Starting phenix.real_space_refine (version: dev)
on Mon Jul 4 00:17:22 2022 by dcliebschner
===============================================================================
Processing files:
-------------------------------------------------------------------------------
Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5tfy_8405/07_2022/5tfy_8405.pdb
Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5tfy_8405/07_2022/5tfy_8405.map
Processing PHIL parameters:
-------------------------------------------------------------------------------
Adding command-line PHIL:
-------------------------
refinement.macro_cycles=10
scattering_table=electron
resolution=3.4
write_initial_geo_file=False
Final processed PHIL parameters:
-------------------------------------------------------------------------------
data_manager {
real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5tfy_8405/07_2022/5tfy_8405.map"
default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5tfy_8405/07_2022/5tfy_8405.map"
model {
file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5tfy_8405/07_2022/5tfy_8405.pdb"
}
default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5tfy_8405/07_2022/5tfy_8405.pdb"
}
resolution = 3.4
write_initial_geo_file = False
refinement {
macro_cycles = 10
}
Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.
Validating inputs
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
Set to: 0
Set model cs if undefined
Decide on map wrapping
Map wrapping is set to: False
Normalize map: mean=0, sd=1
Input map: mean= -0.000 sd= 0.003
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 "I GLU 5": "OE1" <-> "OE2"
Residue "I TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "I TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "I PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "I TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "I GLU 78": "OE1" <-> "OE2"
Residue "I GLU 81": "OE1" <-> "OE2"
Residue "I TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "I TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "A GLU 5": "OE1" <-> "OE2"
Residue "A TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "A TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "A PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "A TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "A GLU 78": "OE1" <-> "OE2"
Residue "A GLU 81": "OE1" <-> "OE2"
Residue "A TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "A TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "B GLU 5": "OE1" <-> "OE2"
Residue "B TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "B TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "B PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "B TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "B GLU 78": "OE1" <-> "OE2"
Residue "B GLU 81": "OE1" <-> "OE2"
Residue "B TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "B TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "C GLU 5": "OE1" <-> "OE2"
Residue "C TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "C TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "C PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "C TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "C GLU 78": "OE1" <-> "OE2"
Residue "C GLU 81": "OE1" <-> "OE2"
Residue "C TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "C TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "D GLU 5": "OE1" <-> "OE2"
Residue "D TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "D TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "D PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "D TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "D GLU 78": "OE1" <-> "OE2"
Residue "D GLU 81": "OE1" <-> "OE2"
Residue "D TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "D TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "E GLU 5": "OE1" <-> "OE2"
Residue "E TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "E TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "E PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "E TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "E GLU 78": "OE1" <-> "OE2"
Residue "E GLU 81": "OE1" <-> "OE2"
Residue "E TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "E TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "F GLU 5": "OE1" <-> "OE2"
Residue "F TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "F TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "F PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "F TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "F GLU 78": "OE1" <-> "OE2"
Residue "F GLU 81": "OE1" <-> "OE2"
Residue "F TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "F TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "G GLU 5": "OE1" <-> "OE2"
Residue "G TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "G TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "G PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "G TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "G GLU 78": "OE1" <-> "OE2"
Residue "G GLU 81": "OE1" <-> "OE2"
Residue "G TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "G TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "H GLU 5": "OE1" <-> "OE2"
Residue "H TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "H TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "H PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "H TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "H GLU 78": "OE1" <-> "OE2"
Residue "H GLU 81": "OE1" <-> "OE2"
Residue "H TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "H TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "J GLU 5": "OE1" <-> "OE2"
Residue "J TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "J TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "J PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "J TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "J GLU 78": "OE1" <-> "OE2"
Residue "J GLU 81": "OE1" <-> "OE2"
Residue "J TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "J TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "K GLU 5": "OE1" <-> "OE2"
Residue "K TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "K TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "K PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "K TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "K GLU 78": "OE1" <-> "OE2"
Residue "K GLU 81": "OE1" <-> "OE2"
Residue "K TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "K TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "L GLU 5": "OE1" <-> "OE2"
Residue "L TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "L TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "L PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "L TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "L GLU 78": "OE1" <-> "OE2"
Residue "L GLU 81": "OE1" <-> "OE2"
Residue "L TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "L TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "M GLU 5": "OE1" <-> "OE2"
Residue "M TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "M TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "M PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "M TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "M GLU 78": "OE1" <-> "OE2"
Residue "M GLU 81": "OE1" <-> "OE2"
Residue "M TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "M TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "N GLU 5": "OE1" <-> "OE2"
Residue "N TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "N TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "N PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "N TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "N GLU 78": "OE1" <-> "OE2"
Residue "N GLU 81": "OE1" <-> "OE2"
Residue "N TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "N TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "O GLU 5": "OE1" <-> "OE2"
Residue "O TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "O TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "O PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "O TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "O GLU 78": "OE1" <-> "OE2"
Residue "O GLU 81": "OE1" <-> "OE2"
Residue "O TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "O TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "P GLU 5": "OE1" <-> "OE2"
Residue "P TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "P TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "P PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "P TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "P GLU 78": "OE1" <-> "OE2"
Residue "P GLU 81": "OE1" <-> "OE2"
Residue "P TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "P TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "Q GLU 5": "OE1" <-> "OE2"
Residue "Q TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "Q TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "Q PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "Q TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "Q GLU 78": "OE1" <-> "OE2"
Residue "Q GLU 81": "OE1" <-> "OE2"
Residue "Q TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "Q TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "R GLU 5": "OE1" <-> "OE2"
Residue "R TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "R TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "R PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "R TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "R GLU 78": "OE1" <-> "OE2"
Residue "R GLU 81": "OE1" <-> "OE2"
Residue "R TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "R TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "S GLU 5": "OE1" <-> "OE2"
Residue "S TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "S TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "S PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "S TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "S GLU 78": "OE1" <-> "OE2"
Residue "S GLU 81": "OE1" <-> "OE2"
Residue "S TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "S TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "T GLU 5": "OE1" <-> "OE2"
Residue "T TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "T TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "T PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "T TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "T GLU 78": "OE1" <-> "OE2"
Residue "T GLU 81": "OE1" <-> "OE2"
Residue "T TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "T TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "U GLU 5": "OE1" <-> "OE2"
Residue "U TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "U TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "U PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "U TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "U GLU 78": "OE1" <-> "OE2"
Residue "U GLU 81": "OE1" <-> "OE2"
Residue "U TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "U TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "V GLU 5": "OE1" <-> "OE2"
Residue "V TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "V TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "V PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "V TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "V GLU 78": "OE1" <-> "OE2"
Residue "V GLU 81": "OE1" <-> "OE2"
Residue "V TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "V TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "W GLU 5": "OE1" <-> "OE2"
Residue "W TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "W TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "W PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "W TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "W GLU 78": "OE1" <-> "OE2"
Residue "W GLU 81": "OE1" <-> "OE2"
Residue "W TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "W TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "X GLU 5": "OE1" <-> "OE2"
Residue "X TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "X TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "X PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "X TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "X GLU 78": "OE1" <-> "OE2"
Residue "X GLU 81": "OE1" <-> "OE2"
Residue "X TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "X TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "Y GLU 5": "OE1" <-> "OE2"
Residue "Y TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "Y TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "Y PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "Y TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "Y GLU 78": "OE1" <-> "OE2"
Residue "Y GLU 81": "OE1" <-> "OE2"
Residue "Y TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "Y TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "Z GLU 5": "OE1" <-> "OE2"
Residue "Z TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "Z TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "Z PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "Z TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "Z GLU 78": "OE1" <-> "OE2"
Residue "Z GLU 81": "OE1" <-> "OE2"
Residue "Z TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "Z TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Time to flip residues: 0.09s
Monomer Library directory:
"/net/cci-filer2/raid1/xp/phenix/phenix-dev-4648/modules/chem_data/mon_lib"
Total number of atoms: 65182
Number of models: 1
Model: ""
Number of chains: 26
Chain: "I"
Number of atoms: 2507
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 164, 2507
Classifications: {'peptide': 164}
Modifications used: {'COO': 1, 'NH3': 1}
Link IDs: {'PTRANS': 6, 'TRANS': 157}
Chain: "A"
Number of atoms: 2507
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 164, 2507
Classifications: {'peptide': 164}
Modifications used: {'COO': 1, 'NH3': 1}
Link IDs: {'PTRANS': 6, 'TRANS': 157}
Chain: "B"
Number of atoms: 2507
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 164, 2507
Classifications: {'peptide': 164}
Modifications used: {'COO': 1, 'NH3': 1}
Link IDs: {'PTRANS': 6, 'TRANS': 157}
Chain: "C"
Number of atoms: 2507
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 164, 2507
Classifications: {'peptide': 164}
Modifications used: {'COO': 1, 'NH3': 1}
Link IDs: {'PTRANS': 6, 'TRANS': 157}
Chain: "D"
Number of atoms: 2507
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 164, 2507
Classifications: {'peptide': 164}
Modifications used: {'COO': 1, 'NH3': 1}
Link IDs: {'PTRANS': 6, 'TRANS': 157}
Chain: "E"
Number of atoms: 2507
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 164, 2507
Classifications: {'peptide': 164}
Modifications used: {'COO': 1, 'NH3': 1}
Link IDs: {'PTRANS': 6, 'TRANS': 157}
Chain: "F"
Number of atoms: 2507
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 164, 2507
Classifications: {'peptide': 164}
Modifications used: {'COO': 1, 'NH3': 1}
Link IDs: {'PTRANS': 6, 'TRANS': 157}
Chain: "G"
Number of atoms: 2507
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 164, 2507
Classifications: {'peptide': 164}
Modifications used: {'COO': 1, 'NH3': 1}
Link IDs: {'PTRANS': 6, 'TRANS': 157}
Chain: "H"
Number of atoms: 2507
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 164, 2507
Classifications: {'peptide': 164}
Modifications used: {'COO': 1, 'NH3': 1}
Link IDs: {'PTRANS': 6, 'TRANS': 157}
Chain: "J"
Number of atoms: 2507
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 164, 2507
Classifications: {'peptide': 164}
Modifications used: {'COO': 1, 'NH3': 1}
Link IDs: {'PTRANS': 6, 'TRANS': 157}
Chain: "K"
Number of atoms: 2507
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 164, 2507
Classifications: {'peptide': 164}
Modifications used: {'COO': 1, 'NH3': 1}
Link IDs: {'PTRANS': 6, 'TRANS': 157}
Chain: "L"
Number of atoms: 2507
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 164, 2507
Classifications: {'peptide': 164}
Modifications used: {'COO': 1, 'NH3': 1}
Link IDs: {'PTRANS': 6, 'TRANS': 157}
Chain: "M"
Number of atoms: 2507
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 164, 2507
Classifications: {'peptide': 164}
Modifications used: {'COO': 1, 'NH3': 1}
Link IDs: {'PTRANS': 6, 'TRANS': 157}
Chain: "N"
Number of atoms: 2507
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 164, 2507
Classifications: {'peptide': 164}
Modifications used: {'COO': 1, 'NH3': 1}
Link IDs: {'PTRANS': 6, 'TRANS': 157}
Chain: "O"
Number of atoms: 2507
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 164, 2507
Classifications: {'peptide': 164}
Modifications used: {'COO': 1, 'NH3': 1}
Link IDs: {'PTRANS': 6, 'TRANS': 157}
Chain: "P"
Number of atoms: 2507
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 164, 2507
Classifications: {'peptide': 164}
Modifications used: {'COO': 1, 'NH3': 1}
Link IDs: {'PTRANS': 6, 'TRANS': 157}
Chain: "Q"
Number of atoms: 2507
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 164, 2507
Classifications: {'peptide': 164}
Modifications used: {'COO': 1, 'NH3': 1}
Link IDs: {'PTRANS': 6, 'TRANS': 157}
Chain: "R"
Number of atoms: 2507
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 164, 2507
Classifications: {'peptide': 164}
Modifications used: {'COO': 1, 'NH3': 1}
Link IDs: {'PTRANS': 6, 'TRANS': 157}
Chain: "S"
Number of atoms: 2507
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 164, 2507
Classifications: {'peptide': 164}
Modifications used: {'COO': 1, 'NH3': 1}
Link IDs: {'PTRANS': 6, 'TRANS': 157}
Chain: "T"
Number of atoms: 2507
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 164, 2507
Classifications: {'peptide': 164}
Modifications used: {'COO': 1, 'NH3': 1}
Link IDs: {'PTRANS': 6, 'TRANS': 157}
Chain: "U"
Number of atoms: 2507
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 164, 2507
Classifications: {'peptide': 164}
Modifications used: {'COO': 1, 'NH3': 1}
Link IDs: {'PTRANS': 6, 'TRANS': 157}
Chain: "V"
Number of atoms: 2507
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 164, 2507
Classifications: {'peptide': 164}
Modifications used: {'COO': 1, 'NH3': 1}
Link IDs: {'PTRANS': 6, 'TRANS': 157}
Chain: "W"
Number of atoms: 2507
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 164, 2507
Classifications: {'peptide': 164}
Modifications used: {'COO': 1, 'NH3': 1}
Link IDs: {'PTRANS': 6, 'TRANS': 157}
Chain: "X"
Number of atoms: 2507
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 164, 2507
Classifications: {'peptide': 164}
Modifications used: {'COO': 1, 'NH3': 1}
Link IDs: {'PTRANS': 6, 'TRANS': 157}
Chain: "Y"
Number of atoms: 2507
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 164, 2507
Classifications: {'peptide': 164}
Modifications used: {'COO': 1, 'NH3': 1}
Link IDs: {'PTRANS': 6, 'TRANS': 157}
Chain: "Z"
Number of atoms: 2507
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 164, 2507
Classifications: {'peptide': 164}
Modifications used: {'COO': 1, 'NH3': 1}
Link IDs: {'PTRANS': 6, 'TRANS': 157}
Time building chain proxies: 21.84, per 1000 atoms: 0.34
Number of scatterers: 65182
At special positions: 0
Unit cell: (102.7, 105.3, 245.7, 90, 90, 90)
Space group: P 1 (No. 1)
Number of sites at special positions: 0
Number of scattering types: 5
Type Number sf(0)
S 78 16.00
O 6110 8.00
N 5096 7.00
C 20852 6.00
H 33046 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: 44.37
Conformation dependent library (CDL) restraints added in 4.1 seconds
8424 Ramachandran restraints generated.
4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2.
Adding C-beta torsion restraints...
Number of C-beta restraints generated: 7592
Finding SS restraints...
Secondary structure from input PDB file:
51 helices and 78 sheets defined
30.4% alpha, 26.3% beta
0 base pairs and 0 stacking pairs defined.
Time for finding SS restraints: 1.54
Creating SS restraints...
Processing helix chain 'I' and resid 2 through 48
removed outlier: 3.937A pdb=" N ALA I 6 " --> pdb=" O SER I 2 " (cutoff:3.500A)
removed outlier: 3.674A pdb=" N ALA I 12 " --> pdb=" O ILE I 8 " (cutoff:3.500A)
removed outlier: 3.648A pdb=" N THR I 39 " --> pdb=" O SER I 35 " (cutoff:3.500A)
removed outlier: 3.509A pdb=" N ALA I 46 " --> pdb=" O GLY I 42 " (cutoff:3.500A)
Processing helix chain 'I' and resid 86 through 88
No H-bonds generated for 'chain 'I' and resid 86 through 88'
Processing helix chain 'A' and resid 2 through 48
removed outlier: 3.939A pdb=" N ALA A 6 " --> pdb=" O SER A 2 " (cutoff:3.500A)
removed outlier: 3.674A pdb=" N ALA A 12 " --> pdb=" O ILE A 8 " (cutoff:3.500A)
removed outlier: 3.656A pdb=" N THR A 39 " --> pdb=" O SER A 35 " (cutoff:3.500A)
Processing helix chain 'A' and resid 86 through 88
No H-bonds generated for 'chain 'A' and resid 86 through 88'
Processing helix chain 'B' and resid 2 through 48
removed outlier: 3.941A pdb=" N ALA B 6 " --> pdb=" O SER B 2 " (cutoff:3.500A)
removed outlier: 3.673A pdb=" N ALA B 12 " --> pdb=" O ILE B 8 " (cutoff:3.500A)
removed outlier: 3.650A pdb=" N THR B 39 " --> pdb=" O SER B 35 " (cutoff:3.500A)
removed outlier: 3.507A pdb=" N ALA B 46 " --> pdb=" O GLY B 42 " (cutoff:3.500A)
Processing helix chain 'B' and resid 86 through 88
No H-bonds generated for 'chain 'B' and resid 86 through 88'
Processing helix chain 'C' and resid 2 through 48
removed outlier: 3.940A pdb=" N ALA C 6 " --> pdb=" O SER C 2 " (cutoff:3.500A)
removed outlier: 3.674A pdb=" N ALA C 12 " --> pdb=" O ILE C 8 " (cutoff:3.500A)
removed outlier: 3.657A pdb=" N THR C 39 " --> pdb=" O SER C 35 " (cutoff:3.500A)
removed outlier: 3.510A pdb=" N ALA C 46 " --> pdb=" O GLY C 42 " (cutoff:3.500A)
Processing helix chain 'C' and resid 86 through 88
No H-bonds generated for 'chain 'C' and resid 86 through 88'
Processing helix chain 'D' and resid 2 through 48
removed outlier: 3.937A pdb=" N ALA D 6 " --> pdb=" O SER D 2 " (cutoff:3.500A)
removed outlier: 3.674A pdb=" N ALA D 12 " --> pdb=" O ILE D 8 " (cutoff:3.500A)
removed outlier: 3.645A pdb=" N THR D 39 " --> pdb=" O SER D 35 " (cutoff:3.500A)
removed outlier: 3.507A pdb=" N ALA D 46 " --> pdb=" O GLY D 42 " (cutoff:3.500A)
Processing helix chain 'D' and resid 86 through 88
No H-bonds generated for 'chain 'D' and resid 86 through 88'
Processing helix chain 'E' and resid 2 through 48
removed outlier: 3.934A pdb=" N ALA E 6 " --> pdb=" O SER E 2 " (cutoff:3.500A)
removed outlier: 3.663A pdb=" N ALA E 12 " --> pdb=" O ILE E 8 " (cutoff:3.500A)
removed outlier: 3.652A pdb=" N THR E 39 " --> pdb=" O SER E 35 " (cutoff:3.500A)
removed outlier: 3.509A pdb=" N ALA E 46 " --> pdb=" O GLY E 42 " (cutoff:3.500A)
Processing helix chain 'E' and resid 86 through 88
No H-bonds generated for 'chain 'E' and resid 86 through 88'
Processing helix chain 'F' and resid 2 through 48
removed outlier: 3.941A pdb=" N ALA F 6 " --> pdb=" O SER F 2 " (cutoff:3.500A)
removed outlier: 3.674A pdb=" N ALA F 12 " --> pdb=" O ILE F 8 " (cutoff:3.500A)
removed outlier: 3.649A pdb=" N THR F 39 " --> pdb=" O SER F 35 " (cutoff:3.500A)
removed outlier: 3.510A pdb=" N ALA F 46 " --> pdb=" O GLY F 42 " (cutoff:3.500A)
Processing helix chain 'G' and resid 2 through 48
removed outlier: 3.942A pdb=" N ALA G 6 " --> pdb=" O SER G 2 " (cutoff:3.500A)
removed outlier: 3.673A pdb=" N ALA G 12 " --> pdb=" O ILE G 8 " (cutoff:3.500A)
removed outlier: 3.658A pdb=" N THR G 39 " --> pdb=" O SER G 35 " (cutoff:3.500A)
removed outlier: 3.510A pdb=" N ALA G 46 " --> pdb=" O GLY G 42 " (cutoff:3.500A)
Processing helix chain 'G' and resid 86 through 88
No H-bonds generated for 'chain 'G' and resid 86 through 88'
Processing helix chain 'H' and resid 2 through 48
removed outlier: 3.931A pdb=" N ALA H 6 " --> pdb=" O SER H 2 " (cutoff:3.500A)
removed outlier: 3.675A pdb=" N ALA H 12 " --> pdb=" O ILE H 8 " (cutoff:3.500A)
removed outlier: 3.647A pdb=" N THR H 39 " --> pdb=" O SER H 35 " (cutoff:3.500A)
removed outlier: 3.505A pdb=" N ALA H 46 " --> pdb=" O GLY H 42 " (cutoff:3.500A)
Processing helix chain 'H' and resid 86 through 88
No H-bonds generated for 'chain 'H' and resid 86 through 88'
Processing helix chain 'J' and resid 2 through 48
removed outlier: 3.936A pdb=" N ALA J 6 " --> pdb=" O SER J 2 " (cutoff:3.500A)
removed outlier: 3.665A pdb=" N ALA J 12 " --> pdb=" O ILE J 8 " (cutoff:3.500A)
removed outlier: 3.655A pdb=" N THR J 39 " --> pdb=" O SER J 35 " (cutoff:3.500A)
removed outlier: 3.508A pdb=" N ALA J 46 " --> pdb=" O GLY J 42 " (cutoff:3.500A)
Processing helix chain 'J' and resid 86 through 88
No H-bonds generated for 'chain 'J' and resid 86 through 88'
Processing helix chain 'K' and resid 2 through 48
removed outlier: 3.938A pdb=" N ALA K 6 " --> pdb=" O SER K 2 " (cutoff:3.500A)
removed outlier: 3.675A pdb=" N ALA K 12 " --> pdb=" O ILE K 8 " (cutoff:3.500A)
removed outlier: 3.653A pdb=" N THR K 39 " --> pdb=" O SER K 35 " (cutoff:3.500A)
removed outlier: 3.507A pdb=" N ALA K 46 " --> pdb=" O GLY K 42 " (cutoff:3.500A)
Processing helix chain 'K' and resid 86 through 88
No H-bonds generated for 'chain 'K' and resid 86 through 88'
Processing helix chain 'L' and resid 2 through 48
removed outlier: 3.942A pdb=" N ALA L 6 " --> pdb=" O SER L 2 " (cutoff:3.500A)
removed outlier: 3.672A pdb=" N ALA L 12 " --> pdb=" O ILE L 8 " (cutoff:3.500A)
removed outlier: 3.652A pdb=" N THR L 39 " --> pdb=" O SER L 35 " (cutoff:3.500A)
removed outlier: 3.507A pdb=" N ALA L 46 " --> pdb=" O GLY L 42 " (cutoff:3.500A)
Processing helix chain 'L' and resid 86 through 88
No H-bonds generated for 'chain 'L' and resid 86 through 88'
Processing helix chain 'M' and resid 2 through 48
removed outlier: 3.941A pdb=" N ALA M 6 " --> pdb=" O SER M 2 " (cutoff:3.500A)
removed outlier: 3.674A pdb=" N ALA M 12 " --> pdb=" O ILE M 8 " (cutoff:3.500A)
removed outlier: 3.653A pdb=" N THR M 39 " --> pdb=" O SER M 35 " (cutoff:3.500A)
removed outlier: 3.508A pdb=" N ALA M 46 " --> pdb=" O GLY M 42 " (cutoff:3.500A)
Processing helix chain 'M' and resid 86 through 88
No H-bonds generated for 'chain 'M' and resid 86 through 88'
Processing helix chain 'N' and resid 2 through 48
removed outlier: 3.942A pdb=" N ALA N 6 " --> pdb=" O SER N 2 " (cutoff:3.500A)
removed outlier: 3.674A pdb=" N ALA N 12 " --> pdb=" O ILE N 8 " (cutoff:3.500A)
removed outlier: 3.654A pdb=" N THR N 39 " --> pdb=" O SER N 35 " (cutoff:3.500A)
removed outlier: 3.511A pdb=" N ALA N 46 " --> pdb=" O GLY N 42 " (cutoff:3.500A)
Processing helix chain 'N' and resid 86 through 88
No H-bonds generated for 'chain 'N' and resid 86 through 88'
Processing helix chain 'O' and resid 2 through 48
removed outlier: 3.942A pdb=" N ALA O 6 " --> pdb=" O SER O 2 " (cutoff:3.500A)
removed outlier: 3.672A pdb=" N ALA O 12 " --> pdb=" O ILE O 8 " (cutoff:3.500A)
removed outlier: 3.651A pdb=" N THR O 39 " --> pdb=" O SER O 35 " (cutoff:3.500A)
removed outlier: 3.509A pdb=" N ALA O 46 " --> pdb=" O GLY O 42 " (cutoff:3.500A)
Processing helix chain 'O' and resid 86 through 88
No H-bonds generated for 'chain 'O' and resid 86 through 88'
Processing helix chain 'P' and resid 2 through 48
removed outlier: 3.935A pdb=" N ALA P 6 " --> pdb=" O SER P 2 " (cutoff:3.500A)
removed outlier: 3.663A pdb=" N ALA P 12 " --> pdb=" O ILE P 8 " (cutoff:3.500A)
removed outlier: 3.650A pdb=" N THR P 39 " --> pdb=" O SER P 35 " (cutoff:3.500A)
removed outlier: 3.508A pdb=" N ALA P 46 " --> pdb=" O GLY P 42 " (cutoff:3.500A)
Processing helix chain 'P' and resid 86 through 88
No H-bonds generated for 'chain 'P' and resid 86 through 88'
Processing helix chain 'Q' and resid 2 through 48
removed outlier: 3.943A pdb=" N ALA Q 6 " --> pdb=" O SER Q 2 " (cutoff:3.500A)
removed outlier: 3.674A pdb=" N ALA Q 12 " --> pdb=" O ILE Q 8 " (cutoff:3.500A)
removed outlier: 3.652A pdb=" N THR Q 39 " --> pdb=" O SER Q 35 " (cutoff:3.500A)
removed outlier: 3.503A pdb=" N ALA Q 46 " --> pdb=" O GLY Q 42 " (cutoff:3.500A)
Processing helix chain 'Q' and resid 86 through 88
No H-bonds generated for 'chain 'Q' and resid 86 through 88'
Processing helix chain 'R' and resid 2 through 48
removed outlier: 3.943A pdb=" N ALA R 6 " --> pdb=" O SER R 2 " (cutoff:3.500A)
removed outlier: 3.674A pdb=" N ALA R 12 " --> pdb=" O ILE R 8 " (cutoff:3.500A)
removed outlier: 3.653A pdb=" N THR R 39 " --> pdb=" O SER R 35 " (cutoff:3.500A)
removed outlier: 3.507A pdb=" N ALA R 46 " --> pdb=" O GLY R 42 " (cutoff:3.500A)
Processing helix chain 'R' and resid 86 through 88
No H-bonds generated for 'chain 'R' and resid 86 through 88'
Processing helix chain 'S' and resid 2 through 48
removed outlier: 3.942A pdb=" N ALA S 6 " --> pdb=" O SER S 2 " (cutoff:3.500A)
removed outlier: 3.673A pdb=" N ALA S 12 " --> pdb=" O ILE S 8 " (cutoff:3.500A)
removed outlier: 3.649A pdb=" N THR S 39 " --> pdb=" O SER S 35 " (cutoff:3.500A)
removed outlier: 3.509A pdb=" N ALA S 46 " --> pdb=" O GLY S 42 " (cutoff:3.500A)
Processing helix chain 'S' and resid 86 through 88
No H-bonds generated for 'chain 'S' and resid 86 through 88'
Processing helix chain 'T' and resid 2 through 48
removed outlier: 3.932A pdb=" N ALA T 6 " --> pdb=" O SER T 2 " (cutoff:3.500A)
removed outlier: 3.674A pdb=" N ALA T 12 " --> pdb=" O ILE T 8 " (cutoff:3.500A)
removed outlier: 3.642A pdb=" N THR T 39 " --> pdb=" O SER T 35 " (cutoff:3.500A)
removed outlier: 3.507A pdb=" N ALA T 46 " --> pdb=" O GLY T 42 " (cutoff:3.500A)
Processing helix chain 'T' and resid 86 through 88
No H-bonds generated for 'chain 'T' and resid 86 through 88'
Processing helix chain 'U' and resid 2 through 48
removed outlier: 3.932A pdb=" N ALA U 6 " --> pdb=" O SER U 2 " (cutoff:3.500A)
removed outlier: 3.664A pdb=" N ALA U 12 " --> pdb=" O ILE U 8 " (cutoff:3.500A)
removed outlier: 3.651A pdb=" N THR U 39 " --> pdb=" O SER U 35 " (cutoff:3.500A)
removed outlier: 3.506A pdb=" N ALA U 46 " --> pdb=" O GLY U 42 " (cutoff:3.500A)
Processing helix chain 'U' and resid 86 through 88
No H-bonds generated for 'chain 'U' and resid 86 through 88'
Processing helix chain 'V' and resid 2 through 48
removed outlier: 3.942A pdb=" N ALA V 6 " --> pdb=" O SER V 2 " (cutoff:3.500A)
removed outlier: 3.674A pdb=" N ALA V 12 " --> pdb=" O ILE V 8 " (cutoff:3.500A)
removed outlier: 3.651A pdb=" N THR V 39 " --> pdb=" O SER V 35 " (cutoff:3.500A)
Processing helix chain 'V' and resid 86 through 88
No H-bonds generated for 'chain 'V' and resid 86 through 88'
Processing helix chain 'W' and resid 2 through 48
removed outlier: 3.942A pdb=" N ALA W 6 " --> pdb=" O SER W 2 " (cutoff:3.500A)
removed outlier: 3.673A pdb=" N ALA W 12 " --> pdb=" O ILE W 8 " (cutoff:3.500A)
removed outlier: 3.652A pdb=" N THR W 39 " --> pdb=" O SER W 35 " (cutoff:3.500A)
removed outlier: 3.506A pdb=" N ALA W 46 " --> pdb=" O GLY W 42 " (cutoff:3.500A)
Processing helix chain 'W' and resid 86 through 88
No H-bonds generated for 'chain 'W' and resid 86 through 88'
Processing helix chain 'X' and resid 2 through 48
removed outlier: 3.946A pdb=" N ALA X 6 " --> pdb=" O SER X 2 " (cutoff:3.500A)
removed outlier: 3.674A pdb=" N ALA X 12 " --> pdb=" O ILE X 8 " (cutoff:3.500A)
removed outlier: 3.651A pdb=" N THR X 39 " --> pdb=" O SER X 35 " (cutoff:3.500A)
removed outlier: 3.507A pdb=" N ALA X 46 " --> pdb=" O GLY X 42 " (cutoff:3.500A)
Processing helix chain 'X' and resid 86 through 88
No H-bonds generated for 'chain 'X' and resid 86 through 88'
Processing helix chain 'Y' and resid 2 through 48
removed outlier: 3.936A pdb=" N ALA Y 6 " --> pdb=" O SER Y 2 " (cutoff:3.500A)
removed outlier: 3.674A pdb=" N ALA Y 12 " --> pdb=" O ILE Y 8 " (cutoff:3.500A)
removed outlier: 3.644A pdb=" N THR Y 39 " --> pdb=" O SER Y 35 " (cutoff:3.500A)
removed outlier: 3.508A pdb=" N ALA Y 46 " --> pdb=" O GLY Y 42 " (cutoff:3.500A)
Processing helix chain 'Y' and resid 86 through 88
No H-bonds generated for 'chain 'Y' and resid 86 through 88'
Processing helix chain 'Z' and resid 2 through 48
removed outlier: 3.934A pdb=" N ALA Z 6 " --> pdb=" O SER Z 2 " (cutoff:3.500A)
removed outlier: 3.663A pdb=" N ALA Z 12 " --> pdb=" O ILE Z 8 " (cutoff:3.500A)
removed outlier: 3.651A pdb=" N THR Z 39 " --> pdb=" O SER Z 35 " (cutoff:3.500A)
removed outlier: 3.507A pdb=" N ALA Z 46 " --> pdb=" O GLY Z 42 " (cutoff:3.500A)
Processing helix chain 'Z' and resid 86 through 88
No H-bonds generated for 'chain 'Z' and resid 86 through 88'
Processing sheet with id=AA1, first strand: chain 'I' and resid 104 through 105
removed outlier: 4.800A pdb=" N SER I 104 " --> pdb=" O THR I 123 " (cutoff:3.500A)
removed outlier: 3.795A pdb=" N GLN I 69 " --> pdb=" O SER I 59 " (cutoff:3.500A)
removed outlier: 4.467A pdb=" N TYR I 73 " --> pdb=" O MET I 55 " (cutoff:3.500A)
removed outlier: 6.795A pdb=" N MET I 55 " --> pdb=" O TYR I 73 " (cutoff:3.500A)
removed outlier: 6.621A pdb=" N LYS I 75 " --> pdb=" O ASP I 53 " (cutoff:3.500A)
removed outlier: 6.501A pdb=" N ASP I 53 " --> pdb=" O LYS I 75 " (cutoff:3.500A)
removed outlier: 4.320A pdb=" N ILE I 56 " --> pdb=" O ILE I 163 " (cutoff:3.500A)
Processing sheet with id=AA2, first strand: chain 'I' and resid 83 through 84
Processing sheet with id=AA3, first strand: chain 'I' and resid 100 through 101
Processing sheet with id=AA4, first strand: chain 'A' and resid 104 through 105
removed outlier: 4.801A pdb=" N SER A 104 " --> pdb=" O THR A 123 " (cutoff:3.500A)
removed outlier: 3.800A pdb=" N GLN A 69 " --> pdb=" O SER A 59 " (cutoff:3.500A)
removed outlier: 4.467A pdb=" N TYR A 73 " --> pdb=" O MET A 55 " (cutoff:3.500A)
removed outlier: 6.795A pdb=" N MET A 55 " --> pdb=" O TYR A 73 " (cutoff:3.500A)
removed outlier: 6.619A pdb=" N LYS A 75 " --> pdb=" O ASP A 53 " (cutoff:3.500A)
removed outlier: 6.503A pdb=" N ASP A 53 " --> pdb=" O LYS A 75 " (cutoff:3.500A)
removed outlier: 4.326A pdb=" N ILE A 56 " --> pdb=" O ILE A 163 " (cutoff:3.500A)
Processing sheet with id=AA5, first strand: chain 'A' and resid 83 through 84
Processing sheet with id=AA6, first strand: chain 'A' and resid 100 through 101
Processing sheet with id=AA7, first strand: chain 'B' and resid 104 through 105
removed outlier: 4.800A pdb=" N SER B 104 " --> pdb=" O THR B 123 " (cutoff:3.500A)
removed outlier: 3.798A pdb=" N GLN B 69 " --> pdb=" O SER B 59 " (cutoff:3.500A)
removed outlier: 4.469A pdb=" N TYR B 73 " --> pdb=" O MET B 55 " (cutoff:3.500A)
removed outlier: 6.794A pdb=" N MET B 55 " --> pdb=" O TYR B 73 " (cutoff:3.500A)
removed outlier: 6.620A pdb=" N LYS B 75 " --> pdb=" O ASP B 53 " (cutoff:3.500A)
removed outlier: 6.504A pdb=" N ASP B 53 " --> pdb=" O LYS B 75 " (cutoff:3.500A)
removed outlier: 4.312A pdb=" N ILE B 56 " --> pdb=" O ILE B 163 " (cutoff:3.500A)
Processing sheet with id=AA8, first strand: chain 'B' and resid 83 through 84
Processing sheet with id=AA9, first strand: chain 'B' and resid 100 through 101
Processing sheet with id=AB1, first strand: chain 'C' and resid 104 through 105
removed outlier: 4.790A pdb=" N SER C 104 " --> pdb=" O THR C 123 " (cutoff:3.500A)
removed outlier: 3.796A pdb=" N GLN C 69 " --> pdb=" O SER C 59 " (cutoff:3.500A)
removed outlier: 4.465A pdb=" N TYR C 73 " --> pdb=" O MET C 55 " (cutoff:3.500A)
removed outlier: 6.802A pdb=" N MET C 55 " --> pdb=" O TYR C 73 " (cutoff:3.500A)
removed outlier: 6.620A pdb=" N LYS C 75 " --> pdb=" O ASP C 53 " (cutoff:3.500A)
removed outlier: 6.495A pdb=" N ASP C 53 " --> pdb=" O LYS C 75 " (cutoff:3.500A)
removed outlier: 4.315A pdb=" N ILE C 56 " --> pdb=" O ILE C 163 " (cutoff:3.500A)
Processing sheet with id=AB2, first strand: chain 'C' and resid 83 through 84
Processing sheet with id=AB3, first strand: chain 'C' and resid 100 through 101
Processing sheet with id=AB4, first strand: chain 'D' and resid 104 through 105
removed outlier: 4.801A pdb=" N SER D 104 " --> pdb=" O THR D 123 " (cutoff:3.500A)
removed outlier: 3.797A pdb=" N GLN D 69 " --> pdb=" O SER D 59 " (cutoff:3.500A)
removed outlier: 4.465A pdb=" N TYR D 73 " --> pdb=" O MET D 55 " (cutoff:3.500A)
removed outlier: 6.805A pdb=" N MET D 55 " --> pdb=" O TYR D 73 " (cutoff:3.500A)
removed outlier: 6.630A pdb=" N LYS D 75 " --> pdb=" O ASP D 53 " (cutoff:3.500A)
removed outlier: 6.494A pdb=" N ASP D 53 " --> pdb=" O LYS D 75 " (cutoff:3.500A)
removed outlier: 4.319A pdb=" N ILE D 56 " --> pdb=" O ILE D 163 " (cutoff:3.500A)
Processing sheet with id=AB5, first strand: chain 'D' and resid 83 through 84
Processing sheet with id=AB6, first strand: chain 'D' and resid 100 through 101
Processing sheet with id=AB7, first strand: chain 'E' and resid 104 through 105
removed outlier: 4.799A pdb=" N SER E 104 " --> pdb=" O THR E 123 " (cutoff:3.500A)
removed outlier: 3.807A pdb=" N GLN E 69 " --> pdb=" O SER E 59 " (cutoff:3.500A)
removed outlier: 4.468A pdb=" N TYR E 73 " --> pdb=" O MET E 55 " (cutoff:3.500A)
removed outlier: 6.803A pdb=" N MET E 55 " --> pdb=" O TYR E 73 " (cutoff:3.500A)
removed outlier: 6.631A pdb=" N LYS E 75 " --> pdb=" O ASP E 53 " (cutoff:3.500A)
removed outlier: 6.496A pdb=" N ASP E 53 " --> pdb=" O LYS E 75 " (cutoff:3.500A)
removed outlier: 4.329A pdb=" N ILE E 56 " --> pdb=" O ILE E 163 " (cutoff:3.500A)
Processing sheet with id=AB8, first strand: chain 'E' and resid 83 through 84
Processing sheet with id=AB9, first strand: chain 'E' and resid 100 through 101
Processing sheet with id=AC1, first strand: chain 'F' and resid 104 through 105
removed outlier: 4.796A pdb=" N SER F 104 " --> pdb=" O THR F 123 " (cutoff:3.500A)
removed outlier: 3.797A pdb=" N GLN F 69 " --> pdb=" O SER F 59 " (cutoff:3.500A)
removed outlier: 4.466A pdb=" N TYR F 73 " --> pdb=" O MET F 55 " (cutoff:3.500A)
removed outlier: 6.796A pdb=" N MET F 55 " --> pdb=" O TYR F 73 " (cutoff:3.500A)
removed outlier: 6.619A pdb=" N LYS F 75 " --> pdb=" O ASP F 53 " (cutoff:3.500A)
removed outlier: 6.502A pdb=" N ASP F 53 " --> pdb=" O LYS F 75 " (cutoff:3.500A)
removed outlier: 4.321A pdb=" N ILE F 56 " --> pdb=" O ILE F 163 " (cutoff:3.500A)
Processing sheet with id=AC2, first strand: chain 'F' and resid 83 through 84
Processing sheet with id=AC3, first strand: chain 'F' and resid 100 through 101
Processing sheet with id=AC4, first strand: chain 'G' and resid 104 through 105
removed outlier: 4.799A pdb=" N SER G 104 " --> pdb=" O THR G 123 " (cutoff:3.500A)
removed outlier: 3.795A pdb=" N GLN G 69 " --> pdb=" O SER G 59 " (cutoff:3.500A)
removed outlier: 4.469A pdb=" N TYR G 73 " --> pdb=" O MET G 55 " (cutoff:3.500A)
removed outlier: 6.795A pdb=" N MET G 55 " --> pdb=" O TYR G 73 " (cutoff:3.500A)
removed outlier: 6.620A pdb=" N LYS G 75 " --> pdb=" O ASP G 53 " (cutoff:3.500A)
removed outlier: 6.505A pdb=" N ASP G 53 " --> pdb=" O LYS G 75 " (cutoff:3.500A)
removed outlier: 4.318A pdb=" N ILE G 56 " --> pdb=" O ILE G 163 " (cutoff:3.500A)
Processing sheet with id=AC5, first strand: chain 'G' and resid 83 through 84
Processing sheet with id=AC6, first strand: chain 'G' and resid 100 through 101
Processing sheet with id=AC7, first strand: chain 'H' and resid 104 through 105
removed outlier: 4.798A pdb=" N SER H 104 " --> pdb=" O THR H 123 " (cutoff:3.500A)
removed outlier: 3.796A pdb=" N GLN H 69 " --> pdb=" O SER H 59 " (cutoff:3.500A)
removed outlier: 4.470A pdb=" N TYR H 73 " --> pdb=" O MET H 55 " (cutoff:3.500A)
removed outlier: 6.804A pdb=" N MET H 55 " --> pdb=" O TYR H 73 " (cutoff:3.500A)
removed outlier: 6.619A pdb=" N LYS H 75 " --> pdb=" O ASP H 53 " (cutoff:3.500A)
removed outlier: 6.495A pdb=" N ASP H 53 " --> pdb=" O LYS H 75 " (cutoff:3.500A)
removed outlier: 4.325A pdb=" N ILE H 56 " --> pdb=" O ILE H 163 " (cutoff:3.500A)
Processing sheet with id=AC8, first strand: chain 'H' and resid 83 through 84
Processing sheet with id=AC9, first strand: chain 'H' and resid 100 through 101
Processing sheet with id=AD1, first strand: chain 'J' and resid 104 through 105
removed outlier: 4.797A pdb=" N SER J 104 " --> pdb=" O THR J 123 " (cutoff:3.500A)
removed outlier: 4.466A pdb=" N TYR J 73 " --> pdb=" O MET J 55 " (cutoff:3.500A)
removed outlier: 6.804A pdb=" N MET J 55 " --> pdb=" O TYR J 73 " (cutoff:3.500A)
removed outlier: 6.629A pdb=" N LYS J 75 " --> pdb=" O ASP J 53 " (cutoff:3.500A)
removed outlier: 6.496A pdb=" N ASP J 53 " --> pdb=" O LYS J 75 " (cutoff:3.500A)
removed outlier: 4.325A pdb=" N ILE J 56 " --> pdb=" O ILE J 163 " (cutoff:3.500A)
Processing sheet with id=AD2, first strand: chain 'J' and resid 83 through 84
Processing sheet with id=AD3, first strand: chain 'J' and resid 100 through 101
Processing sheet with id=AD4, first strand: chain 'K' and resid 104 through 105
removed outlier: 4.799A pdb=" N SER K 104 " --> pdb=" O THR K 123 " (cutoff:3.500A)
removed outlier: 3.808A pdb=" N GLN K 69 " --> pdb=" O SER K 59 " (cutoff:3.500A)
removed outlier: 4.466A pdb=" N TYR K 73 " --> pdb=" O MET K 55 " (cutoff:3.500A)
removed outlier: 6.795A pdb=" N MET K 55 " --> pdb=" O TYR K 73 " (cutoff:3.500A)
removed outlier: 6.630A pdb=" N LYS K 75 " --> pdb=" O ASP K 53 " (cutoff:3.500A)
removed outlier: 6.492A pdb=" N ASP K 53 " --> pdb=" O LYS K 75 " (cutoff:3.500A)
removed outlier: 4.325A pdb=" N ILE K 56 " --> pdb=" O ILE K 163 " (cutoff:3.500A)
Processing sheet with id=AD5, first strand: chain 'K' and resid 83 through 84
Processing sheet with id=AD6, first strand: chain 'K' and resid 100 through 101
Processing sheet with id=AD7, first strand: chain 'L' and resid 104 through 105
removed outlier: 4.793A pdb=" N SER L 104 " --> pdb=" O THR L 123 " (cutoff:3.500A)
removed outlier: 3.797A pdb=" N GLN L 69 " --> pdb=" O SER L 59 " (cutoff:3.500A)
removed outlier: 4.465A pdb=" N TYR L 73 " --> pdb=" O MET L 55 " (cutoff:3.500A)
removed outlier: 6.803A pdb=" N MET L 55 " --> pdb=" O TYR L 73 " (cutoff:3.500A)
removed outlier: 6.620A pdb=" N LYS L 75 " --> pdb=" O ASP L 53 " (cutoff:3.500A)
removed outlier: 6.493A pdb=" N ASP L 53 " --> pdb=" O LYS L 75 " (cutoff:3.500A)
removed outlier: 4.314A pdb=" N ILE L 56 " --> pdb=" O ILE L 163 " (cutoff:3.500A)
Processing sheet with id=AD8, first strand: chain 'L' and resid 83 through 84
Processing sheet with id=AD9, first strand: chain 'L' and resid 100 through 101
Processing sheet with id=AE1, first strand: chain 'M' and resid 104 through 105
removed outlier: 4.797A pdb=" N SER M 104 " --> pdb=" O THR M 123 " (cutoff:3.500A)
removed outlier: 3.793A pdb=" N GLN M 69 " --> pdb=" O SER M 59 " (cutoff:3.500A)
removed outlier: 4.468A pdb=" N TYR M 73 " --> pdb=" O MET M 55 " (cutoff:3.500A)
removed outlier: 6.793A pdb=" N MET M 55 " --> pdb=" O TYR M 73 " (cutoff:3.500A)
removed outlier: 6.619A pdb=" N LYS M 75 " --> pdb=" O ASP M 53 " (cutoff:3.500A)
removed outlier: 6.502A pdb=" N ASP M 53 " --> pdb=" O LYS M 75 " (cutoff:3.500A)
removed outlier: 4.322A pdb=" N ILE M 56 " --> pdb=" O ILE M 163 " (cutoff:3.500A)
Processing sheet with id=AE2, first strand: chain 'M' and resid 83 through 84
Processing sheet with id=AE3, first strand: chain 'M' and resid 100 through 101
Processing sheet with id=AE4, first strand: chain 'N' and resid 104 through 105
removed outlier: 4.798A pdb=" N SER N 104 " --> pdb=" O THR N 123 " (cutoff:3.500A)
removed outlier: 3.797A pdb=" N GLN N 69 " --> pdb=" O SER N 59 " (cutoff:3.500A)
removed outlier: 4.466A pdb=" N TYR N 73 " --> pdb=" O MET N 55 " (cutoff:3.500A)
removed outlier: 6.794A pdb=" N MET N 55 " --> pdb=" O TYR N 73 " (cutoff:3.500A)
removed outlier: 6.620A pdb=" N LYS N 75 " --> pdb=" O ASP N 53 " (cutoff:3.500A)
removed outlier: 6.504A pdb=" N ASP N 53 " --> pdb=" O LYS N 75 " (cutoff:3.500A)
removed outlier: 4.316A pdb=" N ILE N 56 " --> pdb=" O ILE N 163 " (cutoff:3.500A)
Processing sheet with id=AE5, first strand: chain 'N' and resid 83 through 84
Processing sheet with id=AE6, first strand: chain 'N' and resid 100 through 101
Processing sheet with id=AE7, first strand: chain 'O' and resid 104 through 105
removed outlier: 4.793A pdb=" N SER O 104 " --> pdb=" O THR O 123 " (cutoff:3.500A)
removed outlier: 3.796A pdb=" N GLN O 69 " --> pdb=" O SER O 59 " (cutoff:3.500A)
removed outlier: 4.470A pdb=" N TYR O 73 " --> pdb=" O MET O 55 " (cutoff:3.500A)
removed outlier: 6.804A pdb=" N MET O 55 " --> pdb=" O TYR O 73 " (cutoff:3.500A)
removed outlier: 6.619A pdb=" N LYS O 75 " --> pdb=" O ASP O 53 " (cutoff:3.500A)
removed outlier: 6.491A pdb=" N ASP O 53 " --> pdb=" O LYS O 75 " (cutoff:3.500A)
removed outlier: 4.319A pdb=" N ILE O 56 " --> pdb=" O ILE O 163 " (cutoff:3.500A)
Processing sheet with id=AE8, first strand: chain 'O' and resid 83 through 84
Processing sheet with id=AE9, first strand: chain 'O' and resid 100 through 101
Processing sheet with id=AF1, first strand: chain 'P' and resid 104 through 105
removed outlier: 4.800A pdb=" N SER P 104 " --> pdb=" O THR P 123 " (cutoff:3.500A)
removed outlier: 3.804A pdb=" N GLN P 69 " --> pdb=" O SER P 59 " (cutoff:3.500A)
removed outlier: 4.466A pdb=" N TYR P 73 " --> pdb=" O MET P 55 " (cutoff:3.500A)
removed outlier: 6.801A pdb=" N MET P 55 " --> pdb=" O TYR P 73 " (cutoff:3.500A)
removed outlier: 6.630A pdb=" N LYS P 75 " --> pdb=" O ASP P 53 " (cutoff:3.500A)
removed outlier: 6.492A pdb=" N ASP P 53 " --> pdb=" O LYS P 75 " (cutoff:3.500A)
removed outlier: 4.324A pdb=" N ILE P 56 " --> pdb=" O ILE P 163 " (cutoff:3.500A)
Processing sheet with id=AF2, first strand: chain 'P' and resid 83 through 84
Processing sheet with id=AF3, first strand: chain 'P' and resid 100 through 101
Processing sheet with id=AF4, first strand: chain 'Q' and resid 104 through 105
removed outlier: 4.798A pdb=" N SER Q 104 " --> pdb=" O THR Q 123 " (cutoff:3.500A)
removed outlier: 3.808A pdb=" N GLN Q 69 " --> pdb=" O SER Q 59 " (cutoff:3.500A)
removed outlier: 4.469A pdb=" N TYR Q 73 " --> pdb=" O MET Q 55 " (cutoff:3.500A)
removed outlier: 6.796A pdb=" N MET Q 55 " --> pdb=" O TYR Q 73 " (cutoff:3.500A)
removed outlier: 6.629A pdb=" N LYS Q 75 " --> pdb=" O ASP Q 53 " (cutoff:3.500A)
removed outlier: 6.505A pdb=" N ASP Q 53 " --> pdb=" O LYS Q 75 " (cutoff:3.500A)
removed outlier: 4.319A pdb=" N ILE Q 56 " --> pdb=" O ILE Q 163 " (cutoff:3.500A)
Processing sheet with id=AF5, first strand: chain 'Q' and resid 83 through 84
Processing sheet with id=AF6, first strand: chain 'Q' and resid 100 through 101
Processing sheet with id=AF7, first strand: chain 'R' and resid 104 through 105
removed outlier: 4.798A pdb=" N SER R 104 " --> pdb=" O THR R 123 " (cutoff:3.500A)
removed outlier: 3.797A pdb=" N GLN R 69 " --> pdb=" O SER R 59 " (cutoff:3.500A)
removed outlier: 4.471A pdb=" N TYR R 73 " --> pdb=" O MET R 55 " (cutoff:3.500A)
removed outlier: 6.798A pdb=" N MET R 55 " --> pdb=" O TYR R 73 " (cutoff:3.500A)
removed outlier: 6.619A pdb=" N LYS R 75 " --> pdb=" O ASP R 53 " (cutoff:3.500A)
removed outlier: 6.503A pdb=" N ASP R 53 " --> pdb=" O LYS R 75 " (cutoff:3.500A)
removed outlier: 4.324A pdb=" N ILE R 56 " --> pdb=" O ILE R 163 " (cutoff:3.500A)
Processing sheet with id=AF8, first strand: chain 'R' and resid 83 through 84
Processing sheet with id=AF9, first strand: chain 'R' and resid 100 through 101
Processing sheet with id=AG1, first strand: chain 'S' and resid 104 through 105
removed outlier: 4.790A pdb=" N SER S 104 " --> pdb=" O THR S 123 " (cutoff:3.500A)
removed outlier: 3.800A pdb=" N GLN S 69 " --> pdb=" O SER S 59 " (cutoff:3.500A)
removed outlier: 4.466A pdb=" N TYR S 73 " --> pdb=" O MET S 55 " (cutoff:3.500A)
removed outlier: 6.803A pdb=" N MET S 55 " --> pdb=" O TYR S 73 " (cutoff:3.500A)
removed outlier: 6.621A pdb=" N LYS S 75 " --> pdb=" O ASP S 53 " (cutoff:3.500A)
removed outlier: 6.494A pdb=" N ASP S 53 " --> pdb=" O LYS S 75 " (cutoff:3.500A)
removed outlier: 4.315A pdb=" N ILE S 56 " --> pdb=" O ILE S 163 " (cutoff:3.500A)
Processing sheet with id=AG2, first strand: chain 'S' and resid 83 through 84
Processing sheet with id=AG3, first strand: chain 'S' and resid 100 through 101
Processing sheet with id=AG4, first strand: chain 'T' and resid 104 through 105
removed outlier: 4.797A pdb=" N SER T 104 " --> pdb=" O THR T 123 " (cutoff:3.500A)
removed outlier: 3.798A pdb=" N GLN T 69 " --> pdb=" O SER T 59 " (cutoff:3.500A)
removed outlier: 4.469A pdb=" N TYR T 73 " --> pdb=" O MET T 55 " (cutoff:3.500A)
removed outlier: 6.801A pdb=" N MET T 55 " --> pdb=" O TYR T 73 " (cutoff:3.500A)
removed outlier: 6.629A pdb=" N LYS T 75 " --> pdb=" O ASP T 53 " (cutoff:3.500A)
removed outlier: 6.493A pdb=" N ASP T 53 " --> pdb=" O LYS T 75 " (cutoff:3.500A)
removed outlier: 4.323A pdb=" N ILE T 56 " --> pdb=" O ILE T 163 " (cutoff:3.500A)
Processing sheet with id=AG5, first strand: chain 'T' and resid 83 through 84
Processing sheet with id=AG6, first strand: chain 'T' and resid 100 through 101
Processing sheet with id=AG7, first strand: chain 'U' and resid 104 through 105
removed outlier: 4.796A pdb=" N SER U 104 " --> pdb=" O THR U 123 " (cutoff:3.500A)
removed outlier: 3.802A pdb=" N GLN U 69 " --> pdb=" O SER U 59 " (cutoff:3.500A)
removed outlier: 4.465A pdb=" N TYR U 73 " --> pdb=" O MET U 55 " (cutoff:3.500A)
removed outlier: 6.807A pdb=" N MET U 55 " --> pdb=" O TYR U 73 " (cutoff:3.500A)
removed outlier: 6.630A pdb=" N LYS U 75 " --> pdb=" O ASP U 53 " (cutoff:3.500A)
removed outlier: 6.493A pdb=" N ASP U 53 " --> pdb=" O LYS U 75 " (cutoff:3.500A)
removed outlier: 4.324A pdb=" N ILE U 56 " --> pdb=" O ILE U 163 " (cutoff:3.500A)
Processing sheet with id=AG8, first strand: chain 'U' and resid 83 through 84
Processing sheet with id=AG9, first strand: chain 'U' and resid 100 through 101
Processing sheet with id=AH1, first strand: chain 'V' and resid 104 through 105
removed outlier: 4.799A pdb=" N SER V 104 " --> pdb=" O THR V 123 " (cutoff:3.500A)
removed outlier: 3.798A pdb=" N GLN V 69 " --> pdb=" O SER V 59 " (cutoff:3.500A)
removed outlier: 4.468A pdb=" N TYR V 73 " --> pdb=" O MET V 55 " (cutoff:3.500A)
removed outlier: 6.795A pdb=" N MET V 55 " --> pdb=" O TYR V 73 " (cutoff:3.500A)
removed outlier: 6.619A pdb=" N LYS V 75 " --> pdb=" O ASP V 53 " (cutoff:3.500A)
removed outlier: 6.504A pdb=" N ASP V 53 " --> pdb=" O LYS V 75 " (cutoff:3.500A)
removed outlier: 4.322A pdb=" N ILE V 56 " --> pdb=" O ILE V 163 " (cutoff:3.500A)
Processing sheet with id=AH2, first strand: chain 'V' and resid 83 through 84
Processing sheet with id=AH3, first strand: chain 'V' and resid 100 through 101
Processing sheet with id=AH4, first strand: chain 'W' and resid 104 through 105
removed outlier: 4.799A pdb=" N SER W 104 " --> pdb=" O THR W 123 " (cutoff:3.500A)
removed outlier: 3.795A pdb=" N GLN W 69 " --> pdb=" O SER W 59 " (cutoff:3.500A)
removed outlier: 4.467A pdb=" N TYR W 73 " --> pdb=" O MET W 55 " (cutoff:3.500A)
removed outlier: 6.795A pdb=" N MET W 55 " --> pdb=" O TYR W 73 " (cutoff:3.500A)
removed outlier: 6.621A pdb=" N LYS W 75 " --> pdb=" O ASP W 53 " (cutoff:3.500A)
removed outlier: 6.503A pdb=" N ASP W 53 " --> pdb=" O LYS W 75 " (cutoff:3.500A)
removed outlier: 4.312A pdb=" N ILE W 56 " --> pdb=" O ILE W 163 " (cutoff:3.500A)
Processing sheet with id=AH5, first strand: chain 'W' and resid 83 through 84
Processing sheet with id=AH6, first strand: chain 'W' and resid 100 through 101
Processing sheet with id=AH7, first strand: chain 'X' and resid 104 through 105
removed outlier: 4.788A pdb=" N SER X 104 " --> pdb=" O THR X 123 " (cutoff:3.500A)
removed outlier: 3.795A pdb=" N GLN X 69 " --> pdb=" O SER X 59 " (cutoff:3.500A)
removed outlier: 4.468A pdb=" N TYR X 73 " --> pdb=" O MET X 55 " (cutoff:3.500A)
removed outlier: 6.807A pdb=" N MET X 55 " --> pdb=" O TYR X 73 " (cutoff:3.500A)
removed outlier: 6.618A pdb=" N LYS X 75 " --> pdb=" O ASP X 53 " (cutoff:3.500A)
removed outlier: 6.493A pdb=" N ASP X 53 " --> pdb=" O LYS X 75 " (cutoff:3.500A)
removed outlier: 4.315A pdb=" N ILE X 56 " --> pdb=" O ILE X 163 " (cutoff:3.500A)
Processing sheet with id=AH8, first strand: chain 'X' and resid 83 through 84
Processing sheet with id=AH9, first strand: chain 'X' and resid 100 through 101
Processing sheet with id=AI1, first strand: chain 'Y' and resid 104 through 105
removed outlier: 4.794A pdb=" N SER Y 104 " --> pdb=" O THR Y 123 " (cutoff:3.500A)
removed outlier: 3.797A pdb=" N GLN Y 69 " --> pdb=" O SER Y 59 " (cutoff:3.500A)
removed outlier: 4.468A pdb=" N TYR Y 73 " --> pdb=" O MET Y 55 " (cutoff:3.500A)
removed outlier: 6.803A pdb=" N MET Y 55 " --> pdb=" O TYR Y 73 " (cutoff:3.500A)
removed outlier: 6.629A pdb=" N LYS Y 75 " --> pdb=" O ASP Y 53 " (cutoff:3.500A)
removed outlier: 6.492A pdb=" N ASP Y 53 " --> pdb=" O LYS Y 75 " (cutoff:3.500A)
removed outlier: 4.324A pdb=" N ILE Y 56 " --> pdb=" O ILE Y 163 " (cutoff:3.500A)
Processing sheet with id=AI2, first strand: chain 'Y' and resid 83 through 84
Processing sheet with id=AI3, first strand: chain 'Y' and resid 100 through 101
Processing sheet with id=AI4, first strand: chain 'Z' and resid 104 through 105
removed outlier: 4.793A pdb=" N SER Z 104 " --> pdb=" O THR Z 123 " (cutoff:3.500A)
removed outlier: 3.807A pdb=" N GLN Z 69 " --> pdb=" O SER Z 59 " (cutoff:3.500A)
removed outlier: 4.468A pdb=" N TYR Z 73 " --> pdb=" O MET Z 55 " (cutoff:3.500A)
removed outlier: 6.804A pdb=" N MET Z 55 " --> pdb=" O TYR Z 73 " (cutoff:3.500A)
removed outlier: 6.628A pdb=" N LYS Z 75 " --> pdb=" O ASP Z 53 " (cutoff:3.500A)
removed outlier: 6.494A pdb=" N ASP Z 53 " --> pdb=" O LYS Z 75 " (cutoff:3.500A)
removed outlier: 4.325A pdb=" N ILE Z 56 " --> pdb=" O ILE Z 163 " (cutoff:3.500A)
Processing sheet with id=AI5, first strand: chain 'Z' and resid 83 through 84
Processing sheet with id=AI6, first strand: chain 'Z' and resid 100 through 101
1725 hydrogen bonds defined for protein.
4785 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: 23.25
Time building geometry restraints manager: 46.45 seconds
NOTE: a complete listing of the restraints can be obtained by requesting
output of .geo file.
Histogram of bond lengths:
0.83 - 1.02: 32968
1.02 - 1.22: 106
1.22 - 1.42: 13039
1.42 - 1.61: 19537
1.61 - 1.81: 156
Bond restraints: 65806
Sorted by residual:
bond pdb=" N VAL I 99 "
pdb=" H VAL I 99 "
ideal model delta sigma weight residual
0.860 1.115 -0.255 2.00e-02 2.50e+03 1.62e+02
bond pdb=" N VAL Q 99 "
pdb=" H VAL Q 99 "
ideal model delta sigma weight residual
0.860 1.112 -0.252 2.00e-02 2.50e+03 1.59e+02
bond pdb=" N VAL U 99 "
pdb=" H VAL U 99 "
ideal model delta sigma weight residual
0.860 1.110 -0.250 2.00e-02 2.50e+03 1.56e+02
bond pdb=" N VAL W 99 "
pdb=" H VAL W 99 "
ideal model delta sigma weight residual
0.860 1.110 -0.250 2.00e-02 2.50e+03 1.56e+02
bond pdb=" N VAL O 99 "
pdb=" H VAL O 99 "
ideal model delta sigma weight residual
0.860 1.107 -0.247 2.00e-02 2.50e+03 1.53e+02
... (remaining 65801 not shown)
Histogram of bond angle deviations from ideal:
91.09 - 99.76: 257
99.76 - 108.43: 18261
108.43 - 117.10: 71501
117.10 - 125.77: 28864
125.77 - 134.45: 379
Bond angle restraints: 119262
Sorted by residual:
angle pdb=" N THR Y 103 "
pdb=" CA THR Y 103 "
pdb=" C THR Y 103 "
ideal model delta sigma weight residual
111.07 130.07 -19.00 1.07e+00 8.73e-01 3.15e+02
angle pdb=" N THR K 103 "
pdb=" CA THR K 103 "
pdb=" C THR K 103 "
ideal model delta sigma weight residual
111.07 130.04 -18.97 1.07e+00 8.73e-01 3.14e+02
angle pdb=" N THR I 103 "
pdb=" CA THR I 103 "
pdb=" C THR I 103 "
ideal model delta sigma weight residual
111.07 130.02 -18.95 1.07e+00 8.73e-01 3.13e+02
angle pdb=" N THR S 103 "
pdb=" CA THR S 103 "
pdb=" C THR S 103 "
ideal model delta sigma weight residual
111.07 130.00 -18.93 1.07e+00 8.73e-01 3.13e+02
angle pdb=" N THR C 103 "
pdb=" CA THR C 103 "
pdb=" C THR C 103 "
ideal model delta sigma weight residual
111.07 129.98 -18.91 1.07e+00 8.73e-01 3.12e+02
... (remaining 119257 not shown)
Histogram of dihedral angle deviations from ideal:
0.00 - 15.31: 24487
15.31 - 30.61: 1013
30.61 - 45.92: 356
45.92 - 61.22: 144
61.22 - 76.53: 52
Dihedral angle restraints: 26052
sinusoidal: 11856
harmonic: 14196
Sorted by residual:
dihedral pdb=" CA ASP G 156 "
pdb=" C ASP G 156 "
pdb=" N GLY G 157 "
pdb=" CA GLY G 157 "
ideal model delta harmonic sigma weight residual
-180.00 -145.06 -34.94 0 5.00e+00 4.00e-02 4.88e+01
dihedral pdb=" CA ASP T 156 "
pdb=" C ASP T 156 "
pdb=" N GLY T 157 "
pdb=" CA GLY T 157 "
ideal model delta harmonic sigma weight residual
180.00 -145.08 -34.92 0 5.00e+00 4.00e-02 4.88e+01
dihedral pdb=" CA ASP J 156 "
pdb=" C ASP J 156 "
pdb=" N GLY J 157 "
pdb=" CA GLY J 157 "
ideal model delta harmonic sigma weight residual
180.00 -145.17 -34.83 0 5.00e+00 4.00e-02 4.85e+01
... (remaining 26049 not shown)
Histogram of chiral volume deviations from ideal:
0.000 - 0.083: 4387
0.083 - 0.167: 629
0.167 - 0.250: 118
0.250 - 0.333: 81
0.333 - 0.416: 89
Chirality restraints: 5304
Sorted by residual:
chirality pdb=" CA THR U 103 "
pdb=" N THR U 103 "
pdb=" C THR U 103 "
pdb=" CB THR U 103 "
both_signs ideal model delta sigma weight residual
False 2.53 2.11 0.42 2.00e-01 2.50e+01 4.33e+00
chirality pdb=" CA THR E 103 "
pdb=" N THR E 103 "
pdb=" C THR E 103 "
pdb=" CB THR E 103 "
both_signs ideal model delta sigma weight residual
False 2.53 2.11 0.42 2.00e-01 2.50e+01 4.33e+00
chirality pdb=" CA GLN D 110 "
pdb=" N GLN D 110 "
pdb=" C GLN D 110 "
pdb=" CB GLN D 110 "
both_signs ideal model delta sigma weight residual
False 2.51 2.92 -0.41 2.00e-01 2.50e+01 4.26e+00
... (remaining 5301 not shown)
Planarity restraints: 9594
Sorted by residual:
delta sigma weight rms_deltas residual
plane pdb=" C ALA H 98 " -0.132 2.00e-02 2.50e+03 2.17e-01 4.72e+02
pdb=" N VAL H 99 " 0.376 2.00e-02 2.50e+03
pdb=" CA VAL H 99 " -0.121 2.00e-02 2.50e+03
pdb=" H VAL H 99 " -0.124 2.00e-02 2.50e+03
delta sigma weight rms_deltas residual
plane pdb=" C ALA D 98 " -0.132 2.00e-02 2.50e+03 2.17e-01 4.72e+02
pdb=" N VAL D 99 " 0.376 2.00e-02 2.50e+03
pdb=" CA VAL D 99 " -0.122 2.00e-02 2.50e+03
pdb=" H VAL D 99 " -0.122 2.00e-02 2.50e+03
delta sigma weight rms_deltas residual
plane pdb=" C ALA Y 98 " 0.132 2.00e-02 2.50e+03 2.17e-01 4.71e+02
pdb=" N VAL Y 99 " -0.376 2.00e-02 2.50e+03
pdb=" CA VAL Y 99 " 0.121 2.00e-02 2.50e+03
pdb=" H VAL Y 99 " 0.123 2.00e-02 2.50e+03
... (remaining 9591 not shown)
Histogram of nonbonded interaction distances:
1.15 - 1.84: 306
1.84 - 2.53: 61893
2.53 - 3.22: 212773
3.22 - 3.91: 279988
3.91 - 4.60: 454291
Nonbonded interactions: 1009251
Sorted by model distance:
nonbonded pdb=" OD1 ASP I 53 "
pdb=" HH TYR B 22 "
model vdw
1.154 1.850
nonbonded pdb=" OD1 ASP C 53 "
pdb=" HH TYR O 22 "
model vdw
1.154 1.850
nonbonded pdb=" HH TYR F 22 "
pdb=" OD1 ASP V 53 "
model vdw
1.155 1.850
nonbonded pdb=" OD1 ASP F 53 "
pdb=" HH TYR R 22 "
model vdw
1.155 1.850
nonbonded pdb=" HH TYR G 22 "
pdb=" OD1 ASP W 53 "
model vdw
1.155 1.850
... (remaining 1009246 not shown)
NOTE: a complete listing of the restraints can be obtained by requesting
output of .geo file.
Find NCS groups from input model
Found NCS groups:
ncs_group {
reference = chain 'A'
selection = chain 'B'
selection = chain 'C'
selection = chain 'D'
selection = chain 'E'
selection = chain 'F'
selection = chain 'G'
selection = chain 'H'
selection = chain 'I'
selection = chain 'J'
selection = chain 'K'
selection = chain 'L'
selection = chain 'M'
selection = chain 'N'
selection = chain 'O'
selection = chain 'P'
selection = chain 'Q'
selection = chain 'R'
selection = chain 'S'
selection = chain 'T'
selection = chain 'U'
selection = chain 'V'
selection = chain 'W'
selection = chain 'X'
selection = chain 'Y'
selection = chain 'Z'
}
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: 5
Type Number sf(0) Gaussians
S 78 5.16 5
C 20852 2.51 5
N 5096 2.21 5
O 6110 1.98 5
H 33046 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=0.00 max=1.00 mean=0.98
Load rotamer database and sin/cos tables
Set ADP refinement strategy
ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
Set random seed: 0.000
Set model cs if undefined: 0.000
Decide on map wrapping: 0.000
Normalize map: mean=0, sd=1: 0.600
Set stop_for_unknowns flag: 0.000
Assert model is a single copy model: 0.000
Assert all atoms have isotropic ADPs: 0.000
Construct map_model_manager: 0.730
Extract box with map and model: 8.030
Check model and map are aligned: 0.760
Convert atoms to be neutral: 0.410
Process input model: 157.080
Find NCS groups from input model: 2.500
Set up NCS constraints: 0.420
Set refine NCS operators: 0.000
Set scattering table: 0.020
Adjust number of macro_cycles: 0.000
Reset NCS operators: 0.000
Extract rigid body selections: 0.000
Check and reset occupancies: 0.010
Load rotamer database and sin/cos tables:2.770
Set ADP refinement strategy: 0.000
Make a string to write initial .geo file:0.000
Internal consistency checks: 0.000
Total: 173.330
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7435
moved from start: 0.0000
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
Bond : 0.007 0.045 32760 Z= 0.479
Angle : 1.915 19.693 44512 Z= 1.271
Chirality : 0.085 0.416 5304
Planarity : 0.005 0.049 5512
Dihedral : 13.178 76.527 11596
Min Nonbonded Distance : 1.377
Molprobity Statistics.
All-atom Clashscore : 21.59
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 4.94 %
Favored : 95.06 %
Rotamer Outliers : 3.79 %
Cbeta Deviations : 3.27 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.64 %
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: -2.21 (0.11), residues: 4212
helix: -0.54 (0.14), residues: 1170
sheet: -2.03 (0.12), residues: 1170
loop : -1.54 (0.13), residues: 1872
*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
8424 Ramachandran restraints generated.
4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
8424 Ramachandran restraints generated.
4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
2436 residues out of total 3432 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 130
poor density : 2306
time to evaluate : 4.058
Fit side-chains
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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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
outliers start: 130
outliers final: 57
residues processed: 2332
average time/residue: 0.8536
time to fit residues: 3162.7462
Evaluate side-chains
2149 residues out of total 3432 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 57
poor density : 2092
time to evaluate : 3.962
Switching outliers to nearest non-outliers
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
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
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
outliers start: 57
outliers final: 21
residues processed: 57
average time/residue: 0.6939
time to fit residues: 72.2442
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 416
random chunks:
chunk 351 optimal weight: 6.9990
chunk 315 optimal weight: 4.9990
chunk 174 optimal weight: 9.9990
chunk 107 optimal weight: 7.9990
chunk 212 optimal weight: 7.9990
chunk 168 optimal weight: 2.9990
chunk 326 optimal weight: 2.9990
chunk 126 optimal weight: 0.0010
chunk 198 optimal weight: 2.9990
chunk 242 optimal weight: 2.9990
chunk 377 optimal weight: 6.9990
overall best weight: 2.3994
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
I 45 GLN
I 109 ASN
** A 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 109 ASN
** B 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 113 ASN
** D 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 113 ASN
** E 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 109 ASN
** H 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
J 109 ASN
J 113 ASN
K 83 GLN
** K 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 33 GLN
** L 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 113 ASN
N 36 GLN
O 109 ASN
** P 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
P 113 ASN
** Q 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 83 GLN
R 109 ASN
S 109 ASN
S 113 ASN
** T 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
T 113 ASN
U 33 GLN
** U 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** U 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
W 33 GLN
** W 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** W 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** W 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
X 33 GLN
X 45 GLN
** X 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
X 113 ASN
** Y 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** Y 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** Z 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
Total number of N/Q/H flips: 24
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7440
moved from start: 0.4926
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
Bond : 0.004 0.057 32760 Z= 0.278
Angle : 0.699 7.855 44512 Z= 0.391
Chirality : 0.047 0.161 5304
Planarity : 0.004 0.038 5512
Dihedral : 6.444 49.221 4576
Min Nonbonded Distance : 1.878
Molprobity Statistics.
All-atom Clashscore : 21.56
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 3.25 %
Favored : 96.75 %
Rotamer Outliers : 3.15 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: -1.64 (0.11), residues: 4212
helix: 0.65 (0.13), residues: 1144
sheet: -1.66 (0.12), residues: 1248
loop : -1.72 (0.14), residues: 1820
*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
8424 Ramachandran restraints generated.
4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
8424 Ramachandran restraints generated.
4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
2276 residues out of total 3432 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 108
poor density : 2168
time to evaluate : 4.076
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
revert: symmetry clash
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revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
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revert: symmetry clash
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revert: symmetry clash
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revert: symmetry clash
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revert: symmetry clash
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revert: symmetry clash
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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
revert: symmetry clash
revert: symmetry clash
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revert: symmetry clash
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revert: symmetry clash
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revert: symmetry clash
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revert: symmetry clash
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revert: symmetry clash
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revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
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revert: symmetry clash
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revert: symmetry clash
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revert: symmetry clash
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revert: symmetry clash
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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
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revert: symmetry clash
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revert: symmetry clash
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revert: symmetry clash
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revert: symmetry clash
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revert: symmetry clash
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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
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revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
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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
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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revert: symmetry clash
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revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
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revert: symmetry clash
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revert: symmetry clash
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revert: symmetry clash
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revert: symmetry clash
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revert: symmetry clash
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revert: symmetry clash
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revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
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revert: symmetry clash
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revert: symmetry clash
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revert: symmetry clash
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
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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revert: symmetry clash
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revert: symmetry clash
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revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
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
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
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revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
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revert: symmetry clash
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
revert: symmetry clash
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revert: symmetry clash
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revert: symmetry clash
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revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
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revert: symmetry clash
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revert: symmetry clash
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revert: symmetry clash
revert: symmetry clash
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revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
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revert: symmetry clash
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revert: symmetry clash
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revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
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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
revert: symmetry clash
revert: symmetry clash
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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
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
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
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
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
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
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
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
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
outliers start: 108
outliers final: 78
residues processed: 2202
average time/residue: 0.8542
time to fit residues: 2975.4769
Evaluate side-chains
2129 residues out of total 3432 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 78
poor density : 2051
time to evaluate : 4.001
Switching outliers to nearest non-outliers
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
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
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
outliers start: 78
outliers final: 21
residues processed: 78
average time/residue: 0.6131
time to fit residues: 90.7480
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 416
random chunks:
chunk 209 optimal weight: 0.6980
chunk 117 optimal weight: 5.9990
chunk 314 optimal weight: 6.9990
chunk 257 optimal weight: 5.9990
chunk 104 optimal weight: 4.9990
chunk 378 optimal weight: 4.9990
chunk 408 optimal weight: 9.9990
chunk 337 optimal weight: 0.9990
chunk 375 optimal weight: 7.9990
chunk 129 optimal weight: 10.0000
chunk 303 optimal weight: 10.0000
overall best weight: 3.5388
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
I 83 GLN
** A 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 83 GLN
** C 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 83 GLN
F 33 GLN
** G 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 45 GLN
H 109 ASN
** L 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
P 109 ASN
T 96 ASN
** T 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** U 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
U 83 GLN
U 109 ASN
** X 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
X 109 ASN
** Y 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
Y 113 ASN
Total number of N/Q/H flips: 12
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7505
moved from start: 0.6000
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
Bond : 0.004 0.041 32760 Z= 0.284
Angle : 0.624 4.904 44512 Z= 0.349
Chirality : 0.044 0.164 5304
Planarity : 0.004 0.032 5512
Dihedral : 5.666 62.942 4576
Min Nonbonded Distance : 1.857
Molprobity Statistics.
All-atom Clashscore : 22.86
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 3.04 %
Favored : 96.96 %
Rotamer Outliers : 2.74 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: -1.19 (0.12), residues: 4212
helix: 1.19 (0.13), residues: 1144
sheet: -1.37 (0.12), residues: 1274
loop : -1.58 (0.15), residues: 1794
*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
8424 Ramachandran restraints generated.
4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
8424 Ramachandran restraints generated.
4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
2172 residues out of total 3432 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 94
poor density : 2078
time to evaluate : 3.976
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
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
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
revert: symmetry clash
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
revert: symmetry clash
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revert: symmetry clash
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revert: symmetry clash
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revert: symmetry clash
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revert: symmetry clash
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revert: symmetry clash
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revert: symmetry clash
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revert: symmetry clash
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revert: symmetry clash
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revert: symmetry clash
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revert: symmetry clash
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revert: symmetry clash
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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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
outliers start: 94
outliers final: 68
residues processed: 2097
average time/residue: 0.8466
time to fit residues: 2801.0971
Evaluate side-chains
2102 residues out of total 3432 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 68
poor density : 2034
time to evaluate : 3.883
Switching outliers to nearest non-outliers
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
outliers start: 68
outliers final: 3
residues processed: 68
average time/residue: 0.5766
time to fit residues: 76.6635
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 416
random chunks:
chunk 373 optimal weight: 8.9990
chunk 284 optimal weight: 9.9990
chunk 196 optimal weight: 6.9990
chunk 41 optimal weight: 9.9990
chunk 180 optimal weight: 10.0000
chunk 254 optimal weight: 7.9990
chunk 379 optimal weight: 8.9990
chunk 402 optimal weight: 10.0000
chunk 198 optimal weight: 4.9990
chunk 359 optimal weight: 10.0000
chunk 108 optimal weight: 9.9990
overall best weight: 7.5990
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** I 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 109 ASN
** E 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
O 83 GLN
** O 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
S 109 ASN
** T 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** U 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** X 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** Y 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** Z 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
Z 83 GLN
Total number of N/Q/H flips: 4
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7615
moved from start: 0.6714
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
Bond : 0.008 0.050 32760 Z= 0.484
Angle : 0.713 5.834 44512 Z= 0.408
Chirality : 0.045 0.155 5304
Planarity : 0.004 0.032 5512
Dihedral : 5.656 63.651 4576
Min Nonbonded Distance : 1.825
Molprobity Statistics.
All-atom Clashscore : 30.97
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 4.39 %
Favored : 95.61 %
Rotamer Outliers : 4.49 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: -1.41 (0.12), residues: 4212
helix: 1.43 (0.13), residues: 1144
sheet: -1.73 (0.12), residues: 1274
loop : -1.85 (0.14), residues: 1794
*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
8424 Ramachandran restraints generated.
4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
8424 Ramachandran restraints generated.
4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
2167 residues out of total 3432 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 154
poor density : 2013
time to evaluate : 4.610
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
outliers start: 154
outliers final: 110
residues processed: 2071
average time/residue: 0.9464
time to fit residues: 3134.8431
Evaluate side-chains
2084 residues out of total 3432 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 110
poor density : 1974
time to evaluate : 4.116
Switching outliers to nearest non-outliers
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
outliers start: 110
outliers final: 3
residues processed: 110
average time/residue: 0.6439
time to fit residues: 137.6108
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 416
random chunks:
chunk 334 optimal weight: 0.9990
chunk 228 optimal weight: 7.9990
chunk 5 optimal weight: 4.9990
chunk 299 optimal weight: 7.9990
chunk 165 optimal weight: 0.9980
chunk 343 optimal weight: 8.9990
chunk 277 optimal weight: 2.9990
chunk 0 optimal weight: 7.9990
chunk 205 optimal weight: 6.9990
chunk 360 optimal weight: 10.0000
chunk 101 optimal weight: 3.9990
overall best weight: 2.7988
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** I 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 83 GLN
B 109 ASN
** C 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 83 GLN
** L 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
P 83 GLN
P 109 ASN
T 109 ASN
** U 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** W 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
W 109 ASN
** X 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** Y 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** Z 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
Z 83 GLN
Z 109 ASN
Total number of N/Q/H flips: 9
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7514
moved from start: 0.7185
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
Bond : 0.004 0.038 32760 Z= 0.250
Angle : 0.603 6.766 44512 Z= 0.333
Chirality : 0.045 0.172 5304
Planarity : 0.003 0.039 5512
Dihedral : 5.403 69.403 4576
Min Nonbonded Distance : 1.814
Molprobity Statistics.
All-atom Clashscore : 27.61
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 3.44 %
Favored : 96.56 %
Rotamer Outliers : 2.07 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: -1.23 (0.12), residues: 4212
helix: 1.56 (0.13), residues: 1144
sheet: -1.51 (0.13), residues: 1118
loop : -1.86 (0.13), residues: 1950
*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
8424 Ramachandran restraints generated.
4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
8424 Ramachandran restraints generated.
4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
2112 residues out of total 3432 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 71
poor density : 2041
time to evaluate : 3.960
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
outliers start: 71
outliers final: 62
residues processed: 2058
average time/residue: 0.8417
time to fit residues: 2741.7097
Evaluate side-chains
2052 residues out of total 3432 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 62
poor density : 1990
time to evaluate : 3.968
Switching outliers to nearest non-outliers
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
outliers start: 62
outliers final: 4
residues processed: 62
average time/residue: 0.5941
time to fit residues: 71.8130
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 416
random chunks:
chunk 135 optimal weight: 8.9990
chunk 362 optimal weight: 1.9990
chunk 79 optimal weight: 7.9990
chunk 236 optimal weight: 3.9990
chunk 99 optimal weight: 9.9990
chunk 402 optimal weight: 9.9990
chunk 334 optimal weight: 4.9990
chunk 186 optimal weight: 5.9990
chunk 33 optimal weight: 1.9990
chunk 133 optimal weight: 1.9990
chunk 211 optimal weight: 7.9990
overall best weight: 2.9990
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** I 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 83 GLN
** B 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 83 GLN
** G 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 83 GLN
** L 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 159 ASN
** O 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
T 83 GLN
** U 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
U 83 GLN
V 36 GLN
** X 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
Y 83 GLN
** Y 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** Z 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
Total number of N/Q/H flips: 8
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7512
moved from start: 0.7535
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
Bond : 0.004 0.033 32760 Z= 0.255
Angle : 0.609 7.926 44512 Z= 0.334
Chirality : 0.044 0.179 5304
Planarity : 0.003 0.028 5512
Dihedral : 5.338 68.122 4576
Min Nonbonded Distance : 1.805
Molprobity Statistics.
All-atom Clashscore : 28.67
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 3.87 %
Favored : 96.13 %
Rotamer Outliers : 1.52 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: -1.23 (0.12), residues: 4212
helix: 1.58 (0.13), residues: 1170
sheet: -1.55 (0.13), residues: 1144
loop : -1.89 (0.13), residues: 1898
*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
8424 Ramachandran restraints generated.
4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
8424 Ramachandran restraints generated.
4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
2068 residues out of total 3432 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 52
poor density : 2016
time to evaluate : 4.346
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
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
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
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
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
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
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
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
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
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
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
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
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
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revert: symmetry clash
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revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
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revert: symmetry clash
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revert: symmetry clash
revert: symmetry clash
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revert: symmetry clash
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revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
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revert: symmetry clash
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revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
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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
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
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
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
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
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
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
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
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
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
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
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
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
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
outliers start: 52
outliers final: 42
residues processed: 2025
average time/residue: 0.9255
time to fit residues: 3000.3683
Evaluate side-chains
2014 residues out of total 3432 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 42
poor density : 1972
time to evaluate : 4.036
Switching outliers to nearest non-outliers
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
outliers start: 42
outliers final: 6
residues processed: 42
average time/residue: 0.6721
time to fit residues: 57.8449
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 416
random chunks:
chunk 388 optimal weight: 10.0000
chunk 45 optimal weight: 0.0270
chunk 229 optimal weight: 4.9990
chunk 293 optimal weight: 5.9990
chunk 227 optimal weight: 3.9990
chunk 338 optimal weight: 9.9990
chunk 224 optimal weight: 9.9990
chunk 400 optimal weight: 2.9990
chunk 250 optimal weight: 6.9990
chunk 244 optimal weight: 9.9990
chunk 185 optimal weight: 7.9990
overall best weight: 3.6046
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** I 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 109 ASN
** D 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
K 83 GLN
** L 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** U 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
W 83 GLN
** X 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** Y 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** Z 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
Total number of N/Q/H flips: 3
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7518
moved from start: 0.7789
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
Bond : 0.004 0.039 32760 Z= 0.278
Angle : 0.620 8.344 44512 Z= 0.341
Chirality : 0.044 0.170 5304
Planarity : 0.003 0.031 5512
Dihedral : 5.244 64.046 4576
Min Nonbonded Distance : 1.830
Molprobity Statistics.
All-atom Clashscore : 29.87
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 4.18 %
Favored : 95.82 %
Rotamer Outliers : 1.40 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: -1.20 (0.12), residues: 4212
helix: 1.71 (0.13), residues: 1170
sheet: -1.54 (0.13), residues: 1144
loop : -1.94 (0.13), residues: 1898
*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
8424 Ramachandran restraints generated.
4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
8424 Ramachandran restraints generated.
4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
2045 residues out of total 3432 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 48
poor density : 1997
time to evaluate : 4.010
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
revert: symmetry clash
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revert: symmetry clash
revert: symmetry clash
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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
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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revert: symmetry clash
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revert: symmetry clash
revert: symmetry clash
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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
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
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revert: symmetry clash
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revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
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
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
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
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
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revert: symmetry clash
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revert: symmetry clash
revert: symmetry clash
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revert: symmetry clash
revert: symmetry clash
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revert: symmetry clash
revert: symmetry clash
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revert: symmetry clash
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revert: symmetry clash
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
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
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
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
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
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
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
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
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
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
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
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
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
outliers start: 48
outliers final: 43
residues processed: 2001
average time/residue: 0.8614
time to fit residues: 2737.3470
Evaluate side-chains
2003 residues out of total 3432 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 43
poor density : 1960
time to evaluate : 4.040
Switching outliers to nearest non-outliers
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
outliers start: 43
outliers final: 6
residues processed: 43
average time/residue: 0.6036
time to fit residues: 52.3167
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 416
random chunks:
chunk 248 optimal weight: 5.9990
chunk 160 optimal weight: 10.0000
chunk 239 optimal weight: 1.9990
chunk 120 optimal weight: 5.9990
chunk 78 optimal weight: 4.9990
chunk 77 optimal weight: 2.9990
chunk 254 optimal weight: 0.5980
chunk 273 optimal weight: 5.9990
chunk 198 optimal weight: 9.9990
chunk 37 optimal weight: 2.9990
chunk 315 optimal weight: 0.5980
overall best weight: 1.8386
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
I 36 GLN
** I 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 83 GLN
** B 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 45 GLN
J 83 GLN
L 36 GLN
** L 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** P 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** U 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
W 83 GLN
X 45 GLN
** X 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** Y 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** Y 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** Z 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
Total number of N/Q/H flips: 7
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7468
moved from start: 0.8064
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
Bond : 0.003 0.032 32760 Z= 0.214
Angle : 0.608 8.893 44512 Z= 0.330
Chirality : 0.045 0.179 5304
Planarity : 0.003 0.033 5512
Dihedral : 5.173 61.474 4576
Min Nonbonded Distance : 1.827
Molprobity Statistics.
All-atom Clashscore : 28.87
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 3.44 %
Favored : 96.56 %
Rotamer Outliers : 0.70 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: -1.02 (0.12), residues: 4212
helix: 1.85 (0.13), residues: 1170
sheet: -1.40 (0.14), residues: 1144
loop : -1.84 (0.13), residues: 1898
*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
8424 Ramachandran restraints generated.
4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
8424 Ramachandran restraints generated.
4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
2021 residues out of total 3432 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 24
poor density : 1997
time to evaluate : 4.020
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
revert: symmetry clash
outliers start: 24
outliers final: 19
residues processed: 1998
average time/residue: 0.9216
time to fit residues: 2958.5762
Evaluate side-chains
1979 residues out of total 3432 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 19
poor density : 1960
time to evaluate : 4.019
Switching outliers to nearest non-outliers
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
outliers start: 19
outliers final: 5
residues processed: 19
average time/residue: 0.6444
time to fit residues: 27.7124
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 416
random chunks:
chunk 364 optimal weight: 8.9990
chunk 384 optimal weight: 10.0000
chunk 350 optimal weight: 7.9990
chunk 373 optimal weight: 10.0000
chunk 224 optimal weight: 10.0000
chunk 162 optimal weight: 5.9990
chunk 293 optimal weight: 4.9990
chunk 114 optimal weight: 9.9990
chunk 337 optimal weight: 4.9990
chunk 353 optimal weight: 1.9990
chunk 372 optimal weight: 2.9990
overall best weight: 4.1990
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** I 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 83 GLN
** G 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K 83 GLN
** L 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** P 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** P 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** U 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
V 83 GLN
** W 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** X 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** X 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
Y 109 ASN
** Z 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
Total number of N/Q/H flips: 4
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7522
moved from start: 0.8196
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
Bond : 0.005 0.041 32760 Z= 0.307
Angle : 0.646 9.395 44512 Z= 0.358
Chirality : 0.044 0.175 5304
Planarity : 0.003 0.044 5512
Dihedral : 5.305 61.663 4576
Min Nonbonded Distance : 1.804
Molprobity Statistics.
All-atom Clashscore : 33.71
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 4.44 %
Favored : 95.56 %
Rotamer Outliers : 1.14 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: -1.09 (0.12), residues: 4212
helix: 1.84 (0.13), residues: 1170
sheet: -1.45 (0.14), residues: 1144
loop : -1.91 (0.13), residues: 1898
*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
8424 Ramachandran restraints generated.
4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
8424 Ramachandran restraints generated.
4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
1994 residues out of total 3432 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 39
poor density : 1955
time to evaluate : 4.001
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
outliers start: 39
outliers final: 33
residues processed: 1959
average time/residue: 0.8508
time to fit residues: 2648.8536
Evaluate side-chains
1974 residues out of total 3432 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 33
poor density : 1941
time to evaluate : 3.993
Switching outliers to nearest non-outliers
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
outliers start: 33
outliers final: 6
residues processed: 33
average time/residue: 0.5836
time to fit residues: 40.3808
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 416
random chunks:
chunk 245 optimal weight: 8.9990
chunk 395 optimal weight: 6.9990
chunk 241 optimal weight: 0.7980
chunk 187 optimal weight: 0.9980
chunk 274 optimal weight: 8.9990
chunk 414 optimal weight: 1.9990
chunk 381 optimal weight: 0.8980
chunk 330 optimal weight: 0.9980
chunk 34 optimal weight: 6.9990
chunk 254 optimal weight: 2.9990
chunk 202 optimal weight: 0.9990
overall best weight: 0.9382
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** I 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 109 ASN
** R 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** U 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** U 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
V 113 ASN
** X 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** X 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** Y 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** Z 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** Z 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
Total number of N/Q/H flips: 2
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7438
moved from start: 0.8367
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
Bond : 0.003 0.036 32760 Z= 0.204
Angle : 0.634 9.934 44512 Z= 0.342
Chirality : 0.045 0.192 5304
Planarity : 0.003 0.040 5512
Dihedral : 5.327 78.520 4576
Min Nonbonded Distance : 1.800
Molprobity Statistics.
All-atom Clashscore : 29.90
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 3.23 %
Favored : 96.77 %
Rotamer Outliers : 0.41 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: -0.84 (0.12), residues: 4212
helix: 1.94 (0.13), residues: 1170
sheet: -1.16 (0.14), residues: 1118
loop : -1.79 (0.13), residues: 1924
********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
8424 Ramachandran restraints generated.
4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
8424 Ramachandran restraints generated.
4212 Oldfield, 0 Emsley, 4212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
2008 residues out of total 3432 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 14
poor density : 1994
time to evaluate : 4.156
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
outliers start: 14
outliers final: 12
residues processed: 1994
average time/residue: 0.8956
time to fit residues: 2855.5470
Evaluate side-chains
1972 residues out of total 3432 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 12
poor density : 1960
time to evaluate : 4.002
Switching outliers to nearest non-outliers
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
outliers start: 12
outliers final: 4
residues processed: 12
average time/residue: 0.6161
time to fit residues: 18.6837
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 416
random chunks:
chunk 262 optimal weight: 5.9990
chunk 351 optimal weight: 9.9990
chunk 101 optimal weight: 5.9990
chunk 304 optimal weight: 10.0000
chunk 48 optimal weight: 9.9990
chunk 91 optimal weight: 1.9990
chunk 330 optimal weight: 1.9990
chunk 138 optimal weight: 2.9990
chunk 339 optimal weight: 2.9990
chunk 41 optimal weight: 2.9990
chunk 60 optimal weight: 4.9990
overall best weight: 2.5990
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** I 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 45 GLN
** E 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** T 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** U 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** U 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
V 83 GLN
** X 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** X 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** Y 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** Y 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** Z 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** Z 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
Total number of N/Q/H flips: 2
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.097386 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.086519 restraints weight = 301100.278|
|-----------------------------------------------------------------------------|
r_work (start): 0.3376 rms_B_bonded: 5.55
r_work: 0.3367 rms_B_bonded: 5.28 restraints_weight: 2.0000
r_work (final): 0.3367
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7126
moved from start: 0.8524
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
Bond : 0.004 0.041 32760 Z= 0.244
Angle : 0.638 10.242 44512 Z= 0.349
Chirality : 0.044 0.193 5304
Planarity : 0.003 0.041 5512
Dihedral : 5.241 76.864 4576
Min Nonbonded Distance : 1.785
Molprobity Statistics.
All-atom Clashscore : 33.35
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 3.54 %
Favored : 96.46 %
Rotamer Outliers : 0.61 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: -0.87 (0.12), residues: 4212
helix: 2.00 (0.13), residues: 1170
sheet: -1.17 (0.14), residues: 1118
loop : -1.88 (0.13), residues: 1924
===============================================================================
Job complete
usr+sys time: 33839.12 seconds
wall clock time: 578 minutes 58.24 seconds (34738.24 seconds total)