Starting phenix.real_space_refine
on Mon Aug 5 05:51:36 2024 by dcliebschner
===============================================================================
Processing files:
-------------------------------------------------------------------------------
Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8txv_41706/08_2024/8txv_41706.cif
Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8txv_41706/08_2024/8txv_41706.map
Processing PHIL parameters:
-------------------------------------------------------------------------------
Adding command-line PHIL:
-------------------------
refinement.macro_cycles=10
scattering_table=electron
resolution=3.8
write_initial_geo_file=False
Final processed PHIL parameters:
-------------------------------------------------------------------------------
data_manager {
real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8txv_41706/08_2024/8txv_41706.map"
default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8txv_41706/08_2024/8txv_41706.map"
model {
file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8txv_41706/08_2024/8txv_41706.cif"
}
default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8txv_41706/08_2024/8txv_41706.cif"
}
resolution = 3.8
write_initial_geo_file = False
refinement {
macro_cycles = 10
}
qi {
qm_restraints {
package {
program = *test
}
}
}
Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.
Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
Set to: 0
Set model cs if undefined
Decide on map wrapping
Map wrapping is set to: False
Normalize map: mean=0, sd=1
Input map: mean= 0.000 sd= 0.002
Set stop_for_unknowns flag
Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
Set to: electron
Number of scattering types: 5
Type Number sf(0) Gaussians
P 294 5.49 5
S 15 5.16 5
C 7144 2.51 5
N 2407 2.21 5
O 2976 1.98 5
sf(0) = scattering factor at diffraction angle 0.
Process input model
Symmetric amino acids flipped
Residue "A PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "A PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "A GLU 94": "OE1" <-> "OE2"
Residue "A GLU 97": "OE1" <-> "OE2"
Residue "B GLU 52": "OE1" <-> "OE2"
Residue "D ASP 68": "OD1" <-> "OD2"
Residue "D TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "E ASP 123": "OD1" <-> "OD2"
Residue "F GLU 52": "OE1" <-> "OE2"
Residue "F GLU 53": "OE1" <-> "OE2"
Residue "F GLU 74": "OE1" <-> "OE2"
Residue "C TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "C ASP 90": "OD1" <-> "OD2"
Residue "G ASP 72": "OD1" <-> "OD2"
Time to flip residues: 0.03s
Monomer Library directory:
"/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib"
Total number of atoms: 12836
Number of models: 1
Model: ""
Number of chains: 12
Chain: "A"
Number of atoms: 815
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 99, 815
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: "D"
Number of atoms: 740
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 94, 740
Classifications: {'peptide': 94}
Link IDs: {'PTRANS': 2, 'TRANS': 91}
Chain: "E"
Number of atoms: 815
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 99, 815
Classifications: {'peptide': 99}
Link IDs: {'PTRANS': 4, 'TRANS': 94}
Chain: "F"
Number of atoms: 653
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 82, 653
Classifications: {'peptide': 82}
Modifications used: {'COO': 1}
Link IDs: {'PTRANS': 1, 'TRANS': 80}
Chain: "H"
Number of atoms: 743
Number of conformers: 2
Conformer: "A"
Number of residues, atoms: 93, 731
Classifications: {'peptide': 93}
Link IDs: {'PTRANS': 2, 'TRANS': 90}
Conformer: "B"
Number of residues, atoms: 93, 731
Classifications: {'peptide': 93}
Link IDs: {'PTRANS': 2, 'TRANS': 90}
bond proxies already assigned to first conformer: 728
Chain: "I"
Number of atoms: 2996
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 147, 2996
Classifications: {'DNA': 147}
Link IDs: {'rna3p': 146}
Chain: "J"
Number of atoms: 3031
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 147, 3031
Classifications: {'DNA': 147}
Link IDs: {'rna3p': 146}
Chain: "K"
Number of atoms: 117
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 14, 117
Classifications: {'peptide': 14}
Link IDs: {'PTRANS': 1, 'TRANS': 12}
Chain: "M"
Number of atoms: 602
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 76, 602
Classifications: {'peptide': 76}
Modifications used: {'COO': 1}
Link IDs: {'PTRANS': 3, 'TRANS': 72}
Chain: "C"
Number of atoms: 827
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 108, 827
Classifications: {'peptide': 108}
Link IDs: {'PTRANS': 5, 'TRANS': 102}
Chain: "G"
Number of atoms: 836
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 109, 836
Classifications: {'peptide': 109}
Link IDs: {'PTRANS': 5, 'TRANS': 103}
Residues with excluded nonbonded symmetry interactions: 4
residue:
pdb=" N LEU M 73 " occ=0.45
... (6 atoms not shown)
pdb=" CD2 LEU M 73 " occ=0.45
residue:
pdb=" N ARG M 74 " occ=0.45
... (9 atoms not shown)
pdb=" NH2 ARG M 74 " occ=0.45
residue:
pdb=" N GLY M 75 " occ=0.25
... (2 atoms not shown)
pdb=" O GLY M 75 " occ=0.25
residue:
pdb=" N GLY M 76 " occ=0.25
... (3 atoms not shown)
pdb=" OXT GLY M 76 " occ=0.25
Time building chain proxies: 7.77, per 1000 atoms: 0.61
Number of scatterers: 12836
At special positions: 0
Unit cell: (94.288, 124.832, 120.848, 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 15 16.00
P 294 15.00
O 2976 8.00
N 2407 7.00
C 7144 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 - 3.50
Amino acid : False - 1.90
Carbohydrate : True - 1.99
Ligands : True - 1.99
Small molecules : False - 1.98
Amino acid - RNA/DNA : False
Number of custom bonds: simple=0, symmetry=0
Time building additional restraints: 7.32
Conformation dependent library (CDL) restraints added in 1.7 seconds
1678 Ramachandran restraints generated.
839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2.
Adding C-beta torsion restraints...
Number of C-beta restraints generated: 1600
Finding SS restraints...
Secondary structure from input PDB file:
38 helices and 10 sheets defined
66.7% alpha, 4.4% beta
135 base pairs and 243 stacking pairs defined.
Time for finding SS restraints: 5.93
Creating SS restraints...
Processing helix chain 'A' and resid 44 through 55
Processing helix chain 'A' and resid 63 through 79
removed outlier: 3.527A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A)
Processing helix chain 'A' and resid 85 through 114
Processing helix chain 'A' and resid 120 through 131
removed outlier: 3.576A 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 42
Processing helix chain 'B' and resid 49 through 76
removed outlier: 4.010A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A)
removed outlier: 3.972A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A)
removed outlier: 3.766A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A)
Processing helix chain 'B' and resid 82 through 94
Processing helix chain 'D' and resid 37 through 49
removed outlier: 3.596A pdb=" N GLN D 47 " --> pdb=" O LYS D 43 " (cutoff:3.500A)
removed outlier: 3.609A pdb=" N VAL D 48 " --> pdb=" O VAL D 44 " (cutoff:3.500A)
Processing helix chain 'D' and resid 55 through 84
removed outlier: 3.567A pdb=" N ASN D 84 " --> pdb=" O LEU D 80 " (cutoff:3.500A)
Processing helix chain 'D' and resid 90 through 102
Processing helix chain 'D' and resid 104 through 123
removed outlier: 3.881A pdb=" N SER D 112 " --> pdb=" O LYS D 108 " (cutoff:3.500A)
Processing helix chain 'E' and resid 44 through 55
removed outlier: 3.793A pdb=" N LEU E 48 " --> pdb=" O GLY E 44 " (cutoff:3.500A)
removed outlier: 3.904A pdb=" N ARG E 49 " --> pdb=" O THR E 45 " (cutoff:3.500A)
Processing helix chain 'E' and resid 63 through 79
removed outlier: 3.523A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A)
Processing helix chain 'E' and resid 85 through 114
removed outlier: 3.601A pdb=" N ALA E 114 " --> pdb=" O CYS E 110 " (cutoff:3.500A)
Processing helix chain 'E' and resid 120 through 131
Processing helix chain 'F' and resid 25 through 29
Processing helix chain 'F' and resid 30 through 42
Processing helix chain 'F' and resid 49 through 76
removed outlier: 4.014A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A)
removed outlier: 3.731A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A)
removed outlier: 3.678A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A)
Processing helix chain 'F' and resid 82 through 94
removed outlier: 3.504A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A)
Processing helix chain 'H' and resid 37 through 49
Processing helix chain 'H' and resid 55 through 84
removed outlier: 3.629A pdb=" N ASN H 84 " --> pdb=" O LEU H 80 " (cutoff:3.500A)
Processing helix chain 'H' and resid 90 through 102
removed outlier: 3.615A pdb=" N ILE H 94 " --> pdb=" O THR H 90 " (cutoff:3.500A)
Processing helix chain 'H' and resid 103 through 123
removed outlier: 3.712A pdb=" N SER H 123 " --> pdb=" O THR H 119 " (cutoff:3.500A)
Processing helix chain 'M' and resid 22 through 35
Processing helix chain 'M' and resid 37 through 39
No H-bonds generated for 'chain 'M' and resid 37 through 39'
Processing helix chain 'M' and resid 56 through 60
Processing helix chain 'C' and resid 16 through 22
Processing helix chain 'C' and resid 26 through 37
Processing helix chain 'C' and resid 46 through 73
Processing helix chain 'C' and resid 79 through 90
removed outlier: 3.640A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A)
Processing helix chain 'C' and resid 90 through 97
Processing helix chain 'G' and resid 16 through 21
Processing helix chain 'G' and resid 27 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 91 through 97
Processing helix chain 'G' and resid 112 through 116
Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
removed outlier: 6.825A 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
removed outlier: 3.603A pdb=" N ILE A 119 " --> pdb=" O ARG B 45 " (cutoff:3.500A)
No H-bonds generated for sheet with id=AA2
Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98
Processing sheet with id=AA4, first strand: chain 'D' and resid 53 through 54
removed outlier: 7.528A pdb=" N GLY D 53 " --> pdb=" O ILE C 78 " (cutoff:3.500A)
No H-bonds generated for sheet with id=AA4
Processing sheet with id=AA5, first strand: chain 'D' and resid 88 through 89
Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84
removed outlier: 6.709A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A)
No H-bonds generated for sheet with id=AA6
Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119
Processing sheet with id=AA8, first strand: chain 'F' and resid 97 through 98
Processing sheet with id=AA9, first strand: chain 'H' and resid 88 through 89
Processing sheet with id=AB1, first strand: chain 'M' and resid 12 through 16
removed outlier: 8.825A pdb=" N LEU M 67 " --> pdb=" O GLN M 2 " (cutoff:3.500A)
removed outlier: 6.528A pdb=" N PHE M 4 " --> pdb=" O LEU M 67 " (cutoff:3.500A)
removed outlier: 7.318A pdb=" N LEU M 69 " --> pdb=" O PHE M 4 " (cutoff:3.500A)
removed outlier: 6.311A pdb=" N LYS M 6 " --> pdb=" O LEU M 69 " (cutoff:3.500A)
removed outlier: 7.810A pdb=" N LEU M 71 " --> pdb=" O LYS M 6 " (cutoff:3.500A)
420 hydrogen bonds defined for protein.
1228 hydrogen bond angles defined for protein.
Restraints generated for nucleic acids:
348 hydrogen bonds
692 hydrogen bond angles
0 basepair planarities
135 basepair parallelities
243 stacking parallelities
Total time for adding SS restraints: 4.56
Time building geometry restraints manager: 7.67 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: 2529
1.33 - 1.45: 4339
1.45 - 1.57: 6179
1.57 - 1.69: 586
1.69 - 1.81: 26
Bond restraints: 13659
Sorted by residual:
bond pdb=" CG1 ILE A 112 "
pdb=" CD1 ILE A 112 "
ideal model delta sigma weight residual
1.513 1.464 0.049 3.90e-02 6.57e+02 1.59e+00
bond pdb=" CG LEU A 126 "
pdb=" CD1 LEU A 126 "
ideal model delta sigma weight residual
1.521 1.486 0.035 3.30e-02 9.18e+02 1.13e+00
bond pdb=" CB CYS E 96 "
pdb=" SG CYS E 96 "
ideal model delta sigma weight residual
1.808 1.774 0.034 3.30e-02 9.18e+02 1.06e+00
bond pdb=" CB ASP C 72 "
pdb=" CG ASP C 72 "
ideal model delta sigma weight residual
1.516 1.541 -0.025 2.50e-02 1.60e+03 1.01e+00
bond pdb=" CB ASP E 81 "
pdb=" CG ASP E 81 "
ideal model delta sigma weight residual
1.516 1.541 -0.025 2.50e-02 1.60e+03 9.98e-01
... (remaining 13654 not shown)
Histogram of bond angle deviations from ideal:
98.69 - 105.45: 1342
105.45 - 112.22: 7541
112.22 - 118.98: 3419
118.98 - 125.74: 6401
125.74 - 132.51: 995
Bond angle restraints: 19698
Sorted by residual:
angle pdb=" C ARG B 23 "
pdb=" N ASP B 24 "
pdb=" CA ASP B 24 "
ideal model delta sigma weight residual
121.54 128.48 -6.94 1.91e+00 2.74e-01 1.32e+01
angle pdb=" C ARG F 23 "
pdb=" N ASP F 24 "
pdb=" CA ASP F 24 "
ideal model delta sigma weight residual
121.54 127.71 -6.17 1.91e+00 2.74e-01 1.04e+01
angle pdb=" CB ARG B 67 "
pdb=" CG ARG B 67 "
pdb=" CD ARG B 67 "
ideal model delta sigma weight residual
111.30 118.48 -7.18 2.30e+00 1.89e-01 9.74e+00
angle pdb=" CA ARG B 67 "
pdb=" CB ARG B 67 "
pdb=" CG ARG B 67 "
ideal model delta sigma weight residual
114.10 119.28 -5.18 2.00e+00 2.50e-01 6.72e+00
angle pdb=" N GLN A 125 "
pdb=" CA GLN A 125 "
pdb=" CB GLN A 125 "
ideal model delta sigma weight residual
110.28 113.84 -3.56 1.55e+00 4.16e-01 5.28e+00
... (remaining 19693 not shown)
Histogram of dihedral angle deviations from ideal:
0.00 - 29.37: 5858
29.37 - 58.74: 1526
58.74 - 88.12: 103
88.12 - 117.49: 2
117.49 - 146.86: 2
Dihedral angle restraints: 7491
sinusoidal: 5008
harmonic: 2483
Sorted by residual:
dihedral pdb=" C4' DG J 20 "
pdb=" C3' DG J 20 "
pdb=" O3' DG J 20 "
pdb=" P DG J 21 "
ideal model delta sinusoidal sigma weight residual
220.00 73.14 146.86 1 3.50e+01 8.16e-04 1.44e+01
dihedral pdb=" C4' DT J -17 "
pdb=" C3' DT J -17 "
pdb=" O3' DT J -17 "
pdb=" P DT J -16 "
ideal model delta sinusoidal sigma weight residual
220.00 75.89 144.11 1 3.50e+01 8.16e-04 1.42e+01
dihedral pdb=" CB GLU C 56 "
pdb=" CG GLU C 56 "
pdb=" CD GLU C 56 "
pdb=" OE1 GLU C 56 "
ideal model delta sinusoidal sigma weight residual
0.00 89.75 -89.75 1 3.00e+01 1.11e-03 1.06e+01
... (remaining 7488 not shown)
Histogram of chiral volume deviations from ideal:
0.000 - 0.028: 1558
0.028 - 0.055: 471
0.055 - 0.083: 135
0.083 - 0.110: 62
0.110 - 0.138: 14
Chirality restraints: 2240
Sorted by residual:
chirality pdb=" CA ASP B 24 "
pdb=" N ASP B 24 "
pdb=" C ASP B 24 "
pdb=" CB ASP B 24 "
both_signs ideal model delta sigma weight residual
False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.76e-01
chirality pdb=" CA ASP F 24 "
pdb=" N ASP F 24 "
pdb=" C ASP F 24 "
pdb=" CB ASP F 24 "
both_signs ideal model delta sigma weight residual
False 2.51 2.38 0.14 2.00e-01 2.50e+01 4.58e-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 2.56 -0.13 2.00e-01 2.50e+01 3.98e-01
... (remaining 2237 not shown)
Planarity restraints: 1478
Sorted by residual:
delta sigma weight rms_deltas residual
plane pdb=" C1' DA I -35 " 0.021 2.00e-02 2.50e+03 8.92e-03 2.19e+00
pdb=" N9 DA I -35 " -0.018 2.00e-02 2.50e+03
pdb=" C8 DA I -35 " -0.005 2.00e-02 2.50e+03
pdb=" N7 DA I -35 " -0.001 2.00e-02 2.50e+03
pdb=" C5 DA I -35 " 0.003 2.00e-02 2.50e+03
pdb=" C6 DA I -35 " -0.001 2.00e-02 2.50e+03
pdb=" N6 DA I -35 " 0.008 2.00e-02 2.50e+03
pdb=" N1 DA I -35 " 0.001 2.00e-02 2.50e+03
pdb=" C2 DA I -35 " -0.002 2.00e-02 2.50e+03
pdb=" N3 DA I -35 " -0.005 2.00e-02 2.50e+03
pdb=" C4 DA I -35 " -0.002 2.00e-02 2.50e+03
delta sigma weight rms_deltas residual
plane pdb=" C1' DG I 47 " 0.021 2.00e-02 2.50e+03 8.33e-03 2.08e+00
pdb=" N9 DG I 47 " -0.017 2.00e-02 2.50e+03
pdb=" C8 DG I 47 " -0.006 2.00e-02 2.50e+03
pdb=" N7 DG I 47 " -0.002 2.00e-02 2.50e+03
pdb=" C5 DG I 47 " 0.001 2.00e-02 2.50e+03
pdb=" C6 DG I 47 " 0.003 2.00e-02 2.50e+03
pdb=" O6 DG I 47 " 0.007 2.00e-02 2.50e+03
pdb=" N1 DG I 47 " 0.001 2.00e-02 2.50e+03
pdb=" C2 DG I 47 " -0.000 2.00e-02 2.50e+03
pdb=" N2 DG I 47 " -0.003 2.00e-02 2.50e+03
pdb=" N3 DG I 47 " -0.003 2.00e-02 2.50e+03
pdb=" C4 DG I 47 " -0.001 2.00e-02 2.50e+03
delta sigma weight rms_deltas residual
plane pdb=" C1' DG I 26 " 0.018 2.00e-02 2.50e+03 7.34e-03 1.61e+00
pdb=" N9 DG I 26 " -0.015 2.00e-02 2.50e+03
pdb=" C8 DG I 26 " -0.004 2.00e-02 2.50e+03
pdb=" N7 DG I 26 " -0.002 2.00e-02 2.50e+03
pdb=" C5 DG I 26 " 0.001 2.00e-02 2.50e+03
pdb=" C6 DG I 26 " 0.003 2.00e-02 2.50e+03
pdb=" O6 DG I 26 " 0.005 2.00e-02 2.50e+03
pdb=" N1 DG I 26 " 0.003 2.00e-02 2.50e+03
pdb=" C2 DG I 26 " 0.002 2.00e-02 2.50e+03
pdb=" N2 DG I 26 " -0.005 2.00e-02 2.50e+03
pdb=" N3 DG I 26 " -0.002 2.00e-02 2.50e+03
pdb=" C4 DG I 26 " -0.001 2.00e-02 2.50e+03
... (remaining 1475 not shown)
Histogram of nonbonded interaction distances:
1.33 - 2.04: 2
2.04 - 2.76: 1670
2.76 - 3.47: 17444
3.47 - 4.19: 34430
4.19 - 4.90: 52456
Nonbonded interactions: 106002
Sorted by model distance:
nonbonded pdb=" C SER H 123 "
pdb=" N SER G 11 "
model vdw
1.329 3.350
nonbonded pdb=" C SER D 123 "
pdb=" N SER C 11 "
model vdw
1.330 3.350
nonbonded pdb=" O2 DC I 21 "
pdb=" N2 DG J -21 "
model vdw
2.151 2.496
nonbonded pdb=" OG1 THR H 90 "
pdb=" OE1 GLU H 93 "
model vdw
2.219 3.040
nonbonded pdb=" O SER D 123 "
pdb=" N SER C 11 "
model vdw
2.246 3.120
... (remaining 105997 not shown)
NOTE: a complete listing of the restraints can be obtained by requesting
output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
reference = chain 'A'
selection = chain 'E'
}
ncs_group {
reference = (chain 'B' and resid 21 through 102)
selection = (chain 'F' and (resid 21 through 101 or (resid 102 and (name N or name CA or nam \
e C or name O ))))
}
ncs_group {
reference = chain 'C'
selection = (chain 'G' and resid 11 through 118)
}
ncs_group {
reference = (chain 'D' and (resid 31 through 107 or resid 109 through 115 or resid 117 throu \
gh 123))
selection = (chain 'H' and (resid 31 through 107 or resid 109 through 115 or resid 117 throu \
gh 123))
}
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=0.25 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
Set random seed: 0.000
Set model cs if undefined: 0.000
Decide on map wrapping: 0.000
Normalize map: mean=0, sd=1: 0.800
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: 0.010
Extract box with map and model: 0.540
Check model and map are aligned: 0.100
Set scattering table: 0.140
Process input model: 42.300
Find NCS groups from input model: 0.270
Set up NCS constraints: 0.050
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:2.660
Set ADP refinement strategy: 0.000
Make a string to write initial .geo file:0.000
Internal consistency checks: 0.000
Total: 46.870
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8503
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 : 0.003 0.049 13659 Z= 0.178
Angle : 0.557 7.178 19698 Z= 0.330
Chirality : 0.033 0.138 2240
Planarity : 0.003 0.038 1478
Dihedral : 26.649 146.860 5891
Min Nonbonded Distance : 1.329
Molprobity Statistics.
All-atom Clashscore : 7.46
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 2.27 %
Favored : 97.73 %
Rotamer:
Outliers : 0.14 %
Allowed : 0.00 %
Favored : 99.86 %
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: 2.47 (0.30), residues: 839
helix: 2.61 (0.22), residues: 544
sheet: 1.56 (1.19), residues: 26
loop : -0.45 (0.37), residues: 269
Max deviation from planes:
Type MaxDev MeanDev LineInFile
HIS 0.005 0.001 HIS A 113
PHE 0.009 0.001 PHE E 78
TYR 0.020 0.001 TYR H 40
ARG 0.013 0.000 ARG B 67
*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
1678 Ramachandran restraints generated.
839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
1678 Ramachandran restraints generated.
839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
229 residues out of total 717 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 229
time to evaluate : 0.927
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: A 81 ASP cc_start: 0.8392 (m-30) cc_final: 0.7864 (t70)
REVERT: B 31 LYS cc_start: 0.9018 (ttmt) cc_final: 0.8770 (ttpp)
REVERT: B 91 LYS cc_start: 0.9420 (ttmm) cc_final: 0.9160 (ttmt)
REVERT: D 51 ASP cc_start: 0.9279 (p0) cc_final: 0.8711 (p0)
REVERT: D 116 LYS cc_start: 0.9197 (mtmt) cc_final: 0.8989 (ttmt)
REVERT: D 120 LYS cc_start: 0.8988 (ttpt) cc_final: 0.8735 (tttt)
REVERT: E 57 SER cc_start: 0.9388 (p) cc_final: 0.8894 (p)
REVERT: E 59 GLU cc_start: 0.8782 (pm20) cc_final: 0.7941 (pm20)
REVERT: E 82 LEU cc_start: 0.9341 (mt) cc_final: 0.9119 (mm)
REVERT: E 94 GLU cc_start: 0.8653 (mm-30) cc_final: 0.8359 (mm-30)
REVERT: E 110 CYS cc_start: 0.7931 (m) cc_final: 0.7656 (m)
REVERT: E 129 ARG cc_start: 0.8949 (tpt90) cc_final: 0.8743 (tpt-90)
REVERT: F 91 LYS cc_start: 0.9101 (tttp) cc_final: 0.8743 (ttmt)
REVERT: H 59 MET cc_start: 0.8960 (tpt) cc_final: 0.8643 (tpp)
REVERT: H 85 LYS cc_start: 0.9341 (mttm) cc_final: 0.8923 (mttp)
REVERT: M 44 ILE cc_start: 0.5531 (mm) cc_final: 0.4842 (mp)
REVERT: C 64 GLU cc_start: 0.9011 (tm-30) cc_final: 0.8415 (tm-30)
REVERT: G 41 GLU cc_start: 0.8634 (tm-30) cc_final: 0.8178 (tm-30)
REVERT: G 64 GLU cc_start: 0.8913 (tm-30) cc_final: 0.8684 (tm-30)
outliers start: 0
outliers final: 0
residues processed: 229
average time/residue: 0.2984
time to fit residues: 91.1423
Evaluate side-chains
179 residues out of total 717 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 179
time to evaluate : 0.907
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 108
random chunks:
chunk 91 optimal weight: 0.8980
chunk 81 optimal weight: 10.0000
chunk 45 optimal weight: 1.9990
chunk 27 optimal weight: 2.9990
chunk 55 optimal weight: 4.9990
chunk 43 optimal weight: 2.9990
chunk 84 optimal weight: 3.9990
chunk 32 optimal weight: 0.5980
chunk 51 optimal weight: 0.6980
chunk 63 optimal weight: 4.9990
chunk 98 optimal weight: 7.9990
overall best weight: 1.4384
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 68 GLN
Total number of N/Q/H flips: 1
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8564
moved from start: 0.1310
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.005 0.036 13659 Z= 0.292
Angle : 0.610 7.618 19698 Z= 0.355
Chirality : 0.036 0.172 2240
Planarity : 0.004 0.048 1478
Dihedral : 29.689 148.890 4171
Min Nonbonded Distance : 2.130
Molprobity Statistics.
All-atom Clashscore : 8.11
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 2.75 %
Favored : 97.25 %
Rotamer:
Outliers : 2.36 %
Allowed : 11.65 %
Favored : 85.99 %
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: 2.42 (0.29), residues: 839
helix: 2.56 (0.22), residues: 555
sheet: 2.08 (1.30), residues: 18
loop : -0.54 (0.36), residues: 266
Max deviation from planes:
Type MaxDev MeanDev LineInFile
HIS 0.004 0.001 HIS A 113
PHE 0.013 0.001 PHE A 78
TYR 0.015 0.002 TYR B 88
ARG 0.007 0.000 ARG H 33
*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
1678 Ramachandran restraints generated.
839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
1678 Ramachandran restraints generated.
839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
200 residues out of total 717 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 16
poor density : 184
time to evaluate : 1.023
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: A 73 GLU cc_start: 0.8083 (tt0) cc_final: 0.7389 (tt0)
REVERT: A 81 ASP cc_start: 0.8289 (m-30) cc_final: 0.7874 (t70)
REVERT: B 25 ASN cc_start: 0.8644 (m-40) cc_final: 0.7952 (m110)
REVERT: B 31 LYS cc_start: 0.9069 (ttmt) cc_final: 0.8833 (ttpp)
REVERT: B 91 LYS cc_start: 0.9509 (ttmm) cc_final: 0.9236 (ttmt)
REVERT: D 51 ASP cc_start: 0.9316 (p0) cc_final: 0.8859 (p0)
REVERT: D 85 LYS cc_start: 0.9345 (mttm) cc_final: 0.9065 (mmtt)
REVERT: D 120 LYS cc_start: 0.9054 (ttpt) cc_final: 0.8765 (tttt)
REVERT: E 57 SER cc_start: 0.9452 (p) cc_final: 0.8976 (p)
REVERT: E 59 GLU cc_start: 0.8962 (pm20) cc_final: 0.8120 (pm20)
REVERT: E 82 LEU cc_start: 0.9505 (mt) cc_final: 0.9173 (mm)
REVERT: E 105 GLU cc_start: 0.8680 (tp30) cc_final: 0.8272 (tp30)
REVERT: F 88 TYR cc_start: 0.8508 (m-10) cc_final: 0.8181 (m-10)
REVERT: F 91 LYS cc_start: 0.9215 (tttp) cc_final: 0.8849 (ttmt)
REVERT: H 59 MET cc_start: 0.9108 (tpt) cc_final: 0.8865 (tpp)
REVERT: H 83 TYR cc_start: 0.8809 (m-10) cc_final: 0.8505 (m-80)
REVERT: H 85 LYS cc_start: 0.9328 (mttm) cc_final: 0.8899 (mttp)
REVERT: M 44 ILE cc_start: 0.4674 (mm) cc_final: 0.4375 (mp)
REVERT: C 64 GLU cc_start: 0.9062 (tm-30) cc_final: 0.8316 (tm-30)
REVERT: G 41 GLU cc_start: 0.8629 (tm-30) cc_final: 0.8053 (tm-30)
REVERT: G 64 GLU cc_start: 0.8958 (tm-30) cc_final: 0.8725 (tm-30)
outliers start: 16
outliers final: 12
residues processed: 191
average time/residue: 0.2887
time to fit residues: 75.4311
Evaluate side-chains
182 residues out of total 717 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 12
poor density : 170
time to evaluate : 1.020
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 93 GLN
Chi-restraints excluded: chain D residue 118 VAL
Chi-restraints excluded: chain E residue 80 THR
Chi-restraints excluded: chain E residue 115 LYS
Chi-restraints excluded: chain F residue 30 THR
Chi-restraints excluded: chain M residue 25 ASN
Chi-restraints excluded: chain C residue 40 SER
Chi-restraints excluded: chain C residue 79 ILE
Chi-restraints excluded: chain C residue 116 LEU
Chi-restraints excluded: chain G residue 18 SER
Chi-restraints excluded: chain G residue 62 ILE
Chi-restraints excluded: chain G residue 79 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 108
random chunks:
chunk 54 optimal weight: 4.9990
chunk 30 optimal weight: 0.8980
chunk 81 optimal weight: 9.9990
chunk 66 optimal weight: 6.9990
chunk 27 optimal weight: 2.9990
chunk 98 optimal weight: 7.9990
chunk 106 optimal weight: 1.9990
chunk 87 optimal weight: 8.9990
chunk 97 optimal weight: 0.0170
chunk 33 optimal weight: 2.9990
chunk 78 optimal weight: 3.9990
overall best weight: 1.7824
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8589
moved from start: 0.1726
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.006 0.037 13659 Z= 0.334
Angle : 0.624 8.563 19698 Z= 0.361
Chirality : 0.037 0.173 2240
Planarity : 0.004 0.037 1478
Dihedral : 29.780 149.252 4171
Min Nonbonded Distance : 2.116
Molprobity Statistics.
All-atom Clashscore : 8.71
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 3.23 %
Favored : 96.77 %
Rotamer:
Outliers : 3.74 %
Allowed : 14.70 %
Favored : 81.55 %
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: 2.30 (0.29), residues: 839
helix: 2.53 (0.22), residues: 555
sheet: 1.06 (1.16), residues: 26
loop : -0.72 (0.37), residues: 258
Max deviation from planes:
Type MaxDev MeanDev LineInFile
HIS 0.004 0.001 HIS B 75
PHE 0.022 0.002 PHE A 78
TYR 0.025 0.002 TYR B 88
ARG 0.006 0.000 ARG C 29
*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
1678 Ramachandran restraints generated.
839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
1678 Ramachandran restraints generated.
839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
210 residues out of total 717 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 26
poor density : 184
time to evaluate : 1.534
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: A 59 GLU cc_start: 0.8558 (OUTLIER) cc_final: 0.8250 (pm20)
REVERT: A 81 ASP cc_start: 0.8105 (m-30) cc_final: 0.7696 (t70)
REVERT: A 123 ASP cc_start: 0.9373 (m-30) cc_final: 0.9172 (m-30)
REVERT: B 25 ASN cc_start: 0.8667 (m-40) cc_final: 0.7968 (m110)
REVERT: B 91 LYS cc_start: 0.9507 (ttmm) cc_final: 0.9231 (ttmt)
REVERT: D 46 LYS cc_start: 0.9341 (tppt) cc_final: 0.9037 (tppt)
REVERT: D 51 ASP cc_start: 0.9293 (p0) cc_final: 0.8866 (p0)
REVERT: D 59 MET cc_start: 0.9286 (tpp) cc_final: 0.8802 (tpt)
REVERT: D 85 LYS cc_start: 0.9349 (mttm) cc_final: 0.9110 (mmtt)
REVERT: D 120 LYS cc_start: 0.9084 (ttpt) cc_final: 0.8785 (tttt)
REVERT: E 57 SER cc_start: 0.9414 (p) cc_final: 0.8723 (p)
REVERT: E 59 GLU cc_start: 0.8912 (pm20) cc_final: 0.8051 (pm20)
REVERT: E 82 LEU cc_start: 0.9552 (mt) cc_final: 0.9289 (mm)
REVERT: E 105 GLU cc_start: 0.8743 (tp30) cc_final: 0.8351 (tp30)
REVERT: F 88 TYR cc_start: 0.8793 (m-10) cc_final: 0.8364 (m-10)
REVERT: F 91 LYS cc_start: 0.9282 (tttp) cc_final: 0.9016 (ttmt)
REVERT: H 85 LYS cc_start: 0.9312 (mttm) cc_final: 0.8795 (mtmm)
REVERT: C 64 GLU cc_start: 0.9070 (tm-30) cc_final: 0.8316 (tm-30)
REVERT: G 41 GLU cc_start: 0.8693 (tm-30) cc_final: 0.8082 (tm-30)
REVERT: G 64 GLU cc_start: 0.8983 (tm-30) cc_final: 0.8732 (tm-30)
outliers start: 26
outliers final: 22
residues processed: 196
average time/residue: 0.2985
time to fit residues: 80.7623
Evaluate side-chains
195 residues out of total 717 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 23
poor density : 172
time to evaluate : 0.983
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 59 GLU
Chi-restraints excluded: chain A residue 80 THR
Chi-restraints excluded: chain A residue 92 LEU
Chi-restraints excluded: chain A residue 93 GLN
Chi-restraints excluded: chain A residue 110 CYS
Chi-restraints excluded: chain D residue 52 THR
Chi-restraints excluded: chain D residue 118 VAL
Chi-restraints excluded: chain D residue 122 THR
Chi-restraints excluded: chain E residue 80 THR
Chi-restraints excluded: chain E residue 115 LYS
Chi-restraints excluded: chain F residue 30 THR
Chi-restraints excluded: chain F residue 47 SER
Chi-restraints excluded: chain F residue 50 ILE
Chi-restraints excluded: chain H residue 80 LEU
Chi-restraints excluded: chain H residue 101 LEU
Chi-restraints excluded: chain H residue 122 THR
Chi-restraints excluded: chain M residue 25 ASN
Chi-restraints excluded: chain C residue 79 ILE
Chi-restraints excluded: chain C residue 91 GLU
Chi-restraints excluded: chain C residue 116 LEU
Chi-restraints excluded: chain G residue 18 SER
Chi-restraints excluded: chain G residue 62 ILE
Chi-restraints excluded: chain G residue 79 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 108
random chunks:
chunk 97 optimal weight: 1.9990
chunk 73 optimal weight: 3.9990
chunk 50 optimal weight: 0.6980
chunk 10 optimal weight: 0.5980
chunk 46 optimal weight: 0.9980
chunk 65 optimal weight: 5.9990
chunk 98 optimal weight: 0.7980
chunk 104 optimal weight: 1.9990
chunk 51 optimal weight: 0.9990
chunk 93 optimal weight: 0.8980
chunk 28 optimal weight: 3.9990
overall best weight: 0.7980
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 113 HIS
** M 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
M 49 GLN
Total number of N/Q/H flips: 2
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8544
moved from start: 0.1759
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.004 0.031 13659 Z= 0.205
Angle : 0.570 7.774 19698 Z= 0.334
Chirality : 0.034 0.151 2240
Planarity : 0.004 0.037 1478
Dihedral : 29.608 148.386 4171
Min Nonbonded Distance : 2.133
Molprobity Statistics.
All-atom Clashscore : 8.15
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 2.63 %
Favored : 97.37 %
Rotamer:
Outliers : 2.91 %
Allowed : 16.64 %
Favored : 80.44 %
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: 2.52 (0.30), residues: 839
helix: 2.71 (0.22), residues: 554
sheet: 1.11 (1.16), residues: 26
loop : -0.68 (0.37), residues: 259
Max deviation from planes:
Type MaxDev MeanDev LineInFile
HIS 0.005 0.001 HIS H 109
PHE 0.016 0.001 PHE A 78
TYR 0.024 0.001 TYR B 88
ARG 0.007 0.000 ARG H 33
*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
1678 Ramachandran restraints generated.
839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
1678 Ramachandran restraints generated.
839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
214 residues out of total 717 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 20
poor density : 194
time to evaluate : 0.971
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: A 59 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.8161 (pm20)
REVERT: A 81 ASP cc_start: 0.8245 (m-30) cc_final: 0.7906 (t70)
REVERT: A 125 GLN cc_start: 0.8156 (mt0) cc_final: 0.7245 (mp10)
REVERT: B 25 ASN cc_start: 0.8590 (m-40) cc_final: 0.7769 (m110)
REVERT: B 67 ARG cc_start: 0.7382 (mmp80) cc_final: 0.6678 (tpp80)
REVERT: B 88 TYR cc_start: 0.8403 (m-10) cc_final: 0.7976 (m-10)
REVERT: B 91 LYS cc_start: 0.9495 (ttmm) cc_final: 0.9213 (ttmt)
REVERT: D 51 ASP cc_start: 0.9238 (p0) cc_final: 0.8744 (p0)
REVERT: D 83 TYR cc_start: 0.8030 (m-10) cc_final: 0.7665 (m-10)
REVERT: D 85 LYS cc_start: 0.9335 (mttm) cc_final: 0.9127 (mmtt)
REVERT: D 100 LEU cc_start: 0.9332 (mt) cc_final: 0.9104 (mt)
REVERT: D 120 LYS cc_start: 0.9056 (ttpt) cc_final: 0.8740 (tttt)
REVERT: E 57 SER cc_start: 0.9403 (p) cc_final: 0.8610 (p)
REVERT: E 59 GLU cc_start: 0.8865 (pm20) cc_final: 0.8013 (pm20)
REVERT: E 82 LEU cc_start: 0.9481 (mt) cc_final: 0.9137 (mm)
REVERT: F 88 TYR cc_start: 0.8710 (m-10) cc_final: 0.8326 (m-10)
REVERT: F 91 LYS cc_start: 0.9291 (tttp) cc_final: 0.9048 (ttmt)
REVERT: H 85 LYS cc_start: 0.9336 (mttm) cc_final: 0.8827 (mtmm)
REVERT: C 64 GLU cc_start: 0.9047 (tm-30) cc_final: 0.8443 (tm-30)
REVERT: C 74 LYS cc_start: 0.9410 (mtmt) cc_final: 0.9151 (tppt)
REVERT: G 41 GLU cc_start: 0.8666 (tm-30) cc_final: 0.8056 (tm-30)
REVERT: G 64 GLU cc_start: 0.8924 (tm-30) cc_final: 0.8660 (tm-30)
outliers start: 20
outliers final: 14
residues processed: 201
average time/residue: 0.2845
time to fit residues: 78.4195
Evaluate side-chains
194 residues out of total 717 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 15
poor density : 179
time to evaluate : 0.998
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 59 GLU
Chi-restraints excluded: chain A residue 92 LEU
Chi-restraints excluded: chain D residue 118 VAL
Chi-restraints excluded: chain E residue 80 THR
Chi-restraints excluded: chain E residue 110 CYS
Chi-restraints excluded: chain E residue 120 MET
Chi-restraints excluded: chain F residue 30 THR
Chi-restraints excluded: chain F residue 81 VAL
Chi-restraints excluded: chain H residue 80 LEU
Chi-restraints excluded: chain H residue 101 LEU
Chi-restraints excluded: chain C residue 79 ILE
Chi-restraints excluded: chain C residue 116 LEU
Chi-restraints excluded: chain G residue 18 SER
Chi-restraints excluded: chain G residue 62 ILE
Chi-restraints excluded: chain G residue 79 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 108
random chunks:
chunk 86 optimal weight: 8.9990
chunk 59 optimal weight: 4.9990
chunk 1 optimal weight: 0.9990
chunk 77 optimal weight: 3.9990
chunk 43 optimal weight: 0.7980
chunk 89 optimal weight: 2.9990
chunk 72 optimal weight: 3.9990
chunk 0 optimal weight: 3.9990
chunk 53 optimal weight: 5.9990
chunk 93 optimal weight: 0.9990
chunk 26 optimal weight: 4.9990
overall best weight: 1.9588
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
B 93 GLN
F 25 ASN
M 40 GLN
Total number of N/Q/H flips: 3
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8597
moved from start: 0.2032
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.006 0.041 13659 Z= 0.356
Angle : 0.632 12.600 19698 Z= 0.364
Chirality : 0.037 0.152 2240
Planarity : 0.004 0.035 1478
Dihedral : 29.840 150.077 4171
Min Nonbonded Distance : 2.111
Molprobity Statistics.
All-atom Clashscore : 8.84
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 3.23 %
Favored : 96.77 %
Rotamer:
Outliers : 4.16 %
Allowed : 17.20 %
Favored : 78.64 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 2.28 (0.29), residues: 839
helix: 2.50 (0.22), residues: 556
sheet: 1.07 (1.15), residues: 26
loop : -0.74 (0.38), residues: 257
Max deviation from planes:
Type MaxDev MeanDev LineInFile
HIS 0.004 0.001 HIS H 49
PHE 0.016 0.002 PHE A 78
TYR 0.025 0.002 TYR B 88
ARG 0.007 0.000 ARG H 33
*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
1678 Ramachandran restraints generated.
839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
1678 Ramachandran restraints generated.
839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
206 residues out of total 717 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 29
poor density : 177
time to evaluate : 1.078
Fit side-chains
revert: symmetry clash
revert: symmetry clash
REVERT: A 59 GLU cc_start: 0.8516 (OUTLIER) cc_final: 0.8208 (pm20)
REVERT: A 81 ASP cc_start: 0.8134 (m-30) cc_final: 0.7862 (t70)
REVERT: A 123 ASP cc_start: 0.9376 (m-30) cc_final: 0.9088 (m-30)
REVERT: A 125 GLN cc_start: 0.8225 (mt0) cc_final: 0.7492 (mt0)
REVERT: B 25 ASN cc_start: 0.8641 (m-40) cc_final: 0.7866 (m110)
REVERT: B 88 TYR cc_start: 0.8427 (m-10) cc_final: 0.7821 (m-10)
REVERT: B 91 LYS cc_start: 0.9515 (ttmm) cc_final: 0.9243 (ttmt)
REVERT: D 42 TYR cc_start: 0.8515 (t80) cc_final: 0.8277 (t80)
REVERT: D 46 LYS cc_start: 0.9304 (tppt) cc_final: 0.9002 (tppt)
REVERT: D 51 ASP cc_start: 0.9285 (p0) cc_final: 0.8921 (p0)
REVERT: D 59 MET cc_start: 0.9256 (tpp) cc_final: 0.8780 (tpt)
REVERT: D 83 TYR cc_start: 0.8193 (m-10) cc_final: 0.7471 (m-10)
REVERT: D 85 LYS cc_start: 0.9358 (mttm) cc_final: 0.9133 (mmtt)
REVERT: D 120 LYS cc_start: 0.9117 (ttpt) cc_final: 0.8793 (tttt)
REVERT: E 57 SER cc_start: 0.9427 (p) cc_final: 0.8585 (p)
REVERT: E 59 GLU cc_start: 0.8912 (pm20) cc_final: 0.8047 (pm20)
REVERT: E 82 LEU cc_start: 0.9566 (mt) cc_final: 0.9317 (mm)
REVERT: F 88 TYR cc_start: 0.8692 (m-10) cc_final: 0.8368 (m-10)
REVERT: F 91 LYS cc_start: 0.9294 (tttp) cc_final: 0.9054 (ttmt)
REVERT: H 85 LYS cc_start: 0.9311 (mttm) cc_final: 0.8801 (mtmm)
REVERT: M 72 ARG cc_start: 0.5849 (ptt90) cc_final: 0.5464 (mtm110)
REVERT: C 64 GLU cc_start: 0.9076 (tm-30) cc_final: 0.8272 (tm-30)
REVERT: G 41 GLU cc_start: 0.8621 (tm-30) cc_final: 0.8112 (tm-30)
outliers start: 29
outliers final: 23
residues processed: 190
average time/residue: 0.2692
time to fit residues: 71.1179
Evaluate side-chains
196 residues out of total 717 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 24
poor density : 172
time to evaluate : 0.931
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 51 ILE
Chi-restraints excluded: chain A residue 59 GLU
Chi-restraints excluded: chain A residue 80 THR
Chi-restraints excluded: chain A residue 92 LEU
Chi-restraints excluded: chain A residue 93 GLN
Chi-restraints excluded: chain A residue 110 CYS
Chi-restraints excluded: chain D residue 69 ILE
Chi-restraints excluded: chain D residue 118 VAL
Chi-restraints excluded: chain E residue 80 THR
Chi-restraints excluded: chain E residue 110 CYS
Chi-restraints excluded: chain E residue 115 LYS
Chi-restraints excluded: chain F residue 30 THR
Chi-restraints excluded: chain F residue 47 SER
Chi-restraints excluded: chain F residue 50 ILE
Chi-restraints excluded: chain F residue 81 VAL
Chi-restraints excluded: chain H residue 80 LEU
Chi-restraints excluded: chain H residue 101 LEU
Chi-restraints excluded: chain M residue 25 ASN
Chi-restraints excluded: chain C residue 40 SER
Chi-restraints excluded: chain C residue 79 ILE
Chi-restraints excluded: chain C residue 116 LEU
Chi-restraints excluded: chain G residue 18 SER
Chi-restraints excluded: chain G residue 62 ILE
Chi-restraints excluded: chain G residue 79 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 108
random chunks:
chunk 35 optimal weight: 0.7980
chunk 94 optimal weight: 0.9980
chunk 20 optimal weight: 0.5980
chunk 61 optimal weight: 4.9990
chunk 25 optimal weight: 0.8980
chunk 104 optimal weight: 1.9990
chunk 86 optimal weight: 5.9990
chunk 48 optimal weight: 0.9980
chunk 8 optimal weight: 0.9980
chunk 34 optimal weight: 0.9990
chunk 54 optimal weight: 4.9990
overall best weight: 0.8580
-------------------------------------------------------------------------------
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
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8553
moved from start: 0.1979
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.004 0.033 13659 Z= 0.211
Angle : 0.579 9.009 19698 Z= 0.338
Chirality : 0.034 0.155 2240
Planarity : 0.004 0.036 1478
Dihedral : 29.646 148.605 4171
Min Nonbonded Distance : 2.132
Molprobity Statistics.
All-atom Clashscore : 8.06
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 2.51 %
Favored : 97.49 %
Rotamer:
Outliers : 3.05 %
Allowed : 18.31 %
Favored : 78.64 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 2.54 (0.29), residues: 839
helix: 2.74 (0.22), residues: 554
sheet: 1.12 (1.16), residues: 26
loop : -0.71 (0.37), residues: 259
Max deviation from planes:
Type MaxDev MeanDev LineInFile
HIS 0.004 0.001 HIS B 75
PHE 0.015 0.001 PHE A 78
TYR 0.016 0.001 TYR B 88
ARG 0.008 0.000 ARG H 33
*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
1678 Ramachandran restraints generated.
839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
1678 Ramachandran restraints generated.
839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
209 residues out of total 717 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 21
poor density : 188
time to evaluate : 0.982
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: A 59 GLU cc_start: 0.8430 (OUTLIER) cc_final: 0.8164 (pm20)
REVERT: A 81 ASP cc_start: 0.8165 (m-30) cc_final: 0.7955 (t70)
REVERT: A 123 ASP cc_start: 0.9373 (m-30) cc_final: 0.9048 (m-30)
REVERT: A 125 GLN cc_start: 0.8173 (mt0) cc_final: 0.7348 (mt0)
REVERT: B 25 ASN cc_start: 0.8588 (m-40) cc_final: 0.7657 (m110)
REVERT: B 67 ARG cc_start: 0.7317 (mmp80) cc_final: 0.6790 (tpp80)
REVERT: B 88 TYR cc_start: 0.8445 (m-10) cc_final: 0.7963 (m-10)
REVERT: B 91 LYS cc_start: 0.9499 (ttmm) cc_final: 0.9265 (ttmt)
REVERT: D 46 LYS cc_start: 0.9276 (tppt) cc_final: 0.8981 (tppt)
REVERT: D 51 ASP cc_start: 0.9236 (p0) cc_final: 0.8774 (p0)
REVERT: D 83 TYR cc_start: 0.8080 (m-10) cc_final: 0.7626 (m-10)
REVERT: D 85 LYS cc_start: 0.9364 (mttm) cc_final: 0.9151 (mmtt)
REVERT: D 120 LYS cc_start: 0.9066 (ttpt) cc_final: 0.8713 (tttt)
REVERT: E 57 SER cc_start: 0.9380 (p) cc_final: 0.8981 (p)
REVERT: E 59 GLU cc_start: 0.8857 (pm20) cc_final: 0.8135 (pm20)
REVERT: E 82 LEU cc_start: 0.9517 (mt) cc_final: 0.9267 (mm)
REVERT: F 85 ASP cc_start: 0.8956 (m-30) cc_final: 0.8654 (m-30)
REVERT: F 88 TYR cc_start: 0.8683 (m-10) cc_final: 0.8403 (m-10)
REVERT: F 91 LYS cc_start: 0.9269 (tttp) cc_final: 0.9041 (ttmt)
REVERT: H 85 LYS cc_start: 0.9297 (mttm) cc_final: 0.8797 (mtmm)
REVERT: M 72 ARG cc_start: 0.5963 (ptt90) cc_final: 0.5561 (mtm110)
REVERT: C 64 GLU cc_start: 0.9074 (tm-30) cc_final: 0.8458 (tm-30)
REVERT: G 41 GLU cc_start: 0.8594 (tm-30) cc_final: 0.8072 (tm-30)
outliers start: 21
outliers final: 19
residues processed: 196
average time/residue: 0.2747
time to fit residues: 74.3073
Evaluate side-chains
197 residues out of total 717 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 20
poor density : 177
time to evaluate : 1.039
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 59 GLU
Chi-restraints excluded: chain A residue 80 THR
Chi-restraints excluded: chain A residue 92 LEU
Chi-restraints excluded: chain A residue 93 GLN
Chi-restraints excluded: chain B residue 93 GLN
Chi-restraints excluded: chain D residue 118 VAL
Chi-restraints excluded: chain E residue 80 THR
Chi-restraints excluded: chain E residue 110 CYS
Chi-restraints excluded: chain E residue 115 LYS
Chi-restraints excluded: chain F residue 30 THR
Chi-restraints excluded: chain F residue 50 ILE
Chi-restraints excluded: chain F residue 81 VAL
Chi-restraints excluded: chain H residue 101 LEU
Chi-restraints excluded: chain C residue 23 LEU
Chi-restraints excluded: chain C residue 40 SER
Chi-restraints excluded: chain C residue 79 ILE
Chi-restraints excluded: chain C residue 116 LEU
Chi-restraints excluded: chain G residue 18 SER
Chi-restraints excluded: chain G residue 62 ILE
Chi-restraints excluded: chain G residue 79 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 108
random chunks:
chunk 100 optimal weight: 0.7980
chunk 11 optimal weight: 3.9990
chunk 59 optimal weight: 4.9990
chunk 76 optimal weight: 4.9990
chunk 87 optimal weight: 2.9990
chunk 58 optimal weight: 3.9990
chunk 104 optimal weight: 1.9990
chunk 65 optimal weight: 4.9990
chunk 63 optimal weight: 4.9990
chunk 48 optimal weight: 0.8980
chunk 64 optimal weight: 4.9990
overall best weight: 2.1386
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
B 93 GLN
M 62 GLN
Total number of N/Q/H flips: 2
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8606
moved from start: 0.2218
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.007 0.039 13659 Z= 0.386
Angle : 0.651 8.250 19698 Z= 0.374
Chirality : 0.038 0.159 2240
Planarity : 0.004 0.037 1478
Dihedral : 29.900 150.493 4171
Min Nonbonded Distance : 2.107
Molprobity Statistics.
All-atom Clashscore : 8.97
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 3.23 %
Favored : 96.77 %
Rotamer:
Outliers : 4.72 %
Allowed : 17.48 %
Favored : 77.81 %
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: 2.26 (0.29), residues: 839
helix: 2.50 (0.22), residues: 554
sheet: 1.14 (1.14), residues: 26
loop : -0.76 (0.37), residues: 259
Max deviation from planes:
Type MaxDev MeanDev LineInFile
HIS 0.004 0.001 HIS B 75
PHE 0.015 0.002 PHE A 78
TYR 0.025 0.002 TYR B 88
ARG 0.009 0.000 ARG B 67
*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
1678 Ramachandran restraints generated.
839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
1678 Ramachandran restraints generated.
839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
211 residues out of total 717 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 33
poor density : 178
time to evaluate : 0.992
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: A 81 ASP cc_start: 0.8184 (m-30) cc_final: 0.7921 (t70)
REVERT: A 123 ASP cc_start: 0.9405 (m-30) cc_final: 0.9106 (m-30)
REVERT: A 125 GLN cc_start: 0.8169 (mt0) cc_final: 0.7469 (mt0)
REVERT: B 25 ASN cc_start: 0.8653 (m-40) cc_final: 0.7841 (m110)
REVERT: B 88 TYR cc_start: 0.8471 (m-10) cc_final: 0.7870 (m-10)
REVERT: D 42 TYR cc_start: 0.8542 (t80) cc_final: 0.8329 (t80)
REVERT: D 46 LYS cc_start: 0.9333 (tppt) cc_final: 0.9100 (tppt)
REVERT: D 51 ASP cc_start: 0.9303 (p0) cc_final: 0.8945 (p0)
REVERT: D 83 TYR cc_start: 0.8281 (m-10) cc_final: 0.7515 (m-10)
REVERT: D 85 LYS cc_start: 0.9368 (mttm) cc_final: 0.9157 (mmtt)
REVERT: D 120 LYS cc_start: 0.9137 (ttpt) cc_final: 0.8866 (ttmm)
REVERT: E 57 SER cc_start: 0.9334 (p) cc_final: 0.8941 (p)
REVERT: E 59 GLU cc_start: 0.8901 (pm20) cc_final: 0.8216 (pm20)
REVERT: E 82 LEU cc_start: 0.9576 (mt) cc_final: 0.9335 (mm)
REVERT: F 88 TYR cc_start: 0.8731 (m-10) cc_final: 0.8420 (m-10)
REVERT: F 91 LYS cc_start: 0.9315 (tttp) cc_final: 0.9083 (ttmt)
REVERT: H 85 LYS cc_start: 0.9315 (mttm) cc_final: 0.8801 (mtmm)
REVERT: C 64 GLU cc_start: 0.9104 (tm-30) cc_final: 0.8321 (tm-30)
REVERT: G 41 GLU cc_start: 0.8649 (tm-30) cc_final: 0.8120 (tm-30)
outliers start: 33
outliers final: 29
residues processed: 189
average time/residue: 0.2747
time to fit residues: 72.3450
Evaluate side-chains
206 residues out of total 717 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 29
poor density : 177
time to evaluate : 0.991
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 51 ILE
Chi-restraints excluded: chain A residue 80 THR
Chi-restraints excluded: chain A residue 92 LEU
Chi-restraints excluded: chain A residue 93 GLN
Chi-restraints excluded: chain A residue 110 CYS
Chi-restraints excluded: chain B residue 93 GLN
Chi-restraints excluded: chain D residue 52 THR
Chi-restraints excluded: chain D residue 69 ILE
Chi-restraints excluded: chain D residue 118 VAL
Chi-restraints excluded: chain E residue 80 THR
Chi-restraints excluded: chain E residue 110 CYS
Chi-restraints excluded: chain E residue 115 LYS
Chi-restraints excluded: chain F residue 30 THR
Chi-restraints excluded: chain F residue 50 ILE
Chi-restraints excluded: chain F residue 81 VAL
Chi-restraints excluded: chain H residue 101 LEU
Chi-restraints excluded: chain K residue 476 LEU
Chi-restraints excluded: chain C residue 23 LEU
Chi-restraints excluded: chain C residue 40 SER
Chi-restraints excluded: chain C residue 74 LYS
Chi-restraints excluded: chain C residue 79 ILE
Chi-restraints excluded: chain C residue 91 GLU
Chi-restraints excluded: chain C residue 100 VAL
Chi-restraints excluded: chain C residue 116 LEU
Chi-restraints excluded: chain G residue 15 LYS
Chi-restraints excluded: chain G residue 16 THR
Chi-restraints excluded: chain G residue 18 SER
Chi-restraints excluded: chain G residue 62 ILE
Chi-restraints excluded: chain G residue 79 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 108
random chunks:
chunk 41 optimal weight: 0.9990
chunk 62 optimal weight: 3.9990
chunk 31 optimal weight: 0.5980
chunk 20 optimal weight: 0.6980
chunk 66 optimal weight: 5.9990
chunk 70 optimal weight: 3.9990
chunk 51 optimal weight: 0.6980
chunk 9 optimal weight: 0.5980
chunk 81 optimal weight: 9.9990
chunk 94 optimal weight: 1.9990
chunk 99 optimal weight: 1.9990
overall best weight: 0.7182
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
B 93 GLN
M 62 GLN
Total number of N/Q/H flips: 2
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8550
moved from start: 0.2133
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.004 0.033 13659 Z= 0.203
Angle : 0.589 8.451 19698 Z= 0.342
Chirality : 0.034 0.159 2240
Planarity : 0.004 0.041 1478
Dihedral : 29.654 148.647 4171
Min Nonbonded Distance : 2.134
Molprobity Statistics.
All-atom Clashscore : 8.11
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 2.39 %
Favored : 97.61 %
Rotamer:
Outliers : 3.19 %
Allowed : 19.28 %
Favored : 77.53 %
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 (0.29), residues: 839
helix: 2.74 (0.22), residues: 554
sheet: 1.21 (1.12), residues: 26
loop : -0.66 (0.37), residues: 259
Max deviation from planes:
Type MaxDev MeanDev LineInFile
HIS 0.002 0.001 HIS H 109
PHE 0.010 0.001 PHE A 78
TYR 0.014 0.001 TYR B 88
ARG 0.006 0.000 ARG H 33
*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
1678 Ramachandran restraints generated.
839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
1678 Ramachandran restraints generated.
839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
201 residues out of total 717 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 22
poor density : 179
time to evaluate : 1.002
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: A 78 PHE cc_start: 0.7586 (t80) cc_final: 0.7073 (t80)
REVERT: A 123 ASP cc_start: 0.9377 (m-30) cc_final: 0.9049 (m-30)
REVERT: A 125 GLN cc_start: 0.8159 (mt0) cc_final: 0.7371 (mt0)
REVERT: B 25 ASN cc_start: 0.8588 (m-40) cc_final: 0.7765 (m110)
REVERT: B 67 ARG cc_start: 0.7192 (mmp80) cc_final: 0.6862 (tpp80)
REVERT: B 88 TYR cc_start: 0.8476 (m-10) cc_final: 0.7865 (m-10)
REVERT: D 51 ASP cc_start: 0.9255 (p0) cc_final: 0.8878 (p0)
REVERT: D 83 TYR cc_start: 0.8167 (m-10) cc_final: 0.7513 (m-10)
REVERT: D 85 LYS cc_start: 0.9353 (mttm) cc_final: 0.9146 (mmtt)
REVERT: D 120 LYS cc_start: 0.9094 (ttpt) cc_final: 0.8758 (tttt)
REVERT: E 57 SER cc_start: 0.9292 (p) cc_final: 0.8894 (p)
REVERT: E 59 GLU cc_start: 0.8852 (pm20) cc_final: 0.8195 (pm20)
REVERT: E 82 LEU cc_start: 0.9468 (mt) cc_final: 0.9237 (mm)
REVERT: F 85 ASP cc_start: 0.8910 (m-30) cc_final: 0.8573 (m-30)
REVERT: F 91 LYS cc_start: 0.9268 (tttp) cc_final: 0.9042 (ttmt)
REVERT: H 85 LYS cc_start: 0.9302 (mttm) cc_final: 0.8800 (mtmm)
REVERT: C 64 GLU cc_start: 0.9070 (tm-30) cc_final: 0.8272 (tm-30)
REVERT: G 41 GLU cc_start: 0.8620 (tm-30) cc_final: 0.8088 (tm-30)
outliers start: 22
outliers final: 18
residues processed: 187
average time/residue: 0.2645
time to fit residues: 68.9303
Evaluate side-chains
192 residues out of total 717 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 18
poor density : 174
time to evaluate : 1.041
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 80 THR
Chi-restraints excluded: chain A residue 92 LEU
Chi-restraints excluded: chain A residue 93 GLN
Chi-restraints excluded: chain A residue 110 CYS
Chi-restraints excluded: chain D residue 118 VAL
Chi-restraints excluded: chain E residue 110 CYS
Chi-restraints excluded: chain F residue 30 THR
Chi-restraints excluded: chain F residue 50 ILE
Chi-restraints excluded: chain F residue 81 VAL
Chi-restraints excluded: chain H residue 101 LEU
Chi-restraints excluded: chain C residue 23 LEU
Chi-restraints excluded: chain C residue 40 SER
Chi-restraints excluded: chain C residue 79 ILE
Chi-restraints excluded: chain C residue 116 LEU
Chi-restraints excluded: chain G residue 16 THR
Chi-restraints excluded: chain G residue 18 SER
Chi-restraints excluded: chain G residue 62 ILE
Chi-restraints excluded: chain G residue 79 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 108
random chunks:
chunk 90 optimal weight: 2.9990
chunk 97 optimal weight: 0.7980
chunk 99 optimal weight: 0.0970
chunk 58 optimal weight: 3.9990
chunk 42 optimal weight: 2.9990
chunk 76 optimal weight: 4.9990
chunk 29 optimal weight: 0.8980
chunk 87 optimal weight: 5.9990
chunk 91 optimal weight: 0.5980
chunk 96 optimal weight: 3.9990
chunk 63 optimal weight: 4.9990
overall best weight: 1.0780
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
B 93 GLN
K 475 HIS
M 62 GLN
Total number of N/Q/H flips: 3
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8558
moved from start: 0.2164
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.004 0.033 13659 Z= 0.243
Angle : 0.597 8.339 19698 Z= 0.347
Chirality : 0.034 0.163 2240
Planarity : 0.004 0.038 1478
Dihedral : 29.661 149.115 4171
Min Nonbonded Distance : 2.127
Molprobity Statistics.
All-atom Clashscore : 8.24
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 2.63 %
Favored : 97.37 %
Rotamer:
Outliers : 3.47 %
Allowed : 19.42 %
Favored : 77.12 %
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: 2.55 (0.29), residues: 839
helix: 2.70 (0.22), residues: 556
sheet: 1.30 (1.12), residues: 26
loop : -0.63 (0.37), residues: 257
Max deviation from planes:
Type MaxDev MeanDev LineInFile
HIS 0.007 0.001 HIS H 109
PHE 0.013 0.001 PHE A 78
TYR 0.015 0.002 TYR H 83
ARG 0.010 0.000 ARG H 33
*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
1678 Ramachandran restraints generated.
839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
1678 Ramachandran restraints generated.
839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
198 residues out of total 717 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 24
poor density : 174
time to evaluate : 1.022
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: A 78 PHE cc_start: 0.7577 (t80) cc_final: 0.7042 (t80)
REVERT: A 123 ASP cc_start: 0.9383 (m-30) cc_final: 0.9054 (m-30)
REVERT: A 125 GLN cc_start: 0.8167 (mt0) cc_final: 0.7372 (mt0)
REVERT: B 25 ASN cc_start: 0.8635 (m-40) cc_final: 0.7812 (m110)
REVERT: B 88 TYR cc_start: 0.8500 (m-10) cc_final: 0.7945 (m-10)
REVERT: D 51 ASP cc_start: 0.9283 (p0) cc_final: 0.8875 (p0)
REVERT: D 83 TYR cc_start: 0.8157 (m-10) cc_final: 0.7586 (m-10)
REVERT: D 85 LYS cc_start: 0.9357 (mttm) cc_final: 0.9147 (mmtt)
REVERT: D 120 LYS cc_start: 0.9088 (ttpt) cc_final: 0.8827 (ttmm)
REVERT: E 57 SER cc_start: 0.9282 (p) cc_final: 0.8881 (p)
REVERT: E 59 GLU cc_start: 0.8869 (pm20) cc_final: 0.8202 (pm20)
REVERT: E 82 LEU cc_start: 0.9459 (mt) cc_final: 0.9214 (mm)
REVERT: F 85 ASP cc_start: 0.8941 (m-30) cc_final: 0.8588 (m-30)
REVERT: F 88 TYR cc_start: 0.8707 (m-10) cc_final: 0.8259 (m-10)
REVERT: F 91 LYS cc_start: 0.9283 (tttp) cc_final: 0.9056 (ttmt)
REVERT: H 33 ARG cc_start: 0.8032 (mtp-110) cc_final: 0.7377 (mtp-110)
REVERT: H 83 TYR cc_start: 0.8616 (m-10) cc_final: 0.7874 (m-80)
REVERT: H 85 LYS cc_start: 0.9306 (mttm) cc_final: 0.8805 (mtmm)
REVERT: C 64 GLU cc_start: 0.9078 (tm-30) cc_final: 0.8287 (tm-30)
REVERT: G 41 GLU cc_start: 0.8616 (tm-30) cc_final: 0.8088 (tm-30)
outliers start: 24
outliers final: 21
residues processed: 184
average time/residue: 0.2697
time to fit residues: 69.0897
Evaluate side-chains
188 residues out of total 717 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 21
poor density : 167
time to evaluate : 0.994
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 80 THR
Chi-restraints excluded: chain A residue 92 LEU
Chi-restraints excluded: chain A residue 93 GLN
Chi-restraints excluded: chain A residue 110 CYS
Chi-restraints excluded: chain B residue 93 GLN
Chi-restraints excluded: chain D residue 118 VAL
Chi-restraints excluded: chain E residue 110 CYS
Chi-restraints excluded: chain E residue 115 LYS
Chi-restraints excluded: chain F residue 30 THR
Chi-restraints excluded: chain F residue 50 ILE
Chi-restraints excluded: chain F residue 81 VAL
Chi-restraints excluded: chain H residue 101 LEU
Chi-restraints excluded: chain C residue 23 LEU
Chi-restraints excluded: chain C residue 40 SER
Chi-restraints excluded: chain C residue 79 ILE
Chi-restraints excluded: chain C residue 116 LEU
Chi-restraints excluded: chain G residue 15 LYS
Chi-restraints excluded: chain G residue 16 THR
Chi-restraints excluded: chain G residue 18 SER
Chi-restraints excluded: chain G residue 62 ILE
Chi-restraints excluded: chain G residue 79 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 108
random chunks:
chunk 102 optimal weight: 2.9990
chunk 62 optimal weight: 4.9990
chunk 48 optimal weight: 1.9990
chunk 71 optimal weight: 3.9990
chunk 107 optimal weight: 0.8980
chunk 99 optimal weight: 3.9990
chunk 85 optimal weight: 8.9990
chunk 8 optimal weight: 0.0570
chunk 66 optimal weight: 5.9990
chunk 52 optimal weight: 6.9990
chunk 68 optimal weight: 4.9990
overall best weight: 1.9904
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
B 93 GLN
M 62 GLN
Total number of N/Q/H flips: 2
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8596
moved from start: 0.2316
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.006 0.036 13659 Z= 0.368
Angle : 0.653 8.456 19698 Z= 0.374
Chirality : 0.037 0.164 2240
Planarity : 0.004 0.040 1478
Dihedral : 29.834 150.398 4171
Min Nonbonded Distance : 2.112
Molprobity Statistics.
All-atom Clashscore : 8.92
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 3.23 %
Favored : 96.77 %
Rotamer:
Outliers : 3.74 %
Allowed : 19.14 %
Favored : 77.12 %
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 (0.29), residues: 839
helix: 2.56 (0.22), residues: 557
sheet: 1.44 (1.15), residues: 26
loop : -0.75 (0.37), residues: 256
Max deviation from planes:
Type MaxDev MeanDev LineInFile
HIS 0.007 0.001 HIS H 109
PHE 0.010 0.001 PHE E 78
TYR 0.023 0.002 TYR B 88
ARG 0.009 0.000 ARG H 33
********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
1678 Ramachandran restraints generated.
839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
1678 Ramachandran restraints generated.
839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
198 residues out of total 717 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 26
poor density : 172
time to evaluate : 1.015
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: A 123 ASP cc_start: 0.9397 (m-30) cc_final: 0.9096 (m-30)
REVERT: A 125 GLN cc_start: 0.8156 (mt0) cc_final: 0.7439 (mt0)
REVERT: B 25 ASN cc_start: 0.8667 (m-40) cc_final: 0.7980 (m110)
REVERT: B 88 TYR cc_start: 0.8582 (m-10) cc_final: 0.7792 (m-10)
REVERT: D 51 ASP cc_start: 0.9313 (p0) cc_final: 0.8979 (p0)
REVERT: D 83 TYR cc_start: 0.8288 (m-10) cc_final: 0.7513 (m-10)
REVERT: D 85 LYS cc_start: 0.9366 (mttm) cc_final: 0.9158 (mmtt)
REVERT: D 120 LYS cc_start: 0.9135 (ttpt) cc_final: 0.8860 (ttmm)
REVERT: E 57 SER cc_start: 0.9231 (p) cc_final: 0.8549 (p)
REVERT: E 59 GLU cc_start: 0.8876 (pm20) cc_final: 0.8183 (pm20)
REVERT: E 82 LEU cc_start: 0.9497 (mt) cc_final: 0.9257 (mm)
REVERT: F 88 TYR cc_start: 0.8640 (m-10) cc_final: 0.8213 (m-10)
REVERT: F 91 LYS cc_start: 0.9314 (tttp) cc_final: 0.9088 (ttmt)
REVERT: H 85 LYS cc_start: 0.9314 (mttm) cc_final: 0.8795 (mtmm)
REVERT: C 64 GLU cc_start: 0.9107 (tm-30) cc_final: 0.8326 (tm-30)
REVERT: G 41 GLU cc_start: 0.8710 (tm-30) cc_final: 0.8169 (tm-30)
outliers start: 26
outliers final: 24
residues processed: 182
average time/residue: 0.2655
time to fit residues: 67.4144
Evaluate side-chains
194 residues out of total 717 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 24
poor density : 170
time to evaluate : 1.004
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 80 THR
Chi-restraints excluded: chain A residue 92 LEU
Chi-restraints excluded: chain A residue 93 GLN
Chi-restraints excluded: chain A residue 110 CYS
Chi-restraints excluded: chain B residue 93 GLN
Chi-restraints excluded: chain D residue 118 VAL
Chi-restraints excluded: chain E residue 80 THR
Chi-restraints excluded: chain E residue 110 CYS
Chi-restraints excluded: chain E residue 115 LYS
Chi-restraints excluded: chain F residue 30 THR
Chi-restraints excluded: chain F residue 50 ILE
Chi-restraints excluded: chain F residue 81 VAL
Chi-restraints excluded: chain H residue 101 LEU
Chi-restraints excluded: chain C residue 23 LEU
Chi-restraints excluded: chain C residue 40 SER
Chi-restraints excluded: chain C residue 54 VAL
Chi-restraints excluded: chain C residue 79 ILE
Chi-restraints excluded: chain C residue 91 GLU
Chi-restraints excluded: chain C residue 116 LEU
Chi-restraints excluded: chain G residue 15 LYS
Chi-restraints excluded: chain G residue 16 THR
Chi-restraints excluded: chain G residue 18 SER
Chi-restraints excluded: chain G residue 62 ILE
Chi-restraints excluded: chain G residue 79 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 108
random chunks:
chunk 91 optimal weight: 0.9980
chunk 26 optimal weight: 4.9990
chunk 79 optimal weight: 5.9990
chunk 12 optimal weight: 0.9990
chunk 23 optimal weight: 0.3980
chunk 85 optimal weight: 9.9990
chunk 35 optimal weight: 1.9990
chunk 88 optimal weight: 1.9990
chunk 10 optimal weight: 0.4980
chunk 15 optimal weight: 1.9990
chunk 75 optimal weight: 3.9990
overall best weight: 0.9784
-------------------------------------------------------------------------------
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 = 0.3262 r_free = 0.3262 target = 0.086102 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2636 r_free = 0.2636 target = 0.055161 restraints weight = 43448.454|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2684 r_free = 0.2684 target = 0.057279 restraints weight = 20041.501|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.2714 r_free = 0.2714 target = 0.058601 restraints weight = 13011.952|
|-----------------------------------------------------------------------------|
r_work (final): 0.2694
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2694
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2694 r_free = 0.2694 target_work(ls_wunit_k1) = 0.057 |
| occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2693 r_free = 0.2693 target_work(ls_wunit_k1) = 0.057 |
| occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 |
|-----------------------------------------------------------------------------|
r_final: 0.2693
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8697
moved from start: 0.2290
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.004 0.035 13659 Z= 0.230
Angle : 0.606 8.540 19698 Z= 0.350
Chirality : 0.034 0.160 2240
Planarity : 0.004 0.037 1478
Dihedral : 29.728 149.062 4171
Min Nonbonded Distance : 2.130
Molprobity Statistics.
All-atom Clashscore : 8.54
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 2.51 %
Favored : 97.49 %
Rotamer:
Outliers : 3.19 %
Allowed : 19.83 %
Favored : 76.98 %
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 (0.30), residues: 839
helix: 2.68 (0.22), residues: 557
sheet: 1.44 (1.14), residues: 26
loop : -0.69 (0.38), residues: 256
Max deviation from planes:
Type MaxDev MeanDev LineInFile
HIS 0.004 0.001 HIS H 109
PHE 0.011 0.001 PHE A 78
TYR 0.013 0.002 TYR F 88
ARG 0.009 0.000 ARG H 33
Origin is already at (0, 0, 0), no shifts will be applied
===============================================================================
Job complete
usr+sys time: 2313.03 seconds
wall clock time: 42 minutes 9.90 seconds (2529.90 seconds total)