Starting phenix.real_space_refine on Thu Mar 21 01:16:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbh_27284/03_2024/8dbh_27284_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbh_27284/03_2024/8dbh_27284.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbh_27284/03_2024/8dbh_27284.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbh_27284/03_2024/8dbh_27284.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbh_27284/03_2024/8dbh_27284_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbh_27284/03_2024/8dbh_27284_updated.pdb" } resolution = 2.2 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= 0.397 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 17904 2.51 5 N 5040 2.21 5 O 5652 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 ARG 49": "NH1" <-> "NH2" Residue "A GLU 69": "OE1" <-> "OE2" Residue "A ARG 84": "NH1" <-> "NH2" Residue "A ARG 104": "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 ARG 301": "NH1" <-> "NH2" Residue "A ARG 302": "NH1" <-> "NH2" Residue "B ARG 22": "NH1" <-> "NH2" Residue "B ARG 49": "NH1" <-> "NH2" Residue "B GLU 69": "OE1" <-> "OE2" Residue "B ARG 84": "NH1" <-> "NH2" Residue "B ARG 104": "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 ARG 301": "NH1" <-> "NH2" Residue "B ARG 302": "NH1" <-> "NH2" Residue "C ARG 22": "NH1" <-> "NH2" Residue "C ARG 49": "NH1" <-> "NH2" Residue "C GLU 69": "OE1" <-> "OE2" Residue "C ARG 84": "NH1" <-> "NH2" Residue "C ARG 104": "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 ARG 301": "NH1" <-> "NH2" Residue "C ARG 302": "NH1" <-> "NH2" Residue "D ARG 22": "NH1" <-> "NH2" Residue "D ARG 49": "NH1" <-> "NH2" Residue "D GLU 69": "OE1" <-> "OE2" Residue "D ARG 84": "NH1" <-> "NH2" Residue "D ARG 104": "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 ARG 301": "NH1" <-> "NH2" Residue "D ARG 302": "NH1" <-> "NH2" Residue "E ARG 22": "NH1" <-> "NH2" Residue "E ARG 49": "NH1" <-> "NH2" Residue "E GLU 69": "OE1" <-> "OE2" Residue "E ARG 84": "NH1" <-> "NH2" Residue "E ARG 104": "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 ARG 301": "NH1" <-> "NH2" Residue "E ARG 302": "NH1" <-> "NH2" Residue "F ARG 22": "NH1" <-> "NH2" Residue "F ARG 49": "NH1" <-> "NH2" Residue "F GLU 69": "OE1" <-> "OE2" Residue "F ARG 84": "NH1" <-> "NH2" Residue "F ARG 104": "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 ARG 301": "NH1" <-> "NH2" Residue "F ARG 302": "NH1" <-> "NH2" Residue "G ARG 22": "NH1" <-> "NH2" Residue "G ARG 49": "NH1" <-> "NH2" Residue "G GLU 69": "OE1" <-> "OE2" Residue "G ARG 84": "NH1" <-> "NH2" Residue "G ARG 104": "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 ARG 301": "NH1" <-> "NH2" Residue "G ARG 302": "NH1" <-> "NH2" Residue "H ARG 22": "NH1" <-> "NH2" Residue "H ARG 49": "NH1" <-> "NH2" Residue "H GLU 69": "OE1" <-> "OE2" Residue "H ARG 84": "NH1" <-> "NH2" Residue "H ARG 104": "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 ARG 301": "NH1" <-> "NH2" Residue "H ARG 302": "NH1" <-> "NH2" Residue "I ARG 22": "NH1" <-> "NH2" Residue "I ARG 49": "NH1" <-> "NH2" Residue "I GLU 69": "OE1" <-> "OE2" Residue "I ARG 84": "NH1" <-> "NH2" Residue "I ARG 104": "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 ARG 301": "NH1" <-> "NH2" Residue "I ARG 302": "NH1" <-> "NH2" Residue "J ARG 22": "NH1" <-> "NH2" Residue "J ARG 49": "NH1" <-> "NH2" Residue "J GLU 69": "OE1" <-> "OE2" Residue "J ARG 84": "NH1" <-> "NH2" Residue "J ARG 104": "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 ARG 301": "NH1" <-> "NH2" Residue "J ARG 302": "NH1" <-> "NH2" Residue "K ARG 22": "NH1" <-> "NH2" Residue "K ARG 49": "NH1" <-> "NH2" Residue "K GLU 69": "OE1" <-> "OE2" Residue "K ARG 84": "NH1" <-> "NH2" Residue "K ARG 104": "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 ARG 301": "NH1" <-> "NH2" Residue "K ARG 302": "NH1" <-> "NH2" Residue "L ARG 22": "NH1" <-> "NH2" Residue "L ARG 49": "NH1" <-> "NH2" Residue "L GLU 69": "OE1" <-> "OE2" Residue "L ARG 84": "NH1" <-> "NH2" Residue "L ARG 104": "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 ARG 301": "NH1" <-> "NH2" Residue "L ARG 302": "NH1" <-> "NH2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 28884 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: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 43 Unusual residues: {' MG': 2, 'ATP': 1, 'PO4': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 43 Unusual residues: {' MG': 2, 'ATP': 1, 'PO4': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "C" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 43 Unusual residues: {' MG': 2, 'ATP': 1, 'PO4': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "D" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 43 Unusual residues: {' MG': 2, 'ATP': 1, 'PO4': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "E" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 43 Unusual residues: {' MG': 2, 'ATP': 1, 'PO4': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "F" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 43 Unusual residues: {' MG': 2, 'ATP': 1, 'PO4': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "G" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 43 Unusual residues: {' MG': 2, 'ATP': 1, 'PO4': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "H" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 43 Unusual residues: {' MG': 2, 'ATP': 1, 'PO4': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "I" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 43 Unusual residues: {' MG': 2, 'ATP': 1, 'PO4': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "J" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 43 Unusual residues: {' MG': 2, 'ATP': 1, 'PO4': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "K" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 43 Unusual residues: {' MG': 2, 'ATP': 1, 'PO4': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "L" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 43 Unusual residues: {' MG': 2, 'ATP': 1, 'PO4': 2} 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: 14.47, per 1000 atoms: 0.50 Number of scatterers: 28884 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 5652 8.00 N 5040 7.00 C 17904 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: 8.88 Conformation dependent library (CDL) restraints added in 3.9 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: 144 helices and 36 sheets defined 36.2% alpha, 18.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.59 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 162 through 164 No H-bonds generated for 'chain 'A' and resid 162 through 164' Processing helix chain 'A' and resid 175 through 185 Processing helix chain 'A' and resid 227 through 238 Processing helix chain 'A' and resid 257 through 263 Processing helix chain 'A' and resid 278 through 283 removed outlier: 3.667A 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 162 through 164 No H-bonds generated for 'chain 'B' and resid 162 through 164' Processing helix chain 'B' and resid 175 through 185 Processing helix chain 'B' and resid 227 through 238 Processing helix chain 'B' and resid 257 through 263 Processing helix chain 'B' and resid 278 through 283 removed outlier: 3.666A 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 162 through 164 No H-bonds generated for 'chain 'C' and resid 162 through 164' Processing helix chain 'C' and resid 175 through 185 Processing helix chain 'C' and resid 227 through 238 Processing helix chain 'C' and resid 257 through 263 Processing helix chain 'C' and resid 278 through 283 removed outlier: 3.667A 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 162 through 164 No H-bonds generated for 'chain 'D' and resid 162 through 164' Processing helix chain 'D' and resid 175 through 185 Processing helix chain 'D' and resid 227 through 238 Processing helix chain 'D' and resid 257 through 263 Processing helix chain 'D' and resid 278 through 283 removed outlier: 3.668A 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 162 through 164 No H-bonds generated for 'chain 'E' and resid 162 through 164' Processing helix chain 'E' and resid 175 through 185 Processing helix chain 'E' and resid 227 through 238 Processing helix chain 'E' and resid 257 through 263 Processing helix chain 'E' and resid 278 through 283 removed outlier: 3.668A 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 162 through 164 No H-bonds generated for 'chain 'F' and resid 162 through 164' Processing helix chain 'F' and resid 175 through 185 Processing helix chain 'F' and resid 227 through 238 Processing helix chain 'F' and resid 257 through 263 Processing helix chain 'F' and resid 278 through 283 removed outlier: 3.667A 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 162 through 164 No H-bonds generated for 'chain 'G' and resid 162 through 164' Processing helix chain 'G' and resid 175 through 185 Processing helix chain 'G' and resid 227 through 238 Processing helix chain 'G' and resid 257 through 263 Processing helix chain 'G' and resid 278 through 283 removed outlier: 3.668A 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 162 through 164 No H-bonds generated for 'chain 'H' and resid 162 through 164' Processing helix chain 'H' and resid 175 through 185 Processing helix chain 'H' and resid 227 through 238 Processing helix chain 'H' and resid 257 through 263 Processing helix chain 'H' and resid 278 through 283 removed outlier: 3.666A 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 162 through 164 No H-bonds generated for 'chain 'I' and resid 162 through 164' Processing helix chain 'I' and resid 175 through 185 Processing helix chain 'I' and resid 227 through 238 Processing helix chain 'I' and resid 257 through 263 Processing helix chain 'I' and resid 278 through 283 removed outlier: 3.668A 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 162 through 164 No H-bonds generated for 'chain 'J' and resid 162 through 164' Processing helix chain 'J' and resid 175 through 185 Processing helix chain 'J' and resid 227 through 238 Processing helix chain 'J' and resid 257 through 263 Processing helix chain 'J' and resid 278 through 283 removed outlier: 3.667A 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 162 through 164 No H-bonds generated for 'chain 'K' and resid 162 through 164' Processing helix chain 'K' and resid 175 through 185 Processing helix chain 'K' and resid 227 through 238 Processing helix chain 'K' and resid 257 through 263 Processing helix chain 'K' and resid 278 through 283 removed outlier: 3.668A 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 162 through 164 No H-bonds generated for 'chain 'L' and resid 162 through 164' Processing helix chain 'L' and resid 175 through 185 Processing helix chain 'L' and resid 227 through 238 Processing helix chain 'L' and resid 257 through 263 Processing helix chain 'L' and resid 278 through 283 removed outlier: 3.668A 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: 6.352A pdb=" N ASP A 52 " --> pdb=" O LYS A 5 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N PHE A 7 " --> pdb=" O ASP A 52 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N TYR A 54 " --> pdb=" O PHE A 7 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ARG A 84 " --> pdb=" O VAL A 53 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N ILE A 55 " --> pdb=" O ARG A 84 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N THR A 86 " --> pdb=" O ILE A 55 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N HIS A 123 " --> pdb=" O ALA A 87 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N ILE A 89 " --> pdb=" O HIS A 123 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ILE A 125 " --> pdb=" O ILE A 89 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N THR A 126 " --> pdb=" O PRO A 141 " (cutoff:3.500A) removed outlier: 6.112A 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 287 through 290 removed outlier: 6.148A pdb=" N VAL A 269 " --> pdb=" O GLN A 288 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N ILE A 290 " --> pdb=" O VAL A 269 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N VAL A 271 " --> pdb=" O ILE A 290 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ALA A 268 " --> pdb=" O VAL A 244 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ALA A 216 " --> pdb=" O TYR A 245 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N ILE A 247 " --> pdb=" O ALA A 216 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N LEU A 218 " --> pdb=" O ILE A 247 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N THR A 166 " --> pdb=" O ILE A 217 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N VAL A 219 " --> pdb=" O THR A 166 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N VAL A 168 " --> pdb=" O VAL A 219 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ASP A 188 " --> pdb=" O ILE A 167 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N SER A 169 " --> pdb=" O ASP A 188 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ALA A 190 " --> pdb=" O SER A 169 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 4 through 8 removed outlier: 6.351A pdb=" N ASP B 52 " --> pdb=" O LYS B 5 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N PHE B 7 " --> pdb=" O ASP B 52 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N TYR B 54 " --> pdb=" O PHE B 7 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ARG B 84 " --> pdb=" O VAL B 53 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N ILE B 55 " --> pdb=" O ARG B 84 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N THR B 86 " --> pdb=" O ILE B 55 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N HIS B 123 " --> pdb=" O ALA B 87 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N ILE B 89 " --> pdb=" O HIS B 123 " (cutoff:3.500A) removed outlier: 6.338A 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: 6.113A pdb=" N ASP B 143 " --> pdb=" O THR B 126 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'B' and resid 30 through 34 Processing sheet with id= F, first strand: chain 'B' and resid 287 through 290 removed outlier: 6.149A pdb=" N VAL B 269 " --> pdb=" O GLN B 288 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N ILE B 290 " --> pdb=" O VAL B 269 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N VAL B 271 " --> pdb=" O ILE B 290 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ALA B 268 " --> pdb=" O VAL B 244 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ALA B 216 " --> pdb=" O TYR B 245 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N ILE B 247 " --> pdb=" O ALA B 216 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N LEU B 218 " --> pdb=" O ILE B 247 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N THR B 166 " --> pdb=" O ILE B 217 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N VAL B 219 " --> pdb=" O THR B 166 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N VAL B 168 " --> pdb=" O VAL B 219 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ASP B 188 " --> pdb=" O ILE B 167 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N SER B 169 " --> pdb=" O ASP B 188 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ALA B 190 " --> pdb=" O SER B 169 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 4 through 8 removed outlier: 6.352A pdb=" N ASP C 52 " --> pdb=" O LYS C 5 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N PHE C 7 " --> pdb=" O ASP C 52 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N TYR C 54 " --> pdb=" O PHE C 7 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ARG C 84 " --> pdb=" O VAL C 53 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N ILE C 55 " --> pdb=" O ARG C 84 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N THR C 86 " --> pdb=" O ILE C 55 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N HIS C 123 " --> pdb=" O ALA C 87 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N ILE C 89 " --> pdb=" O HIS C 123 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ILE C 125 " --> pdb=" O ILE C 89 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N THR C 126 " --> pdb=" O PRO C 141 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N ASP C 143 " --> pdb=" O THR C 126 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'C' and resid 30 through 34 Processing sheet with id= I, first strand: chain 'C' and resid 287 through 290 removed outlier: 6.148A pdb=" N VAL C 269 " --> pdb=" O GLN C 288 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N ILE C 290 " --> pdb=" O VAL C 269 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N VAL C 271 " --> pdb=" O ILE C 290 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ALA C 268 " --> pdb=" O VAL C 244 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ALA C 216 " --> pdb=" O TYR C 245 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N ILE C 247 " --> pdb=" O ALA C 216 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N LEU C 218 " --> pdb=" O ILE C 247 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N THR C 166 " --> pdb=" O ILE C 217 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N VAL C 219 " --> pdb=" O THR C 166 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N VAL C 168 " --> pdb=" O VAL C 219 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ASP C 188 " --> pdb=" O ILE C 167 " (cutoff:3.500A) removed outlier: 8.142A pdb=" N SER C 169 " --> pdb=" O ASP C 188 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ALA C 190 " --> pdb=" O SER C 169 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 4 through 8 removed outlier: 6.352A pdb=" N ASP D 52 " --> pdb=" O LYS D 5 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N PHE D 7 " --> pdb=" O ASP D 52 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N TYR D 54 " --> pdb=" O PHE D 7 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ARG D 84 " --> pdb=" O VAL D 53 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N ILE D 55 " --> pdb=" O ARG D 84 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N THR D 86 " --> pdb=" O ILE D 55 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N HIS D 123 " --> pdb=" O ALA D 87 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N ILE D 89 " --> pdb=" O HIS D 123 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ILE D 125 " --> pdb=" O ILE D 89 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N THR D 126 " --> pdb=" O PRO D 141 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N ASP D 143 " --> pdb=" O THR D 126 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'D' and resid 30 through 34 Processing sheet with id= L, first strand: chain 'D' and resid 287 through 290 removed outlier: 6.148A pdb=" N VAL D 269 " --> pdb=" O GLN D 288 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N ILE D 290 " --> pdb=" O VAL D 269 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N VAL D 271 " --> pdb=" O ILE D 290 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ALA D 268 " --> pdb=" O VAL D 244 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ALA D 216 " --> pdb=" O TYR D 245 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N ILE D 247 " --> pdb=" O ALA D 216 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N LEU D 218 " --> pdb=" O ILE D 247 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N THR D 166 " --> pdb=" O ILE D 217 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N VAL D 219 " --> pdb=" O THR D 166 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N VAL D 168 " --> pdb=" O VAL D 219 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ASP D 188 " --> pdb=" O ILE D 167 " (cutoff:3.500A) removed outlier: 8.142A pdb=" N SER D 169 " --> pdb=" O ASP D 188 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ALA D 190 " --> pdb=" O SER D 169 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 4 through 8 removed outlier: 6.353A pdb=" N ASP E 52 " --> pdb=" O LYS E 5 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N PHE E 7 " --> pdb=" O ASP E 52 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N TYR E 54 " --> pdb=" O PHE E 7 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ARG E 84 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N ILE E 55 " --> pdb=" O ARG E 84 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N THR E 86 " --> pdb=" O ILE E 55 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N HIS E 123 " --> pdb=" O ALA E 87 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N ILE E 89 " --> pdb=" O HIS E 123 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ILE E 125 " --> pdb=" O ILE E 89 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N THR E 126 " --> pdb=" O PRO E 141 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N ASP E 143 " --> pdb=" O THR E 126 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'E' and resid 30 through 34 Processing sheet with id= O, first strand: chain 'E' and resid 287 through 290 removed outlier: 6.148A pdb=" N VAL E 269 " --> pdb=" O GLN E 288 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N ILE E 290 " --> pdb=" O VAL E 269 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N VAL E 271 " --> pdb=" O ILE E 290 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ALA E 268 " --> pdb=" O VAL E 244 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ALA E 216 " --> pdb=" O TYR E 245 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N ILE E 247 " --> pdb=" O ALA E 216 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N LEU E 218 " --> pdb=" O ILE E 247 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N THR E 166 " --> pdb=" O ILE E 217 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N VAL E 219 " --> pdb=" O THR E 166 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N VAL E 168 " --> pdb=" O VAL E 219 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ASP E 188 " --> pdb=" O ILE E 167 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N SER E 169 " --> pdb=" O ASP E 188 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ALA E 190 " --> pdb=" O SER E 169 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'F' and resid 4 through 8 removed outlier: 6.353A pdb=" N ASP F 52 " --> pdb=" O LYS F 5 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N PHE F 7 " --> pdb=" O ASP F 52 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N TYR F 54 " --> pdb=" O PHE F 7 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ARG F 84 " --> pdb=" O VAL F 53 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N ILE F 55 " --> pdb=" O ARG F 84 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N THR F 86 " --> pdb=" O ILE F 55 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N HIS F 123 " --> pdb=" O ALA F 87 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N ILE F 89 " --> pdb=" O HIS F 123 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ILE F 125 " --> pdb=" O ILE F 89 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N THR F 126 " --> pdb=" O PRO F 141 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N ASP F 143 " --> pdb=" O THR F 126 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'F' and resid 30 through 34 Processing sheet with id= R, first strand: chain 'F' and resid 287 through 290 removed outlier: 6.148A pdb=" N VAL F 269 " --> pdb=" O GLN F 288 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N ILE F 290 " --> pdb=" O VAL F 269 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N VAL F 271 " --> pdb=" O ILE F 290 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ALA F 268 " --> pdb=" O VAL F 244 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ALA F 216 " --> pdb=" O TYR F 245 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N ILE F 247 " --> pdb=" O ALA F 216 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N LEU F 218 " --> pdb=" O ILE F 247 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N THR F 166 " --> pdb=" O ILE F 217 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N VAL F 219 " --> pdb=" O THR F 166 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N VAL F 168 " --> pdb=" O VAL F 219 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ASP F 188 " --> pdb=" O ILE F 167 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N SER F 169 " --> pdb=" O ASP F 188 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ALA F 190 " --> pdb=" O SER F 169 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'G' and resid 4 through 8 removed outlier: 6.352A pdb=" N ASP G 52 " --> pdb=" O LYS G 5 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N PHE G 7 " --> pdb=" O ASP G 52 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N TYR G 54 " --> pdb=" O PHE G 7 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ARG G 84 " --> pdb=" O VAL G 53 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N ILE G 55 " --> pdb=" O ARG G 84 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N THR G 86 " --> pdb=" O ILE G 55 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N HIS G 123 " --> pdb=" O ALA G 87 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N ILE G 89 " --> pdb=" O HIS G 123 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ILE G 125 " --> pdb=" O ILE G 89 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N THR G 126 " --> pdb=" O PRO G 141 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N ASP G 143 " --> pdb=" O THR G 126 " (cutoff:3.500A) No H-bonds generated for sheet with id= S Processing sheet with id= T, first strand: chain 'G' and resid 30 through 34 Processing sheet with id= U, first strand: chain 'G' and resid 287 through 290 removed outlier: 6.148A pdb=" N VAL G 269 " --> pdb=" O GLN G 288 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N ILE G 290 " --> pdb=" O VAL G 269 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N VAL G 271 " --> pdb=" O ILE G 290 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ALA G 268 " --> pdb=" O VAL G 244 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ALA G 216 " --> pdb=" O TYR G 245 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N ILE G 247 " --> pdb=" O ALA G 216 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N LEU G 218 " --> pdb=" O ILE G 247 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N THR G 166 " --> pdb=" O ILE G 217 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N VAL G 219 " --> pdb=" O THR G 166 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N VAL G 168 " --> pdb=" O VAL G 219 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ASP G 188 " --> pdb=" O ILE G 167 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N SER G 169 " --> pdb=" O ASP G 188 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ALA G 190 " --> pdb=" O SER G 169 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'H' and resid 4 through 8 removed outlier: 6.353A pdb=" N ASP H 52 " --> pdb=" O LYS H 5 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N PHE H 7 " --> pdb=" O ASP H 52 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N TYR H 54 " --> pdb=" O PHE H 7 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ARG H 84 " --> pdb=" O VAL H 53 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N ILE H 55 " --> pdb=" O ARG H 84 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N THR H 86 " --> pdb=" O ILE H 55 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N HIS H 123 " --> pdb=" O ALA H 87 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N ILE H 89 " --> pdb=" O HIS H 123 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ILE H 125 " --> pdb=" O ILE H 89 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N THR H 126 " --> pdb=" O PRO H 141 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N ASP H 143 " --> pdb=" O THR H 126 " (cutoff:3.500A) No H-bonds generated for sheet with id= V Processing sheet with id= W, first strand: chain 'H' and resid 30 through 34 Processing sheet with id= X, first strand: chain 'H' and resid 287 through 290 removed outlier: 6.149A pdb=" N VAL H 269 " --> pdb=" O GLN H 288 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N ILE H 290 " --> pdb=" O VAL H 269 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N VAL H 271 " --> pdb=" O ILE H 290 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ALA H 268 " --> pdb=" O VAL H 244 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ALA H 216 " --> pdb=" O TYR H 245 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N ILE H 247 " --> pdb=" O ALA H 216 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N LEU H 218 " --> pdb=" O ILE H 247 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N THR H 166 " --> pdb=" O ILE H 217 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N VAL H 219 " --> pdb=" O THR H 166 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N VAL H 168 " --> pdb=" O VAL H 219 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ASP H 188 " --> pdb=" O ILE H 167 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N SER H 169 " --> pdb=" O ASP H 188 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ALA H 190 " --> pdb=" O SER H 169 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'I' and resid 4 through 8 removed outlier: 6.353A pdb=" N ASP I 52 " --> pdb=" O LYS I 5 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N PHE I 7 " --> pdb=" O ASP I 52 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N TYR I 54 " --> pdb=" O PHE I 7 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ARG I 84 " --> pdb=" O VAL I 53 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N ILE I 55 " --> pdb=" O ARG I 84 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N THR I 86 " --> pdb=" O ILE I 55 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N HIS I 123 " --> pdb=" O ALA I 87 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N ILE I 89 " --> pdb=" O HIS I 123 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ILE I 125 " --> pdb=" O ILE I 89 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N THR I 126 " --> pdb=" O PRO I 141 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N ASP I 143 " --> pdb=" O THR I 126 " (cutoff:3.500A) No H-bonds generated for sheet with id= Y Processing sheet with id= Z, first strand: chain 'I' and resid 30 through 34 Processing sheet with id= AA, first strand: chain 'I' and resid 287 through 290 removed outlier: 6.148A pdb=" N VAL I 269 " --> pdb=" O GLN I 288 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N ILE I 290 " --> pdb=" O VAL I 269 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N VAL I 271 " --> pdb=" O ILE I 290 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ALA I 268 " --> pdb=" O VAL I 244 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ALA I 216 " --> pdb=" O TYR I 245 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N ILE I 247 " --> pdb=" O ALA I 216 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N LEU I 218 " --> pdb=" O ILE I 247 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N THR I 166 " --> pdb=" O ILE I 217 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N VAL I 219 " --> pdb=" O THR I 166 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N VAL I 168 " --> pdb=" O VAL I 219 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ASP I 188 " --> pdb=" O ILE I 167 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N SER I 169 " --> pdb=" O ASP I 188 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ALA I 190 " --> pdb=" O SER I 169 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'J' and resid 4 through 8 removed outlier: 6.352A pdb=" N ASP J 52 " --> pdb=" O LYS J 5 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N PHE J 7 " --> pdb=" O ASP J 52 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N TYR J 54 " --> pdb=" O PHE J 7 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ARG J 84 " --> pdb=" O VAL J 53 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N ILE J 55 " --> pdb=" O ARG J 84 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N THR J 86 " --> pdb=" O ILE J 55 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N HIS J 123 " --> pdb=" O ALA J 87 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N ILE J 89 " --> pdb=" O HIS J 123 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ILE J 125 " --> pdb=" O ILE J 89 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N THR J 126 " --> pdb=" O PRO J 141 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N ASP J 143 " --> pdb=" O THR J 126 " (cutoff:3.500A) No H-bonds generated for sheet with id= AB Processing sheet with id= AC, first strand: chain 'J' and resid 30 through 34 Processing sheet with id= AD, first strand: chain 'J' and resid 287 through 290 removed outlier: 6.148A pdb=" N VAL J 269 " --> pdb=" O GLN J 288 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N ILE J 290 " --> pdb=" O VAL J 269 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N VAL J 271 " --> pdb=" O ILE J 290 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ALA J 268 " --> pdb=" O VAL J 244 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ALA J 216 " --> pdb=" O TYR J 245 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N ILE J 247 " --> pdb=" O ALA J 216 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N LEU J 218 " --> pdb=" O ILE J 247 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N THR J 166 " --> pdb=" O ILE J 217 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N VAL J 219 " --> pdb=" O THR J 166 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N VAL J 168 " --> pdb=" O VAL J 219 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ASP J 188 " --> pdb=" O ILE J 167 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N SER J 169 " --> pdb=" O ASP J 188 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ALA J 190 " --> pdb=" O SER J 169 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'K' and resid 4 through 8 removed outlier: 6.353A pdb=" N ASP K 52 " --> pdb=" O LYS K 5 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N PHE K 7 " --> pdb=" O ASP K 52 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N TYR K 54 " --> pdb=" O PHE K 7 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ARG K 84 " --> pdb=" O VAL K 53 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N ILE K 55 " --> pdb=" O ARG K 84 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N THR K 86 " --> pdb=" O ILE K 55 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N HIS K 123 " --> pdb=" O ALA K 87 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N ILE K 89 " --> pdb=" O HIS K 123 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ILE K 125 " --> pdb=" O ILE K 89 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N THR K 126 " --> pdb=" O PRO K 141 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N ASP K 143 " --> pdb=" O THR K 126 " (cutoff:3.500A) No H-bonds generated for sheet with id= AE Processing sheet with id= AF, first strand: chain 'K' and resid 30 through 34 Processing sheet with id= AG, first strand: chain 'K' and resid 287 through 290 removed outlier: 6.149A pdb=" N VAL K 269 " --> pdb=" O GLN K 288 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N ILE K 290 " --> pdb=" O VAL K 269 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N VAL K 271 " --> pdb=" O ILE K 290 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ALA K 268 " --> pdb=" O VAL K 244 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ALA K 216 " --> pdb=" O TYR K 245 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N ILE K 247 " --> pdb=" O ALA K 216 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N LEU K 218 " --> pdb=" O ILE K 247 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N THR K 166 " --> pdb=" O ILE K 217 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N VAL K 219 " --> pdb=" O THR K 166 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N VAL K 168 " --> pdb=" O VAL K 219 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ASP K 188 " --> pdb=" O ILE K 167 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N SER K 169 " --> pdb=" O ASP K 188 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ALA K 190 " --> pdb=" O SER K 169 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'L' and resid 4 through 8 removed outlier: 6.352A pdb=" N ASP L 52 " --> pdb=" O LYS L 5 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N PHE L 7 " --> pdb=" O ASP L 52 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N TYR L 54 " --> pdb=" O PHE L 7 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ARG L 84 " --> pdb=" O VAL L 53 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N ILE L 55 " --> pdb=" O ARG L 84 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N THR L 86 " --> pdb=" O ILE L 55 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N HIS L 123 " --> pdb=" O ALA L 87 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N ILE L 89 " --> pdb=" O HIS L 123 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ILE L 125 " --> pdb=" O ILE L 89 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N THR L 126 " --> pdb=" O PRO L 141 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N ASP L 143 " --> pdb=" O THR L 126 " (cutoff:3.500A) No H-bonds generated for sheet with id= AH Processing sheet with id= AI, first strand: chain 'L' and resid 30 through 34 Processing sheet with id= AJ, first strand: chain 'L' and resid 287 through 290 removed outlier: 6.148A pdb=" N VAL L 269 " --> pdb=" O GLN L 288 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N ILE L 290 " --> pdb=" O VAL L 269 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N VAL L 271 " --> pdb=" O ILE L 290 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ALA L 268 " --> pdb=" O VAL L 244 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ALA L 216 " --> pdb=" O TYR L 245 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N ILE L 247 " --> pdb=" O ALA L 216 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N LEU L 218 " --> pdb=" O ILE L 247 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N THR L 166 " --> pdb=" O ILE L 217 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N VAL L 219 " --> pdb=" O THR L 166 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N VAL L 168 " --> pdb=" O VAL L 219 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ASP L 188 " --> pdb=" O ILE L 167 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N SER L 169 " --> pdb=" O ASP L 188 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ALA L 190 " --> pdb=" O SER L 169 " (cutoff:3.500A) 936 hydrogen bonds defined for protein. 2664 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: 9.81 Time building geometry restraints manager: 9.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 9333 1.33 - 1.45: 3391 1.45 - 1.57: 16172 1.57 - 1.69: 60 1.69 - 1.81: 300 Bond restraints: 29256 Sorted by residual: bond pdb=" O4 PO4 A 403 " pdb=" P PO4 A 403 " ideal model delta sigma weight residual 1.568 1.497 0.071 2.00e-02 2.50e+03 1.26e+01 bond pdb=" O4 PO4 G 403 " pdb=" P PO4 G 403 " ideal model delta sigma weight residual 1.568 1.498 0.070 2.00e-02 2.50e+03 1.24e+01 bond pdb=" O4 PO4 E 403 " pdb=" P PO4 E 403 " ideal model delta sigma weight residual 1.568 1.498 0.070 2.00e-02 2.50e+03 1.23e+01 bond pdb=" O4 PO4 C 403 " pdb=" P PO4 C 403 " ideal model delta sigma weight residual 1.568 1.498 0.070 2.00e-02 2.50e+03 1.22e+01 bond pdb=" O4 PO4 K 403 " pdb=" P PO4 K 403 " ideal model delta sigma weight residual 1.568 1.498 0.070 2.00e-02 2.50e+03 1.22e+01 ... (remaining 29251 not shown) Histogram of bond angle deviations from ideal: 99.92 - 106.75: 840 106.75 - 113.59: 17176 113.59 - 120.42: 10537 120.42 - 127.26: 10807 127.26 - 134.09: 312 Bond angle restraints: 39672 Sorted by residual: angle pdb=" PB ATP L 401 " pdb=" O3B ATP L 401 " pdb=" PG ATP L 401 " ideal model delta sigma weight residual 139.87 132.33 7.54 1.00e+00 1.00e+00 5.68e+01 angle pdb=" PB ATP F 401 " pdb=" O3B ATP F 401 " pdb=" PG ATP F 401 " ideal model delta sigma weight residual 139.87 132.34 7.53 1.00e+00 1.00e+00 5.66e+01 angle pdb=" PB ATP I 401 " pdb=" O3B ATP I 401 " pdb=" PG ATP I 401 " ideal model delta sigma weight residual 139.87 132.37 7.50 1.00e+00 1.00e+00 5.62e+01 angle pdb=" PB ATP H 401 " pdb=" O3B ATP H 401 " pdb=" PG ATP H 401 " ideal model delta sigma weight residual 139.87 132.38 7.49 1.00e+00 1.00e+00 5.61e+01 angle pdb=" PB ATP C 401 " pdb=" O3B ATP C 401 " pdb=" PG ATP C 401 " ideal model delta sigma weight residual 139.87 132.39 7.48 1.00e+00 1.00e+00 5.59e+01 ... (remaining 39667 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 16036 17.95 - 35.90: 1352 35.90 - 53.85: 432 53.85 - 71.80: 138 71.80 - 89.75: 90 Dihedral angle restraints: 18048 sinusoidal: 7296 harmonic: 10752 Sorted by residual: dihedral pdb=" CA SER K 8 " pdb=" C SER K 8 " pdb=" N GLY K 9 " pdb=" CA GLY K 9 " ideal model delta harmonic sigma weight residual 180.00 160.62 19.38 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" CA SER J 8 " pdb=" C SER J 8 " pdb=" N GLY J 9 " pdb=" CA GLY J 9 " ideal model delta harmonic sigma weight residual 180.00 160.62 19.38 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" CA SER D 8 " pdb=" C SER D 8 " pdb=" N GLY D 9 " pdb=" CA GLY D 9 " ideal model delta harmonic sigma weight residual 180.00 160.63 19.37 0 5.00e+00 4.00e-02 1.50e+01 ... (remaining 18045 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 2634 0.040 - 0.080: 1417 0.080 - 0.120: 489 0.120 - 0.160: 84 0.160 - 0.200: 44 Chirality restraints: 4668 Sorted by residual: chirality pdb=" CG LEU J 248 " pdb=" CB LEU J 248 " pdb=" CD1 LEU J 248 " pdb=" CD2 LEU J 248 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 9.96e-01 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 -2.39 -0.20 2.00e-01 2.50e+01 9.72e-01 chirality pdb=" CG LEU D 248 " pdb=" CB LEU D 248 " pdb=" CD1 LEU D 248 " pdb=" CD2 LEU D 248 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 9.69e-01 ... (remaining 4665 not shown) Planarity restraints: 5004 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER I 180 " 0.009 2.00e-02 2.50e+03 1.71e-02 2.93e+00 pdb=" C SER I 180 " -0.030 2.00e-02 2.50e+03 pdb=" O SER I 180 " 0.011 2.00e-02 2.50e+03 pdb=" N ILE I 181 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER F 180 " -0.009 2.00e-02 2.50e+03 1.71e-02 2.93e+00 pdb=" C SER F 180 " 0.030 2.00e-02 2.50e+03 pdb=" O SER F 180 " -0.011 2.00e-02 2.50e+03 pdb=" N ILE F 181 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER L 180 " -0.009 2.00e-02 2.50e+03 1.70e-02 2.90e+00 pdb=" C SER L 180 " 0.029 2.00e-02 2.50e+03 pdb=" O SER L 180 " -0.011 2.00e-02 2.50e+03 pdb=" N ILE L 181 " -0.010 2.00e-02 2.50e+03 ... (remaining 5001 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 224 2.55 - 3.13: 23430 3.13 - 3.72: 47856 3.72 - 4.31: 67697 4.31 - 4.90: 111322 Nonbonded interactions: 250529 Sorted by model distance: nonbonded pdb="MG MG D 404 " pdb=" O HOH D 501 " model vdw 1.957 2.170 nonbonded pdb="MG MG J 404 " pdb=" O HOH J 501 " model vdw 1.958 2.170 nonbonded pdb="MG MG F 404 " pdb=" O HOH F 501 " model vdw 1.958 2.170 nonbonded pdb="MG MG I 404 " pdb=" O HOH I 501 " model vdw 1.958 2.170 nonbonded pdb="MG MG B 404 " pdb=" O HOH B 501 " model vdw 1.958 2.170 ... (remaining 250524 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: 2.540 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: 8.380 Check model and map are aligned: 0.420 Set scattering table: 0.250 Process input model: 68.850 Find NCS groups from input model: 2.000 Set up NCS constraints: 0.250 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:12.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 95.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 29256 Z= 0.460 Angle : 0.694 7.536 39672 Z= 0.437 Chirality : 0.054 0.200 4668 Planarity : 0.003 0.019 5004 Dihedral : 17.531 89.747 11040 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.94 % Allowed : 12.56 % Favored : 85.50 % 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: 0.54 (0.14), residues: 3660 helix: 1.27 (0.14), residues: 1488 sheet: 0.06 (0.17), residues: 948 loop : -0.38 (0.16), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP E 162 HIS 0.005 0.001 HIS H 130 PHE 0.012 0.002 PHE J 189 TYR 0.023 0.004 TYR D 146 ARG 0.004 0.001 ARG F 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 774 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 713 time to evaluate : 3.220 Fit side-chains REVERT: A 29 LYS cc_start: 0.8257 (mttp) cc_final: 0.8042 (mttm) REVERT: B 294 MET cc_start: 0.8204 (pmm) cc_final: 0.7846 (pmm) REVERT: B 298 GLU cc_start: 0.8228 (mm-30) cc_final: 0.7945 (mm-30) REVERT: C 68 MET cc_start: 0.8302 (tpp) cc_final: 0.8098 (mmm) REVERT: D 281 MET cc_start: 0.6999 (mtp) cc_final: 0.6575 (mtm) REVERT: E 29 LYS cc_start: 0.8144 (mttp) cc_final: 0.7888 (mttm) REVERT: E 51 GLU cc_start: 0.7954 (mm-30) cc_final: 0.7671 (mm-30) REVERT: F 51 GLU cc_start: 0.8010 (mm-30) cc_final: 0.7787 (mm-30) REVERT: F 221 ASP cc_start: 0.7814 (p0) cc_final: 0.7448 (p0) REVERT: F 248 LEU cc_start: 0.8548 (mp) cc_final: 0.8335 (mm) REVERT: G 51 GLU cc_start: 0.8021 (mm-30) cc_final: 0.7800 (mm-30) REVERT: G 221 ASP cc_start: 0.7816 (p0) cc_final: 0.7452 (p0) REVERT: H 29 LYS cc_start: 0.8150 (mttp) cc_final: 0.7884 (mttm) REVERT: H 51 GLU cc_start: 0.7956 (mm-30) cc_final: 0.7676 (mm-30) REVERT: I 281 MET cc_start: 0.7010 (mtp) cc_final: 0.6587 (mtm) REVERT: J 29 LYS cc_start: 0.8162 (mttp) cc_final: 0.7831 (mttm) REVERT: J 46 GLU cc_start: 0.8360 (pt0) cc_final: 0.8157 (pt0) REVERT: K 294 MET cc_start: 0.8213 (pmm) cc_final: 0.7849 (pmm) REVERT: K 298 GLU cc_start: 0.8219 (mm-30) cc_final: 0.7942 (mm-30) REVERT: L 29 LYS cc_start: 0.8271 (mttp) cc_final: 0.8043 (mttm) outliers start: 61 outliers final: 26 residues processed: 761 average time/residue: 1.2622 time to fit residues: 1137.7374 Evaluate side-chains 605 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 579 time to evaluate : 2.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 314 SER Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 314 SER Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 314 SER Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 314 SER Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain H residue 314 SER Chi-restraints excluded: chain I residue 208 VAL Chi-restraints excluded: chain I residue 314 SER Chi-restraints excluded: chain J residue 208 VAL Chi-restraints excluded: chain J residue 314 SER Chi-restraints excluded: chain K residue 208 VAL Chi-restraints excluded: chain K residue 237 LEU Chi-restraints excluded: chain K residue 314 SER Chi-restraints excluded: chain L residue 208 VAL Chi-restraints excluded: chain L residue 314 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 303 optimal weight: 0.4980 chunk 272 optimal weight: 0.0670 chunk 151 optimal weight: 2.9990 chunk 93 optimal weight: 0.6980 chunk 184 optimal weight: 10.0000 chunk 145 optimal weight: 0.8980 chunk 282 optimal weight: 0.5980 chunk 109 optimal weight: 0.6980 chunk 171 optimal weight: 1.9990 chunk 210 optimal weight: 0.9980 chunk 326 optimal weight: 1.9990 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 263 ASN B 288 GLN C 135 GLN D 288 GLN D 305 ASN E 135 GLN F 288 GLN G 288 GLN H 135 GLN I 288 GLN I 305 ASN J 135 GLN K 263 ASN K 288 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.1382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 29256 Z= 0.131 Angle : 0.445 4.361 39672 Z= 0.247 Chirality : 0.046 0.159 4668 Planarity : 0.002 0.024 5004 Dihedral : 12.091 89.687 4360 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 3.02 % Allowed : 12.69 % Favored : 84.29 % 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: 0.99 (0.14), residues: 3660 helix: 1.87 (0.14), residues: 1476 sheet: 0.05 (0.17), residues: 972 loop : -0.24 (0.16), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 162 HIS 0.003 0.001 HIS J 304 PHE 0.009 0.001 PHE B 138 TYR 0.011 0.001 TYR D 146 ARG 0.006 0.000 ARG B 163 *********************** 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 711 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 616 time to evaluate : 3.320 Fit side-chains REVERT: B 294 MET cc_start: 0.8185 (pmm) cc_final: 0.7850 (pmm) REVERT: E 51 GLU cc_start: 0.7937 (mm-30) cc_final: 0.7538 (mm-30) REVERT: E 180 SER cc_start: 0.8742 (t) cc_final: 0.8474 (t) REVERT: H 51 GLU cc_start: 0.7935 (mm-30) cc_final: 0.7536 (mm-30) REVERT: H 180 SER cc_start: 0.8745 (t) cc_final: 0.8476 (t) REVERT: J 29 LYS cc_start: 0.8137 (mttp) cc_final: 0.7763 (mttm) REVERT: K 294 MET cc_start: 0.8185 (pmm) cc_final: 0.7849 (pmm) outliers start: 95 outliers final: 38 residues processed: 671 average time/residue: 1.3565 time to fit residues: 1067.0101 Evaluate side-chains 601 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 563 time to evaluate : 3.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 26 GLU Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 249 THR 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 181 ILE Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 237 LEU Chi-restraints excluded: chain G residue 249 THR Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 181 ILE 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 166 THR Chi-restraints excluded: chain I residue 208 VAL Chi-restraints excluded: chain I residue 249 THR Chi-restraints excluded: chain J residue 62 GLU Chi-restraints excluded: chain J residue 208 VAL Chi-restraints excluded: chain J residue 249 THR Chi-restraints excluded: chain K residue 26 GLU Chi-restraints excluded: chain K residue 208 VAL Chi-restraints excluded: chain K residue 249 THR 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: 3.9990 chunk 101 optimal weight: 5.9990 chunk 272 optimal weight: 0.0060 chunk 222 optimal weight: 7.9990 chunk 90 optimal weight: 6.9990 chunk 327 optimal weight: 6.9990 chunk 353 optimal weight: 0.0670 chunk 291 optimal weight: 6.9990 chunk 324 optimal weight: 7.9990 chunk 111 optimal weight: 0.9990 chunk 262 optimal weight: 0.9980 overall best weight: 1.2138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 HIS A 288 GLN B 12 HIS B 263 ASN C 12 HIS C 38 GLN D 12 HIS E 38 GLN F 263 ASN F 288 GLN G 12 HIS G 263 ASN G 288 GLN H 38 GLN I 12 HIS J 12 HIS K 12 HIS K 263 ASN L 123 HIS L 288 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 29256 Z= 0.183 Angle : 0.470 6.259 39672 Z= 0.262 Chirality : 0.047 0.177 4668 Planarity : 0.003 0.023 5004 Dihedral : 11.194 81.100 4342 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.77 % Allowed : 12.53 % Favored : 84.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.14), residues: 3660 helix: 1.92 (0.14), residues: 1488 sheet: 0.23 (0.17), residues: 936 loop : -0.27 (0.16), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP E 162 HIS 0.005 0.001 HIS L 130 PHE 0.010 0.001 PHE D 138 TYR 0.013 0.002 TYR E 146 ARG 0.005 0.000 ARG B 163 *********************** 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 680 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 593 time to evaluate : 3.103 Fit side-chains REVERT: A 135 GLN cc_start: 0.8988 (OUTLIER) cc_final: 0.8688 (mt0) REVERT: A 188 ASP cc_start: 0.7360 (m-30) cc_final: 0.7089 (m-30) REVERT: B 69 GLU cc_start: 0.8446 (tt0) cc_final: 0.8230 (tt0) REVERT: B 294 MET cc_start: 0.8199 (pmm) cc_final: 0.7885 (pmm) REVERT: E 51 GLU cc_start: 0.7942 (mm-30) cc_final: 0.7640 (mm-30) REVERT: F 208 VAL cc_start: 0.6934 (OUTLIER) cc_final: 0.6727 (p) REVERT: G 208 VAL cc_start: 0.6934 (OUTLIER) cc_final: 0.6721 (p) REVERT: G 298 GLU cc_start: 0.8144 (mm-30) cc_final: 0.7942 (mm-30) REVERT: H 51 GLU cc_start: 0.7944 (mm-30) cc_final: 0.7636 (mm-30) REVERT: K 294 MET cc_start: 0.8204 (pmm) cc_final: 0.7889 (pmm) REVERT: L 135 GLN cc_start: 0.8990 (OUTLIER) cc_final: 0.8688 (mt0) REVERT: L 188 ASP cc_start: 0.7357 (m-30) cc_final: 0.7058 (m-30) outliers start: 87 outliers final: 47 residues processed: 646 average time/residue: 1.3778 time to fit residues: 1041.0264 Evaluate side-chains 623 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 572 time to evaluate : 4.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 135 GLN Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain B residue 12 HIS Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 249 THR 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 C residue 249 THR 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 62 GLU Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 237 LEU Chi-restraints excluded: chain G residue 249 THR Chi-restraints excluded: chain H residue 12 HIS Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 178 VAL Chi-restraints excluded: chain H residue 248 LEU Chi-restraints excluded: chain H residue 249 THR Chi-restraints excluded: chain I residue 166 THR Chi-restraints excluded: chain I residue 208 VAL Chi-restraints excluded: chain I residue 249 THR Chi-restraints excluded: chain J residue 62 GLU Chi-restraints excluded: chain J residue 208 VAL Chi-restraints excluded: chain J residue 248 LEU Chi-restraints excluded: chain J residue 249 THR Chi-restraints excluded: chain K residue 12 HIS Chi-restraints excluded: chain K residue 26 GLU Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain K residue 249 THR Chi-restraints excluded: chain L residue 62 GLU Chi-restraints excluded: chain L residue 135 GLN Chi-restraints excluded: chain L residue 160 SER Chi-restraints excluded: chain L residue 208 VAL Chi-restraints excluded: chain L residue 248 LEU Chi-restraints excluded: chain L residue 249 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 323 optimal weight: 4.9990 chunk 246 optimal weight: 0.7980 chunk 169 optimal weight: 10.0000 chunk 36 optimal weight: 3.9990 chunk 156 optimal weight: 0.9980 chunk 219 optimal weight: 0.0030 chunk 328 optimal weight: 5.9990 chunk 347 optimal weight: 7.9990 chunk 171 optimal weight: 7.9990 chunk 311 optimal weight: 7.9990 chunk 93 optimal weight: 0.8980 overall best weight: 1.3392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 GLN B 263 ASN B 288 GLN D 12 HIS D 288 GLN E 38 GLN F 288 GLN G 263 ASN G 288 GLN H 38 GLN I 12 HIS J 38 GLN K 263 ASN K 288 GLN L 288 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 29256 Z= 0.192 Angle : 0.471 5.601 39672 Z= 0.263 Chirality : 0.047 0.177 4668 Planarity : 0.003 0.024 5004 Dihedral : 11.105 81.027 4340 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.42 % Allowed : 13.10 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.14), residues: 3660 helix: 1.91 (0.14), residues: 1488 sheet: 0.24 (0.17), residues: 936 loop : -0.30 (0.16), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP E 162 HIS 0.005 0.001 HIS L 130 PHE 0.010 0.001 PHE D 138 TYR 0.014 0.002 TYR H 146 ARG 0.006 0.000 ARG G 163 *********************** 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 648 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 572 time to evaluate : 3.220 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 135 GLN cc_start: 0.8985 (OUTLIER) cc_final: 0.8673 (mt0) REVERT: A 188 ASP cc_start: 0.7366 (m-30) cc_final: 0.7067 (m-30) REVERT: B 39 GLU cc_start: 0.8491 (OUTLIER) cc_final: 0.8126 (mt-10) REVERT: B 205 MET cc_start: 0.6671 (mtt) cc_final: 0.6467 (mtt) REVERT: B 294 MET cc_start: 0.8212 (pmm) cc_final: 0.7847 (pmm) REVERT: C 14 ASP cc_start: 0.8002 (t70) cc_final: 0.7767 (t0) REVERT: E 51 GLU cc_start: 0.7909 (mm-30) cc_final: 0.7608 (mm-30) REVERT: F 208 VAL cc_start: 0.6967 (OUTLIER) cc_final: 0.6753 (p) REVERT: G 208 VAL cc_start: 0.6970 (OUTLIER) cc_final: 0.6761 (p) REVERT: H 51 GLU cc_start: 0.7906 (mm-30) cc_final: 0.7601 (mm-30) REVERT: H 180 SER cc_start: 0.8726 (t) cc_final: 0.8417 (t) REVERT: J 14 ASP cc_start: 0.8014 (t70) cc_final: 0.7794 (t0) REVERT: K 39 GLU cc_start: 0.8488 (OUTLIER) cc_final: 0.8124 (mt-10) REVERT: K 205 MET cc_start: 0.6670 (mtt) cc_final: 0.6466 (mtt) REVERT: K 294 MET cc_start: 0.8216 (pmm) cc_final: 0.7850 (pmm) REVERT: L 135 GLN cc_start: 0.8984 (OUTLIER) cc_final: 0.8669 (mt0) REVERT: L 188 ASP cc_start: 0.7368 (m-30) cc_final: 0.7067 (m-30) outliers start: 76 outliers final: 40 residues processed: 622 average time/residue: 1.3599 time to fit residues: 992.3867 Evaluate side-chains 604 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 558 time to evaluate : 3.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 GLN Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain B residue 39 GLU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 249 THR 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 C residue 249 THR Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain E residue 5 LYS Chi-restraints excluded: chain E residue 12 HIS Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 249 THR Chi-restraints excluded: chain H residue 5 LYS Chi-restraints excluded: chain H residue 12 HIS Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 248 LEU Chi-restraints excluded: chain H residue 249 THR Chi-restraints excluded: chain I residue 166 THR Chi-restraints excluded: chain I residue 208 VAL Chi-restraints excluded: chain I residue 249 THR Chi-restraints excluded: chain J residue 62 GLU Chi-restraints excluded: chain J residue 208 VAL Chi-restraints excluded: chain J residue 248 LEU Chi-restraints excluded: chain J residue 249 THR Chi-restraints excluded: chain K residue 39 GLU Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain K residue 249 THR Chi-restraints excluded: chain L residue 135 GLN Chi-restraints excluded: chain L residue 160 SER Chi-restraints excluded: chain L residue 208 VAL Chi-restraints excluded: chain L residue 248 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: 0.3980 chunk 197 optimal weight: 7.9990 chunk 5 optimal weight: 7.9990 chunk 259 optimal weight: 9.9990 chunk 143 optimal weight: 7.9990 chunk 296 optimal weight: 0.4980 chunk 240 optimal weight: 6.9990 chunk 0 optimal weight: 1.9990 chunk 177 optimal weight: 6.9990 chunk 312 optimal weight: 5.9990 chunk 87 optimal weight: 3.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 GLN B 263 ASN B 288 GLN C 123 HIS D 12 HIS E 123 HIS F 12 HIS F 288 GLN G 263 ASN G 288 GLN H 123 HIS I 12 HIS J 38 GLN J 123 HIS K 263 ASN K 288 GLN L 288 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.1829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 29256 Z= 0.318 Angle : 0.541 5.527 39672 Z= 0.303 Chirality : 0.050 0.184 4668 Planarity : 0.003 0.031 5004 Dihedral : 12.223 89.595 4340 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.58 % Allowed : 13.39 % Favored : 84.03 % 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: 0.92 (0.14), residues: 3660 helix: 1.68 (0.14), residues: 1488 sheet: 0.35 (0.17), residues: 912 loop : -0.41 (0.16), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.003 TRP C 162 HIS 0.007 0.001 HIS E 130 PHE 0.011 0.002 PHE I 138 TYR 0.019 0.002 TYR H 146 ARG 0.005 0.000 ARG D 163 *********************** 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 638 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 557 time to evaluate : 3.331 Fit side-chains REVERT: A 135 GLN cc_start: 0.8992 (OUTLIER) cc_final: 0.8690 (mt0) REVERT: A 188 ASP cc_start: 0.7376 (m-30) cc_final: 0.7083 (m-30) REVERT: B 39 GLU cc_start: 0.8625 (OUTLIER) cc_final: 0.8251 (mt-10) REVERT: B 205 MET cc_start: 0.6658 (mtt) cc_final: 0.6433 (mtt) REVERT: B 294 MET cc_start: 0.8215 (pmm) cc_final: 0.7895 (pmm) REVERT: E 5 LYS cc_start: 0.8636 (OUTLIER) cc_final: 0.8267 (mmmt) REVERT: E 51 GLU cc_start: 0.7928 (mm-30) cc_final: 0.7665 (mm-30) REVERT: F 176 LYS cc_start: 0.7956 (OUTLIER) cc_final: 0.7706 (ttpp) REVERT: G 176 LYS cc_start: 0.7960 (OUTLIER) cc_final: 0.7709 (ttpp) REVERT: G 208 VAL cc_start: 0.7060 (OUTLIER) cc_final: 0.6855 (p) REVERT: H 5 LYS cc_start: 0.8633 (OUTLIER) cc_final: 0.8266 (mmmt) REVERT: H 51 GLU cc_start: 0.7929 (mm-30) cc_final: 0.7633 (mm-30) REVERT: K 39 GLU cc_start: 0.8624 (OUTLIER) cc_final: 0.8247 (mt-10) REVERT: K 205 MET cc_start: 0.6659 (mtt) cc_final: 0.6427 (mtt) REVERT: K 294 MET cc_start: 0.8217 (pmm) cc_final: 0.7895 (pmm) REVERT: L 135 GLN cc_start: 0.8993 (OUTLIER) cc_final: 0.8689 (mt0) outliers start: 81 outliers final: 38 residues processed: 611 average time/residue: 1.4870 time to fit residues: 1072.7116 Evaluate side-chains 605 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 558 time to evaluate : 3.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 GLN Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain B residue 39 GLU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain E residue 5 LYS Chi-restraints excluded: chain E residue 12 HIS Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain F residue 152 LEU Chi-restraints excluded: chain F residue 176 LYS Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 282 LYS Chi-restraints excluded: chain G residue 118 VAL Chi-restraints excluded: chain G residue 152 LEU Chi-restraints excluded: chain G residue 176 LYS Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 249 THR Chi-restraints excluded: chain G residue 282 LYS Chi-restraints excluded: chain H residue 5 LYS Chi-restraints excluded: chain H residue 12 HIS Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 248 LEU Chi-restraints excluded: chain H residue 249 THR Chi-restraints excluded: chain I residue 166 THR Chi-restraints excluded: chain I residue 249 THR Chi-restraints excluded: chain J residue 62 GLU Chi-restraints excluded: chain J residue 118 VAL Chi-restraints excluded: chain J residue 208 VAL Chi-restraints excluded: chain J residue 249 THR Chi-restraints excluded: chain K residue 39 GLU Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain K residue 249 THR Chi-restraints excluded: chain L residue 135 GLN Chi-restraints excluded: chain L residue 160 SER Chi-restraints excluded: chain L residue 208 VAL 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: 4.9990 chunk 313 optimal weight: 4.9990 chunk 68 optimal weight: 4.9990 chunk 204 optimal weight: 5.9990 chunk 85 optimal weight: 1.9990 chunk 348 optimal weight: 0.9990 chunk 289 optimal weight: 10.0000 chunk 161 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 chunk 182 optimal weight: 8.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 GLN B 263 ASN B 288 GLN D 12 HIS F 263 ASN F 288 GLN G 263 ASN G 288 GLN I 12 HIS J 38 GLN K 263 ASN K 288 GLN L 288 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 29256 Z= 0.258 Angle : 0.509 5.569 39672 Z= 0.284 Chirality : 0.048 0.177 4668 Planarity : 0.003 0.028 5004 Dihedral : 11.852 86.932 4337 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.13 % Allowed : 13.61 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.14), residues: 3660 helix: 1.68 (0.14), residues: 1488 sheet: 0.20 (0.17), residues: 936 loop : -0.40 (0.16), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP A 162 HIS 0.006 0.001 HIS H 130 PHE 0.012 0.002 PHE D 138 TYR 0.018 0.002 TYR J 146 ARG 0.006 0.000 ARG B 163 *********************** 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 638 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 571 time to evaluate : 4.341 Fit side-chains REVERT: A 135 GLN cc_start: 0.8988 (OUTLIER) cc_final: 0.8708 (mt0) REVERT: A 188 ASP cc_start: 0.7424 (m-30) cc_final: 0.7137 (m-30) REVERT: B 39 GLU cc_start: 0.8568 (OUTLIER) cc_final: 0.8186 (mt-10) REVERT: B 294 MET cc_start: 0.8213 (pmm) cc_final: 0.7889 (pmm) REVERT: E 5 LYS cc_start: 0.8625 (OUTLIER) cc_final: 0.8259 (mmmt) REVERT: E 51 GLU cc_start: 0.7925 (mm-30) cc_final: 0.7654 (mm-30) REVERT: G 208 VAL cc_start: 0.7046 (OUTLIER) cc_final: 0.6841 (p) REVERT: H 5 LYS cc_start: 0.8625 (OUTLIER) cc_final: 0.8261 (mmmt) REVERT: H 51 GLU cc_start: 0.7929 (mm-30) cc_final: 0.7613 (mm-30) REVERT: K 39 GLU cc_start: 0.8568 (OUTLIER) cc_final: 0.8184 (mt-10) REVERT: K 294 MET cc_start: 0.8217 (pmm) cc_final: 0.7894 (pmm) REVERT: L 135 GLN cc_start: 0.8988 (OUTLIER) cc_final: 0.8708 (mt0) outliers start: 67 outliers final: 41 residues processed: 620 average time/residue: 1.3990 time to fit residues: 1013.1131 Evaluate side-chains 601 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 553 time to evaluate : 3.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 GLN Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain B residue 39 GLU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 258 ILE Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain E residue 5 LYS Chi-restraints excluded: chain E residue 12 HIS Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain F residue 118 VAL Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 282 LYS Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 249 THR Chi-restraints excluded: chain G residue 282 LYS Chi-restraints excluded: chain H residue 5 LYS Chi-restraints excluded: chain H residue 12 HIS Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 248 LEU Chi-restraints excluded: chain H residue 249 THR Chi-restraints excluded: chain I residue 166 THR Chi-restraints excluded: chain I residue 249 THR Chi-restraints excluded: chain J residue 62 GLU Chi-restraints excluded: chain J residue 118 VAL Chi-restraints excluded: chain J residue 208 VAL Chi-restraints excluded: chain J residue 249 THR Chi-restraints excluded: chain J residue 258 ILE Chi-restraints excluded: chain K residue 39 GLU Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain K residue 249 THR Chi-restraints excluded: chain L residue 32 THR Chi-restraints excluded: chain L residue 135 GLN Chi-restraints excluded: chain L residue 160 SER Chi-restraints excluded: chain L residue 208 VAL 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: 8.9990 chunk 39 optimal weight: 1.9990 chunk 198 optimal weight: 8.9990 chunk 254 optimal weight: 0.0770 chunk 197 optimal weight: 4.9990 chunk 293 optimal weight: 8.9990 chunk 194 optimal weight: 0.9980 chunk 346 optimal weight: 0.6980 chunk 217 optimal weight: 0.9980 chunk 211 optimal weight: 0.9980 chunk 160 optimal weight: 1.9990 overall best weight: 0.7538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 GLN B 263 ASN B 288 GLN F 263 ASN F 288 GLN G 263 ASN G 288 GLN K 263 ASN K 288 GLN L 288 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 29256 Z= 0.142 Angle : 0.442 5.449 39672 Z= 0.246 Chirality : 0.046 0.166 4668 Planarity : 0.002 0.027 5004 Dihedral : 10.668 79.345 4337 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.75 % Allowed : 14.22 % Favored : 84.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.14), residues: 3660 helix: 1.96 (0.14), residues: 1476 sheet: 0.18 (0.17), residues: 972 loop : -0.30 (0.16), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 162 HIS 0.003 0.001 HIS J 130 PHE 0.011 0.001 PHE B 138 TYR 0.014 0.001 TYR J 146 ARG 0.006 0.000 ARG F 163 *********************** 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 616 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 561 time to evaluate : 3.529 Fit side-chains REVERT: A 135 GLN cc_start: 0.8971 (OUTLIER) cc_final: 0.8687 (mt0) REVERT: B 294 MET cc_start: 0.8208 (pmm) cc_final: 0.7897 (pmm) REVERT: C 14 ASP cc_start: 0.7987 (t70) cc_final: 0.7747 (t0) REVERT: E 5 LYS cc_start: 0.8580 (OUTLIER) cc_final: 0.8241 (mmmt) REVERT: E 46 GLU cc_start: 0.8355 (pt0) cc_final: 0.7914 (pt0) REVERT: E 51 GLU cc_start: 0.7882 (mm-30) cc_final: 0.7569 (mm-30) REVERT: E 163 ARG cc_start: 0.7993 (mtm-85) cc_final: 0.7683 (mtt180) REVERT: H 5 LYS cc_start: 0.8577 (OUTLIER) cc_final: 0.8239 (mmmt) REVERT: H 51 GLU cc_start: 0.7878 (mm-30) cc_final: 0.7568 (mm-30) REVERT: H 163 ARG cc_start: 0.7972 (mtm-85) cc_final: 0.7682 (mtt180) REVERT: H 180 SER cc_start: 0.8740 (t) cc_final: 0.8451 (t) REVERT: J 14 ASP cc_start: 0.7993 (t70) cc_final: 0.7736 (t0) REVERT: K 294 MET cc_start: 0.8213 (pmm) cc_final: 0.7903 (pmm) REVERT: L 135 GLN cc_start: 0.8972 (OUTLIER) cc_final: 0.8688 (mt0) outliers start: 55 outliers final: 35 residues processed: 594 average time/residue: 1.4432 time to fit residues: 997.1344 Evaluate side-chains 592 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 553 time to evaluate : 3.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 GLN Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain B residue 249 THR 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 C residue 249 THR Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain E residue 5 LYS Chi-restraints excluded: chain E residue 12 HIS Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 282 LYS Chi-restraints excluded: chain G residue 249 THR Chi-restraints excluded: chain G residue 282 LYS Chi-restraints excluded: chain H residue 5 LYS Chi-restraints excluded: chain H residue 12 HIS 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 208 VAL Chi-restraints excluded: chain I residue 249 THR Chi-restraints excluded: chain J residue 62 GLU Chi-restraints excluded: chain J residue 208 VAL Chi-restraints excluded: chain J residue 248 LEU Chi-restraints excluded: chain J residue 249 THR Chi-restraints excluded: chain K residue 249 THR Chi-restraints excluded: chain L residue 135 GLN Chi-restraints excluded: chain L residue 160 SER Chi-restraints excluded: chain L residue 208 VAL Chi-restraints excluded: chain L residue 248 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: 0.6980 chunk 138 optimal weight: 0.6980 chunk 207 optimal weight: 5.9990 chunk 104 optimal weight: 1.9990 chunk 68 optimal weight: 5.9990 chunk 67 optimal weight: 3.9990 chunk 220 optimal weight: 6.9990 chunk 236 optimal weight: 0.0070 chunk 171 optimal weight: 6.9990 chunk 32 optimal weight: 0.3980 chunk 272 optimal weight: 2.9990 overall best weight: 0.7600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 263 ASN B 288 GLN F 263 ASN F 288 GLN G 263 ASN G 288 GLN K 263 ASN K 288 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 29256 Z= 0.140 Angle : 0.437 5.621 39672 Z= 0.243 Chirality : 0.045 0.167 4668 Planarity : 0.002 0.025 5004 Dihedral : 10.158 76.051 4336 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.59 % Allowed : 14.50 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.14), residues: 3660 helix: 2.03 (0.14), residues: 1476 sheet: 0.21 (0.16), residues: 972 loop : -0.27 (0.17), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP L 162 HIS 0.003 0.001 HIS J 130 PHE 0.011 0.001 PHE I 138 TYR 0.014 0.001 TYR H 146 ARG 0.006 0.000 ARG F 163 *********************** 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 614 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 564 time to evaluate : 3.284 Fit side-chains REVERT: A 135 GLN cc_start: 0.8975 (OUTLIER) cc_final: 0.8663 (mt0) REVERT: B 294 MET cc_start: 0.8213 (pmm) cc_final: 0.7905 (pmm) REVERT: C 14 ASP cc_start: 0.7988 (t70) cc_final: 0.7737 (t0) REVERT: E 5 LYS cc_start: 0.8582 (OUTLIER) cc_final: 0.8237 (mmmt) REVERT: E 46 GLU cc_start: 0.8346 (pt0) cc_final: 0.7902 (pt0) REVERT: E 51 GLU cc_start: 0.7887 (mm-30) cc_final: 0.7586 (mm-30) REVERT: E 163 ARG cc_start: 0.7963 (mtm-85) cc_final: 0.7670 (mtt180) REVERT: F 298 GLU cc_start: 0.8228 (mm-30) cc_final: 0.7970 (mm-30) REVERT: H 5 LYS cc_start: 0.8577 (OUTLIER) cc_final: 0.8238 (mmmt) REVERT: H 51 GLU cc_start: 0.7885 (mm-30) cc_final: 0.7584 (mm-30) REVERT: H 163 ARG cc_start: 0.7977 (mtm-85) cc_final: 0.7704 (mtt180) REVERT: H 180 SER cc_start: 0.8733 (t) cc_final: 0.8462 (t) REVERT: J 14 ASP cc_start: 0.7996 (t70) cc_final: 0.7743 (t0) REVERT: K 294 MET cc_start: 0.8219 (pmm) cc_final: 0.7917 (pmm) REVERT: L 135 GLN cc_start: 0.8976 (OUTLIER) cc_final: 0.8660 (mt0) outliers start: 50 outliers final: 35 residues processed: 596 average time/residue: 1.4595 time to fit residues: 1009.0508 Evaluate side-chains 601 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 562 time to evaluate : 3.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 GLN Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 249 THR 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 C residue 249 THR Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain E residue 5 LYS Chi-restraints excluded: chain E residue 12 HIS Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain G residue 249 THR Chi-restraints excluded: chain H residue 5 LYS Chi-restraints excluded: chain H residue 12 HIS 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 208 VAL Chi-restraints excluded: chain I residue 249 THR Chi-restraints excluded: chain J residue 62 GLU Chi-restraints excluded: chain J residue 208 VAL Chi-restraints excluded: chain J residue 248 LEU Chi-restraints excluded: chain J residue 249 THR Chi-restraints excluded: chain K residue 249 THR Chi-restraints excluded: chain L residue 135 GLN Chi-restraints excluded: chain L residue 160 SER Chi-restraints excluded: chain L residue 208 VAL Chi-restraints excluded: chain L residue 248 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: 0.7980 chunk 332 optimal weight: 2.9990 chunk 303 optimal weight: 2.9990 chunk 323 optimal weight: 2.9990 chunk 194 optimal weight: 0.6980 chunk 140 optimal weight: 7.9990 chunk 253 optimal weight: 0.9990 chunk 99 optimal weight: 3.9990 chunk 292 optimal weight: 1.9990 chunk 305 optimal weight: 8.9990 chunk 322 optimal weight: 0.9980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 263 ASN B 288 GLN C 123 HIS F 263 ASN F 288 GLN G 263 ASN G 288 GLN J 123 HIS K 263 ASN K 288 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.2051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 29256 Z= 0.168 Angle : 0.458 5.719 39672 Z= 0.255 Chirality : 0.046 0.171 4668 Planarity : 0.003 0.026 5004 Dihedral : 10.314 77.402 4336 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.53 % Allowed : 14.85 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.14), residues: 3660 helix: 1.99 (0.14), residues: 1476 sheet: 0.30 (0.17), residues: 936 loop : -0.37 (0.16), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 162 HIS 0.004 0.001 HIS C 130 PHE 0.011 0.001 PHE D 138 TYR 0.015 0.002 TYR H 146 ARG 0.006 0.000 ARG F 163 *********************** 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 603 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 555 time to evaluate : 3.461 Fit side-chains REVERT: A 135 GLN cc_start: 0.8979 (OUTLIER) cc_final: 0.8670 (mt0) REVERT: B 294 MET cc_start: 0.8210 (pmm) cc_final: 0.7898 (pmm) REVERT: C 14 ASP cc_start: 0.8016 (t70) cc_final: 0.7764 (t0) REVERT: E 5 LYS cc_start: 0.8603 (OUTLIER) cc_final: 0.8241 (mmmt) REVERT: E 51 GLU cc_start: 0.7899 (mm-30) cc_final: 0.7618 (mm-30) REVERT: E 163 ARG cc_start: 0.7942 (mtm-85) cc_final: 0.7648 (mtt180) REVERT: H 5 LYS cc_start: 0.8600 (OUTLIER) cc_final: 0.8253 (mmmt) REVERT: H 51 GLU cc_start: 0.7898 (mm-30) cc_final: 0.7616 (mm-30) REVERT: H 163 ARG cc_start: 0.7974 (mtm-85) cc_final: 0.7705 (mtt180) REVERT: H 180 SER cc_start: 0.8740 (t) cc_final: 0.8457 (t) REVERT: J 14 ASP cc_start: 0.8012 (t70) cc_final: 0.7765 (t0) REVERT: K 294 MET cc_start: 0.8221 (pmm) cc_final: 0.7917 (pmm) REVERT: L 135 GLN cc_start: 0.8980 (OUTLIER) cc_final: 0.8669 (mt0) outliers start: 48 outliers final: 38 residues processed: 593 average time/residue: 1.4471 time to fit residues: 999.8060 Evaluate side-chains 600 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 558 time to evaluate : 3.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 GLN Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 249 THR 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 C residue 249 THR Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain E residue 5 LYS Chi-restraints excluded: chain E residue 12 HIS Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 282 LYS Chi-restraints excluded: chain G residue 249 THR Chi-restraints excluded: chain H residue 5 LYS Chi-restraints excluded: chain H residue 12 HIS Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 248 LEU Chi-restraints excluded: chain H residue 249 THR Chi-restraints excluded: chain I residue 208 VAL Chi-restraints excluded: chain I residue 249 THR Chi-restraints excluded: chain J residue 62 GLU Chi-restraints excluded: chain J residue 208 VAL Chi-restraints excluded: chain J residue 248 LEU Chi-restraints excluded: chain J residue 249 THR Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain K residue 249 THR Chi-restraints excluded: chain L residue 135 GLN Chi-restraints excluded: chain L residue 160 SER Chi-restraints excluded: chain L residue 208 VAL Chi-restraints excluded: chain L residue 248 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: 4.9990 chunk 208 optimal weight: 6.9990 chunk 162 optimal weight: 4.9990 chunk 237 optimal weight: 1.9990 chunk 358 optimal weight: 1.9990 chunk 330 optimal weight: 5.9990 chunk 285 optimal weight: 4.9990 chunk 29 optimal weight: 0.9990 chunk 220 optimal weight: 5.9990 chunk 175 optimal weight: 0.0980 overall best weight: 1.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 263 ASN B 288 GLN D 12 HIS F 263 ASN F 288 GLN G 263 ASN G 288 GLN I 12 HIS K 263 ASN K 288 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.1993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 29256 Z= 0.240 Angle : 0.503 5.980 39672 Z= 0.280 Chirality : 0.048 0.177 4668 Planarity : 0.003 0.026 5004 Dihedral : 11.099 82.709 4336 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.56 % Allowed : 14.82 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.14), residues: 3660 helix: 1.82 (0.14), residues: 1488 sheet: 0.28 (0.17), residues: 936 loop : -0.34 (0.16), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 162 HIS 0.005 0.001 HIS E 130 PHE 0.010 0.002 PHE I 138 TYR 0.019 0.002 TYR E 146 ARG 0.007 0.000 ARG F 163 ********************** 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 613 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 564 time to evaluate : 3.020 Fit side-chains REVERT: A 135 GLN cc_start: 0.8985 (OUTLIER) cc_final: 0.8678 (mt0) REVERT: B 294 MET cc_start: 0.8213 (pmm) cc_final: 0.7849 (pmm) REVERT: E 5 LYS cc_start: 0.8623 (OUTLIER) cc_final: 0.8252 (mmmt) REVERT: E 51 GLU cc_start: 0.7911 (mm-30) cc_final: 0.7643 (mm-30) REVERT: H 5 LYS cc_start: 0.8624 (OUTLIER) cc_final: 0.8265 (mmmt) REVERT: H 51 GLU cc_start: 0.7914 (mm-30) cc_final: 0.7659 (mm-30) REVERT: H 163 ARG cc_start: 0.7944 (mtm-85) cc_final: 0.7655 (mtt180) REVERT: H 180 SER cc_start: 0.8707 (t) cc_final: 0.8390 (t) REVERT: K 294 MET cc_start: 0.8223 (pmm) cc_final: 0.7860 (pmm) REVERT: L 135 GLN cc_start: 0.8986 (OUTLIER) cc_final: 0.8679 (mt0) outliers start: 49 outliers final: 35 residues processed: 605 average time/residue: 1.4335 time to fit residues: 1008.2774 Evaluate side-chains 597 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 558 time to evaluate : 2.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 GLN Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 249 THR 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 C residue 249 THR Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain E residue 5 LYS Chi-restraints excluded: chain E residue 12 HIS Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 282 LYS Chi-restraints excluded: chain G residue 249 THR Chi-restraints excluded: chain H residue 5 LYS Chi-restraints excluded: chain H residue 12 HIS Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 248 LEU Chi-restraints excluded: chain H residue 249 THR Chi-restraints excluded: chain I residue 208 VAL Chi-restraints excluded: chain I residue 249 THR Chi-restraints excluded: chain J residue 62 GLU Chi-restraints excluded: chain J residue 208 VAL Chi-restraints excluded: chain J residue 248 LEU Chi-restraints excluded: chain J residue 249 THR Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain K residue 249 THR Chi-restraints excluded: chain L residue 135 GLN Chi-restraints excluded: chain L residue 160 SER Chi-restraints excluded: chain L residue 208 VAL 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: 0.9980 chunk 304 optimal weight: 0.9980 chunk 87 optimal weight: 2.9990 chunk 263 optimal weight: 9.9990 chunk 42 optimal weight: 8.9990 chunk 79 optimal weight: 3.9990 chunk 286 optimal weight: 0.6980 chunk 119 optimal weight: 2.9990 chunk 293 optimal weight: 10.0000 chunk 36 optimal weight: 1.9990 chunk 52 optimal weight: 7.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 263 ASN B 288 GLN D 12 HIS F 263 ASN F 288 GLN G 263 ASN G 288 GLN I 12 HIS K 263 ASN K 288 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.153745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.118891 restraints weight = 24123.759| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 1.11 r_work: 0.3147 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 2.41 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3060 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3060 r_free = 0.3060 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 648 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2852 r_free = 0.2852 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2852 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8804 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 0.032 29256 Z= 0.212 Angle : 0.488 6.381 39672 Z= 0.271 Chirality : 0.047 0.174 4668 Planarity : 0.003 0.025 5004 Dihedral : 11.032 81.908 4336 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.46 % Allowed : 15.11 % Favored : 83.43 % 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: 0.99 (0.14), residues: 3660 helix: 1.87 (0.14), residues: 1476 sheet: 0.27 (0.17), residues: 936 loop : -0.43 (0.16), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP J 162 HIS 0.005 0.001 HIS E 130 PHE 0.011 0.001 PHE I 138 TYR 0.018 0.002 TYR J 146 ARG 0.007 0.000 ARG B 163 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14519.25 seconds wall clock time: 255 minutes 18.34 seconds (15318.34 seconds total)