Starting phenix.real_space_refine
on Mon Jan 20 13:53:11 2025 by dcliebschner
===============================================================================
Processing files:
-------------------------------------------------------------------------------
Found model, /net/cci-nas-00/data/ceres_data/8vg2_43198/01_2025/8vg2_43198.cif
Found real_map, /net/cci-nas-00/data/ceres_data/8vg2_43198/01_2025/8vg2_43198.map
Processing PHIL parameters:
-------------------------------------------------------------------------------
Adding command-line PHIL:
-------------------------
refinement.macro_cycles=10
scattering_table=electron
resolution=3.04
write_initial_geo_file=False
Final processed PHIL parameters:
-------------------------------------------------------------------------------
data_manager {
real_map_files = "/net/cci-nas-00/data/ceres_data/8vg2_43198/01_2025/8vg2_43198.map"
default_real_map = "/net/cci-nas-00/data/ceres_data/8vg2_43198/01_2025/8vg2_43198.map"
model {
file = "/net/cci-nas-00/data/ceres_data/8vg2_43198/01_2025/8vg2_43198.cif"
}
default_model = "/net/cci-nas-00/data/ceres_data/8vg2_43198/01_2025/8vg2_43198.cif"
}
resolution = 3.04
write_initial_geo_file = False
refinement {
macro_cycles = 10
}
qi {
qm_restraints {
package {
program = *test
}
}
}
Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.
Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
Set to: 0
Set model cs if undefined
Decide on map wrapping
Map wrapping is set to: False
Normalize map: mean=0, sd=1
Input map: mean= 0.000 sd= 0.001
Set stop_for_unknowns flag
Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
Set to: electron
Number of scattering types: 5
Type Number sf(0) Gaussians
P 392 5.49 5
S 21 5.16 5
C 8651 2.51 5
N 2930 2.21 5
O 3695 1.98 5
sf(0) = scattering factor at diffraction angle 0.
Process input model
Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s
Monomer Library directory:
"/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
Total number of atoms: 15689
Number of models: 1
Model: ""
Number of chains: 12
Chain: "A"
Number of atoms: 819
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 99, 819
Classifications: {'peptide': 99}
Link IDs: {'PTRANS': 4, 'TRANS': 94}
Chain: "B"
Number of atoms: 661
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 83, 661
Classifications: {'peptide': 83}
Link IDs: {'PTRANS': 1, 'TRANS': 81}
Chain: "C"
Number of atoms: 858
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 111, 858
Classifications: {'peptide': 111}
Link IDs: {'PTRANS': 5, 'TRANS': 105}
Chain: "D"
Number of atoms: 754
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 96, 754
Classifications: {'peptide': 96}
Link IDs: {'PTRANS': 2, 'TRANS': 93}
Chain: "E"
Number of atoms: 799
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 97, 799
Classifications: {'peptide': 97}
Link IDs: {'PTRANS': 4, 'TRANS': 92}
Chain: "F"
Number of atoms: 661
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 83, 661
Classifications: {'peptide': 83}
Link IDs: {'PTRANS': 1, 'TRANS': 81}
Chain: "G"
Number of atoms: 936
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 121, 936
Classifications: {'peptide': 121}
Link IDs: {'PTRANS': 5, 'TRANS': 115}
Chain: "H"
Number of atoms: 774
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 98, 774
Classifications: {'peptide': 98}
Link IDs: {'PTRANS': 2, 'TRANS': 95}
Chain: "I"
Number of atoms: 3998
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 196, 3998
Classifications: {'DNA': 196}
Link IDs: {'rna3p': 195}
Chain: "J"
Number of atoms: 4038
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 196, 4038
Classifications: {'DNA': 196}
Link IDs: {'rna3p': 195}
Chain: "O"
Number of atoms: 856
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 102, 856
Classifications: {'peptide': 102}
Link IDs: {'PTRANS': 7, 'TRANS': 94}
Chain: "U"
Number of atoms: 535
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 75, 535
Classifications: {'peptide': 75}
Link IDs: {'PTRANS': 2, 'TRANS': 72}
Time building chain proxies: 8.88, per 1000 atoms: 0.57
Number of scatterers: 15689
At special positions: 0
Unit cell: (86.592, 121.44, 195.36, 90, 90, 90)
Space group: P 1 (No. 1)
Number of sites at special positions: 0
Number of scattering types: 5
Type Number sf(0)
S 21 16.00
P 392 15.00
O 3695 8.00
N 2930 7.00
C 8651 6.00
sf(0) = scattering factor at diffraction angle 0.
Number of disulfides: simple=0, symmetry=0
Automatic linking
Parameters for automatic linking
Linking & cutoffs
Metal : Auto - 3.00
Amino acid : True - 1.90
Carbohydrate : True - 1.99
Ligands : True - 1.99
Small molecules : False - 1.98
Amino acid - RNA/DNA : False
Number of custom bonds: simple=0, symmetry=0
Time building additional restraints: 3.61
Conformation dependent library (CDL) restraints added in 1.1 seconds
1890 Ramachandran restraints generated.
945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2.
Adding C-beta torsion restraints...
Number of C-beta restraints generated: 1800
Finding SS restraints...
Secondary structure from input PDB file:
44 helices and 12 sheets defined
68.0% alpha, 3.7% beta
187 base pairs and 339 stacking pairs defined.
Time for finding SS restraints: 7.93
Creating SS restraints...
Processing helix chain 'A' and resid 44 through 57
Processing helix chain 'A' and resid 63 through 79
removed outlier: 3.957A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A)
removed outlier: 4.206A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A)
Processing helix chain 'A' and resid 85 through 114
Processing helix chain 'A' and resid 120 through 132
removed outlier: 3.564A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A)
Processing helix chain 'B' and resid 24 through 29
Processing helix chain 'B' and resid 30 through 41
Processing helix chain 'B' and resid 49 through 76
removed outlier: 3.632A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A)
Processing helix chain 'B' and resid 82 through 93
removed outlier: 3.522A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A)
Processing helix chain 'C' and resid 16 through 22
Processing helix chain 'C' and resid 26 through 37
Processing helix chain 'C' and resid 45 through 73
removed outlier: 4.408A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A)
Processing helix chain 'C' and resid 79 through 90
Processing helix chain 'C' and resid 90 through 97
Processing helix chain 'D' and resid 37 through 49
Processing helix chain 'D' and resid 55 through 84
Processing helix chain 'D' and resid 90 through 102
Processing helix chain 'D' and resid 103 through 125
Processing helix chain 'E' and resid 44 through 56
Processing helix chain 'E' and resid 63 through 77
removed outlier: 3.895A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A)
Processing helix chain 'E' and resid 85 through 114
Processing helix chain 'E' and resid 120 through 132
Processing helix chain 'F' and resid 24 through 29
Processing helix chain 'F' and resid 30 through 41
Processing helix chain 'F' and resid 49 through 76
removed outlier: 3.682A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A)
Processing helix chain 'F' and resid 82 through 94
Processing helix chain 'G' and resid 16 through 22
Processing helix chain 'G' and resid 26 through 37
Processing helix chain 'G' and resid 46 through 73
Processing helix chain 'G' and resid 79 through 90
Processing helix chain 'G' and resid 90 through 97
Processing helix chain 'G' and resid 112 through 116
Processing helix chain 'H' and resid 37 through 49
Processing helix chain 'H' and resid 55 through 84
Processing helix chain 'H' and resid 90 through 102
Processing helix chain 'H' and resid 103 through 125
Processing helix chain 'O' and resid 174 through 186
removed outlier: 3.825A pdb=" N ALA O 186 " --> pdb=" O ALA O 182 " (cutoff:3.500A)
Processing helix chain 'O' and resid 192 through 204
Processing helix chain 'O' and resid 205 through 209
removed outlier: 3.801A pdb=" N GLN O 209 " --> pdb=" O TYR O 206 " (cutoff:3.500A)
Processing helix chain 'O' and resid 210 through 225
Processing helix chain 'O' and resid 248 through 251
Processing helix chain 'U' and resid 38 through 51
removed outlier: 3.606A pdb=" N LEU U 42 " --> pdb=" O PRO U 38 " (cutoff:3.500A)
removed outlier: 3.970A pdb=" N SER U 50 " --> pdb=" O ALA U 46 " (cutoff:3.500A)
removed outlier: 3.647A pdb=" N LYS U 51 " --> pdb=" O VAL U 47 " (cutoff:3.500A)
Processing helix chain 'U' and resid 58 through 69
Processing helix chain 'U' and resid 71 through 74
Processing helix chain 'U' and resid 75 through 89
Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
removed outlier: 7.012A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A)
No H-bonds generated for sheet with id=AA1
Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119
Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98
removed outlier: 6.578A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A)
No H-bonds generated for sheet with id=AA3
Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43
removed outlier: 7.259A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A)
No H-bonds generated for sheet with id=AA4
Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78
Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102
Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84
removed outlier: 6.838A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A)
No H-bonds generated for sheet with id=AA7
Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119
Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43
removed outlier: 6.940A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A)
No H-bonds generated for sheet with id=AA9
Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78
Processing sheet with id=AB2, first strand: chain 'O' and resid 228 through 231
removed outlier: 3.538A pdb=" N TYR O 243 " --> pdb=" O VAL O 231 " (cutoff:3.500A)
Processing sheet with id=AB3, first strand: chain 'U' and resid 56 through 57
486 hydrogen bonds defined for protein.
1422 hydrogen bond angles defined for protein.
Restraints generated for nucleic acids:
471 hydrogen bonds
942 hydrogen bond angles
0 basepair planarities
187 basepair parallelities
339 stacking parallelities
Total time for adding SS restraints: 6.40
Time building geometry restraints manager: 4.27 seconds
NOTE: a complete listing of the restraints can be obtained by requesting
output of .geo file.
Histogram of bond lengths:
1.22 - 1.33: 3115
1.33 - 1.45: 5281
1.45 - 1.57: 7566
1.57 - 1.69: 782
1.69 - 1.81: 35
Bond restraints: 16779
Sorted by residual:
bond pdb=" N LYS H 28 "
pdb=" CA LYS H 28 "
ideal model delta sigma weight residual
1.458 1.492 -0.034 1.90e-02 2.77e+03 3.18e+00
bond pdb=" N LYS B 20 "
pdb=" CA LYS B 20 "
ideal model delta sigma weight residual
1.458 1.491 -0.033 1.90e-02 2.77e+03 3.09e+00
bond pdb=" N LYS A 36 "
pdb=" CA LYS A 36 "
ideal model delta sigma weight residual
1.458 1.491 -0.033 1.90e-02 2.77e+03 3.09e+00
bond pdb=" N LYS G 9 "
pdb=" CA LYS G 9 "
ideal model delta sigma weight residual
1.458 1.491 -0.033 1.90e-02 2.77e+03 2.98e+00
bond pdb=" N LYS D 30 "
pdb=" CA LYS D 30 "
ideal model delta sigma weight residual
1.458 1.491 -0.033 1.90e-02 2.77e+03 2.97e+00
... (remaining 16774 not shown)
Histogram of bond angle deviations from ideal:
0.00 - 1.16: 22684
1.16 - 2.31: 1300
2.31 - 3.47: 303
3.47 - 4.63: 29
4.63 - 5.78: 9
Bond angle restraints: 24325
Sorted by residual:
angle pdb=" CA TRP O 214 "
pdb=" CB TRP O 214 "
pdb=" CG TRP O 214 "
ideal model delta sigma weight residual
113.60 119.13 -5.53 1.90e+00 2.77e-01 8.48e+00
angle pdb=" C2' DT I 88 "
pdb=" C1' DT I 88 "
pdb=" N1 DT I 88 "
ideal model delta sigma weight residual
113.50 117.71 -4.21 1.50e+00 4.44e-01 7.88e+00
angle pdb=" C2' DT J 131 "
pdb=" C1' DT J 131 "
pdb=" N1 DT J 131 "
ideal model delta sigma weight residual
113.50 117.59 -4.09 1.50e+00 4.44e-01 7.42e+00
angle pdb=" C2' DC I 151 "
pdb=" C1' DC I 151 "
pdb=" N1 DC I 151 "
ideal model delta sigma weight residual
113.50 117.30 -3.80 1.50e+00 4.44e-01 6.42e+00
angle pdb=" C2' DC J 50 "
pdb=" C1' DC J 50 "
pdb=" N1 DC J 50 "
ideal model delta sigma weight residual
113.50 117.09 -3.59 1.50e+00 4.44e-01 5.74e+00
... (remaining 24320 not shown)
Histogram of dihedral angle deviations from ideal:
0.00 - 17.10: 6209
17.10 - 34.21: 1286
34.21 - 51.31: 1119
51.31 - 68.41: 490
68.41 - 85.51: 21
Dihedral angle restraints: 9125
sinusoidal: 6332
harmonic: 2793
Sorted by residual:
dihedral pdb=" CA PHE E 84 "
pdb=" C PHE E 84 "
pdb=" N GLN E 85 "
pdb=" CA GLN E 85 "
ideal model delta harmonic sigma weight residual
180.00 164.39 15.61 0 5.00e+00 4.00e-02 9.75e+00
dihedral pdb=" CA ARG E 128 "
pdb=" CB ARG E 128 "
pdb=" CG ARG E 128 "
pdb=" CD ARG E 128 "
ideal model delta sinusoidal sigma weight residual
-180.00 -120.60 -59.40 3 1.50e+01 4.44e-03 9.48e+00
dihedral pdb=" N LYS D 30 "
pdb=" CA LYS D 30 "
pdb=" CB LYS D 30 "
pdb=" CG LYS D 30 "
ideal model delta sinusoidal sigma weight residual
-60.00 -117.86 57.86 3 1.50e+01 4.44e-03 9.45e+00
... (remaining 9122 not shown)
Histogram of chiral volume deviations from ideal:
0.000 - 0.029: 1764
0.029 - 0.058: 581
0.058 - 0.087: 330
0.087 - 0.116: 61
0.116 - 0.146: 8
Chirality restraints: 2744
Sorted by residual:
chirality pdb=" CA ILE B 29 "
pdb=" N ILE B 29 "
pdb=" C ILE B 29 "
pdb=" CB ILE B 29 "
both_signs ideal model delta sigma weight residual
False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.30e-01
chirality pdb=" CA ILE C 111 "
pdb=" N ILE C 111 "
pdb=" C ILE C 111 "
pdb=" CB ILE C 111 "
both_signs ideal model delta sigma weight residual
False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.41e-01
chirality pdb=" CA ILE F 29 "
pdb=" N ILE F 29 "
pdb=" C ILE F 29 "
pdb=" CB ILE F 29 "
both_signs ideal model delta sigma weight residual
False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.36e-01
... (remaining 2741 not shown)
Planarity restraints: 1712
Sorted by residual:
delta sigma weight rms_deltas residual
plane pdb=" C1' DT I 88 " 0.024 2.00e-02 2.50e+03 1.20e-02 3.62e+00
pdb=" N1 DT I 88 " -0.027 2.00e-02 2.50e+03
pdb=" C2 DT I 88 " -0.004 2.00e-02 2.50e+03
pdb=" O2 DT I 88 " -0.003 2.00e-02 2.50e+03
pdb=" N3 DT I 88 " 0.001 2.00e-02 2.50e+03
pdb=" C4 DT I 88 " 0.005 2.00e-02 2.50e+03
pdb=" O4 DT I 88 " 0.009 2.00e-02 2.50e+03
pdb=" C5 DT I 88 " -0.000 2.00e-02 2.50e+03
pdb=" C7 DT I 88 " -0.004 2.00e-02 2.50e+03
pdb=" C6 DT I 88 " 0.000 2.00e-02 2.50e+03
delta sigma weight rms_deltas residual
plane pdb=" C1' DT I 86 " 0.023 2.00e-02 2.50e+03 1.17e-02 3.41e+00
pdb=" N1 DT I 86 " -0.027 2.00e-02 2.50e+03
pdb=" C2 DT I 86 " -0.003 2.00e-02 2.50e+03
pdb=" O2 DT I 86 " -0.003 2.00e-02 2.50e+03
pdb=" N3 DT I 86 " 0.002 2.00e-02 2.50e+03
pdb=" C4 DT I 86 " 0.003 2.00e-02 2.50e+03
pdb=" O4 DT I 86 " 0.008 2.00e-02 2.50e+03
pdb=" C5 DT I 86 " 0.000 2.00e-02 2.50e+03
pdb=" C7 DT I 86 " -0.003 2.00e-02 2.50e+03
pdb=" C6 DT I 86 " -0.002 2.00e-02 2.50e+03
delta sigma weight rms_deltas residual
plane pdb=" C LYS O 237 " 0.030 5.00e-02 4.00e+02 4.49e-02 3.23e+00
pdb=" N PRO O 238 " -0.078 5.00e-02 4.00e+02
pdb=" CA PRO O 238 " 0.023 5.00e-02 4.00e+02
pdb=" CD PRO O 238 " 0.025 5.00e-02 4.00e+02
... (remaining 1709 not shown)
Histogram of nonbonded interaction distances:
2.22 - 2.76: 1841
2.76 - 3.29: 13546
3.29 - 3.83: 30647
3.83 - 4.36: 36360
4.36 - 4.90: 51294
Nonbonded interactions: 133688
Sorted by model distance:
nonbonded pdb=" OG1 THR F 73 "
pdb=" OD2 ASP F 85 "
model vdw
2.219 3.040
nonbonded pdb=" NZ LYS B 91 "
pdb=" OE2 GLU H 71 "
model vdw
2.235 3.120
nonbonded pdb=" OD2 ASP B 68 "
pdb=" NE2 GLN B 93 "
model vdw
2.313 3.120
nonbonded pdb=" OG1 THR H 90 "
pdb=" OE1 GLU H 93 "
model vdw
2.326 3.040
nonbonded pdb=" N GLU E 59 "
pdb=" OE1 GLU E 59 "
model vdw
2.340 3.120
... (remaining 133683 not shown)
NOTE: a complete listing of the restraints can be obtained by requesting
output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
reference = (chain 'A' and resid 37 through 133)
selection = chain 'E'
}
ncs_group {
reference = chain 'B'
selection = chain 'F'
}
ncs_group {
reference = chain 'C'
selection = (chain 'G' and resid 9 through 119)
}
ncs_group {
reference = chain 'D'
selection = (chain 'H' and resid 30 through 125)
}
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: 1.530
Set stop_for_unknowns flag: 0.000
Assert model is a single copy model: 0.000
Assert all atoms have isotropic ADPs: 0.010
Construct map_model_manager: 0.010
Extract box with map and model: 0.540
Check model and map are aligned: 0.120
Set scattering table: 0.150
Process input model: 40.220
Find NCS groups from input model: 0.340
Set up NCS constraints: 0.080
Set refine NCS operators: 0.000
Adjust number of macro_cycles: 0.000
Reset NCS operators: 0.000
Extract rigid body selections: 0.000
Check and reset occupancies: 0.000
Load rotamer database and sin/cos tables:2.850
Set ADP refinement strategy: 0.000
Make a string to write initial .geo file:0.000
Internal consistency checks: 0.000
Total: 45.850
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8670
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 : 0.004 0.041 16779 Z= 0.238
Angle : 0.632 5.783 24325 Z= 0.397
Chirality : 0.037 0.146 2744
Planarity : 0.004 0.045 1712
Dihedral : 25.723 85.514 7325
Min Nonbonded Distance : 2.219
Molprobity Statistics.
All-atom Clashscore : 0.78
Ramachandran Plot:
Outliers : 0.11 %
Allowed : 1.69 %
Favored : 98.20 %
Rotamer:
Outliers : 0.25 %
Allowed : 1.86 %
Favored : 97.89 %
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: 2.46 (0.27), residues: 945
helix: 2.67 (0.21), residues: 616
sheet: -0.74 (1.27), residues: 20
loop : -0.40 (0.33), residues: 309
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.017 0.002 TRP O 214
HIS 0.003 0.001 HIS O 220
PHE 0.007 0.001 PHE A 67
TYR 0.008 0.001 TYR B 51
ARG 0.004 0.000 ARG O 208
*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
1890 Ramachandran restraints generated.
945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
1890 Ramachandran restraints generated.
945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
192 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 2
poor density : 190
time to evaluate : 1.093
Fit side-chains
revert: symmetry clash
revert: symmetry clash
REVERT: A 73 GLU cc_start: 0.8675 (tt0) cc_final: 0.8297 (tt0)
REVERT: A 123 ASP cc_start: 0.9411 (m-30) cc_final: 0.9151 (m-30)
REVERT: D 68 ASP cc_start: 0.9004 (t0) cc_final: 0.8538 (t0)
REVERT: D 72 ARG cc_start: 0.9138 (mtt180) cc_final: 0.8812 (mtt180)
REVERT: F 59 LYS cc_start: 0.9227 (tttp) cc_final: 0.9014 (tttp)
REVERT: G 101 THR cc_start: 0.9178 (t) cc_final: 0.8934 (t)
REVERT: H 68 ASP cc_start: 0.9269 (t0) cc_final: 0.8868 (t0)
REVERT: H 101 LEU cc_start: 0.9300 (mm) cc_final: 0.9006 (mm)
REVERT: H 113 GLU cc_start: 0.8936 (mm-30) cc_final: 0.8593 (mm-30)
REVERT: O 201 MET cc_start: 0.6965 (ttt) cc_final: 0.6383 (tmm)
REVERT: O 214 TRP cc_start: 0.7558 (p-90) cc_final: 0.7253 (p-90)
outliers start: 2
outliers final: 0
residues processed: 191
average time/residue: 0.4313
time to fit residues: 107.9575
Evaluate side-chains
167 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 0
poor density : 167
time to evaluate : 1.134
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 130
random chunks:
chunk 109 optimal weight: 5.9990
chunk 98 optimal weight: 5.9990
chunk 54 optimal weight: 6.9990
chunk 33 optimal weight: 3.9990
chunk 66 optimal weight: 10.0000
chunk 52 optimal weight: 0.9980
chunk 101 optimal weight: 3.9990
chunk 39 optimal weight: 0.7980
chunk 61 optimal weight: 0.9980
chunk 75 optimal weight: 10.0000
chunk 118 optimal weight: 30.0000
overall best weight: 2.1584
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 125 GLN
B 27 GLN
Total number of N/Q/H flips: 2
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.134984 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3084 r_free = 0.3084 target = 0.080608 restraints weight = 27167.749|
|-----------------------------------------------------------------------------|
r_work (start): 0.3000 rms_B_bonded: 1.43
r_work: 0.2829 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.2704 rms_B_bonded: 3.99 restraints_weight: 0.2500
r_work (final): 0.2704
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8830
moved from start: 0.1059
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.006 0.054 16779 Z= 0.324
Angle : 0.572 6.656 24325 Z= 0.344
Chirality : 0.036 0.131 2744
Planarity : 0.004 0.053 1712
Dihedral : 29.831 81.001 5388
Min Nonbonded Distance : 2.555
Molprobity Statistics.
All-atom Clashscore : 1.95
Ramachandran Plot:
Outliers : 0.11 %
Allowed : 2.33 %
Favored : 97.57 %
Rotamer:
Outliers : 0.87 %
Allowed : 4.46 %
Favored : 94.67 %
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: 2.54 (0.27), residues: 945
helix: 2.71 (0.21), residues: 625
sheet: -0.72 (1.21), residues: 20
loop : -0.41 (0.34), residues: 300
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.021 0.002 TRP O 214
HIS 0.003 0.001 HIS D 49
PHE 0.010 0.001 PHE A 67
TYR 0.009 0.001 TYR B 51
ARG 0.005 0.000 ARG D 86
*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
1890 Ramachandran restraints generated.
945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
1890 Ramachandran restraints generated.
945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
174 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 7
poor density : 167
time to evaluate : 1.201
Fit side-chains
revert: symmetry clash
revert: symmetry clash
REVERT: A 123 ASP cc_start: 0.9253 (m-30) cc_final: 0.9032 (m-30)
REVERT: B 93 GLN cc_start: 0.8882 (mm-40) cc_final: 0.8645 (mm110)
REVERT: C 99 ARG cc_start: 0.8771 (mmm160) cc_final: 0.8523 (mtp85)
REVERT: E 73 GLU cc_start: 0.8983 (tt0) cc_final: 0.8720 (tt0)
REVERT: F 35 ARG cc_start: 0.8815 (ttm-80) cc_final: 0.8521 (ttp80)
REVERT: G 92 GLU cc_start: 0.8968 (mm-30) cc_final: 0.8753 (mm-30)
REVERT: H 68 ASP cc_start: 0.9162 (t0) cc_final: 0.8808 (t0)
REVERT: H 101 LEU cc_start: 0.9313 (mm) cc_final: 0.8931 (mm)
REVERT: H 113 GLU cc_start: 0.9022 (mm-30) cc_final: 0.8615 (mm-30)
REVERT: O 201 MET cc_start: 0.6837 (ttt) cc_final: 0.6381 (tmm)
REVERT: O 214 TRP cc_start: 0.7274 (p-90) cc_final: 0.6912 (p-90)
outliers start: 7
outliers final: 5
residues processed: 170
average time/residue: 0.4132
time to fit residues: 93.8181
Evaluate side-chains
166 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 5
poor density : 161
time to evaluate : 1.071
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue 16 THR
Chi-restraints excluded: chain E residue 112 ILE
Chi-restraints excluded: chain F residue 30 THR
Chi-restraints excluded: chain G residue 101 THR
Chi-restraints excluded: chain H residue 71 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 130
random chunks:
chunk 49 optimal weight: 0.7980
chunk 113 optimal weight: 10.0000
chunk 7 optimal weight: 0.8980
chunk 23 optimal weight: 5.9990
chunk 87 optimal weight: 3.9990
chunk 29 optimal weight: 0.8980
chunk 110 optimal weight: 4.9990
chunk 18 optimal weight: 1.9990
chunk 43 optimal weight: 1.9990
chunk 99 optimal weight: 4.9990
chunk 72 optimal weight: 0.9990
overall best weight: 1.1184
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 125 GLN
** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 47 GLN
Total number of N/Q/H flips: 2
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3900 r_free = 0.3900 target = 0.136074 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3106 r_free = 0.3106 target = 0.081838 restraints weight = 27081.746|
|-----------------------------------------------------------------------------|
r_work (start): 0.3017 rms_B_bonded: 1.41
r_work: 0.2843 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.2712 rms_B_bonded: 4.05 restraints_weight: 0.2500
r_work (final): 0.2712
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8823
moved from start: 0.1128
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.004 0.040 16779 Z= 0.216
Angle : 0.547 8.144 24325 Z= 0.331
Chirality : 0.033 0.130 2744
Planarity : 0.004 0.057 1712
Dihedral : 29.794 81.174 5388
Min Nonbonded Distance : 2.545
Molprobity Statistics.
All-atom Clashscore : 2.52
Ramachandran Plot:
Outliers : 0.11 %
Allowed : 1.59 %
Favored : 98.31 %
Rotamer:
Outliers : 0.74 %
Allowed : 6.32 %
Favored : 92.94 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 2.63 (0.27), residues: 945
helix: 2.76 (0.20), residues: 626
sheet: -0.82 (1.20), residues: 20
loop : -0.33 (0.34), residues: 299
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.020 0.002 TRP O 214
HIS 0.002 0.001 HIS F 75
PHE 0.008 0.001 PHE A 67
TYR 0.011 0.001 TYR B 51
ARG 0.005 0.000 ARG D 86
*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
1890 Ramachandran restraints generated.
945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
1890 Ramachandran restraints generated.
945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
168 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 6
poor density : 162
time to evaluate : 1.166
Fit side-chains
revert: symmetry clash
revert: symmetry clash
REVERT: A 123 ASP cc_start: 0.9217 (m-30) cc_final: 0.9001 (m-30)
REVERT: F 35 ARG cc_start: 0.8803 (ttm-80) cc_final: 0.8504 (ttp80)
REVERT: H 68 ASP cc_start: 0.9161 (t0) cc_final: 0.8778 (t0)
REVERT: H 101 LEU cc_start: 0.9309 (mm) cc_final: 0.8882 (mm)
REVERT: H 113 GLU cc_start: 0.8982 (mm-30) cc_final: 0.8586 (mm-30)
REVERT: O 201 MET cc_start: 0.6823 (ttt) cc_final: 0.6387 (tmm)
REVERT: O 214 TRP cc_start: 0.7235 (p-90) cc_final: 0.6868 (p-90)
outliers start: 6
outliers final: 5
residues processed: 164
average time/residue: 0.3967
time to fit residues: 87.1551
Evaluate side-chains
164 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 5
poor density : 159
time to evaluate : 1.222
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue 16 THR
Chi-restraints excluded: chain F residue 31 LYS
Chi-restraints excluded: chain G residue 76 THR
Chi-restraints excluded: chain G residue 101 THR
Chi-restraints excluded: chain H residue 71 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 130
random chunks:
chunk 50 optimal weight: 1.9990
chunk 115 optimal weight: 0.9990
chunk 81 optimal weight: 4.9990
chunk 120 optimal weight: 2.9990
chunk 110 optimal weight: 4.9990
chunk 126 optimal weight: 5.9990
chunk 99 optimal weight: 4.9990
chunk 0 optimal weight: 3.9990
chunk 60 optimal weight: 5.9990
chunk 57 optimal weight: 3.9990
chunk 105 optimal weight: 3.9990
overall best weight: 2.7990
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 125 GLN
** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 73 ASN
Total number of N/Q/H flips: 2
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.133755 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3057 r_free = 0.3057 target = 0.079106 restraints weight = 26999.023|
|-----------------------------------------------------------------------------|
r_work (start): 0.2968 rms_B_bonded: 1.47
r_work: 0.2796 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.2669 rms_B_bonded: 4.05 restraints_weight: 0.2500
r_work (final): 0.2669
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8851
moved from start: 0.1327
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.007 0.054 16779 Z= 0.399
Angle : 0.588 6.120 24325 Z= 0.351
Chirality : 0.038 0.130 2744
Planarity : 0.004 0.059 1712
Dihedral : 30.097 80.833 5388
Min Nonbonded Distance : 2.404
Molprobity Statistics.
All-atom Clashscore : 2.24
Ramachandran Plot:
Outliers : 0.11 %
Allowed : 2.65 %
Favored : 97.25 %
Rotamer:
Outliers : 1.36 %
Allowed : 7.31 %
Favored : 91.33 %
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 (0.27), residues: 945
helix: 2.66 (0.20), residues: 625
sheet: -0.54 (1.21), residues: 20
loop : -0.39 (0.34), residues: 300
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.020 0.002 TRP O 214
HIS 0.003 0.001 HIS D 49
PHE 0.010 0.001 PHE A 67
TYR 0.010 0.002 TYR D 37
ARG 0.005 0.000 ARG D 86
*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
1890 Ramachandran restraints generated.
945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
1890 Ramachandran restraints generated.
945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
181 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 11
poor density : 170
time to evaluate : 1.225
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: A 123 ASP cc_start: 0.9273 (m-30) cc_final: 0.9062 (m-30)
REVERT: E 131 ARG cc_start: 0.9423 (OUTLIER) cc_final: 0.8769 (mtp180)
REVERT: F 35 ARG cc_start: 0.8826 (ttm-80) cc_final: 0.8511 (ttp80)
REVERT: G 92 GLU cc_start: 0.9061 (mm-30) cc_final: 0.8707 (mm-30)
REVERT: H 68 ASP cc_start: 0.9261 (t0) cc_final: 0.8837 (t0)
REVERT: H 101 LEU cc_start: 0.9341 (mm) cc_final: 0.8874 (mm)
REVERT: H 113 GLU cc_start: 0.9039 (mm-30) cc_final: 0.8644 (mm-30)
REVERT: O 201 MET cc_start: 0.6805 (ttt) cc_final: 0.6348 (tmm)
REVERT: O 214 TRP cc_start: 0.7207 (p-90) cc_final: 0.6859 (p-90)
outliers start: 11
outliers final: 8
residues processed: 176
average time/residue: 0.3932
time to fit residues: 92.1170
Evaluate side-chains
177 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 9
poor density : 168
time to evaluate : 1.067
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue 16 THR
Chi-restraints excluded: chain E residue 112 ILE
Chi-restraints excluded: chain E residue 131 ARG
Chi-restraints excluded: chain F residue 30 THR
Chi-restraints excluded: chain F residue 31 LYS
Chi-restraints excluded: chain G residue 76 THR
Chi-restraints excluded: chain G residue 101 THR
Chi-restraints excluded: chain H residue 71 GLU
Chi-restraints excluded: chain O residue 261 ARG
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 130
random chunks:
chunk 83 optimal weight: 2.9990
chunk 34 optimal weight: 0.7980
chunk 112 optimal weight: 10.0000
chunk 37 optimal weight: 0.9990
chunk 8 optimal weight: 0.8980
chunk 129 optimal weight: 20.0000
chunk 76 optimal weight: 10.0000
chunk 82 optimal weight: 2.9990
chunk 13 optimal weight: 0.9990
chunk 58 optimal weight: 0.7980
chunk 23 optimal weight: 2.9990
overall best weight: 0.8984
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 125 GLN
** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 73 ASN
Total number of N/Q/H flips: 2
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.135815 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3116 r_free = 0.3116 target = 0.082153 restraints weight = 27199.051|
|-----------------------------------------------------------------------------|
r_work (start): 0.3021 rms_B_bonded: 1.40
r_work: 0.2854 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.2728 rms_B_bonded: 4.00 restraints_weight: 0.2500
r_work (final): 0.2728
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8821
moved from start: 0.1325
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.033 16779 Z= 0.186
Angle : 0.550 9.598 24325 Z= 0.333
Chirality : 0.034 0.135 2744
Planarity : 0.004 0.059 1712
Dihedral : 30.098 81.659 5388
Min Nonbonded Distance : 2.446
Molprobity Statistics.
All-atom Clashscore : 2.98
Ramachandran Plot:
Outliers : 0.11 %
Allowed : 2.01 %
Favored : 97.88 %
Rotamer:
Outliers : 0.74 %
Allowed : 8.80 %
Favored : 90.46 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 2.56 (0.27), residues: 945
helix: 2.70 (0.20), residues: 625
sheet: -0.62 (1.20), residues: 20
loop : -0.35 (0.34), residues: 300
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.019 0.002 TRP O 214
HIS 0.002 0.000 HIS F 75
PHE 0.008 0.001 PHE A 67
TYR 0.011 0.001 TYR B 51
ARG 0.009 0.000 ARG D 86
*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
1890 Ramachandran restraints generated.
945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
1890 Ramachandran restraints generated.
945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
172 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 6
poor density : 166
time to evaluate : 1.125
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: A 123 ASP cc_start: 0.9223 (m-30) cc_final: 0.9014 (m-30)
REVERT: F 35 ARG cc_start: 0.8740 (ttm-80) cc_final: 0.8453 (ttp80)
REVERT: G 101 THR cc_start: 0.9277 (OUTLIER) cc_final: 0.9028 (t)
REVERT: H 68 ASP cc_start: 0.9193 (t0) cc_final: 0.8772 (t0)
REVERT: H 101 LEU cc_start: 0.9331 (mm) cc_final: 0.8907 (mm)
REVERT: H 113 GLU cc_start: 0.8944 (mm-30) cc_final: 0.8591 (mm-30)
REVERT: O 201 MET cc_start: 0.6868 (ttt) cc_final: 0.6380 (tmm)
REVERT: O 214 TRP cc_start: 0.7265 (p-90) cc_final: 0.6883 (p-90)
outliers start: 6
outliers final: 5
residues processed: 169
average time/residue: 0.3930
time to fit residues: 88.5209
Evaluate side-chains
172 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 6
poor density : 166
time to evaluate : 1.083
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue 16 THR
Chi-restraints excluded: chain E residue 112 ILE
Chi-restraints excluded: chain F residue 31 LYS
Chi-restraints excluded: chain G residue 101 THR
Chi-restraints excluded: chain H residue 71 GLU
Chi-restraints excluded: chain O residue 261 ARG
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 130
random chunks:
chunk 109 optimal weight: 6.9990
chunk 53 optimal weight: 3.9990
chunk 108 optimal weight: 3.9990
chunk 72 optimal weight: 2.9990
chunk 96 optimal weight: 10.0000
chunk 64 optimal weight: 0.8980
chunk 107 optimal weight: 3.9990
chunk 12 optimal weight: 0.7980
chunk 11 optimal weight: 3.9990
chunk 87 optimal weight: 4.9990
chunk 75 optimal weight: 10.0000
overall best weight: 2.5386
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 125 GLN
** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 73 ASN
Total number of N/Q/H flips: 2
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.134039 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3065 r_free = 0.3065 target = 0.079256 restraints weight = 27372.942|
|-----------------------------------------------------------------------------|
r_work (start): 0.2974 rms_B_bonded: 1.59
r_work: 0.2802 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.2675 rms_B_bonded: 4.12 restraints_weight: 0.2500
r_work (final): 0.2675
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8853
moved from start: 0.1403
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.006 0.049 16779 Z= 0.358
Angle : 0.572 6.085 24325 Z= 0.343
Chirality : 0.037 0.132 2744
Planarity : 0.004 0.059 1712
Dihedral : 30.102 80.458 5388
Min Nonbonded Distance : 2.382
Molprobity Statistics.
All-atom Clashscore : 2.63
Ramachandran Plot:
Outliers : 0.11 %
Allowed : 2.43 %
Favored : 97.46 %
Rotamer:
Outliers : 1.36 %
Allowed : 8.30 %
Favored : 90.33 %
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: 2.51 (0.27), residues: 945
helix: 2.68 (0.20), residues: 625
sheet: -0.66 (1.19), residues: 20
loop : -0.41 (0.34), residues: 300
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.020 0.002 TRP O 214
HIS 0.003 0.001 HIS D 49
PHE 0.009 0.001 PHE A 67
TYR 0.010 0.001 TYR G 57
ARG 0.007 0.000 ARG D 86
*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
1890 Ramachandran restraints generated.
945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
1890 Ramachandran restraints generated.
945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
181 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 11
poor density : 170
time to evaluate : 1.062
Fit side-chains
revert: symmetry clash
revert: symmetry clash
REVERT: A 123 ASP cc_start: 0.9283 (m-30) cc_final: 0.9076 (m-30)
REVERT: E 131 ARG cc_start: 0.9425 (OUTLIER) cc_final: 0.8799 (mtp180)
REVERT: F 35 ARG cc_start: 0.8792 (ttm-80) cc_final: 0.8476 (ttp80)
REVERT: G 92 GLU cc_start: 0.8997 (mm-30) cc_final: 0.8778 (mm-30)
REVERT: G 101 THR cc_start: 0.9333 (OUTLIER) cc_final: 0.9100 (t)
REVERT: H 68 ASP cc_start: 0.9262 (t0) cc_final: 0.8838 (t0)
REVERT: H 101 LEU cc_start: 0.9367 (OUTLIER) cc_final: 0.8914 (mm)
REVERT: H 113 GLU cc_start: 0.9028 (mm-30) cc_final: 0.8674 (mm-30)
REVERT: O 201 MET cc_start: 0.6769 (ttt) cc_final: 0.6325 (tmm)
REVERT: O 214 TRP cc_start: 0.7218 (p-90) cc_final: 0.6890 (p-90)
outliers start: 11
outliers final: 6
residues processed: 176
average time/residue: 0.3949
time to fit residues: 91.7148
Evaluate side-chains
175 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 9
poor density : 166
time to evaluate : 1.083
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue 16 THR
Chi-restraints excluded: chain D residue 71 GLU
Chi-restraints excluded: chain E residue 112 ILE
Chi-restraints excluded: chain E residue 131 ARG
Chi-restraints excluded: chain F residue 30 THR
Chi-restraints excluded: chain G residue 101 THR
Chi-restraints excluded: chain H residue 71 GLU
Chi-restraints excluded: chain H residue 101 LEU
Chi-restraints excluded: chain U residue 93 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 130
random chunks:
chunk 16 optimal weight: 0.9990
chunk 125 optimal weight: 10.0000
chunk 115 optimal weight: 10.0000
chunk 10 optimal weight: 0.7980
chunk 19 optimal weight: 1.9990
chunk 78 optimal weight: 4.9990
chunk 85 optimal weight: 2.9990
chunk 61 optimal weight: 0.9980
chunk 37 optimal weight: 0.3980
chunk 103 optimal weight: 2.9990
chunk 121 optimal weight: 0.0270
overall best weight: 0.6440
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 125 GLN
** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 73 ASN
Total number of N/Q/H flips: 2
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.136349 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.082089 restraints weight = 27252.820|
|-----------------------------------------------------------------------------|
r_work (start): 0.3036 rms_B_bonded: 1.41
r_work: 0.2868 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.2738 rms_B_bonded: 4.11 restraints_weight: 0.2500
r_work (final): 0.2738
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8814
moved from start: 0.1447
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.030 16779 Z= 0.172
Angle : 0.551 9.812 24325 Z= 0.331
Chirality : 0.033 0.167 2744
Planarity : 0.004 0.059 1712
Dihedral : 30.047 81.421 5388
Min Nonbonded Distance : 2.400
Molprobity Statistics.
All-atom Clashscore : 3.62
Ramachandran Plot:
Outliers : 0.11 %
Allowed : 2.22 %
Favored : 97.67 %
Rotamer:
Outliers : 1.12 %
Allowed : 9.05 %
Favored : 89.84 %
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: 2.66 (0.27), residues: 945
helix: 2.80 (0.20), residues: 625
sheet: -0.56 (1.21), residues: 20
loop : -0.39 (0.34), residues: 300
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.019 0.002 TRP O 214
HIS 0.002 0.000 HIS F 75
PHE 0.008 0.001 PHE A 67
TYR 0.012 0.001 TYR B 51
ARG 0.010 0.000 ARG D 86
*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
1890 Ramachandran restraints generated.
945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
1890 Ramachandran restraints generated.
945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
175 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 9
poor density : 166
time to evaluate : 1.115
Fit side-chains
revert: symmetry clash
revert: symmetry clash
REVERT: A 123 ASP cc_start: 0.9217 (m-30) cc_final: 0.9014 (m-30)
REVERT: E 131 ARG cc_start: 0.9391 (OUTLIER) cc_final: 0.8662 (mtt180)
REVERT: F 35 ARG cc_start: 0.8775 (ttm-80) cc_final: 0.8490 (ttp80)
REVERT: G 92 GLU cc_start: 0.8930 (mm-30) cc_final: 0.8705 (mm-30)
REVERT: G 101 THR cc_start: 0.9274 (OUTLIER) cc_final: 0.9054 (t)
REVERT: H 68 ASP cc_start: 0.9216 (t0) cc_final: 0.8843 (t0)
REVERT: H 101 LEU cc_start: 0.9332 (OUTLIER) cc_final: 0.8917 (mm)
REVERT: H 113 GLU cc_start: 0.8957 (mm-30) cc_final: 0.8599 (mm-30)
REVERT: O 201 MET cc_start: 0.6894 (ttt) cc_final: 0.6423 (tmm)
REVERT: O 214 TRP cc_start: 0.7282 (p-90) cc_final: 0.6930 (p-90)
outliers start: 9
outliers final: 5
residues processed: 170
average time/residue: 0.4177
time to fit residues: 93.8929
Evaluate side-chains
172 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 8
poor density : 164
time to evaluate : 1.219
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 58 THR
Chi-restraints excluded: chain C residue 16 THR
Chi-restraints excluded: chain E residue 131 ARG
Chi-restraints excluded: chain F residue 31 LYS
Chi-restraints excluded: chain G residue 101 THR
Chi-restraints excluded: chain H residue 71 GLU
Chi-restraints excluded: chain H residue 101 LEU
Chi-restraints excluded: chain U residue 93 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 130
random chunks:
chunk 55 optimal weight: 0.0040
chunk 72 optimal weight: 0.9990
chunk 27 optimal weight: 1.9990
chunk 28 optimal weight: 7.9990
chunk 105 optimal weight: 3.9990
chunk 16 optimal weight: 0.0570
chunk 43 optimal weight: 2.9990
chunk 104 optimal weight: 3.9990
chunk 5 optimal weight: 3.9990
chunk 56 optimal weight: 0.8980
chunk 107 optimal weight: 4.9990
overall best weight: 0.7914
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 93 GLN
F 93 GLN
Total number of N/Q/H flips: 2
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3928 r_free = 0.3928 target = 0.137651 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3157 r_free = 0.3157 target = 0.084155 restraints weight = 27224.938|
|-----------------------------------------------------------------------------|
r_work (start): 0.3071 rms_B_bonded: 1.41
r_work: 0.2908 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.2782 rms_B_bonded: 4.02 restraints_weight: 0.2500
r_work (final): 0.2782
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8784
moved from start: 0.1596
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.028 16779 Z= 0.182
Angle : 0.536 10.150 24325 Z= 0.322
Chirality : 0.032 0.132 2744
Planarity : 0.004 0.059 1712
Dihedral : 29.762 79.035 5388
Min Nonbonded Distance : 2.580
Molprobity Statistics.
All-atom Clashscore : 4.19
Ramachandran Plot:
Outliers : 0.11 %
Allowed : 2.54 %
Favored : 97.35 %
Rotamer:
Outliers : 1.12 %
Allowed : 9.05 %
Favored : 89.84 %
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: 2.85 (0.27), residues: 945
helix: 2.96 (0.20), residues: 626
sheet: -0.43 (1.23), residues: 20
loop : -0.36 (0.34), residues: 299
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.020 0.002 TRP O 214
HIS 0.003 0.001 HIS F 75
PHE 0.009 0.001 PHE A 67
TYR 0.010 0.001 TYR B 51
ARG 0.009 0.000 ARG D 86
*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
1890 Ramachandran restraints generated.
945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
1890 Ramachandran restraints generated.
945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
179 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 9
poor density : 170
time to evaluate : 1.184
Fit side-chains
revert: symmetry clash
revert: symmetry clash
REVERT: E 59 GLU cc_start: 0.9089 (pm20) cc_final: 0.8731 (pm20)
REVERT: F 35 ARG cc_start: 0.8724 (ttm-80) cc_final: 0.8459 (ttp80)
REVERT: F 93 GLN cc_start: 0.8817 (OUTLIER) cc_final: 0.7971 (mp-120)
REVERT: G 101 THR cc_start: 0.9255 (OUTLIER) cc_final: 0.9004 (t)
REVERT: H 68 ASP cc_start: 0.9136 (t0) cc_final: 0.8821 (t0)
REVERT: H 101 LEU cc_start: 0.9313 (OUTLIER) cc_final: 0.8925 (mm)
REVERT: H 113 GLU cc_start: 0.8944 (mm-30) cc_final: 0.8610 (mm-30)
REVERT: O 201 MET cc_start: 0.6942 (ttt) cc_final: 0.6444 (tmm)
REVERT: O 214 TRP cc_start: 0.7332 (p-90) cc_final: 0.6997 (p-90)
outliers start: 9
outliers final: 4
residues processed: 173
average time/residue: 0.3997
time to fit residues: 92.2871
Evaluate side-chains
170 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 7
poor density : 163
time to evaluate : 1.040
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue 16 THR
Chi-restraints excluded: chain D residue 71 GLU
Chi-restraints excluded: chain F residue 93 GLN
Chi-restraints excluded: chain G residue 101 THR
Chi-restraints excluded: chain H residue 71 GLU
Chi-restraints excluded: chain H residue 101 LEU
Chi-restraints excluded: chain U residue 93 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 130
random chunks:
chunk 114 optimal weight: 5.9990
chunk 0 optimal weight: 4.9990
chunk 56 optimal weight: 0.8980
chunk 93 optimal weight: 20.0000
chunk 88 optimal weight: 4.9990
chunk 46 optimal weight: 0.0770
chunk 109 optimal weight: 6.9990
chunk 102 optimal weight: 3.9990
chunk 7 optimal weight: 2.9990
chunk 119 optimal weight: 0.8980
chunk 6 optimal weight: 2.9990
overall best weight: 1.5742
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 125 GLN
B 93 GLN
C 73 ASN
Total number of N/Q/H flips: 3
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.134011 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3066 r_free = 0.3066 target = 0.080123 restraints weight = 27595.996|
|-----------------------------------------------------------------------------|
r_work (start): 0.2979 rms_B_bonded: 1.39
r_work: 0.2802 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.2676 rms_B_bonded: 3.99 restraints_weight: 0.2500
r_work (final): 0.2676
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8814
moved from start: 0.1589
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.005 0.036 16779 Z= 0.257
Angle : 0.556 10.393 24325 Z= 0.331
Chirality : 0.033 0.130 2744
Planarity : 0.004 0.060 1712
Dihedral : 29.914 79.648 5388
Min Nonbonded Distance : 2.313
Molprobity Statistics.
All-atom Clashscore : 3.20
Ramachandran Plot:
Outliers : 0.11 %
Allowed : 2.54 %
Favored : 97.35 %
Rotamer:
Outliers : 0.87 %
Allowed : 10.29 %
Favored : 88.85 %
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: 2.79 (0.27), residues: 945
helix: 2.91 (0.20), residues: 626
sheet: -0.32 (1.23), residues: 20
loop : -0.38 (0.34), residues: 299
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.020 0.002 TRP O 214
HIS 0.003 0.001 HIS F 75
PHE 0.008 0.001 PHE A 67
TYR 0.009 0.001 TYR G 57
ARG 0.009 0.000 ARG D 86
*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
1890 Ramachandran restraints generated.
945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
1890 Ramachandran restraints generated.
945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
172 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 7
poor density : 165
time to evaluate : 1.119
Fit side-chains
revert: symmetry clash
revert: symmetry clash
REVERT: A 123 ASP cc_start: 0.9186 (m-30) cc_final: 0.8967 (m-30)
REVERT: E 59 GLU cc_start: 0.9139 (pm20) cc_final: 0.8723 (pm20)
REVERT: E 131 ARG cc_start: 0.9356 (OUTLIER) cc_final: 0.8644 (mtp180)
REVERT: F 35 ARG cc_start: 0.8751 (ttm-80) cc_final: 0.8441 (ttp80)
REVERT: G 101 THR cc_start: 0.9298 (OUTLIER) cc_final: 0.9064 (t)
REVERT: H 68 ASP cc_start: 0.9213 (t0) cc_final: 0.8815 (t0)
REVERT: H 101 LEU cc_start: 0.9335 (OUTLIER) cc_final: 0.8942 (mm)
REVERT: H 113 GLU cc_start: 0.8989 (mm-30) cc_final: 0.8651 (mm-30)
REVERT: O 201 MET cc_start: 0.6916 (ttt) cc_final: 0.6411 (tmm)
REVERT: O 214 TRP cc_start: 0.7163 (p-90) cc_final: 0.6781 (p-90)
outliers start: 7
outliers final: 4
residues processed: 169
average time/residue: 0.4089
time to fit residues: 91.2753
Evaluate side-chains
172 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 7
poor density : 165
time to evaluate : 1.039
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue 16 THR
Chi-restraints excluded: chain E residue 131 ARG
Chi-restraints excluded: chain F residue 31 LYS
Chi-restraints excluded: chain G residue 101 THR
Chi-restraints excluded: chain H residue 71 GLU
Chi-restraints excluded: chain H residue 101 LEU
Chi-restraints excluded: chain U residue 93 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 130
random chunks:
chunk 48 optimal weight: 0.8980
chunk 96 optimal weight: 10.0000
chunk 78 optimal weight: 4.9990
chunk 42 optimal weight: 0.8980
chunk 29 optimal weight: 1.9990
chunk 81 optimal weight: 3.9990
chunk 70 optimal weight: 2.9990
chunk 59 optimal weight: 0.6980
chunk 45 optimal weight: 0.8980
chunk 1 optimal weight: 0.5980
chunk 104 optimal weight: 2.9990
overall best weight: 0.7980
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
B 93 GLN
Total number of N/Q/H flips: 1
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.134722 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3082 r_free = 0.3082 target = 0.080870 restraints weight = 27713.302|
|-----------------------------------------------------------------------------|
r_work (start): 0.2991 rms_B_bonded: 1.46
r_work: 0.2815 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.2688 rms_B_bonded: 4.05 restraints_weight: 0.2500
r_work (final): 0.2688
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8804
moved from start: 0.1608
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.004 0.040 16779 Z= 0.193
Angle : 0.556 10.751 24325 Z= 0.330
Chirality : 0.032 0.135 2744
Planarity : 0.004 0.059 1712
Dihedral : 29.923 79.954 5388
Min Nonbonded Distance : 2.515
Molprobity Statistics.
All-atom Clashscore : 3.51
Ramachandran Plot:
Outliers : 0.11 %
Allowed : 2.65 %
Favored : 97.25 %
Rotamer:
Outliers : 0.74 %
Allowed : 10.66 %
Favored : 88.60 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 2.83 (0.27), residues: 945
helix: 2.94 (0.20), residues: 626
sheet: -0.30 (1.23), residues: 20
loop : -0.37 (0.34), residues: 299
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.019 0.002 TRP O 214
HIS 0.003 0.001 HIS A 113
PHE 0.009 0.001 PHE A 67
TYR 0.009 0.001 TYR G 57
ARG 0.009 0.000 ARG D 86
********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
1890 Ramachandran restraints generated.
945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
1890 Ramachandran restraints generated.
945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
169 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 6
poor density : 163
time to evaluate : 1.300
Fit side-chains
revert: symmetry clash
revert: symmetry clash
REVERT: A 123 ASP cc_start: 0.9194 (m-30) cc_final: 0.8983 (m-30)
REVERT: E 59 GLU cc_start: 0.9141 (pm20) cc_final: 0.8707 (pm20)
REVERT: F 35 ARG cc_start: 0.8760 (ttm-80) cc_final: 0.8453 (ttp80)
REVERT: G 101 THR cc_start: 0.9295 (OUTLIER) cc_final: 0.9060 (t)
REVERT: H 68 ASP cc_start: 0.9207 (t0) cc_final: 0.8813 (t0)
REVERT: H 101 LEU cc_start: 0.9330 (OUTLIER) cc_final: 0.8935 (mm)
REVERT: H 113 GLU cc_start: 0.9008 (mm-30) cc_final: 0.8658 (mm-30)
REVERT: O 201 MET cc_start: 0.6841 (ttt) cc_final: 0.6383 (tmm)
REVERT: O 214 TRP cc_start: 0.7136 (p-90) cc_final: 0.6756 (p-90)
outliers start: 6
outliers final: 4
residues processed: 166
average time/residue: 0.4002
time to fit residues: 88.9441
Evaluate side-chains
169 residues out of total 807 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 6
poor density : 163
time to evaluate : 1.268
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue 16 THR
Chi-restraints excluded: chain F residue 31 LYS
Chi-restraints excluded: chain G residue 101 THR
Chi-restraints excluded: chain H residue 71 GLU
Chi-restraints excluded: chain H residue 101 LEU
Chi-restraints excluded: chain U residue 93 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 130
random chunks:
chunk 54 optimal weight: 0.0030
chunk 56 optimal weight: 3.9990
chunk 3 optimal weight: 0.0980
chunk 28 optimal weight: 8.9990
chunk 26 optimal weight: 5.9990
chunk 115 optimal weight: 5.9990
chunk 80 optimal weight: 3.9990
chunk 59 optimal weight: 0.8980
chunk 41 optimal weight: 0.9990
chunk 120 optimal weight: 6.9990
chunk 77 optimal weight: 6.9990
overall best weight: 1.1994
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 125 GLN
B 93 GLN
C 73 ASN
Total number of N/Q/H flips: 3
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.134493 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3077 r_free = 0.3077 target = 0.080481 restraints weight = 27702.924|
|-----------------------------------------------------------------------------|
r_work (start): 0.2988 rms_B_bonded: 1.47
r_work: 0.2816 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.2690 rms_B_bonded: 4.12 restraints_weight: 0.2500
r_work (final): 0.2690
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8816
moved from start: 0.1621
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.004 0.032 16779 Z= 0.224
Angle : 0.549 10.931 24325 Z= 0.327
Chirality : 0.032 0.130 2744
Planarity : 0.004 0.059 1712
Dihedral : 29.876 79.875 5388
Min Nonbonded Distance : 2.295
Molprobity Statistics.
All-atom Clashscore : 3.59
Ramachandran Plot:
Outliers : 0.11 %
Allowed : 2.65 %
Favored : 97.25 %
Rotamer:
Outliers : 0.87 %
Allowed : 10.41 %
Favored : 88.72 %
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: 2.84 (0.27), residues: 945
helix: 2.95 (0.20), residues: 626
sheet: -0.29 (1.23), residues: 20
loop : -0.37 (0.34), residues: 299
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.019 0.002 TRP O 214
HIS 0.003 0.001 HIS F 75
PHE 0.009 0.001 PHE A 67
TYR 0.009 0.001 TYR G 57
ARG 0.010 0.000 ARG D 86
Origin is already at (0, 0, 0), no shifts will be applied
===============================================================================
Job complete
usr+sys time: 11372.44 seconds
wall clock time: 201 minutes 11.87 seconds (12071.87 seconds total)