Starting phenix.real_space_refine
on Wed Jan 22 05:13:23 2025 by dcliebschner
===============================================================================
Processing files:
-------------------------------------------------------------------------------
Found model, /net/cci-nas-00/data/ceres_data/9bz8_45056/01_2025/9bz8_45056.cif
Found real_map, /net/cci-nas-00/data/ceres_data/9bz8_45056/01_2025/9bz8_45056.map
Processing PHIL parameters:
-------------------------------------------------------------------------------
Adding command-line PHIL:
-------------------------
refinement.macro_cycles=10
scattering_table=electron
resolution=3.0
write_initial_geo_file=False
Final processed PHIL parameters:
-------------------------------------------------------------------------------
data_manager {
real_map_files = "/net/cci-nas-00/data/ceres_data/9bz8_45056/01_2025/9bz8_45056.map"
default_real_map = "/net/cci-nas-00/data/ceres_data/9bz8_45056/01_2025/9bz8_45056.map"
model {
file = "/net/cci-nas-00/data/ceres_data/9bz8_45056/01_2025/9bz8_45056.cif"
}
default_model = "/net/cci-nas-00/data/ceres_data/9bz8_45056/01_2025/9bz8_45056.cif"
}
resolution = 3.0
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= 0.003
Set stop_for_unknowns flag
Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
Set to: electron
Number of scattering types: 4
Type Number sf(0) Gaussians
S 77 5.16 5
C 12215 2.51 5
N 2814 2.21 5
O 3171 1.98 5
sf(0) = scattering factor at diffraction angle 0.
Process input model
Symmetric amino acids flipped. Time to flip 42 residue(s): 0.06s
Monomer Library directory:
"/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
Total number of atoms: 18277
Number of models: 1
Model: ""
Number of chains: 1
Chain: "A"
Number of atoms: 2611
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 322, 2611
Classifications: {'peptide': 322}
Link IDs: {'PTRANS': 14, 'TRANS': 307}
Chain breaks: 3
Restraints were copied for chains:
C, B, E, D, G, F
Time building chain proxies: 6.27, per 1000 atoms: 0.34
Number of scatterers: 18277
At special positions: 0
Unit cell: (113.42, 113.42, 121.98, 90, 90, 90)
Space group: P 1 (No. 1)
Number of sites at special positions: 0
Number of scattering types: 4
Type Number sf(0)
S 77 16.00
O 3171 8.00
N 2814 7.00
C 12215 6.00
sf(0) = scattering factor at diffraction angle 0.
Number of disulfides: simple=2, symmetry=0
Simple disulfide: pdb=" SG CYS A 66 " - pdb=" SG CYS A 267 " distance=2.03
Simple disulfide: pdb=" SG CYS A 84 " - pdb=" SG CYS A 248 " distance=2.03
Automatic linking
Parameters for automatic linking
Linking & cutoffs
Metal : Auto - 3.00
Amino acid : True - 1.90
Carbohydrate : True - 1.99
Ligands : True - 1.99
Small molecules : False - 1.98
Amino acid - RNA/DNA : False
Number of custom bonds: simple=0, symmetry=0
Time building additional restraints: 4.40
Conformation dependent library (CDL) restraints added in 2.5 seconds
4396 Ramachandran restraints generated.
2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2.
Adding C-beta torsion restraints...
Number of C-beta restraints generated: 4382
Finding SS restraints...
Secondary structure from input PDB file:
98 helices and 7 sheets defined
72.4% alpha, 2.8% beta
0 base pairs and 0 stacking pairs defined.
Time for finding SS restraints: 1.68
Creating SS restraints...
Processing helix chain 'A' and resid 2 through 11
Processing helix chain 'A' and resid 32 through 54
Proline residue: A 46 - end of helix
removed outlier: 3.690A pdb=" N PHE A 54 " --> pdb=" O ILE A 50 " (cutoff:3.500A)
Processing helix chain 'A' and resid 73 through 91
removed outlier: 4.443A pdb=" N GLN A 89 " --> pdb=" O TRP A 85 " (cutoff:3.500A)
removed outlier: 4.261A pdb=" N GLN A 90 " --> pdb=" O ALA A 86 " (cutoff:3.500A)
Processing helix chain 'A' and resid 102 through 131
Proline residue: A 110 - end of helix
Proline residue: A 123 - end of helix
Processing helix chain 'A' and resid 131 through 158
Processing helix chain 'A' and resid 197 through 207
removed outlier: 3.795A pdb=" N ASN A 207 " --> pdb=" O LYS A 203 " (cutoff:3.500A)
Processing helix chain 'A' and resid 209 through 240
Processing helix chain 'A' and resid 252 through 256
removed outlier: 4.280A pdb=" N LEU A 255 " --> pdb=" O THR A 252 " (cutoff:3.500A)
Processing helix chain 'A' and resid 271 through 298
Proline residue: A 291 - end of helix
removed outlier: 3.687A pdb=" N ILE A 294 " --> pdb=" O MET A 290 " (cutoff:3.500A)
Processing helix chain 'A' and resid 307 through 312
removed outlier: 3.919A pdb=" N TYR A 311 " --> pdb=" O VAL A 307 " (cutoff:3.500A)
Processing helix chain 'A' and resid 328 through 340
Processing helix chain 'A' and resid 341 through 344
Processing helix chain 'A' and resid 345 through 360
removed outlier: 3.774A pdb=" N THR A 359 " --> pdb=" O ASN A 355 " (cutoff:3.500A)
removed outlier: 4.283A pdb=" N GLY A 360 " --> pdb=" O ILE A 356 " (cutoff:3.500A)
Processing helix chain 'A' and resid 364 through 372
removed outlier: 4.201A pdb=" N TYR A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A)
Processing helix chain 'B' and resid 3 through 11
Processing helix chain 'B' and resid 32 through 54
Proline residue: B 46 - end of helix
removed outlier: 3.691A pdb=" N PHE B 54 " --> pdb=" O ILE B 50 " (cutoff:3.500A)
Processing helix chain 'B' and resid 73 through 91
removed outlier: 4.442A pdb=" N GLN B 89 " --> pdb=" O TRP B 85 " (cutoff:3.500A)
removed outlier: 4.261A pdb=" N GLN B 90 " --> pdb=" O ALA B 86 " (cutoff:3.500A)
Processing helix chain 'B' and resid 102 through 131
Proline residue: B 110 - end of helix
Proline residue: B 123 - end of helix
Processing helix chain 'B' and resid 131 through 158
Processing helix chain 'B' and resid 197 through 207
removed outlier: 3.794A pdb=" N ASN B 207 " --> pdb=" O LYS B 203 " (cutoff:3.500A)
Processing helix chain 'B' and resid 209 through 240
Processing helix chain 'B' and resid 252 through 256
removed outlier: 4.280A pdb=" N LEU B 255 " --> pdb=" O THR B 252 " (cutoff:3.500A)
Processing helix chain 'B' and resid 271 through 298
Proline residue: B 291 - end of helix
removed outlier: 3.686A pdb=" N ILE B 294 " --> pdb=" O MET B 290 " (cutoff:3.500A)
Processing helix chain 'B' and resid 307 through 312
removed outlier: 3.920A pdb=" N TYR B 311 " --> pdb=" O VAL B 307 " (cutoff:3.500A)
Processing helix chain 'B' and resid 328 through 340
Processing helix chain 'B' and resid 341 through 344
Processing helix chain 'B' and resid 345 through 360
removed outlier: 3.772A pdb=" N THR B 359 " --> pdb=" O ASN B 355 " (cutoff:3.500A)
removed outlier: 4.283A pdb=" N GLY B 360 " --> pdb=" O ILE B 356 " (cutoff:3.500A)
Processing helix chain 'B' and resid 364 through 372
removed outlier: 4.201A pdb=" N TYR B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A)
Processing helix chain 'C' and resid 3 through 11
Processing helix chain 'C' and resid 32 through 54
Proline residue: C 46 - end of helix
removed outlier: 3.690A pdb=" N PHE C 54 " --> pdb=" O ILE C 50 " (cutoff:3.500A)
Processing helix chain 'C' and resid 73 through 91
removed outlier: 4.443A pdb=" N GLN C 89 " --> pdb=" O TRP C 85 " (cutoff:3.500A)
removed outlier: 4.262A pdb=" N GLN C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A)
Processing helix chain 'C' and resid 102 through 131
Proline residue: C 110 - end of helix
Proline residue: C 123 - end of helix
Processing helix chain 'C' and resid 131 through 158
Processing helix chain 'C' and resid 197 through 207
removed outlier: 3.794A pdb=" N ASN C 207 " --> pdb=" O LYS C 203 " (cutoff:3.500A)
Processing helix chain 'C' and resid 209 through 240
Processing helix chain 'C' and resid 252 through 256
removed outlier: 4.279A pdb=" N LEU C 255 " --> pdb=" O THR C 252 " (cutoff:3.500A)
Processing helix chain 'C' and resid 271 through 298
Proline residue: C 291 - end of helix
removed outlier: 3.686A pdb=" N ILE C 294 " --> pdb=" O MET C 290 " (cutoff:3.500A)
Processing helix chain 'C' and resid 307 through 312
removed outlier: 3.920A pdb=" N TYR C 311 " --> pdb=" O VAL C 307 " (cutoff:3.500A)
Processing helix chain 'C' and resid 328 through 340
Processing helix chain 'C' and resid 341 through 344
Processing helix chain 'C' and resid 345 through 360
removed outlier: 3.774A pdb=" N THR C 359 " --> pdb=" O ASN C 355 " (cutoff:3.500A)
removed outlier: 4.283A pdb=" N GLY C 360 " --> pdb=" O ILE C 356 " (cutoff:3.500A)
Processing helix chain 'C' and resid 364 through 372
removed outlier: 4.200A pdb=" N TYR C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A)
Processing helix chain 'D' and resid 3 through 11
Processing helix chain 'D' and resid 32 through 54
Proline residue: D 46 - end of helix
removed outlier: 3.690A pdb=" N PHE D 54 " --> pdb=" O ILE D 50 " (cutoff:3.500A)
Processing helix chain 'D' and resid 73 through 91
removed outlier: 4.442A pdb=" N GLN D 89 " --> pdb=" O TRP D 85 " (cutoff:3.500A)
removed outlier: 4.262A pdb=" N GLN D 90 " --> pdb=" O ALA D 86 " (cutoff:3.500A)
Processing helix chain 'D' and resid 102 through 131
Proline residue: D 110 - end of helix
Proline residue: D 123 - end of helix
Processing helix chain 'D' and resid 131 through 158
Processing helix chain 'D' and resid 197 through 207
removed outlier: 3.794A pdb=" N ASN D 207 " --> pdb=" O LYS D 203 " (cutoff:3.500A)
Processing helix chain 'D' and resid 209 through 240
Processing helix chain 'D' and resid 252 through 256
removed outlier: 4.280A pdb=" N LEU D 255 " --> pdb=" O THR D 252 " (cutoff:3.500A)
Processing helix chain 'D' and resid 271 through 298
Proline residue: D 291 - end of helix
removed outlier: 3.686A pdb=" N ILE D 294 " --> pdb=" O MET D 290 " (cutoff:3.500A)
Processing helix chain 'D' and resid 307 through 312
removed outlier: 3.920A pdb=" N TYR D 311 " --> pdb=" O VAL D 307 " (cutoff:3.500A)
Processing helix chain 'D' and resid 328 through 340
Processing helix chain 'D' and resid 341 through 344
Processing helix chain 'D' and resid 345 through 360
removed outlier: 3.773A pdb=" N THR D 359 " --> pdb=" O ASN D 355 " (cutoff:3.500A)
removed outlier: 4.283A pdb=" N GLY D 360 " --> pdb=" O ILE D 356 " (cutoff:3.500A)
Processing helix chain 'D' and resid 364 through 372
removed outlier: 4.201A pdb=" N TYR D 368 " --> pdb=" O ASP D 364 " (cutoff:3.500A)
Processing helix chain 'E' and resid 3 through 11
Processing helix chain 'E' and resid 32 through 54
Proline residue: E 46 - end of helix
removed outlier: 3.690A pdb=" N PHE E 54 " --> pdb=" O ILE E 50 " (cutoff:3.500A)
Processing helix chain 'E' and resid 73 through 91
removed outlier: 4.442A pdb=" N GLN E 89 " --> pdb=" O TRP E 85 " (cutoff:3.500A)
removed outlier: 4.262A pdb=" N GLN E 90 " --> pdb=" O ALA E 86 " (cutoff:3.500A)
Processing helix chain 'E' and resid 102 through 131
Proline residue: E 110 - end of helix
Proline residue: E 123 - end of helix
Processing helix chain 'E' and resid 131 through 158
Processing helix chain 'E' and resid 197 through 207
removed outlier: 3.795A pdb=" N ASN E 207 " --> pdb=" O LYS E 203 " (cutoff:3.500A)
Processing helix chain 'E' and resid 209 through 240
Processing helix chain 'E' and resid 252 through 256
removed outlier: 4.280A pdb=" N LEU E 255 " --> pdb=" O THR E 252 " (cutoff:3.500A)
Processing helix chain 'E' and resid 271 through 298
Proline residue: E 291 - end of helix
removed outlier: 3.687A pdb=" N ILE E 294 " --> pdb=" O MET E 290 " (cutoff:3.500A)
Processing helix chain 'E' and resid 307 through 312
removed outlier: 3.920A pdb=" N TYR E 311 " --> pdb=" O VAL E 307 " (cutoff:3.500A)
Processing helix chain 'E' and resid 328 through 340
Processing helix chain 'E' and resid 341 through 344
Processing helix chain 'E' and resid 345 through 360
removed outlier: 3.773A pdb=" N THR E 359 " --> pdb=" O ASN E 355 " (cutoff:3.500A)
removed outlier: 4.284A pdb=" N GLY E 360 " --> pdb=" O ILE E 356 " (cutoff:3.500A)
Processing helix chain 'E' and resid 364 through 372
removed outlier: 4.200A pdb=" N TYR E 368 " --> pdb=" O ASP E 364 " (cutoff:3.500A)
Processing helix chain 'F' and resid 3 through 11
Processing helix chain 'F' and resid 32 through 54
Proline residue: F 46 - end of helix
removed outlier: 3.690A pdb=" N PHE F 54 " --> pdb=" O ILE F 50 " (cutoff:3.500A)
Processing helix chain 'F' and resid 73 through 91
removed outlier: 4.443A pdb=" N GLN F 89 " --> pdb=" O TRP F 85 " (cutoff:3.500A)
removed outlier: 4.261A pdb=" N GLN F 90 " --> pdb=" O ALA F 86 " (cutoff:3.500A)
Processing helix chain 'F' and resid 102 through 131
Proline residue: F 110 - end of helix
Proline residue: F 123 - end of helix
Processing helix chain 'F' and resid 131 through 158
Processing helix chain 'F' and resid 197 through 207
removed outlier: 3.795A pdb=" N ASN F 207 " --> pdb=" O LYS F 203 " (cutoff:3.500A)
Processing helix chain 'F' and resid 209 through 240
Processing helix chain 'F' and resid 252 through 256
removed outlier: 4.280A pdb=" N LEU F 255 " --> pdb=" O THR F 252 " (cutoff:3.500A)
Processing helix chain 'F' and resid 271 through 298
Proline residue: F 291 - end of helix
removed outlier: 3.686A pdb=" N ILE F 294 " --> pdb=" O MET F 290 " (cutoff:3.500A)
Processing helix chain 'F' and resid 307 through 312
removed outlier: 3.920A pdb=" N TYR F 311 " --> pdb=" O VAL F 307 " (cutoff:3.500A)
Processing helix chain 'F' and resid 328 through 340
Processing helix chain 'F' and resid 341 through 344
Processing helix chain 'F' and resid 345 through 360
removed outlier: 3.774A pdb=" N THR F 359 " --> pdb=" O ASN F 355 " (cutoff:3.500A)
removed outlier: 4.284A pdb=" N GLY F 360 " --> pdb=" O ILE F 356 " (cutoff:3.500A)
Processing helix chain 'F' and resid 364 through 372
removed outlier: 4.201A pdb=" N TYR F 368 " --> pdb=" O ASP F 364 " (cutoff:3.500A)
Processing helix chain 'G' and resid 3 through 11
Processing helix chain 'G' and resid 32 through 54
Proline residue: G 46 - end of helix
removed outlier: 3.690A pdb=" N PHE G 54 " --> pdb=" O ILE G 50 " (cutoff:3.500A)
Processing helix chain 'G' and resid 73 through 91
removed outlier: 4.443A pdb=" N GLN G 89 " --> pdb=" O TRP G 85 " (cutoff:3.500A)
removed outlier: 4.262A pdb=" N GLN G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A)
Processing helix chain 'G' and resid 102 through 131
Proline residue: G 110 - end of helix
Proline residue: G 123 - end of helix
Processing helix chain 'G' and resid 131 through 158
Processing helix chain 'G' and resid 197 through 207
removed outlier: 3.796A pdb=" N ASN G 207 " --> pdb=" O LYS G 203 " (cutoff:3.500A)
Processing helix chain 'G' and resid 209 through 240
Processing helix chain 'G' and resid 252 through 256
removed outlier: 4.280A pdb=" N LEU G 255 " --> pdb=" O THR G 252 " (cutoff:3.500A)
Processing helix chain 'G' and resid 271 through 298
Proline residue: G 291 - end of helix
removed outlier: 3.686A pdb=" N ILE G 294 " --> pdb=" O MET G 290 " (cutoff:3.500A)
Processing helix chain 'G' and resid 307 through 312
removed outlier: 3.920A pdb=" N TYR G 311 " --> pdb=" O VAL G 307 " (cutoff:3.500A)
Processing helix chain 'G' and resid 328 through 340
Processing helix chain 'G' and resid 341 through 344
Processing helix chain 'G' and resid 345 through 360
removed outlier: 3.773A pdb=" N THR G 359 " --> pdb=" O ASN G 355 " (cutoff:3.500A)
removed outlier: 4.283A pdb=" N GLY G 360 " --> pdb=" O ILE G 356 " (cutoff:3.500A)
Processing helix chain 'G' and resid 364 through 372
removed outlier: 4.201A pdb=" N TYR G 368 " --> pdb=" O ASP G 364 " (cutoff:3.500A)
Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 66
Processing sheet with id=AA2, first strand: chain 'B' and resid 64 through 66
Processing sheet with id=AA3, first strand: chain 'C' and resid 64 through 66
Processing sheet with id=AA4, first strand: chain 'D' and resid 64 through 66
Processing sheet with id=AA5, first strand: chain 'E' and resid 64 through 66
Processing sheet with id=AA6, first strand: chain 'F' and resid 64 through 66
Processing sheet with id=AA7, first strand: chain 'G' and resid 64 through 66
1142 hydrogen bonds defined for protein.
3363 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: 5.47
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:
1.23 - 1.35: 5383
1.35 - 1.47: 4718
1.47 - 1.58: 8519
1.58 - 1.70: 0
1.70 - 1.82: 98
Bond restraints: 18718
Sorted by residual:
bond pdb=" CA VAL A 101 "
pdb=" C VAL A 101 "
ideal model delta sigma weight residual
1.525 1.551 -0.026 2.10e-02 2.27e+03 1.59e+00
bond pdb=" CA VAL C 101 "
pdb=" C VAL C 101 "
ideal model delta sigma weight residual
1.525 1.551 -0.026 2.10e-02 2.27e+03 1.59e+00
bond pdb=" CA VAL G 101 "
pdb=" C VAL G 101 "
ideal model delta sigma weight residual
1.525 1.551 -0.026 2.10e-02 2.27e+03 1.56e+00
bond pdb=" CA VAL B 101 "
pdb=" C VAL B 101 "
ideal model delta sigma weight residual
1.525 1.550 -0.025 2.10e-02 2.27e+03 1.47e+00
bond pdb=" CA VAL F 101 "
pdb=" C VAL F 101 "
ideal model delta sigma weight residual
1.525 1.550 -0.025 2.10e-02 2.27e+03 1.47e+00
... (remaining 18713 not shown)
Histogram of bond angle deviations from ideal:
0.00 - 1.32: 24846
1.32 - 2.65: 445
2.65 - 3.97: 84
3.97 - 5.29: 56
5.29 - 6.61: 14
Bond angle restraints: 25445
Sorted by residual:
angle pdb=" CA VAL B 101 "
pdb=" C VAL B 101 "
pdb=" N PRO B 102 "
ideal model delta sigma weight residual
116.90 120.02 -3.12 1.50e+00 4.44e-01 4.33e+00
angle pdb=" CA VAL F 101 "
pdb=" C VAL F 101 "
pdb=" N PRO F 102 "
ideal model delta sigma weight residual
116.90 120.01 -3.11 1.50e+00 4.44e-01 4.29e+00
angle pdb=" CA VAL C 101 "
pdb=" C VAL C 101 "
pdb=" N PRO C 102 "
ideal model delta sigma weight residual
116.90 119.97 -3.07 1.50e+00 4.44e-01 4.20e+00
angle pdb=" CA VAL D 101 "
pdb=" C VAL D 101 "
pdb=" N PRO D 102 "
ideal model delta sigma weight residual
116.90 119.97 -3.07 1.50e+00 4.44e-01 4.20e+00
angle pdb=" CA VAL E 101 "
pdb=" C VAL E 101 "
pdb=" N PRO E 102 "
ideal model delta sigma weight residual
116.90 119.97 -3.07 1.50e+00 4.44e-01 4.18e+00
... (remaining 25440 not shown)
Histogram of dihedral angle deviations from ideal:
0.00 - 16.87: 9591
16.87 - 33.74: 1082
33.74 - 50.61: 378
50.61 - 67.48: 35
67.48 - 84.36: 22
Dihedral angle restraints: 11108
sinusoidal: 4367
harmonic: 6741
Sorted by residual:
dihedral pdb=" CB CYS A 84 "
pdb=" SG CYS A 84 "
pdb=" SG CYS A 248 "
pdb=" CB CYS A 248 "
ideal model delta sinusoidal sigma weight residual
93.00 15.39 77.61 1 1.00e+01 1.00e-02 7.54e+01
dihedral pdb=" CA ASP E 364 "
pdb=" CB ASP E 364 "
pdb=" CG ASP E 364 "
pdb=" OD1 ASP E 364 "
ideal model delta sinusoidal sigma weight residual
-30.00 -89.73 59.73 1 2.00e+01 2.50e-03 1.19e+01
dihedral pdb=" CA ASP C 364 "
pdb=" CB ASP C 364 "
pdb=" CG ASP C 364 "
pdb=" OD1 ASP C 364 "
ideal model delta sinusoidal sigma weight residual
-30.00 -89.71 59.71 1 2.00e+01 2.50e-03 1.19e+01
... (remaining 11105 not shown)
Histogram of chiral volume deviations from ideal:
0.000 - 0.052: 2539
0.052 - 0.103: 475
0.103 - 0.155: 24
0.155 - 0.206: 0
0.206 - 0.258: 7
Chirality restraints: 3045
Sorted by residual:
chirality pdb=" CB ILE A 217 "
pdb=" CA ILE A 217 "
pdb=" CG1 ILE A 217 "
pdb=" CG2 ILE A 217 "
both_signs ideal model delta sigma weight residual
False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.66e+00
chirality pdb=" CB ILE C 217 "
pdb=" CA ILE C 217 "
pdb=" CG1 ILE C 217 "
pdb=" CG2 ILE C 217 "
both_signs ideal model delta sigma weight residual
False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.63e+00
chirality pdb=" CB ILE G 217 "
pdb=" CA ILE G 217 "
pdb=" CG1 ILE G 217 "
pdb=" CG2 ILE G 217 "
both_signs ideal model delta sigma weight residual
False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.63e+00
... (remaining 3042 not shown)
Planarity restraints: 3052
Sorted by residual:
delta sigma weight rms_deltas residual
plane pdb=" CD ARG B 29 " -0.065 9.50e-02 1.11e+02 2.92e-02 6.65e-01
pdb=" NE ARG B 29 " 0.006 2.00e-02 2.50e+03
pdb=" CZ ARG B 29 " -0.006 2.00e-02 2.50e+03
pdb=" NH1 ARG B 29 " 0.003 2.00e-02 2.50e+03
pdb=" NH2 ARG B 29 " -0.000 2.00e-02 2.50e+03
delta sigma weight rms_deltas residual
plane pdb=" CD ARG D 29 " 0.064 9.50e-02 1.11e+02 2.90e-02 6.64e-01
pdb=" NE ARG D 29 " -0.006 2.00e-02 2.50e+03
pdb=" CZ ARG D 29 " 0.006 2.00e-02 2.50e+03
pdb=" NH1 ARG D 29 " -0.003 2.00e-02 2.50e+03
pdb=" NH2 ARG D 29 " 0.000 2.00e-02 2.50e+03
delta sigma weight rms_deltas residual
plane pdb=" CD ARG C 29 " 0.064 9.50e-02 1.11e+02 2.88e-02 6.61e-01
pdb=" NE ARG C 29 " -0.006 2.00e-02 2.50e+03
pdb=" CZ ARG C 29 " 0.006 2.00e-02 2.50e+03
pdb=" NH1 ARG C 29 " -0.003 2.00e-02 2.50e+03
pdb=" NH2 ARG C 29 " 0.000 2.00e-02 2.50e+03
... (remaining 3049 not shown)
Histogram of nonbonded interaction distances:
2.03 - 2.60: 121
2.60 - 3.18: 15335
3.18 - 3.75: 29563
3.75 - 4.33: 37205
4.33 - 4.90: 65176
Nonbonded interactions: 147400
Sorted by model distance:
nonbonded pdb=" SG CYS B 84 "
pdb=" SG CYS B 248 "
model vdw
2.029 3.760
nonbonded pdb=" SG CYS E 84 "
pdb=" SG CYS E 248 "
model vdw
2.029 3.760
nonbonded pdb=" SG CYS D 84 "
pdb=" SG CYS D 248 "
model vdw
2.029 3.760
nonbonded pdb=" SG CYS C 84 "
pdb=" SG CYS C 248 "
model vdw
2.030 3.760
nonbonded pdb=" SG CYS G 84 "
pdb=" SG CYS G 248 "
model vdw
2.030 3.760
... (remaining 147395 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: 0.12
Found NCS groups:
ncs_group {
reference = chain 'A'
selection = chain 'C'
selection = chain 'B'
selection = chain 'E'
selection = chain 'D'
selection = chain 'G'
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: 0.720
Set stop_for_unknowns flag: 0.000
Assert model is a single copy model: 0.000
Assert all atoms have isotropic ADPs: 0.010
Construct map_model_manager: 0.010
Extract box with map and model: 0.650
Check model and map are aligned: 0.130
Set scattering table: 0.160
Process input model: 35.130
Find NCS groups from input model: 0.310
Set up NCS constraints: 0.030
Set refine NCS operators: 0.000
Adjust number of macro_cycles: 0.000
Reset NCS operators: 0.000
Extract rigid body selections: 0.000
Check and reset occupancies: 0.010
Load rotamer database and sin/cos tables:12.820
Set ADP refinement strategy: 0.000
Make a string to write initial .geo file:0.000
Internal consistency checks: 0.000
Total: 49.980
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8322
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 : 0.002 0.026 18718 Z= 0.140
Angle : 0.512 6.613 25445 Z= 0.259
Chirality : 0.038 0.258 3045
Planarity : 0.003 0.029 3052
Dihedral : 16.193 84.356 6720
Min Nonbonded Distance : 2.029
Molprobity Statistics.
All-atom Clashscore : 7.04
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 2.23 %
Favored : 97.77 %
Rotamer:
Outliers : 2.73 %
Allowed : 22.53 %
Favored : 74.74 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 2.18 (0.18), residues: 2198
helix: 2.54 (0.13), residues: 1505
sheet: 0.26 (0.47), residues: 91
loop : -1.34 (0.26), residues: 602
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.008 0.001 TRP A 74
HIS 0.001 0.000 HIS C 106
PHE 0.008 0.001 PHE B 12
TYR 0.006 0.001 TYR A 232
ARG 0.007 0.001 ARG C 29
*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
4396 Ramachandran restraints generated.
2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
4396 Ramachandran restraints generated.
2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
445 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 56
poor density : 389
time to evaluate : 2.205
Fit side-chains
revert: symmetry clash
revert: symmetry clash
REVERT: A 152 ARG cc_start: 0.6923 (ptm-80) cc_final: 0.6338 (mtm110)
REVERT: A 354 GLU cc_start: 0.8961 (tp30) cc_final: 0.8484 (tp30)
REVERT: A 358 ASN cc_start: 0.8702 (t0) cc_final: 0.8397 (t0)
REVERT: B 152 ARG cc_start: 0.6669 (ptm-80) cc_final: 0.6132 (mtm110)
REVERT: B 354 GLU cc_start: 0.8884 (tp30) cc_final: 0.8602 (tp30)
REVERT: B 358 ASN cc_start: 0.8710 (t0) cc_final: 0.8374 (t0)
REVERT: C 14 ASP cc_start: 0.8010 (m-30) cc_final: 0.7777 (p0)
REVERT: C 152 ARG cc_start: 0.6764 (ptm-80) cc_final: 0.6278 (mtm110)
REVERT: C 354 GLU cc_start: 0.8941 (tp30) cc_final: 0.8694 (tp30)
REVERT: D 152 ARG cc_start: 0.6761 (ptm-80) cc_final: 0.6240 (mtm110)
REVERT: D 240 PHE cc_start: 0.7038 (OUTLIER) cc_final: 0.5983 (m-80)
REVERT: D 354 GLU cc_start: 0.8943 (tp30) cc_final: 0.8691 (tp30)
REVERT: E 152 ARG cc_start: 0.6982 (ptm-80) cc_final: 0.6399 (mtm110)
REVERT: E 354 GLU cc_start: 0.8967 (tp30) cc_final: 0.8702 (tp30)
REVERT: F 152 ARG cc_start: 0.6876 (ptm-80) cc_final: 0.6446 (mtm110)
REVERT: F 354 GLU cc_start: 0.8969 (tp30) cc_final: 0.8553 (tp30)
REVERT: F 358 ASN cc_start: 0.8695 (t0) cc_final: 0.8446 (t0)
REVERT: G 152 ARG cc_start: 0.6832 (ptm-80) cc_final: 0.6233 (mtm110)
REVERT: G 354 GLU cc_start: 0.9005 (tp30) cc_final: 0.8740 (tp30)
outliers start: 56
outliers final: 19
residues processed: 416
average time/residue: 1.4052
time to fit residues: 649.9510
Evaluate side-chains
270 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 20
poor density : 250
time to evaluate : 2.070
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 13 SER
Chi-restraints excluded: chain A residue 124 ASN
Chi-restraints excluded: chain B residue 13 SER
Chi-restraints excluded: chain B residue 101 VAL
Chi-restraints excluded: chain B residue 124 ASN
Chi-restraints excluded: chain C residue 13 SER
Chi-restraints excluded: chain C residue 101 VAL
Chi-restraints excluded: chain C residue 124 ASN
Chi-restraints excluded: chain D residue 13 SER
Chi-restraints excluded: chain D residue 101 VAL
Chi-restraints excluded: chain D residue 124 ASN
Chi-restraints excluded: chain D residue 240 PHE
Chi-restraints excluded: chain E residue 13 SER
Chi-restraints excluded: chain E residue 124 ASN
Chi-restraints excluded: chain E residue 255 LEU
Chi-restraints excluded: chain F residue 13 SER
Chi-restraints excluded: chain F residue 101 VAL
Chi-restraints excluded: chain F residue 124 ASN
Chi-restraints excluded: chain G residue 101 VAL
Chi-restraints excluded: chain G residue 240 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 224
random chunks:
chunk 189 optimal weight: 10.0000
chunk 169 optimal weight: 5.9990
chunk 94 optimal weight: 9.9990
chunk 57 optimal weight: 20.0000
chunk 114 optimal weight: 6.9990
chunk 90 optimal weight: 7.9990
chunk 175 optimal weight: 5.9990
chunk 67 optimal weight: 6.9990
chunk 106 optimal weight: 2.9990
chunk 130 optimal weight: 3.9990
chunk 203 optimal weight: 0.8980
overall best weight: 3.9788
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 266 GLN
A 355 ASN
B 56 GLN
B 266 GLN
B 282 ASN
B 355 ASN
C 266 GLN
C 355 ASN
D 266 GLN
D 355 ASN
E 266 GLN
E 355 ASN
F 266 GLN
F 355 ASN
G 56 GLN
G 266 GLN
G 355 ASN
Total number of N/Q/H flips: 17
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.124592 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3113 r_free = 0.3113 target = 0.082071 restraints weight = 31089.026|
|-----------------------------------------------------------------------------|
r_work (start): 0.3059 rms_B_bonded: 2.46
r_work: 0.2917 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work (final): 0.2917
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8274
moved from start: 0.2066
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.006 0.041 18718 Z= 0.384
Angle : 0.654 8.069 25445 Z= 0.321
Chirality : 0.042 0.215 3045
Planarity : 0.004 0.033 3052
Dihedral : 4.527 48.643 2451
Min Nonbonded Distance : 2.570
Molprobity Statistics.
All-atom Clashscore : 6.42
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 1.82 %
Favored : 98.18 %
Rotamer:
Outliers : 6.58 %
Allowed : 23.84 %
Favored : 69.58 %
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: 1.99 (0.19), residues: 2198
helix: 2.33 (0.13), residues: 1526
sheet: 0.05 (0.48), residues: 126
loop : -1.41 (0.28), residues: 546
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.011 0.002 TRP C 127
HIS 0.005 0.001 HIS B 106
PHE 0.017 0.002 PHE B 333
TYR 0.024 0.002 TYR A 232
ARG 0.005 0.001 ARG B 128
*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
4396 Ramachandran restraints generated.
2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
4396 Ramachandran restraints generated.
2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
392 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 135
poor density : 257
time to evaluate : 2.242
Fit side-chains
revert: symmetry clash
revert: symmetry clash
REVERT: A 14 ASP cc_start: 0.8461 (m-30) cc_final: 0.7980 (t0)
REVERT: A 124 ASN cc_start: 0.8186 (OUTLIER) cc_final: 0.7900 (p0)
REVERT: A 144 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.8043 (mp0)
REVERT: A 152 ARG cc_start: 0.6231 (ptm-80) cc_final: 0.5800 (mtm110)
REVERT: A 240 PHE cc_start: 0.7572 (OUTLIER) cc_final: 0.7047 (m-80)
REVERT: A 358 ASN cc_start: 0.8787 (t0) cc_final: 0.8439 (t0)
REVERT: B 14 ASP cc_start: 0.8661 (m-30) cc_final: 0.7825 (p0)
REVERT: B 144 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.8091 (mp0)
REVERT: B 152 ARG cc_start: 0.6177 (ptm-80) cc_final: 0.5756 (mtm110)
REVERT: B 240 PHE cc_start: 0.7658 (OUTLIER) cc_final: 0.7341 (m-80)
REVERT: B 358 ASN cc_start: 0.8810 (t0) cc_final: 0.8416 (t0)
REVERT: C 14 ASP cc_start: 0.8604 (m-30) cc_final: 0.7747 (p0)
REVERT: C 152 ARG cc_start: 0.6071 (ptm-80) cc_final: 0.5739 (mtm110)
REVERT: C 297 MET cc_start: 0.8132 (OUTLIER) cc_final: 0.7524 (pmm)
REVERT: D 124 ASN cc_start: 0.8204 (OUTLIER) cc_final: 0.7920 (p0)
REVERT: D 152 ARG cc_start: 0.6185 (ptm-80) cc_final: 0.5760 (mtm110)
REVERT: D 306 ASN cc_start: 0.7685 (t0) cc_final: 0.7438 (t0)
REVERT: E 14 ASP cc_start: 0.8591 (m-30) cc_final: 0.7868 (p0)
REVERT: E 144 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7896 (mp0)
REVERT: E 152 ARG cc_start: 0.6220 (ptm-80) cc_final: 0.5770 (mtm110)
REVERT: E 200 GLN cc_start: 0.8869 (mm-40) cc_final: 0.8306 (mm-40)
REVERT: E 297 MET cc_start: 0.7861 (pmm) cc_final: 0.7592 (pmm)
REVERT: E 306 ASN cc_start: 0.7541 (t0) cc_final: 0.7060 (t0)
REVERT: F 14 ASP cc_start: 0.8552 (m-30) cc_final: 0.7899 (t70)
REVERT: F 152 ARG cc_start: 0.6236 (ptm-80) cc_final: 0.5970 (mtp-110)
REVERT: F 358 ASN cc_start: 0.8860 (t0) cc_final: 0.8580 (t0)
REVERT: G 14 ASP cc_start: 0.8603 (m-30) cc_final: 0.7869 (p0)
REVERT: G 144 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7930 (mp0)
REVERT: G 152 ARG cc_start: 0.6131 (ptm-80) cc_final: 0.5669 (mtm110)
REVERT: G 317 PHE cc_start: 0.7912 (OUTLIER) cc_final: 0.7590 (m-80)
outliers start: 135
outliers final: 47
residues processed: 363
average time/residue: 1.2245
time to fit residues: 502.0790
Evaluate side-chains
302 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 57
poor density : 245
time to evaluate : 2.123
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 124 ASN
Chi-restraints excluded: chain A residue 144 GLU
Chi-restraints excluded: chain A residue 154 ILE
Chi-restraints excluded: chain A residue 224 ILE
Chi-restraints excluded: chain A residue 240 PHE
Chi-restraints excluded: chain A residue 242 LEU
Chi-restraints excluded: chain A residue 255 LEU
Chi-restraints excluded: chain A residue 287 VAL
Chi-restraints excluded: chain A residue 313 VAL
Chi-restraints excluded: chain A residue 352 VAL
Chi-restraints excluded: chain B residue 101 VAL
Chi-restraints excluded: chain B residue 144 GLU
Chi-restraints excluded: chain B residue 224 ILE
Chi-restraints excluded: chain B residue 240 PHE
Chi-restraints excluded: chain B residue 242 LEU
Chi-restraints excluded: chain B residue 255 LEU
Chi-restraints excluded: chain B residue 352 VAL
Chi-restraints excluded: chain C residue 16 LEU
Chi-restraints excluded: chain C residue 101 VAL
Chi-restraints excluded: chain C residue 144 GLU
Chi-restraints excluded: chain C residue 224 ILE
Chi-restraints excluded: chain C residue 242 LEU
Chi-restraints excluded: chain C residue 255 LEU
Chi-restraints excluded: chain C residue 287 VAL
Chi-restraints excluded: chain C residue 297 MET
Chi-restraints excluded: chain C residue 352 VAL
Chi-restraints excluded: chain D residue 34 VAL
Chi-restraints excluded: chain D residue 101 VAL
Chi-restraints excluded: chain D residue 124 ASN
Chi-restraints excluded: chain D residue 224 ILE
Chi-restraints excluded: chain D residue 240 PHE
Chi-restraints excluded: chain D residue 242 LEU
Chi-restraints excluded: chain D residue 287 VAL
Chi-restraints excluded: chain E residue 124 ASN
Chi-restraints excluded: chain E residue 144 GLU
Chi-restraints excluded: chain E residue 202 LEU
Chi-restraints excluded: chain E residue 224 ILE
Chi-restraints excluded: chain E residue 242 LEU
Chi-restraints excluded: chain E residue 255 LEU
Chi-restraints excluded: chain E residue 287 VAL
Chi-restraints excluded: chain E residue 352 VAL
Chi-restraints excluded: chain F residue 101 VAL
Chi-restraints excluded: chain F residue 124 ASN
Chi-restraints excluded: chain F residue 224 ILE
Chi-restraints excluded: chain F residue 240 PHE
Chi-restraints excluded: chain F residue 242 LEU
Chi-restraints excluded: chain F residue 255 LEU
Chi-restraints excluded: chain F residue 287 VAL
Chi-restraints excluded: chain F residue 341 VAL
Chi-restraints excluded: chain F residue 352 VAL
Chi-restraints excluded: chain G residue 144 GLU
Chi-restraints excluded: chain G residue 224 ILE
Chi-restraints excluded: chain G residue 240 PHE
Chi-restraints excluded: chain G residue 242 LEU
Chi-restraints excluded: chain G residue 287 VAL
Chi-restraints excluded: chain G residue 317 PHE
Chi-restraints excluded: chain G residue 352 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 224
random chunks:
chunk 35 optimal weight: 9.9990
chunk 55 optimal weight: 0.8980
chunk 110 optimal weight: 9.9990
chunk 84 optimal weight: 2.9990
chunk 141 optimal weight: 5.9990
chunk 39 optimal weight: 2.9990
chunk 6 optimal weight: 3.9990
chunk 18 optimal weight: 2.9990
chunk 164 optimal weight: 2.9990
chunk 210 optimal weight: 2.9990
chunk 144 optimal weight: 0.9990
overall best weight: 2.1788
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
B 355 ASN
C 266 GLN
C 355 ASN
D 355 ASN
E 355 ASN
F 355 ASN
G 5 HIS
G 56 GLN
G 355 ASN
Total number of N/Q/H flips: 9
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.124791 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3114 r_free = 0.3114 target = 0.082228 restraints weight = 30706.831|
|-----------------------------------------------------------------------------|
r_work (start): 0.3065 rms_B_bonded: 2.46
r_work: 0.2925 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.2925
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8287
moved from start: 0.2252
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.004 0.049 18718 Z= 0.251
Angle : 0.598 8.078 25445 Z= 0.289
Chirality : 0.040 0.182 3045
Planarity : 0.003 0.029 3052
Dihedral : 4.332 51.724 2440
Min Nonbonded Distance : 2.617
Molprobity Statistics.
All-atom Clashscore : 5.86
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 1.87 %
Favored : 98.13 %
Rotamer:
Outliers : 6.09 %
Allowed : 23.26 %
Favored : 70.65 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 2.04 (0.19), residues: 2198
helix: 2.36 (0.13), residues: 1526
sheet: 0.25 (0.48), residues: 126
loop : -1.42 (0.28), residues: 546
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.007 0.001 TRP F 85
HIS 0.003 0.001 HIS B 106
PHE 0.010 0.001 PHE D 240
TYR 0.022 0.002 TYR E 232
ARG 0.005 0.001 ARG F 29
*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
4396 Ramachandran restraints generated.
2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
4396 Ramachandran restraints generated.
2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
374 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 125
poor density : 249
time to evaluate : 1.981
Fit side-chains
revert: symmetry clash
REVERT: A 14 ASP cc_start: 0.8435 (m-30) cc_final: 0.7996 (t0)
REVERT: A 124 ASN cc_start: 0.8138 (OUTLIER) cc_final: 0.7853 (p0)
REVERT: A 144 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.7995 (mp0)
REVERT: A 152 ARG cc_start: 0.6295 (ptm-80) cc_final: 0.5803 (mtm110)
REVERT: A 240 PHE cc_start: 0.7702 (OUTLIER) cc_final: 0.7151 (m-80)
REVERT: A 358 ASN cc_start: 0.8802 (t0) cc_final: 0.8458 (t0)
REVERT: B 14 ASP cc_start: 0.8604 (m-30) cc_final: 0.7819 (p0)
REVERT: B 144 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.8014 (mp0)
REVERT: B 152 ARG cc_start: 0.6239 (ptm-80) cc_final: 0.5741 (mtm110)
REVERT: B 240 PHE cc_start: 0.7673 (OUTLIER) cc_final: 0.7376 (m-80)
REVERT: B 266 GLN cc_start: 0.8666 (OUTLIER) cc_final: 0.8243 (tt0)
REVERT: B 306 ASN cc_start: 0.7534 (t0) cc_final: 0.7036 (t0)
REVERT: B 309 LYS cc_start: 0.9084 (mmtt) cc_final: 0.8865 (mmtp)
REVERT: B 358 ASN cc_start: 0.8833 (t0) cc_final: 0.8449 (t0)
REVERT: C 14 ASP cc_start: 0.8462 (m-30) cc_final: 0.7701 (p0)
REVERT: C 152 ARG cc_start: 0.6123 (ptm-80) cc_final: 0.5746 (mtm110)
REVERT: D 14 ASP cc_start: 0.8290 (m-30) cc_final: 0.7593 (p0)
REVERT: D 124 ASN cc_start: 0.8254 (OUTLIER) cc_final: 0.7975 (p0)
REVERT: D 152 ARG cc_start: 0.6203 (ptm-80) cc_final: 0.5707 (mtm110)
REVERT: D 290 MET cc_start: 0.8874 (OUTLIER) cc_final: 0.8639 (mmm)
REVERT: D 306 ASN cc_start: 0.7582 (t0) cc_final: 0.7319 (t0)
REVERT: E 14 ASP cc_start: 0.8505 (m-30) cc_final: 0.7787 (p0)
REVERT: E 144 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7920 (mp0)
REVERT: E 152 ARG cc_start: 0.6210 (ptm-80) cc_final: 0.5752 (mtm110)
REVERT: E 266 GLN cc_start: 0.8747 (OUTLIER) cc_final: 0.8438 (tt0)
REVERT: E 297 MET cc_start: 0.7957 (OUTLIER) cc_final: 0.7714 (pmm)
REVERT: E 306 ASN cc_start: 0.7553 (t0) cc_final: 0.7286 (t0)
REVERT: F 14 ASP cc_start: 0.8573 (m-30) cc_final: 0.7864 (t0)
REVERT: F 124 ASN cc_start: 0.8136 (OUTLIER) cc_final: 0.7828 (p0)
REVERT: F 152 ARG cc_start: 0.6210 (ptm-80) cc_final: 0.5861 (mtm110)
REVERT: F 358 ASN cc_start: 0.8866 (t0) cc_final: 0.8585 (t0)
REVERT: G 14 ASP cc_start: 0.8522 (m-30) cc_final: 0.7824 (p0)
REVERT: G 29 ARG cc_start: 0.8883 (mtm-85) cc_final: 0.8615 (mtt180)
REVERT: G 128 ARG cc_start: 0.8649 (tmm-80) cc_final: 0.8390 (ttt-90)
REVERT: G 144 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7839 (mp0)
REVERT: G 152 ARG cc_start: 0.6259 (ptm-80) cc_final: 0.5728 (mtm110)
REVERT: G 266 GLN cc_start: 0.8909 (OUTLIER) cc_final: 0.8416 (tt0)
REVERT: G 317 PHE cc_start: 0.7905 (OUTLIER) cc_final: 0.7584 (m-80)
outliers start: 125
outliers final: 52
residues processed: 347
average time/residue: 1.0926
time to fit residues: 435.8256
Evaluate side-chains
307 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 67
poor density : 240
time to evaluate : 1.805
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 30 LEU
Chi-restraints excluded: chain A residue 124 ASN
Chi-restraints excluded: chain A residue 144 GLU
Chi-restraints excluded: chain A residue 154 ILE
Chi-restraints excluded: chain A residue 223 LEU
Chi-restraints excluded: chain A residue 224 ILE
Chi-restraints excluded: chain A residue 240 PHE
Chi-restraints excluded: chain A residue 242 LEU
Chi-restraints excluded: chain A residue 255 LEU
Chi-restraints excluded: chain A residue 287 VAL
Chi-restraints excluded: chain A residue 352 VAL
Chi-restraints excluded: chain B residue 144 GLU
Chi-restraints excluded: chain B residue 224 ILE
Chi-restraints excluded: chain B residue 240 PHE
Chi-restraints excluded: chain B residue 242 LEU
Chi-restraints excluded: chain B residue 255 LEU
Chi-restraints excluded: chain B residue 266 GLN
Chi-restraints excluded: chain B residue 352 VAL
Chi-restraints excluded: chain C residue 30 LEU
Chi-restraints excluded: chain C residue 101 VAL
Chi-restraints excluded: chain C residue 144 GLU
Chi-restraints excluded: chain C residue 224 ILE
Chi-restraints excluded: chain C residue 240 PHE
Chi-restraints excluded: chain C residue 242 LEU
Chi-restraints excluded: chain C residue 287 VAL
Chi-restraints excluded: chain C residue 352 VAL
Chi-restraints excluded: chain D residue 30 LEU
Chi-restraints excluded: chain D residue 34 VAL
Chi-restraints excluded: chain D residue 101 VAL
Chi-restraints excluded: chain D residue 124 ASN
Chi-restraints excluded: chain D residue 224 ILE
Chi-restraints excluded: chain D residue 240 PHE
Chi-restraints excluded: chain D residue 242 LEU
Chi-restraints excluded: chain D residue 272 VAL
Chi-restraints excluded: chain D residue 276 ARG
Chi-restraints excluded: chain D residue 287 VAL
Chi-restraints excluded: chain D residue 290 MET
Chi-restraints excluded: chain D residue 352 VAL
Chi-restraints excluded: chain E residue 30 LEU
Chi-restraints excluded: chain E residue 124 ASN
Chi-restraints excluded: chain E residue 144 GLU
Chi-restraints excluded: chain E residue 224 ILE
Chi-restraints excluded: chain E residue 242 LEU
Chi-restraints excluded: chain E residue 255 LEU
Chi-restraints excluded: chain E residue 266 GLN
Chi-restraints excluded: chain E residue 287 VAL
Chi-restraints excluded: chain E residue 297 MET
Chi-restraints excluded: chain E residue 341 VAL
Chi-restraints excluded: chain E residue 352 VAL
Chi-restraints excluded: chain F residue 101 VAL
Chi-restraints excluded: chain F residue 124 ASN
Chi-restraints excluded: chain F residue 224 ILE
Chi-restraints excluded: chain F residue 240 PHE
Chi-restraints excluded: chain F residue 242 LEU
Chi-restraints excluded: chain F residue 287 VAL
Chi-restraints excluded: chain F residue 352 VAL
Chi-restraints excluded: chain G residue 30 LEU
Chi-restraints excluded: chain G residue 101 VAL
Chi-restraints excluded: chain G residue 144 GLU
Chi-restraints excluded: chain G residue 202 LEU
Chi-restraints excluded: chain G residue 224 ILE
Chi-restraints excluded: chain G residue 240 PHE
Chi-restraints excluded: chain G residue 242 LEU
Chi-restraints excluded: chain G residue 266 GLN
Chi-restraints excluded: chain G residue 287 VAL
Chi-restraints excluded: chain G residue 317 PHE
Chi-restraints excluded: chain G residue 352 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 224
random chunks:
chunk 163 optimal weight: 10.0000
chunk 62 optimal weight: 0.0170
chunk 133 optimal weight: 0.7980
chunk 37 optimal weight: 0.9990
chunk 12 optimal weight: 4.9990
chunk 32 optimal weight: 2.9990
chunk 71 optimal weight: 2.9990
chunk 96 optimal weight: 4.9990
chunk 91 optimal weight: 10.0000
chunk 5 optimal weight: 1.9990
chunk 6 optimal weight: 1.9990
overall best weight: 1.1624
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 340 ASN
B 355 ASN
C 266 GLN
C 340 ASN
C 355 ASN
D 340 ASN
D 355 ASN
E 340 ASN
E 355 ASN
F 340 ASN
F 355 ASN
G 56 GLN
G 355 ASN
Total number of N/Q/H flips: 13
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.125938 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3138 r_free = 0.3138 target = 0.083666 restraints weight = 30526.278|
|-----------------------------------------------------------------------------|
r_work (start): 0.3089 rms_B_bonded: 2.46
r_work: 0.2949 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.2949
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8253
moved from start: 0.2321
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.028 18718 Z= 0.184
Angle : 0.593 8.748 25445 Z= 0.282
Chirality : 0.039 0.178 3045
Planarity : 0.003 0.028 3052
Dihedral : 4.341 52.944 2439
Min Nonbonded Distance : 2.417
Molprobity Statistics.
All-atom Clashscore : 5.51
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 1.50 %
Favored : 98.50 %
Rotamer:
Outliers : 5.12 %
Allowed : 24.28 %
Favored : 70.60 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 2.19 (0.19), residues: 2198
helix: 2.48 (0.13), residues: 1519
sheet: 0.26 (0.48), residues: 126
loop : -1.30 (0.28), residues: 553
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.005 0.001 TRP F 85
HIS 0.003 0.001 HIS B 106
PHE 0.010 0.001 PHE D 12
TYR 0.023 0.001 TYR E 232
ARG 0.006 0.001 ARG F 29
*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
4396 Ramachandran restraints generated.
2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
4396 Ramachandran restraints generated.
2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
354 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 105
poor density : 249
time to evaluate : 1.621
Fit side-chains
revert: symmetry clash
REVERT: A 14 ASP cc_start: 0.8454 (m-30) cc_final: 0.7983 (t0)
REVERT: A 124 ASN cc_start: 0.8083 (OUTLIER) cc_final: 0.7729 (p0)
REVERT: A 144 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.8035 (mp0)
REVERT: A 152 ARG cc_start: 0.6301 (ptm-80) cc_final: 0.5796 (mtm110)
REVERT: A 240 PHE cc_start: 0.7661 (OUTLIER) cc_final: 0.7129 (m-80)
REVERT: A 358 ASN cc_start: 0.8809 (t0) cc_final: 0.8464 (t0)
REVERT: B 14 ASP cc_start: 0.8576 (m-30) cc_final: 0.7821 (p0)
REVERT: B 144 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.7993 (mp0)
REVERT: B 152 ARG cc_start: 0.6191 (ptm-80) cc_final: 0.5739 (mtm110)
REVERT: B 203 LYS cc_start: 0.9195 (mmmt) cc_final: 0.8772 (mmtt)
REVERT: B 240 PHE cc_start: 0.7651 (OUTLIER) cc_final: 0.7323 (m-80)
REVERT: B 266 GLN cc_start: 0.8599 (OUTLIER) cc_final: 0.8201 (tt0)
REVERT: B 306 ASN cc_start: 0.7501 (t0) cc_final: 0.6952 (t0)
REVERT: B 309 LYS cc_start: 0.9078 (mmtt) cc_final: 0.8867 (mmtp)
REVERT: B 358 ASN cc_start: 0.8844 (t0) cc_final: 0.8443 (t0)
REVERT: C 14 ASP cc_start: 0.8468 (m-30) cc_final: 0.7709 (p0)
REVERT: C 152 ARG cc_start: 0.6126 (ptm-80) cc_final: 0.5689 (mtm110)
REVERT: C 297 MET cc_start: 0.8154 (OUTLIER) cc_final: 0.7811 (pmt)
REVERT: C 306 ASN cc_start: 0.7293 (t0) cc_final: 0.7032 (t0)
REVERT: C 352 VAL cc_start: 0.8732 (OUTLIER) cc_final: 0.8504 (t)
REVERT: D 14 ASP cc_start: 0.8286 (m-30) cc_final: 0.7582 (p0)
REVERT: D 124 ASN cc_start: 0.8285 (OUTLIER) cc_final: 0.7995 (p0)
REVERT: D 152 ARG cc_start: 0.6196 (ptm-80) cc_final: 0.5711 (mtm110)
REVERT: D 240 PHE cc_start: 0.7633 (OUTLIER) cc_final: 0.6310 (t80)
REVERT: D 266 GLN cc_start: 0.8786 (OUTLIER) cc_final: 0.8405 (tp-100)
REVERT: D 306 ASN cc_start: 0.7575 (t0) cc_final: 0.7300 (t0)
REVERT: D 317 PHE cc_start: 0.7975 (OUTLIER) cc_final: 0.7631 (m-80)
REVERT: E 14 ASP cc_start: 0.8494 (m-30) cc_final: 0.7802 (p0)
REVERT: E 144 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7917 (mp0)
REVERT: E 152 ARG cc_start: 0.6251 (ptm-80) cc_final: 0.5804 (mtm110)
REVERT: E 203 LYS cc_start: 0.9260 (mmmt) cc_final: 0.8845 (mmtt)
REVERT: E 266 GLN cc_start: 0.8658 (OUTLIER) cc_final: 0.8387 (tt0)
REVERT: E 297 MET cc_start: 0.7935 (OUTLIER) cc_final: 0.7695 (pmm)
REVERT: E 306 ASN cc_start: 0.7556 (t0) cc_final: 0.7302 (t0)
REVERT: F 14 ASP cc_start: 0.8561 (m-30) cc_final: 0.7870 (t0)
REVERT: F 124 ASN cc_start: 0.8139 (OUTLIER) cc_final: 0.7815 (p0)
REVERT: F 152 ARG cc_start: 0.6202 (ptm-80) cc_final: 0.5820 (mtm110)
REVERT: F 203 LYS cc_start: 0.9190 (mmmt) cc_final: 0.8838 (mptt)
REVERT: F 266 GLN cc_start: 0.8789 (OUTLIER) cc_final: 0.8187 (tt0)
REVERT: F 358 ASN cc_start: 0.8877 (t0) cc_final: 0.8602 (t0)
REVERT: G 14 ASP cc_start: 0.8483 (m-30) cc_final: 0.7716 (p0)
REVERT: G 29 ARG cc_start: 0.8883 (mtm-85) cc_final: 0.8610 (mtt180)
REVERT: G 128 ARG cc_start: 0.8590 (tmm-80) cc_final: 0.8316 (ttt-90)
REVERT: G 144 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7808 (mp0)
REVERT: G 152 ARG cc_start: 0.6254 (ptm-80) cc_final: 0.5733 (mtm110)
REVERT: G 266 GLN cc_start: 0.8893 (OUTLIER) cc_final: 0.8422 (tt0)
REVERT: G 317 PHE cc_start: 0.7888 (OUTLIER) cc_final: 0.7577 (m-80)
outliers start: 105
outliers final: 46
residues processed: 326
average time/residue: 1.1444
time to fit residues: 424.3173
Evaluate side-chains
307 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 66
poor density : 241
time to evaluate : 2.248
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 90 GLN
Chi-restraints excluded: chain A residue 124 ASN
Chi-restraints excluded: chain A residue 144 GLU
Chi-restraints excluded: chain A residue 223 LEU
Chi-restraints excluded: chain A residue 224 ILE
Chi-restraints excluded: chain A residue 240 PHE
Chi-restraints excluded: chain A residue 242 LEU
Chi-restraints excluded: chain A residue 255 LEU
Chi-restraints excluded: chain A residue 352 VAL
Chi-restraints excluded: chain B residue 101 VAL
Chi-restraints excluded: chain B residue 144 GLU
Chi-restraints excluded: chain B residue 202 LEU
Chi-restraints excluded: chain B residue 224 ILE
Chi-restraints excluded: chain B residue 240 PHE
Chi-restraints excluded: chain B residue 242 LEU
Chi-restraints excluded: chain B residue 255 LEU
Chi-restraints excluded: chain B residue 266 GLN
Chi-restraints excluded: chain B residue 352 VAL
Chi-restraints excluded: chain C residue 30 LEU
Chi-restraints excluded: chain C residue 90 GLN
Chi-restraints excluded: chain C residue 144 GLU
Chi-restraints excluded: chain C residue 224 ILE
Chi-restraints excluded: chain C residue 240 PHE
Chi-restraints excluded: chain C residue 242 LEU
Chi-restraints excluded: chain C residue 297 MET
Chi-restraints excluded: chain C residue 352 VAL
Chi-restraints excluded: chain D residue 30 LEU
Chi-restraints excluded: chain D residue 34 VAL
Chi-restraints excluded: chain D residue 124 ASN
Chi-restraints excluded: chain D residue 224 ILE
Chi-restraints excluded: chain D residue 240 PHE
Chi-restraints excluded: chain D residue 242 LEU
Chi-restraints excluded: chain D residue 266 GLN
Chi-restraints excluded: chain D residue 272 VAL
Chi-restraints excluded: chain D residue 276 ARG
Chi-restraints excluded: chain D residue 290 MET
Chi-restraints excluded: chain D residue 317 PHE
Chi-restraints excluded: chain D residue 352 VAL
Chi-restraints excluded: chain E residue 30 LEU
Chi-restraints excluded: chain E residue 124 ASN
Chi-restraints excluded: chain E residue 144 GLU
Chi-restraints excluded: chain E residue 224 ILE
Chi-restraints excluded: chain E residue 240 PHE
Chi-restraints excluded: chain E residue 242 LEU
Chi-restraints excluded: chain E residue 255 LEU
Chi-restraints excluded: chain E residue 266 GLN
Chi-restraints excluded: chain E residue 297 MET
Chi-restraints excluded: chain E residue 352 VAL
Chi-restraints excluded: chain F residue 30 LEU
Chi-restraints excluded: chain F residue 101 VAL
Chi-restraints excluded: chain F residue 124 ASN
Chi-restraints excluded: chain F residue 224 ILE
Chi-restraints excluded: chain F residue 240 PHE
Chi-restraints excluded: chain F residue 242 LEU
Chi-restraints excluded: chain F residue 266 GLN
Chi-restraints excluded: chain F residue 352 VAL
Chi-restraints excluded: chain G residue 30 LEU
Chi-restraints excluded: chain G residue 101 VAL
Chi-restraints excluded: chain G residue 144 GLU
Chi-restraints excluded: chain G residue 224 ILE
Chi-restraints excluded: chain G residue 240 PHE
Chi-restraints excluded: chain G residue 242 LEU
Chi-restraints excluded: chain G residue 255 LEU
Chi-restraints excluded: chain G residue 266 GLN
Chi-restraints excluded: chain G residue 317 PHE
Chi-restraints excluded: chain G residue 352 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 224
random chunks:
chunk 56 optimal weight: 0.9990
chunk 194 optimal weight: 10.0000
chunk 96 optimal weight: 5.9990
chunk 184 optimal weight: 0.2980
chunk 218 optimal weight: 10.0000
chunk 131 optimal weight: 3.9990
chunk 106 optimal weight: 0.9990
chunk 174 optimal weight: 9.9990
chunk 152 optimal weight: 3.9990
chunk 155 optimal weight: 10.0000
chunk 98 optimal weight: 5.9990
overall best weight: 2.0588
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
B 56 GLN
B 355 ASN
C 266 GLN
C 340 ASN
C 355 ASN
D 355 ASN
E 355 ASN
F 282 ASN
F 355 ASN
G 56 GLN
G 282 ASN
G 355 ASN
Total number of N/Q/H flips: 12
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.124722 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.082382 restraints weight = 30655.617|
|-----------------------------------------------------------------------------|
r_work (start): 0.3068 rms_B_bonded: 2.45
r_work: 0.2924 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.2924
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8280
moved from start: 0.2470
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.004 0.031 18718 Z= 0.238
Angle : 0.606 8.811 25445 Z= 0.289
Chirality : 0.040 0.189 3045
Planarity : 0.003 0.028 3052
Dihedral : 4.310 53.388 2437
Min Nonbonded Distance : 2.627
Molprobity Statistics.
All-atom Clashscore : 5.67
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 1.64 %
Favored : 98.36 %
Rotamer:
Outliers : 6.00 %
Allowed : 23.70 %
Favored : 70.31 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 2.11 (0.19), residues: 2198
helix: 2.38 (0.13), residues: 1519
sheet: 0.37 (0.49), residues: 126
loop : -1.25 (0.28), residues: 553
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.007 0.001 TRP F 85
HIS 0.004 0.001 HIS C 106
PHE 0.010 0.001 PHE B 129
TYR 0.028 0.001 TYR F 232
ARG 0.006 0.000 ARG F 29
*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
4396 Ramachandran restraints generated.
2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
4396 Ramachandran restraints generated.
2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
374 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 123
poor density : 251
time to evaluate : 2.056
Fit side-chains
REVERT: A 14 ASP cc_start: 0.8488 (m-30) cc_final: 0.7614 (p0)
REVERT: A 124 ASN cc_start: 0.8164 (OUTLIER) cc_final: 0.7760 (p0)
REVERT: A 144 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.8010 (mp0)
REVERT: A 152 ARG cc_start: 0.6306 (ptm-80) cc_final: 0.5809 (mtm110)
REVERT: A 240 PHE cc_start: 0.7715 (OUTLIER) cc_final: 0.7254 (m-80)
REVERT: A 358 ASN cc_start: 0.8821 (t0) cc_final: 0.8473 (t0)
REVERT: B 14 ASP cc_start: 0.8564 (m-30) cc_final: 0.7829 (p0)
REVERT: B 144 GLU cc_start: 0.8302 (OUTLIER) cc_final: 0.7964 (mp0)
REVERT: B 152 ARG cc_start: 0.6279 (ptm-80) cc_final: 0.5821 (mtm110)
REVERT: B 203 LYS cc_start: 0.9181 (mmmt) cc_final: 0.8774 (mmtt)
REVERT: B 240 PHE cc_start: 0.7689 (OUTLIER) cc_final: 0.7429 (m-80)
REVERT: B 266 GLN cc_start: 0.8761 (OUTLIER) cc_final: 0.8337 (tt0)
REVERT: B 306 ASN cc_start: 0.7542 (t0) cc_final: 0.6984 (t0)
REVERT: B 309 LYS cc_start: 0.9067 (mmtt) cc_final: 0.8861 (mmtp)
REVERT: B 358 ASN cc_start: 0.8873 (t0) cc_final: 0.8475 (t0)
REVERT: C 14 ASP cc_start: 0.8467 (m-30) cc_final: 0.7693 (p0)
REVERT: C 144 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.7989 (mp0)
REVERT: C 152 ARG cc_start: 0.6096 (ptm-80) cc_final: 0.5657 (mtm110)
REVERT: C 297 MET cc_start: 0.8280 (OUTLIER) cc_final: 0.7983 (pmt)
REVERT: C 306 ASN cc_start: 0.7511 (t0) cc_final: 0.7258 (t0)
REVERT: D 14 ASP cc_start: 0.8300 (m-30) cc_final: 0.7583 (p0)
REVERT: D 124 ASN cc_start: 0.8327 (OUTLIER) cc_final: 0.7977 (p0)
REVERT: D 152 ARG cc_start: 0.6278 (ptm-80) cc_final: 0.5793 (mtm110)
REVERT: D 240 PHE cc_start: 0.7747 (OUTLIER) cc_final: 0.6347 (t80)
REVERT: D 266 GLN cc_start: 0.8862 (OUTLIER) cc_final: 0.8411 (tp-100)
REVERT: D 306 ASN cc_start: 0.7615 (t0) cc_final: 0.7321 (t0)
REVERT: D 317 PHE cc_start: 0.8000 (OUTLIER) cc_final: 0.7608 (m-80)
REVERT: E 14 ASP cc_start: 0.8492 (m-30) cc_final: 0.7804 (p0)
REVERT: E 144 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.7932 (mp0)
REVERT: E 152 ARG cc_start: 0.6219 (ptm-80) cc_final: 0.5766 (mtm110)
REVERT: E 200 GLN cc_start: 0.8761 (mm-40) cc_final: 0.8560 (mm-40)
REVERT: E 203 LYS cc_start: 0.9274 (mmmt) cc_final: 0.8838 (mmtt)
REVERT: E 266 GLN cc_start: 0.8724 (OUTLIER) cc_final: 0.8444 (tt0)
REVERT: E 297 MET cc_start: 0.7788 (OUTLIER) cc_final: 0.7587 (pmm)
REVERT: E 306 ASN cc_start: 0.7595 (t0) cc_final: 0.7319 (t0)
REVERT: F 14 ASP cc_start: 0.8577 (m-30) cc_final: 0.7869 (t0)
REVERT: F 152 ARG cc_start: 0.6212 (ptm-80) cc_final: 0.5833 (mtm110)
REVERT: F 203 LYS cc_start: 0.9234 (mmmt) cc_final: 0.8880 (mptt)
REVERT: F 266 GLN cc_start: 0.8855 (OUTLIER) cc_final: 0.8241 (tt0)
REVERT: F 358 ASN cc_start: 0.8926 (t0) cc_final: 0.8655 (t0)
REVERT: G 14 ASP cc_start: 0.8478 (m-30) cc_final: 0.7711 (p0)
REVERT: G 29 ARG cc_start: 0.8840 (mtm-85) cc_final: 0.8536 (mtt180)
REVERT: G 128 ARG cc_start: 0.8659 (tmm-80) cc_final: 0.8368 (ttt180)
REVERT: G 144 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7836 (mp0)
REVERT: G 152 ARG cc_start: 0.6254 (ptm-80) cc_final: 0.5729 (mtm110)
REVERT: G 203 LYS cc_start: 0.9255 (mmmt) cc_final: 0.8849 (mmtt)
REVERT: G 266 GLN cc_start: 0.8943 (OUTLIER) cc_final: 0.8464 (tt0)
REVERT: G 317 PHE cc_start: 0.7929 (OUTLIER) cc_final: 0.7614 (m-80)
outliers start: 123
outliers final: 56
residues processed: 345
average time/residue: 1.1184
time to fit residues: 440.3215
Evaluate side-chains
319 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 75
poor density : 244
time to evaluate : 2.121
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 30 LEU
Chi-restraints excluded: chain A residue 124 ASN
Chi-restraints excluded: chain A residue 144 GLU
Chi-restraints excluded: chain A residue 154 ILE
Chi-restraints excluded: chain A residue 202 LEU
Chi-restraints excluded: chain A residue 223 LEU
Chi-restraints excluded: chain A residue 224 ILE
Chi-restraints excluded: chain A residue 240 PHE
Chi-restraints excluded: chain A residue 242 LEU
Chi-restraints excluded: chain A residue 255 LEU
Chi-restraints excluded: chain A residue 287 VAL
Chi-restraints excluded: chain A residue 352 VAL
Chi-restraints excluded: chain B residue 3 ILE
Chi-restraints excluded: chain B residue 101 VAL
Chi-restraints excluded: chain B residue 144 GLU
Chi-restraints excluded: chain B residue 202 LEU
Chi-restraints excluded: chain B residue 224 ILE
Chi-restraints excluded: chain B residue 240 PHE
Chi-restraints excluded: chain B residue 242 LEU
Chi-restraints excluded: chain B residue 255 LEU
Chi-restraints excluded: chain B residue 266 GLN
Chi-restraints excluded: chain B residue 352 VAL
Chi-restraints excluded: chain C residue 30 LEU
Chi-restraints excluded: chain C residue 90 GLN
Chi-restraints excluded: chain C residue 101 VAL
Chi-restraints excluded: chain C residue 144 GLU
Chi-restraints excluded: chain C residue 224 ILE
Chi-restraints excluded: chain C residue 240 PHE
Chi-restraints excluded: chain C residue 242 LEU
Chi-restraints excluded: chain C residue 287 VAL
Chi-restraints excluded: chain C residue 297 MET
Chi-restraints excluded: chain C residue 341 VAL
Chi-restraints excluded: chain D residue 30 LEU
Chi-restraints excluded: chain D residue 101 VAL
Chi-restraints excluded: chain D residue 124 ASN
Chi-restraints excluded: chain D residue 223 LEU
Chi-restraints excluded: chain D residue 224 ILE
Chi-restraints excluded: chain D residue 240 PHE
Chi-restraints excluded: chain D residue 242 LEU
Chi-restraints excluded: chain D residue 266 GLN
Chi-restraints excluded: chain D residue 272 VAL
Chi-restraints excluded: chain D residue 276 ARG
Chi-restraints excluded: chain D residue 287 VAL
Chi-restraints excluded: chain D residue 290 MET
Chi-restraints excluded: chain D residue 317 PHE
Chi-restraints excluded: chain D residue 352 VAL
Chi-restraints excluded: chain E residue 30 LEU
Chi-restraints excluded: chain E residue 124 ASN
Chi-restraints excluded: chain E residue 144 GLU
Chi-restraints excluded: chain E residue 202 LEU
Chi-restraints excluded: chain E residue 224 ILE
Chi-restraints excluded: chain E residue 240 PHE
Chi-restraints excluded: chain E residue 242 LEU
Chi-restraints excluded: chain E residue 266 GLN
Chi-restraints excluded: chain E residue 297 MET
Chi-restraints excluded: chain E residue 352 VAL
Chi-restraints excluded: chain F residue 30 LEU
Chi-restraints excluded: chain F residue 124 ASN
Chi-restraints excluded: chain F residue 216 LEU
Chi-restraints excluded: chain F residue 224 ILE
Chi-restraints excluded: chain F residue 240 PHE
Chi-restraints excluded: chain F residue 242 LEU
Chi-restraints excluded: chain F residue 266 GLN
Chi-restraints excluded: chain F residue 352 VAL
Chi-restraints excluded: chain G residue 30 LEU
Chi-restraints excluded: chain G residue 101 VAL
Chi-restraints excluded: chain G residue 144 GLU
Chi-restraints excluded: chain G residue 224 ILE
Chi-restraints excluded: chain G residue 240 PHE
Chi-restraints excluded: chain G residue 242 LEU
Chi-restraints excluded: chain G residue 255 LEU
Chi-restraints excluded: chain G residue 266 GLN
Chi-restraints excluded: chain G residue 287 VAL
Chi-restraints excluded: chain G residue 317 PHE
Chi-restraints excluded: chain G residue 352 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 224
random chunks:
chunk 163 optimal weight: 9.9990
chunk 32 optimal weight: 1.9990
chunk 198 optimal weight: 3.9990
chunk 221 optimal weight: 10.0000
chunk 11 optimal weight: 0.9980
chunk 150 optimal weight: 3.9990
chunk 73 optimal weight: 0.6980
chunk 13 optimal weight: 4.9990
chunk 155 optimal weight: 9.9990
chunk 99 optimal weight: 10.0000
chunk 210 optimal weight: 3.9990
overall best weight: 2.3386
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 355 ASN
B 56 GLN
B 340 ASN
B 355 ASN
C 266 GLN
C 282 ASN
C 340 ASN
C 355 ASN
D 355 ASN
E 355 ASN
F 266 GLN
F 282 ASN
F 340 ASN
G 56 GLN
G 355 ASN
Total number of N/Q/H flips: 15
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.124318 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3100 r_free = 0.3100 target = 0.081527 restraints weight = 30714.473|
|-----------------------------------------------------------------------------|
r_work (start): 0.3052 rms_B_bonded: 2.48
r_work: 0.2912 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.2912
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8292
moved from start: 0.2610
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.004 0.032 18718 Z= 0.260
Angle : 0.621 8.375 25445 Z= 0.297
Chirality : 0.040 0.197 3045
Planarity : 0.003 0.030 3052
Dihedral : 4.266 54.051 2434
Min Nonbonded Distance : 2.624
Molprobity Statistics.
All-atom Clashscore : 5.78
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 1.91 %
Favored : 98.09 %
Rotamer:
Outliers : 5.75 %
Allowed : 23.79 %
Favored : 70.45 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 2.04 (0.19), residues: 2198
helix: 2.36 (0.13), residues: 1512
sheet: 0.34 (0.49), residues: 126
loop : -1.33 (0.28), residues: 560
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.008 0.001 TRP F 85
HIS 0.003 0.001 HIS A 106
PHE 0.010 0.001 PHE A 333
TYR 0.029 0.002 TYR E 232
ARG 0.007 0.001 ARG D 29
*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
4396 Ramachandran restraints generated.
2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
4396 Ramachandran restraints generated.
2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
368 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 118
poor density : 250
time to evaluate : 2.180
Fit side-chains
REVERT: A 14 ASP cc_start: 0.8470 (m-30) cc_final: 0.7609 (p0)
REVERT: A 124 ASN cc_start: 0.8267 (OUTLIER) cc_final: 0.7813 (p0)
REVERT: A 144 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.8000 (mp0)
REVERT: A 152 ARG cc_start: 0.6302 (ptm-80) cc_final: 0.5791 (mtm110)
REVERT: A 240 PHE cc_start: 0.7788 (OUTLIER) cc_final: 0.7339 (m-80)
REVERT: A 317 PHE cc_start: 0.7911 (t80) cc_final: 0.7679 (m-80)
REVERT: A 358 ASN cc_start: 0.8814 (t0) cc_final: 0.8455 (t0)
REVERT: B 14 ASP cc_start: 0.8560 (m-30) cc_final: 0.7852 (p0)
REVERT: B 144 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.7976 (mp0)
REVERT: B 152 ARG cc_start: 0.6289 (ptm-80) cc_final: 0.5825 (mtm110)
REVERT: B 203 LYS cc_start: 0.9182 (mmmt) cc_final: 0.8761 (mmtt)
REVERT: B 240 PHE cc_start: 0.7732 (OUTLIER) cc_final: 0.7475 (m-80)
REVERT: B 266 GLN cc_start: 0.8795 (OUTLIER) cc_final: 0.8364 (tt0)
REVERT: B 306 ASN cc_start: 0.7580 (t0) cc_final: 0.7022 (t0)
REVERT: B 309 LYS cc_start: 0.9074 (mmtt) cc_final: 0.8871 (mmtp)
REVERT: B 317 PHE cc_start: 0.7861 (t80) cc_final: 0.7500 (m-80)
REVERT: B 358 ASN cc_start: 0.8869 (t0) cc_final: 0.8472 (t0)
REVERT: C 14 ASP cc_start: 0.8462 (m-30) cc_final: 0.7714 (p0)
REVERT: C 144 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.7989 (mp0)
REVERT: C 152 ARG cc_start: 0.6119 (ptm-80) cc_final: 0.5659 (mtm110)
REVERT: C 200 GLN cc_start: 0.8514 (mm-40) cc_final: 0.8279 (mm-40)
REVERT: C 297 MET cc_start: 0.8279 (OUTLIER) cc_final: 0.7984 (pmt)
REVERT: C 306 ASN cc_start: 0.7607 (t0) cc_final: 0.7342 (t0)
REVERT: D 14 ASP cc_start: 0.8337 (m-30) cc_final: 0.7600 (p0)
REVERT: D 124 ASN cc_start: 0.8251 (OUTLIER) cc_final: 0.7801 (p0)
REVERT: D 152 ARG cc_start: 0.6216 (ptm-80) cc_final: 0.5745 (mtm110)
REVERT: D 266 GLN cc_start: 0.8883 (OUTLIER) cc_final: 0.8481 (tp-100)
REVERT: D 306 ASN cc_start: 0.7646 (t0) cc_final: 0.7352 (t0)
REVERT: D 317 PHE cc_start: 0.8022 (OUTLIER) cc_final: 0.7594 (m-80)
REVERT: E 14 ASP cc_start: 0.8456 (m-30) cc_final: 0.7757 (p0)
REVERT: E 144 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.7936 (mp0)
REVERT: E 152 ARG cc_start: 0.6252 (ptm-80) cc_final: 0.5761 (mtm110)
REVERT: E 203 LYS cc_start: 0.9258 (mmmt) cc_final: 0.8913 (mptt)
REVERT: E 266 GLN cc_start: 0.8746 (OUTLIER) cc_final: 0.8448 (tt0)
REVERT: E 297 MET cc_start: 0.7772 (OUTLIER) cc_final: 0.7563 (pmm)
REVERT: E 306 ASN cc_start: 0.7568 (t0) cc_final: 0.7270 (t0)
REVERT: F 14 ASP cc_start: 0.8574 (m-30) cc_final: 0.8009 (t0)
REVERT: F 144 GLU cc_start: 0.8482 (mm-30) cc_final: 0.8262 (mp0)
REVERT: F 152 ARG cc_start: 0.6239 (ptm-80) cc_final: 0.5845 (mtm110)
REVERT: F 203 LYS cc_start: 0.9240 (mmmt) cc_final: 0.8901 (mptt)
REVERT: F 280 TYR cc_start: 0.8177 (t80) cc_final: 0.7649 (m-80)
REVERT: F 297 MET cc_start: 0.8114 (pmt) cc_final: 0.7881 (pmt)
REVERT: F 358 ASN cc_start: 0.8973 (t0) cc_final: 0.8697 (t0)
REVERT: G 14 ASP cc_start: 0.8488 (m-30) cc_final: 0.7723 (p0)
REVERT: G 128 ARG cc_start: 0.8671 (tmm-80) cc_final: 0.8465 (ttt-90)
REVERT: G 144 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.7868 (mp0)
REVERT: G 152 ARG cc_start: 0.6243 (ptm-80) cc_final: 0.5746 (mtm110)
REVERT: G 203 LYS cc_start: 0.9248 (mmmt) cc_final: 0.8878 (mmtt)
REVERT: G 266 GLN cc_start: 0.8966 (OUTLIER) cc_final: 0.8474 (tt0)
REVERT: G 317 PHE cc_start: 0.7940 (OUTLIER) cc_final: 0.7634 (m-80)
outliers start: 118
outliers final: 60
residues processed: 344
average time/residue: 1.1258
time to fit residues: 442.4567
Evaluate side-chains
320 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 77
poor density : 243
time to evaluate : 2.235
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 30 LEU
Chi-restraints excluded: chain A residue 124 ASN
Chi-restraints excluded: chain A residue 144 GLU
Chi-restraints excluded: chain A residue 154 ILE
Chi-restraints excluded: chain A residue 202 LEU
Chi-restraints excluded: chain A residue 223 LEU
Chi-restraints excluded: chain A residue 224 ILE
Chi-restraints excluded: chain A residue 240 PHE
Chi-restraints excluded: chain A residue 242 LEU
Chi-restraints excluded: chain A residue 255 LEU
Chi-restraints excluded: chain A residue 287 VAL
Chi-restraints excluded: chain A residue 352 VAL
Chi-restraints excluded: chain B residue 101 VAL
Chi-restraints excluded: chain B residue 144 GLU
Chi-restraints excluded: chain B residue 202 LEU
Chi-restraints excluded: chain B residue 224 ILE
Chi-restraints excluded: chain B residue 240 PHE
Chi-restraints excluded: chain B residue 242 LEU
Chi-restraints excluded: chain B residue 255 LEU
Chi-restraints excluded: chain B residue 266 GLN
Chi-restraints excluded: chain B residue 352 VAL
Chi-restraints excluded: chain C residue 30 LEU
Chi-restraints excluded: chain C residue 90 GLN
Chi-restraints excluded: chain C residue 101 VAL
Chi-restraints excluded: chain C residue 144 GLU
Chi-restraints excluded: chain C residue 224 ILE
Chi-restraints excluded: chain C residue 240 PHE
Chi-restraints excluded: chain C residue 242 LEU
Chi-restraints excluded: chain C residue 287 VAL
Chi-restraints excluded: chain C residue 297 MET
Chi-restraints excluded: chain C residue 341 VAL
Chi-restraints excluded: chain D residue 30 LEU
Chi-restraints excluded: chain D residue 101 VAL
Chi-restraints excluded: chain D residue 124 ASN
Chi-restraints excluded: chain D residue 223 LEU
Chi-restraints excluded: chain D residue 224 ILE
Chi-restraints excluded: chain D residue 240 PHE
Chi-restraints excluded: chain D residue 242 LEU
Chi-restraints excluded: chain D residue 266 GLN
Chi-restraints excluded: chain D residue 272 VAL
Chi-restraints excluded: chain D residue 276 ARG
Chi-restraints excluded: chain D residue 287 VAL
Chi-restraints excluded: chain D residue 317 PHE
Chi-restraints excluded: chain D residue 341 VAL
Chi-restraints excluded: chain D residue 352 VAL
Chi-restraints excluded: chain E residue 30 LEU
Chi-restraints excluded: chain E residue 124 ASN
Chi-restraints excluded: chain E residue 144 GLU
Chi-restraints excluded: chain E residue 202 LEU
Chi-restraints excluded: chain E residue 224 ILE
Chi-restraints excluded: chain E residue 242 LEU
Chi-restraints excluded: chain E residue 255 LEU
Chi-restraints excluded: chain E residue 266 GLN
Chi-restraints excluded: chain E residue 287 VAL
Chi-restraints excluded: chain E residue 297 MET
Chi-restraints excluded: chain E residue 352 VAL
Chi-restraints excluded: chain F residue 30 LEU
Chi-restraints excluded: chain F residue 101 VAL
Chi-restraints excluded: chain F residue 124 ASN
Chi-restraints excluded: chain F residue 216 LEU
Chi-restraints excluded: chain F residue 224 ILE
Chi-restraints excluded: chain F residue 240 PHE
Chi-restraints excluded: chain F residue 242 LEU
Chi-restraints excluded: chain F residue 287 VAL
Chi-restraints excluded: chain F residue 341 VAL
Chi-restraints excluded: chain F residue 352 VAL
Chi-restraints excluded: chain G residue 30 LEU
Chi-restraints excluded: chain G residue 101 VAL
Chi-restraints excluded: chain G residue 144 GLU
Chi-restraints excluded: chain G residue 224 ILE
Chi-restraints excluded: chain G residue 240 PHE
Chi-restraints excluded: chain G residue 242 LEU
Chi-restraints excluded: chain G residue 255 LEU
Chi-restraints excluded: chain G residue 266 GLN
Chi-restraints excluded: chain G residue 287 VAL
Chi-restraints excluded: chain G residue 317 PHE
Chi-restraints excluded: chain G residue 352 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 224
random chunks:
chunk 164 optimal weight: 0.9980
chunk 30 optimal weight: 20.0000
chunk 213 optimal weight: 0.0670
chunk 193 optimal weight: 1.9990
chunk 150 optimal weight: 3.9990
chunk 88 optimal weight: 1.9990
chunk 181 optimal weight: 0.0870
chunk 118 optimal weight: 2.9990
chunk 125 optimal weight: 1.9990
chunk 48 optimal weight: 0.9990
chunk 58 optimal weight: 7.9990
overall best weight: 0.8300
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 355 ASN
B 355 ASN
C 266 GLN
C 340 ASN
C 355 ASN
D 340 ASN
D 355 ASN
E 340 ASN
E 355 ASN
F 340 ASN
G 355 ASN
Total number of N/Q/H flips: 11
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.126382 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3149 r_free = 0.3149 target = 0.084267 restraints weight = 30419.574|
|-----------------------------------------------------------------------------|
r_work (start): 0.3101 rms_B_bonded: 2.47
r_work: 0.2964 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work (final): 0.2964
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8244
moved from start: 0.2561
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.031 18718 Z= 0.168
Angle : 0.604 12.382 25445 Z= 0.286
Chirality : 0.039 0.185 3045
Planarity : 0.003 0.030 3052
Dihedral : 4.308 55.287 2434
Min Nonbonded Distance : 2.625
Molprobity Statistics.
All-atom Clashscore : 5.61
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 1.59 %
Favored : 98.41 %
Rotamer:
Outliers : 4.53 %
Allowed : 25.35 %
Favored : 70.11 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 2.20 (0.19), residues: 2198
helix: 2.46 (0.13), residues: 1512
sheet: 0.34 (0.49), residues: 126
loop : -1.20 (0.28), residues: 560
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.005 0.001 TRP E 74
HIS 0.002 0.001 HIS E 106
PHE 0.010 0.001 PHE D 12
TYR 0.027 0.001 TYR E 232
ARG 0.007 0.001 ARG D 29
*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
4396 Ramachandran restraints generated.
2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
4396 Ramachandran restraints generated.
2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
353 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 93
poor density : 260
time to evaluate : 2.340
Fit side-chains
REVERT: A 14 ASP cc_start: 0.8449 (m-30) cc_final: 0.7510 (p0)
REVERT: A 144 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.8020 (mp0)
REVERT: A 152 ARG cc_start: 0.6232 (ptm-80) cc_final: 0.5745 (mtm110)
REVERT: A 203 LYS cc_start: 0.9257 (mmmt) cc_final: 0.8869 (mptt)
REVERT: A 240 PHE cc_start: 0.7670 (OUTLIER) cc_final: 0.7143 (m-80)
REVERT: A 280 TYR cc_start: 0.8211 (t80) cc_final: 0.7611 (m-80)
REVERT: A 317 PHE cc_start: 0.7863 (t80) cc_final: 0.7655 (m-80)
REVERT: A 358 ASN cc_start: 0.8826 (t0) cc_final: 0.8472 (t0)
REVERT: B 14 ASP cc_start: 0.8492 (m-30) cc_final: 0.7811 (p0)
REVERT: B 144 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.7955 (mp0)
REVERT: B 152 ARG cc_start: 0.6194 (ptm-80) cc_final: 0.5704 (mtm110)
REVERT: B 203 LYS cc_start: 0.9147 (mmmt) cc_final: 0.8759 (mmtt)
REVERT: B 240 PHE cc_start: 0.7631 (OUTLIER) cc_final: 0.7403 (m-80)
REVERT: B 266 GLN cc_start: 0.8650 (OUTLIER) cc_final: 0.8239 (tt0)
REVERT: B 306 ASN cc_start: 0.7563 (t0) cc_final: 0.7004 (t0)
REVERT: B 358 ASN cc_start: 0.8865 (t0) cc_final: 0.8503 (t0)
REVERT: C 14 ASP cc_start: 0.8447 (m-30) cc_final: 0.7641 (p0)
REVERT: C 144 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.7968 (mp0)
REVERT: C 152 ARG cc_start: 0.6107 (ptm-80) cc_final: 0.5656 (mtm110)
REVERT: C 200 GLN cc_start: 0.8521 (mm-40) cc_final: 0.8297 (mm-40)
REVERT: C 306 ASN cc_start: 0.7647 (t0) cc_final: 0.7375 (t0)
REVERT: C 352 VAL cc_start: 0.8795 (OUTLIER) cc_final: 0.8568 (t)
REVERT: D 14 ASP cc_start: 0.8324 (m-30) cc_final: 0.7600 (p0)
REVERT: D 152 ARG cc_start: 0.6298 (ptm-80) cc_final: 0.5774 (mtm110)
REVERT: D 240 PHE cc_start: 0.7747 (OUTLIER) cc_final: 0.6375 (t80)
REVERT: D 306 ASN cc_start: 0.7633 (t0) cc_final: 0.7341 (t0)
REVERT: E 14 ASP cc_start: 0.8416 (m-30) cc_final: 0.7741 (p0)
REVERT: E 144 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.7966 (mp0)
REVERT: E 152 ARG cc_start: 0.6235 (ptm-80) cc_final: 0.5761 (mtm110)
REVERT: E 203 LYS cc_start: 0.9220 (mmmt) cc_final: 0.8910 (mptt)
REVERT: E 266 GLN cc_start: 0.8684 (OUTLIER) cc_final: 0.8421 (tt0)
REVERT: E 297 MET cc_start: 0.7797 (OUTLIER) cc_final: 0.7595 (pmm)
REVERT: E 306 ASN cc_start: 0.7555 (t0) cc_final: 0.7261 (t0)
REVERT: F 14 ASP cc_start: 0.8532 (m-30) cc_final: 0.8006 (t0)
REVERT: F 89 GLN cc_start: 0.8405 (OUTLIER) cc_final: 0.7710 (tt0)
REVERT: F 144 GLU cc_start: 0.8485 (mm-30) cc_final: 0.8255 (mp0)
REVERT: F 152 ARG cc_start: 0.6155 (ptm-80) cc_final: 0.5736 (mtm110)
REVERT: F 203 LYS cc_start: 0.9205 (mmmt) cc_final: 0.8869 (mptt)
REVERT: F 280 TYR cc_start: 0.8150 (t80) cc_final: 0.7623 (m-80)
REVERT: F 358 ASN cc_start: 0.8987 (t0) cc_final: 0.8701 (t0)
REVERT: G 14 ASP cc_start: 0.8465 (m-30) cc_final: 0.7753 (p0)
REVERT: G 128 ARG cc_start: 0.8601 (tmm-80) cc_final: 0.8383 (ttt-90)
REVERT: G 144 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.7865 (mp0)
REVERT: G 152 ARG cc_start: 0.6229 (ptm-80) cc_final: 0.5728 (mtm110)
REVERT: G 203 LYS cc_start: 0.9217 (mmmt) cc_final: 0.8869 (mmtt)
REVERT: G 266 GLN cc_start: 0.8919 (OUTLIER) cc_final: 0.8438 (tt0)
REVERT: G 317 PHE cc_start: 0.7924 (OUTLIER) cc_final: 0.7614 (m-80)
outliers start: 93
outliers final: 51
residues processed: 327
average time/residue: 1.1971
time to fit residues: 444.6234
Evaluate side-chains
313 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 66
poor density : 247
time to evaluate : 2.300
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 30 LEU
Chi-restraints excluded: chain A residue 124 ASN
Chi-restraints excluded: chain A residue 144 GLU
Chi-restraints excluded: chain A residue 223 LEU
Chi-restraints excluded: chain A residue 224 ILE
Chi-restraints excluded: chain A residue 240 PHE
Chi-restraints excluded: chain A residue 242 LEU
Chi-restraints excluded: chain A residue 255 LEU
Chi-restraints excluded: chain A residue 352 VAL
Chi-restraints excluded: chain B residue 101 VAL
Chi-restraints excluded: chain B residue 144 GLU
Chi-restraints excluded: chain B residue 224 ILE
Chi-restraints excluded: chain B residue 240 PHE
Chi-restraints excluded: chain B residue 242 LEU
Chi-restraints excluded: chain B residue 255 LEU
Chi-restraints excluded: chain B residue 266 GLN
Chi-restraints excluded: chain B residue 352 VAL
Chi-restraints excluded: chain C residue 30 LEU
Chi-restraints excluded: chain C residue 90 GLN
Chi-restraints excluded: chain C residue 101 VAL
Chi-restraints excluded: chain C residue 144 GLU
Chi-restraints excluded: chain C residue 224 ILE
Chi-restraints excluded: chain C residue 240 PHE
Chi-restraints excluded: chain C residue 242 LEU
Chi-restraints excluded: chain C residue 352 VAL
Chi-restraints excluded: chain C residue 356 ILE
Chi-restraints excluded: chain D residue 101 VAL
Chi-restraints excluded: chain D residue 124 ASN
Chi-restraints excluded: chain D residue 223 LEU
Chi-restraints excluded: chain D residue 224 ILE
Chi-restraints excluded: chain D residue 240 PHE
Chi-restraints excluded: chain D residue 242 LEU
Chi-restraints excluded: chain D residue 272 VAL
Chi-restraints excluded: chain D residue 276 ARG
Chi-restraints excluded: chain D residue 352 VAL
Chi-restraints excluded: chain E residue 30 LEU
Chi-restraints excluded: chain E residue 124 ASN
Chi-restraints excluded: chain E residue 144 GLU
Chi-restraints excluded: chain E residue 224 ILE
Chi-restraints excluded: chain E residue 240 PHE
Chi-restraints excluded: chain E residue 242 LEU
Chi-restraints excluded: chain E residue 266 GLN
Chi-restraints excluded: chain E residue 297 MET
Chi-restraints excluded: chain E residue 352 VAL
Chi-restraints excluded: chain F residue 30 LEU
Chi-restraints excluded: chain F residue 89 GLN
Chi-restraints excluded: chain F residue 101 VAL
Chi-restraints excluded: chain F residue 124 ASN
Chi-restraints excluded: chain F residue 138 ASP
Chi-restraints excluded: chain F residue 202 LEU
Chi-restraints excluded: chain F residue 216 LEU
Chi-restraints excluded: chain F residue 224 ILE
Chi-restraints excluded: chain F residue 240 PHE
Chi-restraints excluded: chain F residue 242 LEU
Chi-restraints excluded: chain F residue 287 VAL
Chi-restraints excluded: chain F residue 352 VAL
Chi-restraints excluded: chain G residue 30 LEU
Chi-restraints excluded: chain G residue 101 VAL
Chi-restraints excluded: chain G residue 144 GLU
Chi-restraints excluded: chain G residue 224 ILE
Chi-restraints excluded: chain G residue 240 PHE
Chi-restraints excluded: chain G residue 242 LEU
Chi-restraints excluded: chain G residue 255 LEU
Chi-restraints excluded: chain G residue 266 GLN
Chi-restraints excluded: chain G residue 317 PHE
Chi-restraints excluded: chain G residue 352 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 224
random chunks:
chunk 133 optimal weight: 0.5980
chunk 108 optimal weight: 1.9990
chunk 185 optimal weight: 9.9990
chunk 88 optimal weight: 3.9990
chunk 109 optimal weight: 1.9990
chunk 138 optimal weight: 0.8980
chunk 111 optimal weight: 8.9990
chunk 103 optimal weight: 5.9990
chunk 8 optimal weight: 0.8980
chunk 5 optimal weight: 1.9990
chunk 114 optimal weight: 0.8980
overall best weight: 1.0582
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 340 ASN
A 355 ASN
B 56 GLN
B 355 ASN
C 266 GLN
C 282 ASN
C 340 ASN
C 355 ASN
D 355 ASN
E 355 ASN
F 340 ASN
F 355 ASN
G 56 GLN
G 355 ASN
Total number of N/Q/H flips: 14
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.126127 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.084117 restraints weight = 30513.887|
|-----------------------------------------------------------------------------|
r_work (start): 0.3101 rms_B_bonded: 2.47
r_work: 0.2963 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work (final): 0.2963
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8257
moved from start: 0.2604
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.037 18718 Z= 0.181
Angle : 0.618 12.116 25445 Z= 0.292
Chirality : 0.039 0.197 3045
Planarity : 0.003 0.032 3052
Dihedral : 4.388 56.928 2434
Min Nonbonded Distance : 2.621
Molprobity Statistics.
All-atom Clashscore : 5.99
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 1.41 %
Favored : 98.59 %
Rotamer:
Outliers : 4.34 %
Allowed : 25.50 %
Favored : 70.16 %
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: 2.22 (0.19), residues: 2198
helix: 2.48 (0.14), residues: 1512
sheet: 0.32 (0.49), residues: 126
loop : -1.16 (0.28), residues: 560
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.005 0.001 TRP A 104
HIS 0.002 0.001 HIS G 106
PHE 0.010 0.001 PHE D 12
TYR 0.030 0.001 TYR G 232
ARG 0.007 0.001 ARG F 29
*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
4396 Ramachandran restraints generated.
2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
4396 Ramachandran restraints generated.
2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
338 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 89
poor density : 249
time to evaluate : 2.006
Fit side-chains
REVERT: A 14 ASP cc_start: 0.8457 (m-30) cc_final: 0.7517 (p0)
REVERT: A 144 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.8005 (mp0)
REVERT: A 152 ARG cc_start: 0.6252 (ptm-80) cc_final: 0.5731 (mtm110)
REVERT: A 240 PHE cc_start: 0.7647 (OUTLIER) cc_final: 0.7074 (m-80)
REVERT: A 280 TYR cc_start: 0.8225 (t80) cc_final: 0.7628 (m-80)
REVERT: A 358 ASN cc_start: 0.8833 (t0) cc_final: 0.8475 (t0)
REVERT: B 14 ASP cc_start: 0.8483 (m-30) cc_final: 0.7825 (p0)
REVERT: B 144 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.8010 (mp0)
REVERT: B 152 ARG cc_start: 0.6295 (ptm-80) cc_final: 0.5799 (mtm110)
REVERT: B 203 LYS cc_start: 0.9172 (mmmt) cc_final: 0.8809 (mmtt)
REVERT: B 240 PHE cc_start: 0.7633 (OUTLIER) cc_final: 0.7393 (m-80)
REVERT: B 266 GLN cc_start: 0.8781 (OUTLIER) cc_final: 0.8402 (tp40)
REVERT: B 306 ASN cc_start: 0.7603 (t0) cc_final: 0.7394 (t0)
REVERT: B 358 ASN cc_start: 0.8873 (t0) cc_final: 0.8499 (t0)
REVERT: C 14 ASP cc_start: 0.8440 (m-30) cc_final: 0.7646 (p0)
REVERT: C 144 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.8022 (mp0)
REVERT: C 152 ARG cc_start: 0.6122 (ptm-80) cc_final: 0.5662 (mtm110)
REVERT: C 297 MET cc_start: 0.8215 (pmm) cc_final: 0.7994 (pmt)
REVERT: C 306 ASN cc_start: 0.7658 (t0) cc_final: 0.7411 (t0)
REVERT: D 14 ASP cc_start: 0.8334 (m-30) cc_final: 0.7612 (p0)
REVERT: D 152 ARG cc_start: 0.6323 (ptm-80) cc_final: 0.5788 (mtm110)
REVERT: D 240 PHE cc_start: 0.7725 (OUTLIER) cc_final: 0.6429 (t80)
REVERT: D 266 GLN cc_start: 0.8814 (OUTLIER) cc_final: 0.8414 (tp-100)
REVERT: D 306 ASN cc_start: 0.7658 (t0) cc_final: 0.7355 (t0)
REVERT: E 14 ASP cc_start: 0.8419 (m-30) cc_final: 0.7745 (p0)
REVERT: E 144 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.7985 (mp0)
REVERT: E 152 ARG cc_start: 0.6246 (ptm-80) cc_final: 0.5740 (mtm110)
REVERT: E 203 LYS cc_start: 0.9205 (mmmt) cc_final: 0.8900 (mptt)
REVERT: E 266 GLN cc_start: 0.8705 (OUTLIER) cc_final: 0.8433 (tt0)
REVERT: E 297 MET cc_start: 0.7732 (OUTLIER) cc_final: 0.7523 (pmm)
REVERT: E 306 ASN cc_start: 0.7560 (t0) cc_final: 0.7282 (t0)
REVERT: F 14 ASP cc_start: 0.8529 (m-30) cc_final: 0.8010 (t0)
REVERT: F 89 GLN cc_start: 0.8414 (OUTLIER) cc_final: 0.7694 (tt0)
REVERT: F 144 GLU cc_start: 0.8500 (mm-30) cc_final: 0.8247 (mp0)
REVERT: F 152 ARG cc_start: 0.6172 (ptm-80) cc_final: 0.5941 (ptm-80)
REVERT: F 203 LYS cc_start: 0.9226 (mmmt) cc_final: 0.8887 (mptt)
REVERT: F 280 TYR cc_start: 0.8163 (t80) cc_final: 0.7635 (m-80)
REVERT: F 358 ASN cc_start: 0.9001 (t0) cc_final: 0.8713 (t0)
REVERT: G 14 ASP cc_start: 0.8457 (m-30) cc_final: 0.7750 (p0)
REVERT: G 128 ARG cc_start: 0.8590 (tmm-80) cc_final: 0.8366 (ttt-90)
REVERT: G 144 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7922 (mp0)
REVERT: G 152 ARG cc_start: 0.6237 (ptm-80) cc_final: 0.5727 (mtm110)
REVERT: G 203 LYS cc_start: 0.9285 (mmmt) cc_final: 0.8916 (mmtt)
REVERT: G 266 GLN cc_start: 0.8931 (OUTLIER) cc_final: 0.8451 (tt0)
REVERT: G 317 PHE cc_start: 0.7936 (OUTLIER) cc_final: 0.7625 (m-80)
outliers start: 89
outliers final: 53
residues processed: 312
average time/residue: 1.1850
time to fit residues: 420.1411
Evaluate side-chains
312 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 68
poor density : 244
time to evaluate : 2.147
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 124 ASN
Chi-restraints excluded: chain A residue 138 ASP
Chi-restraints excluded: chain A residue 144 GLU
Chi-restraints excluded: chain A residue 223 LEU
Chi-restraints excluded: chain A residue 224 ILE
Chi-restraints excluded: chain A residue 240 PHE
Chi-restraints excluded: chain A residue 242 LEU
Chi-restraints excluded: chain A residue 255 LEU
Chi-restraints excluded: chain A residue 352 VAL
Chi-restraints excluded: chain B residue 101 VAL
Chi-restraints excluded: chain B residue 129 PHE
Chi-restraints excluded: chain B residue 144 GLU
Chi-restraints excluded: chain B residue 224 ILE
Chi-restraints excluded: chain B residue 240 PHE
Chi-restraints excluded: chain B residue 242 LEU
Chi-restraints excluded: chain B residue 255 LEU
Chi-restraints excluded: chain B residue 266 GLN
Chi-restraints excluded: chain B residue 337 LEU
Chi-restraints excluded: chain B residue 352 VAL
Chi-restraints excluded: chain C residue 30 LEU
Chi-restraints excluded: chain C residue 90 GLN
Chi-restraints excluded: chain C residue 101 VAL
Chi-restraints excluded: chain C residue 144 GLU
Chi-restraints excluded: chain C residue 224 ILE
Chi-restraints excluded: chain C residue 240 PHE
Chi-restraints excluded: chain C residue 242 LEU
Chi-restraints excluded: chain C residue 356 ILE
Chi-restraints excluded: chain D residue 30 LEU
Chi-restraints excluded: chain D residue 101 VAL
Chi-restraints excluded: chain D residue 124 ASN
Chi-restraints excluded: chain D residue 223 LEU
Chi-restraints excluded: chain D residue 224 ILE
Chi-restraints excluded: chain D residue 240 PHE
Chi-restraints excluded: chain D residue 242 LEU
Chi-restraints excluded: chain D residue 266 GLN
Chi-restraints excluded: chain D residue 272 VAL
Chi-restraints excluded: chain D residue 276 ARG
Chi-restraints excluded: chain D residue 352 VAL
Chi-restraints excluded: chain E residue 30 LEU
Chi-restraints excluded: chain E residue 124 ASN
Chi-restraints excluded: chain E residue 144 GLU
Chi-restraints excluded: chain E residue 202 LEU
Chi-restraints excluded: chain E residue 224 ILE
Chi-restraints excluded: chain E residue 242 LEU
Chi-restraints excluded: chain E residue 266 GLN
Chi-restraints excluded: chain E residue 297 MET
Chi-restraints excluded: chain E residue 352 VAL
Chi-restraints excluded: chain F residue 30 LEU
Chi-restraints excluded: chain F residue 89 GLN
Chi-restraints excluded: chain F residue 101 VAL
Chi-restraints excluded: chain F residue 124 ASN
Chi-restraints excluded: chain F residue 202 LEU
Chi-restraints excluded: chain F residue 216 LEU
Chi-restraints excluded: chain F residue 224 ILE
Chi-restraints excluded: chain F residue 240 PHE
Chi-restraints excluded: chain F residue 242 LEU
Chi-restraints excluded: chain F residue 287 VAL
Chi-restraints excluded: chain F residue 352 VAL
Chi-restraints excluded: chain G residue 30 LEU
Chi-restraints excluded: chain G residue 101 VAL
Chi-restraints excluded: chain G residue 144 GLU
Chi-restraints excluded: chain G residue 224 ILE
Chi-restraints excluded: chain G residue 240 PHE
Chi-restraints excluded: chain G residue 242 LEU
Chi-restraints excluded: chain G residue 255 LEU
Chi-restraints excluded: chain G residue 266 GLN
Chi-restraints excluded: chain G residue 317 PHE
Chi-restraints excluded: chain G residue 352 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 224
random chunks:
chunk 121 optimal weight: 5.9990
chunk 223 optimal weight: 4.9990
chunk 27 optimal weight: 9.9990
chunk 182 optimal weight: 0.9990
chunk 65 optimal weight: 1.9990
chunk 118 optimal weight: 0.9980
chunk 23 optimal weight: 4.9990
chunk 103 optimal weight: 5.9990
chunk 222 optimal weight: 30.0000
chunk 48 optimal weight: 0.8980
chunk 155 optimal weight: 9.9990
overall best weight: 1.9786
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 355 ASN
B 56 GLN
B 355 ASN
C 266 GLN
C 340 ASN
C 355 ASN
D 355 ASN
E 355 ASN
F 340 ASN
G 355 ASN
Total number of N/Q/H flips: 10
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.124961 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.083180 restraints weight = 30639.308|
|-----------------------------------------------------------------------------|
r_work (start): 0.3073 rms_B_bonded: 2.45
r_work: 0.2931 rms_B_bonded: 3.18 restraints_weight: 0.5000
r_work (final): 0.2931
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8256
moved from start: 0.2658
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.004 0.039 18718 Z= 0.236
Angle : 0.645 11.548 25445 Z= 0.305
Chirality : 0.040 0.214 3045
Planarity : 0.003 0.038 3052
Dihedral : 4.490 59.601 2434
Min Nonbonded Distance : 2.604
Molprobity Statistics.
All-atom Clashscore : 5.88
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 1.46 %
Favored : 98.54 %
Rotamer:
Outliers : 4.29 %
Allowed : 25.30 %
Favored : 70.40 %
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: 2.13 (0.19), residues: 2198
helix: 2.39 (0.14), residues: 1519
sheet: 0.30 (0.49), residues: 126
loop : -1.19 (0.28), residues: 553
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.008 0.001 TRP B 127
HIS 0.003 0.001 HIS G 106
PHE 0.010 0.001 PHE D 12
TYR 0.029 0.001 TYR E 232
ARG 0.007 0.001 ARG D 29
*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
4396 Ramachandran restraints generated.
2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
4396 Ramachandran restraints generated.
2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
331 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 88
poor density : 243
time to evaluate : 2.076
Fit side-chains
REVERT: A 14 ASP cc_start: 0.8473 (m-30) cc_final: 0.7618 (p0)
REVERT: A 144 GLU cc_start: 0.8270 (OUTLIER) cc_final: 0.8012 (mp0)
REVERT: A 152 ARG cc_start: 0.6230 (ptm-80) cc_final: 0.5715 (mtm110)
REVERT: A 240 PHE cc_start: 0.7714 (OUTLIER) cc_final: 0.7195 (m-80)
REVERT: A 358 ASN cc_start: 0.8836 (t0) cc_final: 0.8473 (t0)
REVERT: B 14 ASP cc_start: 0.8501 (m-30) cc_final: 0.7827 (p0)
REVERT: B 144 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.8030 (mp0)
REVERT: B 152 ARG cc_start: 0.6270 (ptm-80) cc_final: 0.5787 (mtm110)
REVERT: B 203 LYS cc_start: 0.9175 (mmmt) cc_final: 0.8809 (mmtt)
REVERT: B 240 PHE cc_start: 0.7641 (OUTLIER) cc_final: 0.7380 (m-80)
REVERT: B 266 GLN cc_start: 0.8778 (OUTLIER) cc_final: 0.8333 (tt0)
REVERT: B 306 ASN cc_start: 0.7512 (t0) cc_final: 0.7263 (t0)
REVERT: B 358 ASN cc_start: 0.8890 (t0) cc_final: 0.8530 (t0)
REVERT: C 14 ASP cc_start: 0.8443 (m-30) cc_final: 0.7730 (p0)
REVERT: C 144 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.7985 (mp0)
REVERT: C 152 ARG cc_start: 0.6092 (ptm-80) cc_final: 0.5613 (mtm110)
REVERT: C 200 GLN cc_start: 0.8568 (mm-40) cc_final: 0.8350 (mm-40)
REVERT: C 297 MET cc_start: 0.8220 (pmm) cc_final: 0.7944 (pmt)
REVERT: C 306 ASN cc_start: 0.7658 (t0) cc_final: 0.7407 (t0)
REVERT: D 14 ASP cc_start: 0.8350 (m-30) cc_final: 0.7610 (p0)
REVERT: D 152 ARG cc_start: 0.6199 (ptm-80) cc_final: 0.5687 (mtm110)
REVERT: D 200 GLN cc_start: 0.8638 (mm-40) cc_final: 0.8422 (mm-40)
REVERT: D 240 PHE cc_start: 0.7749 (OUTLIER) cc_final: 0.6351 (t80)
REVERT: D 266 GLN cc_start: 0.8886 (OUTLIER) cc_final: 0.8485 (tp-100)
REVERT: D 306 ASN cc_start: 0.7660 (t0) cc_final: 0.7360 (t0)
REVERT: D 317 PHE cc_start: 0.7798 (OUTLIER) cc_final: 0.7368 (m-80)
REVERT: E 14 ASP cc_start: 0.8408 (m-30) cc_final: 0.7719 (p0)
REVERT: E 144 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.7997 (mp0)
REVERT: E 152 ARG cc_start: 0.6199 (ptm-80) cc_final: 0.5709 (mtm110)
REVERT: E 203 LYS cc_start: 0.9212 (mmmt) cc_final: 0.8895 (mptt)
REVERT: E 266 GLN cc_start: 0.8772 (OUTLIER) cc_final: 0.8472 (tt0)
REVERT: E 297 MET cc_start: 0.7731 (OUTLIER) cc_final: 0.7520 (pmm)
REVERT: E 306 ASN cc_start: 0.7575 (t0) cc_final: 0.7271 (t0)
REVERT: F 14 ASP cc_start: 0.8534 (m-30) cc_final: 0.7998 (t0)
REVERT: F 152 ARG cc_start: 0.6161 (ptm-80) cc_final: 0.5928 (ptm-80)
REVERT: F 203 LYS cc_start: 0.9231 (mmmt) cc_final: 0.8900 (mptt)
REVERT: F 266 GLN cc_start: 0.8938 (OUTLIER) cc_final: 0.8314 (tt0)
REVERT: F 280 TYR cc_start: 0.8169 (t80) cc_final: 0.7605 (m-80)
REVERT: F 358 ASN cc_start: 0.9033 (t0) cc_final: 0.8735 (t0)
REVERT: G 14 ASP cc_start: 0.8484 (m-30) cc_final: 0.7773 (p0)
REVERT: G 128 ARG cc_start: 0.8584 (tmm-80) cc_final: 0.8358 (ttt-90)
REVERT: G 144 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7938 (mp0)
REVERT: G 152 ARG cc_start: 0.6221 (ptm-80) cc_final: 0.5716 (mtm110)
REVERT: G 203 LYS cc_start: 0.9280 (mmmt) cc_final: 0.8912 (mmtt)
REVERT: G 266 GLN cc_start: 0.8966 (OUTLIER) cc_final: 0.8464 (tt0)
REVERT: G 317 PHE cc_start: 0.7922 (OUTLIER) cc_final: 0.7604 (m-80)
outliers start: 88
outliers final: 52
residues processed: 309
average time/residue: 1.1751
time to fit residues: 412.3182
Evaluate side-chains
307 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 68
poor density : 239
time to evaluate : 2.157
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 124 ASN
Chi-restraints excluded: chain A residue 144 GLU
Chi-restraints excluded: chain A residue 223 LEU
Chi-restraints excluded: chain A residue 224 ILE
Chi-restraints excluded: chain A residue 240 PHE
Chi-restraints excluded: chain A residue 242 LEU
Chi-restraints excluded: chain A residue 255 LEU
Chi-restraints excluded: chain A residue 352 VAL
Chi-restraints excluded: chain B residue 101 VAL
Chi-restraints excluded: chain B residue 129 PHE
Chi-restraints excluded: chain B residue 144 GLU
Chi-restraints excluded: chain B residue 202 LEU
Chi-restraints excluded: chain B residue 224 ILE
Chi-restraints excluded: chain B residue 240 PHE
Chi-restraints excluded: chain B residue 242 LEU
Chi-restraints excluded: chain B residue 255 LEU
Chi-restraints excluded: chain B residue 266 GLN
Chi-restraints excluded: chain B residue 352 VAL
Chi-restraints excluded: chain C residue 30 LEU
Chi-restraints excluded: chain C residue 101 VAL
Chi-restraints excluded: chain C residue 144 GLU
Chi-restraints excluded: chain C residue 224 ILE
Chi-restraints excluded: chain C residue 240 PHE
Chi-restraints excluded: chain C residue 242 LEU
Chi-restraints excluded: chain D residue 30 LEU
Chi-restraints excluded: chain D residue 101 VAL
Chi-restraints excluded: chain D residue 124 ASN
Chi-restraints excluded: chain D residue 202 LEU
Chi-restraints excluded: chain D residue 223 LEU
Chi-restraints excluded: chain D residue 224 ILE
Chi-restraints excluded: chain D residue 240 PHE
Chi-restraints excluded: chain D residue 242 LEU
Chi-restraints excluded: chain D residue 266 GLN
Chi-restraints excluded: chain D residue 272 VAL
Chi-restraints excluded: chain D residue 276 ARG
Chi-restraints excluded: chain D residue 317 PHE
Chi-restraints excluded: chain D residue 352 VAL
Chi-restraints excluded: chain E residue 30 LEU
Chi-restraints excluded: chain E residue 124 ASN
Chi-restraints excluded: chain E residue 144 GLU
Chi-restraints excluded: chain E residue 202 LEU
Chi-restraints excluded: chain E residue 224 ILE
Chi-restraints excluded: chain E residue 242 LEU
Chi-restraints excluded: chain E residue 266 GLN
Chi-restraints excluded: chain E residue 297 MET
Chi-restraints excluded: chain E residue 352 VAL
Chi-restraints excluded: chain F residue 30 LEU
Chi-restraints excluded: chain F residue 101 VAL
Chi-restraints excluded: chain F residue 124 ASN
Chi-restraints excluded: chain F residue 202 LEU
Chi-restraints excluded: chain F residue 216 LEU
Chi-restraints excluded: chain F residue 224 ILE
Chi-restraints excluded: chain F residue 240 PHE
Chi-restraints excluded: chain F residue 242 LEU
Chi-restraints excluded: chain F residue 255 LEU
Chi-restraints excluded: chain F residue 266 GLN
Chi-restraints excluded: chain F residue 287 VAL
Chi-restraints excluded: chain F residue 352 VAL
Chi-restraints excluded: chain G residue 30 LEU
Chi-restraints excluded: chain G residue 101 VAL
Chi-restraints excluded: chain G residue 144 GLU
Chi-restraints excluded: chain G residue 224 ILE
Chi-restraints excluded: chain G residue 240 PHE
Chi-restraints excluded: chain G residue 242 LEU
Chi-restraints excluded: chain G residue 255 LEU
Chi-restraints excluded: chain G residue 266 GLN
Chi-restraints excluded: chain G residue 317 PHE
Chi-restraints excluded: chain G residue 352 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 224
random chunks:
chunk 55 optimal weight: 4.9990
chunk 183 optimal weight: 0.8980
chunk 120 optimal weight: 1.9990
chunk 107 optimal weight: 0.9990
chunk 110 optimal weight: 2.9990
chunk 88 optimal weight: 4.9990
chunk 21 optimal weight: 0.0270
chunk 80 optimal weight: 0.9990
chunk 103 optimal weight: 4.9990
chunk 100 optimal weight: 0.8980
chunk 63 optimal weight: 6.9990
overall best weight: 0.7642
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 355 ASN
B 355 ASN
C 266 GLN
C 340 ASN
C 355 ASN
D 355 ASN
E 355 ASN
F 340 ASN
G 56 GLN
G 355 ASN
Total number of N/Q/H flips: 10
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.126829 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.085213 restraints weight = 30499.112|
|-----------------------------------------------------------------------------|
r_work (start): 0.3114 rms_B_bonded: 2.46
r_work: 0.2973 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.2973
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8235
moved from start: 0.2662
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.041 18718 Z= 0.172
Angle : 0.641 11.381 25445 Z= 0.303
Chirality : 0.039 0.207 3045
Planarity : 0.003 0.031 3052
Dihedral : 4.412 57.189 2434
Min Nonbonded Distance : 2.594
Molprobity Statistics.
All-atom Clashscore : 5.94
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 1.64 %
Favored : 98.36 %
Rotamer:
Outliers : 3.51 %
Allowed : 26.28 %
Favored : 70.21 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 2.27 (0.19), residues: 2198
helix: 2.50 (0.14), residues: 1512
sheet: 0.25 (0.49), residues: 126
loop : -1.09 (0.28), residues: 560
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.006 0.001 TRP E 74
HIS 0.002 0.001 HIS A 106
PHE 0.010 0.001 PHE D 12
TYR 0.028 0.001 TYR E 232
ARG 0.007 0.001 ARG D 29
********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
4396 Ramachandran restraints generated.
2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
4396 Ramachandran restraints generated.
2198 Oldfield, 0 Emsley, 2198 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
324 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 72
poor density : 252
time to evaluate : 2.306
Fit side-chains
REVERT: A 14 ASP cc_start: 0.8459 (m-30) cc_final: 0.7527 (p0)
REVERT: A 144 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.8003 (mp0)
REVERT: A 152 ARG cc_start: 0.6234 (ptm-80) cc_final: 0.5712 (mtm110)
REVERT: A 240 PHE cc_start: 0.7571 (OUTLIER) cc_final: 0.6949 (m-80)
REVERT: A 280 TYR cc_start: 0.8207 (t80) cc_final: 0.7627 (m-80)
REVERT: A 358 ASN cc_start: 0.8847 (t0) cc_final: 0.8483 (t0)
REVERT: B 14 ASP cc_start: 0.8456 (m-30) cc_final: 0.7817 (p0)
REVERT: B 144 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.8032 (mp0)
REVERT: B 152 ARG cc_start: 0.6271 (ptm-80) cc_final: 0.5751 (mtm110)
REVERT: B 203 LYS cc_start: 0.9204 (mmmt) cc_final: 0.8845 (mmtt)
REVERT: B 240 PHE cc_start: 0.7622 (OUTLIER) cc_final: 0.7375 (m-80)
REVERT: B 306 ASN cc_start: 0.7560 (t0) cc_final: 0.7295 (t0)
REVERT: B 358 ASN cc_start: 0.8935 (t0) cc_final: 0.8537 (t0)
REVERT: C 14 ASP cc_start: 0.8430 (m-30) cc_final: 0.7635 (p0)
REVERT: C 144 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.8049 (mp0)
REVERT: C 152 ARG cc_start: 0.6098 (ptm-80) cc_final: 0.5610 (mtm110)
REVERT: C 200 GLN cc_start: 0.8552 (mm-40) cc_final: 0.8335 (mm-40)
REVERT: C 297 MET cc_start: 0.8197 (pmm) cc_final: 0.7914 (pmt)
REVERT: C 306 ASN cc_start: 0.7674 (t0) cc_final: 0.7423 (t0)
REVERT: C 352 VAL cc_start: 0.8821 (p) cc_final: 0.8607 (t)
REVERT: D 14 ASP cc_start: 0.8330 (m-30) cc_final: 0.7631 (p0)
REVERT: D 152 ARG cc_start: 0.6309 (ptm-80) cc_final: 0.5768 (mtm110)
REVERT: D 200 GLN cc_start: 0.8619 (mm-40) cc_final: 0.8397 (mm-40)
REVERT: D 240 PHE cc_start: 0.7711 (OUTLIER) cc_final: 0.6349 (t80)
REVERT: D 266 GLN cc_start: 0.8812 (OUTLIER) cc_final: 0.8407 (tp-100)
REVERT: D 306 ASN cc_start: 0.7669 (t0) cc_final: 0.7401 (t0)
REVERT: E 14 ASP cc_start: 0.8391 (m-30) cc_final: 0.7735 (p0)
REVERT: E 144 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.8003 (mp0)
REVERT: E 152 ARG cc_start: 0.6152 (ptm-80) cc_final: 0.5721 (mtm110)
REVERT: E 203 LYS cc_start: 0.9222 (mmmt) cc_final: 0.8916 (mptt)
REVERT: E 266 GLN cc_start: 0.8692 (OUTLIER) cc_final: 0.8422 (tt0)
REVERT: E 306 ASN cc_start: 0.7554 (t0) cc_final: 0.7268 (t0)
REVERT: F 14 ASP cc_start: 0.8511 (m-30) cc_final: 0.7981 (t0)
REVERT: F 152 ARG cc_start: 0.6109 (ptm-80) cc_final: 0.5858 (ptm-80)
REVERT: F 203 LYS cc_start: 0.9248 (mmmt) cc_final: 0.8908 (mptt)
REVERT: F 266 GLN cc_start: 0.8851 (OUTLIER) cc_final: 0.8238 (tt0)
REVERT: F 280 TYR cc_start: 0.8140 (t80) cc_final: 0.7600 (m-80)
REVERT: F 358 ASN cc_start: 0.9071 (t0) cc_final: 0.8791 (t0)
REVERT: G 14 ASP cc_start: 0.8457 (m-30) cc_final: 0.7752 (p0)
REVERT: G 128 ARG cc_start: 0.8588 (tmm-80) cc_final: 0.8362 (ttt-90)
REVERT: G 144 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.7894 (mp0)
REVERT: G 152 ARG cc_start: 0.6184 (ptm-80) cc_final: 0.5717 (mtm110)
REVERT: G 266 GLN cc_start: 0.8931 (OUTLIER) cc_final: 0.8458 (tt0)
REVERT: G 317 PHE cc_start: 0.7889 (OUTLIER) cc_final: 0.7576 (m-80)
outliers start: 72
outliers final: 51
residues processed: 307
average time/residue: 1.1962
time to fit residues: 416.2946
Evaluate side-chains
306 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 64
poor density : 242
time to evaluate : 1.987
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 124 ASN
Chi-restraints excluded: chain A residue 144 GLU
Chi-restraints excluded: chain A residue 223 LEU
Chi-restraints excluded: chain A residue 224 ILE
Chi-restraints excluded: chain A residue 240 PHE
Chi-restraints excluded: chain A residue 242 LEU
Chi-restraints excluded: chain A residue 255 LEU
Chi-restraints excluded: chain A residue 352 VAL
Chi-restraints excluded: chain B residue 101 VAL
Chi-restraints excluded: chain B residue 129 PHE
Chi-restraints excluded: chain B residue 144 GLU
Chi-restraints excluded: chain B residue 224 ILE
Chi-restraints excluded: chain B residue 240 PHE
Chi-restraints excluded: chain B residue 242 LEU
Chi-restraints excluded: chain B residue 255 LEU
Chi-restraints excluded: chain B residue 352 VAL
Chi-restraints excluded: chain C residue 30 LEU
Chi-restraints excluded: chain C residue 101 VAL
Chi-restraints excluded: chain C residue 144 GLU
Chi-restraints excluded: chain C residue 224 ILE
Chi-restraints excluded: chain C residue 240 PHE
Chi-restraints excluded: chain C residue 242 LEU
Chi-restraints excluded: chain D residue 30 LEU
Chi-restraints excluded: chain D residue 101 VAL
Chi-restraints excluded: chain D residue 124 ASN
Chi-restraints excluded: chain D residue 202 LEU
Chi-restraints excluded: chain D residue 223 LEU
Chi-restraints excluded: chain D residue 224 ILE
Chi-restraints excluded: chain D residue 240 PHE
Chi-restraints excluded: chain D residue 242 LEU
Chi-restraints excluded: chain D residue 266 GLN
Chi-restraints excluded: chain D residue 272 VAL
Chi-restraints excluded: chain D residue 276 ARG
Chi-restraints excluded: chain D residue 352 VAL
Chi-restraints excluded: chain E residue 30 LEU
Chi-restraints excluded: chain E residue 124 ASN
Chi-restraints excluded: chain E residue 144 GLU
Chi-restraints excluded: chain E residue 202 LEU
Chi-restraints excluded: chain E residue 224 ILE
Chi-restraints excluded: chain E residue 242 LEU
Chi-restraints excluded: chain E residue 266 GLN
Chi-restraints excluded: chain E residue 352 VAL
Chi-restraints excluded: chain F residue 30 LEU
Chi-restraints excluded: chain F residue 101 VAL
Chi-restraints excluded: chain F residue 124 ASN
Chi-restraints excluded: chain F residue 202 LEU
Chi-restraints excluded: chain F residue 216 LEU
Chi-restraints excluded: chain F residue 224 ILE
Chi-restraints excluded: chain F residue 240 PHE
Chi-restraints excluded: chain F residue 242 LEU
Chi-restraints excluded: chain F residue 266 GLN
Chi-restraints excluded: chain F residue 287 VAL
Chi-restraints excluded: chain F residue 352 VAL
Chi-restraints excluded: chain G residue 30 LEU
Chi-restraints excluded: chain G residue 101 VAL
Chi-restraints excluded: chain G residue 144 GLU
Chi-restraints excluded: chain G residue 202 LEU
Chi-restraints excluded: chain G residue 224 ILE
Chi-restraints excluded: chain G residue 240 PHE
Chi-restraints excluded: chain G residue 242 LEU
Chi-restraints excluded: chain G residue 255 LEU
Chi-restraints excluded: chain G residue 266 GLN
Chi-restraints excluded: chain G residue 317 PHE
Chi-restraints excluded: chain G residue 352 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 224
random chunks:
chunk 78 optimal weight: 2.9990
chunk 153 optimal weight: 5.9990
chunk 199 optimal weight: 2.9990
chunk 46 optimal weight: 3.9990
chunk 23 optimal weight: 4.9990
chunk 68 optimal weight: 0.6980
chunk 93 optimal weight: 7.9990
chunk 167 optimal weight: 3.9990
chunk 217 optimal weight: 0.7980
chunk 204 optimal weight: 1.9990
chunk 39 optimal weight: 3.9990
overall best weight: 1.8986
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 355 ASN
B 56 GLN
B 355 ASN
C 266 GLN
C 340 ASN
C 355 ASN
D 355 ASN
E 355 ASN
F 340 ASN
G 355 ASN
Total number of N/Q/H flips: 10
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.125107 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3125 r_free = 0.3125 target = 0.082728 restraints weight = 30567.699|
|-----------------------------------------------------------------------------|
r_work (start): 0.3073 rms_B_bonded: 2.48
r_work: 0.2931 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work (final): 0.2931
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8263
moved from start: 0.2756
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.004 0.042 18718 Z= 0.238
Angle : 0.675 12.354 25445 Z= 0.319
Chirality : 0.041 0.214 3045
Planarity : 0.003 0.032 3052
Dihedral : 4.317 55.066 2434
Min Nonbonded Distance : 2.582
Molprobity Statistics.
All-atom Clashscore : 6.12
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 1.64 %
Favored : 98.36 %
Rotamer:
Outliers : 3.80 %
Allowed : 25.99 %
Favored : 70.21 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 2.15 (0.19), residues: 2198
helix: 2.40 (0.14), residues: 1519
sheet: 0.25 (0.49), residues: 126
loop : -1.15 (0.29), residues: 553
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.009 0.001 TRP C 127
HIS 0.003 0.001 HIS B 106
PHE 0.012 0.001 PHE E 15
TYR 0.030 0.001 TYR E 232
ARG 0.008 0.001 ARG C 29
Origin is already at (0, 0, 0), no shifts will be applied
===============================================================================
Job complete
usr+sys time: 11612.82 seconds
wall clock time: 207 minutes 5.26 seconds (12425.26 seconds total)