Starting phenix.real_space_refine
on Mon Jan 13 18:05:16 2025 by dcliebschner
===============================================================================
Processing files:
-------------------------------------------------------------------------------
Found model, /net/cci-nas-00/data/ceres_data/9ern_19927/01_2025/9ern_19927.cif
Found real_map, /net/cci-nas-00/data/ceres_data/9ern_19927/01_2025/9ern_19927.map
Processing PHIL parameters:
-------------------------------------------------------------------------------
Adding command-line PHIL:
-------------------------
refinement.macro_cycles=10
scattering_table=electron
resolution=2.5
write_initial_geo_file=False
Final processed PHIL parameters:
-------------------------------------------------------------------------------
data_manager {
real_map_files = "/net/cci-nas-00/data/ceres_data/9ern_19927/01_2025/9ern_19927.map"
default_real_map = "/net/cci-nas-00/data/ceres_data/9ern_19927/01_2025/9ern_19927.map"
model {
file = "/net/cci-nas-00/data/ceres_data/9ern_19927/01_2025/9ern_19927.cif"
}
default_model = "/net/cci-nas-00/data/ceres_data/9ern_19927/01_2025/9ern_19927.cif"
}
resolution = 2.5
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= 0.001
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 6 5.16 5
C 2160 2.51 5
N 636 2.21 5
O 642 1.98 5
sf(0) = scattering factor at diffraction angle 0.
Process input model
Symmetric amino acids flipped. Time to flip 30 residue(s): 0.02s
Monomer Library directory:
"/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
Total number of atoms: 3444
Number of models: 1
Model: ""
Number of chains: 1
Chain: "A"
Number of atoms: 574
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 75, 574
Classifications: {'peptide': 75}
Link IDs: {'PTRANS': 3, 'TRANS': 71}
Restraints were copied for chains:
C, B, E, D, F
Time building chain proxies: 2.70, per 1000 atoms: 0.78
Number of scatterers: 3444
At special positions: 0
Unit cell: (111.24, 136.784, 39.552, 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 6 16.00
O 642 8.00
N 636 7.00
C 2160 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: 0.75
Conformation dependent library (CDL) restraints added in 387.6 milliseconds
876 Ramachandran restraints generated.
438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2.
Adding C-beta torsion restraints...
Number of C-beta restraints generated: 792
Finding SS restraints...
Secondary structure from input PDB file:
0 helices and 14 sheets defined
0.0% alpha, 60.0% beta
0 base pairs and 0 stacking pairs defined.
Time for finding SS restraints: 0.45
Creating SS restraints...
Processing sheet with id=AA1, first strand: chain 'D' and resid 306 through 310
removed outlier: 6.532A pdb=" N GLN C 307 " --> pdb=" O ILE D 308 " (cutoff:3.500A)
removed outlier: 7.904A pdb=" N TYR D 310 " --> pdb=" O GLN C 307 " (cutoff:3.500A)
removed outlier: 6.631A pdb=" N VAL C 309 " --> pdb=" O TYR D 310 " (cutoff:3.500A)
removed outlier: 6.533A pdb=" N GLN A 307 " --> pdb=" O ILE C 308 " (cutoff:3.500A)
removed outlier: 7.903A pdb=" N TYR C 310 " --> pdb=" O GLN A 307 " (cutoff:3.500A)
removed outlier: 6.631A pdb=" N VAL A 309 " --> pdb=" O TYR C 310 " (cutoff:3.500A)
Processing sheet with id=AA2, first strand: chain 'D' and resid 313 through 314
removed outlier: 6.721A pdb=" N VAL C 313 " --> pdb=" O ASP D 314 " (cutoff:3.500A)
removed outlier: 6.721A pdb=" N VAL A 313 " --> pdb=" O ASP C 314 " (cutoff:3.500A)
Processing sheet with id=AA3, first strand: chain 'D' and resid 317 through 330
removed outlier: 8.811A pdb=" N VAL C 318 " --> pdb=" O THR D 319 " (cutoff:3.500A)
removed outlier: 10.768A pdb=" N LYS D 321 " --> pdb=" O VAL C 318 " (cutoff:3.500A)
removed outlier: 9.205A pdb=" N SER C 320 " --> pdb=" O LYS D 321 " (cutoff:3.500A)
removed outlier: 10.368A pdb=" N GLY D 323 " --> pdb=" O SER C 320 " (cutoff:3.500A)
removed outlier: 6.414A pdb=" N CYS C 322 " --> pdb=" O GLY D 323 " (cutoff:3.500A)
removed outlier: 7.380A pdb=" N LEU D 325 " --> pdb=" O CYS C 322 " (cutoff:3.500A)
removed outlier: 6.109A pdb=" N SER C 324 " --> pdb=" O LEU D 325 " (cutoff:3.500A)
removed outlier: 7.900A pdb=" N ASN D 327 " --> pdb=" O SER C 324 " (cutoff:3.500A)
removed outlier: 9.034A pdb=" N GLY C 326 " --> pdb=" O ASN D 327 " (cutoff:3.500A)
removed outlier: 8.134A pdb=" N HIS D 329 " --> pdb=" O GLY C 326 " (cutoff:3.500A)
removed outlier: 9.240A pdb=" N ILE C 328 " --> pdb=" O HIS D 329 " (cutoff:3.500A)
removed outlier: 8.811A pdb=" N VAL A 318 " --> pdb=" O THR C 319 " (cutoff:3.500A)
removed outlier: 10.769A pdb=" N LYS C 321 " --> pdb=" O VAL A 318 " (cutoff:3.500A)
removed outlier: 9.205A pdb=" N SER A 320 " --> pdb=" O LYS C 321 " (cutoff:3.500A)
removed outlier: 10.368A pdb=" N GLY C 323 " --> pdb=" O SER A 320 " (cutoff:3.500A)
removed outlier: 6.414A pdb=" N CYS A 322 " --> pdb=" O GLY C 323 " (cutoff:3.500A)
removed outlier: 7.379A pdb=" N LEU C 325 " --> pdb=" O CYS A 322 " (cutoff:3.500A)
removed outlier: 6.108A pdb=" N SER A 324 " --> pdb=" O LEU C 325 " (cutoff:3.500A)
removed outlier: 7.900A pdb=" N ASN C 327 " --> pdb=" O SER A 324 " (cutoff:3.500A)
removed outlier: 9.034A pdb=" N GLY A 326 " --> pdb=" O ASN C 327 " (cutoff:3.500A)
removed outlier: 8.134A pdb=" N HIS C 329 " --> pdb=" O GLY A 326 " (cutoff:3.500A)
removed outlier: 9.239A pdb=" N ILE A 328 " --> pdb=" O HIS C 329 " (cutoff:3.500A)
removed outlier: 6.854A pdb=" N VAL E 318 " --> pdb=" O LYS A 317 " (cutoff:3.500A)
removed outlier: 6.953A pdb=" N THR A 319 " --> pdb=" O VAL E 318 " (cutoff:3.500A)
removed outlier: 6.880A pdb=" N SER E 320 " --> pdb=" O THR A 319 " (cutoff:3.500A)
removed outlier: 6.900A pdb=" N LYS A 321 " --> pdb=" O SER E 320 " (cutoff:3.500A)
removed outlier: 6.985A pdb=" N CYS E 322 " --> pdb=" O LYS A 321 " (cutoff:3.500A)
removed outlier: 6.929A pdb=" N GLY A 323 " --> pdb=" O CYS E 322 " (cutoff:3.500A)
removed outlier: 6.869A pdb=" N ILE E 328 " --> pdb=" O ASN A 327 " (cutoff:3.500A)
removed outlier: 6.914A pdb=" N HIS A 329 " --> pdb=" O ILE E 328 " (cutoff:3.500A)
removed outlier: 6.948A pdb=" N HIS E 330 " --> pdb=" O HIS A 329 " (cutoff:3.500A)
Processing sheet with id=AA4, first strand: chain 'D' and resid 337 through 346
removed outlier: 9.063A pdb=" N VAL C 337 " --> pdb=" O GLU D 338 " (cutoff:3.500A)
removed outlier: 10.291A pdb=" N LYS D 340 " --> pdb=" O VAL C 337 " (cutoff:3.500A)
removed outlier: 8.968A pdb=" N VAL C 339 " --> pdb=" O LYS D 340 " (cutoff:3.500A)
removed outlier: 10.293A pdb=" N GLU D 342 " --> pdb=" O VAL C 339 " (cutoff:3.500A)
removed outlier: 9.073A pdb=" N SER C 341 " --> pdb=" O GLU D 342 " (cutoff:3.500A)
removed outlier: 9.261A pdb=" N LEU D 344 " --> pdb=" O SER C 341 " (cutoff:3.500A)
removed outlier: 6.951A pdb=" N LYS C 343 " --> pdb=" O LEU D 344 " (cutoff:3.500A)
removed outlier: 8.181A pdb=" N PHE D 346 " --> pdb=" O LYS C 343 " (cutoff:3.500A)
removed outlier: 6.185A pdb=" N ASP C 345 " --> pdb=" O PHE D 346 " (cutoff:3.500A)
removed outlier: 9.063A pdb=" N VAL A 337 " --> pdb=" O GLU C 338 " (cutoff:3.500A)
removed outlier: 10.291A pdb=" N LYS C 340 " --> pdb=" O VAL A 337 " (cutoff:3.500A)
removed outlier: 8.968A pdb=" N VAL A 339 " --> pdb=" O LYS C 340 " (cutoff:3.500A)
removed outlier: 10.292A pdb=" N GLU C 342 " --> pdb=" O VAL A 339 " (cutoff:3.500A)
removed outlier: 9.073A pdb=" N SER A 341 " --> pdb=" O GLU C 342 " (cutoff:3.500A)
removed outlier: 9.261A pdb=" N LEU C 344 " --> pdb=" O SER A 341 " (cutoff:3.500A)
removed outlier: 6.950A pdb=" N LYS A 343 " --> pdb=" O LEU C 344 " (cutoff:3.500A)
removed outlier: 8.181A pdb=" N PHE C 346 " --> pdb=" O LYS A 343 " (cutoff:3.500A)
removed outlier: 6.185A pdb=" N ASP A 345 " --> pdb=" O PHE C 346 " (cutoff:3.500A)
removed outlier: 6.923A pdb=" N GLU A 338 " --> pdb=" O VAL E 337 " (cutoff:3.500A)
removed outlier: 6.919A pdb=" N VAL E 339 " --> pdb=" O GLU A 338 " (cutoff:3.500A)
removed outlier: 6.925A pdb=" N LYS A 340 " --> pdb=" O VAL E 339 " (cutoff:3.500A)
removed outlier: 6.912A pdb=" N SER E 341 " --> pdb=" O LYS A 340 " (cutoff:3.500A)
removed outlier: 6.928A pdb=" N GLU A 342 " --> pdb=" O SER E 341 " (cutoff:3.500A)
removed outlier: 6.895A pdb=" N LYS E 343 " --> pdb=" O GLU A 342 " (cutoff:3.500A)
Processing sheet with id=AA5, first strand: chain 'D' and resid 350 through 357
removed outlier: 6.567A pdb=" N GLN C 351 " --> pdb=" O SER D 352 " (cutoff:3.500A)
removed outlier: 8.129A pdb=" N ILE D 354 " --> pdb=" O GLN C 351 " (cutoff:3.500A)
removed outlier: 6.499A pdb=" N LYS C 353 " --> pdb=" O ILE D 354 " (cutoff:3.500A)
removed outlier: 7.444A pdb=" N SER D 356 " --> pdb=" O LYS C 353 " (cutoff:3.500A)
removed outlier: 6.119A pdb=" N GLY C 355 " --> pdb=" O SER D 356 " (cutoff:3.500A)
removed outlier: 6.567A pdb=" N GLN A 351 " --> pdb=" O SER C 352 " (cutoff:3.500A)
removed outlier: 8.129A pdb=" N ILE C 354 " --> pdb=" O GLN A 351 " (cutoff:3.500A)
removed outlier: 6.499A pdb=" N LYS A 353 " --> pdb=" O ILE C 354 " (cutoff:3.500A)
removed outlier: 7.445A pdb=" N SER C 356 " --> pdb=" O LYS A 353 " (cutoff:3.500A)
removed outlier: 6.120A pdb=" N GLY A 355 " --> pdb=" O SER C 356 " (cutoff:3.500A)
Processing sheet with id=AA6, first strand: chain 'D' and resid 360 through 362
removed outlier: 6.376A pdb=" N THR A 361 " --> pdb=" O HIS E 362 " (cutoff:3.500A)
Processing sheet with id=AA7, first strand: chain 'D' and resid 369 through 378
removed outlier: 6.358A pdb=" N LYS A 370 " --> pdb=" O ILE E 371 " (cutoff:3.500A)
removed outlier: 8.131A pdb=" N THR E 373 " --> pdb=" O LYS A 370 " (cutoff:3.500A)
removed outlier: 6.778A pdb=" N GLU A 372 " --> pdb=" O THR E 373 " (cutoff:3.500A)
removed outlier: 8.333A pdb=" N LYS E 375 " --> pdb=" O GLU A 372 " (cutoff:3.500A)
removed outlier: 6.508A pdb=" N HIS A 374 " --> pdb=" O LYS E 375 " (cutoff:3.500A)
removed outlier: 7.798A pdb=" N THR E 377 " --> pdb=" O HIS A 374 " (cutoff:3.500A)
removed outlier: 6.460A pdb=" N LEU A 376 " --> pdb=" O THR E 377 " (cutoff:3.500A)
Processing sheet with id=AA8, first strand: chain 'B' and resid 306 through 310
Processing sheet with id=AA9, first strand: chain 'B' and resid 313 through 314
Processing sheet with id=AB1, first strand: chain 'B' and resid 317 through 330
removed outlier: 6.854A pdb=" N VAL F 318 " --> pdb=" O LYS B 317 " (cutoff:3.500A)
removed outlier: 6.953A pdb=" N THR B 319 " --> pdb=" O VAL F 318 " (cutoff:3.500A)
removed outlier: 6.880A pdb=" N SER F 320 " --> pdb=" O THR B 319 " (cutoff:3.500A)
removed outlier: 6.900A pdb=" N LYS B 321 " --> pdb=" O SER F 320 " (cutoff:3.500A)
removed outlier: 6.985A pdb=" N CYS F 322 " --> pdb=" O LYS B 321 " (cutoff:3.500A)
removed outlier: 6.929A pdb=" N GLY B 323 " --> pdb=" O CYS F 322 " (cutoff:3.500A)
removed outlier: 6.869A pdb=" N ILE F 328 " --> pdb=" O ASN B 327 " (cutoff:3.500A)
removed outlier: 6.914A pdb=" N HIS B 329 " --> pdb=" O ILE F 328 " (cutoff:3.500A)
removed outlier: 6.948A pdb=" N HIS F 330 " --> pdb=" O HIS B 329 " (cutoff:3.500A)
Processing sheet with id=AB2, first strand: chain 'B' and resid 337 through 346
removed outlier: 6.923A pdb=" N GLU B 338 " --> pdb=" O VAL F 337 " (cutoff:3.500A)
removed outlier: 6.919A pdb=" N VAL F 339 " --> pdb=" O GLU B 338 " (cutoff:3.500A)
removed outlier: 6.925A pdb=" N LYS B 340 " --> pdb=" O VAL F 339 " (cutoff:3.500A)
removed outlier: 6.912A pdb=" N SER F 341 " --> pdb=" O LYS B 340 " (cutoff:3.500A)
removed outlier: 6.928A pdb=" N GLU B 342 " --> pdb=" O SER F 341 " (cutoff:3.500A)
removed outlier: 6.895A pdb=" N LYS F 343 " --> pdb=" O GLU B 342 " (cutoff:3.500A)
Processing sheet with id=AB3, first strand: chain 'B' and resid 350 through 357
Processing sheet with id=AB4, first strand: chain 'B' and resid 360 through 362
removed outlier: 6.376A pdb=" N THR B 361 " --> pdb=" O HIS F 362 " (cutoff:3.500A)
No H-bonds generated for sheet with id=AB4
Processing sheet with id=AB5, first strand: chain 'B' and resid 369 through 378
removed outlier: 6.358A pdb=" N LYS B 370 " --> pdb=" O ILE F 371 " (cutoff:3.500A)
removed outlier: 8.131A pdb=" N THR F 373 " --> pdb=" O LYS B 370 " (cutoff:3.500A)
removed outlier: 6.777A pdb=" N GLU B 372 " --> pdb=" O THR F 373 " (cutoff:3.500A)
removed outlier: 8.333A pdb=" N LYS F 375 " --> pdb=" O GLU B 372 " (cutoff:3.500A)
removed outlier: 6.508A pdb=" N HIS B 374 " --> pdb=" O LYS F 375 " (cutoff:3.500A)
removed outlier: 7.798A pdb=" N THR F 377 " --> pdb=" O HIS B 374 " (cutoff:3.500A)
removed outlier: 6.460A pdb=" N LEU B 376 " --> pdb=" O THR F 377 " (cutoff:3.500A)
No H-bonds generated for sheet with id=AB5
60 hydrogen bonds defined for protein.
180 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: 0.73
Time building geometry restraints manager: 0.89 seconds
NOTE: a complete listing of the restraints can be obtained by requesting
output of .geo file.
Histogram of bond lengths:
1.22 - 1.34: 796
1.34 - 1.46: 785
1.46 - 1.58: 1911
1.58 - 1.70: 0
1.70 - 1.81: 6
Bond restraints: 3498
Sorted by residual:
bond pdb=" CA SER F 316 "
pdb=" CB SER F 316 "
ideal model delta sigma weight residual
1.529 1.488 0.042 1.64e-02 3.72e+03 6.44e+00
bond pdb=" CA SER D 316 "
pdb=" CB SER D 316 "
ideal model delta sigma weight residual
1.529 1.488 0.042 1.64e-02 3.72e+03 6.42e+00
bond pdb=" CA SER E 316 "
pdb=" CB SER E 316 "
ideal model delta sigma weight residual
1.529 1.488 0.042 1.64e-02 3.72e+03 6.42e+00
bond pdb=" CA SER A 316 "
pdb=" CB SER A 316 "
ideal model delta sigma weight residual
1.529 1.488 0.041 1.64e-02 3.72e+03 6.39e+00
bond pdb=" CA SER B 316 "
pdb=" CB SER B 316 "
ideal model delta sigma weight residual
1.529 1.488 0.041 1.64e-02 3.72e+03 6.32e+00
... (remaining 3493 not shown)
Histogram of bond angle deviations from ideal:
0.00 - 1.29: 3298
1.29 - 2.57: 1073
2.57 - 3.86: 247
3.86 - 5.15: 50
5.15 - 6.43: 12
Bond angle restraints: 4680
Sorted by residual:
angle pdb=" N GLY E 326 "
pdb=" CA GLY E 326 "
pdb=" C GLY E 326 "
ideal model delta sigma weight residual
110.80 116.87 -6.07 1.41e+00 5.03e-01 1.85e+01
angle pdb=" N GLY C 326 "
pdb=" CA GLY C 326 "
pdb=" C GLY C 326 "
ideal model delta sigma weight residual
110.80 116.85 -6.05 1.41e+00 5.03e-01 1.84e+01
angle pdb=" N GLY B 326 "
pdb=" CA GLY B 326 "
pdb=" C GLY B 326 "
ideal model delta sigma weight residual
110.80 116.85 -6.05 1.41e+00 5.03e-01 1.84e+01
angle pdb=" N GLY A 326 "
pdb=" CA GLY A 326 "
pdb=" C GLY A 326 "
ideal model delta sigma weight residual
110.80 116.85 -6.05 1.41e+00 5.03e-01 1.84e+01
angle pdb=" N GLY D 326 "
pdb=" CA GLY D 326 "
pdb=" C GLY D 326 "
ideal model delta sigma weight residual
110.80 116.84 -6.04 1.41e+00 5.03e-01 1.84e+01
... (remaining 4675 not shown)
Histogram of dihedral angle deviations from ideal:
0.00 - 11.49: 1824
11.49 - 22.98: 240
22.98 - 34.47: 42
34.47 - 45.95: 18
45.95 - 57.44: 12
Dihedral angle restraints: 2136
sinusoidal: 894
harmonic: 1242
Sorted by residual:
dihedral pdb=" CA VAL C 318 "
pdb=" C VAL C 318 "
pdb=" N THR C 319 "
pdb=" CA THR C 319 "
ideal model delta harmonic sigma weight residual
-180.00 -155.03 -24.97 0 5.00e+00 4.00e-02 2.49e+01
dihedral pdb=" CA VAL B 318 "
pdb=" C VAL B 318 "
pdb=" N THR B 319 "
pdb=" CA THR B 319 "
ideal model delta harmonic sigma weight residual
-180.00 -155.03 -24.97 0 5.00e+00 4.00e-02 2.49e+01
dihedral pdb=" CA VAL D 318 "
pdb=" C VAL D 318 "
pdb=" N THR D 319 "
pdb=" CA THR D 319 "
ideal model delta harmonic sigma weight residual
-180.00 -155.06 -24.94 0 5.00e+00 4.00e-02 2.49e+01
... (remaining 2133 not shown)
Histogram of chiral volume deviations from ideal:
0.002 - 0.047: 186
0.047 - 0.092: 211
0.092 - 0.137: 101
0.137 - 0.182: 16
0.182 - 0.226: 14
Chirality restraints: 528
Sorted by residual:
chirality pdb=" CB ILE F 328 "
pdb=" CA ILE F 328 "
pdb=" CG1 ILE F 328 "
pdb=" CG2 ILE F 328 "
both_signs ideal model delta sigma weight residual
False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.28e+00
chirality pdb=" CB ILE E 328 "
pdb=" CA ILE E 328 "
pdb=" CG1 ILE E 328 "
pdb=" CG2 ILE E 328 "
both_signs ideal model delta sigma weight residual
False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.27e+00
chirality pdb=" CB ILE B 328 "
pdb=" CA ILE B 328 "
pdb=" CG1 ILE B 328 "
pdb=" CG2 ILE B 328 "
both_signs ideal model delta sigma weight residual
False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.27e+00
... (remaining 525 not shown)
Planarity restraints: 594
Sorted by residual:
delta sigma weight rms_deltas residual
plane pdb=" CB TYR C 310 " -0.029 2.00e-02 2.50e+03 1.70e-02 5.75e+00
pdb=" CG TYR C 310 " 0.036 2.00e-02 2.50e+03
pdb=" CD1 TYR C 310 " 0.008 2.00e-02 2.50e+03
pdb=" CD2 TYR C 310 " 0.003 2.00e-02 2.50e+03
pdb=" CE1 TYR C 310 " -0.006 2.00e-02 2.50e+03
pdb=" CE2 TYR C 310 " -0.000 2.00e-02 2.50e+03
pdb=" CZ TYR C 310 " -0.005 2.00e-02 2.50e+03
pdb=" OH TYR C 310 " -0.006 2.00e-02 2.50e+03
delta sigma weight rms_deltas residual
plane pdb=" CB TYR F 310 " 0.029 2.00e-02 2.50e+03 1.68e-02 5.65e+00
pdb=" CG TYR F 310 " -0.036 2.00e-02 2.50e+03
pdb=" CD1 TYR F 310 " -0.007 2.00e-02 2.50e+03
pdb=" CD2 TYR F 310 " -0.003 2.00e-02 2.50e+03
pdb=" CE1 TYR F 310 " 0.006 2.00e-02 2.50e+03
pdb=" CE2 TYR F 310 " 0.001 2.00e-02 2.50e+03
pdb=" CZ TYR F 310 " 0.005 2.00e-02 2.50e+03
pdb=" OH TYR F 310 " 0.006 2.00e-02 2.50e+03
delta sigma weight rms_deltas residual
plane pdb=" CB TYR E 310 " -0.029 2.00e-02 2.50e+03 1.68e-02 5.65e+00
pdb=" CG TYR E 310 " 0.035 2.00e-02 2.50e+03
pdb=" CD1 TYR E 310 " 0.008 2.00e-02 2.50e+03
pdb=" CD2 TYR E 310 " 0.003 2.00e-02 2.50e+03
pdb=" CE1 TYR E 310 " -0.006 2.00e-02 2.50e+03
pdb=" CE2 TYR E 310 " -0.000 2.00e-02 2.50e+03
pdb=" CZ TYR E 310 " -0.005 2.00e-02 2.50e+03
pdb=" OH TYR E 310 " -0.006 2.00e-02 2.50e+03
... (remaining 591 not shown)
Histogram of nonbonded interaction distances:
2.54 - 3.01: 1736
3.01 - 3.48: 2843
3.48 - 3.96: 5484
3.96 - 4.43: 5487
4.43 - 4.90: 10434
Nonbonded interactions: 25984
Sorted by model distance:
nonbonded pdb=" OG SER F 316 "
pdb=" NZ LYS F 370 "
model vdw
2.539 3.120
nonbonded pdb=" OG SER C 316 "
pdb=" NZ LYS C 370 "
model vdw
2.540 3.120
nonbonded pdb=" OG SER E 316 "
pdb=" NZ LYS E 370 "
model vdw
2.540 3.120
nonbonded pdb=" OG SER A 316 "
pdb=" NZ LYS A 370 "
model vdw
2.540 3.120
nonbonded pdb=" OG SER B 316 "
pdb=" NZ LYS B 370 "
model vdw
2.540 3.120
... (remaining 25979 not shown)
NOTE: a complete listing of the restraints can be obtained by requesting
output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.03
Found NCS groups:
ncs_group {
reference = chain 'A'
selection = chain 'C'
selection = chain 'B'
selection = chain 'E'
selection = chain 'D'
selection = chain 'F'
}
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: 2.780
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: 0.190
Check model and map are aligned: 0.030
Set scattering table: 0.030
Process input model: 12.510
Find NCS groups from input model: 0.070
Set up NCS constraints: 0.010
Set refine NCS operators: 0.000
Adjust number of macro_cycles: 0.000
Reset NCS operators: 0.000
Extract rigid body selections: 0.000
Check and reset occupancies: 0.000
Load rotamer database and sin/cos tables:11.630
Set ADP refinement strategy: 0.000
Make a string to write initial .geo file:0.000
Internal consistency checks: 0.000
Total: 27.260
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8884
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 : 0.009 0.054 3498 Z= 0.606
Angle : 1.379 6.432 4680 Z= 0.910
Chirality : 0.082 0.226 528
Planarity : 0.008 0.034 594
Dihedral : 11.585 57.442 1344
Min Nonbonded Distance : 2.539
Molprobity Statistics.
All-atom Clashscore : 0.00
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 2.74 %
Favored : 97.26 %
Rotamer:
Outliers : 3.03 %
Allowed : 3.03 %
Favored : 93.94 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: -2.81 (0.30), residues: 438
helix: None (None), residues: 0
sheet: None (None), residues: 0
loop : -2.13 (0.23), residues: 438
Max deviation from planes:
Type MaxDev MeanDev LineInFile
HIS 0.012 0.004 HIS B 329
PHE 0.026 0.006 PHE E 346
TYR 0.036 0.011 TYR B 310
ARG 0.001 0.000 ARG E 379
*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
876 Ramachandran restraints generated.
438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
876 Ramachandran restraints generated.
438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
148 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 12
poor density : 136
time to evaluate : 0.445
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: A 340 LYS cc_start: 0.8547 (mtpm) cc_final: 0.8171 (mttp)
REVERT: A 345 ASP cc_start: 0.9016 (m-30) cc_final: 0.8507 (t0)
REVERT: B 338 GLU cc_start: 0.8830 (tt0) cc_final: 0.8604 (tt0)
REVERT: B 340 LYS cc_start: 0.8677 (mtpm) cc_final: 0.8296 (mttp)
REVERT: C 340 LYS cc_start: 0.8596 (mtpm) cc_final: 0.8216 (mttt)
REVERT: C 373 THR cc_start: 0.8702 (m) cc_final: 0.8133 (p)
REVERT: D 317 LYS cc_start: 0.8616 (pttt) cc_final: 0.8393 (ptpt)
REVERT: D 340 LYS cc_start: 0.8786 (mtpm) cc_final: 0.8429 (mttt)
REVERT: D 373 THR cc_start: 0.8887 (m) cc_final: 0.8472 (p)
REVERT: E 340 LYS cc_start: 0.8609 (mtpm) cc_final: 0.8233 (mttp)
REVERT: E 348 ASP cc_start: 0.8979 (t0) cc_final: 0.8722 (t0)
REVERT: E 349 ARG cc_start: 0.9067 (mtt180) cc_final: 0.7437 (tpt90)
REVERT: F 340 LYS cc_start: 0.8596 (mtpm) cc_final: 0.8206 (mttt)
REVERT: F 349 ARG cc_start: 0.9046 (mtt180) cc_final: 0.7331 (tpt90)
outliers start: 12
outliers final: 0
residues processed: 142
average time/residue: 1.4691
time to fit residues: 213.2542
Evaluate side-chains
113 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 0
poor density : 113
time to evaluate : 0.430
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 42
random chunks:
chunk 35 optimal weight: 3.9990
chunk 31 optimal weight: 1.9990
chunk 17 optimal weight: 4.9990
chunk 10 optimal weight: 9.9990
chunk 21 optimal weight: 10.0000
chunk 32 optimal weight: 0.8980
chunk 12 optimal weight: 0.8980
chunk 20 optimal weight: 9.9990
chunk 24 optimal weight: 1.9990
chunk 38 optimal weight: 2.9990
chunk 11 optimal weight: 0.3980
overall best weight: 1.2384
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 330 HIS
A 336 GLN
A 362 HIS
B 327 ASN
B 330 HIS
C 330 HIS
C 336 GLN
C 351 GLN
C 362 HIS
D 330 HIS
D 362 HIS
E 327 ASN
E 336 GLN
E 351 GLN
E 362 HIS
F 330 HIS
F 351 GLN
F 362 HIS
Total number of N/Q/H flips: 18
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4235 r_free = 0.4235 target = 0.161241 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.119570 restraints weight = 3532.500|
|-----------------------------------------------------------------------------|
r_work (start): 0.3754 rms_B_bonded: 1.79
r_work: 0.3639 rms_B_bonded: 1.95 restraints_weight: 0.5000
r_work: 0.3547 rms_B_bonded: 3.21 restraints_weight: 0.2500
r_work (final): 0.3547
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8739
moved from start: 0.2184
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.002 0.018 3498 Z= 0.151
Angle : 0.538 3.817 4680 Z= 0.285
Chirality : 0.049 0.136 528
Planarity : 0.004 0.034 594
Dihedral : 4.993 15.377 462
Min Nonbonded Distance : 2.567
Molprobity Statistics.
All-atom Clashscore : 2.28
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 1.14 %
Favored : 98.86 %
Rotamer:
Outliers : 1.77 %
Allowed : 14.65 %
Favored : 83.59 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: -2.14 (0.32), residues: 438
helix: None (None), residues: 0
sheet: None (None), residues: 0
loop : -1.62 (0.25), residues: 438
Max deviation from planes:
Type MaxDev MeanDev LineInFile
HIS 0.003 0.001 HIS C 329
PHE 0.008 0.001 PHE A 346
TYR 0.015 0.003 TYR B 310
ARG 0.001 0.000 ARG D 379
*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
876 Ramachandran restraints generated.
438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
876 Ramachandran restraints generated.
438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
147 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 7
poor density : 140
time to evaluate : 0.410
Fit side-chains
REVERT: A 340 LYS cc_start: 0.8410 (mtpm) cc_final: 0.8102 (mttt)
REVERT: A 375 LYS cc_start: 0.8029 (tttt) cc_final: 0.7669 (tttm)
REVERT: B 311 LYS cc_start: 0.8425 (mtmt) cc_final: 0.6777 (pptt)
REVERT: B 338 GLU cc_start: 0.8561 (tt0) cc_final: 0.8324 (tt0)
REVERT: B 340 LYS cc_start: 0.8636 (mtpm) cc_final: 0.8255 (mttt)
REVERT: B 347 LYS cc_start: 0.8883 (mptt) cc_final: 0.8652 (mptp)
REVERT: C 340 LYS cc_start: 0.8436 (mtpm) cc_final: 0.8031 (mttt)
REVERT: C 345 ASP cc_start: 0.8393 (m-30) cc_final: 0.8009 (t0)
REVERT: C 375 LYS cc_start: 0.8215 (tttt) cc_final: 0.7853 (tttm)
REVERT: D 311 LYS cc_start: 0.8365 (mtmt) cc_final: 0.6756 (pptt)
REVERT: D 317 LYS cc_start: 0.8537 (pttt) cc_final: 0.8275 (ptpt)
REVERT: D 321 LYS cc_start: 0.8581 (ttpt) cc_final: 0.8331 (mtmm)
REVERT: D 340 LYS cc_start: 0.8610 (mtpm) cc_final: 0.8261 (mttt)
REVERT: D 373 THR cc_start: 0.8639 (m) cc_final: 0.8437 (p)
REVERT: D 375 LYS cc_start: 0.8681 (tttt) cc_final: 0.8476 (tttt)
REVERT: E 311 LYS cc_start: 0.7939 (mtmt) cc_final: 0.7479 (mmtt)
REVERT: E 340 LYS cc_start: 0.8416 (mtpm) cc_final: 0.8055 (mttt)
REVERT: E 349 ARG cc_start: 0.8726 (mtt180) cc_final: 0.7288 (mmp-170)
REVERT: E 375 LYS cc_start: 0.8124 (tttt) cc_final: 0.7691 (tttm)
REVERT: F 311 LYS cc_start: 0.7903 (mtmt) cc_final: 0.7442 (mmtt)
REVERT: F 340 LYS cc_start: 0.8424 (mtpm) cc_final: 0.7970 (mttt)
REVERT: F 347 LYS cc_start: 0.8768 (mptt) cc_final: 0.8521 (mptp)
REVERT: F 349 ARG cc_start: 0.8723 (mtt180) cc_final: 0.7123 (mmp-170)
REVERT: F 373 THR cc_start: 0.8402 (m) cc_final: 0.7897 (p)
REVERT: F 375 LYS cc_start: 0.8059 (tttt) cc_final: 0.7723 (tttt)
outliers start: 7
outliers final: 1
residues processed: 143
average time/residue: 1.4247
time to fit residues: 208.4167
Evaluate side-chains
120 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 1
poor density : 119
time to evaluate : 0.389
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue 320 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 42
random chunks:
chunk 19 optimal weight: 7.9990
chunk 34 optimal weight: 1.9990
chunk 7 optimal weight: 10.0000
chunk 24 optimal weight: 3.9990
chunk 22 optimal weight: 10.0000
chunk 27 optimal weight: 1.9990
chunk 0 optimal weight: 10.0000
chunk 1 optimal weight: 9.9990
chunk 3 optimal weight: 7.9990
chunk 16 optimal weight: 10.0000
chunk 25 optimal weight: 0.8980
overall best weight: 3.3788
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
B 362 HIS
E 330 HIS
E 351 GLN
E 368 ASN
F 351 GLN
F 368 ASN
Total number of N/Q/H flips: 6
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4177 r_free = 0.4177 target = 0.155516 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.113339 restraints weight = 3543.376|
|-----------------------------------------------------------------------------|
r_work (start): 0.3685 rms_B_bonded: 1.81
r_work: 0.3569 rms_B_bonded: 1.94 restraints_weight: 0.5000
r_work: 0.3479 rms_B_bonded: 3.16 restraints_weight: 0.2500
r_work (final): 0.3479
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8796
moved from start: 0.2494
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.005 0.034 3498 Z= 0.318
Angle : 0.616 4.275 4680 Z= 0.321
Chirality : 0.051 0.131 528
Planarity : 0.004 0.027 594
Dihedral : 4.995 15.733 462
Min Nonbonded Distance : 2.586
Molprobity Statistics.
All-atom Clashscore : 2.56
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 0.91 %
Favored : 99.09 %
Rotamer:
Outliers : 2.27 %
Allowed : 19.44 %
Favored : 78.28 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: -1.96 (0.33), residues: 438
helix: None (None), residues: 0
sheet: None (None), residues: 0
loop : -1.48 (0.25), residues: 438
Max deviation from planes:
Type MaxDev MeanDev LineInFile
HIS 0.003 0.001 HIS F 329
PHE 0.011 0.002 PHE A 346
TYR 0.015 0.004 TYR B 310
ARG 0.001 0.000 ARG F 349
*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
876 Ramachandran restraints generated.
438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
876 Ramachandran restraints generated.
438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
136 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 9
poor density : 127
time to evaluate : 0.423
Fit side-chains
revert: symmetry clash
revert: symmetry clash
REVERT: A 340 LYS cc_start: 0.8393 (mtpm) cc_final: 0.8065 (mttt)
REVERT: A 375 LYS cc_start: 0.8030 (tttt) cc_final: 0.7585 (tttm)
REVERT: B 311 LYS cc_start: 0.8457 (mtmt) cc_final: 0.7117 (pptt)
REVERT: B 317 LYS cc_start: 0.8675 (ptpt) cc_final: 0.8470 (ptpt)
REVERT: B 338 GLU cc_start: 0.8548 (tt0) cc_final: 0.8239 (tt0)
REVERT: B 340 LYS cc_start: 0.8693 (mtpm) cc_final: 0.8240 (mttt)
REVERT: B 375 LYS cc_start: 0.8441 (tttm) cc_final: 0.7890 (tppp)
REVERT: C 340 LYS cc_start: 0.8411 (mtpm) cc_final: 0.7990 (mttt)
REVERT: C 373 THR cc_start: 0.8446 (m) cc_final: 0.8023 (p)
REVERT: C 375 LYS cc_start: 0.8304 (tttt) cc_final: 0.7952 (tttm)
REVERT: D 311 LYS cc_start: 0.8394 (mtmt) cc_final: 0.7103 (pptt)
REVERT: D 317 LYS cc_start: 0.8595 (pttt) cc_final: 0.8320 (ptpt)
REVERT: D 340 LYS cc_start: 0.8561 (mtpm) cc_final: 0.8210 (mttt)
REVERT: D 373 THR cc_start: 0.8677 (m) cc_final: 0.8390 (p)
REVERT: E 311 LYS cc_start: 0.8158 (mtmt) cc_final: 0.7718 (mmtt)
REVERT: E 340 LYS cc_start: 0.8422 (mtpm) cc_final: 0.8034 (mttt)
REVERT: E 349 ARG cc_start: 0.8726 (mtt180) cc_final: 0.7295 (mtp180)
REVERT: E 375 LYS cc_start: 0.8157 (tttt) cc_final: 0.7732 (tttm)
REVERT: F 311 LYS cc_start: 0.8069 (mtmt) cc_final: 0.7599 (mmtt)
REVERT: F 331 LYS cc_start: 0.9095 (OUTLIER) cc_final: 0.8810 (ttmt)
REVERT: F 340 LYS cc_start: 0.8411 (mtpm) cc_final: 0.7977 (mttt)
REVERT: F 347 LYS cc_start: 0.8804 (mptt) cc_final: 0.8542 (mptp)
REVERT: F 373 THR cc_start: 0.8457 (m) cc_final: 0.8061 (p)
REVERT: F 375 LYS cc_start: 0.8084 (tttt) cc_final: 0.7756 (tttt)
outliers start: 9
outliers final: 5
residues processed: 132
average time/residue: 1.4746
time to fit residues: 198.9778
Evaluate side-chains
127 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 6
poor density : 121
time to evaluate : 0.422
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 308 ILE
Chi-restraints excluded: chain A residue 320 SER
Chi-restraints excluded: chain B residue 320 SER
Chi-restraints excluded: chain B residue 343 LYS
Chi-restraints excluded: chain C residue 311 LYS
Chi-restraints excluded: chain F residue 331 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 42
random chunks:
chunk 26 optimal weight: 8.9990
chunk 13 optimal weight: 0.3980
chunk 7 optimal weight: 10.0000
chunk 33 optimal weight: 4.9990
chunk 29 optimal weight: 10.0000
chunk 22 optimal weight: 9.9990
chunk 25 optimal weight: 3.9990
chunk 18 optimal weight: 4.9990
chunk 21 optimal weight: 8.9990
chunk 14 optimal weight: 5.9990
chunk 11 optimal weight: 1.9990
overall best weight: 3.2788
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
F 351 GLN
F 368 ASN
Total number of N/Q/H flips: 2
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4173 r_free = 0.4173 target = 0.154830 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.112850 restraints weight = 3599.473|
|-----------------------------------------------------------------------------|
r_work (start): 0.3676 rms_B_bonded: 1.82
r_work: 0.3558 rms_B_bonded: 1.96 restraints_weight: 0.5000
r_work: 0.3468 rms_B_bonded: 3.19 restraints_weight: 0.2500
r_work (final): 0.3468
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8800
moved from start: 0.2763
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.004 0.033 3498 Z= 0.307
Angle : 0.597 4.444 4680 Z= 0.309
Chirality : 0.050 0.131 528
Planarity : 0.003 0.021 594
Dihedral : 4.946 15.659 462
Min Nonbonded Distance : 2.587
Molprobity Statistics.
All-atom Clashscore : 2.56
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 0.91 %
Favored : 99.09 %
Rotamer:
Outliers : 2.53 %
Allowed : 21.21 %
Favored : 76.26 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: -1.88 (0.33), residues: 438
helix: None (None), residues: 0
sheet: None (None), residues: 0
loop : -1.42 (0.25), residues: 438
Max deviation from planes:
Type MaxDev MeanDev LineInFile
HIS 0.002 0.001 HIS E 329
PHE 0.009 0.002 PHE A 346
TYR 0.014 0.004 TYR B 310
ARG 0.001 0.000 ARG F 349
*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
876 Ramachandran restraints generated.
438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
876 Ramachandran restraints generated.
438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
132 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 10
poor density : 122
time to evaluate : 0.362
Fit side-chains
revert: symmetry clash
revert: symmetry clash
REVERT: A 340 LYS cc_start: 0.8384 (mtpm) cc_final: 0.8065 (mttt)
REVERT: A 375 LYS cc_start: 0.7979 (tttt) cc_final: 0.7556 (tttm)
REVERT: B 311 LYS cc_start: 0.8424 (mtmt) cc_final: 0.7218 (pptt)
REVERT: B 338 GLU cc_start: 0.8555 (tt0) cc_final: 0.8308 (tt0)
REVERT: B 340 LYS cc_start: 0.8693 (mtpm) cc_final: 0.8230 (mttt)
REVERT: B 375 LYS cc_start: 0.8363 (tttm) cc_final: 0.7880 (tppp)
REVERT: C 340 LYS cc_start: 0.8440 (mtpm) cc_final: 0.7986 (mttt)
REVERT: C 373 THR cc_start: 0.8460 (m) cc_final: 0.8034 (p)
REVERT: C 375 LYS cc_start: 0.8296 (tttt) cc_final: 0.7962 (tttm)
REVERT: D 311 LYS cc_start: 0.8408 (mtmt) cc_final: 0.7177 (pptt)
REVERT: D 340 LYS cc_start: 0.8544 (mtpm) cc_final: 0.8189 (mttt)
REVERT: D 373 THR cc_start: 0.8676 (m) cc_final: 0.8390 (p)
REVERT: E 311 LYS cc_start: 0.8173 (mtmt) cc_final: 0.7801 (mmtt)
REVERT: E 317 LYS cc_start: 0.8581 (OUTLIER) cc_final: 0.8152 (ptpp)
REVERT: E 340 LYS cc_start: 0.8409 (mtpm) cc_final: 0.8037 (mttt)
REVERT: E 349 ARG cc_start: 0.8753 (mtt180) cc_final: 0.7286 (mtp180)
REVERT: E 375 LYS cc_start: 0.8159 (tttt) cc_final: 0.7738 (tttm)
REVERT: F 311 LYS cc_start: 0.8008 (mtmt) cc_final: 0.7577 (mmtt)
REVERT: F 331 LYS cc_start: 0.9110 (OUTLIER) cc_final: 0.8826 (ttmt)
REVERT: F 340 LYS cc_start: 0.8390 (mtpm) cc_final: 0.7961 (mttt)
REVERT: F 347 LYS cc_start: 0.8783 (mptt) cc_final: 0.8518 (mptp)
REVERT: F 349 ARG cc_start: 0.8734 (mtt180) cc_final: 0.6988 (tpt90)
REVERT: F 373 THR cc_start: 0.8487 (m) cc_final: 0.8121 (p)
REVERT: F 375 LYS cc_start: 0.8053 (tttt) cc_final: 0.7846 (tttm)
outliers start: 10
outliers final: 2
residues processed: 126
average time/residue: 1.3763
time to fit residues: 177.4878
Evaluate side-chains
125 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 4
poor density : 121
time to evaluate : 0.439
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 320 SER
Chi-restraints excluded: chain B residue 320 SER
Chi-restraints excluded: chain E residue 317 LYS
Chi-restraints excluded: chain F residue 331 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 42
random chunks:
chunk 41 optimal weight: 5.9990
chunk 24 optimal weight: 4.9990
chunk 7 optimal weight: 10.0000
chunk 15 optimal weight: 10.0000
chunk 30 optimal weight: 6.9990
chunk 25 optimal weight: 0.7980
chunk 6 optimal weight: 9.9990
chunk 22 optimal weight: 7.9990
chunk 3 optimal weight: 7.9990
chunk 32 optimal weight: 6.9990
chunk 1 optimal weight: 10.0000
overall best weight: 5.1588
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
F 351 GLN
Total number of N/Q/H flips: 1
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4150 r_free = 0.4150 target = 0.151975 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.110054 restraints weight = 3618.712|
|-----------------------------------------------------------------------------|
r_work (start): 0.3641 rms_B_bonded: 1.82
r_work: 0.3525 rms_B_bonded: 1.95 restraints_weight: 0.5000
r_work: 0.3435 rms_B_bonded: 3.17 restraints_weight: 0.2500
r_work (final): 0.3435
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8832
moved from start: 0.2839
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.007 0.051 3498 Z= 0.465
Angle : 0.689 6.136 4680 Z= 0.356
Chirality : 0.053 0.138 528
Planarity : 0.003 0.015 594
Dihedral : 5.203 16.332 462
Min Nonbonded Distance : 2.546
Molprobity Statistics.
All-atom Clashscore : 2.70
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 1.14 %
Favored : 98.86 %
Rotamer:
Outliers : 2.78 %
Allowed : 21.46 %
Favored : 75.76 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: -1.84 (0.34), residues: 438
helix: None (None), residues: 0
sheet: None (None), residues: 0
loop : -1.39 (0.26), residues: 438
Max deviation from planes:
Type MaxDev MeanDev LineInFile
HIS 0.002 0.001 HIS B 329
PHE 0.011 0.002 PHE A 346
TYR 0.015 0.004 TYR C 310
ARG 0.001 0.000 ARG F 349
*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
876 Ramachandran restraints generated.
438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
876 Ramachandran restraints generated.
438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
135 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 11
poor density : 124
time to evaluate : 0.376
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: A 331 LYS cc_start: 0.9071 (OUTLIER) cc_final: 0.8609 (mtmt)
REVERT: A 340 LYS cc_start: 0.8457 (mtpm) cc_final: 0.8014 (mttp)
REVERT: A 375 LYS cc_start: 0.8018 (tttt) cc_final: 0.7641 (tttm)
REVERT: B 311 LYS cc_start: 0.8458 (mtmt) cc_final: 0.7398 (pptt)
REVERT: B 340 LYS cc_start: 0.8683 (mtpm) cc_final: 0.8245 (mttt)
REVERT: B 373 THR cc_start: 0.8820 (m) cc_final: 0.8559 (p)
REVERT: C 340 LYS cc_start: 0.8461 (mtpm) cc_final: 0.8015 (mtmt)
REVERT: C 373 THR cc_start: 0.8491 (m) cc_final: 0.8108 (p)
REVERT: C 375 LYS cc_start: 0.8300 (tttt) cc_final: 0.7977 (tttm)
REVERT: D 311 LYS cc_start: 0.8488 (mtmt) cc_final: 0.7279 (pptt)
REVERT: D 340 LYS cc_start: 0.8539 (mtpm) cc_final: 0.8201 (mttt)
REVERT: D 373 THR cc_start: 0.8682 (m) cc_final: 0.8395 (p)
REVERT: E 311 LYS cc_start: 0.8273 (mtmt) cc_final: 0.7888 (mmtt)
REVERT: E 317 LYS cc_start: 0.8549 (OUTLIER) cc_final: 0.8061 (ptpp)
REVERT: E 331 LYS cc_start: 0.9112 (OUTLIER) cc_final: 0.8735 (mtmm)
REVERT: E 340 LYS cc_start: 0.8403 (mtpm) cc_final: 0.8043 (mttt)
REVERT: E 349 ARG cc_start: 0.8767 (mtt180) cc_final: 0.7355 (mtp180)
REVERT: E 375 LYS cc_start: 0.8203 (tttt) cc_final: 0.7785 (tttm)
REVERT: F 311 LYS cc_start: 0.8134 (mtmt) cc_final: 0.7669 (mmtt)
REVERT: F 331 LYS cc_start: 0.9126 (OUTLIER) cc_final: 0.8894 (ttmt)
REVERT: F 340 LYS cc_start: 0.8398 (mtpm) cc_final: 0.8013 (mttt)
REVERT: F 347 LYS cc_start: 0.8824 (mptt) cc_final: 0.8605 (mptp)
REVERT: F 349 ARG cc_start: 0.8767 (mtt180) cc_final: 0.7022 (tpt90)
outliers start: 11
outliers final: 3
residues processed: 131
average time/residue: 1.4213
time to fit residues: 190.3128
Evaluate side-chains
132 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 7
poor density : 125
time to evaluate : 0.386
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 320 SER
Chi-restraints excluded: chain A residue 331 LYS
Chi-restraints excluded: chain B residue 320 SER
Chi-restraints excluded: chain B residue 343 LYS
Chi-restraints excluded: chain E residue 317 LYS
Chi-restraints excluded: chain E residue 331 LYS
Chi-restraints excluded: chain F residue 331 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 42
random chunks:
chunk 25 optimal weight: 4.9990
chunk 24 optimal weight: 7.9990
chunk 6 optimal weight: 10.0000
chunk 21 optimal weight: 4.9990
chunk 7 optimal weight: 10.0000
chunk 27 optimal weight: 10.0000
chunk 2 optimal weight: 0.8980
chunk 15 optimal weight: 9.9990
chunk 40 optimal weight: 4.9990
chunk 4 optimal weight: 1.9990
chunk 16 optimal weight: 0.9980
overall best weight: 2.7786
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
F 351 GLN
Total number of N/Q/H flips: 1
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4180 r_free = 0.4180 target = 0.154866 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.112899 restraints weight = 3658.033|
|-----------------------------------------------------------------------------|
r_work (start): 0.3682 rms_B_bonded: 1.81
r_work: 0.3568 rms_B_bonded: 1.94 restraints_weight: 0.5000
r_work: 0.3480 rms_B_bonded: 3.15 restraints_weight: 0.2500
r_work (final): 0.3480
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8805
moved from start: 0.2981
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.004 0.030 3498 Z= 0.262
Angle : 0.571 4.529 4680 Z= 0.293
Chirality : 0.050 0.129 528
Planarity : 0.002 0.013 594
Dihedral : 4.914 15.284 462
Min Nonbonded Distance : 2.591
Molprobity Statistics.
All-atom Clashscore : 2.28
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 0.91 %
Favored : 99.09 %
Rotamer:
Outliers : 3.28 %
Allowed : 21.21 %
Favored : 75.51 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: -1.75 (0.34), residues: 438
helix: None (None), residues: 0
sheet: None (None), residues: 0
loop : -1.33 (0.26), residues: 438
Max deviation from planes:
Type MaxDev MeanDev LineInFile
HIS 0.002 0.001 HIS B 329
PHE 0.008 0.001 PHE A 346
TYR 0.012 0.003 TYR A 310
ARG 0.001 0.000 ARG B 379
*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
876 Ramachandran restraints generated.
438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
876 Ramachandran restraints generated.
438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
136 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 13
poor density : 123
time to evaluate : 0.423
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: A 331 LYS cc_start: 0.9026 (OUTLIER) cc_final: 0.8410 (mtmt)
REVERT: A 340 LYS cc_start: 0.8366 (mtpm) cc_final: 0.8029 (mttt)
REVERT: A 375 LYS cc_start: 0.7957 (tttt) cc_final: 0.7711 (tptm)
REVERT: B 311 LYS cc_start: 0.8414 (mtmt) cc_final: 0.7336 (pptt)
REVERT: B 338 GLU cc_start: 0.8535 (tt0) cc_final: 0.8043 (tt0)
REVERT: B 340 LYS cc_start: 0.8674 (mtpm) cc_final: 0.8245 (mtmt)
REVERT: B 373 THR cc_start: 0.8783 (m) cc_final: 0.8529 (p)
REVERT: B 375 LYS cc_start: 0.8326 (tttm) cc_final: 0.7874 (tppp)
REVERT: C 340 LYS cc_start: 0.8395 (mtpm) cc_final: 0.7986 (mtmt)
REVERT: C 373 THR cc_start: 0.8480 (m) cc_final: 0.8066 (p)
REVERT: C 375 LYS cc_start: 0.8253 (tttt) cc_final: 0.7935 (tttm)
REVERT: D 311 LYS cc_start: 0.8437 (mtmt) cc_final: 0.7292 (pptt)
REVERT: D 340 LYS cc_start: 0.8501 (mtpm) cc_final: 0.8160 (mttt)
REVERT: D 373 THR cc_start: 0.8624 (m) cc_final: 0.8372 (p)
REVERT: E 311 LYS cc_start: 0.8214 (mtmt) cc_final: 0.7805 (mmtt)
REVERT: E 317 LYS cc_start: 0.8606 (OUTLIER) cc_final: 0.8128 (ptpp)
REVERT: E 331 LYS cc_start: 0.9069 (OUTLIER) cc_final: 0.8714 (mtmm)
REVERT: E 340 LYS cc_start: 0.8375 (mtpm) cc_final: 0.8046 (mttt)
REVERT: E 349 ARG cc_start: 0.8734 (mtt180) cc_final: 0.7301 (mmp-170)
REVERT: E 375 LYS cc_start: 0.8174 (tttt) cc_final: 0.7764 (tttm)
REVERT: F 311 LYS cc_start: 0.8094 (mtmt) cc_final: 0.7632 (mmtt)
REVERT: F 340 LYS cc_start: 0.8378 (mtpm) cc_final: 0.8000 (mttt)
REVERT: F 347 LYS cc_start: 0.8839 (mptt) cc_final: 0.8613 (mptp)
REVERT: F 349 ARG cc_start: 0.8759 (mtt180) cc_final: 0.7025 (tpt90)
outliers start: 13
outliers final: 2
residues processed: 128
average time/residue: 1.4140
time to fit residues: 185.1507
Evaluate side-chains
120 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 5
poor density : 115
time to evaluate : 0.462
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 331 LYS
Chi-restraints excluded: chain B residue 320 SER
Chi-restraints excluded: chain C residue 311 LYS
Chi-restraints excluded: chain E residue 317 LYS
Chi-restraints excluded: chain E residue 331 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 42
random chunks:
chunk 36 optimal weight: 9.9990
chunk 15 optimal weight: 10.0000
chunk 26 optimal weight: 5.9990
chunk 16 optimal weight: 8.9990
chunk 2 optimal weight: 2.9990
chunk 9 optimal weight: 6.9990
chunk 20 optimal weight: 5.9990
chunk 3 optimal weight: 8.9990
chunk 37 optimal weight: 2.9990
chunk 24 optimal weight: 7.9990
chunk 39 optimal weight: 6.9990
overall best weight: 4.9990
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 368 ASN
F 351 GLN
Total number of N/Q/H flips: 2
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4153 r_free = 0.4153 target = 0.152266 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.110240 restraints weight = 3651.732|
|-----------------------------------------------------------------------------|
r_work (start): 0.3644 rms_B_bonded: 1.82
r_work: 0.3531 rms_B_bonded: 1.93 restraints_weight: 0.5000
r_work: 0.3442 rms_B_bonded: 3.14 restraints_weight: 0.2500
r_work (final): 0.3442
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8830
moved from start: 0.3000
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.007 0.049 3498 Z= 0.448
Angle : 0.678 6.284 4680 Z= 0.348
Chirality : 0.052 0.137 528
Planarity : 0.003 0.017 594
Dihedral : 5.195 16.538 462
Min Nonbonded Distance : 2.554
Molprobity Statistics.
All-atom Clashscore : 2.85
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 1.14 %
Favored : 98.86 %
Rotamer:
Outliers : 2.78 %
Allowed : 22.22 %
Favored : 75.00 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: -1.77 (0.34), residues: 438
helix: None (None), residues: 0
sheet: None (None), residues: 0
loop : -1.34 (0.26), residues: 438
Max deviation from planes:
Type MaxDev MeanDev LineInFile
HIS 0.002 0.001 HIS B 329
PHE 0.011 0.002 PHE A 346
TYR 0.015 0.004 TYR C 310
ARG 0.002 0.000 ARG B 379
*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
876 Ramachandran restraints generated.
438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
876 Ramachandran restraints generated.
438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
129 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 11
poor density : 118
time to evaluate : 0.428
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: A 331 LYS cc_start: 0.9078 (OUTLIER) cc_final: 0.8616 (mtmt)
REVERT: A 340 LYS cc_start: 0.8449 (mtpm) cc_final: 0.8008 (mttp)
REVERT: A 373 THR cc_start: 0.8444 (m) cc_final: 0.7949 (p)
REVERT: A 375 LYS cc_start: 0.7996 (tttt) cc_final: 0.7616 (tttm)
REVERT: B 311 LYS cc_start: 0.8455 (mtmt) cc_final: 0.7405 (pptt)
REVERT: B 340 LYS cc_start: 0.8666 (mtpm) cc_final: 0.8258 (mttt)
REVERT: B 373 THR cc_start: 0.8789 (m) cc_final: 0.8532 (p)
REVERT: C 340 LYS cc_start: 0.8447 (mtpm) cc_final: 0.8009 (mtmt)
REVERT: C 373 THR cc_start: 0.8498 (m) cc_final: 0.8045 (p)
REVERT: C 375 LYS cc_start: 0.8291 (tttt) cc_final: 0.7978 (tttm)
REVERT: D 311 LYS cc_start: 0.8494 (mtmt) cc_final: 0.7322 (pptt)
REVERT: D 314 ASP cc_start: 0.8520 (t0) cc_final: 0.8175 (t0)
REVERT: D 340 LYS cc_start: 0.8539 (mtpm) cc_final: 0.8191 (mttt)
REVERT: D 373 THR cc_start: 0.8675 (m) cc_final: 0.8398 (p)
REVERT: E 311 LYS cc_start: 0.8279 (mtmt) cc_final: 0.7877 (mmtt)
REVERT: E 317 LYS cc_start: 0.8573 (OUTLIER) cc_final: 0.8105 (ptpp)
REVERT: E 331 LYS cc_start: 0.9104 (OUTLIER) cc_final: 0.8726 (mtmm)
REVERT: E 340 LYS cc_start: 0.8380 (mtpm) cc_final: 0.8034 (mttt)
REVERT: E 349 ARG cc_start: 0.8785 (mtt180) cc_final: 0.7358 (mtp180)
REVERT: E 375 LYS cc_start: 0.8176 (tttt) cc_final: 0.7773 (tttm)
REVERT: F 311 LYS cc_start: 0.8148 (mtmt) cc_final: 0.7676 (mmtt)
REVERT: F 340 LYS cc_start: 0.8415 (mtpm) cc_final: 0.8021 (mttt)
REVERT: F 347 LYS cc_start: 0.8848 (mptt) cc_final: 0.8641 (mptp)
REVERT: F 349 ARG cc_start: 0.8767 (mtt180) cc_final: 0.7029 (tpt90)
REVERT: F 375 LYS cc_start: 0.8060 (tttm) cc_final: 0.7658 (tttp)
outliers start: 11
outliers final: 3
residues processed: 124
average time/residue: 1.3566
time to fit residues: 172.2708
Evaluate side-chains
124 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 6
poor density : 118
time to evaluate : 0.451
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 331 LYS
Chi-restraints excluded: chain B residue 320 SER
Chi-restraints excluded: chain C residue 311 LYS
Chi-restraints excluded: chain D residue 324 SER
Chi-restraints excluded: chain E residue 317 LYS
Chi-restraints excluded: chain E residue 331 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 42
random chunks:
chunk 16 optimal weight: 5.9990
chunk 10 optimal weight: 2.9990
chunk 3 optimal weight: 4.9990
chunk 31 optimal weight: 6.9990
chunk 23 optimal weight: 3.9990
chunk 39 optimal weight: 1.9990
chunk 24 optimal weight: 0.0060
chunk 18 optimal weight: 0.8980
chunk 25 optimal weight: 5.9990
chunk 6 optimal weight: 10.0000
chunk 41 optimal weight: 4.9990
overall best weight: 1.9802
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 368 ASN
Total number of N/Q/H flips: 1
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4194 r_free = 0.4194 target = 0.155785 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.113805 restraints weight = 3634.265|
|-----------------------------------------------------------------------------|
r_work (start): 0.3695 rms_B_bonded: 1.82
r_work: 0.3583 rms_B_bonded: 1.94 restraints_weight: 0.5000
r_work: 0.3493 rms_B_bonded: 3.18 restraints_weight: 0.2500
r_work (final): 0.3493
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8796
moved from start: 0.3140
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.027 3498 Z= 0.201
Angle : 0.558 9.181 4680 Z= 0.279
Chirality : 0.050 0.174 528
Planarity : 0.002 0.014 594
Dihedral : 4.808 15.205 462
Min Nonbonded Distance : 2.591
Molprobity Statistics.
All-atom Clashscore : 2.42
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 0.91 %
Favored : 99.09 %
Rotamer:
Outliers : 1.77 %
Allowed : 23.23 %
Favored : 75.00 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: -1.69 (0.34), residues: 438
helix: None (None), residues: 0
sheet: None (None), residues: 0
loop : -1.28 (0.26), residues: 438
Max deviation from planes:
Type MaxDev MeanDev LineInFile
HIS 0.002 0.000 HIS E 329
PHE 0.008 0.001 PHE A 346
TYR 0.011 0.003 TYR B 310
ARG 0.001 0.000 ARG B 379
*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
876 Ramachandran restraints generated.
438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
876 Ramachandran restraints generated.
438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
124 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 7
poor density : 117
time to evaluate : 0.420
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: A 340 LYS cc_start: 0.8338 (mtpm) cc_final: 0.8053 (mttt)
REVERT: A 375 LYS cc_start: 0.7926 (tttt) cc_final: 0.7677 (tptm)
REVERT: B 311 LYS cc_start: 0.8420 (mtmt) cc_final: 0.7366 (pptt)
REVERT: B 338 GLU cc_start: 0.8535 (tt0) cc_final: 0.8287 (tt0)
REVERT: B 340 LYS cc_start: 0.8670 (mtpm) cc_final: 0.8242 (mtmt)
REVERT: B 375 LYS cc_start: 0.8304 (tttm) cc_final: 0.7845 (tppp)
REVERT: C 340 LYS cc_start: 0.8379 (mtpm) cc_final: 0.7972 (mtmt)
REVERT: C 373 THR cc_start: 0.8488 (m) cc_final: 0.8074 (p)
REVERT: C 375 LYS cc_start: 0.8220 (tttt) cc_final: 0.7918 (tttm)
REVERT: D 311 LYS cc_start: 0.8437 (mtmt) cc_final: 0.7315 (pptt)
REVERT: D 314 ASP cc_start: 0.8421 (t0) cc_final: 0.8112 (t0)
REVERT: D 340 LYS cc_start: 0.8482 (mtpm) cc_final: 0.8136 (mttt)
REVERT: D 373 THR cc_start: 0.8581 (m) cc_final: 0.8362 (p)
REVERT: E 311 LYS cc_start: 0.8177 (mtmt) cc_final: 0.7821 (mmtt)
REVERT: E 331 LYS cc_start: 0.9070 (OUTLIER) cc_final: 0.8728 (mtmm)
REVERT: E 340 LYS cc_start: 0.8343 (mtpm) cc_final: 0.8014 (mttp)
REVERT: E 349 ARG cc_start: 0.8743 (mtt180) cc_final: 0.7307 (mmp-170)
REVERT: E 375 LYS cc_start: 0.8146 (tttt) cc_final: 0.7752 (tttm)
REVERT: F 311 LYS cc_start: 0.8083 (mtmt) cc_final: 0.7643 (mmtt)
REVERT: F 340 LYS cc_start: 0.8370 (mtpm) cc_final: 0.7984 (mttt)
REVERT: F 347 LYS cc_start: 0.8837 (mptt) cc_final: 0.8627 (mptp)
outliers start: 7
outliers final: 3
residues processed: 121
average time/residue: 1.3648
time to fit residues: 169.0999
Evaluate side-chains
121 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 4
poor density : 117
time to evaluate : 0.426
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 308 ILE
Chi-restraints excluded: chain B residue 320 SER
Chi-restraints excluded: chain C residue 311 LYS
Chi-restraints excluded: chain E residue 331 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 42
random chunks:
chunk 22 optimal weight: 10.0000
chunk 8 optimal weight: 8.9990
chunk 27 optimal weight: 6.9990
chunk 37 optimal weight: 0.6980
chunk 39 optimal weight: 7.9990
chunk 17 optimal weight: 0.7980
chunk 14 optimal weight: 5.9990
chunk 13 optimal weight: 0.6980
chunk 3 optimal weight: 3.9990
chunk 40 optimal weight: 0.8980
chunk 21 optimal weight: 7.9990
overall best weight: 1.4182
-------------------------------------------------------------------------------
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 = 0.4212 r_free = 0.4212 target = 0.157150 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.115210 restraints weight = 3571.044|
|-----------------------------------------------------------------------------|
r_work (start): 0.3718 rms_B_bonded: 1.80
r_work: 0.3606 rms_B_bonded: 1.94 restraints_weight: 0.5000
r_work: 0.3520 rms_B_bonded: 3.17 restraints_weight: 0.2500
r_work (final): 0.3520
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8776
moved from start: 0.3260
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.002 0.023 3498 Z= 0.159
Angle : 0.528 9.756 4680 Z= 0.260
Chirality : 0.049 0.129 528
Planarity : 0.002 0.014 594
Dihedral : 4.551 14.272 462
Min Nonbonded Distance : 2.594
Molprobity Statistics.
All-atom Clashscore : 2.42
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 0.91 %
Favored : 99.09 %
Rotamer:
Outliers : 1.52 %
Allowed : 23.48 %
Favored : 75.00 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: -1.60 (0.34), residues: 438
helix: None (None), residues: 0
sheet: None (None), residues: 0
loop : -1.21 (0.26), residues: 438
Max deviation from planes:
Type MaxDev MeanDev LineInFile
HIS 0.001 0.000 HIS E 329
PHE 0.008 0.001 PHE A 346
TYR 0.010 0.002 TYR B 310
ARG 0.001 0.000 ARG D 379
*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
876 Ramachandran restraints generated.
438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
876 Ramachandran restraints generated.
438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
127 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 6
poor density : 121
time to evaluate : 0.386
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: A 331 LYS cc_start: 0.9060 (OUTLIER) cc_final: 0.8469 (mtmt)
REVERT: A 340 LYS cc_start: 0.8336 (mtpm) cc_final: 0.8044 (mttt)
REVERT: A 375 LYS cc_start: 0.7913 (tttt) cc_final: 0.7666 (tptm)
REVERT: B 311 LYS cc_start: 0.8414 (mtmt) cc_final: 0.7381 (pptt)
REVERT: B 338 GLU cc_start: 0.8526 (tt0) cc_final: 0.8130 (tt0)
REVERT: B 340 LYS cc_start: 0.8630 (mtpm) cc_final: 0.8217 (mtmt)
REVERT: B 375 LYS cc_start: 0.8272 (tttm) cc_final: 0.7824 (tppp)
REVERT: C 340 LYS cc_start: 0.8350 (mtpm) cc_final: 0.7941 (mtmt)
REVERT: C 373 THR cc_start: 0.8460 (m) cc_final: 0.8023 (p)
REVERT: C 375 LYS cc_start: 0.8154 (tttt) cc_final: 0.7848 (tttm)
REVERT: D 311 LYS cc_start: 0.8463 (mtmt) cc_final: 0.7339 (pptt)
REVERT: D 314 ASP cc_start: 0.8366 (t0) cc_final: 0.8070 (t0)
REVERT: D 340 LYS cc_start: 0.8470 (mtpm) cc_final: 0.8133 (mttt)
REVERT: D 373 THR cc_start: 0.8600 (m) cc_final: 0.8378 (p)
REVERT: E 311 LYS cc_start: 0.8192 (mtmt) cc_final: 0.7814 (mmtt)
REVERT: E 331 LYS cc_start: 0.9060 (OUTLIER) cc_final: 0.8734 (mtmm)
REVERT: E 340 LYS cc_start: 0.8353 (mtpm) cc_final: 0.8011 (mttt)
REVERT: E 349 ARG cc_start: 0.8737 (mtt180) cc_final: 0.7311 (mmp-170)
REVERT: E 375 LYS cc_start: 0.8121 (tttt) cc_final: 0.7873 (tptm)
REVERT: F 311 LYS cc_start: 0.8121 (mtmt) cc_final: 0.7651 (mmtt)
REVERT: F 340 LYS cc_start: 0.8353 (mtpm) cc_final: 0.7961 (mttt)
REVERT: F 347 LYS cc_start: 0.8815 (mptt) cc_final: 0.8586 (mptp)
outliers start: 6
outliers final: 1
residues processed: 123
average time/residue: 1.4371
time to fit residues: 180.7269
Evaluate side-chains
118 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 3
poor density : 115
time to evaluate : 0.425
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 331 LYS
Chi-restraints excluded: chain B residue 320 SER
Chi-restraints excluded: chain E residue 331 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 42
random chunks:
chunk 24 optimal weight: 6.9990
chunk 8 optimal weight: 5.9990
chunk 32 optimal weight: 2.9990
chunk 23 optimal weight: 0.7980
chunk 16 optimal weight: 0.0870
chunk 27 optimal weight: 2.9990
chunk 18 optimal weight: 7.9990
chunk 38 optimal weight: 6.9990
chunk 15 optimal weight: 3.9990
chunk 1 optimal weight: 3.9990
chunk 19 optimal weight: 8.9990
overall best weight: 2.1764
-------------------------------------------------------------------------------
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 = 0.4195 r_free = 0.4195 target = 0.155702 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.113691 restraints weight = 3636.242|
|-----------------------------------------------------------------------------|
r_work (start): 0.3706 rms_B_bonded: 1.80
r_work: 0.3593 rms_B_bonded: 1.93 restraints_weight: 0.5000
r_work: 0.3505 rms_B_bonded: 3.16 restraints_weight: 0.2500
r_work (final): 0.3505
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8791
moved from start: 0.3221
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.027 3498 Z= 0.218
Angle : 0.562 9.699 4680 Z= 0.278
Chirality : 0.049 0.155 528
Planarity : 0.002 0.014 594
Dihedral : 4.653 15.319 462
Min Nonbonded Distance : 2.593
Molprobity Statistics.
All-atom Clashscore : 2.28
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 0.91 %
Favored : 99.09 %
Rotamer:
Outliers : 1.01 %
Allowed : 24.49 %
Favored : 74.49 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: -1.62 (0.34), residues: 438
helix: None (None), residues: 0
sheet: None (None), residues: 0
loop : -1.23 (0.26), residues: 438
Max deviation from planes:
Type MaxDev MeanDev LineInFile
HIS 0.001 0.000 HIS E 329
PHE 0.008 0.001 PHE A 346
TYR 0.010 0.003 TYR B 310
ARG 0.001 0.000 ARG B 379
********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
876 Ramachandran restraints generated.
438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
876 Ramachandran restraints generated.
438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
120 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 4
poor density : 116
time to evaluate : 0.397
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: A 331 LYS cc_start: 0.9039 (OUTLIER) cc_final: 0.8434 (mtmt)
REVERT: A 340 LYS cc_start: 0.8331 (mtpm) cc_final: 0.8047 (mttt)
REVERT: A 375 LYS cc_start: 0.7927 (tttt) cc_final: 0.7669 (tptm)
REVERT: B 311 LYS cc_start: 0.8422 (mtmt) cc_final: 0.7395 (pptt)
REVERT: B 338 GLU cc_start: 0.8533 (tt0) cc_final: 0.8113 (tt0)
REVERT: B 340 LYS cc_start: 0.8650 (mtpm) cc_final: 0.8228 (mtmt)
REVERT: B 375 LYS cc_start: 0.8298 (tttm) cc_final: 0.7837 (tppp)
REVERT: C 340 LYS cc_start: 0.8375 (mtpm) cc_final: 0.7957 (mttt)
REVERT: C 373 THR cc_start: 0.8467 (m) cc_final: 0.8036 (p)
REVERT: C 375 LYS cc_start: 0.8162 (tttt) cc_final: 0.7853 (tttm)
REVERT: D 311 LYS cc_start: 0.8463 (mtmt) cc_final: 0.7391 (pptt)
REVERT: D 340 LYS cc_start: 0.8488 (mtpm) cc_final: 0.8145 (mttt)
REVERT: D 373 THR cc_start: 0.8599 (m) cc_final: 0.8353 (p)
REVERT: E 311 LYS cc_start: 0.8207 (mtmt) cc_final: 0.7803 (mmtt)
REVERT: E 331 LYS cc_start: 0.9075 (OUTLIER) cc_final: 0.8718 (mtmm)
REVERT: E 340 LYS cc_start: 0.8362 (mtpm) cc_final: 0.8009 (mttt)
REVERT: E 349 ARG cc_start: 0.8727 (mtt180) cc_final: 0.7311 (mmp-170)
REVERT: E 375 LYS cc_start: 0.8155 (tttt) cc_final: 0.7767 (tttm)
REVERT: F 311 LYS cc_start: 0.8103 (mtmt) cc_final: 0.7660 (mmtt)
REVERT: F 340 LYS cc_start: 0.8365 (mtpm) cc_final: 0.7982 (mttt)
REVERT: F 347 LYS cc_start: 0.8837 (mptt) cc_final: 0.8607 (mptp)
outliers start: 4
outliers final: 1
residues processed: 120
average time/residue: 1.3911
time to fit residues: 170.8138
Evaluate side-chains
118 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 3
poor density : 115
time to evaluate : 0.425
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 331 LYS
Chi-restraints excluded: chain B residue 320 SER
Chi-restraints excluded: chain E residue 331 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 42
random chunks:
chunk 30 optimal weight: 3.9990
chunk 35 optimal weight: 6.9990
chunk 21 optimal weight: 4.9990
chunk 7 optimal weight: 0.9980
chunk 29 optimal weight: 9.9990
chunk 16 optimal weight: 7.9990
chunk 22 optimal weight: 0.0870
chunk 40 optimal weight: 7.9990
chunk 23 optimal weight: 1.9990
chunk 15 optimal weight: 0.9990
chunk 10 optimal weight: 8.9990
overall best weight: 1.6164
-------------------------------------------------------------------------------
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 = 0.4206 r_free = 0.4206 target = 0.156719 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.114840 restraints weight = 3621.719|
|-----------------------------------------------------------------------------|
r_work (start): 0.3724 rms_B_bonded: 1.79
r_work: 0.3612 rms_B_bonded: 1.94 restraints_weight: 0.5000
r_work: 0.3525 rms_B_bonded: 3.17 restraints_weight: 0.2500
r_work (final): 0.3525
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8779
moved from start: 0.3299
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.024 3498 Z= 0.172
Angle : 0.535 9.626 4680 Z= 0.264
Chirality : 0.049 0.128 528
Planarity : 0.002 0.014 594
Dihedral : 4.525 14.655 462
Min Nonbonded Distance : 2.598
Molprobity Statistics.
All-atom Clashscore : 2.28
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 1.14 %
Favored : 98.86 %
Rotamer:
Outliers : 0.76 %
Allowed : 24.24 %
Favored : 75.00 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: -1.59 (0.34), residues: 438
helix: None (None), residues: 0
sheet: None (None), residues: 0
loop : -1.20 (0.26), residues: 438
Max deviation from planes:
Type MaxDev MeanDev LineInFile
HIS 0.001 0.000 HIS E 329
PHE 0.007 0.001 PHE A 346
TYR 0.010 0.002 TYR B 310
ARG 0.001 0.000 ARG D 379
Origin is already at (0, 0, 0), no shifts will be applied
===============================================================================
Job complete
usr+sys time: 4402.21 seconds
wall clock time: 78 minutes 15.71 seconds (4695.71 seconds total)