Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 28 23:52:43 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbm_27290/04_2023/8dbm_27290_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbm_27290/04_2023/8dbm_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_27290/04_2023/8dbm_27290.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbm_27290/04_2023/8dbm_27290.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbm_27290/04_2023/8dbm_27290_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbm_27290/04_2023/8dbm_27290_updated.pdb" } resolution = 2.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.390 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: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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: 15.16, per 1000 atoms: 0.53 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: 11.48 Conformation dependent library (CDL) restraints added in 4.2 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: 2.75 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: 9.40 Time building geometry restraints manager: 12.26 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: 15809 17.71 - 35.42: 1291 35.42 - 53.12: 384 53.12 - 70.83: 120 70.83 - 88.54: 72 Dihedral angle restraints: 17676 sinusoidal: 6924 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 17673 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: 0.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 6.150 Check model and map are aligned: 0.440 Set scattering table: 0.270 Process input model: 69.610 Find NCS groups from input model: 1.920 Set up NCS constraints: 0.220 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:11.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 91.450 ------------------------------------------------------------------------------- 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 : 16.471 88.539 10668 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 % 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 *********************** 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 : 3.300 Fit side-chains outliers start: 84 outliers final: 38 residues processed: 893 average time/residue: 1.4016 time to fit residues: 1460.4086 Evaluate side-chains 623 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 585 time to evaluate : 3.372 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 35 residues processed: 3 average time/residue: 1.8227 time to fit residues: 10.8117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 303 optimal weight: 2.9990 chunk 272 optimal weight: 0.0040 chunk 151 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 184 optimal weight: 1.9990 chunk 145 optimal weight: 0.7980 chunk 282 optimal weight: 1.9990 chunk 109 optimal weight: 5.9990 chunk 171 optimal weight: 6.9990 chunk 210 optimal weight: 0.7980 chunk 326 optimal weight: 0.9980 overall best weight: 0.9194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 GLN C 97 GLN 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 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: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.031 29076 Z= 0.162 Angle : 0.459 4.817 39396 Z= 0.251 Chirality : 0.047 0.168 4668 Planarity : 0.003 0.022 4992 Dihedral : 4.412 20.758 3960 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer Outliers : 4.17 % 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: 1.36 (0.14), residues: 1404 sheet: -0.44 (0.17), residues: 996 loop : 0.01 (0.17), residues: 1260 *********************** 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 743 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 612 time to evaluate : 3.576 Fit side-chains outliers start: 131 outliers final: 70 residues processed: 692 average time/residue: 1.3999 time to fit residues: 1131.9426 Evaluate side-chains 639 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 569 time to evaluate : 3.448 Switching outliers to nearest non-outliers outliers start: 70 outliers final: 47 residues processed: 23 average time/residue: 1.1475 time to fit residues: 36.3934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 181 optimal weight: 0.3980 chunk 101 optimal weight: 2.9990 chunk 272 optimal weight: 5.9990 chunk 222 optimal weight: 10.0000 chunk 90 optimal weight: 6.9990 chunk 327 optimal weight: 3.9990 chunk 353 optimal weight: 4.9990 chunk 291 optimal weight: 2.9990 chunk 324 optimal weight: 6.9990 chunk 111 optimal weight: 10.0000 chunk 262 optimal weight: 0.9980 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 GLN B 12 HIS C 12 HIS C 97 GLN D 263 ASN E 12 HIS F 263 ASN G 97 GLN G 263 ASN H 12 HIS I 12 HIS I 135 GLN J 97 GLN K 135 GLN K 263 ASN L 12 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.083 29076 Z= 0.303 Angle : 0.528 7.098 39396 Z= 0.287 Chirality : 0.049 0.178 4668 Planarity : 0.004 0.025 4992 Dihedral : 4.981 44.596 3960 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer Outliers : 5.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.14), residues: 3660 helix: 1.19 (0.14), residues: 1392 sheet: -0.18 (0.18), residues: 936 loop : 0.03 (0.17), residues: 1332 *********************** 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 772 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 614 time to evaluate : 3.288 Fit side-chains outliers start: 158 outliers final: 98 residues processed: 714 average time/residue: 1.4630 time to fit residues: 1216.2526 Evaluate side-chains 702 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 604 time to evaluate : 3.301 Switching outliers to nearest non-outliers outliers start: 98 outliers final: 63 residues processed: 35 average time/residue: 1.0370 time to fit residues: 48.6509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 323 optimal weight: 7.9990 chunk 246 optimal weight: 2.9990 chunk 169 optimal weight: 6.9990 chunk 36 optimal weight: 2.9990 chunk 156 optimal weight: 2.9990 chunk 219 optimal weight: 0.4980 chunk 328 optimal weight: 6.9990 chunk 347 optimal weight: 1.9990 chunk 171 optimal weight: 9.9990 chunk 311 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 HIS D 263 ASN E 12 HIS F 263 ASN H 12 HIS H 97 GLN K 263 ASN L 12 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.073 29076 Z= 0.297 Angle : 0.527 7.330 39396 Z= 0.284 Chirality : 0.049 0.177 4668 Planarity : 0.004 0.025 4992 Dihedral : 5.067 51.044 3960 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer Outliers : 5.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.14), residues: 3660 helix: 1.08 (0.14), residues: 1392 sheet: -0.22 (0.18), residues: 936 loop : -0.09 (0.16), residues: 1332 *********************** 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 782 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 624 time to evaluate : 3.426 Fit side-chains outliers start: 158 outliers final: 86 residues processed: 726 average time/residue: 1.4808 time to fit residues: 1244.1414 Evaluate side-chains 693 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 607 time to evaluate : 3.167 Switching outliers to nearest non-outliers outliers start: 86 outliers final: 62 residues processed: 24 average time/residue: 0.8896 time to fit residues: 31.0656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 289 optimal weight: 8.9990 chunk 197 optimal weight: 9.9990 chunk 5 optimal weight: 6.9990 chunk 259 optimal weight: 10.0000 chunk 143 optimal weight: 0.9980 chunk 296 optimal weight: 3.9990 chunk 240 optimal weight: 5.9990 chunk 0 optimal weight: 0.9990 chunk 177 optimal weight: 4.9990 chunk 312 optimal weight: 2.9990 chunk 87 optimal weight: 6.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- 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 135 GLN C 12 HIS D 97 GLN E 12 HIS F 135 GLN F 263 ASN H 12 HIS J 97 GLN K 263 ASN L 12 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.2328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.088 29076 Z= 0.354 Angle : 0.553 6.374 39396 Z= 0.300 Chirality : 0.050 0.180 4668 Planarity : 0.004 0.030 4992 Dihedral : 5.342 53.489 3960 Min Nonbonded Distance : 1.803 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer Outliers : 5.15 % 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: 0.27 (0.14), residues: 3660 helix: 0.97 (0.14), residues: 1392 sheet: -0.25 (0.17), residues: 936 loop : -0.15 (0.16), residues: 1332 *********************** 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 762 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 600 time to evaluate : 3.535 Fit side-chains outliers start: 162 outliers final: 93 residues processed: 710 average time/residue: 1.5479 time to fit residues: 1270.0814 Evaluate side-chains 680 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 587 time to evaluate : 3.612 Switching outliers to nearest non-outliers outliers start: 93 outliers final: 67 residues processed: 27 average time/residue: 1.1157 time to fit residues: 41.5622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 117 optimal weight: 2.9990 chunk 313 optimal weight: 1.9990 chunk 68 optimal weight: 5.9990 chunk 204 optimal weight: 5.9990 chunk 85 optimal weight: 1.9990 chunk 348 optimal weight: 0.9980 chunk 289 optimal weight: 9.9990 chunk 161 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 chunk 115 optimal weight: 0.6980 chunk 182 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 97 GLN E 12 HIS F 263 ASN H 12 HIS H 97 GLN I 97 GLN K 263 ASN L 12 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.030 29076 Z= 0.153 Angle : 0.446 6.532 39396 Z= 0.241 Chirality : 0.046 0.163 4668 Planarity : 0.003 0.038 4992 Dihedral : 4.707 57.225 3960 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer Outliers : 4.17 % 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: 0.50 (0.14), residues: 3660 helix: 1.28 (0.15), residues: 1380 sheet: -0.12 (0.17), residues: 936 loop : -0.18 (0.16), residues: 1344 *********************** 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 734 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 603 time to evaluate : 3.597 Fit side-chains outliers start: 131 outliers final: 87 residues processed: 702 average time/residue: 1.5630 time to fit residues: 1292.2554 Evaluate side-chains 670 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 583 time to evaluate : 3.353 Switching outliers to nearest non-outliers outliers start: 87 outliers final: 73 residues processed: 14 average time/residue: 1.6553 time to fit residues: 32.3656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 335 optimal weight: 8.9990 chunk 39 optimal weight: 3.9990 chunk 198 optimal weight: 10.0000 chunk 254 optimal weight: 0.6980 chunk 197 optimal weight: 4.9990 chunk 293 optimal weight: 7.9990 chunk 194 optimal weight: 0.8980 chunk 346 optimal weight: 6.9990 chunk 217 optimal weight: 1.9990 chunk 211 optimal weight: 0.9990 chunk 160 optimal weight: 3.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- 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 I 97 GLN J 97 GLN K 263 ASN L 12 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.2485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.065 29076 Z= 0.241 Angle : 0.493 7.237 39396 Z= 0.265 Chirality : 0.047 0.173 4668 Planarity : 0.003 0.039 4992 Dihedral : 4.924 51.755 3960 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer Outliers : 4.23 % 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: 0.45 (0.14), residues: 3660 helix: 1.19 (0.15), residues: 1392 sheet: -0.13 (0.17), residues: 936 loop : -0.17 (0.16), residues: 1332 *********************** 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 725 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 592 time to evaluate : 3.619 Fit side-chains outliers start: 133 outliers final: 101 residues processed: 691 average time/residue: 1.5062 time to fit residues: 1206.8063 Evaluate side-chains 680 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 579 time to evaluate : 3.142 Switching outliers to nearest non-outliers outliers start: 101 outliers final: 80 residues processed: 22 average time/residue: 1.2302 time to fit residues: 37.1025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 214 optimal weight: 0.7980 chunk 138 optimal weight: 0.9980 chunk 207 optimal weight: 0.8980 chunk 104 optimal weight: 2.9990 chunk 68 optimal weight: 0.2980 chunk 67 optimal weight: 1.9990 chunk 220 optimal weight: 0.3980 chunk 236 optimal weight: 3.9990 chunk 171 optimal weight: 8.9990 chunk 32 optimal weight: 5.9990 chunk 272 optimal weight: 4.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 12 HIS F 263 ASN H 12 HIS H 97 GLN I 97 GLN K 263 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.2621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 29076 Z= 0.138 Angle : 0.440 7.371 39396 Z= 0.236 Chirality : 0.046 0.162 4668 Planarity : 0.003 0.040 4992 Dihedral : 4.381 42.538 3960 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer Outliers : 3.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.14), residues: 3660 helix: 1.47 (0.15), residues: 1368 sheet: -0.04 (0.17), residues: 936 loop : -0.19 (0.16), residues: 1356 *********************** 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 693 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 587 time to evaluate : 3.368 Fit side-chains outliers start: 106 outliers final: 84 residues processed: 670 average time/residue: 1.5278 time to fit residues: 1189.1678 Evaluate side-chains 669 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 585 time to evaluate : 3.503 Switching outliers to nearest non-outliers outliers start: 84 outliers final: 72 residues processed: 12 average time/residue: 1.6539 time to fit residues: 27.4546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 315 optimal weight: 2.9990 chunk 332 optimal weight: 2.9990 chunk 303 optimal weight: 3.9990 chunk 323 optimal weight: 0.9990 chunk 194 optimal weight: 1.9990 chunk 140 optimal weight: 6.9990 chunk 253 optimal weight: 5.9990 chunk 99 optimal weight: 1.9990 chunk 292 optimal weight: 3.9990 chunk 305 optimal weight: 3.9990 chunk 322 optimal weight: 0.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 GLN A 288 GLN C 12 HIS E 12 HIS F 263 ASN H 12 HIS H 97 GLN I 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: 0.7934 moved from start: 0.2594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.065 29076 Z= 0.247 Angle : 0.500 8.251 39396 Z= 0.267 Chirality : 0.047 0.176 4668 Planarity : 0.003 0.041 4992 Dihedral : 4.739 46.044 3960 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer Outliers : 3.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.14), residues: 3660 helix: 1.26 (0.15), residues: 1392 sheet: -0.08 (0.17), residues: 936 loop : -0.15 (0.16), residues: 1332 *********************** 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 686 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 580 time to evaluate : 3.679 Fit side-chains outliers start: 106 outliers final: 81 residues processed: 668 average time/residue: 1.4793 time to fit residues: 1147.8040 Evaluate side-chains 661 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 580 time to evaluate : 3.265 Switching outliers to nearest non-outliers outliers start: 81 outliers final: 74 residues processed: 8 average time/residue: 1.5777 time to fit residues: 19.0552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 212 optimal weight: 6.9990 chunk 341 optimal weight: 5.9990 chunk 208 optimal weight: 0.8980 chunk 162 optimal weight: 7.9990 chunk 237 optimal weight: 0.9990 chunk 358 optimal weight: 4.9990 chunk 330 optimal weight: 0.9990 chunk 285 optimal weight: 7.9990 chunk 29 optimal weight: 3.9990 chunk 220 optimal weight: 9.9990 chunk 175 optimal weight: 0.0470 overall best weight: 1.3884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 GLN B 97 GLN C 12 HIS E 12 HIS F 263 ASN H 12 HIS H 97 GLN I 97 GLN K 263 ASN L 12 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.2632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 29076 Z= 0.205 Angle : 0.481 7.634 39396 Z= 0.257 Chirality : 0.047 0.169 4668 Planarity : 0.003 0.041 4992 Dihedral : 4.621 47.894 3960 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer Outliers : 2.99 % 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: 0.54 (0.14), residues: 3660 helix: 1.28 (0.15), residues: 1392 sheet: -0.08 (0.17), residues: 936 loop : -0.15 (0.16), residues: 1332 ********************** 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 680 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 586 time to evaluate : 3.647 Fit side-chains outliers start: 94 outliers final: 80 residues processed: 667 average time/residue: 1.5101 time to fit residues: 1169.7593 Evaluate side-chains 665 residues out of total 3144 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 585 time to evaluate : 3.614 Switching outliers to nearest non-outliers outliers start: 80 outliers final: 73 residues processed: 7 average time/residue: 1.5458 time to fit residues: 17.3359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 226 optimal weight: 0.9990 chunk 304 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 263 optimal weight: 0.6980 chunk 42 optimal weight: 10.0000 chunk 79 optimal weight: 6.9990 chunk 286 optimal weight: 0.7980 chunk 119 optimal weight: 0.9990 chunk 293 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 H 97 GLN I 97 GLN J 97 GLN K 263 ASN L 12 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.173042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.124122 restraints weight = 25962.970| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 1.51 r_work: 0.3219 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3099 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3099 r_free = 0.3099 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 648 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2928 r_free = 0.2928 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2928 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.2721 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= 0.155 Angle : 0.454 7.528 39396 Z= 0.242 Chirality : 0.046 0.163 4668 Planarity : 0.003 0.040 4992 Dihedral : 4.378 47.139 3960 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer Outliers : 2.93 % 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: 1.48 (0.15), residues: 1368 sheet: -0.01 (0.17), residues: 936 loop : -0.13 (0.16), residues: 1356 =============================================================================== Job complete usr+sys time: 16163.72 seconds wall clock time: 285 minutes 9.12 seconds (17109.12 seconds total)