Starting phenix.real_space_refine
on Sat Aug 3 05:38:19 2024 by dcliebschner
===============================================================================
Processing files:
-------------------------------------------------------------------------------
Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q9d_18277/08_2024/8q9d_18277.cif
Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q9d_18277/08_2024/8q9d_18277.map
Processing PHIL parameters:
-------------------------------------------------------------------------------
Adding command-line PHIL:
-------------------------
refinement.macro_cycles=10
scattering_table=electron
resolution=3.16
write_initial_geo_file=False
Final processed PHIL parameters:
-------------------------------------------------------------------------------
data_manager {
real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q9d_18277/08_2024/8q9d_18277.map"
default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q9d_18277/08_2024/8q9d_18277.map"
model {
file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q9d_18277/08_2024/8q9d_18277.cif"
}
default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8q9d_18277/08_2024/8q9d_18277.cif"
}
resolution = 3.16
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= 0.002
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 2160 2.51 5
N 636 2.21 5
O 642 1.98 5
H 3588 0.53 5
sf(0) = scattering factor at diffraction angle 0.
Process input model
Symmetric amino acids flipped
Residue "E PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "E PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "A PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "A PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "F PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "F PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "B PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "B PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "C PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "C PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "D PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "D PHE 378": "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: 7032
Number of models: 1
Model: ""
Number of chains: 6
Chain: "E"
Number of atoms: 1172
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 75, 1172
Classifications: {'peptide': 75}
Link IDs: {'PTRANS': 3, 'TRANS': 71}
Chain: "A"
Number of atoms: 1172
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 75, 1172
Classifications: {'peptide': 75}
Link IDs: {'PTRANS': 3, 'TRANS': 71}
Chain: "F"
Number of atoms: 1172
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 75, 1172
Classifications: {'peptide': 75}
Link IDs: {'PTRANS': 3, 'TRANS': 71}
Chain: "B"
Number of atoms: 1172
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 75, 1172
Classifications: {'peptide': 75}
Link IDs: {'PTRANS': 3, 'TRANS': 71}
Chain: "C"
Number of atoms: 1172
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 75, 1172
Classifications: {'peptide': 75}
Link IDs: {'PTRANS': 3, 'TRANS': 71}
Chain: "D"
Number of atoms: 1172
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 75, 1172
Classifications: {'peptide': 75}
Link IDs: {'PTRANS': 3, 'TRANS': 71}
Time building chain proxies: 4.69, per 1000 atoms: 0.67
Number of scatterers: 7032
At special positions: 0
Unit cell: (113.712, 124.424, 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 642 8.00
N 636 7.00
C 2160 6.00
H 3588 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: 5.16
Conformation dependent library (CDL) restraints added in 822.8 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 20 sheets defined
0.0% alpha, 49.3% beta
0 base pairs and 0 stacking pairs defined.
Time for finding SS restraints: 0.77
Creating SS restraints...
Processing sheet with id=AA1, first strand: chain 'E' and resid 306 through 310
removed outlier: 6.512A pdb=" N VAL E 306 " --> pdb=" O GLN F 307 " (cutoff:3.500A)
removed outlier: 7.976A pdb=" N VAL F 309 " --> pdb=" O VAL E 306 " (cutoff:3.500A)
removed outlier: 6.409A pdb=" N ILE E 308 " --> pdb=" O VAL F 309 " (cutoff:3.500A)
Processing sheet with id=AA2, first strand: chain 'E' and resid 313 through 314
removed outlier: 6.749A 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 320
removed outlier: 6.295A pdb=" N LYS A 317 " --> pdb=" O VAL F 318 " (cutoff:3.500A)
removed outlier: 8.434A pdb=" N SER F 320 " --> pdb=" O LYS A 317 " (cutoff:3.500A)
removed outlier: 6.792A pdb=" N THR A 319 " --> pdb=" O SER F 320 " (cutoff:3.500A)
Processing sheet with id=AA4, first strand: chain 'E' and resid 323 through 325
removed outlier: 6.680A pdb=" N SER E 324 " --> pdb=" O LEU F 325 " (cutoff:3.500A)
Processing sheet with id=AA5, first strand: chain 'E' and resid 328 through 330
removed outlier: 6.605A pdb=" N HIS E 329 " --> pdb=" O HIS F 330 " (cutoff:3.500A)
Processing sheet with id=AA6, first strand: chain 'E' and resid 337 through 342
removed outlier: 6.468A pdb=" N GLU A 338 " --> pdb=" O VAL F 339 " (cutoff:3.500A)
removed outlier: 7.919A pdb=" N SER F 341 " --> pdb=" O GLU A 338 " (cutoff:3.500A)
removed outlier: 6.526A pdb=" N LYS A 340 " --> pdb=" O SER F 341 " (cutoff:3.500A)
Processing sheet with id=AA7, first strand: chain 'E' and resid 345 through 346
removed outlier: 6.604A pdb=" N ASP A 345 " --> pdb=" O PHE F 346 " (cutoff:3.500A)
Processing sheet with id=AA8, first strand: chain 'E' and resid 350 through 362
removed outlier: 6.943A pdb=" N GLN E 351 " --> pdb=" O VAL F 350 " (cutoff:3.500A)
removed outlier: 6.930A pdb=" N SER F 352 " --> pdb=" O GLN E 351 " (cutoff:3.500A)
removed outlier: 6.893A pdb=" N LYS E 353 " --> pdb=" O SER F 352 " (cutoff:3.500A)
removed outlier: 6.922A pdb=" N ILE F 354 " --> pdb=" O LYS E 353 " (cutoff:3.500A)
removed outlier: 6.920A pdb=" N GLY E 355 " --> pdb=" O ILE F 354 " (cutoff:3.500A)
removed outlier: 6.811A pdb=" N SER F 356 " --> pdb=" O GLY E 355 " (cutoff:3.500A)
removed outlier: 6.953A pdb=" N GLN F 351 " --> pdb=" O VAL A 350 " (cutoff:3.500A)
removed outlier: 6.951A pdb=" N SER A 352 " --> pdb=" O GLN F 351 " (cutoff:3.500A)
removed outlier: 6.932A pdb=" N LYS F 353 " --> pdb=" O SER A 352 " (cutoff:3.500A)
removed outlier: 6.910A pdb=" N ILE A 354 " --> pdb=" O LYS F 353 " (cutoff:3.500A)
removed outlier: 6.884A pdb=" N GLY F 355 " --> pdb=" O ILE A 354 " (cutoff:3.500A)
removed outlier: 6.774A pdb=" N SER A 356 " --> pdb=" O GLY F 355 " (cutoff:3.500A)
Processing sheet with id=AA9, first strand: chain 'E' and resid 368 through 374
removed outlier: 6.693A pdb=" N ASN E 368 " --> pdb=" O LYS F 369 " (cutoff:3.500A)
removed outlier: 8.014A pdb=" N ILE F 371 " --> pdb=" O ASN E 368 " (cutoff:3.500A)
removed outlier: 6.439A pdb=" N LYS E 370 " --> pdb=" O ILE F 371 " (cutoff:3.500A)
removed outlier: 8.122A pdb=" N THR F 373 " --> pdb=" O LYS E 370 " (cutoff:3.500A)
removed outlier: 6.777A pdb=" N GLU E 372 " --> pdb=" O THR F 373 " (cutoff:3.500A)
removed outlier: 6.503A pdb=" N LYS A 369 " --> pdb=" O LYS F 370 " (cutoff:3.500A)
removed outlier: 7.934A pdb=" N GLU F 372 " --> pdb=" O LYS A 369 " (cutoff:3.500A)
removed outlier: 6.221A pdb=" N ILE A 371 " --> pdb=" O GLU F 372 " (cutoff:3.500A)
removed outlier: 8.043A pdb=" N HIS F 374 " --> pdb=" O ILE A 371 " (cutoff:3.500A)
removed outlier: 6.225A pdb=" N THR A 373 " --> pdb=" O HIS F 374 " (cutoff:3.500A)
No H-bonds generated for sheet with id=AA9
Processing sheet with id=AB1, first strand: chain 'E' and resid 377 through 378
removed outlier: 6.776A pdb=" N THR A 377 " --> pdb=" O PHE F 378 " (cutoff:3.500A)
Processing sheet with id=AB2, first strand: chain 'B' and resid 306 through 310
removed outlier: 6.598A pdb=" N VAL B 306 " --> pdb=" O GLN D 307 " (cutoff:3.500A)
removed outlier: 8.027A pdb=" N VAL D 309 " --> pdb=" O VAL B 306 " (cutoff:3.500A)
removed outlier: 6.388A pdb=" N ILE B 308 " --> pdb=" O VAL D 309 " (cutoff:3.500A)
removed outlier: 6.525A pdb=" N GLN C 307 " --> pdb=" O ILE D 308 " (cutoff:3.500A)
removed outlier: 7.801A pdb=" N TYR D 310 " --> pdb=" O GLN C 307 " (cutoff:3.500A)
removed outlier: 6.616A pdb=" N VAL C 309 " --> pdb=" O TYR D 310 " (cutoff:3.500A)
No H-bonds generated for sheet with id=AB2
Processing sheet with id=AB3, first strand: chain 'B' and resid 313 through 314
removed outlier: 6.759A pdb=" N VAL C 313 " --> pdb=" O ASP D 314 " (cutoff:3.500A)
Processing sheet with id=AB4, first strand: chain 'B' and resid 317 through 320
removed outlier: 6.387A pdb=" N LYS C 317 " --> pdb=" O VAL D 318 " (cutoff:3.500A)
removed outlier: 8.470A pdb=" N SER D 320 " --> pdb=" O LYS C 317 " (cutoff:3.500A)
removed outlier: 6.710A pdb=" N THR C 319 " --> pdb=" O SER D 320 " (cutoff:3.500A)
Processing sheet with id=AB5, first strand: chain 'B' and resid 323 through 325
removed outlier: 6.633A pdb=" N SER B 324 " --> pdb=" O LEU D 325 " (cutoff:3.500A)
Processing sheet with id=AB6, first strand: chain 'B' and resid 328 through 330
removed outlier: 6.549A pdb=" N HIS B 329 " --> pdb=" O HIS D 330 " (cutoff:3.500A)
removed outlier: 6.391A pdb=" N ILE C 328 " --> pdb=" O HIS D 329 " (cutoff:3.500A)
No H-bonds generated for sheet with id=AB6
Processing sheet with id=AB7, first strand: chain 'B' and resid 337 through 342
Processing sheet with id=AB8, first strand: chain 'B' and resid 345 through 346
removed outlier: 6.707A pdb=" N ASP C 345 " --> pdb=" O PHE D 346 " (cutoff:3.500A)
Processing sheet with id=AB9, first strand: chain 'B' and resid 350 through 362
removed outlier: 6.228A pdb=" N VAL B 350 " --> pdb=" O GLN D 351 " (cutoff:3.500A)
removed outlier: 7.872A pdb=" N LYS D 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A)
removed outlier: 6.484A pdb=" N SER B 352 " --> pdb=" O LYS D 353 " (cutoff:3.500A)
removed outlier: 8.287A pdb=" N GLY D 355 " --> pdb=" O SER B 352 " (cutoff:3.500A)
removed outlier: 6.314A pdb=" N ILE B 354 " --> pdb=" O GLY D 355 " (cutoff:3.500A)
removed outlier: 7.238A pdb=" N LEU D 357 " --> pdb=" O ILE B 354 " (cutoff:3.500A)
removed outlier: 7.617A pdb=" N SER B 356 " --> pdb=" O LEU D 357 " (cutoff:3.500A)
removed outlier: 10.375A pdb=" N ASN D 359 " --> pdb=" O SER B 356 " (cutoff:3.500A)
removed outlier: 9.096A pdb=" N ASP B 358 " --> pdb=" O ASN D 359 " (cutoff:3.500A)
removed outlier: 10.089A pdb=" N THR D 361 " --> pdb=" O ASP B 358 " (cutoff:3.500A)
removed outlier: 9.063A pdb=" N ILE B 360 " --> pdb=" O THR D 361 " (cutoff:3.500A)
removed outlier: 6.937A pdb=" N LEU C 357 " --> pdb=" O SER D 356 " (cutoff:3.500A)
removed outlier: 6.904A pdb=" N ASP D 358 " --> pdb=" O LEU C 357 " (cutoff:3.500A)
removed outlier: 6.893A pdb=" N ASN C 359 " --> pdb=" O ASP D 358 " (cutoff:3.500A)
removed outlier: 6.899A pdb=" N ILE D 360 " --> pdb=" O ASN C 359 " (cutoff:3.500A)
removed outlier: 6.909A pdb=" N THR C 361 " --> pdb=" O ILE D 360 " (cutoff:3.500A)
removed outlier: 6.906A pdb=" N HIS D 362 " --> pdb=" O THR C 361 " (cutoff:3.500A)
Processing sheet with id=AC1, first strand: chain 'B' and resid 368 through 374
removed outlier: 6.442A pdb=" N LYS C 369 " --> pdb=" O LYS D 370 " (cutoff:3.500A)
removed outlier: 7.779A pdb=" N GLU D 372 " --> pdb=" O LYS C 369 " (cutoff:3.500A)
removed outlier: 6.476A pdb=" N ILE C 371 " --> pdb=" O GLU D 372 " (cutoff:3.500A)
removed outlier: 8.211A pdb=" N HIS D 374 " --> pdb=" O ILE C 371 " (cutoff:3.500A)
removed outlier: 6.292A pdb=" N THR C 373 " --> pdb=" O HIS D 374 " (cutoff:3.500A)
Processing sheet with id=AC2, first strand: chain 'B' and resid 377 through 378
removed outlier: 6.837A pdb=" N THR C 377 " --> pdb=" O PHE D 378 " (cutoff:3.500A)
61 hydrogen bonds defined for protein.
183 hydrogen bond angles defined for protein.
Restraints generated for nucleic acids:
0 hydrogen bonds
0 hydrogen bond angles
0 basepair planarities
0 basepair parallelities
0 stacking parallelities
Total time for adding SS restraints: 2.29
Time building geometry restraints manager: 5.47 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: 3582
1.12 - 1.29: 570
1.29 - 1.47: 1156
1.47 - 1.64: 1772
1.64 - 1.81: 6
Bond restraints: 7086
Sorted by residual:
bond pdb=" N SER B 316 "
pdb=" H SER B 316 "
ideal model delta sigma weight residual
0.860 1.011 -0.151 2.00e-02 2.50e+03 5.67e+01
bond pdb=" N LYS D 311 "
pdb=" H LYS D 311 "
ideal model delta sigma weight residual
0.860 1.010 -0.150 2.00e-02 2.50e+03 5.65e+01
bond pdb=" CE1 PHE C 346 "
pdb=" HE1 PHE C 346 "
ideal model delta sigma weight residual
0.930 1.080 -0.150 2.00e-02 2.50e+03 5.65e+01
bond pdb=" N PHE E 378 "
pdb=" H PHE E 378 "
ideal model delta sigma weight residual
0.860 1.010 -0.150 2.00e-02 2.50e+03 5.65e+01
bond pdb=" N VAL A 309 "
pdb=" H VAL A 309 "
ideal model delta sigma weight residual
0.860 1.010 -0.150 2.00e-02 2.50e+03 5.64e+01
... (remaining 7081 not shown)
Histogram of bond angle deviations from ideal:
96.09 - 102.72: 24
102.72 - 109.36: 4878
109.36 - 115.99: 4365
115.99 - 122.62: 2963
122.62 - 129.25: 682
Bond angle restraints: 12912
Sorted by residual:
angle pdb=" CB HIS D 330 "
pdb=" CG HIS D 330 "
pdb=" CD2 HIS D 330 "
ideal model delta sigma weight residual
131.20 124.69 6.51 1.30e+00 5.92e-01 2.51e+01
angle pdb=" C ASP A 348 "
pdb=" N ARG A 349 "
pdb=" CA ARG A 349 "
ideal model delta sigma weight residual
121.05 127.97 -6.92 1.43e+00 4.89e-01 2.35e+01
angle pdb=" CA ASP B 348 "
pdb=" CB ASP B 348 "
pdb=" CG ASP B 348 "
ideal model delta sigma weight residual
112.60 117.28 -4.68 1.00e+00 1.00e+00 2.19e+01
angle pdb=" CB HIS A 330 "
pdb=" CG HIS A 330 "
pdb=" CD2 HIS A 330 "
ideal model delta sigma weight residual
131.20 125.26 5.94 1.30e+00 5.92e-01 2.09e+01
angle pdb=" CB HIS C 330 "
pdb=" CG HIS C 330 "
pdb=" CD2 HIS C 330 "
ideal model delta sigma weight residual
131.20 125.36 5.84 1.30e+00 5.92e-01 2.02e+01
... (remaining 12907 not shown)
Histogram of dihedral angle deviations from ideal:
0.00 - 14.25: 2901
14.25 - 28.49: 173
28.49 - 42.73: 69
42.73 - 56.98: 58
56.98 - 71.22: 63
Dihedral angle restraints: 3264
sinusoidal: 1866
harmonic: 1398
Sorted by residual:
dihedral pdb=" CA ASP F 358 "
pdb=" C ASP F 358 "
pdb=" N ASN F 359 "
pdb=" CA ASN F 359 "
ideal model delta harmonic sigma weight residual
180.00 160.44 19.56 0 5.00e+00 4.00e-02 1.53e+01
dihedral pdb=" CA ASP E 358 "
pdb=" C ASP E 358 "
pdb=" N ASN E 359 "
pdb=" CA ASN E 359 "
ideal model delta harmonic sigma weight residual
180.00 161.42 18.58 0 5.00e+00 4.00e-02 1.38e+01
dihedral pdb=" CA GLY A 333 "
pdb=" C GLY A 333 "
pdb=" N GLY A 334 "
pdb=" CA GLY A 334 "
ideal model delta harmonic sigma weight residual
180.00 161.60 18.40 0 5.00e+00 4.00e-02 1.35e+01
... (remaining 3261 not shown)
Histogram of chiral volume deviations from ideal:
0.000 - 0.061: 273
0.061 - 0.121: 182
0.121 - 0.181: 57
0.181 - 0.241: 13
0.241 - 0.302: 3
Chirality restraints: 528
Sorted by residual:
chirality pdb=" CA LYS C 347 "
pdb=" N LYS C 347 "
pdb=" C LYS C 347 "
pdb=" CB LYS C 347 "
both_signs ideal model delta sigma weight residual
False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.28e+00
chirality pdb=" CA LYS A 347 "
pdb=" N LYS A 347 "
pdb=" C LYS A 347 "
pdb=" CB LYS A 347 "
both_signs ideal model delta sigma weight residual
False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.53e+00
chirality pdb=" CA ASP B 348 "
pdb=" N ASP B 348 "
pdb=" C ASP B 348 "
pdb=" CB ASP B 348 "
both_signs ideal model delta sigma weight residual
False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.50e+00
... (remaining 525 not shown)
Planarity restraints: 1020
Sorted by residual:
delta sigma weight rms_deltas residual
plane pdb=" CB TYR A 310 " 0.097 2.00e-02 2.50e+03 4.22e-02 5.33e+01
pdb=" CG TYR A 310 " -0.017 2.00e-02 2.50e+03
pdb=" CD1 TYR A 310 " -0.025 2.00e-02 2.50e+03
pdb=" CD2 TYR A 310 " -0.031 2.00e-02 2.50e+03
pdb=" CE1 TYR A 310 " -0.035 2.00e-02 2.50e+03
pdb=" CE2 TYR A 310 " -0.001 2.00e-02 2.50e+03
pdb=" CZ TYR A 310 " 0.004 2.00e-02 2.50e+03
pdb=" OH TYR A 310 " 0.073 2.00e-02 2.50e+03
pdb=" HD1 TYR A 310 " 0.004 2.00e-02 2.50e+03
pdb=" HD2 TYR A 310 " -0.051 2.00e-02 2.50e+03
pdb=" HE1 TYR A 310 " -0.028 2.00e-02 2.50e+03
pdb=" HE2 TYR A 310 " 0.010 2.00e-02 2.50e+03
delta sigma weight rms_deltas residual
plane pdb=" CB HIS F 330 " -0.083 2.00e-02 2.50e+03 4.61e-02 4.79e+01
pdb=" CG HIS F 330 " 0.048 2.00e-02 2.50e+03
pdb=" ND1 HIS F 330 " 0.026 2.00e-02 2.50e+03
pdb=" CD2 HIS F 330 " 0.053 2.00e-02 2.50e+03
pdb=" CE1 HIS F 330 " 0.015 2.00e-02 2.50e+03
pdb=" NE2 HIS F 330 " 0.023 2.00e-02 2.50e+03
pdb=" HD2 HIS F 330 " 0.011 2.00e-02 2.50e+03
pdb=" HE1 HIS F 330 " -0.022 2.00e-02 2.50e+03
pdb=" HE2 HIS F 330 " -0.071 2.00e-02 2.50e+03
delta sigma weight rms_deltas residual
plane pdb=" CB HIS E 362 " -0.064 2.00e-02 2.50e+03 3.80e-02 3.24e+01
pdb=" CG HIS E 362 " 0.053 2.00e-02 2.50e+03
pdb=" ND1 HIS E 362 " 0.010 2.00e-02 2.50e+03
pdb=" CD2 HIS E 362 " 0.047 2.00e-02 2.50e+03
pdb=" CE1 HIS E 362 " 0.013 2.00e-02 2.50e+03
pdb=" NE2 HIS E 362 " 0.024 2.00e-02 2.50e+03
pdb=" HD2 HIS E 362 " -0.010 2.00e-02 2.50e+03
pdb=" HE1 HIS E 362 " -0.024 2.00e-02 2.50e+03
pdb=" HE2 HIS E 362 " -0.049 2.00e-02 2.50e+03
... (remaining 1017 not shown)
Histogram of nonbonded interaction distances:
1.55 - 2.16: 461
2.16 - 2.77: 11796
2.77 - 3.38: 18028
3.38 - 3.99: 24413
3.99 - 4.60: 33930
Nonbonded interactions: 88628
Sorted by model distance:
nonbonded pdb=" OD1 ASP A 314 "
pdb=" HG SER A 316 "
model vdw
1.547 2.450
nonbonded pdb=" OD1 ASP F 314 "
pdb=" HG SER F 316 "
model vdw
1.559 2.450
nonbonded pdb=" OD1 ASP C 314 "
pdb=" HG SER C 316 "
model vdw
1.563 2.450
nonbonded pdb=" OD1 ASP D 314 "
pdb=" HG SER D 316 "
model vdw
1.572 2.450
nonbonded pdb=" OD1 ASP E 314 "
pdb=" HG SER E 316 "
model vdw
1.605 2.450
... (remaining 88623 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: 2.940
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: 0.090
Extract box with map and model: 0.230
Check model and map are aligned: 0.040
Set scattering table: 0.060
Process input model: 26.820
Find NCS groups from input model: 0.180
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: 0.010
Load rotamer database and sin/cos tables:2.590
Set ADP refinement strategy: 0.000
Make a string to write initial .geo file:0.000
Internal consistency checks: 0.000
Total: 32.980
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7382
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 0.035 3498 Z= 0.726
Angle : 1.800 6.925 4680 Z= 1.189
Chirality : 0.083 0.302 528
Planarity : 0.010 0.083 594
Dihedral : 9.918 46.311 1344
Min Nonbonded Distance : 2.504
Molprobity Statistics.
All-atom Clashscore : 0.00
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 5.02 %
Favored : 94.98 %
Rotamer:
Outliers : 0.00 %
Allowed : 0.25 %
Favored : 99.75 %
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: -1.95 (0.34), residues: 438
helix: None (None), residues: 0
sheet: None (None), residues: 0
loop : -1.48 (0.26), residues: 438
Max deviation from planes:
Type MaxDev MeanDev LineInFile
HIS 0.009 0.003 HIS D 329
PHE 0.049 0.013 PHE E 346
TYR 0.084 0.016 TYR A 310
ARG 0.007 0.001 ARG E 349
*********************** 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
129 residues out of total 396 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 129
time to evaluate : 0.591
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: E 311 LYS cc_start: 0.7839 (mttt) cc_final: 0.7228 (pttp)
REVERT: E 347 LYS cc_start: 0.8576 (mttt) cc_final: 0.7816 (mtmt)
REVERT: E 369 LYS cc_start: 0.8128 (tttt) cc_final: 0.7668 (ttmm)
REVERT: E 371 ILE cc_start: 0.8679 (mt) cc_final: 0.8055 (mt)
REVERT: A 307 GLN cc_start: 0.6964 (tt0) cc_final: 0.6477 (mt0)
REVERT: A 338 GLU cc_start: 0.6756 (tt0) cc_final: 0.6217 (tm-30)
REVERT: A 369 LYS cc_start: 0.7458 (tttt) cc_final: 0.7171 (ttpp)
REVERT: A 375 LYS cc_start: 0.7396 (tttt) cc_final: 0.7091 (tttt)
REVERT: F 307 GLN cc_start: 0.7165 (tt0) cc_final: 0.6604 (mt0)
REVERT: F 317 LYS cc_start: 0.6801 (mttt) cc_final: 0.6299 (mtpt)
REVERT: F 338 GLU cc_start: 0.6879 (tt0) cc_final: 0.6548 (tm-30)
REVERT: F 340 LYS cc_start: 0.7139 (tttt) cc_final: 0.6616 (mttm)
REVERT: F 369 LYS cc_start: 0.7165 (tttt) cc_final: 0.6629 (ttmm)
REVERT: F 371 ILE cc_start: 0.7782 (mt) cc_final: 0.7524 (mp)
REVERT: B 307 GLN cc_start: 0.8218 (tt0) cc_final: 0.7395 (mt0)
REVERT: B 317 LYS cc_start: 0.8017 (mttt) cc_final: 0.7306 (mtpt)
REVERT: B 340 LYS cc_start: 0.8242 (tttt) cc_final: 0.7388 (ttmt)
REVERT: B 353 LYS cc_start: 0.7157 (mttt) cc_final: 0.6773 (tttm)
REVERT: B 369 LYS cc_start: 0.8225 (tttt) cc_final: 0.7650 (tttp)
REVERT: C 311 LYS cc_start: 0.7575 (mttt) cc_final: 0.7343 (mttm)
REVERT: C 317 LYS cc_start: 0.6972 (mttt) cc_final: 0.6681 (mtpp)
REVERT: C 338 GLU cc_start: 0.7053 (tt0) cc_final: 0.6821 (tt0)
REVERT: C 369 LYS cc_start: 0.7752 (tttt) cc_final: 0.7348 (tttp)
REVERT: D 307 GLN cc_start: 0.7497 (tt0) cc_final: 0.7266 (tt0)
REVERT: D 311 LYS cc_start: 0.7490 (mttt) cc_final: 0.7202 (mtmt)
REVERT: D 317 LYS cc_start: 0.6932 (mttt) cc_final: 0.6344 (mtpp)
REVERT: D 340 LYS cc_start: 0.7267 (tttt) cc_final: 0.6595 (ttmt)
REVERT: D 369 LYS cc_start: 0.7547 (tttt) cc_final: 0.7034 (tttp)
REVERT: D 372 GLU cc_start: 0.7486 (tt0) cc_final: 0.7270 (tt0)
outliers start: 0
outliers final: 0
residues processed: 129
average time/residue: 0.6926
time to fit residues: 97.9673
Evaluate side-chains
85 residues out of total 396 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 85
time to evaluate : 0.592
-------------------------------------------------------------------------------
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: 2.9990
chunk 31 optimal weight: 3.9990
chunk 17 optimal weight: 6.9990
chunk 10 optimal weight: 2.9990
chunk 21 optimal weight: 1.9990
chunk 32 optimal weight: 2.9990
chunk 12 optimal weight: 6.9990
chunk 20 optimal weight: 2.9990
chunk 24 optimal weight: 3.9990
chunk 38 optimal weight: 1.9990
chunk 11 optimal weight: 3.9990
overall best weight: 2.5990
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
E 327 ASN
B 327 ASN
B 330 HIS
D 351 GLN
Total number of N/Q/H flips: 4
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7572
moved from start: 0.3692
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.004 0.027 3498 Z= 0.276
Angle : 0.599 4.992 4680 Z= 0.310
Chirality : 0.052 0.137 528
Planarity : 0.003 0.025 594
Dihedral : 5.921 14.474 462
Min Nonbonded Distance : 2.483
Molprobity Statistics.
All-atom Clashscore : 1.14
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 1.60 %
Favored : 98.40 %
Rotamer:
Outliers : 1.01 %
Allowed : 5.05 %
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: -1.18 (0.38), residues: 438
helix: None (None), residues: 0
sheet: None (None), residues: 0
loop : -0.89 (0.29), residues: 438
Max deviation from planes:
Type MaxDev MeanDev LineInFile
HIS 0.004 0.001 HIS B 330
PHE 0.010 0.002 PHE C 346
TYR 0.010 0.003 TYR B 310
ARG 0.004 0.001 ARG E 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
87 residues out of total 396 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 4
poor density : 83
time to evaluate : 0.545
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: E 314 ASP cc_start: 0.7876 (t0) cc_final: 0.7116 (t0)
REVERT: E 369 LYS cc_start: 0.8218 (tttt) cc_final: 0.7683 (ttmm)
REVERT: A 307 GLN cc_start: 0.7001 (tt0) cc_final: 0.6525 (mt0)
REVERT: A 311 LYS cc_start: 0.7638 (mttt) cc_final: 0.6918 (tttt)
REVERT: A 317 LYS cc_start: 0.7035 (mttt) cc_final: 0.6621 (mtpt)
REVERT: A 338 GLU cc_start: 0.7088 (tt0) cc_final: 0.6565 (tm-30)
REVERT: A 369 LYS cc_start: 0.7530 (tttt) cc_final: 0.7047 (ttmm)
REVERT: F 307 GLN cc_start: 0.7314 (tt0) cc_final: 0.6703 (mt0)
REVERT: F 311 LYS cc_start: 0.7519 (mttt) cc_final: 0.6831 (pttp)
REVERT: F 342 GLU cc_start: 0.6738 (mp0) cc_final: 0.6485 (mp0)
REVERT: F 348 ASP cc_start: 0.8390 (t0) cc_final: 0.8154 (t0)
REVERT: F 371 ILE cc_start: 0.7837 (mt) cc_final: 0.7597 (mp)
REVERT: B 317 LYS cc_start: 0.7912 (mttt) cc_final: 0.7269 (mtpt)
REVERT: B 327 ASN cc_start: 0.7968 (m110) cc_final: 0.7754 (m110)
REVERT: B 340 LYS cc_start: 0.8064 (tttt) cc_final: 0.7711 (ttmt)
REVERT: B 353 LYS cc_start: 0.7181 (mttt) cc_final: 0.6846 (tttm)
REVERT: B 369 LYS cc_start: 0.8302 (tttt) cc_final: 0.7732 (tttp)
REVERT: C 307 GLN cc_start: 0.7768 (tt0) cc_final: 0.7427 (tt0)
REVERT: C 311 LYS cc_start: 0.7682 (mttt) cc_final: 0.7358 (mttm)
REVERT: C 317 LYS cc_start: 0.7249 (mttt) cc_final: 0.6862 (mtpp)
REVERT: C 338 GLU cc_start: 0.7203 (tt0) cc_final: 0.6923 (tt0)
REVERT: C 340 LYS cc_start: 0.7324 (tttt) cc_final: 0.6620 (mttm)
REVERT: C 369 LYS cc_start: 0.7820 (tttt) cc_final: 0.7375 (tttp)
REVERT: D 311 LYS cc_start: 0.7680 (mttt) cc_final: 0.7341 (mtmt)
REVERT: D 317 LYS cc_start: 0.6972 (mttt) cc_final: 0.6365 (mtpp)
REVERT: D 340 LYS cc_start: 0.7277 (tttt) cc_final: 0.6611 (mttm)
REVERT: D 369 LYS cc_start: 0.7541 (tttt) cc_final: 0.6981 (tttp)
outliers start: 4
outliers final: 4
residues processed: 87
average time/residue: 0.6925
time to fit residues: 66.7028
Evaluate side-chains
78 residues out of total 396 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 4
poor density : 74
time to evaluate : 0.585
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue 305 SER
Chi-restraints excluded: chain A residue 305 SER
Chi-restraints excluded: chain A residue 372 GLU
Chi-restraints excluded: chain F residue 305 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 42
random chunks:
chunk 31 optimal weight: 6.9990
chunk 25 optimal weight: 5.9990
chunk 10 optimal weight: 8.9990
chunk 38 optimal weight: 0.9980
chunk 41 optimal weight: 4.9990
chunk 34 optimal weight: 3.9990
chunk 37 optimal weight: 5.9990
chunk 13 optimal weight: 4.9990
chunk 30 optimal weight: 0.1980
chunk 28 optimal weight: 5.9990
chunk 19 optimal weight: 7.9990
overall best weight: 3.0386
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
B 307 GLN
Total number of N/Q/H flips: 1
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7602
moved from start: 0.4348
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.004 0.024 3498 Z= 0.273
Angle : 0.561 4.930 4680 Z= 0.287
Chirality : 0.052 0.132 528
Planarity : 0.003 0.020 594
Dihedral : 5.341 13.149 462
Min Nonbonded Distance : 2.473
Molprobity Statistics.
All-atom Clashscore : 1.28
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 1.60 %
Favored : 98.40 %
Rotamer:
Outliers : 2.27 %
Allowed : 5.81 %
Favored : 91.92 %
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: -1.05 (0.39), residues: 438
helix: None (None), residues: 0
sheet: None (None), residues: 0
loop : -0.79 (0.30), residues: 438
Max deviation from planes:
Type MaxDev MeanDev LineInFile
HIS 0.005 0.001 HIS C 329
PHE 0.008 0.002 PHE F 346
TYR 0.013 0.003 TYR A 310
ARG 0.002 0.000 ARG B 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
83 residues out of total 396 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 9
poor density : 74
time to evaluate : 0.637
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: E 314 ASP cc_start: 0.7820 (t0) cc_final: 0.7599 (t0)
REVERT: E 369 LYS cc_start: 0.8144 (tttt) cc_final: 0.7628 (ttmm)
REVERT: A 307 GLN cc_start: 0.7058 (tt0) cc_final: 0.6528 (mt0)
REVERT: A 317 LYS cc_start: 0.7170 (mttt) cc_final: 0.6679 (mtpt)
REVERT: A 338 GLU cc_start: 0.7176 (tt0) cc_final: 0.6625 (tm-30)
REVERT: A 347 LYS cc_start: 0.8548 (mttt) cc_final: 0.8138 (mtpp)
REVERT: A 369 LYS cc_start: 0.7543 (tttt) cc_final: 0.7052 (ttmm)
REVERT: F 307 GLN cc_start: 0.7325 (tt0) cc_final: 0.6688 (mt0)
REVERT: F 311 LYS cc_start: 0.7467 (mttt) cc_final: 0.6721 (pttt)
REVERT: F 341 SER cc_start: 0.8539 (m) cc_final: 0.8032 (m)
REVERT: F 342 GLU cc_start: 0.6856 (mp0) cc_final: 0.6571 (mp0)
REVERT: F 369 LYS cc_start: 0.7393 (tttt) cc_final: 0.6805 (ttmm)
REVERT: F 371 ILE cc_start: 0.7917 (mt) cc_final: 0.7655 (mp)
REVERT: B 307 GLN cc_start: 0.8165 (tt0) cc_final: 0.7933 (tt0)
REVERT: B 317 LYS cc_start: 0.7944 (mttt) cc_final: 0.7356 (mtpt)
REVERT: B 340 LYS cc_start: 0.8143 (tttt) cc_final: 0.7327 (mttm)
REVERT: B 353 LYS cc_start: 0.7228 (mttt) cc_final: 0.6836 (tttm)
REVERT: B 369 LYS cc_start: 0.8373 (tttt) cc_final: 0.7897 (tttp)
REVERT: C 307 GLN cc_start: 0.7774 (tt0) cc_final: 0.7463 (tt0)
REVERT: C 311 LYS cc_start: 0.7903 (mttt) cc_final: 0.7145 (tttt)
REVERT: C 317 LYS cc_start: 0.7335 (mttt) cc_final: 0.6892 (mtpp)
REVERT: C 338 GLU cc_start: 0.7118 (tt0) cc_final: 0.6719 (tt0)
REVERT: C 369 LYS cc_start: 0.7733 (tttt) cc_final: 0.7330 (tttp)
REVERT: D 311 LYS cc_start: 0.7613 (mttt) cc_final: 0.7277 (mtmm)
REVERT: D 317 LYS cc_start: 0.6976 (mttt) cc_final: 0.6398 (mtpp)
REVERT: D 369 LYS cc_start: 0.7506 (tttt) cc_final: 0.6913 (tttp)
outliers start: 9
outliers final: 7
residues processed: 82
average time/residue: 0.6739
time to fit residues: 61.3561
Evaluate side-chains
77 residues out of total 396 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 7
poor density : 70
time to evaluate : 0.563
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue 305 SER
Chi-restraints excluded: chain E residue 315 LEU
Chi-restraints excluded: chain A residue 305 SER
Chi-restraints excluded: chain F residue 305 SER
Chi-restraints excluded: chain C residue 305 SER
Chi-restraints excluded: chain C residue 319 THR
Chi-restraints excluded: chain D residue 324 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 42
random chunks:
chunk 4 optimal weight: 0.9980
chunk 18 optimal weight: 1.9990
chunk 25 optimal weight: 5.9990
chunk 38 optimal weight: 7.9990
chunk 40 optimal weight: 5.9990
chunk 20 optimal weight: 5.9990
chunk 36 optimal weight: 7.9990
chunk 10 optimal weight: 7.9990
chunk 33 optimal weight: 4.9990
chunk 23 optimal weight: 1.9990
chunk 0 optimal weight: 4.9990
overall best weight: 2.9988
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
B 368 ASN
Total number of N/Q/H flips: 1
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7608
moved from start: 0.4611
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.004 0.025 3498 Z= 0.279
Angle : 0.531 4.984 4680 Z= 0.272
Chirality : 0.051 0.136 528
Planarity : 0.003 0.019 594
Dihedral : 5.198 13.455 462
Min Nonbonded Distance : 2.457
Molprobity Statistics.
All-atom Clashscore : 1.57
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 1.37 %
Favored : 98.63 %
Rotamer:
Outliers : 2.27 %
Allowed : 6.57 %
Favored : 91.16 %
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: -0.97 (0.39), residues: 438
helix: None (None), residues: 0
sheet: None (None), residues: 0
loop : -0.73 (0.30), residues: 438
Max deviation from planes:
Type MaxDev MeanDev LineInFile
HIS 0.003 0.001 HIS C 329
PHE 0.006 0.001 PHE B 346
TYR 0.009 0.002 TYR A 310
ARG 0.002 0.000 ARG E 379
*********************** 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
79 residues out of total 396 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 9
poor density : 70
time to evaluate : 0.591
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: E 314 ASP cc_start: 0.7822 (t0) cc_final: 0.7287 (t0)
REVERT: E 369 LYS cc_start: 0.8181 (tttt) cc_final: 0.7651 (ttmm)
REVERT: A 307 GLN cc_start: 0.7114 (tt0) cc_final: 0.6567 (mt0)
REVERT: A 317 LYS cc_start: 0.7144 (mttt) cc_final: 0.6630 (mtpt)
REVERT: A 338 GLU cc_start: 0.7190 (tt0) cc_final: 0.6631 (tm-30)
REVERT: A 347 LYS cc_start: 0.8507 (mttt) cc_final: 0.8133 (mtpp)
REVERT: A 369 LYS cc_start: 0.7518 (tttt) cc_final: 0.7033 (ttmm)
REVERT: A 372 GLU cc_start: 0.7470 (OUTLIER) cc_final: 0.6868 (tm-30)
REVERT: F 307 GLN cc_start: 0.7347 (tt0) cc_final: 0.6666 (mt0)
REVERT: F 311 LYS cc_start: 0.7499 (mttt) cc_final: 0.6733 (pttt)
REVERT: F 341 SER cc_start: 0.8544 (m) cc_final: 0.7997 (m)
REVERT: F 342 GLU cc_start: 0.6830 (mp0) cc_final: 0.6593 (mp0)
REVERT: F 369 LYS cc_start: 0.7436 (tttt) cc_final: 0.6858 (ttmm)
REVERT: F 371 ILE cc_start: 0.7934 (mt) cc_final: 0.7668 (mp)
REVERT: B 307 GLN cc_start: 0.8245 (tt0) cc_final: 0.7998 (tt0)
REVERT: B 317 LYS cc_start: 0.7935 (mttt) cc_final: 0.7226 (mtpp)
REVERT: B 340 LYS cc_start: 0.8083 (tttt) cc_final: 0.7377 (mttm)
REVERT: B 353 LYS cc_start: 0.7213 (mttt) cc_final: 0.6857 (tttm)
REVERT: B 369 LYS cc_start: 0.8487 (tttt) cc_final: 0.8005 (tttp)
REVERT: C 307 GLN cc_start: 0.7818 (tt0) cc_final: 0.7526 (tt0)
REVERT: C 317 LYS cc_start: 0.7395 (mttt) cc_final: 0.6936 (mtpp)
REVERT: C 338 GLU cc_start: 0.7098 (tt0) cc_final: 0.6719 (tt0)
REVERT: C 369 LYS cc_start: 0.7665 (tttt) cc_final: 0.7262 (tttp)
REVERT: D 311 LYS cc_start: 0.7658 (mttt) cc_final: 0.7280 (mtmt)
REVERT: D 317 LYS cc_start: 0.7006 (mttt) cc_final: 0.6387 (mtpp)
REVERT: D 369 LYS cc_start: 0.7490 (tttt) cc_final: 0.6865 (tttp)
outliers start: 9
outliers final: 8
residues processed: 78
average time/residue: 0.6340
time to fit residues: 55.0997
Evaluate side-chains
77 residues out of total 396 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 9
poor density : 68
time to evaluate : 0.583
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue 305 SER
Chi-restraints excluded: chain E residue 315 LEU
Chi-restraints excluded: chain A residue 305 SER
Chi-restraints excluded: chain A residue 315 LEU
Chi-restraints excluded: chain A residue 372 GLU
Chi-restraints excluded: chain F residue 305 SER
Chi-restraints excluded: chain B residue 311 LYS
Chi-restraints excluded: chain C residue 319 THR
Chi-restraints excluded: chain D residue 324 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 42
random chunks:
chunk 30 optimal weight: 5.9990
chunk 16 optimal weight: 3.9990
chunk 34 optimal weight: 5.9990
chunk 28 optimal weight: 4.9990
chunk 0 optimal weight: 4.9990
chunk 20 optimal weight: 6.9990
chunk 36 optimal weight: 7.9990
chunk 10 optimal weight: 7.9990
chunk 13 optimal weight: 1.9990
chunk 8 optimal weight: 0.9990
chunk 23 optimal weight: 0.9990
overall best weight: 2.5990
-------------------------------------------------------------------------------
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: 0.7610
moved from start: 0.4779
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.004 0.023 3498 Z= 0.247
Angle : 0.508 4.963 4680 Z= 0.260
Chirality : 0.051 0.133 528
Planarity : 0.003 0.020 594
Dihedral : 4.991 13.795 462
Min Nonbonded Distance : 2.481
Molprobity Statistics.
All-atom Clashscore : 1.57
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 1.60 %
Favored : 98.40 %
Rotamer:
Outliers : 2.27 %
Allowed : 6.82 %
Favored : 90.91 %
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: -1.01 (0.39), residues: 438
helix: None (None), residues: 0
sheet: None (None), residues: 0
loop : -0.76 (0.30), residues: 438
Max deviation from planes:
Type MaxDev MeanDev LineInFile
HIS 0.003 0.001 HIS C 329
PHE 0.005 0.001 PHE B 346
TYR 0.009 0.002 TYR A 310
ARG 0.002 0.000 ARG F 379
*********************** 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
77 residues out of total 396 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 9
poor density : 68
time to evaluate : 0.590
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: E 314 ASP cc_start: 0.7781 (t0) cc_final: 0.7238 (t0)
REVERT: E 369 LYS cc_start: 0.8178 (tttt) cc_final: 0.7648 (ttmm)
REVERT: A 307 GLN cc_start: 0.7097 (tt0) cc_final: 0.6541 (mt0)
REVERT: A 317 LYS cc_start: 0.7136 (mttt) cc_final: 0.6635 (mtpt)
REVERT: A 338 GLU cc_start: 0.7169 (tt0) cc_final: 0.6617 (tm-30)
REVERT: A 347 LYS cc_start: 0.8497 (mttt) cc_final: 0.8128 (mtpp)
REVERT: A 369 LYS cc_start: 0.7520 (tttt) cc_final: 0.7016 (ttmm)
REVERT: F 307 GLN cc_start: 0.7328 (tt0) cc_final: 0.6642 (mt0)
REVERT: F 311 LYS cc_start: 0.7508 (mttt) cc_final: 0.6756 (pttt)
REVERT: F 315 LEU cc_start: 0.8223 (OUTLIER) cc_final: 0.7983 (mt)
REVERT: F 341 SER cc_start: 0.8515 (m) cc_final: 0.7928 (m)
REVERT: F 342 GLU cc_start: 0.6823 (mp0) cc_final: 0.6619 (mp0)
REVERT: F 369 LYS cc_start: 0.7512 (tttt) cc_final: 0.6953 (ttmm)
REVERT: F 371 ILE cc_start: 0.7921 (mt) cc_final: 0.7654 (mp)
REVERT: B 307 GLN cc_start: 0.8155 (tt0) cc_final: 0.7873 (tt0)
REVERT: B 317 LYS cc_start: 0.7982 (mttt) cc_final: 0.7313 (mtpp)
REVERT: B 340 LYS cc_start: 0.8069 (tttt) cc_final: 0.7367 (mttm)
REVERT: B 353 LYS cc_start: 0.7170 (mttt) cc_final: 0.6839 (tttm)
REVERT: B 369 LYS cc_start: 0.8475 (tttt) cc_final: 0.8037 (tttp)
REVERT: C 307 GLN cc_start: 0.7836 (tt0) cc_final: 0.7539 (tt0)
REVERT: C 317 LYS cc_start: 0.7345 (mttt) cc_final: 0.6870 (mtpp)
REVERT: C 338 GLU cc_start: 0.7120 (tt0) cc_final: 0.6884 (tt0)
REVERT: C 369 LYS cc_start: 0.7674 (tttt) cc_final: 0.7267 (tttp)
REVERT: D 311 LYS cc_start: 0.7659 (mttt) cc_final: 0.7271 (mtmt)
REVERT: D 317 LYS cc_start: 0.6978 (mttt) cc_final: 0.6357 (mtpp)
REVERT: D 369 LYS cc_start: 0.7499 (tttt) cc_final: 0.6878 (tttp)
outliers start: 9
outliers final: 7
residues processed: 76
average time/residue: 0.6564
time to fit residues: 55.7251
Evaluate side-chains
75 residues out of total 396 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 8
poor density : 67
time to evaluate : 0.585
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue 305 SER
Chi-restraints excluded: chain E residue 315 LEU
Chi-restraints excluded: chain A residue 305 SER
Chi-restraints excluded: chain F residue 315 LEU
Chi-restraints excluded: chain B residue 311 LYS
Chi-restraints excluded: chain C residue 305 SER
Chi-restraints excluded: chain C residue 319 THR
Chi-restraints excluded: chain D residue 324 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 42
random chunks:
chunk 10 optimal weight: 6.9990
chunk 40 optimal weight: 7.9990
chunk 33 optimal weight: 0.9980
chunk 18 optimal weight: 0.9990
chunk 3 optimal weight: 5.9990
chunk 13 optimal weight: 3.9990
chunk 21 optimal weight: 4.9990
chunk 39 optimal weight: 3.9990
chunk 4 optimal weight: 0.9980
chunk 23 optimal weight: 3.9990
chunk 29 optimal weight: 0.9990
overall best weight: 1.5986
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
B 368 ASN
Total number of N/Q/H flips: 1
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7606
moved from start: 0.4892
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.002 0.017 3498 Z= 0.166
Angle : 0.468 4.804 4680 Z= 0.238
Chirality : 0.051 0.131 528
Planarity : 0.002 0.018 594
Dihedral : 4.691 12.711 462
Min Nonbonded Distance : 2.500
Molprobity Statistics.
All-atom Clashscore : 1.00
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 1.14 %
Favored : 98.86 %
Rotamer:
Outliers : 2.27 %
Allowed : 7.32 %
Favored : 90.40 %
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: -0.91 (0.40), residues: 438
helix: None (None), residues: 0
sheet: None (None), residues: 0
loop : -0.69 (0.30), residues: 438
Max deviation from planes:
Type MaxDev MeanDev LineInFile
HIS 0.002 0.000 HIS C 329
PHE 0.004 0.001 PHE B 346
TYR 0.006 0.001 TYR A 310
ARG 0.001 0.000 ARG E 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
82 residues out of total 396 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 9
poor density : 73
time to evaluate : 0.569
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: E 314 ASP cc_start: 0.7780 (t0) cc_final: 0.7313 (t0)
REVERT: E 369 LYS cc_start: 0.8163 (tttt) cc_final: 0.7630 (ttmm)
REVERT: A 307 GLN cc_start: 0.7114 (tt0) cc_final: 0.6578 (mt0)
REVERT: A 311 LYS cc_start: 0.7719 (mttt) cc_final: 0.6884 (tttt)
REVERT: A 317 LYS cc_start: 0.7161 (mttt) cc_final: 0.6657 (mtpt)
REVERT: A 338 GLU cc_start: 0.7155 (tt0) cc_final: 0.6614 (tm-30)
REVERT: A 347 LYS cc_start: 0.8525 (mttt) cc_final: 0.8155 (mtpp)
REVERT: A 369 LYS cc_start: 0.7490 (tttt) cc_final: 0.7005 (ttmm)
REVERT: A 372 GLU cc_start: 0.7437 (OUTLIER) cc_final: 0.6869 (tm-30)
REVERT: F 307 GLN cc_start: 0.7319 (tt0) cc_final: 0.6652 (mt0)
REVERT: F 311 LYS cc_start: 0.7487 (mttt) cc_final: 0.6812 (pttt)
REVERT: F 341 SER cc_start: 0.8510 (m) cc_final: 0.7983 (m)
REVERT: F 342 GLU cc_start: 0.6775 (mp0) cc_final: 0.6564 (mp0)
REVERT: F 369 LYS cc_start: 0.7513 (tttt) cc_final: 0.6952 (ttmm)
REVERT: F 371 ILE cc_start: 0.7898 (mt) cc_final: 0.7627 (mp)
REVERT: B 307 GLN cc_start: 0.8113 (tt0) cc_final: 0.7795 (tt0)
REVERT: B 317 LYS cc_start: 0.7929 (mttt) cc_final: 0.7299 (mtpp)
REVERT: B 340 LYS cc_start: 0.8063 (tttt) cc_final: 0.7401 (mttm)
REVERT: B 369 LYS cc_start: 0.8473 (tttt) cc_final: 0.8052 (tttp)
REVERT: C 307 GLN cc_start: 0.7875 (tt0) cc_final: 0.7586 (tt0)
REVERT: C 317 LYS cc_start: 0.7360 (mttt) cc_final: 0.6875 (mtpp)
REVERT: C 369 LYS cc_start: 0.7670 (tttt) cc_final: 0.7271 (tttp)
REVERT: D 311 LYS cc_start: 0.7630 (mttt) cc_final: 0.7229 (mtmt)
REVERT: D 317 LYS cc_start: 0.6955 (mttt) cc_final: 0.6366 (mtpp)
outliers start: 9
outliers final: 8
residues processed: 81
average time/residue: 0.6051
time to fit residues: 55.0185
Evaluate side-chains
78 residues out of total 396 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 9
poor density : 69
time to evaluate : 0.703
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue 305 SER
Chi-restraints excluded: chain E residue 315 LEU
Chi-restraints excluded: chain A residue 305 SER
Chi-restraints excluded: chain A residue 315 LEU
Chi-restraints excluded: chain A residue 372 GLU
Chi-restraints excluded: chain B residue 311 LYS
Chi-restraints excluded: chain C residue 305 SER
Chi-restraints excluded: chain C residue 319 THR
Chi-restraints excluded: chain D residue 324 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 42
random chunks:
chunk 22 optimal weight: 5.9990
chunk 34 optimal weight: 6.9990
chunk 40 optimal weight: 7.9990
chunk 25 optimal weight: 6.9990
chunk 24 optimal weight: 3.9990
chunk 18 optimal weight: 6.9990
chunk 16 optimal weight: 2.9990
chunk 12 optimal weight: 6.9990
chunk 7 optimal weight: 5.9990
chunk 27 optimal weight: 4.9990
chunk 20 optimal weight: 6.9990
overall best weight: 4.7990
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
B 368 ASN
Total number of N/Q/H flips: 1
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7634
moved from start: 0.4961
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.006 0.036 3498 Z= 0.438
Angle : 0.574 4.690 4680 Z= 0.298
Chirality : 0.051 0.131 528
Planarity : 0.004 0.028 594
Dihedral : 5.179 14.240 462
Min Nonbonded Distance : 2.450
Molprobity Statistics.
All-atom Clashscore : 1.99
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 2.97 %
Favored : 97.03 %
Rotamer:
Outliers : 3.03 %
Allowed : 7.07 %
Favored : 89.90 %
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: -1.21 (0.38), residues: 438
helix: None (None), residues: 0
sheet: None (None), residues: 0
loop : -0.91 (0.29), residues: 438
Max deviation from planes:
Type MaxDev MeanDev LineInFile
HIS 0.003 0.001 HIS B 329
PHE 0.009 0.002 PHE F 346
TYR 0.015 0.003 TYR A 310
ARG 0.002 0.001 ARG C 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
82 residues out of total 396 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 12
poor density : 70
time to evaluate : 0.563
Fit side-chains
revert: symmetry clash
REVERT: E 314 ASP cc_start: 0.7787 (t0) cc_final: 0.7280 (t0)
REVERT: E 340 LYS cc_start: 0.7873 (tttt) cc_final: 0.7531 (mmtt)
REVERT: E 347 LYS cc_start: 0.8734 (mttt) cc_final: 0.8300 (mtpp)
REVERT: E 369 LYS cc_start: 0.8186 (tttt) cc_final: 0.7646 (ttmm)
REVERT: A 307 GLN cc_start: 0.7053 (tt0) cc_final: 0.6497 (mt0)
REVERT: A 338 GLU cc_start: 0.7168 (tt0) cc_final: 0.6620 (tm-30)
REVERT: A 340 LYS cc_start: 0.7440 (tttt) cc_final: 0.6718 (mttm)
REVERT: A 347 LYS cc_start: 0.8496 (mttt) cc_final: 0.8125 (mtpp)
REVERT: A 369 LYS cc_start: 0.7536 (tttt) cc_final: 0.7055 (ttmm)
REVERT: A 372 GLU cc_start: 0.7462 (OUTLIER) cc_final: 0.6894 (tm-30)
REVERT: F 307 GLN cc_start: 0.7367 (tt0) cc_final: 0.6726 (mt0)
REVERT: F 311 LYS cc_start: 0.7494 (mttt) cc_final: 0.6673 (pttt)
REVERT: F 341 SER cc_start: 0.8512 (m) cc_final: 0.7844 (m)
REVERT: F 371 ILE cc_start: 0.7905 (mt) cc_final: 0.7641 (mp)
REVERT: F 372 GLU cc_start: 0.7417 (tt0) cc_final: 0.7212 (tt0)
REVERT: B 307 GLN cc_start: 0.8212 (tt0) cc_final: 0.7925 (tt0)
REVERT: B 317 LYS cc_start: 0.8068 (mttt) cc_final: 0.7414 (mtpp)
REVERT: B 340 LYS cc_start: 0.8169 (tttt) cc_final: 0.7454 (mttm)
REVERT: B 353 LYS cc_start: 0.7229 (mttt) cc_final: 0.6901 (tttm)
REVERT: B 369 LYS cc_start: 0.8476 (tttt) cc_final: 0.7994 (tttp)
REVERT: C 307 GLN cc_start: 0.7805 (tt0) cc_final: 0.7557 (tt0)
REVERT: C 311 LYS cc_start: 0.7927 (mttt) cc_final: 0.7057 (tttt)
REVERT: C 317 LYS cc_start: 0.7257 (mttt) cc_final: 0.6801 (mtpp)
REVERT: C 338 GLU cc_start: 0.7245 (tt0) cc_final: 0.6763 (tt0)
REVERT: C 369 LYS cc_start: 0.7679 (tttt) cc_final: 0.7272 (tttp)
REVERT: D 311 LYS cc_start: 0.7639 (mttt) cc_final: 0.7286 (mtmt)
REVERT: D 317 LYS cc_start: 0.7047 (mttt) cc_final: 0.6467 (mtpp)
REVERT: D 340 LYS cc_start: 0.7294 (tttt) cc_final: 0.6566 (mttm)
REVERT: D 369 LYS cc_start: 0.7514 (tttt) cc_final: 0.6852 (tttp)
outliers start: 12
outliers final: 11
residues processed: 81
average time/residue: 0.6581
time to fit residues: 59.5606
Evaluate side-chains
81 residues out of total 396 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 12
poor density : 69
time to evaluate : 0.581
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue 305 SER
Chi-restraints excluded: chain E residue 315 LEU
Chi-restraints excluded: chain A residue 305 SER
Chi-restraints excluded: chain A residue 315 LEU
Chi-restraints excluded: chain A residue 353 LYS
Chi-restraints excluded: chain A residue 372 GLU
Chi-restraints excluded: chain F residue 315 LEU
Chi-restraints excluded: chain B residue 311 LYS
Chi-restraints excluded: chain C residue 305 SER
Chi-restraints excluded: chain C residue 319 THR
Chi-restraints excluded: chain C residue 324 SER
Chi-restraints excluded: chain D residue 324 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 42
random chunks:
chunk 3 optimal weight: 9.9990
chunk 31 optimal weight: 7.9990
chunk 36 optimal weight: 5.9990
chunk 38 optimal weight: 2.9990
chunk 35 optimal weight: 3.9990
chunk 37 optimal weight: 4.9990
chunk 22 optimal weight: 0.8980
chunk 16 optimal weight: 3.9990
chunk 29 optimal weight: 0.7980
chunk 11 optimal weight: 6.9990
chunk 34 optimal weight: 0.9980
overall best weight: 1.9384
-------------------------------------------------------------------------------
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: 0.7617
moved from start: 0.5030
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.019 3498 Z= 0.196
Angle : 0.495 5.187 4680 Z= 0.253
Chirality : 0.051 0.131 528
Planarity : 0.003 0.018 594
Dihedral : 4.851 12.747 462
Min Nonbonded Distance : 2.491
Molprobity Statistics.
All-atom Clashscore : 1.42
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 1.37 %
Favored : 98.63 %
Rotamer:
Outliers : 2.27 %
Allowed : 8.33 %
Favored : 89.39 %
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: -1.15 (0.39), residues: 438
helix: None (None), residues: 0
sheet: None (None), residues: 0
loop : -0.87 (0.29), residues: 438
Max deviation from planes:
Type MaxDev MeanDev LineInFile
HIS 0.002 0.000 HIS C 329
PHE 0.004 0.001 PHE B 346
TYR 0.007 0.002 TYR A 310
ARG 0.001 0.000 ARG B 349
*********************** 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
80 residues out of total 396 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 9
poor density : 71
time to evaluate : 0.585
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: E 314 ASP cc_start: 0.7766 (t0) cc_final: 0.7302 (t0)
REVERT: E 347 LYS cc_start: 0.8725 (mttt) cc_final: 0.8278 (mtpp)
REVERT: E 369 LYS cc_start: 0.8176 (tttt) cc_final: 0.7640 (ttmm)
REVERT: A 307 GLN cc_start: 0.7136 (tt0) cc_final: 0.6588 (mt0)
REVERT: A 317 LYS cc_start: 0.7144 (mttt) cc_final: 0.6654 (mtpt)
REVERT: A 338 GLU cc_start: 0.7169 (tt0) cc_final: 0.6621 (tm-30)
REVERT: A 347 LYS cc_start: 0.8568 (mttt) cc_final: 0.8177 (mtpp)
REVERT: A 369 LYS cc_start: 0.7506 (tttt) cc_final: 0.7011 (ttmm)
REVERT: F 307 GLN cc_start: 0.7331 (tt0) cc_final: 0.6732 (mt0)
REVERT: F 311 LYS cc_start: 0.7483 (mttt) cc_final: 0.6706 (pttt)
REVERT: F 369 LYS cc_start: 0.7524 (tttt) cc_final: 0.6958 (ttmm)
REVERT: F 371 ILE cc_start: 0.7918 (mt) cc_final: 0.7651 (mp)
REVERT: B 307 GLN cc_start: 0.8174 (tt0) cc_final: 0.7842 (tt0)
REVERT: B 317 LYS cc_start: 0.7924 (mttt) cc_final: 0.7312 (mtpp)
REVERT: B 340 LYS cc_start: 0.8111 (tttt) cc_final: 0.7367 (mttm)
REVERT: B 353 LYS cc_start: 0.7149 (mttt) cc_final: 0.6791 (tttm)
REVERT: B 369 LYS cc_start: 0.8496 (tttt) cc_final: 0.8052 (tttp)
REVERT: C 307 GLN cc_start: 0.7822 (tt0) cc_final: 0.7534 (tt0)
REVERT: C 317 LYS cc_start: 0.7364 (mttt) cc_final: 0.6904 (mtpp)
REVERT: C 369 LYS cc_start: 0.7677 (tttt) cc_final: 0.7277 (tttp)
REVERT: D 311 LYS cc_start: 0.7636 (mttt) cc_final: 0.7234 (mtmt)
REVERT: D 317 LYS cc_start: 0.6998 (mttt) cc_final: 0.6421 (mtpp)
REVERT: D 369 LYS cc_start: 0.7493 (tttt) cc_final: 0.6879 (tttp)
outliers start: 9
outliers final: 9
residues processed: 79
average time/residue: 0.6594
time to fit residues: 57.9027
Evaluate side-chains
79 residues out of total 396 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 9
poor density : 70
time to evaluate : 0.570
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue 305 SER
Chi-restraints excluded: chain E residue 315 LEU
Chi-restraints excluded: chain A residue 305 SER
Chi-restraints excluded: chain A residue 353 LYS
Chi-restraints excluded: chain B residue 311 LYS
Chi-restraints excluded: chain C residue 305 SER
Chi-restraints excluded: chain C residue 319 THR
Chi-restraints excluded: chain C residue 324 SER
Chi-restraints excluded: chain D residue 324 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 42
random chunks:
chunk 35 optimal weight: 4.9990
chunk 37 optimal weight: 6.9990
chunk 24 optimal weight: 7.9990
chunk 39 optimal weight: 5.9990
chunk 18 optimal weight: 6.9990
chunk 27 optimal weight: 2.9990
chunk 41 optimal weight: 2.9990
chunk 38 optimal weight: 0.9990
chunk 33 optimal weight: 5.9990
chunk 3 optimal weight: 5.9990
chunk 25 optimal weight: 0.9990
overall best weight: 2.5990
-------------------------------------------------------------------------------
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: 0.7624
moved from start: 0.5078
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.004 0.023 3498 Z= 0.251
Angle : 0.505 4.947 4680 Z= 0.260
Chirality : 0.050 0.133 528
Planarity : 0.003 0.018 594
Dihedral : 4.846 12.742 462
Min Nonbonded Distance : 2.484
Molprobity Statistics.
All-atom Clashscore : 1.28
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 2.05 %
Favored : 97.95 %
Rotamer:
Outliers : 2.53 %
Allowed : 8.08 %
Favored : 89.39 %
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: -1.16 (0.39), residues: 438
helix: None (None), residues: 0
sheet: None (None), residues: 0
loop : -0.88 (0.29), residues: 438
Max deviation from planes:
Type MaxDev MeanDev LineInFile
HIS 0.002 0.000 HIS B 329
PHE 0.005 0.001 PHE E 378
TYR 0.010 0.002 TYR A 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
79 residues out of total 396 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 10
poor density : 69
time to evaluate : 0.599
Fit side-chains
revert: symmetry clash
REVERT: E 314 ASP cc_start: 0.7748 (t0) cc_final: 0.7281 (t0)
REVERT: E 347 LYS cc_start: 0.8722 (mttt) cc_final: 0.8267 (mtpp)
REVERT: E 369 LYS cc_start: 0.8167 (tttt) cc_final: 0.7628 (ttmm)
REVERT: E 372 GLU cc_start: 0.7435 (mm-30) cc_final: 0.7210 (mp0)
REVERT: A 307 GLN cc_start: 0.7111 (tt0) cc_final: 0.6569 (mt0)
REVERT: A 317 LYS cc_start: 0.7145 (mttt) cc_final: 0.6633 (mtpt)
REVERT: A 338 GLU cc_start: 0.7177 (tt0) cc_final: 0.6635 (tm-30)
REVERT: A 340 LYS cc_start: 0.7460 (tttt) cc_final: 0.6870 (mttm)
REVERT: A 347 LYS cc_start: 0.8570 (mttt) cc_final: 0.8176 (mtpp)
REVERT: A 369 LYS cc_start: 0.7596 (tttt) cc_final: 0.7105 (ttmm)
REVERT: F 307 GLN cc_start: 0.7287 (tt0) cc_final: 0.6748 (mt0)
REVERT: F 311 LYS cc_start: 0.7470 (mttt) cc_final: 0.6649 (pttt)
REVERT: F 369 LYS cc_start: 0.7578 (tttt) cc_final: 0.6998 (ttmm)
REVERT: F 371 ILE cc_start: 0.7864 (mt) cc_final: 0.7591 (mp)
REVERT: F 372 GLU cc_start: 0.7654 (tt0) cc_final: 0.7362 (tt0)
REVERT: B 307 GLN cc_start: 0.8182 (tt0) cc_final: 0.7831 (tt0)
REVERT: B 317 LYS cc_start: 0.7958 (mttt) cc_final: 0.7363 (mtpp)
REVERT: B 340 LYS cc_start: 0.8116 (tttt) cc_final: 0.7403 (mttm)
REVERT: B 353 LYS cc_start: 0.7168 (mttt) cc_final: 0.6823 (tttm)
REVERT: B 369 LYS cc_start: 0.8506 (tttt) cc_final: 0.8059 (tttp)
REVERT: C 307 GLN cc_start: 0.7826 (tt0) cc_final: 0.7607 (tt0)
REVERT: C 311 LYS cc_start: 0.7855 (mttt) cc_final: 0.7083 (tttt)
REVERT: C 317 LYS cc_start: 0.7266 (mttt) cc_final: 0.6836 (mtpp)
REVERT: C 369 LYS cc_start: 0.7691 (tttt) cc_final: 0.7292 (tttp)
REVERT: D 311 LYS cc_start: 0.7637 (mttt) cc_final: 0.7283 (mtmt)
REVERT: D 317 LYS cc_start: 0.7065 (mttt) cc_final: 0.6501 (mtpp)
REVERT: D 369 LYS cc_start: 0.7478 (tttt) cc_final: 0.6834 (tttp)
outliers start: 10
outliers final: 9
residues processed: 78
average time/residue: 0.6563
time to fit residues: 56.9143
Evaluate side-chains
77 residues out of total 396 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 9
poor density : 68
time to evaluate : 0.650
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue 305 SER
Chi-restraints excluded: chain E residue 315 LEU
Chi-restraints excluded: chain A residue 305 SER
Chi-restraints excluded: chain A residue 353 LYS
Chi-restraints excluded: chain B residue 311 LYS
Chi-restraints excluded: chain C residue 305 SER
Chi-restraints excluded: chain C residue 319 THR
Chi-restraints excluded: chain C residue 324 SER
Chi-restraints excluded: chain D residue 324 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 42
random chunks:
chunk 20 optimal weight: 4.9990
chunk 26 optimal weight: 5.9990
chunk 35 optimal weight: 1.9990
chunk 10 optimal weight: 8.9990
chunk 30 optimal weight: 4.9990
chunk 4 optimal weight: 0.0070
chunk 9 optimal weight: 2.9990
chunk 33 optimal weight: 1.9990
chunk 13 optimal weight: 1.9990
chunk 34 optimal weight: 0.9990
chunk 6 optimal weight: 1.9990
overall best weight: 1.4006
-------------------------------------------------------------------------------
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: 0.7612
moved from start: 0.5162
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.002 0.021 3498 Z= 0.163
Angle : 0.472 4.929 4680 Z= 0.241
Chirality : 0.051 0.130 528
Planarity : 0.002 0.017 594
Dihedral : 4.580 12.019 462
Min Nonbonded Distance : 2.503
Molprobity Statistics.
All-atom Clashscore : 1.42
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 1.37 %
Favored : 98.63 %
Rotamer:
Outliers : 2.02 %
Allowed : 9.34 %
Favored : 88.64 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: -1.07 (0.39), residues: 438
helix: None (None), residues: 0
sheet: None (None), residues: 0
loop : -0.81 (0.30), residues: 438
Max deviation from planes:
Type MaxDev MeanDev LineInFile
HIS 0.002 0.000 HIS C 362
PHE 0.003 0.001 PHE B 346
TYR 0.006 0.001 TYR E 310
ARG 0.001 0.000 ARG F 349
********************** 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
79 residues out of total 396 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 8
poor density : 71
time to evaluate : 0.644
Fit side-chains
revert: symmetry clash
revert: symmetry clash
REVERT: E 314 ASP cc_start: 0.7796 (t0) cc_final: 0.7366 (t0)
REVERT: E 347 LYS cc_start: 0.8721 (mttt) cc_final: 0.8258 (mtpp)
REVERT: E 369 LYS cc_start: 0.8159 (tttt) cc_final: 0.7626 (ttmm)
REVERT: A 307 GLN cc_start: 0.7142 (tt0) cc_final: 0.6612 (mt0)
REVERT: A 311 LYS cc_start: 0.7665 (mttt) cc_final: 0.6846 (tttt)
REVERT: A 317 LYS cc_start: 0.7156 (mttt) cc_final: 0.6651 (mtpt)
REVERT: A 338 GLU cc_start: 0.7146 (tt0) cc_final: 0.6601 (tm-30)
REVERT: A 347 LYS cc_start: 0.8563 (mttt) cc_final: 0.8171 (mtpp)
REVERT: A 353 LYS cc_start: 0.8466 (OUTLIER) cc_final: 0.8215 (tttt)
REVERT: A 369 LYS cc_start: 0.7603 (tttt) cc_final: 0.7108 (ttmm)
REVERT: F 307 GLN cc_start: 0.7281 (tt0) cc_final: 0.6757 (mt0)
REVERT: F 311 LYS cc_start: 0.7508 (mttt) cc_final: 0.6802 (pttt)
REVERT: F 369 LYS cc_start: 0.7560 (tttt) cc_final: 0.6982 (ttmm)
REVERT: F 371 ILE cc_start: 0.7877 (mt) cc_final: 0.7607 (mp)
REVERT: F 372 GLU cc_start: 0.7648 (tt0) cc_final: 0.7297 (tt0)
REVERT: B 307 GLN cc_start: 0.8144 (tt0) cc_final: 0.7792 (tp40)
REVERT: B 317 LYS cc_start: 0.7890 (mttt) cc_final: 0.7331 (mtpp)
REVERT: B 340 LYS cc_start: 0.8095 (tttt) cc_final: 0.7364 (mttm)
REVERT: B 369 LYS cc_start: 0.8453 (tttt) cc_final: 0.8037 (tttp)
REVERT: C 307 GLN cc_start: 0.7831 (tt0) cc_final: 0.7551 (tt0)
REVERT: C 317 LYS cc_start: 0.7386 (mttt) cc_final: 0.6933 (mtpp)
REVERT: C 369 LYS cc_start: 0.7705 (tttt) cc_final: 0.7310 (tttp)
REVERT: D 311 LYS cc_start: 0.7654 (mttt) cc_final: 0.7241 (mtmt)
REVERT: D 317 LYS cc_start: 0.6966 (mttt) cc_final: 0.6388 (mtpp)
outliers start: 8
outliers final: 7
residues processed: 78
average time/residue: 0.6453
time to fit residues: 55.9236
Evaluate side-chains
77 residues out of total 396 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 8
poor density : 69
time to evaluate : 0.548
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue 315 LEU
Chi-restraints excluded: chain A residue 305 SER
Chi-restraints excluded: chain A residue 315 LEU
Chi-restraints excluded: chain A residue 353 LYS
Chi-restraints excluded: chain B residue 311 LYS
Chi-restraints excluded: chain C residue 305 SER
Chi-restraints excluded: chain C residue 324 SER
Chi-restraints excluded: chain D residue 324 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 42
random chunks:
chunk 29 optimal weight: 4.9990
chunk 1 optimal weight: 5.9990
chunk 24 optimal weight: 3.9990
chunk 38 optimal weight: 4.9990
chunk 22 optimal weight: 4.9990
chunk 28 optimal weight: 4.9990
chunk 26 optimal weight: 1.9990
chunk 25 optimal weight: 0.9990
chunk 16 optimal weight: 1.9990
chunk 15 optimal weight: 3.9990
chunk 41 optimal weight: 5.9990
overall best weight: 2.5990
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
D 327 ASN
Total number of N/Q/H flips: 1
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3951 r_free = 0.3951 target = 0.128932 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.113940 restraints weight = 13361.195|
|-----------------------------------------------------------------------------|
r_work (start): 0.3772 rms_B_bonded: 1.91
r_work: 0.3696 rms_B_bonded: 1.86 restraints_weight: 0.5000
r_work: 0.3608 rms_B_bonded: 3.21 restraints_weight: 0.2500
r_work (final): 0.3608
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8394
moved from start: 0.5163
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.004 0.023 3498 Z= 0.248
Angle : 0.500 4.758 4680 Z= 0.258
Chirality : 0.050 0.130 528
Planarity : 0.003 0.017 594
Dihedral : 4.749 12.356 462
Min Nonbonded Distance : 2.486
Molprobity Statistics.
All-atom Clashscore : 1.85
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 2.05 %
Favored : 97.95 %
Rotamer:
Outliers : 2.02 %
Allowed : 9.60 %
Favored : 88.38 %
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: -1.13 (0.39), residues: 438
helix: None (None), residues: 0
sheet: None (None), residues: 0
loop : -0.85 (0.30), residues: 438
Max deviation from planes:
Type MaxDev MeanDev LineInFile
HIS 0.002 0.000 HIS B 329
PHE 0.005 0.001 PHE E 378
TYR 0.009 0.002 TYR A 310
ARG 0.001 0.000 ARG A 379
Origin is already at (0, 0, 0), no shifts will be applied
===============================================================================
Job complete
usr+sys time: 3028.22 seconds
wall clock time: 53 minutes 6.44 seconds (3186.44 seconds total)