Starting phenix.real_space_refine
on Sat Jan 18 09:38:11 2025 by dcliebschner
===============================================================================
Processing files:
-------------------------------------------------------------------------------
Found model, /net/cci-nas-00/data/ceres_data/8vpq_43413/01_2025/8vpq_43413.cif
Found real_map, /net/cci-nas-00/data/ceres_data/8vpq_43413/01_2025/8vpq_43413.map
Processing PHIL parameters:
-------------------------------------------------------------------------------
Adding command-line PHIL:
-------------------------
refinement.macro_cycles=10
scattering_table=electron
resolution=3.3
write_initial_geo_file=False
Final processed PHIL parameters:
-------------------------------------------------------------------------------
data_manager {
real_map_files = "/net/cci-nas-00/data/ceres_data/8vpq_43413/01_2025/8vpq_43413.map"
default_real_map = "/net/cci-nas-00/data/ceres_data/8vpq_43413/01_2025/8vpq_43413.map"
model {
file = "/net/cci-nas-00/data/ceres_data/8vpq_43413/01_2025/8vpq_43413.cif"
}
default_model = "/net/cci-nas-00/data/ceres_data/8vpq_43413/01_2025/8vpq_43413.cif"
}
resolution = 3.3
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= 0.025
Set stop_for_unknowns flag
Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
Set to: electron
Number of scattering types: 6
Type Number sf(0) Gaussians
Zn 1 6.06 5
P 6 5.49 5
S 75 5.16 5
C 7665 2.51 5
N 2055 2.21 5
O 2288 1.98 5
sf(0) = scattering factor at diffraction angle 0.
Process input model
Symmetric amino acids flipped. Time to flip 4 residue(s): 0.04s
Monomer Library directory:
"/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
Total number of atoms: 12090
Number of models: 1
Model: ""
Number of chains: 6
Chain: "A"
Number of atoms: 3947
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 499, 3947
Classifications: {'peptide': 499}
Link IDs: {'CIS': 1, 'PTRANS': 13, 'TRANS': 484}
Chain breaks: 3
Chain: "B"
Number of atoms: 4001
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 506, 4001
Classifications: {'peptide': 506}
Link IDs: {'PTRANS': 13, 'TRANS': 492}
Chain breaks: 1
Chain: "C"
Number of atoms: 2985
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 369, 2985
Classifications: {'peptide': 369}
Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 353}
Chain: "D"
Number of atoms: 1120
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 135, 1120
Classifications: {'peptide': 135}
Link IDs: {'PTRANS': 8, 'TRANS': 126}
Chain: "C"
Number of atoms: 1
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 1, 1
Unusual residues: {' ZN': 1}
Classifications: {'undetermined': 1}
Chain: "D"
Number of atoms: 36
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 1, 36
Unusual residues: {'IHP': 1}
Classifications: {'undetermined': 1}
Time building chain proxies: 8.57, per 1000 atoms: 0.71
Number of scatterers: 12090
At special positions: 0
Unit cell: (77.28, 136.08, 154.56, 90, 90, 90)
Space group: P 1 (No. 1)
Number of sites at special positions: 0
Number of scattering types: 6
Type Number sf(0)
Zn 1 29.99
S 75 16.00
P 6 15.00
O 2288 8.00
N 2055 7.00
C 7665 6.00
sf(0) = scattering factor at diffraction angle 0.
Number of disulfides: simple=0, symmetry=0
Automatic linking
Parameters for automatic linking
Linking & cutoffs
Metal : Auto - 3.00
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: 3.14
Conformation dependent library (CDL) restraints added in 1.7 seconds
Dynamic metal coordination
Zn2+ tetrahedral coordination
pdb=" ZN C 600 "
pdb="ZN ZN C 600 " - pdb=" ND1 HIS C 178 "
2986 Ramachandran restraints generated.
1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2.
Adding C-beta torsion restraints...
Number of C-beta restraints generated: 2840
Finding SS restraints...
Secondary structure from input PDB file:
46 helices and 20 sheets defined
31.2% alpha, 14.7% beta
0 base pairs and 0 stacking pairs defined.
Time for finding SS restraints: 1.37
Creating SS restraints...
Processing helix chain 'A' and resid 41 through 54
removed outlier: 3.505A pdb=" N ARG A 45 " --> pdb=" O SER A 41 " (cutoff:3.500A)
Processing helix chain 'A' and resid 75 through 83
removed outlier: 3.801A pdb=" N LEU A 79 " --> pdb=" O HIS A 75 " (cutoff:3.500A)
Processing helix chain 'A' and resid 84 through 90
Processing helix chain 'A' and resid 111 through 120
Processing helix chain 'A' and resid 130 through 141
removed outlier: 3.866A pdb=" N ILE A 134 " --> pdb=" O GLU A 130 " (cutoff:3.500A)
removed outlier: 3.821A pdb=" N ASP A 139 " --> pdb=" O TYR A 135 " (cutoff:3.500A)
Processing helix chain 'A' and resid 143 through 156
Processing helix chain 'A' and resid 159 through 162
Processing helix chain 'A' and resid 163 through 173
removed outlier: 3.912A pdb=" N TRP A 168 " --> pdb=" O LEU A 164 " (cutoff:3.500A)
removed outlier: 3.601A pdb=" N HIS A 173 " --> pdb=" O LEU A 169 " (cutoff:3.500A)
Processing helix chain 'A' and resid 175 through 189
removed outlier: 4.158A pdb=" N CYS A 185 " --> pdb=" O ALA A 181 " (cutoff:3.500A)
removed outlier: 3.731A pdb=" N ALA A 186 " --> pdb=" O ALA A 182 " (cutoff:3.500A)
Processing helix chain 'A' and resid 203 through 212
Processing helix chain 'A' and resid 216 through 219
removed outlier: 3.529A pdb=" N GLN A 219 " --> pdb=" O PRO A 216 " (cutoff:3.500A)
No H-bonds generated for 'chain 'A' and resid 216 through 219'
Processing helix chain 'A' and resid 220 through 230
removed outlier: 3.530A pdb=" N ALA A 224 " --> pdb=" O ASN A 220 " (cutoff:3.500A)
removed outlier: 3.724A pdb=" N GLU A 226 " --> pdb=" O THR A 222 " (cutoff:3.500A)
Processing helix chain 'A' and resid 239 through 244
Processing helix chain 'B' and resid 41 through 54
removed outlier: 3.879A pdb=" N ARG B 45 " --> pdb=" O SER B 41 " (cutoff:3.500A)
removed outlier: 3.758A pdb=" N LYS B 52 " --> pdb=" O GLN B 48 " (cutoff:3.500A)
Processing helix chain 'B' and resid 75 through 81
removed outlier: 3.632A pdb=" N LEU B 79 " --> pdb=" O HIS B 75 " (cutoff:3.500A)
Processing helix chain 'B' and resid 83 through 91
Processing helix chain 'B' and resid 111 through 120
Processing helix chain 'B' and resid 131 through 142
Processing helix chain 'B' and resid 143 through 157
removed outlier: 3.699A pdb=" N THR B 157 " --> pdb=" O PHE B 153 " (cutoff:3.500A)
Processing helix chain 'B' and resid 162 through 170
removed outlier: 3.509A pdb=" N MET B 167 " --> pdb=" O CYS B 163 " (cutoff:3.500A)
Processing helix chain 'B' and resid 175 through 188
removed outlier: 3.727A pdb=" N CYS B 185 " --> pdb=" O ALA B 181 " (cutoff:3.500A)
removed outlier: 4.081A pdb=" N ALA B 186 " --> pdb=" O ALA B 182 " (cutoff:3.500A)
Processing helix chain 'B' and resid 190 through 194
Processing helix chain 'B' and resid 203 through 212
Processing helix chain 'B' and resid 216 through 220
Processing helix chain 'B' and resid 221 through 230
Processing helix chain 'B' and resid 232 through 237
Processing helix chain 'B' and resid 238 through 240
No H-bonds generated for 'chain 'B' and resid 238 through 240'
Processing helix chain 'C' and resid 18 through 22
removed outlier: 3.913A pdb=" N ASN C 21 " --> pdb=" O ASP C 18 " (cutoff:3.500A)
removed outlier: 3.530A pdb=" N TYR C 22 " --> pdb=" O VAL C 19 " (cutoff:3.500A)
No H-bonds generated for 'chain 'C' and resid 18 through 22'
Processing helix chain 'C' and resid 32 through 43
removed outlier: 4.234A pdb=" N ARG C 36 " --> pdb=" O PRO C 32 " (cutoff:3.500A)
Processing helix chain 'C' and resid 69 through 78
removed outlier: 3.511A pdb=" N ILE C 73 " --> pdb=" O SER C 69 " (cutoff:3.500A)
Processing helix chain 'C' and resid 88 through 94
Processing helix chain 'C' and resid 106 through 125
Processing helix chain 'C' and resid 154 through 164
Processing helix chain 'C' and resid 180 through 187
Processing helix chain 'C' and resid 233 through 253
removed outlier: 3.618A pdb=" N TYR C 237 " --> pdb=" O ASP C 233 " (cutoff:3.500A)
Proline residue: C 243 - end of helix
Processing helix chain 'C' and resid 277 through 290
removed outlier: 3.563A pdb=" N HIS C 281 " --> pdb=" O THR C 277 " (cutoff:3.500A)
Processing helix chain 'C' and resid 304 through 320
Processing helix chain 'C' and resid 356 through 371
Processing helix chain 'D' and resid 15 through 19
Processing helix chain 'D' and resid 20 through 25
removed outlier: 3.683A pdb=" N SER D 23 " --> pdb=" O ALA D 20 " (cutoff:3.500A)
removed outlier: 3.618A pdb=" N GLN D 24 " --> pdb=" O ARG D 21 " (cutoff:3.500A)
Processing helix chain 'D' and resid 41 through 55
Processing helix chain 'D' and resid 61 through 69
Processing helix chain 'D' and resid 73 through 80
Processing helix chain 'D' and resid 92 through 106
Processing helix chain 'D' and resid 109 through 114
Processing helix chain 'D' and resid 122 through 131
Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 26
removed outlier: 6.515A pdb=" N PHE B 469 " --> pdb=" O SER A 26 " (cutoff:3.500A)
Processing sheet with id=AA2, first strand: chain 'A' and resid 34 through 38
Processing sheet with id=AA3, first strand: chain 'A' and resid 70 through 74
Processing sheet with id=AA4, first strand: chain 'A' and resid 123 through 127
removed outlier: 3.626A pdb=" N TYR B 35 " --> pdb=" O LEU A 126 " (cutoff:3.500A)
Processing sheet with id=AA5, first strand: chain 'A' and resid 280 through 283
removed outlier: 3.821A pdb=" N SER A 280 " --> pdb=" O ALA A 276 " (cutoff:3.500A)
removed outlier: 4.653A pdb=" N ILE A 256 " --> pdb=" O LEU A 273 " (cutoff:3.500A)
removed outlier: 3.614A pdb=" N ILE A 259 " --> pdb=" O PHE A 533 " (cutoff:3.500A)
removed outlier: 3.797A pdb=" N PHE A 533 " --> pdb=" O ILE A 259 " (cutoff:3.500A)
removed outlier: 6.027A pdb=" N LYS A 261 " --> pdb=" O LEU A 531 " (cutoff:3.500A)
removed outlier: 4.872A pdb=" N LEU A 531 " --> pdb=" O LYS A 261 " (cutoff:3.500A)
Processing sheet with id=AA6, first strand: chain 'A' and resid 295 through 299
removed outlier: 4.527A pdb=" N LEU A 303 " --> pdb=" O CYS A 319 " (cutoff:3.500A)
Processing sheet with id=AA7, first strand: chain 'A' and resid 340 through 344
Processing sheet with id=AA8, first strand: chain 'A' and resid 355 through 356
removed outlier: 4.143A pdb=" N GLY A 355 " --> pdb=" O SER A 363 " (cutoff:3.500A)
Processing sheet with id=AA9, first strand: chain 'A' and resid 390 through 394
removed outlier: 3.567A pdb=" N LYS A 427 " --> pdb=" O ASP A 422 " (cutoff:3.500A)
Processing sheet with id=AB1, first strand: chain 'A' and resid 404 through 406
Processing sheet with id=AB2, first strand: chain 'A' and resid 442 through 446
Processing sheet with id=AB3, first strand: chain 'A' and resid 485 through 489
Processing sheet with id=AB4, first strand: chain 'B' and resid 70 through 74
Processing sheet with id=AB5, first strand: chain 'B' and resid 268 through 271
removed outlier: 6.951A pdb=" N LYS B 261 " --> pdb=" O LEU B 531 " (cutoff:3.500A)
removed outlier: 6.051A pdb=" N LEU B 531 " --> pdb=" O LYS B 261 " (cutoff:3.500A)
Processing sheet with id=AB6, first strand: chain 'B' and resid 295 through 299
Processing sheet with id=AB7, first strand: chain 'B' and resid 340 through 342
removed outlier: 3.544A pdb=" N ILE B 367 " --> pdb=" O SER B 352 " (cutoff:3.500A)
Processing sheet with id=AB8, first strand: chain 'B' and resid 390 through 394
Processing sheet with id=AB9, first strand: chain 'B' and resid 405 through 406
Processing sheet with id=AC1, first strand: chain 'B' and resid 486 through 488
removed outlier: 4.121A pdb=" N ILE B 494 " --> pdb=" O LEU B 511 " (cutoff:3.500A)
Processing sheet with id=AC2, first strand: chain 'C' and resid 223 through 228
removed outlier: 7.924A pdb=" N VAL C 224 " --> pdb=" O VAL C 193 " (cutoff:3.500A)
removed outlier: 5.973A pdb=" N THR C 195 " --> pdb=" O VAL C 224 " (cutoff:3.500A)
removed outlier: 7.247A pdb=" N TYR C 226 " --> pdb=" O THR C 195 " (cutoff:3.500A)
removed outlier: 6.649A pdb=" N SER C 197 " --> pdb=" O TYR C 226 " (cutoff:3.500A)
removed outlier: 7.262A pdb=" N LEU C 228 " --> pdb=" O SER C 197 " (cutoff:3.500A)
removed outlier: 6.942A pdb=" N HIS C 199 " --> pdb=" O LEU C 228 " (cutoff:3.500A)
removed outlier: 6.855A pdb=" N VAL C 170 " --> pdb=" O MET C 194 " (cutoff:3.500A)
removed outlier: 7.735A pdb=" N VAL C 196 " --> pdb=" O VAL C 170 " (cutoff:3.500A)
removed outlier: 6.003A pdb=" N TYR C 172 " --> pdb=" O VAL C 196 " (cutoff:3.500A)
removed outlier: 7.622A pdb=" N PHE C 198 " --> pdb=" O TYR C 172 " (cutoff:3.500A)
removed outlier: 6.214A pdb=" N ASP C 174 " --> pdb=" O PHE C 198 " (cutoff:3.500A)
removed outlier: 8.351A pdb=" N LYS C 200 " --> pdb=" O ASP C 174 " (cutoff:3.500A)
removed outlier: 6.692A pdb=" N LEU C 171 " --> pdb=" O VAL C 258 " (cutoff:3.500A)
removed outlier: 7.756A pdb=" N GLN C 260 " --> pdb=" O LEU C 171 " (cutoff:3.500A)
removed outlier: 6.928A pdb=" N ILE C 173 " --> pdb=" O GLN C 260 " (cutoff:3.500A)
removed outlier: 6.963A pdb=" N VAL C 257 " --> pdb=" O LEU C 296 " (cutoff:3.500A)
removed outlier: 7.974A pdb=" N LEU C 298 " --> pdb=" O VAL C 257 " (cutoff:3.500A)
removed outlier: 7.206A pdb=" N LEU C 259 " --> pdb=" O LEU C 298 " (cutoff:3.500A)
removed outlier: 6.432A pdb=" N ALA C 132 " --> pdb=" O MET C 297 " (cutoff:3.500A)
removed outlier: 7.031A pdb=" N VAL C 11 " --> pdb=" O GLU C 52 " (cutoff:3.500A)
removed outlier: 8.005A pdb=" N TYR C 54 " --> pdb=" O VAL C 11 " (cutoff:3.500A)
removed outlier: 6.726A pdb=" N TYR C 13 " --> pdb=" O TYR C 54 " (cutoff:3.500A)
removed outlier: 3.529A pdb=" N MET D 31 " --> pdb=" O ARG C 55 " (cutoff:3.500A)
420 hydrogen bonds defined for protein.
1140 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: 4.11
Time building geometry restraints manager: 3.46 seconds
NOTE: a complete listing of the restraints can be obtained by requesting
output of .geo file.
Histogram of bond lengths:
1.23 - 1.34: 3955
1.34 - 1.46: 2696
1.46 - 1.58: 5598
1.58 - 1.69: 6
1.69 - 1.81: 110
Bond restraints: 12365
Sorted by residual:
bond pdb=" C5 IHP D 701 "
pdb=" O15 IHP D 701 "
ideal model delta sigma weight residual
1.389 1.443 -0.054 2.00e-02 2.50e+03 7.34e+00
bond pdb=" C1 IHP D 701 "
pdb=" O11 IHP D 701 "
ideal model delta sigma weight residual
1.392 1.443 -0.051 2.00e-02 2.50e+03 6.42e+00
bond pdb=" C3 IHP D 701 "
pdb=" O13 IHP D 701 "
ideal model delta sigma weight residual
1.393 1.443 -0.050 2.00e-02 2.50e+03 6.19e+00
bond pdb=" C6 IHP D 701 "
pdb=" O16 IHP D 701 "
ideal model delta sigma weight residual
1.394 1.443 -0.049 2.00e-02 2.50e+03 6.04e+00
bond pdb=" O15 IHP D 701 "
pdb=" P5 IHP D 701 "
ideal model delta sigma weight residual
1.675 1.626 0.049 2.00e-02 2.50e+03 5.99e+00
... (remaining 12360 not shown)
Histogram of bond angle deviations from ideal:
0.00 - 1.83: 16124
1.83 - 3.65: 564
3.65 - 5.48: 54
5.48 - 7.31: 12
7.31 - 9.14: 5
Bond angle restraints: 16759
Sorted by residual:
angle pdb=" N ASN A 232 "
pdb=" CA ASN A 232 "
pdb=" C ASN A 232 "
ideal model delta sigma weight residual
114.62 107.20 7.42 1.14e+00 7.69e-01 4.24e+01
angle pdb=" C LYS A 447 "
pdb=" CA LYS A 447 "
pdb=" CB LYS A 447 "
ideal model delta sigma weight residual
117.23 110.75 6.48 1.36e+00 5.41e-01 2.27e+01
angle pdb=" CA GLN B 105 "
pdb=" C GLN B 105 "
pdb=" N ASP B 106 "
ideal model delta sigma weight residual
119.56 116.87 2.69 5.80e-01 2.97e+00 2.15e+01
angle pdb=" C GLY C 338 "
pdb=" N PRO C 339 "
pdb=" CA PRO C 339 "
ideal model delta sigma weight residual
119.84 124.54 -4.70 1.25e+00 6.40e-01 1.41e+01
angle pdb=" CA LYS A 447 "
pdb=" C LYS A 447 "
pdb=" N ASP A 448 "
ideal model delta sigma weight residual
119.98 116.94 3.04 8.50e-01 1.38e+00 1.28e+01
... (remaining 16754 not shown)
Histogram of dihedral angle deviations from ideal:
0.00 - 15.24: 7035
15.24 - 30.47: 268
30.47 - 45.71: 56
45.71 - 60.94: 2
60.94 - 76.18: 8
Dihedral angle restraints: 7369
sinusoidal: 2957
harmonic: 4412
Sorted by residual:
dihedral pdb=" CA ALA A 454 "
pdb=" C ALA A 454 "
pdb=" N GLU A 455 "
pdb=" CA GLU A 455 "
ideal model delta harmonic sigma weight residual
-180.00 -157.26 -22.74 0 5.00e+00 4.00e-02 2.07e+01
dihedral pdb=" CA GLY C 202 "
pdb=" C GLY C 202 "
pdb=" N GLU C 203 "
pdb=" CA GLU C 203 "
ideal model delta harmonic sigma weight residual
180.00 158.27 21.73 0 5.00e+00 4.00e-02 1.89e+01
dihedral pdb=" CA LEU B 314 "
pdb=" C LEU B 314 "
pdb=" N ARG B 315 "
pdb=" CA ARG B 315 "
ideal model delta harmonic sigma weight residual
180.00 -159.42 -20.58 0 5.00e+00 4.00e-02 1.69e+01
... (remaining 7366 not shown)
Histogram of chiral volume deviations from ideal:
0.000 - 0.052: 1480
0.052 - 0.105: 302
0.105 - 0.157: 54
0.157 - 0.210: 2
0.210 - 0.262: 2
Chirality restraints: 1840
Sorted by residual:
chirality pdb=" C1 IHP D 701 "
pdb=" C2 IHP D 701 "
pdb=" C6 IHP D 701 "
pdb=" O11 IHP D 701 "
both_signs ideal model delta sigma weight residual
False 2.32 2.58 -0.26 2.00e-01 2.50e+01 1.72e+00
chirality pdb=" C3 IHP D 701 "
pdb=" C2 IHP D 701 "
pdb=" C4 IHP D 701 "
pdb=" O13 IHP D 701 "
both_signs ideal model delta sigma weight residual
False -2.34 -2.59 0.25 2.00e-01 2.50e+01 1.62e+00
chirality pdb=" C5 IHP D 701 "
pdb=" C4 IHP D 701 "
pdb=" C6 IHP D 701 "
pdb=" O15 IHP D 701 "
both_signs ideal model delta sigma weight residual
False -2.42 -2.60 0.18 2.00e-01 2.50e+01 7.99e-01
... (remaining 1837 not shown)
Planarity restraints: 2149
Sorted by residual:
delta sigma weight rms_deltas residual
plane pdb=" C LEU B 332 " 0.036 5.00e-02 4.00e+02 5.41e-02 4.68e+00
pdb=" N PRO B 333 " -0.094 5.00e-02 4.00e+02
pdb=" CA PRO B 333 " 0.028 5.00e-02 4.00e+02
pdb=" CD PRO B 333 " 0.030 5.00e-02 4.00e+02
delta sigma weight rms_deltas residual
plane pdb=" CB TYR B 351 " -0.016 2.00e-02 2.50e+03 1.33e-02 3.52e+00
pdb=" CG TYR B 351 " 0.031 2.00e-02 2.50e+03
pdb=" CD1 TYR B 351 " -0.010 2.00e-02 2.50e+03
pdb=" CD2 TYR B 351 " -0.002 2.00e-02 2.50e+03
pdb=" CE1 TYR B 351 " 0.006 2.00e-02 2.50e+03
pdb=" CE2 TYR B 351 " -0.002 2.00e-02 2.50e+03
pdb=" CZ TYR B 351 " -0.003 2.00e-02 2.50e+03
pdb=" OH TYR B 351 " -0.004 2.00e-02 2.50e+03
delta sigma weight rms_deltas residual
plane pdb=" C LYS A 431 " -0.029 5.00e-02 4.00e+02 4.41e-02 3.11e+00
pdb=" N PRO A 432 " 0.076 5.00e-02 4.00e+02
pdb=" CA PRO A 432 " -0.023 5.00e-02 4.00e+02
pdb=" CD PRO A 432 " -0.025 5.00e-02 4.00e+02
... (remaining 2146 not shown)
Histogram of nonbonded interaction distances:
2.04 - 2.61: 113
2.61 - 3.18: 10618
3.18 - 3.75: 17167
3.75 - 4.33: 25121
4.33 - 4.90: 41772
Nonbonded interactions: 94791
Sorted by model distance:
nonbonded pdb=" OD2 ASP C 176 "
pdb="ZN ZN C 600 "
model vdw
2.036 2.230
nonbonded pdb=" OH TYR B 351 "
pdb=" OG1 THR B 423 "
model vdw
2.103 3.040
nonbonded pdb=" OG SER A 468 "
pdb=" OH TYR B 31 "
model vdw
2.111 3.040
nonbonded pdb=" OE2 GLU A 149 "
pdb=" OH TYR B 35 "
model vdw
2.124 3.040
nonbonded pdb=" O HIS C 28 "
pdb=" NZ LYS C 31 "
model vdw
2.137 3.120
... (remaining 94786 not shown)
NOTE: a complete listing of the restraints can be obtained by requesting
output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
reference = (chain 'A' and resid 26 through 536)
selection = (chain 'B' and (resid 26 through 93 or resid 99 through 307 or resid 312 through \
476 or resid 483 through 536))
}
Set up NCS constraints
No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
Set random seed: 0.000
Set model cs if undefined: 0.000
Decide on map wrapping: 0.000
Normalize map: mean=0, sd=1: 2.420
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: 0.570
Check model and map are aligned: 0.100
Set scattering table: 0.110
Process input model: 33.150
Find NCS groups from input model: 0.380
Set up NCS constraints: 0.050
Set refine NCS operators: 0.000
Adjust number of macro_cycles: 0.000
Reset NCS operators: 0.000
Extract rigid body selections: 0.000
Check and reset occupancies: 0.010
Load rotamer database and sin/cos tables:3.090
Set ADP refinement strategy: 0.000
Make a string to write initial .geo file:0.000
Internal consistency checks: 0.000
Total: 39.890
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7400
moved from start: 0.0000
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.004 0.058 12365 Z= 0.260
Angle : 0.787 9.135 16759 Z= 0.470
Chirality : 0.044 0.262 1840
Planarity : 0.004 0.054 2149
Dihedral : 9.419 76.178 4529
Min Nonbonded Distance : 2.036
Molprobity Statistics.
All-atom Clashscore : 10.44
Ramachandran Plot:
Outliers : 3.01 %
Allowed : 13.80 %
Favored : 83.19 %
Rotamer:
Outliers : 0.00 %
Allowed : 1.59 %
Favored : 98.41 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 2.04 %
Cis-general : 0.07 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: -4.85 (0.17), residues: 1493
helix: -3.21 (0.17), residues: 457
sheet: -2.89 (0.27), residues: 305
loop : -3.35 (0.19), residues: 731
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.023 0.002 TRP A 485
HIS 0.006 0.001 HIS C 28
PHE 0.022 0.002 PHE B 153
TYR 0.031 0.002 TYR B 351
ARG 0.004 0.000 ARG A 156
*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
2986 Ramachandran restraints generated.
1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
2986 Ramachandran restraints generated.
1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
221 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 0
poor density : 221
time to evaluate : 1.731
Fit side-chains
REVERT: A 89 MET cc_start: 0.7566 (ttm) cc_final: 0.7291 (ttm)
REVERT: A 440 ARG cc_start: 0.7550 (tpp80) cc_final: 0.7336 (ttm-80)
REVERT: A 498 ARG cc_start: 0.6907 (tpm-80) cc_final: 0.6620 (mpt180)
REVERT: B 249 GLU cc_start: 0.7114 (tp30) cc_final: 0.6733 (tp30)
REVERT: B 261 LYS cc_start: 0.7874 (ttmm) cc_final: 0.7583 (tttt)
REVERT: B 356 LYS cc_start: 0.8154 (ttpt) cc_final: 0.7856 (ttmm)
REVERT: B 374 ASN cc_start: 0.6992 (m-40) cc_final: 0.6740 (m-40)
REVERT: B 411 PHE cc_start: 0.6834 (m-80) cc_final: 0.6074 (m-10)
REVERT: C 10 LYS cc_start: 0.8651 (ttmt) cc_final: 0.8287 (ttpp)
REVERT: C 18 ASP cc_start: 0.7197 (t0) cc_final: 0.6788 (t0)
REVERT: C 48 TYR cc_start: 0.5157 (p90) cc_final: 0.4876 (p90)
REVERT: C 221 TYR cc_start: 0.7951 (m-10) cc_final: 0.7695 (m-10)
REVERT: C 253 GLN cc_start: 0.8073 (mm-40) cc_final: 0.7674 (mt0)
REVERT: D 60 MET cc_start: 0.5891 (tpt) cc_final: 0.5341 (tpp)
outliers start: 0
outliers final: 0
residues processed: 221
average time/residue: 0.2959
time to fit residues: 89.9855
Evaluate side-chains
124 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 0
poor density : 124
time to evaluate : 1.392
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 148
random chunks:
chunk 124 optimal weight: 0.7980
chunk 112 optimal weight: 3.9990
chunk 62 optimal weight: 1.9990
chunk 38 optimal weight: 3.9990
chunk 75 optimal weight: 0.0770
chunk 59 optimal weight: 1.9990
chunk 116 optimal weight: 1.9990
chunk 44 optimal weight: 0.9990
chunk 70 optimal weight: 2.9990
chunk 86 optimal weight: 0.4980
chunk 134 optimal weight: 0.8980
overall best weight: 0.6540
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 82 GLN
A 189 HIS
A 201 HIS
A 446 HIS
** B 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 82 GLN
B 286 GLN
B 287 ASN
B 299 HIS
B 395 ASN
B 446 HIS
C 40 ASN
C 57 HIS
** C 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 326 ASN
Total number of N/Q/H flips: 13
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4520 r_free = 0.4520 target = 0.225502 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.4093 r_free = 0.4093 target = 0.186811 restraints weight = 13805.865|
|-----------------------------------------------------------------------------|
r_work (start): 0.4133 rms_B_bonded: 2.51
r_work: 0.3868 rms_B_bonded: 3.67 restraints_weight: 0.5000
r_work (final): 0.3868
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8140
moved from start: 0.1821
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.034 12365 Z= 0.226
Angle : 0.632 12.280 16759 Z= 0.327
Chirality : 0.045 0.173 1840
Planarity : 0.004 0.048 2149
Dihedral : 5.581 43.527 1685
Min Nonbonded Distance : 2.058
Molprobity Statistics.
All-atom Clashscore : 7.50
Ramachandran Plot:
Outliers : 0.80 %
Allowed : 7.50 %
Favored : 91.69 %
Rotamer:
Outliers : 1.21 %
Allowed : 6.68 %
Favored : 92.11 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 2.04 %
Cis-general : 0.07 %
Twisted Proline : 0.00 %
Twisted General : 0.07 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: -3.35 (0.19), residues: 1493
helix: -1.33 (0.22), residues: 470
sheet: -2.17 (0.27), residues: 323
loop : -2.86 (0.20), residues: 700
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.017 0.002 TRP D 91
HIS 0.005 0.001 HIS C 140
PHE 0.016 0.002 PHE A 153
TYR 0.024 0.002 TYR B 351
ARG 0.006 0.001 ARG C 212
*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
2986 Ramachandran restraints generated.
1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
2986 Ramachandran restraints generated.
1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
156 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 16
poor density : 140
time to evaluate : 1.486
Fit side-chains
revert: symmetry clash
REVERT: A 89 MET cc_start: 0.8059 (ttm) cc_final: 0.7680 (ttm)
REVERT: A 404 GLU cc_start: 0.8268 (pt0) cc_final: 0.7933 (mt-10)
REVERT: A 457 ASP cc_start: 0.7202 (t70) cc_final: 0.6658 (t0)
REVERT: A 498 ARG cc_start: 0.7180 (tpm-80) cc_final: 0.6597 (mpt180)
REVERT: B 217 CYS cc_start: 0.7847 (p) cc_final: 0.7097 (p)
REVERT: B 347 LYS cc_start: 0.7807 (OUTLIER) cc_final: 0.7506 (pttt)
REVERT: B 411 PHE cc_start: 0.7205 (m-80) cc_final: 0.6494 (m-10)
REVERT: C 10 LYS cc_start: 0.8623 (ttmt) cc_final: 0.7526 (tptt)
REVERT: C 48 TYR cc_start: 0.6048 (p90) cc_final: 0.5637 (p90)
REVERT: C 253 GLN cc_start: 0.8403 (mm-40) cc_final: 0.8202 (mt0)
REVERT: D 60 MET cc_start: 0.6747 (tpt) cc_final: 0.5977 (tpp)
REVERT: D 130 TYR cc_start: 0.8133 (m-80) cc_final: 0.7844 (m-80)
outliers start: 16
outliers final: 6
residues processed: 152
average time/residue: 0.2947
time to fit residues: 62.2293
Evaluate side-chains
120 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 7
poor density : 113
time to evaluate : 1.394
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 101 VAL
Chi-restraints excluded: chain A residue 160 VAL
Chi-restraints excluded: chain A residue 255 HIS
Chi-restraints excluded: chain A residue 314 LEU
Chi-restraints excluded: chain A residue 485 TRP
Chi-restraints excluded: chain B residue 347 LYS
Chi-restraints excluded: chain C residue 177 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 148
random chunks:
chunk 106 optimal weight: 7.9990
chunk 64 optimal weight: 0.7980
chunk 76 optimal weight: 0.4980
chunk 40 optimal weight: 0.6980
chunk 7 optimal weight: 0.7980
chunk 137 optimal weight: 5.9990
chunk 129 optimal weight: 0.9990
chunk 70 optimal weight: 10.0000
chunk 83 optimal weight: 0.9990
chunk 59 optimal weight: 0.0470
chunk 79 optimal weight: 1.9990
overall best weight: 0.5678
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** C 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
Total number of N/Q/H flips: 0
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4394 r_free = 0.4394 target = 0.208137 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.4063 r_free = 0.4063 target = 0.174294 restraints weight = 13259.571|
|-----------------------------------------------------------------------------|
r_work (start): 0.4180 rms_B_bonded: 1.93
r_work: 0.3899 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work (final): 0.3899
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8095
moved from start: 0.2264
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.033 12365 Z= 0.192
Angle : 0.554 7.367 16759 Z= 0.287
Chirality : 0.043 0.158 1840
Planarity : 0.004 0.045 2149
Dihedral : 5.159 43.051 1685
Min Nonbonded Distance : 2.040
Molprobity Statistics.
All-atom Clashscore : 6.83
Ramachandran Plot:
Outliers : 0.74 %
Allowed : 7.90 %
Favored : 91.36 %
Rotamer:
Outliers : 1.29 %
Allowed : 7.97 %
Favored : 90.74 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 2.04 %
Cis-general : 0.07 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: -2.60 (0.20), residues: 1493
helix: -0.59 (0.24), residues: 472
sheet: -1.70 (0.29), residues: 318
loop : -2.54 (0.20), residues: 703
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.011 0.001 TRP D 91
HIS 0.007 0.001 HIS A 189
PHE 0.019 0.002 PHE A 153
TYR 0.021 0.001 TYR B 351
ARG 0.005 0.000 ARG B 416
*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
2986 Ramachandran restraints generated.
1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
2986 Ramachandran restraints generated.
1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
132 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 17
poor density : 115
time to evaluate : 1.330
Fit side-chains
revert: symmetry clash
REVERT: A 89 MET cc_start: 0.7998 (ttm) cc_final: 0.7622 (ttm)
REVERT: A 313 MET cc_start: 0.6761 (tpp) cc_final: 0.6371 (tpt)
REVERT: A 404 GLU cc_start: 0.8114 (pt0) cc_final: 0.7843 (mt-10)
REVERT: B 347 LYS cc_start: 0.7826 (OUTLIER) cc_final: 0.7554 (pttt)
REVERT: B 411 PHE cc_start: 0.7241 (m-80) cc_final: 0.6693 (m-10)
REVERT: C 48 TYR cc_start: 0.5892 (p90) cc_final: 0.5572 (p90)
REVERT: D 60 MET cc_start: 0.6716 (tpt) cc_final: 0.6096 (tpp)
outliers start: 17
outliers final: 11
residues processed: 129
average time/residue: 0.2465
time to fit residues: 46.9303
Evaluate side-chains
111 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 12
poor density : 99
time to evaluate : 1.475
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 38 LYS
Chi-restraints excluded: chain A residue 101 VAL
Chi-restraints excluded: chain A residue 160 VAL
Chi-restraints excluded: chain A residue 196 THR
Chi-restraints excluded: chain A residue 255 HIS
Chi-restraints excluded: chain A residue 314 LEU
Chi-restraints excluded: chain A residue 429 HIS
Chi-restraints excluded: chain A residue 485 TRP
Chi-restraints excluded: chain B residue 347 LYS
Chi-restraints excluded: chain B residue 394 LEU
Chi-restraints excluded: chain C residue 155 ASP
Chi-restraints excluded: chain C residue 177 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 148
random chunks:
chunk 47 optimal weight: 2.9990
chunk 13 optimal weight: 0.7980
chunk 12 optimal weight: 0.9980
chunk 144 optimal weight: 6.9990
chunk 77 optimal weight: 1.9990
chunk 138 optimal weight: 5.9990
chunk 51 optimal weight: 0.5980
chunk 9 optimal weight: 0.9980
chunk 76 optimal weight: 0.5980
chunk 40 optimal weight: 0.5980
chunk 28 optimal weight: 10.0000
overall best weight: 0.7180
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4504 r_free = 0.4504 target = 0.224059 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.4071 r_free = 0.4071 target = 0.185223 restraints weight = 13708.319|
|-----------------------------------------------------------------------------|
r_work (start): 0.3960 rms_B_bonded: 2.37
r_work: 0.3763 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work (final): 0.3763
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8113
moved from start: 0.2577
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.036 12365 Z= 0.214
Angle : 0.547 7.258 16759 Z= 0.283
Chirality : 0.043 0.156 1840
Planarity : 0.003 0.039 2149
Dihedral : 5.029 41.459 1685
Min Nonbonded Distance : 2.057
Molprobity Statistics.
All-atom Clashscore : 6.54
Ramachandran Plot:
Outliers : 0.67 %
Allowed : 6.70 %
Favored : 92.63 %
Rotamer:
Outliers : 1.97 %
Allowed : 8.19 %
Favored : 89.83 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 2.04 %
Cis-general : 0.07 %
Twisted Proline : 0.00 %
Twisted General : 0.07 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: -2.13 (0.21), residues: 1493
helix: -0.22 (0.24), residues: 475
sheet: -1.42 (0.29), residues: 324
loop : -2.26 (0.21), residues: 694
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.009 0.001 TRP B 228
HIS 0.006 0.001 HIS A 429
PHE 0.013 0.001 PHE B 32
TYR 0.019 0.002 TYR B 351
ARG 0.004 0.000 ARG C 212
*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
2986 Ramachandran restraints generated.
1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
2986 Ramachandran restraints generated.
1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
149 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 26
poor density : 123
time to evaluate : 1.428
Fit side-chains
revert: symmetry clash
REVERT: A 48 GLN cc_start: 0.7854 (OUTLIER) cc_final: 0.7331 (mp10)
REVERT: A 89 MET cc_start: 0.8011 (ttm) cc_final: 0.7605 (ttm)
REVERT: A 313 MET cc_start: 0.6768 (tpp) cc_final: 0.6418 (tpt)
REVERT: A 404 GLU cc_start: 0.8086 (pt0) cc_final: 0.7850 (mt-10)
REVERT: A 448 ASP cc_start: 0.7471 (t0) cc_final: 0.7128 (t0)
REVERT: A 457 ASP cc_start: 0.7144 (t70) cc_final: 0.6575 (t0)
REVERT: B 347 LYS cc_start: 0.7812 (OUTLIER) cc_final: 0.7523 (pttt)
REVERT: B 411 PHE cc_start: 0.7183 (m-80) cc_final: 0.6792 (m-10)
REVERT: C 48 TYR cc_start: 0.5907 (p90) cc_final: 0.5615 (p90)
REVERT: D 60 MET cc_start: 0.6783 (tpt) cc_final: 0.6249 (tpp)
outliers start: 26
outliers final: 16
residues processed: 143
average time/residue: 0.2707
time to fit residues: 55.5250
Evaluate side-chains
132 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 18
poor density : 114
time to evaluate : 1.370
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 38 LYS
Chi-restraints excluded: chain A residue 48 GLN
Chi-restraints excluded: chain A residue 51 MET
Chi-restraints excluded: chain A residue 101 VAL
Chi-restraints excluded: chain A residue 160 VAL
Chi-restraints excluded: chain A residue 196 THR
Chi-restraints excluded: chain A residue 255 HIS
Chi-restraints excluded: chain A residue 314 LEU
Chi-restraints excluded: chain A residue 429 HIS
Chi-restraints excluded: chain A residue 485 TRP
Chi-restraints excluded: chain B residue 103 VAL
Chi-restraints excluded: chain B residue 347 LYS
Chi-restraints excluded: chain B residue 394 LEU
Chi-restraints excluded: chain B residue 459 LEU
Chi-restraints excluded: chain B residue 511 LEU
Chi-restraints excluded: chain C residue 130 ASP
Chi-restraints excluded: chain C residue 155 ASP
Chi-restraints excluded: chain C residue 177 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 148
random chunks:
chunk 101 optimal weight: 0.7980
chunk 104 optimal weight: 4.9990
chunk 55 optimal weight: 0.0870
chunk 49 optimal weight: 1.9990
chunk 129 optimal weight: 0.5980
chunk 11 optimal weight: 0.7980
chunk 3 optimal weight: 0.0870
chunk 48 optimal weight: 0.8980
chunk 82 optimal weight: 0.6980
chunk 130 optimal weight: 0.3980
chunk 146 optimal weight: 0.7980
overall best weight: 0.3736
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
B 82 GLN
B 286 GLN
Total number of N/Q/H flips: 2
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4526 r_free = 0.4526 target = 0.226271 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.4151 r_free = 0.4151 target = 0.188066 restraints weight = 13703.133|
|-----------------------------------------------------------------------------|
r_work (start): 0.4164 rms_B_bonded: 2.53
r_work: 0.3890 rms_B_bonded: 3.40 restraints_weight: 0.5000
r_work (final): 0.3890
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8103
moved from start: 0.2779
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.002 0.026 12365 Z= 0.151
Angle : 0.512 9.473 16759 Z= 0.266
Chirality : 0.042 0.155 1840
Planarity : 0.003 0.038 2149
Dihedral : 4.812 40.515 1685
Min Nonbonded Distance : 2.071
Molprobity Statistics.
All-atom Clashscore : 6.08
Ramachandran Plot:
Outliers : 0.47 %
Allowed : 6.10 %
Favored : 93.44 %
Rotamer:
Outliers : 1.82 %
Allowed : 9.18 %
Favored : 89.00 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 2.04 %
Cis-general : 0.07 %
Twisted Proline : 0.00 %
Twisted General : 0.07 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: -1.81 (0.21), residues: 1493
helix: 0.14 (0.25), residues: 469
sheet: -1.17 (0.30), residues: 319
loop : -2.17 (0.21), residues: 705
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.010 0.001 TRP D 132
HIS 0.006 0.001 HIS A 429
PHE 0.010 0.001 PHE B 437
TYR 0.012 0.001 TYR B 351
ARG 0.003 0.000 ARG C 212
*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
2986 Ramachandran restraints generated.
1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
2986 Ramachandran restraints generated.
1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
144 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 24
poor density : 120
time to evaluate : 1.330
Fit side-chains
REVERT: A 48 GLN cc_start: 0.7870 (OUTLIER) cc_final: 0.7369 (mp10)
REVERT: A 89 MET cc_start: 0.8102 (ttm) cc_final: 0.7728 (ttm)
REVERT: A 448 ASP cc_start: 0.7512 (t0) cc_final: 0.7219 (t0)
REVERT: A 466 LEU cc_start: 0.7955 (OUTLIER) cc_final: 0.7721 (pp)
REVERT: A 498 ARG cc_start: 0.7007 (tpm-80) cc_final: 0.6444 (mpt180)
REVERT: B 347 LYS cc_start: 0.7781 (OUTLIER) cc_final: 0.7516 (pttt)
REVERT: B 411 PHE cc_start: 0.7188 (m-80) cc_final: 0.6888 (m-10)
REVERT: C 48 TYR cc_start: 0.5956 (p90) cc_final: 0.5610 (p90)
REVERT: D 60 MET cc_start: 0.6821 (tpt) cc_final: 0.6296 (tpp)
REVERT: D 130 TYR cc_start: 0.8119 (m-80) cc_final: 0.7616 (m-80)
outliers start: 24
outliers final: 15
residues processed: 137
average time/residue: 0.2516
time to fit residues: 50.5995
Evaluate side-chains
122 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 18
poor density : 104
time to evaluate : 1.303
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 38 LYS
Chi-restraints excluded: chain A residue 48 GLN
Chi-restraints excluded: chain A residue 51 MET
Chi-restraints excluded: chain A residue 101 VAL
Chi-restraints excluded: chain A residue 160 VAL
Chi-restraints excluded: chain A residue 196 THR
Chi-restraints excluded: chain A residue 314 LEU
Chi-restraints excluded: chain A residue 429 HIS
Chi-restraints excluded: chain A residue 466 LEU
Chi-restraints excluded: chain A residue 485 TRP
Chi-restraints excluded: chain B residue 347 LYS
Chi-restraints excluded: chain B residue 394 LEU
Chi-restraints excluded: chain B residue 459 LEU
Chi-restraints excluded: chain B residue 511 LEU
Chi-restraints excluded: chain C residue 122 VAL
Chi-restraints excluded: chain C residue 130 ASP
Chi-restraints excluded: chain C residue 155 ASP
Chi-restraints excluded: chain C residue 177 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 148
random chunks:
chunk 121 optimal weight: 0.8980
chunk 127 optimal weight: 0.8980
chunk 118 optimal weight: 1.9990
chunk 62 optimal weight: 1.9990
chunk 123 optimal weight: 0.6980
chunk 124 optimal weight: 0.5980
chunk 77 optimal weight: 0.6980
chunk 33 optimal weight: 6.9990
chunk 12 optimal weight: 0.9980
chunk 16 optimal weight: 4.9990
chunk 42 optimal weight: 0.7980
overall best weight: 0.7380
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 75 HIS
Total number of N/Q/H flips: 1
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4503 r_free = 0.4503 target = 0.223834 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.4116 r_free = 0.4116 target = 0.185020 restraints weight = 13940.582|
|-----------------------------------------------------------------------------|
r_work (start): 0.4128 rms_B_bonded: 2.65
r_work: 0.3845 rms_B_bonded: 3.52 restraints_weight: 0.5000
r_work (final): 0.3845
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8162
moved from start: 0.2938
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.033 12365 Z= 0.213
Angle : 0.540 10.012 16759 Z= 0.276
Chirality : 0.043 0.153 1840
Planarity : 0.003 0.040 2149
Dihedral : 4.806 39.760 1685
Min Nonbonded Distance : 2.050
Molprobity Statistics.
All-atom Clashscore : 5.83
Ramachandran Plot:
Outliers : 0.47 %
Allowed : 6.83 %
Favored : 92.70 %
Rotamer:
Outliers : 2.28 %
Allowed : 9.86 %
Favored : 87.86 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 2.04 %
Cis-general : 0.07 %
Twisted Proline : 0.00 %
Twisted General : 0.07 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: -1.64 (0.21), residues: 1493
helix: 0.24 (0.25), residues: 471
sheet: -1.04 (0.30), residues: 328
loop : -2.06 (0.22), residues: 694
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.007 0.001 TRP A 485
HIS 0.006 0.001 HIS A 429
PHE 0.014 0.001 PHE A 153
TYR 0.014 0.001 TYR B 462
ARG 0.008 0.000 ARG C 212
*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
2986 Ramachandran restraints generated.
1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
2986 Ramachandran restraints generated.
1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
147 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 30
poor density : 117
time to evaluate : 1.367
Fit side-chains
REVERT: A 38 LYS cc_start: 0.8614 (OUTLIER) cc_final: 0.8340 (mtpp)
REVERT: A 48 GLN cc_start: 0.7957 (OUTLIER) cc_final: 0.7453 (mp10)
REVERT: A 89 MET cc_start: 0.8094 (ttm) cc_final: 0.7712 (ttm)
REVERT: A 448 ASP cc_start: 0.7549 (t0) cc_final: 0.7231 (t0)
REVERT: A 457 ASP cc_start: 0.7247 (t70) cc_final: 0.6626 (t0)
REVERT: A 498 ARG cc_start: 0.7086 (tpm-80) cc_final: 0.6811 (ttp80)
REVERT: B 347 LYS cc_start: 0.7831 (OUTLIER) cc_final: 0.7567 (pttt)
REVERT: B 411 PHE cc_start: 0.7237 (m-80) cc_final: 0.6840 (m-10)
REVERT: B 437 PHE cc_start: 0.8845 (OUTLIER) cc_final: 0.8629 (p90)
REVERT: C 48 TYR cc_start: 0.6063 (p90) cc_final: 0.5731 (p90)
REVERT: D 60 MET cc_start: 0.6910 (tpt) cc_final: 0.6391 (tpp)
REVERT: D 134 LYS cc_start: 0.6420 (mttp) cc_final: 0.5364 (pttp)
outliers start: 30
outliers final: 21
residues processed: 139
average time/residue: 0.2578
time to fit residues: 51.6995
Evaluate side-chains
139 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 25
poor density : 114
time to evaluate : 1.346
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 38 LYS
Chi-restraints excluded: chain A residue 48 GLN
Chi-restraints excluded: chain A residue 51 MET
Chi-restraints excluded: chain A residue 63 VAL
Chi-restraints excluded: chain A residue 101 VAL
Chi-restraints excluded: chain A residue 160 VAL
Chi-restraints excluded: chain A residue 196 THR
Chi-restraints excluded: chain A residue 255 HIS
Chi-restraints excluded: chain A residue 314 LEU
Chi-restraints excluded: chain A residue 429 HIS
Chi-restraints excluded: chain A residue 485 TRP
Chi-restraints excluded: chain B residue 103 VAL
Chi-restraints excluded: chain B residue 157 THR
Chi-restraints excluded: chain B residue 290 CYS
Chi-restraints excluded: chain B residue 347 LYS
Chi-restraints excluded: chain B residue 394 LEU
Chi-restraints excluded: chain B residue 437 PHE
Chi-restraints excluded: chain B residue 459 LEU
Chi-restraints excluded: chain B residue 511 LEU
Chi-restraints excluded: chain C residue 40 ASN
Chi-restraints excluded: chain C residue 122 VAL
Chi-restraints excluded: chain C residue 130 ASP
Chi-restraints excluded: chain C residue 155 ASP
Chi-restraints excluded: chain C residue 177 ILE
Chi-restraints excluded: chain C residue 334 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 148
random chunks:
chunk 12 optimal weight: 0.5980
chunk 111 optimal weight: 0.9980
chunk 38 optimal weight: 2.9990
chunk 54 optimal weight: 0.0980
chunk 22 optimal weight: 2.9990
chunk 55 optimal weight: 0.5980
chunk 118 optimal weight: 0.5980
chunk 57 optimal weight: 0.0050
chunk 86 optimal weight: 0.9990
chunk 139 optimal weight: 6.9990
chunk 76 optimal weight: 1.9990
overall best weight: 0.3794
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 75 HIS
Total number of N/Q/H flips: 1
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4404 r_free = 0.4404 target = 0.209452 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.4098 r_free = 0.4098 target = 0.177358 restraints weight = 13233.214|
|-----------------------------------------------------------------------------|
r_work (start): 0.4201 rms_B_bonded: 1.67
r_work: 0.3909 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work (final): 0.3909
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8080
moved from start: 0.3084
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.002 0.023 12365 Z= 0.144
Angle : 0.503 7.693 16759 Z= 0.259
Chirality : 0.042 0.145 1840
Planarity : 0.003 0.038 2149
Dihedral : 4.620 39.057 1685
Min Nonbonded Distance : 2.085
Molprobity Statistics.
All-atom Clashscore : 5.11
Ramachandran Plot:
Outliers : 0.40 %
Allowed : 6.03 %
Favored : 93.57 %
Rotamer:
Outliers : 2.12 %
Allowed : 10.24 %
Favored : 87.63 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 2.04 %
Cis-general : 0.07 %
Twisted Proline : 0.00 %
Twisted General : 0.07 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: -1.42 (0.22), residues: 1493
helix: 0.46 (0.25), residues: 471
sheet: -0.91 (0.30), residues: 334
loop : -1.96 (0.22), residues: 688
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.008 0.001 TRP A 485
HIS 0.006 0.001 HIS A 429
PHE 0.009 0.001 PHE A 153
TYR 0.010 0.001 TYR B 462
ARG 0.006 0.000 ARG C 212
*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
2986 Ramachandran restraints generated.
1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
2986 Ramachandran restraints generated.
1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
145 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 28
poor density : 117
time to evaluate : 1.465
Fit side-chains
REVERT: A 48 GLN cc_start: 0.7938 (OUTLIER) cc_final: 0.7463 (mp10)
REVERT: A 89 MET cc_start: 0.8056 (ttm) cc_final: 0.7690 (ttm)
REVERT: A 448 ASP cc_start: 0.7393 (t0) cc_final: 0.7163 (t0)
REVERT: A 457 ASP cc_start: 0.7123 (t70) cc_final: 0.6487 (t0)
REVERT: B 411 PHE cc_start: 0.7211 (m-80) cc_final: 0.6892 (m-10)
REVERT: B 441 MET cc_start: 0.8269 (mtm) cc_final: 0.8042 (mtm)
outliers start: 28
outliers final: 20
residues processed: 137
average time/residue: 0.2423
time to fit residues: 49.0851
Evaluate side-chains
129 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 21
poor density : 108
time to evaluate : 1.529
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 48 GLN
Chi-restraints excluded: chain A residue 51 MET
Chi-restraints excluded: chain A residue 101 VAL
Chi-restraints excluded: chain A residue 160 VAL
Chi-restraints excluded: chain A residue 196 THR
Chi-restraints excluded: chain A residue 255 HIS
Chi-restraints excluded: chain A residue 314 LEU
Chi-restraints excluded: chain A residue 429 HIS
Chi-restraints excluded: chain A residue 485 TRP
Chi-restraints excluded: chain B residue 64 THR
Chi-restraints excluded: chain B residue 103 VAL
Chi-restraints excluded: chain B residue 157 THR
Chi-restraints excluded: chain B residue 394 LEU
Chi-restraints excluded: chain B residue 459 LEU
Chi-restraints excluded: chain B residue 461 CYS
Chi-restraints excluded: chain B residue 511 LEU
Chi-restraints excluded: chain C residue 122 VAL
Chi-restraints excluded: chain C residue 130 ASP
Chi-restraints excluded: chain C residue 155 ASP
Chi-restraints excluded: chain C residue 177 ILE
Chi-restraints excluded: chain C residue 334 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 148
random chunks:
chunk 66 optimal weight: 0.0970
chunk 87 optimal weight: 0.0970
chunk 90 optimal weight: 0.5980
chunk 115 optimal weight: 2.9990
chunk 107 optimal weight: 0.0170
chunk 19 optimal weight: 5.9990
chunk 53 optimal weight: 1.9990
chunk 11 optimal weight: 0.2980
chunk 54 optimal weight: 1.9990
chunk 145 optimal weight: 2.9990
chunk 55 optimal weight: 1.9990
overall best weight: 0.2214
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 507 ASN
** B 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 281 HIS
Total number of N/Q/H flips: 2
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4545 r_free = 0.4545 target = 0.228791 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.4117 r_free = 0.4117 target = 0.190982 restraints weight = 13843.060|
|-----------------------------------------------------------------------------|
r_work (start): 0.4156 rms_B_bonded: 2.64
r_work: 0.3846 rms_B_bonded: 4.32 restraints_weight: 0.5000
r_work (final): 0.3846
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8153
moved from start: 0.3292
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.002 0.027 12365 Z= 0.130
Angle : 0.511 11.037 16759 Z= 0.261
Chirality : 0.042 0.213 1840
Planarity : 0.003 0.039 2149
Dihedral : 4.468 38.047 1685
Min Nonbonded Distance : 2.069
Molprobity Statistics.
All-atom Clashscore : 5.32
Ramachandran Plot:
Outliers : 0.40 %
Allowed : 5.96 %
Favored : 93.64 %
Rotamer:
Outliers : 1.90 %
Allowed : 11.00 %
Favored : 87.10 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 2.04 %
Cis-general : 0.07 %
Twisted Proline : 0.00 %
Twisted General : 0.07 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: -1.26 (0.22), residues: 1493
helix: 0.62 (0.25), residues: 473
sheet: -0.77 (0.30), residues: 329
loop : -1.92 (0.22), residues: 691
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.008 0.001 TRP D 34
HIS 0.006 0.001 HIS A 429
PHE 0.008 0.001 PHE B 437
TYR 0.010 0.001 TYR C 13
ARG 0.007 0.000 ARG C 212
*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
2986 Ramachandran restraints generated.
1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
2986 Ramachandran restraints generated.
1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
146 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 25
poor density : 121
time to evaluate : 1.360
Fit side-chains
REVERT: A 48 GLN cc_start: 0.8001 (OUTLIER) cc_final: 0.7739 (mm-40)
REVERT: A 89 MET cc_start: 0.8169 (ttm) cc_final: 0.7771 (ttm)
REVERT: A 448 ASP cc_start: 0.7576 (t0) cc_final: 0.7339 (t0)
REVERT: A 457 ASP cc_start: 0.7281 (t70) cc_final: 0.6633 (t0)
REVERT: A 498 ARG cc_start: 0.7621 (OUTLIER) cc_final: 0.7217 (ttm-80)
REVERT: B 411 PHE cc_start: 0.7271 (m-80) cc_final: 0.6902 (m-10)
REVERT: D 130 TYR cc_start: 0.8111 (m-80) cc_final: 0.7870 (m-80)
outliers start: 25
outliers final: 18
residues processed: 139
average time/residue: 0.2435
time to fit residues: 50.4288
Evaluate side-chains
134 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 20
poor density : 114
time to evaluate : 1.464
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 48 GLN
Chi-restraints excluded: chain A residue 51 MET
Chi-restraints excluded: chain A residue 63 VAL
Chi-restraints excluded: chain A residue 101 VAL
Chi-restraints excluded: chain A residue 160 VAL
Chi-restraints excluded: chain A residue 196 THR
Chi-restraints excluded: chain A residue 314 LEU
Chi-restraints excluded: chain A residue 429 HIS
Chi-restraints excluded: chain A residue 485 TRP
Chi-restraints excluded: chain A residue 498 ARG
Chi-restraints excluded: chain B residue 64 THR
Chi-restraints excluded: chain B residue 459 LEU
Chi-restraints excluded: chain B residue 461 CYS
Chi-restraints excluded: chain B residue 511 LEU
Chi-restraints excluded: chain C residue 40 ASN
Chi-restraints excluded: chain C residue 122 VAL
Chi-restraints excluded: chain C residue 130 ASP
Chi-restraints excluded: chain C residue 155 ASP
Chi-restraints excluded: chain C residue 177 ILE
Chi-restraints excluded: chain C residue 334 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 148
random chunks:
chunk 130 optimal weight: 0.9980
chunk 46 optimal weight: 3.9990
chunk 126 optimal weight: 0.9990
chunk 48 optimal weight: 0.0980
chunk 129 optimal weight: 0.5980
chunk 59 optimal weight: 1.9990
chunk 100 optimal weight: 3.9990
chunk 133 optimal weight: 0.1980
chunk 66 optimal weight: 0.6980
chunk 33 optimal weight: 5.9990
chunk 76 optimal weight: 2.9990
overall best weight: 0.5180
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
C 344 HIS
Total number of N/Q/H flips: 1
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4403 r_free = 0.4403 target = 0.209398 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 85)----------------|
| r_work = 0.4070 r_free = 0.4070 target = 0.174919 restraints weight = 13093.931|
|-----------------------------------------------------------------------------|
r_work (start): 0.4179 rms_B_bonded: 1.91
r_work: 0.3919 rms_B_bonded: 2.99 restraints_weight: 0.5000
r_work: 0.3762 rms_B_bonded: 4.98 restraints_weight: 0.2500
r_work (final): 0.3762
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8233
moved from start: 0.3336
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.032 12365 Z= 0.170
Angle : 0.520 10.451 16759 Z= 0.266
Chirality : 0.042 0.186 1840
Planarity : 0.003 0.044 2149
Dihedral : 4.508 37.459 1685
Min Nonbonded Distance : 2.014
Molprobity Statistics.
All-atom Clashscore : 5.16
Ramachandran Plot:
Outliers : 0.40 %
Allowed : 6.36 %
Favored : 93.24 %
Rotamer:
Outliers : 1.82 %
Allowed : 11.61 %
Favored : 86.57 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 2.04 %
Cis-general : 0.07 %
Twisted Proline : 0.00 %
Twisted General : 0.07 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: -1.22 (0.22), residues: 1493
helix: 0.62 (0.25), residues: 475
sheet: -0.79 (0.30), residues: 338
loop : -1.86 (0.22), residues: 680
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.008 0.001 TRP A 485
HIS 0.006 0.001 HIS A 429
PHE 0.009 0.001 PHE C 252
TYR 0.013 0.001 TYR B 135
ARG 0.007 0.000 ARG C 212
*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
2986 Ramachandran restraints generated.
1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
2986 Ramachandran restraints generated.
1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
140 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 24
poor density : 116
time to evaluate : 1.323
Fit side-chains
REVERT: A 48 GLN cc_start: 0.8095 (OUTLIER) cc_final: 0.7845 (mm-40)
REVERT: A 89 MET cc_start: 0.8270 (ttm) cc_final: 0.7888 (ttm)
REVERT: A 448 ASP cc_start: 0.7684 (t0) cc_final: 0.7428 (t0)
REVERT: A 457 ASP cc_start: 0.7356 (t70) cc_final: 0.6711 (t0)
REVERT: A 498 ARG cc_start: 0.7720 (OUTLIER) cc_final: 0.6237 (mtt90)
REVERT: A 533 PHE cc_start: 0.7564 (OUTLIER) cc_final: 0.6193 (p90)
REVERT: B 167 MET cc_start: 0.8147 (ttm) cc_final: 0.7832 (ttt)
REVERT: B 411 PHE cc_start: 0.7268 (m-80) cc_final: 0.6952 (m-10)
REVERT: D 60 MET cc_start: 0.6338 (tpt) cc_final: 0.4346 (tpp)
REVERT: D 130 TYR cc_start: 0.8144 (m-80) cc_final: 0.7906 (m-80)
outliers start: 24
outliers final: 19
residues processed: 135
average time/residue: 0.2521
time to fit residues: 50.8516
Evaluate side-chains
134 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 22
poor density : 112
time to evaluate : 1.514
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 48 GLN
Chi-restraints excluded: chain A residue 51 MET
Chi-restraints excluded: chain A residue 63 VAL
Chi-restraints excluded: chain A residue 101 VAL
Chi-restraints excluded: chain A residue 160 VAL
Chi-restraints excluded: chain A residue 196 THR
Chi-restraints excluded: chain A residue 255 HIS
Chi-restraints excluded: chain A residue 314 LEU
Chi-restraints excluded: chain A residue 429 HIS
Chi-restraints excluded: chain A residue 485 TRP
Chi-restraints excluded: chain A residue 498 ARG
Chi-restraints excluded: chain A residue 533 PHE
Chi-restraints excluded: chain B residue 64 THR
Chi-restraints excluded: chain B residue 459 LEU
Chi-restraints excluded: chain B residue 461 CYS
Chi-restraints excluded: chain B residue 511 LEU
Chi-restraints excluded: chain C residue 40 ASN
Chi-restraints excluded: chain C residue 122 VAL
Chi-restraints excluded: chain C residue 130 ASP
Chi-restraints excluded: chain C residue 155 ASP
Chi-restraints excluded: chain C residue 177 ILE
Chi-restraints excluded: chain C residue 334 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 148
random chunks:
chunk 69 optimal weight: 0.9990
chunk 99 optimal weight: 3.9990
chunk 22 optimal weight: 5.9990
chunk 66 optimal weight: 0.2980
chunk 76 optimal weight: 1.9990
chunk 79 optimal weight: 0.6980
chunk 118 optimal weight: 0.5980
chunk 13 optimal weight: 0.2980
chunk 129 optimal weight: 0.5980
chunk 90 optimal weight: 0.8980
chunk 51 optimal weight: 1.9990
overall best weight: 0.4980
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4403 r_free = 0.4403 target = 0.209402 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.4073 r_free = 0.4073 target = 0.175070 restraints weight = 13139.688|
|-----------------------------------------------------------------------------|
r_work (start): 0.4182 rms_B_bonded: 1.90
r_work: 0.3916 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work (final): 0.3916
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8071
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 0.031 12365 Z= 0.168
Angle : 0.521 9.995 16759 Z= 0.268
Chirality : 0.042 0.217 1840
Planarity : 0.003 0.042 2149
Dihedral : 4.469 37.013 1685
Min Nonbonded Distance : 2.022
Molprobity Statistics.
All-atom Clashscore : 5.28
Ramachandran Plot:
Outliers : 0.40 %
Allowed : 6.03 %
Favored : 93.57 %
Rotamer:
Outliers : 1.59 %
Allowed : 11.99 %
Favored : 86.42 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 2.04 %
Cis-general : 0.07 %
Twisted Proline : 0.00 %
Twisted General : 0.07 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: -1.16 (0.22), residues: 1493
helix: 0.66 (0.25), residues: 474
sheet: -0.72 (0.30), residues: 323
loop : -1.82 (0.22), residues: 696
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.009 0.001 TRP A 485
HIS 0.006 0.001 HIS A 429
PHE 0.008 0.001 PHE C 252
TYR 0.012 0.001 TYR B 135
ARG 0.007 0.000 ARG C 212
********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
2986 Ramachandran restraints generated.
1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
2986 Ramachandran restraints generated.
1493 Oldfield, 0 Emsley, 1493 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
140 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 21
poor density : 119
time to evaluate : 1.340
Fit side-chains
REVERT: A 48 GLN cc_start: 0.7937 (OUTLIER) cc_final: 0.7675 (mm-40)
REVERT: A 89 MET cc_start: 0.8074 (ttm) cc_final: 0.7699 (ttm)
REVERT: A 448 ASP cc_start: 0.7426 (t0) cc_final: 0.7209 (t0)
REVERT: A 457 ASP cc_start: 0.7184 (t70) cc_final: 0.6584 (t0)
REVERT: A 533 PHE cc_start: 0.7468 (OUTLIER) cc_final: 0.6129 (p90)
REVERT: B 167 MET cc_start: 0.8053 (ttm) cc_final: 0.7654 (ttt)
REVERT: B 411 PHE cc_start: 0.7205 (m-80) cc_final: 0.6914 (m-10)
REVERT: D 130 TYR cc_start: 0.8198 (m-80) cc_final: 0.7936 (m-80)
outliers start: 21
outliers final: 18
residues processed: 133
average time/residue: 0.2317
time to fit residues: 46.3602
Evaluate side-chains
135 residues out of total 1318 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 20
poor density : 115
time to evaluate : 1.335
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 48 GLN
Chi-restraints excluded: chain A residue 51 MET
Chi-restraints excluded: chain A residue 63 VAL
Chi-restraints excluded: chain A residue 101 VAL
Chi-restraints excluded: chain A residue 160 VAL
Chi-restraints excluded: chain A residue 196 THR
Chi-restraints excluded: chain A residue 314 LEU
Chi-restraints excluded: chain A residue 429 HIS
Chi-restraints excluded: chain A residue 485 TRP
Chi-restraints excluded: chain A residue 533 PHE
Chi-restraints excluded: chain B residue 64 THR
Chi-restraints excluded: chain B residue 459 LEU
Chi-restraints excluded: chain B residue 461 CYS
Chi-restraints excluded: chain B residue 511 LEU
Chi-restraints excluded: chain C residue 40 ASN
Chi-restraints excluded: chain C residue 122 VAL
Chi-restraints excluded: chain C residue 130 ASP
Chi-restraints excluded: chain C residue 155 ASP
Chi-restraints excluded: chain C residue 177 ILE
Chi-restraints excluded: chain C residue 334 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 148
random chunks:
chunk 72 optimal weight: 0.9990
chunk 98 optimal weight: 0.0980
chunk 145 optimal weight: 2.9990
chunk 96 optimal weight: 2.9990
chunk 117 optimal weight: 2.9990
chunk 102 optimal weight: 0.9990
chunk 78 optimal weight: 2.9990
chunk 94 optimal weight: 2.9990
chunk 93 optimal weight: 2.9990
chunk 146 optimal weight: 2.9990
chunk 25 optimal weight: 4.9990
overall best weight: 1.6188
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
B 339 HIS
Total number of N/Q/H flips: 1
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.160259 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.127841 restraints weight = 13695.506|
|-----------------------------------------------------------------------------|
r_work (start): 0.3447 rms_B_bonded: 1.52
r_work: 0.3219 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.3082 rms_B_bonded: 3.77 restraints_weight: 0.2500
r_work (final): 0.3082
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8258
moved from start: 0.3331
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.006 0.055 12365 Z= 0.398
Angle : 0.652 9.345 16759 Z= 0.332
Chirality : 0.048 0.217 1840
Planarity : 0.004 0.043 2149
Dihedral : 5.074 39.002 1685
Min Nonbonded Distance : 1.984
Molprobity Statistics.
All-atom Clashscore : 6.75
Ramachandran Plot:
Outliers : 0.40 %
Allowed : 8.17 %
Favored : 91.43 %
Rotamer:
Outliers : 2.05 %
Allowed : 12.06 %
Favored : 85.89 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 2.04 %
Cis-general : 0.07 %
Twisted Proline : 0.00 %
Twisted General : 0.07 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: -1.54 (0.21), residues: 1493
helix: 0.16 (0.24), residues: 479
sheet: -0.84 (0.31), residues: 304
loop : -1.95 (0.22), residues: 710
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.013 0.001 TRP A 485
HIS 0.008 0.001 HIS A 429
PHE 0.017 0.002 PHE B 32
TYR 0.023 0.002 TYR B 135
ARG 0.007 0.001 ARG C 212
Origin is already at (0, 0, 0), no shifts will be applied
===============================================================================
Job complete
usr+sys time: 5622.41 seconds
wall clock time: 100 minutes 45.65 seconds (6045.65 seconds total)