Starting phenix.real_space_refine (version: 1.21rc1) on Sat Apr 29 01:47:08 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbh_27284/04_2023/8dbh_27284_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbh_27284/04_2023/8dbh_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_27284/04_2023/8dbh_27284.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbh_27284/04_2023/8dbh_27284.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbh_27284/04_2023/8dbh_27284_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbh_27284/04_2023/8dbh_27284_updated.pdb" } resolution = 2.2 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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-1.21rc1-4938/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: 15.34, per 1000 atoms: 0.53 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: 12.32 Conformation dependent library (CDL) restraints added in 4.3 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: 2.89 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: 9.93 Time building geometry restraints manager: 13.19 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 - 16.94: 15872 16.94 - 33.89: 1276 33.89 - 50.83: 384 50.83 - 67.78: 96 67.78 - 84.72: 48 Dihedral angle restraints: 17676 sinusoidal: 6924 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 17673 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: 1.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 9.620 Check model and map are aligned: 0.550 Set scattering table: 0.280 Process input model: 73.770 Find NCS groups from input model: 2.040 Set up NCS constraints: 0.240 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 102.020 ------------------------------------------------------------------------------- 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 : 15.178 84.723 10668 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 % 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 *********************** 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 : 3.622 Fit side-chains outliers start: 61 outliers final: 26 residues processed: 761 average time/residue: 1.2907 time to fit residues: 1163.0859 Evaluate side-chains 603 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 577 time to evaluate : 3.455 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 26 residues processed: 0 time to fit residues: 4.7830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0000 chunk 151 optimal weight: 2.9990 chunk 93 optimal weight: 0.6980 chunk 184 optimal weight: 0.9990 chunk 145 optimal weight: 0.8980 chunk 282 optimal weight: 0.5980 chunk 109 optimal weight: 0.6980 chunk 171 optimal weight: 3.9990 chunk 210 optimal weight: 0.9980 chunk 326 optimal weight: 1.9990 overall best weight: 0.4984 ------------------------------------------------------------------------------- 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: 0.8229 moved from start: 0.1371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.023 29256 Z= 0.124 Angle : 0.441 5.639 39672 Z= 0.242 Chirality : 0.046 0.159 4668 Planarity : 0.002 0.026 5004 Dihedral : 7.264 89.215 3960 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer Outliers : 3.40 % 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: 1.00 (0.14), residues: 3660 helix: 1.88 (0.14), residues: 1476 sheet: 0.07 (0.17), residues: 972 loop : -0.24 (0.16), residues: 1212 *********************** 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 721 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 614 time to evaluate : 3.693 Fit side-chains outliers start: 107 outliers final: 55 residues processed: 681 average time/residue: 1.3920 time to fit residues: 1112.0463 Evaluate side-chains 633 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 578 time to evaluate : 3.473 Switching outliers to nearest non-outliers outliers start: 55 outliers final: 37 residues processed: 18 average time/residue: 1.0566 time to fit residues: 27.8949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 181 optimal weight: 4.9990 chunk 101 optimal weight: 5.9990 chunk 272 optimal weight: 0.2980 chunk 222 optimal weight: 7.9990 chunk 90 optimal weight: 6.9990 chunk 327 optimal weight: 6.9990 chunk 353 optimal weight: 0.0170 chunk 291 optimal weight: 6.9990 chunk 324 optimal weight: 7.9990 chunk 111 optimal weight: 4.9990 chunk 262 optimal weight: 0.9980 overall best weight: 2.2622 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 GLN D 12 HIS D 288 GLN F 12 HIS F 263 ASN F 288 GLN G 12 HIS G 263 ASN G 288 GLN I 12 HIS I 288 GLN ** J 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 12 HIS K 263 ASN L 123 HIS L 288 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.032 29256 Z= 0.283 Angle : 0.530 6.208 39672 Z= 0.294 Chirality : 0.050 0.184 4668 Planarity : 0.003 0.031 5004 Dihedral : 7.124 88.489 3960 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer Outliers : 3.09 % 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: 0.98 (0.14), residues: 3660 helix: 1.77 (0.14), residues: 1488 sheet: 0.21 (0.17), residues: 936 loop : -0.27 (0.16), residues: 1236 *********************** 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 664 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 567 time to evaluate : 3.710 Fit side-chains outliers start: 97 outliers final: 55 residues processed: 639 average time/residue: 1.3760 time to fit residues: 1030.7946 Evaluate side-chains 610 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 555 time to evaluate : 3.173 Switching outliers to nearest non-outliers outliers start: 55 outliers final: 48 residues processed: 7 average time/residue: 1.5432 time to fit residues: 16.6319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 323 optimal weight: 0.4980 chunk 246 optimal weight: 3.9990 chunk 169 optimal weight: 8.9990 chunk 36 optimal weight: 3.9990 chunk 156 optimal weight: 2.9990 chunk 219 optimal weight: 1.9990 chunk 328 optimal weight: 1.9990 chunk 347 optimal weight: 5.9990 chunk 171 optimal weight: 7.9990 chunk 311 optimal weight: 7.9990 chunk 93 optimal weight: 1.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- 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 38 GLN C 123 HIS D 12 HIS D 288 GLN E 123 HIS F 263 ASN F 288 GLN G 263 ASN G 288 GLN H 123 HIS I 12 HIS I 288 GLN J 38 GLN J 123 HIS K 263 ASN K 288 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.028 29256 Z= 0.244 Angle : 0.501 5.589 39672 Z= 0.278 Chirality : 0.048 0.178 4668 Planarity : 0.003 0.028 5004 Dihedral : 6.759 89.054 3960 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer Outliers : 3.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.14), residues: 3660 helix: 1.76 (0.14), residues: 1488 sheet: 0.20 (0.17), residues: 936 loop : -0.35 (0.16), residues: 1236 *********************** 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 669 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 568 time to evaluate : 3.772 Fit side-chains outliers start: 101 outliers final: 62 residues processed: 643 average time/residue: 1.4180 time to fit residues: 1068.3788 Evaluate side-chains 615 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 553 time to evaluate : 3.513 Switching outliers to nearest non-outliers outliers start: 62 outliers final: 58 residues processed: 4 average time/residue: 1.9851 time to fit residues: 13.5985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 289 optimal weight: 10.0000 chunk 197 optimal weight: 0.3980 chunk 5 optimal weight: 6.9990 chunk 259 optimal weight: 9.9990 chunk 143 optimal weight: 5.9990 chunk 296 optimal weight: 4.9990 chunk 240 optimal weight: 6.9990 chunk 0 optimal weight: 0.9980 chunk 177 optimal weight: 0.5980 chunk 312 optimal weight: 6.9990 chunk 87 optimal weight: 3.9990 overall best weight: 2.1984 ------------------------------------------------------------------------------- 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 D 288 GLN F 263 ASN F 288 GLN G 263 ASN G 288 GLN I 12 HIS I 288 GLN K 263 ASN K 288 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.030 29256 Z= 0.276 Angle : 0.518 5.595 39672 Z= 0.288 Chirality : 0.049 0.181 4668 Planarity : 0.003 0.029 5004 Dihedral : 6.805 89.950 3960 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer Outliers : 3.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.14), residues: 3660 helix: 1.68 (0.14), residues: 1488 sheet: 0.19 (0.17), residues: 936 loop : -0.38 (0.16), residues: 1236 *********************** 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 651 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 555 time to evaluate : 3.410 Fit side-chains outliers start: 96 outliers final: 67 residues processed: 623 average time/residue: 1.4506 time to fit residues: 1067.6284 Evaluate side-chains 628 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 561 time to evaluate : 3.738 Switching outliers to nearest non-outliers outliers start: 67 outliers final: 58 residues processed: 9 average time/residue: 1.1192 time to fit residues: 17.3926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 6.9990 chunk 85 optimal weight: 0.8980 chunk 348 optimal weight: 0.9990 chunk 289 optimal weight: 8.9990 chunk 161 optimal weight: 3.9990 chunk 28 optimal weight: 0.5980 chunk 115 optimal weight: 0.6980 chunk 182 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 263 ASN D 12 HIS D 288 GLN F 263 ASN F 288 GLN G 263 ASN G 288 GLN I 12 HIS I 288 GLN K 263 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.1910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 29256 Z= 0.181 Angle : 0.463 5.714 39672 Z= 0.256 Chirality : 0.046 0.172 4668 Planarity : 0.003 0.026 5004 Dihedral : 6.348 88.463 3960 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer Outliers : 2.74 % 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: 0.97 (0.14), residues: 3660 helix: 1.83 (0.14), residues: 1488 sheet: 0.22 (0.17), residues: 936 loop : -0.38 (0.16), residues: 1236 *********************** 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 672 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 586 time to evaluate : 3.281 Fit side-chains outliers start: 86 outliers final: 66 residues processed: 650 average time/residue: 1.3962 time to fit residues: 1063.0883 Evaluate side-chains 629 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 563 time to evaluate : 3.471 Switching outliers to nearest non-outliers outliers start: 66 outliers final: 58 residues processed: 8 average time/residue: 1.3431 time to fit residues: 17.3191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 335 optimal weight: 7.9990 chunk 39 optimal weight: 1.9990 chunk 198 optimal weight: 0.3980 chunk 254 optimal weight: 0.5980 chunk 197 optimal weight: 5.9990 chunk 293 optimal weight: 9.9990 chunk 194 optimal weight: 0.0170 chunk 346 optimal weight: 0.7980 chunk 217 optimal weight: 1.9990 chunk 211 optimal weight: 0.9980 chunk 160 optimal weight: 8.9990 overall best weight: 0.5618 ------------------------------------------------------------------------------- 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: 0.8241 moved from start: 0.2058 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= 0.121 Angle : 0.423 5.933 39672 Z= 0.231 Chirality : 0.045 0.163 4668 Planarity : 0.002 0.024 5004 Dihedral : 5.549 82.750 3960 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer Outliers : 2.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.14), residues: 3660 helix: 2.05 (0.14), residues: 1476 sheet: 0.20 (0.17), residues: 972 loop : -0.28 (0.17), residues: 1212 *********************** 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 655 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 580 time to evaluate : 3.707 Fit side-chains outliers start: 75 outliers final: 58 residues processed: 640 average time/residue: 1.4465 time to fit residues: 1084.6749 Evaluate side-chains 622 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 564 time to evaluate : 3.389 Switching outliers to nearest non-outliers outliers start: 58 outliers final: 51 residues processed: 7 average time/residue: 1.5429 time to fit residues: 17.0967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 207 optimal weight: 5.9990 chunk 104 optimal weight: 0.9990 chunk 68 optimal weight: 6.9990 chunk 67 optimal weight: 3.9990 chunk 220 optimal weight: 7.9990 chunk 236 optimal weight: 8.9990 chunk 171 optimal weight: 8.9990 chunk 32 optimal weight: 0.0570 chunk 272 optimal weight: 0.0570 overall best weight: 1.1620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 12 HIS B 263 ASN B 288 GLN C 123 HIS D 12 HIS F 263 ASN F 288 GLN G 263 ASN G 288 GLN I 12 HIS J 123 HIS K 12 HIS K 263 ASN K 288 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 29256 Z= 0.172 Angle : 0.454 5.496 39672 Z= 0.250 Chirality : 0.046 0.170 4668 Planarity : 0.003 0.026 5004 Dihedral : 5.794 85.331 3960 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer Outliers : 2.39 % 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: 1.94 (0.14), residues: 1488 sheet: 0.30 (0.17), residues: 936 loop : -0.31 (0.16), residues: 1236 *********************** 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 641 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 566 time to evaluate : 3.210 Fit side-chains outliers start: 75 outliers final: 58 residues processed: 624 average time/residue: 1.4220 time to fit residues: 1037.3507 Evaluate side-chains 617 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 559 time to evaluate : 3.608 Switching outliers to nearest non-outliers outliers start: 58 outliers final: 51 residues processed: 7 average time/residue: 1.6686 time to fit residues: 17.8687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 323 optimal weight: 3.9990 chunk 194 optimal weight: 1.9990 chunk 140 optimal weight: 3.9990 chunk 253 optimal weight: 0.8980 chunk 99 optimal weight: 0.0040 chunk 292 optimal weight: 0.9990 chunk 305 optimal weight: 2.9990 chunk 322 optimal weight: 2.9990 overall best weight: 0.9396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 12 HIS B 263 ASN B 288 GLN F 263 ASN F 288 GLN G 263 ASN G 288 GLN K 12 HIS K 263 ASN K 288 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.032 29256 Z= 0.153 Angle : 0.450 8.712 39672 Z= 0.246 Chirality : 0.046 0.168 4668 Planarity : 0.003 0.027 5004 Dihedral : 5.583 85.383 3960 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer Outliers : 2.04 % 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: 2.01 (0.14), residues: 1476 sheet: 0.24 (0.17), residues: 972 loop : -0.27 (0.17), residues: 1212 *********************** 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 616 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 552 time to evaluate : 3.508 Fit side-chains outliers start: 64 outliers final: 56 residues processed: 608 average time/residue: 1.4643 time to fit residues: 1045.8106 Evaluate side-chains 616 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 560 time to evaluate : 3.618 Switching outliers to nearest non-outliers outliers start: 56 outliers final: 51 residues processed: 5 average time/residue: 1.6526 time to fit residues: 14.3758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 162 optimal weight: 5.9990 chunk 237 optimal weight: 0.7980 chunk 358 optimal weight: 5.9990 chunk 330 optimal weight: 5.9990 chunk 285 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 220 optimal weight: 5.9990 chunk 175 optimal weight: 0.8980 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 12 HIS B 263 ASN B 288 GLN C 38 GLN D 12 HIS F 263 ASN F 288 GLN G 263 ASN G 288 GLN I 12 HIS J 38 GLN K 12 HIS K 263 ASN K 288 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 29256 Z= 0.270 Angle : 0.520 8.894 39672 Z= 0.286 Chirality : 0.048 0.178 4668 Planarity : 0.003 0.026 5004 Dihedral : 6.181 87.443 3960 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer Outliers : 2.00 % 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: 1.00 (0.14), residues: 3660 helix: 1.80 (0.14), residues: 1488 sheet: 0.29 (0.17), residues: 936 loop : -0.34 (0.16), residues: 1236 ********************** 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 616 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 553 time to evaluate : 3.858 Fit side-chains outliers start: 63 outliers final: 52 residues processed: 611 average time/residue: 1.4304 time to fit residues: 1021.3415 Evaluate side-chains 606 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 554 time to evaluate : 3.452 Switching outliers to nearest non-outliers outliers start: 52 outliers final: 51 residues processed: 1 average time/residue: 0.3737 time to fit residues: 5.1846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 226 optimal weight: 0.7980 chunk 304 optimal weight: 0.9980 chunk 87 optimal weight: 0.7980 chunk 263 optimal weight: 8.9990 chunk 42 optimal weight: 8.9990 chunk 79 optimal weight: 0.0470 chunk 286 optimal weight: 0.8980 chunk 119 optimal weight: 0.7980 chunk 293 optimal weight: 7.9990 chunk 36 optimal weight: 2.9990 chunk 52 optimal weight: 6.9990 overall best weight: 0.6678 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.155353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.120725 restraints weight = 23965.405| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 1.12 r_work: 0.3195 rms_B_bonded: 1.49 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 2.44 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3060 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3060 r_free = 0.3060 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 648 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2861 r_free = 0.2861 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2861 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8775 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.032 29256 Z= 0.132 Angle : 0.443 8.825 39672 Z= 0.241 Chirality : 0.045 0.167 4668 Planarity : 0.002 0.026 5004 Dihedral : 5.463 87.756 3960 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer Outliers : 1.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.14), residues: 3660 helix: 2.03 (0.14), residues: 1476 sheet: 0.24 (0.17), residues: 972 loop : -0.28 (0.17), residues: 1212 =============================================================================== Job complete usr+sys time: 14821.88 seconds wall clock time: 262 minutes 5.94 seconds (15725.94 seconds total)