Starting phenix.real_space_refine
on Wed Jan 15 17:55:35 2025 by dcliebschner
===============================================================================
Processing files:
-------------------------------------------------------------------------------
Found model, /net/cci-nas-00/data/ceres_data/8yh6_39282/01_2025/8yh6_39282.cif
Found real_map, /net/cci-nas-00/data/ceres_data/8yh6_39282/01_2025/8yh6_39282.map
Processing PHIL parameters:
-------------------------------------------------------------------------------
Adding command-line PHIL:
-------------------------
refinement.macro_cycles=10
scattering_table=electron
resolution=3.62
write_initial_geo_file=False
Final processed PHIL parameters:
-------------------------------------------------------------------------------
data_manager {
real_map_files = "/net/cci-nas-00/data/ceres_data/8yh6_39282/01_2025/8yh6_39282.map"
default_real_map = "/net/cci-nas-00/data/ceres_data/8yh6_39282/01_2025/8yh6_39282.map"
model {
file = "/net/cci-nas-00/data/ceres_data/8yh6_39282/01_2025/8yh6_39282.cif"
}
default_model = "/net/cci-nas-00/data/ceres_data/8yh6_39282/01_2025/8yh6_39282.cif"
}
resolution = 3.62
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= 0.005 sd= 1.069
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: 6
Type Number sf(0) Gaussians
I 1 10.91 5
S 66 5.16 5
Cl 1 4.86 5
C 5570 2.51 5
N 1464 2.21 5
O 1604 1.98 5
sf(0) = scattering factor at diffraction angle 0.
Process input model
Symmetric amino acids flipped. Time to flip 12 residue(s): 0.03s
Monomer Library directory:
"/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
Total number of atoms: 8706
Number of models: 1
Model: ""
Number of chains: 6
Chain: "B"
Number of atoms: 2583
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 336, 2583
Classifications: {'peptide': 336}
Link IDs: {'PTRANS': 5, 'TRANS': 330}
Chain: "G"
Number of atoms: 407
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 53, 407
Classifications: {'peptide': 53}
Link IDs: {'PTRANS': 4, 'TRANS': 48}
Chain: "S"
Number of atoms: 1783
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 232, 1783
Classifications: {'peptide': 232}
Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221}
Chain breaks: 1
Chain: "R"
Number of atoms: 2198
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 271, 2198
Classifications: {'peptide': 271}
Link IDs: {'PTRANS': 8, 'TRANS': 262}
Chain breaks: 1
Chain: "A"
Number of atoms: 1705
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 212, 1705
Classifications: {'peptide': 212}
Modifications used: {'COO': 1}
Incomplete info: {'truncation_to_alanine': 1}
Link IDs: {'PTRANS': 2, 'TRANS': 209}
Chain breaks: 2
Unresolved non-hydrogen bonds: 3
Unresolved non-hydrogen angles: 4
Unresolved non-hydrogen dihedrals: 2
Planarities with less than four sites: {'ASP:plan': 1}
Unresolved non-hydrogen planarities: 3
Chain: "R"
Number of atoms: 30
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 1, 30
Unusual residues: {'XS0': 1}
Classifications: {'undetermined': 1}
Time building chain proxies: 5.16, per 1000 atoms: 0.59
Number of scatterers: 8706
At special positions: 0
Unit cell: (91.02, 123.21, 127.65, 90, 90, 90)
Space group: P 1 (No. 1)
Number of sites at special positions: 0
Number of scattering types: 6
Type Number sf(0)
I 1 52.95
Cl 1 17.00
S 66 16.00
O 1604 8.00
N 1464 7.00
C 5570 6.00
sf(0) = scattering factor at diffraction angle 0.
Number of disulfides: simple=4, symmetry=0
Simple disulfide: pdb=" SG CYS B 103 " - pdb=" SG CYS B 114 " distance=1.70
Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03
Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " distance=2.05
Simple disulfide: pdb=" SG CYS R 83 " - pdb=" SG CYS R 165 " distance=2.03
Automatic linking
Parameters for automatic linking
Linking & cutoffs
Metal : Auto - 3.00
Amino acid : True - 1.90
Carbohydrate : True - 1.99
Ligands : True - 1.99
Small molecules : False - 1.98
Amino acid - RNA/DNA : False
Number of custom bonds: simple=0, symmetry=0
Time building additional restraints: 2.22
Conformation dependent library (CDL) restraints added in 1.2 seconds
2172 Ramachandran restraints generated.
1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
Adding C-beta torsion restraints...
Number of C-beta restraints generated: 2068
Finding SS restraints...
Secondary structure from input PDB file:
29 helices and 12 sheets defined
37.3% alpha, 21.8% beta
0 base pairs and 0 stacking pairs defined.
Time for finding SS restraints: 0.89
Creating SS restraints...
Processing helix chain 'B' and resid 6 through 25
removed outlier: 3.637A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A)
Processing helix chain 'B' and resid 29 through 35
removed outlier: 3.833A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A)
Processing helix chain 'G' and resid 12 through 22
Processing helix chain 'G' and resid 33 through 44
removed outlier: 3.556A pdb=" N LEU G 37 " --> pdb=" O ALA G 33 " (cutoff:3.500A)
Processing helix chain 'S' and resid 28 through 32
removed outlier: 3.529A pdb=" N PHE S 32 " --> pdb=" O PHE S 29 " (cutoff:3.500A)
Processing helix chain 'S' and resid 53 through 56
removed outlier: 3.928A pdb=" N GLY S 56 " --> pdb=" O SER S 53 " (cutoff:3.500A)
No H-bonds generated for 'chain 'S' and resid 53 through 56'
Processing helix chain 'R' and resid 10 through 40
Processing helix chain 'R' and resid 41 through 44
Processing helix chain 'R' and resid 45 through 64
Processing helix chain 'R' and resid 64 through 75
Processing helix chain 'R' and resid 79 through 115
Processing helix chain 'R' and resid 116 through 122
removed outlier: 4.435A pdb=" N ARG R 120 " --> pdb=" O VAL R 116 " (cutoff:3.500A)
Processing helix chain 'R' and resid 123 through 144
Processing helix chain 'R' and resid 145 through 148
Processing helix chain 'R' and resid 150 through 154
Processing helix chain 'R' and resid 166 through 171
removed outlier: 3.574A pdb=" N VAL R 170 " --> pdb=" O ARG R 166 " (cutoff:3.500A)
Processing helix chain 'R' and resid 172 through 179
removed outlier: 3.570A pdb=" N MET R 176 " --> pdb=" O ARG R 172 " (cutoff:3.500A)
Processing helix chain 'R' and resid 179 through 185
Processing helix chain 'R' and resid 185 through 207
Processing helix chain 'R' and resid 225 through 254
Proline residue: R 244 - end of helix
Processing helix chain 'R' and resid 259 through 282
removed outlier: 3.824A pdb=" N MET R 275 " --> pdb=" O HIS R 271 " (cutoff:3.500A)
Proline residue: R 278 - end of helix
Processing helix chain 'R' and resid 285 through 295
Processing helix chain 'A' and resid 6 through 31
removed outlier: 4.118A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A)
removed outlier: 3.586A pdb=" N LYS A 29 " --> pdb=" O GLU A 25 " (cutoff:3.500A)
Processing helix chain 'A' and resid 45 through 53
Processing helix chain 'A' and resid 211 through 216
Processing helix chain 'A' and resid 242 through 256
Processing helix chain 'A' and resid 275 through 281
removed outlier: 3.886A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A)
Processing helix chain 'A' and resid 295 through 310
removed outlier: 3.615A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A)
Processing helix chain 'A' and resid 330 through 352
Processing sheet with id=AA1, first strand: chain 'B' and resid 47 through 51
removed outlier: 3.994A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A)
removed outlier: 6.650A pdb=" N ALA B 328 " --> pdb=" O LEU B 318 " (cutoff:3.500A)
removed outlier: 4.503A pdb=" N LEU B 318 " --> pdb=" O ALA B 328 " (cutoff:3.500A)
removed outlier: 6.680A pdb=" N GLY B 330 " --> pdb=" O SER B 316 " (cutoff:3.500A)
Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63
removed outlier: 3.673A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A)
removed outlier: 4.096A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A)
removed outlier: 6.425A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A)
removed outlier: 4.304A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A)
removed outlier: 6.465A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A)
Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 105
removed outlier: 4.301A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A)
removed outlier: 4.855A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A)
removed outlier: 6.156A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A)
removed outlier: 6.183A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A)
Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 153
removed outlier: 5.007A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A)
removed outlier: 3.704A pdb=" N SER B 160 " --> pdb=" O CYS B 148 " (cutoff:3.500A)
removed outlier: 6.527A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A)
removed outlier: 3.595A pdb=" N SER B 161 " --> pdb=" O THR B 165 " (cutoff:3.500A)
removed outlier: 4.493A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A)
Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192
removed outlier: 3.517A pdb=" N VAL B 200 " --> pdb=" O SER B 191 " (cutoff:3.500A)
removed outlier: 3.962A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A)
removed outlier: 7.201A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A)
removed outlier: 6.499A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A)
Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234
removed outlier: 6.912A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A)
removed outlier: 4.920A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A)
removed outlier: 7.232A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A)
removed outlier: 5.059A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A)
removed outlier: 7.137A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A)
removed outlier: 6.689A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A)
removed outlier: 4.799A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A)
removed outlier: 6.606A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A)
Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 276
removed outlier: 6.515A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A)
removed outlier: 4.858A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A)
removed outlier: 6.920A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A)
removed outlier: 3.866A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A)
removed outlier: 6.295A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A)
removed outlier: 6.354A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A)
Processing sheet with id=AA8, first strand: chain 'S' and resid 3 through 6
Processing sheet with id=AA9, first strand: chain 'S' and resid 10 through 12
removed outlier: 6.191A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A)
removed outlier: 6.751A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A)
removed outlier: 4.473A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A)
removed outlier: 6.532A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A)
removed outlier: 3.911A pdb=" N GLY S 44 " --> pdb=" O ALA S 40 " (cutoff:3.500A)
Processing sheet with id=AB1, first strand: chain 'S' and resid 128 through 130
removed outlier: 3.636A pdb=" N ALA S 199 " --> pdb=" O SER S 196 " (cutoff:3.500A)
Processing sheet with id=AB2, first strand: chain 'S' and resid 135 through 136
removed outlier: 6.143A pdb=" N VAL S 135 " --> pdb=" O GLU S 234 " (cutoff:3.500A)
removed outlier: 3.713A pdb=" N GLY S 213 " --> pdb=" O LEU S 233 " (cutoff:3.500A)
removed outlier: 6.472A pdb=" N TRP S 164 " --> pdb=" O LEU S 176 " (cutoff:3.500A)
Processing sheet with id=AB3, first strand: chain 'A' and resid 185 through 191
removed outlier: 6.270A pdb=" N VAL A 34 " --> pdb=" O LYS A 197 " (cutoff:3.500A)
removed outlier: 7.288A pdb=" N PHE A 199 " --> pdb=" O VAL A 34 " (cutoff:3.500A)
removed outlier: 6.807A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A)
removed outlier: 9.159A pdb=" N ALA A 220 " --> pdb=" O GLU A 33 " (cutoff:3.500A)
removed outlier: 7.013A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A)
removed outlier: 7.843A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A)
removed outlier: 6.679A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A)
removed outlier: 7.991A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A)
removed outlier: 7.190A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A)
removed outlier: 6.400A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A)
removed outlier: 7.472A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A)
removed outlier: 7.083A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A)
removed outlier: 6.447A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A)
removed outlier: 7.808A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A)
removed outlier: 6.930A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A)
414 hydrogen bonds defined for protein.
1170 hydrogen bond angles defined for protein.
Restraints generated for nucleic acids:
0 hydrogen bonds
0 hydrogen bond angles
0 basepair planarities
0 basepair parallelities
0 stacking parallelities
Total time for adding SS restraints: 1.96
Time building geometry restraints manager: 2.52 seconds
NOTE: a complete listing of the restraints can be obtained by requesting
output of .geo file.
Histogram of bond lengths:
1.18 - 1.36: 2831
1.36 - 1.55: 5959
1.55 - 1.73: 0
1.73 - 1.92: 99
1.92 - 2.10: 1
Bond restraints: 8890
Sorted by residual:
bond pdb=" C SER A 6 "
pdb=" O SER A 6 "
ideal model delta sigma weight residual
1.234 1.305 -0.071 1.35e-02 5.49e+03 2.77e+01
bond pdb=" C ASP A 200 "
pdb=" O ASP A 200 "
ideal model delta sigma weight residual
1.236 1.299 -0.063 1.22e-02 6.72e+03 2.67e+01
bond pdb=" C PHE A 307 "
pdb=" O PHE A 307 "
ideal model delta sigma weight residual
1.237 1.181 0.056 1.19e-02 7.06e+03 2.19e+01
bond pdb=" N VAL R 170 "
pdb=" CA VAL R 170 "
ideal model delta sigma weight residual
1.459 1.498 -0.039 9.10e-03 1.21e+04 1.87e+01
bond pdb=" CA SER A 6 "
pdb=" CB SER A 6 "
ideal model delta sigma weight residual
1.528 1.462 0.066 1.61e-02 3.86e+03 1.69e+01
... (remaining 8885 not shown)
Histogram of bond angle deviations from ideal:
0.00 - 1.89: 10006
1.89 - 3.78: 1844
3.78 - 5.66: 168
5.66 - 7.55: 17
7.55 - 9.44: 6
Bond angle restraints: 12041
Sorted by residual:
angle pdb=" N ILE R 248 "
pdb=" CA ILE R 248 "
pdb=" C ILE R 248 "
ideal model delta sigma weight residual
110.42 100.98 9.44 9.60e-01 1.09e+00 9.67e+01
angle pdb=" N LYS A 210 "
pdb=" CA LYS A 210 "
pdb=" C LYS A 210 "
ideal model delta sigma weight residual
112.92 103.60 9.32 1.23e+00 6.61e-01 5.74e+01
angle pdb=" N LEU A 268 "
pdb=" CA LEU A 268 "
pdb=" C LEU A 268 "
ideal model delta sigma weight residual
108.54 100.39 8.15 1.41e+00 5.03e-01 3.34e+01
angle pdb=" C ASP R 255 "
pdb=" N GLY R 256 "
pdb=" CA GLY R 256 "
ideal model delta sigma weight residual
122.27 116.74 5.53 9.90e-01 1.02e+00 3.12e+01
angle pdb=" CA ARG B 52 "
pdb=" C ARG B 52 "
pdb=" O ARG B 52 "
ideal model delta sigma weight residual
121.58 115.15 6.43 1.16e+00 7.43e-01 3.07e+01
... (remaining 12036 not shown)
Histogram of dihedral angle deviations from ideal:
0.00 - 30.67: 5132
30.67 - 61.35: 139
61.35 - 92.02: 7
92.02 - 122.70: 0
122.70 - 153.37: 4
Dihedral angle restraints: 5282
sinusoidal: 2077
harmonic: 3205
Sorted by residual:
dihedral pdb=" CB CYS B 103 "
pdb=" SG CYS B 103 "
pdb=" SG CYS B 114 "
pdb=" CB CYS B 114 "
ideal model delta sinusoidal sigma weight residual
93.00 19.91 73.09 1 1.00e+01 1.00e-02 6.81e+01
dihedral pdb=" CD ARG B 137 "
pdb=" NE ARG B 137 "
pdb=" CZ ARG B 137 "
pdb=" NH1 ARG B 137 "
ideal model delta sinusoidal sigma weight residual
0.00 51.93 -51.93 1 1.00e+01 1.00e-02 3.68e+01
dihedral pdb=" CA TYR S 223 "
pdb=" C TYR S 223 "
pdb=" N PRO S 224 "
pdb=" CA PRO S 224 "
ideal model delta harmonic sigma weight residual
0.00 29.00 -29.00 0 5.00e+00 4.00e-02 3.36e+01
... (remaining 5279 not shown)
Histogram of chiral volume deviations from ideal:
0.000 - 0.051: 497
0.051 - 0.103: 497
0.103 - 0.154: 272
0.154 - 0.206: 89
0.206 - 0.257: 22
Chirality restraints: 1377
Sorted by residual:
chirality pdb=" CB VAL R 234 "
pdb=" CA VAL R 234 "
pdb=" CG1 VAL R 234 "
pdb=" CG2 VAL R 234 "
both_signs ideal model delta sigma weight residual
False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.65e+00
chirality pdb=" CA VAL B 327 "
pdb=" N VAL B 327 "
pdb=" C VAL B 327 "
pdb=" CB VAL B 327 "
both_signs ideal model delta sigma weight residual
False 2.44 2.69 -0.25 2.00e-01 2.50e+01 1.60e+00
chirality pdb=" CB ILE R 98 "
pdb=" CA ILE R 98 "
pdb=" CG1 ILE R 98 "
pdb=" CG2 ILE R 98 "
both_signs ideal model delta sigma weight residual
False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.55e+00
... (remaining 1374 not shown)
Planarity restraints: 1501
Sorted by residual:
delta sigma weight rms_deltas residual
plane pdb=" C08 XS0 R 801 " 0.173 2.00e-02 2.50e+03 7.77e-02 1.81e+02
pdb=" C11 XS0 R 801 " -0.016 2.00e-02 2.50e+03
pdb=" C13 XS0 R 801 " -0.081 2.00e-02 2.50e+03
pdb=" C14 XS0 R 801 " -0.010 2.00e-02 2.50e+03
pdb=" C16 XS0 R 801 " -0.017 2.00e-02 2.50e+03
pdb=" C18 XS0 R 801 " -0.080 2.00e-02 2.50e+03
pdb=" N10 XS0 R 801 " -0.032 2.00e-02 2.50e+03
pdb=" N12 XS0 R 801 " -0.045 2.00e-02 2.50e+03
pdb=" N15 XS0 R 801 " 0.006 2.00e-02 2.50e+03
pdb=" N17 XS0 R 801 " -0.067 2.00e-02 2.50e+03
pdb=" N20 XS0 R 801 " 0.143 2.00e-02 2.50e+03
pdb="CL19 XS0 R 801 " 0.027 2.00e-02 2.50e+03
delta sigma weight rms_deltas residual
plane pdb=" CD ARG B 137 " -0.856 9.50e-02 1.11e+02 3.84e-01 8.93e+01
pdb=" NE ARG B 137 " 0.051 2.00e-02 2.50e+03
pdb=" CZ ARG B 137 " 0.008 2.00e-02 2.50e+03
pdb=" NH1 ARG B 137 " 0.002 2.00e-02 2.50e+03
pdb=" NH2 ARG B 137 " -0.023 2.00e-02 2.50e+03
delta sigma weight rms_deltas residual
plane pdb=" CD ARG A 205 " -0.726 9.50e-02 1.11e+02 3.25e-01 6.45e+01
pdb=" NE ARG A 205 " 0.042 2.00e-02 2.50e+03
pdb=" CZ ARG A 205 " 0.012 2.00e-02 2.50e+03
pdb=" NH1 ARG A 205 " 0.002 2.00e-02 2.50e+03
pdb=" NH2 ARG A 205 " -0.024 2.00e-02 2.50e+03
... (remaining 1498 not shown)
Histogram of nonbonded interaction distances:
2.22 - 2.76: 1312
2.76 - 3.31: 8871
3.31 - 3.86: 14990
3.86 - 4.41: 18911
4.41 - 4.96: 31539
Nonbonded interactions: 75623
Sorted by model distance:
nonbonded pdb=" OG1 THR B 274 "
pdb=" OD1 ASP B 290 "
model vdw
2.215 3.040
nonbonded pdb=" O MET G 21 "
pdb=" CG1 ILE G 25 "
model vdw
2.238 3.440
nonbonded pdb=" O LEU A 249 "
pdb=" OG SER A 252 "
model vdw
2.255 3.040
nonbonded pdb=" O GLY B 162 "
pdb=" OD1 ASP B 186 "
model vdw
2.258 3.040
nonbonded pdb=" OG SER B 74 "
pdb=" OD1 ASP B 76 "
model vdw
2.279 3.040
... (remaining 75618 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
========== WARNING! ============
No NCS relation were found !!!
================================
Found NCS groups:
found none.
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 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: 0.570
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: 0.330
Check model and map are aligned: 0.060
Set scattering table: 0.080
Process input model: 21.550
Find NCS groups from input model: 0.090
Set up NCS constraints: 0.040
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:2.830
Set ADP refinement strategy: 0.000
Make a string to write initial .geo file:0.000
Internal consistency checks: 0.000
Total: 25.560
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4927
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 : 0.012 0.071 8890 Z= 0.810
Angle : 1.430 9.438 12041 Z= 1.034
Chirality : 0.092 0.257 1377
Planarity : 0.028 0.384 1501
Dihedral : 14.434 153.370 3202
Min Nonbonded Distance : 2.215
Molprobity Statistics.
All-atom Clashscore : 12.85
Ramachandran Plot:
Outliers : 0.09 %
Allowed : 4.88 %
Favored : 95.03 %
Rotamer:
Outliers : 0.94 %
Allowed : 6.82 %
Favored : 92.24 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 3.45 %
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: -2.37 (0.23), residues: 1086
helix: -0.85 (0.24), residues: 374
sheet: -1.81 (0.30), residues: 239
loop : -1.92 (0.26), residues: 473
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.028 0.004 TRP S 36
HIS 0.013 0.003 HIS A 188
PHE 0.081 0.006 PHE A 199
TYR 0.039 0.005 TYR R 15
ARG 0.011 0.002 ARG B 49
*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
2172 Ramachandran restraints generated.
1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
2172 Ramachandran restraints generated.
1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
298 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 9
poor density : 289
time to evaluate : 0.996
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: B 308 LEU cc_start: 0.7028 (mt) cc_final: 0.6653 (mt)
REVERT: G 55 PRO cc_start: 0.5700 (Cg_exo) cc_final: 0.5484 (Cg_endo)
outliers start: 9
outliers final: 2
residues processed: 294
average time/residue: 0.2399
time to fit residues: 93.3512
Evaluate side-chains
170 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 2
poor density : 168
time to evaluate : 1.015
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue 103 CYS
Chi-restraints excluded: chain B residue 119 ASN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 109
random chunks:
chunk 92 optimal weight: 6.9990
chunk 82 optimal weight: 4.9990
chunk 45 optimal weight: 1.9990
chunk 28 optimal weight: 0.8980
chunk 55 optimal weight: 0.4980
chunk 44 optimal weight: 4.9990
chunk 85 optimal weight: 1.9990
chunk 33 optimal weight: 8.9990
chunk 51 optimal weight: 9.9990
chunk 63 optimal weight: 0.9980
chunk 98 optimal weight: 0.7980
overall best weight: 1.0382
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
B 88 ASN
B 91 HIS
** B 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 44 HIS
** S 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 79 HIS
A 22 ASN
A 52 GLN
A 213 HIS
** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 311 ASN
** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 347 ASN
Total number of N/Q/H flips: 9
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4580 r_free = 0.4580 target = 0.163397 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.4254 r_free = 0.4254 target = 0.141084 restraints weight = 25102.097|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.4303 r_free = 0.4303 target = 0.144226 restraints weight = 14913.794|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.4341 r_free = 0.4341 target = 0.146916 restraints weight = 10666.923|
|-----------------------------------------------------------------------------|
r_work (final): 0.4324
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5856
moved from start: 0.4134
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.059 8890 Z= 0.224
Angle : 0.702 14.127 12041 Z= 0.371
Chirality : 0.044 0.169 1377
Planarity : 0.005 0.042 1501
Dihedral : 9.336 131.046 1223
Min Nonbonded Distance : 2.427
Molprobity Statistics.
All-atom Clashscore : 12.68
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 2.85 %
Favored : 97.15 %
Rotamer:
Outliers : 2.83 %
Allowed : 16.05 %
Favored : 81.11 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 3.45 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: -1.29 (0.24), residues: 1086
helix: 0.50 (0.25), residues: 380
sheet: -1.27 (0.30), residues: 276
loop : -1.74 (0.28), residues: 430
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.041 0.002 TRP R 128
HIS 0.007 0.001 HIS A 188
PHE 0.012 0.002 PHE A 196
TYR 0.015 0.002 TYR B 105
ARG 0.007 0.001 ARG B 52
*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
2172 Ramachandran restraints generated.
1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
2172 Ramachandran restraints generated.
1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
228 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 27
poor density : 201
time to evaluate : 1.053
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: B 188 MET cc_start: 0.3513 (mmp) cc_final: 0.3298 (mmp)
REVERT: G 55 PRO cc_start: 0.5749 (Cg_exo) cc_final: 0.5518 (Cg_endo)
REVERT: S 93 MET cc_start: 0.6434 (mpp) cc_final: 0.5872 (ptp)
REVERT: S 182 ASN cc_start: 0.7253 (m-40) cc_final: 0.7017 (m-40)
REVERT: S 218 MET cc_start: 0.4163 (ttp) cc_final: 0.3728 (tmm)
REVERT: R 86 MET cc_start: 0.7229 (mmm) cc_final: 0.6985 (mtt)
REVERT: R 99 MET cc_start: 0.7636 (mmt) cc_final: 0.7335 (mmp)
REVERT: R 184 TRP cc_start: 0.5911 (m100) cc_final: 0.5635 (m100)
REVERT: A 22 ASN cc_start: 0.7031 (m110) cc_final: 0.6561 (m110)
REVERT: A 26 ASP cc_start: 0.7709 (p0) cc_final: 0.7330 (p0)
REVERT: A 247 MET cc_start: 0.6499 (mmm) cc_final: 0.6177 (mmt)
REVERT: A 256 ASN cc_start: 0.8466 (m110) cc_final: 0.7953 (m110)
REVERT: A 345 LYS cc_start: 0.8482 (mttp) cc_final: 0.8100 (tmtt)
outliers start: 27
outliers final: 11
residues processed: 220
average time/residue: 0.2196
time to fit residues: 65.6064
Evaluate side-chains
173 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 11
poor density : 162
time to evaluate : 0.931
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue 119 ASN
Chi-restraints excluded: chain B residue 249 THR
Chi-restraints excluded: chain B residue 307 VAL
Chi-restraints excluded: chain G residue 36 ASP
Chi-restraints excluded: chain S residue 51 ILE
Chi-restraints excluded: chain S residue 202 LEU
Chi-restraints excluded: chain R residue 56 LEU
Chi-restraints excluded: chain R residue 83 CYS
Chi-restraints excluded: chain R residue 104 ILE
Chi-restraints excluded: chain R residue 226 LYS
Chi-restraints excluded: chain A residue 276 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 109
random chunks:
chunk 63 optimal weight: 1.9990
chunk 50 optimal weight: 8.9990
chunk 34 optimal weight: 20.0000
chunk 30 optimal weight: 0.2980
chunk 80 optimal weight: 0.9980
chunk 82 optimal weight: 4.9990
chunk 89 optimal weight: 8.9990
chunk 36 optimal weight: 0.0670
chunk 93 optimal weight: 6.9990
chunk 17 optimal weight: 20.0000
chunk 67 optimal weight: 7.9990
overall best weight: 1.6722
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
B 176 GLN
B 266 HIS
B 293 ASN
S 130 GLN
S 159 ASN
** S 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
S 220 HIS
** R 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 256 ASN
** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 346 ASN
Total number of N/Q/H flips: 8
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4503 r_free = 0.4503 target = 0.157610 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.4157 r_free = 0.4157 target = 0.134847 restraints weight = 26162.209|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.4204 r_free = 0.4204 target = 0.137720 restraints weight = 16124.080|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4237 r_free = 0.4237 target = 0.139910 restraints weight = 11790.260|
|-----------------------------------------------------------------------------|
r_work (final): 0.4168
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6115
moved from start: 0.5709
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.004 0.045 8890 Z= 0.242
Angle : 0.737 21.161 12041 Z= 0.380
Chirality : 0.044 0.200 1377
Planarity : 0.005 0.062 1501
Dihedral : 7.398 84.214 1222
Min Nonbonded Distance : 2.469
Molprobity Statistics.
All-atom Clashscore : 15.04
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 3.78 %
Favored : 96.22 %
Rotamer:
Outliers : 3.15 %
Allowed : 18.89 %
Favored : 77.96 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 3.45 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: -0.83 (0.25), residues: 1086
helix: 0.80 (0.26), residues: 375
sheet: -1.07 (0.30), residues: 290
loop : -1.29 (0.30), residues: 421
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.022 0.002 TRP R 128
HIS 0.012 0.002 HIS G 44
PHE 0.015 0.002 PHE B 253
TYR 0.019 0.002 TYR B 105
ARG 0.006 0.001 ARG B 52
*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
2172 Ramachandran restraints generated.
1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
2172 Ramachandran restraints generated.
1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
199 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 30
poor density : 169
time to evaluate : 1.074
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: B 57 LYS cc_start: 0.7823 (mtmm) cc_final: 0.7471 (ttmt)
REVERT: B 268 ASN cc_start: 0.7638 (t0) cc_final: 0.7326 (t0)
REVERT: B 325 MET cc_start: 0.7815 (mmm) cc_final: 0.7433 (mmt)
REVERT: G 55 PRO cc_start: 0.6159 (Cg_exo) cc_final: 0.5929 (Cg_endo)
REVERT: S 93 MET cc_start: 0.6935 (mpp) cc_final: 0.6381 (ptt)
REVERT: S 103 TYR cc_start: 0.6568 (t80) cc_final: 0.6126 (t80)
REVERT: S 148 ARG cc_start: 0.7089 (mtm-85) cc_final: 0.6801 (mtm-85)
REVERT: S 218 MET cc_start: 0.4040 (ttp) cc_final: 0.3691 (tmm)
REVERT: R 86 MET cc_start: 0.7540 (mmm) cc_final: 0.7282 (mtt)
REVERT: R 99 MET cc_start: 0.7628 (mmt) cc_final: 0.7130 (mmp)
REVERT: R 109 TYR cc_start: 0.8143 (t80) cc_final: 0.7937 (t80)
REVERT: R 183 LEU cc_start: 0.8202 (tp) cc_final: 0.7773 (tp)
REVERT: A 198 MET cc_start: 0.7649 (mtp) cc_final: 0.7439 (mtp)
REVERT: A 247 MET cc_start: 0.7046 (mmt) cc_final: 0.6551 (mmt)
REVERT: A 256 ASN cc_start: 0.8608 (m-40) cc_final: 0.8097 (m110)
REVERT: A 309 ASP cc_start: 0.9033 (t0) cc_final: 0.8795 (t0)
outliers start: 30
outliers final: 19
residues processed: 188
average time/residue: 0.2140
time to fit residues: 55.2955
Evaluate side-chains
175 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 19
poor density : 156
time to evaluate : 1.021
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue 87 THR
Chi-restraints excluded: chain B residue 103 CYS
Chi-restraints excluded: chain B residue 114 CYS
Chi-restraints excluded: chain B residue 233 CYS
Chi-restraints excluded: chain B residue 247 ASP
Chi-restraints excluded: chain B residue 249 THR
Chi-restraints excluded: chain B residue 263 THR
Chi-restraints excluded: chain B residue 270 ILE
Chi-restraints excluded: chain B residue 307 VAL
Chi-restraints excluded: chain G residue 36 ASP
Chi-restraints excluded: chain S residue 51 ILE
Chi-restraints excluded: chain S residue 159 ASN
Chi-restraints excluded: chain S residue 202 LEU
Chi-restraints excluded: chain S residue 203 THR
Chi-restraints excluded: chain R residue 56 LEU
Chi-restraints excluded: chain R residue 175 TYR
Chi-restraints excluded: chain R residue 226 LYS
Chi-restraints excluded: chain R residue 287 LYS
Chi-restraints excluded: chain A residue 273 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 109
random chunks:
chunk 38 optimal weight: 0.0060
chunk 21 optimal weight: 6.9990
chunk 50 optimal weight: 10.0000
chunk 87 optimal weight: 0.9990
chunk 98 optimal weight: 5.9990
chunk 19 optimal weight: 7.9990
chunk 107 optimal weight: 1.9990
chunk 88 optimal weight: 4.9990
chunk 89 optimal weight: 8.9990
chunk 67 optimal weight: 5.9990
chunk 82 optimal weight: 2.9990
overall best weight: 2.2004
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
B 88 ASN
** S 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 22 ASN
** A 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
Total number of N/Q/H flips: 2
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4430 r_free = 0.4430 target = 0.153791 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.4061 r_free = 0.4061 target = 0.130350 restraints weight = 27599.295|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 58)----------------|
| r_work = 0.4108 r_free = 0.4108 target = 0.133107 restraints weight = 17219.927|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 55)----------------|
| r_work = 0.4141 r_free = 0.4141 target = 0.135213 restraints weight = 12647.097|
|-----------------------------------------------------------------------------|
r_work (final): 0.4074
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6283
moved from start: 0.6847
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.004 0.039 8890 Z= 0.264
Angle : 0.736 17.149 12041 Z= 0.381
Chirality : 0.045 0.151 1377
Planarity : 0.005 0.045 1501
Dihedral : 5.899 53.821 1220
Min Nonbonded Distance : 2.476
Molprobity Statistics.
All-atom Clashscore : 15.67
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 4.33 %
Favored : 95.67 %
Rotamer:
Outliers : 4.09 %
Allowed : 18.68 %
Favored : 77.23 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 3.45 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: -0.74 (0.25), residues: 1086
helix: 0.76 (0.26), residues: 368
sheet: -0.89 (0.31), residues: 288
loop : -1.19 (0.30), residues: 430
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.027 0.002 TRP B 82
HIS 0.005 0.001 HIS R 95
PHE 0.019 0.002 PHE R 179
TYR 0.026 0.002 TYR B 105
ARG 0.003 0.001 ARG S 168
*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
2172 Ramachandran restraints generated.
1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
2172 Ramachandran restraints generated.
1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
207 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 39
poor density : 168
time to evaluate : 1.219
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: B 57 LYS cc_start: 0.8121 (mtmm) cc_final: 0.7801 (ttmt)
REVERT: B 101 MET cc_start: 0.7428 (tpp) cc_final: 0.6885 (tpp)
REVERT: B 234 PHE cc_start: 0.7381 (OUTLIER) cc_final: 0.6175 (m-80)
REVERT: B 296 VAL cc_start: 0.7995 (t) cc_final: 0.7730 (p)
REVERT: B 325 MET cc_start: 0.7725 (mmm) cc_final: 0.7208 (mmt)
REVERT: G 55 PRO cc_start: 0.5812 (Cg_exo) cc_final: 0.5572 (Cg_endo)
REVERT: S 159 ASN cc_start: 0.8411 (OUTLIER) cc_final: 0.8155 (p0)
REVERT: S 218 MET cc_start: 0.4331 (ttp) cc_final: 0.4069 (tmm)
REVERT: R 99 MET cc_start: 0.7687 (mmt) cc_final: 0.7206 (mmp)
REVERT: R 183 LEU cc_start: 0.8219 (tp) cc_final: 0.7743 (tp)
REVERT: R 275 MET cc_start: 0.8328 (tmm) cc_final: 0.7933 (tmm)
REVERT: R 288 PHE cc_start: 0.8246 (t80) cc_final: 0.8026 (t80)
REVERT: A 247 MET cc_start: 0.7354 (mmm) cc_final: 0.6945 (mmt)
REVERT: A 256 ASN cc_start: 0.8556 (m-40) cc_final: 0.7937 (m110)
outliers start: 39
outliers final: 26
residues processed: 188
average time/residue: 0.2201
time to fit residues: 57.5463
Evaluate side-chains
176 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 28
poor density : 148
time to evaluate : 1.077
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue 17 GLN
Chi-restraints excluded: chain B residue 87 THR
Chi-restraints excluded: chain B residue 103 CYS
Chi-restraints excluded: chain B residue 114 CYS
Chi-restraints excluded: chain B residue 230 ASN
Chi-restraints excluded: chain B residue 234 PHE
Chi-restraints excluded: chain B residue 247 ASP
Chi-restraints excluded: chain B residue 270 ILE
Chi-restraints excluded: chain B residue 307 VAL
Chi-restraints excluded: chain G residue 36 ASP
Chi-restraints excluded: chain S residue 51 ILE
Chi-restraints excluded: chain S residue 159 ASN
Chi-restraints excluded: chain S residue 203 THR
Chi-restraints excluded: chain R residue 22 ILE
Chi-restraints excluded: chain R residue 56 LEU
Chi-restraints excluded: chain R residue 83 CYS
Chi-restraints excluded: chain R residue 89 LEU
Chi-restraints excluded: chain R residue 104 ILE
Chi-restraints excluded: chain R residue 122 THR
Chi-restraints excluded: chain R residue 177 VAL
Chi-restraints excluded: chain R residue 226 LYS
Chi-restraints excluded: chain R residue 241 CYS
Chi-restraints excluded: chain R residue 243 LEU
Chi-restraints excluded: chain R residue 246 SER
Chi-restraints excluded: chain R residue 280 VAL
Chi-restraints excluded: chain R residue 287 LYS
Chi-restraints excluded: chain A residue 273 LEU
Chi-restraints excluded: chain A residue 331 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 109
random chunks:
chunk 50 optimal weight: 20.0000
chunk 24 optimal weight: 6.9990
chunk 104 optimal weight: 0.9990
chunk 37 optimal weight: 0.0870
chunk 72 optimal weight: 3.9990
chunk 41 optimal weight: 5.9990
chunk 70 optimal weight: 1.9990
chunk 45 optimal weight: 0.4980
chunk 49 optimal weight: 0.8980
chunk 60 optimal weight: 3.9990
chunk 56 optimal weight: 3.9990
overall best weight: 0.8962
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** R 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
Total number of N/Q/H flips: 0
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4464 r_free = 0.4464 target = 0.154743 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.4107 r_free = 0.4107 target = 0.131967 restraints weight = 27141.326|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.4155 r_free = 0.4155 target = 0.134874 restraints weight = 16338.926|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.4192 r_free = 0.4192 target = 0.137244 restraints weight = 11740.810|
|-----------------------------------------------------------------------------|
r_work (final): 0.4133
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6220
moved from start: 0.7277
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.036 8890 Z= 0.183
Angle : 0.681 13.420 12041 Z= 0.350
Chirality : 0.043 0.176 1377
Planarity : 0.004 0.040 1501
Dihedral : 5.200 51.815 1220
Min Nonbonded Distance : 2.487
Molprobity Statistics.
All-atom Clashscore : 13.54
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 3.59 %
Favored : 96.41 %
Rotamer:
Outliers : 2.52 %
Allowed : 22.46 %
Favored : 75.03 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 3.45 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: -0.37 (0.25), residues: 1086
helix: 1.08 (0.26), residues: 368
sheet: -0.62 (0.32), residues: 280
loop : -1.05 (0.30), residues: 438
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.014 0.002 TRP R 128
HIS 0.004 0.001 HIS B 54
PHE 0.019 0.002 PHE A 259
TYR 0.018 0.001 TYR S 178
ARG 0.009 0.000 ARG S 168
*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
2172 Ramachandran restraints generated.
1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
2172 Ramachandran restraints generated.
1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
181 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 24
poor density : 157
time to evaluate : 0.941
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: B 57 LYS cc_start: 0.7759 (mtmm) cc_final: 0.7453 (ttmt)
REVERT: B 101 MET cc_start: 0.7045 (tpp) cc_final: 0.6659 (tpp)
REVERT: B 234 PHE cc_start: 0.6995 (OUTLIER) cc_final: 0.5836 (m-80)
REVERT: B 296 VAL cc_start: 0.7795 (t) cc_final: 0.7540 (p)
REVERT: B 325 MET cc_start: 0.7816 (mmm) cc_final: 0.7288 (mmt)
REVERT: G 55 PRO cc_start: 0.5757 (Cg_exo) cc_final: 0.5489 (Cg_endo)
REVERT: S 103 TYR cc_start: 0.6383 (t80) cc_final: 0.6061 (t80)
REVERT: S 218 MET cc_start: 0.4666 (ttp) cc_final: 0.4324 (tmm)
REVERT: R 86 MET cc_start: 0.7716 (mtt) cc_final: 0.7511 (mtp)
REVERT: R 99 MET cc_start: 0.7535 (mmt) cc_final: 0.7224 (mmp)
REVERT: R 173 MET cc_start: 0.5161 (mmm) cc_final: 0.4565 (mmp)
REVERT: R 183 LEU cc_start: 0.8165 (tp) cc_final: 0.7698 (tp)
REVERT: R 275 MET cc_start: 0.7925 (tmm) cc_final: 0.7697 (tmm)
REVERT: A 247 MET cc_start: 0.7366 (mmm) cc_final: 0.6870 (mmt)
REVERT: A 256 ASN cc_start: 0.8553 (m-40) cc_final: 0.8012 (m110)
outliers start: 24
outliers final: 18
residues processed: 174
average time/residue: 0.2034
time to fit residues: 48.7922
Evaluate side-chains
164 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 19
poor density : 145
time to evaluate : 1.043
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue 17 GLN
Chi-restraints excluded: chain B residue 84 SER
Chi-restraints excluded: chain B residue 87 THR
Chi-restraints excluded: chain B residue 103 CYS
Chi-restraints excluded: chain B residue 114 CYS
Chi-restraints excluded: chain B residue 234 PHE
Chi-restraints excluded: chain B residue 247 ASP
Chi-restraints excluded: chain B residue 270 ILE
Chi-restraints excluded: chain B residue 307 VAL
Chi-restraints excluded: chain G residue 36 ASP
Chi-restraints excluded: chain S residue 202 LEU
Chi-restraints excluded: chain S residue 203 THR
Chi-restraints excluded: chain R residue 36 VAL
Chi-restraints excluded: chain R residue 56 LEU
Chi-restraints excluded: chain R residue 83 CYS
Chi-restraints excluded: chain R residue 177 VAL
Chi-restraints excluded: chain R residue 226 LYS
Chi-restraints excluded: chain R residue 280 VAL
Chi-restraints excluded: chain R residue 287 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 109
random chunks:
chunk 54 optimal weight: 3.9990
chunk 33 optimal weight: 0.8980
chunk 59 optimal weight: 3.9990
chunk 67 optimal weight: 3.9990
chunk 2 optimal weight: 4.9990
chunk 88 optimal weight: 20.0000
chunk 97 optimal weight: 7.9990
chunk 51 optimal weight: 8.9990
chunk 40 optimal weight: 5.9990
chunk 6 optimal weight: 0.5980
chunk 86 optimal weight: 0.7980
overall best weight: 2.0584
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
B 266 HIS
S 159 ASN
** R 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
Total number of N/Q/H flips: 2
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4406 r_free = 0.4406 target = 0.151668 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4035 r_free = 0.4035 target = 0.128333 restraints weight = 27283.742|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4080 r_free = 0.4080 target = 0.130935 restraints weight = 17299.466|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.4111 r_free = 0.4111 target = 0.132863 restraints weight = 12779.418|
|-----------------------------------------------------------------------------|
r_work (final): 0.4043
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6363
moved from start: 0.7883
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.004 0.038 8890 Z= 0.251
Angle : 0.718 13.219 12041 Z= 0.370
Chirality : 0.045 0.182 1377
Planarity : 0.004 0.033 1501
Dihedral : 5.200 50.274 1220
Min Nonbonded Distance : 2.468
Molprobity Statistics.
All-atom Clashscore : 15.27
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 4.51 %
Favored : 95.49 %
Rotamer:
Outliers : 3.36 %
Allowed : 22.67 %
Favored : 73.98 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 3.45 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: -0.52 (0.25), residues: 1086
helix: 0.84 (0.26), residues: 369
sheet: -0.72 (0.32), residues: 274
loop : -1.00 (0.29), residues: 443
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.013 0.002 TRP S 164
HIS 0.006 0.002 HIS R 95
PHE 0.034 0.002 PHE R 288
TYR 0.022 0.002 TYR B 105
ARG 0.005 0.001 ARG A 32
*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
2172 Ramachandran restraints generated.
1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
2172 Ramachandran restraints generated.
1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
190 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 32
poor density : 158
time to evaluate : 0.958
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: B 57 LYS cc_start: 0.7900 (mtmm) cc_final: 0.7700 (ttmt)
REVERT: B 234 PHE cc_start: 0.7445 (OUTLIER) cc_final: 0.6221 (m-80)
REVERT: B 296 VAL cc_start: 0.8225 (t) cc_final: 0.7960 (p)
REVERT: B 325 MET cc_start: 0.7867 (mmm) cc_final: 0.7394 (mmt)
REVERT: G 55 PRO cc_start: 0.5462 (Cg_exo) cc_final: 0.5223 (Cg_endo)
REVERT: S 34 MET cc_start: 0.4969 (mtp) cc_final: 0.4020 (ptp)
REVERT: S 103 TYR cc_start: 0.6558 (t80) cc_final: 0.6145 (t80)
REVERT: S 168 ARG cc_start: 0.8365 (OUTLIER) cc_final: 0.7908 (mtm110)
REVERT: R 99 MET cc_start: 0.7590 (mmt) cc_final: 0.7314 (mmp)
REVERT: R 183 LEU cc_start: 0.8082 (tp) cc_final: 0.7616 (tp)
REVERT: A 256 ASN cc_start: 0.8584 (m-40) cc_final: 0.8085 (m110)
outliers start: 32
outliers final: 23
residues processed: 177
average time/residue: 0.2031
time to fit residues: 50.3351
Evaluate side-chains
172 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 25
poor density : 147
time to evaluate : 1.043
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue 17 GLN
Chi-restraints excluded: chain B residue 84 SER
Chi-restraints excluded: chain B residue 93 ILE
Chi-restraints excluded: chain B residue 103 CYS
Chi-restraints excluded: chain B residue 114 CYS
Chi-restraints excluded: chain B residue 117 LEU
Chi-restraints excluded: chain B residue 234 PHE
Chi-restraints excluded: chain B residue 247 ASP
Chi-restraints excluded: chain B residue 270 ILE
Chi-restraints excluded: chain B residue 307 VAL
Chi-restraints excluded: chain G residue 36 ASP
Chi-restraints excluded: chain S residue 51 ILE
Chi-restraints excluded: chain S residue 168 ARG
Chi-restraints excluded: chain S residue 202 LEU
Chi-restraints excluded: chain S residue 203 THR
Chi-restraints excluded: chain R residue 22 ILE
Chi-restraints excluded: chain R residue 36 VAL
Chi-restraints excluded: chain R residue 56 LEU
Chi-restraints excluded: chain R residue 83 CYS
Chi-restraints excluded: chain R residue 104 ILE
Chi-restraints excluded: chain R residue 177 VAL
Chi-restraints excluded: chain R residue 226 LYS
Chi-restraints excluded: chain R residue 246 SER
Chi-restraints excluded: chain R residue 287 LYS
Chi-restraints excluded: chain A residue 273 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 109
random chunks:
chunk 63 optimal weight: 0.2980
chunk 12 optimal weight: 0.0970
chunk 0 optimal weight: 50.0000
chunk 23 optimal weight: 1.9990
chunk 100 optimal weight: 0.9980
chunk 103 optimal weight: 6.9990
chunk 16 optimal weight: 1.9990
chunk 18 optimal weight: 4.9990
chunk 21 optimal weight: 4.9990
chunk 84 optimal weight: 0.9980
chunk 44 optimal weight: 6.9990
overall best weight: 0.8780
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
B 266 HIS
** R 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 322 HIS
Total number of N/Q/H flips: 2
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4485 r_free = 0.4485 target = 0.154796 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.4137 r_free = 0.4137 target = 0.132530 restraints weight = 27493.843|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 54)----------------|
| r_work = 0.4184 r_free = 0.4184 target = 0.135366 restraints weight = 16562.213|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.4220 r_free = 0.4220 target = 0.137529 restraints weight = 11967.856|
|-----------------------------------------------------------------------------|
r_work (final): 0.4153
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6267
moved from start: 0.8158
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.034 8890 Z= 0.183
Angle : 0.683 12.603 12041 Z= 0.347
Chirality : 0.043 0.187 1377
Planarity : 0.004 0.039 1501
Dihedral : 4.768 42.973 1220
Min Nonbonded Distance : 2.485
Molprobity Statistics.
All-atom Clashscore : 13.94
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 3.59 %
Favored : 96.41 %
Rotamer:
Outliers : 2.83 %
Allowed : 24.24 %
Favored : 72.93 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 3.45 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: -0.18 (0.26), residues: 1086
helix: 1.21 (0.27), residues: 365
sheet: -0.55 (0.32), residues: 273
loop : -0.87 (0.30), residues: 448
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.011 0.001 TRP R 35
HIS 0.004 0.001 HIS R 95
PHE 0.020 0.001 PHE R 288
TYR 0.019 0.001 TYR R 109
ARG 0.005 0.000 ARG A 32
*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
2172 Ramachandran restraints generated.
1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
2172 Ramachandran restraints generated.
1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
185 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 27
poor density : 158
time to evaluate : 1.162
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: B 234 PHE cc_start: 0.7182 (OUTLIER) cc_final: 0.5978 (m-80)
REVERT: B 296 VAL cc_start: 0.8103 (t) cc_final: 0.7854 (p)
REVERT: B 325 MET cc_start: 0.7844 (mmm) cc_final: 0.7409 (mmt)
REVERT: G 55 PRO cc_start: 0.5348 (Cg_exo) cc_final: 0.5038 (Cg_endo)
REVERT: S 34 MET cc_start: 0.5035 (mtp) cc_final: 0.4158 (ptp)
REVERT: S 103 TYR cc_start: 0.6434 (t80) cc_final: 0.5861 (t80)
REVERT: S 168 ARG cc_start: 0.8246 (ttp-110) cc_final: 0.7845 (mtm110)
REVERT: S 234 GLU cc_start: 0.8565 (tp30) cc_final: 0.8294 (tp30)
REVERT: R 99 MET cc_start: 0.7546 (mmt) cc_final: 0.7217 (mmp)
REVERT: R 173 MET cc_start: 0.4989 (tpt) cc_final: 0.4491 (mmp)
REVERT: R 183 LEU cc_start: 0.7875 (tp) cc_final: 0.7301 (tp)
REVERT: A 5 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8673 (tp)
REVERT: A 247 MET cc_start: 0.7393 (mmt) cc_final: 0.6741 (mmt)
REVERT: A 256 ASN cc_start: 0.8475 (m-40) cc_final: 0.8048 (m110)
outliers start: 27
outliers final: 21
residues processed: 178
average time/residue: 0.2411
time to fit residues: 59.1477
Evaluate side-chains
170 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 23
poor density : 147
time to evaluate : 1.161
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue 17 GLN
Chi-restraints excluded: chain B residue 71 VAL
Chi-restraints excluded: chain B residue 103 CYS
Chi-restraints excluded: chain B residue 114 CYS
Chi-restraints excluded: chain B residue 117 LEU
Chi-restraints excluded: chain B residue 234 PHE
Chi-restraints excluded: chain B residue 247 ASP
Chi-restraints excluded: chain B residue 270 ILE
Chi-restraints excluded: chain B residue 307 VAL
Chi-restraints excluded: chain G residue 36 ASP
Chi-restraints excluded: chain G residue 54 VAL
Chi-restraints excluded: chain S residue 202 LEU
Chi-restraints excluded: chain S residue 203 THR
Chi-restraints excluded: chain R residue 36 VAL
Chi-restraints excluded: chain R residue 56 LEU
Chi-restraints excluded: chain R residue 83 CYS
Chi-restraints excluded: chain R residue 177 VAL
Chi-restraints excluded: chain R residue 226 LYS
Chi-restraints excluded: chain R residue 243 LEU
Chi-restraints excluded: chain R residue 246 SER
Chi-restraints excluded: chain R residue 287 LYS
Chi-restraints excluded: chain A residue 5 LEU
Chi-restraints excluded: chain A residue 194 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 109
random chunks:
chunk 10 optimal weight: 2.9990
chunk 68 optimal weight: 5.9990
chunk 108 optimal weight: 0.9990
chunk 21 optimal weight: 4.9990
chunk 56 optimal weight: 0.0370
chunk 47 optimal weight: 0.9980
chunk 73 optimal weight: 5.9990
chunk 103 optimal weight: 1.9990
chunk 18 optimal weight: 0.9990
chunk 74 optimal weight: 2.9990
chunk 86 optimal weight: 4.9990
overall best weight: 1.0064
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** R 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
Total number of N/Q/H flips: 0
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4449 r_free = 0.4449 target = 0.159090 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4170 r_free = 0.4170 target = 0.132545 restraints weight = 20597.788|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.4180 r_free = 0.4180 target = 0.132465 restraints weight = 14010.902|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4198 r_free = 0.4198 target = 0.133703 restraints weight = 10614.488|
|-----------------------------------------------------------------------------|
r_work (final): 0.4163
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6334
moved from start: 0.8430
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.036 8890 Z= 0.193
Angle : 0.698 12.426 12041 Z= 0.358
Chirality : 0.043 0.186 1377
Planarity : 0.004 0.040 1501
Dihedral : 4.777 45.355 1220
Min Nonbonded Distance : 2.503
Molprobity Statistics.
All-atom Clashscore : 14.86
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 3.87 %
Favored : 96.13 %
Rotamer:
Outliers : 3.04 %
Allowed : 24.45 %
Favored : 72.51 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 3.45 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: -0.14 (0.26), residues: 1086
helix: 1.16 (0.27), residues: 369
sheet: -0.37 (0.32), residues: 272
loop : -0.90 (0.30), residues: 445
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.010 0.001 TRP R 242
HIS 0.004 0.001 HIS R 95
PHE 0.019 0.001 PHE R 288
TYR 0.020 0.001 TYR R 109
ARG 0.007 0.000 ARG S 148
*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
2172 Ramachandran restraints generated.
1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
2172 Ramachandran restraints generated.
1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
182 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 29
poor density : 153
time to evaluate : 0.964
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: B 234 PHE cc_start: 0.7169 (OUTLIER) cc_final: 0.5925 (m-80)
REVERT: B 296 VAL cc_start: 0.8128 (t) cc_final: 0.7895 (p)
REVERT: B 325 MET cc_start: 0.7713 (mmm) cc_final: 0.7267 (mmt)
REVERT: S 34 MET cc_start: 0.4886 (mtp) cc_final: 0.4139 (ptp)
REVERT: S 83 MET cc_start: 0.2077 (mmt) cc_final: 0.1793 (mmp)
REVERT: S 93 MET cc_start: 0.6404 (OUTLIER) cc_final: 0.5820 (tmm)
REVERT: S 103 TYR cc_start: 0.6413 (t80) cc_final: 0.5803 (t80)
REVERT: S 168 ARG cc_start: 0.8348 (ttp-110) cc_final: 0.7898 (mtm110)
REVERT: S 234 GLU cc_start: 0.8784 (tp30) cc_final: 0.7911 (mp0)
REVERT: R 99 MET cc_start: 0.7482 (mmt) cc_final: 0.7151 (mmp)
REVERT: R 171 MET cc_start: 0.7893 (tpp) cc_final: 0.7540 (tpp)
REVERT: R 183 LEU cc_start: 0.7877 (tp) cc_final: 0.7476 (tp)
REVERT: A 5 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8462 (tp)
REVERT: A 256 ASN cc_start: 0.8515 (m-40) cc_final: 0.8027 (m110)
outliers start: 29
outliers final: 24
residues processed: 170
average time/residue: 0.2128
time to fit residues: 50.3452
Evaluate side-chains
172 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 27
poor density : 145
time to evaluate : 1.098
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue 17 GLN
Chi-restraints excluded: chain B residue 103 CYS
Chi-restraints excluded: chain B residue 114 CYS
Chi-restraints excluded: chain B residue 234 PHE
Chi-restraints excluded: chain B residue 247 ASP
Chi-restraints excluded: chain B residue 270 ILE
Chi-restraints excluded: chain B residue 307 VAL
Chi-restraints excluded: chain G residue 36 ASP
Chi-restraints excluded: chain G residue 54 VAL
Chi-restraints excluded: chain S residue 93 MET
Chi-restraints excluded: chain S residue 202 LEU
Chi-restraints excluded: chain S residue 203 THR
Chi-restraints excluded: chain R residue 22 ILE
Chi-restraints excluded: chain R residue 36 VAL
Chi-restraints excluded: chain R residue 56 LEU
Chi-restraints excluded: chain R residue 83 CYS
Chi-restraints excluded: chain R residue 104 ILE
Chi-restraints excluded: chain R residue 138 SER
Chi-restraints excluded: chain R residue 177 VAL
Chi-restraints excluded: chain R residue 226 LYS
Chi-restraints excluded: chain R residue 243 LEU
Chi-restraints excluded: chain R residue 246 SER
Chi-restraints excluded: chain R residue 287 LYS
Chi-restraints excluded: chain A residue 5 LEU
Chi-restraints excluded: chain A residue 53 MET
Chi-restraints excluded: chain A residue 194 LEU
Chi-restraints excluded: chain A residue 273 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 109
random chunks:
chunk 70 optimal weight: 1.9990
chunk 60 optimal weight: 0.8980
chunk 99 optimal weight: 0.8980
chunk 15 optimal weight: 1.9990
chunk 50 optimal weight: 5.9990
chunk 85 optimal weight: 0.9990
chunk 27 optimal weight: 4.9990
chunk 10 optimal weight: 0.9990
chunk 69 optimal weight: 0.8980
chunk 108 optimal weight: 0.9980
chunk 1 optimal weight: 5.9990
overall best weight: 0.9382
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** S 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
Total number of N/Q/H flips: 0
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4486 r_free = 0.4486 target = 0.154595 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.4138 r_free = 0.4138 target = 0.132320 restraints weight = 28156.229|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.4186 r_free = 0.4186 target = 0.135177 restraints weight = 16986.901|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4220 r_free = 0.4220 target = 0.137376 restraints weight = 12224.534|
|-----------------------------------------------------------------------------|
r_work (final): 0.4154
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6280
moved from start: 0.8678
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.034 8890 Z= 0.191
Angle : 0.699 12.023 12041 Z= 0.356
Chirality : 0.044 0.186 1377
Planarity : 0.004 0.040 1501
Dihedral : 4.780 47.233 1220
Min Nonbonded Distance : 2.486
Molprobity Statistics.
All-atom Clashscore : 14.58
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 3.41 %
Favored : 96.59 %
Rotamer:
Outliers : 2.94 %
Allowed : 24.97 %
Favored : 72.09 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 3.45 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: -0.13 (0.26), residues: 1086
helix: 1.19 (0.26), residues: 369
sheet: -0.40 (0.33), residues: 267
loop : -0.90 (0.30), residues: 450
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.012 0.001 TRP R 242
HIS 0.005 0.001 HIS B 311
PHE 0.022 0.001 PHE R 167
TYR 0.021 0.001 TYR R 109
ARG 0.003 0.000 ARG B 49
*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
2172 Ramachandran restraints generated.
1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
2172 Ramachandran restraints generated.
1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
179 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 28
poor density : 151
time to evaluate : 1.125
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: B 234 PHE cc_start: 0.7152 (OUTLIER) cc_final: 0.5909 (m-80)
REVERT: B 296 VAL cc_start: 0.7997 (t) cc_final: 0.7755 (p)
REVERT: B 325 MET cc_start: 0.7813 (mmm) cc_final: 0.7416 (mmt)
REVERT: S 34 MET cc_start: 0.5092 (mtp) cc_final: 0.4231 (ptp)
REVERT: S 93 MET cc_start: 0.6509 (OUTLIER) cc_final: 0.5915 (tmm)
REVERT: S 103 TYR cc_start: 0.6374 (t80) cc_final: 0.5960 (t80)
REVERT: S 168 ARG cc_start: 0.8385 (ttp-110) cc_final: 0.7921 (mtm110)
REVERT: S 234 GLU cc_start: 0.8780 (tp30) cc_final: 0.7984 (mp0)
REVERT: R 99 MET cc_start: 0.7490 (mmt) cc_final: 0.7208 (mmm)
REVERT: R 176 MET cc_start: 0.7980 (mpp) cc_final: 0.7333 (mpp)
REVERT: R 183 LEU cc_start: 0.7784 (tp) cc_final: 0.7372 (tp)
REVERT: R 277 ASN cc_start: 0.7260 (t0) cc_final: 0.6770 (m-40)
REVERT: A 5 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8605 (tp)
REVERT: A 216 GLU cc_start: 0.7972 (mt-10) cc_final: 0.7765 (mt-10)
REVERT: A 247 MET cc_start: 0.7794 (mmt) cc_final: 0.6838 (mmt)
REVERT: A 256 ASN cc_start: 0.8473 (m-40) cc_final: 0.8076 (m110)
outliers start: 28
outliers final: 21
residues processed: 169
average time/residue: 0.2037
time to fit residues: 48.0440
Evaluate side-chains
167 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 24
poor density : 143
time to evaluate : 0.955
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue 17 GLN
Chi-restraints excluded: chain B residue 103 CYS
Chi-restraints excluded: chain B residue 114 CYS
Chi-restraints excluded: chain B residue 234 PHE
Chi-restraints excluded: chain B residue 247 ASP
Chi-restraints excluded: chain B residue 270 ILE
Chi-restraints excluded: chain B residue 307 VAL
Chi-restraints excluded: chain G residue 36 ASP
Chi-restraints excluded: chain G residue 54 VAL
Chi-restraints excluded: chain S residue 93 MET
Chi-restraints excluded: chain S residue 202 LEU
Chi-restraints excluded: chain S residue 203 THR
Chi-restraints excluded: chain R residue 56 LEU
Chi-restraints excluded: chain R residue 83 CYS
Chi-restraints excluded: chain R residue 104 ILE
Chi-restraints excluded: chain R residue 138 SER
Chi-restraints excluded: chain R residue 177 VAL
Chi-restraints excluded: chain R residue 226 LYS
Chi-restraints excluded: chain R residue 243 LEU
Chi-restraints excluded: chain R residue 246 SER
Chi-restraints excluded: chain R residue 287 LYS
Chi-restraints excluded: chain A residue 5 LEU
Chi-restraints excluded: chain A residue 18 MET
Chi-restraints excluded: chain A residue 194 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 109
random chunks:
chunk 100 optimal weight: 0.0040
chunk 95 optimal weight: 5.9990
chunk 48 optimal weight: 0.8980
chunk 40 optimal weight: 10.0000
chunk 38 optimal weight: 1.9990
chunk 5 optimal weight: 6.9990
chunk 82 optimal weight: 0.0010
chunk 63 optimal weight: 9.9990
chunk 27 optimal weight: 5.9990
chunk 33 optimal weight: 0.0870
chunk 4 optimal weight: 3.9990
overall best weight: 0.5978
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4508 r_free = 0.4508 target = 0.155999 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4167 r_free = 0.4167 target = 0.134115 restraints weight = 27427.722|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4214 r_free = 0.4214 target = 0.136883 restraints weight = 16514.320|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.4249 r_free = 0.4249 target = 0.139057 restraints weight = 11883.338|
|-----------------------------------------------------------------------------|
r_work (final): 0.4184
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6244
moved from start: 0.8830
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.043 8890 Z= 0.186
Angle : 0.725 12.673 12041 Z= 0.366
Chirality : 0.044 0.220 1377
Planarity : 0.004 0.043 1501
Dihedral : 4.751 47.153 1220
Min Nonbonded Distance : 2.487
Molprobity Statistics.
All-atom Clashscore : 14.52
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 3.50 %
Favored : 96.50 %
Rotamer:
Outliers : 2.41 %
Allowed : 25.29 %
Favored : 72.30 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 3.45 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: -0.06 (0.26), residues: 1086
helix: 1.31 (0.27), residues: 367
sheet: -0.38 (0.33), residues: 256
loop : -0.89 (0.30), residues: 463
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.017 0.002 TRP B 82
HIS 0.004 0.001 HIS B 266
PHE 0.030 0.002 PHE R 181
TYR 0.019 0.001 TYR R 109
ARG 0.007 0.000 ARG S 148
********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
2172 Ramachandran restraints generated.
1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
2172 Ramachandran restraints generated.
1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
177 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 23
poor density : 154
time to evaluate : 0.962
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: B 234 PHE cc_start: 0.7077 (OUTLIER) cc_final: 0.5762 (m-80)
REVERT: B 296 VAL cc_start: 0.7910 (t) cc_final: 0.7689 (p)
REVERT: B 325 MET cc_start: 0.7795 (mmm) cc_final: 0.7398 (mmt)
REVERT: S 34 MET cc_start: 0.5102 (mtp) cc_final: 0.4214 (ptp)
REVERT: S 168 ARG cc_start: 0.8422 (ttp-110) cc_final: 0.7950 (mtm110)
REVERT: S 234 GLU cc_start: 0.8766 (tp30) cc_final: 0.8086 (mp0)
REVERT: R 30 ASN cc_start: 0.5414 (m-40) cc_final: 0.4945 (m-40)
REVERT: R 64 LEU cc_start: 0.8300 (tt) cc_final: 0.8099 (tp)
REVERT: R 99 MET cc_start: 0.7393 (mmt) cc_final: 0.7091 (mmm)
REVERT: R 173 MET cc_start: 0.5335 (tpt) cc_final: 0.4337 (mmp)
REVERT: R 176 MET cc_start: 0.8023 (mpp) cc_final: 0.7302 (mpp)
REVERT: R 183 LEU cc_start: 0.7801 (tp) cc_final: 0.7281 (tp)
REVERT: R 206 ARG cc_start: 0.7803 (mmm160) cc_final: 0.7267 (mmp80)
REVERT: A 247 MET cc_start: 0.7738 (mmt) cc_final: 0.6834 (mmt)
REVERT: A 256 ASN cc_start: 0.8428 (m-40) cc_final: 0.8117 (m110)
outliers start: 23
outliers final: 20
residues processed: 170
average time/residue: 0.2071
time to fit residues: 49.1398
Evaluate side-chains
169 residues out of total 954 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 21
poor density : 148
time to evaluate : 1.010
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue 17 GLN
Chi-restraints excluded: chain B residue 103 CYS
Chi-restraints excluded: chain B residue 114 CYS
Chi-restraints excluded: chain B residue 234 PHE
Chi-restraints excluded: chain B residue 247 ASP
Chi-restraints excluded: chain B residue 270 ILE
Chi-restraints excluded: chain B residue 307 VAL
Chi-restraints excluded: chain G residue 36 ASP
Chi-restraints excluded: chain G residue 54 VAL
Chi-restraints excluded: chain S residue 202 LEU
Chi-restraints excluded: chain S residue 203 THR
Chi-restraints excluded: chain R residue 56 LEU
Chi-restraints excluded: chain R residue 83 CYS
Chi-restraints excluded: chain R residue 104 ILE
Chi-restraints excluded: chain R residue 138 SER
Chi-restraints excluded: chain R residue 226 LYS
Chi-restraints excluded: chain R residue 243 LEU
Chi-restraints excluded: chain R residue 246 SER
Chi-restraints excluded: chain R residue 287 LYS
Chi-restraints excluded: chain A residue 5 LEU
Chi-restraints excluded: chain A residue 194 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 109
random chunks:
chunk 86 optimal weight: 5.9990
chunk 65 optimal weight: 3.9990
chunk 102 optimal weight: 4.9990
chunk 34 optimal weight: 5.9990
chunk 92 optimal weight: 8.9990
chunk 99 optimal weight: 2.9990
chunk 62 optimal weight: 0.9980
chunk 19 optimal weight: 3.9990
chunk 54 optimal weight: 0.9990
chunk 6 optimal weight: 2.9990
chunk 91 optimal weight: 2.9990
overall best weight: 2.1988
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
B 142 HIS
S 219 GLN
Total number of N/Q/H flips: 2
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4438 r_free = 0.4438 target = 0.151137 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.4074 r_free = 0.4074 target = 0.128527 restraints weight = 28039.750|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4123 r_free = 0.4123 target = 0.131309 restraints weight = 17202.616|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 64)----------------|
| r_work = 0.4157 r_free = 0.4157 target = 0.133582 restraints weight = 12442.260|
|-----------------------------------------------------------------------------|
r_work (final): 0.4089
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6394
moved from start: 0.9145
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.004 0.043 8890 Z= 0.268
Angle : 0.765 12.517 12041 Z= 0.391
Chirality : 0.045 0.197 1377
Planarity : 0.004 0.044 1501
Dihedral : 5.061 47.821 1220
Min Nonbonded Distance : 2.467
Molprobity Statistics.
All-atom Clashscore : 17.46
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 4.60 %
Favored : 95.40 %
Rotamer:
Outliers : 3.04 %
Allowed : 24.76 %
Favored : 72.19 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 3.45 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: -0.24 (0.26), residues: 1086
helix: 0.99 (0.27), residues: 371
sheet: -0.64 (0.32), residues: 281
loop : -0.71 (0.31), residues: 434
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.016 0.002 TRP B 99
HIS 0.009 0.002 HIS B 311
PHE 0.041 0.002 PHE R 181
TYR 0.023 0.002 TYR B 105
ARG 0.004 0.000 ARG S 67
Origin is already at (0, 0, 0), no shifts will be applied
===============================================================================
Job complete
usr+sys time: 3523.14 seconds
wall clock time: 63 minutes 53.61 seconds (3833.61 seconds total)