Starting phenix.real_space_refine (version: dev)
on Thu Jul 7 12:39:39 2022 by dcliebschner
===============================================================================
Processing files:
-------------------------------------------------------------------------------
Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5n6w_3595/07_2022/5n6w_3595.pdb
Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5n6w_3595/07_2022/5n6w_3595.map
Processing PHIL parameters:
-------------------------------------------------------------------------------
Adding command-line PHIL:
-------------------------
refinement.macro_cycles=10
scattering_table=electron
resolution=4.2
write_initial_geo_file=False
Final processed PHIL parameters:
-------------------------------------------------------------------------------
data_manager {
real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5n6w_3595/07_2022/5n6w_3595.map"
default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5n6w_3595/07_2022/5n6w_3595.map"
model {
file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5n6w_3595/07_2022/5n6w_3595.pdb"
}
default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5n6w_3595/07_2022/5n6w_3595.pdb"
}
resolution = 4.2
write_initial_geo_file = False
refinement {
macro_cycles = 10
}
Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.
Validating inputs
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
Set to: 0
Set model cs if undefined
Decide on map wrapping
Map wrapping is set to: False
Normalize map: mean=0, sd=1
Input map: mean= 0.000 sd= 0.004
Set stop_for_unknowns flag
Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Convert atoms to be neutral
Process input model
Symmetric amino acids flipped
Residue "A PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "A TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "A PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "A ASP 118": "OD1" <-> "OD2"
Residue "A TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "A TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "A ARG 160": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
Residue "A TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "A PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "A ARG 209": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
Residue "B PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "B TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "B PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "B ASP 118": "OD1" <-> "OD2"
Residue "B TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "B TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "B ARG 160": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
Residue "B TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "B PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "B ARG 209": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
Residue "C PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "C TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "C PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "C ASP 118": "OD1" <-> "OD2"
Residue "C TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "C TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "C ARG 160": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
Residue "C TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "C PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "C ARG 209": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
Residue "D PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "D TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "D PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "D ASP 118": "OD1" <-> "OD2"
Residue "D TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "D TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "D ARG 160": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
Residue "D TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "D PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "D ARG 209": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
Residue "E PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "E TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "E PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "E ASP 118": "OD1" <-> "OD2"
Residue "E TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "E TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "E ARG 160": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
Residue "E TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "E PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "E ARG 209": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
Residue "F PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "F TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "F PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "F ASP 118": "OD1" <-> "OD2"
Residue "F TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "F TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "F ARG 160": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
Residue "F TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "F PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "F ARG 209": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
Residue "G PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "G TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "G PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "G ASP 118": "OD1" <-> "OD2"
Residue "G TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "G TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "G ARG 160": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
Residue "G TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "G PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "G ARG 209": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
Residue "H PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "H TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "H PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "H ASP 118": "OD1" <-> "OD2"
Residue "H TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "H TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "H ARG 160": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
Residue "H TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "H PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "H ARG 209": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
Residue "I PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "I TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "I PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "I ASP 118": "OD1" <-> "OD2"
Residue "I TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "I TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "I ARG 160": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
Residue "I TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "I PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "I ARG 209": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
Residue "J PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "J TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "J PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "J ASP 118": "OD1" <-> "OD2"
Residue "J TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "J TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "J ARG 160": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
Residue "J TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "J PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "J ARG 209": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
Residue "K PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "K TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "K PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "K ASP 118": "OD1" <-> "OD2"
Residue "K TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "K TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "K ARG 160": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
Residue "K TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "K PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "K ARG 209": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
Residue "L PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "L TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "L PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "L ASP 118": "OD1" <-> "OD2"
Residue "L TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "L TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "L ARG 160": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
Residue "L TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "L PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "L ARG 209": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
Residue "M PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "M TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "M PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "M ASP 118": "OD1" <-> "OD2"
Residue "M TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "M TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "M ARG 160": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
Residue "M TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "M PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "M ARG 209": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
Residue "N PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "N TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "N PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "N ASP 118": "OD1" <-> "OD2"
Residue "N TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "N TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "N ARG 160": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
Residue "N TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "N PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "N ARG 209": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
Residue "O PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "O TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "O PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "O ASP 118": "OD1" <-> "OD2"
Residue "O TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "O TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "O ARG 160": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
Residue "O TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "O PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "O ARG 209": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
Residue "P PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "P TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "P PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "P ASP 118": "OD1" <-> "OD2"
Residue "P TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "P TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "P ARG 160": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
Residue "P TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "P PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "P ARG 209": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
Time to flip residues: 0.07s
Monomer Library directory:
"/net/cci-filer2/raid1/xp/phenix/phenix-dev-4648/modules/chem_data/mon_lib"
Total number of atoms: 40752
Number of models: 1
Model: ""
Number of chains: 16
Chain: "A"
Number of atoms: 2547
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 157, 2547
Classifications: {'peptide': 157}
Link IDs: {'PTRANS': 7, 'TRANS': 149}
Chain: "B"
Number of atoms: 2547
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 157, 2547
Classifications: {'peptide': 157}
Link IDs: {'PTRANS': 7, 'TRANS': 149}
Chain: "C"
Number of atoms: 2547
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 157, 2547
Classifications: {'peptide': 157}
Link IDs: {'PTRANS': 7, 'TRANS': 149}
Chain: "D"
Number of atoms: 2547
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 157, 2547
Classifications: {'peptide': 157}
Link IDs: {'PTRANS': 7, 'TRANS': 149}
Chain: "E"
Number of atoms: 2547
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 157, 2547
Classifications: {'peptide': 157}
Link IDs: {'PTRANS': 7, 'TRANS': 149}
Chain: "F"
Number of atoms: 2547
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 157, 2547
Classifications: {'peptide': 157}
Link IDs: {'PTRANS': 7, 'TRANS': 149}
Chain: "G"
Number of atoms: 2547
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 157, 2547
Classifications: {'peptide': 157}
Link IDs: {'PTRANS': 7, 'TRANS': 149}
Chain: "H"
Number of atoms: 2547
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 157, 2547
Classifications: {'peptide': 157}
Link IDs: {'PTRANS': 7, 'TRANS': 149}
Chain: "I"
Number of atoms: 2547
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 157, 2547
Classifications: {'peptide': 157}
Link IDs: {'PTRANS': 7, 'TRANS': 149}
Chain: "J"
Number of atoms: 2547
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 157, 2547
Classifications: {'peptide': 157}
Link IDs: {'PTRANS': 7, 'TRANS': 149}
Chain: "K"
Number of atoms: 2547
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 157, 2547
Classifications: {'peptide': 157}
Link IDs: {'PTRANS': 7, 'TRANS': 149}
Chain: "L"
Number of atoms: 2547
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 157, 2547
Classifications: {'peptide': 157}
Link IDs: {'PTRANS': 7, 'TRANS': 149}
Chain: "M"
Number of atoms: 2547
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 157, 2547
Classifications: {'peptide': 157}
Link IDs: {'PTRANS': 7, 'TRANS': 149}
Chain: "N"
Number of atoms: 2547
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 157, 2547
Classifications: {'peptide': 157}
Link IDs: {'PTRANS': 7, 'TRANS': 149}
Chain: "O"
Number of atoms: 2547
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 157, 2547
Classifications: {'peptide': 157}
Link IDs: {'PTRANS': 7, 'TRANS': 149}
Chain: "P"
Number of atoms: 2547
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 157, 2547
Classifications: {'peptide': 157}
Link IDs: {'PTRANS': 7, 'TRANS': 149}
Time building chain proxies: 19.09, per 1000 atoms: 0.47
Number of scatterers: 40752
At special positions: 0
Unit cell: (145.77, 145.77, 86.43, 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 112 16.00
O 3792 8.00
N 3600 7.00
C 13216 6.00
H 20032 1.00
sf(0) = scattering factor at diffraction angle 0.
Number of disulfides: simple=16, symmetry=0
Simple disulfide: pdb=" SG CYS A 63 " - pdb=" SG CYS A 219 " distance=2.03
Simple disulfide: pdb=" SG CYS B 63 " - pdb=" SG CYS B 219 " distance=2.03
Simple disulfide: pdb=" SG CYS C 63 " - pdb=" SG CYS C 219 " distance=2.03
Simple disulfide: pdb=" SG CYS D 63 " - pdb=" SG CYS D 219 " distance=2.03
Simple disulfide: pdb=" SG CYS E 63 " - pdb=" SG CYS E 219 " distance=2.03
Simple disulfide: pdb=" SG CYS F 63 " - pdb=" SG CYS F 219 " distance=2.03
Simple disulfide: pdb=" SG CYS G 63 " - pdb=" SG CYS G 219 " distance=2.03
Simple disulfide: pdb=" SG CYS H 63 " - pdb=" SG CYS H 219 " distance=2.03
Simple disulfide: pdb=" SG CYS I 63 " - pdb=" SG CYS I 219 " distance=2.03
Simple disulfide: pdb=" SG CYS J 63 " - pdb=" SG CYS J 219 " distance=2.03
Simple disulfide: pdb=" SG CYS K 63 " - pdb=" SG CYS K 219 " distance=2.03
Simple disulfide: pdb=" SG CYS L 63 " - pdb=" SG CYS L 219 " distance=2.03
Simple disulfide: pdb=" SG CYS M 63 " - pdb=" SG CYS M 219 " distance=2.03
Simple disulfide: pdb=" SG CYS N 63 " - pdb=" SG CYS N 219 " distance=2.03
Simple disulfide: pdb=" SG CYS O 63 " - pdb=" SG CYS O 219 " distance=2.03
Simple disulfide: pdb=" SG CYS P 63 " - pdb=" SG CYS P 219 " distance=2.03
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: 29.07
Conformation dependent library (CDL) restraints added in 3.2 seconds
4960 Ramachandran restraints generated.
2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2.
Adding C-beta torsion restraints...
Number of C-beta restraints generated: 4704
Finding SS restraints...
Secondary structure from input PDB file:
0 helices and 32 sheets defined
0.0% alpha, 10.2% beta
0 base pairs and 0 stacking pairs defined.
Time for finding SS restraints: 0.66
Creating SS restraints...
Processing sheet with id=AA1, first strand: chain 'A' and resid 194 through 196
removed outlier: 3.922A pdb=" N ILE A 194 " --> pdb=" O ILE A 133 " (cutoff:3.500A)
removed outlier: 3.506A pdb=" N SER A 196 " --> pdb=" O LYS A 131 " (cutoff:3.500A)
removed outlier: 4.967A pdb=" N LEU A 217 " --> pdb=" O SER A 134 " (cutoff:3.500A)
Processing sheet with id=AA2, first strand: chain 'A' and resid 163 through 164
removed outlier: 3.889A pdb=" N TRP A 163 " --> pdb=" O TYR A 155 " (cutoff:3.500A)
removed outlier: 3.556A pdb=" N TYR A 155 " --> pdb=" O TRP A 163 " (cutoff:3.500A)
removed outlier: 3.619A pdb=" N ARG A 200 " --> pdb=" O GLN A 154 " (cutoff:3.500A)
removed outlier: 3.656A pdb=" N ARG A 156 " --> pdb=" O PHE A 198 " (cutoff:3.500A)
removed outlier: 4.368A pdb=" N PHE A 198 " --> pdb=" O ARG A 156 " (cutoff:3.500A)
Processing sheet with id=AA3, first strand: chain 'B' and resid 194 through 196
removed outlier: 3.921A pdb=" N ILE B 194 " --> pdb=" O ILE B 133 " (cutoff:3.500A)
removed outlier: 3.505A pdb=" N SER B 196 " --> pdb=" O LYS B 131 " (cutoff:3.500A)
removed outlier: 4.967A pdb=" N LEU B 217 " --> pdb=" O SER B 134 " (cutoff:3.500A)
Processing sheet with id=AA4, first strand: chain 'B' and resid 163 through 164
removed outlier: 3.890A pdb=" N TRP B 163 " --> pdb=" O TYR B 155 " (cutoff:3.500A)
removed outlier: 3.556A pdb=" N TYR B 155 " --> pdb=" O TRP B 163 " (cutoff:3.500A)
removed outlier: 3.618A pdb=" N ARG B 200 " --> pdb=" O GLN B 154 " (cutoff:3.500A)
removed outlier: 3.655A pdb=" N ARG B 156 " --> pdb=" O PHE B 198 " (cutoff:3.500A)
removed outlier: 4.369A pdb=" N PHE B 198 " --> pdb=" O ARG B 156 " (cutoff:3.500A)
Processing sheet with id=AA5, first strand: chain 'C' and resid 194 through 196
removed outlier: 3.920A pdb=" N ILE C 194 " --> pdb=" O ILE C 133 " (cutoff:3.500A)
removed outlier: 3.505A pdb=" N SER C 196 " --> pdb=" O LYS C 131 " (cutoff:3.500A)
removed outlier: 4.967A pdb=" N LEU C 217 " --> pdb=" O SER C 134 " (cutoff:3.500A)
Processing sheet with id=AA6, first strand: chain 'C' and resid 163 through 164
removed outlier: 3.890A pdb=" N TRP C 163 " --> pdb=" O TYR C 155 " (cutoff:3.500A)
removed outlier: 3.556A pdb=" N TYR C 155 " --> pdb=" O TRP C 163 " (cutoff:3.500A)
removed outlier: 3.619A pdb=" N ARG C 200 " --> pdb=" O GLN C 154 " (cutoff:3.500A)
removed outlier: 3.656A pdb=" N ARG C 156 " --> pdb=" O PHE C 198 " (cutoff:3.500A)
removed outlier: 4.369A pdb=" N PHE C 198 " --> pdb=" O ARG C 156 " (cutoff:3.500A)
Processing sheet with id=AA7, first strand: chain 'D' and resid 194 through 196
removed outlier: 3.921A pdb=" N ILE D 194 " --> pdb=" O ILE D 133 " (cutoff:3.500A)
removed outlier: 3.506A pdb=" N SER D 196 " --> pdb=" O LYS D 131 " (cutoff:3.500A)
removed outlier: 4.968A pdb=" N LEU D 217 " --> pdb=" O SER D 134 " (cutoff:3.500A)
Processing sheet with id=AA8, first strand: chain 'D' and resid 163 through 164
removed outlier: 3.891A pdb=" N TRP D 163 " --> pdb=" O TYR D 155 " (cutoff:3.500A)
removed outlier: 3.558A pdb=" N TYR D 155 " --> pdb=" O TRP D 163 " (cutoff:3.500A)
removed outlier: 3.618A pdb=" N ARG D 200 " --> pdb=" O GLN D 154 " (cutoff:3.500A)
removed outlier: 3.656A pdb=" N ARG D 156 " --> pdb=" O PHE D 198 " (cutoff:3.500A)
removed outlier: 4.371A pdb=" N PHE D 198 " --> pdb=" O ARG D 156 " (cutoff:3.500A)
Processing sheet with id=AA9, first strand: chain 'E' and resid 194 through 196
removed outlier: 3.927A pdb=" N ILE E 194 " --> pdb=" O ILE E 133 " (cutoff:3.500A)
removed outlier: 3.522A pdb=" N SER E 196 " --> pdb=" O LYS E 131 " (cutoff:3.500A)
removed outlier: 4.970A pdb=" N LEU E 217 " --> pdb=" O SER E 134 " (cutoff:3.500A)
Processing sheet with id=AB1, first strand: chain 'E' and resid 163 through 164
removed outlier: 3.886A pdb=" N TRP E 163 " --> pdb=" O TYR E 155 " (cutoff:3.500A)
removed outlier: 3.554A pdb=" N TYR E 155 " --> pdb=" O TRP E 163 " (cutoff:3.500A)
removed outlier: 3.619A pdb=" N ARG E 200 " --> pdb=" O GLN E 154 " (cutoff:3.500A)
removed outlier: 3.656A pdb=" N ARG E 156 " --> pdb=" O PHE E 198 " (cutoff:3.500A)
removed outlier: 4.367A pdb=" N PHE E 198 " --> pdb=" O ARG E 156 " (cutoff:3.500A)
Processing sheet with id=AB2, first strand: chain 'F' and resid 194 through 196
removed outlier: 3.921A pdb=" N ILE F 194 " --> pdb=" O ILE F 133 " (cutoff:3.500A)
removed outlier: 3.511A pdb=" N SER F 196 " --> pdb=" O LYS F 131 " (cutoff:3.500A)
removed outlier: 4.968A pdb=" N LEU F 217 " --> pdb=" O SER F 134 " (cutoff:3.500A)
Processing sheet with id=AB3, first strand: chain 'F' and resid 163 through 164
removed outlier: 3.905A pdb=" N TRP F 163 " --> pdb=" O TYR F 155 " (cutoff:3.500A)
removed outlier: 3.574A pdb=" N TYR F 155 " --> pdb=" O TRP F 163 " (cutoff:3.500A)
removed outlier: 3.616A pdb=" N ARG F 200 " --> pdb=" O GLN F 154 " (cutoff:3.500A)
removed outlier: 3.657A pdb=" N ARG F 156 " --> pdb=" O PHE F 198 " (cutoff:3.500A)
removed outlier: 4.372A pdb=" N PHE F 198 " --> pdb=" O ARG F 156 " (cutoff:3.500A)
Processing sheet with id=AB4, first strand: chain 'G' and resid 194 through 196
removed outlier: 3.923A pdb=" N ILE G 194 " --> pdb=" O ILE G 133 " (cutoff:3.500A)
removed outlier: 3.506A pdb=" N SER G 196 " --> pdb=" O LYS G 131 " (cutoff:3.500A)
removed outlier: 4.966A pdb=" N LEU G 217 " --> pdb=" O SER G 134 " (cutoff:3.500A)
Processing sheet with id=AB5, first strand: chain 'G' and resid 163 through 164
removed outlier: 3.891A pdb=" N TRP G 163 " --> pdb=" O TYR G 155 " (cutoff:3.500A)
removed outlier: 3.556A pdb=" N TYR G 155 " --> pdb=" O TRP G 163 " (cutoff:3.500A)
removed outlier: 3.619A pdb=" N ARG G 200 " --> pdb=" O GLN G 154 " (cutoff:3.500A)
removed outlier: 3.656A pdb=" N ARG G 156 " --> pdb=" O PHE G 198 " (cutoff:3.500A)
removed outlier: 4.372A pdb=" N PHE G 198 " --> pdb=" O ARG G 156 " (cutoff:3.500A)
Processing sheet with id=AB6, first strand: chain 'H' and resid 194 through 196
removed outlier: 3.923A pdb=" N ILE H 194 " --> pdb=" O ILE H 133 " (cutoff:3.500A)
removed outlier: 3.522A pdb=" N SER H 196 " --> pdb=" O LYS H 131 " (cutoff:3.500A)
removed outlier: 4.970A pdb=" N LEU H 217 " --> pdb=" O SER H 134 " (cutoff:3.500A)
Processing sheet with id=AB7, first strand: chain 'H' and resid 163 through 164
removed outlier: 3.890A pdb=" N TRP H 163 " --> pdb=" O TYR H 155 " (cutoff:3.500A)
removed outlier: 3.557A pdb=" N TYR H 155 " --> pdb=" O TRP H 163 " (cutoff:3.500A)
removed outlier: 3.618A pdb=" N ARG H 200 " --> pdb=" O GLN H 154 " (cutoff:3.500A)
removed outlier: 3.656A pdb=" N ARG H 156 " --> pdb=" O PHE H 198 " (cutoff:3.500A)
removed outlier: 4.368A pdb=" N PHE H 198 " --> pdb=" O ARG H 156 " (cutoff:3.500A)
Processing sheet with id=AB8, first strand: chain 'I' and resid 194 through 196
removed outlier: 3.920A pdb=" N ILE I 194 " --> pdb=" O ILE I 133 " (cutoff:3.500A)
removed outlier: 3.506A pdb=" N SER I 196 " --> pdb=" O LYS I 131 " (cutoff:3.500A)
removed outlier: 4.967A pdb=" N LEU I 217 " --> pdb=" O SER I 134 " (cutoff:3.500A)
Processing sheet with id=AB9, first strand: chain 'I' and resid 163 through 164
removed outlier: 3.889A pdb=" N TRP I 163 " --> pdb=" O TYR I 155 " (cutoff:3.500A)
removed outlier: 3.556A pdb=" N TYR I 155 " --> pdb=" O TRP I 163 " (cutoff:3.500A)
removed outlier: 3.619A pdb=" N ARG I 200 " --> pdb=" O GLN I 154 " (cutoff:3.500A)
removed outlier: 3.656A pdb=" N ARG I 156 " --> pdb=" O PHE I 198 " (cutoff:3.500A)
removed outlier: 4.368A pdb=" N PHE I 198 " --> pdb=" O ARG I 156 " (cutoff:3.500A)
Processing sheet with id=AC1, first strand: chain 'J' and resid 194 through 196
removed outlier: 3.921A pdb=" N ILE J 194 " --> pdb=" O ILE J 133 " (cutoff:3.500A)
removed outlier: 3.506A pdb=" N SER J 196 " --> pdb=" O LYS J 131 " (cutoff:3.500A)
removed outlier: 4.967A pdb=" N LEU J 217 " --> pdb=" O SER J 134 " (cutoff:3.500A)
Processing sheet with id=AC2, first strand: chain 'J' and resid 163 through 164
removed outlier: 3.893A pdb=" N TRP J 163 " --> pdb=" O TYR J 155 " (cutoff:3.500A)
removed outlier: 3.559A pdb=" N TYR J 155 " --> pdb=" O TRP J 163 " (cutoff:3.500A)
removed outlier: 3.619A pdb=" N ARG J 200 " --> pdb=" O GLN J 154 " (cutoff:3.500A)
removed outlier: 3.656A pdb=" N ARG J 156 " --> pdb=" O PHE J 198 " (cutoff:3.500A)
removed outlier: 4.370A pdb=" N PHE J 198 " --> pdb=" O ARG J 156 " (cutoff:3.500A)
Processing sheet with id=AC3, first strand: chain 'K' and resid 194 through 196
removed outlier: 3.921A pdb=" N ILE K 194 " --> pdb=" O ILE K 133 " (cutoff:3.500A)
removed outlier: 3.505A pdb=" N SER K 196 " --> pdb=" O LYS K 131 " (cutoff:3.500A)
removed outlier: 4.968A pdb=" N LEU K 217 " --> pdb=" O SER K 134 " (cutoff:3.500A)
Processing sheet with id=AC4, first strand: chain 'K' and resid 163 through 164
removed outlier: 3.890A pdb=" N TRP K 163 " --> pdb=" O TYR K 155 " (cutoff:3.500A)
removed outlier: 3.557A pdb=" N TYR K 155 " --> pdb=" O TRP K 163 " (cutoff:3.500A)
removed outlier: 3.619A pdb=" N ARG K 200 " --> pdb=" O GLN K 154 " (cutoff:3.500A)
removed outlier: 3.656A pdb=" N ARG K 156 " --> pdb=" O PHE K 198 " (cutoff:3.500A)
removed outlier: 4.368A pdb=" N PHE K 198 " --> pdb=" O ARG K 156 " (cutoff:3.500A)
Processing sheet with id=AC5, first strand: chain 'L' and resid 194 through 196
removed outlier: 3.921A pdb=" N ILE L 194 " --> pdb=" O ILE L 133 " (cutoff:3.500A)
removed outlier: 3.505A pdb=" N SER L 196 " --> pdb=" O LYS L 131 " (cutoff:3.500A)
removed outlier: 4.967A pdb=" N LEU L 217 " --> pdb=" O SER L 134 " (cutoff:3.500A)
Processing sheet with id=AC6, first strand: chain 'L' and resid 163 through 164
removed outlier: 3.889A pdb=" N TRP L 163 " --> pdb=" O TYR L 155 " (cutoff:3.500A)
removed outlier: 3.556A pdb=" N TYR L 155 " --> pdb=" O TRP L 163 " (cutoff:3.500A)
removed outlier: 3.621A pdb=" N ARG L 200 " --> pdb=" O GLN L 154 " (cutoff:3.500A)
removed outlier: 3.657A pdb=" N ARG L 156 " --> pdb=" O PHE L 198 " (cutoff:3.500A)
removed outlier: 4.371A pdb=" N PHE L 198 " --> pdb=" O ARG L 156 " (cutoff:3.500A)
Processing sheet with id=AC7, first strand: chain 'M' and resid 194 through 196
removed outlier: 3.922A pdb=" N ILE M 194 " --> pdb=" O ILE M 133 " (cutoff:3.500A)
removed outlier: 3.505A pdb=" N SER M 196 " --> pdb=" O LYS M 131 " (cutoff:3.500A)
removed outlier: 4.967A pdb=" N LEU M 217 " --> pdb=" O SER M 134 " (cutoff:3.500A)
Processing sheet with id=AC8, first strand: chain 'M' and resid 163 through 164
removed outlier: 3.905A pdb=" N TRP M 163 " --> pdb=" O TYR M 155 " (cutoff:3.500A)
removed outlier: 3.574A pdb=" N TYR M 155 " --> pdb=" O TRP M 163 " (cutoff:3.500A)
removed outlier: 3.616A pdb=" N ARG M 200 " --> pdb=" O GLN M 154 " (cutoff:3.500A)
removed outlier: 3.656A pdb=" N ARG M 156 " --> pdb=" O PHE M 198 " (cutoff:3.500A)
removed outlier: 4.372A pdb=" N PHE M 198 " --> pdb=" O ARG M 156 " (cutoff:3.500A)
Processing sheet with id=AC9, first strand: chain 'N' and resid 194 through 196
removed outlier: 3.923A pdb=" N ILE N 194 " --> pdb=" O ILE N 133 " (cutoff:3.500A)
removed outlier: 3.506A pdb=" N SER N 196 " --> pdb=" O LYS N 131 " (cutoff:3.500A)
removed outlier: 4.966A pdb=" N LEU N 217 " --> pdb=" O SER N 134 " (cutoff:3.500A)
Processing sheet with id=AD1, first strand: chain 'N' and resid 163 through 164
removed outlier: 3.906A pdb=" N TRP N 163 " --> pdb=" O TYR N 155 " (cutoff:3.500A)
removed outlier: 3.573A pdb=" N TYR N 155 " --> pdb=" O TRP N 163 " (cutoff:3.500A)
removed outlier: 3.615A pdb=" N ARG N 200 " --> pdb=" O GLN N 154 " (cutoff:3.500A)
removed outlier: 3.656A pdb=" N ARG N 156 " --> pdb=" O PHE N 198 " (cutoff:3.500A)
removed outlier: 4.373A pdb=" N PHE N 198 " --> pdb=" O ARG N 156 " (cutoff:3.500A)
Processing sheet with id=AD2, first strand: chain 'O' and resid 194 through 196
removed outlier: 3.921A pdb=" N ILE O 194 " --> pdb=" O ILE O 133 " (cutoff:3.500A)
removed outlier: 3.505A pdb=" N SER O 196 " --> pdb=" O LYS O 131 " (cutoff:3.500A)
removed outlier: 4.966A pdb=" N LEU O 217 " --> pdb=" O SER O 134 " (cutoff:3.500A)
Processing sheet with id=AD3, first strand: chain 'O' and resid 163 through 164
removed outlier: 3.890A pdb=" N TRP O 163 " --> pdb=" O TYR O 155 " (cutoff:3.500A)
removed outlier: 3.555A pdb=" N TYR O 155 " --> pdb=" O TRP O 163 " (cutoff:3.500A)
removed outlier: 3.619A pdb=" N ARG O 200 " --> pdb=" O GLN O 154 " (cutoff:3.500A)
removed outlier: 3.655A pdb=" N ARG O 156 " --> pdb=" O PHE O 198 " (cutoff:3.500A)
removed outlier: 4.370A pdb=" N PHE O 198 " --> pdb=" O ARG O 156 " (cutoff:3.500A)
Processing sheet with id=AD4, first strand: chain 'P' and resid 194 through 196
removed outlier: 3.918A pdb=" N ILE P 194 " --> pdb=" O ILE P 133 " (cutoff:3.500A)
removed outlier: 3.506A pdb=" N SER P 196 " --> pdb=" O LYS P 131 " (cutoff:3.500A)
removed outlier: 4.968A pdb=" N LEU P 217 " --> pdb=" O SER P 134 " (cutoff:3.500A)
Processing sheet with id=AD5, first strand: chain 'P' and resid 163 through 164
removed outlier: 3.897A pdb=" N TRP P 163 " --> pdb=" O TYR P 155 " (cutoff:3.500A)
removed outlier: 3.561A pdb=" N TYR P 155 " --> pdb=" O TRP P 163 " (cutoff:3.500A)
removed outlier: 3.618A pdb=" N ARG P 200 " --> pdb=" O GLN P 154 " (cutoff:3.500A)
removed outlier: 3.654A pdb=" N ARG P 156 " --> pdb=" O PHE P 198 " (cutoff:3.500A)
removed outlier: 4.369A pdb=" N PHE P 198 " --> pdb=" O ARG P 156 " (cutoff:3.500A)
64 hydrogen bonds defined for protein.
144 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: 12.28
Time building geometry restraints manager: 30.34 seconds
NOTE: a complete listing of the restraints can be obtained by requesting
output of .geo file.
Histogram of bond lengths:
0.84 - 1.03: 19984
1.03 - 1.23: 80
1.23 - 1.42: 9376
1.42 - 1.62: 11744
1.62 - 1.81: 144
Bond restraints: 41328
Sorted by residual:
bond pdb=" N GLY I 140 "
pdb=" CA GLY I 140 "
ideal model delta sigma weight residual
1.445 1.452 -0.007 8.30e-03 1.45e+04 7.43e-01
bond pdb=" N GLY H 140 "
pdb=" CA GLY H 140 "
ideal model delta sigma weight residual
1.445 1.452 -0.007 8.30e-03 1.45e+04 7.33e-01
bond pdb=" N GLY N 140 "
pdb=" CA GLY N 140 "
ideal model delta sigma weight residual
1.445 1.452 -0.007 8.30e-03 1.45e+04 7.09e-01
bond pdb=" N GLY P 140 "
pdb=" CA GLY P 140 "
ideal model delta sigma weight residual
1.445 1.451 -0.007 8.30e-03 1.45e+04 6.62e-01
bond pdb=" N GLY M 140 "
pdb=" CA GLY M 140 "
ideal model delta sigma weight residual
1.445 1.451 -0.007 8.30e-03 1.45e+04 6.47e-01
... (remaining 41323 not shown)
Histogram of bond angle deviations from ideal:
100.84 - 107.46: 1428
107.46 - 114.09: 47955
114.09 - 120.72: 12753
120.72 - 127.35: 11768
127.35 - 133.97: 384
Bond angle restraints: 74288
Sorted by residual:
angle pdb=" N TRP C 92 "
pdb=" CA TRP C 92 "
pdb=" C TRP C 92 "
ideal model delta sigma weight residual
114.56 110.93 3.63 1.27e+00 6.20e-01 8.15e+00
angle pdb=" N TRP E 92 "
pdb=" CA TRP E 92 "
pdb=" C TRP E 92 "
ideal model delta sigma weight residual
114.56 110.93 3.63 1.27e+00 6.20e-01 8.15e+00
angle pdb=" N TRP H 92 "
pdb=" CA TRP H 92 "
pdb=" C TRP H 92 "
ideal model delta sigma weight residual
114.56 110.94 3.62 1.27e+00 6.20e-01 8.14e+00
angle pdb=" N TRP L 92 "
pdb=" CA TRP L 92 "
pdb=" C TRP L 92 "
ideal model delta sigma weight residual
114.56 110.96 3.60 1.27e+00 6.20e-01 8.03e+00
angle pdb=" N TRP P 92 "
pdb=" CA TRP P 92 "
pdb=" C TRP P 92 "
ideal model delta sigma weight residual
114.56 110.97 3.59 1.27e+00 6.20e-01 8.00e+00
... (remaining 74283 not shown)
Histogram of dihedral angle deviations from ideal:
0.00 - 8.93: 15946
8.93 - 17.86: 584
17.86 - 26.79: 158
26.79 - 35.73: 96
35.73 - 44.66: 16
Dihedral angle restraints: 16800
sinusoidal: 7744
harmonic: 9056
Sorted by residual:
dihedral pdb=" SG CYS H 63 "
pdb=" CB CYS H 219 "
pdb=" SG CYS H 219 "
pdb=" CA CYS H 219 "
ideal model delta sinusoidal sigma weight residual
-73.00 -117.66 44.66 1 2.00e+01 2.50e-03 6.93e+00
dihedral pdb=" SG CYS E 63 "
pdb=" CB CYS E 219 "
pdb=" SG CYS E 219 "
pdb=" CA CYS E 219 "
ideal model delta sinusoidal sigma weight residual
-73.00 -117.65 44.65 1 2.00e+01 2.50e-03 6.93e+00
dihedral pdb=" SG CYS A 63 "
pdb=" CB CYS A 219 "
pdb=" SG CYS A 219 "
pdb=" CA CYS A 219 "
ideal model delta sinusoidal sigma weight residual
-73.00 -117.64 44.64 1 2.00e+01 2.50e-03 6.92e+00
... (remaining 16797 not shown)
Histogram of chiral volume deviations from ideal:
0.000 - 0.026: 1919
0.026 - 0.052: 717
0.052 - 0.079: 68
0.079 - 0.105: 172
0.105 - 0.131: 148
Chirality restraints: 3024
Sorted by residual:
chirality pdb=" CA ILE E 125 "
pdb=" N ILE E 125 "
pdb=" C ILE E 125 "
pdb=" CB ILE E 125 "
both_signs ideal model delta sigma weight residual
False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.29e-01
chirality pdb=" CA ILE D 125 "
pdb=" N ILE D 125 "
pdb=" C ILE D 125 "
pdb=" CB ILE D 125 "
both_signs ideal model delta sigma weight residual
False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.29e-01
chirality pdb=" CA ILE O 125 "
pdb=" N ILE O 125 "
pdb=" C ILE O 125 "
pdb=" CB ILE O 125 "
both_signs ideal model delta sigma weight residual
False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.24e-01
... (remaining 3021 not shown)
Planarity restraints: 6064
Sorted by residual:
delta sigma weight rms_deltas residual
plane pdb=" CG GLN G 187 " 0.142 2.00e-02 2.50e+03 1.59e-01 3.81e+02
pdb=" CD GLN G 187 " -0.008 2.00e-02 2.50e+03
pdb=" OE1 GLN G 187 " -0.139 2.00e-02 2.50e+03
pdb=" NE2 GLN G 187 " 0.002 2.00e-02 2.50e+03
pdb="HE21 GLN G 187 " -0.236 2.00e-02 2.50e+03
pdb="HE22 GLN G 187 " 0.239 2.00e-02 2.50e+03
delta sigma weight rms_deltas residual
plane pdb=" CG GLN L 187 " 0.142 2.00e-02 2.50e+03 1.59e-01 3.80e+02
pdb=" CD GLN L 187 " -0.009 2.00e-02 2.50e+03
pdb=" OE1 GLN L 187 " -0.139 2.00e-02 2.50e+03
pdb=" NE2 GLN L 187 " 0.002 2.00e-02 2.50e+03
pdb="HE21 GLN L 187 " -0.236 2.00e-02 2.50e+03
pdb="HE22 GLN L 187 " 0.239 2.00e-02 2.50e+03
delta sigma weight rms_deltas residual
plane pdb=" CG GLN D 187 " 0.142 2.00e-02 2.50e+03 1.59e-01 3.80e+02
pdb=" CD GLN D 187 " -0.008 2.00e-02 2.50e+03
pdb=" OE1 GLN D 187 " -0.139 2.00e-02 2.50e+03
pdb=" NE2 GLN D 187 " 0.002 2.00e-02 2.50e+03
pdb="HE21 GLN D 187 " -0.236 2.00e-02 2.50e+03
pdb="HE22 GLN D 187 " 0.239 2.00e-02 2.50e+03
... (remaining 6061 not shown)
Histogram of nonbonded interaction distances:
1.72 - 2.30: 6348
2.30 - 2.87: 91425
2.87 - 3.45: 91171
3.45 - 4.02: 124081
4.02 - 4.60: 190048
Nonbonded interactions: 503073
Sorted by model distance:
nonbonded pdb=" O ALA E 98 "
pdb=" HE ARG E 102 "
model vdw
1.720 1.850
nonbonded pdb=" O ALA H 98 "
pdb=" HE ARG H 102 "
model vdw
1.721 1.850
nonbonded pdb=" O ALA M 98 "
pdb=" HE ARG M 102 "
model vdw
1.721 1.850
nonbonded pdb=" O ALA C 98 "
pdb=" HE ARG C 102 "
model vdw
1.721 1.850
nonbonded pdb=" O ALA P 98 "
pdb=" HE ARG P 102 "
model vdw
1.721 1.850
... (remaining 503068 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'
}
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 112 5.16 5
C 13216 2.51 5
N 3600 2.21 5
O 3792 1.98 5
H 20032 0.53 5
sf(0) = scattering factor at diffraction angle 0.
Adjust number of macro_cycles
Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
Set random seed: 0.000
Set model cs if undefined: 0.000
Decide on map wrapping: 0.000
Normalize map: mean=0, sd=1: 0.950
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: 0.560
Extract box with map and model: 7.640
Check model and map are aligned: 0.580
Convert atoms to be neutral: 0.350
Process input model: 110.520
Find NCS groups from input model: 1.970
Set up NCS constraints: 0.240
Set refine NCS operators: 0.000
Set scattering table: 0.010
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:2.740
Set ADP refinement strategy: 0.000
Make a string to write initial .geo file:0.000
Internal consistency checks: 0.000
Total: 125.570
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.2746
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 : 0.001 0.013 21296 Z= 0.099
Angle : 0.360 3.625 28928 Z= 0.217
Chirality : 0.041 0.131 3024
Planarity : 0.001 0.011 3680
Dihedral : 4.916 31.060 7792
Min Nonbonded Distance : 2.309
Molprobity Statistics.
All-atom Clashscore : 3.73
Ramachandran Plot:
Outliers : 2.58 %
Allowed : 17.70 %
Favored : 79.72 %
Rotamer Outliers : 0.00 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: -5.61 (0.12), residues: 2480
helix: None (None), residues: 0
sheet: -4.79 (0.17), residues: 160
loop : -4.14 (0.10), residues: 2320
*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
4960 Ramachandran restraints generated.
2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
4960 Ramachandran restraints generated.
2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Evaluate side-chains
782 residues out of total 2288 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 782
time to evaluate : 3.238
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
outliers start: 0
outliers final: 0
residues processed: 782
average time/residue: 0.8855
time to fit residues: 1003.3569
Evaluate side-chains
534 residues out of total 2288 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 534
time to evaluate : 3.259
Switching outliers to nearest non-outliers
outliers start: 0
outliers final: 0
residues processed: 0
time to fit residues: 4.3233
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 240
random chunks:
chunk 202 optimal weight: 4.9990
chunk 181 optimal weight: 9.9990
chunk 100 optimal weight: 8.9990
chunk 62 optimal weight: 4.9990
chunk 122 optimal weight: 5.9990
chunk 97 optimal weight: 5.9990
chunk 188 optimal weight: 6.9990
chunk 72 optimal weight: 5.9990
chunk 114 optimal weight: 0.9990
chunk 140 optimal weight: 5.9990
chunk 217 optimal weight: 7.9990
overall best weight: 4.5990
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 85 ASN
A 187 GLN
B 187 GLN
C 187 GLN
D 187 GLN
E 187 GLN
F 187 GLN
G 85 ASN
G 187 GLN
H 187 GLN
I 187 GLN
J 121 GLN
J 187 GLN
K 187 GLN
L 187 GLN
M 187 GLN
N 187 GLN
O 187 GLN
P 187 GLN
Total number of N/Q/H flips: 19
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4008
moved from start: 0.6752
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
Bond : 0.007 0.062 21296 Z= 0.454
Angle : 0.884 8.926 28928 Z= 0.468
Chirality : 0.048 0.191 3024
Planarity : 0.009 0.122 3680
Dihedral : 5.263 23.287 2784
Min Nonbonded Distance : 1.804
Molprobity Statistics.
All-atom Clashscore : 28.16
Ramachandran Plot:
Outliers : 1.29 %
Allowed : 11.53 %
Favored : 87.18 %
Rotamer Outliers : 0.00 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: -4.80 (0.13), residues: 2480
helix: None (None), residues: 0
sheet: -2.37 (0.19), residues: 160
loop : -3.69 (0.11), residues: 2320
*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
4960 Ramachandran restraints generated.
2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
4960 Ramachandran restraints generated.
2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Evaluate side-chains
688 residues out of total 2288 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 688
time to evaluate : 3.385
Fit side-chains
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revert: symmetry clash
revert: symmetry clash
outliers start: 0
outliers final: 0
residues processed: 688
average time/residue: 0.8043
time to fit residues: 806.6735
Evaluate side-chains
528 residues out of total 2288 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 528
time to evaluate : 3.359
Switching outliers to nearest non-outliers
outliers start: 0
outliers final: 0
residues processed: 0
time to fit residues: 4.2588
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 240
random chunks:
chunk 121 optimal weight: 7.9990
chunk 67 optimal weight: 0.8980
chunk 181 optimal weight: 6.9990
chunk 148 optimal weight: 6.9990
chunk 60 optimal weight: 1.9990
chunk 218 optimal weight: 6.9990
chunk 235 optimal weight: 8.9990
chunk 194 optimal weight: 0.7980
chunk 216 optimal weight: 5.9990
chunk 74 optimal weight: 0.7980
chunk 175 optimal weight: 6.9990
overall best weight: 2.0984
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
B 207 HIS
D 207 HIS
J 207 HIS
K 124 GLN
L 207 HIS
N 124 GLN
N 207 HIS
O 124 GLN
Total number of N/Q/H flips: 8
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4061
moved from start: 0.7914
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
Bond : 0.004 0.148 21296 Z= 0.236
Angle : 0.530 17.732 28928 Z= 0.276
Chirality : 0.041 0.190 3024
Planarity : 0.005 0.080 3680
Dihedral : 4.113 17.344 2784
Min Nonbonded Distance : 2.078
Molprobity Statistics.
All-atom Clashscore : 14.13
Ramachandran Plot:
Outliers : 1.25 %
Allowed : 11.09 %
Favored : 87.66 %
Rotamer Outliers : 0.04 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: -4.47 (0.13), residues: 2480
helix: None (None), residues: 0
sheet: -2.07 (0.20), residues: 224
loop : -3.46 (0.11), residues: 2256
*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
4960 Ramachandran restraints generated.
2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
4960 Ramachandran restraints generated.
2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Evaluate side-chains
646 residues out of total 2288 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 1
poor density : 645
time to evaluate : 3.337
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
outliers start: 1
outliers final: 0
residues processed: 646
average time/residue: 0.7705
time to fit residues: 730.9093
Evaluate side-chains
493 residues out of total 2288 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 493
time to evaluate : 3.448
Switching outliers to nearest non-outliers
outliers start: 0
outliers final: 0
residues processed: 0
time to fit residues: 4.4113
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 240
random chunks:
chunk 215 optimal weight: 1.9990
chunk 164 optimal weight: 5.9990
chunk 113 optimal weight: 7.9990
chunk 24 optimal weight: 1.9990
chunk 104 optimal weight: 0.2980
chunk 146 optimal weight: 9.9990
chunk 219 optimal weight: 5.9990
chunk 231 optimal weight: 4.9990
chunk 114 optimal weight: 1.9990
chunk 207 optimal weight: 4.9990
chunk 62 optimal weight: 7.9990
overall best weight: 2.2588
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 207 HIS
F 207 HIS
H 85 ASN
H 207 HIS
I 104 ASN
N 85 ASN
N 124 GLN
P 85 ASN
Total number of N/Q/H flips: 8
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4292
moved from start: 0.9202
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
Bond : 0.004 0.123 21296 Z= 0.227
Angle : 0.549 20.353 28928 Z= 0.286
Chirality : 0.041 0.179 3024
Planarity : 0.004 0.068 3680
Dihedral : 4.287 18.102 2784
Min Nonbonded Distance : 1.878
Molprobity Statistics.
All-atom Clashscore : 15.87
Ramachandran Plot:
Outliers : 0.69 %
Allowed : 10.52 %
Favored : 88.79 %
Rotamer Outliers : 0.04 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: -4.17 (0.14), residues: 2480
helix: None (None), residues: 0
sheet: -0.96 (0.23), residues: 224
loop : -3.35 (0.11), residues: 2256
*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
4960 Ramachandran restraints generated.
2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
4960 Ramachandran restraints generated.
2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Evaluate side-chains
640 residues out of total 2288 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 1
poor density : 639
time to evaluate : 3.521
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
outliers start: 1
outliers final: 0
residues processed: 640
average time/residue: 0.7874
time to fit residues: 756.2485
Evaluate side-chains
538 residues out of total 2288 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 538
time to evaluate : 3.364
Switching outliers to nearest non-outliers
outliers start: 0
outliers final: 0
residues processed: 0
time to fit residues: 4.2958
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 240
random chunks:
chunk 193 optimal weight: 5.9990
chunk 131 optimal weight: 10.0000
chunk 3 optimal weight: 4.9990
chunk 172 optimal weight: 5.9990
chunk 95 optimal weight: 9.9990
chunk 197 optimal weight: 6.9990
chunk 160 optimal weight: 1.9990
chunk 0 optimal weight: 7.9990
chunk 118 optimal weight: 0.9980
chunk 208 optimal weight: 4.9990
chunk 58 optimal weight: 1.9990
overall best weight: 2.9988
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
B 207 HIS
** D 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 207 HIS
F 207 HIS
G 124 GLN
H 124 GLN
** J 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
J 207 HIS
L 124 GLN
** M 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Total number of N/Q/H flips: 7
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4313
moved from start: 0.9360
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
Bond : 0.014 1.175 21296 Z= 1.053
Angle : 1.137 95.069 28928 Z= 0.477
Chirality : 0.043 0.343 3024
Planarity : 0.005 0.082 3680
Dihedral : 4.334 16.988 2784
Min Nonbonded Distance : 1.880
Molprobity Statistics.
All-atom Clashscore : 20.70
Ramachandran Plot:
Outliers : 0.69 %
Allowed : 11.17 %
Favored : 88.15 %
Rotamer Outliers : 0.04 %
Cbeta Deviations : 0.09 %
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: -4.12 (0.14), residues: 2480
helix: None (None), residues: 0
sheet: -0.78 (0.24), residues: 224
loop : -3.33 (0.11), residues: 2256
*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
4960 Ramachandran restraints generated.
2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
4960 Ramachandran restraints generated.
2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Evaluate side-chains
620 residues out of total 2288 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 1
poor density : 619
time to evaluate : 3.298
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
outliers start: 1
outliers final: 0
residues processed: 620
average time/residue: 0.7399
time to fit residues: 685.2583
Evaluate side-chains
532 residues out of total 2288 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 532
time to evaluate : 3.392
Switching outliers to nearest non-outliers
outliers start: 0
outliers final: 0
residues processed: 0
time to fit residues: 4.3188
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 240
random chunks:
chunk 78 optimal weight: 20.0000
chunk 208 optimal weight: 0.7980
chunk 45 optimal weight: 6.9990
chunk 136 optimal weight: 0.0570
chunk 57 optimal weight: 7.9990
chunk 232 optimal weight: 6.9990
chunk 192 optimal weight: 2.9990
chunk 107 optimal weight: 7.9990
chunk 19 optimal weight: 8.9990
chunk 76 optimal weight: 2.9990
chunk 121 optimal weight: 5.9990
overall best weight: 2.5704
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 99 ASN
B 162 ASN
B 207 HIS
D 207 HIS
F 207 HIS
I 162 ASN
** I 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
K 124 GLN
M 104 ASN
M 187 GLN
O 104 ASN
Total number of N/Q/H flips: 10
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4320
moved from start: 0.9425
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
Bond : 0.017 1.221 21296 Z= 1.105
Angle : 1.335 100.957 28928 Z= 0.539
Chirality : 0.043 0.286 3024
Planarity : 0.005 0.067 3680
Dihedral : 4.351 16.699 2784
Min Nonbonded Distance : 1.891
Molprobity Statistics.
All-atom Clashscore : 22.15
Ramachandran Plot:
Outliers : 0.65 %
Allowed : 11.65 %
Favored : 87.70 %
Rotamer Outliers : 0.13 %
Cbeta Deviations : 0.09 %
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: -4.11 (0.14), residues: 2480
helix: None (None), residues: 0
sheet: -0.70 (0.24), residues: 224
loop : -3.33 (0.11), residues: 2256
*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
4960 Ramachandran restraints generated.
2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
4960 Ramachandran restraints generated.
2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Evaluate side-chains
613 residues out of total 2288 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 3
poor density : 610
time to evaluate : 3.348
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
outliers start: 3
outliers final: 1
residues processed: 611
average time/residue: 0.7376
time to fit residues: 673.1525
Evaluate side-chains
530 residues out of total 2288 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 1
poor density : 529
time to evaluate : 3.349
Switching outliers to nearest non-outliers
outliers start: 1
outliers final: 0
residues processed: 1
average time/residue: 0.4164
time to fit residues: 5.0216
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 240
random chunks:
chunk 223 optimal weight: 5.9990
chunk 26 optimal weight: 10.0000
chunk 132 optimal weight: 1.9990
chunk 169 optimal weight: 8.9990
chunk 131 optimal weight: 10.0000
chunk 195 optimal weight: 0.3980
chunk 129 optimal weight: 4.9990
chunk 231 optimal weight: 4.9990
chunk 144 optimal weight: 3.9990
chunk 141 optimal weight: 1.9990
chunk 106 optimal weight: 7.9990
overall best weight: 2.6788
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
B 162 ASN
B 207 HIS
D 207 HIS
** E 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
J 104 ASN
M 104 ASN
N 187 GLN
O 104 ASN
Total number of N/Q/H flips: 7
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4319
moved from start: 0.9443
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
Bond : 0.021 1.149 21296 Z= 1.422
Angle : 1.561 99.201 28928 Z= 0.622
Chirality : 0.044 0.351 3024
Planarity : 0.005 0.074 3680
Dihedral : 4.343 16.566 2784
Min Nonbonded Distance : 1.892
Molprobity Statistics.
All-atom Clashscore : 23.20
Ramachandran Plot:
Outliers : 0.65 %
Allowed : 11.81 %
Favored : 87.54 %
Rotamer Outliers : 0.04 %
Cbeta Deviations : 0.04 %
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: -4.11 (0.14), residues: 2480
helix: None (None), residues: 0
sheet: -0.67 (0.24), residues: 224
loop : -3.33 (0.11), residues: 2256
*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
4960 Ramachandran restraints generated.
2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
4960 Ramachandran restraints generated.
2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Evaluate side-chains
606 residues out of total 2288 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 1
poor density : 605
time to evaluate : 3.815
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
outliers start: 1
outliers final: 0
residues processed: 605
average time/residue: 0.7385
time to fit residues: 666.7414
Evaluate side-chains
527 residues out of total 2288 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 527
time to evaluate : 3.329
Switching outliers to nearest non-outliers
outliers start: 0
outliers final: 0
residues processed: 0
time to fit residues: 4.3402
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 240
random chunks:
chunk 143 optimal weight: 0.8980
chunk 92 optimal weight: 5.9990
chunk 138 optimal weight: 20.0000
chunk 69 optimal weight: 1.9990
chunk 45 optimal weight: 5.9990
chunk 44 optimal weight: 0.9990
chunk 147 optimal weight: 5.9990
chunk 157 optimal weight: 0.7980
chunk 114 optimal weight: 1.9990
chunk 21 optimal weight: 3.9990
chunk 181 optimal weight: 0.8980
overall best weight: 1.1184
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
B 162 ASN
B 207 HIS
D 207 HIS
** E 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
J 104 ASN
K 124 GLN
M 104 ASN
O 104 ASN
P 104 ASN
Total number of N/Q/H flips: 8
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4322
moved from start: 0.9464
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
Bond : 0.020 1.149 21296 Z= 1.421
Angle : 1.567 99.201 28928 Z= 0.627
Chirality : 0.044 0.351 3024
Planarity : 0.005 0.070 3680
Dihedral : 4.343 16.566 2784
Min Nonbonded Distance : 1.587
Molprobity Statistics.
All-atom Clashscore : 23.55
Ramachandran Plot:
Outliers : 0.65 %
Allowed : 11.81 %
Favored : 87.54 %
Rotamer Outliers : 0.04 %
Cbeta Deviations : 0.04 %
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: -4.11 (0.14), residues: 2480
helix: None (None), residues: 0
sheet: -0.67 (0.24), residues: 224
loop : -3.33 (0.11), residues: 2256
*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
4960 Ramachandran restraints generated.
2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
4960 Ramachandran restraints generated.
2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Evaluate side-chains
605 residues out of total 2288 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 1
poor density : 604
time to evaluate : 3.490
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
outliers start: 1
outliers final: 0
residues processed: 604
average time/residue: 0.7539
time to fit residues: 681.6184
Evaluate side-chains
528 residues out of total 2288 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 528
time to evaluate : 3.298
Switching outliers to nearest non-outliers
outliers start: 0
outliers final: 0
residues processed: 0
time to fit residues: 4.3334
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 240
random chunks:
chunk 210 optimal weight: 4.9990
chunk 221 optimal weight: 8.9990
chunk 202 optimal weight: 1.9990
chunk 215 optimal weight: 3.9990
chunk 129 optimal weight: 6.9990
chunk 93 optimal weight: 8.9990
chunk 169 optimal weight: 10.0000
chunk 66 optimal weight: 3.9990
chunk 194 optimal weight: 5.9990
chunk 203 optimal weight: 4.9990
chunk 214 optimal weight: 0.6980
overall best weight: 3.1388
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
B 162 ASN
B 207 HIS
D 207 HIS
** E 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
J 104 ASN
K 124 GLN
M 104 ASN
O 104 ASN
P 104 ASN
Total number of N/Q/H flips: 8
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4322
moved from start: 0.9465
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
Bond : 0.020 1.149 21296 Z= 1.421
Angle : 1.562 99.201 28928 Z= 0.628
Chirality : 0.044 0.351 3024
Planarity : 0.006 0.150 3680
Dihedral : 4.343 16.566 2784
Min Nonbonded Distance : 1.587
Molprobity Statistics.
All-atom Clashscore : 23.57
Ramachandran Plot:
Outliers : 0.65 %
Allowed : 11.81 %
Favored : 87.54 %
Rotamer Outliers : 0.04 %
Cbeta Deviations : 0.04 %
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: -4.11 (0.14), residues: 2480
helix: None (None), residues: 0
sheet: -0.67 (0.24), residues: 224
loop : -3.33 (0.11), residues: 2256
*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
4960 Ramachandran restraints generated.
2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
4960 Ramachandran restraints generated.
2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Evaluate side-chains
605 residues out of total 2288 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 1
poor density : 604
time to evaluate : 3.370
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
outliers start: 1
outliers final: 0
residues processed: 604
average time/residue: 0.7427
time to fit residues: 669.4475
Evaluate side-chains
528 residues out of total 2288 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 528
time to evaluate : 3.310
Switching outliers to nearest non-outliers
outliers start: 0
outliers final: 0
residues processed: 0
time to fit residues: 4.1921
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 240
random chunks:
chunk 141 optimal weight: 4.9990
chunk 227 optimal weight: 5.9990
chunk 139 optimal weight: 4.9990
chunk 108 optimal weight: 20.0000
chunk 158 optimal weight: 4.9990
chunk 239 optimal weight: 4.9990
chunk 220 optimal weight: 4.9990
chunk 190 optimal weight: 0.9990
chunk 19 optimal weight: 6.9990
chunk 147 optimal weight: 4.9990
chunk 116 optimal weight: 0.5980
overall best weight: 3.3188
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
B 162 ASN
B 207 HIS
D 207 HIS
** E 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
J 104 ASN
K 124 GLN
M 104 ASN
O 104 ASN
P 104 ASN
Total number of N/Q/H flips: 8
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4322
moved from start: 0.9465
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
Bond : 0.020 1.149 21296 Z= 1.421
Angle : 1.562 99.201 28928 Z= 0.628
Chirality : 0.044 0.351 3024
Planarity : 0.006 0.150 3680
Dihedral : 4.343 16.566 2784
Min Nonbonded Distance : 1.587
Molprobity Statistics.
All-atom Clashscore : 23.57
Ramachandran Plot:
Outliers : 0.65 %
Allowed : 11.81 %
Favored : 87.54 %
Rotamer Outliers : 0.04 %
Cbeta Deviations : 0.04 %
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: -4.11 (0.14), residues: 2480
helix: None (None), residues: 0
sheet: -0.67 (0.24), residues: 224
loop : -3.33 (0.11), residues: 2256
********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
4960 Ramachandran restraints generated.
2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
4960 Ramachandran restraints generated.
2480 Oldfield, 0 Emsley, 2480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Residue TYR 177 is missing expected H atoms. Skipping.
Evaluate side-chains
605 residues out of total 2288 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 1
poor density : 604
time to evaluate : 3.184
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
outliers start: 1
outliers final: 0
residues processed: 604
average time/residue: 0.7359
time to fit residues: 665.8898
Evaluate side-chains
528 residues out of total 2288 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 528
time to evaluate : 3.368
Switching outliers to nearest non-outliers
outliers start: 0
outliers final: 0
residues processed: 0
time to fit residues: 4.3280
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 240
random chunks:
chunk 151 optimal weight: 2.9990
chunk 202 optimal weight: 2.9990
chunk 58 optimal weight: 0.8980
chunk 175 optimal weight: 2.9990
chunk 28 optimal weight: 0.6980
chunk 52 optimal weight: 0.9990
chunk 190 optimal weight: 0.9990
chunk 79 optimal weight: 8.9990
chunk 195 optimal weight: 0.8980
chunk 24 optimal weight: 2.9990
chunk 35 optimal weight: 5.9990
overall best weight: 0.8984
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
B 162 ASN
B 207 HIS
D 207 HIS
** E 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
J 104 ASN
K 124 GLN
M 104 ASN
O 104 ASN
P 104 ASN
Total number of N/Q/H flips: 8
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4887 r_free = 0.4887 target = 0.198210 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4588 r_free = 0.4588 target = 0.164297 restraints weight = 154094.248|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4633 r_free = 0.4633 target = 0.168980 restraints weight = 108903.958|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4665 r_free = 0.4665 target = 0.172681 restraints weight = 83832.682|
|-----------------------------------------------------------------------------|
r_work (final): 0.4627
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6385
moved from start: 0.9465
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
Bond : 0.020 1.149 21296 Z= 1.421
Angle : 1.562 99.201 28928 Z= 0.628
Chirality : 0.044 0.351 3024
Planarity : 0.006 0.150 3680
Dihedral : 4.343 16.566 2784
Min Nonbonded Distance : 1.587
Molprobity Statistics.
All-atom Clashscore : 23.57
Ramachandran Plot:
Outliers : 0.65 %
Allowed : 11.81 %
Favored : 87.54 %
Rotamer Outliers : 0.04 %
Cbeta Deviations : 0.04 %
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: -4.11 (0.14), residues: 2480
helix: None (None), residues: 0
sheet: -0.67 (0.24), residues: 224
loop : -3.33 (0.11), residues: 2256
===============================================================================
Job complete
usr+sys time: 11491.73 seconds
wall clock time: 203 minutes 8.49 seconds (12188.49 seconds total)