Starting phenix.real_space_refine (version: dev)
on Mon Jul 4 10:18:25 2022 by dcliebschner
===============================================================================
Processing files:
-------------------------------------------------------------------------------
Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wp9_8874/07_2022/5wp9_8874_updated.pdb
Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wp9_8874/07_2022/5wp9_8874.map
Processing PHIL parameters:
-------------------------------------------------------------------------------
Adding command-line PHIL:
-------------------------
refinement.macro_cycles=10
scattering_table=electron
resolution=4.22
write_initial_geo_file=False
Final processed PHIL parameters:
-------------------------------------------------------------------------------
data_manager {
real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wp9_8874/07_2022/5wp9_8874.map"
default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wp9_8874/07_2022/5wp9_8874.map"
model {
file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wp9_8874/07_2022/5wp9_8874_updated.pdb"
}
default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wp9_8874/07_2022/5wp9_8874_updated.pdb"
}
resolution = 4.22
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= 0.027 sd= 2.837
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
Convert atoms to be neutral
Process input model
Symmetric amino acids flipped
Residue "A PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "A PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "A PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "A TYR 273": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "A TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "A TYR 322": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "A TYR 344": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "A TYR 368": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "A PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "A TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "A PHE 457": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "A PHE 647": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "B TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "B PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "B PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "B PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "B PHE 243": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "C PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "C PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "C PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "C TYR 273": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "C TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "C TYR 322": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "C TYR 344": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "C TYR 368": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "C PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "C TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "C PHE 457": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "C PHE 647": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "D TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "D PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "D PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "D PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "D PHE 243": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "E PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "E PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "E PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "E TYR 273": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "E TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "E TYR 322": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "E TYR 344": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "E TYR 368": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "E PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "E TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "E PHE 457": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "E PHE 647": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "F TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "F PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "F PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "F PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "F PHE 243": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "G PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "G PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "G PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "G TYR 273": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "G TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "G TYR 322": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "G TYR 344": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "G TYR 368": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "G PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "G TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "G PHE 457": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "G PHE 647": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "H TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "H PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "H PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "H PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "H PHE 243": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "I PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "I PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "I PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "I TYR 273": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "I TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "I TYR 322": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "I TYR 344": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "I TYR 368": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "I PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "I TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "I PHE 457": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "I PHE 647": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "J TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "J PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "J PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "J PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "J PHE 243": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "K PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "K PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "K PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "K TYR 273": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "K TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "K TYR 322": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "K TYR 344": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "K TYR 368": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "K PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "K TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "K PHE 457": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "K PHE 647": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "L TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "L PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "L PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "L PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "L PHE 243": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "M PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "M PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "M PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "M TYR 273": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "M TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "M TYR 322": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "M TYR 344": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "M TYR 368": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "M PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "M TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "M PHE 457": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "M PHE 647": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "N TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "N PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "N PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "N PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "N PHE 243": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "O PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "O PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "O PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "O TYR 273": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "O TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "O TYR 322": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "O TYR 344": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "O TYR 368": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "O PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "O TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "O PHE 457": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "O PHE 647": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "P TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "P PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "P PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "P PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "P PHE 243": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Time to flip residues: 0.16s
Monomer Library directory:
"/net/cci-filer2/raid1/xp/phenix/phenix-dev-4648/modules/chem_data/mon_lib"
Total number of atoms: 117048
Number of models: 1
Model: ""
Number of chains: 24
Chain: "A"
Number of atoms: 9471
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 590, 9471
Classifications: {'peptide': 590}
Modifications used: {'COO': 1, 'NH1NOTPRO': 1}
Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 564}
Chain breaks: 2
Chain: "B"
Number of atoms: 5127
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 329, 5127
Classifications: {'peptide': 329}
Modifications used: {'COO': 1, 'NH1NOTPRO': 1}
Link IDs: {'PTRANS': 19, 'TRANS': 309}
Chain: "C"
Number of atoms: 9471
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 590, 9471
Classifications: {'peptide': 590}
Modifications used: {'COO': 1, 'NH1NOTPRO': 1}
Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 564}
Chain breaks: 2
Chain: "D"
Number of atoms: 5127
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 329, 5127
Classifications: {'peptide': 329}
Modifications used: {'COO': 1, 'NH1NOTPRO': 1}
Link IDs: {'PTRANS': 19, 'TRANS': 309}
Chain: "E"
Number of atoms: 9471
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 590, 9471
Classifications: {'peptide': 590}
Modifications used: {'COO': 1, 'NH1NOTPRO': 1}
Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 564}
Chain breaks: 2
Chain: "F"
Number of atoms: 5127
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 329, 5127
Classifications: {'peptide': 329}
Modifications used: {'COO': 1, 'NH1NOTPRO': 1}
Link IDs: {'PTRANS': 19, 'TRANS': 309}
Chain: "G"
Number of atoms: 9471
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 590, 9471
Classifications: {'peptide': 590}
Modifications used: {'COO': 1, 'NH1NOTPRO': 1}
Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 564}
Chain breaks: 2
Chain: "H"
Number of atoms: 5127
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 329, 5127
Classifications: {'peptide': 329}
Modifications used: {'COO': 1, 'NH1NOTPRO': 1}
Link IDs: {'PTRANS': 19, 'TRANS': 309}
Chain: "I"
Number of atoms: 9471
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 590, 9471
Classifications: {'peptide': 590}
Modifications used: {'COO': 1, 'NH1NOTPRO': 1}
Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 564}
Chain breaks: 2
Chain: "J"
Number of atoms: 5127
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 329, 5127
Classifications: {'peptide': 329}
Modifications used: {'COO': 1, 'NH1NOTPRO': 1}
Link IDs: {'PTRANS': 19, 'TRANS': 309}
Chain: "K"
Number of atoms: 9471
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 590, 9471
Classifications: {'peptide': 590}
Modifications used: {'COO': 1, 'NH1NOTPRO': 1}
Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 564}
Chain breaks: 2
Chain: "L"
Number of atoms: 5127
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 329, 5127
Classifications: {'peptide': 329}
Modifications used: {'COO': 1, 'NH1NOTPRO': 1}
Link IDs: {'PTRANS': 19, 'TRANS': 309}
Chain: "M"
Number of atoms: 9471
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 590, 9471
Classifications: {'peptide': 590}
Modifications used: {'COO': 1, 'NH1NOTPRO': 1}
Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 564}
Chain breaks: 2
Chain: "N"
Number of atoms: 5127
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 329, 5127
Classifications: {'peptide': 329}
Modifications used: {'COO': 1, 'NH1NOTPRO': 1}
Link IDs: {'PTRANS': 19, 'TRANS': 309}
Chain: "O"
Number of atoms: 9471
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 590, 9471
Classifications: {'peptide': 590}
Modifications used: {'COO': 1, 'NH1NOTPRO': 1}
Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 564}
Chain breaks: 2
Chain: "P"
Number of atoms: 5127
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 329, 5127
Classifications: {'peptide': 329}
Modifications used: {'COO': 1, 'NH1NOTPRO': 1}
Link IDs: {'PTRANS': 19, 'TRANS': 309}
Chain: "A"
Number of atoms: 33
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 2, 33
Unusual residues: {' MG': 1, 'GCP': 1}
Classifications: {'undetermined': 2}
Link IDs: {None: 1}
Chain: "C"
Number of atoms: 33
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 2, 33
Unusual residues: {' MG': 1, 'GCP': 1}
Classifications: {'undetermined': 2}
Link IDs: {None: 1}
Chain: "E"
Number of atoms: 33
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 2, 33
Unusual residues: {' MG': 1, 'GCP': 1}
Classifications: {'undetermined': 2}
Link IDs: {None: 1}
Chain: "G"
Number of atoms: 33
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 2, 33
Unusual residues: {' MG': 1, 'GCP': 1}
Classifications: {'undetermined': 2}
Link IDs: {None: 1}
Chain: "I"
Number of atoms: 33
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 2, 33
Unusual residues: {' MG': 1, 'GCP': 1}
Classifications: {'undetermined': 2}
Link IDs: {None: 1}
Chain: "K"
Number of atoms: 33
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 2, 33
Unusual residues: {' MG': 1, 'GCP': 1}
Classifications: {'undetermined': 2}
Link IDs: {None: 1}
Chain: "M"
Number of atoms: 33
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 2, 33
Unusual residues: {' MG': 1, 'GCP': 1}
Classifications: {'undetermined': 2}
Link IDs: {None: 1}
Chain: "O"
Number of atoms: 33
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 2, 33
Unusual residues: {' MG': 1, 'GCP': 1}
Classifications: {'undetermined': 2}
Link IDs: {None: 1}
Time building chain proxies: 38.31, per 1000 atoms: 0.33
Number of scatterers: 117048
At special positions: 0
Unit cell: (153.72, 161.04, 361.12, 90, 90, 90)
Space group: P 1 (No. 1)
Number of sites at special positions: 0
Number of scattering types: 7
Type Number sf(0)
S 224 16.00
P 24 15.00
Mg 8 11.99
O 10880 8.00
N 10136 7.00
C 36696 6.00
H 59080 1.00
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: 80.41
Conformation dependent library (CDL) restraints added in 7.2 seconds
14576 Ramachandran restraints generated.
7288 Oldfield, 0 Emsley, 7288 emsley8k and 0 Phi/Psi/2.
Adding C-beta torsion restraints...
Number of C-beta restraints generated: 13840
Finding SS restraints...
Warning!!! ksdssp method is not applicable forstructures with more than 99999 atoms!
Switching to from_ca.
running find_ss_from_ca liberal...
Secondary structure from input PDB file:
256 helices and 32 sheets defined
60.4% alpha, 9.4% beta
0 base pairs and 0 stacking pairs defined.
Time for finding SS restraints: 7.52
Creating SS restraints...
Processing helix chain 'A' and resid 2 through 19
Proline residue: A 6 - end of helix
removed outlier: 4.609A pdb=" N PHE A 15 " --> pdb=" O LEU A 11 " (cutoff:3.500A)
removed outlier: 4.087A pdb=" N VAL A 18 " --> pdb=" O VAL A 14 " (cutoff:3.500A)
Processing helix chain 'A' and resid 37 through 47
Processing helix chain 'A' and resid 103 through 119
Processing helix chain 'A' and resid 161 through 175
removed outlier: 4.087A pdb=" N PHE A 173 " --> pdb=" O LEU A 169 " (cutoff:3.500A)
Processing helix chain 'A' and resid 194 through 204
removed outlier: 3.858A pdb=" N GLU A 202 " --> pdb=" O LYS A 198 " (cutoff:3.500A)
removed outlier: 3.906A pdb=" N VAL A 203 " --> pdb=" O ILE A 199 " (cutoff:3.500A)
Processing helix chain 'A' and resid 226 through 232
Processing helix chain 'A' and resid 248 through 255
Processing helix chain 'A' and resid 257 through 273
Processing helix chain 'A' and resid 276 through 281
Processing helix chain 'A' and resid 282 through 323
removed outlier: 4.185A pdb=" N CYS A 300 " --> pdb=" O HIS A 296 " (cutoff:3.500A)
removed outlier: 3.634A pdb=" N LEU A 301 " --> pdb=" O ILE A 297 " (cutoff:3.500A)
Proline residue: A 302 - end of helix
removed outlier: 4.297A pdb=" N TYR A 322 " --> pdb=" O LEU A 318 " (cutoff:3.500A)
Processing helix chain 'A' and resid 328 through 350
removed outlier: 5.254A pdb=" N THR A 332 " --> pdb=" O ASP A 328 " (cutoff:3.500A)
Processing helix chain 'A' and resid 362 through 382
removed outlier: 5.078A pdb=" N ILE A 366 " --> pdb=" O GLY A 362 " (cutoff:3.500A)
removed outlier: 3.892A pdb=" N THR A 373 " --> pdb=" O ILE A 369 " (cutoff:3.500A)
removed outlier: 5.159A pdb=" N PHE A 374 " --> pdb=" O PHE A 370 " (cutoff:3.500A)
removed outlier: 4.338A pdb=" N ARG A 376 " --> pdb=" O GLU A 372 " (cutoff:3.500A)
removed outlier: 3.636A pdb=" N VAL A 381 " --> pdb=" O THR A 377 " (cutoff:3.500A)
removed outlier: 5.555A pdb=" N ASP A 382 " --> pdb=" O LEU A 378 " (cutoff:3.500A)
Processing helix chain 'A' and resid 388 through 401
Processing helix chain 'A' and resid 410 through 450
removed outlier: 4.099A pdb=" N LYS A 418 " --> pdb=" O GLU A 414 " (cutoff:3.500A)
removed outlier: 3.610A pdb=" N LEU A 424 " --> pdb=" O GLN A 420 " (cutoff:3.500A)
removed outlier: 3.830A pdb=" N GLU A 425 " --> pdb=" O ILE A 421 " (cutoff:3.500A)
removed outlier: 4.338A pdb=" N GLU A 426 " --> pdb=" O LYS A 422 " (cutoff:3.500A)
Proline residue: A 427 - end of helix
removed outlier: 4.013A pdb=" N ILE A 443 " --> pdb=" O MET A 439 " (cutoff:3.500A)
removed outlier: 3.555A pdb=" N GLN A 444 " --> pdb=" O GLN A 440 " (cutoff:3.500A)
removed outlier: 3.738A pdb=" N ASN A 448 " --> pdb=" O GLN A 444 " (cutoff:3.500A)
removed outlier: 4.445A pdb=" N TYR A 449 " --> pdb=" O HIS A 445 " (cutoff:3.500A)
removed outlier: 4.826A pdb=" N SER A 450 " --> pdb=" O CYS A 446 " (cutoff:3.500A)
Processing helix chain 'A' and resid 451 through 458
removed outlier: 4.291A pdb=" N ARG A 456 " --> pdb=" O GLN A 452 " (cutoff:3.500A)
removed outlier: 4.166A pdb=" N PHE A 457 " --> pdb=" O GLU A 453 " (cutoff:3.500A)
Proline residue: A 458 - end of helix
Processing helix chain 'A' and resid 459 through 494
Proline residue: A 477 - end of helix
removed outlier: 3.749A pdb=" N TYR A 493 " --> pdb=" O ILE A 489 " (cutoff:3.500A)
removed outlier: 5.045A pdb=" N ILE A 494 " --> pdb=" O GLU A 490 " (cutoff:3.500A)
Processing helix chain 'A' and resid 612 through 644
removed outlier: 3.815A pdb=" N ASP A 638 " --> pdb=" O LYS A 634 " (cutoff:3.500A)
Proline residue: A 641 - end of helix
Processing helix chain 'A' and resid 649 through 660
removed outlier: 3.585A pdb=" N ASP A 654 " --> pdb=" O ASN A 650 " (cutoff:3.500A)
removed outlier: 5.477A pdb=" N GLN A 657 " --> pdb=" O LYS A 653 " (cutoff:3.500A)
removed outlier: 4.512A pdb=" N SER A 658 " --> pdb=" O ASP A 654 " (cutoff:3.500A)
Processing helix chain 'A' and resid 666 through 673
removed outlier: 4.050A pdb=" N ASP A 671 " --> pdb=" O SER A 667 " (cutoff:3.500A)
Processing helix chain 'A' and resid 677 through 710
removed outlier: 4.060A pdb=" N GLN A 699 " --> pdb=" O GLN A 695 " (cutoff:3.500A)
removed outlier: 3.819A pdb=" N HIS A 708 " --> pdb=" O ILE A 704 " (cutoff:3.500A)
removed outlier: 3.906A pdb=" N LEU A 709 " --> pdb=" O ARG A 705 " (cutoff:3.500A)
removed outlier: 5.057A pdb=" N TRP A 710 " --> pdb=" O GLU A 706 " (cutoff:3.500A)
Processing helix chain 'C' and resid 2 through 19
Proline residue: C 6 - end of helix
removed outlier: 4.610A pdb=" N PHE C 15 " --> pdb=" O LEU C 11 " (cutoff:3.500A)
removed outlier: 4.087A pdb=" N VAL C 18 " --> pdb=" O VAL C 14 " (cutoff:3.500A)
Processing helix chain 'C' and resid 37 through 47
Processing helix chain 'C' and resid 103 through 119
Processing helix chain 'C' and resid 161 through 175
removed outlier: 4.087A pdb=" N PHE C 173 " --> pdb=" O LEU C 169 " (cutoff:3.500A)
Processing helix chain 'C' and resid 194 through 204
removed outlier: 3.859A pdb=" N GLU C 202 " --> pdb=" O LYS C 198 " (cutoff:3.500A)
removed outlier: 3.906A pdb=" N VAL C 203 " --> pdb=" O ILE C 199 " (cutoff:3.500A)
Processing helix chain 'C' and resid 226 through 232
Processing helix chain 'C' and resid 248 through 255
Processing helix chain 'C' and resid 257 through 273
Processing helix chain 'C' and resid 276 through 281
Processing helix chain 'C' and resid 282 through 323
removed outlier: 4.185A pdb=" N CYS C 300 " --> pdb=" O HIS C 296 " (cutoff:3.500A)
removed outlier: 3.634A pdb=" N LEU C 301 " --> pdb=" O ILE C 297 " (cutoff:3.500A)
Proline residue: C 302 - end of helix
removed outlier: 4.297A pdb=" N TYR C 322 " --> pdb=" O LEU C 318 " (cutoff:3.500A)
Processing helix chain 'C' and resid 328 through 350
removed outlier: 5.254A pdb=" N THR C 332 " --> pdb=" O ASP C 328 " (cutoff:3.500A)
Processing helix chain 'C' and resid 362 through 382
removed outlier: 5.077A pdb=" N ILE C 366 " --> pdb=" O GLY C 362 " (cutoff:3.500A)
removed outlier: 3.892A pdb=" N THR C 373 " --> pdb=" O ILE C 369 " (cutoff:3.500A)
removed outlier: 5.159A pdb=" N PHE C 374 " --> pdb=" O PHE C 370 " (cutoff:3.500A)
removed outlier: 4.339A pdb=" N ARG C 376 " --> pdb=" O GLU C 372 " (cutoff:3.500A)
removed outlier: 3.635A pdb=" N VAL C 381 " --> pdb=" O THR C 377 " (cutoff:3.500A)
removed outlier: 5.556A pdb=" N ASP C 382 " --> pdb=" O LEU C 378 " (cutoff:3.500A)
Processing helix chain 'C' and resid 388 through 401
Processing helix chain 'C' and resid 410 through 450
removed outlier: 4.098A pdb=" N LYS C 418 " --> pdb=" O GLU C 414 " (cutoff:3.500A)
removed outlier: 3.610A pdb=" N LEU C 424 " --> pdb=" O GLN C 420 " (cutoff:3.500A)
removed outlier: 3.830A pdb=" N GLU C 425 " --> pdb=" O ILE C 421 " (cutoff:3.500A)
removed outlier: 4.338A pdb=" N GLU C 426 " --> pdb=" O LYS C 422 " (cutoff:3.500A)
Proline residue: C 427 - end of helix
removed outlier: 4.013A pdb=" N ILE C 443 " --> pdb=" O MET C 439 " (cutoff:3.500A)
removed outlier: 3.555A pdb=" N GLN C 444 " --> pdb=" O GLN C 440 " (cutoff:3.500A)
removed outlier: 3.738A pdb=" N ASN C 448 " --> pdb=" O GLN C 444 " (cutoff:3.500A)
removed outlier: 4.445A pdb=" N TYR C 449 " --> pdb=" O HIS C 445 " (cutoff:3.500A)
removed outlier: 4.827A pdb=" N SER C 450 " --> pdb=" O CYS C 446 " (cutoff:3.500A)
Processing helix chain 'C' and resid 451 through 458
removed outlier: 4.291A pdb=" N ARG C 456 " --> pdb=" O GLN C 452 " (cutoff:3.500A)
removed outlier: 4.166A pdb=" N PHE C 457 " --> pdb=" O GLU C 453 " (cutoff:3.500A)
Proline residue: C 458 - end of helix
Processing helix chain 'C' and resid 459 through 494
Proline residue: C 477 - end of helix
removed outlier: 3.750A pdb=" N TYR C 493 " --> pdb=" O ILE C 489 " (cutoff:3.500A)
removed outlier: 5.046A pdb=" N ILE C 494 " --> pdb=" O GLU C 490 " (cutoff:3.500A)
Processing helix chain 'C' and resid 612 through 644
removed outlier: 3.815A pdb=" N ASP C 638 " --> pdb=" O LYS C 634 " (cutoff:3.500A)
Proline residue: C 641 - end of helix
Processing helix chain 'C' and resid 649 through 660
removed outlier: 3.585A pdb=" N ASP C 654 " --> pdb=" O ASN C 650 " (cutoff:3.500A)
removed outlier: 5.477A pdb=" N GLN C 657 " --> pdb=" O LYS C 653 " (cutoff:3.500A)
removed outlier: 4.513A pdb=" N SER C 658 " --> pdb=" O ASP C 654 " (cutoff:3.500A)
Processing helix chain 'C' and resid 666 through 673
removed outlier: 4.049A pdb=" N ASP C 671 " --> pdb=" O SER C 667 " (cutoff:3.500A)
Processing helix chain 'C' and resid 677 through 710
removed outlier: 4.060A pdb=" N GLN C 699 " --> pdb=" O GLN C 695 " (cutoff:3.500A)
removed outlier: 3.819A pdb=" N HIS C 708 " --> pdb=" O ILE C 704 " (cutoff:3.500A)
removed outlier: 3.907A pdb=" N LEU C 709 " --> pdb=" O ARG C 705 " (cutoff:3.500A)
removed outlier: 5.056A pdb=" N TRP C 710 " --> pdb=" O GLU C 706 " (cutoff:3.500A)
Processing helix chain 'E' and resid 2 through 19
Proline residue: E 6 - end of helix
removed outlier: 4.610A pdb=" N PHE E 15 " --> pdb=" O LEU E 11 " (cutoff:3.500A)
removed outlier: 4.087A pdb=" N VAL E 18 " --> pdb=" O VAL E 14 " (cutoff:3.500A)
Processing helix chain 'E' and resid 37 through 47
Processing helix chain 'E' and resid 103 through 119
Processing helix chain 'E' and resid 161 through 175
removed outlier: 4.086A pdb=" N PHE E 173 " --> pdb=" O LEU E 169 " (cutoff:3.500A)
Processing helix chain 'E' and resid 194 through 204
removed outlier: 3.859A pdb=" N GLU E 202 " --> pdb=" O LYS E 198 " (cutoff:3.500A)
removed outlier: 3.905A pdb=" N VAL E 203 " --> pdb=" O ILE E 199 " (cutoff:3.500A)
Processing helix chain 'E' and resid 226 through 232
Processing helix chain 'E' and resid 248 through 255
Processing helix chain 'E' and resid 257 through 273
Processing helix chain 'E' and resid 276 through 281
Processing helix chain 'E' and resid 282 through 323
removed outlier: 4.185A pdb=" N CYS E 300 " --> pdb=" O HIS E 296 " (cutoff:3.500A)
removed outlier: 3.634A pdb=" N LEU E 301 " --> pdb=" O ILE E 297 " (cutoff:3.500A)
Proline residue: E 302 - end of helix
removed outlier: 4.298A pdb=" N TYR E 322 " --> pdb=" O LEU E 318 " (cutoff:3.500A)
Processing helix chain 'E' and resid 328 through 350
removed outlier: 5.254A pdb=" N THR E 332 " --> pdb=" O ASP E 328 " (cutoff:3.500A)
Processing helix chain 'E' and resid 362 through 382
removed outlier: 5.077A pdb=" N ILE E 366 " --> pdb=" O GLY E 362 " (cutoff:3.500A)
removed outlier: 3.892A pdb=" N THR E 373 " --> pdb=" O ILE E 369 " (cutoff:3.500A)
removed outlier: 5.159A pdb=" N PHE E 374 " --> pdb=" O PHE E 370 " (cutoff:3.500A)
removed outlier: 4.338A pdb=" N ARG E 376 " --> pdb=" O GLU E 372 " (cutoff:3.500A)
removed outlier: 3.635A pdb=" N VAL E 381 " --> pdb=" O THR E 377 " (cutoff:3.500A)
removed outlier: 5.556A pdb=" N ASP E 382 " --> pdb=" O LEU E 378 " (cutoff:3.500A)
Processing helix chain 'E' and resid 388 through 401
Processing helix chain 'E' and resid 410 through 450
removed outlier: 4.098A pdb=" N LYS E 418 " --> pdb=" O GLU E 414 " (cutoff:3.500A)
removed outlier: 3.610A pdb=" N LEU E 424 " --> pdb=" O GLN E 420 " (cutoff:3.500A)
removed outlier: 3.830A pdb=" N GLU E 425 " --> pdb=" O ILE E 421 " (cutoff:3.500A)
removed outlier: 4.338A pdb=" N GLU E 426 " --> pdb=" O LYS E 422 " (cutoff:3.500A)
Proline residue: E 427 - end of helix
removed outlier: 4.013A pdb=" N ILE E 443 " --> pdb=" O MET E 439 " (cutoff:3.500A)
removed outlier: 3.556A pdb=" N GLN E 444 " --> pdb=" O GLN E 440 " (cutoff:3.500A)
removed outlier: 3.737A pdb=" N ASN E 448 " --> pdb=" O GLN E 444 " (cutoff:3.500A)
removed outlier: 4.445A pdb=" N TYR E 449 " --> pdb=" O HIS E 445 " (cutoff:3.500A)
removed outlier: 4.826A pdb=" N SER E 450 " --> pdb=" O CYS E 446 " (cutoff:3.500A)
Processing helix chain 'E' and resid 451 through 458
removed outlier: 4.291A pdb=" N ARG E 456 " --> pdb=" O GLN E 452 " (cutoff:3.500A)
removed outlier: 4.166A pdb=" N PHE E 457 " --> pdb=" O GLU E 453 " (cutoff:3.500A)
Proline residue: E 458 - end of helix
Processing helix chain 'E' and resid 459 through 494
Proline residue: E 477 - end of helix
removed outlier: 3.751A pdb=" N TYR E 493 " --> pdb=" O ILE E 489 " (cutoff:3.500A)
removed outlier: 5.045A pdb=" N ILE E 494 " --> pdb=" O GLU E 490 " (cutoff:3.500A)
Processing helix chain 'E' and resid 612 through 644
removed outlier: 3.815A pdb=" N ASP E 638 " --> pdb=" O LYS E 634 " (cutoff:3.500A)
Proline residue: E 641 - end of helix
Processing helix chain 'E' and resid 649 through 660
removed outlier: 3.585A pdb=" N ASP E 654 " --> pdb=" O ASN E 650 " (cutoff:3.500A)
removed outlier: 5.478A pdb=" N GLN E 657 " --> pdb=" O LYS E 653 " (cutoff:3.500A)
removed outlier: 4.512A pdb=" N SER E 658 " --> pdb=" O ASP E 654 " (cutoff:3.500A)
Processing helix chain 'E' and resid 666 through 673
removed outlier: 4.050A pdb=" N ASP E 671 " --> pdb=" O SER E 667 " (cutoff:3.500A)
Processing helix chain 'E' and resid 677 through 710
removed outlier: 4.060A pdb=" N GLN E 699 " --> pdb=" O GLN E 695 " (cutoff:3.500A)
removed outlier: 3.819A pdb=" N HIS E 708 " --> pdb=" O ILE E 704 " (cutoff:3.500A)
removed outlier: 3.906A pdb=" N LEU E 709 " --> pdb=" O ARG E 705 " (cutoff:3.500A)
removed outlier: 5.056A pdb=" N TRP E 710 " --> pdb=" O GLU E 706 " (cutoff:3.500A)
Processing helix chain 'G' and resid 2 through 19
Proline residue: G 6 - end of helix
removed outlier: 4.609A pdb=" N PHE G 15 " --> pdb=" O LEU G 11 " (cutoff:3.500A)
removed outlier: 4.087A pdb=" N VAL G 18 " --> pdb=" O VAL G 14 " (cutoff:3.500A)
Processing helix chain 'G' and resid 37 through 47
Processing helix chain 'G' and resid 103 through 119
Processing helix chain 'G' and resid 161 through 175
removed outlier: 4.086A pdb=" N PHE G 173 " --> pdb=" O LEU G 169 " (cutoff:3.500A)
Processing helix chain 'G' and resid 194 through 204
removed outlier: 3.859A pdb=" N GLU G 202 " --> pdb=" O LYS G 198 " (cutoff:3.500A)
removed outlier: 3.905A pdb=" N VAL G 203 " --> pdb=" O ILE G 199 " (cutoff:3.500A)
Processing helix chain 'G' and resid 226 through 232
Processing helix chain 'G' and resid 248 through 255
Processing helix chain 'G' and resid 257 through 273
Processing helix chain 'G' and resid 276 through 281
Processing helix chain 'G' and resid 282 through 323
removed outlier: 4.185A pdb=" N CYS G 300 " --> pdb=" O HIS G 296 " (cutoff:3.500A)
removed outlier: 3.634A pdb=" N LEU G 301 " --> pdb=" O ILE G 297 " (cutoff:3.500A)
Proline residue: G 302 - end of helix
removed outlier: 4.298A pdb=" N TYR G 322 " --> pdb=" O LEU G 318 " (cutoff:3.500A)
Processing helix chain 'G' and resid 328 through 350
removed outlier: 5.253A pdb=" N THR G 332 " --> pdb=" O ASP G 328 " (cutoff:3.500A)
Processing helix chain 'G' and resid 362 through 382
removed outlier: 5.077A pdb=" N ILE G 366 " --> pdb=" O GLY G 362 " (cutoff:3.500A)
removed outlier: 3.892A pdb=" N THR G 373 " --> pdb=" O ILE G 369 " (cutoff:3.500A)
removed outlier: 5.159A pdb=" N PHE G 374 " --> pdb=" O PHE G 370 " (cutoff:3.500A)
removed outlier: 4.339A pdb=" N ARG G 376 " --> pdb=" O GLU G 372 " (cutoff:3.500A)
removed outlier: 3.635A pdb=" N VAL G 381 " --> pdb=" O THR G 377 " (cutoff:3.500A)
removed outlier: 5.556A pdb=" N ASP G 382 " --> pdb=" O LEU G 378 " (cutoff:3.500A)
Processing helix chain 'G' and resid 388 through 401
Processing helix chain 'G' and resid 410 through 450
removed outlier: 4.097A pdb=" N LYS G 418 " --> pdb=" O GLU G 414 " (cutoff:3.500A)
removed outlier: 3.610A pdb=" N LEU G 424 " --> pdb=" O GLN G 420 " (cutoff:3.500A)
removed outlier: 3.829A pdb=" N GLU G 425 " --> pdb=" O ILE G 421 " (cutoff:3.500A)
removed outlier: 4.337A pdb=" N GLU G 426 " --> pdb=" O LYS G 422 " (cutoff:3.500A)
Proline residue: G 427 - end of helix
removed outlier: 4.014A pdb=" N ILE G 443 " --> pdb=" O MET G 439 " (cutoff:3.500A)
removed outlier: 3.555A pdb=" N GLN G 444 " --> pdb=" O GLN G 440 " (cutoff:3.500A)
removed outlier: 3.737A pdb=" N ASN G 448 " --> pdb=" O GLN G 444 " (cutoff:3.500A)
removed outlier: 4.445A pdb=" N TYR G 449 " --> pdb=" O HIS G 445 " (cutoff:3.500A)
removed outlier: 4.826A pdb=" N SER G 450 " --> pdb=" O CYS G 446 " (cutoff:3.500A)
Processing helix chain 'G' and resid 451 through 458
removed outlier: 4.291A pdb=" N ARG G 456 " --> pdb=" O GLN G 452 " (cutoff:3.500A)
removed outlier: 4.166A pdb=" N PHE G 457 " --> pdb=" O GLU G 453 " (cutoff:3.500A)
Proline residue: G 458 - end of helix
Processing helix chain 'G' and resid 459 through 494
Proline residue: G 477 - end of helix
removed outlier: 3.749A pdb=" N TYR G 493 " --> pdb=" O ILE G 489 " (cutoff:3.500A)
removed outlier: 5.046A pdb=" N ILE G 494 " --> pdb=" O GLU G 490 " (cutoff:3.500A)
Processing helix chain 'G' and resid 612 through 644
removed outlier: 3.816A pdb=" N ASP G 638 " --> pdb=" O LYS G 634 " (cutoff:3.500A)
Proline residue: G 641 - end of helix
Processing helix chain 'G' and resid 649 through 660
removed outlier: 3.585A pdb=" N ASP G 654 " --> pdb=" O ASN G 650 " (cutoff:3.500A)
removed outlier: 5.477A pdb=" N GLN G 657 " --> pdb=" O LYS G 653 " (cutoff:3.500A)
removed outlier: 4.512A pdb=" N SER G 658 " --> pdb=" O ASP G 654 " (cutoff:3.500A)
Processing helix chain 'G' and resid 666 through 673
removed outlier: 4.050A pdb=" N ASP G 671 " --> pdb=" O SER G 667 " (cutoff:3.500A)
Processing helix chain 'G' and resid 677 through 710
removed outlier: 4.059A pdb=" N GLN G 699 " --> pdb=" O GLN G 695 " (cutoff:3.500A)
removed outlier: 3.819A pdb=" N HIS G 708 " --> pdb=" O ILE G 704 " (cutoff:3.500A)
removed outlier: 3.906A pdb=" N LEU G 709 " --> pdb=" O ARG G 705 " (cutoff:3.500A)
removed outlier: 5.056A pdb=" N TRP G 710 " --> pdb=" O GLU G 706 " (cutoff:3.500A)
Processing helix chain 'I' and resid 2 through 19
Proline residue: I 6 - end of helix
removed outlier: 4.609A pdb=" N PHE I 15 " --> pdb=" O LEU I 11 " (cutoff:3.500A)
removed outlier: 4.087A pdb=" N VAL I 18 " --> pdb=" O VAL I 14 " (cutoff:3.500A)
Processing helix chain 'I' and resid 37 through 47
Processing helix chain 'I' and resid 103 through 119
Processing helix chain 'I' and resid 161 through 175
removed outlier: 4.087A pdb=" N PHE I 173 " --> pdb=" O LEU I 169 " (cutoff:3.500A)
Processing helix chain 'I' and resid 194 through 204
removed outlier: 3.859A pdb=" N GLU I 202 " --> pdb=" O LYS I 198 " (cutoff:3.500A)
removed outlier: 3.905A pdb=" N VAL I 203 " --> pdb=" O ILE I 199 " (cutoff:3.500A)
Processing helix chain 'I' and resid 226 through 232
Processing helix chain 'I' and resid 248 through 255
Processing helix chain 'I' and resid 257 through 273
Processing helix chain 'I' and resid 276 through 281
Processing helix chain 'I' and resid 282 through 323
removed outlier: 4.185A pdb=" N CYS I 300 " --> pdb=" O HIS I 296 " (cutoff:3.500A)
removed outlier: 3.634A pdb=" N LEU I 301 " --> pdb=" O ILE I 297 " (cutoff:3.500A)
Proline residue: I 302 - end of helix
removed outlier: 4.298A pdb=" N TYR I 322 " --> pdb=" O LEU I 318 " (cutoff:3.500A)
Processing helix chain 'I' and resid 328 through 350
removed outlier: 5.254A pdb=" N THR I 332 " --> pdb=" O ASP I 328 " (cutoff:3.500A)
Processing helix chain 'I' and resid 362 through 382
removed outlier: 5.077A pdb=" N ILE I 366 " --> pdb=" O GLY I 362 " (cutoff:3.500A)
removed outlier: 3.892A pdb=" N THR I 373 " --> pdb=" O ILE I 369 " (cutoff:3.500A)
removed outlier: 5.159A pdb=" N PHE I 374 " --> pdb=" O PHE I 370 " (cutoff:3.500A)
removed outlier: 4.339A pdb=" N ARG I 376 " --> pdb=" O GLU I 372 " (cutoff:3.500A)
removed outlier: 3.636A pdb=" N VAL I 381 " --> pdb=" O THR I 377 " (cutoff:3.500A)
removed outlier: 5.556A pdb=" N ASP I 382 " --> pdb=" O LEU I 378 " (cutoff:3.500A)
Processing helix chain 'I' and resid 388 through 401
Processing helix chain 'I' and resid 410 through 450
removed outlier: 4.098A pdb=" N LYS I 418 " --> pdb=" O GLU I 414 " (cutoff:3.500A)
removed outlier: 3.609A pdb=" N LEU I 424 " --> pdb=" O GLN I 420 " (cutoff:3.500A)
removed outlier: 3.829A pdb=" N GLU I 425 " --> pdb=" O ILE I 421 " (cutoff:3.500A)
removed outlier: 4.338A pdb=" N GLU I 426 " --> pdb=" O LYS I 422 " (cutoff:3.500A)
Proline residue: I 427 - end of helix
removed outlier: 4.014A pdb=" N ILE I 443 " --> pdb=" O MET I 439 " (cutoff:3.500A)
removed outlier: 3.555A pdb=" N GLN I 444 " --> pdb=" O GLN I 440 " (cutoff:3.500A)
removed outlier: 3.738A pdb=" N ASN I 448 " --> pdb=" O GLN I 444 " (cutoff:3.500A)
removed outlier: 4.446A pdb=" N TYR I 449 " --> pdb=" O HIS I 445 " (cutoff:3.500A)
removed outlier: 4.826A pdb=" N SER I 450 " --> pdb=" O CYS I 446 " (cutoff:3.500A)
Processing helix chain 'I' and resid 451 through 458
removed outlier: 4.291A pdb=" N ARG I 456 " --> pdb=" O GLN I 452 " (cutoff:3.500A)
removed outlier: 4.166A pdb=" N PHE I 457 " --> pdb=" O GLU I 453 " (cutoff:3.500A)
Proline residue: I 458 - end of helix
Processing helix chain 'I' and resid 459 through 494
Proline residue: I 477 - end of helix
removed outlier: 3.750A pdb=" N TYR I 493 " --> pdb=" O ILE I 489 " (cutoff:3.500A)
removed outlier: 5.045A pdb=" N ILE I 494 " --> pdb=" O GLU I 490 " (cutoff:3.500A)
Processing helix chain 'I' and resid 612 through 644
removed outlier: 3.815A pdb=" N ASP I 638 " --> pdb=" O LYS I 634 " (cutoff:3.500A)
Proline residue: I 641 - end of helix
Processing helix chain 'I' and resid 649 through 660
removed outlier: 3.585A pdb=" N ASP I 654 " --> pdb=" O ASN I 650 " (cutoff:3.500A)
removed outlier: 5.478A pdb=" N GLN I 657 " --> pdb=" O LYS I 653 " (cutoff:3.500A)
removed outlier: 4.513A pdb=" N SER I 658 " --> pdb=" O ASP I 654 " (cutoff:3.500A)
Processing helix chain 'I' and resid 666 through 673
removed outlier: 4.050A pdb=" N ASP I 671 " --> pdb=" O SER I 667 " (cutoff:3.500A)
Processing helix chain 'I' and resid 677 through 710
removed outlier: 4.060A pdb=" N GLN I 699 " --> pdb=" O GLN I 695 " (cutoff:3.500A)
removed outlier: 3.819A pdb=" N HIS I 708 " --> pdb=" O ILE I 704 " (cutoff:3.500A)
removed outlier: 3.907A pdb=" N LEU I 709 " --> pdb=" O ARG I 705 " (cutoff:3.500A)
removed outlier: 5.056A pdb=" N TRP I 710 " --> pdb=" O GLU I 706 " (cutoff:3.500A)
Processing helix chain 'K' and resid 2 through 19
Proline residue: K 6 - end of helix
removed outlier: 4.609A pdb=" N PHE K 15 " --> pdb=" O LEU K 11 " (cutoff:3.500A)
removed outlier: 4.087A pdb=" N VAL K 18 " --> pdb=" O VAL K 14 " (cutoff:3.500A)
Processing helix chain 'K' and resid 37 through 47
Processing helix chain 'K' and resid 103 through 119
Processing helix chain 'K' and resid 161 through 175
removed outlier: 4.087A pdb=" N PHE K 173 " --> pdb=" O LEU K 169 " (cutoff:3.500A)
Processing helix chain 'K' and resid 194 through 204
removed outlier: 3.858A pdb=" N GLU K 202 " --> pdb=" O LYS K 198 " (cutoff:3.500A)
removed outlier: 3.905A pdb=" N VAL K 203 " --> pdb=" O ILE K 199 " (cutoff:3.500A)
Processing helix chain 'K' and resid 226 through 232
Processing helix chain 'K' and resid 248 through 255
Processing helix chain 'K' and resid 257 through 273
Processing helix chain 'K' and resid 276 through 281
Processing helix chain 'K' and resid 282 through 323
removed outlier: 4.185A pdb=" N CYS K 300 " --> pdb=" O HIS K 296 " (cutoff:3.500A)
removed outlier: 3.633A pdb=" N LEU K 301 " --> pdb=" O ILE K 297 " (cutoff:3.500A)
Proline residue: K 302 - end of helix
removed outlier: 4.298A pdb=" N TYR K 322 " --> pdb=" O LEU K 318 " (cutoff:3.500A)
Processing helix chain 'K' and resid 328 through 350
removed outlier: 5.254A pdb=" N THR K 332 " --> pdb=" O ASP K 328 " (cutoff:3.500A)
Processing helix chain 'K' and resid 362 through 382
removed outlier: 5.077A pdb=" N ILE K 366 " --> pdb=" O GLY K 362 " (cutoff:3.500A)
removed outlier: 3.892A pdb=" N THR K 373 " --> pdb=" O ILE K 369 " (cutoff:3.500A)
removed outlier: 5.159A pdb=" N PHE K 374 " --> pdb=" O PHE K 370 " (cutoff:3.500A)
removed outlier: 4.339A pdb=" N ARG K 376 " --> pdb=" O GLU K 372 " (cutoff:3.500A)
removed outlier: 3.635A pdb=" N VAL K 381 " --> pdb=" O THR K 377 " (cutoff:3.500A)
removed outlier: 5.557A pdb=" N ASP K 382 " --> pdb=" O LEU K 378 " (cutoff:3.500A)
Processing helix chain 'K' and resid 388 through 401
Processing helix chain 'K' and resid 410 through 450
removed outlier: 4.099A pdb=" N LYS K 418 " --> pdb=" O GLU K 414 " (cutoff:3.500A)
removed outlier: 3.610A pdb=" N LEU K 424 " --> pdb=" O GLN K 420 " (cutoff:3.500A)
removed outlier: 3.830A pdb=" N GLU K 425 " --> pdb=" O ILE K 421 " (cutoff:3.500A)
removed outlier: 4.337A pdb=" N GLU K 426 " --> pdb=" O LYS K 422 " (cutoff:3.500A)
Proline residue: K 427 - end of helix
removed outlier: 4.014A pdb=" N ILE K 443 " --> pdb=" O MET K 439 " (cutoff:3.500A)
removed outlier: 3.556A pdb=" N GLN K 444 " --> pdb=" O GLN K 440 " (cutoff:3.500A)
removed outlier: 3.738A pdb=" N ASN K 448 " --> pdb=" O GLN K 444 " (cutoff:3.500A)
removed outlier: 4.445A pdb=" N TYR K 449 " --> pdb=" O HIS K 445 " (cutoff:3.500A)
removed outlier: 4.826A pdb=" N SER K 450 " --> pdb=" O CYS K 446 " (cutoff:3.500A)
Processing helix chain 'K' and resid 451 through 458
removed outlier: 4.290A pdb=" N ARG K 456 " --> pdb=" O GLN K 452 " (cutoff:3.500A)
removed outlier: 4.166A pdb=" N PHE K 457 " --> pdb=" O GLU K 453 " (cutoff:3.500A)
Proline residue: K 458 - end of helix
Processing helix chain 'K' and resid 459 through 494
Proline residue: K 477 - end of helix
removed outlier: 3.750A pdb=" N TYR K 493 " --> pdb=" O ILE K 489 " (cutoff:3.500A)
removed outlier: 5.046A pdb=" N ILE K 494 " --> pdb=" O GLU K 490 " (cutoff:3.500A)
Processing helix chain 'K' and resid 612 through 644
removed outlier: 3.815A pdb=" N ASP K 638 " --> pdb=" O LYS K 634 " (cutoff:3.500A)
Proline residue: K 641 - end of helix
Processing helix chain 'K' and resid 649 through 660
removed outlier: 3.586A pdb=" N ASP K 654 " --> pdb=" O ASN K 650 " (cutoff:3.500A)
removed outlier: 5.477A pdb=" N GLN K 657 " --> pdb=" O LYS K 653 " (cutoff:3.500A)
removed outlier: 4.512A pdb=" N SER K 658 " --> pdb=" O ASP K 654 " (cutoff:3.500A)
Processing helix chain 'K' and resid 666 through 673
removed outlier: 4.050A pdb=" N ASP K 671 " --> pdb=" O SER K 667 " (cutoff:3.500A)
Processing helix chain 'K' and resid 677 through 710
removed outlier: 4.060A pdb=" N GLN K 699 " --> pdb=" O GLN K 695 " (cutoff:3.500A)
removed outlier: 3.818A pdb=" N HIS K 708 " --> pdb=" O ILE K 704 " (cutoff:3.500A)
removed outlier: 3.906A pdb=" N LEU K 709 " --> pdb=" O ARG K 705 " (cutoff:3.500A)
removed outlier: 5.056A pdb=" N TRP K 710 " --> pdb=" O GLU K 706 " (cutoff:3.500A)
Processing helix chain 'M' and resid 2 through 19
Proline residue: M 6 - end of helix
removed outlier: 4.610A pdb=" N PHE M 15 " --> pdb=" O LEU M 11 " (cutoff:3.500A)
removed outlier: 4.087A pdb=" N VAL M 18 " --> pdb=" O VAL M 14 " (cutoff:3.500A)
Processing helix chain 'M' and resid 37 through 47
Processing helix chain 'M' and resid 103 through 119
Processing helix chain 'M' and resid 161 through 175
removed outlier: 4.087A pdb=" N PHE M 173 " --> pdb=" O LEU M 169 " (cutoff:3.500A)
Processing helix chain 'M' and resid 194 through 204
removed outlier: 3.859A pdb=" N GLU M 202 " --> pdb=" O LYS M 198 " (cutoff:3.500A)
removed outlier: 3.905A pdb=" N VAL M 203 " --> pdb=" O ILE M 199 " (cutoff:3.500A)
Processing helix chain 'M' and resid 226 through 232
Processing helix chain 'M' and resid 248 through 255
Processing helix chain 'M' and resid 257 through 273
Processing helix chain 'M' and resid 276 through 281
Processing helix chain 'M' and resid 282 through 323
removed outlier: 4.185A pdb=" N CYS M 300 " --> pdb=" O HIS M 296 " (cutoff:3.500A)
removed outlier: 3.634A pdb=" N LEU M 301 " --> pdb=" O ILE M 297 " (cutoff:3.500A)
Proline residue: M 302 - end of helix
removed outlier: 4.298A pdb=" N TYR M 322 " --> pdb=" O LEU M 318 " (cutoff:3.500A)
Processing helix chain 'M' and resid 328 through 350
removed outlier: 5.254A pdb=" N THR M 332 " --> pdb=" O ASP M 328 " (cutoff:3.500A)
Processing helix chain 'M' and resid 362 through 382
removed outlier: 5.078A pdb=" N ILE M 366 " --> pdb=" O GLY M 362 " (cutoff:3.500A)
removed outlier: 3.892A pdb=" N THR M 373 " --> pdb=" O ILE M 369 " (cutoff:3.500A)
removed outlier: 5.159A pdb=" N PHE M 374 " --> pdb=" O PHE M 370 " (cutoff:3.500A)
removed outlier: 4.338A pdb=" N ARG M 376 " --> pdb=" O GLU M 372 " (cutoff:3.500A)
removed outlier: 3.635A pdb=" N VAL M 381 " --> pdb=" O THR M 377 " (cutoff:3.500A)
removed outlier: 5.556A pdb=" N ASP M 382 " --> pdb=" O LEU M 378 " (cutoff:3.500A)
Processing helix chain 'M' and resid 388 through 401
Processing helix chain 'M' and resid 410 through 450
removed outlier: 4.097A pdb=" N LYS M 418 " --> pdb=" O GLU M 414 " (cutoff:3.500A)
removed outlier: 3.610A pdb=" N LEU M 424 " --> pdb=" O GLN M 420 " (cutoff:3.500A)
removed outlier: 3.830A pdb=" N GLU M 425 " --> pdb=" O ILE M 421 " (cutoff:3.500A)
removed outlier: 4.338A pdb=" N GLU M 426 " --> pdb=" O LYS M 422 " (cutoff:3.500A)
Proline residue: M 427 - end of helix
removed outlier: 4.013A pdb=" N ILE M 443 " --> pdb=" O MET M 439 " (cutoff:3.500A)
removed outlier: 3.555A pdb=" N GLN M 444 " --> pdb=" O GLN M 440 " (cutoff:3.500A)
removed outlier: 3.738A pdb=" N ASN M 448 " --> pdb=" O GLN M 444 " (cutoff:3.500A)
removed outlier: 4.445A pdb=" N TYR M 449 " --> pdb=" O HIS M 445 " (cutoff:3.500A)
removed outlier: 4.827A pdb=" N SER M 450 " --> pdb=" O CYS M 446 " (cutoff:3.500A)
Processing helix chain 'M' and resid 451 through 458
removed outlier: 4.291A pdb=" N ARG M 456 " --> pdb=" O GLN M 452 " (cutoff:3.500A)
removed outlier: 4.166A pdb=" N PHE M 457 " --> pdb=" O GLU M 453 " (cutoff:3.500A)
Proline residue: M 458 - end of helix
Processing helix chain 'M' and resid 459 through 494
Proline residue: M 477 - end of helix
removed outlier: 3.750A pdb=" N TYR M 493 " --> pdb=" O ILE M 489 " (cutoff:3.500A)
removed outlier: 5.046A pdb=" N ILE M 494 " --> pdb=" O GLU M 490 " (cutoff:3.500A)
Processing helix chain 'M' and resid 612 through 644
removed outlier: 3.815A pdb=" N ASP M 638 " --> pdb=" O LYS M 634 " (cutoff:3.500A)
Proline residue: M 641 - end of helix
Processing helix chain 'M' and resid 649 through 660
removed outlier: 3.585A pdb=" N ASP M 654 " --> pdb=" O ASN M 650 " (cutoff:3.500A)
removed outlier: 5.477A pdb=" N GLN M 657 " --> pdb=" O LYS M 653 " (cutoff:3.500A)
removed outlier: 4.512A pdb=" N SER M 658 " --> pdb=" O ASP M 654 " (cutoff:3.500A)
Processing helix chain 'M' and resid 666 through 673
removed outlier: 4.049A pdb=" N ASP M 671 " --> pdb=" O SER M 667 " (cutoff:3.500A)
Processing helix chain 'M' and resid 677 through 710
removed outlier: 4.060A pdb=" N GLN M 699 " --> pdb=" O GLN M 695 " (cutoff:3.500A)
removed outlier: 3.818A pdb=" N HIS M 708 " --> pdb=" O ILE M 704 " (cutoff:3.500A)
removed outlier: 3.906A pdb=" N LEU M 709 " --> pdb=" O ARG M 705 " (cutoff:3.500A)
removed outlier: 5.056A pdb=" N TRP M 710 " --> pdb=" O GLU M 706 " (cutoff:3.500A)
Processing helix chain 'O' and resid 2 through 19
Proline residue: O 6 - end of helix
removed outlier: 4.609A pdb=" N PHE O 15 " --> pdb=" O LEU O 11 " (cutoff:3.500A)
removed outlier: 4.087A pdb=" N VAL O 18 " --> pdb=" O VAL O 14 " (cutoff:3.500A)
Processing helix chain 'O' and resid 37 through 47
Processing helix chain 'O' and resid 103 through 119
Processing helix chain 'O' and resid 161 through 175
removed outlier: 4.086A pdb=" N PHE O 173 " --> pdb=" O LEU O 169 " (cutoff:3.500A)
Processing helix chain 'O' and resid 194 through 204
removed outlier: 3.859A pdb=" N GLU O 202 " --> pdb=" O LYS O 198 " (cutoff:3.500A)
removed outlier: 3.906A pdb=" N VAL O 203 " --> pdb=" O ILE O 199 " (cutoff:3.500A)
Processing helix chain 'O' and resid 226 through 232
Processing helix chain 'O' and resid 248 through 255
Processing helix chain 'O' and resid 257 through 273
Processing helix chain 'O' and resid 276 through 281
Processing helix chain 'O' and resid 282 through 323
removed outlier: 4.185A pdb=" N CYS O 300 " --> pdb=" O HIS O 296 " (cutoff:3.500A)
removed outlier: 3.634A pdb=" N LEU O 301 " --> pdb=" O ILE O 297 " (cutoff:3.500A)
Proline residue: O 302 - end of helix
removed outlier: 4.297A pdb=" N TYR O 322 " --> pdb=" O LEU O 318 " (cutoff:3.500A)
Processing helix chain 'O' and resid 328 through 350
removed outlier: 5.253A pdb=" N THR O 332 " --> pdb=" O ASP O 328 " (cutoff:3.500A)
Processing helix chain 'O' and resid 362 through 382
removed outlier: 5.077A pdb=" N ILE O 366 " --> pdb=" O GLY O 362 " (cutoff:3.500A)
removed outlier: 3.892A pdb=" N THR O 373 " --> pdb=" O ILE O 369 " (cutoff:3.500A)
removed outlier: 5.159A pdb=" N PHE O 374 " --> pdb=" O PHE O 370 " (cutoff:3.500A)
removed outlier: 4.338A pdb=" N ARG O 376 " --> pdb=" O GLU O 372 " (cutoff:3.500A)
removed outlier: 3.634A pdb=" N VAL O 381 " --> pdb=" O THR O 377 " (cutoff:3.500A)
removed outlier: 5.556A pdb=" N ASP O 382 " --> pdb=" O LEU O 378 " (cutoff:3.500A)
Processing helix chain 'O' and resid 388 through 401
Processing helix chain 'O' and resid 410 through 450
removed outlier: 4.098A pdb=" N LYS O 418 " --> pdb=" O GLU O 414 " (cutoff:3.500A)
removed outlier: 3.611A pdb=" N LEU O 424 " --> pdb=" O GLN O 420 " (cutoff:3.500A)
removed outlier: 3.830A pdb=" N GLU O 425 " --> pdb=" O ILE O 421 " (cutoff:3.500A)
removed outlier: 4.338A pdb=" N GLU O 426 " --> pdb=" O LYS O 422 " (cutoff:3.500A)
Proline residue: O 427 - end of helix
removed outlier: 4.014A pdb=" N ILE O 443 " --> pdb=" O MET O 439 " (cutoff:3.500A)
removed outlier: 3.555A pdb=" N GLN O 444 " --> pdb=" O GLN O 440 " (cutoff:3.500A)
removed outlier: 3.738A pdb=" N ASN O 448 " --> pdb=" O GLN O 444 " (cutoff:3.500A)
removed outlier: 4.445A pdb=" N TYR O 449 " --> pdb=" O HIS O 445 " (cutoff:3.500A)
removed outlier: 4.826A pdb=" N SER O 450 " --> pdb=" O CYS O 446 " (cutoff:3.500A)
Processing helix chain 'O' and resid 451 through 458
removed outlier: 4.291A pdb=" N ARG O 456 " --> pdb=" O GLN O 452 " (cutoff:3.500A)
removed outlier: 4.167A pdb=" N PHE O 457 " --> pdb=" O GLU O 453 " (cutoff:3.500A)
Proline residue: O 458 - end of helix
Processing helix chain 'O' and resid 459 through 494
Proline residue: O 477 - end of helix
removed outlier: 3.750A pdb=" N TYR O 493 " --> pdb=" O ILE O 489 " (cutoff:3.500A)
removed outlier: 5.045A pdb=" N ILE O 494 " --> pdb=" O GLU O 490 " (cutoff:3.500A)
Processing helix chain 'O' and resid 612 through 644
removed outlier: 3.816A pdb=" N ASP O 638 " --> pdb=" O LYS O 634 " (cutoff:3.500A)
Proline residue: O 641 - end of helix
Processing helix chain 'O' and resid 649 through 660
removed outlier: 3.586A pdb=" N ASP O 654 " --> pdb=" O ASN O 650 " (cutoff:3.500A)
removed outlier: 5.478A pdb=" N GLN O 657 " --> pdb=" O LYS O 653 " (cutoff:3.500A)
removed outlier: 4.513A pdb=" N SER O 658 " --> pdb=" O ASP O 654 " (cutoff:3.500A)
Processing helix chain 'O' and resid 666 through 673
removed outlier: 4.049A pdb=" N ASP O 671 " --> pdb=" O SER O 667 " (cutoff:3.500A)
Processing helix chain 'O' and resid 677 through 710
removed outlier: 4.059A pdb=" N GLN O 699 " --> pdb=" O GLN O 695 " (cutoff:3.500A)
removed outlier: 3.819A pdb=" N HIS O 708 " --> pdb=" O ILE O 704 " (cutoff:3.500A)
removed outlier: 3.906A pdb=" N LEU O 709 " --> pdb=" O ARG O 705 " (cutoff:3.500A)
removed outlier: 5.056A pdb=" N TRP O 710 " --> pdb=" O GLU O 706 " (cutoff:3.500A)
Processing helix chain 'B' and resid 126 through 138
Processing helix chain 'B' and resid 142 through 168
Processing helix chain 'B' and resid 211 through 216
removed outlier: 3.941A pdb=" N THR B 215 " --> pdb=" O PRO B 211 " (cutoff:3.500A)
removed outlier: 5.040A pdb=" N VAL B 216 " --> pdb=" O GLY B 212 " (cutoff:3.500A)
No H-bonds generated for 'chain 'B' and resid 211 through 216'
Processing helix chain 'B' and resid 240 through 245
removed outlier: 3.857A pdb=" N LEU B 244 " --> pdb=" O TRP B 240 " (cutoff:3.500A)
removed outlier: 5.814A pdb=" N VAL B 245 " --> pdb=" O ASP B 241 " (cutoff:3.500A)
No H-bonds generated for 'chain 'B' and resid 240 through 245'
Processing helix chain 'B' and resid 250 through 264
Processing helix chain 'B' and resid 267 through 276
Processing helix chain 'B' and resid 334 through 350
removed outlier: 3.881A pdb=" N ASP B 349 " --> pdb=" O LEU B 345 " (cutoff:3.500A)
Processing helix chain 'B' and resid 352 through 368
removed outlier: 4.754A pdb=" N SER B 368 " --> pdb=" O CYS B 364 " (cutoff:3.500A)
Processing helix chain 'B' and resid 374 through 387
Processing helix chain 'B' and resid 393 through 415
removed outlier: 3.892A pdb=" N LEU B 397 " --> pdb=" O THR B 393 " (cutoff:3.500A)
removed outlier: 5.227A pdb=" N GLY B 398 " --> pdb=" O GLU B 394 " (cutoff:3.500A)
removed outlier: 5.817A pdb=" N GLU B 399 " --> pdb=" O GLU B 395 " (cutoff:3.500A)
Processing helix chain 'B' and resid 432 through 450
Proline residue: B 450 - end of helix
Processing helix chain 'B' and resid 180 through 185
removed outlier: 5.622A pdb=" N GLY B 185 " --> pdb=" O GLY B 180 " (cutoff:3.500A)
No H-bonds generated for 'chain 'B' and resid 180 through 185'
Processing helix chain 'D' and resid 126 through 138
Processing helix chain 'D' and resid 142 through 168
Processing helix chain 'D' and resid 211 through 216
removed outlier: 3.942A pdb=" N THR D 215 " --> pdb=" O PRO D 211 " (cutoff:3.500A)
removed outlier: 5.040A pdb=" N VAL D 216 " --> pdb=" O GLY D 212 " (cutoff:3.500A)
No H-bonds generated for 'chain 'D' and resid 211 through 216'
Processing helix chain 'D' and resid 240 through 245
removed outlier: 3.857A pdb=" N LEU D 244 " --> pdb=" O TRP D 240 " (cutoff:3.500A)
removed outlier: 5.814A pdb=" N VAL D 245 " --> pdb=" O ASP D 241 " (cutoff:3.500A)
No H-bonds generated for 'chain 'D' and resid 240 through 245'
Processing helix chain 'D' and resid 250 through 264
Processing helix chain 'D' and resid 267 through 276
Processing helix chain 'D' and resid 334 through 350
removed outlier: 3.882A pdb=" N ASP D 349 " --> pdb=" O LEU D 345 " (cutoff:3.500A)
Processing helix chain 'D' and resid 352 through 368
removed outlier: 4.754A pdb=" N SER D 368 " --> pdb=" O CYS D 364 " (cutoff:3.500A)
Processing helix chain 'D' and resid 374 through 387
Processing helix chain 'D' and resid 393 through 415
removed outlier: 3.892A pdb=" N LEU D 397 " --> pdb=" O THR D 393 " (cutoff:3.500A)
removed outlier: 5.226A pdb=" N GLY D 398 " --> pdb=" O GLU D 394 " (cutoff:3.500A)
removed outlier: 5.816A pdb=" N GLU D 399 " --> pdb=" O GLU D 395 " (cutoff:3.500A)
Processing helix chain 'D' and resid 432 through 450
Proline residue: D 450 - end of helix
Processing helix chain 'D' and resid 180 through 185
removed outlier: 5.622A pdb=" N GLY D 185 " --> pdb=" O GLY D 180 " (cutoff:3.500A)
No H-bonds generated for 'chain 'D' and resid 180 through 185'
Processing helix chain 'F' and resid 126 through 138
Processing helix chain 'F' and resid 142 through 168
Processing helix chain 'F' and resid 211 through 216
removed outlier: 3.941A pdb=" N THR F 215 " --> pdb=" O PRO F 211 " (cutoff:3.500A)
removed outlier: 5.040A pdb=" N VAL F 216 " --> pdb=" O GLY F 212 " (cutoff:3.500A)
No H-bonds generated for 'chain 'F' and resid 211 through 216'
Processing helix chain 'F' and resid 240 through 245
removed outlier: 3.857A pdb=" N LEU F 244 " --> pdb=" O TRP F 240 " (cutoff:3.500A)
removed outlier: 5.814A pdb=" N VAL F 245 " --> pdb=" O ASP F 241 " (cutoff:3.500A)
No H-bonds generated for 'chain 'F' and resid 240 through 245'
Processing helix chain 'F' and resid 250 through 264
Processing helix chain 'F' and resid 267 through 276
Processing helix chain 'F' and resid 334 through 350
removed outlier: 3.881A pdb=" N ASP F 349 " --> pdb=" O LEU F 345 " (cutoff:3.500A)
Processing helix chain 'F' and resid 352 through 368
removed outlier: 4.753A pdb=" N SER F 368 " --> pdb=" O CYS F 364 " (cutoff:3.500A)
Processing helix chain 'F' and resid 374 through 387
Processing helix chain 'F' and resid 393 through 415
removed outlier: 3.892A pdb=" N LEU F 397 " --> pdb=" O THR F 393 " (cutoff:3.500A)
removed outlier: 5.226A pdb=" N GLY F 398 " --> pdb=" O GLU F 394 " (cutoff:3.500A)
removed outlier: 5.817A pdb=" N GLU F 399 " --> pdb=" O GLU F 395 " (cutoff:3.500A)
Processing helix chain 'F' and resid 432 through 450
Proline residue: F 450 - end of helix
Processing helix chain 'F' and resid 180 through 185
removed outlier: 5.621A pdb=" N GLY F 185 " --> pdb=" O GLY F 180 " (cutoff:3.500A)
No H-bonds generated for 'chain 'F' and resid 180 through 185'
Processing helix chain 'H' and resid 126 through 138
Processing helix chain 'H' and resid 142 through 168
Processing helix chain 'H' and resid 211 through 216
removed outlier: 3.941A pdb=" N THR H 215 " --> pdb=" O PRO H 211 " (cutoff:3.500A)
removed outlier: 5.040A pdb=" N VAL H 216 " --> pdb=" O GLY H 212 " (cutoff:3.500A)
No H-bonds generated for 'chain 'H' and resid 211 through 216'
Processing helix chain 'H' and resid 240 through 245
removed outlier: 3.856A pdb=" N LEU H 244 " --> pdb=" O TRP H 240 " (cutoff:3.500A)
removed outlier: 5.813A pdb=" N VAL H 245 " --> pdb=" O ASP H 241 " (cutoff:3.500A)
No H-bonds generated for 'chain 'H' and resid 240 through 245'
Processing helix chain 'H' and resid 250 through 264
Processing helix chain 'H' and resid 267 through 276
Processing helix chain 'H' and resid 334 through 350
removed outlier: 3.881A pdb=" N ASP H 349 " --> pdb=" O LEU H 345 " (cutoff:3.500A)
Processing helix chain 'H' and resid 352 through 368
removed outlier: 4.753A pdb=" N SER H 368 " --> pdb=" O CYS H 364 " (cutoff:3.500A)
Processing helix chain 'H' and resid 374 through 387
Processing helix chain 'H' and resid 393 through 415
removed outlier: 3.892A pdb=" N LEU H 397 " --> pdb=" O THR H 393 " (cutoff:3.500A)
removed outlier: 5.226A pdb=" N GLY H 398 " --> pdb=" O GLU H 394 " (cutoff:3.500A)
removed outlier: 5.817A pdb=" N GLU H 399 " --> pdb=" O GLU H 395 " (cutoff:3.500A)
Processing helix chain 'H' and resid 432 through 450
Proline residue: H 450 - end of helix
Processing helix chain 'H' and resid 180 through 185
removed outlier: 5.623A pdb=" N GLY H 185 " --> pdb=" O GLY H 180 " (cutoff:3.500A)
No H-bonds generated for 'chain 'H' and resid 180 through 185'
Processing helix chain 'J' and resid 126 through 138
Processing helix chain 'J' and resid 142 through 168
Processing helix chain 'J' and resid 211 through 216
removed outlier: 3.941A pdb=" N THR J 215 " --> pdb=" O PRO J 211 " (cutoff:3.500A)
removed outlier: 5.040A pdb=" N VAL J 216 " --> pdb=" O GLY J 212 " (cutoff:3.500A)
No H-bonds generated for 'chain 'J' and resid 211 through 216'
Processing helix chain 'J' and resid 240 through 245
removed outlier: 3.857A pdb=" N LEU J 244 " --> pdb=" O TRP J 240 " (cutoff:3.500A)
removed outlier: 5.814A pdb=" N VAL J 245 " --> pdb=" O ASP J 241 " (cutoff:3.500A)
No H-bonds generated for 'chain 'J' and resid 240 through 245'
Processing helix chain 'J' and resid 250 through 264
Processing helix chain 'J' and resid 267 through 276
Processing helix chain 'J' and resid 334 through 350
removed outlier: 3.881A pdb=" N ASP J 349 " --> pdb=" O LEU J 345 " (cutoff:3.500A)
Processing helix chain 'J' and resid 352 through 368
removed outlier: 4.754A pdb=" N SER J 368 " --> pdb=" O CYS J 364 " (cutoff:3.500A)
Processing helix chain 'J' and resid 374 through 387
Processing helix chain 'J' and resid 393 through 415
removed outlier: 3.892A pdb=" N LEU J 397 " --> pdb=" O THR J 393 " (cutoff:3.500A)
removed outlier: 5.227A pdb=" N GLY J 398 " --> pdb=" O GLU J 394 " (cutoff:3.500A)
removed outlier: 5.817A pdb=" N GLU J 399 " --> pdb=" O GLU J 395 " (cutoff:3.500A)
Processing helix chain 'J' and resid 432 through 450
Proline residue: J 450 - end of helix
Processing helix chain 'J' and resid 180 through 185
removed outlier: 5.622A pdb=" N GLY J 185 " --> pdb=" O GLY J 180 " (cutoff:3.500A)
No H-bonds generated for 'chain 'J' and resid 180 through 185'
Processing helix chain 'L' and resid 126 through 138
Processing helix chain 'L' and resid 142 through 168
Processing helix chain 'L' and resid 211 through 216
removed outlier: 3.941A pdb=" N THR L 215 " --> pdb=" O PRO L 211 " (cutoff:3.500A)
removed outlier: 5.040A pdb=" N VAL L 216 " --> pdb=" O GLY L 212 " (cutoff:3.500A)
No H-bonds generated for 'chain 'L' and resid 211 through 216'
Processing helix chain 'L' and resid 240 through 245
removed outlier: 3.857A pdb=" N LEU L 244 " --> pdb=" O TRP L 240 " (cutoff:3.500A)
removed outlier: 5.813A pdb=" N VAL L 245 " --> pdb=" O ASP L 241 " (cutoff:3.500A)
No H-bonds generated for 'chain 'L' and resid 240 through 245'
Processing helix chain 'L' and resid 250 through 264
Processing helix chain 'L' and resid 267 through 276
Processing helix chain 'L' and resid 334 through 350
removed outlier: 3.881A pdb=" N ASP L 349 " --> pdb=" O LEU L 345 " (cutoff:3.500A)
Processing helix chain 'L' and resid 352 through 368
removed outlier: 4.754A pdb=" N SER L 368 " --> pdb=" O CYS L 364 " (cutoff:3.500A)
Processing helix chain 'L' and resid 374 through 387
Processing helix chain 'L' and resid 393 through 415
removed outlier: 3.892A pdb=" N LEU L 397 " --> pdb=" O THR L 393 " (cutoff:3.500A)
removed outlier: 5.226A pdb=" N GLY L 398 " --> pdb=" O GLU L 394 " (cutoff:3.500A)
removed outlier: 5.817A pdb=" N GLU L 399 " --> pdb=" O GLU L 395 " (cutoff:3.500A)
Processing helix chain 'L' and resid 432 through 450
Proline residue: L 450 - end of helix
Processing helix chain 'L' and resid 180 through 185
removed outlier: 5.622A pdb=" N GLY L 185 " --> pdb=" O GLY L 180 " (cutoff:3.500A)
No H-bonds generated for 'chain 'L' and resid 180 through 185'
Processing helix chain 'N' and resid 126 through 138
Processing helix chain 'N' and resid 142 through 168
Processing helix chain 'N' and resid 211 through 216
removed outlier: 3.941A pdb=" N THR N 215 " --> pdb=" O PRO N 211 " (cutoff:3.500A)
removed outlier: 5.040A pdb=" N VAL N 216 " --> pdb=" O GLY N 212 " (cutoff:3.500A)
No H-bonds generated for 'chain 'N' and resid 211 through 216'
Processing helix chain 'N' and resid 240 through 245
removed outlier: 3.857A pdb=" N LEU N 244 " --> pdb=" O TRP N 240 " (cutoff:3.500A)
removed outlier: 5.813A pdb=" N VAL N 245 " --> pdb=" O ASP N 241 " (cutoff:3.500A)
No H-bonds generated for 'chain 'N' and resid 240 through 245'
Processing helix chain 'N' and resid 250 through 264
Processing helix chain 'N' and resid 267 through 276
Processing helix chain 'N' and resid 334 through 350
removed outlier: 3.881A pdb=" N ASP N 349 " --> pdb=" O LEU N 345 " (cutoff:3.500A)
Processing helix chain 'N' and resid 352 through 368
removed outlier: 4.754A pdb=" N SER N 368 " --> pdb=" O CYS N 364 " (cutoff:3.500A)
Processing helix chain 'N' and resid 374 through 387
Processing helix chain 'N' and resid 393 through 415
removed outlier: 3.892A pdb=" N LEU N 397 " --> pdb=" O THR N 393 " (cutoff:3.500A)
removed outlier: 5.226A pdb=" N GLY N 398 " --> pdb=" O GLU N 394 " (cutoff:3.500A)
removed outlier: 5.817A pdb=" N GLU N 399 " --> pdb=" O GLU N 395 " (cutoff:3.500A)
Processing helix chain 'N' and resid 432 through 450
Proline residue: N 450 - end of helix
Processing helix chain 'N' and resid 180 through 185
removed outlier: 5.623A pdb=" N GLY N 185 " --> pdb=" O GLY N 180 " (cutoff:3.500A)
No H-bonds generated for 'chain 'N' and resid 180 through 185'
Processing helix chain 'P' and resid 126 through 138
Processing helix chain 'P' and resid 142 through 168
Processing helix chain 'P' and resid 211 through 216
removed outlier: 3.941A pdb=" N THR P 215 " --> pdb=" O PRO P 211 " (cutoff:3.500A)
removed outlier: 5.040A pdb=" N VAL P 216 " --> pdb=" O GLY P 212 " (cutoff:3.500A)
No H-bonds generated for 'chain 'P' and resid 211 through 216'
Processing helix chain 'P' and resid 240 through 245
removed outlier: 3.857A pdb=" N LEU P 244 " --> pdb=" O TRP P 240 " (cutoff:3.500A)
removed outlier: 5.813A pdb=" N VAL P 245 " --> pdb=" O ASP P 241 " (cutoff:3.500A)
No H-bonds generated for 'chain 'P' and resid 240 through 245'
Processing helix chain 'P' and resid 250 through 264
Processing helix chain 'P' and resid 267 through 276
Processing helix chain 'P' and resid 334 through 350
removed outlier: 3.881A pdb=" N ASP P 349 " --> pdb=" O LEU P 345 " (cutoff:3.500A)
Processing helix chain 'P' and resid 352 through 368
removed outlier: 4.753A pdb=" N SER P 368 " --> pdb=" O CYS P 364 " (cutoff:3.500A)
Processing helix chain 'P' and resid 374 through 387
Processing helix chain 'P' and resid 393 through 415
removed outlier: 3.893A pdb=" N LEU P 397 " --> pdb=" O THR P 393 " (cutoff:3.500A)
removed outlier: 5.226A pdb=" N GLY P 398 " --> pdb=" O GLU P 394 " (cutoff:3.500A)
removed outlier: 5.817A pdb=" N GLU P 399 " --> pdb=" O GLU P 395 " (cutoff:3.500A)
Processing helix chain 'P' and resid 432 through 450
Proline residue: P 450 - end of helix
Processing helix chain 'P' and resid 180 through 185
removed outlier: 5.622A pdb=" N GLY P 185 " --> pdb=" O GLY P 180 " (cutoff:3.500A)
No H-bonds generated for 'chain 'P' and resid 180 through 185'
Processing sheet with id= 1, first strand: chain 'A' and resid 27 through 33
removed outlier: 6.018A pdb=" N ILE A 28 " --> pdb=" O LEU A 144 " (cutoff:3.500A)
removed outlier: 5.387A pdb=" N ASP A 146 " --> pdb=" O ILE A 28 " (cutoff:3.500A)
removed outlier: 7.135A pdb=" N VAL A 30 " --> pdb=" O ASP A 146 " (cutoff:3.500A)
removed outlier: 5.567A pdb=" N GLY A 32 " --> pdb=" O PRO A 148 " (cutoff:3.500A)
removed outlier: 7.114A pdb=" N VAL A 140 " --> pdb=" O HIS A 69 " (cutoff:3.500A)
removed outlier: 4.870A pdb=" N HIS A 69 " --> pdb=" O VAL A 140 " (cutoff:3.500A)
removed outlier: 7.784A pdb=" N HIS A 131 " --> pdb=" O LEU A 94 " (cutoff:3.500A)
Processing sheet with id= 2, first strand: chain 'A' and resid 180 through 186
Processing sheet with id= 3, first strand: chain 'C' and resid 27 through 33
removed outlier: 6.017A pdb=" N ILE C 28 " --> pdb=" O LEU C 144 " (cutoff:3.500A)
removed outlier: 5.387A pdb=" N ASP C 146 " --> pdb=" O ILE C 28 " (cutoff:3.500A)
removed outlier: 7.135A pdb=" N VAL C 30 " --> pdb=" O ASP C 146 " (cutoff:3.500A)
removed outlier: 5.567A pdb=" N GLY C 32 " --> pdb=" O PRO C 148 " (cutoff:3.500A)
removed outlier: 7.115A pdb=" N VAL C 140 " --> pdb=" O HIS C 69 " (cutoff:3.500A)
removed outlier: 4.868A pdb=" N HIS C 69 " --> pdb=" O VAL C 140 " (cutoff:3.500A)
removed outlier: 7.784A pdb=" N HIS C 131 " --> pdb=" O LEU C 94 " (cutoff:3.500A)
Processing sheet with id= 4, first strand: chain 'C' and resid 180 through 186
Processing sheet with id= 5, first strand: chain 'E' and resid 27 through 33
removed outlier: 6.017A pdb=" N ILE E 28 " --> pdb=" O LEU E 144 " (cutoff:3.500A)
removed outlier: 5.387A pdb=" N ASP E 146 " --> pdb=" O ILE E 28 " (cutoff:3.500A)
removed outlier: 7.135A pdb=" N VAL E 30 " --> pdb=" O ASP E 146 " (cutoff:3.500A)
removed outlier: 5.567A pdb=" N GLY E 32 " --> pdb=" O PRO E 148 " (cutoff:3.500A)
removed outlier: 7.115A pdb=" N VAL E 140 " --> pdb=" O HIS E 69 " (cutoff:3.500A)
removed outlier: 4.870A pdb=" N HIS E 69 " --> pdb=" O VAL E 140 " (cutoff:3.500A)
removed outlier: 7.784A pdb=" N HIS E 131 " --> pdb=" O LEU E 94 " (cutoff:3.500A)
Processing sheet with id= 6, first strand: chain 'E' and resid 180 through 186
Processing sheet with id= 7, first strand: chain 'G' and resid 27 through 33
removed outlier: 6.017A pdb=" N ILE G 28 " --> pdb=" O LEU G 144 " (cutoff:3.500A)
removed outlier: 5.387A pdb=" N ASP G 146 " --> pdb=" O ILE G 28 " (cutoff:3.500A)
removed outlier: 7.135A pdb=" N VAL G 30 " --> pdb=" O ASP G 146 " (cutoff:3.500A)
removed outlier: 5.566A pdb=" N GLY G 32 " --> pdb=" O PRO G 148 " (cutoff:3.500A)
removed outlier: 7.115A pdb=" N VAL G 140 " --> pdb=" O HIS G 69 " (cutoff:3.500A)
removed outlier: 4.868A pdb=" N HIS G 69 " --> pdb=" O VAL G 140 " (cutoff:3.500A)
removed outlier: 7.784A pdb=" N HIS G 131 " --> pdb=" O LEU G 94 " (cutoff:3.500A)
Processing sheet with id= 8, first strand: chain 'G' and resid 180 through 186
Processing sheet with id= 9, first strand: chain 'I' and resid 27 through 33
removed outlier: 6.017A pdb=" N ILE I 28 " --> pdb=" O LEU I 144 " (cutoff:3.500A)
removed outlier: 5.387A pdb=" N ASP I 146 " --> pdb=" O ILE I 28 " (cutoff:3.500A)
removed outlier: 7.135A pdb=" N VAL I 30 " --> pdb=" O ASP I 146 " (cutoff:3.500A)
removed outlier: 5.567A pdb=" N GLY I 32 " --> pdb=" O PRO I 148 " (cutoff:3.500A)
removed outlier: 7.115A pdb=" N VAL I 140 " --> pdb=" O HIS I 69 " (cutoff:3.500A)
removed outlier: 4.869A pdb=" N HIS I 69 " --> pdb=" O VAL I 140 " (cutoff:3.500A)
removed outlier: 7.784A pdb=" N HIS I 131 " --> pdb=" O LEU I 94 " (cutoff:3.500A)
Processing sheet with id= 10, first strand: chain 'I' and resid 180 through 186
Processing sheet with id= 11, first strand: chain 'K' and resid 27 through 33
removed outlier: 6.018A pdb=" N ILE K 28 " --> pdb=" O LEU K 144 " (cutoff:3.500A)
removed outlier: 5.387A pdb=" N ASP K 146 " --> pdb=" O ILE K 28 " (cutoff:3.500A)
removed outlier: 7.134A pdb=" N VAL K 30 " --> pdb=" O ASP K 146 " (cutoff:3.500A)
removed outlier: 5.567A pdb=" N GLY K 32 " --> pdb=" O PRO K 148 " (cutoff:3.500A)
removed outlier: 7.114A pdb=" N VAL K 140 " --> pdb=" O HIS K 69 " (cutoff:3.500A)
removed outlier: 4.869A pdb=" N HIS K 69 " --> pdb=" O VAL K 140 " (cutoff:3.500A)
removed outlier: 7.784A pdb=" N HIS K 131 " --> pdb=" O LEU K 94 " (cutoff:3.500A)
Processing sheet with id= 12, first strand: chain 'K' and resid 180 through 186
Processing sheet with id= 13, first strand: chain 'M' and resid 27 through 33
removed outlier: 6.017A pdb=" N ILE M 28 " --> pdb=" O LEU M 144 " (cutoff:3.500A)
removed outlier: 5.387A pdb=" N ASP M 146 " --> pdb=" O ILE M 28 " (cutoff:3.500A)
removed outlier: 7.134A pdb=" N VAL M 30 " --> pdb=" O ASP M 146 " (cutoff:3.500A)
removed outlier: 5.567A pdb=" N GLY M 32 " --> pdb=" O PRO M 148 " (cutoff:3.500A)
removed outlier: 7.115A pdb=" N VAL M 140 " --> pdb=" O HIS M 69 " (cutoff:3.500A)
removed outlier: 4.869A pdb=" N HIS M 69 " --> pdb=" O VAL M 140 " (cutoff:3.500A)
removed outlier: 7.783A pdb=" N HIS M 131 " --> pdb=" O LEU M 94 " (cutoff:3.500A)
Processing sheet with id= 14, first strand: chain 'M' and resid 180 through 186
Processing sheet with id= 15, first strand: chain 'O' and resid 27 through 33
removed outlier: 6.017A pdb=" N ILE O 28 " --> pdb=" O LEU O 144 " (cutoff:3.500A)
removed outlier: 5.387A pdb=" N ASP O 146 " --> pdb=" O ILE O 28 " (cutoff:3.500A)
removed outlier: 7.135A pdb=" N VAL O 30 " --> pdb=" O ASP O 146 " (cutoff:3.500A)
removed outlier: 5.568A pdb=" N GLY O 32 " --> pdb=" O PRO O 148 " (cutoff:3.500A)
removed outlier: 7.115A pdb=" N VAL O 140 " --> pdb=" O HIS O 69 " (cutoff:3.500A)
removed outlier: 4.868A pdb=" N HIS O 69 " --> pdb=" O VAL O 140 " (cutoff:3.500A)
removed outlier: 7.784A pdb=" N HIS O 131 " --> pdb=" O LEU O 94 " (cutoff:3.500A)
Processing sheet with id= 16, first strand: chain 'O' and resid 180 through 186
Processing sheet with id= 17, first strand: chain 'B' and resid 176 through 179
removed outlier: 5.443A pdb=" N GLU B 286 " --> pdb=" O VAL B 303 " (cutoff:3.500A)
removed outlier: 5.937A pdb=" N GLU B 287 " --> pdb=" O SER B 282 " (cutoff:3.500A)
removed outlier: 6.373A pdb=" N LEU B 278 " --> pdb=" O GLU B 291 " (cutoff:3.500A)
Processing sheet with id= 18, first strand: chain 'B' and resid 206 through 210
removed outlier: 4.866A pdb=" N LEU B 206 " --> pdb=" O THR B 228 " (cutoff:3.500A)
Processing sheet with id= 19, first strand: chain 'D' and resid 176 through 179
removed outlier: 5.443A pdb=" N GLU D 286 " --> pdb=" O VAL D 303 " (cutoff:3.500A)
removed outlier: 5.937A pdb=" N GLU D 287 " --> pdb=" O SER D 282 " (cutoff:3.500A)
removed outlier: 6.373A pdb=" N LEU D 278 " --> pdb=" O GLU D 291 " (cutoff:3.500A)
Processing sheet with id= 20, first strand: chain 'D' and resid 206 through 210
removed outlier: 4.865A pdb=" N LEU D 206 " --> pdb=" O THR D 228 " (cutoff:3.500A)
Processing sheet with id= 21, first strand: chain 'F' and resid 176 through 179
removed outlier: 5.443A pdb=" N GLU F 286 " --> pdb=" O VAL F 303 " (cutoff:3.500A)
removed outlier: 5.938A pdb=" N GLU F 287 " --> pdb=" O SER F 282 " (cutoff:3.500A)
removed outlier: 6.373A pdb=" N LEU F 278 " --> pdb=" O GLU F 291 " (cutoff:3.500A)
Processing sheet with id= 22, first strand: chain 'F' and resid 206 through 210
removed outlier: 4.866A pdb=" N LEU F 206 " --> pdb=" O THR F 228 " (cutoff:3.500A)
Processing sheet with id= 23, first strand: chain 'H' and resid 176 through 179
removed outlier: 5.443A pdb=" N GLU H 286 " --> pdb=" O VAL H 303 " (cutoff:3.500A)
removed outlier: 5.938A pdb=" N GLU H 287 " --> pdb=" O SER H 282 " (cutoff:3.500A)
removed outlier: 6.373A pdb=" N LEU H 278 " --> pdb=" O GLU H 291 " (cutoff:3.500A)
Processing sheet with id= 24, first strand: chain 'H' and resid 206 through 210
removed outlier: 4.866A pdb=" N LEU H 206 " --> pdb=" O THR H 228 " (cutoff:3.500A)
Processing sheet with id= 25, first strand: chain 'J' and resid 176 through 179
removed outlier: 5.443A pdb=" N GLU J 286 " --> pdb=" O VAL J 303 " (cutoff:3.500A)
removed outlier: 5.937A pdb=" N GLU J 287 " --> pdb=" O SER J 282 " (cutoff:3.500A)
removed outlier: 6.373A pdb=" N LEU J 278 " --> pdb=" O GLU J 291 " (cutoff:3.500A)
Processing sheet with id= 26, first strand: chain 'J' and resid 206 through 210
removed outlier: 4.865A pdb=" N LEU J 206 " --> pdb=" O THR J 228 " (cutoff:3.500A)
Processing sheet with id= 27, first strand: chain 'L' and resid 176 through 179
removed outlier: 5.442A pdb=" N GLU L 286 " --> pdb=" O VAL L 303 " (cutoff:3.500A)
removed outlier: 5.937A pdb=" N GLU L 287 " --> pdb=" O SER L 282 " (cutoff:3.500A)
removed outlier: 6.373A pdb=" N LEU L 278 " --> pdb=" O GLU L 291 " (cutoff:3.500A)
Processing sheet with id= 28, first strand: chain 'L' and resid 206 through 210
removed outlier: 4.866A pdb=" N LEU L 206 " --> pdb=" O THR L 228 " (cutoff:3.500A)
Processing sheet with id= 29, first strand: chain 'N' and resid 176 through 179
removed outlier: 5.442A pdb=" N GLU N 286 " --> pdb=" O VAL N 303 " (cutoff:3.500A)
removed outlier: 5.937A pdb=" N GLU N 287 " --> pdb=" O SER N 282 " (cutoff:3.500A)
removed outlier: 6.373A pdb=" N LEU N 278 " --> pdb=" O GLU N 291 " (cutoff:3.500A)
Processing sheet with id= 30, first strand: chain 'N' and resid 206 through 210
removed outlier: 4.866A pdb=" N LEU N 206 " --> pdb=" O THR N 228 " (cutoff:3.500A)
Processing sheet with id= 31, first strand: chain 'P' and resid 176 through 179
removed outlier: 5.443A pdb=" N GLU P 286 " --> pdb=" O VAL P 303 " (cutoff:3.500A)
removed outlier: 5.938A pdb=" N GLU P 287 " --> pdb=" O SER P 282 " (cutoff:3.500A)
removed outlier: 6.373A pdb=" N LEU P 278 " --> pdb=" O GLU P 291 " (cutoff:3.500A)
Processing sheet with id= 32, first strand: chain 'P' and resid 206 through 210
removed outlier: 4.865A pdb=" N LEU P 206 " --> pdb=" O THR P 228 " (cutoff:3.500A)
3264 hydrogen bonds defined for protein.
9768 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: 41.19
Time building geometry restraints manager: 84.11 seconds
NOTE: a complete listing of the restraints can be obtained by requesting
output of .geo file.
Histogram of bond lengths:
0.96 - 1.13: 58960
1.13 - 1.30: 9864
1.30 - 1.47: 22066
1.47 - 1.64: 26790
1.64 - 1.82: 344
Bond restraints: 118024
Sorted by residual:
bond pdb=" CE1 HIS H 348 "
pdb=" HE1 HIS H 348 "
ideal model delta sigma weight residual
0.930 1.095 -0.165 2.00e-02 2.50e+03 6.82e+01
bond pdb=" CE1 HIS D 348 "
pdb=" HE1 HIS D 348 "
ideal model delta sigma weight residual
0.930 1.095 -0.165 2.00e-02 2.50e+03 6.81e+01
bond pdb=" CE1 HIS J 348 "
pdb=" HE1 HIS J 348 "
ideal model delta sigma weight residual
0.930 1.095 -0.165 2.00e-02 2.50e+03 6.79e+01
bond pdb=" CE1 HIS P 348 "
pdb=" HE1 HIS P 348 "
ideal model delta sigma weight residual
0.930 1.095 -0.165 2.00e-02 2.50e+03 6.79e+01
bond pdb=" CE1 HIS N 348 "
pdb=" HE1 HIS N 348 "
ideal model delta sigma weight residual
0.930 1.095 -0.165 2.00e-02 2.50e+03 6.78e+01
... (remaining 118019 not shown)
Histogram of bond angle deviations from ideal:
95.70 - 103.90: 933
103.90 - 112.09: 139263
112.09 - 120.29: 46531
120.29 - 128.49: 27185
128.49 - 136.68: 480
Bond angle restraints: 214392
Sorted by residual:
angle pdb=" C GLY F 180 "
pdb=" N PRO F 181 "
pdb=" CA PRO F 181 "
ideal model delta sigma weight residual
119.84 128.70 -8.86 1.25e+00 6.40e-01 5.03e+01
angle pdb=" C GLY B 180 "
pdb=" N PRO B 181 "
pdb=" CA PRO B 181 "
ideal model delta sigma weight residual
119.84 128.69 -8.85 1.25e+00 6.40e-01 5.01e+01
angle pdb=" C GLY E 401 "
pdb=" N PRO E 402 "
pdb=" CA PRO E 402 "
ideal model delta sigma weight residual
119.56 126.78 -7.22 1.02e+00 9.61e-01 5.01e+01
angle pdb=" C GLY L 180 "
pdb=" N PRO L 181 "
pdb=" CA PRO L 181 "
ideal model delta sigma weight residual
119.84 128.67 -8.83 1.25e+00 6.40e-01 4.99e+01
angle pdb=" C GLY G 401 "
pdb=" N PRO G 402 "
pdb=" CA PRO G 402 "
ideal model delta sigma weight residual
119.56 126.76 -7.20 1.02e+00 9.61e-01 4.98e+01
... (remaining 214387 not shown)
Histogram of dihedral angle deviations from ideal:
0.00 - 16.60: 45289
16.60 - 33.20: 1043
33.20 - 49.80: 232
49.80 - 66.40: 124
66.40 - 83.00: 16
Dihedral angle restraints: 46704
sinusoidal: 22896
harmonic: 23808
Sorted by residual:
dihedral pdb=" CA VAL K 411 "
pdb=" C VAL K 411 "
pdb=" N SER K 412 "
pdb=" CA SER K 412 "
ideal model delta harmonic sigma weight residual
180.00 159.39 20.61 0 5.00e+00 4.00e-02 1.70e+01
dihedral pdb=" CA VAL I 411 "
pdb=" C VAL I 411 "
pdb=" N SER I 412 "
pdb=" CA SER I 412 "
ideal model delta harmonic sigma weight residual
180.00 159.39 20.61 0 5.00e+00 4.00e-02 1.70e+01
dihedral pdb=" CA VAL O 411 "
pdb=" C VAL O 411 "
pdb=" N SER O 412 "
pdb=" CA SER O 412 "
ideal model delta harmonic sigma weight residual
180.00 159.39 20.61 0 5.00e+00 4.00e-02 1.70e+01
... (remaining 46701 not shown)
Histogram of chiral volume deviations from ideal:
0.000 - 0.041: 5719
0.041 - 0.082: 2421
0.082 - 0.123: 1186
0.123 - 0.165: 91
0.165 - 0.206: 23
Chirality restraints: 9440
Sorted by residual:
chirality pdb=" CA VAL J 307 "
pdb=" N VAL J 307 "
pdb=" C VAL J 307 "
pdb=" CB VAL J 307 "
both_signs ideal model delta sigma weight residual
False 2.44 2.65 -0.21 2.00e-01 2.50e+01 1.06e+00
chirality pdb=" CA VAL L 307 "
pdb=" N VAL L 307 "
pdb=" C VAL L 307 "
pdb=" CB VAL L 307 "
both_signs ideal model delta sigma weight residual
False 2.44 2.65 -0.20 2.00e-01 2.50e+01 1.05e+00
chirality pdb=" CA VAL H 307 "
pdb=" N VAL H 307 "
pdb=" C VAL H 307 "
pdb=" CB VAL H 307 "
both_signs ideal model delta sigma weight residual
False 2.44 2.64 -0.20 2.00e-01 2.50e+01 1.04e+00
... (remaining 9437 not shown)
Planarity restraints: 17272
Sorted by residual:
delta sigma weight rms_deltas residual
plane pdb=" CB HIS I 69 " 0.058 2.00e-02 2.50e+03 6.01e-02 8.12e+01
pdb=" CG HIS I 69 " 0.033 2.00e-02 2.50e+03
pdb=" ND1 HIS I 69 " 0.053 2.00e-02 2.50e+03
pdb=" CD2 HIS I 69 " -0.015 2.00e-02 2.50e+03
pdb=" CE1 HIS I 69 " 0.030 2.00e-02 2.50e+03
pdb=" NE2 HIS I 69 " -0.016 2.00e-02 2.50e+03
pdb=" HD1 HIS I 69 " -0.139 2.00e-02 2.50e+03
pdb=" HD2 HIS I 69 " -0.049 2.00e-02 2.50e+03
pdb=" HE1 HIS I 69 " 0.045 2.00e-02 2.50e+03
delta sigma weight rms_deltas residual
plane pdb=" CB HIS E 69 " 0.057 2.00e-02 2.50e+03 6.01e-02 8.11e+01
pdb=" CG HIS E 69 " 0.034 2.00e-02 2.50e+03
pdb=" ND1 HIS E 69 " 0.053 2.00e-02 2.50e+03
pdb=" CD2 HIS E 69 " -0.015 2.00e-02 2.50e+03
pdb=" CE1 HIS E 69 " 0.030 2.00e-02 2.50e+03
pdb=" NE2 HIS E 69 " -0.016 2.00e-02 2.50e+03
pdb=" HD1 HIS E 69 " -0.139 2.00e-02 2.50e+03
pdb=" HD2 HIS E 69 " -0.049 2.00e-02 2.50e+03
pdb=" HE1 HIS E 69 " 0.045 2.00e-02 2.50e+03
delta sigma weight rms_deltas residual
plane pdb=" CB HIS G 69 " 0.057 2.00e-02 2.50e+03 6.00e-02 8.10e+01
pdb=" CG HIS G 69 " 0.034 2.00e-02 2.50e+03
pdb=" ND1 HIS G 69 " 0.053 2.00e-02 2.50e+03
pdb=" CD2 HIS G 69 " -0.015 2.00e-02 2.50e+03
pdb=" CE1 HIS G 69 " 0.030 2.00e-02 2.50e+03
pdb=" NE2 HIS G 69 " -0.016 2.00e-02 2.50e+03
pdb=" HD1 HIS G 69 " -0.139 2.00e-02 2.50e+03
pdb=" HD2 HIS G 69 " -0.049 2.00e-02 2.50e+03
pdb=" HE1 HIS G 69 " 0.045 2.00e-02 2.50e+03
... (remaining 17269 not shown)
Histogram of nonbonded interaction distances:
1.28 - 1.94: 2581
1.94 - 2.61: 138440
2.61 - 3.27: 386016
3.27 - 3.94: 482914
3.94 - 4.60: 744033
Nonbonded interactions: 1753984
Sorted by model distance:
nonbonded pdb=" OE1 GLN M 657 "
pdb=" H GLN M 657 "
model vdw
1.278 1.850
nonbonded pdb=" OE1 GLN K 657 "
pdb=" H GLN K 657 "
model vdw
1.279 1.850
nonbonded pdb=" OE1 GLN O 657 "
pdb=" H GLN O 657 "
model vdw
1.279 1.850
nonbonded pdb=" OE1 GLN A 657 "
pdb=" H GLN A 657 "
model vdw
1.279 1.850
nonbonded pdb=" OE1 GLN G 657 "
pdb=" H GLN G 657 "
model vdw
1.279 1.850
... (remaining 1753979 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 'C'
selection = chain 'E'
selection = chain 'G'
selection = chain 'I'
selection = chain 'K'
selection = chain 'M'
selection = chain 'O'
}
ncs_group {
reference = chain 'B'
selection = chain 'D'
selection = chain 'F'
selection = chain 'H'
selection = chain 'J'
selection = chain 'L'
selection = chain 'N'
selection = chain 'P'
}
Set up NCS constraints
No NCS constraints will be used in refinement.
Set refine NCS operators
Set scattering table
Set to: electron
Number of scattering types: 7
Type Number sf(0) Gaussians
P 24 5.49 5
Mg 8 5.21 5
S 224 5.16 5
C 36696 2.51 5
N 10136 2.21 5
O 10880 1.98 5
H 59080 0.53 5
sf(0) = scattering factor at diffraction angle 0.
Adjust number of macro_cycles
Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
Set random seed: 0.010
Set model cs if undefined: 0.000
Decide on map wrapping: 0.000
Normalize map: mean=0, sd=1: 1.300
Set stop_for_unknowns flag: 0.000
Assert model is a single copy model: 0.000
Assert all atoms have isotropic ADPs: 0.000
Construct map_model_manager: 1.260
Extract box with map and model: 15.860
Check model and map are aligned: 1.250
Convert atoms to be neutral: 0.740
Process input model: 276.580
Find NCS groups from input model: 4.580
Set up NCS constraints: 0.680
Set refine NCS operators: 0.000
Set scattering table: 0.030
Adjust number of macro_cycles: 0.000
Reset NCS operators: 0.000
Extract rigid body selections: 0.000
Check and reset occupancies: 0.020
Load rotamer database and sin/cos tables:2.850
Set ADP refinement strategy: 0.000
Make a string to write initial .geo file:0.000
Internal consistency checks: 0.000
Total: 305.160
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6355
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 0.089 58944 Z= 0.749
Angle : 1.242 11.774 80072 Z= 0.778
Chirality : 0.052 0.206 9440
Planarity : 0.022 0.145 10304
Dihedral : 10.028 83.002 22192
Min Nonbonded Distance : 1.918
Molprobity Statistics.
All-atom Clashscore : 2.77
Ramachandran Plot:
Outliers : 1.43 %
Allowed : 5.46 %
Favored : 93.11 %
Rotamer Outliers : 0.63 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 2.27 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: -0.58 (0.09), residues: 7288
helix: 0.15 (0.07), residues: 4008
sheet: -1.55 (0.23), residues: 488
loop : -0.78 (0.12), residues: 2792
*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
14576 Ramachandran restraints generated.
7288 Oldfield, 0 Emsley, 7288 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
14576 Ramachandran restraints generated.
7288 Oldfield, 0 Emsley, 7288 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
3470 residues out of total 6368 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 40
poor density : 3430
time to evaluate : 6.907
Fit side-chains
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outliers start: 40
outliers final: 12
residues processed: 3466
average time/residue: 1.5288
time to fit residues: 8379.8490
Evaluate side-chains
2659 residues out of total 6368 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 12
poor density : 2647
time to evaluate : 6.870
Switching outliers to nearest non-outliers
outliers start: 12
outliers final: 0
residues processed: 12
average time/residue: 0.9142
time to fit residues: 30.4145
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 728
random chunks:
chunk 614 optimal weight: 5.9990
chunk 551 optimal weight: 5.9990
chunk 306 optimal weight: 0.9990
chunk 188 optimal weight: 6.9990
chunk 372 optimal weight: 1.9990
chunk 294 optimal weight: 5.9990
chunk 570 optimal weight: 5.9990
chunk 220 optimal weight: 0.9990
chunk 346 optimal weight: 5.9990
chunk 424 optimal weight: 7.9990
chunk 661 optimal weight: 5.9990
overall best weight: 3.1990
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** A 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 95 HIS
B 161 GLN
C 9 ASN
C 95 HIS
C 270 GLN
** C 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 161 GLN
D 267 ASN
D 294 HIS
D 348 HIS
** D 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 9 ASN
** E 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F 161 GLN
F 267 ASN
F 414 GLN
G 9 ASN
G 314 GLN
** G 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 161 GLN
** I 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
I 270 GLN
** I 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
J 161 GLN
** K 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 161 GLN
L 294 HIS
L 377 HIS
** M 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
N 161 GLN
N 294 HIS
** N 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
O 9 ASN
** O 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
P 161 GLN
P 229 GLN
P 294 HIS
P 348 HIS
P 380 GLN
Total number of N/Q/H flips: 29
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6654
moved from start: 0.4466
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
Bond : 0.005 0.044 58944 Z= 0.309
Angle : 0.649 8.168 80072 Z= 0.374
Chirality : 0.040 0.174 9440
Planarity : 0.011 0.094 10304
Dihedral : 5.434 65.324 8024
Min Nonbonded Distance : 1.752
Molprobity Statistics.
All-atom Clashscore : 10.78
Ramachandran Plot:
Outliers : 0.38 %
Allowed : 3.87 %
Favored : 95.75 %
Rotamer Outliers : 0.03 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 2.27 %
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: -0.30 (0.09), residues: 7288
helix: 0.37 (0.08), residues: 4064
sheet: -1.33 (0.20), residues: 600
loop : -0.62 (0.12), residues: 2624
*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
14576 Ramachandran restraints generated.
7288 Oldfield, 0 Emsley, 7288 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
14576 Ramachandran restraints generated.
7288 Oldfield, 0 Emsley, 7288 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
2997 residues out of total 6368 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 2
poor density : 2995
time to evaluate : 6.869
Fit side-chains
revert: symmetry clash
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outliers start: 2
outliers final: 1
residues processed: 2996
average time/residue: 1.4280
time to fit residues: 6997.7872
Evaluate side-chains
2569 residues out of total 6368 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 1
poor density : 2568
time to evaluate : 6.880
Switching outliers to nearest non-outliers
outliers start: 1
outliers final: 0
residues processed: 1
average time/residue: 1.0169
time to fit residues: 11.0928
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 728
random chunks:
chunk 367 optimal weight: 10.0000
chunk 205 optimal weight: 10.0000
chunk 550 optimal weight: 5.9990
chunk 450 optimal weight: 7.9990
chunk 182 optimal weight: 6.9990
chunk 662 optimal weight: 5.9990
chunk 715 optimal weight: 6.9990
chunk 589 optimal weight: 1.9990
chunk 656 optimal weight: 10.0000
chunk 225 optimal weight: 0.5980
chunk 531 optimal weight: 8.9990
overall best weight: 4.3188
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 9 ASN
A 27 GLN
A 270 GLN
** A 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 708 HIS
** B 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 27 GLN
** C 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 635 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 708 HIS
E 27 GLN
E 270 GLN
E 295 HIS
** E 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 708 HIS
G 27 GLN
G 270 GLN
G 708 HIS
I 9 ASN
I 27 GLN
I 95 HIS
** I 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
J 187 GLN
K 27 GLN
K 95 HIS
K 270 GLN
** K 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K 708 HIS
M 27 GLN
M 270 GLN
** M 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
N 414 GLN
O 27 GLN
O 95 HIS
** O 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** O 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
O 480 ASN
** O 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
P 161 GLN
Total number of N/Q/H flips: 28
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6961
moved from start: 0.6229
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
Bond : 0.006 0.064 58944 Z= 0.391
Angle : 0.750 7.763 80072 Z= 0.424
Chirality : 0.040 0.225 9440
Planarity : 0.009 0.094 10304
Dihedral : 5.405 42.103 8024
Min Nonbonded Distance : 1.894
Molprobity Statistics.
All-atom Clashscore : 19.21
Ramachandran Plot:
Outliers : 0.38 %
Allowed : 5.79 %
Favored : 93.83 %
Rotamer Outliers : 0.08 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 2.27 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: -1.06 (0.09), residues: 7288
helix: -0.34 (0.07), residues: 4128
sheet: -1.49 (0.19), residues: 600
loop : -0.85 (0.12), residues: 2560
*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
14576 Ramachandran restraints generated.
7288 Oldfield, 0 Emsley, 7288 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
14576 Ramachandran restraints generated.
7288 Oldfield, 0 Emsley, 7288 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
2823 residues out of total 6368 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 5
poor density : 2818
time to evaluate : 6.921
Fit side-chains
revert: symmetry clash
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revert: symmetry clash
outliers start: 5
outliers final: 4
residues processed: 2820
average time/residue: 1.4246
time to fit residues: 6546.9693
Evaluate side-chains
2500 residues out of total 6368 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 4
poor density : 2496
time to evaluate : 6.886
Switching outliers to nearest non-outliers
outliers start: 4
outliers final: 0
residues processed: 4
average time/residue: 0.9959
time to fit residues: 16.5370
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 728
random chunks:
chunk 654 optimal weight: 10.0000
chunk 497 optimal weight: 1.9990
chunk 343 optimal weight: 0.9990
chunk 73 optimal weight: 5.9990
chunk 316 optimal weight: 3.9990
chunk 444 optimal weight: 0.8980
chunk 664 optimal weight: 3.9990
chunk 703 optimal weight: 5.9990
chunk 347 optimal weight: 0.9990
chunk 629 optimal weight: 10.0000
chunk 189 optimal weight: 7.9990
overall best weight: 1.7788
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** A 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 187 GLN
** E 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
I 95 HIS
I 249 GLN
I 254 ASN
** I 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
K 290 ASN
** K 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
M 249 GLN
** M 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
O 270 GLN
** O 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** O 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Total number of N/Q/H flips: 7
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6881
moved from start: 0.6697
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
Bond : 0.003 0.056 58944 Z= 0.208
Angle : 0.563 7.534 80072 Z= 0.306
Chirality : 0.039 0.155 9440
Planarity : 0.006 0.077 10304
Dihedral : 4.910 34.620 8024
Min Nonbonded Distance : 1.872
Molprobity Statistics.
All-atom Clashscore : 12.18
Ramachandran Plot:
Outliers : 0.38 %
Allowed : 3.98 %
Favored : 95.64 %
Rotamer Outliers : 0.00 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 2.27 %
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: -0.28 (0.09), residues: 7288
helix: 0.43 (0.07), residues: 4072
sheet: -1.45 (0.20), residues: 600
loop : -0.67 (0.13), residues: 2616
*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
14576 Ramachandran restraints generated.
7288 Oldfield, 0 Emsley, 7288 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
14576 Ramachandran restraints generated.
7288 Oldfield, 0 Emsley, 7288 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
2805 residues out of total 6368 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 2805
time to evaluate : 6.963
Fit side-chains
revert: symmetry clash
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revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
outliers start: 0
outliers final: 0
residues processed: 2805
average time/residue: 1.4056
time to fit residues: 6438.9121
Evaluate side-chains
2521 residues out of total 6368 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 2521
time to evaluate : 6.866
Switching outliers to nearest non-outliers
outliers start: 0
outliers final: 0
residues processed: 0
time to fit residues: 8.7957
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 728
random chunks:
chunk 586 optimal weight: 2.9990
chunk 399 optimal weight: 0.7980
chunk 10 optimal weight: 1.9990
chunk 523 optimal weight: 7.9990
chunk 290 optimal weight: 9.9990
chunk 600 optimal weight: 0.9980
chunk 486 optimal weight: 0.9990
chunk 0 optimal weight: 5.9990
chunk 359 optimal weight: 10.0000
chunk 631 optimal weight: 8.9990
chunk 177 optimal weight: 1.9990
overall best weight: 1.3586
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 290 ASN
** C 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 249 GLN
C 635 ASN
D 187 GLN
E 420 GLN
** E 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 420 GLN
I 420 GLN
** K 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
M 708 HIS
** O 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** O 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** O 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Total number of N/Q/H flips: 8
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6880
moved from start: 0.7039
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
Bond : 0.003 0.082 58944 Z= 0.187
Angle : 0.542 7.421 80072 Z= 0.291
Chirality : 0.039 0.173 9440
Planarity : 0.005 0.072 10304
Dihedral : 4.609 30.973 8024
Min Nonbonded Distance : 1.922
Molprobity Statistics.
All-atom Clashscore : 11.45
Ramachandran Plot:
Outliers : 0.27 %
Allowed : 4.64 %
Favored : 95.09 %
Rotamer Outliers : 0.00 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 2.27 %
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: 0.18 (0.10), residues: 7288
helix: 0.91 (0.08), residues: 4048
sheet: -1.46 (0.20), residues: 576
loop : -0.60 (0.13), residues: 2664
*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
14576 Ramachandran restraints generated.
7288 Oldfield, 0 Emsley, 7288 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
14576 Ramachandran restraints generated.
7288 Oldfield, 0 Emsley, 7288 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
2767 residues out of total 6368 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 2767
time to evaluate : 6.926
Fit side-chains
revert: symmetry clash
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revert: symmetry clash
outliers start: 0
outliers final: 0
residues processed: 2767
average time/residue: 1.3598
time to fit residues: 6115.4345
Evaluate side-chains
2495 residues out of total 6368 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 2495
time to evaluate : 7.052
Switching outliers to nearest non-outliers
outliers start: 0
outliers final: 0
residues processed: 0
time to fit residues: 9.1011
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 728
random chunks:
chunk 236 optimal weight: 3.9990
chunk 633 optimal weight: 10.0000
chunk 139 optimal weight: 0.0870
chunk 413 optimal weight: 5.9990
chunk 173 optimal weight: 7.9990
chunk 704 optimal weight: 9.9990
chunk 584 optimal weight: 3.9990
chunk 326 optimal weight: 2.9990
chunk 58 optimal weight: 1.9990
chunk 232 optimal weight: 4.9990
chunk 369 optimal weight: 5.9990
overall best weight: 2.6166
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 249 GLN
** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 9 ASN
** C 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 398 ASN
E 420 GLN
** E 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 27 GLN
G 249 GLN
G 295 HIS
** G 420 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 635 ASN
I 27 GLN
I 66 GLN
** I 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
K 9 ASN
M 9 ASN
M 290 ASN
O 9 ASN
** O 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** O 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** O 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
O 708 HIS
Total number of N/Q/H flips: 15
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7007
moved from start: 0.7495
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
Bond : 0.004 0.060 58944 Z= 0.262
Angle : 0.604 7.795 80072 Z= 0.330
Chirality : 0.039 0.147 9440
Planarity : 0.006 0.074 10304
Dihedral : 4.658 32.252 8024
Min Nonbonded Distance : 1.842
Molprobity Statistics.
All-atom Clashscore : 14.27
Ramachandran Plot:
Outliers : 0.27 %
Allowed : 4.90 %
Favored : 94.83 %
Rotamer Outliers : 0.00 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 2.27 %
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: -0.07 (0.10), residues: 7288
helix: 0.67 (0.08), residues: 4072
sheet: -1.48 (0.20), residues: 576
loop : -0.69 (0.13), residues: 2640
*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
14576 Ramachandran restraints generated.
7288 Oldfield, 0 Emsley, 7288 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
14576 Ramachandran restraints generated.
7288 Oldfield, 0 Emsley, 7288 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
2748 residues out of total 6368 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 2748
time to evaluate : 6.989
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
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outliers start: 0
outliers final: 0
residues processed: 2748
average time/residue: 1.3383
time to fit residues: 5973.8933
Evaluate side-chains
2497 residues out of total 6368 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 2497
time to evaluate : 6.920
Switching outliers to nearest non-outliers
outliers start: 0
outliers final: 0
residues processed: 0
time to fit residues: 8.9728
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 728
random chunks:
chunk 679 optimal weight: 4.9990
chunk 79 optimal weight: 10.0000
chunk 401 optimal weight: 0.4980
chunk 514 optimal weight: 9.9990
chunk 398 optimal weight: 4.9990
chunk 592 optimal weight: 1.9990
chunk 393 optimal weight: 6.9990
chunk 701 optimal weight: 6.9990
chunk 439 optimal weight: 0.2980
chunk 427 optimal weight: 0.7980
chunk 323 optimal weight: 2.9990
overall best weight: 1.3184
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** B 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 293 GLN
G 290 ASN
G 420 GLN
I 34 GLN
I 420 GLN
K 448 ASN
** L 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
M 420 GLN
O 316 GLN
O 320 ASN
O 420 GLN
** O 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** O 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Total number of N/Q/H flips: 10
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6952
moved from start: 0.7696
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
Bond : 0.003 0.074 58944 Z= 0.180
Angle : 0.542 7.650 80072 Z= 0.289
Chirality : 0.039 0.152 9440
Planarity : 0.005 0.094 10304
Dihedral : 4.473 31.697 8024
Min Nonbonded Distance : 1.908
Molprobity Statistics.
All-atom Clashscore : 12.19
Ramachandran Plot:
Outliers : 0.26 %
Allowed : 4.14 %
Favored : 95.60 %
Rotamer Outliers : 0.00 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 2.27 %
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: 0.41 (0.10), residues: 7288
helix: 1.14 (0.08), residues: 4016
sheet: -1.47 (0.20), residues: 592
loop : -0.54 (0.13), residues: 2680
*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
14576 Ramachandran restraints generated.
7288 Oldfield, 0 Emsley, 7288 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
14576 Ramachandran restraints generated.
7288 Oldfield, 0 Emsley, 7288 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
2782 residues out of total 6368 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 2782
time to evaluate : 7.215
Fit side-chains
revert: symmetry clash
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outliers start: 0
outliers final: 0
residues processed: 2782
average time/residue: 1.3822
time to fit residues: 6263.1488
Evaluate side-chains
2511 residues out of total 6368 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 2511
time to evaluate : 6.943
Switching outliers to nearest non-outliers
outliers start: 0
outliers final: 0
residues processed: 0
time to fit residues: 8.9682
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 728
random chunks:
chunk 434 optimal weight: 6.9990
chunk 280 optimal weight: 0.9990
chunk 419 optimal weight: 2.9990
chunk 211 optimal weight: 5.9990
chunk 137 optimal weight: 0.0870
chunk 135 optimal weight: 2.9990
chunk 446 optimal weight: 5.9990
chunk 478 optimal weight: 1.9990
chunk 346 optimal weight: 0.9990
chunk 65 optimal weight: 9.9990
chunk 551 optimal weight: 0.4980
overall best weight: 0.9164
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** A 682 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 9 ASN
E 249 GLN
** E 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
K 27 GLN
K 249 GLN
K 448 ASN
O 420 GLN
** O 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** O 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
O 448 ASN
Total number of N/Q/H flips: 7
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6940
moved from start: 0.7864
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
Bond : 0.002 0.075 58944 Z= 0.164
Angle : 0.526 7.609 80072 Z= 0.279
Chirality : 0.039 0.157 9440
Planarity : 0.005 0.072 10304
Dihedral : 4.330 29.874 8024
Min Nonbonded Distance : 1.919
Molprobity Statistics.
All-atom Clashscore : 11.39
Ramachandran Plot:
Outliers : 0.26 %
Allowed : 3.84 %
Favored : 95.90 %
Rotamer Outliers : 0.00 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 2.27 %
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: 0.69 (0.10), residues: 7288
helix: 1.40 (0.08), residues: 4048
sheet: -1.29 (0.21), residues: 576
loop : -0.51 (0.13), residues: 2664
*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
14576 Ramachandran restraints generated.
7288 Oldfield, 0 Emsley, 7288 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
14576 Ramachandran restraints generated.
7288 Oldfield, 0 Emsley, 7288 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
2816 residues out of total 6368 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 2816
time to evaluate : 6.907
Fit side-chains
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revert: symmetry clash
revert: symmetry clash
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revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
outliers start: 0
outliers final: 0
residues processed: 2816
average time/residue: 1.3679
time to fit residues: 6273.3589
Evaluate side-chains
2531 residues out of total 6368 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 2531
time to evaluate : 6.876
Switching outliers to nearest non-outliers
outliers start: 0
outliers final: 0
residues processed: 0
time to fit residues: 8.9008
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 728
random chunks:
chunk 638 optimal weight: 3.9990
chunk 672 optimal weight: 2.9990
chunk 613 optimal weight: 3.9990
chunk 653 optimal weight: 3.9990
chunk 393 optimal weight: 6.9990
chunk 284 optimal weight: 2.9990
chunk 513 optimal weight: 4.9990
chunk 200 optimal weight: 8.9990
chunk 590 optimal weight: 0.5980
chunk 618 optimal weight: 5.9990
chunk 651 optimal weight: 0.8980
overall best weight: 2.2986
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** A 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 682 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K 448 ASN
** L 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
O 448 ASN
** O 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
Total number of N/Q/H flips: 2
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7037
moved from start: 0.8125
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
Bond : 0.004 0.097 58944 Z= 0.235
Angle : 0.573 7.500 80072 Z= 0.311
Chirality : 0.038 0.195 9440
Planarity : 0.005 0.070 10304
Dihedral : 4.405 31.676 8024
Min Nonbonded Distance : 1.887
Molprobity Statistics.
All-atom Clashscore : 14.34
Ramachandran Plot:
Outliers : 0.27 %
Allowed : 4.47 %
Favored : 95.25 %
Rotamer Outliers : 0.00 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 2.27 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 0.40 (0.10), residues: 7288
helix: 1.15 (0.08), residues: 4056
sheet: -1.27 (0.21), residues: 576
loop : -0.66 (0.13), residues: 2656
*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
14576 Ramachandran restraints generated.
7288 Oldfield, 0 Emsley, 7288 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
14576 Ramachandran restraints generated.
7288 Oldfield, 0 Emsley, 7288 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
2748 residues out of total 6368 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 2748
time to evaluate : 6.956
Fit side-chains
revert: symmetry clash
revert: symmetry clash
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revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
outliers start: 0
outliers final: 0
residues processed: 2748
average time/residue: 1.3313
time to fit residues: 5955.9645
Evaluate side-chains
2494 residues out of total 6368 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 2494
time to evaluate : 6.929
Switching outliers to nearest non-outliers
outliers start: 0
outliers final: 0
residues processed: 0
time to fit residues: 8.9201
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 728
random chunks:
chunk 429 optimal weight: 20.0000
chunk 691 optimal weight: 1.9990
chunk 422 optimal weight: 4.9990
chunk 328 optimal weight: 4.9990
chunk 480 optimal weight: 4.9990
chunk 725 optimal weight: 4.9990
chunk 667 optimal weight: 0.6980
chunk 577 optimal weight: 2.9990
chunk 59 optimal weight: 8.9990
chunk 446 optimal weight: 9.9990
chunk 354 optimal weight: 9.9990
overall best weight: 3.1388
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 290 ASN
C 66 GLN
C 95 HIS
D 161 GLN
** E 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 66 GLN
** E 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K 448 ASN
L 161 GLN
O 448 ASN
** O 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
Total number of N/Q/H flips: 8
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7136
moved from start: 0.8517
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
Bond : 0.004 0.073 58944 Z= 0.295
Angle : 0.635 7.846 80072 Z= 0.348
Chirality : 0.040 0.184 9440
Planarity : 0.006 0.079 10304
Dihedral : 4.699 33.927 8024
Min Nonbonded Distance : 1.833
Molprobity Statistics.
All-atom Clashscore : 17.37
Ramachandran Plot:
Outliers : 0.27 %
Allowed : 5.21 %
Favored : 94.51 %
Rotamer Outliers : 0.00 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 2.27 %
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: -0.17 (0.10), residues: 7288
helix: 0.67 (0.08), residues: 4056
sheet: -1.32 (0.20), residues: 576
loop : -0.92 (0.12), residues: 2656
********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
14576 Ramachandran restraints generated.
7288 Oldfield, 0 Emsley, 7288 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
14576 Ramachandran restraints generated.
7288 Oldfield, 0 Emsley, 7288 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
2752 residues out of total 6368 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 2752
time to evaluate : 6.912
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
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outliers start: 0
outliers final: 0
residues processed: 2752
average time/residue: 1.3701
time to fit residues: 6170.8438
Evaluate side-chains
2446 residues out of total 6368 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 2446
time to evaluate : 6.882
Switching outliers to nearest non-outliers
outliers start: 0
outliers final: 0
residues processed: 0
time to fit residues: 8.8434
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 728
random chunks:
chunk 458 optimal weight: 9.9990
chunk 615 optimal weight: 7.9990
chunk 176 optimal weight: 3.9990
chunk 532 optimal weight: 10.0000
chunk 85 optimal weight: 6.9990
chunk 160 optimal weight: 0.3980
chunk 578 optimal weight: 1.9990
chunk 242 optimal weight: 7.9990
chunk 593 optimal weight: 1.9990
chunk 73 optimal weight: 0.5980
chunk 106 optimal weight: 4.9990
overall best weight: 1.7986
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 290 ASN
** A 682 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 290 ASN
** E 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 66 GLN
** E 346 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 309 ASN
K 448 ASN
** L 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
M 295 HIS
** N 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** O 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** O 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
O 290 ASN
O 448 ASN
Total number of N/Q/H flips: 8
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4202 r_free = 0.4202 target = 0.139765 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.089534 restraints weight = 399083.579|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.095659 restraints weight = 196501.846|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.099775 restraints weight = 118779.682|
|-----------------------------------------------------------------------------|
r_work (final): 0.3740
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6932
moved from start: 0.8646
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
Bond : 0.003 0.113 58944 Z= 0.209
Angle : 0.565 8.450 80072 Z= 0.302
Chirality : 0.039 0.177 9440
Planarity : 0.005 0.068 10304
Dihedral : 4.543 30.660 8024
Min Nonbonded Distance : 1.866
Molprobity Statistics.
All-atom Clashscore : 14.52
Ramachandran Plot:
Outliers : 0.27 %
Allowed : 4.50 %
Favored : 95.23 %
Rotamer Outliers : 0.00 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 2.27 %
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: 0.15 (0.10), residues: 7288
helix: 0.95 (0.08), residues: 4064
sheet: -1.29 (0.20), residues: 576
loop : -0.81 (0.13), residues: 2648
===============================================================================
Job complete
usr+sys time: 72258.07 seconds
wall clock time: 1228 minutes 44.72 seconds (73724.72 seconds total)