Starting phenix.real_space_refine on Thu Mar 21 00:03:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbm_27290/03_2024/8dbm_27290_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbm_27290/03_2024/8dbm_27290.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbm_27290/03_2024/8dbm_27290.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbm_27290/03_2024/8dbm_27290.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbm_27290/03_2024/8dbm_27290_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbm_27290/03_2024/8dbm_27290_updated.pdb" } resolution = 2.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.390 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 48 5.49 5 Mg 24 5.21 5 S 204 5.16 5 C 17844 2.51 5 N 4980 2.21 5 O 5616 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 51": "OE1" <-> "OE2" Residue "A GLU 69": "OE1" <-> "OE2" Residue "A ARG 84": "NH1" <-> "NH2" Residue "A ARG 104": "NH1" <-> "NH2" 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 51": "OE1" <-> "OE2" Residue "B GLU 69": "OE1" <-> "OE2" Residue "B ARG 84": "NH1" <-> "NH2" Residue "B ARG 104": "NH1" <-> "NH2" 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 51": "OE1" <-> "OE2" Residue "C GLU 69": "OE1" <-> "OE2" Residue "C ARG 84": "NH1" <-> "NH2" Residue "C ARG 104": "NH1" <-> "NH2" 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 51": "OE1" <-> "OE2" Residue "D GLU 69": "OE1" <-> "OE2" Residue "D ARG 84": "NH1" <-> "NH2" Residue "D ARG 104": "NH1" <-> "NH2" 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 51": "OE1" <-> "OE2" Residue "E GLU 69": "OE1" <-> "OE2" Residue "E ARG 84": "NH1" <-> "NH2" Residue "E ARG 104": "NH1" <-> "NH2" 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 51": "OE1" <-> "OE2" Residue "F GLU 69": "OE1" <-> "OE2" Residue "F ARG 84": "NH1" <-> "NH2" Residue "F ARG 104": "NH1" <-> "NH2" 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 51": "OE1" <-> "OE2" Residue "G GLU 69": "OE1" <-> "OE2" Residue "G ARG 84": "NH1" <-> "NH2" Residue "G ARG 104": "NH1" <-> "NH2" 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 51": "OE1" <-> "OE2" Residue "H GLU 69": "OE1" <-> "OE2" Residue "H ARG 84": "NH1" <-> "NH2" Residue "H ARG 104": "NH1" <-> "NH2" 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 51": "OE1" <-> "OE2" Residue "I GLU 69": "OE1" <-> "OE2" Residue "I ARG 84": "NH1" <-> "NH2" Residue "I ARG 104": "NH1" <-> "NH2" 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 51": "OE1" <-> "OE2" Residue "J GLU 69": "OE1" <-> "OE2" Residue "J ARG 84": "NH1" <-> "NH2" Residue "J ARG 104": "NH1" <-> "NH2" 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 51": "OE1" <-> "OE2" Residue "K GLU 69": "OE1" <-> "OE2" Residue "K ARG 84": "NH1" <-> "NH2" Residue "K ARG 104": "NH1" <-> "NH2" 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 51": "OE1" <-> "OE2" Residue "L GLU 69": "OE1" <-> "OE2" Residue "L ARG 84": "NH1" <-> "NH2" Residue "L ARG 104": "NH1" <-> "NH2" 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: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 28716 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: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 29 Unusual residues: {' MG': 2, 'PO4': 1, 'PRP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 29 Unusual residues: {' MG': 2, 'PO4': 1, 'PRP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 29 Unusual residues: {' MG': 2, 'PO4': 1, 'PRP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 29 Unusual residues: {' MG': 2, 'PO4': 1, 'PRP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 29 Unusual residues: {' MG': 2, 'PO4': 1, 'PRP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 29 Unusual residues: {' MG': 2, 'PO4': 1, 'PRP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "G" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 29 Unusual residues: {' MG': 2, 'PO4': 1, 'PRP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "H" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 29 Unusual residues: {' MG': 2, 'PO4': 1, 'PRP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "I" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 29 Unusual residues: {' MG': 2, 'PO4': 1, 'PRP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "J" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 29 Unusual residues: {' MG': 2, 'PO4': 1, 'PRP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "K" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 29 Unusual residues: {' MG': 2, 'PO4': 1, 'PRP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "L" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 29 Unusual residues: {' MG': 2, 'PO4': 1, 'PRP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 636 residue: pdb=" N HIS A 12 " occ=0.58 ... (8 atoms not shown) pdb=" NE2 HIS A 12 " occ=0.58 residue: pdb=" N ARG A 22 " occ=0.80 ... (9 atoms not shown) pdb=" NH2 ARG A 22 " occ=0.80 residue: pdb=" N GLU A 26 " occ=0.40 ... (7 atoms not shown) pdb=" OE2 GLU A 26 " occ=0.40 residue: pdb=" N LYS A 29 " occ=0.40 ... (7 atoms not shown) pdb=" NZ LYS A 29 " occ=0.40 residue: pdb=" N LYS A 33 " occ=0.01 ... (7 atoms not shown) pdb=" NZ LYS A 33 " occ=0.01 residue: pdb=" N SER A 36 " occ=0.01 ... (4 atoms not shown) pdb=" OG SER A 36 " occ=0.01 residue: pdb=" N ASN A 37 " occ=0.50 ... (6 atoms not shown) pdb=" ND2 ASN A 37 " occ=0.50 residue: pdb=" N CYS A 41 " occ=0.89 ... (4 atoms not shown) pdb=" SG CYS A 41 " occ=0.89 residue: pdb=" N GLU A 43 " occ=0.40 ... (7 atoms not shown) pdb=" OE2 GLU A 43 " occ=0.40 residue: pdb=" N GLU A 46 " occ=0.88 ... (7 atoms not shown) pdb=" OE2 GLU A 46 " occ=0.88 residue: pdb=" N SER A 58 " occ=0.10 ... (4 atoms not shown) pdb=" OG SER A 58 " occ=0.10 residue: pdb=" N GLY A 59 " occ=0.01 ... (2 atoms not shown) pdb=" O GLY A 59 " occ=0.01 ... (remaining 624 not shown) Time building chain proxies: 13.86, per 1000 atoms: 0.48 Number of scatterers: 28716 At special positions: 0 Unit cell: (128.018, 138.598, 140.714, 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 48 15.00 Mg 24 11.99 O 5616 8.00 N 4980 7.00 C 17844 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: 11.39 Conformation dependent library (CDL) restraints added in 5.1 seconds 7320 Ramachandran restraints generated. 3660 Oldfield, 0 Emsley, 3660 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7008 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 132 helices and 36 sheets defined 37.2% alpha, 18.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.37 Creating SS restraints... Processing helix chain 'A' and resid 13 through 22 Processing helix chain 'A' and resid 63 through 79 Processing helix chain 'A' and resid 108 through 119 Processing helix chain 'A' and resid 132 through 137 Processing helix chain 'A' and resid 148 through 158 Processing helix chain 'A' and resid 172 through 185 removed outlier: 5.017A pdb=" N LYS A 176 " --> pdb=" O GLY A 173 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ARG A 177 " --> pdb=" O GLY A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 238 Processing helix chain 'A' and resid 255 through 263 removed outlier: 4.420A pdb=" N ILE A 258 " --> pdb=" O GLY A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 283 removed outlier: 3.666A 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 314 Processing helix chain 'B' and resid 13 through 22 Processing helix chain 'B' and resid 63 through 79 Processing helix chain 'B' and resid 108 through 119 Processing helix chain 'B' and resid 132 through 137 Processing helix chain 'B' and resid 148 through 158 Processing helix chain 'B' and resid 172 through 185 removed outlier: 5.018A pdb=" N LYS B 176 " --> pdb=" O GLY B 173 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ARG B 177 " --> pdb=" O GLY B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 238 Processing helix chain 'B' and resid 255 through 263 removed outlier: 4.420A pdb=" N ILE B 258 " --> pdb=" O GLY B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 283 removed outlier: 3.667A 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 314 Processing helix chain 'C' and resid 13 through 22 Processing helix chain 'C' and resid 63 through 79 Processing helix chain 'C' and resid 108 through 119 Processing helix chain 'C' and resid 132 through 137 Processing helix chain 'C' and resid 148 through 158 Processing helix chain 'C' and resid 172 through 185 removed outlier: 5.017A pdb=" N LYS C 176 " --> pdb=" O GLY C 173 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ARG C 177 " --> pdb=" O GLY C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 238 Processing helix chain 'C' and resid 255 through 263 removed outlier: 4.419A pdb=" N ILE C 258 " --> pdb=" O GLY C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 283 removed outlier: 3.666A 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 314 Processing helix chain 'D' and resid 13 through 22 Processing helix chain 'D' and resid 63 through 79 Processing helix chain 'D' and resid 108 through 119 Processing helix chain 'D' and resid 132 through 137 Processing helix chain 'D' and resid 148 through 158 Processing helix chain 'D' and resid 172 through 185 removed outlier: 5.017A pdb=" N LYS D 176 " --> pdb=" O GLY D 173 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ARG D 177 " --> pdb=" O GLY D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 238 Processing helix chain 'D' and resid 255 through 263 removed outlier: 4.421A pdb=" N ILE D 258 " --> pdb=" O GLY D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 278 through 283 removed outlier: 3.666A 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 314 Processing helix chain 'E' and resid 13 through 22 Processing helix chain 'E' and resid 63 through 79 Processing helix chain 'E' and resid 108 through 119 Processing helix chain 'E' and resid 132 through 137 Processing helix chain 'E' and resid 148 through 158 Processing helix chain 'E' and resid 172 through 185 removed outlier: 5.016A pdb=" N LYS E 176 " --> pdb=" O GLY E 173 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ARG E 177 " --> pdb=" O GLY E 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 227 through 238 Processing helix chain 'E' and resid 255 through 263 removed outlier: 4.421A pdb=" N ILE E 258 " --> pdb=" O GLY E 255 " (cutoff:3.500A) Processing helix chain 'E' and resid 278 through 283 removed outlier: 3.666A 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 314 Processing helix chain 'F' and resid 13 through 22 Processing helix chain 'F' and resid 63 through 79 Processing helix chain 'F' and resid 108 through 119 Processing helix chain 'F' and resid 132 through 137 Processing helix chain 'F' and resid 148 through 158 Processing helix chain 'F' and resid 172 through 185 removed outlier: 5.017A pdb=" N LYS F 176 " --> pdb=" O GLY F 173 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ARG F 177 " --> pdb=" O GLY F 174 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 238 Processing helix chain 'F' and resid 255 through 263 removed outlier: 4.421A pdb=" N ILE F 258 " --> pdb=" O GLY F 255 " (cutoff:3.500A) 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 314 Processing helix chain 'G' and resid 13 through 22 Processing helix chain 'G' and resid 63 through 79 Processing helix chain 'G' and resid 108 through 119 Processing helix chain 'G' and resid 132 through 137 Processing helix chain 'G' and resid 148 through 158 Processing helix chain 'G' and resid 172 through 185 removed outlier: 5.016A pdb=" N LYS G 176 " --> pdb=" O GLY G 173 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ARG G 177 " --> pdb=" O GLY G 174 " (cutoff:3.500A) Processing helix chain 'G' and resid 227 through 238 Processing helix chain 'G' and resid 255 through 263 removed outlier: 4.420A pdb=" N ILE G 258 " --> pdb=" O GLY G 255 " (cutoff:3.500A) Processing helix chain 'G' and resid 278 through 283 removed outlier: 3.667A 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 314 Processing helix chain 'H' and resid 13 through 22 Processing helix chain 'H' and resid 63 through 79 Processing helix chain 'H' and resid 108 through 119 Processing helix chain 'H' and resid 132 through 137 Processing helix chain 'H' and resid 148 through 158 Processing helix chain 'H' and resid 172 through 185 removed outlier: 5.018A pdb=" N LYS H 176 " --> pdb=" O GLY H 173 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ARG H 177 " --> pdb=" O GLY H 174 " (cutoff:3.500A) Processing helix chain 'H' and resid 227 through 238 Processing helix chain 'H' and resid 255 through 263 removed outlier: 4.420A pdb=" N ILE H 258 " --> pdb=" O GLY H 255 " (cutoff:3.500A) 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 314 Processing helix chain 'I' and resid 13 through 22 Processing helix chain 'I' and resid 63 through 79 Processing helix chain 'I' and resid 108 through 119 Processing helix chain 'I' and resid 132 through 137 Processing helix chain 'I' and resid 148 through 158 Processing helix chain 'I' and resid 172 through 185 removed outlier: 5.017A pdb=" N LYS I 176 " --> pdb=" O GLY I 173 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ARG I 177 " --> pdb=" O GLY I 174 " (cutoff:3.500A) Processing helix chain 'I' and resid 227 through 238 Processing helix chain 'I' and resid 255 through 263 removed outlier: 4.419A pdb=" N ILE I 258 " --> pdb=" O GLY I 255 " (cutoff:3.500A) Processing helix chain 'I' and resid 278 through 283 removed outlier: 3.666A 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 314 Processing helix chain 'J' and resid 13 through 22 Processing helix chain 'J' and resid 63 through 79 Processing helix chain 'J' and resid 108 through 119 Processing helix chain 'J' and resid 132 through 137 Processing helix chain 'J' and resid 148 through 158 Processing helix chain 'J' and resid 172 through 185 removed outlier: 5.017A pdb=" N LYS J 176 " --> pdb=" O GLY J 173 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ARG J 177 " --> pdb=" O GLY J 174 " (cutoff:3.500A) Processing helix chain 'J' and resid 227 through 238 Processing helix chain 'J' and resid 255 through 263 removed outlier: 4.420A pdb=" N ILE J 258 " --> pdb=" O GLY J 255 " (cutoff:3.500A) 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 314 Processing helix chain 'K' and resid 13 through 22 Processing helix chain 'K' and resid 63 through 79 Processing helix chain 'K' and resid 108 through 119 Processing helix chain 'K' and resid 132 through 137 Processing helix chain 'K' and resid 148 through 158 Processing helix chain 'K' and resid 172 through 185 removed outlier: 5.016A pdb=" N LYS K 176 " --> pdb=" O GLY K 173 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ARG K 177 " --> pdb=" O GLY K 174 " (cutoff:3.500A) Processing helix chain 'K' and resid 227 through 238 Processing helix chain 'K' and resid 255 through 263 removed outlier: 4.421A pdb=" N ILE K 258 " --> pdb=" O GLY K 255 " (cutoff:3.500A) Processing helix chain 'K' and resid 278 through 283 removed outlier: 3.666A 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 314 Processing helix chain 'L' and resid 13 through 22 Processing helix chain 'L' and resid 63 through 79 Processing helix chain 'L' and resid 108 through 119 Processing helix chain 'L' and resid 132 through 137 Processing helix chain 'L' and resid 148 through 158 Processing helix chain 'L' and resid 172 through 185 removed outlier: 5.016A pdb=" N LYS L 176 " --> pdb=" O GLY L 173 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ARG L 177 " --> pdb=" O GLY L 174 " (cutoff:3.500A) Processing helix chain 'L' and resid 227 through 238 Processing helix chain 'L' and resid 255 through 263 removed outlier: 4.421A pdb=" N ILE L 258 " --> pdb=" O GLY L 255 " (cutoff:3.500A) Processing helix chain 'L' and resid 278 through 283 removed outlier: 3.666A 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 314 Processing sheet with id= A, first strand: chain 'A' and resid 4 through 8 removed outlier: 6.287A pdb=" N ASP A 52 " --> pdb=" O LYS A 5 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N PHE A 7 " --> pdb=" O ASP A 52 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N TYR A 54 " --> pdb=" O PHE A 7 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N ARG A 84 " --> pdb=" O VAL A 53 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N ILE A 55 " --> pdb=" O ARG A 84 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N THR A 86 " --> pdb=" O ILE A 55 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N HIS A 123 " --> pdb=" O ALA A 87 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N ILE A 89 " --> pdb=" O HIS A 123 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ILE A 125 " --> pdb=" O ILE A 89 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N THR A 126 " --> pdb=" O PRO A 141 " (cutoff:3.500A) removed outlier: 6.037A 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: 6.306A pdb=" N VAL A 269 " --> pdb=" O GLN A 288 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N ILE A 290 " --> pdb=" O VAL A 269 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL A 271 " --> pdb=" O ILE A 290 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ALA A 268 " --> pdb=" O VAL A 244 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ALA A 216 " --> pdb=" O TYR A 245 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N ILE A 247 " --> pdb=" O ALA A 216 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N LEU A 218 " --> pdb=" O ILE A 247 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N THR A 166 " --> pdb=" O ILE A 217 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N VAL A 219 " --> pdb=" O THR A 166 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N VAL A 168 " --> pdb=" O VAL A 219 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N ASP A 188 " --> pdb=" O ILE A 167 " (cutoff:3.500A) removed outlier: 8.741A pdb=" N SER A 169 " --> pdb=" O ASP A 188 " (cutoff:3.500A) removed outlier: 7.659A 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: 6.286A pdb=" N ASP B 52 " --> pdb=" O LYS B 5 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N PHE B 7 " --> pdb=" O ASP B 52 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N TYR B 54 " --> pdb=" O PHE B 7 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N ARG B 84 " --> pdb=" O VAL B 53 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N ILE B 55 " --> pdb=" O ARG B 84 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N THR B 86 " --> pdb=" O ILE B 55 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N HIS B 123 " --> pdb=" O ALA B 87 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N ILE B 89 " --> pdb=" O HIS B 123 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ILE B 125 " --> pdb=" O ILE B 89 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N THR B 126 " --> pdb=" O PRO B 141 " (cutoff:3.500A) removed outlier: 6.037A 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: 6.305A pdb=" N VAL B 269 " --> pdb=" O GLN B 288 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N ILE B 290 " --> pdb=" O VAL B 269 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N VAL B 271 " --> pdb=" O ILE B 290 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ALA B 268 " --> pdb=" O VAL B 244 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ALA B 216 " --> pdb=" O TYR B 245 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N ILE B 247 " --> pdb=" O ALA B 216 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N LEU B 218 " --> pdb=" O ILE B 247 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N THR B 166 " --> pdb=" O ILE B 217 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N VAL B 219 " --> pdb=" O THR B 166 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N VAL B 168 " --> pdb=" O VAL B 219 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N ASP B 188 " --> pdb=" O ILE B 167 " (cutoff:3.500A) removed outlier: 8.742A pdb=" N SER B 169 " --> pdb=" O ASP B 188 " (cutoff:3.500A) removed outlier: 7.658A 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: 6.287A pdb=" N ASP C 52 " --> pdb=" O LYS C 5 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N PHE C 7 " --> pdb=" O ASP C 52 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N TYR C 54 " --> pdb=" O PHE C 7 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N ARG C 84 " --> pdb=" O VAL C 53 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N ILE C 55 " --> pdb=" O ARG C 84 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N THR C 86 " --> pdb=" O ILE C 55 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N HIS C 123 " --> pdb=" O ALA C 87 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N ILE C 89 " --> pdb=" O HIS C 123 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ILE C 125 " --> pdb=" O ILE C 89 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N THR C 126 " --> pdb=" O PRO C 141 " (cutoff:3.500A) removed outlier: 6.038A 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: 6.306A pdb=" N VAL C 269 " --> pdb=" O GLN C 288 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N ILE C 290 " --> pdb=" O VAL C 269 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL C 271 " --> pdb=" O ILE C 290 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ALA C 268 " --> pdb=" O VAL C 244 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ALA C 216 " --> pdb=" O TYR C 245 " (cutoff:3.500A) removed outlier: 7.850A 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: 6.541A pdb=" N THR C 166 " --> pdb=" O ILE C 217 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N VAL C 219 " --> pdb=" O THR C 166 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N VAL C 168 " --> pdb=" O VAL C 219 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N ASP C 188 " --> pdb=" O ILE C 167 " (cutoff:3.500A) removed outlier: 8.741A pdb=" N SER C 169 " --> pdb=" O ASP C 188 " (cutoff:3.500A) removed outlier: 7.659A 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: 6.288A pdb=" N ASP D 52 " --> pdb=" O LYS D 5 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N PHE D 7 " --> pdb=" O ASP D 52 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N TYR D 54 " --> pdb=" O PHE D 7 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ARG D 84 " --> pdb=" O VAL D 53 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N ILE D 55 " --> pdb=" O ARG D 84 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N THR D 86 " --> pdb=" O ILE D 55 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N HIS D 123 " --> pdb=" O ALA D 87 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N ILE D 89 " --> pdb=" O HIS D 123 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ILE D 125 " --> pdb=" O ILE D 89 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N THR D 126 " --> pdb=" O PRO D 141 " (cutoff:3.500A) removed outlier: 6.038A 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: 6.306A pdb=" N VAL D 269 " --> pdb=" O GLN D 288 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N ILE D 290 " --> pdb=" O VAL D 269 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N VAL D 271 " --> pdb=" O ILE D 290 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ALA D 268 " --> pdb=" O VAL D 244 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ALA D 216 " --> pdb=" O TYR D 245 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N ILE D 247 " --> pdb=" O ALA D 216 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N LEU D 218 " --> pdb=" O ILE D 247 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N THR D 166 " --> pdb=" O ILE D 217 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N VAL D 219 " --> pdb=" O THR D 166 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N VAL D 168 " --> pdb=" O VAL D 219 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N ASP D 188 " --> pdb=" O ILE D 167 " (cutoff:3.500A) removed outlier: 8.742A pdb=" N SER D 169 " --> pdb=" O ASP D 188 " (cutoff:3.500A) removed outlier: 7.657A 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: 6.287A pdb=" N ASP E 52 " --> pdb=" O LYS E 5 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N PHE E 7 " --> pdb=" O ASP E 52 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N TYR E 54 " --> pdb=" O PHE E 7 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N ARG E 84 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N ILE E 55 " --> pdb=" O ARG E 84 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N THR E 86 " --> pdb=" O ILE E 55 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N HIS E 123 " --> pdb=" O ALA E 87 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N ILE E 89 " --> pdb=" O HIS E 123 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ILE E 125 " --> pdb=" O ILE E 89 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N THR E 126 " --> pdb=" O PRO E 141 " (cutoff:3.500A) removed outlier: 6.037A 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: 6.306A pdb=" N VAL E 269 " --> pdb=" O GLN E 288 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N ILE E 290 " --> pdb=" O VAL E 269 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N VAL E 271 " --> pdb=" O ILE E 290 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ALA E 268 " --> pdb=" O VAL E 244 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ALA E 216 " --> pdb=" O TYR E 245 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N ILE E 247 " --> pdb=" O ALA E 216 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N LEU E 218 " --> pdb=" O ILE E 247 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N THR E 166 " --> pdb=" O ILE E 217 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N VAL E 219 " --> pdb=" O THR E 166 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N VAL E 168 " --> pdb=" O VAL E 219 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N ASP E 188 " --> pdb=" O ILE E 167 " (cutoff:3.500A) removed outlier: 8.741A pdb=" N SER E 169 " --> pdb=" O ASP E 188 " (cutoff:3.500A) removed outlier: 7.659A 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: 6.287A pdb=" N ASP F 52 " --> pdb=" O LYS F 5 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N PHE F 7 " --> pdb=" O ASP F 52 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N TYR F 54 " --> pdb=" O PHE F 7 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ARG F 84 " --> pdb=" O VAL F 53 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N ILE F 55 " --> pdb=" O ARG F 84 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N THR F 86 " --> pdb=" O ILE F 55 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N HIS F 123 " --> pdb=" O ALA F 87 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N ILE F 89 " --> pdb=" O HIS F 123 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ILE F 125 " --> pdb=" O ILE F 89 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N THR F 126 " --> pdb=" O PRO F 141 " (cutoff:3.500A) removed outlier: 6.038A 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: 6.306A pdb=" N VAL F 269 " --> pdb=" O GLN F 288 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N ILE F 290 " --> pdb=" O VAL F 269 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N VAL F 271 " --> pdb=" O ILE F 290 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ALA F 268 " --> pdb=" O VAL F 244 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ALA F 216 " --> pdb=" O TYR F 245 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N ILE F 247 " --> pdb=" O ALA F 216 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N LEU F 218 " --> pdb=" O ILE F 247 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N THR F 166 " --> pdb=" O ILE F 217 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N VAL F 219 " --> pdb=" O THR F 166 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N VAL F 168 " --> pdb=" O VAL F 219 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N ASP F 188 " --> pdb=" O ILE F 167 " (cutoff:3.500A) removed outlier: 8.741A pdb=" N SER F 169 " --> pdb=" O ASP F 188 " (cutoff:3.500A) removed outlier: 7.658A 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: 6.287A pdb=" N ASP G 52 " --> pdb=" O LYS G 5 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N PHE G 7 " --> pdb=" O ASP G 52 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N TYR G 54 " --> pdb=" O PHE G 7 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N ARG G 84 " --> pdb=" O VAL G 53 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N ILE G 55 " --> pdb=" O ARG G 84 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N THR G 86 " --> pdb=" O ILE G 55 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N HIS G 123 " --> pdb=" O ALA G 87 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N ILE G 89 " --> pdb=" O HIS G 123 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ILE G 125 " --> pdb=" O ILE G 89 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N THR G 126 " --> pdb=" O PRO G 141 " (cutoff:3.500A) removed outlier: 6.038A 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: 6.306A pdb=" N VAL G 269 " --> pdb=" O GLN G 288 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N ILE G 290 " --> pdb=" O VAL G 269 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL G 271 " --> pdb=" O ILE G 290 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ALA G 268 " --> pdb=" O VAL G 244 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ALA G 216 " --> pdb=" O TYR G 245 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N ILE G 247 " --> pdb=" O ALA G 216 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N LEU G 218 " --> pdb=" O ILE G 247 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N THR G 166 " --> pdb=" O ILE G 217 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N VAL G 219 " --> pdb=" O THR G 166 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N VAL G 168 " --> pdb=" O VAL G 219 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N ASP G 188 " --> pdb=" O ILE G 167 " (cutoff:3.500A) removed outlier: 8.741A pdb=" N SER G 169 " --> pdb=" O ASP G 188 " (cutoff:3.500A) removed outlier: 7.659A 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: 6.287A pdb=" N ASP H 52 " --> pdb=" O LYS H 5 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N PHE H 7 " --> pdb=" O ASP H 52 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N TYR H 54 " --> pdb=" O PHE H 7 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N ARG H 84 " --> pdb=" O VAL H 53 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N ILE H 55 " --> pdb=" O ARG H 84 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N THR H 86 " --> pdb=" O ILE H 55 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N HIS H 123 " --> pdb=" O ALA H 87 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N ILE H 89 " --> pdb=" O HIS H 123 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ILE H 125 " --> pdb=" O ILE H 89 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N THR H 126 " --> pdb=" O PRO H 141 " (cutoff:3.500A) removed outlier: 6.038A 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: 6.306A pdb=" N VAL H 269 " --> pdb=" O GLN H 288 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N ILE H 290 " --> pdb=" O VAL H 269 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N VAL H 271 " --> pdb=" O ILE H 290 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ALA H 268 " --> pdb=" O VAL H 244 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ALA H 216 " --> pdb=" O TYR H 245 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N ILE H 247 " --> pdb=" O ALA H 216 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N LEU H 218 " --> pdb=" O ILE H 247 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N THR H 166 " --> pdb=" O ILE H 217 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N VAL H 219 " --> pdb=" O THR H 166 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N VAL H 168 " --> pdb=" O VAL H 219 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N ASP H 188 " --> pdb=" O ILE H 167 " (cutoff:3.500A) removed outlier: 8.742A pdb=" N SER H 169 " --> pdb=" O ASP H 188 " (cutoff:3.500A) removed outlier: 7.659A 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: 6.286A pdb=" N ASP I 52 " --> pdb=" O LYS I 5 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N PHE I 7 " --> pdb=" O ASP I 52 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N TYR I 54 " --> pdb=" O PHE I 7 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N ARG I 84 " --> pdb=" O VAL I 53 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N ILE I 55 " --> pdb=" O ARG I 84 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N THR I 86 " --> pdb=" O ILE I 55 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N HIS I 123 " --> pdb=" O ALA I 87 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N ILE I 89 " --> pdb=" O HIS I 123 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ILE I 125 " --> pdb=" O ILE I 89 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N THR I 126 " --> pdb=" O PRO I 141 " (cutoff:3.500A) removed outlier: 6.037A 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: 6.306A pdb=" N VAL I 269 " --> pdb=" O GLN I 288 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N ILE I 290 " --> pdb=" O VAL I 269 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL I 271 " --> pdb=" O ILE I 290 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ALA I 268 " --> pdb=" O VAL I 244 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ALA I 216 " --> pdb=" O TYR I 245 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N ILE I 247 " --> pdb=" O ALA I 216 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N LEU I 218 " --> pdb=" O ILE I 247 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N THR I 166 " --> pdb=" O ILE I 217 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N VAL I 219 " --> pdb=" O THR I 166 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N VAL I 168 " --> pdb=" O VAL I 219 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N ASP I 188 " --> pdb=" O ILE I 167 " (cutoff:3.500A) removed outlier: 8.741A pdb=" N SER I 169 " --> pdb=" O ASP I 188 " (cutoff:3.500A) removed outlier: 7.658A 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: 6.286A pdb=" N ASP J 52 " --> pdb=" O LYS J 5 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N PHE J 7 " --> pdb=" O ASP J 52 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N TYR J 54 " --> pdb=" O PHE J 7 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N ARG J 84 " --> pdb=" O VAL J 53 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N ILE J 55 " --> pdb=" O ARG J 84 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N THR J 86 " --> pdb=" O ILE J 55 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N HIS J 123 " --> pdb=" O ALA J 87 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N ILE J 89 " --> pdb=" O HIS J 123 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ILE J 125 " --> pdb=" O ILE J 89 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N THR J 126 " --> pdb=" O PRO J 141 " (cutoff:3.500A) removed outlier: 6.037A 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: 6.306A pdb=" N VAL J 269 " --> pdb=" O GLN J 288 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N ILE J 290 " --> pdb=" O VAL J 269 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N VAL J 271 " --> pdb=" O ILE J 290 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ALA J 268 " --> pdb=" O VAL J 244 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ALA J 216 " --> pdb=" O TYR J 245 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N ILE J 247 " --> pdb=" O ALA J 216 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N LEU J 218 " --> pdb=" O ILE J 247 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N THR J 166 " --> pdb=" O ILE J 217 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N VAL J 219 " --> pdb=" O THR J 166 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N VAL J 168 " --> pdb=" O VAL J 219 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N ASP J 188 " --> pdb=" O ILE J 167 " (cutoff:3.500A) removed outlier: 8.741A pdb=" N SER J 169 " --> pdb=" O ASP J 188 " (cutoff:3.500A) removed outlier: 7.658A 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: 6.287A pdb=" N ASP K 52 " --> pdb=" O LYS K 5 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N PHE K 7 " --> pdb=" O ASP K 52 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N TYR K 54 " --> pdb=" O PHE K 7 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ARG K 84 " --> pdb=" O VAL K 53 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N ILE K 55 " --> pdb=" O ARG K 84 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N THR K 86 " --> pdb=" O ILE K 55 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N HIS K 123 " --> pdb=" O ALA K 87 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N ILE K 89 " --> pdb=" O HIS K 123 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ILE K 125 " --> pdb=" O ILE K 89 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N THR K 126 " --> pdb=" O PRO K 141 " (cutoff:3.500A) removed outlier: 6.037A 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: 6.305A pdb=" N VAL K 269 " --> pdb=" O GLN K 288 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N ILE K 290 " --> pdb=" O VAL K 269 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N VAL K 271 " --> pdb=" O ILE K 290 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ALA K 268 " --> pdb=" O VAL K 244 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ALA K 216 " --> pdb=" O TYR K 245 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N ILE K 247 " --> pdb=" O ALA K 216 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N LEU K 218 " --> pdb=" O ILE K 247 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N THR K 166 " --> pdb=" O ILE K 217 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N VAL K 219 " --> pdb=" O THR K 166 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N VAL K 168 " --> pdb=" O VAL K 219 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N ASP K 188 " --> pdb=" O ILE K 167 " (cutoff:3.500A) removed outlier: 8.741A pdb=" N SER K 169 " --> pdb=" O ASP K 188 " (cutoff:3.500A) removed outlier: 7.658A 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: 6.287A pdb=" N ASP L 52 " --> pdb=" O LYS L 5 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N PHE L 7 " --> pdb=" O ASP L 52 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N TYR L 54 " --> pdb=" O PHE L 7 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N ARG L 84 " --> pdb=" O VAL L 53 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N ILE L 55 " --> pdb=" O ARG L 84 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N THR L 86 " --> pdb=" O ILE L 55 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N HIS L 123 " --> pdb=" O ALA L 87 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N ILE L 89 " --> pdb=" O HIS L 123 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ILE L 125 " --> pdb=" O ILE L 89 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N THR L 126 " --> pdb=" O PRO L 141 " (cutoff:3.500A) removed outlier: 6.038A 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: 6.306A pdb=" N VAL L 269 " --> pdb=" O GLN L 288 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N ILE L 290 " --> pdb=" O VAL L 269 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL L 271 " --> pdb=" O ILE L 290 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ALA L 268 " --> pdb=" O VAL L 244 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ALA L 216 " --> pdb=" O TYR L 245 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N ILE L 247 " --> pdb=" O ALA L 216 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N LEU L 218 " --> pdb=" O ILE L 247 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N THR L 166 " --> pdb=" O ILE L 217 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N VAL L 219 " --> pdb=" O THR L 166 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N VAL L 168 " --> pdb=" O VAL L 219 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N ASP L 188 " --> pdb=" O ILE L 167 " (cutoff:3.500A) removed outlier: 8.741A pdb=" N SER L 169 " --> pdb=" O ASP L 188 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N ALA L 190 " --> pdb=" O SER L 169 " (cutoff:3.500A) 996 hydrogen bonds defined for protein. 2304 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: 9.96 Time building geometry restraints manager: 12.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9550 1.34 - 1.46: 4209 1.46 - 1.57: 14969 1.57 - 1.69: 48 1.69 - 1.81: 300 Bond restraints: 29076 Sorted by residual: bond pdb=" C1 PRP B 401 " pdb=" O4 PRP B 401 " ideal model delta sigma weight residual 1.656 1.420 0.236 2.00e-02 2.50e+03 1.39e+02 bond pdb=" C1 PRP C 401 " pdb=" O4 PRP C 401 " ideal model delta sigma weight residual 1.656 1.420 0.236 2.00e-02 2.50e+03 1.39e+02 bond pdb=" C1 PRP H 401 " pdb=" O4 PRP H 401 " ideal model delta sigma weight residual 1.656 1.420 0.236 2.00e-02 2.50e+03 1.39e+02 bond pdb=" C1 PRP G 401 " pdb=" O4 PRP G 401 " ideal model delta sigma weight residual 1.656 1.421 0.235 2.00e-02 2.50e+03 1.39e+02 bond pdb=" C1 PRP I 401 " pdb=" O4 PRP I 401 " ideal model delta sigma weight residual 1.656 1.421 0.235 2.00e-02 2.50e+03 1.38e+02 ... (remaining 29071 not shown) Histogram of bond angle deviations from ideal: 99.21 - 106.19: 754 106.19 - 113.16: 16789 113.16 - 120.13: 9865 120.13 - 127.11: 11736 127.11 - 134.08: 252 Bond angle restraints: 39396 Sorted by residual: angle pdb=" C THR C 272 " pdb=" CA THR C 272 " pdb=" CB THR C 272 " ideal model delta sigma weight residual 109.51 117.40 -7.89 1.71e+00 3.42e-01 2.13e+01 angle pdb=" C THR H 272 " pdb=" CA THR H 272 " pdb=" CB THR H 272 " ideal model delta sigma weight residual 109.51 117.39 -7.88 1.71e+00 3.42e-01 2.12e+01 angle pdb=" C THR G 272 " pdb=" CA THR G 272 " pdb=" CB THR G 272 " ideal model delta sigma weight residual 109.51 117.38 -7.87 1.71e+00 3.42e-01 2.12e+01 angle pdb=" C THR I 272 " pdb=" CA THR I 272 " pdb=" CB THR I 272 " ideal model delta sigma weight residual 109.51 117.37 -7.86 1.71e+00 3.42e-01 2.12e+01 angle pdb=" C THR F 272 " pdb=" CA THR F 272 " pdb=" CB THR F 272 " ideal model delta sigma weight residual 109.51 117.37 -7.86 1.71e+00 3.42e-01 2.11e+01 ... (remaining 39391 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 16031 17.71 - 35.42: 1315 35.42 - 53.12: 414 53.12 - 70.83: 120 70.83 - 88.54: 72 Dihedral angle restraints: 17952 sinusoidal: 7200 harmonic: 10752 Sorted by residual: dihedral pdb=" CA GLU K 62 " pdb=" C GLU K 62 " pdb=" N ILE K 63 " pdb=" CA ILE K 63 " ideal model delta harmonic sigma weight residual -180.00 -160.91 -19.09 0 5.00e+00 4.00e-02 1.46e+01 dihedral pdb=" CA GLU C 62 " pdb=" C GLU C 62 " pdb=" N ILE C 63 " pdb=" CA ILE C 63 " ideal model delta harmonic sigma weight residual -180.00 -160.91 -19.09 0 5.00e+00 4.00e-02 1.46e+01 dihedral pdb=" CA GLU E 62 " pdb=" C GLU E 62 " pdb=" N ILE E 63 " pdb=" CA ILE E 63 " ideal model delta harmonic sigma weight residual -180.00 -160.91 -19.09 0 5.00e+00 4.00e-02 1.46e+01 ... (remaining 17949 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 2677 0.041 - 0.083: 1314 0.083 - 0.124: 526 0.124 - 0.165: 91 0.165 - 0.206: 60 Chirality restraints: 4668 Sorted by residual: chirality pdb=" CA THR J 272 " pdb=" N THR J 272 " pdb=" C THR J 272 " pdb=" CB THR J 272 " both_signs ideal model delta sigma weight residual False 2.53 2.32 0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CA THR D 272 " pdb=" N THR D 272 " pdb=" C THR D 272 " pdb=" CB THR D 272 " both_signs ideal model delta sigma weight residual False 2.53 2.32 0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CA THR L 272 " pdb=" N THR L 272 " pdb=" C THR L 272 " pdb=" CB THR L 272 " both_signs ideal model delta sigma weight residual False 2.53 2.32 0.21 2.00e-01 2.50e+01 1.06e+00 ... (remaining 4665 not shown) Planarity restraints: 4992 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP I 221 " 0.012 2.00e-02 2.50e+03 2.46e-02 6.05e+00 pdb=" CG ASP I 221 " -0.043 2.00e-02 2.50e+03 pdb=" OD1 ASP I 221 " 0.015 2.00e-02 2.50e+03 pdb=" OD2 ASP I 221 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP E 221 " 0.012 2.00e-02 2.50e+03 2.46e-02 6.03e+00 pdb=" CG ASP E 221 " -0.042 2.00e-02 2.50e+03 pdb=" OD1 ASP E 221 " 0.015 2.00e-02 2.50e+03 pdb=" OD2 ASP E 221 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP K 221 " 0.012 2.00e-02 2.50e+03 2.46e-02 6.03e+00 pdb=" CG ASP K 221 " -0.042 2.00e-02 2.50e+03 pdb=" OD1 ASP K 221 " 0.015 2.00e-02 2.50e+03 pdb=" OD2 ASP K 221 " 0.015 2.00e-02 2.50e+03 ... (remaining 4989 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.49: 216 2.49 - 3.09: 20987 3.09 - 3.69: 45082 3.69 - 4.30: 69196 4.30 - 4.90: 112117 Nonbonded interactions: 247598 Sorted by model distance: nonbonded pdb=" O3B PRP K 401 " pdb="MG MG K 403 " model vdw 1.884 2.170 nonbonded pdb=" O3B PRP E 401 " pdb="MG MG E 403 " model vdw 1.885 2.170 nonbonded pdb=" O3B PRP C 401 " pdb="MG MG C 403 " model vdw 1.885 2.170 nonbonded pdb=" O1B PRP F 401 " pdb="MG MG F 403 " model vdw 1.885 2.170 nonbonded pdb=" O3B PRP I 401 " pdb="MG MG I 403 " model vdw 1.886 2.170 ... (remaining 247593 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: 0.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 5.250 Check model and map are aligned: 0.430 Set scattering table: 0.260 Process input model: 73.970 Find NCS groups from input model: 2.170 Set up NCS constraints: 0.260 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 95.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 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 : 0.011 0.236 29076 Z= 0.722 Angle : 0.823 9.813 39396 Z= 0.455 Chirality : 0.057 0.206 4668 Planarity : 0.003 0.025 4992 Dihedral : 16.538 88.539 10944 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.67 % Allowed : 15.27 % Favored : 82.06 % 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: 0.14 (0.15), residues: 3660 helix: 1.25 (0.14), residues: 1476 sheet: -0.62 (0.17), residues: 1044 loop : -0.54 (0.19), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP E 162 HIS 0.003 0.001 HIS D 193 PHE 0.017 0.002 PHE K 138 TYR 0.027 0.004 TYR C 245 ARG 0.004 0.001 ARG I 177 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7320 Ramachandran restraints generated. 3660 Oldfield, 0 Emsley, 3660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7320 Ramachandran restraints generated. 3660 Oldfield, 0 Emsley, 3660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 915 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 831 time to evaluate : 3.326 Fit side-chains REVERT: A 5 LYS cc_start: 0.8587 (OUTLIER) cc_final: 0.8270 (mmmt) REVERT: A 103 SER cc_start: 0.7538 (m) cc_final: 0.7283 (p) REVERT: A 128 ASP cc_start: 0.8352 (m-30) cc_final: 0.8103 (m-30) REVERT: A 180 SER cc_start: 0.8115 (t) cc_final: 0.7741 (t) REVERT: A 281 MET cc_start: 0.7565 (mtp) cc_final: 0.7350 (mtm) REVERT: B 5 LYS cc_start: 0.8351 (OUTLIER) cc_final: 0.8124 (mmtt) REVERT: B 14 ASP cc_start: 0.7548 (t0) cc_final: 0.7313 (t70) REVERT: B 152 LEU cc_start: 0.8164 (mt) cc_final: 0.7900 (mt) REVERT: B 158 ASN cc_start: 0.7999 (m-40) cc_final: 0.7355 (m-40) REVERT: B 191 LEU cc_start: 0.7511 (mp) cc_final: 0.6428 (tt) REVERT: B 220 ASP cc_start: 0.8083 (t0) cc_final: 0.7758 (t0) REVERT: C 5 LYS cc_start: 0.8512 (OUTLIER) cc_final: 0.8184 (mmtp) REVERT: C 46 GLU cc_start: 0.8288 (pt0) cc_final: 0.7942 (pt0) REVERT: C 128 ASP cc_start: 0.8407 (m-30) cc_final: 0.8129 (m-30) REVERT: C 260 ARG cc_start: 0.8229 (mtt180) cc_final: 0.7880 (mtt180) REVERT: C 281 MET cc_start: 0.7366 (mtp) cc_final: 0.7125 (mtm) REVERT: D 69 GLU cc_start: 0.8279 (tt0) cc_final: 0.8077 (tt0) REVERT: D 158 ASN cc_start: 0.8065 (m-40) cc_final: 0.7671 (m110) REVERT: D 191 LEU cc_start: 0.7625 (mp) cc_final: 0.6581 (tt) REVERT: D 261 ILE cc_start: 0.8623 (mt) cc_final: 0.8388 (mm) REVERT: E 14 ASP cc_start: 0.7704 (t0) cc_final: 0.7314 (t70) REVERT: E 46 GLU cc_start: 0.8400 (pt0) cc_final: 0.8090 (pt0) REVERT: E 103 SER cc_start: 0.7473 (m) cc_final: 0.7164 (p) REVERT: E 180 SER cc_start: 0.8147 (t) cc_final: 0.7743 (t) REVERT: E 267 GLU cc_start: 0.7503 (tp30) cc_final: 0.7210 (tp30) REVERT: F 158 ASN cc_start: 0.8005 (m-40) cc_final: 0.7791 (m110) REVERT: F 169 SER cc_start: 0.7771 (t) cc_final: 0.7459 (p) REVERT: F 180 SER cc_start: 0.8470 (t) cc_final: 0.7763 (t) REVERT: F 261 ILE cc_start: 0.8623 (mt) cc_final: 0.8407 (mm) REVERT: F 294 MET cc_start: 0.8556 (pmm) cc_final: 0.8221 (pmm) REVERT: G 158 ASN cc_start: 0.8243 (m-40) cc_final: 0.7876 (m110) REVERT: G 191 LEU cc_start: 0.7627 (mp) cc_final: 0.6583 (tt) REVERT: G 261 ILE cc_start: 0.8620 (mt) cc_final: 0.8410 (mm) REVERT: H 5 LYS cc_start: 0.8496 (OUTLIER) cc_final: 0.8161 (mmtp) REVERT: H 46 GLU cc_start: 0.8282 (pt0) cc_final: 0.7992 (pt0) REVERT: H 128 ASP cc_start: 0.8414 (m-30) cc_final: 0.8120 (m-30) REVERT: H 260 ARG cc_start: 0.8223 (mtt180) cc_final: 0.7890 (mtt180) REVERT: H 281 MET cc_start: 0.7463 (mtp) cc_final: 0.7216 (mtm) REVERT: I 5 LYS cc_start: 0.8384 (OUTLIER) cc_final: 0.8158 (mmtt) REVERT: I 52 ASP cc_start: 0.8534 (t0) cc_final: 0.8284 (t0) REVERT: I 158 ASN cc_start: 0.8006 (m-40) cc_final: 0.7260 (m110) REVERT: I 191 LEU cc_start: 0.7516 (mp) cc_final: 0.6416 (tt) REVERT: I 220 ASP cc_start: 0.8134 (t0) cc_final: 0.7790 (t0) REVERT: J 5 LYS cc_start: 0.8583 (OUTLIER) cc_final: 0.8273 (mmmt) REVERT: J 103 SER cc_start: 0.7579 (m) cc_final: 0.7331 (p) REVERT: J 128 ASP cc_start: 0.8367 (m-30) cc_final: 0.8061 (m-30) REVERT: J 180 SER cc_start: 0.8180 (t) cc_final: 0.7763 (t) REVERT: J 281 MET cc_start: 0.7598 (mtp) cc_final: 0.7343 (mtm) REVERT: K 78 LYS cc_start: 0.8505 (tptm) cc_final: 0.7732 (ttmt) REVERT: K 158 ASN cc_start: 0.8018 (m-40) cc_final: 0.7801 (m110) REVERT: K 169 SER cc_start: 0.7781 (t) cc_final: 0.7459 (p) REVERT: K 191 LEU cc_start: 0.7460 (mp) cc_final: 0.6458 (tt) REVERT: K 217 ILE cc_start: 0.8352 (mt) cc_final: 0.8150 (mm) REVERT: K 261 ILE cc_start: 0.8651 (mt) cc_final: 0.8438 (mm) REVERT: K 294 MET cc_start: 0.8576 (pmm) cc_final: 0.8252 (pmm) REVERT: L 14 ASP cc_start: 0.7720 (t0) cc_final: 0.7324 (t70) REVERT: L 46 GLU cc_start: 0.8408 (pt0) cc_final: 0.8087 (pt0) REVERT: L 103 SER cc_start: 0.7520 (m) cc_final: 0.7218 (p) REVERT: L 180 SER cc_start: 0.8172 (t) cc_final: 0.7774 (t) REVERT: L 267 GLU cc_start: 0.7506 (tp30) cc_final: 0.7225 (tp30) outliers start: 84 outliers final: 38 residues processed: 893 average time/residue: 1.3908 time to fit residues: 1443.8977 Evaluate side-chains 638 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 594 time to evaluate : 3.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LYS Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain B residue 5 LYS Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 278 GLU Chi-restraints excluded: chain C residue 5 LYS Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain E residue 278 GLU Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 259 SER Chi-restraints excluded: chain F residue 278 GLU Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 249 THR Chi-restraints excluded: chain H residue 5 LYS Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain H residue 249 THR Chi-restraints excluded: chain H residue 278 GLU Chi-restraints excluded: chain I residue 5 LYS Chi-restraints excluded: chain I residue 208 VAL Chi-restraints excluded: chain I residue 249 THR Chi-restraints excluded: chain I residue 259 SER Chi-restraints excluded: chain I residue 278 GLU Chi-restraints excluded: chain J residue 5 LYS Chi-restraints excluded: chain J residue 208 VAL Chi-restraints excluded: chain J residue 249 THR Chi-restraints excluded: chain J residue 278 GLU Chi-restraints excluded: chain K residue 208 VAL Chi-restraints excluded: chain K residue 249 THR Chi-restraints excluded: chain K residue 259 SER Chi-restraints excluded: chain K residue 278 GLU Chi-restraints excluded: chain L residue 208 VAL Chi-restraints excluded: chain L residue 249 THR Chi-restraints excluded: chain L residue 278 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 303 optimal weight: 2.9990 chunk 272 optimal weight: 0.0040 chunk 151 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 184 optimal weight: 1.9990 chunk 145 optimal weight: 0.8980 chunk 282 optimal weight: 2.9990 chunk 109 optimal weight: 0.9990 chunk 171 optimal weight: 6.9990 chunk 210 optimal weight: 0.7980 chunk 326 optimal weight: 0.9980 overall best weight: 0.7394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 GLN B 305 ASN C 97 GLN C 305 ASN D 263 ASN D 305 ASN E 97 GLN E 277 GLN E 305 ASN F 263 ASN F 305 ASN G 263 ASN G 305 ASN H 97 GLN H 305 ASN I 305 ASN J 97 GLN K 263 ASN K 305 ASN L 97 GLN L 277 GLN L 305 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.1623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 29076 Z= 0.143 Angle : 0.450 5.684 39396 Z= 0.244 Chirality : 0.047 0.171 4668 Planarity : 0.003 0.021 4992 Dihedral : 8.337 64.630 4318 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 4.33 % Allowed : 15.14 % Favored : 80.53 % 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: 0.56 (0.14), residues: 3660 helix: 1.53 (0.14), residues: 1368 sheet: -0.44 (0.17), residues: 996 loop : -0.03 (0.17), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 162 HIS 0.003 0.001 HIS B 123 PHE 0.012 0.001 PHE H 35 TYR 0.013 0.001 TYR A 311 ARG 0.004 0.000 ARG B 184 *********************** 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 757 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 621 time to evaluate : 3.430 Fit side-chains REVERT: A 5 LYS cc_start: 0.8519 (OUTLIER) cc_final: 0.8272 (mmmt) REVERT: A 68 MET cc_start: 0.8327 (tpt) cc_final: 0.7889 (mmm) REVERT: A 103 SER cc_start: 0.7560 (m) cc_final: 0.7321 (p) REVERT: A 128 ASP cc_start: 0.8297 (m-30) cc_final: 0.8080 (m-30) REVERT: B 14 ASP cc_start: 0.7394 (t0) cc_final: 0.7169 (t70) REVERT: B 52 ASP cc_start: 0.8386 (t0) cc_final: 0.8184 (t0) REVERT: B 152 LEU cc_start: 0.8117 (mt) cc_final: 0.7883 (mt) REVERT: B 191 LEU cc_start: 0.7315 (mp) cc_final: 0.6375 (tt) REVERT: B 220 ASP cc_start: 0.8082 (t0) cc_final: 0.7668 (t0) REVERT: C 5 LYS cc_start: 0.8432 (OUTLIER) cc_final: 0.8169 (mmtp) REVERT: C 128 ASP cc_start: 0.8339 (m-30) cc_final: 0.8083 (m-30) REVERT: C 288 GLN cc_start: 0.8325 (OUTLIER) cc_final: 0.7857 (mt0) REVERT: C 294 MET cc_start: 0.8482 (pmm) cc_final: 0.8159 (pmm) REVERT: D 29 LYS cc_start: 0.8011 (mtmm) cc_final: 0.7785 (mtmt) REVERT: D 158 ASN cc_start: 0.8063 (m-40) cc_final: 0.7818 (m110) REVERT: E 14 ASP cc_start: 0.7478 (t0) cc_final: 0.7119 (t70) REVERT: E 46 GLU cc_start: 0.8491 (pt0) cc_final: 0.8150 (pt0) REVERT: E 103 SER cc_start: 0.7290 (m) cc_final: 0.7050 (p) REVERT: E 180 SER cc_start: 0.7897 (t) cc_final: 0.7674 (t) REVERT: E 254 SER cc_start: 0.8488 (p) cc_final: 0.8278 (p) REVERT: E 259 SER cc_start: 0.8145 (m) cc_final: 0.7898 (p) REVERT: E 267 GLU cc_start: 0.7436 (tp30) cc_final: 0.7234 (tp30) REVERT: E 282 LYS cc_start: 0.7605 (OUTLIER) cc_final: 0.7387 (mmtp) REVERT: F 169 SER cc_start: 0.7586 (t) cc_final: 0.7321 (p) REVERT: F 294 MET cc_start: 0.8540 (pmm) cc_final: 0.8127 (pmm) REVERT: G 158 ASN cc_start: 0.8082 (m-40) cc_final: 0.7648 (m110) REVERT: G 191 LEU cc_start: 0.7256 (mp) cc_final: 0.6311 (tt) REVERT: H 5 LYS cc_start: 0.8457 (OUTLIER) cc_final: 0.8185 (mmtp) REVERT: H 35 PHE cc_start: 0.7952 (m-80) cc_final: 0.7749 (m-80) REVERT: H 128 ASP cc_start: 0.8380 (m-30) cc_final: 0.8105 (m-30) REVERT: H 288 GLN cc_start: 0.8321 (OUTLIER) cc_final: 0.7864 (mt0) REVERT: H 294 MET cc_start: 0.8484 (pmm) cc_final: 0.8157 (pmm) REVERT: I 191 LEU cc_start: 0.7270 (mp) cc_final: 0.6139 (tm) REVERT: J 5 LYS cc_start: 0.8500 (OUTLIER) cc_final: 0.8278 (mmmt) REVERT: J 68 MET cc_start: 0.8315 (tpt) cc_final: 0.7891 (mmm) REVERT: J 103 SER cc_start: 0.7565 (m) cc_final: 0.7336 (p) REVERT: J 128 ASP cc_start: 0.8279 (m-30) cc_final: 0.8024 (m-30) REVERT: K 169 SER cc_start: 0.7619 (t) cc_final: 0.7352 (p) REVERT: K 294 MET cc_start: 0.8528 (pmm) cc_final: 0.8091 (pmm) REVERT: L 14 ASP cc_start: 0.7488 (t0) cc_final: 0.7135 (t70) REVERT: L 46 GLU cc_start: 0.8418 (pt0) cc_final: 0.8121 (pt0) REVERT: L 103 SER cc_start: 0.7319 (m) cc_final: 0.7086 (p) REVERT: L 180 SER cc_start: 0.7958 (t) cc_final: 0.7738 (t) outliers start: 136 outliers final: 71 residues processed: 706 average time/residue: 1.4275 time to fit residues: 1171.0467 Evaluate side-chains 657 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 579 time to evaluate : 3.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LYS Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain B residue 36 SER Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 278 GLU Chi-restraints excluded: chain C residue 5 LYS Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 286 LYS Chi-restraints excluded: chain C residue 288 GLN Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 132 SER Chi-restraints excluded: chain D residue 169 SER Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain E residue 36 SER Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 132 SER Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain E residue 278 GLU Chi-restraints excluded: chain E residue 282 LYS Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 278 GLU Chi-restraints excluded: chain G residue 36 SER Chi-restraints excluded: chain G residue 62 GLU Chi-restraints excluded: chain G residue 132 SER Chi-restraints excluded: chain G residue 169 SER Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 249 THR Chi-restraints excluded: chain H residue 5 LYS Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain H residue 249 THR Chi-restraints excluded: chain H residue 278 GLU Chi-restraints excluded: chain H residue 288 GLN Chi-restraints excluded: chain I residue 36 SER Chi-restraints excluded: chain I residue 62 GLU Chi-restraints excluded: chain I residue 169 SER Chi-restraints excluded: chain I residue 208 VAL Chi-restraints excluded: chain I residue 249 THR Chi-restraints excluded: chain I residue 259 SER Chi-restraints excluded: chain I residue 278 GLU Chi-restraints excluded: chain J residue 5 LYS Chi-restraints excluded: chain J residue 36 SER Chi-restraints excluded: chain J residue 62 GLU Chi-restraints excluded: chain J residue 169 SER Chi-restraints excluded: chain J residue 208 VAL Chi-restraints excluded: chain J residue 249 THR Chi-restraints excluded: chain J residue 278 GLU Chi-restraints excluded: chain K residue 12 HIS Chi-restraints excluded: chain K residue 62 GLU Chi-restraints excluded: chain K residue 208 VAL Chi-restraints excluded: chain K residue 249 THR Chi-restraints excluded: chain K residue 278 GLU Chi-restraints excluded: chain L residue 36 SER Chi-restraints excluded: chain L residue 62 GLU Chi-restraints excluded: chain L residue 132 SER Chi-restraints excluded: chain L residue 208 VAL Chi-restraints excluded: chain L residue 249 THR Chi-restraints excluded: chain L residue 278 GLU 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: 4.9990 chunk 272 optimal weight: 6.9990 chunk 222 optimal weight: 9.9990 chunk 90 optimal weight: 6.9990 chunk 327 optimal weight: 6.9990 chunk 353 optimal weight: 10.0000 chunk 291 optimal weight: 4.9990 chunk 324 optimal weight: 6.9990 chunk 111 optimal weight: 10.0000 chunk 262 optimal weight: 0.7980 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 HIS A 97 GLN A 123 HIS B 12 HIS B 135 GLN C 12 HIS C 97 GLN D 97 GLN D 263 ASN E 12 HIS F 135 GLN F 263 ASN G 12 HIS G 263 ASN H 12 HIS H 97 GLN I 12 HIS I 135 GLN J 12 HIS J 97 GLN J 123 HIS K 135 GLN K 263 ASN L 12 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.139 29076 Z= 0.542 Angle : 0.662 9.456 39396 Z= 0.356 Chirality : 0.055 0.192 4668 Planarity : 0.005 0.042 4992 Dihedral : 8.412 59.953 4308 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 5.57 % Allowed : 13.87 % Favored : 80.57 % 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: 0.03 (0.14), residues: 3660 helix: 0.60 (0.14), residues: 1476 sheet: -0.29 (0.18), residues: 936 loop : -0.19 (0.17), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP L 162 HIS 0.008 0.002 HIS G 123 PHE 0.021 0.003 PHE C 35 TYR 0.020 0.003 TYR E 146 ARG 0.006 0.001 ARG I 104 *********************** 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 801 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 175 poor density : 626 time to evaluate : 3.361 Fit side-chains REVERT: A 5 LYS cc_start: 0.8675 (OUTLIER) cc_final: 0.8408 (mmmt) REVERT: A 13 GLN cc_start: 0.7789 (OUTLIER) cc_final: 0.7457 (tm-30) REVERT: A 68 MET cc_start: 0.8551 (tpt) cc_final: 0.8187 (tpp) REVERT: A 288 GLN cc_start: 0.8397 (mt0) cc_final: 0.8166 (mt0) REVERT: B 14 ASP cc_start: 0.7526 (t0) cc_final: 0.7290 (t70) REVERT: B 52 ASP cc_start: 0.8407 (t0) cc_final: 0.8150 (t0) REVERT: B 288 GLN cc_start: 0.8515 (OUTLIER) cc_final: 0.7898 (mt0) REVERT: C 5 LYS cc_start: 0.8679 (OUTLIER) cc_final: 0.8410 (mmmt) REVERT: C 13 GLN cc_start: 0.7855 (OUTLIER) cc_final: 0.7522 (tm-30) REVERT: C 115 MET cc_start: 0.8682 (mtp) cc_final: 0.8469 (mtp) REVERT: C 128 ASP cc_start: 0.8418 (m-30) cc_final: 0.8206 (m-30) REVERT: C 260 ARG cc_start: 0.8045 (mtt180) cc_final: 0.7693 (mtt180) REVERT: C 281 MET cc_start: 0.7137 (mtm) cc_final: 0.6756 (mtm) REVERT: C 288 GLN cc_start: 0.8341 (OUTLIER) cc_final: 0.7751 (mt0) REVERT: C 294 MET cc_start: 0.8526 (pmm) cc_final: 0.8229 (pmm) REVERT: D 78 LYS cc_start: 0.8813 (OUTLIER) cc_final: 0.8193 (ttmt) REVERT: D 217 ILE cc_start: 0.8774 (mt) cc_final: 0.8473 (mm) REVERT: D 288 GLN cc_start: 0.8631 (OUTLIER) cc_final: 0.8311 (mt0) REVERT: E 13 GLN cc_start: 0.7811 (OUTLIER) cc_final: 0.7108 (tm-30) REVERT: E 14 ASP cc_start: 0.7684 (t0) cc_final: 0.7297 (t70) REVERT: E 46 GLU cc_start: 0.8442 (pt0) cc_final: 0.8086 (pt0) REVERT: E 180 SER cc_start: 0.7874 (t) cc_final: 0.7654 (t) REVERT: E 267 GLU cc_start: 0.7511 (tp30) cc_final: 0.7171 (tp30) REVERT: E 288 GLN cc_start: 0.8555 (OUTLIER) cc_final: 0.8180 (mp10) REVERT: F 97 GLN cc_start: 0.7775 (OUTLIER) cc_final: 0.6034 (mp10) REVERT: F 169 SER cc_start: 0.7348 (t) cc_final: 0.7101 (p) REVERT: F 191 LEU cc_start: 0.7899 (OUTLIER) cc_final: 0.6641 (tm) REVERT: F 288 GLN cc_start: 0.8379 (OUTLIER) cc_final: 0.7959 (mt0) REVERT: G 78 LYS cc_start: 0.8809 (OUTLIER) cc_final: 0.8204 (ttmt) REVERT: G 97 GLN cc_start: 0.7818 (OUTLIER) cc_final: 0.6167 (mp10) REVERT: G 288 GLN cc_start: 0.8617 (OUTLIER) cc_final: 0.8293 (mt0) REVERT: H 5 LYS cc_start: 0.8679 (OUTLIER) cc_final: 0.8422 (mmmt) REVERT: H 13 GLN cc_start: 0.7857 (OUTLIER) cc_final: 0.7511 (tm-30) REVERT: H 39 GLU cc_start: 0.8304 (mt-10) cc_final: 0.7902 (mt-10) REVERT: H 115 MET cc_start: 0.8661 (mtp) cc_final: 0.8450 (mtp) REVERT: H 128 ASP cc_start: 0.8417 (m-30) cc_final: 0.8212 (m-30) REVERT: H 248 LEU cc_start: 0.8264 (OUTLIER) cc_final: 0.7825 (mt) REVERT: H 260 ARG cc_start: 0.8028 (mtt180) cc_final: 0.7680 (mtt180) REVERT: H 281 MET cc_start: 0.7177 (mtm) cc_final: 0.6776 (mtm) REVERT: H 288 GLN cc_start: 0.8359 (OUTLIER) cc_final: 0.7780 (mt0) REVERT: H 294 MET cc_start: 0.8538 (pmm) cc_final: 0.8227 (pmm) REVERT: I 14 ASP cc_start: 0.7623 (t0) cc_final: 0.7394 (t70) REVERT: I 97 GLN cc_start: 0.7626 (OUTLIER) cc_final: 0.5719 (mp10) REVERT: I 288 GLN cc_start: 0.8494 (OUTLIER) cc_final: 0.7882 (mt0) REVERT: J 5 LYS cc_start: 0.8650 (OUTLIER) cc_final: 0.8384 (mmmt) REVERT: J 13 GLN cc_start: 0.7817 (OUTLIER) cc_final: 0.7488 (tm-30) REVERT: J 68 MET cc_start: 0.8539 (tpt) cc_final: 0.8176 (tpp) REVERT: J 288 GLN cc_start: 0.8396 (mt0) cc_final: 0.8170 (mt0) REVERT: K 39 GLU cc_start: 0.8466 (mt-10) cc_final: 0.8261 (mt-10) REVERT: K 97 GLN cc_start: 0.7824 (OUTLIER) cc_final: 0.6077 (mp10) REVERT: K 169 SER cc_start: 0.7375 (t) cc_final: 0.7139 (p) REVERT: K 191 LEU cc_start: 0.7901 (OUTLIER) cc_final: 0.6690 (tm) REVERT: K 288 GLN cc_start: 0.8451 (OUTLIER) cc_final: 0.7996 (mt0) REVERT: L 13 GLN cc_start: 0.7828 (OUTLIER) cc_final: 0.7128 (tm-30) REVERT: L 14 ASP cc_start: 0.7700 (t0) cc_final: 0.7311 (t70) REVERT: L 46 GLU cc_start: 0.8477 (pt0) cc_final: 0.8180 (pt0) REVERT: L 180 SER cc_start: 0.7865 (t) cc_final: 0.7644 (t) outliers start: 175 outliers final: 99 residues processed: 742 average time/residue: 1.4549 time to fit residues: 1248.9301 Evaluate side-chains 731 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 604 time to evaluate : 3.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LYS Chi-restraints excluded: chain A residue 13 GLN Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 97 GLN Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 282 LYS Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain B residue 16 SER Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 259 SER Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 278 GLU Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain B residue 288 GLN Chi-restraints excluded: chain B residue 307 GLU Chi-restraints excluded: chain C residue 5 LYS Chi-restraints excluded: chain C residue 13 GLN Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 169 SER Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 286 LYS Chi-restraints excluded: chain C residue 288 GLN Chi-restraints excluded: chain C residue 314 SER Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 78 LYS Chi-restraints excluded: chain D residue 97 GLN Chi-restraints excluded: chain D residue 132 SER Chi-restraints excluded: chain D residue 169 SER Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 285 SER Chi-restraints excluded: chain D residue 288 GLN Chi-restraints excluded: chain E residue 13 GLN Chi-restraints excluded: chain E residue 36 SER Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain E residue 278 GLU Chi-restraints excluded: chain E residue 288 GLN Chi-restraints excluded: chain E residue 314 SER Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 97 GLN Chi-restraints excluded: chain F residue 118 VAL Chi-restraints excluded: chain F residue 191 LEU Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 278 GLU Chi-restraints excluded: chain F residue 285 SER Chi-restraints excluded: chain F residue 288 GLN Chi-restraints excluded: chain G residue 62 GLU Chi-restraints excluded: chain G residue 78 LYS Chi-restraints excluded: chain G residue 97 GLN Chi-restraints excluded: chain G residue 132 SER Chi-restraints excluded: chain G residue 169 SER Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 249 THR Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 285 SER Chi-restraints excluded: chain G residue 288 GLN Chi-restraints excluded: chain H residue 5 LYS Chi-restraints excluded: chain H residue 13 GLN Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 97 GLN Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain H residue 248 LEU Chi-restraints excluded: chain H residue 249 THR Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 278 GLU Chi-restraints excluded: chain H residue 286 LYS Chi-restraints excluded: chain H residue 288 GLN Chi-restraints excluded: chain H residue 314 SER Chi-restraints excluded: chain I residue 62 GLU Chi-restraints excluded: chain I residue 97 GLN Chi-restraints excluded: chain I residue 132 SER Chi-restraints excluded: chain I residue 169 SER Chi-restraints excluded: chain I residue 208 VAL Chi-restraints excluded: chain I residue 249 THR Chi-restraints excluded: chain I residue 259 SER Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain I residue 278 GLU Chi-restraints excluded: chain I residue 285 SER Chi-restraints excluded: chain I residue 288 GLN Chi-restraints excluded: chain I residue 298 GLU Chi-restraints excluded: chain I residue 307 GLU Chi-restraints excluded: chain J residue 5 LYS Chi-restraints excluded: chain J residue 13 GLN Chi-restraints excluded: chain J residue 36 SER Chi-restraints excluded: chain J residue 62 GLU Chi-restraints excluded: chain J residue 97 GLN Chi-restraints excluded: chain J residue 132 SER Chi-restraints excluded: chain J residue 169 SER Chi-restraints excluded: chain J residue 208 VAL Chi-restraints excluded: chain J residue 249 THR Chi-restraints excluded: chain J residue 278 GLU Chi-restraints excluded: chain K residue 62 GLU Chi-restraints excluded: chain K residue 97 GLN Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain K residue 191 LEU Chi-restraints excluded: chain K residue 208 VAL Chi-restraints excluded: chain K residue 249 THR Chi-restraints excluded: chain K residue 278 GLU Chi-restraints excluded: chain K residue 285 SER Chi-restraints excluded: chain K residue 288 GLN Chi-restraints excluded: chain L residue 13 GLN Chi-restraints excluded: chain L residue 36 SER Chi-restraints excluded: chain L residue 62 GLU Chi-restraints excluded: chain L residue 118 VAL Chi-restraints excluded: chain L residue 208 VAL Chi-restraints excluded: chain L residue 249 THR Chi-restraints excluded: chain L residue 259 SER Chi-restraints excluded: chain L residue 278 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 323 optimal weight: 5.9990 chunk 246 optimal weight: 1.9990 chunk 169 optimal weight: 0.0170 chunk 36 optimal weight: 1.9990 chunk 156 optimal weight: 0.8980 chunk 219 optimal weight: 2.9990 chunk 328 optimal weight: 0.9980 chunk 347 optimal weight: 5.9990 chunk 171 optimal weight: 1.9990 chunk 311 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 overall best weight: 0.9820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 GLN B 97 GLN B 263 ASN E 12 HIS F 263 ASN J 97 GLN K 263 ASN L 12 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 29076 Z= 0.165 Angle : 0.468 9.202 39396 Z= 0.251 Chirality : 0.046 0.169 4668 Planarity : 0.003 0.024 4992 Dihedral : 7.425 59.361 4308 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 4.23 % Allowed : 15.33 % Favored : 80.44 % 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: 0.43 (0.14), residues: 3660 helix: 1.16 (0.14), residues: 1380 sheet: -0.18 (0.18), residues: 936 loop : -0.12 (0.16), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP E 162 HIS 0.003 0.001 HIS C 123 PHE 0.014 0.001 PHE H 35 TYR 0.015 0.002 TYR E 146 ARG 0.005 0.000 ARG D 22 *********************** 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 737 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 604 time to evaluate : 3.162 Fit side-chains REVERT: A 68 MET cc_start: 0.8558 (tpt) cc_final: 0.8214 (tpp) REVERT: B 14 ASP cc_start: 0.7432 (t0) cc_final: 0.7215 (t70) REVERT: B 52 ASP cc_start: 0.8383 (t0) cc_final: 0.8154 (t0) REVERT: B 191 LEU cc_start: 0.7437 (mp) cc_final: 0.6445 (tt) REVERT: C 5 LYS cc_start: 0.8542 (OUTLIER) cc_final: 0.8315 (mmmt) REVERT: C 13 GLN cc_start: 0.7814 (OUTLIER) cc_final: 0.7465 (tm-30) REVERT: C 115 MET cc_start: 0.8612 (mtp) cc_final: 0.8408 (mtp) REVERT: C 128 ASP cc_start: 0.8369 (m-30) cc_final: 0.8145 (m-30) REVERT: D 68 MET cc_start: 0.8262 (tpp) cc_final: 0.8044 (tpt) REVERT: D 78 LYS cc_start: 0.8796 (OUTLIER) cc_final: 0.8253 (ttmt) REVERT: D 217 ILE cc_start: 0.8790 (mt) cc_final: 0.8499 (mm) REVERT: D 277 GLN cc_start: 0.8572 (mm-40) cc_final: 0.8304 (mm110) REVERT: E 14 ASP cc_start: 0.7590 (t0) cc_final: 0.7220 (t70) REVERT: E 46 GLU cc_start: 0.8432 (pt0) cc_final: 0.8092 (pt0) REVERT: E 153 LYS cc_start: 0.7314 (ttpp) cc_final: 0.7107 (tttm) REVERT: E 222 MET cc_start: 0.8297 (ptp) cc_final: 0.8080 (ptp) REVERT: E 267 GLU cc_start: 0.7431 (tp30) cc_final: 0.7107 (tp30) REVERT: F 191 LEU cc_start: 0.7823 (OUTLIER) cc_final: 0.6616 (tm) REVERT: G 68 MET cc_start: 0.8276 (tpp) cc_final: 0.8048 (tpt) REVERT: G 78 LYS cc_start: 0.8799 (OUTLIER) cc_final: 0.8258 (ttmt) REVERT: G 97 GLN cc_start: 0.7751 (OUTLIER) cc_final: 0.6079 (mp10) REVERT: G 217 ILE cc_start: 0.8781 (mt) cc_final: 0.8481 (mm) REVERT: G 298 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.7868 (mm-30) REVERT: H 5 LYS cc_start: 0.8558 (OUTLIER) cc_final: 0.8340 (mmmt) REVERT: H 13 GLN cc_start: 0.7805 (OUTLIER) cc_final: 0.7443 (tm-30) REVERT: H 260 ARG cc_start: 0.8052 (mtt180) cc_final: 0.7733 (mtt180) REVERT: I 52 ASP cc_start: 0.8367 (t0) cc_final: 0.8160 (t0) REVERT: I 191 LEU cc_start: 0.7466 (mp) cc_final: 0.6180 (tm) REVERT: J 13 GLN cc_start: 0.7731 (OUTLIER) cc_final: 0.7353 (tm-30) REVERT: J 68 MET cc_start: 0.8548 (tpt) cc_final: 0.8197 (tpp) REVERT: K 191 LEU cc_start: 0.7835 (OUTLIER) cc_final: 0.6650 (tm) REVERT: K 288 GLN cc_start: 0.8350 (OUTLIER) cc_final: 0.8077 (mt0) REVERT: L 14 ASP cc_start: 0.7595 (t0) cc_final: 0.7236 (t70) REVERT: L 46 GLU cc_start: 0.8432 (pt0) cc_final: 0.8129 (pt0) REVERT: L 314 SER cc_start: 0.6824 (OUTLIER) cc_final: 0.6558 (p) outliers start: 133 outliers final: 77 residues processed: 680 average time/residue: 1.4662 time to fit residues: 1152.3903 Evaluate side-chains 689 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 599 time to evaluate : 3.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 97 GLN Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain B residue 16 SER Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 97 GLN Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 278 GLU Chi-restraints excluded: chain C residue 5 LYS Chi-restraints excluded: chain C residue 13 GLN Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 286 LYS Chi-restraints excluded: chain D residue 12 HIS Chi-restraints excluded: chain D residue 34 LYS Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 78 LYS Chi-restraints excluded: chain D residue 132 SER Chi-restraints excluded: chain D residue 169 SER Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain E residue 36 SER Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 132 SER Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain E residue 278 GLU Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 191 LEU Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 278 GLU Chi-restraints excluded: chain G residue 62 GLU Chi-restraints excluded: chain G residue 78 LYS Chi-restraints excluded: chain G residue 97 GLN Chi-restraints excluded: chain G residue 132 SER Chi-restraints excluded: chain G residue 169 SER Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 249 THR Chi-restraints excluded: chain G residue 298 GLU Chi-restraints excluded: chain H residue 5 LYS Chi-restraints excluded: chain H residue 13 GLN Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 178 VAL Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain H residue 249 THR Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 278 GLU Chi-restraints excluded: chain H residue 286 LYS Chi-restraints excluded: chain I residue 62 GLU Chi-restraints excluded: chain I residue 208 VAL Chi-restraints excluded: chain I residue 249 THR Chi-restraints excluded: chain I residue 278 GLU Chi-restraints excluded: chain I residue 298 GLU Chi-restraints excluded: chain J residue 13 GLN Chi-restraints excluded: chain J residue 36 SER Chi-restraints excluded: chain J residue 62 GLU Chi-restraints excluded: chain J residue 97 GLN Chi-restraints excluded: chain J residue 132 SER Chi-restraints excluded: chain J residue 169 SER Chi-restraints excluded: chain J residue 208 VAL Chi-restraints excluded: chain J residue 249 THR Chi-restraints excluded: chain J residue 278 GLU Chi-restraints excluded: chain K residue 62 GLU Chi-restraints excluded: chain K residue 191 LEU Chi-restraints excluded: chain K residue 208 VAL Chi-restraints excluded: chain K residue 249 THR Chi-restraints excluded: chain K residue 278 GLU Chi-restraints excluded: chain K residue 288 GLN Chi-restraints excluded: chain L residue 36 SER Chi-restraints excluded: chain L residue 62 GLU Chi-restraints excluded: chain L residue 118 VAL Chi-restraints excluded: chain L residue 132 SER Chi-restraints excluded: chain L residue 155 ILE Chi-restraints excluded: chain L residue 208 VAL Chi-restraints excluded: chain L residue 249 THR Chi-restraints excluded: chain L residue 278 GLU Chi-restraints excluded: chain L residue 314 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 289 optimal weight: 9.9990 chunk 197 optimal weight: 9.9990 chunk 5 optimal weight: 4.9990 chunk 259 optimal weight: 2.9990 chunk 143 optimal weight: 2.9990 chunk 296 optimal weight: 7.9990 chunk 240 optimal weight: 6.9990 chunk 0 optimal weight: 0.9990 chunk 177 optimal weight: 0.7980 chunk 312 optimal weight: 6.9990 chunk 87 optimal weight: 0.0470 overall best weight: 1.5684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 GLN C 12 HIS D 97 GLN E 12 HIS F 263 ASN H 12 HIS H 97 GLN J 97 GLN K 263 ASN L 12 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 29076 Z= 0.223 Angle : 0.480 8.230 39396 Z= 0.259 Chirality : 0.047 0.176 4668 Planarity : 0.003 0.026 4992 Dihedral : 7.018 59.613 4298 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 4.87 % Allowed : 15.14 % Favored : 79.99 % 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: 0.44 (0.14), residues: 3660 helix: 1.16 (0.14), residues: 1392 sheet: -0.15 (0.17), residues: 936 loop : -0.13 (0.16), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP L 162 HIS 0.003 0.001 HIS H 123 PHE 0.013 0.002 PHE B 138 TYR 0.016 0.002 TYR L 146 ARG 0.006 0.000 ARG B 22 *********************** 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 748 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 595 time to evaluate : 3.477 Fit side-chains REVERT: A 13 GLN cc_start: 0.7738 (OUTLIER) cc_final: 0.7357 (tm-30) REVERT: A 68 MET cc_start: 0.8564 (tpt) cc_final: 0.8208 (tpp) REVERT: B 14 ASP cc_start: 0.7464 (t0) cc_final: 0.7240 (t70) REVERT: B 52 ASP cc_start: 0.8372 (t0) cc_final: 0.8126 (t0) REVERT: B 191 LEU cc_start: 0.7447 (mp) cc_final: 0.6448 (tt) REVERT: B 288 GLN cc_start: 0.8383 (OUTLIER) cc_final: 0.7974 (mt0) REVERT: C 13 GLN cc_start: 0.7825 (OUTLIER) cc_final: 0.7487 (tm-30) REVERT: C 128 ASP cc_start: 0.8382 (m-30) cc_final: 0.8161 (m-30) REVERT: C 281 MET cc_start: 0.7405 (mtm) cc_final: 0.7177 (mtm) REVERT: C 288 GLN cc_start: 0.8387 (OUTLIER) cc_final: 0.7827 (mt0) REVERT: D 78 LYS cc_start: 0.8782 (OUTLIER) cc_final: 0.8218 (ttmt) REVERT: D 191 LEU cc_start: 0.7305 (OUTLIER) cc_final: 0.6288 (tt) REVERT: D 217 ILE cc_start: 0.8832 (mt) cc_final: 0.8539 (mm) REVERT: D 277 GLN cc_start: 0.8604 (mm-40) cc_final: 0.8321 (mm110) REVERT: E 13 GLN cc_start: 0.7810 (OUTLIER) cc_final: 0.7093 (tm-30) REVERT: E 14 ASP cc_start: 0.7617 (t0) cc_final: 0.7240 (t70) REVERT: E 46 GLU cc_start: 0.8463 (pt0) cc_final: 0.8149 (pt0) REVERT: E 97 GLN cc_start: 0.7833 (OUTLIER) cc_final: 0.6764 (mp10) REVERT: E 267 GLU cc_start: 0.7441 (tp30) cc_final: 0.7102 (tp30) REVERT: F 97 GLN cc_start: 0.7582 (OUTLIER) cc_final: 0.5908 (mp10) REVERT: F 191 LEU cc_start: 0.7852 (OUTLIER) cc_final: 0.6635 (tm) REVERT: F 314 SER cc_start: 0.6960 (OUTLIER) cc_final: 0.6579 (p) REVERT: G 78 LYS cc_start: 0.8747 (OUTLIER) cc_final: 0.8201 (ttmt) REVERT: G 97 GLN cc_start: 0.7800 (OUTLIER) cc_final: 0.6151 (mp10) REVERT: G 217 ILE cc_start: 0.8818 (mt) cc_final: 0.8521 (mm) REVERT: H 13 GLN cc_start: 0.7831 (OUTLIER) cc_final: 0.7478 (tm-30) REVERT: H 39 GLU cc_start: 0.8236 (mt-10) cc_final: 0.7936 (mt-10) REVERT: H 248 LEU cc_start: 0.8210 (OUTLIER) cc_final: 0.7850 (mt) REVERT: H 260 ARG cc_start: 0.8029 (mtt180) cc_final: 0.7685 (mtt180) REVERT: H 288 GLN cc_start: 0.8431 (OUTLIER) cc_final: 0.7866 (mt0) REVERT: I 14 ASP cc_start: 0.7482 (t0) cc_final: 0.7271 (t70) REVERT: I 52 ASP cc_start: 0.8340 (t0) cc_final: 0.8091 (t0) REVERT: I 288 GLN cc_start: 0.8369 (OUTLIER) cc_final: 0.7960 (mt0) REVERT: J 13 GLN cc_start: 0.7757 (OUTLIER) cc_final: 0.7375 (tm-30) REVERT: J 68 MET cc_start: 0.8557 (tpt) cc_final: 0.8194 (tpp) REVERT: K 97 GLN cc_start: 0.7599 (OUTLIER) cc_final: 0.5929 (mp10) REVERT: K 191 LEU cc_start: 0.7868 (OUTLIER) cc_final: 0.6679 (tm) REVERT: K 247 ILE cc_start: 0.8993 (mt) cc_final: 0.8790 (mm) REVERT: K 314 SER cc_start: 0.6993 (OUTLIER) cc_final: 0.6607 (p) REVERT: L 13 GLN cc_start: 0.7816 (OUTLIER) cc_final: 0.7090 (tm-30) REVERT: L 14 ASP cc_start: 0.7615 (t0) cc_final: 0.7242 (t70) REVERT: L 46 GLU cc_start: 0.8473 (pt0) cc_final: 0.8177 (pt0) REVERT: L 97 GLN cc_start: 0.7832 (OUTLIER) cc_final: 0.6757 (mp10) REVERT: L 314 SER cc_start: 0.6852 (OUTLIER) cc_final: 0.6618 (p) outliers start: 153 outliers final: 86 residues processed: 693 average time/residue: 1.4451 time to fit residues: 1157.7033 Evaluate side-chains 690 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 580 time to evaluate : 3.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 GLN Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 97 GLN Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain B residue 16 SER Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 278 GLU Chi-restraints excluded: chain B residue 288 GLN Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 307 GLU Chi-restraints excluded: chain C residue 13 GLN Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 286 LYS Chi-restraints excluded: chain C residue 288 GLN Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 78 LYS Chi-restraints excluded: chain D residue 132 SER Chi-restraints excluded: chain D residue 169 SER Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain E residue 13 GLN Chi-restraints excluded: chain E residue 36 SER Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 97 GLN Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 155 ILE Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 97 GLN Chi-restraints excluded: chain F residue 118 VAL Chi-restraints excluded: chain F residue 169 SER Chi-restraints excluded: chain F residue 191 LEU Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 278 GLU Chi-restraints excluded: chain F residue 285 SER Chi-restraints excluded: chain F residue 314 SER Chi-restraints excluded: chain G residue 62 GLU Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain G residue 78 LYS Chi-restraints excluded: chain G residue 97 GLN Chi-restraints excluded: chain G residue 132 SER Chi-restraints excluded: chain G residue 169 SER Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 249 THR Chi-restraints excluded: chain G residue 314 SER Chi-restraints excluded: chain H residue 13 GLN Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 178 VAL Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain H residue 248 LEU Chi-restraints excluded: chain H residue 249 THR Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 278 GLU Chi-restraints excluded: chain H residue 286 LYS Chi-restraints excluded: chain H residue 288 GLN Chi-restraints excluded: chain I residue 62 GLU Chi-restraints excluded: chain I residue 132 SER Chi-restraints excluded: chain I residue 169 SER Chi-restraints excluded: chain I residue 208 VAL Chi-restraints excluded: chain I residue 249 THR Chi-restraints excluded: chain I residue 278 GLU Chi-restraints excluded: chain I residue 288 GLN Chi-restraints excluded: chain J residue 13 GLN Chi-restraints excluded: chain J residue 36 SER Chi-restraints excluded: chain J residue 62 GLU Chi-restraints excluded: chain J residue 97 GLN Chi-restraints excluded: chain J residue 132 SER Chi-restraints excluded: chain J residue 169 SER Chi-restraints excluded: chain J residue 208 VAL Chi-restraints excluded: chain J residue 249 THR Chi-restraints excluded: chain J residue 278 GLU Chi-restraints excluded: chain J residue 314 SER Chi-restraints excluded: chain K residue 62 GLU Chi-restraints excluded: chain K residue 97 GLN Chi-restraints excluded: chain K residue 169 SER Chi-restraints excluded: chain K residue 191 LEU Chi-restraints excluded: chain K residue 208 VAL Chi-restraints excluded: chain K residue 249 THR Chi-restraints excluded: chain K residue 285 SER Chi-restraints excluded: chain K residue 314 SER Chi-restraints excluded: chain L residue 13 GLN Chi-restraints excluded: chain L residue 36 SER Chi-restraints excluded: chain L residue 62 GLU Chi-restraints excluded: chain L residue 97 GLN Chi-restraints excluded: chain L residue 118 VAL Chi-restraints excluded: chain L residue 132 SER Chi-restraints excluded: chain L residue 155 ILE Chi-restraints excluded: chain L residue 178 VAL Chi-restraints excluded: chain L residue 208 VAL Chi-restraints excluded: chain L residue 249 THR Chi-restraints excluded: chain L residue 314 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 117 optimal weight: 0.9990 chunk 313 optimal weight: 1.9990 chunk 68 optimal weight: 5.9990 chunk 204 optimal weight: 4.9990 chunk 85 optimal weight: 4.9990 chunk 348 optimal weight: 4.9990 chunk 289 optimal weight: 9.9990 chunk 161 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 chunk 115 optimal weight: 4.9990 chunk 182 optimal weight: 0.5980 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 GLN A 123 HIS B 97 GLN C 12 HIS D 97 GLN E 12 HIS F 263 ASN G 277 GLN H 12 HIS H 97 GLN J 97 GLN K 263 ASN L 12 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.2343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 29076 Z= 0.236 Angle : 0.485 7.559 39396 Z= 0.262 Chirality : 0.047 0.175 4668 Planarity : 0.003 0.043 4992 Dihedral : 6.638 55.100 4281 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 4.87 % Allowed : 15.14 % Favored : 79.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.14), residues: 3660 helix: 1.16 (0.14), residues: 1392 sheet: -0.15 (0.17), residues: 936 loop : -0.17 (0.16), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP L 162 HIS 0.003 0.001 HIS H 123 PHE 0.013 0.002 PHE L 35 TYR 0.017 0.002 TYR L 146 ARG 0.008 0.000 ARG B 22 *********************** 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 745 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 592 time to evaluate : 3.305 Fit side-chains REVERT: A 13 GLN cc_start: 0.7778 (OUTLIER) cc_final: 0.7386 (tm-30) REVERT: A 68 MET cc_start: 0.8565 (tpt) cc_final: 0.8202 (tpp) REVERT: B 14 ASP cc_start: 0.7428 (t0) cc_final: 0.7222 (t70) REVERT: B 52 ASP cc_start: 0.8357 (t0) cc_final: 0.8103 (t0) REVERT: B 191 LEU cc_start: 0.7440 (mp) cc_final: 0.6444 (tt) REVERT: C 13 GLN cc_start: 0.7825 (OUTLIER) cc_final: 0.7466 (tm-30) REVERT: C 128 ASP cc_start: 0.8383 (m-30) cc_final: 0.8150 (m-30) REVERT: C 281 MET cc_start: 0.7402 (mtm) cc_final: 0.7104 (mtm) REVERT: C 288 GLN cc_start: 0.8386 (OUTLIER) cc_final: 0.7802 (mt0) REVERT: D 78 LYS cc_start: 0.8802 (OUTLIER) cc_final: 0.8256 (ttmt) REVERT: D 191 LEU cc_start: 0.7285 (OUTLIER) cc_final: 0.6257 (tt) REVERT: D 217 ILE cc_start: 0.8840 (mt) cc_final: 0.8554 (mm) REVERT: D 277 GLN cc_start: 0.8590 (mm-40) cc_final: 0.8281 (mm110) REVERT: E 13 GLN cc_start: 0.7805 (OUTLIER) cc_final: 0.7090 (tm-30) REVERT: E 14 ASP cc_start: 0.7609 (t0) cc_final: 0.7234 (t70) REVERT: E 46 GLU cc_start: 0.8460 (pt0) cc_final: 0.8152 (pt0) REVERT: E 248 LEU cc_start: 0.8156 (OUTLIER) cc_final: 0.7813 (mt) REVERT: E 267 GLU cc_start: 0.7478 (tp30) cc_final: 0.7138 (tp30) REVERT: E 288 GLN cc_start: 0.8540 (OUTLIER) cc_final: 0.8201 (mp10) REVERT: F 97 GLN cc_start: 0.7702 (OUTLIER) cc_final: 0.5992 (mp10) REVERT: F 314 SER cc_start: 0.6989 (OUTLIER) cc_final: 0.6589 (p) REVERT: G 78 LYS cc_start: 0.8805 (OUTLIER) cc_final: 0.8261 (ttmt) REVERT: G 97 GLN cc_start: 0.7800 (OUTLIER) cc_final: 0.6147 (mp10) REVERT: G 217 ILE cc_start: 0.8842 (mt) cc_final: 0.8550 (mm) REVERT: G 245 TYR cc_start: 0.7723 (m-80) cc_final: 0.7465 (m-80) REVERT: H 13 GLN cc_start: 0.7819 (OUTLIER) cc_final: 0.7462 (tm-30) REVERT: H 248 LEU cc_start: 0.8208 (OUTLIER) cc_final: 0.7843 (mt) REVERT: H 288 GLN cc_start: 0.8444 (OUTLIER) cc_final: 0.7858 (mt0) REVERT: I 14 ASP cc_start: 0.7476 (t0) cc_final: 0.7271 (t70) REVERT: I 52 ASP cc_start: 0.8345 (t0) cc_final: 0.8102 (t0) REVERT: J 13 GLN cc_start: 0.7764 (OUTLIER) cc_final: 0.7377 (tm-30) REVERT: J 68 MET cc_start: 0.8557 (tpt) cc_final: 0.8196 (tpp) REVERT: J 291 ASP cc_start: 0.8841 (t0) cc_final: 0.8569 (t70) REVERT: K 97 GLN cc_start: 0.7723 (OUTLIER) cc_final: 0.6002 (mp10) REVERT: K 314 SER cc_start: 0.7018 (OUTLIER) cc_final: 0.6620 (p) REVERT: L 13 GLN cc_start: 0.7813 (OUTLIER) cc_final: 0.7080 (tm-30) REVERT: L 14 ASP cc_start: 0.7605 (t0) cc_final: 0.7233 (t70) REVERT: L 46 GLU cc_start: 0.8472 (pt0) cc_final: 0.8181 (pt0) REVERT: L 248 LEU cc_start: 0.8159 (OUTLIER) cc_final: 0.7832 (mt) REVERT: L 314 SER cc_start: 0.6863 (OUTLIER) cc_final: 0.6644 (p) outliers start: 153 outliers final: 100 residues processed: 693 average time/residue: 1.4767 time to fit residues: 1181.2837 Evaluate side-chains 710 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 589 time to evaluate : 3.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 GLN Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 97 GLN Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain B residue 16 SER Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 97 GLN Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain B residue 307 GLU Chi-restraints excluded: chain C residue 13 GLN Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 286 LYS Chi-restraints excluded: chain C residue 288 GLN Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 78 LYS Chi-restraints excluded: chain D residue 97 GLN Chi-restraints excluded: chain D residue 132 SER Chi-restraints excluded: chain D residue 169 SER Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain E residue 13 GLN Chi-restraints excluded: chain E residue 36 SER Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 132 SER Chi-restraints excluded: chain E residue 155 ILE Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain E residue 288 GLN Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 97 GLN Chi-restraints excluded: chain F residue 118 VAL Chi-restraints excluded: chain F residue 169 SER Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 285 SER Chi-restraints excluded: chain F residue 314 SER Chi-restraints excluded: chain G residue 62 GLU Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain G residue 78 LYS Chi-restraints excluded: chain G residue 97 GLN Chi-restraints excluded: chain G residue 132 SER Chi-restraints excluded: chain G residue 169 SER Chi-restraints excluded: chain G residue 207 LEU Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 249 THR Chi-restraints excluded: chain G residue 314 SER Chi-restraints excluded: chain H residue 13 GLN Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 178 VAL Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain H residue 248 LEU Chi-restraints excluded: chain H residue 249 THR Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 278 GLU Chi-restraints excluded: chain H residue 286 LYS Chi-restraints excluded: chain H residue 288 GLN Chi-restraints excluded: chain H residue 314 SER Chi-restraints excluded: chain I residue 62 GLU Chi-restraints excluded: chain I residue 132 SER Chi-restraints excluded: chain I residue 169 SER Chi-restraints excluded: chain I residue 207 LEU Chi-restraints excluded: chain I residue 208 VAL Chi-restraints excluded: chain I residue 249 THR Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain I residue 278 GLU Chi-restraints excluded: chain I residue 285 SER Chi-restraints excluded: chain I residue 307 GLU Chi-restraints excluded: chain J residue 13 GLN Chi-restraints excluded: chain J residue 36 SER Chi-restraints excluded: chain J residue 62 GLU Chi-restraints excluded: chain J residue 97 GLN Chi-restraints excluded: chain J residue 132 SER Chi-restraints excluded: chain J residue 169 SER Chi-restraints excluded: chain J residue 208 VAL Chi-restraints excluded: chain J residue 249 THR Chi-restraints excluded: chain J residue 278 GLU Chi-restraints excluded: chain K residue 62 GLU Chi-restraints excluded: chain K residue 97 GLN Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain K residue 169 SER Chi-restraints excluded: chain K residue 208 VAL Chi-restraints excluded: chain K residue 249 THR Chi-restraints excluded: chain K residue 285 SER Chi-restraints excluded: chain K residue 314 SER Chi-restraints excluded: chain L residue 13 GLN Chi-restraints excluded: chain L residue 36 SER Chi-restraints excluded: chain L residue 62 GLU Chi-restraints excluded: chain L residue 118 VAL Chi-restraints excluded: chain L residue 132 SER Chi-restraints excluded: chain L residue 155 ILE Chi-restraints excluded: chain L residue 178 VAL Chi-restraints excluded: chain L residue 208 VAL Chi-restraints excluded: chain L residue 248 LEU Chi-restraints excluded: chain L residue 249 THR Chi-restraints excluded: chain L residue 314 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 335 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 chunk 198 optimal weight: 3.9990 chunk 254 optimal weight: 4.9990 chunk 197 optimal weight: 4.9990 chunk 293 optimal weight: 7.9990 chunk 194 optimal weight: 0.7980 chunk 346 optimal weight: 2.9990 chunk 217 optimal weight: 0.7980 chunk 211 optimal weight: 2.9990 chunk 160 optimal weight: 0.0870 overall best weight: 1.3362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 GLN B 97 GLN C 12 HIS D 97 GLN E 12 HIS F 263 ASN H 12 HIS H 97 GLN J 97 GLN K 263 ASN L 12 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 29076 Z= 0.199 Angle : 0.469 7.637 39396 Z= 0.253 Chirality : 0.046 0.172 4668 Planarity : 0.003 0.029 4992 Dihedral : 6.328 53.549 4275 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 4.83 % Allowed : 15.39 % Favored : 79.77 % 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: 0.49 (0.14), residues: 3660 helix: 1.26 (0.15), residues: 1380 sheet: -0.12 (0.17), residues: 936 loop : -0.15 (0.16), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP L 162 HIS 0.003 0.001 HIS E 304 PHE 0.012 0.001 PHE B 138 TYR 0.016 0.002 TYR L 146 ARG 0.007 0.000 ARG B 22 *********************** 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 745 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 593 time to evaluate : 3.019 Fit side-chains REVERT: A 13 GLN cc_start: 0.7776 (OUTLIER) cc_final: 0.7390 (tm-30) REVERT: A 68 MET cc_start: 0.8563 (tpt) cc_final: 0.8200 (tpp) REVERT: B 14 ASP cc_start: 0.7454 (t0) cc_final: 0.7207 (t70) REVERT: B 38 GLN cc_start: 0.7470 (mm110) cc_final: 0.7265 (mm110) REVERT: B 52 ASP cc_start: 0.8342 (t0) cc_final: 0.8089 (t0) REVERT: B 288 GLN cc_start: 0.8342 (OUTLIER) cc_final: 0.7944 (mt0) REVERT: C 13 GLN cc_start: 0.7821 (OUTLIER) cc_final: 0.7457 (tm-30) REVERT: C 128 ASP cc_start: 0.8379 (m-30) cc_final: 0.8158 (m-30) REVERT: C 281 MET cc_start: 0.7407 (mtm) cc_final: 0.7125 (mtm) REVERT: C 288 GLN cc_start: 0.8389 (OUTLIER) cc_final: 0.7786 (mt0) REVERT: D 78 LYS cc_start: 0.8764 (OUTLIER) cc_final: 0.8237 (ttmt) REVERT: D 191 LEU cc_start: 0.7275 (OUTLIER) cc_final: 0.6247 (tt) REVERT: D 217 ILE cc_start: 0.8831 (mt) cc_final: 0.8548 (mm) REVERT: D 277 GLN cc_start: 0.8573 (mm-40) cc_final: 0.8265 (mm110) REVERT: E 13 GLN cc_start: 0.7799 (OUTLIER) cc_final: 0.7087 (tm-30) REVERT: E 14 ASP cc_start: 0.7603 (t0) cc_final: 0.7228 (t70) REVERT: E 46 GLU cc_start: 0.8461 (pt0) cc_final: 0.8150 (pt0) REVERT: E 267 GLU cc_start: 0.7461 (tp30) cc_final: 0.7115 (tp30) REVERT: E 288 GLN cc_start: 0.8536 (OUTLIER) cc_final: 0.8207 (mp10) REVERT: F 314 SER cc_start: 0.6994 (OUTLIER) cc_final: 0.6599 (p) REVERT: G 78 LYS cc_start: 0.8764 (OUTLIER) cc_final: 0.8245 (ttmt) REVERT: G 97 GLN cc_start: 0.7778 (OUTLIER) cc_final: 0.6117 (mp10) REVERT: G 191 LEU cc_start: 0.7258 (OUTLIER) cc_final: 0.6233 (tt) REVERT: G 217 ILE cc_start: 0.8857 (mt) cc_final: 0.8574 (mm) REVERT: G 245 TYR cc_start: 0.7729 (m-80) cc_final: 0.7464 (m-80) REVERT: H 13 GLN cc_start: 0.7817 (OUTLIER) cc_final: 0.7465 (tm-30) REVERT: H 248 LEU cc_start: 0.8203 (OUTLIER) cc_final: 0.7837 (mt) REVERT: H 288 GLN cc_start: 0.8436 (OUTLIER) cc_final: 0.7842 (mt0) REVERT: H 314 SER cc_start: 0.6047 (OUTLIER) cc_final: 0.5596 (p) REVERT: I 52 ASP cc_start: 0.8338 (t0) cc_final: 0.8097 (t0) REVERT: I 288 GLN cc_start: 0.8332 (OUTLIER) cc_final: 0.7938 (mt0) REVERT: J 13 GLN cc_start: 0.7786 (OUTLIER) cc_final: 0.7393 (tm-30) REVERT: J 68 MET cc_start: 0.8554 (tpt) cc_final: 0.8194 (tpp) REVERT: K 97 GLN cc_start: 0.7728 (OUTLIER) cc_final: 0.5854 (mp10) REVERT: K 191 LEU cc_start: 0.7849 (OUTLIER) cc_final: 0.6670 (tm) REVERT: L 13 GLN cc_start: 0.7809 (OUTLIER) cc_final: 0.7078 (tm-30) REVERT: L 14 ASP cc_start: 0.7599 (t0) cc_final: 0.7234 (t70) REVERT: L 46 GLU cc_start: 0.8466 (pt0) cc_final: 0.8179 (pt0) REVERT: L 288 GLN cc_start: 0.8407 (mt0) cc_final: 0.8033 (mt0) REVERT: L 314 SER cc_start: 0.6829 (OUTLIER) cc_final: 0.6599 (p) outliers start: 152 outliers final: 97 residues processed: 695 average time/residue: 1.4648 time to fit residues: 1176.2762 Evaluate side-chains 706 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 587 time to evaluate : 3.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 GLN Chi-restraints excluded: chain A residue 36 SER Chi-restraints excluded: chain A residue 97 GLN Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain B residue 16 SER Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain B residue 288 GLN Chi-restraints excluded: chain C residue 13 GLN Chi-restraints excluded: chain C residue 36 SER Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 286 LYS Chi-restraints excluded: chain C residue 288 GLN Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 78 LYS Chi-restraints excluded: chain D residue 132 SER Chi-restraints excluded: chain D residue 169 SER Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain E residue 13 GLN Chi-restraints excluded: chain E residue 36 SER Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 132 SER Chi-restraints excluded: chain E residue 155 ILE Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain E residue 288 GLN Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 118 VAL Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 285 SER Chi-restraints excluded: chain F residue 314 SER Chi-restraints excluded: chain G residue 62 GLU Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain G residue 78 LYS Chi-restraints excluded: chain G residue 97 GLN Chi-restraints excluded: chain G residue 132 SER Chi-restraints excluded: chain G residue 169 SER Chi-restraints excluded: chain G residue 191 LEU Chi-restraints excluded: chain G residue 207 LEU Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 249 THR Chi-restraints excluded: chain H residue 13 GLN Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 178 VAL Chi-restraints excluded: chain H residue 207 LEU Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain H residue 248 LEU Chi-restraints excluded: chain H residue 249 THR Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 278 GLU Chi-restraints excluded: chain H residue 286 LYS Chi-restraints excluded: chain H residue 288 GLN Chi-restraints excluded: chain H residue 314 SER Chi-restraints excluded: chain I residue 62 GLU Chi-restraints excluded: chain I residue 132 SER Chi-restraints excluded: chain I residue 169 SER Chi-restraints excluded: chain I residue 207 LEU Chi-restraints excluded: chain I residue 208 VAL Chi-restraints excluded: chain I residue 249 THR Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain I residue 285 SER Chi-restraints excluded: chain I residue 288 GLN Chi-restraints excluded: chain I residue 307 GLU Chi-restraints excluded: chain J residue 13 GLN Chi-restraints excluded: chain J residue 36 SER Chi-restraints excluded: chain J residue 62 GLU Chi-restraints excluded: chain J residue 97 GLN Chi-restraints excluded: chain J residue 132 SER Chi-restraints excluded: chain J residue 169 SER Chi-restraints excluded: chain J residue 208 VAL Chi-restraints excluded: chain J residue 249 THR Chi-restraints excluded: chain J residue 278 GLU Chi-restraints excluded: chain J residue 314 SER Chi-restraints excluded: chain K residue 62 GLU Chi-restraints excluded: chain K residue 97 GLN Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain K residue 191 LEU Chi-restraints excluded: chain K residue 208 VAL Chi-restraints excluded: chain K residue 249 THR Chi-restraints excluded: chain K residue 285 SER Chi-restraints excluded: chain L residue 13 GLN Chi-restraints excluded: chain L residue 36 SER Chi-restraints excluded: chain L residue 62 GLU Chi-restraints excluded: chain L residue 118 VAL Chi-restraints excluded: chain L residue 132 SER Chi-restraints excluded: chain L residue 155 ILE Chi-restraints excluded: chain L residue 178 VAL Chi-restraints excluded: chain L residue 207 LEU Chi-restraints excluded: chain L residue 208 VAL Chi-restraints excluded: chain L residue 249 THR Chi-restraints excluded: chain L residue 314 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 214 optimal weight: 4.9990 chunk 138 optimal weight: 5.9990 chunk 207 optimal weight: 0.0070 chunk 104 optimal weight: 0.8980 chunk 68 optimal weight: 7.9990 chunk 67 optimal weight: 4.9990 chunk 220 optimal weight: 0.9990 chunk 236 optimal weight: 3.9990 chunk 171 optimal weight: 8.9990 chunk 32 optimal weight: 0.0980 chunk 272 optimal weight: 0.5980 overall best weight: 0.5200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 GLN B 97 GLN F 263 ASN J 97 GLN J 123 HIS K 263 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 29076 Z= 0.126 Angle : 0.432 7.903 39396 Z= 0.230 Chirality : 0.045 0.162 4668 Planarity : 0.003 0.030 4992 Dihedral : 5.786 48.886 4272 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.59 % Allowed : 16.35 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.14), residues: 3660 helix: 1.44 (0.15), residues: 1380 sheet: 0.00 (0.17), residues: 936 loop : -0.11 (0.16), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP E 162 HIS 0.004 0.001 HIS J 193 PHE 0.013 0.001 PHE B 35 TYR 0.011 0.001 TYR A 311 ARG 0.009 0.000 ARG D 22 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7320 Ramachandran restraints generated. 3660 Oldfield, 0 Emsley, 3660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7320 Ramachandran restraints generated. 3660 Oldfield, 0 Emsley, 3660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 727 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 614 time to evaluate : 3.202 Fit side-chains REVERT: A 13 GLN cc_start: 0.7758 (OUTLIER) cc_final: 0.7354 (tm-30) REVERT: A 68 MET cc_start: 0.8547 (tpt) cc_final: 0.8194 (tpp) REVERT: B 38 GLN cc_start: 0.7360 (mm110) cc_final: 0.7145 (mm110) REVERT: B 52 ASP cc_start: 0.8325 (t0) cc_final: 0.8075 (t0) REVERT: B 288 GLN cc_start: 0.8359 (OUTLIER) cc_final: 0.7976 (mt0) REVERT: C 281 MET cc_start: 0.7345 (mtm) cc_final: 0.7143 (mtm) REVERT: D 191 LEU cc_start: 0.7227 (OUTLIER) cc_final: 0.6245 (tt) REVERT: D 217 ILE cc_start: 0.8799 (mt) cc_final: 0.8516 (mm) REVERT: E 14 ASP cc_start: 0.7570 (t0) cc_final: 0.7214 (t70) REVERT: E 46 GLU cc_start: 0.8457 (pt0) cc_final: 0.8127 (pt0) REVERT: E 267 GLU cc_start: 0.7466 (tp30) cc_final: 0.7147 (tp30) REVERT: E 288 GLN cc_start: 0.8509 (OUTLIER) cc_final: 0.8187 (mp10) REVERT: F 191 LEU cc_start: 0.7542 (OUTLIER) cc_final: 0.6471 (tm) REVERT: G 191 LEU cc_start: 0.7213 (OUTLIER) cc_final: 0.6206 (tt) REVERT: G 217 ILE cc_start: 0.8819 (mt) cc_final: 0.8530 (mm) REVERT: G 245 TYR cc_start: 0.7532 (m-80) cc_final: 0.7239 (m-80) REVERT: I 21 ASP cc_start: 0.7897 (m-30) cc_final: 0.7440 (m-30) REVERT: I 52 ASP cc_start: 0.8292 (t0) cc_final: 0.8057 (t0) REVERT: J 68 MET cc_start: 0.8551 (tpt) cc_final: 0.8202 (tpp) REVERT: K 191 LEU cc_start: 0.7569 (OUTLIER) cc_final: 0.6505 (tm) REVERT: K 288 GLN cc_start: 0.8339 (mt0) cc_final: 0.8064 (mt0) REVERT: L 14 ASP cc_start: 0.7566 (t0) cc_final: 0.7225 (t70) REVERT: L 46 GLU cc_start: 0.8454 (pt0) cc_final: 0.8153 (pt0) outliers start: 113 outliers final: 75 residues processed: 690 average time/residue: 1.4421 time to fit residues: 1153.4845 Evaluate side-chains 672 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 590 time to evaluate : 3.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 GLN Chi-restraints excluded: chain A residue 97 GLN Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain B residue 16 SER Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain B residue 288 GLN Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 286 LYS Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 132 SER Chi-restraints excluded: chain D residue 169 SER Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain E residue 36 SER Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain E residue 288 GLN Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 118 VAL Chi-restraints excluded: chain F residue 169 SER Chi-restraints excluded: chain F residue 191 LEU Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain G residue 62 GLU Chi-restraints excluded: chain G residue 132 SER Chi-restraints excluded: chain G residue 169 SER Chi-restraints excluded: chain G residue 191 LEU Chi-restraints excluded: chain G residue 207 LEU Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 248 LEU Chi-restraints excluded: chain G residue 249 THR Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 178 VAL Chi-restraints excluded: chain H residue 207 LEU Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain H residue 249 THR Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 278 GLU Chi-restraints excluded: chain I residue 208 VAL Chi-restraints excluded: chain I residue 249 THR Chi-restraints excluded: chain I residue 285 SER Chi-restraints excluded: chain J residue 36 SER Chi-restraints excluded: chain J residue 62 GLU Chi-restraints excluded: chain J residue 97 GLN Chi-restraints excluded: chain J residue 132 SER Chi-restraints excluded: chain J residue 208 VAL Chi-restraints excluded: chain J residue 249 THR Chi-restraints excluded: chain J residue 278 GLU Chi-restraints excluded: chain K residue 62 GLU Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain K residue 169 SER Chi-restraints excluded: chain K residue 191 LEU Chi-restraints excluded: chain K residue 207 LEU Chi-restraints excluded: chain K residue 208 VAL Chi-restraints excluded: chain K residue 249 THR Chi-restraints excluded: chain L residue 36 SER Chi-restraints excluded: chain L residue 62 GLU Chi-restraints excluded: chain L residue 118 VAL Chi-restraints excluded: chain L residue 132 SER Chi-restraints excluded: chain L residue 178 VAL Chi-restraints excluded: chain L residue 207 LEU Chi-restraints excluded: chain L residue 208 VAL Chi-restraints excluded: chain L residue 249 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 315 optimal weight: 2.9990 chunk 332 optimal weight: 0.9980 chunk 303 optimal weight: 2.9990 chunk 323 optimal weight: 3.9990 chunk 194 optimal weight: 0.9980 chunk 140 optimal weight: 9.9990 chunk 253 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 chunk 292 optimal weight: 3.9990 chunk 305 optimal weight: 5.9990 chunk 322 optimal weight: 0.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 GLN B 97 GLN C 12 HIS E 12 HIS F 263 ASN H 12 HIS I 97 GLN J 97 GLN K 263 ASN L 12 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.2579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 29076 Z= 0.187 Angle : 0.462 7.870 39396 Z= 0.247 Chirality : 0.046 0.168 4668 Planarity : 0.003 0.028 4992 Dihedral : 5.928 48.423 4272 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 3.50 % Allowed : 16.89 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.14), residues: 3660 helix: 1.41 (0.15), residues: 1380 sheet: -0.01 (0.17), residues: 936 loop : -0.06 (0.16), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP G 154 HIS 0.004 0.001 HIS J 193 PHE 0.014 0.001 PHE H 35 TYR 0.013 0.002 TYR L 146 ARG 0.007 0.000 ARG B 22 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7320 Ramachandran restraints generated. 3660 Oldfield, 0 Emsley, 3660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7320 Ramachandran restraints generated. 3660 Oldfield, 0 Emsley, 3660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 706 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 596 time to evaluate : 3.093 Fit side-chains REVERT: A 13 GLN cc_start: 0.7782 (OUTLIER) cc_final: 0.7393 (tm-30) REVERT: A 68 MET cc_start: 0.8546 (tpt) cc_final: 0.8182 (tpp) REVERT: B 14 ASP cc_start: 0.7433 (t70) cc_final: 0.7146 (t70) REVERT: B 38 GLN cc_start: 0.7271 (mm110) cc_final: 0.7038 (mm110) REVERT: B 52 ASP cc_start: 0.8345 (t0) cc_final: 0.8074 (t0) REVERT: B 97 GLN cc_start: 0.7705 (OUTLIER) cc_final: 0.7140 (mt0) REVERT: B 288 GLN cc_start: 0.8359 (OUTLIER) cc_final: 0.7958 (mt0) REVERT: C 222 MET cc_start: 0.8252 (ptp) cc_final: 0.8036 (ptm) REVERT: C 281 MET cc_start: 0.7369 (mtm) cc_final: 0.7131 (mtm) REVERT: D 191 LEU cc_start: 0.7280 (OUTLIER) cc_final: 0.6276 (tt) REVERT: D 217 ILE cc_start: 0.8810 (mt) cc_final: 0.8517 (mm) REVERT: D 245 TYR cc_start: 0.7553 (m-80) cc_final: 0.7261 (m-80) REVERT: E 13 GLN cc_start: 0.7801 (OUTLIER) cc_final: 0.7092 (tm-30) REVERT: E 14 ASP cc_start: 0.7613 (t0) cc_final: 0.7255 (t70) REVERT: E 46 GLU cc_start: 0.8476 (pt0) cc_final: 0.8154 (pt0) REVERT: E 97 GLN cc_start: 0.7801 (OUTLIER) cc_final: 0.6739 (mp10) REVERT: E 248 LEU cc_start: 0.8072 (OUTLIER) cc_final: 0.7702 (mt) REVERT: E 267 GLU cc_start: 0.7454 (tp30) cc_final: 0.7141 (tp30) REVERT: E 288 GLN cc_start: 0.8538 (OUTLIER) cc_final: 0.8190 (mp10) REVERT: F 97 GLN cc_start: 0.7577 (OUTLIER) cc_final: 0.5743 (mp10) REVERT: F 191 LEU cc_start: 0.7579 (OUTLIER) cc_final: 0.6503 (tm) REVERT: F 294 MET cc_start: 0.8496 (pmt) cc_final: 0.8073 (pmm) REVERT: G 191 LEU cc_start: 0.7231 (OUTLIER) cc_final: 0.6210 (tt) REVERT: G 217 ILE cc_start: 0.8815 (mt) cc_final: 0.8532 (mm) REVERT: G 245 TYR cc_start: 0.7562 (m-80) cc_final: 0.7269 (m-80) REVERT: H 288 GLN cc_start: 0.8430 (OUTLIER) cc_final: 0.7825 (mt0) REVERT: I 52 ASP cc_start: 0.8301 (t0) cc_final: 0.8056 (t0) REVERT: J 68 MET cc_start: 0.8557 (tpt) cc_final: 0.8194 (tpp) REVERT: K 191 LEU cc_start: 0.7603 (OUTLIER) cc_final: 0.6530 (tm) REVERT: K 294 MET cc_start: 0.8492 (pmt) cc_final: 0.8163 (pmm) REVERT: K 314 SER cc_start: 0.6876 (OUTLIER) cc_final: 0.6505 (p) REVERT: L 13 GLN cc_start: 0.7815 (OUTLIER) cc_final: 0.7105 (tm-30) REVERT: L 14 ASP cc_start: 0.7612 (t0) cc_final: 0.7258 (t70) REVERT: L 46 GLU cc_start: 0.8474 (pt0) cc_final: 0.8174 (pt0) REVERT: L 97 GLN cc_start: 0.7818 (OUTLIER) cc_final: 0.6747 (mp10) REVERT: L 248 LEU cc_start: 0.8084 (OUTLIER) cc_final: 0.7716 (mt) outliers start: 110 outliers final: 81 residues processed: 667 average time/residue: 1.4695 time to fit residues: 1131.1830 Evaluate side-chains 689 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 591 time to evaluate : 3.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 GLN Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain B residue 16 SER Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 97 GLN Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain B residue 288 GLN Chi-restraints excluded: chain B residue 307 GLU Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 286 LYS Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 132 SER Chi-restraints excluded: chain D residue 169 SER Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain E residue 13 GLN Chi-restraints excluded: chain E residue 36 SER Chi-restraints excluded: chain E residue 97 GLN Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 132 SER Chi-restraints excluded: chain E residue 155 ILE Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain E residue 288 GLN Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 97 GLN Chi-restraints excluded: chain F residue 118 VAL Chi-restraints excluded: chain F residue 169 SER Chi-restraints excluded: chain F residue 191 LEU Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain G residue 62 GLU Chi-restraints excluded: chain G residue 132 SER Chi-restraints excluded: chain G residue 169 SER Chi-restraints excluded: chain G residue 191 LEU Chi-restraints excluded: chain G residue 207 LEU Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 249 THR Chi-restraints excluded: chain G residue 314 SER Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 178 VAL Chi-restraints excluded: chain H residue 207 LEU Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain H residue 249 THR Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 278 GLU Chi-restraints excluded: chain H residue 288 GLN Chi-restraints excluded: chain I residue 208 VAL Chi-restraints excluded: chain I residue 249 THR Chi-restraints excluded: chain I residue 307 GLU Chi-restraints excluded: chain J residue 36 SER Chi-restraints excluded: chain J residue 62 GLU Chi-restraints excluded: chain J residue 97 GLN Chi-restraints excluded: chain J residue 132 SER Chi-restraints excluded: chain J residue 207 LEU Chi-restraints excluded: chain J residue 208 VAL Chi-restraints excluded: chain J residue 249 THR Chi-restraints excluded: chain J residue 278 GLU Chi-restraints excluded: chain K residue 62 GLU Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain K residue 169 SER Chi-restraints excluded: chain K residue 191 LEU Chi-restraints excluded: chain K residue 207 LEU Chi-restraints excluded: chain K residue 208 VAL Chi-restraints excluded: chain K residue 249 THR Chi-restraints excluded: chain K residue 285 SER Chi-restraints excluded: chain K residue 314 SER Chi-restraints excluded: chain L residue 13 GLN Chi-restraints excluded: chain L residue 36 SER Chi-restraints excluded: chain L residue 62 GLU Chi-restraints excluded: chain L residue 97 GLN Chi-restraints excluded: chain L residue 118 VAL Chi-restraints excluded: chain L residue 132 SER Chi-restraints excluded: chain L residue 178 VAL Chi-restraints excluded: chain L residue 207 LEU Chi-restraints excluded: chain L residue 208 VAL Chi-restraints excluded: chain L residue 248 LEU Chi-restraints excluded: chain L residue 249 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 212 optimal weight: 6.9990 chunk 341 optimal weight: 0.8980 chunk 208 optimal weight: 1.9990 chunk 162 optimal weight: 0.8980 chunk 237 optimal weight: 5.9990 chunk 358 optimal weight: 3.9990 chunk 330 optimal weight: 0.9990 chunk 285 optimal weight: 7.9990 chunk 29 optimal weight: 0.9980 chunk 220 optimal weight: 4.9990 chunk 175 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 GLN A 288 GLN B 97 GLN C 12 HIS E 12 HIS F 263 ASN H 12 HIS I 97 GLN J 97 GLN J 288 GLN K 263 ASN L 12 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.2586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 29076 Z= 0.183 Angle : 0.463 7.794 39396 Z= 0.247 Chirality : 0.046 0.169 4668 Planarity : 0.003 0.030 4992 Dihedral : 5.920 48.253 4272 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 3.53 % Allowed : 16.98 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.14), residues: 3660 helix: 1.39 (0.15), residues: 1380 sheet: -0.01 (0.17), residues: 936 loop : -0.05 (0.16), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP E 162 HIS 0.003 0.001 HIS C 123 PHE 0.011 0.001 PHE B 138 TYR 0.015 0.002 TYR E 146 ARG 0.007 0.000 ARG D 22 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7320 Ramachandran restraints generated. 3660 Oldfield, 0 Emsley, 3660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7320 Ramachandran restraints generated. 3660 Oldfield, 0 Emsley, 3660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 702 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 591 time to evaluate : 3.394 Fit side-chains REVERT: A 13 GLN cc_start: 0.7779 (OUTLIER) cc_final: 0.7394 (tm-30) REVERT: A 68 MET cc_start: 0.8550 (tpt) cc_final: 0.8190 (tpp) REVERT: A 260 ARG cc_start: 0.8083 (mtt180) cc_final: 0.7784 (mtm-85) REVERT: B 14 ASP cc_start: 0.7429 (t70) cc_final: 0.7144 (t70) REVERT: B 38 GLN cc_start: 0.7197 (mm110) cc_final: 0.6946 (mm110) REVERT: B 52 ASP cc_start: 0.8320 (t0) cc_final: 0.8052 (t0) REVERT: C 222 MET cc_start: 0.8232 (ptp) cc_final: 0.8017 (ptm) REVERT: C 281 MET cc_start: 0.7370 (mtm) cc_final: 0.7128 (mtm) REVERT: D 191 LEU cc_start: 0.7273 (OUTLIER) cc_final: 0.6272 (tt) REVERT: D 217 ILE cc_start: 0.8799 (mt) cc_final: 0.8531 (mm) REVERT: D 245 TYR cc_start: 0.7551 (m-80) cc_final: 0.7266 (m-80) REVERT: E 13 GLN cc_start: 0.7796 (OUTLIER) cc_final: 0.7093 (tm-30) REVERT: E 14 ASP cc_start: 0.7609 (t0) cc_final: 0.7245 (t70) REVERT: E 46 GLU cc_start: 0.8477 (pt0) cc_final: 0.8155 (pt0) REVERT: E 97 GLN cc_start: 0.7803 (OUTLIER) cc_final: 0.6732 (mp10) REVERT: E 248 LEU cc_start: 0.8053 (OUTLIER) cc_final: 0.7683 (mt) REVERT: E 267 GLU cc_start: 0.7453 (tp30) cc_final: 0.7135 (tp30) REVERT: E 288 GLN cc_start: 0.8536 (OUTLIER) cc_final: 0.8182 (mp10) REVERT: F 191 LEU cc_start: 0.7576 (OUTLIER) cc_final: 0.6509 (tm) REVERT: F 294 MET cc_start: 0.8489 (pmt) cc_final: 0.8066 (pmm) REVERT: G 191 LEU cc_start: 0.7241 (OUTLIER) cc_final: 0.6230 (tt) REVERT: G 217 ILE cc_start: 0.8815 (mt) cc_final: 0.8530 (mm) REVERT: G 245 TYR cc_start: 0.7558 (m-80) cc_final: 0.7266 (m-80) REVERT: H 222 MET cc_start: 0.8227 (ptp) cc_final: 0.8018 (ptm) REVERT: H 288 GLN cc_start: 0.8430 (OUTLIER) cc_final: 0.7881 (mt0) REVERT: I 52 ASP cc_start: 0.8299 (t0) cc_final: 0.8053 (t0) REVERT: J 13 GLN cc_start: 0.7792 (OUTLIER) cc_final: 0.7405 (tm-30) REVERT: J 68 MET cc_start: 0.8539 (tpt) cc_final: 0.8183 (tpp) REVERT: J 248 LEU cc_start: 0.8203 (OUTLIER) cc_final: 0.7967 (mt) REVERT: J 260 ARG cc_start: 0.8090 (mtt180) cc_final: 0.7835 (mtm-85) REVERT: K 191 LEU cc_start: 0.7594 (OUTLIER) cc_final: 0.6518 (tm) REVERT: K 288 GLN cc_start: 0.8339 (OUTLIER) cc_final: 0.8112 (mt0) REVERT: K 294 MET cc_start: 0.8507 (pmt) cc_final: 0.8078 (pmm) REVERT: K 314 SER cc_start: 0.6870 (OUTLIER) cc_final: 0.6505 (p) REVERT: L 14 ASP cc_start: 0.7608 (t0) cc_final: 0.7264 (t70) REVERT: L 46 GLU cc_start: 0.8483 (pt0) cc_final: 0.8185 (pt0) REVERT: L 97 GLN cc_start: 0.7819 (OUTLIER) cc_final: 0.6751 (mp10) REVERT: L 248 LEU cc_start: 0.8083 (OUTLIER) cc_final: 0.7714 (mt) outliers start: 111 outliers final: 80 residues processed: 664 average time/residue: 1.5194 time to fit residues: 1165.1210 Evaluate side-chains 685 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 589 time to evaluate : 3.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 GLN Chi-restraints excluded: chain A residue 132 SER Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain B residue 16 SER Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 285 SER Chi-restraints excluded: chain B residue 307 GLU Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 132 SER Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 278 GLU Chi-restraints excluded: chain C residue 286 LYS Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 132 SER Chi-restraints excluded: chain D residue 169 SER Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain E residue 13 GLN Chi-restraints excluded: chain E residue 36 SER Chi-restraints excluded: chain E residue 97 GLN Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 249 THR Chi-restraints excluded: chain E residue 288 GLN Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 118 VAL Chi-restraints excluded: chain F residue 169 SER Chi-restraints excluded: chain F residue 191 LEU Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 285 SER Chi-restraints excluded: chain G residue 62 GLU Chi-restraints excluded: chain G residue 132 SER Chi-restraints excluded: chain G residue 169 SER Chi-restraints excluded: chain G residue 191 LEU Chi-restraints excluded: chain G residue 207 LEU Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 249 THR Chi-restraints excluded: chain H residue 36 SER Chi-restraints excluded: chain H residue 62 GLU Chi-restraints excluded: chain H residue 178 VAL Chi-restraints excluded: chain H residue 207 LEU Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain H residue 249 THR Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 278 GLU Chi-restraints excluded: chain H residue 288 GLN Chi-restraints excluded: chain I residue 208 VAL Chi-restraints excluded: chain I residue 249 THR Chi-restraints excluded: chain I residue 307 GLU Chi-restraints excluded: chain J residue 13 GLN Chi-restraints excluded: chain J residue 36 SER Chi-restraints excluded: chain J residue 62 GLU Chi-restraints excluded: chain J residue 97 GLN Chi-restraints excluded: chain J residue 132 SER Chi-restraints excluded: chain J residue 207 LEU Chi-restraints excluded: chain J residue 208 VAL Chi-restraints excluded: chain J residue 248 LEU Chi-restraints excluded: chain J residue 249 THR Chi-restraints excluded: chain J residue 278 GLU Chi-restraints excluded: chain K residue 62 GLU Chi-restraints excluded: chain K residue 118 VAL Chi-restraints excluded: chain K residue 169 SER Chi-restraints excluded: chain K residue 191 LEU Chi-restraints excluded: chain K residue 207 LEU Chi-restraints excluded: chain K residue 208 VAL Chi-restraints excluded: chain K residue 249 THR Chi-restraints excluded: chain K residue 285 SER Chi-restraints excluded: chain K residue 288 GLN Chi-restraints excluded: chain K residue 314 SER Chi-restraints excluded: chain L residue 36 SER Chi-restraints excluded: chain L residue 62 GLU Chi-restraints excluded: chain L residue 97 GLN Chi-restraints excluded: chain L residue 118 VAL Chi-restraints excluded: chain L residue 132 SER Chi-restraints excluded: chain L residue 178 VAL Chi-restraints excluded: chain L residue 207 LEU Chi-restraints excluded: chain L residue 208 VAL Chi-restraints excluded: chain L residue 248 LEU Chi-restraints excluded: chain L residue 249 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 226 optimal weight: 0.9980 chunk 304 optimal weight: 0.5980 chunk 87 optimal weight: 5.9990 chunk 263 optimal weight: 9.9990 chunk 42 optimal weight: 10.0000 chunk 79 optimal weight: 0.9990 chunk 286 optimal weight: 0.9990 chunk 119 optimal weight: 1.9990 chunk 293 optimal weight: 7.9990 chunk 36 optimal weight: 5.9990 chunk 52 optimal weight: 4.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 GLN A 288 GLN B 97 GLN C 12 HIS E 12 HIS F 263 ASN H 12 HIS J 97 GLN J 288 GLN K 263 ASN L 12 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.171277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.129611 restraints weight = 25925.925| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 1.61 r_work: 0.3210 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3089 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3089 r_free = 0.3089 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 648 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2913 r_free = 0.2913 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2913 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.2611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 29076 Z= 0.180 Angle : 0.460 7.714 39396 Z= 0.246 Chirality : 0.046 0.168 4668 Planarity : 0.003 0.029 4992 Dihedral : 5.905 48.206 4272 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 3.66 % Allowed : 16.79 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.14), residues: 3660 helix: 1.39 (0.15), residues: 1380 sheet: -0.01 (0.17), residues: 936 loop : -0.04 (0.16), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP E 162 HIS 0.003 0.001 HIS E 304 PHE 0.013 0.001 PHE C 35 TYR 0.014 0.002 TYR E 146 ARG 0.007 0.000 ARG D 22 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16059.30 seconds wall clock time: 281 minutes 41.42 seconds (16901.42 seconds total)