Starting phenix.real_space_refine
on Sat Jan 25 15:28:22 2025 by dcliebschner
===============================================================================
Processing files:
-------------------------------------------------------------------------------
Found model, /net/cci-nas-00/data/ceres_data/9ewx_50025/01_2025/9ewx_50025.cif
Found real_map, /net/cci-nas-00/data/ceres_data/9ewx_50025/01_2025/9ewx_50025.map
Processing PHIL parameters:
-------------------------------------------------------------------------------
Adding command-line PHIL:
-------------------------
refinement.macro_cycles=10
scattering_table=electron
resolution=3.17
write_initial_geo_file=False
Final processed PHIL parameters:
-------------------------------------------------------------------------------
data_manager {
real_map_files = "/net/cci-nas-00/data/ceres_data/9ewx_50025/01_2025/9ewx_50025.map"
default_real_map = "/net/cci-nas-00/data/ceres_data/9ewx_50025/01_2025/9ewx_50025.map"
model {
file = "/net/cci-nas-00/data/ceres_data/9ewx_50025/01_2025/9ewx_50025.cif"
}
default_model = "/net/cci-nas-00/data/ceres_data/9ewx_50025/01_2025/9ewx_50025.cif"
}
resolution = 3.17
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= 0.005
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 92 5.16 5
C 15111 2.51 5
N 3933 2.21 5
O 4853 1.98 5
sf(0) = scattering factor at diffraction angle 0.
Process input model
Symmetric amino acids flipped. Time to flip 92 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: 23989
Number of models: 1
Model: ""
Number of chains: 1
Chain: "A"
Number of atoms: 1043
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 143, 1043
Classifications: {'peptide': 143}
Modifications used: {'COO': 1}
Link IDs: {'PTRANS': 6, 'TRANS': 136}
Restraints were copied for chains:
C, B, E, D, G, F, I, H, K, J, M, L, O, N, Q, P, S, R, U, T, W, V
Time building chain proxies: 7.05, per 1000 atoms: 0.29
Number of scatterers: 23989
At special positions: 0
Unit cell: (71.688, 71.688, 319.712, 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 92 16.00
O 4853 8.00
N 3933 7.00
C 15111 6.00
sf(0) = scattering factor at diffraction angle 0.
Number of disulfides: simple=1, symmetry=0
Simple disulfide: pdb=" SG CYS A 134 " - pdb=" SG CYS A 147 " 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: 5.23
Conformation dependent library (CDL) restraints added in 3.4 seconds
6486 Ramachandran restraints generated.
3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2.
Adding C-beta torsion restraints...
Number of C-beta restraints generated: 6026
Finding SS restraints...
Secondary structure from input PDB file:
92 helices and 46 sheets defined
34.3% alpha, 16.1% beta
0 base pairs and 0 stacking pairs defined.
Time for finding SS restraints: 2.69
Creating SS restraints...
Processing helix chain 'A' and resid 8 through 23
Processing helix chain 'A' and resid 30 through 47
Processing helix chain 'A' and resid 48 through 59
removed outlier: 3.595A pdb=" N THR A 52 " --> pdb=" O PRO A 48 " (cutoff:3.500A)
Processing helix chain 'A' and resid 62 through 64
No H-bonds generated for 'chain 'A' and resid 62 through 64'
Processing helix chain 'B' and resid 8 through 23
Processing helix chain 'B' and resid 30 through 47
Processing helix chain 'B' and resid 48 through 59
removed outlier: 3.595A pdb=" N THR B 52 " --> pdb=" O PRO B 48 " (cutoff:3.500A)
Processing helix chain 'B' and resid 62 through 64
No H-bonds generated for 'chain 'B' and resid 62 through 64'
Processing helix chain 'C' and resid 8 through 23
Processing helix chain 'C' and resid 30 through 47
Processing helix chain 'C' and resid 48 through 59
removed outlier: 3.595A pdb=" N THR C 52 " --> pdb=" O PRO C 48 " (cutoff:3.500A)
Processing helix chain 'C' and resid 62 through 64
No H-bonds generated for 'chain 'C' and resid 62 through 64'
Processing helix chain 'D' and resid 8 through 23
Processing helix chain 'D' and resid 30 through 47
Processing helix chain 'D' and resid 48 through 59
removed outlier: 3.595A pdb=" N THR D 52 " --> pdb=" O PRO D 48 " (cutoff:3.500A)
Processing helix chain 'D' and resid 62 through 64
No H-bonds generated for 'chain 'D' and resid 62 through 64'
Processing helix chain 'E' and resid 8 through 23
Processing helix chain 'E' and resid 30 through 47
Processing helix chain 'E' and resid 48 through 59
removed outlier: 3.595A pdb=" N THR E 52 " --> pdb=" O PRO E 48 " (cutoff:3.500A)
Processing helix chain 'E' and resid 62 through 64
No H-bonds generated for 'chain 'E' and resid 62 through 64'
Processing helix chain 'F' and resid 8 through 23
Processing helix chain 'F' and resid 30 through 47
Processing helix chain 'F' and resid 48 through 59
removed outlier: 3.595A pdb=" N THR F 52 " --> pdb=" O PRO F 48 " (cutoff:3.500A)
Processing helix chain 'F' and resid 62 through 64
No H-bonds generated for 'chain 'F' and resid 62 through 64'
Processing helix chain 'G' and resid 8 through 23
Processing helix chain 'G' and resid 30 through 47
Processing helix chain 'G' and resid 48 through 59
removed outlier: 3.596A pdb=" N THR G 52 " --> pdb=" O PRO G 48 " (cutoff:3.500A)
Processing helix chain 'G' and resid 62 through 64
No H-bonds generated for 'chain 'G' and resid 62 through 64'
Processing helix chain 'H' and resid 8 through 23
Processing helix chain 'H' and resid 30 through 47
Processing helix chain 'H' and resid 48 through 59
removed outlier: 3.595A pdb=" N THR H 52 " --> pdb=" O PRO H 48 " (cutoff:3.500A)
Processing helix chain 'H' and resid 62 through 64
No H-bonds generated for 'chain 'H' and resid 62 through 64'
Processing helix chain 'I' and resid 8 through 23
Processing helix chain 'I' and resid 30 through 47
Processing helix chain 'I' and resid 48 through 59
removed outlier: 3.594A pdb=" N THR I 52 " --> pdb=" O PRO I 48 " (cutoff:3.500A)
Processing helix chain 'I' and resid 62 through 64
No H-bonds generated for 'chain 'I' and resid 62 through 64'
Processing helix chain 'J' and resid 8 through 23
Processing helix chain 'J' and resid 30 through 47
Processing helix chain 'J' and resid 48 through 59
removed outlier: 3.595A pdb=" N THR J 52 " --> pdb=" O PRO J 48 " (cutoff:3.500A)
Processing helix chain 'J' and resid 62 through 64
No H-bonds generated for 'chain 'J' and resid 62 through 64'
Processing helix chain 'K' and resid 8 through 23
Processing helix chain 'K' and resid 30 through 47
Processing helix chain 'K' and resid 48 through 59
removed outlier: 3.595A pdb=" N THR K 52 " --> pdb=" O PRO K 48 " (cutoff:3.500A)
Processing helix chain 'K' and resid 62 through 64
No H-bonds generated for 'chain 'K' and resid 62 through 64'
Processing helix chain 'L' and resid 8 through 23
Processing helix chain 'L' and resid 30 through 47
Processing helix chain 'L' and resid 48 through 59
removed outlier: 3.595A pdb=" N THR L 52 " --> pdb=" O PRO L 48 " (cutoff:3.500A)
Processing helix chain 'L' and resid 62 through 64
No H-bonds generated for 'chain 'L' and resid 62 through 64'
Processing helix chain 'M' and resid 8 through 23
Processing helix chain 'M' and resid 30 through 47
Processing helix chain 'M' and resid 48 through 59
removed outlier: 3.595A pdb=" N THR M 52 " --> pdb=" O PRO M 48 " (cutoff:3.500A)
Processing helix chain 'M' and resid 62 through 64
No H-bonds generated for 'chain 'M' and resid 62 through 64'
Processing helix chain 'N' and resid 8 through 23
Processing helix chain 'N' and resid 30 through 47
Processing helix chain 'N' and resid 48 through 59
removed outlier: 3.595A pdb=" N THR N 52 " --> pdb=" O PRO N 48 " (cutoff:3.500A)
Processing helix chain 'N' and resid 62 through 64
No H-bonds generated for 'chain 'N' and resid 62 through 64'
Processing helix chain 'O' and resid 8 through 23
Processing helix chain 'O' and resid 30 through 47
Processing helix chain 'O' and resid 48 through 59
removed outlier: 3.595A pdb=" N THR O 52 " --> pdb=" O PRO O 48 " (cutoff:3.500A)
Processing helix chain 'O' and resid 62 through 64
No H-bonds generated for 'chain 'O' and resid 62 through 64'
Processing helix chain 'P' and resid 8 through 23
Processing helix chain 'P' and resid 30 through 47
Processing helix chain 'P' and resid 48 through 59
removed outlier: 3.595A pdb=" N THR P 52 " --> pdb=" O PRO P 48 " (cutoff:3.500A)
Processing helix chain 'P' and resid 62 through 64
No H-bonds generated for 'chain 'P' and resid 62 through 64'
Processing helix chain 'Q' and resid 8 through 23
Processing helix chain 'Q' and resid 30 through 47
Processing helix chain 'Q' and resid 48 through 59
removed outlier: 3.595A pdb=" N THR Q 52 " --> pdb=" O PRO Q 48 " (cutoff:3.500A)
Processing helix chain 'Q' and resid 62 through 64
No H-bonds generated for 'chain 'Q' and resid 62 through 64'
Processing helix chain 'R' and resid 8 through 23
Processing helix chain 'R' and resid 30 through 47
Processing helix chain 'R' and resid 48 through 59
removed outlier: 3.595A pdb=" N THR R 52 " --> pdb=" O PRO R 48 " (cutoff:3.500A)
Processing helix chain 'R' and resid 62 through 64
No H-bonds generated for 'chain 'R' and resid 62 through 64'
Processing helix chain 'S' and resid 8 through 23
Processing helix chain 'S' and resid 30 through 47
Processing helix chain 'S' and resid 48 through 59
removed outlier: 3.595A pdb=" N THR S 52 " --> pdb=" O PRO S 48 " (cutoff:3.500A)
Processing helix chain 'S' and resid 62 through 64
No H-bonds generated for 'chain 'S' and resid 62 through 64'
Processing helix chain 'T' and resid 8 through 23
Processing helix chain 'T' and resid 30 through 47
Processing helix chain 'T' and resid 48 through 59
removed outlier: 3.595A pdb=" N THR T 52 " --> pdb=" O PRO T 48 " (cutoff:3.500A)
Processing helix chain 'T' and resid 62 through 64
No H-bonds generated for 'chain 'T' and resid 62 through 64'
Processing helix chain 'U' and resid 8 through 23
Processing helix chain 'U' and resid 30 through 47
Processing helix chain 'U' and resid 48 through 59
removed outlier: 3.595A pdb=" N THR U 52 " --> pdb=" O PRO U 48 " (cutoff:3.500A)
Processing helix chain 'U' and resid 62 through 64
No H-bonds generated for 'chain 'U' and resid 62 through 64'
Processing helix chain 'V' and resid 8 through 23
Processing helix chain 'V' and resid 30 through 47
Processing helix chain 'V' and resid 48 through 59
removed outlier: 3.595A pdb=" N THR V 52 " --> pdb=" O PRO V 48 " (cutoff:3.500A)
Processing helix chain 'V' and resid 62 through 64
No H-bonds generated for 'chain 'V' and resid 62 through 64'
Processing helix chain 'W' and resid 8 through 23
Processing helix chain 'W' and resid 30 through 47
Processing helix chain 'W' and resid 48 through 59
removed outlier: 3.594A pdb=" N THR W 52 " --> pdb=" O PRO W 48 " (cutoff:3.500A)
Processing helix chain 'W' and resid 62 through 64
No H-bonds generated for 'chain 'W' and resid 62 through 64'
Processing sheet with id=AA1, first strand: chain 'A' and resid 66 through 67
Processing sheet with id=AA2, first strand: chain 'A' and resid 90 through 96
Processing sheet with id=AA3, first strand: chain 'B' and resid 66 through 67
Processing sheet with id=AA4, first strand: chain 'B' and resid 90 through 96
Processing sheet with id=AA5, first strand: chain 'C' and resid 66 through 67
Processing sheet with id=AA6, first strand: chain 'C' and resid 90 through 96
Processing sheet with id=AA7, first strand: chain 'D' and resid 66 through 67
Processing sheet with id=AA8, first strand: chain 'D' and resid 90 through 96
Processing sheet with id=AA9, first strand: chain 'E' and resid 66 through 67
Processing sheet with id=AB1, first strand: chain 'E' and resid 90 through 96
Processing sheet with id=AB2, first strand: chain 'F' and resid 66 through 67
Processing sheet with id=AB3, first strand: chain 'F' and resid 90 through 96
Processing sheet with id=AB4, first strand: chain 'G' and resid 66 through 67
Processing sheet with id=AB5, first strand: chain 'G' and resid 90 through 96
Processing sheet with id=AB6, first strand: chain 'H' and resid 66 through 67
Processing sheet with id=AB7, first strand: chain 'H' and resid 90 through 96
Processing sheet with id=AB8, first strand: chain 'I' and resid 66 through 67
Processing sheet with id=AB9, first strand: chain 'I' and resid 90 through 96
Processing sheet with id=AC1, first strand: chain 'J' and resid 66 through 67
Processing sheet with id=AC2, first strand: chain 'J' and resid 90 through 96
Processing sheet with id=AC3, first strand: chain 'K' and resid 66 through 67
Processing sheet with id=AC4, first strand: chain 'K' and resid 90 through 96
Processing sheet with id=AC5, first strand: chain 'L' and resid 66 through 67
Processing sheet with id=AC6, first strand: chain 'L' and resid 90 through 96
Processing sheet with id=AC7, first strand: chain 'M' and resid 66 through 67
Processing sheet with id=AC8, first strand: chain 'M' and resid 90 through 96
Processing sheet with id=AC9, first strand: chain 'N' and resid 66 through 67
Processing sheet with id=AD1, first strand: chain 'N' and resid 90 through 96
Processing sheet with id=AD2, first strand: chain 'O' and resid 66 through 67
Processing sheet with id=AD3, first strand: chain 'O' and resid 90 through 96
Processing sheet with id=AD4, first strand: chain 'P' and resid 66 through 67
Processing sheet with id=AD5, first strand: chain 'P' and resid 90 through 96
Processing sheet with id=AD6, first strand: chain 'Q' and resid 66 through 67
Processing sheet with id=AD7, first strand: chain 'Q' and resid 90 through 96
Processing sheet with id=AD8, first strand: chain 'R' and resid 66 through 67
Processing sheet with id=AD9, first strand: chain 'R' and resid 90 through 96
Processing sheet with id=AE1, first strand: chain 'S' and resid 66 through 67
Processing sheet with id=AE2, first strand: chain 'S' and resid 90 through 96
Processing sheet with id=AE3, first strand: chain 'T' and resid 66 through 67
Processing sheet with id=AE4, first strand: chain 'T' and resid 90 through 96
Processing sheet with id=AE5, first strand: chain 'U' and resid 66 through 67
Processing sheet with id=AE6, first strand: chain 'U' and resid 90 through 96
Processing sheet with id=AE7, first strand: chain 'V' and resid 66 through 67
Processing sheet with id=AE8, first strand: chain 'V' and resid 90 through 96
Processing sheet with id=AE9, first strand: chain 'W' and resid 66 through 67
Processing sheet with id=AF1, first strand: chain 'W' and resid 90 through 96
1150 hydrogen bonds defined for protein.
3381 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: 7.68
Time building geometry restraints manager: 6.16 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: 7843
1.35 - 1.46: 4991
1.46 - 1.58: 11339
1.58 - 1.69: 0
1.69 - 1.81: 138
Bond restraints: 24311
Sorted by residual:
bond pdb=" CG GLN K 109 "
pdb=" CD GLN K 109 "
ideal model delta sigma weight residual
1.516 1.535 -0.019 2.50e-02 1.60e+03 5.54e-01
bond pdb=" CG GLN F 109 "
pdb=" CD GLN F 109 "
ideal model delta sigma weight residual
1.516 1.534 -0.018 2.50e-02 1.60e+03 5.47e-01
bond pdb=" CG GLN J 109 "
pdb=" CD GLN J 109 "
ideal model delta sigma weight residual
1.516 1.534 -0.018 2.50e-02 1.60e+03 5.36e-01
bond pdb=" CG GLN O 109 "
pdb=" CD GLN O 109 "
ideal model delta sigma weight residual
1.516 1.534 -0.018 2.50e-02 1.60e+03 5.35e-01
bond pdb=" CG GLN P 109 "
pdb=" CD GLN P 109 "
ideal model delta sigma weight residual
1.516 1.534 -0.018 2.50e-02 1.60e+03 5.30e-01
... (remaining 24306 not shown)
Histogram of bond angle deviations from ideal:
0.00 - 0.91: 32130
0.91 - 1.81: 682
1.81 - 2.72: 216
2.72 - 3.63: 92
3.63 - 4.54: 23
Bond angle restraints: 33143
Sorted by residual:
angle pdb=" CB GLN E 109 "
pdb=" CG GLN E 109 "
pdb=" CD GLN E 109 "
ideal model delta sigma weight residual
112.60 115.48 -2.88 1.70e+00 3.46e-01 2.87e+00
angle pdb=" CB GLN R 109 "
pdb=" CG GLN R 109 "
pdb=" CD GLN R 109 "
ideal model delta sigma weight residual
112.60 115.47 -2.87 1.70e+00 3.46e-01 2.86e+00
angle pdb=" CB GLN H 109 "
pdb=" CG GLN H 109 "
pdb=" CD GLN H 109 "
ideal model delta sigma weight residual
112.60 115.46 -2.86 1.70e+00 3.46e-01 2.84e+00
angle pdb=" CB GLN P 109 "
pdb=" CG GLN P 109 "
pdb=" CD GLN P 109 "
ideal model delta sigma weight residual
112.60 115.46 -2.86 1.70e+00 3.46e-01 2.83e+00
angle pdb=" CB GLN N 109 "
pdb=" CG GLN N 109 "
pdb=" CD GLN N 109 "
ideal model delta sigma weight residual
112.60 115.45 -2.85 1.70e+00 3.46e-01 2.81e+00
... (remaining 33138 not shown)
Histogram of dihedral angle deviations from ideal:
0.00 - 16.52: 12721
16.52 - 33.04: 1426
33.04 - 49.56: 369
49.56 - 66.07: 46
66.07 - 82.59: 115
Dihedral angle restraints: 14677
sinusoidal: 5316
harmonic: 9361
Sorted by residual:
dihedral pdb=" CA GLU B 77 "
pdb=" CB GLU B 77 "
pdb=" CG GLU B 77 "
pdb=" CD GLU B 77 "
ideal model delta sinusoidal sigma weight residual
60.00 115.07 -55.07 3 1.50e+01 4.44e-03 9.32e+00
dihedral pdb=" CA GLU R 77 "
pdb=" CB GLU R 77 "
pdb=" CG GLU R 77 "
pdb=" CD GLU R 77 "
ideal model delta sinusoidal sigma weight residual
60.00 115.07 -55.07 3 1.50e+01 4.44e-03 9.32e+00
dihedral pdb=" CA GLU L 77 "
pdb=" CB GLU L 77 "
pdb=" CG GLU L 77 "
pdb=" CD GLU L 77 "
ideal model delta sinusoidal sigma weight residual
60.00 115.07 -55.07 3 1.50e+01 4.44e-03 9.32e+00
... (remaining 14674 not shown)
Histogram of chiral volume deviations from ideal:
0.000 - 0.026: 2396
0.026 - 0.052: 967
0.052 - 0.078: 412
0.078 - 0.104: 238
0.104 - 0.131: 173
Chirality restraints: 4186
Sorted by residual:
chirality pdb=" CA ILE B 104 "
pdb=" N ILE B 104 "
pdb=" C ILE B 104 "
pdb=" CB ILE B 104 "
both_signs ideal model delta sigma weight residual
False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.26e-01
chirality pdb=" CA ILE F 104 "
pdb=" N ILE F 104 "
pdb=" C ILE F 104 "
pdb=" CB ILE F 104 "
both_signs ideal model delta sigma weight residual
False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.25e-01
chirality pdb=" CA ILE V 104 "
pdb=" N ILE V 104 "
pdb=" C ILE V 104 "
pdb=" CB ILE V 104 "
both_signs ideal model delta sigma weight residual
False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.20e-01
... (remaining 4183 not shown)
Planarity restraints: 4209
Sorted by residual:
delta sigma weight rms_deltas residual
plane pdb=" CA ILE S 10 " 0.004 2.00e-02 2.50e+03 7.66e-03 5.87e-01
pdb=" C ILE S 10 " -0.013 2.00e-02 2.50e+03
pdb=" O ILE S 10 " 0.005 2.00e-02 2.50e+03
pdb=" N GLU S 11 " 0.004 2.00e-02 2.50e+03
delta sigma weight rms_deltas residual
plane pdb=" CA ILE P 10 " 0.004 2.00e-02 2.50e+03 7.46e-03 5.56e-01
pdb=" C ILE P 10 " -0.013 2.00e-02 2.50e+03
pdb=" O ILE P 10 " 0.005 2.00e-02 2.50e+03
pdb=" N GLU P 11 " 0.004 2.00e-02 2.50e+03
delta sigma weight rms_deltas residual
plane pdb=" CA ILE W 10 " 0.004 2.00e-02 2.50e+03 7.42e-03 5.50e-01
pdb=" C ILE W 10 " -0.013 2.00e-02 2.50e+03
pdb=" O ILE W 10 " 0.005 2.00e-02 2.50e+03
pdb=" N GLU W 11 " 0.004 2.00e-02 2.50e+03
... (remaining 4206 not shown)
Histogram of nonbonded interaction distances:
2.03 - 2.60: 137
2.60 - 3.18: 21554
3.18 - 3.75: 36500
3.75 - 4.33: 53745
4.33 - 4.90: 90824
Nonbonded interactions: 202760
Sorted by model distance:
nonbonded pdb=" SG CYS P 134 "
pdb=" SG CYS P 147 "
model vdw
2.031 3.760
nonbonded pdb=" SG CYS W 134 "
pdb=" SG CYS W 147 "
model vdw
2.031 3.760
nonbonded pdb=" SG CYS D 134 "
pdb=" SG CYS D 147 "
model vdw
2.031 3.760
nonbonded pdb=" SG CYS O 134 "
pdb=" SG CYS O 147 "
model vdw
2.031 3.760
nonbonded pdb=" SG CYS M 134 "
pdb=" SG CYS M 147 "
model vdw
2.032 3.760
... (remaining 202755 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: 0.25
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'
selection = chain 'I'
selection = chain 'H'
selection = chain 'K'
selection = chain 'J'
selection = chain 'M'
selection = chain 'L'
selection = chain 'O'
selection = chain 'N'
selection = chain 'Q'
selection = chain 'P'
selection = chain 'S'
selection = chain 'R'
selection = chain 'U'
selection = chain 'T'
selection = chain 'W'
selection = chain 'V'
}
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: 9.180
Set stop_for_unknowns flag: 0.000
Assert model is a single copy model: 0.000
Assert all atoms have isotropic ADPs: 0.000
Construct map_model_manager: 0.000
Extract box with map and model: 0.960
Check model and map are aligned: 0.190
Set scattering table: 0.230
Process input model: 44.020
Find NCS groups from input model: 0.760
Set up NCS constraints: 0.100
Set refine NCS operators: 0.000
Adjust number of macro_cycles: 0.000
Reset NCS operators: 0.000
Extract rigid body selections: 0.000
Check and reset occupancies: 0.010
Load rotamer database and sin/cos tables:2.510
Set ADP refinement strategy: 0.000
Make a string to write initial .geo file:0.000
Internal consistency checks: 0.000
Total: 57.960
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8517
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 0.019 24311 Z= 0.136
Angle : 0.416 4.536 33143 Z= 0.226
Chirality : 0.044 0.131 4186
Planarity : 0.003 0.017 4209
Dihedral : 17.574 82.593 8648
Min Nonbonded Distance : 2.031
Molprobity Statistics.
All-atom Clashscore : 3.78
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 0.71 %
Favored : 99.29 %
Rotamer:
Outliers : 0.88 %
Allowed : 26.36 %
Favored : 72.76 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 2.80 (0.15), residues: 3243
helix: 2.22 (0.17), residues: 1081
sheet: 0.79 (0.20), residues: 713
loop : 2.47 (0.16), residues: 1449
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.004 0.001 TRP T 132
PHE 0.004 0.001 PHE Q 142
TYR 0.006 0.001 TYR D 33
ARG 0.001 0.000 ARG L 59
*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
6486 Ramachandran restraints generated.
3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
6486 Ramachandran restraints generated.
3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
639 residues out of total 2599 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 23
poor density : 616
time to evaluate : 2.972
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: A 82 VAL cc_start: 0.8742 (m) cc_final: 0.8461 (m)
REVERT: A 136 SER cc_start: 0.8544 (t) cc_final: 0.8274 (p)
REVERT: B 65 LYS cc_start: 0.8414 (mmtt) cc_final: 0.7720 (mttt)
REVERT: B 77 GLU cc_start: 0.8336 (mp0) cc_final: 0.7999 (mp0)
REVERT: C 124 LEU cc_start: 0.9135 (mt) cc_final: 0.8883 (mp)
REVERT: D 65 LYS cc_start: 0.8698 (mmtt) cc_final: 0.8327 (mmtp)
REVERT: E 103 ASP cc_start: 0.8694 (p0) cc_final: 0.8433 (p0)
REVERT: I 70 THR cc_start: 0.8556 (p) cc_final: 0.8238 (m)
REVERT: I 97 GLU cc_start: 0.8029 (mt-10) cc_final: 0.7731 (mm-30)
REVERT: I 116 LYS cc_start: 0.8061 (mmtm) cc_final: 0.7784 (mmtt)
REVERT: K 29 GLN cc_start: 0.7969 (tt0) cc_final: 0.7512 (tt0)
REVERT: L 103 ASP cc_start: 0.8283 (p0) cc_final: 0.7895 (p0)
REVERT: M 29 GLN cc_start: 0.7881 (tt0) cc_final: 0.7350 (mt0)
REVERT: M 70 THR cc_start: 0.8636 (p) cc_final: 0.8315 (m)
REVERT: N 129 ASP cc_start: 0.7671 (m-30) cc_final: 0.7330 (m-30)
REVERT: O 29 GLN cc_start: 0.7816 (tt0) cc_final: 0.7514 (mt0)
REVERT: O 43 LEU cc_start: 0.9028 (tp) cc_final: 0.8805 (tp)
REVERT: O 61 ILE cc_start: 0.8400 (mt) cc_final: 0.8197 (mt)
REVERT: P 29 GLN cc_start: 0.7492 (tt0) cc_final: 0.7146 (mt0)
REVERT: P 85 ASP cc_start: 0.7915 (p0) cc_final: 0.7667 (p0)
REVERT: Q 116 LYS cc_start: 0.8613 (mmtm) cc_final: 0.8377 (mmtp)
REVERT: Q 125 ASN cc_start: 0.8845 (t0) cc_final: 0.8610 (t0)
REVERT: Q 135 LYS cc_start: 0.7812 (tptt) cc_final: 0.7470 (tttm)
outliers start: 23
outliers final: 3
residues processed: 638
average time/residue: 0.3704
time to fit residues: 364.9291
Evaluate side-chains
454 residues out of total 2599 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 3
poor density : 451
time to evaluate : 2.762
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue 52 THR
Chi-restraints excluded: chain O residue 52 THR
Chi-restraints excluded: chain U residue 52 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 322
random chunks:
chunk 271 optimal weight: 9.9990
chunk 244 optimal weight: 10.0000
chunk 135 optimal weight: 10.0000
chunk 83 optimal weight: 3.9990
chunk 164 optimal weight: 6.9990
chunk 130 optimal weight: 0.9990
chunk 252 optimal weight: 1.9990
chunk 97 optimal weight: 0.7980
chunk 153 optimal weight: 0.0970
chunk 187 optimal weight: 0.5980
chunk 292 optimal weight: 7.9990
overall best weight: 0.8982
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 149 ASN
B 29 GLN
B 47 ASN
** B 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 149 ASN
** C 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 125 ASN
C 149 ASN
** D 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 125 ASN
D 149 ASN
E 31 GLN
E 149 ASN
F 29 GLN
** F 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 149 ASN
G 109 GLN
G 149 ASN
H 149 ASN
** I 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
I 149 ASN
** J 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
J 149 ASN
K 29 GLN
K 149 ASN
L 29 GLN
L 87 ASN
L 149 ASN
M 29 GLN
M 109 GLN
M 149 ASN
N 149 ASN
O 87 ASN
O 149 ASN
P 149 ASN
** R 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 149 ASN
S 29 GLN
** S 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
S 149 ASN
T 149 ASN
U 149 ASN
V 149 ASN
W 149 ASN
Total number of N/Q/H flips: 36
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3075 r_free = 0.3075 target = 0.099798 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2947 r_free = 0.2947 target = 0.091237 restraints weight = 33056.464|
|-----------------------------------------------------------------------------|
r_work (start): 0.2948 rms_B_bonded: 1.17
r_work: 0.2874 rms_B_bonded: 1.65 restraints_weight: 0.5000
r_work: 0.2768 rms_B_bonded: 2.96 restraints_weight: 0.2500
r_work (final): 0.2768
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8570
moved from start: 0.1598
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.002 0.023 24311 Z= 0.142
Angle : 0.442 4.543 33143 Z= 0.238
Chirality : 0.046 0.146 4186
Planarity : 0.003 0.020 4209
Dihedral : 3.497 14.534 3430
Min Nonbonded Distance : 2.571
Molprobity Statistics.
All-atom Clashscore : 4.54
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 0.77 %
Favored : 99.23 %
Rotamer:
Outliers : 3.39 %
Allowed : 21.16 %
Favored : 75.45 %
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: 3.18 (0.15), residues: 3243
helix: 2.50 (0.17), residues: 1081
sheet: 1.33 (0.20), residues: 713
loop : 2.51 (0.16), residues: 1449
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.005 0.001 TRP Q 132
PHE 0.006 0.001 PHE R 108
TYR 0.008 0.001 TYR G 33
ARG 0.002 0.000 ARG R 126
*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
6486 Ramachandran restraints generated.
3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
6486 Ramachandran restraints generated.
3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
575 residues out of total 2599 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 88
poor density : 487
time to evaluate : 2.719
Fit side-chains
revert: symmetry clash
REVERT: A 82 VAL cc_start: 0.8591 (m) cc_final: 0.8303 (m)
REVERT: B 43 LEU cc_start: 0.9084 (tp) cc_final: 0.8871 (tp)
REVERT: B 65 LYS cc_start: 0.8276 (mmtt) cc_final: 0.7305 (mttt)
REVERT: C 135 LYS cc_start: 0.8138 (tptt) cc_final: 0.7885 (mttp)
REVERT: D 65 LYS cc_start: 0.8594 (mmtt) cc_final: 0.8108 (mmtp)
REVERT: I 70 THR cc_start: 0.8682 (p) cc_final: 0.8438 (m)
REVERT: I 91 VAL cc_start: 0.9193 (m) cc_final: 0.8924 (t)
REVERT: I 97 GLU cc_start: 0.8005 (mt-10) cc_final: 0.7686 (mm-30)
REVERT: I 116 LYS cc_start: 0.8147 (mmtm) cc_final: 0.7876 (mmtt)
REVERT: I 148 ASP cc_start: 0.7929 (m-30) cc_final: 0.7505 (t0)
REVERT: K 91 VAL cc_start: 0.9006 (m) cc_final: 0.8724 (t)
REVERT: L 135 LYS cc_start: 0.8229 (tmtt) cc_final: 0.7856 (mtpt)
REVERT: M 29 GLN cc_start: 0.7888 (OUTLIER) cc_final: 0.7526 (mt0)
REVERT: N 129 ASP cc_start: 0.7683 (m-30) cc_final: 0.7394 (m-30)
REVERT: O 43 LEU cc_start: 0.8999 (tp) cc_final: 0.8732 (tp)
REVERT: P 135 LYS cc_start: 0.8359 (mmtt) cc_final: 0.7805 (mptt)
REVERT: Q 135 LYS cc_start: 0.7997 (tptt) cc_final: 0.7704 (tttm)
REVERT: R 135 LYS cc_start: 0.8262 (tptt) cc_final: 0.7793 (ttpp)
REVERT: R 141 MET cc_start: 0.8579 (OUTLIER) cc_final: 0.8256 (ptm)
REVERT: W 8 THR cc_start: 0.6777 (OUTLIER) cc_final: 0.6350 (m)
REVERT: W 135 LYS cc_start: 0.8404 (tptt) cc_final: 0.8118 (mtpp)
outliers start: 88
outliers final: 58
residues processed: 544
average time/residue: 0.3480
time to fit residues: 300.2088
Evaluate side-chains
497 residues out of total 2599 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 61
poor density : 436
time to evaluate : 2.720
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 112 THR
Chi-restraints excluded: chain B residue 8 THR
Chi-restraints excluded: chain B residue 11 GLU
Chi-restraints excluded: chain C residue 107 THR
Chi-restraints excluded: chain C residue 112 THR
Chi-restraints excluded: chain D residue 73 SER
Chi-restraints excluded: chain D residue 110 THR
Chi-restraints excluded: chain E residue 73 SER
Chi-restraints excluded: chain E residue 112 THR
Chi-restraints excluded: chain F residue 112 THR
Chi-restraints excluded: chain G residue 112 THR
Chi-restraints excluded: chain H residue 78 THR
Chi-restraints excluded: chain H residue 112 THR
Chi-restraints excluded: chain I residue 8 THR
Chi-restraints excluded: chain I residue 19 ILE
Chi-restraints excluded: chain I residue 85 ASP
Chi-restraints excluded: chain I residue 112 THR
Chi-restraints excluded: chain J residue 73 SER
Chi-restraints excluded: chain J residue 92 ILE
Chi-restraints excluded: chain J residue 103 ASP
Chi-restraints excluded: chain J residue 141 MET
Chi-restraints excluded: chain K residue 8 THR
Chi-restraints excluded: chain K residue 52 THR
Chi-restraints excluded: chain K residue 73 SER
Chi-restraints excluded: chain K residue 112 THR
Chi-restraints excluded: chain L residue 29 GLN
Chi-restraints excluded: chain L residue 85 ASP
Chi-restraints excluded: chain M residue 29 GLN
Chi-restraints excluded: chain M residue 112 THR
Chi-restraints excluded: chain M residue 147 CYS
Chi-restraints excluded: chain N residue 73 SER
Chi-restraints excluded: chain O residue 73 SER
Chi-restraints excluded: chain O residue 82 VAL
Chi-restraints excluded: chain O residue 112 THR
Chi-restraints excluded: chain O residue 141 MET
Chi-restraints excluded: chain P residue 8 THR
Chi-restraints excluded: chain P residue 116 LYS
Chi-restraints excluded: chain Q residue 8 THR
Chi-restraints excluded: chain Q residue 41 SER
Chi-restraints excluded: chain Q residue 78 THR
Chi-restraints excluded: chain Q residue 85 ASP
Chi-restraints excluded: chain Q residue 112 THR
Chi-restraints excluded: chain R residue 8 THR
Chi-restraints excluded: chain R residue 82 VAL
Chi-restraints excluded: chain R residue 141 MET
Chi-restraints excluded: chain T residue 8 THR
Chi-restraints excluded: chain T residue 11 GLU
Chi-restraints excluded: chain T residue 52 THR
Chi-restraints excluded: chain T residue 112 THR
Chi-restraints excluded: chain U residue 8 THR
Chi-restraints excluded: chain U residue 73 SER
Chi-restraints excluded: chain U residue 98 ASP
Chi-restraints excluded: chain U residue 110 THR
Chi-restraints excluded: chain U residue 141 MET
Chi-restraints excluded: chain V residue 97 GLU
Chi-restraints excluded: chain V residue 136 SER
Chi-restraints excluded: chain W residue 8 THR
Chi-restraints excluded: chain W residue 64 SER
Chi-restraints excluded: chain W residue 73 SER
Chi-restraints excluded: chain W residue 82 VAL
Chi-restraints excluded: chain W residue 112 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 322
random chunks:
chunk 193 optimal weight: 4.9990
chunk 129 optimal weight: 0.9980
chunk 180 optimal weight: 6.9990
chunk 35 optimal weight: 4.9990
chunk 159 optimal weight: 9.9990
chunk 318 optimal weight: 8.9990
chunk 63 optimal weight: 8.9990
chunk 136 optimal weight: 0.8980
chunk 305 optimal weight: 6.9990
chunk 17 optimal weight: 6.9990
chunk 90 optimal weight: 10.0000
overall best weight: 3.7786
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
B 47 ASN
B 138 GLN
B 149 ASN
** C 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 125 ASN
D 31 GLN
** D 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 125 ASN
F 149 ASN
** G 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 149 ASN
** H 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 149 ASN
I 109 GLN
** J 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
M 109 GLN
O 29 GLN
O 149 ASN
P 149 ASN
R 109 GLN
R 125 ASN
S 109 GLN
T 109 GLN
U 109 GLN
U 138 GLN
U 149 ASN
Total number of N/Q/H flips: 21
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2952 r_free = 0.2952 target = 0.091841 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 23)----------------|
| r_work = 0.2816 r_free = 0.2816 target = 0.083192 restraints weight = 33524.148|
|-----------------------------------------------------------------------------|
r_work (start): 0.2817 rms_B_bonded: 1.17
r_work: 0.2742 rms_B_bonded: 1.63 restraints_weight: 0.5000
r_work: 0.2635 rms_B_bonded: 2.91 restraints_weight: 0.2500
r_work (final): 0.2635
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8693
moved from start: 0.2506
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.006 0.043 24311 Z= 0.385
Angle : 0.563 4.840 33143 Z= 0.307
Chirality : 0.051 0.209 4186
Planarity : 0.004 0.038 4209
Dihedral : 4.532 25.038 3427
Min Nonbonded Distance : 2.517
Molprobity Statistics.
All-atom Clashscore : 5.08
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 2.31 %
Favored : 97.69 %
Rotamer:
Outliers : 5.04 %
Allowed : 19.85 %
Favored : 75.11 %
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: 2.65 (0.15), residues: 3243
helix: 2.04 (0.17), residues: 1081
sheet: 1.28 (0.19), residues: 713
loop : 2.07 (0.16), residues: 1449
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.012 0.002 TRP F 132
PHE 0.013 0.002 PHE E 142
TYR 0.012 0.002 TYR I 30
ARG 0.004 0.001 ARG Q 59
*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
6486 Ramachandran restraints generated.
3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
6486 Ramachandran restraints generated.
3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
571 residues out of total 2599 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 131
poor density : 440
time to evaluate : 2.667
Fit side-chains
revert: symmetry clash
revert: symmetry clash
REVERT: B 22 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8610 (mp)
REVERT: B 31 GLN cc_start: 0.8458 (OUTLIER) cc_final: 0.8203 (pt0)
REVERT: B 65 LYS cc_start: 0.8307 (mmtt) cc_final: 0.7379 (mttt)
REVERT: C 22 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.8124 (mp)
REVERT: C 135 LYS cc_start: 0.8305 (tptt) cc_final: 0.8025 (mptt)
REVERT: C 148 ASP cc_start: 0.7518 (OUTLIER) cc_final: 0.7145 (m-30)
REVERT: D 65 LYS cc_start: 0.8574 (mmtt) cc_final: 0.8093 (mmtp)
REVERT: E 141 MET cc_start: 0.8537 (OUTLIER) cc_final: 0.8137 (ptt)
REVERT: F 22 LEU cc_start: 0.8447 (OUTLIER) cc_final: 0.8084 (mp)
REVERT: I 91 VAL cc_start: 0.9284 (m) cc_final: 0.9066 (t)
REVERT: I 97 GLU cc_start: 0.8063 (mt-10) cc_final: 0.7732 (mm-30)
REVERT: I 148 ASP cc_start: 0.8002 (m-30) cc_final: 0.7661 (m-30)
REVERT: J 22 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8076 (mp)
REVERT: K 31 GLN cc_start: 0.8221 (OUTLIER) cc_final: 0.7845 (pt0)
REVERT: L 22 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8285 (mp)
REVERT: L 135 LYS cc_start: 0.8154 (tmtt) cc_final: 0.7819 (mtpt)
REVERT: M 7 PHE cc_start: 0.7423 (OUTLIER) cc_final: 0.7009 (t80)
REVERT: M 22 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8122 (mp)
REVERT: M 135 LYS cc_start: 0.8861 (mmtt) cc_final: 0.8496 (tttp)
REVERT: N 87 ASN cc_start: 0.9076 (t0) cc_final: 0.8755 (t0)
REVERT: N 129 ASP cc_start: 0.7671 (OUTLIER) cc_final: 0.7402 (m-30)
REVERT: O 7 PHE cc_start: 0.7929 (OUTLIER) cc_final: 0.7537 (t80)
REVERT: O 129 ASP cc_start: 0.8330 (t70) cc_final: 0.7800 (t0)
REVERT: P 22 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8394 (mp)
REVERT: P 135 LYS cc_start: 0.8388 (mmtt) cc_final: 0.8182 (tttp)
REVERT: Q 22 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8320 (mp)
REVERT: Q 87 ASN cc_start: 0.8670 (t0) cc_final: 0.8433 (t0)
REVERT: Q 135 LYS cc_start: 0.8033 (tptt) cc_final: 0.7672 (tttm)
REVERT: R 135 LYS cc_start: 0.8405 (tptt) cc_final: 0.7747 (ttpp)
REVERT: S 22 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8392 (mp)
REVERT: T 135 LYS cc_start: 0.8479 (tptt) cc_final: 0.8130 (mmtm)
outliers start: 131
outliers final: 85
residues processed: 536
average time/residue: 0.3483
time to fit residues: 297.5247
Evaluate side-chains
517 residues out of total 2599 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 101
poor density : 416
time to evaluate : 2.941
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 31 GLN
Chi-restraints excluded: chain A residue 78 THR
Chi-restraints excluded: chain A residue 112 THR
Chi-restraints excluded: chain A residue 136 SER
Chi-restraints excluded: chain B residue 8 THR
Chi-restraints excluded: chain B residue 11 GLU
Chi-restraints excluded: chain B residue 22 LEU
Chi-restraints excluded: chain B residue 31 GLN
Chi-restraints excluded: chain C residue 22 LEU
Chi-restraints excluded: chain C residue 73 SER
Chi-restraints excluded: chain C residue 82 VAL
Chi-restraints excluded: chain C residue 91 VAL
Chi-restraints excluded: chain C residue 107 THR
Chi-restraints excluded: chain C residue 112 THR
Chi-restraints excluded: chain C residue 148 ASP
Chi-restraints excluded: chain D residue 7 PHE
Chi-restraints excluded: chain D residue 70 THR
Chi-restraints excluded: chain D residue 73 SER
Chi-restraints excluded: chain D residue 110 THR
Chi-restraints excluded: chain E residue 64 SER
Chi-restraints excluded: chain E residue 73 SER
Chi-restraints excluded: chain E residue 112 THR
Chi-restraints excluded: chain E residue 141 MET
Chi-restraints excluded: chain F residue 22 LEU
Chi-restraints excluded: chain F residue 29 GLN
Chi-restraints excluded: chain F residue 31 GLN
Chi-restraints excluded: chain F residue 112 THR
Chi-restraints excluded: chain G residue 31 GLN
Chi-restraints excluded: chain G residue 112 THR
Chi-restraints excluded: chain H residue 76 THR
Chi-restraints excluded: chain H residue 112 THR
Chi-restraints excluded: chain I residue 78 THR
Chi-restraints excluded: chain I residue 85 ASP
Chi-restraints excluded: chain I residue 112 THR
Chi-restraints excluded: chain J residue 22 LEU
Chi-restraints excluded: chain J residue 73 SER
Chi-restraints excluded: chain K residue 8 THR
Chi-restraints excluded: chain K residue 31 GLN
Chi-restraints excluded: chain K residue 52 THR
Chi-restraints excluded: chain K residue 73 SER
Chi-restraints excluded: chain K residue 112 THR
Chi-restraints excluded: chain L residue 8 THR
Chi-restraints excluded: chain L residue 22 LEU
Chi-restraints excluded: chain L residue 78 THR
Chi-restraints excluded: chain M residue 7 PHE
Chi-restraints excluded: chain M residue 8 THR
Chi-restraints excluded: chain M residue 21 ILE
Chi-restraints excluded: chain M residue 22 LEU
Chi-restraints excluded: chain M residue 112 THR
Chi-restraints excluded: chain N residue 8 THR
Chi-restraints excluded: chain N residue 73 SER
Chi-restraints excluded: chain N residue 103 ASP
Chi-restraints excluded: chain N residue 129 ASP
Chi-restraints excluded: chain N residue 147 CYS
Chi-restraints excluded: chain O residue 7 PHE
Chi-restraints excluded: chain O residue 73 SER
Chi-restraints excluded: chain O residue 82 VAL
Chi-restraints excluded: chain O residue 112 THR
Chi-restraints excluded: chain O residue 141 MET
Chi-restraints excluded: chain P residue 8 THR
Chi-restraints excluded: chain P residue 22 LEU
Chi-restraints excluded: chain P residue 116 LYS
Chi-restraints excluded: chain Q residue 8 THR
Chi-restraints excluded: chain Q residue 22 LEU
Chi-restraints excluded: chain Q residue 41 SER
Chi-restraints excluded: chain Q residue 74 THR
Chi-restraints excluded: chain Q residue 78 THR
Chi-restraints excluded: chain Q residue 82 VAL
Chi-restraints excluded: chain Q residue 85 ASP
Chi-restraints excluded: chain Q residue 112 THR
Chi-restraints excluded: chain R residue 8 THR
Chi-restraints excluded: chain R residue 73 SER
Chi-restraints excluded: chain R residue 78 THR
Chi-restraints excluded: chain R residue 82 VAL
Chi-restraints excluded: chain R residue 110 THR
Chi-restraints excluded: chain R residue 129 ASP
Chi-restraints excluded: chain S residue 22 LEU
Chi-restraints excluded: chain S residue 73 SER
Chi-restraints excluded: chain S residue 78 THR
Chi-restraints excluded: chain S residue 91 VAL
Chi-restraints excluded: chain S residue 112 THR
Chi-restraints excluded: chain T residue 8 THR
Chi-restraints excluded: chain T residue 52 THR
Chi-restraints excluded: chain T residue 85 ASP
Chi-restraints excluded: chain T residue 103 ASP
Chi-restraints excluded: chain T residue 112 THR
Chi-restraints excluded: chain T residue 125 ASN
Chi-restraints excluded: chain T residue 141 MET
Chi-restraints excluded: chain U residue 8 THR
Chi-restraints excluded: chain U residue 73 SER
Chi-restraints excluded: chain U residue 98 ASP
Chi-restraints excluded: chain U residue 110 THR
Chi-restraints excluded: chain U residue 125 ASN
Chi-restraints excluded: chain U residue 141 MET
Chi-restraints excluded: chain U residue 147 CYS
Chi-restraints excluded: chain V residue 139 ASP
Chi-restraints excluded: chain W residue 64 SER
Chi-restraints excluded: chain W residue 73 SER
Chi-restraints excluded: chain W residue 80 VAL
Chi-restraints excluded: chain W residue 82 VAL
Chi-restraints excluded: chain W residue 112 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 322
random chunks:
chunk 201 optimal weight: 5.9990
chunk 232 optimal weight: 3.9990
chunk 196 optimal weight: 4.9990
chunk 282 optimal weight: 0.8980
chunk 94 optimal weight: 0.0670
chunk 236 optimal weight: 9.9990
chunk 225 optimal weight: 0.9990
chunk 319 optimal weight: 9.9990
chunk 173 optimal weight: 5.9990
chunk 318 optimal weight: 5.9990
chunk 180 optimal weight: 2.9990
overall best weight: 1.7924
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
B 47 ASN
B 138 GLN
D 109 GLN
D 125 ASN
G 109 GLN
H 109 GLN
J 109 GLN
M 109 GLN
P 149 ASN
U 29 GLN
U 138 GLN
V 31 GLN
Total number of N/Q/H flips: 12
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2988 r_free = 0.2988 target = 0.094318 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2856 r_free = 0.2856 target = 0.085748 restraints weight = 33587.674|
|-----------------------------------------------------------------------------|
r_work (start): 0.2856 rms_B_bonded: 1.16
r_work: 0.2783 rms_B_bonded: 1.63 restraints_weight: 0.5000
r_work: 0.2677 rms_B_bonded: 2.92 restraints_weight: 0.2500
r_work (final): 0.2677
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8659
moved from start: 0.2560
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.027 24311 Z= 0.207
Angle : 0.465 5.203 33143 Z= 0.251
Chirality : 0.047 0.156 4186
Planarity : 0.003 0.028 4209
Dihedral : 4.096 25.002 3427
Min Nonbonded Distance : 2.586
Molprobity Statistics.
All-atom Clashscore : 5.14
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 1.36 %
Favored : 98.64 %
Rotamer:
Outliers : 4.27 %
Allowed : 20.85 %
Favored : 74.87 %
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: 2.77 (0.15), residues: 3243
helix: 2.30 (0.17), residues: 1081
sheet: 1.19 (0.19), residues: 713
loop : 2.09 (0.16), residues: 1449
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.008 0.001 TRP O 132
PHE 0.007 0.001 PHE W 108
TYR 0.007 0.001 TYR B 33
ARG 0.002 0.000 ARG E 59
*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
6486 Ramachandran restraints generated.
3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
6486 Ramachandran restraints generated.
3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
543 residues out of total 2599 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 111
poor density : 432
time to evaluate : 3.396
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: A 85 ASP cc_start: 0.8082 (p0) cc_final: 0.7776 (p0)
REVERT: B 31 GLN cc_start: 0.8370 (OUTLIER) cc_final: 0.8104 (pt0)
REVERT: B 65 LYS cc_start: 0.8328 (mmtt) cc_final: 0.7403 (mttt)
REVERT: B 77 GLU cc_start: 0.8174 (mp0) cc_final: 0.7782 (mp0)
REVERT: C 77 GLU cc_start: 0.8254 (mp0) cc_final: 0.7910 (mp0)
REVERT: C 135 LYS cc_start: 0.8358 (tptt) cc_final: 0.8022 (mptt)
REVERT: D 65 LYS cc_start: 0.8614 (mmtt) cc_final: 0.8101 (mmtp)
REVERT: E 141 MET cc_start: 0.8529 (OUTLIER) cc_final: 0.8174 (ptt)
REVERT: I 97 GLU cc_start: 0.8102 (mt-10) cc_final: 0.7760 (mm-30)
REVERT: I 148 ASP cc_start: 0.8038 (m-30) cc_final: 0.7688 (m-30)
REVERT: J 13 MET cc_start: 0.8606 (OUTLIER) cc_final: 0.8321 (mmm)
REVERT: K 22 LEU cc_start: 0.8283 (OUTLIER) cc_final: 0.8063 (mp)
REVERT: K 31 GLN cc_start: 0.8105 (OUTLIER) cc_final: 0.7718 (pt0)
REVERT: K 91 VAL cc_start: 0.9002 (m) cc_final: 0.8729 (t)
REVERT: L 103 ASP cc_start: 0.8020 (OUTLIER) cc_final: 0.7535 (p0)
REVERT: L 129 ASP cc_start: 0.7617 (t0) cc_final: 0.7377 (t0)
REVERT: L 135 LYS cc_start: 0.8169 (tmtt) cc_final: 0.7837 (mtpt)
REVERT: M 7 PHE cc_start: 0.7424 (OUTLIER) cc_final: 0.6985 (t80)
REVERT: M 29 GLN cc_start: 0.8144 (tt0) cc_final: 0.7571 (mt0)
REVERT: M 135 LYS cc_start: 0.8848 (mmtt) cc_final: 0.8506 (tttp)
REVERT: N 22 LEU cc_start: 0.9098 (OUTLIER) cc_final: 0.8571 (mp)
REVERT: N 129 ASP cc_start: 0.7647 (m-30) cc_final: 0.7345 (m-30)
REVERT: O 7 PHE cc_start: 0.7951 (OUTLIER) cc_final: 0.7576 (t80)
REVERT: O 129 ASP cc_start: 0.8321 (t70) cc_final: 0.7754 (t0)
REVERT: P 135 LYS cc_start: 0.8397 (mmtt) cc_final: 0.8185 (tttp)
REVERT: Q 77 GLU cc_start: 0.8329 (mt-10) cc_final: 0.8058 (mt-10)
REVERT: Q 87 ASN cc_start: 0.8624 (t0) cc_final: 0.8420 (t0)
REVERT: Q 135 LYS cc_start: 0.8081 (tptt) cc_final: 0.7677 (tttm)
REVERT: R 135 LYS cc_start: 0.8387 (tptt) cc_final: 0.7778 (ttpp)
REVERT: S 7 PHE cc_start: 0.7484 (OUTLIER) cc_final: 0.7257 (t80)
REVERT: S 91 VAL cc_start: 0.9221 (m) cc_final: 0.8985 (t)
REVERT: T 135 LYS cc_start: 0.8497 (tptt) cc_final: 0.8136 (mmtm)
REVERT: W 10 ILE cc_start: 0.8436 (OUTLIER) cc_final: 0.8179 (mm)
outliers start: 111
outliers final: 80
residues processed: 511
average time/residue: 0.3584
time to fit residues: 292.9084
Evaluate side-chains
502 residues out of total 2599 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 91
poor density : 411
time to evaluate : 2.747
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 78 THR
Chi-restraints excluded: chain A residue 112 THR
Chi-restraints excluded: chain A residue 136 SER
Chi-restraints excluded: chain B residue 7 PHE
Chi-restraints excluded: chain B residue 8 THR
Chi-restraints excluded: chain B residue 11 GLU
Chi-restraints excluded: chain B residue 31 GLN
Chi-restraints excluded: chain B residue 82 VAL
Chi-restraints excluded: chain B residue 138 GLN
Chi-restraints excluded: chain C residue 73 SER
Chi-restraints excluded: chain C residue 107 THR
Chi-restraints excluded: chain C residue 112 THR
Chi-restraints excluded: chain D residue 7 PHE
Chi-restraints excluded: chain D residue 73 SER
Chi-restraints excluded: chain D residue 76 THR
Chi-restraints excluded: chain D residue 110 THR
Chi-restraints excluded: chain D residue 136 SER
Chi-restraints excluded: chain E residue 64 SER
Chi-restraints excluded: chain E residue 73 SER
Chi-restraints excluded: chain E residue 112 THR
Chi-restraints excluded: chain E residue 141 MET
Chi-restraints excluded: chain F residue 8 THR
Chi-restraints excluded: chain F residue 29 GLN
Chi-restraints excluded: chain F residue 112 THR
Chi-restraints excluded: chain G residue 31 GLN
Chi-restraints excluded: chain H residue 82 VAL
Chi-restraints excluded: chain H residue 112 THR
Chi-restraints excluded: chain I residue 8 THR
Chi-restraints excluded: chain I residue 78 THR
Chi-restraints excluded: chain I residue 85 ASP
Chi-restraints excluded: chain I residue 112 THR
Chi-restraints excluded: chain J residue 13 MET
Chi-restraints excluded: chain J residue 73 SER
Chi-restraints excluded: chain J residue 103 ASP
Chi-restraints excluded: chain K residue 22 LEU
Chi-restraints excluded: chain K residue 29 GLN
Chi-restraints excluded: chain K residue 31 GLN
Chi-restraints excluded: chain K residue 52 THR
Chi-restraints excluded: chain K residue 73 SER
Chi-restraints excluded: chain K residue 112 THR
Chi-restraints excluded: chain L residue 8 THR
Chi-restraints excluded: chain L residue 103 ASP
Chi-restraints excluded: chain L residue 112 THR
Chi-restraints excluded: chain L residue 141 MET
Chi-restraints excluded: chain M residue 7 PHE
Chi-restraints excluded: chain M residue 8 THR
Chi-restraints excluded: chain M residue 92 ILE
Chi-restraints excluded: chain M residue 112 THR
Chi-restraints excluded: chain N residue 22 LEU
Chi-restraints excluded: chain N residue 73 SER
Chi-restraints excluded: chain N residue 92 ILE
Chi-restraints excluded: chain O residue 7 PHE
Chi-restraints excluded: chain O residue 8 THR
Chi-restraints excluded: chain O residue 22 LEU
Chi-restraints excluded: chain O residue 73 SER
Chi-restraints excluded: chain O residue 82 VAL
Chi-restraints excluded: chain O residue 112 THR
Chi-restraints excluded: chain O residue 141 MET
Chi-restraints excluded: chain Q residue 8 THR
Chi-restraints excluded: chain Q residue 41 SER
Chi-restraints excluded: chain Q residue 78 THR
Chi-restraints excluded: chain Q residue 85 ASP
Chi-restraints excluded: chain R residue 8 THR
Chi-restraints excluded: chain R residue 73 SER
Chi-restraints excluded: chain R residue 78 THR
Chi-restraints excluded: chain R residue 82 VAL
Chi-restraints excluded: chain R residue 110 THR
Chi-restraints excluded: chain R residue 129 ASP
Chi-restraints excluded: chain S residue 7 PHE
Chi-restraints excluded: chain S residue 73 SER
Chi-restraints excluded: chain S residue 112 THR
Chi-restraints excluded: chain T residue 8 THR
Chi-restraints excluded: chain T residue 52 THR
Chi-restraints excluded: chain T residue 85 ASP
Chi-restraints excluded: chain T residue 91 VAL
Chi-restraints excluded: chain T residue 112 THR
Chi-restraints excluded: chain T residue 141 MET
Chi-restraints excluded: chain U residue 8 THR
Chi-restraints excluded: chain U residue 73 SER
Chi-restraints excluded: chain U residue 110 THR
Chi-restraints excluded: chain U residue 125 ASN
Chi-restraints excluded: chain U residue 141 MET
Chi-restraints excluded: chain V residue 31 GLN
Chi-restraints excluded: chain V residue 85 ASP
Chi-restraints excluded: chain V residue 103 ASP
Chi-restraints excluded: chain W residue 10 ILE
Chi-restraints excluded: chain W residue 64 SER
Chi-restraints excluded: chain W residue 73 SER
Chi-restraints excluded: chain W residue 82 VAL
Chi-restraints excluded: chain W residue 112 THR
Chi-restraints excluded: chain W residue 135 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 322
random chunks:
chunk 175 optimal weight: 8.9990
chunk 61 optimal weight: 3.9990
chunk 233 optimal weight: 0.0060
chunk 313 optimal weight: 5.9990
chunk 39 optimal weight: 6.9990
chunk 252 optimal weight: 0.0980
chunk 35 optimal weight: 10.0000
chunk 193 optimal weight: 6.9990
chunk 267 optimal weight: 8.9990
chunk 234 optimal weight: 7.9990
chunk 265 optimal weight: 4.9990
overall best weight: 3.0202
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
B 47 ASN
B 138 GLN
** C 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 125 ASN
E 149 ASN
** G 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 109 GLN
I 109 GLN
** J 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K 149 ASN
** M 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
P 29 GLN
P 149 ASN
R 109 GLN
T 87 ASN
T 149 ASN
V 31 GLN
Total number of N/Q/H flips: 13
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2954 r_free = 0.2954 target = 0.092010 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2815 r_free = 0.2815 target = 0.083124 restraints weight = 33831.938|
|-----------------------------------------------------------------------------|
r_work (start): 0.2816 rms_B_bonded: 1.25
r_work: 0.2737 rms_B_bonded: 1.73 restraints_weight: 0.5000
r_work: 0.2628 rms_B_bonded: 3.06 restraints_weight: 0.2500
r_work (final): 0.2628
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8687
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 : 0.005 0.041 24311 Z= 0.319
Angle : 0.519 7.368 33143 Z= 0.281
Chirality : 0.049 0.174 4186
Planarity : 0.004 0.034 4209
Dihedral : 4.429 31.196 3427
Min Nonbonded Distance : 2.544
Molprobity Statistics.
All-atom Clashscore : 5.18
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 2.53 %
Favored : 97.47 %
Rotamer:
Outliers : 5.43 %
Allowed : 19.35 %
Favored : 75.22 %
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: 2.49 (0.15), residues: 3243
helix: 2.10 (0.17), residues: 1081
sheet: 0.96 (0.19), residues: 713
loop : 1.94 (0.16), residues: 1449
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.010 0.001 TRP F 132
PHE 0.010 0.001 PHE E 142
TYR 0.014 0.001 TYR G 33
ARG 0.003 0.001 ARG S 59
*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
6486 Ramachandran restraints generated.
3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
6486 Ramachandran restraints generated.
3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
557 residues out of total 2599 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 141
poor density : 416
time to evaluate : 2.769
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: B 31 GLN cc_start: 0.8426 (OUTLIER) cc_final: 0.8154 (pt0)
REVERT: B 65 LYS cc_start: 0.8306 (mmtt) cc_final: 0.7367 (mttt)
REVERT: B 77 GLU cc_start: 0.8201 (mp0) cc_final: 0.7860 (mp0)
REVERT: C 22 LEU cc_start: 0.8580 (OUTLIER) cc_final: 0.8146 (mp)
REVERT: C 135 LYS cc_start: 0.8248 (tptt) cc_final: 0.7936 (mptt)
REVERT: D 65 LYS cc_start: 0.8599 (mmtt) cc_final: 0.8059 (mmtp)
REVERT: E 141 MET cc_start: 0.8613 (OUTLIER) cc_final: 0.8218 (ptt)
REVERT: F 22 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.8090 (mp)
REVERT: H 31 GLN cc_start: 0.7733 (OUTLIER) cc_final: 0.7416 (pt0)
REVERT: I 97 GLU cc_start: 0.8063 (mt-10) cc_final: 0.7675 (mm-30)
REVERT: I 129 ASP cc_start: 0.8099 (t70) cc_final: 0.7877 (t70)
REVERT: J 22 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.8035 (mp)
REVERT: J 129 ASP cc_start: 0.7564 (m-30) cc_final: 0.6816 (t70)
REVERT: K 22 LEU cc_start: 0.8374 (OUTLIER) cc_final: 0.8016 (mp)
REVERT: K 31 GLN cc_start: 0.8160 (OUTLIER) cc_final: 0.7770 (pt0)
REVERT: L 22 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8239 (mp)
REVERT: L 103 ASP cc_start: 0.8047 (OUTLIER) cc_final: 0.7554 (p0)
REVERT: L 135 LYS cc_start: 0.8164 (tmtt) cc_final: 0.7800 (mtpt)
REVERT: M 7 PHE cc_start: 0.7418 (OUTLIER) cc_final: 0.7003 (t80)
REVERT: M 22 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8091 (mp)
REVERT: M 135 LYS cc_start: 0.8850 (mmtt) cc_final: 0.8535 (tttp)
REVERT: N 22 LEU cc_start: 0.9088 (OUTLIER) cc_final: 0.8540 (mp)
REVERT: N 129 ASP cc_start: 0.7651 (OUTLIER) cc_final: 0.7349 (m-30)
REVERT: O 7 PHE cc_start: 0.8053 (OUTLIER) cc_final: 0.7770 (t80)
REVERT: O 11 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.7937 (tt0)
REVERT: O 129 ASP cc_start: 0.8302 (t70) cc_final: 0.7720 (t0)
REVERT: P 22 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8338 (mp)
REVERT: P 135 LYS cc_start: 0.8412 (mmtt) cc_final: 0.8197 (tttp)
REVERT: Q 31 GLN cc_start: 0.8307 (OUTLIER) cc_final: 0.8016 (pt0)
REVERT: Q 77 GLU cc_start: 0.8377 (mt-10) cc_final: 0.8113 (mt-10)
REVERT: Q 87 ASN cc_start: 0.8685 (t0) cc_final: 0.8448 (t0)
REVERT: Q 135 LYS cc_start: 0.8196 (tptt) cc_final: 0.7718 (tttm)
REVERT: R 135 LYS cc_start: 0.8450 (tptt) cc_final: 0.7828 (ttpp)
REVERT: R 141 MET cc_start: 0.8623 (OUTLIER) cc_final: 0.8288 (ptm)
REVERT: S 7 PHE cc_start: 0.7539 (OUTLIER) cc_final: 0.7324 (t80)
REVERT: S 22 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8359 (mp)
REVERT: S 91 VAL cc_start: 0.9173 (m) cc_final: 0.8928 (t)
REVERT: T 135 LYS cc_start: 0.8517 (tptt) cc_final: 0.8199 (mmtm)
REVERT: V 135 LYS cc_start: 0.8533 (mptt) cc_final: 0.8123 (mttt)
REVERT: W 10 ILE cc_start: 0.8522 (mt) cc_final: 0.8296 (mm)
REVERT: W 31 GLN cc_start: 0.8056 (OUTLIER) cc_final: 0.7831 (pt0)
outliers start: 141
outliers final: 103
residues processed: 518
average time/residue: 0.3408
time to fit residues: 282.6507
Evaluate side-chains
531 residues out of total 2599 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 125
poor density : 406
time to evaluate : 2.931
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 31 GLN
Chi-restraints excluded: chain A residue 78 THR
Chi-restraints excluded: chain A residue 112 THR
Chi-restraints excluded: chain A residue 136 SER
Chi-restraints excluded: chain B residue 7 PHE
Chi-restraints excluded: chain B residue 8 THR
Chi-restraints excluded: chain B residue 11 GLU
Chi-restraints excluded: chain B residue 31 GLN
Chi-restraints excluded: chain B residue 82 VAL
Chi-restraints excluded: chain C residue 22 LEU
Chi-restraints excluded: chain C residue 73 SER
Chi-restraints excluded: chain C residue 82 VAL
Chi-restraints excluded: chain C residue 91 VAL
Chi-restraints excluded: chain C residue 107 THR
Chi-restraints excluded: chain C residue 112 THR
Chi-restraints excluded: chain D residue 7 PHE
Chi-restraints excluded: chain D residue 73 SER
Chi-restraints excluded: chain D residue 76 THR
Chi-restraints excluded: chain D residue 110 THR
Chi-restraints excluded: chain D residue 136 SER
Chi-restraints excluded: chain E residue 64 SER
Chi-restraints excluded: chain E residue 73 SER
Chi-restraints excluded: chain E residue 112 THR
Chi-restraints excluded: chain E residue 141 MET
Chi-restraints excluded: chain F residue 22 LEU
Chi-restraints excluded: chain F residue 29 GLN
Chi-restraints excluded: chain F residue 31 GLN
Chi-restraints excluded: chain F residue 76 THR
Chi-restraints excluded: chain F residue 112 THR
Chi-restraints excluded: chain G residue 31 GLN
Chi-restraints excluded: chain G residue 112 THR
Chi-restraints excluded: chain H residue 31 GLN
Chi-restraints excluded: chain H residue 76 THR
Chi-restraints excluded: chain H residue 82 VAL
Chi-restraints excluded: chain H residue 112 THR
Chi-restraints excluded: chain I residue 8 THR
Chi-restraints excluded: chain I residue 78 THR
Chi-restraints excluded: chain I residue 85 ASP
Chi-restraints excluded: chain I residue 112 THR
Chi-restraints excluded: chain J residue 22 LEU
Chi-restraints excluded: chain J residue 73 SER
Chi-restraints excluded: chain J residue 78 THR
Chi-restraints excluded: chain J residue 103 ASP
Chi-restraints excluded: chain K residue 8 THR
Chi-restraints excluded: chain K residue 22 LEU
Chi-restraints excluded: chain K residue 29 GLN
Chi-restraints excluded: chain K residue 31 GLN
Chi-restraints excluded: chain K residue 52 THR
Chi-restraints excluded: chain K residue 73 SER
Chi-restraints excluded: chain K residue 112 THR
Chi-restraints excluded: chain L residue 8 THR
Chi-restraints excluded: chain L residue 22 LEU
Chi-restraints excluded: chain L residue 85 ASP
Chi-restraints excluded: chain L residue 103 ASP
Chi-restraints excluded: chain L residue 112 THR
Chi-restraints excluded: chain L residue 141 MET
Chi-restraints excluded: chain M residue 7 PHE
Chi-restraints excluded: chain M residue 8 THR
Chi-restraints excluded: chain M residue 22 LEU
Chi-restraints excluded: chain M residue 92 ILE
Chi-restraints excluded: chain M residue 112 THR
Chi-restraints excluded: chain N residue 22 LEU
Chi-restraints excluded: chain N residue 73 SER
Chi-restraints excluded: chain N residue 74 THR
Chi-restraints excluded: chain N residue 92 ILE
Chi-restraints excluded: chain N residue 103 ASP
Chi-restraints excluded: chain N residue 129 ASP
Chi-restraints excluded: chain O residue 7 PHE
Chi-restraints excluded: chain O residue 8 THR
Chi-restraints excluded: chain O residue 11 GLU
Chi-restraints excluded: chain O residue 22 LEU
Chi-restraints excluded: chain O residue 73 SER
Chi-restraints excluded: chain O residue 82 VAL
Chi-restraints excluded: chain O residue 92 ILE
Chi-restraints excluded: chain O residue 112 THR
Chi-restraints excluded: chain O residue 141 MET
Chi-restraints excluded: chain P residue 8 THR
Chi-restraints excluded: chain P residue 22 LEU
Chi-restraints excluded: chain P residue 77 GLU
Chi-restraints excluded: chain Q residue 8 THR
Chi-restraints excluded: chain Q residue 31 GLN
Chi-restraints excluded: chain Q residue 41 SER
Chi-restraints excluded: chain Q residue 78 THR
Chi-restraints excluded: chain Q residue 82 VAL
Chi-restraints excluded: chain Q residue 85 ASP
Chi-restraints excluded: chain R residue 7 PHE
Chi-restraints excluded: chain R residue 8 THR
Chi-restraints excluded: chain R residue 73 SER
Chi-restraints excluded: chain R residue 78 THR
Chi-restraints excluded: chain R residue 82 VAL
Chi-restraints excluded: chain R residue 110 THR
Chi-restraints excluded: chain R residue 141 MET
Chi-restraints excluded: chain R residue 148 ASP
Chi-restraints excluded: chain S residue 7 PHE
Chi-restraints excluded: chain S residue 22 LEU
Chi-restraints excluded: chain S residue 73 SER
Chi-restraints excluded: chain S residue 78 THR
Chi-restraints excluded: chain S residue 112 THR
Chi-restraints excluded: chain T residue 8 THR
Chi-restraints excluded: chain T residue 22 LEU
Chi-restraints excluded: chain T residue 52 THR
Chi-restraints excluded: chain T residue 85 ASP
Chi-restraints excluded: chain T residue 87 ASN
Chi-restraints excluded: chain T residue 91 VAL
Chi-restraints excluded: chain T residue 112 THR
Chi-restraints excluded: chain T residue 125 ASN
Chi-restraints excluded: chain T residue 141 MET
Chi-restraints excluded: chain U residue 8 THR
Chi-restraints excluded: chain U residue 73 SER
Chi-restraints excluded: chain U residue 78 THR
Chi-restraints excluded: chain U residue 110 THR
Chi-restraints excluded: chain U residue 125 ASN
Chi-restraints excluded: chain U residue 141 MET
Chi-restraints excluded: chain V residue 85 ASP
Chi-restraints excluded: chain V residue 103 ASP
Chi-restraints excluded: chain V residue 112 THR
Chi-restraints excluded: chain V residue 139 ASP
Chi-restraints excluded: chain W residue 31 GLN
Chi-restraints excluded: chain W residue 64 SER
Chi-restraints excluded: chain W residue 73 SER
Chi-restraints excluded: chain W residue 80 VAL
Chi-restraints excluded: chain W residue 82 VAL
Chi-restraints excluded: chain W residue 112 THR
Chi-restraints excluded: chain W residue 135 LYS
Chi-restraints excluded: chain W residue 148 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 322
random chunks:
chunk 139 optimal weight: 8.9990
chunk 298 optimal weight: 0.9980
chunk 137 optimal weight: 9.9990
chunk 282 optimal weight: 3.9990
chunk 131 optimal weight: 5.9990
chunk 159 optimal weight: 7.9990
chunk 156 optimal weight: 0.9990
chunk 190 optimal weight: 9.9990
chunk 92 optimal weight: 7.9990
chunk 88 optimal weight: 2.9990
chunk 297 optimal weight: 5.9990
overall best weight: 2.9988
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
B 29 GLN
B 47 ASN
** B 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 125 ASN
** G 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
M 109 GLN
T 87 ASN
V 31 GLN
Total number of N/Q/H flips: 6
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2948 r_free = 0.2948 target = 0.091610 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2815 r_free = 0.2815 target = 0.083106 restraints weight = 33717.269|
|-----------------------------------------------------------------------------|
r_work (start): 0.2819 rms_B_bonded: 1.16
r_work: 0.2745 rms_B_bonded: 1.62 restraints_weight: 0.5000
r_work: 0.2639 rms_B_bonded: 2.88 restraints_weight: 0.2500
r_work (final): 0.2639
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8696
moved from start: 0.2854
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.005 0.036 24311 Z= 0.315
Angle : 0.520 7.277 33143 Z= 0.282
Chirality : 0.049 0.168 4186
Planarity : 0.004 0.033 4209
Dihedral : 4.493 32.943 3427
Min Nonbonded Distance : 2.539
Molprobity Statistics.
All-atom Clashscore : 5.24
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 2.31 %
Favored : 97.69 %
Rotamer:
Outliers : 5.50 %
Allowed : 19.43 %
Favored : 75.07 %
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: 2.36 (0.15), residues: 3243
helix: 2.06 (0.17), residues: 1081
sheet: 0.79 (0.18), residues: 713
loop : 1.86 (0.16), residues: 1449
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.010 0.001 TRP F 132
PHE 0.009 0.001 PHE E 142
TYR 0.013 0.001 TYR G 33
ARG 0.004 0.001 ARG P 59
*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
6486 Ramachandran restraints generated.
3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
6486 Ramachandran restraints generated.
3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
556 residues out of total 2599 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 143
poor density : 413
time to evaluate : 2.713
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: B 31 GLN cc_start: 0.8387 (OUTLIER) cc_final: 0.8173 (pt0)
REVERT: B 65 LYS cc_start: 0.8338 (mmtt) cc_final: 0.7416 (mttt)
REVERT: B 77 GLU cc_start: 0.8165 (mp0) cc_final: 0.7669 (mp0)
REVERT: C 22 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8174 (mp)
REVERT: C 135 LYS cc_start: 0.8229 (tptt) cc_final: 0.7880 (mttp)
REVERT: D 65 LYS cc_start: 0.8628 (mmtt) cc_final: 0.8106 (mmtp)
REVERT: E 141 MET cc_start: 0.8600 (OUTLIER) cc_final: 0.8210 (ptt)
REVERT: F 22 LEU cc_start: 0.8386 (OUTLIER) cc_final: 0.8148 (mp)
REVERT: H 31 GLN cc_start: 0.7770 (OUTLIER) cc_final: 0.7464 (pt0)
REVERT: I 97 GLU cc_start: 0.8072 (mt-10) cc_final: 0.7708 (mm-30)
REVERT: I 129 ASP cc_start: 0.8077 (t70) cc_final: 0.7823 (t70)
REVERT: J 22 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.8058 (mp)
REVERT: J 129 ASP cc_start: 0.7549 (m-30) cc_final: 0.6904 (t70)
REVERT: K 22 LEU cc_start: 0.8379 (OUTLIER) cc_final: 0.8032 (mp)
REVERT: K 31 GLN cc_start: 0.8153 (OUTLIER) cc_final: 0.7764 (pt0)
REVERT: L 22 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8274 (mp)
REVERT: L 103 ASP cc_start: 0.7942 (OUTLIER) cc_final: 0.7465 (p0)
REVERT: L 135 LYS cc_start: 0.8138 (tmtt) cc_final: 0.7749 (mtpt)
REVERT: M 7 PHE cc_start: 0.7403 (OUTLIER) cc_final: 0.7000 (t80)
REVERT: M 22 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.8100 (mp)
REVERT: M 135 LYS cc_start: 0.8868 (mmtt) cc_final: 0.8526 (tttp)
REVERT: N 22 LEU cc_start: 0.9097 (OUTLIER) cc_final: 0.8531 (mp)
REVERT: N 129 ASP cc_start: 0.7626 (OUTLIER) cc_final: 0.7376 (m-30)
REVERT: O 11 GLU cc_start: 0.8333 (OUTLIER) cc_final: 0.7913 (tt0)
REVERT: O 129 ASP cc_start: 0.8323 (t70) cc_final: 0.7747 (t0)
REVERT: P 22 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8331 (mp)
REVERT: P 135 LYS cc_start: 0.8432 (mmtt) cc_final: 0.8193 (tttp)
REVERT: Q 31 GLN cc_start: 0.8313 (OUTLIER) cc_final: 0.8020 (pt0)
REVERT: Q 77 GLU cc_start: 0.8358 (mt-10) cc_final: 0.8087 (mt-10)
REVERT: Q 87 ASN cc_start: 0.8679 (t0) cc_final: 0.8442 (t0)
REVERT: Q 135 LYS cc_start: 0.8269 (tptt) cc_final: 0.7832 (tttm)
REVERT: R 135 LYS cc_start: 0.8438 (tptt) cc_final: 0.7844 (ttpp)
REVERT: R 141 MET cc_start: 0.8603 (OUTLIER) cc_final: 0.8285 (ptm)
REVERT: S 22 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8352 (mp)
REVERT: S 91 VAL cc_start: 0.9213 (m) cc_final: 0.8948 (t)
REVERT: T 135 LYS cc_start: 0.8479 (tptt) cc_final: 0.8177 (mmtm)
REVERT: V 135 LYS cc_start: 0.8522 (mptt) cc_final: 0.8179 (mttt)
REVERT: W 31 GLN cc_start: 0.8047 (OUTLIER) cc_final: 0.7832 (pt0)
outliers start: 143
outliers final: 109
residues processed: 519
average time/residue: 0.3469
time to fit residues: 287.9852
Evaluate side-chains
534 residues out of total 2599 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 129
poor density : 405
time to evaluate : 2.902
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 31 GLN
Chi-restraints excluded: chain A residue 78 THR
Chi-restraints excluded: chain A residue 112 THR
Chi-restraints excluded: chain A residue 136 SER
Chi-restraints excluded: chain B residue 7 PHE
Chi-restraints excluded: chain B residue 8 THR
Chi-restraints excluded: chain B residue 11 GLU
Chi-restraints excluded: chain B residue 31 GLN
Chi-restraints excluded: chain B residue 82 VAL
Chi-restraints excluded: chain C residue 22 LEU
Chi-restraints excluded: chain C residue 73 SER
Chi-restraints excluded: chain C residue 82 VAL
Chi-restraints excluded: chain C residue 91 VAL
Chi-restraints excluded: chain C residue 107 THR
Chi-restraints excluded: chain C residue 112 THR
Chi-restraints excluded: chain D residue 7 PHE
Chi-restraints excluded: chain D residue 70 THR
Chi-restraints excluded: chain D residue 73 SER
Chi-restraints excluded: chain D residue 76 THR
Chi-restraints excluded: chain D residue 110 THR
Chi-restraints excluded: chain D residue 136 SER
Chi-restraints excluded: chain E residue 64 SER
Chi-restraints excluded: chain E residue 73 SER
Chi-restraints excluded: chain E residue 112 THR
Chi-restraints excluded: chain E residue 141 MET
Chi-restraints excluded: chain F residue 22 LEU
Chi-restraints excluded: chain F residue 29 GLN
Chi-restraints excluded: chain F residue 31 GLN
Chi-restraints excluded: chain F residue 76 THR
Chi-restraints excluded: chain F residue 112 THR
Chi-restraints excluded: chain G residue 31 GLN
Chi-restraints excluded: chain G residue 112 THR
Chi-restraints excluded: chain H residue 31 GLN
Chi-restraints excluded: chain H residue 76 THR
Chi-restraints excluded: chain H residue 82 VAL
Chi-restraints excluded: chain H residue 112 THR
Chi-restraints excluded: chain I residue 8 THR
Chi-restraints excluded: chain I residue 78 THR
Chi-restraints excluded: chain I residue 85 ASP
Chi-restraints excluded: chain I residue 112 THR
Chi-restraints excluded: chain J residue 22 LEU
Chi-restraints excluded: chain J residue 73 SER
Chi-restraints excluded: chain J residue 78 THR
Chi-restraints excluded: chain J residue 103 ASP
Chi-restraints excluded: chain K residue 8 THR
Chi-restraints excluded: chain K residue 22 LEU
Chi-restraints excluded: chain K residue 29 GLN
Chi-restraints excluded: chain K residue 31 GLN
Chi-restraints excluded: chain K residue 52 THR
Chi-restraints excluded: chain K residue 73 SER
Chi-restraints excluded: chain K residue 112 THR
Chi-restraints excluded: chain K residue 149 ASN
Chi-restraints excluded: chain L residue 7 PHE
Chi-restraints excluded: chain L residue 8 THR
Chi-restraints excluded: chain L residue 22 LEU
Chi-restraints excluded: chain L residue 78 THR
Chi-restraints excluded: chain L residue 103 ASP
Chi-restraints excluded: chain L residue 112 THR
Chi-restraints excluded: chain L residue 141 MET
Chi-restraints excluded: chain L residue 148 ASP
Chi-restraints excluded: chain M residue 7 PHE
Chi-restraints excluded: chain M residue 8 THR
Chi-restraints excluded: chain M residue 11 GLU
Chi-restraints excluded: chain M residue 22 LEU
Chi-restraints excluded: chain M residue 92 ILE
Chi-restraints excluded: chain M residue 112 THR
Chi-restraints excluded: chain N residue 22 LEU
Chi-restraints excluded: chain N residue 73 SER
Chi-restraints excluded: chain N residue 74 THR
Chi-restraints excluded: chain N residue 92 ILE
Chi-restraints excluded: chain N residue 103 ASP
Chi-restraints excluded: chain N residue 129 ASP
Chi-restraints excluded: chain O residue 8 THR
Chi-restraints excluded: chain O residue 11 GLU
Chi-restraints excluded: chain O residue 22 LEU
Chi-restraints excluded: chain O residue 73 SER
Chi-restraints excluded: chain O residue 82 VAL
Chi-restraints excluded: chain O residue 92 ILE
Chi-restraints excluded: chain O residue 112 THR
Chi-restraints excluded: chain O residue 141 MET
Chi-restraints excluded: chain P residue 8 THR
Chi-restraints excluded: chain P residue 22 LEU
Chi-restraints excluded: chain P residue 77 GLU
Chi-restraints excluded: chain Q residue 8 THR
Chi-restraints excluded: chain Q residue 31 GLN
Chi-restraints excluded: chain Q residue 41 SER
Chi-restraints excluded: chain Q residue 78 THR
Chi-restraints excluded: chain Q residue 82 VAL
Chi-restraints excluded: chain Q residue 85 ASP
Chi-restraints excluded: chain R residue 7 PHE
Chi-restraints excluded: chain R residue 8 THR
Chi-restraints excluded: chain R residue 73 SER
Chi-restraints excluded: chain R residue 78 THR
Chi-restraints excluded: chain R residue 82 VAL
Chi-restraints excluded: chain R residue 110 THR
Chi-restraints excluded: chain R residue 141 MET
Chi-restraints excluded: chain R residue 148 ASP
Chi-restraints excluded: chain S residue 22 LEU
Chi-restraints excluded: chain S residue 73 SER
Chi-restraints excluded: chain S residue 78 THR
Chi-restraints excluded: chain S residue 112 THR
Chi-restraints excluded: chain T residue 8 THR
Chi-restraints excluded: chain T residue 22 LEU
Chi-restraints excluded: chain T residue 52 THR
Chi-restraints excluded: chain T residue 85 ASP
Chi-restraints excluded: chain T residue 87 ASN
Chi-restraints excluded: chain T residue 91 VAL
Chi-restraints excluded: chain T residue 112 THR
Chi-restraints excluded: chain T residue 125 ASN
Chi-restraints excluded: chain T residue 141 MET
Chi-restraints excluded: chain U residue 8 THR
Chi-restraints excluded: chain U residue 73 SER
Chi-restraints excluded: chain U residue 78 THR
Chi-restraints excluded: chain U residue 110 THR
Chi-restraints excluded: chain U residue 125 ASN
Chi-restraints excluded: chain U residue 141 MET
Chi-restraints excluded: chain U residue 149 ASN
Chi-restraints excluded: chain V residue 85 ASP
Chi-restraints excluded: chain V residue 103 ASP
Chi-restraints excluded: chain V residue 112 THR
Chi-restraints excluded: chain V residue 139 ASP
Chi-restraints excluded: chain W residue 31 GLN
Chi-restraints excluded: chain W residue 64 SER
Chi-restraints excluded: chain W residue 73 SER
Chi-restraints excluded: chain W residue 80 VAL
Chi-restraints excluded: chain W residue 82 VAL
Chi-restraints excluded: chain W residue 112 THR
Chi-restraints excluded: chain W residue 135 LYS
Chi-restraints excluded: chain W residue 148 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 322
random chunks:
chunk 126 optimal weight: 2.9990
chunk 208 optimal weight: 6.9990
chunk 229 optimal weight: 3.9990
chunk 4 optimal weight: 0.9990
chunk 59 optimal weight: 0.9990
chunk 254 optimal weight: 8.9990
chunk 147 optimal weight: 3.9990
chunk 320 optimal weight: 7.9990
chunk 317 optimal weight: 1.9990
chunk 77 optimal weight: 4.9990
chunk 209 optimal weight: 0.9990
overall best weight: 1.5990
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
B 47 ASN
B 109 GLN
** C 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 125 ASN
G 29 GLN
G 109 GLN
** J 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
M 109 GLN
Total number of N/Q/H flips: 6
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2985 r_free = 0.2985 target = 0.094048 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2854 r_free = 0.2854 target = 0.085529 restraints weight = 33475.806|
|-----------------------------------------------------------------------------|
r_work (start): 0.2854 rms_B_bonded: 1.16
r_work: 0.2784 rms_B_bonded: 1.61 restraints_weight: 0.5000
r_work: 0.2678 rms_B_bonded: 2.89 restraints_weight: 0.2500
r_work (final): 0.2678
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8661
moved from start: 0.2803
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.024 24311 Z= 0.192
Angle : 0.461 6.319 33143 Z= 0.248
Chirality : 0.047 0.149 4186
Planarity : 0.004 0.031 4209
Dihedral : 4.119 29.752 3427
Min Nonbonded Distance : 2.559
Molprobity Statistics.
All-atom Clashscore : 5.41
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 1.60 %
Favored : 98.40 %
Rotamer:
Outliers : 4.69 %
Allowed : 20.39 %
Favored : 74.91 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 2.57 (0.15), residues: 3243
helix: 2.32 (0.17), residues: 1081
sheet: 0.81 (0.18), residues: 713
loop : 1.97 (0.16), residues: 1449
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.007 0.001 TRP O 132
PHE 0.006 0.001 PHE W 108
TYR 0.009 0.001 TYR G 33
ARG 0.003 0.000 ARG S 126
*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
6486 Ramachandran restraints generated.
3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
6486 Ramachandran restraints generated.
3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
546 residues out of total 2599 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 122
poor density : 424
time to evaluate : 2.659
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: A 125 ASN cc_start: 0.8262 (t0) cc_final: 0.7898 (t0)
REVERT: B 31 GLN cc_start: 0.8372 (OUTLIER) cc_final: 0.8094 (pt0)
REVERT: B 65 LYS cc_start: 0.8340 (mmtt) cc_final: 0.7436 (mttt)
REVERT: B 77 GLU cc_start: 0.8169 (mp0) cc_final: 0.7729 (mp0)
REVERT: C 22 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8184 (mp)
REVERT: C 77 GLU cc_start: 0.8207 (mp0) cc_final: 0.7918 (mp0)
REVERT: C 135 LYS cc_start: 0.8226 (tptt) cc_final: 0.7991 (mtmm)
REVERT: D 65 LYS cc_start: 0.8636 (mmtt) cc_final: 0.8100 (mmtp)
REVERT: E 141 MET cc_start: 0.8555 (OUTLIER) cc_final: 0.8199 (ptt)
REVERT: H 31 GLN cc_start: 0.7625 (OUTLIER) cc_final: 0.7349 (pt0)
REVERT: I 97 GLU cc_start: 0.8060 (mt-10) cc_final: 0.7708 (mm-30)
REVERT: I 129 ASP cc_start: 0.8034 (t70) cc_final: 0.7813 (t70)
REVERT: J 22 LEU cc_start: 0.8342 (OUTLIER) cc_final: 0.8063 (mp)
REVERT: J 129 ASP cc_start: 0.7503 (m-30) cc_final: 0.6856 (t70)
REVERT: K 22 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.8031 (mp)
REVERT: K 31 GLN cc_start: 0.8108 (OUTLIER) cc_final: 0.7709 (pt0)
REVERT: L 22 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8291 (mp)
REVERT: L 103 ASP cc_start: 0.7910 (OUTLIER) cc_final: 0.7383 (p0)
REVERT: L 135 LYS cc_start: 0.8130 (tmtt) cc_final: 0.7755 (mtpt)
REVERT: M 7 PHE cc_start: 0.7422 (OUTLIER) cc_final: 0.7031 (t80)
REVERT: M 22 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.8043 (mp)
REVERT: M 29 GLN cc_start: 0.8134 (tt0) cc_final: 0.7577 (mt0)
REVERT: M 67 LYS cc_start: 0.8449 (mtmt) cc_final: 0.8192 (mtmt)
REVERT: M 135 LYS cc_start: 0.8824 (mmtt) cc_final: 0.8490 (tttp)
REVERT: N 22 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8511 (mp)
REVERT: N 129 ASP cc_start: 0.7543 (OUTLIER) cc_final: 0.7282 (m-30)
REVERT: O 129 ASP cc_start: 0.8326 (t70) cc_final: 0.7767 (t0)
REVERT: Q 77 GLU cc_start: 0.8389 (mt-10) cc_final: 0.8132 (mt-10)
REVERT: Q 135 LYS cc_start: 0.8262 (tptt) cc_final: 0.7820 (tttm)
REVERT: R 135 LYS cc_start: 0.8428 (tptt) cc_final: 0.7846 (ttpp)
REVERT: R 141 MET cc_start: 0.8590 (OUTLIER) cc_final: 0.8244 (ptm)
REVERT: S 22 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8419 (mp)
REVERT: S 91 VAL cc_start: 0.9195 (m) cc_final: 0.8973 (t)
REVERT: T 135 LYS cc_start: 0.8466 (tptt) cc_final: 0.8157 (mmtm)
REVERT: V 135 LYS cc_start: 0.8520 (mptt) cc_final: 0.8157 (mttt)
REVERT: W 31 GLN cc_start: 0.7994 (OUTLIER) cc_final: 0.7787 (pt0)
outliers start: 122
outliers final: 89
residues processed: 514
average time/residue: 0.3363
time to fit residues: 276.4402
Evaluate side-chains
518 residues out of total 2599 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 105
poor density : 413
time to evaluate : 2.811
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 7 PHE
Chi-restraints excluded: chain A residue 78 THR
Chi-restraints excluded: chain A residue 112 THR
Chi-restraints excluded: chain A residue 136 SER
Chi-restraints excluded: chain B residue 7 PHE
Chi-restraints excluded: chain B residue 8 THR
Chi-restraints excluded: chain B residue 31 GLN
Chi-restraints excluded: chain B residue 82 VAL
Chi-restraints excluded: chain C residue 22 LEU
Chi-restraints excluded: chain C residue 73 SER
Chi-restraints excluded: chain C residue 82 VAL
Chi-restraints excluded: chain C residue 91 VAL
Chi-restraints excluded: chain C residue 107 THR
Chi-restraints excluded: chain C residue 112 THR
Chi-restraints excluded: chain D residue 7 PHE
Chi-restraints excluded: chain D residue 73 SER
Chi-restraints excluded: chain D residue 76 THR
Chi-restraints excluded: chain D residue 110 THR
Chi-restraints excluded: chain D residue 136 SER
Chi-restraints excluded: chain E residue 64 SER
Chi-restraints excluded: chain E residue 73 SER
Chi-restraints excluded: chain E residue 112 THR
Chi-restraints excluded: chain E residue 141 MET
Chi-restraints excluded: chain F residue 29 GLN
Chi-restraints excluded: chain F residue 76 THR
Chi-restraints excluded: chain F residue 112 THR
Chi-restraints excluded: chain G residue 31 GLN
Chi-restraints excluded: chain G residue 112 THR
Chi-restraints excluded: chain H residue 31 GLN
Chi-restraints excluded: chain H residue 82 VAL
Chi-restraints excluded: chain H residue 112 THR
Chi-restraints excluded: chain I residue 8 THR
Chi-restraints excluded: chain I residue 78 THR
Chi-restraints excluded: chain I residue 85 ASP
Chi-restraints excluded: chain I residue 112 THR
Chi-restraints excluded: chain J residue 22 LEU
Chi-restraints excluded: chain J residue 73 SER
Chi-restraints excluded: chain J residue 103 ASP
Chi-restraints excluded: chain K residue 22 LEU
Chi-restraints excluded: chain K residue 29 GLN
Chi-restraints excluded: chain K residue 31 GLN
Chi-restraints excluded: chain K residue 52 THR
Chi-restraints excluded: chain K residue 73 SER
Chi-restraints excluded: chain K residue 112 THR
Chi-restraints excluded: chain L residue 7 PHE
Chi-restraints excluded: chain L residue 8 THR
Chi-restraints excluded: chain L residue 22 LEU
Chi-restraints excluded: chain L residue 103 ASP
Chi-restraints excluded: chain L residue 112 THR
Chi-restraints excluded: chain L residue 141 MET
Chi-restraints excluded: chain M residue 7 PHE
Chi-restraints excluded: chain M residue 8 THR
Chi-restraints excluded: chain M residue 11 GLU
Chi-restraints excluded: chain M residue 22 LEU
Chi-restraints excluded: chain M residue 92 ILE
Chi-restraints excluded: chain M residue 112 THR
Chi-restraints excluded: chain N residue 22 LEU
Chi-restraints excluded: chain N residue 73 SER
Chi-restraints excluded: chain N residue 92 ILE
Chi-restraints excluded: chain N residue 103 ASP
Chi-restraints excluded: chain N residue 129 ASP
Chi-restraints excluded: chain O residue 8 THR
Chi-restraints excluded: chain O residue 22 LEU
Chi-restraints excluded: chain O residue 73 SER
Chi-restraints excluded: chain O residue 82 VAL
Chi-restraints excluded: chain O residue 92 ILE
Chi-restraints excluded: chain O residue 112 THR
Chi-restraints excluded: chain O residue 141 MET
Chi-restraints excluded: chain P residue 8 THR
Chi-restraints excluded: chain P residue 74 THR
Chi-restraints excluded: chain P residue 77 GLU
Chi-restraints excluded: chain Q residue 8 THR
Chi-restraints excluded: chain Q residue 41 SER
Chi-restraints excluded: chain Q residue 78 THR
Chi-restraints excluded: chain R residue 8 THR
Chi-restraints excluded: chain R residue 73 SER
Chi-restraints excluded: chain R residue 76 THR
Chi-restraints excluded: chain R residue 78 THR
Chi-restraints excluded: chain R residue 82 VAL
Chi-restraints excluded: chain R residue 110 THR
Chi-restraints excluded: chain R residue 141 MET
Chi-restraints excluded: chain R residue 148 ASP
Chi-restraints excluded: chain S residue 22 LEU
Chi-restraints excluded: chain S residue 73 SER
Chi-restraints excluded: chain S residue 78 THR
Chi-restraints excluded: chain S residue 112 THR
Chi-restraints excluded: chain T residue 8 THR
Chi-restraints excluded: chain T residue 22 LEU
Chi-restraints excluded: chain T residue 52 THR
Chi-restraints excluded: chain T residue 112 THR
Chi-restraints excluded: chain T residue 141 MET
Chi-restraints excluded: chain U residue 8 THR
Chi-restraints excluded: chain U residue 73 SER
Chi-restraints excluded: chain U residue 78 THR
Chi-restraints excluded: chain U residue 110 THR
Chi-restraints excluded: chain V residue 7 PHE
Chi-restraints excluded: chain V residue 13 MET
Chi-restraints excluded: chain V residue 103 ASP
Chi-restraints excluded: chain V residue 112 THR
Chi-restraints excluded: chain W residue 31 GLN
Chi-restraints excluded: chain W residue 64 SER
Chi-restraints excluded: chain W residue 73 SER
Chi-restraints excluded: chain W residue 82 VAL
Chi-restraints excluded: chain W residue 112 THR
Chi-restraints excluded: chain W residue 135 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 322
random chunks:
chunk 216 optimal weight: 8.9990
chunk 224 optimal weight: 4.9990
chunk 215 optimal weight: 4.9990
chunk 303 optimal weight: 0.6980
chunk 26 optimal weight: 9.9990
chunk 207 optimal weight: 5.9990
chunk 120 optimal weight: 7.9990
chunk 168 optimal weight: 1.9990
chunk 10 optimal weight: 3.9990
chunk 300 optimal weight: 7.9990
chunk 124 optimal weight: 5.9990
overall best weight: 3.3388
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
B 47 ASN
B 109 GLN
** C 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 125 ASN
D 149 ASN
** H 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
I 31 GLN
** J 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L 149 ASN
Total number of N/Q/H flips: 6
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2942 r_free = 0.2942 target = 0.091302 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2809 r_free = 0.2809 target = 0.082826 restraints weight = 33743.635|
|-----------------------------------------------------------------------------|
r_work (start): 0.2814 rms_B_bonded: 1.16
r_work: 0.2741 rms_B_bonded: 1.61 restraints_weight: 0.5000
r_work: 0.2635 rms_B_bonded: 2.86 restraints_weight: 0.2500
r_work (final): 0.2635
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8705
moved from start: 0.2934
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.005 0.048 24311 Z= 0.345
Angle : 0.536 8.316 33143 Z= 0.290
Chirality : 0.050 0.173 4186
Planarity : 0.004 0.033 4209
Dihedral : 4.587 33.116 3427
Min Nonbonded Distance : 2.525
Molprobity Statistics.
All-atom Clashscore : 5.47
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 2.81 %
Favored : 97.19 %
Rotamer:
Outliers : 5.31 %
Allowed : 19.85 %
Favored : 74.84 %
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 (0.15), residues: 3243
helix: 2.03 (0.17), residues: 1081
sheet: 0.66 (0.18), residues: 713
loop : 1.81 (0.16), residues: 1449
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.008 0.001 TRP A 132
PHE 0.010 0.001 PHE E 142
TYR 0.014 0.001 TYR G 33
ARG 0.004 0.001 ARG P 59
*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
6486 Ramachandran restraints generated.
3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
6486 Ramachandran restraints generated.
3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
546 residues out of total 2599 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 138
poor density : 408
time to evaluate : 2.820
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: A 125 ASN cc_start: 0.8282 (t0) cc_final: 0.7871 (t0)
REVERT: B 31 GLN cc_start: 0.8462 (OUTLIER) cc_final: 0.8208 (pt0)
REVERT: B 65 LYS cc_start: 0.8354 (mmtt) cc_final: 0.7442 (mttt)
REVERT: B 77 GLU cc_start: 0.8177 (mp0) cc_final: 0.7754 (mp0)
REVERT: C 22 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8120 (mp)
REVERT: C 135 LYS cc_start: 0.8256 (tptt) cc_final: 0.7990 (mtmm)
REVERT: D 65 LYS cc_start: 0.8631 (mmtt) cc_final: 0.8108 (mmtp)
REVERT: E 141 MET cc_start: 0.8618 (OUTLIER) cc_final: 0.8234 (ptt)
REVERT: H 31 GLN cc_start: 0.7787 (OUTLIER) cc_final: 0.7496 (pt0)
REVERT: I 97 GLU cc_start: 0.8078 (mt-10) cc_final: 0.7717 (mm-30)
REVERT: J 22 LEU cc_start: 0.8392 (OUTLIER) cc_final: 0.8066 (mp)
REVERT: J 129 ASP cc_start: 0.7541 (m-30) cc_final: 0.6959 (t70)
REVERT: K 22 LEU cc_start: 0.8398 (OUTLIER) cc_final: 0.8035 (mp)
REVERT: K 31 GLN cc_start: 0.8199 (OUTLIER) cc_final: 0.7808 (pt0)
REVERT: L 22 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8255 (mp)
REVERT: L 103 ASP cc_start: 0.7919 (p0) cc_final: 0.7460 (p0)
REVERT: L 129 ASP cc_start: 0.7891 (t0) cc_final: 0.7616 (t0)
REVERT: L 135 LYS cc_start: 0.8141 (tmtt) cc_final: 0.7771 (mtpt)
REVERT: M 7 PHE cc_start: 0.7390 (OUTLIER) cc_final: 0.7009 (t80)
REVERT: M 22 LEU cc_start: 0.8485 (OUTLIER) cc_final: 0.8121 (mp)
REVERT: M 67 LYS cc_start: 0.8471 (mtmt) cc_final: 0.8261 (mtmt)
REVERT: M 135 LYS cc_start: 0.8870 (mmtt) cc_final: 0.8547 (tttp)
REVERT: N 129 ASP cc_start: 0.7586 (OUTLIER) cc_final: 0.7313 (m-30)
REVERT: O 129 ASP cc_start: 0.8314 (t70) cc_final: 0.7729 (t0)
REVERT: P 7 PHE cc_start: 0.8159 (OUTLIER) cc_final: 0.7889 (t80)
REVERT: P 22 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8335 (mp)
REVERT: Q 31 GLN cc_start: 0.8336 (OUTLIER) cc_final: 0.8027 (pt0)
REVERT: Q 77 GLU cc_start: 0.8382 (mt-10) cc_final: 0.8116 (mt-10)
REVERT: Q 135 LYS cc_start: 0.8207 (tptt) cc_final: 0.7776 (tttm)
REVERT: R 135 LYS cc_start: 0.8433 (tptt) cc_final: 0.7870 (ttpp)
REVERT: R 141 MET cc_start: 0.8592 (OUTLIER) cc_final: 0.8283 (ptm)
REVERT: S 22 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8402 (mp)
REVERT: S 91 VAL cc_start: 0.9194 (m) cc_final: 0.8928 (t)
REVERT: T 135 LYS cc_start: 0.8451 (tptt) cc_final: 0.8163 (mmtm)
REVERT: V 22 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8430 (mp)
REVERT: V 97 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7620 (mp0)
REVERT: V 135 LYS cc_start: 0.8520 (mptt) cc_final: 0.8151 (mttt)
REVERT: W 31 GLN cc_start: 0.8102 (OUTLIER) cc_final: 0.7891 (pt0)
outliers start: 138
outliers final: 109
residues processed: 512
average time/residue: 0.3441
time to fit residues: 280.3024
Evaluate side-chains
529 residues out of total 2599 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 128
poor density : 401
time to evaluate : 2.665
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 31 GLN
Chi-restraints excluded: chain A residue 78 THR
Chi-restraints excluded: chain A residue 112 THR
Chi-restraints excluded: chain A residue 136 SER
Chi-restraints excluded: chain B residue 7 PHE
Chi-restraints excluded: chain B residue 8 THR
Chi-restraints excluded: chain B residue 11 GLU
Chi-restraints excluded: chain B residue 31 GLN
Chi-restraints excluded: chain B residue 82 VAL
Chi-restraints excluded: chain B residue 109 GLN
Chi-restraints excluded: chain C residue 22 LEU
Chi-restraints excluded: chain C residue 73 SER
Chi-restraints excluded: chain C residue 82 VAL
Chi-restraints excluded: chain C residue 91 VAL
Chi-restraints excluded: chain C residue 107 THR
Chi-restraints excluded: chain C residue 112 THR
Chi-restraints excluded: chain D residue 7 PHE
Chi-restraints excluded: chain D residue 70 THR
Chi-restraints excluded: chain D residue 73 SER
Chi-restraints excluded: chain D residue 76 THR
Chi-restraints excluded: chain D residue 110 THR
Chi-restraints excluded: chain D residue 136 SER
Chi-restraints excluded: chain D residue 149 ASN
Chi-restraints excluded: chain E residue 64 SER
Chi-restraints excluded: chain E residue 73 SER
Chi-restraints excluded: chain E residue 112 THR
Chi-restraints excluded: chain E residue 141 MET
Chi-restraints excluded: chain F residue 29 GLN
Chi-restraints excluded: chain F residue 76 THR
Chi-restraints excluded: chain F residue 112 THR
Chi-restraints excluded: chain F residue 141 MET
Chi-restraints excluded: chain G residue 31 GLN
Chi-restraints excluded: chain G residue 112 THR
Chi-restraints excluded: chain G residue 148 ASP
Chi-restraints excluded: chain H residue 31 GLN
Chi-restraints excluded: chain H residue 76 THR
Chi-restraints excluded: chain H residue 82 VAL
Chi-restraints excluded: chain H residue 112 THR
Chi-restraints excluded: chain I residue 8 THR
Chi-restraints excluded: chain I residue 78 THR
Chi-restraints excluded: chain I residue 85 ASP
Chi-restraints excluded: chain I residue 112 THR
Chi-restraints excluded: chain J residue 22 LEU
Chi-restraints excluded: chain J residue 73 SER
Chi-restraints excluded: chain J residue 78 THR
Chi-restraints excluded: chain J residue 103 ASP
Chi-restraints excluded: chain K residue 22 LEU
Chi-restraints excluded: chain K residue 29 GLN
Chi-restraints excluded: chain K residue 31 GLN
Chi-restraints excluded: chain K residue 52 THR
Chi-restraints excluded: chain K residue 73 SER
Chi-restraints excluded: chain K residue 112 THR
Chi-restraints excluded: chain K residue 149 ASN
Chi-restraints excluded: chain L residue 7 PHE
Chi-restraints excluded: chain L residue 8 THR
Chi-restraints excluded: chain L residue 22 LEU
Chi-restraints excluded: chain L residue 112 THR
Chi-restraints excluded: chain L residue 141 MET
Chi-restraints excluded: chain L residue 148 ASP
Chi-restraints excluded: chain M residue 7 PHE
Chi-restraints excluded: chain M residue 8 THR
Chi-restraints excluded: chain M residue 11 GLU
Chi-restraints excluded: chain M residue 22 LEU
Chi-restraints excluded: chain M residue 92 ILE
Chi-restraints excluded: chain M residue 112 THR
Chi-restraints excluded: chain N residue 22 LEU
Chi-restraints excluded: chain N residue 73 SER
Chi-restraints excluded: chain N residue 92 ILE
Chi-restraints excluded: chain N residue 103 ASP
Chi-restraints excluded: chain N residue 129 ASP
Chi-restraints excluded: chain O residue 8 THR
Chi-restraints excluded: chain O residue 22 LEU
Chi-restraints excluded: chain O residue 73 SER
Chi-restraints excluded: chain O residue 82 VAL
Chi-restraints excluded: chain O residue 92 ILE
Chi-restraints excluded: chain O residue 112 THR
Chi-restraints excluded: chain O residue 141 MET
Chi-restraints excluded: chain P residue 7 PHE
Chi-restraints excluded: chain P residue 8 THR
Chi-restraints excluded: chain P residue 22 LEU
Chi-restraints excluded: chain P residue 74 THR
Chi-restraints excluded: chain P residue 77 GLU
Chi-restraints excluded: chain P residue 116 LYS
Chi-restraints excluded: chain Q residue 8 THR
Chi-restraints excluded: chain Q residue 31 GLN
Chi-restraints excluded: chain Q residue 41 SER
Chi-restraints excluded: chain Q residue 78 THR
Chi-restraints excluded: chain Q residue 82 VAL
Chi-restraints excluded: chain R residue 8 THR
Chi-restraints excluded: chain R residue 22 LEU
Chi-restraints excluded: chain R residue 73 SER
Chi-restraints excluded: chain R residue 76 THR
Chi-restraints excluded: chain R residue 78 THR
Chi-restraints excluded: chain R residue 82 VAL
Chi-restraints excluded: chain R residue 110 THR
Chi-restraints excluded: chain R residue 141 MET
Chi-restraints excluded: chain R residue 148 ASP
Chi-restraints excluded: chain S residue 22 LEU
Chi-restraints excluded: chain S residue 73 SER
Chi-restraints excluded: chain S residue 78 THR
Chi-restraints excluded: chain S residue 112 THR
Chi-restraints excluded: chain T residue 8 THR
Chi-restraints excluded: chain T residue 22 LEU
Chi-restraints excluded: chain T residue 52 THR
Chi-restraints excluded: chain T residue 85 ASP
Chi-restraints excluded: chain T residue 112 THR
Chi-restraints excluded: chain T residue 125 ASN
Chi-restraints excluded: chain T residue 141 MET
Chi-restraints excluded: chain U residue 8 THR
Chi-restraints excluded: chain U residue 73 SER
Chi-restraints excluded: chain U residue 78 THR
Chi-restraints excluded: chain U residue 110 THR
Chi-restraints excluded: chain U residue 125 ASN
Chi-restraints excluded: chain U residue 141 MET
Chi-restraints excluded: chain U residue 149 ASN
Chi-restraints excluded: chain V residue 22 LEU
Chi-restraints excluded: chain V residue 97 GLU
Chi-restraints excluded: chain V residue 103 ASP
Chi-restraints excluded: chain V residue 112 THR
Chi-restraints excluded: chain V residue 139 ASP
Chi-restraints excluded: chain W residue 31 GLN
Chi-restraints excluded: chain W residue 64 SER
Chi-restraints excluded: chain W residue 73 SER
Chi-restraints excluded: chain W residue 80 VAL
Chi-restraints excluded: chain W residue 82 VAL
Chi-restraints excluded: chain W residue 112 THR
Chi-restraints excluded: chain W residue 135 LYS
Chi-restraints excluded: chain W residue 148 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 322
random chunks:
chunk 161 optimal weight: 2.9990
chunk 10 optimal weight: 1.9990
chunk 121 optimal weight: 0.0270
chunk 76 optimal weight: 5.9990
chunk 108 optimal weight: 0.0970
chunk 199 optimal weight: 0.8980
chunk 237 optimal weight: 0.9980
chunk 292 optimal weight: 1.9990
chunk 207 optimal weight: 0.8980
chunk 189 optimal weight: 6.9990
chunk 303 optimal weight: 6.9990
overall best weight: 0.5836
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
B 47 ASN
** C 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 125 ASN
G 29 GLN
G 109 GLN
I 31 GLN
** J 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K 87 ASN
Q 87 ASN
Q 149 ASN
Total number of N/Q/H flips: 8
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3032 r_free = 0.3032 target = 0.097196 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2904 r_free = 0.2904 target = 0.088732 restraints weight = 33266.511|
|-----------------------------------------------------------------------------|
r_work (start): 0.2902 rms_B_bonded: 1.16
r_work: 0.2831 rms_B_bonded: 1.62 restraints_weight: 0.5000
r_work: 0.2727 rms_B_bonded: 2.91 restraints_weight: 0.2500
r_work (final): 0.2727
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8618
moved from start: 0.2846
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.002 0.028 24311 Z= 0.125
Angle : 0.434 7.877 33143 Z= 0.232
Chirality : 0.046 0.146 4186
Planarity : 0.003 0.029 4209
Dihedral : 3.848 25.569 3427
Min Nonbonded Distance : 2.551
Molprobity Statistics.
All-atom Clashscore : 5.57
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 0.89 %
Favored : 99.11 %
Rotamer:
Outliers : 3.27 %
Allowed : 21.97 %
Favored : 74.76 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 2.69 (0.15), residues: 3243
helix: 2.47 (0.17), residues: 1081
sheet: 0.84 (0.19), residues: 713
loop : 2.02 (0.16), residues: 1449
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.006 0.001 TRP B 132
PHE 0.005 0.001 PHE B 108
TYR 0.008 0.001 TYR I 33
ARG 0.004 0.000 ARG P 59
*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
6486 Ramachandran restraints generated.
3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
6486 Ramachandran restraints generated.
3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
527 residues out of total 2599 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 85
poor density : 442
time to evaluate : 2.934
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: A 85 ASP cc_start: 0.8026 (p0) cc_final: 0.7680 (p0)
REVERT: A 125 ASN cc_start: 0.8170 (t0) cc_final: 0.7811 (t0)
REVERT: B 65 LYS cc_start: 0.8341 (mmtt) cc_final: 0.7418 (mttt)
REVERT: B 77 GLU cc_start: 0.8131 (mp0) cc_final: 0.7775 (mp0)
REVERT: C 22 LEU cc_start: 0.8434 (OUTLIER) cc_final: 0.8174 (mp)
REVERT: C 77 GLU cc_start: 0.8214 (mp0) cc_final: 0.7855 (mp0)
REVERT: C 135 LYS cc_start: 0.8239 (tptt) cc_final: 0.7978 (mtmm)
REVERT: D 65 LYS cc_start: 0.8625 (mmtt) cc_final: 0.8059 (mmtp)
REVERT: E 141 MET cc_start: 0.8504 (OUTLIER) cc_final: 0.8181 (ptt)
REVERT: G 85 ASP cc_start: 0.8267 (p0) cc_final: 0.7971 (p0)
REVERT: G 141 MET cc_start: 0.8466 (ptp) cc_final: 0.8177 (ptm)
REVERT: H 31 GLN cc_start: 0.7469 (OUTLIER) cc_final: 0.7229 (pt0)
REVERT: I 97 GLU cc_start: 0.8057 (mt-10) cc_final: 0.7738 (mm-30)
REVERT: J 67 LYS cc_start: 0.8736 (mmtt) cc_final: 0.8486 (mmtt)
REVERT: J 129 ASP cc_start: 0.7496 (m-30) cc_final: 0.6859 (t70)
REVERT: K 31 GLN cc_start: 0.8039 (OUTLIER) cc_final: 0.7651 (pt0)
REVERT: K 65 LYS cc_start: 0.8542 (mmtm) cc_final: 0.8336 (mmtp)
REVERT: K 91 VAL cc_start: 0.8950 (m) cc_final: 0.8697 (t)
REVERT: L 135 LYS cc_start: 0.8159 (tmtt) cc_final: 0.7768 (mtpt)
REVERT: M 7 PHE cc_start: 0.7436 (OUTLIER) cc_final: 0.6948 (t80)
REVERT: M 22 LEU cc_start: 0.8282 (OUTLIER) cc_final: 0.8014 (mp)
REVERT: M 29 GLN cc_start: 0.8021 (tt0) cc_final: 0.7479 (mt0)
REVERT: M 67 LYS cc_start: 0.8456 (mtmt) cc_final: 0.8200 (mtmt)
REVERT: M 135 LYS cc_start: 0.8863 (mmtt) cc_final: 0.8519 (tttp)
REVERT: N 22 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8495 (mp)
REVERT: N 87 ASN cc_start: 0.9135 (t0) cc_final: 0.8897 (t0)
REVERT: O 43 LEU cc_start: 0.9016 (tp) cc_final: 0.8740 (tp)
REVERT: O 129 ASP cc_start: 0.8405 (t70) cc_final: 0.7932 (t0)
REVERT: P 7 PHE cc_start: 0.8108 (OUTLIER) cc_final: 0.7849 (t80)
REVERT: Q 77 GLU cc_start: 0.8387 (mt-10) cc_final: 0.8128 (mt-10)
REVERT: Q 135 LYS cc_start: 0.8213 (tptt) cc_final: 0.7813 (tttm)
REVERT: R 135 LYS cc_start: 0.8346 (tptt) cc_final: 0.7759 (ttpp)
REVERT: S 91 VAL cc_start: 0.9225 (m) cc_final: 0.9015 (t)
REVERT: T 135 LYS cc_start: 0.8436 (tptt) cc_final: 0.8110 (mmtm)
REVERT: V 22 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8482 (mp)
REVERT: V 97 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.7414 (mp0)
REVERT: V 103 ASP cc_start: 0.8163 (OUTLIER) cc_final: 0.7858 (p0)
REVERT: V 135 LYS cc_start: 0.8492 (mptt) cc_final: 0.8156 (mttt)
REVERT: W 77 GLU cc_start: 0.8085 (mt-10) cc_final: 0.7688 (mt-10)
outliers start: 85
outliers final: 56
residues processed: 502
average time/residue: 0.3436
time to fit residues: 274.7982
Evaluate side-chains
489 residues out of total 2599 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 67
poor density : 422
time to evaluate : 2.677
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 7 PHE
Chi-restraints excluded: chain A residue 31 GLN
Chi-restraints excluded: chain A residue 78 THR
Chi-restraints excluded: chain B residue 7 PHE
Chi-restraints excluded: chain B residue 8 THR
Chi-restraints excluded: chain B residue 11 GLU
Chi-restraints excluded: chain C residue 22 LEU
Chi-restraints excluded: chain C residue 91 VAL
Chi-restraints excluded: chain C residue 107 THR
Chi-restraints excluded: chain D residue 22 LEU
Chi-restraints excluded: chain D residue 73 SER
Chi-restraints excluded: chain D residue 136 SER
Chi-restraints excluded: chain E residue 73 SER
Chi-restraints excluded: chain E residue 141 MET
Chi-restraints excluded: chain F residue 29 GLN
Chi-restraints excluded: chain G residue 112 THR
Chi-restraints excluded: chain H residue 31 GLN
Chi-restraints excluded: chain H residue 82 VAL
Chi-restraints excluded: chain I residue 8 THR
Chi-restraints excluded: chain I residue 78 THR
Chi-restraints excluded: chain I residue 85 ASP
Chi-restraints excluded: chain J residue 73 SER
Chi-restraints excluded: chain J residue 103 ASP
Chi-restraints excluded: chain K residue 8 THR
Chi-restraints excluded: chain K residue 29 GLN
Chi-restraints excluded: chain K residue 31 GLN
Chi-restraints excluded: chain K residue 52 THR
Chi-restraints excluded: chain K residue 73 SER
Chi-restraints excluded: chain L residue 8 THR
Chi-restraints excluded: chain L residue 141 MET
Chi-restraints excluded: chain L residue 148 ASP
Chi-restraints excluded: chain M residue 7 PHE
Chi-restraints excluded: chain M residue 8 THR
Chi-restraints excluded: chain M residue 11 GLU
Chi-restraints excluded: chain M residue 22 LEU
Chi-restraints excluded: chain M residue 92 ILE
Chi-restraints excluded: chain M residue 112 THR
Chi-restraints excluded: chain N residue 22 LEU
Chi-restraints excluded: chain N residue 73 SER
Chi-restraints excluded: chain N residue 92 ILE
Chi-restraints excluded: chain N residue 129 ASP
Chi-restraints excluded: chain O residue 8 THR
Chi-restraints excluded: chain O residue 82 VAL
Chi-restraints excluded: chain O residue 141 MET
Chi-restraints excluded: chain P residue 7 PHE
Chi-restraints excluded: chain P residue 8 THR
Chi-restraints excluded: chain P residue 74 THR
Chi-restraints excluded: chain Q residue 29 GLN
Chi-restraints excluded: chain Q residue 41 SER
Chi-restraints excluded: chain R residue 78 THR
Chi-restraints excluded: chain R residue 141 MET
Chi-restraints excluded: chain S residue 73 SER
Chi-restraints excluded: chain S residue 78 THR
Chi-restraints excluded: chain S residue 112 THR
Chi-restraints excluded: chain T residue 8 THR
Chi-restraints excluded: chain T residue 78 THR
Chi-restraints excluded: chain U residue 8 THR
Chi-restraints excluded: chain U residue 73 SER
Chi-restraints excluded: chain U residue 78 THR
Chi-restraints excluded: chain U residue 141 MET
Chi-restraints excluded: chain V residue 7 PHE
Chi-restraints excluded: chain V residue 22 LEU
Chi-restraints excluded: chain V residue 97 GLU
Chi-restraints excluded: chain V residue 103 ASP
Chi-restraints excluded: chain V residue 112 THR
Chi-restraints excluded: chain W residue 73 SER
Chi-restraints excluded: chain W residue 82 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 322
random chunks:
chunk 248 optimal weight: 0.7980
chunk 33 optimal weight: 7.9990
chunk 75 optimal weight: 4.9990
chunk 167 optimal weight: 1.9990
chunk 223 optimal weight: 4.9990
chunk 24 optimal weight: 7.9990
chunk 253 optimal weight: 8.9990
chunk 246 optimal weight: 2.9990
chunk 318 optimal weight: 0.1980
chunk 268 optimal weight: 4.9990
chunk 90 optimal weight: 0.0980
overall best weight: 1.2184
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
B 47 ASN
B 109 GLN
** C 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 125 ASN
G 29 GLN
G 109 GLN
H 29 GLN
** H 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
M 109 GLN
T 149 ASN
Total number of N/Q/H flips: 8
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3008 r_free = 0.3008 target = 0.095563 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2880 r_free = 0.2880 target = 0.087077 restraints weight = 33406.185|
|-----------------------------------------------------------------------------|
r_work (start): 0.2887 rms_B_bonded: 1.16
r_work: 0.2815 rms_B_bonded: 1.61 restraints_weight: 0.5000
r_work: 0.2709 rms_B_bonded: 2.90 restraints_weight: 0.2500
r_work (final): 0.2709
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8640
moved from start: 0.2849
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.029 24311 Z= 0.164
Angle : 0.450 7.593 33143 Z= 0.240
Chirality : 0.046 0.147 4186
Planarity : 0.003 0.030 4209
Dihedral : 3.890 23.596 3427
Min Nonbonded Distance : 2.548
Molprobity Statistics.
All-atom Clashscore : 5.63
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 1.82 %
Favored : 98.18 %
Rotamer:
Outliers : 2.81 %
Allowed : 22.82 %
Favored : 74.37 %
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: 2.74 (0.15), residues: 3243
helix: 2.50 (0.17), residues: 1081
sheet: 0.86 (0.19), residues: 713
loop : 2.05 (0.16), residues: 1449
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.006 0.001 TRP B 132
PHE 0.006 0.001 PHE W 7
TYR 0.009 0.001 TYR I 33
ARG 0.003 0.000 ARG P 59
********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
6486 Ramachandran restraints generated.
3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
6486 Ramachandran restraints generated.
3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
499 residues out of total 2599 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 73
poor density : 426
time to evaluate : 2.775
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: A 85 ASP cc_start: 0.8002 (p0) cc_final: 0.7651 (p0)
REVERT: A 125 ASN cc_start: 0.8204 (t0) cc_final: 0.7836 (t0)
REVERT: B 65 LYS cc_start: 0.8345 (mmtt) cc_final: 0.7420 (mttt)
REVERT: B 77 GLU cc_start: 0.8131 (mp0) cc_final: 0.7749 (mp0)
REVERT: C 22 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.8126 (mp)
REVERT: C 77 GLU cc_start: 0.8190 (mp0) cc_final: 0.7923 (mp0)
REVERT: C 135 LYS cc_start: 0.8265 (tptt) cc_final: 0.8013 (mtmm)
REVERT: D 65 LYS cc_start: 0.8622 (mmtt) cc_final: 0.8073 (mmtp)
REVERT: E 141 MET cc_start: 0.8539 (OUTLIER) cc_final: 0.8214 (ptt)
REVERT: G 141 MET cc_start: 0.8458 (ptp) cc_final: 0.8161 (ptm)
REVERT: H 31 GLN cc_start: 0.7523 (OUTLIER) cc_final: 0.7271 (pt0)
REVERT: I 97 GLU cc_start: 0.8119 (mt-10) cc_final: 0.7766 (mm-30)
REVERT: J 67 LYS cc_start: 0.8764 (mmtt) cc_final: 0.8495 (mmtt)
REVERT: J 129 ASP cc_start: 0.7523 (m-30) cc_final: 0.6900 (t70)
REVERT: K 31 GLN cc_start: 0.8106 (OUTLIER) cc_final: 0.7702 (pt0)
REVERT: K 65 LYS cc_start: 0.8542 (mmtm) cc_final: 0.8329 (mmtp)
REVERT: L 135 LYS cc_start: 0.8152 (tmtt) cc_final: 0.7795 (mtpt)
REVERT: M 7 PHE cc_start: 0.7378 (OUTLIER) cc_final: 0.6938 (t80)
REVERT: M 22 LEU cc_start: 0.8329 (OUTLIER) cc_final: 0.8002 (mp)
REVERT: M 29 GLN cc_start: 0.8120 (tt0) cc_final: 0.7564 (mt0)
REVERT: M 67 LYS cc_start: 0.8470 (mtmt) cc_final: 0.8211 (mtmt)
REVERT: M 135 LYS cc_start: 0.8878 (mmtt) cc_final: 0.8516 (tttp)
REVERT: N 87 ASN cc_start: 0.9136 (t0) cc_final: 0.8873 (t0)
REVERT: O 129 ASP cc_start: 0.8358 (t70) cc_final: 0.7845 (t0)
REVERT: P 7 PHE cc_start: 0.8128 (OUTLIER) cc_final: 0.7895 (t80)
REVERT: Q 77 GLU cc_start: 0.8400 (mt-10) cc_final: 0.8136 (mt-10)
REVERT: Q 135 LYS cc_start: 0.8183 (tptt) cc_final: 0.7617 (tttm)
REVERT: R 135 LYS cc_start: 0.8382 (tptt) cc_final: 0.7753 (ttpp)
REVERT: S 91 VAL cc_start: 0.9221 (m) cc_final: 0.8987 (t)
REVERT: T 135 LYS cc_start: 0.8403 (tptt) cc_final: 0.8101 (mmtm)
REVERT: V 22 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8487 (mp)
REVERT: V 97 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7446 (mp0)
REVERT: V 103 ASP cc_start: 0.8178 (OUTLIER) cc_final: 0.7863 (p0)
REVERT: V 135 LYS cc_start: 0.8495 (mptt) cc_final: 0.8153 (mttt)
REVERT: W 77 GLU cc_start: 0.8097 (mt-10) cc_final: 0.7690 (mt-10)
outliers start: 73
outliers final: 59
residues processed: 479
average time/residue: 0.3426
time to fit residues: 260.5507
Evaluate side-chains
488 residues out of total 2599 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 69
poor density : 419
time to evaluate : 2.721
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 7 PHE
Chi-restraints excluded: chain A residue 31 GLN
Chi-restraints excluded: chain A residue 78 THR
Chi-restraints excluded: chain B residue 7 PHE
Chi-restraints excluded: chain B residue 8 THR
Chi-restraints excluded: chain B residue 11 GLU
Chi-restraints excluded: chain B residue 109 GLN
Chi-restraints excluded: chain C residue 22 LEU
Chi-restraints excluded: chain C residue 91 VAL
Chi-restraints excluded: chain C residue 107 THR
Chi-restraints excluded: chain D residue 22 LEU
Chi-restraints excluded: chain D residue 73 SER
Chi-restraints excluded: chain D residue 136 SER
Chi-restraints excluded: chain E residue 73 SER
Chi-restraints excluded: chain E residue 141 MET
Chi-restraints excluded: chain F residue 29 GLN
Chi-restraints excluded: chain F residue 112 THR
Chi-restraints excluded: chain G residue 112 THR
Chi-restraints excluded: chain H residue 31 GLN
Chi-restraints excluded: chain H residue 82 VAL
Chi-restraints excluded: chain I residue 8 THR
Chi-restraints excluded: chain I residue 78 THR
Chi-restraints excluded: chain I residue 85 ASP
Chi-restraints excluded: chain J residue 73 SER
Chi-restraints excluded: chain J residue 78 THR
Chi-restraints excluded: chain J residue 103 ASP
Chi-restraints excluded: chain K residue 29 GLN
Chi-restraints excluded: chain K residue 31 GLN
Chi-restraints excluded: chain K residue 52 THR
Chi-restraints excluded: chain K residue 73 SER
Chi-restraints excluded: chain K residue 149 ASN
Chi-restraints excluded: chain L residue 8 THR
Chi-restraints excluded: chain L residue 141 MET
Chi-restraints excluded: chain L residue 148 ASP
Chi-restraints excluded: chain M residue 7 PHE
Chi-restraints excluded: chain M residue 11 GLU
Chi-restraints excluded: chain M residue 22 LEU
Chi-restraints excluded: chain M residue 92 ILE
Chi-restraints excluded: chain M residue 112 THR
Chi-restraints excluded: chain N residue 22 LEU
Chi-restraints excluded: chain N residue 73 SER
Chi-restraints excluded: chain N residue 92 ILE
Chi-restraints excluded: chain N residue 129 ASP
Chi-restraints excluded: chain O residue 8 THR
Chi-restraints excluded: chain O residue 82 VAL
Chi-restraints excluded: chain O residue 141 MET
Chi-restraints excluded: chain P residue 7 PHE
Chi-restraints excluded: chain P residue 8 THR
Chi-restraints excluded: chain P residue 74 THR
Chi-restraints excluded: chain Q residue 41 SER
Chi-restraints excluded: chain R residue 78 THR
Chi-restraints excluded: chain S residue 73 SER
Chi-restraints excluded: chain S residue 78 THR
Chi-restraints excluded: chain S residue 112 THR
Chi-restraints excluded: chain T residue 8 THR
Chi-restraints excluded: chain T residue 78 THR
Chi-restraints excluded: chain T residue 149 ASN
Chi-restraints excluded: chain U residue 8 THR
Chi-restraints excluded: chain U residue 73 SER
Chi-restraints excluded: chain U residue 78 THR
Chi-restraints excluded: chain U residue 141 MET
Chi-restraints excluded: chain V residue 7 PHE
Chi-restraints excluded: chain V residue 22 LEU
Chi-restraints excluded: chain V residue 97 GLU
Chi-restraints excluded: chain V residue 103 ASP
Chi-restraints excluded: chain V residue 112 THR
Chi-restraints excluded: chain W residue 64 SER
Chi-restraints excluded: chain W residue 73 SER
Chi-restraints excluded: chain W residue 82 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 322
random chunks:
chunk 250 optimal weight: 7.9990
chunk 241 optimal weight: 0.7980
chunk 155 optimal weight: 7.9990
chunk 106 optimal weight: 10.0000
chunk 156 optimal weight: 0.8980
chunk 103 optimal weight: 1.9990
chunk 23 optimal weight: 8.9990
chunk 6 optimal weight: 7.9990
chunk 174 optimal weight: 8.9990
chunk 319 optimal weight: 8.9990
chunk 60 optimal weight: 0.9990
overall best weight: 2.5386
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
B 47 ASN
B 109 GLN
** C 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 125 ASN
F 31 GLN
G 29 GLN
** G 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Q 87 ASN
Q 149 ASN
Total number of N/Q/H flips: 7
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2963 r_free = 0.2963 target = 0.092483 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.2832 r_free = 0.2832 target = 0.084000 restraints weight = 33612.784|
|-----------------------------------------------------------------------------|
r_work (start): 0.2833 rms_B_bonded: 1.16
r_work: 0.2760 rms_B_bonded: 1.61 restraints_weight: 0.5000
r_work: 0.2654 rms_B_bonded: 2.88 restraints_weight: 0.2500
r_work (final): 0.2654
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8683
moved from start: 0.2936
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.004 0.040 24311 Z= 0.276
Angle : 0.509 7.841 33143 Z= 0.274
Chirality : 0.049 0.161 4186
Planarity : 0.004 0.031 4209
Dihedral : 4.312 26.743 3427
Min Nonbonded Distance : 2.542
Molprobity Statistics.
All-atom Clashscore : 5.51
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 2.68 %
Favored : 97.32 %
Rotamer:
Outliers : 2.96 %
Allowed : 22.66 %
Favored : 74.37 %
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: 2.50 (0.15), residues: 3243
helix: 2.27 (0.17), residues: 1081
sheet: 0.71 (0.19), residues: 713
loop : 1.96 (0.16), residues: 1449
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.008 0.001 TRP F 132
PHE 0.008 0.001 PHE E 142
TYR 0.013 0.001 TYR H 33
ARG 0.007 0.001 ARG P 59
Origin is already at (0, 0, 0), no shifts will be applied
===============================================================================
Job complete
usr+sys time: 10461.38 seconds
wall clock time: 189 minutes 54.69 seconds (11394.69 seconds total)