG 243": "NH1" <-> "NH2" Residue "B ARG 260": "NH1" <-> "NH2" Residue "B GLU 267": "OE1" <-> "OE2" Residue "B GLU 298": "OE1" <-> "OE2" Residue "B ARG 301": "NH1" <-> "NH2" Residue "B ARG 302": "NH1" <-> "NH2" Residue "B GLU 307": "OE1" <-> "OE2" Residue "C ARG 22": "NH1" <-> "NH2" Residue "C GLU 39": "OE1" <-> "OE2" Residue "C ARG 49": "NH1" <-> "NH2" Residue "C GLU 69": "OE1" <-> "OE2" Residue "C ARG 84": "NH1" <-> "NH2" Residue "C GLU 148": "OE1" <-> "OE2" Residue "C ARG 156": "NH1" <-> "NH2" Residue "C ARG 163": "NH1" <-> "NH2" Residue "C ARG 177": "NH1" <-> "NH2" Residue "C ARG 184": "NH1" <-> "NH2" Residue "C ARG 204": "NH1" <-> "NH2" Residue "C ARG 214": "NH1" <-> "NH2" Residue "C ARG 243": "NH1" <-> "NH2" Residue "C ARG 260": "NH1" <-> "NH2" Residue "C GLU 267": "OE1" <-> "OE2" Residue "C GLU 298": "OE1" <-> "OE2" Residue "C ARG 301": "NH1" <-> "NH2" Residue "C ARG 302": "NH1" <-> "NH2" Residue "C GLU 307": "OE1" <-> "OE2" Residue "D ARG 22": "NH1" <-> "NH2" Residue "D GLU 39": "OE1" <-> "OE2" Residue "D ARG 49": "NH1" <-> "NH2" Residue "D GLU 69": "OE1" <-> "OE2" Residue "D ARG 84": "NH1" <-> "NH2" Residue "D GLU 148": "OE1" <-> "OE2" Residue "D ARG 156": "NH1" <-> "NH2" Residue "D ARG 163": "NH1" <-> "NH2" Residue "D ARG 177": "NH1" <-> "NH2" Residue "D ARG 184": "NH1" <-> "NH2" Residue "D ARG 204": "NH1" <-> "NH2" Residue "D ARG 214": "NH1" <-> "NH2" Residue "D ARG 243": "NH1" <-> "NH2" Residue "D ARG 260": "NH1" <-> "NH2" Residue "D GLU 267": "OE1" <-> "OE2" Residue "D GLU 298": "OE1" <-> "OE2" Residue "D ARG 301": "NH1" <-> "NH2" Residue "D ARG 302": "NH1" <-> "NH2" Residue "D GLU 307": "OE1" <-> "OE2" Residue "E ARG 22": "NH1" <-> "NH2" Residue "E GLU 39": "OE1" <-> "OE2" Residue "E ARG 49": "NH1" <-> "NH2" Residue "E GLU 69": "OE1" <-> "OE2" Residue "E ARG 84": "NH1" <-> "NH2" Residue "E GLU 148": "OE1" <-> "OE2" Residue "E ARG 156": "NH1" <-> "NH2" Residue "E ARG 163": "NH1" <-> "NH2" Residue "E ARG 177": "NH1" <-> "NH2" Residue "E ARG 184": "NH1" <-> "NH2" Residue "E ARG 204": "NH1" <-> "NH2" Residue "E ARG 214": "NH1" <-> "NH2" Residue "E ARG 243": "NH1" <-> "NH2" Residue "E ARG 260": "NH1" <-> "NH2" Residue "E GLU 267": "OE1" <-> "OE2" Residue "E GLU 298": "OE1" <-> "OE2" Residue "E ARG 301": "NH1" <-> "NH2" Residue "E ARG 302": "NH1" <-> "NH2" Residue "E GLU 307": "OE1" <-> "OE2" Residue "F ARG 22": "NH1" <-> "NH2" Residue "F GLU 39": "OE1" <-> "OE2" Residue "F ARG 49": "NH1" <-> "NH2" Residue "F GLU 69": "OE1" <-> "OE2" Residue "F ARG 84": "NH1" <-> "NH2" Residue "F GLU 148": "OE1" <-> "OE2" Residue "F ARG 156": "NH1" <-> "NH2" Residue "F ARG 163": "NH1" <-> "NH2" Residue "F ARG 177": "NH1" <-> "NH2" Residue "F ARG 184": "NH1" <-> "NH2" Residue "F ARG 204": "NH1" <-> "NH2" Residue "F ARG 214": "NH1" <-> "NH2" Residue "F ARG 243": "NH1" <-> "NH2" Residue "F ARG 260": "NH1" <-> "NH2" Residue "F GLU 267": "OE1" <-> "OE2" Residue "F GLU 298": "OE1" <-> "OE2" Residue "F ARG 301": "NH1" <-> "NH2" Residue "F ARG 302": "NH1" <-> "NH2" Residue "F GLU 307": "OE1" <-> "OE2" Residue "G ARG 22": "NH1" <-> "NH2" Residue "G GLU 39": "OE1" <-> "OE2" Residue "G ARG 49": "NH1" <-> "NH2" Residue "G GLU 69": "OE1" <-> "OE2" Residue "G ARG 84": "NH1" <-> "NH2" Residue "G GLU 148": "OE1" <-> "OE2" Residue "G ARG 156": "NH1" <-> "NH2" Residue "G ARG 163": "NH1" <-> "NH2" Residue "G ARG 177": "NH1" <-> "NH2" Residue "G ARG 184": "NH1" <-> "NH2" Residue "G ARG 204": "NH1" <-> "NH2" Residue "G ARG 214": "NH1" <-> "NH2" Residue "G ARG 243": "NH1" <-> "NH2" Residue "G ARG 260": "NH1" <-> "NH2" Residue "G GLU 267": "OE1" <-> "OE2" Residue "G GLU 298": "OE1" <-> "OE2" Residue "G ARG 301": "NH1" <-> "NH2" Residue "G ARG 302": "NH1" <-> "NH2" Residue "G GLU 307": "OE1" <-> "OE2" Residue "H ARG 22": "NH1" <-> "NH2" Residue "H GLU 39": "OE1" <-> "OE2" Residue "H ARG 49": "NH1" <-> "NH2" Residue "H GLU 69": "OE1" <-> "OE2" Residue "H ARG 84": "NH1" <-> "NH2" Residue "H GLU 148": "OE1" <-> "OE2" Residue "H ARG 156": "NH1" <-> "NH2" Residue "H ARG 163": "NH1" <-> "NH2" Residue "H ARG 177": "NH1" <-> "NH2" Residue "H ARG 184": "NH1" <-> "NH2" Residue "H ARG 204": "NH1" <-> "NH2" Residue "H ARG 214": "NH1" <-> "NH2" Residue "H ARG 243": "NH1" <-> "NH2" Residue "H ARG 260": "NH1" <-> "NH2" Residue "H GLU 267": "OE1" <-> "OE2" Residue "H GLU 298": "OE1" <-> "OE2" Residue "H ARG 301": "NH1" <-> "NH2" Residue "H ARG 302": "NH1" <-> "NH2" Residue "H GLU 307": "OE1" <-> "OE2" Residue "I ARG 22": "NH1" <-> "NH2" Residue "I GLU 39": "OE1" <-> "OE2" Residue "I ARG 49": "NH1" <-> "NH2" Residue "I GLU 69": "OE1" <-> "OE2" Residue "I ARG 84": "NH1" <-> "NH2" Residue "I GLU 148": "OE1" <-> "OE2" Residue "I ARG 156": "NH1" <-> "NH2" Residue "I ARG 163": "NH1" <-> "NH2" Residue "I ARG 177": "NH1" <-> "NH2" Residue "I ARG 184": "NH1" <-> "NH2" Residue "I ARG 204": "NH1" <-> "NH2" Residue "I ARG 214": "NH1" <-> "NH2" Residue "I ARG 243": "NH1" <-> "NH2" Residue "I ARG 260": "NH1" <-> "NH2" Residue "I GLU 267": "OE1" <-> "OE2" Residue "I GLU 298": "OE1" <-> "OE2" Residue "I ARG 301": "NH1" <-> "NH2" Residue "I ARG 302": "NH1" <-> "NH2" Residue "I GLU 307": "OE1" <-> "OE2" Residue "J ARG 22": "NH1" <-> "NH2" Residue "J GLU 39": "OE1" <-> "OE2" Residue "J ARG 49": "NH1" <-> "NH2" Residue "J GLU 69": "OE1" <-> "OE2" Residue "J ARG 84": "NH1" <-> "NH2" Residue "J GLU 148": "OE1" <-> "OE2" Residue "J ARG 156": "NH1" <-> "NH2" Residue "J ARG 163": "NH1" <-> "NH2" Residue "J ARG 177": "NH1" <-> "NH2" Residue "J ARG 184": "NH1" <-> "NH2" Residue "J ARG 204": "NH1" <-> "NH2" Residue "J ARG 214": "NH1" <-> "NH2" Residue "J ARG 243": "NH1" <-> "NH2" Residue "J ARG 260": "NH1" <-> "NH2" Residue "J GLU 267": "OE1" <-> "OE2" Residue "J GLU 298": "OE1" <-> "OE2" Residue "J ARG 301": "NH1" <-> "NH2" Residue "J ARG 302": "NH1" <-> "NH2" Residue "J GLU 307": "OE1" <-> "OE2" Residue "K ARG 22": "NH1" <-> "NH2" Residue "K GLU 39": "OE1" <-> "OE2" Residue "K ARG 49": "NH1" <-> "NH2" Residue "K GLU 69": "OE1" <-> "OE2" Residue "K ARG 84": "NH1" <-> "NH2" Residue "K GLU 148": "OE1" <-> "OE2" Residue "K ARG 156": "NH1" <-> "NH2" Residue "K ARG 163": "NH1" <-> "NH2" Residue "K ARG 177": "NH1" <-> "NH2" Residue "K ARG 184": "NH1" <-> "NH2" Residue "K ARG 204": "NH1" <-> "NH2" Residue "K ARG 214": "NH1" <-> "NH2" Residue "K ARG 243": "NH1" <-> "NH2" Residue "K ARG 260": "NH1" <-> "NH2" Residue "K GLU 267": "OE1" <-> "OE2" Residue "K GLU 298": "OE1" <-> "OE2" Residue "K ARG 301": "NH1" <-> "NH2" Residue "K ARG 302": "NH1" <-> "NH2" Residue "K GLU 307": "OE1" <-> "OE2" Residue "L ARG 22": "NH1" <-> "NH2" Residue "L GLU 39": "OE1" <-> "OE2" Residue "L ARG 49": "NH1" <-> "NH2" Residue "L GLU 69": "OE1" <-> "OE2" Residue "L ARG 84": "NH1" <-> "NH2" Residue "L GLU 148": "OE1" <-> "OE2" Residue "L ARG 156": "NH1" <-> "NH2" Residue "L ARG 163": "NH1" <-> "NH2" Residue "L ARG 177": "NH1" <-> "NH2" Residue "L ARG 184": "NH1" <-> "NH2" Residue "L ARG 204": "NH1" <-> "NH2" Residue "L ARG 214": "NH1" <-> "NH2" Residue "L ARG 243": "NH1" <-> "NH2" Residue "L ARG 260": "NH1" <-> "NH2" Residue "L GLU 267": "OE1" <-> "OE2" Residue "L GLU 298": "OE1" <-> "OE2" Residue "L ARG 301": "NH1" <-> "NH2" Residue "L ARG 302": "NH1" <-> "NH2" Residue "L GLU 307": "OE1" <-> "OE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 28992 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 2362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2362 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 9, 'TRANS': 299} Chain breaks: 1 Chain: "B" Number of atoms: 2362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2362 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 9, 'TRANS': 299} Chain breaks: 1 Chain: "C" Number of atoms: 2362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2362 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 9, 'TRANS': 299} Chain breaks: 1 Chain: "D" Number of atoms: 2362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2362 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 9, 'TRANS': 299} Chain breaks: 1 Chain: "E" Number of atoms: 2362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2362 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 9, 'TRANS': 299} Chain breaks: 1 Chain: "F" Number of atoms: 2362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2362 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 9, 'TRANS': 299} Chain breaks: 1 Chain: "G" Number of atoms: 2362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2362 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 9, 'TRANS': 299} Chain breaks: 1 Chain: "H" Number of atoms: 2362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2362 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 9, 'TRANS': 299} Chain breaks: 1 Chain: "I" Number of atoms: 2362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2362 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 9, 'TRANS': 299} Chain breaks: 1 Chain: "J" Number of atoms: 2362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2362 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 9, 'TRANS': 299} Chain breaks: 1 Chain: "K" Number of atoms: 2362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2362 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 9, 'TRANS': 299} Chain breaks: 1 Chain: "L" Number of atoms: 2362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2362 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 9, 'TRANS': 299} Chain breaks: 1 Chain: "A" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 52 Unusual residues: {' MG': 2, 'ATP': 1, 'HSX': 1, 'PO4': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 52 Unusual residues: {' MG': 2, 'ATP': 1, 'HSX': 1, 'PO4': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "C" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 52 Unusual residues: {' MG': 2, 'ATP': 1, 'HSX': 1, 'PO4': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "D" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 52 Unusual residues: {' MG': 2, 'ATP': 1, 'HSX': 1, 'PO4': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "E" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 52 Unusual residues: {' MG': 2, 'ATP': 1, 'HSX': 1, 'PO4': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "F" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 52 Unusual residues: {' MG': 2, 'ATP': 1, 'HSX': 1, 'PO4': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "G" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 52 Unusual residues: {' MG': 2, 'ATP': 1, 'HSX': 1, 'PO4': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "H" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 52 Unusual residues: {' MG': 2, 'ATP': 1, 'HSX': 1, 'PO4': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "I" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 52 Unusual residues: {' MG': 2, 'ATP': 1, 'HSX': 1, 'PO4': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "J" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 52 Unusual residues: {' MG': 2, 'ATP': 1, 'HSX': 1, 'PO4': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "K" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 52 Unusual residues: {' MG': 2, 'ATP': 1, 'HSX': 1, 'PO4': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "L" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 52 Unusual residues: {' MG': 2, 'ATP': 1, 'HSX': 1, 'PO4': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 636 residue: pdb=" N HIS A 12 " occ=0.58 ... (8 atoms not shown) pdb=" NE2 HIS A 12 " occ=0.58 residue: pdb=" N ARG A 22 " occ=0.80 ... (9 atoms not shown) pdb=" NH2 ARG A 22 " occ=0.80 residue: pdb=" N GLU A 26 " occ=0.40 ... (7 atoms not shown) pdb=" OE2 GLU A 26 " occ=0.40 residue: pdb=" N LYS A 29 " occ=0.40 ... (7 atoms not shown) pdb=" NZ LYS A 29 " occ=0.40 residue: pdb=" N LYS A 33 " occ=0.01 ... (7 atoms not shown) pdb=" NZ LYS A 33 " occ=0.01 residue: pdb=" N SER A 36 " occ=0.01 ... (4 atoms not shown) pdb=" OG SER A 36 " occ=0.01 residue: pdb=" N ASN A 37 " occ=0.50 ... (6 atoms not shown) pdb=" ND2 ASN A 37 " occ=0.50 residue: pdb=" N CYS A 41 " occ=0.89 ... (4 atoms not shown) pdb=" SG CYS A 41 " occ=0.89 residue: pdb=" N GLU A 43 " occ=0.40 ... (7 atoms not shown) pdb=" OE2 GLU A 43 " occ=0.40 residue: pdb=" N GLU A 46 " occ=0.88 ... (7 atoms not shown) pdb=" OE2 GLU A 46 " occ=0.88 residue: pdb=" N SER A 58 " occ=0.10 ... (4 atoms not shown) pdb=" OG SER A 58 " occ=0.10 residue: pdb=" N GLY A 59 " occ=0.01 ... (2 atoms not shown) pdb=" O GLY A 59 " occ=0.01 ... (remaining 624 not shown) Time building chain proxies: 13.76, per 1000 atoms: 0.47 Number of scatterers: 28992 At special positions: 0 Unit cell: (126.531, 138.109, 139.763, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 204 16.00 P 60 15.00 Mg 24 11.99 O 5700 8.00 N 5040 7.00 C 17964 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: 12.27 Conformation dependent library (CDL) restraints added in 4.9 seconds 7320 Ramachandran restraints generated. 3660 Oldfield, 0 Emsley, 3660 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7008 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 132 helices and 48 sheets defined 36.6% alpha, 17.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.90 Creating SS restraints... Processing helix chain 'A' and resid 13 through 22 Processing helix chain 'A' and resid 63 through 79 Processing helix chain 'A' and resid 108 through 119 Processing helix chain 'A' and resid 132 through 137 Processing helix chain 'A' and resid 148 through 158 Processing helix chain 'A' and resid 172 through 185 removed outlier: 3.551A pdb=" N ALA A 175 " --> pdb=" O ALA A 172 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N LYS A 176 " --> pdb=" O GLY A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 239 Processing helix chain 'A' and resid 257 through 263 Processing helix chain 'A' and resid 278 through 283 removed outlier: 3.692A pdb=" N HIS A 283 " --> pdb=" O ASP A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 305 Processing helix chain 'A' and resid 310 through 313 Processing helix chain 'B' and resid 13 through 22 Processing helix chain 'B' and resid 63 through 79 Processing helix chain 'B' and resid 108 through 119 Processing helix chain 'B' and resid 132 through 137 Processing helix chain 'B' and resid 148 through 158 Processing helix chain 'B' and resid 172 through 185 removed outlier: 3.551A pdb=" N ALA B 175 " --> pdb=" O ALA B 172 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N LYS B 176 " --> pdb=" O GLY B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 239 Processing helix chain 'B' and resid 257 through 263 Processing helix chain 'B' and resid 278 through 283 removed outlier: 3.691A pdb=" N HIS B 283 " --> pdb=" O ASP B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 305 Processing helix chain 'B' and resid 310 through 313 Processing helix chain 'C' and resid 13 through 22 Processing helix chain 'C' and resid 63 through 79 Processing helix chain 'C' and resid 108 through 119 Processing helix chain 'C' and resid 132 through 137 Processing helix chain 'C' and resid 148 through 158 Processing helix chain 'C' and resid 172 through 185 removed outlier: 3.552A pdb=" N ALA C 175 " --> pdb=" O ALA C 172 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N LYS C 176 " --> pdb=" O GLY C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 239 Processing helix chain 'C' and resid 257 through 263 Processing helix chain 'C' and resid 278 through 283 removed outlier: 3.691A pdb=" N HIS C 283 " --> pdb=" O ASP C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 305 Processing helix chain 'C' and resid 310 through 313 Processing helix chain 'D' and resid 13 through 22 Processing helix chain 'D' and resid 63 through 79 Processing helix chain 'D' and resid 108 through 119 Processing helix chain 'D' and resid 132 through 137 Processing helix chain 'D' and resid 148 through 158 Processing helix chain 'D' and resid 172 through 185 removed outlier: 3.551A pdb=" N ALA D 175 " --> pdb=" O ALA D 172 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N LYS D 176 " --> pdb=" O GLY D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 239 Processing helix chain 'D' and resid 257 through 263 Processing helix chain 'D' and resid 278 through 283 removed outlier: 3.690A pdb=" N HIS D 283 " --> pdb=" O ASP D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 through 305 Processing helix chain 'D' and resid 310 through 313 Processing helix chain 'E' and resid 13 through 22 Processing helix chain 'E' and resid 63 through 79 Processing helix chain 'E' and resid 108 through 119 Processing helix chain 'E' and resid 132 through 137 Processing helix chain 'E' and resid 148 through 158 Processing helix chain 'E' and resid 172 through 185 removed outlier: 3.551A pdb=" N ALA E 175 " --> pdb=" O ALA E 172 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N LYS E 176 " --> pdb=" O GLY E 173 " (cutoff:3.500A) Processing helix chain 'E' and resid 227 through 239 Processing helix chain 'E' and resid 257 through 263 Processing helix chain 'E' and resid 278 through 283 removed outlier: 3.691A pdb=" N HIS E 283 " --> pdb=" O ASP E 279 " (cutoff:3.500A) Processing helix chain 'E' and resid 293 through 305 Processing helix chain 'E' and resid 310 through 313 Processing helix chain 'F' and resid 13 through 22 Processing helix chain 'F' and resid 63 through 79 Processing helix chain 'F' and resid 108 through 119 Processing helix chain 'F' and resid 132 through 137 Processing helix chain 'F' and resid 148 through 158 Processing helix chain 'F' and resid 172 through 185 removed outlier: 3.552A pdb=" N ALA F 175 " --> pdb=" O ALA F 172 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N LYS F 176 " --> pdb=" O GLY F 173 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 239 Processing helix chain 'F' and resid 257 through 263 Processing helix chain 'F' and resid 278 through 283 removed outlier: 3.691A pdb=" N HIS F 283 " --> pdb=" O ASP F 279 " (cutoff:3.500A) Processing helix chain 'F' and resid 293 through 305 Processing helix chain 'F' and resid 310 through 313 Processing helix chain 'G' and resid 13 through 22 Processing helix chain 'G' and resid 63 through 79 Processing helix chain 'G' and resid 108 through 119 Processing helix chain 'G' and resid 132 through 137 Processing helix chain 'G' and resid 148 through 158 Processing helix chain 'G' and resid 172 through 185 removed outlier: 3.551A pdb=" N ALA G 175 " --> pdb=" O ALA G 172 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N LYS G 176 " --> pdb=" O GLY G 173 " (cutoff:3.500A) Processing helix chain 'G' and resid 227 through 239 Processing helix chain 'G' and resid 257 through 263 Processing helix chain 'G' and resid 278 through 283 removed outlier: 3.690A pdb=" N HIS G 283 " --> pdb=" O ASP G 279 " (cutoff:3.500A) Processing helix chain 'G' and resid 293 through 305 Processing helix chain 'G' and resid 310 through 313 Processing helix chain 'H' and resid 13 through 22 Processing helix chain 'H' and resid 63 through 79 Processing helix chain 'H' and resid 108 through 119 Processing helix chain 'H' and resid 132 through 137 Processing helix chain 'H' and resid 148 through 158 Processing helix chain 'H' and resid 172 through 185 removed outlier: 3.551A pdb=" N ALA H 175 " --> pdb=" O ALA H 172 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N LYS H 176 " --> pdb=" O GLY H 173 " (cutoff:3.500A) Processing helix chain 'H' and resid 227 through 239 Processing helix chain 'H' and resid 257 through 263 Processing helix chain 'H' and resid 278 through 283 removed outlier: 3.691A pdb=" N HIS H 283 " --> pdb=" O ASP H 279 " (cutoff:3.500A) Processing helix chain 'H' and resid 293 through 305 Processing helix chain 'H' and resid 310 through 313 Processing helix chain 'I' and resid 13 through 22 Processing helix chain 'I' and resid 63 through 79 Processing helix chain 'I' and resid 108 through 119 Processing helix chain 'I' and resid 132 through 137 Processing helix chain 'I' and resid 148 through 158 Processing helix chain 'I' and resid 172 through 185 removed outlier: 3.552A pdb=" N ALA I 175 " --> pdb=" O ALA I 172 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N LYS I 176 " --> pdb=" O GLY I 173 " (cutoff:3.500A) Processing helix chain 'I' and resid 227 through 239 Processing helix chain 'I' and resid 257 through 263 Processing helix chain 'I' and resid 278 through 283 removed outlier: 3.690A pdb=" N HIS I 283 " --> pdb=" O ASP I 279 " (cutoff:3.500A) Processing helix chain 'I' and resid 293 through 305 Processing helix chain 'I' and resid 310 through 313 Processing helix chain 'J' and resid 13 through 22 Processing helix chain 'J' and resid 63 through 79 Processing helix chain 'J' and resid 108 through 119 Processing helix chain 'J' and resid 132 through 137 Processing helix chain 'J' and resid 148 through 158 Processing helix chain 'J' and resid 172 through 185 removed outlier: 3.551A pdb=" N ALA J 175 " --> pdb=" O ALA J 172 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N LYS J 176 " --> pdb=" O GLY J 173 " (cutoff:3.500A) Processing helix chain 'J' and resid 227 through 239 Processing helix chain 'J' and resid 257 through 263 Processing helix chain 'J' and resid 278 through 283 removed outlier: 3.689A pdb=" N HIS J 283 " --> pdb=" O ASP J 279 " (cutoff:3.500A) Processing helix chain 'J' and resid 293 through 305 Processing helix chain 'J' and resid 310 through 313 Processing helix chain 'K' and resid 13 through 22 Processing helix chain 'K' and resid 63 through 79 Processing helix chain 'K' and resid 108 through 119 Processing helix chain 'K' and resid 132 through 137 Processing helix chain 'K' and resid 148 through 158 Processing helix chain 'K' and resid 172 through 185 removed outlier: 3.551A pdb=" N ALA K 175 " --> pdb=" O ALA K 172 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N LYS K 176 " --> pdb=" O GLY K 173 " (cutoff:3.500A) Processing helix chain 'K' and resid 227 through 239 Processing helix chain 'K' and resid 257 through 263 Processing helix chain 'K' and resid 278 through 283 removed outlier: 3.692A pdb=" N HIS K 283 " --> pdb=" O ASP K 279 " (cutoff:3.500A) Processing helix chain 'K' and resid 293 through 305 Processing helix chain 'K' and resid 310 through 313 Processing helix chain 'L' and resid 13 through 22 Processing helix chain 'L' and resid 63 through 79 Processing helix chain 'L' and resid 108 through 119 Processing helix chain 'L' and resid 132 through 137 Processing helix chain 'L' and resid 148 through 158 Processing helix chain 'L' and resid 172 through 185 removed outlier: 3.552A pdb=" N ALA L 175 " --> pdb=" O ALA L 172 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N LYS L 176 " --> pdb=" O GLY L 173 " (cutoff:3.500A) Processing helix chain 'L' and resid 227 through 239 Processing helix chain 'L' and resid 257 through 263 Processing helix chain 'L' and resid 278 through 283 removed outlier: 3.691A pdb=" N HIS L 283 " --> pdb=" O ASP L 279 " (cutoff:3.500A) Processing helix chain 'L' and resid 293 through 305 Processing helix chain 'L' and resid 310 through 313 Processing sheet with id= A, first strand: chain 'A' and resid 4 through 8 removed outlier: 6.261A pdb=" N ASP A 52 " --> pdb=" O LYS A 5 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N PHE A 7 " --> pdb=" O ASP A 52 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N TYR A 54 " --> pdb=" O PHE A 7 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ARG A 84 " --> pdb=" O VAL A 53 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N ILE A 55 " --> pdb=" O ARG A 84 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N THR A 86 " --> pdb=" O ILE A 55 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N HIS A 123 " --> pdb=" O ALA A 87 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N ILE A 89 " --> pdb=" O HIS A 123 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ILE A 125 " --> pdb=" O ILE A 89 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N THR A 126 " --> pdb=" O PRO A 141 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N ASP A 143 " --> pdb=" O THR A 126 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 30 through 34 Processing sheet with id= C, first strand: chain 'A' and resid 166 through 169 removed outlier: 6.354A pdb=" N ARG A 243 " --> pdb=" O ALA A 216 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N LEU A 218 " --> pdb=" O ARG A 243 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N TYR A 245 " --> pdb=" O LEU A 218 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N ASP A 220 " --> pdb=" O TYR A 245 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ILE A 247 " --> pdb=" O ASP A 220 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N ALA A 268 " --> pdb=" O ALA A 246 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N LEU A 248 " --> pdb=" O ALA A 268 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N VAL A 270 " --> pdb=" O LEU A 248 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 191 through 194 Processing sheet with id= E, first strand: chain 'B' and resid 4 through 8 removed outlier: 6.261A pdb=" N ASP B 52 " --> pdb=" O LYS B 5 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N PHE B 7 " --> pdb=" O ASP B 52 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N TYR B 54 " --> pdb=" O PHE B 7 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ARG B 84 " --> pdb=" O VAL B 53 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N ILE B 55 " --> pdb=" O ARG B 84 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N THR B 86 " --> pdb=" O ILE B 55 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N HIS B 123 " --> pdb=" O ALA B 87 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N ILE B 89 " --> pdb=" O HIS B 123 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N ILE B 125 " --> pdb=" O ILE B 89 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N THR B 126 " --> pdb=" O PRO B 141 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N ASP B 143 " --> pdb=" O THR B 126 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'B' and resid 30 through 34 Processing sheet with id= G, first strand: chain 'B' and resid 166 through 169 removed outlier: 6.353A pdb=" N ARG B 243 " --> pdb=" O ALA B 216 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N LEU B 218 " --> pdb=" O ARG B 243 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N TYR B 245 " --> pdb=" O LEU B 218 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N ASP B 220 " --> pdb=" O TYR B 245 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ILE B 247 " --> pdb=" O ASP B 220 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N ALA B 268 " --> pdb=" O ALA B 246 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N LEU B 248 " --> pdb=" O ALA B 268 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N VAL B 270 " --> pdb=" O LEU B 248 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 191 through 194 Processing sheet with id= I, first strand: chain 'C' and resid 4 through 8 removed outlier: 6.262A pdb=" N ASP C 52 " --> pdb=" O LYS C 5 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N PHE C 7 " --> pdb=" O ASP C 52 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N TYR C 54 " --> pdb=" O PHE C 7 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ARG C 84 " --> pdb=" O VAL C 53 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N ILE C 55 " --> pdb=" O ARG C 84 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N THR C 86 " --> pdb=" O ILE C 55 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N HIS C 123 " --> pdb=" O ALA C 87 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N ILE C 89 " --> pdb=" O HIS C 123 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ILE C 125 " --> pdb=" O ILE C 89 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N THR C 126 " --> pdb=" O PRO C 141 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N ASP C 143 " --> pdb=" O THR C 126 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'C' and resid 30 through 34 Processing sheet with id= K, first strand: chain 'C' and resid 166 through 169 removed outlier: 6.354A pdb=" N ARG C 243 " --> pdb=" O ALA C 216 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N LEU C 218 " --> pdb=" O ARG C 243 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N TYR C 245 " --> pdb=" O LEU C 218 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N ASP C 220 " --> pdb=" O TYR C 245 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ILE C 247 " --> pdb=" O ASP C 220 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N ALA C 268 " --> pdb=" O ALA C 246 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N LEU C 248 " --> pdb=" O ALA C 268 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N VAL C 270 " --> pdb=" O LEU C 248 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 191 through 194 Processing sheet with id= M, first strand: chain 'D' and resid 4 through 8 removed outlier: 6.260A pdb=" N ASP D 52 " --> pdb=" O LYS D 5 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N PHE D 7 " --> pdb=" O ASP D 52 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N TYR D 54 " --> pdb=" O PHE D 7 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ARG D 84 " --> pdb=" O VAL D 53 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N ILE D 55 " --> pdb=" O ARG D 84 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N THR D 86 " --> pdb=" O ILE D 55 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N HIS D 123 " --> pdb=" O ALA D 87 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N ILE D 89 " --> pdb=" O HIS D 123 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N ILE D 125 " --> pdb=" O ILE D 89 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N THR D 126 " --> pdb=" O PRO D 141 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N ASP D 143 " --> pdb=" O THR D 126 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'D' and resid 30 through 34 Processing sheet with id= O, first strand: chain 'D' and resid 166 through 169 removed outlier: 6.352A pdb=" N ARG D 243 " --> pdb=" O ALA D 216 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N LEU D 218 " --> pdb=" O ARG D 243 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N TYR D 245 " --> pdb=" O LEU D 218 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N ASP D 220 " --> pdb=" O TYR D 245 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ILE D 247 " --> pdb=" O ASP D 220 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N ALA D 268 " --> pdb=" O ALA D 246 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N LEU D 248 " --> pdb=" O ALA D 268 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N VAL D 270 " --> pdb=" O LEU D 248 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 191 through 194 Processing sheet with id= Q, first strand: chain 'E' and resid 4 through 8 removed outlier: 6.261A pdb=" N ASP E 52 " --> pdb=" O LYS E 5 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N PHE E 7 " --> pdb=" O ASP E 52 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N TYR E 54 " --> pdb=" O PHE E 7 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ARG E 84 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N ILE E 55 " --> pdb=" O ARG E 84 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N THR E 86 " --> pdb=" O ILE E 55 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N HIS E 123 " --> pdb=" O ALA E 87 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N ILE E 89 " --> pdb=" O HIS E 123 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ILE E 125 " --> pdb=" O ILE E 89 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N THR E 126 " --> pdb=" O PRO E 141 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N ASP E 143 " --> pdb=" O THR E 126 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'E' and resid 30 through 34 Processing sheet with id= S, first strand: chain 'E' and resid 166 through 169 removed outlier: 6.353A pdb=" N ARG E 243 " --> pdb=" O ALA E 216 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N LEU E 218 " --> pdb=" O ARG E 243 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N TYR E 245 " --> pdb=" O LEU E 218 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N ASP E 220 " --> pdb=" O TYR E 245 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ILE E 247 " --> pdb=" O ASP E 220 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N ALA E 268 " --> pdb=" O ALA E 246 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N LEU E 248 " --> pdb=" O ALA E 268 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N VAL E 270 " --> pdb=" O LEU E 248 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 191 through 194 Processing sheet with id= U, first strand: chain 'F' and resid 4 through 8 removed outlier: 6.260A pdb=" N ASP F 52 " --> pdb=" O LYS F 5 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N PHE F 7 " --> pdb=" O ASP F 52 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N TYR F 54 " --> pdb=" O PHE F 7 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ARG F 84 " --> pdb=" O VAL F 53 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N ILE F 55 " --> pdb=" O ARG F 84 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N THR F 86 " --> pdb=" O ILE F 55 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N HIS F 123 " --> pdb=" O ALA F 87 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N ILE F 89 " --> pdb=" O HIS F 123 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N ILE F 125 " --> pdb=" O ILE F 89 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N THR F 126 " --> pdb=" O PRO F 141 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N ASP F 143 " --> pdb=" O THR F 126 " (cutoff:3.500A) No H-bonds generated for sheet with id= U Processing sheet with id= V, first strand: chain 'F' and resid 30 through 34 Processing sheet with id= W, first strand: chain 'F' and resid 166 through 169 removed outlier: 6.353A pdb=" N ARG F 243 " --> pdb=" O ALA F 216 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N LEU F 218 " --> pdb=" O ARG F 243 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N TYR F 245 " --> pdb=" O LEU F 218 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N ASP F 220 " --> pdb=" O TYR F 245 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ILE F 247 " --> pdb=" O ASP F 220 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N ALA F 268 " --> pdb=" O ALA F 246 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N LEU F 248 " --> pdb=" O ALA F 268 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N VAL F 270 " --> pdb=" O LEU F 248 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'F' and resid 191 through 194 Processing sheet with id= Y, first strand: chain 'G' and resid 4 through 8 removed outlier: 6.260A pdb=" N ASP G 52 " --> pdb=" O LYS G 5 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N PHE G 7 " --> pdb=" O ASP G 52 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N TYR G 54 " --> pdb=" O PHE G 7 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ARG G 84 " --> pdb=" O VAL G 53 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N ILE G 55 " --> pdb=" O ARG G 84 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N THR G 86 " --> pdb=" O ILE G 55 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N HIS G 123 " --> pdb=" O ALA G 87 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N ILE G 89 " --> pdb=" O HIS G 123 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ILE G 125 " --> pdb=" O ILE G 89 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N THR G 126 " --> pdb=" O PRO G 141 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N ASP G 143 " --> pdb=" O THR G 126 " (cutoff:3.500A) No H-bonds generated for sheet with id= Y Processing sheet with id= Z, first strand: chain 'G' and resid 30 through 34 Processing sheet with id= AA, first strand: chain 'G' and resid 166 through 169 removed outlier: 6.353A pdb=" N ARG G 243 " --> pdb=" O ALA G 216 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N LEU G 218 " --> pdb=" O ARG G 243 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N TYR G 245 " --> pdb=" O LEU G 218 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N ASP G 220 " --> pdb=" O TYR G 245 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ILE G 247 " --> pdb=" O ASP G 220 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N ALA G 268 " --> pdb=" O ALA G 246 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N LEU G 248 " --> pdb=" O ALA G 268 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N VAL G 270 " --> pdb=" O LEU G 248 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'G' and resid 191 through 194 Processing sheet with id= AC, first strand: chain 'H' and resid 4 through 8 removed outlier: 6.261A pdb=" N ASP H 52 " --> pdb=" O LYS H 5 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N PHE H 7 " --> pdb=" O ASP H 52 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N TYR H 54 " --> pdb=" O PHE H 7 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ARG H 84 " --> pdb=" O VAL H 53 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N ILE H 55 " --> pdb=" O ARG H 84 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N THR H 86 " --> pdb=" O ILE H 55 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N HIS H 123 " --> pdb=" O ALA H 87 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N ILE H 89 " --> pdb=" O HIS H 123 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ILE H 125 " --> pdb=" O ILE H 89 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N THR H 126 " --> pdb=" O PRO H 141 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N ASP H 143 " --> pdb=" O THR H 126 " (cutoff:3.500A) No H-bonds generated for sheet with id= AC Processing sheet with id= AD, first strand: chain 'H' and resid 30 through 34 Processing sheet with id= AE, first strand: chain 'H' and resid 166 through 169 removed outlier: 6.353A pdb=" N ARG H 243 " --> pdb=" O ALA H 216 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N LEU H 218 " --> pdb=" O ARG H 243 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N TYR H 245 " --> pdb=" O LEU H 218 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N ASP H 220 " --> pdb=" O TYR H 245 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ILE H 247 " --> pdb=" O ASP H 220 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N ALA H 268 " --> pdb=" O ALA H 246 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N LEU H 248 " --> pdb=" O ALA H 268 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N VAL H 270 " --> pdb=" O LEU H 248 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'H' and resid 191 through 194 Processing sheet with id= AG, first strand: chain 'I' and resid 4 through 8 removed outlier: 6.261A pdb=" N ASP I 52 " --> pdb=" O LYS I 5 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N PHE I 7 " --> pdb=" O ASP I 52 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N TYR I 54 " --> pdb=" O PHE I 7 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ARG I 84 " --> pdb=" O VAL I 53 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N ILE I 55 " --> pdb=" O ARG I 84 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N THR I 86 " --> pdb=" O ILE I 55 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N HIS I 123 " --> pdb=" O ALA I 87 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N ILE I 89 " --> pdb=" O HIS I 123 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ILE I 125 " --> pdb=" O ILE I 89 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N THR I 126 " --> pdb=" O PRO I 141 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N ASP I 143 " --> pdb=" O THR I 126 " (cutoff:3.500A) No H-bonds generated for sheet with id= AG Processing sheet with id= AH, first strand: chain 'I' and resid 30 through 34 Processing sheet with id= AI, first strand: chain 'I' and resid 166 through 169 removed outlier: 6.354A pdb=" N ARG I 243 " --> pdb=" O ALA I 216 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N LEU I 218 " --> pdb=" O ARG I 243 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N TYR I 245 " --> pdb=" O LEU I 218 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N ASP I 220 " --> pdb=" O TYR I 245 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ILE I 247 " --> pdb=" O ASP I 220 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N ALA I 268 " --> pdb=" O ALA I 246 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N LEU I 248 " --> pdb=" O ALA I 268 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N VAL I 270 " --> pdb=" O LEU I 248 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'I' and resid 191 through 194 Processing sheet with id= AK, first strand: chain 'J' and resid 4 through 8 removed outlier: 6.261A pdb=" N ASP J 52 " --> pdb=" O LYS J 5 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N PHE J 7 " --> pdb=" O ASP J 52 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N TYR J 54 " --> pdb=" O PHE J 7 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ARG J 84 " --> pdb=" O VAL J 53 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N ILE J 55 " --> pdb=" O ARG J 84 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N THR J 86 " --> pdb=" O ILE J 55 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N HIS J 123 " --> pdb=" O ALA J 87 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N ILE J 89 " --> pdb=" O HIS J 123 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ILE J 125 " --> pdb=" O ILE J 89 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N THR J 126 " --> pdb=" O PRO J 141 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N ASP J 143 " --> pdb=" O THR J 126 " (cutoff:3.500A) No H-bonds generated for sheet with id= AK Processing sheet with id= AL, first strand: chain 'J' and resid 30 through 34 Processing sheet with id= AM, first strand: chain 'J' and resid 166 through 169 removed outlier: 6.354A pdb=" N ARG J 243 " --> pdb=" O ALA J 216 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N LEU J 218 " --> pdb=" O ARG J 243 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N TYR J 245 " --> pdb=" O LEU J 218 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N ASP J 220 " --> pdb=" O TYR J 245 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ILE J 247 " --> pdb=" O ASP J 220 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N ALA J 268 " --> pdb=" O ALA J 246 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N LEU J 248 " --> pdb=" O ALA J 268 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N VAL J 270 " --> pdb=" O LEU J 248 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'J' and resid 191 through 194 Processing sheet with id= AO, first strand: chain 'K' and resid 4 through 8 removed outlier: 6.261A pdb=" N ASP K 52 " --> pdb=" O LYS K 5 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N PHE K 7 " --> pdb=" O ASP K 52 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N TYR K 54 " --> pdb=" O PHE K 7 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ARG K 84 " --> pdb=" O VAL K 53 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N ILE K 55 " --> pdb=" O ARG K 84 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N THR K 86 " --> pdb=" O ILE K 55 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N HIS K 123 " --> pdb=" O ALA K 87 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N ILE K 89 " --> pdb=" O HIS K 123 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ILE K 125 " --> pdb=" O ILE K 89 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N THR K 126 " --> pdb=" O PRO K 141 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N ASP K 143 " --> pdb=" O THR K 126 " (cutoff:3.500A) No H-bonds generated for sheet with id= AO Processing sheet with id= AP, first strand: chain 'K' and resid 30 through 34 Processing sheet with id= AQ, first strand: chain 'K' and resid 166 through 169 removed outlier: 6.353A pdb=" N ARG K 243 " --> pdb=" O ALA K 216 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N LEU K 218 " --> pdb=" O ARG K 243 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N TYR K 245 " --> pdb=" O LEU K 218 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N ASP K 220 " --> pdb=" O TYR K 245 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ILE K 247 " --> pdb=" O ASP K 220 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N ALA K 268 " --> pdb=" O ALA K 246 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N LEU K 248 " --> pdb=" O ALA K 268 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N VAL K 270 " --> pdb=" O LEU K 248 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'K' and resid 191 through 194 Processing sheet with id= AS, first strand: chain 'L' and resid 4 through 8 removed outlier: 6.261A pdb=" N ASP L 52 " --> pdb=" O LYS L 5 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N PHE L 7 " --> pdb=" O ASP L 52 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N TYR L 54 " --> pdb=" O PHE L 7 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ARG L 84 " --> pdb=" O VAL L 53 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N ILE L 55 " --> pdb=" O ARG L 84 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N THR L 86 " --> pdb=" O ILE L 55 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N HIS L 123 " --> pdb=" O ALA L 87 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N ILE L 89 " --> pdb=" O HIS L 123 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N ILE L 125 " --> pdb=" O ILE L 89 " (cutoff:3.500A) removed outlier: 8.069A pdb=" N THR L 126 " --> pdb=" O PRO L 141 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N ASP L 143 " --> pdb=" O THR L 126 " (cutoff:3.500A) No H-bonds generated for sheet with id= AS Processing sheet with id= AT, first strand: chain 'L' and resid 30 through 34 Processing sheet with id= AU, first strand: chain 'L' and resid 166 through 169 removed outlier: 6.354A pdb=" N ARG L 243 " --> pdb=" O ALA L 216 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N LEU L 218 " --> pdb=" O ARG L 243 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N TYR L 245 " --> pdb=" O LEU L 218 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N ASP L 220 " --> pdb=" O TYR L 245 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ILE L 247 " --> pdb=" O ASP L 220 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N ALA L 268 " --> pdb=" O ALA L 246 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N LEU L 248 " --> pdb=" O ALA L 268 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N VAL L 270 " --> pdb=" O LEU L 248 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'L' and resid 191 through 194 1008 hydrogen bonds defined for protein. 2484 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: 10.48 Time building geometry restraints manager: 13.22 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: 9635 1.34 - 1.46: 3781 1.46 - 1.57: 15588 1.57 - 1.69: 72 1.69 - 1.81: 300 Bond restraints: 29376 Sorted by residual: bond pdb=" C3' ATP C 401 " pdb=" C4' ATP C 401 " ideal model delta sigma weight residual 1.305 1.531 -0.226 2.00e-02 2.50e+03 1.27e+02 bond pdb=" C3' ATP B 401 " pdb=" C4' ATP B 401 " ideal model delta sigma weight residual 1.305 1.530 -0.225 2.00e-02 2.50e+03 1.27e+02 bond pdb=" C3' ATP K 401 " pdb=" C4' ATP K 401 " ideal model delta sigma weight residual 1.305 1.530 -0.225 2.00e-02 2.50e+03 1.27e+02 bond pdb=" C3' ATP I 401 " pdb=" C4' ATP I 401 " ideal model delta sigma weight residual 1.305 1.530 -0.225 2.00e-02 2.50e+03 1.27e+02 bond pdb=" C3' ATP D 401 " pdb=" C4' ATP D 401 " ideal model delta sigma weight residual 1.305 1.530 -0.225 2.00e-02 2.50e+03 1.27e+02 ... (remaining 29371 not shown) Histogram of bond angle deviations from ideal: 98.83 - 105.88: 671 105.88 - 112.92: 16837 112.92 - 119.97: 9617 119.97 - 127.01: 12371 127.01 - 134.06: 356 Bond angle restraints: 39852 Sorted by residual: angle pdb=" C1' ATP A 401 " pdb=" N9 ATP A 401 " pdb=" C8 ATP A 401 " ideal model delta sigma weight residual 92.72 126.91 -34.19 3.00e+00 1.11e-01 1.30e+02 angle pdb=" C1' ATP H 401 " pdb=" N9 ATP H 401 " pdb=" C8 ATP H 401 " ideal model delta sigma weight residual 92.72 126.87 -34.15 3.00e+00 1.11e-01 1.30e+02 angle pdb=" C1' ATP L 401 " pdb=" N9 ATP L 401 " pdb=" C8 ATP L 401 " ideal model delta sigma weight residual 92.72 126.85 -34.13 3.00e+00 1.11e-01 1.29e+02 angle pdb=" C1' ATP B 401 " pdb=" N9 ATP B 401 " pdb=" C8 ATP B 401 " ideal model delta sigma weight residual 92.72 126.85 -34.13 3.00e+00 1.11e-01 1.29e+02 angle pdb=" C1' ATP K 401 " pdb=" N9 ATP K 401 " pdb=" C8 ATP K 401 " ideal model delta sigma weight residual 92.72 126.85 -34.13 3.00e+00 1.11e-01 1.29e+02 ... (remaining 39847 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.89: 16823 26.89 - 53.78: 931 53.78 - 80.68: 162 80.68 - 107.57: 24 107.57 - 134.46: 36 Dihedral angle restraints: 17976 sinusoidal: 7224 harmonic: 10752 Sorted by residual: dihedral pdb=" CA ASP G 101 " pdb=" C ASP G 101 " pdb=" N LYS G 102 " pdb=" CA LYS G 102 " ideal model delta harmonic sigma weight residual 180.00 156.28 23.72 0 5.00e+00 4.00e-02 2.25e+01 dihedral pdb=" CA ASP H 101 " pdb=" C ASP H 101 " pdb=" N LYS H 102 " pdb=" CA LYS H 102 " ideal model delta harmonic sigma weight residual 180.00 156.29 23.71 0 5.00e+00 4.00e-02 2.25e+01 dihedral pdb=" CA ASP A 101 " pdb=" C ASP A 101 " pdb=" N LYS A 102 " pdb=" CA LYS A 102 " ideal model delta harmonic sigma weight residual 180.00 156.30 23.70 0 5.00e+00 4.00e-02 2.25e+01 ... (remaining 17973 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 2873 0.048 - 0.097: 1290 0.097 - 0.145: 394 0.145 - 0.193: 39 0.193 - 0.242: 24 Chirality restraints: 4620 Sorted by residual: chirality pdb=" CG LEU E 248 " pdb=" CB LEU E 248 " pdb=" CD1 LEU E 248 " pdb=" CD2 LEU E 248 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" CG LEU I 248 " pdb=" CB LEU I 248 " pdb=" CD1 LEU I 248 " pdb=" CD2 LEU I 248 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" CG LEU H 248 " pdb=" CB LEU H 248 " pdb=" CD1 LEU H 248 " pdb=" CD2 LEU H 248 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.24 2.00e-01 2.50e+01 1.45e+00 ... (remaining 4617 not shown) Planarity restraints: 5028 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 HSX D 402 " -0.273 2.00e-02 2.50e+03 6.78e-01 1.03e+04 pdb=" C2 HSX D 402 " -0.852 2.00e-02 2.50e+03 pdb=" C3 HSX D 402 " 0.038 2.00e-02 2.50e+03 pdb=" C4 HSX D 402 " 0.320 2.00e-02 2.50e+03 pdb=" C5 HSX D 402 " -0.562 2.00e-02 2.50e+03 pdb=" O1 HSX D 402 " 0.781 2.00e-02 2.50e+03 pdb=" O2 HSX D 402 " -0.858 2.00e-02 2.50e+03 pdb=" O3 HSX D 402 " 1.241 2.00e-02 2.50e+03 pdb=" O4 HSX D 402 " 0.165 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 HSX A 402 " -0.273 2.00e-02 2.50e+03 6.78e-01 1.03e+04 pdb=" C2 HSX A 402 " -0.851 2.00e-02 2.50e+03 pdb=" C3 HSX A 402 " 0.038 2.00e-02 2.50e+03 pdb=" C4 HSX A 402 " 0.320 2.00e-02 2.50e+03 pdb=" C5 HSX A 402 " -0.562 2.00e-02 2.50e+03 pdb=" O1 HSX A 402 " 0.780 2.00e-02 2.50e+03 pdb=" O2 HSX A 402 " -0.858 2.00e-02 2.50e+03 pdb=" O3 HSX A 402 " 1.242 2.00e-02 2.50e+03 pdb=" O4 HSX A 402 " 0.165 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 HSX J 402 " -0.273 2.00e-02 2.50e+03 6.78e-01 1.03e+04 pdb=" C2 HSX J 402 " -0.852 2.00e-02 2.50e+03 pdb=" C3 HSX J 402 " 0.038 2.00e-02 2.50e+03 pdb=" C4 HSX J 402 " 0.320 2.00e-02 2.50e+03 pdb=" C5 HSX J 402 " -0.562 2.00e-02 2.50e+03 pdb=" O1 HSX J 402 " 0.781 2.00e-02 2.50e+03 pdb=" O2 HSX J 402 " -0.858 2.00e-02 2.50e+03 pdb=" O3 HSX J 402 " 1.241 2.00e-02 2.50e+03 pdb=" O4 HSX J 402 " 0.165 2.00e-02 2.50e+03 ... (remaining 5025 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 210 2.51 - 3.11: 21864 3.11 - 3.70: 47278 3.70 - 4.30: 69170 4.30 - 4.90: 111854 Nonbonded interactions: 250376 Sorted by model distance: nonbonded pdb=" CE MET G 68 " pdb=" CE MET L 68 " model vdw 1.910 3.880 nonbonded pdb=" CE MET A 68 " pdb=" CE MET F 68 " model vdw 1.910 3.880 nonbonded pdb=" CE MET B 68 " pdb=" CE MET C 68 " model vdw 1.910 3.880 nonbonded pdb=" CE MET H 68 " pdb=" CE MET I 68 " model vdw 1.910 3.880 nonbonded pdb=" CE MET D 68 " pdb=" CE MET E 68 " model vdw 1.912 3.880 ... (remaining 250371 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } 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=0.01 max=1.00 mean=0.91 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 8.250 Check model and map are aligned: 0.430 Set scattering table: 0.260 Process input model: 75.360 Find NCS groups from input model: 2.170 Set up NCS constraints: 0.290 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 102.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 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 : 0.012 0.226 29376 Z= 0.847 Angle : 1.174 34.191 39852 Z= 0.524 Chirality : 0.057 0.242 4620 Planarity : 0.042 0.678 5028 Dihedral : 18.164 134.462 10968 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 1.15 % Allowed : 11.83 % Favored : 87.02 % 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: 0.57 (0.14), residues: 3660 helix: 1.71 (0.14), residues: 1464 sheet: -0.63 (0.16), residues: 996 loop : -0.22 (0.17), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.004 TRP H 162 HIS 0.005 0.002 HIS C 231 PHE 0.018 0.002 PHE J 189 TYR 0.022 0.003 TYR B 146 ARG 0.011 0.001 ARG H 177 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7320 Ramachandran restraints generated. 3660 Oldfield, 0 Emsley, 3660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7320 Ramachandran restraints generated. 3660 Oldfield, 0 Emsley, 3660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 624 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 588 time to evaluate : 3.200 Fit side-chains REVERT: A 128 ASP cc_start: 0.8872 (m-30) cc_final: 0.8541 (m-30) REVERT: A 178 VAL cc_start: 0.8484 (m) cc_final: 0.8253 (t) REVERT: A 298 GLU cc_start: 0.8702 (mm-30) cc_final: 0.8492 (mm-30) REVERT: B 178 VAL cc_start: 0.8765 (m) cc_final: 0.8529 (t) REVERT: C 177 ARG cc_start: 0.7664 (ttm110) cc_final: 0.7361 (ttm110) REVERT: C 178 VAL cc_start: 0.8582 (m) cc_final: 0.8306 (t) REVERT: D 156 ARG cc_start: 0.8086 (mtt90) cc_final: 0.7805 (mtt180) REVERT: D 178 VAL cc_start: 0.8770 (m) cc_final: 0.8529 (t) REVERT: E 178 VAL cc_start: 0.8523 (m) cc_final: 0.8271 (t) REVERT: F 127 MET cc_start: 0.8729 (ttm) cc_final: 0.8521 (ttm) REVERT: G 127 MET cc_start: 0.8698 (ttm) cc_final: 0.8490 (ttm) REVERT: G 178 VAL cc_start: 0.8829 (m) cc_final: 0.8610 (t) REVERT: H 178 VAL cc_start: 0.8507 (m) cc_final: 0.8220 (t) REVERT: I 156 ARG cc_start: 0.8082 (mtt90) cc_final: 0.7806 (mtt180) REVERT: I 178 VAL cc_start: 0.8778 (m) cc_final: 0.8563 (t) REVERT: J 177 ARG cc_start: 0.7654 (ttm110) cc_final: 0.7371 (ttm110) REVERT: J 178 VAL cc_start: 0.8581 (m) cc_final: 0.8266 (t) REVERT: K 115 MET cc_start: 0.8357 (mtm) cc_final: 0.8154 (mtm) REVERT: K 178 VAL cc_start: 0.8785 (m) cc_final: 0.8574 (t) REVERT: L 128 ASP cc_start: 0.8860 (m-30) cc_final: 0.8527 (m-30) REVERT: L 178 VAL cc_start: 0.8481 (m) cc_final: 0.8221 (t) outliers start: 36 outliers final: 18 residues processed: 611 average time/residue: 1.5340 time to fit residues: 1081.1557 Evaluate side-chains 516 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 498 time to evaluate : 2.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 314 SER Chi-restraints excluded: chain G residue 249 THR Chi-restraints excluded: chain G residue 314 SER Chi-restraints excluded: chain H residue 249 THR Chi-restraints excluded: chain H residue 314 SER Chi-restraints excluded: chain I residue 249 THR Chi-restraints excluded: chain I residue 314 SER Chi-restraints excluded: chain J residue 249 THR Chi-restraints excluded: chain J residue 314 SER Chi-restraints excluded: chain K residue 314 SER Chi-restraints excluded: chain L residue 249 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 303 optimal weight: 0.9990 chunk 272 optimal weight: 4.9990 chunk 151 optimal weight: 7.9990 chunk 93 optimal weight: 4.9990 chunk 184 optimal weight: 2.9990 chunk 145 optimal weight: 0.0980 chunk 282 optimal weight: 0.7980 chunk 109 optimal weight: 5.9990 chunk 171 optimal weight: 6.9990 chunk 210 optimal weight: 4.9990 chunk 326 optimal weight: 0.0070 overall best weight: 0.9802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 288 GLN C 38 GLN D 135 GLN D 288 GLN E 38 GLN F 135 GLN G 135 GLN G 288 GLN H 38 GLN I 17 GLN I 135 GLN I 288 GLN J 38 GLN K 288 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.1350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 29376 Z= 0.187 Angle : 1.626 45.918 39852 Z= 0.590 Chirality : 0.048 0.173 4620 Planarity : 0.004 0.020 5028 Dihedral : 16.416 114.664 4278 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.48 % Allowed : 11.10 % 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: 0.73 (0.14), residues: 3660 helix: 1.81 (0.15), residues: 1464 sheet: -0.44 (0.16), residues: 996 loop : -0.21 (0.17), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP K 162 HIS 0.003 0.001 HIS A 193 PHE 0.015 0.002 PHE H 189 TYR 0.010 0.001 TYR D 146 ARG 0.004 0.000 ARG E 243 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7320 Ramachandran restraints generated. 3660 Oldfield, 0 Emsley, 3660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7320 Ramachandran restraints generated. 3660 Oldfield, 0 Emsley, 3660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 594 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 516 time to evaluate : 3.348 Fit side-chains REVERT: C 191 LEU cc_start: 0.6917 (OUTLIER) cc_final: 0.6696 (mp) REVERT: D 156 ARG cc_start: 0.8066 (mtt90) cc_final: 0.7692 (mtt180) REVERT: D 177 ARG cc_start: 0.8051 (OUTLIER) cc_final: 0.7111 (ttm-80) REVERT: D 191 LEU cc_start: 0.6567 (OUTLIER) cc_final: 0.5601 (tm) REVERT: E 191 LEU cc_start: 0.6833 (OUTLIER) cc_final: 0.6551 (mt) REVERT: H 191 LEU cc_start: 0.6811 (OUTLIER) cc_final: 0.6542 (mt) REVERT: H 281 MET cc_start: 0.7395 (mtp) cc_final: 0.7158 (mtp) REVERT: I 156 ARG cc_start: 0.8061 (mtt90) cc_final: 0.7690 (mtt180) REVERT: I 191 LEU cc_start: 0.6543 (OUTLIER) cc_final: 0.5583 (tm) REVERT: J 191 LEU cc_start: 0.6894 (OUTLIER) cc_final: 0.6679 (mp) REVERT: K 115 MET cc_start: 0.8443 (mtm) cc_final: 0.8177 (mtm) outliers start: 78 outliers final: 43 residues processed: 567 average time/residue: 1.4663 time to fit residues: 964.9428 Evaluate side-chains 528 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 478 time to evaluate : 3.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 HIS Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain C residue 12 HIS Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 177 ARG Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain E residue 12 HIS Chi-restraints excluded: chain E residue 43 GLU Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain G residue 62 GLU Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 249 THR Chi-restraints excluded: chain H residue 12 HIS Chi-restraints excluded: chain H residue 43 GLU Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 191 LEU Chi-restraints excluded: chain H residue 249 THR Chi-restraints excluded: chain I residue 62 GLU Chi-restraints excluded: chain I residue 191 LEU Chi-restraints excluded: chain I residue 208 VAL Chi-restraints excluded: chain I residue 249 THR Chi-restraints excluded: chain J residue 12 HIS Chi-restraints excluded: chain J residue 26 GLU Chi-restraints excluded: chain J residue 62 GLU Chi-restraints excluded: chain J residue 191 LEU Chi-restraints excluded: chain J residue 208 VAL Chi-restraints excluded: chain J residue 249 THR Chi-restraints excluded: chain K residue 62 GLU Chi-restraints excluded: chain K residue 208 VAL Chi-restraints excluded: chain K residue 259 SER Chi-restraints excluded: chain L residue 12 HIS Chi-restraints excluded: chain L residue 62 GLU Chi-restraints excluded: chain L residue 208 VAL Chi-restraints excluded: chain L residue 249 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 181 optimal weight: 8.9990 chunk 101 optimal weight: 2.9990 chunk 272 optimal weight: 0.1980 chunk 222 optimal weight: 2.9990 chunk 90 optimal weight: 8.9990 chunk 327 optimal weight: 0.9990 chunk 353 optimal weight: 9.9990 chunk 291 optimal weight: 9.9990 chunk 324 optimal weight: 5.9990 chunk 111 optimal weight: 3.9990 chunk 262 optimal weight: 0.9980 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 288 GLN C 38 GLN D 17 GLN E 123 HIS H 123 HIS I 17 GLN I 288 GLN J 38 GLN K 288 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 29376 Z= 0.230 Angle : 1.636 46.352 39852 Z= 0.596 Chirality : 0.049 0.180 4620 Planarity : 0.003 0.023 5028 Dihedral : 14.929 99.374 4270 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.10 % Allowed : 12.12 % Favored : 85.78 % 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: 0.58 (0.14), residues: 3660 helix: 1.58 (0.15), residues: 1464 sheet: -0.43 (0.16), residues: 996 loop : -0.20 (0.17), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP I 162 HIS 0.005 0.001 HIS A 193 PHE 0.015 0.002 PHE A 189 TYR 0.011 0.002 TYR I 146 ARG 0.003 0.000 ARG B 49 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7320 Ramachandran restraints generated. 3660 Oldfield, 0 Emsley, 3660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7320 Ramachandran restraints generated. 3660 Oldfield, 0 Emsley, 3660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 554 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 488 time to evaluate : 3.335 Fit side-chains REVERT: C 191 LEU cc_start: 0.6963 (OUTLIER) cc_final: 0.6736 (mp) REVERT: D 156 ARG cc_start: 0.8098 (mtt90) cc_final: 0.7686 (mtt180) REVERT: D 191 LEU cc_start: 0.6600 (OUTLIER) cc_final: 0.5578 (tm) REVERT: D 248 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.7928 (mp) REVERT: E 294 MET cc_start: 0.8562 (pmm) cc_final: 0.8355 (pmm) REVERT: H 191 LEU cc_start: 0.6891 (OUTLIER) cc_final: 0.6604 (mt) REVERT: H 294 MET cc_start: 0.8563 (pmm) cc_final: 0.8355 (pmm) REVERT: I 156 ARG cc_start: 0.8101 (mtt90) cc_final: 0.7823 (mtt180) REVERT: I 191 LEU cc_start: 0.6580 (OUTLIER) cc_final: 0.5578 (tm) REVERT: J 191 LEU cc_start: 0.6964 (OUTLIER) cc_final: 0.6727 (mp) REVERT: K 115 MET cc_start: 0.8430 (mtm) cc_final: 0.8117 (mtm) outliers start: 66 outliers final: 32 residues processed: 525 average time/residue: 1.5094 time to fit residues: 916.5187 Evaluate side-chains 499 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 461 time to evaluate : 3.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain C residue 12 HIS Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain G residue 62 GLU Chi-restraints excluded: chain G residue 249 THR Chi-restraints excluded: chain H residue 43 GLU Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 191 LEU Chi-restraints excluded: chain H residue 249 THR Chi-restraints excluded: chain I residue 62 GLU Chi-restraints excluded: chain I residue 191 LEU Chi-restraints excluded: chain I residue 208 VAL Chi-restraints excluded: chain I residue 249 THR Chi-restraints excluded: chain J residue 12 HIS Chi-restraints excluded: chain J residue 62 GLU Chi-restraints excluded: chain J residue 191 LEU Chi-restraints excluded: chain J residue 208 VAL Chi-restraints excluded: chain J residue 249 THR Chi-restraints excluded: chain K residue 62 GLU Chi-restraints excluded: chain K residue 208 VAL Chi-restraints excluded: chain L residue 62 GLU Chi-restraints excluded: chain L residue 208 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 323 optimal weight: 9.9990 chunk 246 optimal weight: 6.9990 chunk 169 optimal weight: 0.0570 chunk 36 optimal weight: 0.6980 chunk 156 optimal weight: 0.4980 chunk 219 optimal weight: 0.8980 chunk 328 optimal weight: 4.9990 chunk 347 optimal weight: 3.9990 chunk 171 optimal weight: 5.9990 chunk 311 optimal weight: 5.9990 chunk 93 optimal weight: 3.9990 overall best weight: 1.2300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN B 288 GLN C 17 GLN C 38 GLN D 17 GLN F 17 GLN F 288 GLN G 17 GLN I 17 GLN J 38 GLN K 288 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 29376 Z= 0.194 Angle : 1.616 46.793 39852 Z= 0.583 Chirality : 0.048 0.172 4620 Planarity : 0.003 0.021 5028 Dihedral : 12.782 88.920 4268 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.58 % Allowed : 11.61 % Favored : 85.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.14), residues: 3660 helix: 1.60 (0.15), residues: 1464 sheet: -0.39 (0.16), residues: 996 loop : -0.20 (0.17), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP I 162 HIS 0.004 0.001 HIS H 193 PHE 0.013 0.002 PHE A 189 TYR 0.009 0.001 TYR I 146 ARG 0.003 0.000 ARG G 243 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7320 Ramachandran restraints generated. 3660 Oldfield, 0 Emsley, 3660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7320 Ramachandran restraints generated. 3660 Oldfield, 0 Emsley, 3660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 568 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 487 time to evaluate : 3.256 Fit side-chains REVERT: D 156 ARG cc_start: 0.8078 (mtt90) cc_final: 0.7657 (mtt180) REVERT: D 248 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.7848 (mp) REVERT: E 191 LEU cc_start: 0.6867 (OUTLIER) cc_final: 0.6575 (mt) REVERT: I 156 ARG cc_start: 0.8094 (mtt90) cc_final: 0.7649 (mtt180) REVERT: K 115 MET cc_start: 0.8459 (mtm) cc_final: 0.8196 (mtm) outliers start: 81 outliers final: 41 residues processed: 536 average time/residue: 1.4632 time to fit residues: 908.7177 Evaluate side-chains 520 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 477 time to evaluate : 3.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 HIS Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 153 LYS Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain E residue 12 HIS Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain G residue 62 GLU Chi-restraints excluded: chain G residue 249 THR Chi-restraints excluded: chain H residue 12 HIS Chi-restraints excluded: chain H residue 43 GLU Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 249 THR Chi-restraints excluded: chain I residue 62 GLU Chi-restraints excluded: chain I residue 208 VAL Chi-restraints excluded: chain I residue 249 THR Chi-restraints excluded: chain J residue 26 GLU Chi-restraints excluded: chain J residue 62 GLU Chi-restraints excluded: chain J residue 208 VAL Chi-restraints excluded: chain K residue 62 GLU Chi-restraints excluded: chain K residue 153 LYS Chi-restraints excluded: chain K residue 180 SER Chi-restraints excluded: chain K residue 208 VAL Chi-restraints excluded: chain K residue 249 THR Chi-restraints excluded: chain K residue 259 SER Chi-restraints excluded: chain L residue 12 HIS Chi-restraints excluded: chain L residue 62 GLU Chi-restraints excluded: chain L residue 191 LEU Chi-restraints excluded: chain L residue 249 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 289 optimal weight: 0.9990 chunk 197 optimal weight: 0.8980 chunk 5 optimal weight: 9.9990 chunk 259 optimal weight: 6.9990 chunk 143 optimal weight: 10.0000 chunk 296 optimal weight: 0.7980 chunk 240 optimal weight: 10.0000 chunk 0 optimal weight: 4.9990 chunk 177 optimal weight: 2.9990 chunk 312 optimal weight: 0.9980 chunk 87 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN B 288 GLN C 38 GLN D 17 GLN F 288 GLN I 17 GLN I 288 GLN J 17 GLN J 38 GLN K 17 GLN K 288 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 29376 Z= 0.173 Angle : 1.604 46.843 39852 Z= 0.576 Chirality : 0.047 0.168 4620 Planarity : 0.003 0.020 5028 Dihedral : 11.435 80.768 4266 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.32 % Allowed : 11.93 % Favored : 85.75 % 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: 0.68 (0.14), residues: 3660 helix: 1.67 (0.15), residues: 1464 sheet: -0.36 (0.16), residues: 996 loop : -0.18 (0.17), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 162 HIS 0.004 0.001 HIS H 193 PHE 0.011 0.001 PHE C 189 TYR 0.007 0.001 TYR I 146 ARG 0.002 0.000 ARG H 243 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7320 Ramachandran restraints generated. 3660 Oldfield, 0 Emsley, 3660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7320 Ramachandran restraints generated. 3660 Oldfield, 0 Emsley, 3660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 562 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 489 time to evaluate : 3.264 Fit side-chains REVERT: D 156 ARG cc_start: 0.8059 (mtt90) cc_final: 0.7651 (mtt180) REVERT: D 248 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.7846 (mp) REVERT: E 294 MET cc_start: 0.8546 (pmm) cc_final: 0.8336 (pmm) REVERT: H 294 MET cc_start: 0.8553 (pmm) cc_final: 0.8322 (pmm) REVERT: I 156 ARG cc_start: 0.8059 (mtt90) cc_final: 0.7643 (mtt180) REVERT: K 115 MET cc_start: 0.8458 (mtm) cc_final: 0.8195 (mtm) outliers start: 73 outliers final: 45 residues processed: 537 average time/residue: 1.5223 time to fit residues: 945.5472 Evaluate side-chains 512 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 466 time to evaluate : 4.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 HIS Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 153 LYS Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain C residue 12 HIS Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain E residue 12 HIS Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain F residue 12 HIS Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain G residue 62 GLU Chi-restraints excluded: chain G residue 207 LEU Chi-restraints excluded: chain G residue 249 THR Chi-restraints excluded: chain H residue 12 HIS Chi-restraints excluded: chain H residue 43 GLU Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 249 THR Chi-restraints excluded: chain I residue 62 GLU Chi-restraints excluded: chain I residue 180 SER Chi-restraints excluded: chain I residue 249 THR Chi-restraints excluded: chain J residue 12 HIS Chi-restraints excluded: chain J residue 26 GLU Chi-restraints excluded: chain J residue 62 GLU Chi-restraints excluded: chain J residue 208 VAL Chi-restraints excluded: chain K residue 62 GLU Chi-restraints excluded: chain K residue 153 LYS Chi-restraints excluded: chain K residue 180 SER Chi-restraints excluded: chain K residue 208 VAL Chi-restraints excluded: chain K residue 249 THR Chi-restraints excluded: chain K residue 259 SER Chi-restraints excluded: chain L residue 12 HIS Chi-restraints excluded: chain L residue 62 GLU Chi-restraints excluded: chain L residue 249 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 117 optimal weight: 3.9990 chunk 313 optimal weight: 0.5980 chunk 68 optimal weight: 4.9990 chunk 204 optimal weight: 5.9990 chunk 85 optimal weight: 5.9990 chunk 348 optimal weight: 4.9990 chunk 289 optimal weight: 9.9990 chunk 161 optimal weight: 6.9990 chunk 28 optimal weight: 7.9990 chunk 115 optimal weight: 0.7980 chunk 182 optimal weight: 6.9990 overall best weight: 3.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 GLN A 123 HIS B 17 GLN B 288 GLN C 38 GLN D 12 HIS D 17 GLN F 288 GLN I 17 GLN J 38 GLN K 17 GLN K 288 GLN L 13 GLN L 123 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 29376 Z= 0.349 Angle : 1.673 46.758 39852 Z= 0.621 Chirality : 0.052 0.215 4620 Planarity : 0.004 0.032 5028 Dihedral : 12.417 91.537 4266 Min Nonbonded Distance : 1.772 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.26 % Allowed : 11.93 % Favored : 85.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.14), residues: 3660 helix: 1.28 (0.15), residues: 1476 sheet: -0.42 (0.16), residues: 996 loop : -0.21 (0.17), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP K 162 HIS 0.007 0.001 HIS L 193 PHE 0.018 0.002 PHE A 189 TYR 0.017 0.002 TYR I 146 ARG 0.005 0.001 ARG E 49 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7320 Ramachandran restraints generated. 3660 Oldfield, 0 Emsley, 3660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7320 Ramachandran restraints generated. 3660 Oldfield, 0 Emsley, 3660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 459 time to evaluate : 3.293 Fit side-chains REVERT: D 156 ARG cc_start: 0.8154 (mtt90) cc_final: 0.7842 (mtt180) REVERT: D 248 LEU cc_start: 0.8684 (OUTLIER) cc_final: 0.7908 (mp) REVERT: E 294 MET cc_start: 0.8614 (pmm) cc_final: 0.8357 (pmm) REVERT: I 156 ARG cc_start: 0.8153 (mtt90) cc_final: 0.7832 (mtt180) REVERT: K 115 MET cc_start: 0.8453 (mtm) cc_final: 0.8138 (mtm) outliers start: 71 outliers final: 44 residues processed: 502 average time/residue: 1.4553 time to fit residues: 848.6175 Evaluate side-chains 491 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 446 time to evaluate : 3.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 153 LYS Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain C residue 12 HIS Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain G residue 62 GLU Chi-restraints excluded: chain G residue 249 THR Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 249 THR Chi-restraints excluded: chain I residue 62 GLU Chi-restraints excluded: chain I residue 180 SER Chi-restraints excluded: chain I residue 208 VAL Chi-restraints excluded: chain I residue 249 THR Chi-restraints excluded: chain J residue 12 HIS Chi-restraints excluded: chain J residue 43 GLU Chi-restraints excluded: chain J residue 62 GLU Chi-restraints excluded: chain J residue 207 LEU Chi-restraints excluded: chain J residue 248 LEU Chi-restraints excluded: chain K residue 62 GLU Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain K residue 153 LYS Chi-restraints excluded: chain K residue 207 LEU Chi-restraints excluded: chain K residue 208 VAL Chi-restraints excluded: chain K residue 249 THR Chi-restraints excluded: chain K residue 259 SER Chi-restraints excluded: chain L residue 62 GLU Chi-restraints excluded: chain L residue 207 LEU Chi-restraints excluded: chain L residue 249 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 335 optimal weight: 10.0000 chunk 39 optimal weight: 0.0970 chunk 198 optimal weight: 0.6980 chunk 254 optimal weight: 0.9980 chunk 197 optimal weight: 4.9990 chunk 293 optimal weight: 9.9990 chunk 194 optimal weight: 6.9990 chunk 346 optimal weight: 5.9990 chunk 217 optimal weight: 4.9990 chunk 211 optimal weight: 3.9990 chunk 160 optimal weight: 3.9990 overall best weight: 1.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 GLN B 17 GLN B 288 GLN C 38 GLN F 288 GLN I 17 GLN J 38 GLN K 17 GLN K 288 GLN L 13 GLN L 123 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.1893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 29376 Z= 0.253 Angle : 1.636 46.838 39852 Z= 0.597 Chirality : 0.050 0.193 4620 Planarity : 0.004 0.025 5028 Dihedral : 12.039 88.992 4266 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.91 % Allowed : 12.53 % Favored : 85.56 % 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: 0.42 (0.14), residues: 3660 helix: 1.33 (0.15), residues: 1476 sheet: -0.41 (0.16), residues: 996 loop : -0.25 (0.17), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP E 162 HIS 0.005 0.001 HIS H 193 PHE 0.014 0.002 PHE A 189 TYR 0.014 0.002 TYR I 146 ARG 0.003 0.000 ARG B 49 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7320 Ramachandran restraints generated. 3660 Oldfield, 0 Emsley, 3660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7320 Ramachandran restraints generated. 3660 Oldfield, 0 Emsley, 3660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 458 time to evaluate : 3.238 Fit side-chains REVERT: D 156 ARG cc_start: 0.8108 (mtt90) cc_final: 0.7805 (mtt180) REVERT: I 156 ARG cc_start: 0.8131 (mtt90) cc_final: 0.7816 (mtt180) REVERT: K 115 MET cc_start: 0.8462 (mtm) cc_final: 0.8205 (mtm) outliers start: 60 outliers final: 48 residues processed: 495 average time/residue: 1.5162 time to fit residues: 867.5796 Evaluate side-chains 500 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 452 time to evaluate : 3.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 153 LYS Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain C residue 12 HIS Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain G residue 62 GLU Chi-restraints excluded: chain G residue 207 LEU Chi-restraints excluded: chain G residue 249 THR Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 248 LEU Chi-restraints excluded: chain H residue 249 THR Chi-restraints excluded: chain I residue 62 GLU Chi-restraints excluded: chain I residue 207 LEU Chi-restraints excluded: chain I residue 208 VAL Chi-restraints excluded: chain I residue 249 THR Chi-restraints excluded: chain J residue 12 HIS Chi-restraints excluded: chain J residue 62 GLU Chi-restraints excluded: chain J residue 207 LEU Chi-restraints excluded: chain J residue 248 LEU Chi-restraints excluded: chain K residue 62 GLU Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain K residue 153 LYS Chi-restraints excluded: chain K residue 207 LEU Chi-restraints excluded: chain K residue 208 VAL Chi-restraints excluded: chain K residue 249 THR Chi-restraints excluded: chain K residue 259 SER Chi-restraints excluded: chain L residue 62 GLU Chi-restraints excluded: chain L residue 207 LEU Chi-restraints excluded: chain L residue 249 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 214 optimal weight: 2.9990 chunk 138 optimal weight: 2.9990 chunk 207 optimal weight: 0.8980 chunk 104 optimal weight: 0.0870 chunk 68 optimal weight: 7.9990 chunk 67 optimal weight: 0.9990 chunk 220 optimal weight: 2.9990 chunk 236 optimal weight: 4.9990 chunk 171 optimal weight: 7.9990 chunk 32 optimal weight: 4.9990 chunk 272 optimal weight: 5.9990 overall best weight: 1.5964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 GLN B 17 GLN B 288 GLN C 38 GLN F 17 GLN F 288 GLN H 17 GLN I 17 GLN J 38 GLN K 17 GLN K 288 GLN L 13 GLN L 123 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 29376 Z= 0.225 Angle : 1.627 47.078 39852 Z= 0.591 Chirality : 0.049 0.182 4620 Planarity : 0.003 0.024 5028 Dihedral : 11.792 86.158 4266 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.00 % Allowed : 12.34 % Favored : 85.66 % 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: 0.47 (0.14), residues: 3660 helix: 1.40 (0.15), residues: 1476 sheet: -0.40 (0.16), residues: 996 loop : -0.25 (0.17), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP E 162 HIS 0.004 0.001 HIS E 193 PHE 0.014 0.002 PHE L 189 TYR 0.012 0.002 TYR I 146 ARG 0.003 0.000 ARG D 22 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7320 Ramachandran restraints generated. 3660 Oldfield, 0 Emsley, 3660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7320 Ramachandran restraints generated. 3660 Oldfield, 0 Emsley, 3660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 452 time to evaluate : 3.207 Fit side-chains REVERT: D 156 ARG cc_start: 0.8096 (mtt90) cc_final: 0.7798 (mtt180) REVERT: I 156 ARG cc_start: 0.8122 (mtt90) cc_final: 0.7813 (mtt180) REVERT: K 115 MET cc_start: 0.8457 (mtm) cc_final: 0.8203 (mtm) outliers start: 63 outliers final: 51 residues processed: 489 average time/residue: 1.5745 time to fit residues: 893.8234 Evaluate side-chains 496 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 445 time to evaluate : 3.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 153 LYS Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain C residue 12 HIS Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain G residue 62 GLU Chi-restraints excluded: chain G residue 207 LEU Chi-restraints excluded: chain G residue 249 THR Chi-restraints excluded: chain H residue 43 GLU Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 207 LEU Chi-restraints excluded: chain H residue 248 LEU Chi-restraints excluded: chain H residue 249 THR Chi-restraints excluded: chain I residue 62 GLU Chi-restraints excluded: chain I residue 207 LEU Chi-restraints excluded: chain I residue 208 VAL Chi-restraints excluded: chain I residue 249 THR Chi-restraints excluded: chain J residue 12 HIS Chi-restraints excluded: chain J residue 26 GLU Chi-restraints excluded: chain J residue 62 GLU Chi-restraints excluded: chain J residue 207 LEU Chi-restraints excluded: chain J residue 248 LEU Chi-restraints excluded: chain K residue 62 GLU Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain K residue 153 LYS Chi-restraints excluded: chain K residue 180 SER Chi-restraints excluded: chain K residue 207 LEU Chi-restraints excluded: chain K residue 208 VAL Chi-restraints excluded: chain K residue 249 THR Chi-restraints excluded: chain K residue 259 SER Chi-restraints excluded: chain L residue 62 GLU Chi-restraints excluded: chain L residue 207 LEU Chi-restraints excluded: chain L residue 249 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 315 optimal weight: 0.9980 chunk 332 optimal weight: 8.9990 chunk 303 optimal weight: 6.9990 chunk 323 optimal weight: 7.9990 chunk 194 optimal weight: 0.0040 chunk 140 optimal weight: 9.9990 chunk 253 optimal weight: 2.9990 chunk 99 optimal weight: 0.5980 chunk 292 optimal weight: 4.9990 chunk 305 optimal weight: 9.9990 chunk 322 optimal weight: 0.9990 overall best weight: 1.1196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 GLN B 17 GLN B 288 GLN C 38 GLN F 288 GLN G 17 GLN I 17 GLN J 38 GLN K 17 GLN K 288 GLN L 13 GLN L 123 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 29376 Z= 0.189 Angle : 1.611 47.176 39852 Z= 0.581 Chirality : 0.048 0.172 4620 Planarity : 0.003 0.027 5028 Dihedral : 11.424 86.275 4266 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.97 % Allowed : 12.69 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.14), residues: 3660 helix: 1.51 (0.15), residues: 1476 sheet: -0.36 (0.16), residues: 996 loop : -0.26 (0.17), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 162 HIS 0.003 0.001 HIS L 193 PHE 0.012 0.002 PHE L 189 TYR 0.010 0.001 TYR I 146 ARG 0.003 0.000 ARG D 22 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7320 Ramachandran restraints generated. 3660 Oldfield, 0 Emsley, 3660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7320 Ramachandran restraints generated. 3660 Oldfield, 0 Emsley, 3660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 462 time to evaluate : 3.272 Fit side-chains REVERT: D 156 ARG cc_start: 0.8091 (mtt90) cc_final: 0.7739 (mtt180) REVERT: I 156 ARG cc_start: 0.8079 (mtt90) cc_final: 0.7641 (mtt180) REVERT: K 115 MET cc_start: 0.8470 (mtm) cc_final: 0.8210 (mtm) outliers start: 62 outliers final: 50 residues processed: 499 average time/residue: 1.5324 time to fit residues: 882.5361 Evaluate side-chains 508 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 458 time to evaluate : 3.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 153 LYS Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain C residue 12 HIS Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain G residue 62 GLU Chi-restraints excluded: chain G residue 207 LEU Chi-restraints excluded: chain G residue 249 THR Chi-restraints excluded: chain H residue 43 GLU Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 207 LEU Chi-restraints excluded: chain H residue 249 THR Chi-restraints excluded: chain I residue 62 GLU Chi-restraints excluded: chain I residue 180 SER Chi-restraints excluded: chain I residue 207 LEU Chi-restraints excluded: chain I residue 208 VAL Chi-restraints excluded: chain I residue 249 THR Chi-restraints excluded: chain J residue 12 HIS Chi-restraints excluded: chain J residue 62 GLU Chi-restraints excluded: chain J residue 207 LEU Chi-restraints excluded: chain K residue 62 GLU Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain K residue 153 LYS Chi-restraints excluded: chain K residue 180 SER Chi-restraints excluded: chain K residue 207 LEU Chi-restraints excluded: chain K residue 208 VAL Chi-restraints excluded: chain K residue 249 THR Chi-restraints excluded: chain K residue 259 SER Chi-restraints excluded: chain L residue 62 GLU Chi-restraints excluded: chain L residue 207 LEU Chi-restraints excluded: chain L residue 249 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 212 optimal weight: 3.9990 chunk 341 optimal weight: 1.9990 chunk 208 optimal weight: 6.9990 chunk 162 optimal weight: 0.8980 chunk 237 optimal weight: 5.9990 chunk 358 optimal weight: 1.9990 chunk 330 optimal weight: 6.9990 chunk 285 optimal weight: 5.9990 chunk 29 optimal weight: 0.8980 chunk 220 optimal weight: 0.2980 chunk 175 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN B 288 GLN C 38 GLN D 17 GLN I 17 GLN J 38 GLN K 17 GLN K 288 GLN L 123 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.2020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 29376 Z= 0.197 Angle : 1.617 47.141 39852 Z= 0.585 Chirality : 0.048 0.175 4620 Planarity : 0.003 0.028 5028 Dihedral : 11.441 87.579 4266 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.65 % Allowed : 12.98 % Favored : 85.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.14), residues: 3660 helix: 1.51 (0.15), residues: 1476 sheet: -0.35 (0.16), residues: 996 loop : -0.27 (0.17), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP E 162 HIS 0.004 0.001 HIS L 193 PHE 0.013 0.002 PHE L 189 TYR 0.010 0.001 TYR I 146 ARG 0.004 0.000 ARG D 22 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7320 Ramachandran restraints generated. 3660 Oldfield, 0 Emsley, 3660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7320 Ramachandran restraints generated. 3660 Oldfield, 0 Emsley, 3660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 455 time to evaluate : 3.857 Fit side-chains REVERT: D 156 ARG cc_start: 0.8090 (mtt90) cc_final: 0.7742 (mtt180) REVERT: I 156 ARG cc_start: 0.8076 (mtt90) cc_final: 0.7649 (mtt180) REVERT: K 115 MET cc_start: 0.8468 (mtm) cc_final: 0.8214 (mtm) outliers start: 52 outliers final: 50 residues processed: 486 average time/residue: 1.5869 time to fit residues: 887.7416 Evaluate side-chains 500 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 450 time to evaluate : 3.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 153 LYS Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain C residue 12 HIS Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain G residue 62 GLU Chi-restraints excluded: chain G residue 207 LEU Chi-restraints excluded: chain G residue 249 THR Chi-restraints excluded: chain H residue 43 GLU Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 207 LEU Chi-restraints excluded: chain H residue 249 THR Chi-restraints excluded: chain I residue 62 GLU Chi-restraints excluded: chain I residue 180 SER Chi-restraints excluded: chain I residue 207 LEU Chi-restraints excluded: chain I residue 208 VAL Chi-restraints excluded: chain I residue 249 THR Chi-restraints excluded: chain J residue 12 HIS Chi-restraints excluded: chain J residue 62 GLU Chi-restraints excluded: chain J residue 207 LEU Chi-restraints excluded: chain K residue 62 GLU Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain K residue 153 LYS Chi-restraints excluded: chain K residue 180 SER Chi-restraints excluded: chain K residue 207 LEU Chi-restraints excluded: chain K residue 208 VAL Chi-restraints excluded: chain K residue 249 THR Chi-restraints excluded: chain K residue 259 SER Chi-restraints excluded: chain L residue 62 GLU Chi-restraints excluded: chain L residue 207 LEU Chi-restraints excluded: chain L residue 249 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 226 optimal weight: 0.9990 chunk 304 optimal weight: 0.9980 chunk 87 optimal weight: 0.9980 chunk 263 optimal weight: 5.9990 chunk 42 optimal weight: 7.9990 chunk 79 optimal weight: 0.6980 chunk 286 optimal weight: 0.9990 chunk 119 optimal weight: 0.6980 chunk 293 optimal weight: 9.9990 chunk 36 optimal weight: 0.9990 chunk 52 optimal weight: 10.0000 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 288 GLN C 38 GLN D 17 GLN E 13 GLN F 13 GLN J 38 GLN K 288 GLN L 123 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.159562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.122310 restraints weight = 21892.193| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 1.05 r_work: 0.3214 rms_B_bonded: 1.34 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 2.17 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3108 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3108 r_free = 0.3108 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 648 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2929 r_free = 0.2929 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2929 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8787 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 29376 Z= 0.174 Angle : 1.605 47.207 39852 Z= 0.577 Chirality : 0.047 0.170 4620 Planarity : 0.003 0.027 5028 Dihedral : 11.274 88.588 4266 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.78 % Allowed : 13.14 % Favored : 85.08 % 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: 0.68 (0.14), residues: 3660 helix: 1.63 (0.15), residues: 1464 sheet: -0.31 (0.16), residues: 996 loop : -0.20 (0.17), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP E 162 HIS 0.003 0.000 HIS L 193 PHE 0.012 0.001 PHE L 189 TYR 0.009 0.001 TYR I 146 ARG 0.003 0.000 ARG D 22 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13785.64 seconds wall clock time: 243 minutes 26.33 seconds (14606.33 seconds total)