Starting phenix.real_space_refine
on Wed Jan 15 07:56:04 2025 by dcliebschner
===============================================================================
Processing files:
-------------------------------------------------------------------------------
Found model, /net/cci-nas-00/data/ceres_data/9c2b_45153/01_2025/9c2b_45153.cif
Found real_map, /net/cci-nas-00/data/ceres_data/9c2b_45153/01_2025/9c2b_45153.map
Processing PHIL parameters:
-------------------------------------------------------------------------------
Adding command-line PHIL:
-------------------------
refinement.macro_cycles=10
scattering_table=electron
resolution=2.42
write_initial_geo_file=False
Final processed PHIL parameters:
-------------------------------------------------------------------------------
data_manager {
real_map_files = "/net/cci-nas-00/data/ceres_data/9c2b_45153/01_2025/9c2b_45153.map"
default_real_map = "/net/cci-nas-00/data/ceres_data/9c2b_45153/01_2025/9c2b_45153.map"
model {
file = "/net/cci-nas-00/data/ceres_data/9c2b_45153/01_2025/9c2b_45153.cif"
}
default_model = "/net/cci-nas-00/data/ceres_data/9c2b_45153/01_2025/9c2b_45153.cif"
}
resolution = 2.42
write_initial_geo_file = False
refinement {
macro_cycles = 10
}
qi {
qm_restraints {
package {
program = *test
}
}
}
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
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
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= 0.001 sd= 0.030
Set stop_for_unknowns flag
Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
Set to: electron
Number of scattering types: 6
Type Number sf(0) Gaussians
P 9 5.49 5
Mg 3 5.21 5
S 42 5.16 5
C 5178 2.51 5
N 1350 2.21 5
O 1626 1.98 5
sf(0) = scattering factor at diffraction angle 0.
Process input model
Symmetric amino acids flipped. Time to flip 7 residue(s): 0.05s
Monomer Library directory:
"/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
Total number of atoms: 8208
Number of models: 1
Model: ""
Number of chains: 15
Chain: "A"
Number of atoms: 2576
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 330, 2576
Classifications: {'peptide': 330}
Incomplete info: {'truncation_to_alanine': 8}
Link IDs: {'PCIS': 3, 'PTRANS': 12, 'TRANS': 314}
Unresolved non-hydrogen bonds: 29
Unresolved non-hydrogen angles: 34
Unresolved non-hydrogen dihedrals: 24
Unresolved non-hydrogen chiralities: 2
Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1}
Unresolved non-hydrogen planarities: 11
Chain: "B"
Number of atoms: 2576
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 330, 2576
Classifications: {'peptide': 330}
Incomplete info: {'truncation_to_alanine': 8}
Link IDs: {'PCIS': 3, 'PTRANS': 12, 'TRANS': 314}
Unresolved non-hydrogen bonds: 29
Unresolved non-hydrogen angles: 34
Unresolved non-hydrogen dihedrals: 24
Unresolved non-hydrogen chiralities: 2
Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1}
Unresolved non-hydrogen planarities: 11
Chain: "C"
Number of atoms: 2576
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 330, 2576
Classifications: {'peptide': 330}
Incomplete info: {'truncation_to_alanine': 8}
Link IDs: {'PCIS': 3, 'PTRANS': 12, 'TRANS': 314}
Unresolved non-hydrogen bonds: 29
Unresolved non-hydrogen angles: 34
Unresolved non-hydrogen dihedrals: 24
Unresolved non-hydrogen chiralities: 2
Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1}
Unresolved non-hydrogen planarities: 11
Chain: "D"
Number of atoms: 39
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 3, 39
Unusual residues: {'BMA': 1, 'NAG': 2}
Classifications: {'undetermined': 3}
Link IDs: {None: 2}
Unresolved non-hydrogen bonds: 3
Unresolved non-hydrogen angles: 6
Unresolved non-hydrogen dihedrals: 9
Unresolved non-hydrogen chiralities: 3
Chain: "E"
Number of atoms: 28
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 2, 28
Unusual residues: {'NAG': 2}
Classifications: {'undetermined': 2}
Link IDs: {None: 1}
Unresolved non-hydrogen bonds: 2
Unresolved non-hydrogen angles: 4
Unresolved non-hydrogen dihedrals: 6
Unresolved non-hydrogen chiralities: 2
Chain: "F"
Number of atoms: 39
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 3, 39
Unusual residues: {'BMA': 1, 'NAG': 2}
Classifications: {'undetermined': 3}
Link IDs: {None: 2}
Unresolved non-hydrogen bonds: 3
Unresolved non-hydrogen angles: 6
Unresolved non-hydrogen dihedrals: 9
Unresolved non-hydrogen chiralities: 3
Chain: "G"
Number of atoms: 28
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 2, 28
Unusual residues: {'NAG': 2}
Classifications: {'undetermined': 2}
Link IDs: {None: 1}
Unresolved non-hydrogen bonds: 2
Unresolved non-hydrogen angles: 4
Unresolved non-hydrogen dihedrals: 6
Unresolved non-hydrogen chiralities: 2
Chain: "H"
Number of atoms: 39
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 3, 39
Unusual residues: {'BMA': 1, 'NAG': 2}
Classifications: {'undetermined': 3}
Link IDs: {None: 2}
Unresolved non-hydrogen bonds: 3
Unresolved non-hydrogen angles: 6
Unresolved non-hydrogen dihedrals: 9
Unresolved non-hydrogen chiralities: 3
Chain: "I"
Number of atoms: 28
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 2, 28
Unusual residues: {'NAG': 2}
Classifications: {'undetermined': 2}
Link IDs: {None: 1}
Unresolved non-hydrogen bonds: 2
Unresolved non-hydrogen angles: 4
Unresolved non-hydrogen dihedrals: 6
Unresolved non-hydrogen chiralities: 2
Chain: "A"
Number of atoms: 46
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 3, 46
Unusual residues: {' MG': 1, 'ATP': 1, 'NAG': 1}
Classifications: {'undetermined': 3}
Link IDs: {None: 2}
Unresolved non-hydrogen bonds: 1
Unresolved non-hydrogen angles: 2
Unresolved non-hydrogen dihedrals: 3
Unresolved non-hydrogen chiralities: 1
Chain: "B"
Number of atoms: 46
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 3, 46
Unusual residues: {' MG': 1, 'ATP': 1, 'NAG': 1}
Classifications: {'undetermined': 3}
Link IDs: {None: 2}
Unresolved non-hydrogen bonds: 1
Unresolved non-hydrogen angles: 2
Unresolved non-hydrogen dihedrals: 3
Unresolved non-hydrogen chiralities: 1
Chain: "C"
Number of atoms: 46
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 3, 46
Unusual residues: {' MG': 1, 'ATP': 1, 'NAG': 1}
Classifications: {'undetermined': 3}
Link IDs: {None: 2}
Unresolved non-hydrogen bonds: 1
Unresolved non-hydrogen angles: 2
Unresolved non-hydrogen dihedrals: 3
Unresolved non-hydrogen chiralities: 1
Chain: "A"
Number of atoms: 47
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 47, 47
Classifications: {'water': 47}
Link IDs: {None: 46}
Chain: "B"
Number of atoms: 47
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 47, 47
Classifications: {'water': 47}
Link IDs: {None: 46}
Chain: "C"
Number of atoms: 47
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 47, 47
Classifications: {'water': 47}
Link IDs: {None: 46}
Time building chain proxies: 6.44, per 1000 atoms: 0.78
Number of scatterers: 8208
At special positions: 0
Unit cell: (90.832, 88.8856, 118.082, 90, 90, 90)
Space group: P 1 (No. 1)
Number of sites at special positions: 0
Number of scattering types: 6
Type Number sf(0)
S 42 16.00
P 9 15.00
Mg 3 11.99
O 1626 8.00
N 1350 7.00
C 5178 6.00
sf(0) = scattering factor at diffraction angle 0.
Number of disulfides: simple=12, symmetry=0
Simple disulfide: pdb=" SG CYS A 117 " - pdb=" SG CYS A 165 " distance=2.03
Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 149 " distance=2.04
Simple disulfide: pdb=" SG CYS A 217 " - pdb=" SG CYS A 227 " distance=2.03
Simple disulfide: pdb=" SG CYS A 261 " - pdb=" SG CYS A 270 " distance=2.03
Simple disulfide: pdb=" SG CYS B 117 " - pdb=" SG CYS B 165 " distance=2.03
Simple disulfide: pdb=" SG CYS B 126 " - pdb=" SG CYS B 149 " distance=2.04
Simple disulfide: pdb=" SG CYS B 217 " - pdb=" SG CYS B 227 " distance=2.03
Simple disulfide: pdb=" SG CYS B 261 " - pdb=" SG CYS B 270 " distance=2.03
Simple disulfide: pdb=" SG CYS C 117 " - pdb=" SG CYS C 165 " distance=2.03
Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 149 " distance=2.03
Simple disulfide: pdb=" SG CYS C 217 " - pdb=" SG CYS C 227 " distance=2.03
Simple disulfide: pdb=" SG CYS C 261 " - pdb=" SG CYS C 270 " distance=2.03
Automatic linking
Parameters for automatic linking
Linking & cutoffs
Metal : Auto - 3.00
Amino acid : True - 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
Links applied
BETA1-4
" NAG D 1 " - " NAG D 2 "
" NAG D 2 " - " BMA D 3 "
" NAG E 1 " - " NAG E 2 "
" NAG F 1 " - " NAG F 2 "
" NAG F 2 " - " BMA F 3 "
" NAG G 1 " - " NAG G 2 "
" NAG H 1 " - " NAG H 2 "
" NAG H 2 " - " BMA H 3 "
" NAG I 1 " - " NAG I 2 "
NAG-ASN
" NAG A 502 " - " ASN A 242 "
" NAG B 502 " - " ASN B 242 "
" NAG C 403 " - " ASN C 242 "
" NAG D 1 " - " ASN A 153 "
" NAG E 1 " - " ASN A 184 "
" NAG F 1 " - " ASN B 153 "
" NAG G 1 " - " ASN B 184 "
" NAG H 1 " - " ASN C 153 "
" NAG I 1 " - " ASN C 184 "
Time building additional restraints: 2.46
Conformation dependent library (CDL) restraints added in 941.8 milliseconds
1968 Ramachandran restraints generated.
984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2.
Adding C-beta torsion restraints...
Number of C-beta restraints generated: 1794
Finding SS restraints...
Secondary structure from input PDB file:
30 helices and 9 sheets defined
30.7% alpha, 25.8% beta
0 base pairs and 0 stacking pairs defined.
Time for finding SS restraints: 0.78
Creating SS restraints...
Processing helix chain 'A' and resid 27 through 47
Processing helix chain 'A' and resid 86 through 90
Processing helix chain 'A' and resid 120 through 124
Processing helix chain 'A' and resid 128 through 132
Processing helix chain 'A' and resid 179 through 184
Processing helix chain 'A' and resid 210 through 217
removed outlier: 3.565A pdb=" N THR A 216 " --> pdb=" O ALA A 212 " (cutoff:3.500A)
Processing helix chain 'A' and resid 232 through 239
Processing helix chain 'A' and resid 242 through 250
removed outlier: 3.691A pdb=" N GLU A 248 " --> pdb=" O SER A 244 " (cutoff:3.500A)
removed outlier: 3.893A pdb=" N LYS A 249 " --> pdb=" O THR A 245 " (cutoff:3.500A)
Processing helix chain 'A' and resid 266 through 270
Processing helix chain 'A' and resid 327 through 356
Processing helix chain 'B' and resid 28 through 47
Processing helix chain 'B' and resid 86 through 90
Processing helix chain 'B' and resid 120 through 124
Processing helix chain 'B' and resid 128 through 132
Processing helix chain 'B' and resid 179 through 184
Processing helix chain 'B' and resid 210 through 217
removed outlier: 3.564A pdb=" N THR B 216 " --> pdb=" O ALA B 212 " (cutoff:3.500A)
Processing helix chain 'B' and resid 232 through 239
Processing helix chain 'B' and resid 242 through 250
removed outlier: 3.691A pdb=" N GLU B 248 " --> pdb=" O SER B 244 " (cutoff:3.500A)
removed outlier: 3.893A pdb=" N LYS B 249 " --> pdb=" O THR B 245 " (cutoff:3.500A)
Processing helix chain 'B' and resid 266 through 270
Processing helix chain 'B' and resid 327 through 356
Processing helix chain 'C' and resid 28 through 47
Processing helix chain 'C' and resid 86 through 90
Processing helix chain 'C' and resid 120 through 124
Processing helix chain 'C' and resid 128 through 132
Processing helix chain 'C' and resid 179 through 184
Processing helix chain 'C' and resid 210 through 217
removed outlier: 3.565A pdb=" N THR C 216 " --> pdb=" O ALA C 212 " (cutoff:3.500A)
Processing helix chain 'C' and resid 232 through 239
Processing helix chain 'C' and resid 242 through 250
removed outlier: 3.690A pdb=" N GLU C 248 " --> pdb=" O SER C 244 " (cutoff:3.500A)
removed outlier: 3.892A pdb=" N LYS C 249 " --> pdb=" O THR C 245 " (cutoff:3.500A)
Processing helix chain 'C' and resid 266 through 270
Processing helix chain 'C' and resid 327 through 356
Processing sheet with id=AA1, first strand: chain 'A' and resid 56 through 60
WARNING: can't find start of bonding for strands!
previous: chain 'A' and resid 56 through 60
current: chain 'A' and resid 99 through 118
WARNING: can't find start of bonding for strands!
previous: chain 'A' and resid 99 through 118
current: chain 'A' and resid 157 through 165
WARNING: can't find start of bonding for strands!
previous: chain 'A' and resid 157 through 165
current: chain 'A' and resid 273 through 277
WARNING: can't find start of bonding for strands!
previous: chain 'A' and resid 273 through 277
current: chain 'A' and resid 302 through 326
No H-bonds generated for sheet with id=AA1
Processing sheet with id=AA2, first strand: chain 'A' and resid 62 through 70
Processing sheet with id=AA3, first strand: chain 'A' and resid 73 through 76
Processing sheet with id=AA4, first strand: chain 'B' and resid 56 through 60
WARNING: can't find start of bonding for strands!
previous: chain 'B' and resid 56 through 60
current: chain 'B' and resid 99 through 118
WARNING: can't find start of bonding for strands!
previous: chain 'B' and resid 99 through 118
current: chain 'B' and resid 157 through 165
WARNING: can't find start of bonding for strands!
previous: chain 'B' and resid 157 through 165
current: chain 'B' and resid 273 through 277
WARNING: can't find start of bonding for strands!
previous: chain 'B' and resid 273 through 277
current: chain 'B' and resid 302 through 326
No H-bonds generated for sheet with id=AA4
Processing sheet with id=AA5, first strand: chain 'B' and resid 62 through 70
Processing sheet with id=AA6, first strand: chain 'B' and resid 73 through 76
Processing sheet with id=AA7, first strand: chain 'C' and resid 56 through 60
WARNING: can't find start of bonding for strands!
previous: chain 'C' and resid 56 through 60
current: chain 'C' and resid 99 through 118
WARNING: can't find start of bonding for strands!
previous: chain 'C' and resid 99 through 118
current: chain 'C' and resid 157 through 165
WARNING: can't find start of bonding for strands!
previous: chain 'C' and resid 157 through 165
current: chain 'C' and resid 273 through 277
WARNING: can't find start of bonding for strands!
previous: chain 'C' and resid 273 through 277
current: chain 'C' and resid 302 through 326
No H-bonds generated for sheet with id=AA7
Processing sheet with id=AA8, first strand: chain 'C' and resid 62 through 70
Processing sheet with id=AA9, first strand: chain 'C' and resid 73 through 76
241 hydrogen bonds defined for protein.
606 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: 2.09
Time building geometry restraints manager: 2.77 seconds
NOTE: a complete listing of the restraints can be obtained by requesting
output of .geo file.
Histogram of bond lengths:
1.22 - 1.34: 2523
1.34 - 1.46: 1934
1.46 - 1.58: 3754
1.58 - 1.70: 12
1.70 - 1.82: 51
Bond restraints: 8274
Sorted by residual:
bond pdb=" C4 ATP C 401 "
pdb=" C5 ATP C 401 "
ideal model delta sigma weight residual
1.388 1.435 -0.047 1.00e-02 1.00e+04 2.17e+01
bond pdb=" C4 ATP A 500 "
pdb=" C5 ATP A 500 "
ideal model delta sigma weight residual
1.388 1.434 -0.046 1.00e-02 1.00e+04 2.13e+01
bond pdb=" C4 ATP B 500 "
pdb=" C5 ATP B 500 "
ideal model delta sigma weight residual
1.388 1.434 -0.046 1.00e-02 1.00e+04 2.09e+01
bond pdb=" C4 ATP A 500 "
pdb=" N9 ATP A 500 "
ideal model delta sigma weight residual
1.374 1.334 0.040 1.00e-02 1.00e+04 1.57e+01
bond pdb=" C8 ATP B 500 "
pdb=" N7 ATP B 500 "
ideal model delta sigma weight residual
1.310 1.349 -0.039 1.00e-02 1.00e+04 1.54e+01
... (remaining 8269 not shown)
Histogram of bond angle deviations from ideal:
0.00 - 3.69: 11195
3.69 - 7.39: 52
7.39 - 11.08: 3
11.08 - 14.78: 0
14.78 - 18.47: 6
Bond angle restraints: 11256
Sorted by residual:
angle pdb=" PB ATP A 500 "
pdb=" O3B ATP A 500 "
pdb=" PG ATP A 500 "
ideal model delta sigma weight residual
139.87 121.40 18.47 1.00e+00 1.00e+00 3.41e+02
angle pdb=" PB ATP C 401 "
pdb=" O3B ATP C 401 "
pdb=" PG ATP C 401 "
ideal model delta sigma weight residual
139.87 121.41 18.46 1.00e+00 1.00e+00 3.41e+02
angle pdb=" PB ATP B 500 "
pdb=" O3B ATP B 500 "
pdb=" PG ATP B 500 "
ideal model delta sigma weight residual
139.87 121.44 18.43 1.00e+00 1.00e+00 3.40e+02
angle pdb=" PA ATP C 401 "
pdb=" O3A ATP C 401 "
pdb=" PB ATP C 401 "
ideal model delta sigma weight residual
136.83 121.74 15.09 1.00e+00 1.00e+00 2.28e+02
angle pdb=" PA ATP A 500 "
pdb=" O3A ATP A 500 "
pdb=" PB ATP A 500 "
ideal model delta sigma weight residual
136.83 121.79 15.04 1.00e+00 1.00e+00 2.26e+02
... (remaining 11251 not shown)
Histogram of dihedral angle deviations from ideal:
0.00 - 21.12: 4551
21.12 - 42.24: 419
42.24 - 63.35: 94
63.35 - 84.47: 21
84.47 - 105.59: 21
Dihedral angle restraints: 5106
sinusoidal: 2298
harmonic: 2808
Sorted by residual:
dihedral pdb=" CA PHE B 308 "
pdb=" C PHE B 308 "
pdb=" N LYS B 309 "
pdb=" CA LYS B 309 "
ideal model delta harmonic sigma weight residual
180.00 161.47 18.53 0 5.00e+00 4.00e-02 1.37e+01
dihedral pdb=" CA PHE C 308 "
pdb=" C PHE C 308 "
pdb=" N LYS C 309 "
pdb=" CA LYS C 309 "
ideal model delta harmonic sigma weight residual
180.00 161.47 18.53 0 5.00e+00 4.00e-02 1.37e+01
dihedral pdb=" CA PHE A 308 "
pdb=" C PHE A 308 "
pdb=" N LYS A 309 "
pdb=" CA LYS A 309 "
ideal model delta harmonic sigma weight residual
180.00 161.51 18.49 0 5.00e+00 4.00e-02 1.37e+01
... (remaining 5103 not shown)
Histogram of chiral volume deviations from ideal:
0.000 - 0.052: 866
0.052 - 0.103: 289
0.103 - 0.155: 120
0.155 - 0.206: 18
0.206 - 0.258: 9
Chirality restraints: 1302
Sorted by residual:
chirality pdb=" C1 NAG H 2 "
pdb=" O4 NAG H 1 "
pdb=" C2 NAG H 2 "
pdb=" O5 NAG H 2 "
both_signs ideal model delta sigma weight residual
False -2.40 -2.28 -0.12 2.00e-02 2.50e+03 3.82e+01
chirality pdb=" C1 NAG F 2 "
pdb=" O4 NAG F 1 "
pdb=" C2 NAG F 2 "
pdb=" O5 NAG F 2 "
both_signs ideal model delta sigma weight residual
False -2.40 -2.28 -0.12 2.00e-02 2.50e+03 3.72e+01
chirality pdb=" C1 NAG D 2 "
pdb=" O4 NAG D 1 "
pdb=" C2 NAG D 2 "
pdb=" O5 NAG D 2 "
both_signs ideal model delta sigma weight residual
False -2.40 -2.28 -0.12 2.00e-02 2.50e+03 3.68e+01
... (remaining 1299 not shown)
Planarity restraints: 1404
Sorted by residual:
delta sigma weight rms_deltas residual
plane pdb=" C2 NAG D 1 " -0.085 2.00e-02 2.50e+03 7.04e-02 6.20e+01
pdb=" C7 NAG D 1 " 0.028 2.00e-02 2.50e+03
pdb=" C8 NAG D 1 " -0.065 2.00e-02 2.50e+03
pdb=" N2 NAG D 1 " 0.111 2.00e-02 2.50e+03
pdb=" O7 NAG D 1 " 0.012 2.00e-02 2.50e+03
delta sigma weight rms_deltas residual
plane pdb=" C2 NAG F 1 " 0.085 2.00e-02 2.50e+03 7.01e-02 6.14e+01
pdb=" C7 NAG F 1 " -0.027 2.00e-02 2.50e+03
pdb=" C8 NAG F 1 " 0.065 2.00e-02 2.50e+03
pdb=" N2 NAG F 1 " -0.111 2.00e-02 2.50e+03
pdb=" O7 NAG F 1 " -0.012 2.00e-02 2.50e+03
delta sigma weight rms_deltas residual
plane pdb=" C2 NAG H 1 " -0.085 2.00e-02 2.50e+03 7.00e-02 6.13e+01
pdb=" C7 NAG H 1 " 0.027 2.00e-02 2.50e+03
pdb=" C8 NAG H 1 " -0.065 2.00e-02 2.50e+03
pdb=" N2 NAG H 1 " 0.111 2.00e-02 2.50e+03
pdb=" O7 NAG H 1 " 0.012 2.00e-02 2.50e+03
... (remaining 1401 not shown)
Histogram of nonbonded interaction distances:
2.16 - 2.71: 393
2.71 - 3.26: 7929
3.26 - 3.80: 14664
3.80 - 4.35: 18955
4.35 - 4.90: 29682
Nonbonded interactions: 71623
Sorted by model distance:
nonbonded pdb=" O1G ATP B 500 "
pdb="MG MG C 402 "
model vdw
2.161 2.170
nonbonded pdb=" O1G ATP A 500 "
pdb="MG MG B 501 "
model vdw
2.161 2.170
nonbonded pdb="MG MG A 501 "
pdb=" O1G ATP C 401 "
model vdw
2.162 2.170
nonbonded pdb=" O HOH A 608 "
pdb=" O HOH A 645 "
model vdw
2.218 3.040
nonbonded pdb=" O HOH B 608 "
pdb=" O HOH B 645 "
model vdw
2.226 3.040
... (remaining 71618 not shown)
NOTE: a complete listing of the restraints can be obtained by requesting
output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.03
Found NCS groups:
ncs_group {
reference = (chain 'A' and resid 27 through 356)
selection = (chain 'B' and resid 27 through 356)
selection = (chain 'C' and resid 27 through 356)
}
ncs_group {
reference = chain 'D'
selection = chain 'F'
selection = chain 'H'
}
ncs_group {
reference = chain 'E'
selection = chain 'G'
selection = chain 'I'
}
Set up NCS constraints
No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
Set random seed: 0.000
Set model cs if undefined: 0.000
Decide on map wrapping: 0.000
Normalize map: mean=0, sd=1: 4.090
Set stop_for_unknowns flag: 0.000
Assert model is a single copy model: 0.000
Assert all atoms have isotropic ADPs: 0.000
Construct map_model_manager: 0.000
Extract box with map and model: 0.370
Check model and map are aligned: 0.060
Set scattering table: 0.090
Process input model: 22.760
Find NCS groups from input model: 0.410
Set up NCS constraints: 0.050
Set refine NCS operators: 0.000
Adjust number of macro_cycles: 0.000
Reset NCS operators: 0.000
Extract rigid body selections: 0.000
Check and reset occupancies: 0.000
Load rotamer database and sin/cos tables:12.930
Set ADP refinement strategy: 0.000
Make a string to write initial .geo file:0.000
Internal consistency checks: 0.000
Total: 40.760
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8273
moved from start: 0.0000
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.007 0.053 8274 Z= 0.451
Angle : 0.976 18.470 11256 Z= 0.707
Chirality : 0.063 0.258 1302
Planarity : 0.007 0.070 1395
Dihedral : 18.261 105.589 3276
Min Nonbonded Distance : 2.161
Molprobity Statistics.
All-atom Clashscore : 3.71
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 2.13 %
Favored : 97.87 %
Rotamer:
Outliers : 0.00 %
Allowed : 16.67 %
Favored : 83.33 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 20.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 0.27 (0.27), residues: 984
helix: -0.27 (0.33), residues: 273
sheet: 0.47 (0.28), residues: 309
loop : 0.52 (0.33), residues: 402
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.010 0.002 TRP C 85
HIS 0.004 0.001 HIS A 355
PHE 0.013 0.002 PHE A 276
TYR 0.019 0.002 TYR B 51
ARG 0.007 0.001 ARG A 180
*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
1968 Ramachandran restraints generated.
984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
1968 Ramachandran restraints generated.
984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
128 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 0
poor density : 128
time to evaluate : 0.915
Fit side-chains
revert: symmetry clash
REVERT: C 215 LYS cc_start: 0.8178 (tttp) cc_final: 0.7892 (ttmm)
outliers start: 0
outliers final: 0
residues processed: 128
average time/residue: 1.5687
time to fit residues: 211.3161
Evaluate side-chains
115 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 0
poor density : 115
time to evaluate : 0.869
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 99
random chunks:
chunk 83 optimal weight: 0.2980
chunk 75 optimal weight: 3.9990
chunk 41 optimal weight: 3.9990
chunk 25 optimal weight: 4.9990
chunk 50 optimal weight: 3.9990
chunk 40 optimal weight: 1.9990
chunk 77 optimal weight: 0.9990
chunk 30 optimal weight: 3.9990
chunk 47 optimal weight: 3.9990
chunk 57 optimal weight: 0.0370
chunk 89 optimal weight: 0.5980
overall best weight: 0.7862
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
B 237 GLN
Total number of N/Q/H flips: 1
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.162379 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.114511 restraints weight = 7332.623|
|-----------------------------------------------------------------------------|
r_work (start): 0.3348 rms_B_bonded: 1.67
r_work: 0.3239 rms_B_bonded: 2.08 restraints_weight: 0.5000
r_work: 0.3125 rms_B_bonded: 3.37 restraints_weight: 0.2500
r_work (final): 0.3125
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8588
moved from start: 0.1068
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.040 8274 Z= 0.209
Angle : 0.572 7.348 11256 Z= 0.297
Chirality : 0.046 0.180 1302
Planarity : 0.004 0.045 1395
Dihedral : 12.877 89.640 1530
Min Nonbonded Distance : 1.938
Molprobity Statistics.
All-atom Clashscore : 3.33
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 1.32 %
Favored : 98.68 %
Rotamer:
Outliers : 2.66 %
Allowed : 16.79 %
Favored : 80.56 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 20.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 1.05 (0.28), residues: 984
helix: 1.21 (0.34), residues: 273
sheet: 0.51 (0.28), residues: 309
loop : 0.69 (0.34), residues: 402
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.008 0.001 TRP A 85
HIS 0.003 0.001 HIS B 220
PHE 0.014 0.002 PHE A 326
TYR 0.017 0.002 TYR C 90
ARG 0.007 0.001 ARG B 180
*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
1968 Ramachandran restraints generated.
984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
1968 Ramachandran restraints generated.
984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
140 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 22
poor density : 118
time to evaluate : 0.879
Fit side-chains
REVERT: A 275 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.7538 (mp0)
REVERT: B 138 LYS cc_start: 0.8678 (OUTLIER) cc_final: 0.8203 (tttt)
REVERT: B 197 ARG cc_start: 0.8306 (ttm-80) cc_final: 0.7897 (ttm110)
REVERT: B 215 LYS cc_start: 0.8382 (tttp) cc_final: 0.7997 (ttmm)
REVERT: B 275 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.7345 (mp0)
REVERT: C 52 GLU cc_start: 0.7956 (OUTLIER) cc_final: 0.7580 (mt-10)
REVERT: C 138 LYS cc_start: 0.8713 (OUTLIER) cc_final: 0.8109 (tttt)
REVERT: C 148 LYS cc_start: 0.8375 (mppt) cc_final: 0.7828 (mmtt)
outliers start: 22
outliers final: 5
residues processed: 134
average time/residue: 1.3357
time to fit residues: 189.6662
Evaluate side-chains
126 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 10
poor density : 116
time to evaluate : 0.883
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 72 LEU
Chi-restraints excluded: chain A residue 275 GLU
Chi-restraints excluded: chain B residue 72 LEU
Chi-restraints excluded: chain B residue 128 GLU
Chi-restraints excluded: chain B residue 138 LYS
Chi-restraints excluded: chain B residue 258 ASP
Chi-restraints excluded: chain B residue 275 GLU
Chi-restraints excluded: chain C residue 52 GLU
Chi-restraints excluded: chain C residue 62 ILE
Chi-restraints excluded: chain C residue 138 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 99
random chunks:
chunk 91 optimal weight: 3.9990
chunk 14 optimal weight: 0.9980
chunk 25 optimal weight: 4.9990
chunk 86 optimal weight: 1.9990
chunk 83 optimal weight: 0.9990
chunk 76 optimal weight: 0.3980
chunk 71 optimal weight: 0.0470
chunk 84 optimal weight: 2.9990
chunk 47 optimal weight: 0.8980
chunk 9 optimal weight: 1.9990
chunk 24 optimal weight: 0.8980
overall best weight: 0.6478
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 237 GLN
C 114 GLN
Total number of N/Q/H flips: 2
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.163346 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.115450 restraints weight = 7444.391|
|-----------------------------------------------------------------------------|
r_work (start): 0.3357 rms_B_bonded: 1.69
r_work: 0.3247 rms_B_bonded: 2.11 restraints_weight: 0.5000
r_work: 0.3135 rms_B_bonded: 3.40 restraints_weight: 0.2500
r_work (final): 0.3135
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8578
moved from start: 0.1195
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.043 8274 Z= 0.181
Angle : 0.542 6.474 11256 Z= 0.279
Chirality : 0.045 0.183 1302
Planarity : 0.004 0.044 1395
Dihedral : 11.331 89.938 1530
Min Nonbonded Distance : 1.937
Molprobity Statistics.
All-atom Clashscore : 3.08
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 1.12 %
Favored : 98.88 %
Rotamer:
Outliers : 2.78 %
Allowed : 18.36 %
Favored : 78.86 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 20.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 1.17 (0.28), residues: 984
helix: 1.47 (0.34), residues: 273
sheet: 0.45 (0.27), residues: 309
loop : 0.76 (0.35), residues: 402
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.007 0.001 TRP B 259
HIS 0.002 0.001 HIS B 355
PHE 0.010 0.001 PHE B 243
TYR 0.016 0.001 TYR C 90
ARG 0.007 0.000 ARG B 180
*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
1968 Ramachandran restraints generated.
984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
1968 Ramachandran restraints generated.
984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
145 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 23
poor density : 122
time to evaluate : 0.897
Fit side-chains
REVERT: A 52 GLU cc_start: 0.7985 (tp30) cc_final: 0.7653 (mt-10)
REVERT: A 138 LYS cc_start: 0.8681 (OUTLIER) cc_final: 0.8304 (tttt)
REVERT: A 275 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.7483 (mp0)
REVERT: A 332 MET cc_start: 0.7588 (OUTLIER) cc_final: 0.6051 (mpm)
REVERT: B 138 LYS cc_start: 0.8665 (OUTLIER) cc_final: 0.8183 (tttt)
REVERT: B 197 ARG cc_start: 0.8302 (ttm-80) cc_final: 0.7902 (ttm110)
REVERT: B 215 LYS cc_start: 0.8381 (tttp) cc_final: 0.7998 (ttmm)
REVERT: B 275 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.7313 (mp0)
REVERT: B 332 MET cc_start: 0.7687 (OUTLIER) cc_final: 0.6242 (mpm)
REVERT: C 138 LYS cc_start: 0.8718 (OUTLIER) cc_final: 0.8177 (tttt)
REVERT: C 148 LYS cc_start: 0.8372 (mppt) cc_final: 0.7831 (mmtt)
REVERT: C 215 LYS cc_start: 0.8350 (tttp) cc_final: 0.8021 (ttmm)
outliers start: 23
outliers final: 8
residues processed: 135
average time/residue: 1.3746
time to fit residues: 196.3193
Evaluate side-chains
131 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 15
poor density : 116
time to evaluate : 0.852
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 62 ILE
Chi-restraints excluded: chain A residue 72 LEU
Chi-restraints excluded: chain A residue 138 LYS
Chi-restraints excluded: chain A residue 246 LEU
Chi-restraints excluded: chain A residue 258 ASP
Chi-restraints excluded: chain A residue 275 GLU
Chi-restraints excluded: chain A residue 332 MET
Chi-restraints excluded: chain B residue 62 ILE
Chi-restraints excluded: chain B residue 72 LEU
Chi-restraints excluded: chain B residue 128 GLU
Chi-restraints excluded: chain B residue 138 LYS
Chi-restraints excluded: chain B residue 237 GLN
Chi-restraints excluded: chain B residue 275 GLU
Chi-restraints excluded: chain B residue 332 MET
Chi-restraints excluded: chain C residue 138 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 99
random chunks:
chunk 0 optimal weight: 10.0000
chunk 69 optimal weight: 5.9990
chunk 65 optimal weight: 2.9990
chunk 48 optimal weight: 0.4980
chunk 34 optimal weight: 0.9990
chunk 36 optimal weight: 0.8980
chunk 18 optimal weight: 7.9990
chunk 67 optimal weight: 0.8980
chunk 78 optimal weight: 5.9990
chunk 31 optimal weight: 7.9990
chunk 83 optimal weight: 0.9990
overall best weight: 0.8584
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 114 GLN
A 237 GLN
B 114 GLN
Total number of N/Q/H flips: 3
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.162596 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.114840 restraints weight = 7361.852|
|-----------------------------------------------------------------------------|
r_work (start): 0.3352 rms_B_bonded: 1.66
r_work: 0.3244 rms_B_bonded: 2.06 restraints_weight: 0.5000
r_work: 0.3132 rms_B_bonded: 3.33 restraints_weight: 0.2500
r_work (final): 0.3132
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8568
moved from start: 0.1279
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.045 8274 Z= 0.207
Angle : 0.546 6.988 11256 Z= 0.280
Chirality : 0.046 0.185 1302
Planarity : 0.004 0.044 1395
Dihedral : 10.181 88.462 1530
Min Nonbonded Distance : 1.919
Molprobity Statistics.
All-atom Clashscore : 2.83
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 0.91 %
Favored : 99.09 %
Rotamer:
Outliers : 3.50 %
Allowed : 17.39 %
Favored : 79.11 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 20.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 1.26 (0.28), residues: 984
helix: 1.62 (0.35), residues: 273
sheet: 0.51 (0.27), residues: 324
loop : 0.76 (0.35), residues: 387
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.007 0.001 TRP C 259
HIS 0.002 0.001 HIS C 260
PHE 0.012 0.002 PHE A 243
TYR 0.016 0.001 TYR C 90
ARG 0.007 0.000 ARG B 180
*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
1968 Ramachandran restraints generated.
984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
1968 Ramachandran restraints generated.
984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
148 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 29
poor density : 119
time to evaluate : 0.922
Fit side-chains
REVERT: A 138 LYS cc_start: 0.8658 (OUTLIER) cc_final: 0.8287 (tttt)
REVERT: A 275 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.7483 (mp0)
REVERT: A 332 MET cc_start: 0.7595 (OUTLIER) cc_final: 0.6014 (mpm)
REVERT: B 138 LYS cc_start: 0.8676 (OUTLIER) cc_final: 0.8185 (tttt)
REVERT: B 197 ARG cc_start: 0.8305 (ttm-80) cc_final: 0.7911 (ttm110)
REVERT: B 215 LYS cc_start: 0.8364 (tttp) cc_final: 0.7980 (ttmm)
REVERT: B 267 VAL cc_start: 0.7896 (m) cc_final: 0.7536 (p)
REVERT: B 275 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.7255 (mp0)
REVERT: B 332 MET cc_start: 0.7686 (OUTLIER) cc_final: 0.6217 (mpm)
REVERT: C 52 GLU cc_start: 0.7970 (tp30) cc_final: 0.7554 (mt-10)
REVERT: C 138 LYS cc_start: 0.8706 (OUTLIER) cc_final: 0.8187 (tttt)
REVERT: C 148 LYS cc_start: 0.8319 (mppt) cc_final: 0.7767 (mmtt)
REVERT: C 215 LYS cc_start: 0.8354 (tttp) cc_final: 0.8015 (ttmm)
REVERT: C 332 MET cc_start: 0.7625 (OUTLIER) cc_final: 0.6081 (mpm)
outliers start: 29
outliers final: 11
residues processed: 138
average time/residue: 1.4341
time to fit residues: 208.8589
Evaluate side-chains
134 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 19
poor density : 115
time to evaluate : 0.959
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 62 ILE
Chi-restraints excluded: chain A residue 72 LEU
Chi-restraints excluded: chain A residue 138 LYS
Chi-restraints excluded: chain A residue 246 LEU
Chi-restraints excluded: chain A residue 258 ASP
Chi-restraints excluded: chain A residue 275 GLU
Chi-restraints excluded: chain A residue 318 LEU
Chi-restraints excluded: chain A residue 332 MET
Chi-restraints excluded: chain B residue 62 ILE
Chi-restraints excluded: chain B residue 72 LEU
Chi-restraints excluded: chain B residue 128 GLU
Chi-restraints excluded: chain B residue 138 LYS
Chi-restraints excluded: chain B residue 237 GLN
Chi-restraints excluded: chain B residue 275 GLU
Chi-restraints excluded: chain B residue 332 MET
Chi-restraints excluded: chain C residue 138 LYS
Chi-restraints excluded: chain C residue 275 GLU
Chi-restraints excluded: chain C residue 318 LEU
Chi-restraints excluded: chain C residue 332 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 99
random chunks:
chunk 33 optimal weight: 10.0000
chunk 63 optimal weight: 1.9990
chunk 85 optimal weight: 0.9990
chunk 64 optimal weight: 10.0000
chunk 73 optimal weight: 5.9990
chunk 71 optimal weight: 3.9990
chunk 3 optimal weight: 0.9990
chunk 56 optimal weight: 0.9980
chunk 92 optimal weight: 0.6980
chunk 75 optimal weight: 0.8980
chunk 66 optimal weight: 10.0000
overall best weight: 0.9184
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 114 GLN
C 114 GLN
Total number of N/Q/H flips: 2
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.162668 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.114848 restraints weight = 7363.092|
|-----------------------------------------------------------------------------|
r_work (start): 0.3349 rms_B_bonded: 1.68
r_work: 0.3240 rms_B_bonded: 2.09 restraints_weight: 0.5000
r_work: 0.3126 rms_B_bonded: 3.40 restraints_weight: 0.2500
r_work (final): 0.3126
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8588
moved from start: 0.1367
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.046 8274 Z= 0.213
Angle : 0.538 7.297 11256 Z= 0.280
Chirality : 0.045 0.169 1302
Planarity : 0.004 0.044 1395
Dihedral : 9.487 88.505 1530
Min Nonbonded Distance : 1.915
Molprobity Statistics.
All-atom Clashscore : 2.51
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 0.71 %
Favored : 99.29 %
Rotamer:
Outliers : 3.38 %
Allowed : 17.51 %
Favored : 79.11 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 20.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 1.30 (0.29), residues: 984
helix: 1.70 (0.35), residues: 273
sheet: 0.49 (0.27), residues: 324
loop : 0.79 (0.36), residues: 387
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.007 0.001 TRP B 259
HIS 0.002 0.001 HIS C 260
PHE 0.010 0.002 PHE B 276
TYR 0.015 0.001 TYR C 90
ARG 0.008 0.001 ARG B 180
*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
1968 Ramachandran restraints generated.
984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
1968 Ramachandran restraints generated.
984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
147 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 28
poor density : 119
time to evaluate : 0.988
Fit side-chains
REVERT: A 52 GLU cc_start: 0.7977 (tp30) cc_final: 0.7640 (mt-10)
REVERT: A 138 LYS cc_start: 0.8673 (OUTLIER) cc_final: 0.8317 (tttt)
REVERT: A 275 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.7510 (mp0)
REVERT: A 332 MET cc_start: 0.7650 (OUTLIER) cc_final: 0.6102 (mpm)
REVERT: B 138 LYS cc_start: 0.8696 (OUTLIER) cc_final: 0.8226 (tttt)
REVERT: B 215 LYS cc_start: 0.8400 (tttp) cc_final: 0.8027 (ttmm)
REVERT: B 267 VAL cc_start: 0.7912 (m) cc_final: 0.7601 (p)
REVERT: B 275 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7262 (mp0)
REVERT: B 332 MET cc_start: 0.7736 (OUTLIER) cc_final: 0.6312 (mpm)
REVERT: C 52 GLU cc_start: 0.7999 (tp30) cc_final: 0.7598 (mt-10)
REVERT: C 138 LYS cc_start: 0.8713 (OUTLIER) cc_final: 0.8211 (tttt)
REVERT: C 148 LYS cc_start: 0.8336 (mppt) cc_final: 0.7770 (mmtt)
REVERT: C 215 LYS cc_start: 0.8375 (tttp) cc_final: 0.8044 (ttmm)
REVERT: C 332 MET cc_start: 0.7650 (OUTLIER) cc_final: 0.6111 (mpm)
outliers start: 28
outliers final: 9
residues processed: 138
average time/residue: 1.4375
time to fit residues: 209.4848
Evaluate side-chains
135 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 17
poor density : 118
time to evaluate : 0.916
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 62 ILE
Chi-restraints excluded: chain A residue 72 LEU
Chi-restraints excluded: chain A residue 138 LYS
Chi-restraints excluded: chain A residue 246 LEU
Chi-restraints excluded: chain A residue 258 ASP
Chi-restraints excluded: chain A residue 275 GLU
Chi-restraints excluded: chain A residue 318 LEU
Chi-restraints excluded: chain A residue 332 MET
Chi-restraints excluded: chain B residue 62 ILE
Chi-restraints excluded: chain B residue 72 LEU
Chi-restraints excluded: chain B residue 128 GLU
Chi-restraints excluded: chain B residue 138 LYS
Chi-restraints excluded: chain B residue 237 GLN
Chi-restraints excluded: chain B residue 275 GLU
Chi-restraints excluded: chain B residue 332 MET
Chi-restraints excluded: chain C residue 138 LYS
Chi-restraints excluded: chain C residue 332 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 99
random chunks:
chunk 15 optimal weight: 0.6980
chunk 78 optimal weight: 3.9990
chunk 95 optimal weight: 6.9990
chunk 80 optimal weight: 0.6980
chunk 7 optimal weight: 0.8980
chunk 86 optimal weight: 2.9990
chunk 98 optimal weight: 0.3980
chunk 93 optimal weight: 0.0070
chunk 90 optimal weight: 1.9990
chunk 1 optimal weight: 8.9990
chunk 36 optimal weight: 1.9990
overall best weight: 0.5398
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 114 GLN
A 237 GLN
B 114 GLN
C 114 GLN
Total number of N/Q/H flips: 4
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3870 r_free = 0.3870 target = 0.163974 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.116590 restraints weight = 7346.798|
|-----------------------------------------------------------------------------|
r_work (start): 0.3378 rms_B_bonded: 1.67
r_work: 0.3270 rms_B_bonded: 2.11 restraints_weight: 0.5000
r_work: 0.3159 rms_B_bonded: 3.41 restraints_weight: 0.2500
r_work (final): 0.3159
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8555
moved from start: 0.1508
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.043 8274 Z= 0.161
Angle : 0.509 7.444 11256 Z= 0.265
Chirality : 0.044 0.141 1302
Planarity : 0.004 0.043 1395
Dihedral : 9.126 87.778 1530
Min Nonbonded Distance : 1.947
Molprobity Statistics.
All-atom Clashscore : 2.51
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 1.12 %
Favored : 98.88 %
Rotamer:
Outliers : 2.90 %
Allowed : 18.36 %
Favored : 78.74 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 20.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 1.34 (0.29), residues: 984
helix: 1.75 (0.35), residues: 273
sheet: 0.67 (0.29), residues: 297
loop : 0.65 (0.35), residues: 414
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.006 0.001 TRP C 259
HIS 0.001 0.001 HIS A 296
PHE 0.011 0.001 PHE A 243
TYR 0.015 0.001 TYR C 90
ARG 0.008 0.000 ARG B 180
*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
1968 Ramachandran restraints generated.
984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
1968 Ramachandran restraints generated.
984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
141 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 24
poor density : 117
time to evaluate : 0.885
Fit side-chains
REVERT: A 52 GLU cc_start: 0.7975 (tp30) cc_final: 0.7635 (mt-10)
REVERT: A 138 LYS cc_start: 0.8654 (OUTLIER) cc_final: 0.8282 (tttt)
REVERT: A 267 VAL cc_start: 0.7979 (m) cc_final: 0.7689 (p)
REVERT: A 275 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.7499 (mp0)
REVERT: A 332 MET cc_start: 0.7611 (OUTLIER) cc_final: 0.6059 (mpm)
REVERT: B 215 LYS cc_start: 0.8355 (tttp) cc_final: 0.7983 (ttmm)
REVERT: B 267 VAL cc_start: 0.7886 (m) cc_final: 0.7615 (p)
REVERT: B 275 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.7255 (mp0)
REVERT: B 332 MET cc_start: 0.7709 (OUTLIER) cc_final: 0.6270 (mpm)
REVERT: C 52 GLU cc_start: 0.7964 (tp30) cc_final: 0.7587 (mt-10)
REVERT: C 148 LYS cc_start: 0.8332 (mppt) cc_final: 0.7785 (mmtt)
REVERT: C 215 LYS cc_start: 0.8346 (tttp) cc_final: 0.7976 (ttmm)
REVERT: C 332 MET cc_start: 0.7619 (OUTLIER) cc_final: 0.6083 (mpm)
outliers start: 24
outliers final: 9
residues processed: 133
average time/residue: 1.4058
time to fit residues: 197.3900
Evaluate side-chains
134 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 15
poor density : 119
time to evaluate : 0.975
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 62 ILE
Chi-restraints excluded: chain A residue 138 LYS
Chi-restraints excluded: chain A residue 246 LEU
Chi-restraints excluded: chain A residue 258 ASP
Chi-restraints excluded: chain A residue 275 GLU
Chi-restraints excluded: chain A residue 318 LEU
Chi-restraints excluded: chain A residue 332 MET
Chi-restraints excluded: chain B residue 62 ILE
Chi-restraints excluded: chain B residue 72 LEU
Chi-restraints excluded: chain B residue 128 GLU
Chi-restraints excluded: chain B residue 237 GLN
Chi-restraints excluded: chain B residue 275 GLU
Chi-restraints excluded: chain B residue 332 MET
Chi-restraints excluded: chain C residue 318 LEU
Chi-restraints excluded: chain C residue 332 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 99
random chunks:
chunk 83 optimal weight: 0.0370
chunk 0 optimal weight: 10.0000
chunk 94 optimal weight: 4.9990
chunk 75 optimal weight: 3.9990
chunk 38 optimal weight: 5.9990
chunk 89 optimal weight: 3.9990
chunk 33 optimal weight: 10.0000
chunk 58 optimal weight: 3.9990
chunk 62 optimal weight: 7.9990
chunk 31 optimal weight: 9.9990
chunk 72 optimal weight: 2.9990
overall best weight: 3.0066
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 114 GLN
A 237 GLN
B 114 GLN
B 237 GLN
C 114 GLN
Total number of N/Q/H flips: 5
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.158506 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.109996 restraints weight = 7353.842|
|-----------------------------------------------------------------------------|
r_work (start): 0.3289 rms_B_bonded: 1.66
r_work: 0.3180 rms_B_bonded: 2.04 restraints_weight: 0.5000
r_work: 0.3066 rms_B_bonded: 3.30 restraints_weight: 0.2500
r_work (final): 0.3066
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8640
moved from start: 0.1359
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.008 0.082 8274 Z= 0.534
Angle : 0.719 8.358 11256 Z= 0.378
Chirality : 0.053 0.313 1302
Planarity : 0.006 0.047 1395
Dihedral : 10.280 85.384 1530
Min Nonbonded Distance : 1.876
Molprobity Statistics.
All-atom Clashscore : 3.45
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 1.93 %
Favored : 98.07 %
Rotamer:
Outliers : 4.23 %
Allowed : 17.15 %
Favored : 78.62 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 20.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 1.15 (0.28), residues: 984
helix: 1.60 (0.35), residues: 273
sheet: 0.42 (0.27), residues: 324
loop : 0.66 (0.35), residues: 387
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.013 0.003 TRP A 259
HIS 0.005 0.002 HIS C 260
PHE 0.021 0.003 PHE A 276
TYR 0.018 0.003 TYR C 90
ARG 0.008 0.001 ARG B 180
*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
1968 Ramachandran restraints generated.
984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
1968 Ramachandran restraints generated.
984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
144 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 35
poor density : 109
time to evaluate : 0.876
Fit side-chains
REVERT: A 138 LYS cc_start: 0.8720 (OUTLIER) cc_final: 0.8372 (tttt)
REVERT: A 215 LYS cc_start: 0.8438 (tttt) cc_final: 0.8105 (ttmm)
REVERT: A 275 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.7510 (mp0)
REVERT: A 332 MET cc_start: 0.7686 (OUTLIER) cc_final: 0.6172 (mpm)
REVERT: B 138 LYS cc_start: 0.8696 (OUTLIER) cc_final: 0.8234 (tttt)
REVERT: B 197 ARG cc_start: 0.8369 (ttm-80) cc_final: 0.7958 (ttm110)
REVERT: B 215 LYS cc_start: 0.8486 (tttp) cc_final: 0.8094 (ttmm)
REVERT: B 275 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.7310 (mp0)
REVERT: B 332 MET cc_start: 0.7759 (OUTLIER) cc_final: 0.6392 (mpm)
REVERT: C 148 LYS cc_start: 0.8316 (mppt) cc_final: 0.7682 (mmtt)
REVERT: C 215 LYS cc_start: 0.8412 (tttp) cc_final: 0.8069 (ttmm)
REVERT: C 246 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8604 (mp)
REVERT: C 332 MET cc_start: 0.7700 (OUTLIER) cc_final: 0.6268 (mpm)
outliers start: 35
outliers final: 8
residues processed: 132
average time/residue: 1.4057
time to fit residues: 196.4435
Evaluate side-chains
124 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 16
poor density : 108
time to evaluate : 0.950
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 72 LEU
Chi-restraints excluded: chain A residue 138 LYS
Chi-restraints excluded: chain A residue 258 ASP
Chi-restraints excluded: chain A residue 275 GLU
Chi-restraints excluded: chain A residue 332 MET
Chi-restraints excluded: chain B residue 72 LEU
Chi-restraints excluded: chain B residue 128 GLU
Chi-restraints excluded: chain B residue 138 LYS
Chi-restraints excluded: chain B residue 275 GLU
Chi-restraints excluded: chain B residue 318 LEU
Chi-restraints excluded: chain B residue 332 MET
Chi-restraints excluded: chain C residue 62 ILE
Chi-restraints excluded: chain C residue 246 LEU
Chi-restraints excluded: chain C residue 275 GLU
Chi-restraints excluded: chain C residue 318 LEU
Chi-restraints excluded: chain C residue 332 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 99
random chunks:
chunk 29 optimal weight: 6.9990
chunk 94 optimal weight: 0.6980
chunk 69 optimal weight: 9.9990
chunk 98 optimal weight: 4.9990
chunk 28 optimal weight: 0.9980
chunk 36 optimal weight: 2.9990
chunk 89 optimal weight: 0.9990
chunk 45 optimal weight: 8.9990
chunk 92 optimal weight: 0.9980
chunk 21 optimal weight: 0.5980
chunk 85 optimal weight: 0.6980
overall best weight: 0.7980
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 237 GLN
B 114 GLN
B 237 GLN
Total number of N/Q/H flips: 3
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.162400 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.114525 restraints weight = 7454.664|
|-----------------------------------------------------------------------------|
r_work (start): 0.3352 rms_B_bonded: 1.67
r_work: 0.3244 rms_B_bonded: 2.09 restraints_weight: 0.5000
r_work: 0.3130 rms_B_bonded: 3.40 restraints_weight: 0.2500
r_work (final): 0.3130
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8587
moved from start: 0.1476
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.046 8274 Z= 0.204
Angle : 0.584 8.471 11256 Z= 0.308
Chirality : 0.047 0.307 1302
Planarity : 0.004 0.043 1395
Dihedral : 9.759 89.036 1530
Min Nonbonded Distance : 1.942
Molprobity Statistics.
All-atom Clashscore : 2.83
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 1.12 %
Favored : 98.88 %
Rotamer:
Outliers : 2.66 %
Allowed : 18.72 %
Favored : 78.62 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 20.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 1.20 (0.28), residues: 984
helix: 1.71 (0.36), residues: 273
sheet: 0.41 (0.27), residues: 324
loop : 0.69 (0.35), residues: 387
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.009 0.001 TRP B 85
HIS 0.002 0.001 HIS B 220
PHE 0.009 0.002 PHE B 289
TYR 0.016 0.001 TYR B 90
ARG 0.008 0.001 ARG B 180
*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
1968 Ramachandran restraints generated.
984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
1968 Ramachandran restraints generated.
984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
139 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 22
poor density : 117
time to evaluate : 0.907
Fit side-chains
REVERT: A 138 LYS cc_start: 0.8698 (OUTLIER) cc_final: 0.8342 (tttt)
REVERT: A 275 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.7525 (mp0)
REVERT: A 332 MET cc_start: 0.7680 (OUTLIER) cc_final: 0.6142 (mpm)
REVERT: B 215 LYS cc_start: 0.8428 (tttp) cc_final: 0.8051 (ttmm)
REVERT: B 267 VAL cc_start: 0.7911 (m) cc_final: 0.7614 (p)
REVERT: B 275 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7273 (mp0)
REVERT: B 332 MET cc_start: 0.7748 (OUTLIER) cc_final: 0.6314 (mpm)
REVERT: C 52 GLU cc_start: 0.7993 (tp30) cc_final: 0.7624 (mt-10)
REVERT: C 148 LYS cc_start: 0.8314 (mppt) cc_final: 0.7695 (mmtt)
REVERT: C 275 GLU cc_start: 0.8304 (OUTLIER) cc_final: 0.7317 (mp0)
REVERT: C 332 MET cc_start: 0.7694 (OUTLIER) cc_final: 0.6203 (mpm)
outliers start: 22
outliers final: 9
residues processed: 129
average time/residue: 1.4515
time to fit residues: 197.6249
Evaluate side-chains
131 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 16
poor density : 115
time to evaluate : 0.791
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 138 LYS
Chi-restraints excluded: chain A residue 258 ASP
Chi-restraints excluded: chain A residue 275 GLU
Chi-restraints excluded: chain A residue 318 LEU
Chi-restraints excluded: chain A residue 332 MET
Chi-restraints excluded: chain B residue 62 ILE
Chi-restraints excluded: chain B residue 72 LEU
Chi-restraints excluded: chain B residue 128 GLU
Chi-restraints excluded: chain B residue 275 GLU
Chi-restraints excluded: chain B residue 318 LEU
Chi-restraints excluded: chain B residue 332 MET
Chi-restraints excluded: chain C residue 62 ILE
Chi-restraints excluded: chain C residue 72 LEU
Chi-restraints excluded: chain C residue 275 GLU
Chi-restraints excluded: chain C residue 318 LEU
Chi-restraints excluded: chain C residue 332 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 99
random chunks:
chunk 20 optimal weight: 3.9990
chunk 77 optimal weight: 0.5980
chunk 64 optimal weight: 9.9990
chunk 59 optimal weight: 0.8980
chunk 11 optimal weight: 3.9990
chunk 12 optimal weight: 3.9990
chunk 36 optimal weight: 0.9980
chunk 94 optimal weight: 3.9990
chunk 33 optimal weight: 10.0000
chunk 62 optimal weight: 1.9990
chunk 41 optimal weight: 3.9990
overall best weight: 1.6984
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 237 GLN
B 114 GLN
C 114 GLN
Total number of N/Q/H flips: 3
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.160452 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.112252 restraints weight = 7499.652|
|-----------------------------------------------------------------------------|
r_work (start): 0.3319 rms_B_bonded: 1.67
r_work: 0.3206 rms_B_bonded: 2.10 restraints_weight: 0.5000
r_work: 0.3092 rms_B_bonded: 3.40 restraints_weight: 0.2500
r_work (final): 0.3092
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8626
moved from start: 0.1469
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.005 0.052 8274 Z= 0.334
Angle : 0.642 8.386 11256 Z= 0.338
Chirality : 0.050 0.382 1302
Planarity : 0.005 0.043 1395
Dihedral : 9.860 88.844 1530
Min Nonbonded Distance : 1.888
Molprobity Statistics.
All-atom Clashscore : 3.27
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 1.52 %
Favored : 98.48 %
Rotamer:
Outliers : 2.90 %
Allowed : 18.24 %
Favored : 78.86 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 20.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 1.15 (0.28), residues: 984
helix: 1.64 (0.35), residues: 273
sheet: 0.35 (0.27), residues: 324
loop : 0.70 (0.35), residues: 387
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.009 0.002 TRP A 259
HIS 0.003 0.001 HIS C 260
PHE 0.017 0.002 PHE A 243
TYR 0.016 0.002 TYR C 90
ARG 0.008 0.001 ARG B 180
*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
1968 Ramachandran restraints generated.
984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
1968 Ramachandran restraints generated.
984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
133 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 24
poor density : 109
time to evaluate : 0.883
Fit side-chains
REVERT: A 138 LYS cc_start: 0.8694 (OUTLIER) cc_final: 0.8335 (tttt)
REVERT: A 275 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.7525 (mp0)
REVERT: A 332 MET cc_start: 0.7694 (OUTLIER) cc_final: 0.6163 (mpm)
REVERT: B 138 LYS cc_start: 0.8693 (OUTLIER) cc_final: 0.8212 (tttt)
REVERT: B 215 LYS cc_start: 0.8441 (tttp) cc_final: 0.8060 (ttmm)
REVERT: B 275 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.7330 (mp0)
REVERT: B 332 MET cc_start: 0.7755 (OUTLIER) cc_final: 0.6351 (mpm)
REVERT: C 52 GLU cc_start: 0.8005 (tp30) cc_final: 0.7598 (mt-10)
REVERT: C 148 LYS cc_start: 0.8335 (mppt) cc_final: 0.7700 (mmtt)
REVERT: C 215 LYS cc_start: 0.8402 (tttp) cc_final: 0.8069 (ttmm)
REVERT: C 332 MET cc_start: 0.7744 (OUTLIER) cc_final: 0.6322 (mpm)
outliers start: 24
outliers final: 9
residues processed: 122
average time/residue: 1.4926
time to fit residues: 191.9775
Evaluate side-chains
125 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 16
poor density : 109
time to evaluate : 0.904
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 138 LYS
Chi-restraints excluded: chain A residue 258 ASP
Chi-restraints excluded: chain A residue 275 GLU
Chi-restraints excluded: chain A residue 332 MET
Chi-restraints excluded: chain B residue 62 ILE
Chi-restraints excluded: chain B residue 72 LEU
Chi-restraints excluded: chain B residue 128 GLU
Chi-restraints excluded: chain B residue 138 LYS
Chi-restraints excluded: chain B residue 237 GLN
Chi-restraints excluded: chain B residue 248 GLU
Chi-restraints excluded: chain B residue 275 GLU
Chi-restraints excluded: chain B residue 318 LEU
Chi-restraints excluded: chain B residue 332 MET
Chi-restraints excluded: chain C residue 62 ILE
Chi-restraints excluded: chain C residue 318 LEU
Chi-restraints excluded: chain C residue 332 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 99
random chunks:
chunk 11 optimal weight: 1.9990
chunk 48 optimal weight: 0.0070
chunk 64 optimal weight: 8.9990
chunk 20 optimal weight: 5.9990
chunk 72 optimal weight: 2.9990
chunk 85 optimal weight: 0.2980
chunk 43 optimal weight: 5.9990
chunk 57 optimal weight: 2.9990
chunk 96 optimal weight: 0.0000
chunk 91 optimal weight: 0.9990
chunk 81 optimal weight: 0.9990
overall best weight: 0.4606
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 237 GLN
C 114 GLN
Total number of N/Q/H flips: 2
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.163601 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.116214 restraints weight = 7377.977|
|-----------------------------------------------------------------------------|
r_work (start): 0.3374 rms_B_bonded: 1.67
r_work: 0.3269 rms_B_bonded: 2.06 restraints_weight: 0.5000
r_work: 0.3156 rms_B_bonded: 3.35 restraints_weight: 0.2500
r_work (final): 0.3156
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8544
moved from start: 0.1601
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.043 8274 Z= 0.163
Angle : 0.550 8.284 11256 Z= 0.285
Chirality : 0.046 0.337 1302
Planarity : 0.004 0.042 1395
Dihedral : 9.288 89.254 1530
Min Nonbonded Distance : 1.955
Molprobity Statistics.
All-atom Clashscore : 3.01
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 1.32 %
Favored : 98.68 %
Rotamer:
Outliers : 1.93 %
Allowed : 19.32 %
Favored : 78.74 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 20.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 1.28 (0.29), residues: 984
helix: 1.73 (0.36), residues: 273
sheet: 0.40 (0.27), residues: 318
loop : 0.81 (0.35), residues: 393
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.008 0.001 TRP C 259
HIS 0.002 0.001 HIS A 296
PHE 0.008 0.001 PHE A 230
TYR 0.016 0.001 TYR B 90
ARG 0.009 0.001 ARG B 180
********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
1968 Ramachandran restraints generated.
984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
1968 Ramachandran restraints generated.
984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
132 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 16
poor density : 116
time to evaluate : 1.006
Fit side-chains
REVERT: A 138 LYS cc_start: 0.8687 (OUTLIER) cc_final: 0.8338 (tttt)
REVERT: A 267 VAL cc_start: 0.7960 (m) cc_final: 0.7680 (p)
REVERT: A 275 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.7469 (mp0)
REVERT: A 332 MET cc_start: 0.7645 (OUTLIER) cc_final: 0.6104 (mpm)
REVERT: B 215 LYS cc_start: 0.8389 (tttp) cc_final: 0.7996 (ttmm)
REVERT: B 267 VAL cc_start: 0.7853 (m) cc_final: 0.7586 (p)
REVERT: B 275 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7873 (tp30)
REVERT: B 332 MET cc_start: 0.7691 (OUTLIER) cc_final: 0.6235 (mpm)
REVERT: C 52 GLU cc_start: 0.7941 (tp30) cc_final: 0.7573 (mt-10)
REVERT: C 148 LYS cc_start: 0.8266 (mppt) cc_final: 0.7634 (mmtt)
REVERT: C 249 LYS cc_start: 0.8839 (mttt) cc_final: 0.8638 (mttm)
REVERT: C 267 VAL cc_start: 0.7807 (m) cc_final: 0.7543 (p)
REVERT: C 332 MET cc_start: 0.7676 (OUTLIER) cc_final: 0.6193 (mpm)
outliers start: 16
outliers final: 8
residues processed: 123
average time/residue: 1.4230
time to fit residues: 184.9330
Evaluate side-chains
129 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 14
poor density : 115
time to evaluate : 0.966
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 138 LYS
Chi-restraints excluded: chain A residue 275 GLU
Chi-restraints excluded: chain A residue 318 LEU
Chi-restraints excluded: chain A residue 332 MET
Chi-restraints excluded: chain B residue 62 ILE
Chi-restraints excluded: chain B residue 72 LEU
Chi-restraints excluded: chain B residue 128 GLU
Chi-restraints excluded: chain B residue 237 GLN
Chi-restraints excluded: chain B residue 275 GLU
Chi-restraints excluded: chain B residue 318 LEU
Chi-restraints excluded: chain B residue 332 MET
Chi-restraints excluded: chain C residue 62 ILE
Chi-restraints excluded: chain C residue 318 LEU
Chi-restraints excluded: chain C residue 332 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 99
random chunks:
chunk 48 optimal weight: 0.6980
chunk 41 optimal weight: 3.9990
chunk 92 optimal weight: 3.9990
chunk 55 optimal weight: 4.9990
chunk 46 optimal weight: 3.9990
chunk 63 optimal weight: 0.0870
chunk 7 optimal weight: 0.7980
chunk 72 optimal weight: 3.9990
chunk 85 optimal weight: 4.9990
chunk 21 optimal weight: 0.9980
chunk 42 optimal weight: 1.9990
overall best weight: 0.9160
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 237 GLN
B 114 GLN
C 114 GLN
Total number of N/Q/H flips: 3
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.162395 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.114593 restraints weight = 7443.681|
|-----------------------------------------------------------------------------|
r_work (start): 0.3352 rms_B_bonded: 1.67
r_work: 0.3243 rms_B_bonded: 2.11 restraints_weight: 0.5000
r_work: 0.3131 rms_B_bonded: 3.41 restraints_weight: 0.2500
r_work (final): 0.3131
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8584
moved from start: 0.1588
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.046 8274 Z= 0.215
Angle : 0.571 8.324 11256 Z= 0.297
Chirality : 0.046 0.283 1302
Planarity : 0.004 0.043 1395
Dihedral : 9.383 89.795 1530
Min Nonbonded Distance : 1.907
Molprobity Statistics.
All-atom Clashscore : 3.14
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 1.22 %
Favored : 98.78 %
Rotamer:
Outliers : 1.81 %
Allowed : 19.69 %
Favored : 78.50 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 20.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 1.30 (0.29), residues: 984
helix: 1.73 (0.36), residues: 273
sheet: 0.41 (0.27), residues: 318
loop : 0.83 (0.36), residues: 393
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.008 0.001 TRP C 259
HIS 0.002 0.001 HIS A 296
PHE 0.012 0.002 PHE A 243
TYR 0.015 0.001 TYR B 90
ARG 0.008 0.001 ARG B 180
Origin is already at (0, 0, 0), no shifts will be applied
===============================================================================
Job complete
usr+sys time: 7425.32 seconds
wall clock time: 131 minutes 32.87 seconds (7892.87 seconds total)