Starting phenix.real_space_refine
on Sat Aug 3 00:18:20 2024 by dcliebschner
===============================================================================
Processing files:
-------------------------------------------------------------------------------
Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q9k_18284/08_2024/8q9k_18284.cif
Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q9k_18284/08_2024/8q9k_18284.map
Processing PHIL parameters:
-------------------------------------------------------------------------------
Adding command-line PHIL:
-------------------------
refinement.macro_cycles=10
scattering_table=electron
resolution=3.2
write_initial_geo_file=False
Final processed PHIL parameters:
-------------------------------------------------------------------------------
data_manager {
real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q9k_18284/08_2024/8q9k_18284.map"
default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q9k_18284/08_2024/8q9k_18284.map"
model {
file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q9k_18284/08_2024/8q9k_18284.cif"
}
default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q9k_18284/08_2024/8q9k_18284.cif"
}
resolution = 3.2
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: 5
Type Number sf(0) Gaussians
S 6 5.16 5
C 1932 2.51 5
N 570 2.21 5
O 582 1.98 5
H 3216 0.53 5
sf(0) = scattering factor at diffraction angle 0.
Process input model
Symmetric amino acids flipped
Residue "A TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "A GLU 338": "OE1" <-> "OE2"
Residue "A PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "E TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "E GLU 338": "OE1" <-> "OE2"
Residue "E PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "C TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "C GLU 338": "OE1" <-> "OE2"
Residue "C PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "D TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "D GLU 338": "OE1" <-> "OE2"
Residue "D PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "B TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "B GLU 338": "OE1" <-> "OE2"
Residue "B PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "F TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "F GLU 338": "OE1" <-> "OE2"
Residue "F PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Time to flip residues: 0.01s
Monomer Library directory:
"/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib"
Total number of atoms: 6306
Number of models: 1
Model: ""
Number of chains: 6
Chain: "A"
Number of atoms: 1051
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 68, 1051
Classifications: {'peptide': 68}
Link IDs: {'PTRANS': 3, 'TRANS': 64}
Chain: "E"
Number of atoms: 1051
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 68, 1051
Classifications: {'peptide': 68}
Link IDs: {'PTRANS': 3, 'TRANS': 64}
Chain: "C"
Number of atoms: 1051
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 68, 1051
Classifications: {'peptide': 68}
Link IDs: {'PTRANS': 3, 'TRANS': 64}
Chain: "D"
Number of atoms: 1051
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 68, 1051
Classifications: {'peptide': 68}
Link IDs: {'PTRANS': 3, 'TRANS': 64}
Chain: "B"
Number of atoms: 1051
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 68, 1051
Classifications: {'peptide': 68}
Link IDs: {'PTRANS': 3, 'TRANS': 64}
Chain: "F"
Number of atoms: 1051
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 68, 1051
Classifications: {'peptide': 68}
Link IDs: {'PTRANS': 3, 'TRANS': 64}
Time building chain proxies: 3.92, per 1000 atoms: 0.62
Number of scatterers: 6306
At special positions: 0
Unit cell: (139.256, 84.048, 41.2, 90, 90, 90)
Space group: P 1 (No. 1)
Number of sites at special positions: 0
Number of scattering types: 5
Type Number sf(0)
S 6 16.00
O 582 8.00
N 570 7.00
C 1932 6.00
H 3216 1.00
sf(0) = scattering factor at diffraction angle 0.
Number of disulfides: simple=0, symmetry=0
Automatic linking
Parameters for automatic linking
Linking & cutoffs
Metal : Auto - 3.50
Amino acid : False - 1.90
Carbohydrate : True - 1.99
Ligands : True - 1.99
Small molecules : False - 1.98
Amino acid - RNA/DNA : False
Number of custom bonds: simple=0, symmetry=0
Time building additional restraints: 4.92
Conformation dependent library (CDL) restraints added in 660.8 milliseconds
792 Ramachandran restraints generated.
396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2.
Adding C-beta torsion restraints...
Number of C-beta restraints generated: 708
Finding SS restraints...
Secondary structure from input PDB file:
0 helices and 18 sheets defined
0.0% alpha, 45.3% beta
0 base pairs and 0 stacking pairs defined.
Time for finding SS restraints: 0.66
Creating SS restraints...
Processing sheet with id=AA1, first strand: chain 'E' and resid 309 through 310
removed outlier: 6.552A pdb=" N VAL A 309 " --> pdb=" O TYR F 310 " (cutoff:3.500A)
Processing sheet with id=AA2, first strand: chain 'E' and resid 313 through 314
removed outlier: 6.837A pdb=" N VAL A 313 " --> pdb=" O ASP F 314 " (cutoff:3.500A)
Processing sheet with id=AA3, first strand: chain 'E' and resid 317 through 322
removed outlier: 6.415A pdb=" N LYS A 317 " --> pdb=" O VAL F 318 " (cutoff:3.500A)
removed outlier: 8.334A pdb=" N SER F 320 " --> pdb=" O LYS A 317 " (cutoff:3.500A)
removed outlier: 6.976A pdb=" N THR A 319 " --> pdb=" O SER F 320 " (cutoff:3.500A)
removed outlier: 8.456A pdb=" N CYS F 322 " --> pdb=" O THR A 319 " (cutoff:3.500A)
removed outlier: 6.413A pdb=" N LYS A 321 " --> pdb=" O CYS F 322 " (cutoff:3.500A)
Processing sheet with id=AA4, first strand: chain 'E' and resid 325 through 330
removed outlier: 6.913A pdb=" N GLY A 326 " --> pdb=" O LEU E 325 " (cutoff:3.500A)
removed outlier: 6.795A pdb=" N ASN E 327 " --> pdb=" O GLY A 326 " (cutoff:3.500A)
removed outlier: 7.002A pdb=" N GLY F 326 " --> pdb=" O LEU A 325 " (cutoff:3.500A)
removed outlier: 6.826A pdb=" N ASN A 327 " --> pdb=" O GLY F 326 " (cutoff:3.500A)
Processing sheet with id=AA5, first strand: chain 'E' and resid 337 through 341
removed outlier: 6.613A pdb=" N VAL A 337 " --> pdb=" O GLU E 338 " (cutoff:3.500A)
removed outlier: 8.198A pdb=" N LYS E 340 " --> pdb=" O VAL A 337 " (cutoff:3.500A)
removed outlier: 6.625A pdb=" N VAL A 339 " --> pdb=" O LYS E 340 " (cutoff:3.500A)
Processing sheet with id=AA6, first strand: chain 'E' and resid 345 through 346
removed outlier: 6.648A pdb=" N ASP A 345 " --> pdb=" O PHE F 346 " (cutoff:3.500A)
Processing sheet with id=AA7, first strand: chain 'E' and resid 350 through 354
removed outlier: 6.381A pdb=" N VAL A 350 " --> pdb=" O GLN E 351 " (cutoff:3.500A)
removed outlier: 8.299A pdb=" N LYS E 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A)
removed outlier: 6.557A pdb=" N SER A 352 " --> pdb=" O LYS E 353 " (cutoff:3.500A)
Processing sheet with id=AA8, first strand: chain 'E' and resid 357 through 362
removed outlier: 6.440A pdb=" N ASP A 358 " --> pdb=" O ASN F 359 " (cutoff:3.500A)
removed outlier: 8.061A pdb=" N THR F 361 " --> pdb=" O ASP A 358 " (cutoff:3.500A)
removed outlier: 6.560A pdb=" N ILE A 360 " --> pdb=" O THR F 361 " (cutoff:3.500A)
Processing sheet with id=AA9, first strand: chain 'E' and resid 369 through 374
removed outlier: 6.568A pdb=" N LYS A 369 " --> pdb=" O LYS F 370 " (cutoff:3.500A)
removed outlier: 8.080A pdb=" N GLU F 372 " --> pdb=" O LYS A 369 " (cutoff:3.500A)
removed outlier: 6.305A pdb=" N ILE A 371 " --> pdb=" O GLU F 372 " (cutoff:3.500A)
removed outlier: 8.130A pdb=" N HIS F 374 " --> pdb=" O ILE A 371 " (cutoff:3.500A)
removed outlier: 6.456A pdb=" N THR A 373 " --> pdb=" O HIS F 374 " (cutoff:3.500A)
Processing sheet with id=AB1, first strand: chain 'C' and resid 309 through 310
removed outlier: 6.488A pdb=" N VAL C 309 " --> pdb=" O TYR D 310 " (cutoff:3.500A)
removed outlier: 6.535A pdb=" N VAL D 309 " --> pdb=" O TYR B 310 " (cutoff:3.500A)
No H-bonds generated for sheet with id=AB1
Processing sheet with id=AB2, first strand: chain 'C' and resid 313 through 314
removed outlier: 6.753A pdb=" N VAL C 313 " --> pdb=" O ASP D 314 " (cutoff:3.500A)
removed outlier: 6.848A pdb=" N VAL D 313 " --> pdb=" O ASP B 314 " (cutoff:3.500A)
No H-bonds generated for sheet with id=AB2
Processing sheet with id=AB3, first strand: chain 'C' and resid 317 through 322
removed outlier: 6.424A pdb=" N LYS C 317 " --> pdb=" O VAL D 318 " (cutoff:3.500A)
removed outlier: 8.295A pdb=" N SER D 320 " --> pdb=" O LYS C 317 " (cutoff:3.500A)
removed outlier: 7.004A pdb=" N THR C 319 " --> pdb=" O SER D 320 " (cutoff:3.500A)
removed outlier: 8.444A pdb=" N CYS D 322 " --> pdb=" O THR C 319 " (cutoff:3.500A)
removed outlier: 6.388A pdb=" N LYS C 321 " --> pdb=" O CYS D 322 " (cutoff:3.500A)
removed outlier: 6.442A pdb=" N LYS D 317 " --> pdb=" O VAL B 318 " (cutoff:3.500A)
removed outlier: 8.336A pdb=" N SER B 320 " --> pdb=" O LYS D 317 " (cutoff:3.500A)
removed outlier: 7.015A pdb=" N THR D 319 " --> pdb=" O SER B 320 " (cutoff:3.500A)
removed outlier: 8.501A pdb=" N CYS B 322 " --> pdb=" O THR D 319 " (cutoff:3.500A)
removed outlier: 6.382A pdb=" N LYS D 321 " --> pdb=" O CYS B 322 " (cutoff:3.500A)
No H-bonds generated for sheet with id=AB3
Processing sheet with id=AB4, first strand: chain 'C' and resid 325 through 330
removed outlier: 8.850A pdb=" N LEU C 325 " --> pdb=" O GLY D 326 " (cutoff:3.500A)
removed outlier: 9.832A pdb=" N ILE D 328 " --> pdb=" O LEU C 325 " (cutoff:3.500A)
removed outlier: 6.901A pdb=" N ASN C 327 " --> pdb=" O ILE D 328 " (cutoff:3.500A)
removed outlier: 7.893A pdb=" N HIS D 330 " --> pdb=" O ASN C 327 " (cutoff:3.500A)
removed outlier: 6.365A pdb=" N HIS C 329 " --> pdb=" O HIS D 330 " (cutoff:3.500A)
removed outlier: 8.894A pdb=" N LEU D 325 " --> pdb=" O GLY B 326 " (cutoff:3.500A)
removed outlier: 9.761A pdb=" N ILE B 328 " --> pdb=" O LEU D 325 " (cutoff:3.500A)
removed outlier: 6.878A pdb=" N ASN D 327 " --> pdb=" O ILE B 328 " (cutoff:3.500A)
removed outlier: 7.921A pdb=" N HIS B 330 " --> pdb=" O ASN D 327 " (cutoff:3.500A)
removed outlier: 6.402A pdb=" N HIS D 329 " --> pdb=" O HIS B 330 " (cutoff:3.500A)
No H-bonds generated for sheet with id=AB4
Processing sheet with id=AB5, first strand: chain 'C' and resid 337 through 340
Processing sheet with id=AB6, first strand: chain 'C' and resid 345 through 346
removed outlier: 6.564A pdb=" N ASP C 345 " --> pdb=" O PHE D 346 " (cutoff:3.500A)
removed outlier: 6.628A pdb=" N ASP D 345 " --> pdb=" O PHE B 346 " (cutoff:3.500A)
No H-bonds generated for sheet with id=AB6
Processing sheet with id=AB7, first strand: chain 'C' and resid 350 through 354
Processing sheet with id=AB8, first strand: chain 'C' and resid 357 through 362
removed outlier: 6.440A pdb=" N ASP C 358 " --> pdb=" O ASN D 359 " (cutoff:3.500A)
removed outlier: 8.112A pdb=" N THR D 361 " --> pdb=" O ASP C 358 " (cutoff:3.500A)
removed outlier: 6.594A pdb=" N ILE C 360 " --> pdb=" O THR D 361 " (cutoff:3.500A)
removed outlier: 6.403A pdb=" N ASP D 358 " --> pdb=" O ASN B 359 " (cutoff:3.500A)
removed outlier: 8.042A pdb=" N THR B 361 " --> pdb=" O ASP D 358 " (cutoff:3.500A)
removed outlier: 6.563A pdb=" N ILE D 360 " --> pdb=" O THR B 361 " (cutoff:3.500A)
No H-bonds generated for sheet with id=AB8
Processing sheet with id=AB9, first strand: chain 'C' and resid 369 through 374
removed outlier: 6.501A pdb=" N LYS C 369 " --> pdb=" O LYS D 370 " (cutoff:3.500A)
removed outlier: 7.998A pdb=" N GLU D 372 " --> pdb=" O LYS C 369 " (cutoff:3.500A)
removed outlier: 6.356A pdb=" N ILE C 371 " --> pdb=" O GLU D 372 " (cutoff:3.500A)
removed outlier: 8.098A pdb=" N HIS D 374 " --> pdb=" O ILE C 371 " (cutoff:3.500A)
removed outlier: 6.351A pdb=" N THR C 373 " --> pdb=" O HIS D 374 " (cutoff:3.500A)
removed outlier: 6.549A pdb=" N LYS D 369 " --> pdb=" O LYS B 370 " (cutoff:3.500A)
removed outlier: 8.092A pdb=" N GLU B 372 " --> pdb=" O LYS D 369 " (cutoff:3.500A)
removed outlier: 6.282A pdb=" N ILE D 371 " --> pdb=" O GLU B 372 " (cutoff:3.500A)
removed outlier: 8.104A pdb=" N HIS B 374 " --> pdb=" O ILE D 371 " (cutoff:3.500A)
removed outlier: 6.315A pdb=" N THR D 373 " --> pdb=" O HIS B 374 " (cutoff:3.500A)
No H-bonds generated for sheet with id=AB9
47 hydrogen bonds defined for protein.
141 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: 1.91
Time building geometry restraints manager: 5.21 seconds
NOTE: a complete listing of the restraints can be obtained by requesting
output of .geo file.
Histogram of bond lengths:
0.95 - 1.12: 3210
1.12 - 1.29: 522
1.29 - 1.46: 891
1.46 - 1.63: 1725
1.63 - 1.81: 6
Bond restraints: 6354
Sorted by residual:
bond pdb=" N SER C 324 "
pdb=" H SER C 324 "
ideal model delta sigma weight residual
0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01
bond pdb=" NE ARG A 349 "
pdb=" HE ARG A 349 "
ideal model delta sigma weight residual
0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01
bond pdb=" CD2 PHE E 346 "
pdb=" HD2 PHE E 346 "
ideal model delta sigma weight residual
0.930 1.081 -0.151 2.00e-02 2.50e+03 5.69e+01
bond pdb=" N GLU F 338 "
pdb=" H GLU F 338 "
ideal model delta sigma weight residual
0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01
bond pdb=" N LYS C 311 "
pdb=" H LYS C 311 "
ideal model delta sigma weight residual
0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01
... (remaining 6349 not shown)
Histogram of bond angle deviations from ideal:
97.00 - 103.39: 44
103.39 - 109.78: 5471
109.78 - 116.17: 2920
116.17 - 122.56: 2504
122.56 - 128.96: 665
Bond angle restraints: 11604
Sorted by residual:
angle pdb=" N GLY D 326 "
pdb=" CA GLY D 326 "
pdb=" C GLY D 326 "
ideal model delta sigma weight residual
110.69 117.98 -7.29 1.33e+00 5.65e-01 3.00e+01
angle pdb=" C LYS C 340 "
pdb=" N SER C 341 "
pdb=" H SER C 341 "
ideal model delta sigma weight residual
123.83 108.35 15.48 3.00e+00 1.11e-01 2.66e+01
angle pdb=" C LYS B 340 "
pdb=" N SER B 341 "
pdb=" H SER B 341 "
ideal model delta sigma weight residual
123.83 108.63 15.20 3.00e+00 1.11e-01 2.57e+01
angle pdb=" N ARG D 349 "
pdb=" CA ARG D 349 "
pdb=" C ARG D 349 "
ideal model delta sigma weight residual
110.35 117.23 -6.88 1.36e+00 5.41e-01 2.56e+01
angle pdb=" C LYS D 340 "
pdb=" N SER D 341 "
pdb=" H SER D 341 "
ideal model delta sigma weight residual
123.83 108.95 14.88 3.00e+00 1.11e-01 2.46e+01
... (remaining 11599 not shown)
Histogram of dihedral angle deviations from ideal:
0.00 - 13.63: 2579
13.63 - 27.26: 156
27.26 - 40.89: 58
40.89 - 54.52: 42
54.52 - 68.15: 87
Dihedral angle restraints: 2922
sinusoidal: 1680
harmonic: 1242
Sorted by residual:
dihedral pdb=" C ARG B 349 "
pdb=" N ARG B 349 "
pdb=" CA ARG B 349 "
pdb=" CB ARG B 349 "
ideal model delta harmonic sigma weight residual
-122.60 -133.04 10.44 0 2.50e+00 1.60e-01 1.75e+01
dihedral pdb=" C ARG F 349 "
pdb=" N ARG F 349 "
pdb=" CA ARG F 349 "
pdb=" CB ARG F 349 "
ideal model delta harmonic sigma weight residual
-122.60 -132.63 10.03 0 2.50e+00 1.60e-01 1.61e+01
dihedral pdb=" N ARG B 349 "
pdb=" C ARG B 349 "
pdb=" CA ARG B 349 "
pdb=" CB ARG B 349 "
ideal model delta harmonic sigma weight residual
122.80 131.83 -9.03 0 2.50e+00 1.60e-01 1.31e+01
... (remaining 2919 not shown)
Histogram of chiral volume deviations from ideal:
0.000 - 0.085: 323
0.085 - 0.169: 124
0.169 - 0.254: 16
0.254 - 0.338: 2
0.338 - 0.423: 3
Chirality restraints: 468
Sorted by residual:
chirality pdb=" CA ARG B 349 "
pdb=" N ARG B 349 "
pdb=" C ARG B 349 "
pdb=" CB ARG B 349 "
both_signs ideal model delta sigma weight residual
False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.47e+00
chirality pdb=" CA ARG F 349 "
pdb=" N ARG F 349 "
pdb=" C ARG F 349 "
pdb=" CB ARG F 349 "
both_signs ideal model delta sigma weight residual
False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.02e+00
chirality pdb=" CA ARG D 349 "
pdb=" N ARG D 349 "
pdb=" C ARG D 349 "
pdb=" CB ARG D 349 "
both_signs ideal model delta sigma weight residual
False 2.51 2.14 0.38 2.00e-01 2.50e+01 3.52e+00
... (remaining 465 not shown)
Planarity restraints: 918
Sorted by residual:
delta sigma weight rms_deltas residual
plane pdb=" C LYS B 340 " 0.046 2.00e-02 2.50e+03 8.41e-02 7.07e+01
pdb=" N SER B 341 " -0.145 2.00e-02 2.50e+03
pdb=" CA SER B 341 " 0.045 2.00e-02 2.50e+03
pdb=" H SER B 341 " 0.055 2.00e-02 2.50e+03
delta sigma weight rms_deltas residual
plane pdb=" C LYS C 340 " 0.044 2.00e-02 2.50e+03 7.88e-02 6.21e+01
pdb=" N SER C 341 " -0.136 2.00e-02 2.50e+03
pdb=" CA SER C 341 " 0.042 2.00e-02 2.50e+03
pdb=" H SER C 341 " 0.051 2.00e-02 2.50e+03
delta sigma weight rms_deltas residual
plane pdb=" C LYS D 340 " 0.041 2.00e-02 2.50e+03 7.42e-02 5.51e+01
pdb=" N SER D 341 " -0.128 2.00e-02 2.50e+03
pdb=" CA SER D 341 " 0.039 2.00e-02 2.50e+03
pdb=" H SER D 341 " 0.048 2.00e-02 2.50e+03
... (remaining 915 not shown)
Histogram of nonbonded interaction distances:
1.57 - 2.18: 475
2.18 - 2.78: 10985
2.78 - 3.39: 16438
3.39 - 3.99: 21542
3.99 - 4.60: 30268
Nonbonded interactions: 79708
Sorted by model distance:
nonbonded pdb=" OD1 ASP E 314 "
pdb=" HG SER E 316 "
model vdw
1.571 2.450
nonbonded pdb=" OD1 ASP C 314 "
pdb=" HG SER C 316 "
model vdw
1.573 2.450
nonbonded pdb=" OD1 ASP D 314 "
pdb=" HG SER D 316 "
model vdw
1.579 2.450
nonbonded pdb=" OD1 ASP A 314 "
pdb=" HG SER A 316 "
model vdw
1.583 2.450
nonbonded pdb=" OD1 ASP F 314 "
pdb=" HG SER F 316 "
model vdw
1.597 2.450
... (remaining 79703 not shown)
NOTE: a complete listing of the restraints can be obtained by requesting
output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
reference = chain 'A'
selection = chain 'B'
selection = chain 'C'
selection = chain 'D'
selection = chain 'E'
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: 2.640
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: 0.100
Extract box with map and model: 0.270
Check model and map are aligned: 0.050
Set scattering table: 0.050
Process input model: 24.810
Find NCS groups from input model: 0.150
Set up NCS constraints: 0.020
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:2.740
Set ADP refinement strategy: 0.000
Make a string to write initial .geo file:0.000
Internal consistency checks: 0.000
Total: 30.830
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8005
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 : 0.011 0.038 3138 Z= 0.741
Angle : 1.997 7.291 4194 Z= 1.327
Chirality : 0.088 0.423 468
Planarity : 0.011 0.092 534
Dihedral : 9.094 65.306 1212
Min Nonbonded Distance : 2.527
Molprobity Statistics.
All-atom Clashscore : 0.79
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 5.05 %
Favored : 94.95 %
Rotamer:
Outliers : 0.00 %
Allowed : 0.00 %
Favored : 100.00 %
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: -1.94 (0.34), residues: 396
helix: None (None), residues: 0
sheet: None (None), residues: 0
loop : -1.47 (0.26), residues: 396
Max deviation from planes:
Type MaxDev MeanDev LineInFile
HIS 0.016 0.003 HIS B 330
PHE 0.037 0.018 PHE D 346
TYR 0.049 0.014 TYR D 310
ARG 0.007 0.001 ARG F 349
*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
792 Ramachandran restraints generated.
396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
792 Ramachandran restraints generated.
396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
151 residues out of total 354 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 151
time to evaluate : 0.513
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: E 317 LYS cc_start: 0.8756 (pttt) cc_final: 0.7914 (mmmt)
REVERT: C 317 LYS cc_start: 0.8615 (pttt) cc_final: 0.7747 (mmtt)
REVERT: C 345 ASP cc_start: 0.7730 (t0) cc_final: 0.7432 (t70)
REVERT: F 340 LYS cc_start: 0.7983 (ttmt) cc_final: 0.7594 (tttm)
outliers start: 0
outliers final: 0
residues processed: 151
average time/residue: 0.5712
time to fit residues: 95.3644
Evaluate side-chains
90 residues out of total 354 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 90
time to evaluate : 0.484
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 36
random chunks:
chunk 30 optimal weight: 5.9990
chunk 27 optimal weight: 0.9990
chunk 15 optimal weight: 1.9990
chunk 9 optimal weight: 1.9990
chunk 18 optimal weight: 5.9990
chunk 14 optimal weight: 0.8980
chunk 28 optimal weight: 0.9990
chunk 10 optimal weight: 2.9990
chunk 17 optimal weight: 2.9990
chunk 21 optimal weight: 0.9990
chunk 32 optimal weight: 4.9990
overall best weight: 1.1788
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8081
moved from start: 0.5172
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.002 0.023 3138 Z= 0.170
Angle : 0.549 4.293 4194 Z= 0.288
Chirality : 0.052 0.135 468
Planarity : 0.004 0.032 534
Dihedral : 5.534 19.103 414
Min Nonbonded Distance : 2.560
Molprobity Statistics.
All-atom Clashscore : 1.75
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 3.54 %
Favored : 96.46 %
Rotamer:
Outliers : 1.13 %
Allowed : 7.63 %
Favored : 91.24 %
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: -1.78 (0.34), residues: 396
helix: None (None), residues: 0
sheet: None (None), residues: 0
loop : -1.35 (0.26), residues: 396
Max deviation from planes:
Type MaxDev MeanDev LineInFile
HIS 0.002 0.000 HIS D 330
PHE 0.006 0.002 PHE D 346
TYR 0.003 0.001 TYR E 310
ARG 0.001 0.000 ARG C 349
*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
792 Ramachandran restraints generated.
396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
792 Ramachandran restraints generated.
396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
108 residues out of total 354 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 4
poor density : 104
time to evaluate : 0.713
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: E 317 LYS cc_start: 0.8709 (pttt) cc_final: 0.7672 (mmmt)
REVERT: C 317 LYS cc_start: 0.8483 (pttt) cc_final: 0.7451 (mmmt)
REVERT: D 345 ASP cc_start: 0.7853 (t70) cc_final: 0.7466 (t0)
REVERT: F 369 LYS cc_start: 0.8757 (mtmt) cc_final: 0.8508 (mtmm)
outliers start: 4
outliers final: 4
residues processed: 106
average time/residue: 0.4901
time to fit residues: 59.8121
Evaluate side-chains
91 residues out of total 354 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 4
poor density : 87
time to evaluate : 0.485
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue 313 VAL
Chi-restraints excluded: chain B residue 356 SER
Chi-restraints excluded: chain F residue 309 VAL
Chi-restraints excluded: chain F residue 356 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 36
random chunks:
chunk 18 optimal weight: 9.9990
chunk 10 optimal weight: 3.9990
chunk 27 optimal weight: 4.9990
chunk 22 optimal weight: 3.9990
chunk 9 optimal weight: 3.9990
chunk 32 optimal weight: 0.9980
chunk 35 optimal weight: 4.9990
chunk 29 optimal weight: 0.8980
chunk 11 optimal weight: 4.9990
chunk 26 optimal weight: 0.8980
chunk 24 optimal weight: 2.9990
overall best weight: 1.9584
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8132
moved from start: 0.5797
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.023 3138 Z= 0.217
Angle : 0.531 4.078 4194 Z= 0.276
Chirality : 0.052 0.131 468
Planarity : 0.004 0.035 534
Dihedral : 5.148 18.733 414
Min Nonbonded Distance : 2.415
Molprobity Statistics.
All-atom Clashscore : 2.86
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 3.28 %
Favored : 96.72 %
Rotamer:
Outliers : 2.26 %
Allowed : 7.91 %
Favored : 89.83 %
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: -1.67 (0.34), residues: 396
helix: None (None), residues: 0
sheet: None (None), residues: 0
loop : -1.27 (0.26), residues: 396
Max deviation from planes:
Type MaxDev MeanDev LineInFile
HIS 0.003 0.001 HIS A 329
PHE 0.005 0.001 PHE E 346
TYR 0.004 0.001 TYR E 310
ARG 0.001 0.000 ARG D 349
*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
792 Ramachandran restraints generated.
396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
792 Ramachandran restraints generated.
396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
95 residues out of total 354 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 8
poor density : 87
time to evaluate : 0.547
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: E 317 LYS cc_start: 0.8688 (pttt) cc_final: 0.7642 (mmmt)
REVERT: D 345 ASP cc_start: 0.7850 (t0) cc_final: 0.7527 (t0)
REVERT: F 345 ASP cc_start: 0.7755 (t0) cc_final: 0.7221 (t0)
REVERT: F 347 LYS cc_start: 0.8645 (mmtt) cc_final: 0.8418 (mmtt)
outliers start: 8
outliers final: 8
residues processed: 90
average time/residue: 0.4068
time to fit residues: 42.2234
Evaluate side-chains
89 residues out of total 354 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 8
poor density : 81
time to evaluate : 0.560
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 308 ILE
Chi-restraints excluded: chain E residue 309 VAL
Chi-restraints excluded: chain E residue 356 SER
Chi-restraints excluded: chain C residue 309 VAL
Chi-restraints excluded: chain D residue 308 ILE
Chi-restraints excluded: chain D residue 348 ASP
Chi-restraints excluded: chain B residue 356 SER
Chi-restraints excluded: chain F residue 309 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 36
random chunks:
chunk 16 optimal weight: 5.9990
chunk 3 optimal weight: 0.9980
chunk 15 optimal weight: 2.9990
chunk 21 optimal weight: 2.9990
chunk 32 optimal weight: 0.5980
chunk 34 optimal weight: 0.7980
chunk 17 optimal weight: 3.9990
chunk 31 optimal weight: 4.9990
chunk 9 optimal weight: 0.9990
chunk 28 optimal weight: 5.9990
chunk 19 optimal weight: 9.9990
overall best weight: 1.2784
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
E 336 GLN
Total number of N/Q/H flips: 1
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8107
moved from start: 0.6048
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.002 0.021 3138 Z= 0.168
Angle : 0.499 4.368 4194 Z= 0.258
Chirality : 0.052 0.133 468
Planarity : 0.004 0.038 534
Dihedral : 4.875 17.318 414
Min Nonbonded Distance : 2.491
Molprobity Statistics.
All-atom Clashscore : 2.38
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 3.54 %
Favored : 96.46 %
Rotamer:
Outliers : 1.69 %
Allowed : 9.04 %
Favored : 89.27 %
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: -1.64 (0.34), residues: 396
helix: None (None), residues: 0
sheet: None (None), residues: 0
loop : -1.24 (0.26), residues: 396
Max deviation from planes:
Type MaxDev MeanDev LineInFile
HIS 0.002 0.001 HIS A 329
PHE 0.004 0.001 PHE C 346
TYR 0.004 0.001 TYR E 310
ARG 0.001 0.000 ARG D 349
*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
792 Ramachandran restraints generated.
396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
792 Ramachandran restraints generated.
396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
92 residues out of total 354 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 6
poor density : 86
time to evaluate : 0.539
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: E 317 LYS cc_start: 0.8667 (pttt) cc_final: 0.7625 (mmmt)
REVERT: E 349 ARG cc_start: 0.7779 (ptp-170) cc_final: 0.5580 (mmm-85)
REVERT: C 349 ARG cc_start: 0.7826 (ptp-170) cc_final: 0.5615 (mmm-85)
outliers start: 6
outliers final: 6
residues processed: 89
average time/residue: 0.4270
time to fit residues: 43.6035
Evaluate side-chains
89 residues out of total 354 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 6
poor density : 83
time to evaluate : 0.485
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue 356 SER
Chi-restraints excluded: chain D residue 348 ASP
Chi-restraints excluded: chain D residue 356 SER
Chi-restraints excluded: chain B residue 356 SER
Chi-restraints excluded: chain F residue 309 VAL
Chi-restraints excluded: chain F residue 356 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 36
random chunks:
chunk 0 optimal weight: 10.0000
chunk 25 optimal weight: 6.9990
chunk 14 optimal weight: 4.9990
chunk 29 optimal weight: 3.9990
chunk 24 optimal weight: 0.7980
chunk 17 optimal weight: 0.7980
chunk 31 optimal weight: 0.9990
chunk 8 optimal weight: 4.9990
chunk 11 optimal weight: 3.9990
chunk 6 optimal weight: 6.9990
chunk 20 optimal weight: 0.7980
overall best weight: 1.4784
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8120
moved from start: 0.6180
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.029 3138 Z= 0.189
Angle : 0.497 4.132 4194 Z= 0.256
Chirality : 0.051 0.133 468
Planarity : 0.004 0.038 534
Dihedral : 4.751 16.682 414
Min Nonbonded Distance : 2.525
Molprobity Statistics.
All-atom Clashscore : 2.54
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 3.54 %
Favored : 96.46 %
Rotamer:
Outliers : 1.98 %
Allowed : 10.73 %
Favored : 87.29 %
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: -1.58 (0.34), residues: 396
helix: None (None), residues: 0
sheet: None (None), residues: 0
loop : -1.20 (0.26), residues: 396
Max deviation from planes:
Type MaxDev MeanDev LineInFile
HIS 0.002 0.001 HIS A 329
PHE 0.004 0.001 PHE E 346
TYR 0.004 0.001 TYR E 310
ARG 0.001 0.000 ARG D 349
*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
792 Ramachandran restraints generated.
396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
792 Ramachandran restraints generated.
396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
91 residues out of total 354 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 7
poor density : 84
time to evaluate : 0.531
Fit side-chains
revert: symmetry clash
revert: symmetry clash
REVERT: E 317 LYS cc_start: 0.8709 (pttt) cc_final: 0.7664 (mmmt)
REVERT: E 349 ARG cc_start: 0.7826 (ptp-170) cc_final: 0.5665 (mmm-85)
REVERT: C 345 ASP cc_start: 0.8049 (t0) cc_final: 0.7689 (t0)
REVERT: C 349 ARG cc_start: 0.7854 (ptp-170) cc_final: 0.5769 (mmm-85)
REVERT: F 345 ASP cc_start: 0.7799 (t0) cc_final: 0.7291 (t0)
outliers start: 7
outliers final: 7
residues processed: 88
average time/residue: 0.4590
time to fit residues: 46.2904
Evaluate side-chains
88 residues out of total 354 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 7
poor density : 81
time to evaluate : 0.543
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue 309 VAL
Chi-restraints excluded: chain E residue 356 SER
Chi-restraints excluded: chain D residue 348 ASP
Chi-restraints excluded: chain D residue 356 SER
Chi-restraints excluded: chain B residue 356 SER
Chi-restraints excluded: chain F residue 309 VAL
Chi-restraints excluded: chain F residue 356 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 36
random chunks:
chunk 8 optimal weight: 0.9990
chunk 34 optimal weight: 3.9990
chunk 28 optimal weight: 0.7980
chunk 16 optimal weight: 5.9990
chunk 2 optimal weight: 0.7980
chunk 11 optimal weight: 3.9990
chunk 18 optimal weight: 10.0000
chunk 33 optimal weight: 1.9990
chunk 3 optimal weight: 0.8980
chunk 19 optimal weight: 10.0000
chunk 25 optimal weight: 2.9990
overall best weight: 1.0984
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8104
moved from start: 0.6295
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.002 0.024 3138 Z= 0.166
Angle : 0.489 4.341 4194 Z= 0.252
Chirality : 0.051 0.132 468
Planarity : 0.004 0.040 534
Dihedral : 4.603 16.211 414
Min Nonbonded Distance : 2.535
Molprobity Statistics.
All-atom Clashscore : 2.70
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 4.04 %
Favored : 95.96 %
Rotamer:
Outliers : 1.98 %
Allowed : 12.43 %
Favored : 85.59 %
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: -1.56 (0.34), residues: 396
helix: None (None), residues: 0
sheet: None (None), residues: 0
loop : -1.18 (0.26), residues: 396
Max deviation from planes:
Type MaxDev MeanDev LineInFile
HIS 0.002 0.000 HIS B 329
PHE 0.003 0.001 PHE D 346
TYR 0.004 0.001 TYR E 310
ARG 0.003 0.000 ARG D 349
*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
792 Ramachandran restraints generated.
396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
792 Ramachandran restraints generated.
396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
90 residues out of total 354 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 7
poor density : 83
time to evaluate : 0.592
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: E 317 LYS cc_start: 0.8703 (pttt) cc_final: 0.7669 (mmmt)
REVERT: E 349 ARG cc_start: 0.7765 (ptp-170) cc_final: 0.5950 (mmm160)
outliers start: 7
outliers final: 7
residues processed: 87
average time/residue: 0.4363
time to fit residues: 43.9226
Evaluate side-chains
85 residues out of total 354 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 7
poor density : 78
time to evaluate : 0.534
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue 309 VAL
Chi-restraints excluded: chain E residue 356 SER
Chi-restraints excluded: chain C residue 309 VAL
Chi-restraints excluded: chain D residue 348 ASP
Chi-restraints excluded: chain D residue 356 SER
Chi-restraints excluded: chain B residue 356 SER
Chi-restraints excluded: chain F residue 356 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 36
random chunks:
chunk 19 optimal weight: 10.0000
chunk 29 optimal weight: 0.8980
chunk 34 optimal weight: 4.9990
chunk 21 optimal weight: 4.9990
chunk 16 optimal weight: 4.9990
chunk 13 optimal weight: 1.9990
chunk 20 optimal weight: 0.9980
chunk 10 optimal weight: 0.8980
chunk 6 optimal weight: 10.0000
chunk 22 optimal weight: 0.8980
chunk 23 optimal weight: 0.7980
overall best weight: 0.8980
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8090
moved from start: 0.6432
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.002 0.027 3138 Z= 0.157
Angle : 0.476 4.327 4194 Z= 0.244
Chirality : 0.051 0.134 468
Planarity : 0.004 0.038 534
Dihedral : 4.417 15.824 414
Min Nonbonded Distance : 2.534
Molprobity Statistics.
All-atom Clashscore : 2.54
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 3.54 %
Favored : 96.46 %
Rotamer:
Outliers : 2.26 %
Allowed : 11.86 %
Favored : 85.88 %
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: -1.46 (0.35), residues: 396
helix: None (None), residues: 0
sheet: None (None), residues: 0
loop : -1.10 (0.27), residues: 396
Max deviation from planes:
Type MaxDev MeanDev LineInFile
HIS 0.001 0.000 HIS A 329
PHE 0.002 0.001 PHE D 346
TYR 0.004 0.001 TYR E 310
ARG 0.002 0.000 ARG D 349
*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
792 Ramachandran restraints generated.
396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
792 Ramachandran restraints generated.
396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
94 residues out of total 354 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 8
poor density : 86
time to evaluate : 0.554
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: E 317 LYS cc_start: 0.8670 (pttt) cc_final: 0.7603 (mmmt)
REVERT: E 349 ARG cc_start: 0.7741 (ptp-170) cc_final: 0.5696 (mmp80)
REVERT: B 372 GLU cc_start: 0.7358 (mm-30) cc_final: 0.6984 (mm-30)
REVERT: F 347 LYS cc_start: 0.8602 (mmtt) cc_final: 0.8376 (mmtt)
outliers start: 8
outliers final: 8
residues processed: 91
average time/residue: 0.4329
time to fit residues: 45.5083
Evaluate side-chains
92 residues out of total 354 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 8
poor density : 84
time to evaluate : 0.564
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue 309 VAL
Chi-restraints excluded: chain E residue 356 SER
Chi-restraints excluded: chain C residue 309 VAL
Chi-restraints excluded: chain D residue 348 ASP
Chi-restraints excluded: chain D residue 356 SER
Chi-restraints excluded: chain B residue 356 SER
Chi-restraints excluded: chain F residue 309 VAL
Chi-restraints excluded: chain F residue 356 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 36
random chunks:
chunk 17 optimal weight: 3.9990
chunk 3 optimal weight: 5.9990
chunk 27 optimal weight: 3.9990
chunk 31 optimal weight: 2.9990
chunk 33 optimal weight: 1.9990
chunk 30 optimal weight: 1.9990
chunk 32 optimal weight: 1.9990
chunk 19 optimal weight: 9.9990
chunk 14 optimal weight: 0.7980
chunk 25 optimal weight: 4.9990
chunk 9 optimal weight: 0.9990
overall best weight: 1.5588
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8114
moved from start: 0.6467
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.036 3138 Z= 0.198
Angle : 0.504 4.325 4194 Z= 0.261
Chirality : 0.051 0.134 468
Planarity : 0.004 0.038 534
Dihedral : 4.560 15.333 414
Min Nonbonded Distance : 2.533
Molprobity Statistics.
All-atom Clashscore : 3.17
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 4.04 %
Favored : 95.96 %
Rotamer:
Outliers : 2.26 %
Allowed : 12.99 %
Favored : 84.75 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: -1.54 (0.34), residues: 396
helix: None (None), residues: 0
sheet: None (None), residues: 0
loop : -1.16 (0.26), residues: 396
Max deviation from planes:
Type MaxDev MeanDev LineInFile
HIS 0.003 0.001 HIS A 329
PHE 0.004 0.001 PHE D 346
TYR 0.004 0.001 TYR E 310
ARG 0.001 0.000 ARG D 349
*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
792 Ramachandran restraints generated.
396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
792 Ramachandran restraints generated.
396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
91 residues out of total 354 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 8
poor density : 83
time to evaluate : 0.555
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: E 317 LYS cc_start: 0.8714 (pttt) cc_final: 0.7637 (mmmt)
REVERT: E 349 ARG cc_start: 0.7842 (ptp-170) cc_final: 0.5893 (mmm160)
REVERT: C 317 LYS cc_start: 0.8581 (pttt) cc_final: 0.7532 (mmmt)
REVERT: B 372 GLU cc_start: 0.7323 (mm-30) cc_final: 0.6960 (mm-30)
REVERT: F 345 ASP cc_start: 0.7707 (t0) cc_final: 0.7373 (t0)
outliers start: 8
outliers final: 7
residues processed: 88
average time/residue: 0.4664
time to fit residues: 47.0778
Evaluate side-chains
88 residues out of total 354 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 7
poor density : 81
time to evaluate : 0.521
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue 309 VAL
Chi-restraints excluded: chain E residue 356 SER
Chi-restraints excluded: chain C residue 309 VAL
Chi-restraints excluded: chain D residue 348 ASP
Chi-restraints excluded: chain D residue 356 SER
Chi-restraints excluded: chain B residue 356 SER
Chi-restraints excluded: chain F residue 356 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 36
random chunks:
chunk 29 optimal weight: 4.9990
chunk 30 optimal weight: 10.0000
chunk 32 optimal weight: 2.9990
chunk 21 optimal weight: 5.9990
chunk 34 optimal weight: 4.9990
chunk 20 optimal weight: 2.9990
chunk 16 optimal weight: 4.9990
chunk 23 optimal weight: 0.7980
chunk 35 optimal weight: 0.8980
chunk 33 optimal weight: 0.7980
chunk 28 optimal weight: 0.6980
overall best weight: 1.2382
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8106
moved from start: 0.6540
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.028 3138 Z= 0.179
Angle : 0.504 4.534 4194 Z= 0.258
Chirality : 0.051 0.133 468
Planarity : 0.004 0.036 534
Dihedral : 4.483 15.419 414
Min Nonbonded Distance : 2.524
Molprobity Statistics.
All-atom Clashscore : 3.33
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 3.54 %
Favored : 96.46 %
Rotamer:
Outliers : 1.69 %
Allowed : 13.56 %
Favored : 84.75 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: -1.45 (0.35), residues: 396
helix: None (None), residues: 0
sheet: None (None), residues: 0
loop : -1.10 (0.26), residues: 396
Max deviation from planes:
Type MaxDev MeanDev LineInFile
HIS 0.002 0.001 HIS A 329
PHE 0.003 0.001 PHE F 346
TYR 0.003 0.001 TYR E 310
ARG 0.001 0.000 ARG D 349
*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
792 Ramachandran restraints generated.
396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
792 Ramachandran restraints generated.
396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
90 residues out of total 354 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 6
poor density : 84
time to evaluate : 0.494
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: E 317 LYS cc_start: 0.8704 (pttt) cc_final: 0.7646 (mmmt)
REVERT: E 349 ARG cc_start: 0.7824 (ptp-170) cc_final: 0.5883 (mmm160)
REVERT: C 317 LYS cc_start: 0.8586 (pttt) cc_final: 0.7540 (mmmt)
REVERT: B 372 GLU cc_start: 0.7313 (mm-30) cc_final: 0.6964 (mm-30)
outliers start: 6
outliers final: 6
residues processed: 88
average time/residue: 0.4566
time to fit residues: 46.2028
Evaluate side-chains
87 residues out of total 354 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 6
poor density : 81
time to evaluate : 0.533
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue 356 SER
Chi-restraints excluded: chain C residue 309 VAL
Chi-restraints excluded: chain D residue 348 ASP
Chi-restraints excluded: chain D residue 356 SER
Chi-restraints excluded: chain B residue 356 SER
Chi-restraints excluded: chain F residue 356 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 36
random chunks:
chunk 2 optimal weight: 2.9990
chunk 22 optimal weight: 5.9990
chunk 17 optimal weight: 3.9990
chunk 30 optimal weight: 1.9990
chunk 8 optimal weight: 0.7980
chunk 26 optimal weight: 2.9990
chunk 4 optimal weight: 5.9990
chunk 7 optimal weight: 2.9990
chunk 28 optimal weight: 0.9980
chunk 11 optimal weight: 2.9990
chunk 29 optimal weight: 1.9990
overall best weight: 1.7586
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8125
moved from start: 0.6614
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.029 3138 Z= 0.215
Angle : 0.523 4.732 4194 Z= 0.270
Chirality : 0.051 0.137 468
Planarity : 0.004 0.035 534
Dihedral : 4.597 15.063 414
Min Nonbonded Distance : 2.533
Molprobity Statistics.
All-atom Clashscore : 3.65
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 4.04 %
Favored : 95.96 %
Rotamer:
Outliers : 1.69 %
Allowed : 13.84 %
Favored : 84.46 %
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: -1.55 (0.34), residues: 396
helix: None (None), residues: 0
sheet: None (None), residues: 0
loop : -1.17 (0.26), residues: 396
Max deviation from planes:
Type MaxDev MeanDev LineInFile
HIS 0.003 0.001 HIS A 329
PHE 0.004 0.001 PHE D 346
TYR 0.005 0.001 TYR E 310
ARG 0.001 0.000 ARG D 349
********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
792 Ramachandran restraints generated.
396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
792 Ramachandran restraints generated.
396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
87 residues out of total 354 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 6
poor density : 81
time to evaluate : 0.506
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: E 317 LYS cc_start: 0.8721 (pttt) cc_final: 0.7667 (mmmt)
REVERT: E 349 ARG cc_start: 0.7885 (ptp-170) cc_final: 0.5965 (mmm160)
REVERT: E 369 LYS cc_start: 0.8638 (mtmt) cc_final: 0.8296 (mtmm)
REVERT: C 317 LYS cc_start: 0.8639 (pttt) cc_final: 0.7596 (mmmt)
REVERT: B 372 GLU cc_start: 0.7319 (mm-30) cc_final: 0.6978 (mm-30)
outliers start: 6
outliers final: 6
residues processed: 85
average time/residue: 0.4968
time to fit residues: 48.4494
Evaluate side-chains
85 residues out of total 354 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 6
poor density : 79
time to evaluate : 0.554
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue 356 SER
Chi-restraints excluded: chain C residue 309 VAL
Chi-restraints excluded: chain D residue 348 ASP
Chi-restraints excluded: chain D residue 356 SER
Chi-restraints excluded: chain B residue 356 SER
Chi-restraints excluded: chain F residue 356 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 36
random chunks:
chunk 3 optimal weight: 4.9990
chunk 5 optimal weight: 3.9990
chunk 25 optimal weight: 3.9990
chunk 1 optimal weight: 10.0000
chunk 20 optimal weight: 2.9990
chunk 32 optimal weight: 2.9990
chunk 19 optimal weight: 5.9990
chunk 24 optimal weight: 0.0060
chunk 0 optimal weight: 10.0000
chunk 22 optimal weight: 4.9990
chunk 21 optimal weight: 0.7980
overall best weight: 2.1602
-------------------------------------------------------------------------------
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 = 0.4461 r_free = 0.4461 target = 0.168291 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4174 r_free = 0.4174 target = 0.131219 restraints weight = 10865.033|
|-----------------------------------------------------------------------------|
r_work (start): 0.4171 rms_B_bonded: 2.45
r_work: 0.4080 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.3979 rms_B_bonded: 3.88 restraints_weight: 0.2500
r_work (final): 0.3979
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8365
moved from start: 0.6671
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.029 3138 Z= 0.241
Angle : 0.533 4.710 4194 Z= 0.274
Chirality : 0.051 0.132 468
Planarity : 0.004 0.038 534
Dihedral : 4.712 15.420 414
Min Nonbonded Distance : 2.537
Molprobity Statistics.
All-atom Clashscore : 3.81
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 4.04 %
Favored : 95.96 %
Rotamer:
Outliers : 1.98 %
Allowed : 14.12 %
Favored : 83.90 %
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: -1.61 (0.34), residues: 396
helix: None (None), residues: 0
sheet: None (None), residues: 0
loop : -1.22 (0.26), residues: 396
Max deviation from planes:
Type MaxDev MeanDev LineInFile
HIS 0.003 0.001 HIS A 329
PHE 0.005 0.001 PHE C 346
TYR 0.005 0.001 TYR E 310
ARG 0.001 0.000 ARG D 349
Origin is already at (0, 0, 0), no shifts will be applied
===============================================================================
Job complete
usr+sys time: 2842.09 seconds
wall clock time: 49 minutes 58.94 seconds (2998.94 seconds total)