Starting phenix.real_space_refine (version: dev)
on Mon Sep 6 08:40:11 2021 by dcliebschner
===============================================================================
Processing files:
-------------------------------------------------------------------------------
Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5n6w_3595/09_2021/5n6w_3595.pdb
Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5n6w_3595/09_2021/5n6w_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_3595/09_2021/5n6w_3595.map"
default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5n6w_3595/09_2021/5n6w_3595.map"
model {
file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5n6w_3595/09_2021/5n6w_3595.pdb"
}
default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5n6w_3595/09_2021/5n6w_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
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-4346/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: 18.48, per 1000 atoms: 0.45
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'
}
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
Amimo 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: 32.57
Conformation dependent library (CDL) restraints added in 3.5 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: 0.72
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: 13.49
Time building geometry restraints manager: 33.59 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.
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
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: 0.750
Set stop_for_unknowns flag: 0.000
Assert model is a single copy model: 0.000
Construct map_model_manager: 0.070
Extract box with map and model: 7.750
Check model and map are aligned: 0.630
Convert atoms to be neutral: 0.380
Process input model: 117.290
Set up NCS constraints: 0.240
Set refine NCS operators: 0.000
Set scattering table: 0.020
Adjust number of macro_cycles: 0.000
Reset NCS operators: 0.000
Extract rigid body selections: 0.000
Check and reset occupancies: 0.010
Load rotamer database and sin/cos tables:2.160
Set ADP refinement strategy: 0.000
Internal consistency checks: 0.000
Total: 129.300
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.2753
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 : 3.773
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: 0.8504
time to fit residues: 956.2082
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: 4.1786
-------------------------------------------------------------------------------
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
** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 85 ASN
B 187 GLN
** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 85 ASN
** C 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 187 GLN
D 187 GLN
** D 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 85 ASN
E 187 GLN
** E 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F 187 GLN
F 207 HIS
G 85 ASN
G 187 GLN
** G 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H 85 ASN
H 187 GLN
** H 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
I 85 ASN
I 187 GLN
** I 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
J 187 GLN
K 85 ASN
** K 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
K 187 GLN
** K 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
L 187 GLN
** L 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
M 85 ASN
M 187 GLN
** M 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
N 85 ASN
N 187 GLN
O 85 ASN
O 187 GLN
** O 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
P 85 ASN
P 187 GLN
** P 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
Total number of N/Q/H flips: 29
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4514
moved from start: 0.9474
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
Bond : 0.007 0.082 21296 Z= 0.467
Angle : 0.871 6.857 28928 Z= 0.471
Chirality : 0.047 0.198 3024
Planarity : 0.009 0.118 3680
Dihedral : 6.486 23.532 2784
Min Nonbonded Distance : 1.868
Molprobity Statistics.
All-atom Clashscore : 33.41
Ramachandran Plot:
Outliers : 1.29 %
Allowed : 13.71 %
Favored : 85.00 %
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: -5.05 (0.12), residues: 2480
helix: None (None), residues: 0
sheet: -2.82 (0.17), residues: 160
loop : -3.85 (0.10), 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
753 residues out of total 2288 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 1
poor density : 752
time to evaluate : 3.538
Fit side-chains
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outliers start: 1
outliers final: 1
residues processed: 752
average time/residue: 0.8227
time to fit residues: 914.8999
Evaluate side-chains
584 residues out of total 2288 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 1
poor density : 583
time to evaluate : 3.470
Switching outliers to nearest non-outliers
outliers start: 1
outliers final: 0
residues processed: 1
average time/residue: 0.4368
time to fit residues: 5.1099
-------------------------------------------------------------------------------
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: 6.9990
chunk 67 optimal weight: 3.9990
chunk 181 optimal weight: 3.9990
chunk 148 optimal weight: 3.9990
chunk 60 optimal weight: 7.9990
chunk 218 optimal weight: 0.9990
chunk 235 optimal weight: 8.9990
chunk 194 optimal weight: 3.9990
chunk 216 optimal weight: 4.9990
chunk 74 optimal weight: 4.9990
chunk 175 optimal weight: 7.9990
overall best weight: 3.3990
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
F 85 ASN
J 85 ASN
L 85 ASN
Total number of N/Q/H flips: 3
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4645
moved from start: 1.0720
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
Bond : 0.021 1.174 21296 Z= 1.521
Angle : 1.571 101.693 28928 Z= 0.605
Chirality : 0.044 0.204 3024
Planarity : 0.006 0.078 3680
Dihedral : 5.636 20.300 2784
Min Nonbonded Distance : 1.846
Molprobity Statistics.
All-atom Clashscore : 22.86
Ramachandran Plot:
Outliers : 1.29 %
Allowed : 12.94 %
Favored : 85.77 %
Rotamer Outliers : 0.35 %
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: -4.51 (0.14), residues: 2480
helix: None (None), residues: 0
sheet: -1.52 (0.21), residues: 224
loop : -3.57 (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
716 residues out of total 2288 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 8
poor density : 708
time to evaluate : 3.615
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
outliers start: 8
outliers final: 1
residues processed: 710
average time/residue: 0.8039
time to fit residues: 854.7305
Evaluate side-chains
572 residues out of total 2288 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 1
poor density : 571
time to evaluate : 3.518
Switching outliers to nearest non-outliers
outliers start: 1
outliers final: 0
residues processed: 1
average time/residue: 0.4411
time to fit residues: 5.3184
-------------------------------------------------------------------------------
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: 10.0000
chunk 164 optimal weight: 0.0000
chunk 113 optimal weight: 6.9990
chunk 24 optimal weight: 2.9990
chunk 104 optimal weight: 7.9990
chunk 146 optimal weight: 6.9990
chunk 219 optimal weight: 5.9990
chunk 231 optimal weight: 5.9990
chunk 114 optimal weight: 0.1980
chunk 207 optimal weight: 1.9990
chunk 62 optimal weight: 2.9990
overall best weight: 1.6390
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** A 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 207 HIS
** E 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
I 104 ASN
** J 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
J 207 HIS
L 207 HIS
M 104 ASN
N 104 ASN
** N 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
P 162 ASN
Total number of N/Q/H flips: 7
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4631
moved from start: 1.0961
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
Bond : 0.028 1.272 21296 Z= 2.005
Angle : 1.876 106.098 28928 Z= 0.726
Chirality : 0.045 0.322 3024
Planarity : 0.007 0.219 3680
Dihedral : 5.623 26.202 2784
Min Nonbonded Distance : 1.721
Molprobity Statistics.
All-atom Clashscore : 27.91
Ramachandran Plot:
Outliers : 0.73 %
Allowed : 13.99 %
Favored : 85.28 %
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: -4.57 (0.14), residues: 2480
helix: None (None), residues: 0
sheet: -3.37 (0.18), residues: 384
loop : -3.30 (0.12), residues: 2096
*********************** 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
644 residues out of total 2288 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 3
poor density : 641
time to evaluate : 3.621
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
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revert: symmetry clash
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revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
outliers start: 3
outliers final: 0
residues processed: 643
average time/residue: 0.7709
time to fit residues: 737.5096
Evaluate side-chains
549 residues out of total 2288 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 549
time to evaluate : 3.729
Switching outliers to nearest non-outliers
outliers start: 0
outliers final: 0
residues processed: 0
time to fit residues: 4.6956
-------------------------------------------------------------------------------
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: 0.9990
chunk 131 optimal weight: 3.9990
chunk 3 optimal weight: 20.0000
chunk 172 optimal weight: 0.8980
chunk 95 optimal weight: 10.0000
chunk 197 optimal weight: 9.9990
chunk 160 optimal weight: 0.5980
chunk 0 optimal weight: 2.9990
chunk 118 optimal weight: 1.9990
chunk 208 optimal weight: 2.9990
chunk 58 optimal weight: 7.9990
overall best weight: 1.4986
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** A 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 207 HIS
** E 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 124 GLN
I 162 ASN
I 207 HIS
J 207 HIS
M 104 ASN
O 162 ASN
P 162 ASN
Total number of N/Q/H flips: 8
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4603
moved from start: 1.1039
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
Bond : 0.025 1.270 21296 Z= 1.685
Angle : 1.790 106.100 28928 Z= 0.678
Chirality : 0.044 0.299 3024
Planarity : 0.008 0.189 3680
Dihedral : 5.572 22.290 2784
Min Nonbonded Distance : 1.570
Molprobity Statistics.
All-atom Clashscore : 26.93
Ramachandran Plot:
Outliers : 0.73 %
Allowed : 14.15 %
Favored : 85.12 %
Rotamer Outliers : 0.13 %
Cbeta Deviations : 0.21 %
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: -4.51 (0.14), residues: 2480
helix: None (None), residues: 0
sheet: -3.25 (0.19), residues: 384
loop : -3.27 (0.12), residues: 2096
*********************** 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
653 residues out of total 2288 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 3
poor density : 650
time to evaluate : 3.476
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
outliers start: 3
outliers final: 1
residues processed: 650
average time/residue: 0.7743
time to fit residues: 750.8492
Evaluate side-chains
553 residues out of total 2288 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 1
poor density : 552
time to evaluate : 3.353
Switching outliers to nearest non-outliers
outliers start: 1
outliers final: 0
residues processed: 1
average time/residue: 0.3931
time to fit residues: 4.9114
-------------------------------------------------------------------------------
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: 7.9990
chunk 208 optimal weight: 10.0000
chunk 45 optimal weight: 0.6980
chunk 136 optimal weight: 0.8980
chunk 57 optimal weight: 5.9990
chunk 232 optimal weight: 0.8980
chunk 192 optimal weight: 0.9990
chunk 107 optimal weight: 0.0670
chunk 19 optimal weight: 7.9990
chunk 76 optimal weight: 2.9990
chunk 121 optimal weight: 5.9990
overall best weight: 0.7120
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** A 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 162 ASN
B 207 HIS
** C 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 207 HIS
** E 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
I 162 ASN
I 207 HIS
** J 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
J 207 HIS
** K 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
M 104 ASN
M 162 ASN
M 207 HIS
P 162 ASN
Total number of N/Q/H flips: 10
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4597
moved from start: 1.1073
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
Bond : 0.028 1.201 21296 Z= 1.979
Angle : 2.033 106.100 28928 Z= 0.799
Chirality : 0.046 0.396 3024
Planarity : 0.008 0.172 3680
Dihedral : 5.563 21.354 2784
Min Nonbonded Distance : 1.889
Molprobity Statistics.
All-atom Clashscore : 28.65
Ramachandran Plot:
Outliers : 0.81 %
Allowed : 13.87 %
Favored : 85.32 %
Rotamer Outliers : 0.17 %
Cbeta Deviations : 0.21 %
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: -4.49 (0.14), residues: 2480
helix: None (None), residues: 0
sheet: -3.22 (0.19), residues: 384
loop : -3.26 (0.12), residues: 2096
*********************** 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
624 residues out of total 2288 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 4
poor density : 620
time to evaluate : 3.486
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
outliers start: 4
outliers final: 0
residues processed: 620
average time/residue: 0.7634
time to fit residues: 700.1607
Evaluate side-chains
537 residues out of total 2288 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 537
time to evaluate : 3.474
Switching outliers to nearest non-outliers
outliers start: 0
outliers final: 0
residues processed: 0
time to fit residues: 4.3710
-------------------------------------------------------------------------------
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: 3.9990
chunk 26 optimal weight: 0.8980
chunk 132 optimal weight: 3.9990
chunk 169 optimal weight: 10.0000
chunk 131 optimal weight: 7.9990
chunk 195 optimal weight: 0.9990
chunk 129 optimal weight: 0.9980
chunk 231 optimal weight: 3.9990
chunk 144 optimal weight: 6.9990
chunk 141 optimal weight: 4.9990
chunk 106 optimal weight: 6.9990
overall best weight: 2.1786
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** A 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 162 ASN
** B 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 207 HIS
** C 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 207 HIS
** E 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
I 162 ASN
I 207 HIS
** J 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
J 207 HIS
** K 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
M 104 ASN
M 162 ASN
P 162 ASN
Total number of N/Q/H flips: 9
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4604
moved from start: 1.1093
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
Bond : 0.028 1.220 21296 Z= 1.944
Angle : 2.000 106.100 28928 Z= 0.791
Chirality : 0.046 0.447 3024
Planarity : 0.008 0.196 3680
Dihedral : 5.566 21.668 2784
Min Nonbonded Distance : 1.818
Molprobity Statistics.
All-atom Clashscore : 29.46
Ramachandran Plot:
Outliers : 0.85 %
Allowed : 13.87 %
Favored : 85.28 %
Rotamer Outliers : 0.17 %
Cbeta Deviations : 0.17 %
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: -4.48 (0.14), residues: 2480
helix: None (None), residues: 0
sheet: -3.21 (0.19), residues: 384
loop : -3.26 (0.12), residues: 2096
*********************** 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
617 residues out of total 2288 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 4
poor density : 613
time to evaluate : 3.685
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
outliers start: 4
outliers final: 0
residues processed: 613
average time/residue: 0.7824
time to fit residues: 710.9030
Evaluate side-chains
538 residues out of total 2288 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 538
time to evaluate : 3.493
Switching outliers to nearest non-outliers
outliers start: 0
outliers final: 0
residues processed: 0
time to fit residues: 4.5879
-------------------------------------------------------------------------------
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: 0.9980
chunk 92 optimal weight: 10.0000
chunk 138 optimal weight: 8.9990
chunk 69 optimal weight: 4.9990
chunk 45 optimal weight: 0.8980
chunk 44 optimal weight: 2.9990
chunk 147 optimal weight: 5.9990
chunk 157 optimal weight: 0.9980
chunk 114 optimal weight: 6.9990
chunk 21 optimal weight: 1.9990
chunk 181 optimal weight: 4.9990
overall best weight: 1.5784
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** A 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 162 ASN
** B 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 207 HIS
** C 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 207 HIS
** E 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
I 162 ASN
I 207 HIS
** J 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
J 207 HIS
** K 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 104 ASN
** L 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
M 104 ASN
M 162 ASN
P 162 ASN
Total number of N/Q/H flips: 10
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4603
moved from start: 1.1094
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
Bond : 0.028 1.220 21296 Z= 1.944
Angle : 2.000 106.100 28928 Z= 0.791
Chirality : 0.046 0.447 3024
Planarity : 0.008 0.179 3680
Dihedral : 5.566 21.668 2784
Min Nonbonded Distance : 1.888
Molprobity Statistics.
All-atom Clashscore : 29.63
Ramachandran Plot:
Outliers : 0.85 %
Allowed : 13.87 %
Favored : 85.28 %
Rotamer Outliers : 0.17 %
Cbeta Deviations : 0.17 %
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: -4.48 (0.14), residues: 2480
helix: None (None), residues: 0
sheet: -3.21 (0.19), residues: 384
loop : -3.26 (0.12), residues: 2096
*********************** 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
616 residues out of total 2288 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 4
poor density : 612
time to evaluate : 3.774
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
outliers start: 4
outliers final: 0
residues processed: 612
average time/residue: 0.7854
time to fit residues: 713.0762
Evaluate side-chains
537 residues out of total 2288 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 537
time to evaluate : 3.633
Switching outliers to nearest non-outliers
outliers start: 0
outliers final: 0
residues processed: 0
time to fit residues: 4.7130
-------------------------------------------------------------------------------
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: 0.8980
chunk 221 optimal weight: 9.9990
chunk 202 optimal weight: 0.9990
chunk 215 optimal weight: 9.9990
chunk 129 optimal weight: 0.9990
chunk 93 optimal weight: 10.0000
chunk 169 optimal weight: 8.9990
chunk 66 optimal weight: 0.2980
chunk 194 optimal weight: 0.3980
chunk 203 optimal weight: 2.9990
chunk 214 optimal weight: 5.9990
overall best weight: 0.7184
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** A 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 162 ASN
** B 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 207 HIS
** C 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 207 HIS
** E 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
I 162 ASN
I 207 HIS
** J 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
J 207 HIS
** K 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 104 ASN
** L 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
M 104 ASN
M 162 ASN
P 162 ASN
Total number of N/Q/H flips: 10
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4604
moved from start: 1.1099
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
Bond : 0.028 1.220 21296 Z= 1.944
Angle : 2.000 106.100 28928 Z= 0.791
Chirality : 0.046 0.447 3024
Planarity : 0.008 0.179 3680
Dihedral : 5.566 21.668 2784
Min Nonbonded Distance : 1.888
Molprobity Statistics.
All-atom Clashscore : 29.56
Ramachandran Plot:
Outliers : 0.85 %
Allowed : 13.87 %
Favored : 85.28 %
Rotamer Outliers : 0.17 %
Cbeta Deviations : 0.17 %
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: -4.48 (0.14), residues: 2480
helix: None (None), residues: 0
sheet: -3.21 (0.19), residues: 384
loop : -3.26 (0.12), residues: 2096
*********************** 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
616 residues out of total 2288 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 4
poor density : 612
time to evaluate : 3.522
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
outliers start: 4
outliers final: 0
residues processed: 612
average time/residue: 0.7562
time to fit residues: 684.0899
Evaluate side-chains
538 residues out of total 2288 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 538
time to evaluate : 3.484
Switching outliers to nearest non-outliers
outliers start: 0
outliers final: 0
residues processed: 0
time to fit residues: 4.3108
-------------------------------------------------------------------------------
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: 3.9990
chunk 227 optimal weight: 4.9990
chunk 139 optimal weight: 7.9990
chunk 108 optimal weight: 20.0000
chunk 158 optimal weight: 5.9990
chunk 239 optimal weight: 0.8980
chunk 220 optimal weight: 1.9990
chunk 190 optimal weight: 0.9980
chunk 19 optimal weight: 2.9990
chunk 147 optimal weight: 5.9990
chunk 116 optimal weight: 8.9990
overall best weight: 2.1786
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** A 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 162 ASN
** B 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 207 HIS
** C 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 207 HIS
** E 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
I 162 ASN
I 207 HIS
** J 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
J 207 HIS
** K 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 104 ASN
** L 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
M 104 ASN
M 162 ASN
P 162 ASN
Total number of N/Q/H flips: 10
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4604
moved from start: 1.1099
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
Bond : 0.028 1.220 21296 Z= 1.944
Angle : 2.000 106.100 28928 Z= 0.791
Chirality : 0.046 0.447 3024
Planarity : 0.008 0.179 3680
Dihedral : 5.566 21.668 2784
Min Nonbonded Distance : 1.888
Molprobity Statistics.
All-atom Clashscore : 29.61
Ramachandran Plot:
Outliers : 0.85 %
Allowed : 13.87 %
Favored : 85.28 %
Rotamer Outliers : 0.17 %
Cbeta Deviations : 0.17 %
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: -4.48 (0.14), residues: 2480
helix: None (None), residues: 0
sheet: -3.21 (0.19), residues: 384
loop : -3.26 (0.12), residues: 2096
********************** 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
616 residues out of total 2288 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 4
poor density : 612
time to evaluate : 3.510
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
outliers start: 4
outliers final: 0
residues processed: 612
average time/residue: 0.7662
time to fit residues: 694.3936
Evaluate side-chains
537 residues out of total 2288 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 537
time to evaluate : 3.474
Switching outliers to nearest non-outliers
outliers start: 0
outliers final: 0
residues processed: 0
time to fit residues: 4.3754
-------------------------------------------------------------------------------
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: 4.9990
chunk 202 optimal weight: 1.9990
chunk 58 optimal weight: 10.0000
chunk 175 optimal weight: 6.9990
chunk 28 optimal weight: 0.0370
chunk 52 optimal weight: 2.9990
chunk 190 optimal weight: 0.9980
chunk 79 optimal weight: 7.9990
chunk 195 optimal weight: 0.9980
chunk 24 optimal weight: 3.9990
chunk 35 optimal weight: 4.9990
overall best weight: 1.4062
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** A 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 162 ASN
** B 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 207 HIS
** C 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 207 HIS
** E 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
I 162 ASN
I 207 HIS
** J 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
J 207 HIS
** K 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 104 ASN
** L 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
M 104 ASN
M 162 ASN
P 162 ASN
Total number of N/Q/H flips: 10
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4719 r_free = 0.4719 target = 0.177892 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4405 r_free = 0.4405 target = 0.146680 restraints weight = 178320.398|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4451 r_free = 0.4451 target = 0.150877 restraints weight = 126474.749|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4485 r_free = 0.4485 target = 0.154144 restraints weight = 97486.849|
|-----------------------------------------------------------------------------|
GEOMETRY RESTRAINTS LIBRARY: GEOSTD + MONOMER LIBRARY + CDL V1.2
DEVIATIONS FROM IDEAL VALUES - RMSD. RMSZ FOR BONDS AND ANGLES.
BOND : 0.028 1.220 21296 Z= 1.944
ANGLE : 2.000 106.100 28928 Z= 0.791
CHIRALITY : 0.046 0.447 3024
PLANARITY : 0.008 0.179 3680
DIHEDRAL : 5.566 21.668 2784
MIN NONBONDED DISTANCE : 1.888
MOLPROBITY STATISTICS.
ALL-ATOM CLASHSCORE : 29.56
RAMACHANDRAN PLOT:
OUTLIERS : 0.85 %
ALLOWED : 13.87 %
FAVORED : 85.28 %
ROTAMER OUTLIERS : 0.17 %
CBETA DEVIATIONS : 0.17 %
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: -4.48 (0.14), RESIDUES: 2480
HELIX: NONE (NONE), RESIDUES: 0
SHEET: -3.21 (0.19), RESIDUES: 384
LOOP : -3.26 (0.12), RESIDUES: 2096
-------------------------------------------------------------------------------
Occupancy refinement
********************
GEOMETRY RESTRAINTS LIBRARY: GEOSTD + MONOMER LIBRARY + CDL V1.2
DEVIATIONS FROM IDEAL VALUES - RMSD. RMSZ FOR BONDS AND ANGLES.
BOND : 0.028 1.220 21296 Z= 1.944
ANGLE : 2.000 106.100 28928 Z= 0.791
CHIRALITY : 0.046 0.447 3024
PLANARITY : 0.008 0.179 3680
DIHEDRAL : 5.566 21.668 2784
MIN NONBONDED DISTANCE : 1.888
MOLPROBITY STATISTICS.
ALL-ATOM CLASHSCORE : 29.56
RAMACHANDRAN PLOT:
OUTLIERS : 0.85 %
ALLOWED : 13.87 %
FAVORED : 85.28 %
ROTAMER OUTLIERS : 0.17 %
CBETA DEVIATIONS : 0.17 %
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: -4.48 (0.14), RESIDUES: 2480
HELIX: NONE (NONE), RESIDUES: 0
SHEET: -3.21 (0.19), RESIDUES: 384
LOOP : -3.26 (0.12), RESIDUES: 2096
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6599
moved from start: 1.1099
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
Bond : 0.028 1.220 21296 Z= 1.944
Angle : 2.000 106.100 28928 Z= 0.791
Chirality : 0.046 0.447 3024
Planarity : 0.008 0.179 3680
Dihedral : 5.566 21.668 2784
Min Nonbonded Distance : 1.888
Molprobity Statistics.
All-atom Clashscore : 29.56
Ramachandran Plot:
Outliers : 0.85 %
Allowed : 13.87 %
Favored : 85.28 %
Rotamer Outliers : 0.17 %
Cbeta Deviations : 0.17 %
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: -4.48 (0.14), residues: 2480
helix: None (None), residues: 0
sheet: -3.21 (0.19), residues: 384
loop : -3.26 (0.12), residues: 2096
===============================================================================
Job complete
usr+sys time: 11957.42 seconds
wall clock time: 211 minutes 42.08 seconds (12702.08 seconds total)