Starting phenix.real_space_refine
on Thu Jan 16 04:36:46 2025 by dcliebschner
===============================================================================
Processing files:
-------------------------------------------------------------------------------
Found model, /net/cci-nas-00/data/ceres_data/8xwq_38741/01_2025/8xwq_38741.cif
Found real_map, /net/cci-nas-00/data/ceres_data/8xwq_38741/01_2025/8xwq_38741.map
Processing PHIL parameters:
-------------------------------------------------------------------------------
Adding command-line PHIL:
-------------------------
refinement.macro_cycles=10
scattering_table=electron
resolution=4.6
write_initial_geo_file=False
Final processed PHIL parameters:
-------------------------------------------------------------------------------
data_manager {
real_map_files = "/net/cci-nas-00/data/ceres_data/8xwq_38741/01_2025/8xwq_38741.map"
default_real_map = "/net/cci-nas-00/data/ceres_data/8xwq_38741/01_2025/8xwq_38741.map"
model {
file = "/net/cci-nas-00/data/ceres_data/8xwq_38741/01_2025/8xwq_38741.cif"
}
default_model = "/net/cci-nas-00/data/ceres_data/8xwq_38741/01_2025/8xwq_38741.cif"
}
resolution = 4.6
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= 0.006
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: 4
Type Number sf(0) Gaussians
S 70 5.16 5
C 5795 2.51 5
N 1527 2.21 5
O 1684 1.98 5
sf(0) = scattering factor at diffraction angle 0.
Process input model
Symmetric amino acids flipped. Time to flip 20 residue(s): 0.03s
Monomer Library directory:
"/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
Total number of atoms: 9076
Number of models: 1
Model: ""
Number of chains: 6
Chain: "R"
Number of atoms: 2404
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 302, 2404
Classifications: {'peptide': 302}
Incomplete info: {'truncation_to_alanine': 3}
Link IDs: {'PTRANS': 13, 'TRANS': 288}
Chain breaks: 1
Unresolved non-hydrogen bonds: 11
Unresolved non-hydrogen angles: 12
Unresolved non-hydrogen dihedrals: 10
Planarities with less than four sites: {'ASP:plan': 1}
Unresolved non-hydrogen planarities: 3
Chain: "L"
Number of atoms: 171
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 21, 171
Classifications: {'peptide': 21}
Modifications used: {'COO': 1}
Link IDs: {'TRANS': 20}
Chain: "A"
Number of atoms: 1751
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 218, 1751
Classifications: {'peptide': 218}
Modifications used: {'COO': 1}
Incomplete info: {'truncation_to_alanine': 2}
Link IDs: {'PTRANS': 2, 'TRANS': 215}
Chain breaks: 2
Unresolved non-hydrogen bonds: 7
Unresolved non-hydrogen angles: 8
Unresolved non-hydrogen dihedrals: 6
Unresolved non-hydrogen chiralities: 1
Chain: "B"
Number of atoms: 2584
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 338, 2584
Classifications: {'peptide': 338}
Modifications used: {'COO': 1}
Incomplete info: {'truncation_to_alanine': 4}
Link IDs: {'PTRANS': 5, 'TRANS': 332}
Unresolved non-hydrogen bonds: 17
Unresolved non-hydrogen angles: 20
Unresolved non-hydrogen dihedrals: 14
Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1}
Unresolved non-hydrogen planarities: 12
Chain: "C"
Number of atoms: 404
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 53, 404
Classifications: {'peptide': 53}
Incomplete info: {'truncation_to_alanine': 1}
Link IDs: {'PTRANS': 4, 'TRANS': 48}
Unresolved non-hydrogen bonds: 3
Unresolved non-hydrogen angles: 4
Unresolved non-hydrogen dihedrals: 2
Planarities with less than four sites: {'ASP:plan': 1}
Unresolved non-hydrogen planarities: 3
Chain: "D"
Number of atoms: 1762
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 231, 1762
Classifications: {'peptide': 231}
Incomplete info: {'truncation_to_alanine': 5}
Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220}
Chain breaks: 1
Unresolved non-hydrogen bonds: 15
Unresolved non-hydrogen angles: 19
Unresolved non-hydrogen dihedrals: 11
Unresolved non-hydrogen chiralities: 1
Planarities with less than four sites: {'GLU:plan': 3}
Unresolved non-hydrogen planarities: 12
Time building chain proxies: 5.48, per 1000 atoms: 0.60
Number of scatterers: 9076
At special positions: 0
Unit cell: (120.34, 126.904, 109.4, 90, 90, 90)
Space group: P 1 (No. 1)
Number of sites at special positions: 0
Number of scattering types: 4
Type Number sf(0)
S 70 16.00
O 1684 8.00
N 1527 7.00
C 5795 6.00
sf(0) = scattering factor at diffraction angle 0.
Number of disulfides: simple=6, symmetry=0
Simple disulfide: pdb=" SG CYS R 90 " - pdb=" SG CYS R 358 " distance=2.03
Simple disulfide: pdb=" SG CYS R 174 " - pdb=" SG CYS R 255 " distance=2.03
Simple disulfide: pdb=" SG CYS L 1 " - pdb=" SG CYS L 15 " distance=2.03
Simple disulfide: pdb=" SG CYS L 3 " - pdb=" SG CYS L 11 " distance=2.03
Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 149 " distance=2.04
Simple disulfide: pdb=" SG CYS D 147 " - pdb=" SG CYS D 217 " distance=2.03
Automatic linking
Parameters for automatic linking
Linking & cutoffs
Metal : Auto - 3.00
Amino acid : True - 1.90
Carbohydrate : True - 1.99
Ligands : True - 1.99
Small molecules : False - 1.98
Amino acid - RNA/DNA : False
Number of custom bonds: simple=0, symmetry=0
Time building additional restraints: 2.82
Conformation dependent library (CDL) restraints added in 1.0 seconds
2286 Ramachandran restraints generated.
1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
Adding C-beta torsion restraints...
Number of C-beta restraints generated: 2180
Finding SS restraints...
Secondary structure from input PDB file:
27 helices and 14 sheets defined
37.4% alpha, 19.4% beta
0 base pairs and 0 stacking pairs defined.
Time for finding SS restraints: 1.06
Creating SS restraints...
Processing helix chain 'R' and resid 97 through 129
removed outlier: 3.633A pdb=" N VAL R 106 " --> pdb=" O TYR R 102 " (cutoff:3.500A)
Processing helix chain 'R' and resid 134 through 162
Proline residue: R 156 - end of helix
removed outlier: 3.729A pdb=" N LEU R 162 " --> pdb=" O ASN R 158 " (cutoff:3.500A)
Processing helix chain 'R' and resid 170 through 205
Proline residue: R 178 - end of helix
removed outlier: 4.603A pdb=" N VAL R 203 " --> pdb=" O ARG R 199 " (cutoff:3.500A)
Processing helix chain 'R' and resid 217 through 238
removed outlier: 3.752A pdb=" N VAL R 230 " --> pdb=" O TRP R 226 " (cutoff:3.500A)
Proline residue: R 235 - end of helix
removed outlier: 3.611A pdb=" N ILE R 238 " --> pdb=" O VAL R 234 " (cutoff:3.500A)
Processing helix chain 'R' and resid 263 through 272
removed outlier: 4.154A pdb=" N ALA R 272 " --> pdb=" O PHE R 268 " (cutoff:3.500A)
Processing helix chain 'R' and resid 272 through 282
removed outlier: 3.675A pdb=" N TRP R 276 " --> pdb=" O ALA R 272 " (cutoff:3.500A)
Processing helix chain 'R' and resid 282 through 301
Processing helix chain 'R' and resid 313 through 349
Proline residue: R 338 - end of helix
Processing helix chain 'R' and resid 356 through 388
removed outlier: 3.745A pdb=" N ASN R 382 " --> pdb=" O ASN R 378 " (cutoff:3.500A)
Proline residue: R 383 - end of helix
Processing helix chain 'R' and resid 390 through 398
Processing helix chain 'L' and resid 10 through 18
Processing helix chain 'A' and resid 6 through 32
Processing helix chain 'A' and resid 45 through 53
Processing helix chain 'A' and resid 211 through 216
Processing helix chain 'A' and resid 228 through 230
No H-bonds generated for 'chain 'A' and resid 228 through 230'
Processing helix chain 'A' and resid 242 through 255
Processing helix chain 'A' and resid 270 through 281
Processing helix chain 'A' and resid 295 through 310
removed outlier: 3.676A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A)
Processing helix chain 'A' and resid 329 through 351
Processing helix chain 'B' and resid 4 through 26
Processing helix chain 'B' and resid 30 through 35
removed outlier: 3.553A pdb=" N ASN B 35 " --> pdb=" O SER B 31 " (cutoff:3.500A)
Processing helix chain 'C' and resid 10 through 24
Processing helix chain 'C' and resid 29 through 44
Processing helix chain 'D' and resid 28 through 32
removed outlier: 3.651A pdb=" N PHE D 32 " --> pdb=" O PHE D 29 " (cutoff:3.500A)
Processing helix chain 'D' and resid 53 through 56
Processing helix chain 'D' and resid 62 through 65
removed outlier: 3.742A pdb=" N LYS D 65 " --> pdb=" O ASP D 62 " (cutoff:3.500A)
No H-bonds generated for 'chain 'D' and resid 62 through 65'
Processing helix chain 'D' and resid 74 through 76
No H-bonds generated for 'chain 'D' and resid 74 through 76'
Processing sheet with id=AA1, first strand: chain 'R' and resid 240 through 243
Processing sheet with id=AA2, first strand: chain 'R' and resid 246 through 247
Processing sheet with id=AA3, first strand: chain 'A' and resid 185 through 188
removed outlier: 3.630A pdb=" N LEU A 38 " --> pdb=" O PHE A 199 " (cutoff:3.500A)
removed outlier: 3.643A pdb=" N CYS A 224 " --> pdb=" O LEU A 39 " (cutoff:3.500A)
Processing sheet with id=AA4, first strand: chain 'B' and resid 47 through 51
removed outlier: 3.722A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A)
removed outlier: 3.790A pdb=" N LEU B 336 " --> pdb=" O LEU B 51 " (cutoff:3.500A)
Processing sheet with id=AA5, first strand: chain 'B' and resid 58 through 63
removed outlier: 4.132A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A)
removed outlier: 4.313A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A)
removed outlier: 3.786A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A)
removed outlier: 7.113A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A)
removed outlier: 6.552A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A)
Processing sheet with id=AA6, first strand: chain 'B' and resid 100 through 105
removed outlier: 3.778A pdb=" N CYS B 121 " --> pdb=" O LEU B 139 " (cutoff:3.500A)
removed outlier: 6.011A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A)
removed outlier: 6.240A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A)
Processing sheet with id=AA7, first strand: chain 'B' and resid 146 through 151
removed outlier: 6.656A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A)
removed outlier: 4.533A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A)
removed outlier: 6.670A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A)
Processing sheet with id=AA8, first strand: chain 'B' and resid 187 through 192
removed outlier: 7.134A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A)
removed outlier: 4.969A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A)
removed outlier: 7.065A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A)
removed outlier: 5.433A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A)
removed outlier: 7.612A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A)
removed outlier: 3.624A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A)
removed outlier: 3.755A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A)
removed outlier: 5.917A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A)
removed outlier: 5.946A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A)
Processing sheet with id=AA9, first strand: chain 'B' and resid 229 through 234
removed outlier: 6.856A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A)
removed outlier: 4.899A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A)
removed outlier: 7.094A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A)
removed outlier: 5.277A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A)
removed outlier: 7.233A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A)
Processing sheet with id=AB1, first strand: chain 'B' and resid 273 through 278
removed outlier: 3.588A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A)
removed outlier: 6.427A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A)
removed outlier: 6.870A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A)
Processing sheet with id=AB2, first strand: chain 'D' and resid 3 through 7
Processing sheet with id=AB3, first strand: chain 'D' and resid 58 through 60
removed outlier: 6.478A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A)
removed outlier: 4.519A pdb=" N TYR D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A)
removed outlier: 6.757A pdb=" N MET D 34 " --> pdb=" O TYR D 50 " (cutoff:3.500A)
Processing sheet with id=AB4, first strand: chain 'D' and resid 128 through 129
Processing sheet with id=AB5, first strand: chain 'D' and resid 134 through 136
removed outlier: 6.429A pdb=" N VAL D 135 " --> pdb=" O GLU D 234 " (cutoff:3.500A)
removed outlier: 6.557A pdb=" N LEU D 162 " --> pdb=" O TYR D 178 " (cutoff:3.500A)
removed outlier: 4.681A pdb=" N TYR D 178 " --> pdb=" O LEU D 162 " (cutoff:3.500A)
removed outlier: 6.529A pdb=" N TRP D 164 " --> pdb=" O LEU D 176 " (cutoff:3.500A)
449 hydrogen bonds defined for protein.
1269 hydrogen bond angles defined for protein.
Restraints generated for nucleic acids:
0 hydrogen bonds
0 hydrogen bond angles
0 basepair planarities
0 basepair parallelities
0 stacking parallelities
Total time for adding SS restraints: 2.59
Time building geometry restraints manager: 3.19 seconds
NOTE: a complete listing of the restraints can be obtained by requesting
output of .geo file.
Histogram of bond lengths:
1.23 - 1.35: 2906
1.35 - 1.47: 2282
1.47 - 1.59: 3980
1.59 - 1.71: 0
1.71 - 1.83: 98
Bond restraints: 9266
Sorted by residual:
bond pdb=" CA ARG R 208 "
pdb=" CB ARG R 208 "
ideal model delta sigma weight residual
1.523 1.541 -0.018 1.21e-02 6.83e+03 2.19e+00
bond pdb=" CA LYS L 9 "
pdb=" C LYS L 9 "
ideal model delta sigma weight residual
1.522 1.504 0.018 1.38e-02 5.25e+03 1.67e+00
bond pdb=" CA VAL R 234 "
pdb=" C VAL R 234 "
ideal model delta sigma weight residual
1.520 1.530 -0.010 8.80e-03 1.29e+04 1.34e+00
bond pdb=" CB ARG R 208 "
pdb=" CG ARG R 208 "
ideal model delta sigma weight residual
1.520 1.550 -0.030 3.00e-02 1.11e+03 1.01e+00
bond pdb=" CA ALA B 92 "
pdb=" C ALA B 92 "
ideal model delta sigma weight residual
1.528 1.518 0.010 1.18e-02 7.18e+03 7.90e-01
... (remaining 9261 not shown)
Histogram of bond angle deviations from ideal:
0.00 - 1.22: 12053
1.22 - 2.43: 419
2.43 - 3.65: 66
3.65 - 4.87: 11
4.87 - 6.08: 5
Bond angle restraints: 12554
Sorted by residual:
angle pdb=" C VAL R 234 "
pdb=" CA VAL R 234 "
pdb=" CB VAL R 234 "
ideal model delta sigma weight residual
114.35 109.69 4.66 1.06e+00 8.90e-01 1.94e+01
angle pdb=" N MET L 7 "
pdb=" CA MET L 7 "
pdb=" C MET L 7 "
ideal model delta sigma weight residual
114.39 110.35 4.04 1.45e+00 4.76e-01 7.77e+00
angle pdb=" CA ARG R 208 "
pdb=" CB ARG R 208 "
pdb=" CG ARG R 208 "
ideal model delta sigma weight residual
114.10 119.44 -5.34 2.00e+00 2.50e-01 7.13e+00
angle pdb=" C ALA R 233 "
pdb=" N VAL R 234 "
pdb=" CA VAL R 234 "
ideal model delta sigma weight residual
120.24 121.90 -1.66 6.30e-01 2.52e+00 6.94e+00
angle pdb=" C ARG D 179 "
pdb=" N MET D 180 "
pdb=" CA MET D 180 "
ideal model delta sigma weight residual
121.54 125.90 -4.36 1.91e+00 2.74e-01 5.22e+00
... (remaining 12549 not shown)
Histogram of dihedral angle deviations from ideal:
0.00 - 17.60: 5086
17.60 - 35.19: 325
35.19 - 52.79: 89
52.79 - 70.38: 14
70.38 - 87.98: 2
Dihedral angle restraints: 5516
sinusoidal: 2140
harmonic: 3376
Sorted by residual:
dihedral pdb=" CB CYS R 174 "
pdb=" SG CYS R 174 "
pdb=" SG CYS R 255 "
pdb=" CB CYS R 255 "
ideal model delta sinusoidal sigma weight residual
-86.00 -126.43 40.43 1 1.00e+01 1.00e-02 2.29e+01
dihedral pdb=" CA LEU R 256 "
pdb=" C LEU R 256 "
pdb=" N LEU R 257 "
pdb=" CA LEU R 257 "
ideal model delta harmonic sigma weight residual
180.00 161.11 18.89 0 5.00e+00 4.00e-02 1.43e+01
dihedral pdb=" CA ARG A 208 "
pdb=" C ARG A 208 "
pdb=" N LYS A 209 "
pdb=" CA LYS A 209 "
ideal model delta harmonic sigma weight residual
-180.00 -162.59 -17.41 0 5.00e+00 4.00e-02 1.21e+01
... (remaining 5513 not shown)
Histogram of chiral volume deviations from ideal:
0.000 - 0.026: 871
0.026 - 0.053: 339
0.053 - 0.079: 128
0.079 - 0.106: 70
0.106 - 0.132: 24
Chirality restraints: 1432
Sorted by residual:
chirality pdb=" CA ILE D 51 "
pdb=" N ILE D 51 "
pdb=" C ILE D 51 "
pdb=" CB ILE D 51 "
both_signs ideal model delta sigma weight residual
False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.36e-01
chirality pdb=" CA PRO R 338 "
pdb=" N PRO R 338 "
pdb=" C PRO R 338 "
pdb=" CB PRO R 338 "
both_signs ideal model delta sigma weight residual
False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.12e-01
chirality pdb=" CA ILE D 145 "
pdb=" N ILE D 145 "
pdb=" C ILE D 145 "
pdb=" CB ILE D 145 "
both_signs ideal model delta sigma weight residual
False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.10e-01
... (remaining 1429 not shown)
Planarity restraints: 1579
Sorted by residual:
delta sigma weight rms_deltas residual
plane pdb=" CA ILE R 370 " 0.008 2.00e-02 2.50e+03 1.68e-02 2.83e+00
pdb=" C ILE R 370 " -0.029 2.00e-02 2.50e+03
pdb=" O ILE R 370 " 0.011 2.00e-02 2.50e+03
pdb=" N GLY R 371 " 0.010 2.00e-02 2.50e+03
delta sigma weight rms_deltas residual
plane pdb=" CA TYR R 369 " -0.008 2.00e-02 2.50e+03 1.57e-02 2.47e+00
pdb=" C TYR R 369 " 0.027 2.00e-02 2.50e+03
pdb=" O TYR R 369 " -0.010 2.00e-02 2.50e+03
pdb=" N ILE R 370 " -0.009 2.00e-02 2.50e+03
delta sigma weight rms_deltas residual
plane pdb=" CA SER R 279 " 0.007 2.00e-02 2.50e+03 1.46e-02 2.14e+00
pdb=" C SER R 279 " -0.025 2.00e-02 2.50e+03
pdb=" O SER R 279 " 0.010 2.00e-02 2.50e+03
pdb=" N PHE R 280 " 0.008 2.00e-02 2.50e+03
... (remaining 1576 not shown)
Histogram of nonbonded interaction distances:
2.14 - 2.70: 304
2.70 - 3.25: 9489
3.25 - 3.80: 15106
3.80 - 4.35: 18987
4.35 - 4.90: 31340
Nonbonded interactions: 75226
Sorted by model distance:
nonbonded pdb=" O GLN B 75 "
pdb=" OG SER B 98 "
model vdw
2.145 3.040
nonbonded pdb=" OG SER B 331 "
pdb=" OD1 ASP B 333 "
model vdw
2.174 3.040
nonbonded pdb=" OE2 GLU R 236 "
pdb=" OH TYR R 269 "
model vdw
2.191 3.040
nonbonded pdb=" O GLU R 359 "
pdb=" OG SER R 362 "
model vdw
2.217 3.040
nonbonded pdb=" OG1 THR B 65 "
pdb=" O PRO B 107 "
model vdw
2.217 3.040
... (remaining 75221 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
========== WARNING! ============
No NCS relation were found !!!
================================
Found NCS groups:
found none.
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: 0.400
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: 0.010
Extract box with map and model: 0.270
Check model and map are aligned: 0.060
Set scattering table: 0.070
Process input model: 23.710
Find NCS groups from input model: 0.110
Set up NCS constraints: 0.030
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: 0.010
Load rotamer database and sin/cos tables:2.830
Set ADP refinement strategy: 0.000
Make a string to write initial .geo file:0.000
Internal consistency checks: 0.000
Total: 27.500
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7535
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 : 0.003 0.036 9266 Z= 0.172
Angle : 0.546 6.083 12554 Z= 0.323
Chirality : 0.038 0.132 1432
Planarity : 0.003 0.036 1579
Dihedral : 12.776 87.977 3318
Min Nonbonded Distance : 2.145
Molprobity Statistics.
All-atom Clashscore : 14.35
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 3.59 %
Favored : 96.41 %
Rotamer:
Outliers : 7.98 %
Allowed : 9.19 %
Favored : 82.83 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 2.94 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: -0.12 (0.25), residues: 1143
helix: 1.47 (0.27), residues: 413
sheet: -0.12 (0.35), residues: 228
loop : -1.40 (0.27), residues: 502
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.012 0.001 TRP R 336
HIS 0.003 0.001 HIS B 266
PHE 0.014 0.001 PHE R 291
TYR 0.009 0.001 TYR D 223
ARG 0.002 0.000 ARG B 68
*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
2286 Ramachandran restraints generated.
1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
2286 Ramachandran restraints generated.
1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
504 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 79
poor density : 425
time to evaluate : 1.112
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: R 94 ILE cc_start: 0.8348 (mt) cc_final: 0.6448 (pt)
REVERT: R 126 ILE cc_start: 0.8485 (mp) cc_final: 0.8267 (mp)
REVERT: R 134 ASN cc_start: 0.7224 (p0) cc_final: 0.6938 (t0)
REVERT: R 138 ILE cc_start: 0.8766 (mt) cc_final: 0.8507 (pt)
REVERT: R 175 LYS cc_start: 0.7442 (tttp) cc_final: 0.6965 (pttt)
REVERT: R 190 LEU cc_start: 0.9594 (mt) cc_final: 0.9379 (mt)
REVERT: R 236 GLU cc_start: 0.8157 (mp0) cc_final: 0.7310 (mp0)
REVERT: R 240 PHE cc_start: 0.8987 (m-80) cc_final: 0.8201 (m-80)
REVERT: R 280 PHE cc_start: 0.8633 (t80) cc_final: 0.8129 (m-10)
REVERT: R 293 TYR cc_start: 0.8758 (m-10) cc_final: 0.8526 (m-10)
REVERT: R 295 LEU cc_start: 0.9002 (mt) cc_final: 0.8802 (mt)
REVERT: R 313 ASP cc_start: 0.8472 (t70) cc_final: 0.8260 (t70)
REVERT: R 319 ARG cc_start: 0.7525 (mtt180) cc_final: 0.7059 (tmt170)
REVERT: R 323 LYS cc_start: 0.5326 (OUTLIER) cc_final: 0.5108 (pttt)
REVERT: R 326 PHE cc_start: 0.8362 (m-10) cc_final: 0.7704 (t80)
REVERT: R 327 CYS cc_start: 0.9019 (OUTLIER) cc_final: 0.8459 (t)
REVERT: R 336 TRP cc_start: 0.8793 (m100) cc_final: 0.8519 (m100)
REVERT: R 370 ILE cc_start: 0.9045 (mm) cc_final: 0.8651 (tt)
REVERT: L 8 ASP cc_start: 0.4458 (OUTLIER) cc_final: 0.3732 (p0)
REVERT: L 10 GLU cc_start: 0.8476 (mp0) cc_final: 0.8112 (pm20)
REVERT: A 21 ARG cc_start: 0.8954 (mtm110) cc_final: 0.8592 (ptm160)
REVERT: A 43 GLU cc_start: 0.6963 (pm20) cc_final: 0.5885 (tt0)
REVERT: A 213 HIS cc_start: 0.8726 (p90) cc_final: 0.7710 (p90)
REVERT: A 215 PHE cc_start: 0.8907 (m-80) cc_final: 0.8705 (m-80)
REVERT: A 216 GLU cc_start: 0.8803 (tt0) cc_final: 0.8313 (tp30)
REVERT: A 224 CYS cc_start: 0.9306 (m) cc_final: 0.7989 (t)
REVERT: A 230 TYR cc_start: 0.5349 (OUTLIER) cc_final: 0.4792 (p90)
REVERT: A 242 ARG cc_start: 0.8426 (mtp85) cc_final: 0.8029 (mmp-170)
REVERT: A 250 PHE cc_start: 0.9485 (t80) cc_final: 0.9023 (t80)
REVERT: A 256 ASN cc_start: 0.9127 (m-40) cc_final: 0.8829 (t0)
REVERT: A 269 ASN cc_start: 0.8824 (OUTLIER) cc_final: 0.8517 (p0)
REVERT: A 298 GLU cc_start: 0.9023 (OUTLIER) cc_final: 0.8735 (pp20)
REVERT: A 304 GLN cc_start: 0.9405 (tt0) cc_final: 0.9114 (tm-30)
REVERT: A 320 TYR cc_start: 0.8764 (m-80) cc_final: 0.7256 (m-80)
REVERT: A 348 LEU cc_start: 0.9593 (mt) cc_final: 0.9101 (tp)
REVERT: A 349 LYS cc_start: 0.9402 (ttmm) cc_final: 0.9182 (mtmm)
REVERT: B 45 MET cc_start: 0.8663 (mmm) cc_final: 0.8282 (mmm)
REVERT: B 57 LYS cc_start: 0.9067 (pttp) cc_final: 0.8465 (ptpt)
REVERT: B 59 TYR cc_start: 0.8001 (m-80) cc_final: 0.7097 (m-80)
REVERT: B 63 TRP cc_start: 0.9314 (m100) cc_final: 0.8928 (m100)
REVERT: B 81 ILE cc_start: 0.9529 (mt) cc_final: 0.9225 (tp)
REVERT: B 89 LYS cc_start: 0.8889 (mptt) cc_final: 0.8529 (mmtp)
REVERT: B 119 ASN cc_start: 0.8559 (OUTLIER) cc_final: 0.8208 (m-40)
REVERT: B 146 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8063 (tp)
REVERT: B 157 ILE cc_start: 0.9489 (tt) cc_final: 0.9187 (tt)
REVERT: B 180 PHE cc_start: 0.8319 (m-80) cc_final: 0.7891 (m-80)
REVERT: B 192 LEU cc_start: 0.8573 (mt) cc_final: 0.8076 (pt)
REVERT: B 222 PHE cc_start: 0.8236 (m-80) cc_final: 0.7955 (m-80)
REVERT: B 234 PHE cc_start: 0.8234 (OUTLIER) cc_final: 0.7977 (t80)
REVERT: B 243 THR cc_start: 0.8301 (p) cc_final: 0.8062 (t)
REVERT: B 267 ASP cc_start: 0.9042 (OUTLIER) cc_final: 0.8651 (p0)
REVERT: B 278 PHE cc_start: 0.8340 (m-80) cc_final: 0.8108 (m-80)
REVERT: B 283 ARG cc_start: 0.8593 (tpt90) cc_final: 0.8339 (tpt170)
REVERT: B 289 TYR cc_start: 0.8087 (m-80) cc_final: 0.6525 (m-80)
REVERT: B 335 PHE cc_start: 0.6297 (OUTLIER) cc_final: 0.5704 (m-10)
REVERT: C 24 ASN cc_start: 0.9216 (t0) cc_final: 0.8783 (p0)
REVERT: C 36 ASP cc_start: 0.9132 (m-30) cc_final: 0.8891 (m-30)
REVERT: D 35 HIS cc_start: 0.9054 (m-70) cc_final: 0.8486 (m-70)
REVERT: D 36 TRP cc_start: 0.8295 (m100) cc_final: 0.7440 (m100)
REVERT: D 73 ASP cc_start: 0.8855 (t70) cc_final: 0.8636 (t0)
REVERT: D 74 ASP cc_start: 0.9082 (m-30) cc_final: 0.8808 (m-30)
REVERT: D 77 ASN cc_start: 0.8784 (m-40) cc_final: 0.8424 (p0)
REVERT: D 78 THR cc_start: 0.9066 (m) cc_final: 0.8624 (p)
REVERT: D 79 LEU cc_start: 0.9500 (tp) cc_final: 0.9213 (tp)
REVERT: D 108 PHE cc_start: 0.9011 (m-80) cc_final: 0.8763 (m-80)
REVERT: D 111 TRP cc_start: 0.8265 (m100) cc_final: 0.7502 (m-10)
REVERT: D 165 PHE cc_start: 0.9072 (m-80) cc_final: 0.8729 (m-80)
outliers start: 79
outliers final: 24
residues processed: 470
average time/residue: 0.2513
time to fit residues: 153.9907
Evaluate side-chains
311 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 35
poor density : 276
time to evaluate : 1.042
-------------------------------------------------------------------------------
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: 1.9990
chunk 86 optimal weight: 7.9990
chunk 47 optimal weight: 6.9990
chunk 29 optimal weight: 0.9990
chunk 58 optimal weight: 5.9990
chunk 46 optimal weight: 10.0000
chunk 89 optimal weight: 1.9990
chunk 34 optimal weight: 3.9990
chunk 54 optimal weight: 9.9990
chunk 66 optimal weight: 0.9990
chunk 103 optimal weight: 20.0000
overall best weight: 1.9990
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
R 150 HIS
R 181 GLN
R 258 HIS
R 317 GLN
A 188 HIS
A 195 HIS
A 244 HIS
A 294 ASN
A 304 GLN
B 32 GLN
B 156 GLN
B 268 ASN
D 167 GLN
Total number of N/Q/H flips: 13
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.076476 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.060186 restraints weight = 40231.293|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.062439 restraints weight = 26425.607|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3191 r_free = 0.3191 target = 0.064051 restraints weight = 19190.461|
|-----------------------------------------------------------------------------|
r_work (final): 0.3188
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7565
moved from start: 0.3409
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.044 9266 Z= 0.226
Angle : 0.648 7.683 12554 Z= 0.347
Chirality : 0.044 0.223 1432
Planarity : 0.005 0.054 1579
Dihedral : 4.669 30.178 1251
Min Nonbonded Distance : 2.544
Molprobity Statistics.
All-atom Clashscore : 15.73
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 4.37 %
Favored : 95.63 %
Rotamer:
Outliers : 0.20 %
Allowed : 4.14 %
Favored : 95.66 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 2.94 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: -0.17 (0.25), residues: 1143
helix: 1.26 (0.25), residues: 401
sheet: -0.23 (0.33), residues: 239
loop : -1.17 (0.28), residues: 503
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.015 0.002 TRP D 36
HIS 0.013 0.002 HIS B 225
PHE 0.016 0.002 PHE R 397
TYR 0.019 0.002 TYR D 161
ARG 0.007 0.001 ARG R 392
*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
2286 Ramachandran restraints generated.
1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
2286 Ramachandran restraints generated.
1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
350 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 2
poor density : 348
time to evaluate : 0.980
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: R 94 ILE cc_start: 0.8135 (mt) cc_final: 0.7678 (mp)
REVERT: R 134 ASN cc_start: 0.7036 (p0) cc_final: 0.6358 (t0)
REVERT: R 138 ILE cc_start: 0.8710 (mt) cc_final: 0.8502 (pt)
REVERT: R 257 LEU cc_start: 0.8945 (mm) cc_final: 0.8633 (mm)
REVERT: R 280 PHE cc_start: 0.8510 (t80) cc_final: 0.7844 (m-80)
REVERT: R 326 PHE cc_start: 0.8326 (m-10) cc_final: 0.7666 (t80)
REVERT: L 7 MET cc_start: 0.7710 (tmm) cc_final: 0.7375 (tmm)
REVERT: L 10 GLU cc_start: 0.8322 (mp0) cc_final: 0.7901 (pm20)
REVERT: L 13 TYR cc_start: 0.8214 (t80) cc_final: 0.7803 (t80)
REVERT: A 5 LEU cc_start: 0.7830 (mt) cc_final: 0.7598 (pt)
REVERT: A 24 ARG cc_start: 0.7862 (mtt180) cc_final: 0.7402 (mmm-85)
REVERT: A 188 HIS cc_start: 0.8369 (OUTLIER) cc_final: 0.8081 (t-90)
REVERT: A 213 HIS cc_start: 0.8667 (p90) cc_final: 0.7586 (p90)
REVERT: A 215 PHE cc_start: 0.8991 (m-80) cc_final: 0.8782 (m-80)
REVERT: A 216 GLU cc_start: 0.8771 (tt0) cc_final: 0.8284 (tp30)
REVERT: A 223 PHE cc_start: 0.8666 (t80) cc_final: 0.8366 (t80)
REVERT: A 224 CYS cc_start: 0.9164 (m) cc_final: 0.7647 (t)
REVERT: A 243 MET cc_start: 0.9214 (ttp) cc_final: 0.8404 (tmm)
REVERT: A 247 MET cc_start: 0.9179 (mtm) cc_final: 0.8324 (mtm)
REVERT: A 248 LYS cc_start: 0.9296 (mtmm) cc_final: 0.9072 (mttt)
REVERT: A 256 ASN cc_start: 0.9068 (m-40) cc_final: 0.8850 (m110)
REVERT: A 269 ASN cc_start: 0.9151 (m110) cc_final: 0.7608 (m-40)
REVERT: A 304 GLN cc_start: 0.9439 (tt0) cc_final: 0.9152 (tm-30)
REVERT: A 317 LYS cc_start: 0.8342 (pttt) cc_final: 0.8135 (pttp)
REVERT: A 348 LEU cc_start: 0.9502 (mt) cc_final: 0.9186 (tp)
REVERT: B 51 LEU cc_start: 0.9023 (mp) cc_final: 0.8585 (tp)
REVERT: B 57 LYS cc_start: 0.9052 (pttp) cc_final: 0.8737 (ptpt)
REVERT: B 63 TRP cc_start: 0.9346 (m100) cc_final: 0.9033 (m100)
REVERT: B 69 LEU cc_start: 0.9534 (mt) cc_final: 0.8661 (pp)
REVERT: B 146 LEU cc_start: 0.7427 (mp) cc_final: 0.6963 (mp)
REVERT: B 180 PHE cc_start: 0.8432 (m-80) cc_final: 0.8039 (m-80)
REVERT: B 192 LEU cc_start: 0.8508 (mt) cc_final: 0.8116 (pt)
REVERT: B 222 PHE cc_start: 0.8203 (m-80) cc_final: 0.7990 (m-80)
REVERT: B 254 ASP cc_start: 0.7482 (t70) cc_final: 0.7262 (t0)
REVERT: B 283 ARG cc_start: 0.9067 (tpt90) cc_final: 0.8828 (tpt170)
REVERT: B 289 TYR cc_start: 0.7868 (m-80) cc_final: 0.6371 (m-80)
REVERT: C 24 ASN cc_start: 0.8942 (t0) cc_final: 0.8549 (p0)
REVERT: D 35 HIS cc_start: 0.8920 (m-70) cc_final: 0.8320 (m-70)
REVERT: D 46 GLU cc_start: 0.9031 (mm-30) cc_final: 0.8730 (mm-30)
REVERT: D 73 ASP cc_start: 0.9090 (t70) cc_final: 0.8586 (t0)
REVERT: D 78 THR cc_start: 0.9155 (m) cc_final: 0.8737 (p)
REVERT: D 89 GLU cc_start: 0.8835 (mp0) cc_final: 0.8318 (pm20)
REVERT: D 111 TRP cc_start: 0.8314 (m100) cc_final: 0.7752 (m-10)
REVERT: D 145 ILE cc_start: 0.8624 (pt) cc_final: 0.8379 (pt)
REVERT: D 164 TRP cc_start: 0.8124 (m100) cc_final: 0.7391 (m-10)
REVERT: D 165 PHE cc_start: 0.8907 (m-80) cc_final: 0.8566 (m-80)
REVERT: D 202 LEU cc_start: 0.9190 (tt) cc_final: 0.8483 (tt)
outliers start: 2
outliers final: 1
residues processed: 348
average time/residue: 0.2428
time to fit residues: 112.5221
Evaluate side-chains
259 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 2
poor density : 257
time to evaluate : 0.970
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 114
random chunks:
chunk 73 optimal weight: 4.9990
chunk 55 optimal weight: 3.9990
chunk 13 optimal weight: 6.9990
chunk 22 optimal weight: 9.9990
chunk 51 optimal weight: 0.9990
chunk 65 optimal weight: 9.9990
chunk 99 optimal weight: 5.9990
chunk 24 optimal weight: 7.9990
chunk 28 optimal weight: 9.9990
chunk 77 optimal weight: 0.0040
chunk 19 optimal weight: 7.9990
overall best weight: 3.2000
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
R 119 ASN
R 150 HIS
R 181 GLN
R 258 HIS
A 195 HIS
B 32 GLN
Total number of N/Q/H flips: 6
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.075310 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3090 r_free = 0.3090 target = 0.058993 restraints weight = 41157.278|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3133 r_free = 0.3133 target = 0.061215 restraints weight = 26834.677|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.062862 restraints weight = 19478.974|
|-----------------------------------------------------------------------------|
r_work (final): 0.3161
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7619
moved from start: 0.4068
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.004 0.047 9266 Z= 0.264
Angle : 0.644 8.694 12554 Z= 0.339
Chirality : 0.044 0.178 1432
Planarity : 0.004 0.041 1579
Dihedral : 4.777 24.919 1251
Min Nonbonded Distance : 2.550
Molprobity Statistics.
All-atom Clashscore : 15.73
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 4.72 %
Favored : 95.28 %
Rotamer:
Outliers : 0.51 %
Allowed : 4.65 %
Favored : 94.85 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 2.94 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: -0.35 (0.25), residues: 1143
helix: 1.05 (0.25), residues: 402
sheet: -0.32 (0.34), residues: 240
loop : -1.22 (0.27), residues: 501
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.021 0.002 TRP R 336
HIS 0.006 0.001 HIS R 258
PHE 0.030 0.002 PHE D 68
TYR 0.013 0.002 TYR R 251
ARG 0.007 0.001 ARG D 206
*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
2286 Ramachandran restraints generated.
1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
2286 Ramachandran restraints generated.
1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
315 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 5
poor density : 310
time to evaluate : 0.994
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: R 242 ILE cc_start: 0.8726 (tp) cc_final: 0.8348 (mt)
REVERT: R 245 MET cc_start: 0.9046 (mpp) cc_final: 0.8725 (mpp)
REVERT: R 280 PHE cc_start: 0.8517 (t80) cc_final: 0.7877 (m-80)
REVERT: R 293 TYR cc_start: 0.8551 (m-10) cc_final: 0.8300 (m-80)
REVERT: R 295 LEU cc_start: 0.8591 (mt) cc_final: 0.8290 (mt)
REVERT: R 320 GLU cc_start: 0.8684 (mt-10) cc_final: 0.8381 (mt-10)
REVERT: R 326 PHE cc_start: 0.8403 (m-10) cc_final: 0.7701 (t80)
REVERT: L 7 MET cc_start: 0.7773 (tmm) cc_final: 0.7320 (tmm)
REVERT: L 10 GLU cc_start: 0.8404 (mp0) cc_final: 0.7941 (pm20)
REVERT: L 13 TYR cc_start: 0.8368 (t80) cc_final: 0.8098 (t80)
REVERT: A 213 HIS cc_start: 0.8708 (p90) cc_final: 0.7628 (p90)
REVERT: A 223 PHE cc_start: 0.8722 (t80) cc_final: 0.8276 (t80)
REVERT: A 224 CYS cc_start: 0.9281 (m) cc_final: 0.7729 (t)
REVERT: A 225 VAL cc_start: 0.9170 (OUTLIER) cc_final: 0.8899 (m)
REVERT: A 256 ASN cc_start: 0.9126 (m-40) cc_final: 0.8862 (m110)
REVERT: A 269 ASN cc_start: 0.9245 (m110) cc_final: 0.7864 (m-40)
REVERT: A 304 GLN cc_start: 0.9414 (tt0) cc_final: 0.9109 (tm-30)
REVERT: A 317 LYS cc_start: 0.8344 (pttt) cc_final: 0.7989 (pttp)
REVERT: A 332 VAL cc_start: 0.9498 (t) cc_final: 0.9170 (t)
REVERT: A 333 GLN cc_start: 0.8739 (mp10) cc_final: 0.8348 (mp10)
REVERT: B 57 LYS cc_start: 0.9157 (pttp) cc_final: 0.8690 (ptpt)
REVERT: B 63 TRP cc_start: 0.9421 (m100) cc_final: 0.8993 (m100)
REVERT: B 192 LEU cc_start: 0.8564 (mt) cc_final: 0.8191 (pt)
REVERT: B 222 PHE cc_start: 0.8181 (m-80) cc_final: 0.7745 (m-80)
REVERT: B 252 LEU cc_start: 0.9697 (tt) cc_final: 0.9324 (mt)
REVERT: B 254 ASP cc_start: 0.7610 (t70) cc_final: 0.7303 (t0)
REVERT: B 283 ARG cc_start: 0.9056 (tpt90) cc_final: 0.8808 (tpt170)
REVERT: B 289 TYR cc_start: 0.7779 (m-80) cc_final: 0.6308 (m-80)
REVERT: D 19 LYS cc_start: 0.9108 (ttmm) cc_final: 0.8715 (tttm)
REVERT: D 35 HIS cc_start: 0.8827 (m-70) cc_final: 0.8516 (m-70)
REVERT: D 37 VAL cc_start: 0.9615 (m) cc_final: 0.9341 (p)
REVERT: D 45 LEU cc_start: 0.9413 (mt) cc_final: 0.8732 (mt)
REVERT: D 73 ASP cc_start: 0.9119 (t70) cc_final: 0.8600 (t0)
REVERT: D 78 THR cc_start: 0.9098 (m) cc_final: 0.8470 (p)
REVERT: D 80 PHE cc_start: 0.8769 (m-80) cc_final: 0.8511 (m-10)
REVERT: D 111 TRP cc_start: 0.8402 (m100) cc_final: 0.7851 (m-10)
REVERT: D 159 ASN cc_start: 0.9205 (m110) cc_final: 0.8814 (t0)
REVERT: D 164 TRP cc_start: 0.8189 (m100) cc_final: 0.7197 (m-10)
REVERT: D 165 PHE cc_start: 0.8466 (m-80) cc_final: 0.8012 (m-80)
REVERT: D 202 LEU cc_start: 0.9203 (tt) cc_final: 0.8544 (tt)
outliers start: 5
outliers final: 0
residues processed: 312
average time/residue: 0.2174
time to fit residues: 91.4357
Evaluate side-chains
235 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 1
poor density : 234
time to evaluate : 1.071
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 114
random chunks:
chunk 101 optimal weight: 0.3980
chunk 83 optimal weight: 20.0000
chunk 2 optimal weight: 9.9990
chunk 14 optimal weight: 20.0000
chunk 104 optimal weight: 7.9990
chunk 91 optimal weight: 20.0000
chunk 108 optimal weight: 6.9990
chunk 44 optimal weight: 5.9990
chunk 97 optimal weight: 0.8980
chunk 109 optimal weight: 10.0000
chunk 70 optimal weight: 20.0000
overall best weight: 4.4586
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** R 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 150 HIS
R 181 GLN
A 188 HIS
A 195 HIS
A 294 ASN
B 32 GLN
** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 219 GLN
Total number of N/Q/H flips: 7
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.073464 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3061 r_free = 0.3061 target = 0.057627 restraints weight = 42137.122|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3102 r_free = 0.3102 target = 0.059675 restraints weight = 28165.364|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3133 r_free = 0.3133 target = 0.061197 restraints weight = 20839.848|
|-----------------------------------------------------------------------------|
r_work (final): 0.3130
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7667
moved from start: 0.4559
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.005 0.065 9266 Z= 0.323
Angle : 0.683 6.627 12554 Z= 0.365
Chirality : 0.045 0.200 1432
Planarity : 0.005 0.047 1579
Dihedral : 5.125 23.907 1251
Min Nonbonded Distance : 2.446
Molprobity Statistics.
All-atom Clashscore : 18.61
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 4.90 %
Favored : 95.10 %
Rotamer:
Outliers : 0.40 %
Allowed : 5.15 %
Favored : 94.44 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 2.94 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: -0.70 (0.24), residues: 1143
helix: 0.49 (0.25), residues: 401
sheet: -0.36 (0.33), residues: 257
loop : -1.26 (0.28), residues: 485
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.025 0.002 TRP R 217
HIS 0.009 0.002 HIS B 142
PHE 0.024 0.002 PHE D 68
TYR 0.017 0.002 TYR R 369
ARG 0.010 0.001 ARG D 206
*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
2286 Ramachandran restraints generated.
1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
2286 Ramachandran restraints generated.
1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
283 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 4
poor density : 279
time to evaluate : 0.959
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: R 132 MET cc_start: 0.6400 (ttt) cc_final: 0.6115 (ttt)
REVERT: R 190 LEU cc_start: 0.9549 (mt) cc_final: 0.9342 (mt)
REVERT: R 236 GLU cc_start: 0.8271 (mp0) cc_final: 0.8026 (mp0)
REVERT: R 280 PHE cc_start: 0.8647 (t80) cc_final: 0.7908 (m-80)
REVERT: R 293 TYR cc_start: 0.8649 (m-10) cc_final: 0.8407 (m-80)
REVERT: R 295 LEU cc_start: 0.8636 (mt) cc_final: 0.8402 (mt)
REVERT: R 320 GLU cc_start: 0.8618 (mt-10) cc_final: 0.8269 (mt-10)
REVERT: R 326 PHE cc_start: 0.8335 (m-10) cc_final: 0.7793 (t80)
REVERT: L 7 MET cc_start: 0.7990 (tmm) cc_final: 0.7481 (tmm)
REVERT: L 10 GLU cc_start: 0.8391 (mp0) cc_final: 0.8132 (pm20)
REVERT: L 13 TYR cc_start: 0.8698 (t80) cc_final: 0.8344 (t80)
REVERT: A 5 LEU cc_start: 0.8016 (mm) cc_final: 0.7390 (pt)
REVERT: A 188 HIS cc_start: 0.8500 (OUTLIER) cc_final: 0.8198 (t-90)
REVERT: A 213 HIS cc_start: 0.8731 (p90) cc_final: 0.7735 (p90)
REVERT: A 223 PHE cc_start: 0.8824 (t80) cc_final: 0.8444 (t80)
REVERT: A 224 CYS cc_start: 0.9222 (m) cc_final: 0.7822 (t)
REVERT: A 256 ASN cc_start: 0.9160 (m-40) cc_final: 0.8838 (m110)
REVERT: A 269 ASN cc_start: 0.9130 (m110) cc_final: 0.7910 (m-40)
REVERT: A 304 GLN cc_start: 0.9458 (tt0) cc_final: 0.9099 (tm-30)
REVERT: A 349 LYS cc_start: 0.9429 (mtmt) cc_final: 0.8732 (tmtt)
REVERT: B 57 LYS cc_start: 0.9147 (pttp) cc_final: 0.8569 (ptpt)
REVERT: B 192 LEU cc_start: 0.8578 (mt) cc_final: 0.8227 (pt)
REVERT: B 252 LEU cc_start: 0.9745 (tt) cc_final: 0.9410 (mt)
REVERT: B 254 ASP cc_start: 0.7646 (t70) cc_final: 0.7286 (t0)
REVERT: B 283 ARG cc_start: 0.9194 (tpt90) cc_final: 0.8948 (tpt170)
REVERT: B 289 TYR cc_start: 0.7821 (m-80) cc_final: 0.6289 (m-80)
REVERT: C 21 MET cc_start: 0.9068 (mmm) cc_final: 0.8640 (mmm)
REVERT: C 38 MET cc_start: 0.9269 (ptp) cc_final: 0.9028 (ptp)
REVERT: D 73 ASP cc_start: 0.9163 (t70) cc_final: 0.8496 (t0)
REVERT: D 78 THR cc_start: 0.8985 (m) cc_final: 0.8320 (p)
REVERT: D 80 PHE cc_start: 0.8919 (m-80) cc_final: 0.8225 (m-10)
REVERT: D 111 TRP cc_start: 0.8597 (m100) cc_final: 0.8162 (m-10)
REVERT: D 159 ASN cc_start: 0.9192 (m110) cc_final: 0.8927 (m110)
REVERT: D 164 TRP cc_start: 0.8354 (m100) cc_final: 0.7956 (m-10)
REVERT: D 202 LEU cc_start: 0.9212 (tt) cc_final: 0.8765 (tt)
outliers start: 4
outliers final: 1
residues processed: 280
average time/residue: 0.2408
time to fit residues: 89.9101
Evaluate side-chains
219 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 2
poor density : 217
time to evaluate : 0.974
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 114
random chunks:
chunk 10 optimal weight: 0.8980
chunk 17 optimal weight: 2.9990
chunk 60 optimal weight: 8.9990
chunk 106 optimal weight: 0.9990
chunk 20 optimal weight: 0.9980
chunk 88 optimal weight: 0.9990
chunk 23 optimal weight: 5.9990
chunk 18 optimal weight: 3.9990
chunk 62 optimal weight: 2.9990
chunk 43 optimal weight: 1.9990
chunk 32 optimal weight: 10.0000
overall best weight: 1.1786
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** R 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 150 HIS
R 181 GLN
A 195 HIS
B 32 GLN
** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
Total number of N/Q/H flips: 4
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.077023 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3129 r_free = 0.3129 target = 0.061058 restraints weight = 40762.227|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.063293 restraints weight = 27121.814|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.064965 restraints weight = 19794.026|
|-----------------------------------------------------------------------------|
r_work (final): 0.3200
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7587
moved from start: 0.4937
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.043 9266 Z= 0.187
Angle : 0.631 8.967 12554 Z= 0.329
Chirality : 0.044 0.169 1432
Planarity : 0.004 0.049 1579
Dihedral : 4.791 22.274 1251
Min Nonbonded Distance : 2.388
Molprobity Statistics.
All-atom Clashscore : 14.46
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 3.85 %
Favored : 96.15 %
Rotamer:
Outliers : 0.00 %
Allowed : 3.43 %
Favored : 96.57 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 2.94 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: -0.53 (0.25), residues: 1143
helix: 0.60 (0.25), residues: 401
sheet: -0.31 (0.33), residues: 252
loop : -1.10 (0.29), residues: 490
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.024 0.002 TRP D 36
HIS 0.005 0.001 HIS R 258
PHE 0.030 0.002 PHE A 307
TYR 0.019 0.001 TYR R 369
ARG 0.009 0.000 ARG D 206
*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
2286 Ramachandran restraints generated.
1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
2286 Ramachandran restraints generated.
1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
296 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 0
poor density : 296
time to evaluate : 1.053
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: R 94 ILE cc_start: 0.8222 (mt) cc_final: 0.7626 (mp)
REVERT: R 119 ASN cc_start: 0.8659 (m-40) cc_final: 0.8195 (m110)
REVERT: R 190 LEU cc_start: 0.9553 (mt) cc_final: 0.9345 (mt)
REVERT: R 280 PHE cc_start: 0.8533 (t80) cc_final: 0.7839 (m-80)
REVERT: R 293 TYR cc_start: 0.8655 (m-10) cc_final: 0.8363 (m-80)
REVERT: R 295 LEU cc_start: 0.8575 (mt) cc_final: 0.8339 (mt)
REVERT: R 316 LYS cc_start: 0.8515 (mtmt) cc_final: 0.8285 (mmtt)
REVERT: R 320 GLU cc_start: 0.8612 (mt-10) cc_final: 0.8242 (mt-10)
REVERT: R 326 PHE cc_start: 0.8126 (m-10) cc_final: 0.7731 (t80)
REVERT: R 374 MET cc_start: 0.5056 (mmt) cc_final: 0.4586 (mmt)
REVERT: R 381 ILE cc_start: 0.8877 (tp) cc_final: 0.8654 (tp)
REVERT: L 7 MET cc_start: 0.7789 (tmm) cc_final: 0.7238 (tmm)
REVERT: L 13 TYR cc_start: 0.8581 (t80) cc_final: 0.8293 (t80)
REVERT: A 5 LEU cc_start: 0.8197 (mm) cc_final: 0.7566 (pt)
REVERT: A 213 HIS cc_start: 0.8813 (p90) cc_final: 0.7798 (p90)
REVERT: A 224 CYS cc_start: 0.9193 (m) cc_final: 0.8070 (t)
REVERT: A 256 ASN cc_start: 0.9195 (m-40) cc_final: 0.8677 (m110)
REVERT: A 304 GLN cc_start: 0.9450 (tt0) cc_final: 0.8592 (tm-30)
REVERT: A 348 LEU cc_start: 0.9301 (mm) cc_final: 0.8971 (tp)
REVERT: A 349 LYS cc_start: 0.9441 (mtmt) cc_final: 0.8820 (tptp)
REVERT: B 49 ARG cc_start: 0.8943 (mmt180) cc_final: 0.8559 (mmt90)
REVERT: B 57 LYS cc_start: 0.9128 (pttp) cc_final: 0.8590 (ptpt)
REVERT: B 69 LEU cc_start: 0.9512 (mt) cc_final: 0.8668 (pp)
REVERT: B 127 LYS cc_start: 0.9242 (mtpp) cc_final: 0.8935 (mttp)
REVERT: B 192 LEU cc_start: 0.8478 (mt) cc_final: 0.8169 (pt)
REVERT: B 219 ARG cc_start: 0.8340 (tpt170) cc_final: 0.8002 (tpt90)
REVERT: B 222 PHE cc_start: 0.8117 (m-80) cc_final: 0.7880 (m-10)
REVERT: B 254 ASP cc_start: 0.7711 (t70) cc_final: 0.7424 (t0)
REVERT: B 264 TYR cc_start: 0.7357 (m-10) cc_final: 0.7052 (m-80)
REVERT: B 283 ARG cc_start: 0.9083 (tpt90) cc_final: 0.8861 (tpt170)
REVERT: B 289 TYR cc_start: 0.7502 (m-80) cc_final: 0.6321 (m-80)
REVERT: C 38 MET cc_start: 0.9210 (ptp) cc_final: 0.8932 (ptp)
REVERT: D 73 ASP cc_start: 0.9037 (t70) cc_final: 0.8631 (t0)
REVERT: D 78 THR cc_start: 0.8979 (m) cc_final: 0.8209 (p)
REVERT: D 80 PHE cc_start: 0.8829 (m-80) cc_final: 0.8427 (m-10)
REVERT: D 81 LEU cc_start: 0.8643 (tp) cc_final: 0.8375 (tp)
REVERT: D 111 TRP cc_start: 0.8258 (m100) cc_final: 0.7838 (m-10)
REVERT: D 159 ASN cc_start: 0.9375 (m110) cc_final: 0.9001 (t0)
REVERT: D 164 TRP cc_start: 0.8167 (m100) cc_final: 0.7388 (m-10)
REVERT: D 165 PHE cc_start: 0.8510 (m-80) cc_final: 0.8046 (m-80)
REVERT: D 202 LEU cc_start: 0.9189 (tt) cc_final: 0.8629 (tt)
REVERT: D 218 MET cc_start: 0.8220 (tmm) cc_final: 0.7763 (tmm)
REVERT: D 227 PHE cc_start: 0.8530 (m-80) cc_final: 0.8142 (m-80)
outliers start: 0
outliers final: 0
residues processed: 296
average time/residue: 0.2278
time to fit residues: 91.4309
Evaluate side-chains
234 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 0
poor density : 234
time to evaluate : 1.191
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 114
random chunks:
chunk 90 optimal weight: 20.0000
chunk 24 optimal weight: 3.9990
chunk 101 optimal weight: 6.9990
chunk 68 optimal weight: 7.9990
chunk 25 optimal weight: 5.9990
chunk 67 optimal weight: 5.9990
chunk 27 optimal weight: 4.9990
chunk 110 optimal weight: 0.0980
chunk 22 optimal weight: 5.9990
chunk 111 optimal weight: 0.9980
chunk 3 optimal weight: 7.9990
overall best weight: 3.2186
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** R 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 150 HIS
R 181 GLN
A 188 HIS
A 195 HIS
A 294 ASN
A 304 GLN
B 32 GLN
** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Total number of N/Q/H flips: 7
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.074211 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3088 r_free = 0.3088 target = 0.058547 restraints weight = 41251.590|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3130 r_free = 0.3130 target = 0.060624 restraints weight = 27449.497|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.062158 restraints weight = 20187.710|
|-----------------------------------------------------------------------------|
r_work (final): 0.3158
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7685
moved from start: 0.5107
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.004 0.051 9266 Z= 0.267
Angle : 0.655 6.257 12554 Z= 0.347
Chirality : 0.045 0.224 1432
Planarity : 0.004 0.054 1579
Dihedral : 4.925 24.075 1251
Min Nonbonded Distance : 2.399
Molprobity Statistics.
All-atom Clashscore : 16.67
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 4.90 %
Favored : 95.10 %
Rotamer:
Outliers : 0.40 %
Allowed : 2.73 %
Favored : 96.87 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 2.94 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: -0.60 (0.25), residues: 1143
helix: 0.57 (0.25), residues: 402
sheet: -0.28 (0.34), residues: 242
loop : -1.20 (0.28), residues: 499
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.024 0.002 TRP B 211
HIS 0.011 0.002 HIS D 35
PHE 0.027 0.002 PHE D 68
TYR 0.020 0.002 TYR R 369
ARG 0.005 0.001 ARG D 206
*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
2286 Ramachandran restraints generated.
1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
2286 Ramachandran restraints generated.
1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
285 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 4
poor density : 281
time to evaluate : 0.925
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: R 190 LEU cc_start: 0.9582 (mt) cc_final: 0.9380 (mt)
REVERT: R 253 ARG cc_start: 0.7966 (tpp-160) cc_final: 0.7670 (mtt180)
REVERT: R 280 PHE cc_start: 0.8556 (t80) cc_final: 0.7784 (m-80)
REVERT: R 293 TYR cc_start: 0.8612 (m-10) cc_final: 0.8323 (m-80)
REVERT: R 320 GLU cc_start: 0.8522 (mt-10) cc_final: 0.8155 (mt-10)
REVERT: R 326 PHE cc_start: 0.8270 (m-10) cc_final: 0.7698 (t80)
REVERT: R 374 MET cc_start: 0.5087 (mmt) cc_final: 0.4590 (mmt)
REVERT: L 7 MET cc_start: 0.7914 (tmm) cc_final: 0.7365 (tmm)
REVERT: L 13 TYR cc_start: 0.8656 (t80) cc_final: 0.8346 (t80)
REVERT: A 5 LEU cc_start: 0.8364 (mm) cc_final: 0.7690 (pt)
REVERT: A 188 HIS cc_start: 0.8367 (OUTLIER) cc_final: 0.8085 (t-90)
REVERT: A 198 MET cc_start: 0.8562 (ttm) cc_final: 0.8342 (ttp)
REVERT: A 213 HIS cc_start: 0.8813 (p90) cc_final: 0.8076 (p90)
REVERT: A 224 CYS cc_start: 0.9167 (m) cc_final: 0.8098 (t)
REVERT: A 253 ILE cc_start: 0.9637 (pt) cc_final: 0.9403 (pt)
REVERT: A 256 ASN cc_start: 0.9224 (m-40) cc_final: 0.8802 (m110)
REVERT: A 304 GLN cc_start: 0.9429 (tt0) cc_final: 0.8547 (tm-30)
REVERT: A 348 LEU cc_start: 0.9367 (mm) cc_final: 0.9048 (tp)
REVERT: B 57 LYS cc_start: 0.9151 (pttp) cc_final: 0.8632 (ptpt)
REVERT: B 89 LYS cc_start: 0.9037 (mmtt) cc_final: 0.8654 (mmtm)
REVERT: B 192 LEU cc_start: 0.8615 (mt) cc_final: 0.8246 (pt)
REVERT: B 222 PHE cc_start: 0.8098 (m-80) cc_final: 0.7831 (m-10)
REVERT: B 254 ASP cc_start: 0.7659 (t70) cc_final: 0.7449 (t0)
REVERT: B 289 TYR cc_start: 0.7416 (m-80) cc_final: 0.6335 (m-80)
REVERT: C 25 ILE cc_start: 0.7781 (pt) cc_final: 0.7347 (pt)
REVERT: C 27 ARG cc_start: 0.8076 (ptp90) cc_final: 0.7764 (ptp90)
REVERT: C 38 MET cc_start: 0.9155 (ptp) cc_final: 0.8887 (ptp)
REVERT: D 35 HIS cc_start: 0.8866 (m-70) cc_final: 0.8394 (m-70)
REVERT: D 73 ASP cc_start: 0.9055 (t70) cc_final: 0.8503 (t0)
REVERT: D 78 THR cc_start: 0.8879 (m) cc_final: 0.8124 (p)
REVERT: D 80 PHE cc_start: 0.8625 (m-80) cc_final: 0.8233 (m-10)
REVERT: D 93 MET cc_start: 0.8010 (tpt) cc_final: 0.7786 (tpt)
REVERT: D 111 TRP cc_start: 0.8247 (m100) cc_final: 0.7908 (m-10)
REVERT: D 159 ASN cc_start: 0.9366 (m110) cc_final: 0.8965 (t0)
REVERT: D 164 TRP cc_start: 0.8197 (m100) cc_final: 0.7387 (m-10)
REVERT: D 202 LEU cc_start: 0.9201 (tt) cc_final: 0.8602 (tt)
REVERT: D 218 MET cc_start: 0.8294 (tmm) cc_final: 0.7918 (tmm)
REVERT: D 227 PHE cc_start: 0.8298 (m-80) cc_final: 0.7983 (m-80)
outliers start: 4
outliers final: 1
residues processed: 283
average time/residue: 0.2287
time to fit residues: 86.8748
Evaluate side-chains
220 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 2
poor density : 218
time to evaluate : 1.025
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 114
random chunks:
chunk 80 optimal weight: 9.9990
chunk 82 optimal weight: 7.9990
chunk 8 optimal weight: 10.0000
chunk 13 optimal weight: 6.9990
chunk 32 optimal weight: 8.9990
chunk 86 optimal weight: 6.9990
chunk 51 optimal weight: 1.9990
chunk 71 optimal weight: 10.0000
chunk 103 optimal weight: 0.9990
chunk 93 optimal weight: 10.0000
chunk 46 optimal weight: 6.9990
overall best weight: 4.7990
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** R 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 150 HIS
** R 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 188 HIS
B 32 GLN
** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 77 ASN
** D 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Total number of N/Q/H flips: 4
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.072348 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3055 r_free = 0.3055 target = 0.056966 restraints weight = 43366.554|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3095 r_free = 0.3095 target = 0.058992 restraints weight = 29035.706|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3125 r_free = 0.3125 target = 0.060485 restraints weight = 21385.541|
|-----------------------------------------------------------------------------|
r_work (final): 0.3120
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7747
moved from start: 0.5338
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.005 0.066 9266 Z= 0.349
Angle : 0.719 6.453 12554 Z= 0.382
Chirality : 0.046 0.257 1432
Planarity : 0.005 0.058 1579
Dihedral : 5.242 26.480 1251
Min Nonbonded Distance : 2.450
Molprobity Statistics.
All-atom Clashscore : 19.77
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 5.07 %
Favored : 94.93 %
Rotamer:
Outliers : 0.10 %
Allowed : 2.22 %
Favored : 97.68 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 2.94 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: -0.78 (0.25), residues: 1143
helix: 0.31 (0.25), residues: 402
sheet: -0.31 (0.34), residues: 236
loop : -1.24 (0.27), residues: 505
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.023 0.003 TRP R 206
HIS 0.010 0.002 HIS D 35
PHE 0.014 0.002 PHE R 240
TYR 0.016 0.002 TYR B 124
ARG 0.007 0.001 ARG D 206
*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
2286 Ramachandran restraints generated.
1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
2286 Ramachandran restraints generated.
1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
269 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 1
poor density : 268
time to evaluate : 1.033
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: R 280 PHE cc_start: 0.8591 (t80) cc_final: 0.7732 (m-80)
REVERT: R 293 TYR cc_start: 0.8629 (m-10) cc_final: 0.8367 (m-80)
REVERT: R 320 GLU cc_start: 0.8569 (mt-10) cc_final: 0.8198 (mt-10)
REVERT: R 326 PHE cc_start: 0.8429 (m-10) cc_final: 0.7721 (t80)
REVERT: R 374 MET cc_start: 0.5095 (mmt) cc_final: 0.4726 (mmt)
REVERT: L 7 MET cc_start: 0.7959 (tmm) cc_final: 0.7402 (tmm)
REVERT: L 13 TYR cc_start: 0.8747 (t80) cc_final: 0.8389 (t80)
REVERT: A 213 HIS cc_start: 0.8736 (p90) cc_final: 0.8016 (p90)
REVERT: A 269 ASN cc_start: 0.9008 (m110) cc_final: 0.8563 (m110)
REVERT: A 274 PHE cc_start: 0.9095 (t80) cc_final: 0.8770 (t80)
REVERT: A 275 GLU cc_start: 0.9247 (tm-30) cc_final: 0.8832 (tm-30)
REVERT: A 304 GLN cc_start: 0.9480 (tt0) cc_final: 0.9076 (tm-30)
REVERT: A 348 LEU cc_start: 0.9353 (mm) cc_final: 0.9100 (tp)
REVERT: B 57 LYS cc_start: 0.9188 (pttp) cc_final: 0.8636 (ptpt)
REVERT: B 101 MET cc_start: 0.8926 (mpp) cc_final: 0.8381 (mpp)
REVERT: B 146 LEU cc_start: 0.8053 (mp) cc_final: 0.7779 (mp)
REVERT: B 192 LEU cc_start: 0.8613 (mt) cc_final: 0.8216 (pt)
REVERT: B 222 PHE cc_start: 0.8203 (m-80) cc_final: 0.7508 (m-80)
REVERT: B 289 TYR cc_start: 0.7525 (m-80) cc_final: 0.6337 (m-80)
REVERT: C 27 ARG cc_start: 0.8065 (ptp90) cc_final: 0.7672 (ptp90)
REVERT: C 38 MET cc_start: 0.9118 (ptp) cc_final: 0.8860 (ptp)
REVERT: D 73 ASP cc_start: 0.9107 (t70) cc_final: 0.8261 (t0)
REVERT: D 78 THR cc_start: 0.8938 (m) cc_final: 0.8555 (p)
REVERT: D 80 PHE cc_start: 0.8680 (m-80) cc_final: 0.8227 (m-80)
REVERT: D 93 MET cc_start: 0.8018 (tpt) cc_final: 0.7727 (tpt)
REVERT: D 111 TRP cc_start: 0.8292 (m100) cc_final: 0.7834 (m-10)
REVERT: D 159 ASN cc_start: 0.9260 (m110) cc_final: 0.8729 (t0)
REVERT: D 164 TRP cc_start: 0.8192 (m100) cc_final: 0.7451 (m-10)
REVERT: D 202 LEU cc_start: 0.9195 (tt) cc_final: 0.8765 (tt)
REVERT: D 218 MET cc_start: 0.8504 (tmm) cc_final: 0.8029 (tmm)
REVERT: D 227 PHE cc_start: 0.8398 (m-80) cc_final: 0.8057 (m-80)
outliers start: 1
outliers final: 0
residues processed: 268
average time/residue: 0.2254
time to fit residues: 81.2353
Evaluate side-chains
212 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 0
poor density : 212
time to evaluate : 1.010
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 114
random chunks:
chunk 14 optimal weight: 2.9990
chunk 66 optimal weight: 6.9990
chunk 75 optimal weight: 4.9990
chunk 29 optimal weight: 1.9990
chunk 57 optimal weight: 0.0670
chunk 43 optimal weight: 9.9990
chunk 15 optimal weight: 0.7980
chunk 101 optimal weight: 0.6980
chunk 109 optimal weight: 0.5980
chunk 96 optimal weight: 4.9990
chunk 3 optimal weight: 6.9990
overall best weight: 0.8320
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** R 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 150 HIS
R 181 GLN
A 188 HIS
A 294 ASN
A 306 GLN
** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Total number of N/Q/H flips: 5
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.076359 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3125 r_free = 0.3125 target = 0.060249 restraints weight = 41219.605|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3166 r_free = 0.3166 target = 0.062448 restraints weight = 27210.349|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.064081 restraints weight = 19848.645|
|-----------------------------------------------------------------------------|
r_work (final): 0.3194
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7630
moved from start: 0.5560
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.055 9266 Z= 0.193
Angle : 0.669 8.910 12554 Z= 0.343
Chirality : 0.044 0.158 1432
Planarity : 0.004 0.064 1579
Dihedral : 4.863 25.508 1251
Min Nonbonded Distance : 2.365
Molprobity Statistics.
All-atom Clashscore : 14.51
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 3.76 %
Favored : 96.24 %
Rotamer:
Outliers : 0.30 %
Allowed : 1.52 %
Favored : 98.18 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 2.94 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: -0.67 (0.25), residues: 1143
helix: 0.51 (0.25), residues: 404
sheet: -0.55 (0.32), residues: 270
loop : -1.13 (0.29), residues: 469
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.016 0.002 TRP B 297
HIS 0.006 0.001 HIS B 142
PHE 0.013 0.001 PHE A 223
TYR 0.020 0.001 TYR R 369
ARG 0.016 0.000 ARG D 206
*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
2286 Ramachandran restraints generated.
1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
2286 Ramachandran restraints generated.
1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
295 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 3
poor density : 292
time to evaluate : 1.159
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: R 94 ILE cc_start: 0.7183 (mt) cc_final: 0.6468 (mm)
REVERT: R 119 ASN cc_start: 0.8755 (m-40) cc_final: 0.8375 (m-40)
REVERT: R 253 ARG cc_start: 0.7335 (mtt180) cc_final: 0.6793 (mtp180)
REVERT: R 280 PHE cc_start: 0.8485 (t80) cc_final: 0.7716 (m-80)
REVERT: R 293 TYR cc_start: 0.8722 (m-10) cc_final: 0.8482 (m-80)
REVERT: R 320 GLU cc_start: 0.8578 (mt-10) cc_final: 0.8213 (mt-10)
REVERT: R 374 MET cc_start: 0.4617 (mmt) cc_final: 0.4236 (mmt)
REVERT: R 381 ILE cc_start: 0.8847 (tp) cc_final: 0.8603 (tp)
REVERT: L 7 MET cc_start: 0.7713 (tmm) cc_final: 0.7109 (tmm)
REVERT: L 13 TYR cc_start: 0.8703 (t80) cc_final: 0.8488 (t80)
REVERT: A 188 HIS cc_start: 0.8338 (OUTLIER) cc_final: 0.8104 (t-90)
REVERT: A 213 HIS cc_start: 0.8815 (p90) cc_final: 0.8023 (p90)
REVERT: A 224 CYS cc_start: 0.8941 (m) cc_final: 0.8175 (p)
REVERT: A 247 MET cc_start: 0.9285 (mtm) cc_final: 0.8293 (mtm)
REVERT: A 248 LYS cc_start: 0.9465 (mtmm) cc_final: 0.9257 (mttt)
REVERT: A 256 ASN cc_start: 0.9240 (m-40) cc_final: 0.8772 (m110)
REVERT: A 274 PHE cc_start: 0.9121 (t80) cc_final: 0.8724 (t80)
REVERT: A 296 TYR cc_start: 0.8434 (t80) cc_final: 0.7699 (t80)
REVERT: A 304 GLN cc_start: 0.9462 (tt0) cc_final: 0.8584 (tm-30)
REVERT: A 313 ARG cc_start: 0.8141 (mtt90) cc_final: 0.7926 (mpt180)
REVERT: A 348 LEU cc_start: 0.9317 (mm) cc_final: 0.8925 (tp)
REVERT: B 57 LYS cc_start: 0.9136 (pttp) cc_final: 0.8617 (ptpt)
REVERT: B 101 MET cc_start: 0.8961 (mpp) cc_final: 0.8529 (mpp)
REVERT: B 146 LEU cc_start: 0.7913 (mp) cc_final: 0.7607 (mp)
REVERT: B 192 LEU cc_start: 0.8534 (mt) cc_final: 0.8179 (pt)
REVERT: B 222 PHE cc_start: 0.8121 (m-80) cc_final: 0.7918 (m-10)
REVERT: B 283 ARG cc_start: 0.9096 (tpt170) cc_final: 0.8847 (tpt170)
REVERT: B 289 TYR cc_start: 0.7338 (m-80) cc_final: 0.6287 (m-80)
REVERT: B 292 PHE cc_start: 0.9215 (m-10) cc_final: 0.8638 (m-80)
REVERT: B 325 MET cc_start: 0.9045 (mtp) cc_final: 0.8447 (ttt)
REVERT: C 25 ILE cc_start: 0.7700 (pt) cc_final: 0.6817 (pt)
REVERT: C 27 ARG cc_start: 0.7955 (ptp90) cc_final: 0.7699 (ptp90)
REVERT: D 29 PHE cc_start: 0.8824 (t80) cc_final: 0.8474 (t80)
REVERT: D 73 ASP cc_start: 0.9048 (t70) cc_final: 0.8245 (t0)
REVERT: D 93 MET cc_start: 0.8101 (tpt) cc_final: 0.7875 (tpt)
REVERT: D 111 TRP cc_start: 0.8002 (m100) cc_final: 0.7554 (m-10)
REVERT: D 159 ASN cc_start: 0.9358 (m110) cc_final: 0.8932 (t0)
REVERT: D 164 TRP cc_start: 0.8026 (m100) cc_final: 0.7263 (m-10)
REVERT: D 165 PHE cc_start: 0.8592 (m-80) cc_final: 0.8297 (m-80)
REVERT: D 202 LEU cc_start: 0.9239 (tt) cc_final: 0.8726 (tt)
REVERT: D 218 MET cc_start: 0.8303 (tmm) cc_final: 0.7797 (tmm)
REVERT: D 227 PHE cc_start: 0.8418 (m-80) cc_final: 0.7964 (m-80)
outliers start: 3
outliers final: 1
residues processed: 294
average time/residue: 0.2291
time to fit residues: 92.0961
Evaluate side-chains
231 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 2
poor density : 229
time to evaluate : 1.058
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 114
random chunks:
chunk 101 optimal weight: 7.9990
chunk 22 optimal weight: 2.9990
chunk 52 optimal weight: 5.9990
chunk 79 optimal weight: 0.8980
chunk 86 optimal weight: 4.9990
chunk 0 optimal weight: 30.0000
chunk 26 optimal weight: 10.0000
chunk 110 optimal weight: 30.0000
chunk 64 optimal weight: 4.9990
chunk 8 optimal weight: 9.9990
chunk 75 optimal weight: 7.9990
overall best weight: 3.9788
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** R 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 150 HIS
** R 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 188 HIS
B 32 GLN
** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 35 HIS
** D 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Total number of N/Q/H flips: 4
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.073243 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3067 r_free = 0.3067 target = 0.057544 restraints weight = 41893.090|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3109 r_free = 0.3109 target = 0.059648 restraints weight = 27738.611|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.061200 restraints weight = 20285.020|
|-----------------------------------------------------------------------------|
r_work (final): 0.3137
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7705
moved from start: 0.5751
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.005 0.064 9266 Z= 0.308
Angle : 0.704 8.090 12554 Z= 0.373
Chirality : 0.045 0.160 1432
Planarity : 0.006 0.116 1579
Dihedral : 5.044 26.618 1251
Min Nonbonded Distance : 2.300
Molprobity Statistics.
All-atom Clashscore : 18.56
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 4.99 %
Favored : 95.01 %
Rotamer:
Outliers : 0.10 %
Allowed : 0.91 %
Favored : 98.99 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 2.94 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: -0.87 (0.24), residues: 1143
helix: 0.22 (0.25), residues: 408
sheet: -0.51 (0.33), residues: 253
loop : -1.22 (0.28), residues: 482
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.026 0.003 TRP R 336
HIS 0.009 0.002 HIS B 142
PHE 0.018 0.002 PHE D 29
TYR 0.025 0.002 TYR R 369
ARG 0.014 0.001 ARG D 206
*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
2286 Ramachandran restraints generated.
1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
2286 Ramachandran restraints generated.
1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
270 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 1
poor density : 269
time to evaluate : 1.155
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: R 94 ILE cc_start: 0.6866 (mt) cc_final: 0.6361 (mm)
REVERT: R 253 ARG cc_start: 0.7295 (mtt180) cc_final: 0.6799 (mtp180)
REVERT: R 280 PHE cc_start: 0.8594 (t80) cc_final: 0.7716 (m-80)
REVERT: R 295 LEU cc_start: 0.8429 (mt) cc_final: 0.8191 (mt)
REVERT: R 299 GLU cc_start: 0.5787 (mp0) cc_final: 0.5452 (mp0)
REVERT: R 320 GLU cc_start: 0.8536 (mt-10) cc_final: 0.8202 (mt-10)
REVERT: R 330 LEU cc_start: 0.8887 (tp) cc_final: 0.8615 (mt)
REVERT: R 374 MET cc_start: 0.4780 (mmt) cc_final: 0.4397 (mmt)
REVERT: R 381 ILE cc_start: 0.8910 (tp) cc_final: 0.8677 (tp)
REVERT: L 7 MET cc_start: 0.7823 (tmm) cc_final: 0.7405 (tmm)
REVERT: L 13 TYR cc_start: 0.8838 (t80) cc_final: 0.8532 (t80)
REVERT: A 198 MET cc_start: 0.8547 (ttm) cc_final: 0.8224 (ttp)
REVERT: A 200 ASP cc_start: 0.8373 (t0) cc_final: 0.8087 (t0)
REVERT: A 213 HIS cc_start: 0.8762 (p90) cc_final: 0.8047 (p90)
REVERT: A 224 CYS cc_start: 0.9050 (m) cc_final: 0.8268 (p)
REVERT: A 274 PHE cc_start: 0.9216 (t80) cc_final: 0.8836 (t80)
REVERT: A 275 GLU cc_start: 0.9218 (tm-30) cc_final: 0.9001 (tm-30)
REVERT: A 304 GLN cc_start: 0.9475 (tt0) cc_final: 0.8544 (tm-30)
REVERT: A 313 ARG cc_start: 0.8286 (mtt90) cc_final: 0.7960 (mpt180)
REVERT: A 348 LEU cc_start: 0.9351 (mm) cc_final: 0.9076 (tp)
REVERT: B 57 LYS cc_start: 0.9173 (pttp) cc_final: 0.8613 (ptpt)
REVERT: B 69 LEU cc_start: 0.9552 (mt) cc_final: 0.8550 (pp)
REVERT: B 101 MET cc_start: 0.8935 (mpp) cc_final: 0.8288 (mpp)
REVERT: B 146 LEU cc_start: 0.8279 (mp) cc_final: 0.7773 (mp)
REVERT: B 190 LEU cc_start: 0.8869 (tp) cc_final: 0.8154 (tp)
REVERT: B 192 LEU cc_start: 0.8549 (mt) cc_final: 0.8202 (pt)
REVERT: B 222 PHE cc_start: 0.8239 (m-80) cc_final: 0.7574 (m-80)
REVERT: B 262 MET cc_start: 0.8550 (pmm) cc_final: 0.8159 (pmm)
REVERT: B 289 TYR cc_start: 0.7530 (m-80) cc_final: 0.6446 (m-80)
REVERT: D 29 PHE cc_start: 0.8933 (t80) cc_final: 0.8507 (t80)
REVERT: D 73 ASP cc_start: 0.8998 (t70) cc_final: 0.8267 (t0)
REVERT: D 81 LEU cc_start: 0.8901 (pp) cc_final: 0.8343 (pp)
REVERT: D 93 MET cc_start: 0.8211 (tpt) cc_final: 0.7948 (tpt)
REVERT: D 111 TRP cc_start: 0.8414 (m100) cc_final: 0.7991 (m-10)
REVERT: D 159 ASN cc_start: 0.9201 (m110) cc_final: 0.8649 (t0)
REVERT: D 164 TRP cc_start: 0.8203 (m100) cc_final: 0.7679 (m-10)
REVERT: D 202 LEU cc_start: 0.9239 (tt) cc_final: 0.8733 (tt)
REVERT: D 218 MET cc_start: 0.8451 (tmm) cc_final: 0.8019 (tmm)
REVERT: D 225 LEU cc_start: 0.7710 (mt) cc_final: 0.7461 (mt)
outliers start: 1
outliers final: 0
residues processed: 269
average time/residue: 0.2332
time to fit residues: 84.9407
Evaluate side-chains
208 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 0
poor density : 208
time to evaluate : 1.035
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 114
random chunks:
chunk 87 optimal weight: 20.0000
chunk 65 optimal weight: 0.5980
chunk 80 optimal weight: 9.9990
chunk 48 optimal weight: 8.9990
chunk 12 optimal weight: 0.6980
chunk 64 optimal weight: 4.9990
chunk 44 optimal weight: 2.9990
chunk 78 optimal weight: 0.9980
chunk 88 optimal weight: 0.0010
chunk 46 optimal weight: 0.9980
chunk 21 optimal weight: 5.9990
overall best weight: 0.6586
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** R 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 150 HIS
R 181 GLN
A 188 HIS
A 294 ASN
** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Total number of N/Q/H flips: 4
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.077017 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.060883 restraints weight = 40722.715|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.063110 restraints weight = 26901.839|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.064750 restraints weight = 19639.820|
|-----------------------------------------------------------------------------|
r_work (final): 0.3213
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7621
moved from start: 0.5905
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.049 9266 Z= 0.193
Angle : 0.697 11.862 12554 Z= 0.362
Chirality : 0.045 0.194 1432
Planarity : 0.005 0.081 1579
Dihedral : 4.807 22.910 1251
Min Nonbonded Distance : 2.340
Molprobity Statistics.
All-atom Clashscore : 14.01
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 3.24 %
Favored : 96.76 %
Rotamer:
Outliers : 0.30 %
Allowed : 0.30 %
Favored : 99.39 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 2.94 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: -0.69 (0.25), residues: 1143
helix: 0.43 (0.25), residues: 407
sheet: -0.60 (0.32), residues: 265
loop : -1.05 (0.29), residues: 471
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.020 0.002 TRP B 169
HIS 0.010 0.002 HIS R 150
PHE 0.020 0.002 PHE A 336
TYR 0.026 0.001 TYR R 369
ARG 0.019 0.001 ARG D 206
********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
2286 Ramachandran restraints generated.
1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
2286 Ramachandran restraints generated.
1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
283 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 3
poor density : 280
time to evaluate : 0.982
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: R 94 ILE cc_start: 0.7020 (mt) cc_final: 0.6233 (mm)
REVERT: R 119 ASN cc_start: 0.8713 (m-40) cc_final: 0.8335 (m110)
REVERT: R 253 ARG cc_start: 0.7296 (mtt180) cc_final: 0.6786 (mtp180)
REVERT: R 280 PHE cc_start: 0.8479 (t80) cc_final: 0.7672 (m-80)
REVERT: R 282 PHE cc_start: 0.8852 (t80) cc_final: 0.8502 (t80)
REVERT: R 295 LEU cc_start: 0.8220 (mt) cc_final: 0.7900 (mt)
REVERT: R 299 GLU cc_start: 0.5322 (mp0) cc_final: 0.4991 (mp0)
REVERT: R 320 GLU cc_start: 0.8557 (mt-10) cc_final: 0.8219 (mt-10)
REVERT: R 374 MET cc_start: 0.4386 (mmt) cc_final: 0.3940 (mmt)
REVERT: R 381 ILE cc_start: 0.8882 (tp) cc_final: 0.8662 (tp)
REVERT: L 7 MET cc_start: 0.7610 (tmm) cc_final: 0.7192 (tmm)
REVERT: L 13 TYR cc_start: 0.8721 (t80) cc_final: 0.8455 (t80)
REVERT: A 188 HIS cc_start: 0.8359 (OUTLIER) cc_final: 0.8087 (t-90)
REVERT: A 200 ASP cc_start: 0.8413 (t0) cc_final: 0.8114 (t0)
REVERT: A 213 HIS cc_start: 0.8775 (p90) cc_final: 0.8014 (p90)
REVERT: A 224 CYS cc_start: 0.9052 (m) cc_final: 0.8332 (p)
REVERT: A 274 PHE cc_start: 0.9144 (t80) cc_final: 0.8809 (t80)
REVERT: A 304 GLN cc_start: 0.9462 (tt0) cc_final: 0.8654 (tm-30)
REVERT: A 313 ARG cc_start: 0.8153 (mtt90) cc_final: 0.7848 (mpt180)
REVERT: A 317 LYS cc_start: 0.8759 (pttt) cc_final: 0.8536 (pttt)
REVERT: A 348 LEU cc_start: 0.9321 (mm) cc_final: 0.9050 (tp)
REVERT: B 57 LYS cc_start: 0.9180 (pttp) cc_final: 0.8672 (ptpt)
REVERT: B 101 MET cc_start: 0.8921 (mpp) cc_final: 0.8512 (mpp)
REVERT: B 146 LEU cc_start: 0.8052 (mp) cc_final: 0.7707 (mp)
REVERT: B 190 LEU cc_start: 0.8659 (tp) cc_final: 0.8352 (tp)
REVERT: B 192 LEU cc_start: 0.8541 (mt) cc_final: 0.8187 (pt)
REVERT: B 283 ARG cc_start: 0.9153 (tpt170) cc_final: 0.8900 (tpt170)
REVERT: B 289 TYR cc_start: 0.7313 (m-80) cc_final: 0.6269 (m-80)
REVERT: B 292 PHE cc_start: 0.9239 (m-10) cc_final: 0.8648 (m-80)
REVERT: B 311 HIS cc_start: 0.8292 (m-70) cc_final: 0.8036 (m-70)
REVERT: B 337 LYS cc_start: 0.8998 (mttp) cc_final: 0.8772 (mttt)
REVERT: D 29 PHE cc_start: 0.8615 (t80) cc_final: 0.8414 (t80)
REVERT: D 45 LEU cc_start: 0.8921 (mt) cc_final: 0.8696 (mt)
REVERT: D 73 ASP cc_start: 0.8783 (t70) cc_final: 0.8212 (t0)
REVERT: D 93 MET cc_start: 0.8126 (tpt) cc_final: 0.7830 (tpt)
REVERT: D 111 TRP cc_start: 0.7933 (m100) cc_final: 0.7506 (m-10)
REVERT: D 159 ASN cc_start: 0.9319 (m110) cc_final: 0.8858 (t0)
REVERT: D 164 TRP cc_start: 0.7959 (m100) cc_final: 0.7112 (m-10)
REVERT: D 165 PHE cc_start: 0.8575 (m-80) cc_final: 0.8294 (m-80)
REVERT: D 202 LEU cc_start: 0.9205 (tt) cc_final: 0.8687 (tt)
REVERT: D 218 MET cc_start: 0.8425 (tmm) cc_final: 0.8007 (tmm)
outliers start: 3
outliers final: 2
residues processed: 281
average time/residue: 0.2297
time to fit residues: 86.6242
Evaluate side-chains
224 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 3
poor density : 221
time to evaluate : 1.081
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 114
random chunks:
chunk 6 optimal weight: 0.0270
chunk 69 optimal weight: 7.9990
chunk 89 optimal weight: 3.9990
chunk 105 optimal weight: 6.9990
chunk 27 optimal weight: 0.9980
chunk 83 optimal weight: 3.9990
chunk 60 optimal weight: 0.0170
chunk 26 optimal weight: 6.9990
chunk 50 optimal weight: 8.9990
chunk 59 optimal weight: 1.9990
chunk 35 optimal weight: 5.9990
overall best weight: 1.4080
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** R 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 181 GLN
A 188 HIS
** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 35 HIS
D 219 GLN
Total number of N/Q/H flips: 4
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.076704 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3136 r_free = 0.3136 target = 0.060565 restraints weight = 41302.324|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.062808 restraints weight = 27079.966|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.064409 restraints weight = 19696.336|
|-----------------------------------------------------------------------------|
r_work (final): 0.3205
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7621
moved from start: 0.6064
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.072 9266 Z= 0.210
Angle : 0.690 10.375 12554 Z= 0.359
Chirality : 0.045 0.182 1432
Planarity : 0.005 0.072 1579
Dihedral : 4.709 23.899 1251
Min Nonbonded Distance : 2.351
Molprobity Statistics.
All-atom Clashscore : 15.34
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 4.11 %
Favored : 95.89 %
Rotamer:
Outliers : 0.10 %
Allowed : 0.30 %
Favored : 99.60 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 2.94 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: -0.62 (0.25), residues: 1143
helix: 0.42 (0.25), residues: 407
sheet: -0.51 (0.33), residues: 262
loop : -0.98 (0.29), residues: 474
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.039 0.002 TRP R 336
HIS 0.008 0.001 HIS D 35
PHE 0.024 0.002 PHE D 227
TYR 0.060 0.002 TYR R 369
ARG 0.005 0.000 ARG B 219
Origin is already at (0, 0, 0), no shifts will be applied
===============================================================================
Job complete
usr+sys time: 2942.53 seconds
wall clock time: 53 minutes 55.20 seconds (3235.20 seconds total)