Starting phenix.real_space_refine
on Tue Aug 6 17:52:57 2024 by dcliebschner
===============================================================================
Processing files:
-------------------------------------------------------------------------------
Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tzk_41761/08_2024/8tzk_41761.cif
Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tzk_41761/08_2024/8tzk_41761.map
Processing PHIL parameters:
-------------------------------------------------------------------------------
Adding command-line PHIL:
-------------------------
refinement.macro_cycles=10
scattering_table=electron
resolution=3.55
write_initial_geo_file=False
Final processed PHIL parameters:
-------------------------------------------------------------------------------
data_manager {
real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tzk_41761/08_2024/8tzk_41761.map"
default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tzk_41761/08_2024/8tzk_41761.map"
model {
file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tzk_41761/08_2024/8tzk_41761.cif"
}
default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tzk_41761/08_2024/8tzk_41761.cif"
}
resolution = 3.55
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= 0.000 sd= 0.017
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: 7
Type Number sf(0) Gaussians
P 4 5.49 5
Mg 2 5.21 5
S 27 5.16 5
C 5491 2.51 5
N 1550 2.21 5
O 1535 1.98 5
H 8468 0.53 5
sf(0) = scattering factor at diffraction angle 0.
Process input model
Symmetric amino acids flipped
Residue "A PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Time to flip residues: 0.03s
Monomer Library directory:
"/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib"
Total number of atoms: 17077
Number of models: 1
Model: ""
Number of chains: 7
Chain: "A"
Number of atoms: 3494
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 220, 3494
Classifications: {'peptide': 220}
Link IDs: {'PTRANS': 9, 'TRANS': 210}
Unresolved non-hydrogen bonds: 12
Unresolved non-hydrogen angles: 15
Unresolved non-hydrogen dihedrals: 9
Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1}
Unresolved non-hydrogen planarities: 11
Chain: "B"
Number of atoms: 3494
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 220, 3494
Classifications: {'peptide': 220}
Link IDs: {'PTRANS': 9, 'TRANS': 210}
Unresolved non-hydrogen bonds: 12
Unresolved non-hydrogen angles: 15
Unresolved non-hydrogen dihedrals: 9
Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1}
Unresolved non-hydrogen planarities: 11
Chain: "C"
Number of atoms: 4369
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 304, 4369
Classifications: {'peptide': 304}
Link IDs: {'PTRANS': 10, 'TRANS': 293}
Unresolved non-hydrogen bonds: 173
Unresolved non-hydrogen angles: 215
Unresolved non-hydrogen dihedrals: 133
Unresolved non-hydrogen chiralities: 11
Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 10, 'ASP:plan': 9, 'ARG:plan': 6, 'HIS:plan': 1}
Unresolved non-hydrogen planarities: 118
Chain: "D"
Number of atoms: 4359
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 304, 4359
Classifications: {'peptide': 304}
Link IDs: {'PTRANS': 10, 'TRANS': 293}
Unresolved chain link angles: 3
Unresolved non-hydrogen bonds: 166
Unresolved non-hydrogen angles: 208
Unresolved non-hydrogen dihedrals: 127
Unresolved non-hydrogen chiralities: 15
Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 9, 'ARG:plan': 5, 'ASP:plan': 8}
Unresolved non-hydrogen planarities: 93
Chain: "E"
Number of atoms: 1305
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 101, 1305
Classifications: {'peptide': 101}
Link IDs: {'TRANS': 100}
Unresolved non-hydrogen bonds: 131
Unresolved non-hydrogen angles: 165
Unresolved non-hydrogen dihedrals: 97
Unresolved non-hydrogen chiralities: 11
Planarities with less than four sites: {'GLN:plan1': 7, 'GLU:plan': 6, 'ASN:plan1': 6, 'ASP:plan': 1, 'ARG:plan': 3}
Unresolved non-hydrogen planarities: 88
Chain: "A"
Number of atoms: 28
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 2, 28
Unusual residues: {' MG': 1, 'ADP': 1}
Classifications: {'undetermined': 2}
Link IDs: {None: 1}
Chain: "B"
Number of atoms: 28
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 2, 28
Unusual residues: {' MG': 1, 'ADP': 1}
Classifications: {'undetermined': 2}
Link IDs: {None: 1}
Time building chain proxies: 9.77, per 1000 atoms: 0.57
Number of scatterers: 17077
At special positions: 0
Unit cell: (105.84, 83.16, 149.04, 90, 90, 90)
Space group: P 1 (No. 1)
Number of sites at special positions: 0
Number of scattering types: 7
Type Number sf(0)
S 27 16.00
P 4 15.00
Mg 2 11.99
O 1535 8.00
N 1550 7.00
C 5491 6.00
H 8468 1.00
sf(0) = scattering factor at diffraction angle 0.
Number of disulfides: simple=0, symmetry=0
Automatic linking
Parameters for automatic linking
Linking & cutoffs
Metal : Auto - 3.50
Amino acid : False - 1.90
Carbohydrate : True - 1.99
Ligands : True - 1.99
Small molecules : False - 1.98
Amino acid - RNA/DNA : False
Number of custom bonds: simple=0, symmetry=0
Time building additional restraints: 13.82
Conformation dependent library (CDL) restraints added in 2.1 seconds
2278 Ramachandran restraints generated.
1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2.
Adding C-beta torsion restraints...
Number of C-beta restraints generated: 2168
Finding SS restraints...
Secondary structure from input PDB file:
35 helices and 10 sheets defined
62.6% alpha, 7.0% beta
0 base pairs and 0 stacking pairs defined.
Time for finding SS restraints: 1.37
Creating SS restraints...
Processing helix chain 'A' and resid 49 through 58
removed outlier: 3.651A pdb=" N CYS A 58 " --> pdb=" O LEU A 54 " (cutoff:3.500A)
Processing helix chain 'A' and resid 82 through 89
removed outlier: 3.784A pdb=" N ASN A 89 " --> pdb=" O PHE A 85 " (cutoff:3.500A)
Processing helix chain 'A' and resid 104 through 116
Proline residue: A 112 - end of helix
removed outlier: 3.739A pdb=" N GLU A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A)
Processing helix chain 'A' and resid 119 through 134
Processing helix chain 'A' and resid 148 through 162
Processing helix chain 'A' and resid 178 through 196
removed outlier: 3.709A pdb=" N ARG A 184 " --> pdb=" O GLU A 180 " (cutoff:3.500A)
Processing helix chain 'A' and resid 205 through 212
removed outlier: 3.770A pdb=" N ARG A 212 " --> pdb=" O LEU A 208 " (cutoff:3.500A)
Processing helix chain 'B' and resid 49 through 58
removed outlier: 3.648A pdb=" N CYS B 58 " --> pdb=" O LEU B 54 " (cutoff:3.500A)
Processing helix chain 'B' and resid 82 through 89
removed outlier: 3.766A pdb=" N ASN B 89 " --> pdb=" O PHE B 85 " (cutoff:3.500A)
Processing helix chain 'B' and resid 104 through 116
Proline residue: B 112 - end of helix
removed outlier: 3.759A pdb=" N GLU B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A)
Processing helix chain 'B' and resid 119 through 134
Processing helix chain 'B' and resid 148 through 162
Processing helix chain 'B' and resid 178 through 196
removed outlier: 3.671A pdb=" N ARG B 184 " --> pdb=" O GLU B 180 " (cutoff:3.500A)
Processing helix chain 'B' and resid 205 through 212
removed outlier: 3.766A pdb=" N ARG B 212 " --> pdb=" O LEU B 208 " (cutoff:3.500A)
Processing helix chain 'C' and resid 31 through 47
removed outlier: 3.511A pdb=" N ILE C 35 " --> pdb=" O SER C 31 " (cutoff:3.500A)
removed outlier: 3.629A pdb=" N HIS C 36 " --> pdb=" O PHE C 32 " (cutoff:3.500A)
removed outlier: 3.566A pdb=" N LEU C 47 " --> pdb=" O SER C 43 " (cutoff:3.500A)
Processing helix chain 'C' and resid 50 through 86
removed outlier: 3.604A pdb=" N THR C 57 " --> pdb=" O GLY C 53 " (cutoff:3.500A)
removed outlier: 3.553A pdb=" N LEU C 58 " --> pdb=" O ASN C 54 " (cutoff:3.500A)
Proline residue: C 68 - end of helix
removed outlier: 4.217A pdb=" N ALA C 86 " --> pdb=" O ALA C 82 " (cutoff:3.500A)
Processing helix chain 'C' and resid 100 through 114
removed outlier: 3.571A pdb=" N ILE C 104 " --> pdb=" O PRO C 100 " (cutoff:3.500A)
removed outlier: 3.898A pdb=" N ILE C 105 " --> pdb=" O GLU C 101 " (cutoff:3.500A)
removed outlier: 3.673A pdb=" N VAL C 106 " --> pdb=" O PRO C 102 " (cutoff:3.500A)
Processing helix chain 'C' and resid 124 through 136
Processing helix chain 'C' and resid 162 through 178
Processing helix chain 'C' and resid 193 through 229
removed outlier: 3.812A pdb=" N HIS C 197 " --> pdb=" O ASP C 193 " (cutoff:3.500A)
removed outlier: 4.103A pdb=" N ALA C 199 " --> pdb=" O ILE C 195 " (cutoff:3.500A)
removed outlier: 4.812A pdb=" N THR C 200 " --> pdb=" O ARG C 196 " (cutoff:3.500A)
removed outlier: 3.868A pdb=" N GLY C 219 " --> pdb=" O PHE C 215 " (cutoff:3.500A)
Processing helix chain 'C' and resid 229 through 240
Processing helix chain 'C' and resid 242 through 287
Proline residue: C 249 - end of helix
removed outlier: 4.651A pdb=" N GLY C 278 " --> pdb=" O ILE C 274 " (cutoff:3.500A)
removed outlier: 4.749A pdb=" N ALA C 279 " --> pdb=" O LEU C 275 " (cutoff:3.500A)
removed outlier: 3.584A pdb=" N LEU C 286 " --> pdb=" O ALA C 282 " (cutoff:3.500A)
removed outlier: 3.529A pdb=" N TYR C 287 " --> pdb=" O LEU C 283 " (cutoff:3.500A)
Processing helix chain 'C' and resid 297 through 326
removed outlier: 3.909A pdb=" N LEU C 302 " --> pdb=" O TRP C 298 " (cutoff:3.500A)
removed outlier: 4.186A pdb=" N GLU C 326 " --> pdb=" O ARG C 322 " (cutoff:3.500A)
Processing helix chain 'D' and resid 31 through 47
removed outlier: 3.529A pdb=" N HIS D 36 " --> pdb=" O PHE D 32 " (cutoff:3.500A)
removed outlier: 3.675A pdb=" N LEU D 47 " --> pdb=" O SER D 43 " (cutoff:3.500A)
Processing helix chain 'D' and resid 50 through 85
Proline residue: D 68 - end of helix
Processing helix chain 'D' and resid 100 through 114
Processing helix chain 'D' and resid 124 through 135
removed outlier: 4.046A pdb=" N TYR D 135 " --> pdb=" O ASP D 131 " (cutoff:3.500A)
Processing helix chain 'D' and resid 138 through 145
Processing helix chain 'D' and resid 162 through 176
Processing helix chain 'D' and resid 188 through 229
removed outlier: 3.678A pdb=" N LEU D 192 " --> pdb=" O TRP D 188 " (cutoff:3.500A)
removed outlier: 3.624A pdb=" N GLY D 219 " --> pdb=" O PHE D 215 " (cutoff:3.500A)
removed outlier: 3.575A pdb=" N ASN D 229 " --> pdb=" O ASN D 225 " (cutoff:3.500A)
Processing helix chain 'D' and resid 229 through 239
Processing helix chain 'D' and resid 242 through 286
removed outlier: 3.570A pdb=" N ILE D 246 " --> pdb=" O THR D 242 " (cutoff:3.500A)
Proline residue: D 249 - end of helix
removed outlier: 3.727A pdb=" N LEU D 275 " --> pdb=" O LEU D 271 " (cutoff:3.500A)
removed outlier: 3.716A pdb=" N LEU D 286 " --> pdb=" O ALA D 282 " (cutoff:3.500A)
Processing helix chain 'D' and resid 297 through 326
removed outlier: 3.632A pdb=" N LEU D 302 " --> pdb=" O TRP D 298 " (cutoff:3.500A)
removed outlier: 4.081A pdb=" N GLU D 326 " --> pdb=" O ARG D 322 " (cutoff:3.500A)
Processing helix chain 'E' and resid 92 through 129
removed outlier: 3.632A pdb=" N ARG E 96 " --> pdb=" O GLU E 92 " (cutoff:3.500A)
Processing helix chain 'E' and resid 144 through 191
Processing sheet with id=AA1, first strand: chain 'A' and resid 33 through 34
removed outlier: 3.945A pdb=" N ILE A 11 " --> pdb=" O LEU A 34 " (cutoff:3.500A)
removed outlier: 3.529A pdb=" N LYS A 67 " --> pdb=" O GLN A 14 " (cutoff:3.500A)
Processing sheet with id=AA2, first strand: chain 'A' and resid 16 through 18
removed outlier: 3.605A pdb=" N VAL A 16 " --> pdb=" O VAL A 30 " (cutoff:3.500A)
removed outlier: 7.479A pdb=" N LYS A 18 " --> pdb=" O GLN A 28 " (cutoff:3.500A)
removed outlier: 5.443A pdb=" N GLN A 28 " --> pdb=" O LYS A 18 " (cutoff:3.500A)
Processing sheet with id=AA3, first strand: chain 'A' and resid 39 through 40
removed outlier: 5.752A pdb=" N ALA A 40 " --> pdb=" O LEU A 201 " (cutoff:3.500A)
removed outlier: 3.574A pdb=" N ALA A 170 " --> pdb=" O LEU A 200 " (cutoff:3.500A)
removed outlier: 6.255A pdb=" N GLY A 91 " --> pdb=" O LEU A 169 " (cutoff:3.500A)
removed outlier: 7.758A pdb=" N ASP A 171 " --> pdb=" O GLY A 91 " (cutoff:3.500A)
removed outlier: 6.920A pdb=" N VAL A 93 " --> pdb=" O ASP A 171 " (cutoff:3.500A)
Processing sheet with id=AA4, first strand: chain 'A' and resid 43 through 44
removed outlier: 6.570A pdb=" N GLY A 43 " --> pdb=" O LEU A 220 " (cutoff:3.500A)
Processing sheet with id=AA5, first strand: chain 'B' and resid 33 through 34
removed outlier: 3.920A pdb=" N ILE B 11 " --> pdb=" O LEU B 34 " (cutoff:3.500A)
removed outlier: 3.508A pdb=" N LYS B 67 " --> pdb=" O GLN B 14 " (cutoff:3.500A)
Processing sheet with id=AA6, first strand: chain 'B' and resid 16 through 18
removed outlier: 3.622A pdb=" N VAL B 16 " --> pdb=" O VAL B 30 " (cutoff:3.500A)
removed outlier: 7.517A pdb=" N LYS B 18 " --> pdb=" O GLN B 28 " (cutoff:3.500A)
removed outlier: 5.469A pdb=" N GLN B 28 " --> pdb=" O LYS B 18 " (cutoff:3.500A)
Processing sheet with id=AA7, first strand: chain 'B' and resid 39 through 40
removed outlier: 5.745A pdb=" N ALA B 40 " --> pdb=" O LEU B 201 " (cutoff:3.500A)
removed outlier: 3.536A pdb=" N ALA B 170 " --> pdb=" O LEU B 200 " (cutoff:3.500A)
removed outlier: 6.285A pdb=" N GLY B 91 " --> pdb=" O LEU B 169 " (cutoff:3.500A)
removed outlier: 7.781A pdb=" N ASP B 171 " --> pdb=" O GLY B 91 " (cutoff:3.500A)
removed outlier: 6.959A pdb=" N VAL B 93 " --> pdb=" O ASP B 171 " (cutoff:3.500A)
Processing sheet with id=AA8, first strand: chain 'B' and resid 43 through 44
removed outlier: 6.571A pdb=" N GLY B 43 " --> pdb=" O LEU B 220 " (cutoff:3.500A)
Processing sheet with id=AA9, first strand: chain 'C' and resid 91 through 94
removed outlier: 3.633A pdb=" N VAL C 153 " --> pdb=" O ILE C 123 " (cutoff:3.500A)
Processing sheet with id=AB1, first strand: chain 'D' and resid 117 through 123
removed outlier: 3.978A pdb=" N LYS D 119 " --> pdb=" O THR D 157 " (cutoff:3.500A)
removed outlier: 3.648A pdb=" N VAL D 153 " --> pdb=" O ILE D 123 " (cutoff:3.500A)
removed outlier: 3.612A pdb=" N ASP D 181 " --> pdb=" O TYR D 94 " (cutoff:3.500A)
558 hydrogen bonds defined for protein.
1662 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: 6.02
Time building geometry restraints manager: 14.60 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: 8462
1.03 - 1.23: 6
1.23 - 1.42: 3534
1.42 - 1.61: 5162
1.61 - 1.81: 54
Bond restraints: 17218
Sorted by residual:
bond pdb=" C6 ADP A 302 "
pdb=" N6 ADP A 302 "
ideal model delta sigma weight residual
1.355 1.450 -0.095 2.00e-02 2.50e+03 2.24e+01
bond pdb=" C6 ADP B 302 "
pdb=" N6 ADP B 302 "
ideal model delta sigma weight residual
1.355 1.449 -0.094 2.00e-02 2.50e+03 2.22e+01
bond pdb=" C4 ADP A 302 "
pdb=" C5 ADP A 302 "
ideal model delta sigma weight residual
1.490 1.397 0.093 2.00e-02 2.50e+03 2.18e+01
bond pdb=" C4 ADP B 302 "
pdb=" C5 ADP B 302 "
ideal model delta sigma weight residual
1.490 1.397 0.093 2.00e-02 2.50e+03 2.17e+01
bond pdb=" O3A ADP B 302 "
pdb=" PB ADP B 302 "
ideal model delta sigma weight residual
1.610 1.684 -0.074 2.00e-02 2.50e+03 1.37e+01
... (remaining 17213 not shown)
Histogram of bond angle deviations from ideal:
100.58 - 107.34: 1792
107.34 - 114.11: 19164
114.11 - 120.87: 6409
120.87 - 127.63: 3676
127.63 - 134.39: 75
Bond angle restraints: 31116
Sorted by residual:
angle pdb=" O2B ADP B 302 "
pdb=" PB ADP B 302 "
pdb=" O3B ADP B 302 "
ideal model delta sigma weight residual
119.90 109.35 10.55 3.00e+00 1.11e-01 1.24e+01
angle pdb=" O2B ADP A 302 "
pdb=" PB ADP A 302 "
pdb=" O3B ADP A 302 "
ideal model delta sigma weight residual
119.90 109.45 10.45 3.00e+00 1.11e-01 1.21e+01
angle pdb=" N ILE D 239 "
pdb=" CA ILE D 239 "
pdb=" C ILE D 239 "
ideal model delta sigma weight residual
110.21 106.30 3.91 1.13e+00 7.83e-01 1.20e+01
angle pdb=" O1B ADP B 302 "
pdb=" PB ADP B 302 "
pdb=" O3B ADP B 302 "
ideal model delta sigma weight residual
119.90 109.67 10.23 3.00e+00 1.11e-01 1.16e+01
angle pdb=" O1B ADP B 302 "
pdb=" PB ADP B 302 "
pdb=" O2B ADP B 302 "
ideal model delta sigma weight residual
119.90 109.72 10.18 3.00e+00 1.11e-01 1.15e+01
... (remaining 31111 not shown)
Histogram of dihedral angle deviations from ideal:
0.00 - 24.87: 7770
24.87 - 49.73: 219
49.73 - 74.60: 65
74.60 - 99.46: 1
99.46 - 124.33: 6
Dihedral angle restraints: 8061
sinusoidal: 4289
harmonic: 3772
Sorted by residual:
dihedral pdb=" O2A ADP B 302 "
pdb=" O3A ADP B 302 "
pdb=" PA ADP B 302 "
pdb=" PB ADP B 302 "
ideal model delta sinusoidal sigma weight residual
-60.00 64.33 -124.33 1 2.00e+01 2.50e-03 3.75e+01
dihedral pdb=" O1B ADP A 302 "
pdb=" O3A ADP A 302 "
pdb=" PB ADP A 302 "
pdb=" PA ADP A 302 "
ideal model delta sinusoidal sigma weight residual
-60.00 61.90 -121.90 1 2.00e+01 2.50e-03 3.67e+01
dihedral pdb=" O1B ADP B 302 "
pdb=" O3A ADP B 302 "
pdb=" PB ADP B 302 "
pdb=" PA ADP B 302 "
ideal model delta sinusoidal sigma weight residual
-60.00 59.60 -119.60 1 2.00e+01 2.50e-03 3.59e+01
... (remaining 8058 not shown)
Histogram of chiral volume deviations from ideal:
0.000 - 0.042: 1173
0.042 - 0.084: 179
0.084 - 0.126: 61
0.126 - 0.168: 5
0.168 - 0.211: 6
Chirality restraints: 1424
Sorted by residual:
chirality pdb=" C2' ADP A 302 "
pdb=" C1' ADP A 302 "
pdb=" C3' ADP A 302 "
pdb=" O2' ADP A 302 "
both_signs ideal model delta sigma weight residual
False -2.51 -2.72 0.21 2.00e-01 2.50e+01 1.11e+00
chirality pdb=" C3' ADP A 302 "
pdb=" C2' ADP A 302 "
pdb=" C4' ADP A 302 "
pdb=" O3' ADP A 302 "
both_signs ideal model delta sigma weight residual
False -2.51 -2.72 0.21 2.00e-01 2.50e+01 1.09e+00
chirality pdb=" C3' ADP B 302 "
pdb=" C2' ADP B 302 "
pdb=" C4' ADP B 302 "
pdb=" O3' ADP B 302 "
both_signs ideal model delta sigma weight residual
False -2.51 -2.72 0.21 2.00e-01 2.50e+01 1.07e+00
... (remaining 1421 not shown)
Planarity restraints: 2615
Sorted by residual:
delta sigma weight rms_deltas residual
plane pdb=" C GLU C 87 " 0.014 5.00e-02 4.00e+02 2.13e-02 7.24e-01
pdb=" N PRO C 88 " -0.037 5.00e-02 4.00e+02
pdb=" CA PRO C 88 " 0.011 5.00e-02 4.00e+02
pdb=" CD PRO C 88 " 0.012 5.00e-02 4.00e+02
delta sigma weight rms_deltas residual
plane pdb=" C ARG B 212 " 0.013 5.00e-02 4.00e+02 2.02e-02 6.54e-01
pdb=" N PRO B 213 " -0.035 5.00e-02 4.00e+02
pdb=" CA PRO B 213 " 0.010 5.00e-02 4.00e+02
pdb=" CD PRO B 213 " 0.011 5.00e-02 4.00e+02
delta sigma weight rms_deltas residual
plane pdb=" C GLU C 101 " 0.012 5.00e-02 4.00e+02 1.84e-02 5.40e-01
pdb=" N PRO C 102 " -0.032 5.00e-02 4.00e+02
pdb=" CA PRO C 102 " 0.009 5.00e-02 4.00e+02
pdb=" CD PRO C 102 " 0.010 5.00e-02 4.00e+02
... (remaining 2612 not shown)
Histogram of nonbonded interaction distances:
1.51 - 2.13: 379
2.13 - 2.75: 31413
2.75 - 3.36: 46217
3.36 - 3.98: 55796
3.98 - 4.60: 90294
Nonbonded interactions: 224099
Sorted by model distance:
nonbonded pdb=" O GLU B 116 "
pdb=" HG SER B 117 "
model vdw
1.511 2.450
nonbonded pdb=" O LEU E 122 "
pdb=" HG1 THR E 125 "
model vdw
1.588 2.450
nonbonded pdb=" O GLU A 116 "
pdb=" HG SER A 117 "
model vdw
1.623 2.450
nonbonded pdb=" HD1 HIS D 36 "
pdb=" OH TYR D 252 "
model vdw
1.643 2.450
nonbonded pdb="HE21 GLN A 25 "
pdb=" OE1 GLN A 28 "
model vdw
1.668 2.450
... (remaining 224094 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: 0.00
Found NCS groups:
ncs_group {
reference = chain 'A'
selection = chain 'B'
}
ncs_group {
reference = (chain 'C' and (resid 27 through 83 or (resid 84 and (name N or name CA or name \
C or name O or name CB or name H or name HA )) or resid 85 through 91 or (resid \
92 and (name N or name CA or name C or name O or name CB or name H or name HA )) \
or resid 93 through 99 or (resid 100 and (name N or name CA or name C or name O \
or name CB or name HA )) or resid 101 or (resid 102 and (name N or name CA or n \
ame C or name O or name CB or name HA )) or (resid 103 through 117 and (name N o \
r name CA or name C or name O or name CB or name H or name HA )) or resid 118 th \
rough 120 or (resid 121 and (name N or name CA or name C or name O or name CB or \
name H or name HA )) or resid 122 through 123 or (resid 124 and (name N or name \
CA or name C or name O or name CB or name H or name HA )) or resid 125 through \
152 or (resid 153 and (name N or name CA or name C or name O or name CB or name \
H or name HA )) or resid 154 or (resid 155 through 157 and (name N or name CA or \
name C or name O or name CB or name H or name HA )) or (resid 158 and (name N o \
r name CA or name C or name O or name CB or name HA )) or resid 159 through 230 \
or (resid 231 and (name N or name CA or name C or name O or name CB or name H or \
name HA )) or resid 232 through 241 or (resid 242 through 243 and (name N or na \
me CA or name C or name O or name CB or name H or name HA )) or resid 244 throug \
h 291 or (resid 292 and (name N or name CA or name C or name O or name CB or nam \
e H or name HA )) or resid 293 or (resid 294 and (name N or name CA or name C or \
name O or name CB or name H or name HA )) or resid 295 through 330))
selection = (chain 'D' and (resid 27 or (resid 28 and (name N or name CA or name C or name O \
or name CB or name H or name HA )) or resid 29 through 35 or (resid 36 and (nam \
e N or name CA or name C or name O or name CB or name CG or name ND1 or name CD2 \
or name CE1 or name NE2 or name H or name HA or name HB2 or name HB3 or name HD \
2 or name HE1 or name HE2)) or resid 37 through 82 or (resid 83 through 84 and ( \
name N or name CA or name C or name O or name CB or name H or name HA )) or resi \
d 85 through 89 or (resid 90 and (name N or name CA or name C or name O or name \
CB or name H or name HA )) or resid 91 through 94 or (resid 95 through 96 and (n \
ame N or name CA or name C or name O or name CB or name H or name HA )) or resid \
97 through 110 or (resid 111 through 117 and (name N or name CA or name C or na \
me O or name CB or name H or name HA )) or resid 118 through 148 or (resid 149 a \
nd (name N or name CA or name C or name O or name CB or name H or name HA )) or \
resid 150 through 162 or (resid 163 through 169 and (name N or name CA or name C \
or name O or name CB or name H or name HA )) or resid 170 through 172 or (resid \
173 through 174 and (name N or name CA or name C or name O or name CB or name H \
or name HA )) or resid 175 through 178 or (resid 179 and (name N or name CA or \
name C or name O or name CB or name H or name HA )) or resid 180 or (resid 181 a \
nd (name N or name CA or name C or name O or name CB or name H or name HA )) or \
resid 182 through 183 or (resid 184 through 187 and (name N or name CA or name C \
or name O or name CB or name H or name HA )) or resid 188 through 191 or (resid \
192 through 193 and (name N or name CA or name C or name O or name CB or name H \
or name HA )) or resid 194 through 195 or (resid 196 and (name N or name CA or \
name C or name O or name CB or name H or name HA )) or resid 197 through 287 or \
(resid 288 and (name N or name CA or name C or name O or name CB or name H or na \
me HA )) or resid 289 through 330))
}
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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
Set random seed: 0.000
Set model cs if undefined: 0.000
Decide on map wrapping: 0.000
Normalize map: mean=0, sd=1: 10.590
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: 0.940
Check model and map are aligned: 0.000
Set scattering table: 0.000
Process input model: 58.630
Find NCS groups from input model: 0.470
Set up NCS constraints: 0.080
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: 0.020
Load rotamer database and sin/cos tables:3.140
Set ADP refinement strategy: 0.000
Make a string to write initial .geo file:0.000
Internal consistency checks: 0.000
Total: 73.870
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7808
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 : 0.004 0.095 8750 Z= 0.248
Angle : 0.527 10.553 11890 Z= 0.246
Chirality : 0.037 0.211 1424
Planarity : 0.002 0.021 1509
Dihedral : 11.132 124.329 3110
Min Nonbonded Distance : 1.922
Molprobity Statistics.
All-atom Clashscore : 2.51
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 3.07 %
Favored : 96.93 %
Rotamer:
Outliers : 0.00 %
Allowed : 2.53 %
Favored : 97.47 %
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: 3.24 (0.26), residues: 1139
helix: 3.71 (0.19), residues: 672
sheet: 0.47 (0.56), residues: 103
loop : -0.50 (0.33), residues: 364
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.004 0.001 TRP C 298
HIS 0.002 0.001 HIS B 97
PHE 0.006 0.001 PHE C 257
TYR 0.008 0.001 TYR D 252
ARG 0.003 0.000 ARG B 126
*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
2278 Ramachandran restraints generated.
1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
2278 Ramachandran restraints generated.
1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER 46 is missing expected H atoms. Skipping.
Residue SER 51 is missing expected H atoms. Skipping.
Residue SER 46 is missing expected H atoms. Skipping.
Residue SER 51 is missing expected H atoms. Skipping.
Residue LYS 28 is missing expected H atoms. Skipping.
Residue LEU 95 is missing expected H atoms. Skipping.
Residue THR 99 is missing expected H atoms. Skipping.
Residue LEU 111 is missing expected H atoms. Skipping.
Residue LYS 119 is missing expected H atoms. Skipping.
Residue THR 149 is missing expected H atoms. Skipping.
Residue LYS 159 is missing expected H atoms. Skipping.
Residue VAL 160 is missing expected H atoms. Skipping.
Residue SER 162 is missing expected H atoms. Skipping.
Residue ILE 166 is missing expected H atoms. Skipping.
Residue THR 168 is missing expected H atoms. Skipping.
Residue LEU 169 is missing expected H atoms. Skipping.
Residue LYS 171 is missing expected H atoms. Skipping.
Residue LEU 173 is missing expected H atoms. Skipping.
Residue VAL 179 is missing expected H atoms. Skipping.
Residue MET 184 is missing expected H atoms. Skipping.
Residue LEU 192 is missing expected H atoms. Skipping.
Residue SER 92 is missing expected H atoms. Skipping.
Residue THR 99 is missing expected H atoms. Skipping.
Residue ILE 104 is missing expected H atoms. Skipping.
Residue ILE 105 is missing expected H atoms. Skipping.
Residue VAL 106 is missing expected H atoms. Skipping.
Residue LEU 107 is missing expected H atoms. Skipping.
Residue LYS 108 is missing expected H atoms. Skipping.
Residue ILE 117 is missing expected H atoms. Skipping.
Residue LYS 119 is missing expected H atoms. Skipping.
Residue LYS 121 is missing expected H atoms. Skipping.
Residue SER 124 is missing expected H atoms. Skipping.
Residue VAL 153 is missing expected H atoms. Skipping.
Residue VAL 155 is missing expected H atoms. Skipping.
Residue VAL 156 is missing expected H atoms. Skipping.
Residue THR 157 is missing expected H atoms. Skipping.
Residue LYS 159 is missing expected H atoms. Skipping.
Residue VAL 160 is missing expected H atoms. Skipping.
Residue SER 162 is missing expected H atoms. Skipping.
Residue ILE 166 is missing expected H atoms. Skipping.
Residue THR 168 is missing expected H atoms. Skipping.
Residue LYS 171 is missing expected H atoms. Skipping.
Residue THR 242 is missing expected H atoms. Skipping.
Residue ILE 294 is missing expected H atoms. Skipping.
Residue LEU 91 is missing expected H atoms. Skipping.
Residue ILE 98 is missing expected H atoms. Skipping.
Residue LEU 101 is missing expected H atoms. Skipping.
Residue SER 103 is missing expected H atoms. Skipping.
Residue ILE 105 is missing expected H atoms. Skipping.
Residue LEU 108 is missing expected H atoms. Skipping.
Residue THR 110 is missing expected H atoms. Skipping.
Residue THR 171 is missing expected H atoms. Skipping.
Residue SER 175 is missing expected H atoms. Skipping.
Residue LYS 178 is missing expected H atoms. Skipping.
Residue THR 182 is missing expected H atoms. Skipping.
Residue ILE 187 is missing expected H atoms. Skipping.
Residue LYS 189 is missing expected H atoms. Skipping.
Residue LEU 190 is missing expected H atoms. Skipping.
Evaluate side-chains
195 residues out of total 973 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 195
time to evaluate : 1.437
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: B 101 MET cc_start: 0.8660 (mmm) cc_final: 0.8317 (mmt)
REVERT: C 41 LYS cc_start: 0.8721 (tttt) cc_final: 0.8507 (ttmm)
REVERT: C 63 MET cc_start: 0.8253 (mtm) cc_final: 0.7980 (mtt)
REVERT: D 223 ARG cc_start: 0.7435 (ttm-80) cc_final: 0.7216 (ttp-170)
REVERT: E 123 LEU cc_start: 0.9022 (tt) cc_final: 0.8536 (mt)
REVERT: E 141 ARG cc_start: 0.7904 (mtp180) cc_final: 0.7580 (tpm170)
REVERT: E 170 GLN cc_start: 0.8658 (tm-30) cc_final: 0.8416 (tm-30)
outliers start: 0
outliers final: 0
residues processed: 195
average time/residue: 0.6410
time to fit residues: 157.7154
Evaluate side-chains
114 residues out of total 973 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 114
time to evaluate : 1.394
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 114
random chunks:
chunk 96 optimal weight: 0.8980
chunk 86 optimal weight: 2.9990
chunk 47 optimal weight: 0.4980
chunk 29 optimal weight: 0.6980
chunk 58 optimal weight: 7.9990
chunk 46 optimal weight: 0.3980
chunk 89 optimal weight: 1.9990
chunk 34 optimal weight: 0.9980
chunk 54 optimal weight: 1.9990
chunk 66 optimal weight: 0.6980
chunk 103 optimal weight: 0.0980
overall best weight: 0.4780
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 80 ASN
B 80 ASN
E 111 GLN
E 161 GLN
Total number of N/Q/H flips: 4
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7867
moved from start: 0.2073
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.029 8750 Z= 0.205
Angle : 0.554 7.021 11890 Z= 0.280
Chirality : 0.037 0.165 1424
Planarity : 0.003 0.031 1509
Dihedral : 8.119 131.566 1262
Min Nonbonded Distance : 2.098
Molprobity Statistics.
All-atom Clashscore : 4.15
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 3.07 %
Favored : 96.93 %
Rotamer:
Outliers : 1.08 %
Allowed : 8.07 %
Favored : 90.84 %
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: 3.00 (0.26), residues: 1139
helix: 3.50 (0.19), residues: 682
sheet: 0.15 (0.54), residues: 100
loop : -0.62 (0.33), residues: 357
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.003 0.001 TRP C 298
HIS 0.003 0.001 HIS A 33
PHE 0.016 0.001 PHE C 215
TYR 0.014 0.001 TYR D 252
ARG 0.003 0.000 ARG E 159
*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
2278 Ramachandran restraints generated.
1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
2278 Ramachandran restraints generated.
1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER 46 is missing expected H atoms. Skipping.
Residue SER 51 is missing expected H atoms. Skipping.
Residue SER 46 is missing expected H atoms. Skipping.
Residue SER 51 is missing expected H atoms. Skipping.
Residue LYS 28 is missing expected H atoms. Skipping.
Residue LEU 95 is missing expected H atoms. Skipping.
Residue THR 99 is missing expected H atoms. Skipping.
Residue LEU 111 is missing expected H atoms. Skipping.
Residue LYS 119 is missing expected H atoms. Skipping.
Residue THR 149 is missing expected H atoms. Skipping.
Residue LYS 159 is missing expected H atoms. Skipping.
Residue VAL 160 is missing expected H atoms. Skipping.
Residue SER 162 is missing expected H atoms. Skipping.
Residue ILE 166 is missing expected H atoms. Skipping.
Residue THR 168 is missing expected H atoms. Skipping.
Residue LEU 169 is missing expected H atoms. Skipping.
Residue LYS 171 is missing expected H atoms. Skipping.
Residue LEU 173 is missing expected H atoms. Skipping.
Residue VAL 179 is missing expected H atoms. Skipping.
Residue MET 184 is missing expected H atoms. Skipping.
Residue LEU 192 is missing expected H atoms. Skipping.
Residue SER 92 is missing expected H atoms. Skipping.
Residue THR 99 is missing expected H atoms. Skipping.
Residue ILE 104 is missing expected H atoms. Skipping.
Residue ILE 105 is missing expected H atoms. Skipping.
Residue VAL 106 is missing expected H atoms. Skipping.
Residue LEU 107 is missing expected H atoms. Skipping.
Residue LYS 108 is missing expected H atoms. Skipping.
Residue ILE 117 is missing expected H atoms. Skipping.
Residue LYS 119 is missing expected H atoms. Skipping.
Residue LYS 121 is missing expected H atoms. Skipping.
Residue SER 124 is missing expected H atoms. Skipping.
Residue VAL 153 is missing expected H atoms. Skipping.
Residue VAL 155 is missing expected H atoms. Skipping.
Residue VAL 156 is missing expected H atoms. Skipping.
Residue THR 157 is missing expected H atoms. Skipping.
Residue LYS 159 is missing expected H atoms. Skipping.
Residue VAL 160 is missing expected H atoms. Skipping.
Residue SER 162 is missing expected H atoms. Skipping.
Residue ILE 166 is missing expected H atoms. Skipping.
Residue THR 168 is missing expected H atoms. Skipping.
Residue LYS 171 is missing expected H atoms. Skipping.
Residue THR 242 is missing expected H atoms. Skipping.
Residue ILE 294 is missing expected H atoms. Skipping.
Residue LEU 91 is missing expected H atoms. Skipping.
Residue ILE 98 is missing expected H atoms. Skipping.
Residue LEU 101 is missing expected H atoms. Skipping.
Residue SER 103 is missing expected H atoms. Skipping.
Residue ILE 105 is missing expected H atoms. Skipping.
Residue LEU 108 is missing expected H atoms. Skipping.
Residue THR 110 is missing expected H atoms. Skipping.
Residue THR 171 is missing expected H atoms. Skipping.
Residue SER 175 is missing expected H atoms. Skipping.
Residue LYS 178 is missing expected H atoms. Skipping.
Residue THR 182 is missing expected H atoms. Skipping.
Residue ILE 187 is missing expected H atoms. Skipping.
Residue LYS 189 is missing expected H atoms. Skipping.
Residue LEU 190 is missing expected H atoms. Skipping.
Evaluate side-chains
134 residues out of total 973 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 9
poor density : 125
time to evaluate : 1.389
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: B 101 MET cc_start: 0.8695 (mmm) cc_final: 0.8396 (mmt)
REVERT: C 41 LYS cc_start: 0.8726 (tttt) cc_final: 0.8510 (ttmm)
REVERT: C 127 GLN cc_start: 0.8178 (mm-40) cc_final: 0.7963 (mm-40)
REVERT: D 223 ARG cc_start: 0.7472 (ttm-80) cc_final: 0.7246 (ttp-170)
REVERT: D 306 MET cc_start: 0.6697 (tmm) cc_final: 0.6459 (tmm)
REVERT: E 123 LEU cc_start: 0.9034 (tt) cc_final: 0.8534 (mt)
REVERT: E 141 ARG cc_start: 0.7932 (mtp180) cc_final: 0.7611 (tpm170)
REVERT: E 170 GLN cc_start: 0.8692 (tm-30) cc_final: 0.8459 (tm-30)
outliers start: 9
outliers final: 7
residues processed: 132
average time/residue: 0.5512
time to fit residues: 95.2713
Evaluate side-chains
119 residues out of total 973 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 7
poor density : 112
time to evaluate : 1.427
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 80 ASN
Chi-restraints excluded: chain A residue 136 LEU
Chi-restraints excluded: chain B residue 80 ASN
Chi-restraints excluded: chain B residue 96 ASP
Chi-restraints excluded: chain B residue 174 THR
Chi-restraints excluded: chain C residue 191 ARG
Chi-restraints excluded: chain C residue 203 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 114
random chunks:
chunk 57 optimal weight: 0.0030
chunk 32 optimal weight: 0.8980
chunk 86 optimal weight: 2.9990
chunk 70 optimal weight: 0.9980
chunk 28 optimal weight: 0.9980
chunk 103 optimal weight: 0.9980
chunk 112 optimal weight: 3.9990
chunk 92 optimal weight: 0.9990
chunk 102 optimal weight: 0.6980
chunk 35 optimal weight: 0.5980
chunk 83 optimal weight: 0.8980
overall best weight: 0.6190
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7887
moved from start: 0.2375
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.031 8750 Z= 0.227
Angle : 0.531 5.770 11890 Z= 0.270
Chirality : 0.036 0.152 1424
Planarity : 0.003 0.027 1509
Dihedral : 7.653 126.551 1262
Min Nonbonded Distance : 2.024
Molprobity Statistics.
All-atom Clashscore : 3.80
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 2.99 %
Favored : 97.01 %
Rotamer:
Outliers : 1.33 %
Allowed : 9.04 %
Favored : 89.64 %
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: 2.88 (0.25), residues: 1139
helix: 3.47 (0.19), residues: 682
sheet: -0.03 (0.52), residues: 100
loop : -0.77 (0.32), residues: 357
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.003 0.001 TRP C 298
HIS 0.003 0.001 HIS B 97
PHE 0.023 0.001 PHE C 291
TYR 0.012 0.001 TYR D 252
ARG 0.011 0.000 ARG A 126
*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
2278 Ramachandran restraints generated.
1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
2278 Ramachandran restraints generated.
1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER 46 is missing expected H atoms. Skipping.
Residue SER 51 is missing expected H atoms. Skipping.
Residue SER 46 is missing expected H atoms. Skipping.
Residue SER 51 is missing expected H atoms. Skipping.
Residue LYS 28 is missing expected H atoms. Skipping.
Residue LEU 95 is missing expected H atoms. Skipping.
Residue THR 99 is missing expected H atoms. Skipping.
Residue LEU 111 is missing expected H atoms. Skipping.
Residue LYS 119 is missing expected H atoms. Skipping.
Residue THR 149 is missing expected H atoms. Skipping.
Residue LYS 159 is missing expected H atoms. Skipping.
Residue VAL 160 is missing expected H atoms. Skipping.
Residue SER 162 is missing expected H atoms. Skipping.
Residue ILE 166 is missing expected H atoms. Skipping.
Residue THR 168 is missing expected H atoms. Skipping.
Residue LEU 169 is missing expected H atoms. Skipping.
Residue LYS 171 is missing expected H atoms. Skipping.
Residue LEU 173 is missing expected H atoms. Skipping.
Residue VAL 179 is missing expected H atoms. Skipping.
Residue MET 184 is missing expected H atoms. Skipping.
Residue LEU 192 is missing expected H atoms. Skipping.
Residue SER 92 is missing expected H atoms. Skipping.
Residue THR 99 is missing expected H atoms. Skipping.
Residue ILE 104 is missing expected H atoms. Skipping.
Residue ILE 105 is missing expected H atoms. Skipping.
Residue VAL 106 is missing expected H atoms. Skipping.
Residue LEU 107 is missing expected H atoms. Skipping.
Residue LYS 108 is missing expected H atoms. Skipping.
Residue ILE 117 is missing expected H atoms. Skipping.
Residue LYS 119 is missing expected H atoms. Skipping.
Residue LYS 121 is missing expected H atoms. Skipping.
Residue SER 124 is missing expected H atoms. Skipping.
Residue VAL 153 is missing expected H atoms. Skipping.
Residue VAL 155 is missing expected H atoms. Skipping.
Residue VAL 156 is missing expected H atoms. Skipping.
Residue THR 157 is missing expected H atoms. Skipping.
Residue LYS 159 is missing expected H atoms. Skipping.
Residue VAL 160 is missing expected H atoms. Skipping.
Residue SER 162 is missing expected H atoms. Skipping.
Residue ILE 166 is missing expected H atoms. Skipping.
Residue THR 168 is missing expected H atoms. Skipping.
Residue LYS 171 is missing expected H atoms. Skipping.
Residue THR 242 is missing expected H atoms. Skipping.
Residue ILE 294 is missing expected H atoms. Skipping.
Residue LEU 91 is missing expected H atoms. Skipping.
Residue ILE 98 is missing expected H atoms. Skipping.
Residue LEU 101 is missing expected H atoms. Skipping.
Residue SER 103 is missing expected H atoms. Skipping.
Residue ILE 105 is missing expected H atoms. Skipping.
Residue LEU 108 is missing expected H atoms. Skipping.
Residue THR 110 is missing expected H atoms. Skipping.
Residue THR 171 is missing expected H atoms. Skipping.
Residue SER 175 is missing expected H atoms. Skipping.
Residue LYS 178 is missing expected H atoms. Skipping.
Residue THR 182 is missing expected H atoms. Skipping.
Residue ILE 187 is missing expected H atoms. Skipping.
Residue LYS 189 is missing expected H atoms. Skipping.
Residue LEU 190 is missing expected H atoms. Skipping.
Evaluate side-chains
128 residues out of total 973 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 11
poor density : 117
time to evaluate : 1.305
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: A 61 GLU cc_start: 0.7918 (mt-10) cc_final: 0.7524 (mt-10)
REVERT: B 101 MET cc_start: 0.8700 (mmm) cc_final: 0.8374 (mmt)
REVERT: C 41 LYS cc_start: 0.8720 (tttt) cc_final: 0.8516 (ttmm)
REVERT: C 291 PHE cc_start: 0.7362 (t80) cc_final: 0.6954 (t80)
REVERT: D 223 ARG cc_start: 0.7428 (ttm-80) cc_final: 0.7219 (ttp-170)
REVERT: D 306 MET cc_start: 0.6742 (tmm) cc_final: 0.6486 (tmm)
REVERT: E 123 LEU cc_start: 0.9026 (tt) cc_final: 0.8534 (mt)
REVERT: E 141 ARG cc_start: 0.7950 (mtp180) cc_final: 0.7615 (tpm170)
REVERT: E 170 GLN cc_start: 0.8696 (tm-30) cc_final: 0.8457 (tm-30)
outliers start: 11
outliers final: 11
residues processed: 123
average time/residue: 0.5818
time to fit residues: 92.9860
Evaluate side-chains
122 residues out of total 973 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 11
poor density : 111
time to evaluate : 1.315
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 136 LEU
Chi-restraints excluded: chain A residue 176 ASN
Chi-restraints excluded: chain B residue 96 ASP
Chi-restraints excluded: chain B residue 174 THR
Chi-restraints excluded: chain C residue 191 ARG
Chi-restraints excluded: chain C residue 203 VAL
Chi-restraints excluded: chain D residue 29 THR
Chi-restraints excluded: chain D residue 185 ASP
Chi-restraints excluded: chain D residue 214 VAL
Chi-restraints excluded: chain D residue 324 LEU
Chi-restraints excluded: chain E residue 149 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 114
random chunks:
chunk 102 optimal weight: 0.8980
chunk 77 optimal weight: 0.9990
chunk 53 optimal weight: 2.9990
chunk 11 optimal weight: 0.6980
chunk 49 optimal weight: 0.7980
chunk 69 optimal weight: 0.9980
chunk 104 optimal weight: 20.0000
chunk 110 optimal weight: 1.9990
chunk 54 optimal weight: 0.9990
chunk 98 optimal weight: 0.9990
chunk 29 optimal weight: 0.6980
overall best weight: 0.8180
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 80 ASN
E 111 GLN
Total number of N/Q/H flips: 2
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7926
moved from start: 0.2594
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.004 0.043 8750 Z= 0.279
Angle : 0.537 5.796 11890 Z= 0.277
Chirality : 0.037 0.154 1424
Planarity : 0.003 0.025 1509
Dihedral : 7.300 120.548 1262
Min Nonbonded Distance : 2.018
Molprobity Statistics.
All-atom Clashscore : 4.39
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 2.90 %
Favored : 97.10 %
Rotamer:
Outliers : 1.69 %
Allowed : 9.52 %
Favored : 88.80 %
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: 2.66 (0.25), residues: 1139
helix: 3.30 (0.19), residues: 682
sheet: -0.20 (0.51), residues: 102
loop : -0.83 (0.32), residues: 355
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.004 0.001 TRP D 256
HIS 0.004 0.001 HIS B 97
PHE 0.010 0.001 PHE A 32
TYR 0.011 0.001 TYR D 252
ARG 0.003 0.000 ARG B 24
*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
2278 Ramachandran restraints generated.
1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
2278 Ramachandran restraints generated.
1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER 46 is missing expected H atoms. Skipping.
Residue SER 51 is missing expected H atoms. Skipping.
Residue SER 46 is missing expected H atoms. Skipping.
Residue SER 51 is missing expected H atoms. Skipping.
Residue LYS 28 is missing expected H atoms. Skipping.
Residue LEU 95 is missing expected H atoms. Skipping.
Residue THR 99 is missing expected H atoms. Skipping.
Residue LEU 111 is missing expected H atoms. Skipping.
Residue LYS 119 is missing expected H atoms. Skipping.
Residue THR 149 is missing expected H atoms. Skipping.
Residue LYS 159 is missing expected H atoms. Skipping.
Residue VAL 160 is missing expected H atoms. Skipping.
Residue SER 162 is missing expected H atoms. Skipping.
Residue ILE 166 is missing expected H atoms. Skipping.
Residue THR 168 is missing expected H atoms. Skipping.
Residue LEU 169 is missing expected H atoms. Skipping.
Residue LYS 171 is missing expected H atoms. Skipping.
Residue LEU 173 is missing expected H atoms. Skipping.
Residue VAL 179 is missing expected H atoms. Skipping.
Residue MET 184 is missing expected H atoms. Skipping.
Residue LEU 192 is missing expected H atoms. Skipping.
Residue SER 92 is missing expected H atoms. Skipping.
Residue THR 99 is missing expected H atoms. Skipping.
Residue ILE 104 is missing expected H atoms. Skipping.
Residue ILE 105 is missing expected H atoms. Skipping.
Residue VAL 106 is missing expected H atoms. Skipping.
Residue LEU 107 is missing expected H atoms. Skipping.
Residue LYS 108 is missing expected H atoms. Skipping.
Residue ILE 117 is missing expected H atoms. Skipping.
Residue LYS 119 is missing expected H atoms. Skipping.
Residue LYS 121 is missing expected H atoms. Skipping.
Residue SER 124 is missing expected H atoms. Skipping.
Residue VAL 153 is missing expected H atoms. Skipping.
Residue VAL 155 is missing expected H atoms. Skipping.
Residue VAL 156 is missing expected H atoms. Skipping.
Residue THR 157 is missing expected H atoms. Skipping.
Residue LYS 159 is missing expected H atoms. Skipping.
Residue VAL 160 is missing expected H atoms. Skipping.
Residue SER 162 is missing expected H atoms. Skipping.
Residue ILE 166 is missing expected H atoms. Skipping.
Residue THR 168 is missing expected H atoms. Skipping.
Residue LYS 171 is missing expected H atoms. Skipping.
Residue THR 242 is missing expected H atoms. Skipping.
Residue ILE 294 is missing expected H atoms. Skipping.
Residue LEU 91 is missing expected H atoms. Skipping.
Residue ILE 98 is missing expected H atoms. Skipping.
Residue LEU 101 is missing expected H atoms. Skipping.
Residue SER 103 is missing expected H atoms. Skipping.
Residue ILE 105 is missing expected H atoms. Skipping.
Residue LEU 108 is missing expected H atoms. Skipping.
Residue THR 110 is missing expected H atoms. Skipping.
Residue THR 171 is missing expected H atoms. Skipping.
Residue SER 175 is missing expected H atoms. Skipping.
Residue LYS 178 is missing expected H atoms. Skipping.
Residue THR 182 is missing expected H atoms. Skipping.
Residue ILE 187 is missing expected H atoms. Skipping.
Residue LYS 189 is missing expected H atoms. Skipping.
Residue LEU 190 is missing expected H atoms. Skipping.
Evaluate side-chains
132 residues out of total 973 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 14
poor density : 118
time to evaluate : 1.496
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: A 61 GLU cc_start: 0.7991 (mt-10) cc_final: 0.7605 (mt-10)
REVERT: B 101 MET cc_start: 0.8714 (mmm) cc_final: 0.8419 (mmt)
REVERT: C 41 LYS cc_start: 0.8746 (tttt) cc_final: 0.8537 (ttmm)
REVERT: C 291 PHE cc_start: 0.7386 (t80) cc_final: 0.7066 (t80)
REVERT: D 306 MET cc_start: 0.6789 (tmm) cc_final: 0.6495 (tmm)
REVERT: E 123 LEU cc_start: 0.9038 (tt) cc_final: 0.8546 (mt)
REVERT: E 141 ARG cc_start: 0.7929 (mtp180) cc_final: 0.7629 (tpm170)
REVERT: E 170 GLN cc_start: 0.8679 (tm-30) cc_final: 0.8442 (tm-30)
outliers start: 14
outliers final: 12
residues processed: 125
average time/residue: 0.5631
time to fit residues: 91.7823
Evaluate side-chains
124 residues out of total 973 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 12
poor density : 112
time to evaluate : 1.411
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 136 LEU
Chi-restraints excluded: chain A residue 176 ASN
Chi-restraints excluded: chain B residue 96 ASP
Chi-restraints excluded: chain B residue 174 THR
Chi-restraints excluded: chain C residue 55 ILE
Chi-restraints excluded: chain C residue 191 ARG
Chi-restraints excluded: chain C residue 203 VAL
Chi-restraints excluded: chain D residue 29 THR
Chi-restraints excluded: chain D residue 144 LEU
Chi-restraints excluded: chain D residue 185 ASP
Chi-restraints excluded: chain D residue 214 VAL
Chi-restraints excluded: chain E residue 149 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 114
random chunks:
chunk 91 optimal weight: 0.9990
chunk 62 optimal weight: 0.9990
chunk 1 optimal weight: 0.5980
chunk 82 optimal weight: 3.9990
chunk 45 optimal weight: 0.9990
chunk 94 optimal weight: 0.9990
chunk 76 optimal weight: 1.9990
chunk 0 optimal weight: 0.9980
chunk 56 optimal weight: 2.9990
chunk 98 optimal weight: 0.8980
chunk 27 optimal weight: 0.8980
overall best weight: 0.8782
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 28 GLN
Total number of N/Q/H flips: 1
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7941
moved from start: 0.2765
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.004 0.042 8750 Z= 0.293
Angle : 0.542 5.838 11890 Z= 0.280
Chirality : 0.037 0.158 1424
Planarity : 0.003 0.026 1509
Dihedral : 7.300 120.476 1262
Min Nonbonded Distance : 2.005
Molprobity Statistics.
All-atom Clashscore : 4.68
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 3.34 %
Favored : 96.66 %
Rotamer:
Outliers : 1.69 %
Allowed : 10.72 %
Favored : 87.59 %
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: 2.54 (0.25), residues: 1139
helix: 3.23 (0.19), residues: 682
sheet: -0.31 (0.50), residues: 102
loop : -0.93 (0.31), residues: 355
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.009 0.001 TRP C 298
HIS 0.006 0.001 HIS B 97
PHE 0.011 0.001 PHE C 291
TYR 0.012 0.001 TYR C 250
ARG 0.005 0.000 ARG A 126
*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
2278 Ramachandran restraints generated.
1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
2278 Ramachandran restraints generated.
1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER 46 is missing expected H atoms. Skipping.
Residue SER 51 is missing expected H atoms. Skipping.
Residue SER 46 is missing expected H atoms. Skipping.
Residue SER 51 is missing expected H atoms. Skipping.
Residue LYS 28 is missing expected H atoms. Skipping.
Residue LEU 95 is missing expected H atoms. Skipping.
Residue THR 99 is missing expected H atoms. Skipping.
Residue LEU 111 is missing expected H atoms. Skipping.
Residue LYS 119 is missing expected H atoms. Skipping.
Residue THR 149 is missing expected H atoms. Skipping.
Residue LYS 159 is missing expected H atoms. Skipping.
Residue VAL 160 is missing expected H atoms. Skipping.
Residue SER 162 is missing expected H atoms. Skipping.
Residue ILE 166 is missing expected H atoms. Skipping.
Residue THR 168 is missing expected H atoms. Skipping.
Residue LEU 169 is missing expected H atoms. Skipping.
Residue LYS 171 is missing expected H atoms. Skipping.
Residue LEU 173 is missing expected H atoms. Skipping.
Residue VAL 179 is missing expected H atoms. Skipping.
Residue MET 184 is missing expected H atoms. Skipping.
Residue LEU 192 is missing expected H atoms. Skipping.
Residue SER 92 is missing expected H atoms. Skipping.
Residue THR 99 is missing expected H atoms. Skipping.
Residue ILE 104 is missing expected H atoms. Skipping.
Residue ILE 105 is missing expected H atoms. Skipping.
Residue VAL 106 is missing expected H atoms. Skipping.
Residue LEU 107 is missing expected H atoms. Skipping.
Residue LYS 108 is missing expected H atoms. Skipping.
Residue ILE 117 is missing expected H atoms. Skipping.
Residue LYS 119 is missing expected H atoms. Skipping.
Residue LYS 121 is missing expected H atoms. Skipping.
Residue SER 124 is missing expected H atoms. Skipping.
Residue VAL 153 is missing expected H atoms. Skipping.
Residue VAL 155 is missing expected H atoms. Skipping.
Residue VAL 156 is missing expected H atoms. Skipping.
Residue THR 157 is missing expected H atoms. Skipping.
Residue LYS 159 is missing expected H atoms. Skipping.
Residue VAL 160 is missing expected H atoms. Skipping.
Residue SER 162 is missing expected H atoms. Skipping.
Residue ILE 166 is missing expected H atoms. Skipping.
Residue THR 168 is missing expected H atoms. Skipping.
Residue LYS 171 is missing expected H atoms. Skipping.
Residue THR 242 is missing expected H atoms. Skipping.
Residue ILE 294 is missing expected H atoms. Skipping.
Residue LEU 91 is missing expected H atoms. Skipping.
Residue ILE 98 is missing expected H atoms. Skipping.
Residue LEU 101 is missing expected H atoms. Skipping.
Residue SER 103 is missing expected H atoms. Skipping.
Residue ILE 105 is missing expected H atoms. Skipping.
Residue LEU 108 is missing expected H atoms. Skipping.
Residue THR 110 is missing expected H atoms. Skipping.
Residue THR 171 is missing expected H atoms. Skipping.
Residue SER 175 is missing expected H atoms. Skipping.
Residue LYS 178 is missing expected H atoms. Skipping.
Residue THR 182 is missing expected H atoms. Skipping.
Residue ILE 187 is missing expected H atoms. Skipping.
Residue LYS 189 is missing expected H atoms. Skipping.
Residue LEU 190 is missing expected H atoms. Skipping.
Evaluate side-chains
128 residues out of total 973 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 14
poor density : 114
time to evaluate : 1.328
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: A 61 GLU cc_start: 0.7994 (mt-10) cc_final: 0.7613 (mt-10)
REVERT: B 101 MET cc_start: 0.8715 (mmm) cc_final: 0.8411 (mmt)
REVERT: C 41 LYS cc_start: 0.8765 (tttt) cc_final: 0.8543 (ttmm)
REVERT: C 291 PHE cc_start: 0.7430 (t80) cc_final: 0.6982 (t80)
REVERT: D 306 MET cc_start: 0.6805 (tmm) cc_final: 0.6484 (tmm)
REVERT: E 123 LEU cc_start: 0.9020 (tt) cc_final: 0.8556 (mt)
REVERT: E 141 ARG cc_start: 0.7954 (mtp180) cc_final: 0.7636 (tpm170)
REVERT: E 170 GLN cc_start: 0.8696 (tm-30) cc_final: 0.8413 (tm-30)
outliers start: 14
outliers final: 11
residues processed: 121
average time/residue: 0.5652
time to fit residues: 89.3895
Evaluate side-chains
123 residues out of total 973 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 11
poor density : 112
time to evaluate : 1.392
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 136 LEU
Chi-restraints excluded: chain A residue 176 ASN
Chi-restraints excluded: chain B residue 123 ILE
Chi-restraints excluded: chain B residue 174 THR
Chi-restraints excluded: chain C residue 191 ARG
Chi-restraints excluded: chain C residue 203 VAL
Chi-restraints excluded: chain D residue 29 THR
Chi-restraints excluded: chain D residue 144 LEU
Chi-restraints excluded: chain D residue 185 ASP
Chi-restraints excluded: chain D residue 214 VAL
Chi-restraints excluded: chain E residue 149 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 114
random chunks:
chunk 37 optimal weight: 0.9990
chunk 99 optimal weight: 0.9980
chunk 21 optimal weight: 0.9980
chunk 64 optimal weight: 0.0970
chunk 27 optimal weight: 1.9990
chunk 110 optimal weight: 0.8980
chunk 91 optimal weight: 0.9990
chunk 51 optimal weight: 0.9990
chunk 9 optimal weight: 0.9980
chunk 36 optimal weight: 0.3980
chunk 57 optimal weight: 8.9990
overall best weight: 0.6778
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7934
moved from start: 0.2849
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.004 0.044 8750 Z= 0.236
Angle : 0.522 5.993 11890 Z= 0.266
Chirality : 0.037 0.160 1424
Planarity : 0.003 0.026 1509
Dihedral : 7.156 119.541 1262
Min Nonbonded Distance : 1.999
Molprobity Statistics.
All-atom Clashscore : 4.56
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 3.51 %
Favored : 96.49 %
Rotamer:
Outliers : 1.69 %
Allowed : 10.84 %
Favored : 87.47 %
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: 2.59 (0.25), residues: 1139
helix: 3.31 (0.19), residues: 678
sheet: -0.43 (0.49), residues: 102
loop : -0.91 (0.31), residues: 359
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.004 0.001 TRP C 298
HIS 0.005 0.001 HIS B 97
PHE 0.009 0.001 PHE A 32
TYR 0.011 0.001 TYR D 252
ARG 0.003 0.000 ARG C 50
*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
2278 Ramachandran restraints generated.
1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
2278 Ramachandran restraints generated.
1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER 46 is missing expected H atoms. Skipping.
Residue SER 51 is missing expected H atoms. Skipping.
Residue SER 46 is missing expected H atoms. Skipping.
Residue SER 51 is missing expected H atoms. Skipping.
Residue LYS 28 is missing expected H atoms. Skipping.
Residue LEU 95 is missing expected H atoms. Skipping.
Residue THR 99 is missing expected H atoms. Skipping.
Residue LEU 111 is missing expected H atoms. Skipping.
Residue LYS 119 is missing expected H atoms. Skipping.
Residue THR 149 is missing expected H atoms. Skipping.
Residue LYS 159 is missing expected H atoms. Skipping.
Residue VAL 160 is missing expected H atoms. Skipping.
Residue SER 162 is missing expected H atoms. Skipping.
Residue ILE 166 is missing expected H atoms. Skipping.
Residue THR 168 is missing expected H atoms. Skipping.
Residue LEU 169 is missing expected H atoms. Skipping.
Residue LYS 171 is missing expected H atoms. Skipping.
Residue LEU 173 is missing expected H atoms. Skipping.
Residue VAL 179 is missing expected H atoms. Skipping.
Residue MET 184 is missing expected H atoms. Skipping.
Residue LEU 192 is missing expected H atoms. Skipping.
Residue SER 92 is missing expected H atoms. Skipping.
Residue THR 99 is missing expected H atoms. Skipping.
Residue ILE 104 is missing expected H atoms. Skipping.
Residue ILE 105 is missing expected H atoms. Skipping.
Residue VAL 106 is missing expected H atoms. Skipping.
Residue LEU 107 is missing expected H atoms. Skipping.
Residue LYS 108 is missing expected H atoms. Skipping.
Residue ILE 117 is missing expected H atoms. Skipping.
Residue LYS 119 is missing expected H atoms. Skipping.
Residue LYS 121 is missing expected H atoms. Skipping.
Residue SER 124 is missing expected H atoms. Skipping.
Residue VAL 153 is missing expected H atoms. Skipping.
Residue VAL 155 is missing expected H atoms. Skipping.
Residue VAL 156 is missing expected H atoms. Skipping.
Residue THR 157 is missing expected H atoms. Skipping.
Residue LYS 159 is missing expected H atoms. Skipping.
Residue VAL 160 is missing expected H atoms. Skipping.
Residue SER 162 is missing expected H atoms. Skipping.
Residue ILE 166 is missing expected H atoms. Skipping.
Residue THR 168 is missing expected H atoms. Skipping.
Residue LYS 171 is missing expected H atoms. Skipping.
Residue THR 242 is missing expected H atoms. Skipping.
Residue ILE 294 is missing expected H atoms. Skipping.
Residue LEU 91 is missing expected H atoms. Skipping.
Residue ILE 98 is missing expected H atoms. Skipping.
Residue LEU 101 is missing expected H atoms. Skipping.
Residue SER 103 is missing expected H atoms. Skipping.
Residue ILE 105 is missing expected H atoms. Skipping.
Residue LEU 108 is missing expected H atoms. Skipping.
Residue THR 110 is missing expected H atoms. Skipping.
Residue THR 171 is missing expected H atoms. Skipping.
Residue SER 175 is missing expected H atoms. Skipping.
Residue LYS 178 is missing expected H atoms. Skipping.
Residue THR 182 is missing expected H atoms. Skipping.
Residue ILE 187 is missing expected H atoms. Skipping.
Residue LYS 189 is missing expected H atoms. Skipping.
Residue LEU 190 is missing expected H atoms. Skipping.
Evaluate side-chains
130 residues out of total 973 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 14
poor density : 116
time to evaluate : 1.476
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: A 61 GLU cc_start: 0.7976 (mt-10) cc_final: 0.7597 (mt-10)
REVERT: B 101 MET cc_start: 0.8689 (mmm) cc_final: 0.8400 (mmt)
REVERT: C 41 LYS cc_start: 0.8761 (tttt) cc_final: 0.8542 (ttmm)
REVERT: C 291 PHE cc_start: 0.7415 (t80) cc_final: 0.7014 (t80)
REVERT: D 306 MET cc_start: 0.6882 (tmm) cc_final: 0.6535 (tmm)
REVERT: D 326 GLU cc_start: 0.8540 (pp20) cc_final: 0.8196 (pp20)
REVERT: E 123 LEU cc_start: 0.9020 (tt) cc_final: 0.8563 (mt)
REVERT: E 141 ARG cc_start: 0.7948 (mtp180) cc_final: 0.7670 (tpm170)
REVERT: E 170 GLN cc_start: 0.8681 (tm-30) cc_final: 0.8427 (tm-30)
outliers start: 14
outliers final: 12
residues processed: 124
average time/residue: 0.5645
time to fit residues: 91.7936
Evaluate side-chains
126 residues out of total 973 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 12
poor density : 114
time to evaluate : 1.279
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 136 LEU
Chi-restraints excluded: chain A residue 176 ASN
Chi-restraints excluded: chain B residue 123 ILE
Chi-restraints excluded: chain B residue 174 THR
Chi-restraints excluded: chain C residue 191 ARG
Chi-restraints excluded: chain C residue 203 VAL
Chi-restraints excluded: chain D residue 29 THR
Chi-restraints excluded: chain D residue 144 LEU
Chi-restraints excluded: chain D residue 185 ASP
Chi-restraints excluded: chain D residue 214 VAL
Chi-restraints excluded: chain D residue 302 LEU
Chi-restraints excluded: chain E residue 149 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 114
random chunks:
chunk 106 optimal weight: 2.9990
chunk 12 optimal weight: 1.9990
chunk 62 optimal weight: 0.9980
chunk 80 optimal weight: 0.2980
chunk 92 optimal weight: 0.3980
chunk 61 optimal weight: 0.0270
chunk 109 optimal weight: 2.9990
chunk 68 optimal weight: 0.9990
chunk 66 optimal weight: 0.6980
chunk 50 optimal weight: 0.9990
chunk 67 optimal weight: 0.6980
overall best weight: 0.4238
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 25 GLN
A 28 GLN
Total number of N/Q/H flips: 2
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7912
moved from start: 0.2919
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.043 8750 Z= 0.171
Angle : 0.505 6.248 11890 Z= 0.253
Chirality : 0.036 0.172 1424
Planarity : 0.003 0.028 1509
Dihedral : 6.937 118.380 1262
Min Nonbonded Distance : 2.024
Molprobity Statistics.
All-atom Clashscore : 4.21
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 3.34 %
Favored : 96.66 %
Rotamer:
Outliers : 1.33 %
Allowed : 11.20 %
Favored : 87.47 %
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: 2.76 (0.25), residues: 1139
helix: 3.43 (0.19), residues: 681
sheet: -0.38 (0.50), residues: 102
loop : -0.83 (0.32), residues: 356
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.004 0.000 TRP C 298
HIS 0.004 0.001 HIS B 97
PHE 0.008 0.001 PHE A 32
TYR 0.010 0.001 TYR D 252
ARG 0.004 0.000 ARG C 50
*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
2278 Ramachandran restraints generated.
1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
2278 Ramachandran restraints generated.
1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER 46 is missing expected H atoms. Skipping.
Residue SER 51 is missing expected H atoms. Skipping.
Residue SER 46 is missing expected H atoms. Skipping.
Residue SER 51 is missing expected H atoms. Skipping.
Residue LYS 28 is missing expected H atoms. Skipping.
Residue LEU 95 is missing expected H atoms. Skipping.
Residue THR 99 is missing expected H atoms. Skipping.
Residue LEU 111 is missing expected H atoms. Skipping.
Residue LYS 119 is missing expected H atoms. Skipping.
Residue THR 149 is missing expected H atoms. Skipping.
Residue LYS 159 is missing expected H atoms. Skipping.
Residue VAL 160 is missing expected H atoms. Skipping.
Residue SER 162 is missing expected H atoms. Skipping.
Residue ILE 166 is missing expected H atoms. Skipping.
Residue THR 168 is missing expected H atoms. Skipping.
Residue LEU 169 is missing expected H atoms. Skipping.
Residue LYS 171 is missing expected H atoms. Skipping.
Residue LEU 173 is missing expected H atoms. Skipping.
Residue VAL 179 is missing expected H atoms. Skipping.
Residue MET 184 is missing expected H atoms. Skipping.
Residue LEU 192 is missing expected H atoms. Skipping.
Residue SER 92 is missing expected H atoms. Skipping.
Residue THR 99 is missing expected H atoms. Skipping.
Residue ILE 104 is missing expected H atoms. Skipping.
Residue ILE 105 is missing expected H atoms. Skipping.
Residue VAL 106 is missing expected H atoms. Skipping.
Residue LEU 107 is missing expected H atoms. Skipping.
Residue LYS 108 is missing expected H atoms. Skipping.
Residue ILE 117 is missing expected H atoms. Skipping.
Residue LYS 119 is missing expected H atoms. Skipping.
Residue LYS 121 is missing expected H atoms. Skipping.
Residue SER 124 is missing expected H atoms. Skipping.
Residue VAL 153 is missing expected H atoms. Skipping.
Residue VAL 155 is missing expected H atoms. Skipping.
Residue VAL 156 is missing expected H atoms. Skipping.
Residue THR 157 is missing expected H atoms. Skipping.
Residue LYS 159 is missing expected H atoms. Skipping.
Residue VAL 160 is missing expected H atoms. Skipping.
Residue SER 162 is missing expected H atoms. Skipping.
Residue ILE 166 is missing expected H atoms. Skipping.
Residue THR 168 is missing expected H atoms. Skipping.
Residue LYS 171 is missing expected H atoms. Skipping.
Residue THR 242 is missing expected H atoms. Skipping.
Residue ILE 294 is missing expected H atoms. Skipping.
Residue LEU 91 is missing expected H atoms. Skipping.
Residue ILE 98 is missing expected H atoms. Skipping.
Residue LEU 101 is missing expected H atoms. Skipping.
Residue SER 103 is missing expected H atoms. Skipping.
Residue ILE 105 is missing expected H atoms. Skipping.
Residue LEU 108 is missing expected H atoms. Skipping.
Residue THR 110 is missing expected H atoms. Skipping.
Residue THR 171 is missing expected H atoms. Skipping.
Residue SER 175 is missing expected H atoms. Skipping.
Residue LYS 178 is missing expected H atoms. Skipping.
Residue THR 182 is missing expected H atoms. Skipping.
Residue ILE 187 is missing expected H atoms. Skipping.
Residue LYS 189 is missing expected H atoms. Skipping.
Residue LEU 190 is missing expected H atoms. Skipping.
Evaluate side-chains
130 residues out of total 973 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 11
poor density : 119
time to evaluate : 1.343
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: A 61 GLU cc_start: 0.7940 (mt-10) cc_final: 0.7577 (mt-10)
REVERT: B 101 MET cc_start: 0.8670 (mmm) cc_final: 0.8370 (mmt)
REVERT: C 41 LYS cc_start: 0.8739 (tttt) cc_final: 0.8527 (ttmm)
REVERT: C 291 PHE cc_start: 0.7434 (t80) cc_final: 0.6978 (t80)
REVERT: D 306 MET cc_start: 0.6863 (tmm) cc_final: 0.6520 (tmm)
REVERT: D 326 GLU cc_start: 0.8605 (pp20) cc_final: 0.8234 (pp20)
REVERT: E 123 LEU cc_start: 0.9054 (tt) cc_final: 0.8597 (mt)
REVERT: E 141 ARG cc_start: 0.7941 (mtp180) cc_final: 0.7671 (tpm170)
REVERT: E 170 GLN cc_start: 0.8710 (tm-30) cc_final: 0.8407 (tm-30)
outliers start: 11
outliers final: 11
residues processed: 124
average time/residue: 0.5501
time to fit residues: 89.0994
Evaluate side-chains
125 residues out of total 973 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 11
poor density : 114
time to evaluate : 1.330
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 136 LEU
Chi-restraints excluded: chain A residue 176 ASN
Chi-restraints excluded: chain B residue 123 ILE
Chi-restraints excluded: chain B residue 174 THR
Chi-restraints excluded: chain C residue 191 ARG
Chi-restraints excluded: chain C residue 203 VAL
Chi-restraints excluded: chain D residue 29 THR
Chi-restraints excluded: chain D residue 144 LEU
Chi-restraints excluded: chain D residue 185 ASP
Chi-restraints excluded: chain D residue 214 VAL
Chi-restraints excluded: chain E residue 149 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 114
random chunks:
chunk 43 optimal weight: 0.9990
chunk 65 optimal weight: 0.9990
chunk 33 optimal weight: 0.9980
chunk 21 optimal weight: 0.6980
chunk 69 optimal weight: 0.9990
chunk 74 optimal weight: 0.0050
chunk 54 optimal weight: 1.9990
chunk 10 optimal weight: 0.8980
chunk 86 optimal weight: 0.9980
chunk 99 optimal weight: 0.9980
chunk 105 optimal weight: 6.9990
overall best weight: 0.7194
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 28 GLN
B 80 ASN
Total number of N/Q/H flips: 2
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7938
moved from start: 0.3029
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.004 0.047 8750 Z= 0.254
Angle : 0.530 6.001 11890 Z= 0.269
Chirality : 0.037 0.170 1424
Planarity : 0.003 0.029 1509
Dihedral : 6.975 119.610 1262
Min Nonbonded Distance : 2.040
Molprobity Statistics.
All-atom Clashscore : 4.80
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 3.42 %
Favored : 96.58 %
Rotamer:
Outliers : 1.57 %
Allowed : 11.69 %
Favored : 86.75 %
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: 2.64 (0.25), residues: 1139
helix: 3.37 (0.19), residues: 679
sheet: -0.10 (0.51), residues: 92
loop : -1.02 (0.31), residues: 368
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.004 0.001 TRP C 298
HIS 0.005 0.001 HIS B 97
PHE 0.011 0.001 PHE A 32
TYR 0.011 0.001 TYR C 250
ARG 0.004 0.000 ARG B 126
*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
2278 Ramachandran restraints generated.
1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
2278 Ramachandran restraints generated.
1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER 46 is missing expected H atoms. Skipping.
Residue SER 51 is missing expected H atoms. Skipping.
Residue SER 46 is missing expected H atoms. Skipping.
Residue SER 51 is missing expected H atoms. Skipping.
Residue LYS 28 is missing expected H atoms. Skipping.
Residue LEU 95 is missing expected H atoms. Skipping.
Residue THR 99 is missing expected H atoms. Skipping.
Residue LEU 111 is missing expected H atoms. Skipping.
Residue LYS 119 is missing expected H atoms. Skipping.
Residue THR 149 is missing expected H atoms. Skipping.
Residue LYS 159 is missing expected H atoms. Skipping.
Residue VAL 160 is missing expected H atoms. Skipping.
Residue SER 162 is missing expected H atoms. Skipping.
Residue ILE 166 is missing expected H atoms. Skipping.
Residue THR 168 is missing expected H atoms. Skipping.
Residue LEU 169 is missing expected H atoms. Skipping.
Residue LYS 171 is missing expected H atoms. Skipping.
Residue LEU 173 is missing expected H atoms. Skipping.
Residue VAL 179 is missing expected H atoms. Skipping.
Residue MET 184 is missing expected H atoms. Skipping.
Residue LEU 192 is missing expected H atoms. Skipping.
Residue SER 92 is missing expected H atoms. Skipping.
Residue THR 99 is missing expected H atoms. Skipping.
Residue ILE 104 is missing expected H atoms. Skipping.
Residue ILE 105 is missing expected H atoms. Skipping.
Residue VAL 106 is missing expected H atoms. Skipping.
Residue LEU 107 is missing expected H atoms. Skipping.
Residue LYS 108 is missing expected H atoms. Skipping.
Residue ILE 117 is missing expected H atoms. Skipping.
Residue LYS 119 is missing expected H atoms. Skipping.
Residue LYS 121 is missing expected H atoms. Skipping.
Residue SER 124 is missing expected H atoms. Skipping.
Residue VAL 153 is missing expected H atoms. Skipping.
Residue VAL 155 is missing expected H atoms. Skipping.
Residue VAL 156 is missing expected H atoms. Skipping.
Residue THR 157 is missing expected H atoms. Skipping.
Residue LYS 159 is missing expected H atoms. Skipping.
Residue VAL 160 is missing expected H atoms. Skipping.
Residue SER 162 is missing expected H atoms. Skipping.
Residue ILE 166 is missing expected H atoms. Skipping.
Residue THR 168 is missing expected H atoms. Skipping.
Residue LYS 171 is missing expected H atoms. Skipping.
Residue THR 242 is missing expected H atoms. Skipping.
Residue ILE 294 is missing expected H atoms. Skipping.
Residue LEU 91 is missing expected H atoms. Skipping.
Residue ILE 98 is missing expected H atoms. Skipping.
Residue LEU 101 is missing expected H atoms. Skipping.
Residue SER 103 is missing expected H atoms. Skipping.
Residue ILE 105 is missing expected H atoms. Skipping.
Residue LEU 108 is missing expected H atoms. Skipping.
Residue THR 110 is missing expected H atoms. Skipping.
Residue THR 171 is missing expected H atoms. Skipping.
Residue SER 175 is missing expected H atoms. Skipping.
Residue LYS 178 is missing expected H atoms. Skipping.
Residue THR 182 is missing expected H atoms. Skipping.
Residue ILE 187 is missing expected H atoms. Skipping.
Residue LYS 189 is missing expected H atoms. Skipping.
Residue LEU 190 is missing expected H atoms. Skipping.
Evaluate side-chains
129 residues out of total 973 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 13
poor density : 116
time to evaluate : 1.430
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: A 61 GLU cc_start: 0.7971 (mt-10) cc_final: 0.7614 (mt-10)
REVERT: B 101 MET cc_start: 0.8687 (mmm) cc_final: 0.8376 (mmt)
REVERT: C 41 LYS cc_start: 0.8757 (tttt) cc_final: 0.8538 (ttmm)
REVERT: C 291 PHE cc_start: 0.7486 (t80) cc_final: 0.7074 (t80)
REVERT: D 326 GLU cc_start: 0.8611 (pp20) cc_final: 0.8264 (pp20)
REVERT: E 123 LEU cc_start: 0.9033 (tt) cc_final: 0.8576 (mt)
REVERT: E 141 ARG cc_start: 0.7943 (mtp180) cc_final: 0.7654 (tpm170)
REVERT: E 170 GLN cc_start: 0.8640 (tm-30) cc_final: 0.8386 (tm-30)
outliers start: 13
outliers final: 11
residues processed: 123
average time/residue: 0.5781
time to fit residues: 92.7513
Evaluate side-chains
125 residues out of total 973 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 11
poor density : 114
time to evaluate : 1.396
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 136 LEU
Chi-restraints excluded: chain A residue 176 ASN
Chi-restraints excluded: chain B residue 123 ILE
Chi-restraints excluded: chain B residue 174 THR
Chi-restraints excluded: chain C residue 191 ARG
Chi-restraints excluded: chain C residue 203 VAL
Chi-restraints excluded: chain D residue 29 THR
Chi-restraints excluded: chain D residue 185 ASP
Chi-restraints excluded: chain D residue 214 VAL
Chi-restraints excluded: chain D residue 302 LEU
Chi-restraints excluded: chain E residue 149 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 114
random chunks:
chunk 96 optimal weight: 0.7980
chunk 102 optimal weight: 0.3980
chunk 105 optimal weight: 6.9990
chunk 61 optimal weight: 0.8980
chunk 44 optimal weight: 0.0010
chunk 80 optimal weight: 0.6980
chunk 31 optimal weight: 0.9980
chunk 92 optimal weight: 0.9990
chunk 67 optimal weight: 0.9990
chunk 108 optimal weight: 1.9990
chunk 66 optimal weight: 0.0970
overall best weight: 0.3984
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
B 80 ASN
Total number of N/Q/H flips: 1
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7915
moved from start: 0.3049
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.049 8750 Z= 0.172
Angle : 0.514 6.633 11890 Z= 0.256
Chirality : 0.036 0.174 1424
Planarity : 0.003 0.030 1509
Dihedral : 6.825 118.094 1262
Min Nonbonded Distance : 2.046
Molprobity Statistics.
All-atom Clashscore : 5.03
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 3.42 %
Favored : 96.58 %
Rotamer:
Outliers : 1.45 %
Allowed : 11.45 %
Favored : 87.11 %
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: 2.78 (0.25), residues: 1139
helix: 3.45 (0.19), residues: 681
sheet: -0.06 (0.51), residues: 92
loop : -0.93 (0.32), residues: 366
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.004 0.000 TRP C 298
HIS 0.005 0.001 HIS B 97
PHE 0.007 0.001 PHE A 32
TYR 0.010 0.001 TYR D 252
ARG 0.004 0.000 ARG C 50
*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
2278 Ramachandran restraints generated.
1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
2278 Ramachandran restraints generated.
1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER 46 is missing expected H atoms. Skipping.
Residue SER 51 is missing expected H atoms. Skipping.
Residue SER 46 is missing expected H atoms. Skipping.
Residue SER 51 is missing expected H atoms. Skipping.
Residue LYS 28 is missing expected H atoms. Skipping.
Residue LEU 95 is missing expected H atoms. Skipping.
Residue THR 99 is missing expected H atoms. Skipping.
Residue LEU 111 is missing expected H atoms. Skipping.
Residue LYS 119 is missing expected H atoms. Skipping.
Residue THR 149 is missing expected H atoms. Skipping.
Residue LYS 159 is missing expected H atoms. Skipping.
Residue VAL 160 is missing expected H atoms. Skipping.
Residue SER 162 is missing expected H atoms. Skipping.
Residue ILE 166 is missing expected H atoms. Skipping.
Residue THR 168 is missing expected H atoms. Skipping.
Residue LEU 169 is missing expected H atoms. Skipping.
Residue LYS 171 is missing expected H atoms. Skipping.
Residue LEU 173 is missing expected H atoms. Skipping.
Residue VAL 179 is missing expected H atoms. Skipping.
Residue MET 184 is missing expected H atoms. Skipping.
Residue LEU 192 is missing expected H atoms. Skipping.
Residue SER 92 is missing expected H atoms. Skipping.
Residue THR 99 is missing expected H atoms. Skipping.
Residue ILE 104 is missing expected H atoms. Skipping.
Residue ILE 105 is missing expected H atoms. Skipping.
Residue VAL 106 is missing expected H atoms. Skipping.
Residue LEU 107 is missing expected H atoms. Skipping.
Residue LYS 108 is missing expected H atoms. Skipping.
Residue ILE 117 is missing expected H atoms. Skipping.
Residue LYS 119 is missing expected H atoms. Skipping.
Residue LYS 121 is missing expected H atoms. Skipping.
Residue SER 124 is missing expected H atoms. Skipping.
Residue VAL 153 is missing expected H atoms. Skipping.
Residue VAL 155 is missing expected H atoms. Skipping.
Residue VAL 156 is missing expected H atoms. Skipping.
Residue THR 157 is missing expected H atoms. Skipping.
Residue LYS 159 is missing expected H atoms. Skipping.
Residue VAL 160 is missing expected H atoms. Skipping.
Residue SER 162 is missing expected H atoms. Skipping.
Residue ILE 166 is missing expected H atoms. Skipping.
Residue THR 168 is missing expected H atoms. Skipping.
Residue LYS 171 is missing expected H atoms. Skipping.
Residue THR 242 is missing expected H atoms. Skipping.
Residue ILE 294 is missing expected H atoms. Skipping.
Residue LEU 91 is missing expected H atoms. Skipping.
Residue ILE 98 is missing expected H atoms. Skipping.
Residue LEU 101 is missing expected H atoms. Skipping.
Residue SER 103 is missing expected H atoms. Skipping.
Residue ILE 105 is missing expected H atoms. Skipping.
Residue LEU 108 is missing expected H atoms. Skipping.
Residue THR 110 is missing expected H atoms. Skipping.
Residue THR 171 is missing expected H atoms. Skipping.
Residue SER 175 is missing expected H atoms. Skipping.
Residue LYS 178 is missing expected H atoms. Skipping.
Residue THR 182 is missing expected H atoms. Skipping.
Residue ILE 187 is missing expected H atoms. Skipping.
Residue LYS 189 is missing expected H atoms. Skipping.
Residue LEU 190 is missing expected H atoms. Skipping.
Evaluate side-chains
126 residues out of total 973 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 12
poor density : 114
time to evaluate : 1.334
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: A 61 GLU cc_start: 0.7940 (mt-10) cc_final: 0.7582 (mt-10)
REVERT: C 41 LYS cc_start: 0.8739 (tttt) cc_final: 0.8524 (ttmm)
REVERT: C 291 PHE cc_start: 0.7512 (t80) cc_final: 0.7062 (t80)
REVERT: D 326 GLU cc_start: 0.8590 (pp20) cc_final: 0.8264 (pp20)
REVERT: E 123 LEU cc_start: 0.9057 (tt) cc_final: 0.8605 (mt)
REVERT: E 141 ARG cc_start: 0.7928 (mtp180) cc_final: 0.7645 (tpm170)
REVERT: E 170 GLN cc_start: 0.8727 (tm-30) cc_final: 0.8421 (tm-30)
outliers start: 12
outliers final: 11
residues processed: 121
average time/residue: 0.6086
time to fit residues: 97.5375
Evaluate side-chains
123 residues out of total 973 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 11
poor density : 112
time to evaluate : 1.299
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 136 LEU
Chi-restraints excluded: chain A residue 176 ASN
Chi-restraints excluded: chain B residue 123 ILE
Chi-restraints excluded: chain B residue 174 THR
Chi-restraints excluded: chain C residue 191 ARG
Chi-restraints excluded: chain C residue 203 VAL
Chi-restraints excluded: chain D residue 29 THR
Chi-restraints excluded: chain D residue 185 ASP
Chi-restraints excluded: chain D residue 214 VAL
Chi-restraints excluded: chain D residue 302 LEU
Chi-restraints excluded: chain E residue 149 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 114
random chunks:
chunk 51 optimal weight: 0.9990
chunk 75 optimal weight: 0.8980
chunk 113 optimal weight: 40.0000
chunk 104 optimal weight: 30.0000
chunk 90 optimal weight: 0.9990
chunk 9 optimal weight: 0.9990
chunk 69 optimal weight: 0.9980
chunk 55 optimal weight: 0.9990
chunk 71 optimal weight: 0.9980
chunk 96 optimal weight: 0.2980
chunk 27 optimal weight: 0.4980
overall best weight: 0.7380
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
B 80 ASN
E 111 GLN
Total number of N/Q/H flips: 2
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7943
moved from start: 0.3124
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.004 0.054 8750 Z= 0.260
Angle : 0.541 6.600 11890 Z= 0.274
Chirality : 0.037 0.174 1424
Planarity : 0.003 0.031 1509
Dihedral : 6.915 120.108 1262
Min Nonbonded Distance : 2.052
Molprobity Statistics.
All-atom Clashscore : 5.44
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 3.42 %
Favored : 96.58 %
Rotamer:
Outliers : 1.57 %
Allowed : 11.45 %
Favored : 86.99 %
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: 2.66 (0.25), residues: 1139
helix: 3.36 (0.19), residues: 679
sheet: 0.27 (0.57), residues: 70
loop : -0.99 (0.30), residues: 390
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.005 0.001 TRP C 298
HIS 0.006 0.001 HIS B 97
PHE 0.011 0.001 PHE A 32
TYR 0.010 0.001 TYR C 250
ARG 0.006 0.000 ARG B 103
********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
2278 Ramachandran restraints generated.
1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
2278 Ramachandran restraints generated.
1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER 46 is missing expected H atoms. Skipping.
Residue SER 51 is missing expected H atoms. Skipping.
Residue SER 46 is missing expected H atoms. Skipping.
Residue SER 51 is missing expected H atoms. Skipping.
Residue LYS 28 is missing expected H atoms. Skipping.
Residue LEU 95 is missing expected H atoms. Skipping.
Residue THR 99 is missing expected H atoms. Skipping.
Residue LEU 111 is missing expected H atoms. Skipping.
Residue LYS 119 is missing expected H atoms. Skipping.
Residue THR 149 is missing expected H atoms. Skipping.
Residue LYS 159 is missing expected H atoms. Skipping.
Residue VAL 160 is missing expected H atoms. Skipping.
Residue SER 162 is missing expected H atoms. Skipping.
Residue ILE 166 is missing expected H atoms. Skipping.
Residue THR 168 is missing expected H atoms. Skipping.
Residue LEU 169 is missing expected H atoms. Skipping.
Residue LYS 171 is missing expected H atoms. Skipping.
Residue LEU 173 is missing expected H atoms. Skipping.
Residue VAL 179 is missing expected H atoms. Skipping.
Residue MET 184 is missing expected H atoms. Skipping.
Residue LEU 192 is missing expected H atoms. Skipping.
Residue SER 92 is missing expected H atoms. Skipping.
Residue THR 99 is missing expected H atoms. Skipping.
Residue ILE 104 is missing expected H atoms. Skipping.
Residue ILE 105 is missing expected H atoms. Skipping.
Residue VAL 106 is missing expected H atoms. Skipping.
Residue LEU 107 is missing expected H atoms. Skipping.
Residue LYS 108 is missing expected H atoms. Skipping.
Residue ILE 117 is missing expected H atoms. Skipping.
Residue LYS 119 is missing expected H atoms. Skipping.
Residue LYS 121 is missing expected H atoms. Skipping.
Residue SER 124 is missing expected H atoms. Skipping.
Residue VAL 153 is missing expected H atoms. Skipping.
Residue VAL 155 is missing expected H atoms. Skipping.
Residue VAL 156 is missing expected H atoms. Skipping.
Residue THR 157 is missing expected H atoms. Skipping.
Residue LYS 159 is missing expected H atoms. Skipping.
Residue VAL 160 is missing expected H atoms. Skipping.
Residue SER 162 is missing expected H atoms. Skipping.
Residue ILE 166 is missing expected H atoms. Skipping.
Residue THR 168 is missing expected H atoms. Skipping.
Residue LYS 171 is missing expected H atoms. Skipping.
Residue THR 242 is missing expected H atoms. Skipping.
Residue ILE 294 is missing expected H atoms. Skipping.
Residue LEU 91 is missing expected H atoms. Skipping.
Residue ILE 98 is missing expected H atoms. Skipping.
Residue LEU 101 is missing expected H atoms. Skipping.
Residue SER 103 is missing expected H atoms. Skipping.
Residue ILE 105 is missing expected H atoms. Skipping.
Residue LEU 108 is missing expected H atoms. Skipping.
Residue THR 110 is missing expected H atoms. Skipping.
Residue THR 171 is missing expected H atoms. Skipping.
Residue SER 175 is missing expected H atoms. Skipping.
Residue LYS 178 is missing expected H atoms. Skipping.
Residue THR 182 is missing expected H atoms. Skipping.
Residue ILE 187 is missing expected H atoms. Skipping.
Residue LYS 189 is missing expected H atoms. Skipping.
Residue LEU 190 is missing expected H atoms. Skipping.
Evaluate side-chains
126 residues out of total 973 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 13
poor density : 113
time to evaluate : 1.483
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: A 61 GLU cc_start: 0.7965 (mt-10) cc_final: 0.7612 (mt-10)
REVERT: B 101 MET cc_start: 0.8381 (mmt) cc_final: 0.8064 (mmt)
REVERT: C 41 LYS cc_start: 0.8761 (tttt) cc_final: 0.8541 (ttmm)
REVERT: C 291 PHE cc_start: 0.7532 (t80) cc_final: 0.7079 (t80)
REVERT: D 326 GLU cc_start: 0.8638 (pp20) cc_final: 0.8290 (pp20)
REVERT: E 123 LEU cc_start: 0.9049 (tt) cc_final: 0.8617 (mt)
REVERT: E 141 ARG cc_start: 0.7960 (mtp180) cc_final: 0.7656 (tpm170)
REVERT: E 167 GLU cc_start: 0.8652 (mm-30) cc_final: 0.8436 (mm-30)
REVERT: E 170 GLN cc_start: 0.8676 (tm-30) cc_final: 0.8399 (tm-30)
outliers start: 13
outliers final: 11
residues processed: 120
average time/residue: 0.6352
time to fit residues: 99.7372
Evaluate side-chains
124 residues out of total 973 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 11
poor density : 113
time to evaluate : 1.297
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 136 LEU
Chi-restraints excluded: chain A residue 176 ASN
Chi-restraints excluded: chain B residue 123 ILE
Chi-restraints excluded: chain B residue 174 THR
Chi-restraints excluded: chain C residue 191 ARG
Chi-restraints excluded: chain C residue 203 VAL
Chi-restraints excluded: chain D residue 29 THR
Chi-restraints excluded: chain D residue 185 ASP
Chi-restraints excluded: chain D residue 214 VAL
Chi-restraints excluded: chain D residue 302 LEU
Chi-restraints excluded: chain E residue 149 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 114
random chunks:
chunk 83 optimal weight: 1.9990
chunk 13 optimal weight: 0.8980
chunk 25 optimal weight: 0.0060
chunk 90 optimal weight: 0.9990
chunk 37 optimal weight: 0.9990
chunk 93 optimal weight: 0.9980
chunk 11 optimal weight: 0.9990
chunk 16 optimal weight: 0.0570
chunk 79 optimal weight: 0.9990
chunk 5 optimal weight: 0.9990
chunk 65 optimal weight: 0.9980
overall best weight: 0.5914
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
B 80 ASN
Total number of N/Q/H flips: 1
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.109818 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.086151 restraints weight = 48468.817|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 61)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.090198 restraints weight = 19927.751|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.092616 restraints weight = 11089.145|
|-----------------------------------------------------------------------------|
r_work (final): 0.3399
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7960
moved from start: 0.3176
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.049 8750 Z= 0.214
Angle : 0.535 7.073 11890 Z= 0.270
Chirality : 0.037 0.175 1424
Planarity : 0.003 0.032 1509
Dihedral : 6.859 119.188 1262
Min Nonbonded Distance : 2.057
Molprobity Statistics.
All-atom Clashscore : 5.56
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 3.60 %
Favored : 96.40 %
Rotamer:
Outliers : 1.45 %
Allowed : 11.81 %
Favored : 86.75 %
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: 2.69 (0.25), residues: 1139
helix: 3.37 (0.19), residues: 679
sheet: 0.23 (0.56), residues: 70
loop : -0.97 (0.30), residues: 390
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.005 0.001 TRP C 298
HIS 0.005 0.001 HIS B 97
PHE 0.009 0.001 PHE A 32
TYR 0.010 0.001 TYR D 252
ARG 0.011 0.000 ARG B 103
Origin is already at (0, 0, 0), no shifts will be applied
===============================================================================
Job complete
usr+sys time: 3931.78 seconds
wall clock time: 69 minutes 5.91 seconds (4145.91 seconds total)