Starting phenix.real_space_refine
on Sat Aug 3 15:08:56 2024 by dcliebschner
===============================================================================
Processing files:
-------------------------------------------------------------------------------
Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w88_37348/08_2024/8w88_37348_neut.cif
Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w88_37348/08_2024/8w88_37348.map
Processing PHIL parameters:
-------------------------------------------------------------------------------
Adding command-line PHIL:
-------------------------
refinement.macro_cycles=10
scattering_table=electron
resolution=2.6
write_initial_geo_file=False
Final processed PHIL parameters:
-------------------------------------------------------------------------------
data_manager {
real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w88_37348/08_2024/8w88_37348.map"
default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w88_37348/08_2024/8w88_37348.map"
model {
file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w88_37348/08_2024/8w88_37348_neut.cif"
}
default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w88_37348/08_2024/8w88_37348_neut.cif"
}
resolution = 2.6
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= 0.001 sd= 0.131
Set stop_for_unknowns flag
Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
Set to: electron
Number of scattering types: 4
Type Number sf(0) Gaussians
S 62 5.16 5
C 5307 2.51 5
N 1419 2.21 5
O 1519 1.98 5
sf(0) = scattering factor at diffraction angle 0.
Process input model
Symmetric amino acids flipped
Residue "A GLU 20": "OE1" <-> "OE2"
Residue "A GLU 313": "OE1" <-> "OE2"
Residue "A GLU 326": "OE1" <-> "OE2"
Residue "A GLU 343": "OE1" <-> "OE2"
Residue "B GLU 151": "OE1" <-> "OE2"
Residue "B PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "B GLU 185": "OE1" <-> "OE2"
Residue "G GLU 16": "OE1" <-> "OE2"
Residue "G GLU 41": "OE1" <-> "OE2"
Residue "N GLU 7": "OE1" <-> "OE2"
Residue "N GLU 47": "OE1" <-> "OE2"
Residue "R GLU 93": "OE1" <-> "OE2"
Time to flip residues: 0.02s
Monomer Library directory:
"/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib"
Total number of atoms: 8307
Number of models: 1
Model: ""
Number of chains: 6
Chain: "A"
Number of atoms: 1957
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 236, 1957
Classifications: {'peptide': 236}
Link IDs: {'PTRANS': 6, 'TRANS': 229}
Chain breaks: 2
Chain: "B"
Number of atoms: 2600
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 338, 2600
Classifications: {'peptide': 338}
Link IDs: {'PTRANS': 5, 'TRANS': 332}
Chain: "G"
Number of atoms: 433
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 57, 433
Classifications: {'peptide': 57}
Link IDs: {'PTRANS': 4, 'TRANS': 52}
Chain: "N"
Number of atoms: 967
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 127, 967
Classifications: {'peptide': 127}
Link IDs: {'PTRANS': 5, 'TRANS': 121}
Chain: "R"
Number of atoms: 2254
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 281, 2254
Classifications: {'peptide': 281}
Incomplete info: {'truncation_to_alanine': 5}
Link IDs: {'PTRANS': 11, 'TRANS': 269}
Chain breaks: 1
Unresolved non-hydrogen bonds: 24
Unresolved non-hydrogen angles: 28
Unresolved non-hydrogen dihedrals: 22
Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'HIS:plan': 1}
Unresolved non-hydrogen planarities: 14
Chain: "R"
Number of atoms: 96
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 4, 96
Unusual residues: {'CLR': 3, 'UJL': 1}
Classifications: {'undetermined': 4}
Link IDs: {None: 3}
Time building chain proxies: 5.13, per 1000 atoms: 0.62
Number of scatterers: 8307
At special positions: 0
Unit cell: (83.224, 99.704, 135.136, 90, 90, 90)
Space group: P 1 (No. 1)
Number of sites at special positions: 0
Number of scattering types: 4
Type Number sf(0)
S 62 16.00
O 1519 8.00
N 1419 7.00
C 5307 6.00
sf(0) = scattering factor at diffraction angle 0.
Number of disulfides: simple=1, symmetry=0
Simple disulfide: pdb=" SG CYS R 96 " - pdb=" SG CYS R 182 " distance=2.28
Automatic linking
Parameters for automatic linking
Linking & cutoffs
Metal : Auto - 3.50
Amino acid : False - 1.90
Carbohydrate : True - 1.99
Ligands : True - 1.99
Small molecules : False - 1.98
Amino acid - RNA/DNA : False
Number of custom bonds: simple=0, symmetry=0
Time building additional restraints: 3.05
Conformation dependent library (CDL) restraints added in 1.6 seconds
2046 Ramachandran restraints generated.
1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2.
Adding C-beta torsion restraints...
Number of C-beta restraints generated: 1956
Finding SS restraints...
Secondary structure from input PDB file:
30 helices and 10 sheets defined
44.6% alpha, 20.7% beta
0 base pairs and 0 stacking pairs defined.
Time for finding SS restraints: 0.86
Creating SS restraints...
Processing helix chain 'A' and resid 8 through 37
removed outlier: 3.558A pdb=" N LYS A 31 " --> pdb=" O LYS A 27 " (cutoff:3.500A)
removed outlier: 3.667A pdb=" N VAL A 35 " --> pdb=" O LYS A 31 " (cutoff:3.500A)
Processing helix chain 'A' and resid 51 through 60
Processing helix chain 'A' and resid 234 through 238
removed outlier: 3.522A pdb=" N ASN A 238 " --> pdb=" O GLN A 235 " (cutoff:3.500A)
Processing helix chain 'A' and resid 263 through 278
removed outlier: 3.815A pdb=" N GLU A 267 " --> pdb=" O ASN A 263 " (cutoff:3.500A)
Processing helix chain 'A' and resid 292 through 302
Processing helix chain 'A' and resid 306 through 311
Processing helix chain 'A' and resid 312 through 317
Processing helix chain 'A' and resid 330 through 351
removed outlier: 3.506A pdb=" N PHE A 344 " --> pdb=" O ILE A 340 " (cutoff:3.500A)
removed outlier: 3.876A pdb=" N ILE A 347 " --> pdb=" O GLU A 343 " (cutoff:3.500A)
removed outlier: 3.878A pdb=" N SER A 351 " --> pdb=" O ILE A 347 " (cutoff:3.500A)
Processing helix chain 'A' and resid 368 through 390
removed outlier: 4.494A pdb=" N ARG A 372 " --> pdb=" O THR A 368 " (cutoff:3.500A)
Processing helix chain 'B' and resid 17 through 39
removed outlier: 3.520A pdb=" N ARG B 21 " --> pdb=" O LEU B 17 " (cutoff:3.500A)
Processing helix chain 'B' and resid 42 through 47
Processing helix chain 'B' and resid 48 through 50
No H-bonds generated for 'chain 'B' and resid 48 through 50'
Processing helix chain 'G' and resid 5 through 23
Processing helix chain 'G' and resid 28 through 43
Processing helix chain 'N' and resid 29 through 33
Processing helix chain 'N' and resid 75 through 77
No H-bonds generated for 'chain 'N' and resid 75 through 77'
Processing helix chain 'N' and resid 88 through 92
Processing helix chain 'R' and resid 20 through 51
Processing helix chain 'R' and resid 52 through 55
Processing helix chain 'R' and resid 56 through 76
Processing helix chain 'R' and resid 76 through 86
Processing helix chain 'R' and resid 92 through 127
removed outlier: 3.685A pdb=" N LYS R 97 " --> pdb=" O GLU R 93 " (cutoff:3.500A)
Processing helix chain 'R' and resid 130 through 135
Processing helix chain 'R' and resid 136 through 160
Proline residue: R 151 - end of helix
Processing helix chain 'R' and resid 168 through 179
removed outlier: 3.740A pdb=" N HIS R 177 " --> pdb=" O TYR R 173 " (cutoff:3.500A)
Processing helix chain 'R' and resid 187 through 199
Processing helix chain 'R' and resid 199 through 229
Processing helix chain 'R' and resid 248 through 277
removed outlier: 3.683A pdb=" N PHE R 260 " --> pdb=" O VAL R 256 " (cutoff:3.500A)
Proline residue: R 266 - end of helix
Proline residue: R 275 - end of helix
Processing helix chain 'R' and resid 282 through 305
removed outlier: 3.585A pdb=" N ASN R 286 " --> pdb=" O PRO R 282 " (cutoff:3.500A)
removed outlier: 3.722A pdb=" N SER R 297 " --> pdb=" O GLY R 293 " (cutoff:3.500A)
Proline residue: R 301 - end of helix
Processing helix chain 'R' and resid 308 through 316
removed outlier: 3.514A pdb=" N ALA R 314 " --> pdb=" O TRP R 310 " (cutoff:3.500A)
Processing sheet with id=AA1, first strand: chain 'A' and resid 206 through 213
removed outlier: 6.407A pdb=" N HIS A 40 " --> pdb=" O HIS A 219 " (cutoff:3.500A)
removed outlier: 7.586A pdb=" N PHE A 221 " --> pdb=" O HIS A 40 " (cutoff:3.500A)
removed outlier: 6.643A pdb=" N LEU A 42 " --> pdb=" O PHE A 221 " (cutoff:3.500A)
removed outlier: 8.081A pdb=" N VAL A 223 " --> pdb=" O LEU A 42 " (cutoff:3.500A)
removed outlier: 8.564A pdb=" N LEU A 44 " --> pdb=" O VAL A 223 " (cutoff:3.500A)
removed outlier: 4.164A pdb=" N ALA A 242 " --> pdb=" O ARG A 41 " (cutoff:3.500A)
removed outlier: 6.242A pdb=" N ILE A 243 " --> pdb=" O ILE A 287 " (cutoff:3.500A)
removed outlier: 7.078A pdb=" N PHE A 289 " --> pdb=" O ILE A 243 " (cutoff:3.500A)
removed outlier: 6.610A pdb=" N PHE A 245 " --> pdb=" O PHE A 289 " (cutoff:3.500A)
removed outlier: 6.739A pdb=" N ASN A 291 " --> pdb=" O PHE A 245 " (cutoff:3.500A)
removed outlier: 6.315A pdb=" N VAL A 247 " --> pdb=" O ASN A 291 " (cutoff:3.500A)
Processing sheet with id=AA2, first strand: chain 'B' and resid 59 through 64
removed outlier: 6.308A pdb=" N THR B 60 " --> pdb=" O ASN B 353 " (cutoff:3.500A)
removed outlier: 7.124A pdb=" N ASN B 353 " --> pdb=" O THR B 60 " (cutoff:3.500A)
removed outlier: 3.606A pdb=" N CYS B 330 " --> pdb=" O GLY B 343 " (cutoff:3.500A)
Processing sheet with id=AA3, first strand: chain 'B' and resid 71 through 76
removed outlier: 3.690A pdb=" N LYS B 91 " --> pdb=" O SER B 87 " (cutoff:3.500A)
removed outlier: 6.025A pdb=" N LEU B 92 " --> pdb=" O ALA B 105 " (cutoff:3.500A)
removed outlier: 4.539A pdb=" N ALA B 105 " --> pdb=" O LEU B 92 " (cutoff:3.500A)
removed outlier: 6.552A pdb=" N ILE B 94 " --> pdb=" O VAL B 103 " (cutoff:3.500A)
Processing sheet with id=AA4, first strand: chain 'B' and resid 113 through 118
removed outlier: 6.657A pdb=" N GLY B 128 " --> pdb=" O MET B 114 " (cutoff:3.500A)
removed outlier: 4.579A pdb=" N CYS B 116 " --> pdb=" O ALA B 126 " (cutoff:3.500A)
removed outlier: 6.390A pdb=" N ALA B 126 " --> pdb=" O CYS B 116 " (cutoff:3.500A)
removed outlier: 4.894A pdb=" N TYR B 118 " --> pdb=" O TYR B 124 " (cutoff:3.500A)
removed outlier: 7.053A pdb=" N TYR B 124 " --> pdb=" O TYR B 118 " (cutoff:3.500A)
removed outlier: 5.889A pdb=" N ASN B 138 " --> pdb=" O VAL B 148 " (cutoff:3.500A)
removed outlier: 6.122A pdb=" N VAL B 148 " --> pdb=" O ASN B 138 " (cutoff:3.500A)
Processing sheet with id=AA5, first strand: chain 'B' and resid 159 through 164
removed outlier: 3.609A pdb=" N CYS B 161 " --> pdb=" O SER B 173 " (cutoff:3.500A)
removed outlier: 3.564A pdb=" N ILE B 170 " --> pdb=" O TRP B 182 " (cutoff:3.500A)
removed outlier: 6.371A pdb=" N ASP B 183 " --> pdb=" O GLN B 189 " (cutoff:3.500A)
removed outlier: 5.955A pdb=" N GLN B 189 " --> pdb=" O ASP B 183 " (cutoff:3.500A)
Processing sheet with id=AA6, first strand: chain 'B' and resid 200 through 205
removed outlier: 6.786A pdb=" N GLY B 215 " --> pdb=" O MET B 201 " (cutoff:3.500A)
removed outlier: 4.278A pdb=" N LEU B 203 " --> pdb=" O VAL B 213 " (cutoff:3.500A)
removed outlier: 6.635A pdb=" N VAL B 213 " --> pdb=" O LEU B 203 " (cutoff:3.500A)
removed outlier: 5.058A pdb=" N LEU B 205 " --> pdb=" O LEU B 211 " (cutoff:3.500A)
removed outlier: 7.273A pdb=" N LEU B 211 " --> pdb=" O LEU B 205 " (cutoff:3.500A)
removed outlier: 6.502A pdb=" N ALA B 221 " --> pdb=" O THR B 234 " (cutoff:3.500A)
removed outlier: 4.437A pdb=" N THR B 234 " --> pdb=" O ALA B 221 " (cutoff:3.500A)
removed outlier: 6.606A pdb=" N LEU B 223 " --> pdb=" O ARG B 232 " (cutoff:3.500A)
Processing sheet with id=AA7, first strand: chain 'B' and resid 242 through 247
removed outlier: 6.579A pdb=" N CYS B 263 " --> pdb=" O THR B 276 " (cutoff:3.500A)
removed outlier: 4.538A pdb=" N THR B 276 " --> pdb=" O CYS B 263 " (cutoff:3.500A)
removed outlier: 6.547A pdb=" N LEU B 265 " --> pdb=" O LEU B 274 " (cutoff:3.500A)
removed outlier: 3.847A pdb=" N GLN B 272 " --> pdb=" O ASP B 267 " (cutoff:3.500A)
Processing sheet with id=AA8, first strand: chain 'B' and resid 286 through 291
removed outlier: 3.713A pdb=" N SER B 288 " --> pdb=" O GLY B 301 " (cutoff:3.500A)
removed outlier: 6.197A pdb=" N ASP B 311 " --> pdb=" O ARG B 317 " (cutoff:3.500A)
removed outlier: 6.275A pdb=" N ARG B 317 " --> pdb=" O ASP B 311 " (cutoff:3.500A)
Processing sheet with id=AA9, first strand: chain 'N' and resid 4 through 8
removed outlier: 3.522A pdb=" N THR N 79 " --> pdb=" O ASP N 74 " (cutoff:3.500A)
Processing sheet with id=AB1, first strand: chain 'N' and resid 11 through 13
removed outlier: 6.004A pdb=" N GLY N 11 " --> pdb=" O THR N 126 " (cutoff:3.500A)
removed outlier: 6.798A pdb=" N MET N 35 " --> pdb=" O ASP N 51 " (cutoff:3.500A)
removed outlier: 4.443A pdb=" N ASP N 51 " --> pdb=" O MET N 35 " (cutoff:3.500A)
removed outlier: 6.481A pdb=" N TRP N 37 " --> pdb=" O VAL N 49 " (cutoff:3.500A)
438 hydrogen bonds defined for protein.
1260 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: 2.26
Time building geometry restraints manager: 3.32 seconds
NOTE: a complete listing of the restraints can be obtained by requesting
output of .geo file.
Histogram of bond lengths:
1.22 - 1.34: 2655
1.34 - 1.46: 1381
1.46 - 1.57: 4369
1.57 - 1.69: 1
1.69 - 1.81: 88
Bond restraints: 8494
Sorted by residual:
bond pdb=" C8 UJL R 404 "
pdb=" S1 UJL R 404 "
ideal model delta sigma weight residual
1.725 1.526 0.199 2.00e-02 2.50e+03 9.94e+01
bond pdb=" C6 UJL R 404 "
pdb=" C7 UJL R 404 "
ideal model delta sigma weight residual
1.428 1.613 -0.185 2.00e-02 2.50e+03 8.54e+01
bond pdb=" C9 UJL R 404 "
pdb=" S1 UJL R 404 "
ideal model delta sigma weight residual
1.730 1.564 0.166 2.00e-02 2.50e+03 6.90e+01
bond pdb=" C7 UJL R 404 "
pdb=" C8 UJL R 404 "
ideal model delta sigma weight residual
1.364 1.428 -0.064 2.00e-02 2.50e+03 1.03e+01
bond pdb=" C3 UJL R 404 "
pdb=" C9 UJL R 404 "
ideal model delta sigma weight residual
1.503 1.557 -0.054 2.00e-02 2.50e+03 7.31e+00
... (remaining 8489 not shown)
Histogram of bond angle deviations from ideal:
99.46 - 106.39: 191
106.39 - 113.31: 4624
113.31 - 120.24: 3110
120.24 - 127.16: 3499
127.16 - 134.09: 94
Bond angle restraints: 11518
Sorted by residual:
angle pdb=" C8 UJL R 404 "
pdb=" S1 UJL R 404 "
pdb=" C9 UJL R 404 "
ideal model delta sigma weight residual
91.70 107.43 -15.73 3.00e+00 1.11e-01 2.75e+01
angle pdb=" N HIS B 238 "
pdb=" CA HIS B 238 "
pdb=" C HIS B 238 "
ideal model delta sigma weight residual
110.43 116.41 -5.98 1.31e+00 5.83e-01 2.08e+01
angle pdb=" CA PRO N 89 "
pdb=" N PRO N 89 "
pdb=" CD PRO N 89 "
ideal model delta sigma weight residual
112.00 107.65 4.35 1.40e+00 5.10e-01 9.67e+00
angle pdb=" C4 UJL R 404 "
pdb=" C5 UJL R 404 "
pdb=" C6 UJL R 404 "
ideal model delta sigma weight residual
109.30 118.13 -8.83 3.00e+00 1.11e-01 8.66e+00
angle pdb=" C3 UJL R 404 "
pdb=" C9 UJL R 404 "
pdb=" S1 UJL R 404 "
ideal model delta sigma weight residual
124.67 133.40 -8.73 3.00e+00 1.11e-01 8.47e+00
... (remaining 11513 not shown)
Histogram of dihedral angle deviations from ideal:
0.00 - 17.21: 4652
17.21 - 34.43: 402
34.43 - 51.64: 100
51.64 - 68.85: 22
68.85 - 86.06: 15
Dihedral angle restraints: 5191
sinusoidal: 2165
harmonic: 3026
Sorted by residual:
dihedral pdb=" CA LYS A 306 "
pdb=" C LYS A 306 "
pdb=" N ILE A 307 "
pdb=" CA ILE A 307 "
ideal model delta harmonic sigma weight residual
-180.00 -161.24 -18.76 0 5.00e+00 4.00e-02 1.41e+01
dihedral pdb=" CA TRP B 95 "
pdb=" C TRP B 95 "
pdb=" N ASP B 96 "
pdb=" CA ASP B 96 "
ideal model delta harmonic sigma weight residual
180.00 162.04 17.96 0 5.00e+00 4.00e-02 1.29e+01
dihedral pdb=" CA ILE A 307 "
pdb=" C ILE A 307 "
pdb=" N GLU A 308 "
pdb=" CA GLU A 308 "
ideal model delta harmonic sigma weight residual
-180.00 -162.53 -17.47 0 5.00e+00 4.00e-02 1.22e+01
... (remaining 5188 not shown)
Histogram of chiral volume deviations from ideal:
0.000 - 0.043: 966
0.043 - 0.086: 251
0.086 - 0.129: 70
0.129 - 0.172: 6
0.172 - 0.215: 2
Chirality restraints: 1295
Sorted by residual:
chirality pdb=" CA ASN R 41 "
pdb=" N ASN R 41 "
pdb=" C ASN R 41 "
pdb=" CB ASN R 41 "
both_signs ideal model delta sigma weight residual
False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.15e+00
chirality pdb=" CA HIS B 238 "
pdb=" N HIS B 238 "
pdb=" C HIS B 238 "
pdb=" CB HIS B 238 "
both_signs ideal model delta sigma weight residual
False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.69e-01
chirality pdb=" CA ILE R 281 "
pdb=" N ILE R 281 "
pdb=" C ILE R 281 "
pdb=" CB ILE R 281 "
both_signs ideal model delta sigma weight residual
False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.24e-01
... (remaining 1292 not shown)
Planarity restraints: 1446
Sorted by residual:
delta sigma weight rms_deltas residual
plane pdb=" C LYS N 88 " 0.051 5.00e-02 4.00e+02 7.59e-02 9.21e+00
pdb=" N PRO N 89 " -0.131 5.00e-02 4.00e+02
pdb=" CA PRO N 89 " 0.038 5.00e-02 4.00e+02
pdb=" CD PRO N 89 " 0.042 5.00e-02 4.00e+02
delta sigma weight rms_deltas residual
plane pdb=" CD ARG N 106 " 0.248 9.50e-02 1.11e+02 1.12e-01 8.65e+00
pdb=" NE ARG N 106 " -0.021 2.00e-02 2.50e+03
pdb=" CZ ARG N 106 " 0.015 2.00e-02 2.50e+03
pdb=" NH1 ARG N 106 " -0.008 2.00e-02 2.50e+03
pdb=" NH2 ARG N 106 " 0.003 2.00e-02 2.50e+03
delta sigma weight rms_deltas residual
plane pdb=" CD ARG A 264 " -0.130 9.50e-02 1.11e+02 5.86e-02 2.20e+00
pdb=" NE ARG A 264 " 0.010 2.00e-02 2.50e+03
pdb=" CZ ARG A 264 " -0.004 2.00e-02 2.50e+03
pdb=" NH1 ARG A 264 " 0.003 2.00e-02 2.50e+03
pdb=" NH2 ARG A 264 " -0.003 2.00e-02 2.50e+03
... (remaining 1443 not shown)
Histogram of nonbonded interaction distances:
2.14 - 2.69: 202
2.69 - 3.25: 8166
3.25 - 3.80: 13317
3.80 - 4.35: 18534
4.35 - 4.90: 31063
Nonbonded interactions: 71282
Sorted by model distance:
nonbonded pdb=" N GLU A 326 "
pdb=" OE1 GLU A 326 "
model vdw
2.143 3.120
nonbonded pdb=" OG SER B 294 "
pdb=" OD2 ASP G 47 "
model vdw
2.210 3.040
nonbonded pdb=" OH TYR A 317 "
pdb=" OD2 ASP A 342 "
model vdw
2.229 3.040
nonbonded pdb=" O PHE R 145 "
pdb=" OG SER R 149 "
model vdw
2.231 3.040
nonbonded pdb=" O ASP B 208 "
pdb=" OG1 THR B 209 "
model vdw
2.266 3.040
... (remaining 71277 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=0.01 max=1.00 mean=0.94
Load rotamer database and sin/cos tables
Set ADP refinement strategy
ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
Set random seed: 0.000
Set model cs if undefined: 0.000
Decide on map wrapping: 0.000
Normalize map: mean=0, sd=1: 1.640
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: 0.300
Check model and map are aligned: 0.060
Set scattering table: 0.070
Process input model: 24.990
Find NCS groups from input model: 0.080
Set up NCS constraints: 0.030
Set refine NCS operators: 0.000
Adjust number of macro_cycles: 0.000
Reset NCS operators: 0.000
Extract rigid body selections: 0.000
Check and reset occupancies: 0.000
Load rotamer database and sin/cos tables:13.490
Set ADP refinement strategy: 0.000
Make a string to write initial .geo file:0.000
Internal consistency checks: 0.000
Total: 40.670
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8390
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 : 0.006 0.199 8494 Z= 0.402
Angle : 0.638 15.729 11518 Z= 0.342
Chirality : 0.042 0.215 1295
Planarity : 0.005 0.112 1446
Dihedral : 14.725 86.062 3232
Min Nonbonded Distance : 2.143
Molprobity Statistics.
All-atom Clashscore : 4.00
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 2.74 %
Favored : 97.26 %
Rotamer:
Outliers : 0.34 %
Allowed : 14.77 %
Favored : 84.90 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 1.00 (0.26), residues: 1023
helix: 2.06 (0.26), residues: 409
sheet: 0.04 (0.34), residues: 216
loop : -0.39 (0.30), residues: 398
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.018 0.002 TRP R 291
HIS 0.004 0.001 HIS B 67
PHE 0.014 0.002 PHE R 160
TYR 0.013 0.001 TYR R 304
ARG 0.018 0.001 ARG N 106
*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
2046 Ramachandran restraints generated.
1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
2046 Ramachandran restraints generated.
1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
131 residues out of total 899 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 3
poor density : 128
time to evaluate : 0.849
Fit side-chains
revert: symmetry clash
REVERT: A 326 GLU cc_start: 0.6524 (mp0) cc_final: 0.6294 (tp30)
REVERT: B 72 TYR cc_start: 0.9043 (OUTLIER) cc_final: 0.7863 (m-80)
REVERT: N 47 GLU cc_start: 0.8111 (tt0) cc_final: 0.7891 (tt0)
outliers start: 3
outliers final: 2
residues processed: 130
average time/residue: 1.3585
time to fit residues: 187.1885
Evaluate side-chains
117 residues out of total 899 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 3
poor density : 114
time to evaluate : 0.895
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue 72 TYR
Chi-restraints excluded: chain B residue 159 LEU
Chi-restraints excluded: chain B residue 287 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 101
random chunks:
chunk 85 optimal weight: 0.6980
chunk 76 optimal weight: 0.9990
chunk 42 optimal weight: 4.9990
chunk 26 optimal weight: 0.8980
chunk 51 optimal weight: 0.9990
chunk 40 optimal weight: 3.9990
chunk 79 optimal weight: 1.9990
chunk 30 optimal weight: 2.9990
chunk 48 optimal weight: 0.5980
chunk 58 optimal weight: 8.9990
chunk 91 optimal weight: 0.8980
overall best weight: 0.8182
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 13 ASN
A 34 GLN
B 189 GLN
B 238 HIS
B 272 GLN
N 4 GLN
N 6 GLN
R 175 HIS
R 296 ASN
Total number of N/Q/H flips: 9
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8331
moved from start: 0.1165
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.045 8494 Z= 0.191
Angle : 0.540 6.069 11518 Z= 0.292
Chirality : 0.043 0.159 1295
Planarity : 0.004 0.052 1446
Dihedral : 5.182 58.441 1344
Min Nonbonded Distance : 2.506
Molprobity Statistics.
All-atom Clashscore : 3.45
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 1.96 %
Favored : 98.04 %
Rotamer:
Outliers : 2.57 %
Allowed : 13.87 %
Favored : 83.56 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 1.21 (0.26), residues: 1023
helix: 2.24 (0.25), residues: 413
sheet: 0.05 (0.34), residues: 228
loop : -0.26 (0.31), residues: 382
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.020 0.002 TRP R 291
HIS 0.004 0.001 HIS R 113
PHE 0.013 0.001 PHE R 160
TYR 0.015 0.001 TYR R 79
ARG 0.005 0.000 ARG A 264
*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
2046 Ramachandran restraints generated.
1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
2046 Ramachandran restraints generated.
1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
155 residues out of total 899 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 23
poor density : 132
time to evaluate : 0.921
Fit side-chains
revert: symmetry clash
revert: symmetry clash
REVERT: A 295 LEU cc_start: 0.8262 (mp) cc_final: 0.8030 (tp)
REVERT: A 316 ARG cc_start: 0.7282 (OUTLIER) cc_final: 0.6937 (ptt90)
REVERT: B 83 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8607 (pp)
REVERT: N 107 ASP cc_start: 0.7885 (p0) cc_final: 0.7562 (p0)
outliers start: 23
outliers final: 11
residues processed: 147
average time/residue: 1.2682
time to fit residues: 198.2724
Evaluate side-chains
131 residues out of total 899 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 13
poor density : 118
time to evaluate : 0.914
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 316 ARG
Chi-restraints excluded: chain B residue 53 VAL
Chi-restraints excluded: chain B residue 72 TYR
Chi-restraints excluded: chain B residue 83 LEU
Chi-restraints excluded: chain B residue 111 SER
Chi-restraints excluded: chain B residue 159 LEU
Chi-restraints excluded: chain B residue 177 THR
Chi-restraints excluded: chain B residue 191 THR
Chi-restraints excluded: chain B residue 247 PHE
Chi-restraints excluded: chain B residue 275 MET
Chi-restraints excluded: chain B residue 287 THR
Chi-restraints excluded: chain N residue 105 THR
Chi-restraints excluded: chain N residue 115 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 101
random chunks:
chunk 50 optimal weight: 0.9980
chunk 28 optimal weight: 3.9990
chunk 76 optimal weight: 5.9990
chunk 62 optimal weight: 4.9990
chunk 25 optimal weight: 0.5980
chunk 91 optimal weight: 0.6980
chunk 99 optimal weight: 0.9990
chunk 81 optimal weight: 6.9990
chunk 31 optimal weight: 0.7980
chunk 73 optimal weight: 9.9990
chunk 90 optimal weight: 0.9990
overall best weight: 0.8182
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 34 GLN
** A 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 291 ASN
B 233 GLN
B 272 GLN
N 4 GLN
N 6 GLN
Total number of N/Q/H flips: 6
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8322
moved from start: 0.1541
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.041 8494 Z= 0.178
Angle : 0.505 6.666 11518 Z= 0.273
Chirality : 0.042 0.134 1295
Planarity : 0.004 0.062 1446
Dihedral : 5.060 59.914 1344
Min Nonbonded Distance : 2.519
Molprobity Statistics.
All-atom Clashscore : 3.81
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 1.86 %
Favored : 98.14 %
Rotamer:
Outliers : 3.13 %
Allowed : 14.54 %
Favored : 82.33 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 1.35 (0.26), residues: 1023
helix: 2.45 (0.25), residues: 413
sheet: -0.01 (0.34), residues: 226
loop : -0.20 (0.31), residues: 384
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.018 0.002 TRP R 291
HIS 0.003 0.001 HIS R 63
PHE 0.011 0.001 PHE R 95
TYR 0.015 0.001 TYR R 79
ARG 0.005 0.000 ARG A 264
*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
2046 Ramachandran restraints generated.
1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
2046 Ramachandran restraints generated.
1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
145 residues out of total 899 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 28
poor density : 117
time to evaluate : 0.895
Fit side-chains
revert: symmetry clash
revert: symmetry clash
REVERT: A 212 GLN cc_start: 0.8903 (OUTLIER) cc_final: 0.8630 (tt0)
REVERT: A 316 ARG cc_start: 0.7281 (OUTLIER) cc_final: 0.6918 (ptt90)
REVERT: B 83 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8613 (pp)
REVERT: B 247 PHE cc_start: 0.9127 (OUTLIER) cc_final: 0.8184 (t80)
REVERT: N 107 ASP cc_start: 0.7780 (p0) cc_final: 0.7537 (p0)
outliers start: 28
outliers final: 13
residues processed: 139
average time/residue: 1.1892
time to fit residues: 175.9205
Evaluate side-chains
128 residues out of total 899 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 17
poor density : 111
time to evaluate : 0.935
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 212 GLN
Chi-restraints excluded: chain A residue 316 ARG
Chi-restraints excluded: chain A residue 366 VAL
Chi-restraints excluded: chain B residue 53 VAL
Chi-restraints excluded: chain B residue 72 TYR
Chi-restraints excluded: chain B residue 83 LEU
Chi-restraints excluded: chain B residue 111 SER
Chi-restraints excluded: chain B residue 177 THR
Chi-restraints excluded: chain B residue 191 THR
Chi-restraints excluded: chain B residue 247 PHE
Chi-restraints excluded: chain B residue 275 MET
Chi-restraints excluded: chain B residue 287 THR
Chi-restraints excluded: chain N residue 60 SER
Chi-restraints excluded: chain N residue 105 THR
Chi-restraints excluded: chain N residue 115 THR
Chi-restraints excluded: chain R residue 209 VAL
Chi-restraints excluded: chain R residue 219 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 101
random chunks:
chunk 69 optimal weight: 8.9990
chunk 47 optimal weight: 0.9990
chunk 10 optimal weight: 10.0000
chunk 43 optimal weight: 8.9990
chunk 61 optimal weight: 6.9990
chunk 92 optimal weight: 3.9990
chunk 97 optimal weight: 3.9990
chunk 48 optimal weight: 0.1980
chunk 87 optimal weight: 7.9990
chunk 26 optimal weight: 6.9990
chunk 81 optimal weight: 6.9990
overall best weight: 3.2388
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** A 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 233 GLN
B 272 GLN
N 4 GLN
N 6 GLN
N 32 ASN
Total number of N/Q/H flips: 5
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8419
moved from start: 0.1544
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.007 0.071 8494 Z= 0.485
Angle : 0.656 9.774 11518 Z= 0.349
Chirality : 0.049 0.224 1295
Planarity : 0.005 0.064 1446
Dihedral : 5.640 55.945 1342
Min Nonbonded Distance : 2.487
Molprobity Statistics.
All-atom Clashscore : 4.72
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 3.13 %
Favored : 96.87 %
Rotamer:
Outliers : 4.47 %
Allowed : 14.09 %
Favored : 81.43 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 0.92 (0.26), residues: 1023
helix: 1.97 (0.25), residues: 415
sheet: -0.20 (0.34), residues: 223
loop : -0.32 (0.30), residues: 385
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.020 0.003 TRP R 291
HIS 0.008 0.001 HIS R 63
PHE 0.025 0.002 PHE R 160
TYR 0.019 0.002 TYR R 79
ARG 0.006 0.001 ARG A 37
*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
2046 Ramachandran restraints generated.
1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
2046 Ramachandran restraints generated.
1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
146 residues out of total 899 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 40
poor density : 106
time to evaluate : 0.934
Fit side-chains
revert: symmetry clash
revert: symmetry clash
REVERT: A 316 ARG cc_start: 0.7339 (OUTLIER) cc_final: 0.6963 (ptt90)
REVERT: B 72 TYR cc_start: 0.9091 (OUTLIER) cc_final: 0.8810 (m-80)
outliers start: 40
outliers final: 20
residues processed: 134
average time/residue: 1.2226
time to fit residues: 174.6111
Evaluate side-chains
124 residues out of total 899 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 22
poor density : 102
time to evaluate : 0.849
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 212 GLN
Chi-restraints excluded: chain A residue 299 LYS
Chi-restraints excluded: chain A residue 316 ARG
Chi-restraints excluded: chain A residue 366 VAL
Chi-restraints excluded: chain B residue 53 VAL
Chi-restraints excluded: chain B residue 72 TYR
Chi-restraints excluded: chain B residue 111 SER
Chi-restraints excluded: chain B residue 114 MET
Chi-restraints excluded: chain B residue 116 CYS
Chi-restraints excluded: chain B residue 159 LEU
Chi-restraints excluded: chain B residue 177 THR
Chi-restraints excluded: chain B residue 191 THR
Chi-restraints excluded: chain B residue 247 PHE
Chi-restraints excluded: chain B residue 275 MET
Chi-restraints excluded: chain B residue 287 THR
Chi-restraints excluded: chain B residue 330 CYS
Chi-restraints excluded: chain N residue 60 SER
Chi-restraints excluded: chain N residue 105 THR
Chi-restraints excluded: chain N residue 109 PHE
Chi-restraints excluded: chain N residue 115 THR
Chi-restraints excluded: chain R residue 183 SER
Chi-restraints excluded: chain R residue 209 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 101
random chunks:
chunk 55 optimal weight: 1.9990
chunk 1 optimal weight: 1.9990
chunk 72 optimal weight: 5.9990
chunk 40 optimal weight: 0.0570
chunk 83 optimal weight: 0.6980
chunk 67 optimal weight: 3.9990
chunk 0 optimal weight: 6.9990
chunk 49 optimal weight: 0.9990
chunk 87 optimal weight: 5.9990
chunk 24 optimal weight: 0.9980
chunk 32 optimal weight: 2.9990
overall best weight: 0.9502
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** A 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 272 GLN
N 4 GLN
N 6 GLN
N 78 ASN
Total number of N/Q/H flips: 4
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8356
moved from start: 0.1757
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.042 8494 Z= 0.195
Angle : 0.525 9.395 11518 Z= 0.281
Chirality : 0.042 0.158 1295
Planarity : 0.004 0.062 1446
Dihedral : 5.091 57.952 1342
Min Nonbonded Distance : 2.516
Molprobity Statistics.
All-atom Clashscore : 4.48
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 1.96 %
Favored : 98.04 %
Rotamer:
Outliers : 2.91 %
Allowed : 15.66 %
Favored : 81.43 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 1.13 (0.26), residues: 1023
helix: 2.26 (0.25), residues: 413
sheet: -0.22 (0.33), residues: 225
loop : -0.25 (0.31), residues: 385
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.021 0.002 TRP R 291
HIS 0.003 0.001 HIS R 63
PHE 0.012 0.001 PHE B 164
TYR 0.017 0.001 TYR R 79
ARG 0.006 0.000 ARG A 37
*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
2046 Ramachandran restraints generated.
1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
2046 Ramachandran restraints generated.
1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
136 residues out of total 899 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 26
poor density : 110
time to evaluate : 0.951
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: A 212 GLN cc_start: 0.8936 (OUTLIER) cc_final: 0.8643 (tt0)
REVERT: A 316 ARG cc_start: 0.7312 (OUTLIER) cc_final: 0.6883 (ptt90)
REVERT: B 247 PHE cc_start: 0.9111 (OUTLIER) cc_final: 0.8162 (t80)
REVERT: R 193 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8257 (mm)
outliers start: 26
outliers final: 16
residues processed: 127
average time/residue: 1.2303
time to fit residues: 166.2404
Evaluate side-chains
126 residues out of total 899 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 20
poor density : 106
time to evaluate : 0.829
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 212 GLN
Chi-restraints excluded: chain A residue 316 ARG
Chi-restraints excluded: chain A residue 366 VAL
Chi-restraints excluded: chain B residue 53 VAL
Chi-restraints excluded: chain B residue 72 TYR
Chi-restraints excluded: chain B residue 111 SER
Chi-restraints excluded: chain B residue 114 MET
Chi-restraints excluded: chain B residue 116 CYS
Chi-restraints excluded: chain B residue 159 LEU
Chi-restraints excluded: chain B residue 177 THR
Chi-restraints excluded: chain B residue 191 THR
Chi-restraints excluded: chain B residue 247 PHE
Chi-restraints excluded: chain B residue 275 MET
Chi-restraints excluded: chain B residue 287 THR
Chi-restraints excluded: chain N residue 105 THR
Chi-restraints excluded: chain N residue 109 PHE
Chi-restraints excluded: chain N residue 115 THR
Chi-restraints excluded: chain R residue 193 LEU
Chi-restraints excluded: chain R residue 209 VAL
Chi-restraints excluded: chain R residue 280 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 101
random chunks:
chunk 87 optimal weight: 6.9990
chunk 19 optimal weight: 0.0000
chunk 57 optimal weight: 5.9990
chunk 24 optimal weight: 0.6980
chunk 97 optimal weight: 2.9990
chunk 81 optimal weight: 1.9990
chunk 45 optimal weight: 6.9990
chunk 8 optimal weight: 1.9990
chunk 32 optimal weight: 0.9990
chunk 51 optimal weight: 4.9990
chunk 94 optimal weight: 1.9990
overall best weight: 1.1390
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** A 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 272 GLN
N 4 GLN
N 6 GLN
N 78 ASN
Total number of N/Q/H flips: 4
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8355
moved from start: 0.1889
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.040 8494 Z= 0.213
Angle : 0.518 8.740 11518 Z= 0.277
Chirality : 0.042 0.147 1295
Planarity : 0.004 0.063 1446
Dihedral : 4.999 58.481 1342
Min Nonbonded Distance : 2.524
Molprobity Statistics.
All-atom Clashscore : 4.30
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 2.44 %
Favored : 97.56 %
Rotamer:
Outliers : 3.47 %
Allowed : 16.11 %
Favored : 80.43 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 1.16 (0.26), residues: 1023
helix: 2.34 (0.25), residues: 413
sheet: -0.29 (0.33), residues: 223
loop : -0.23 (0.31), residues: 387
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.020 0.002 TRP R 291
HIS 0.004 0.001 HIS R 63
PHE 0.012 0.001 PHE R 160
TYR 0.015 0.001 TYR R 79
ARG 0.006 0.000 ARG A 264
*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
2046 Ramachandran restraints generated.
1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
2046 Ramachandran restraints generated.
1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
140 residues out of total 899 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 31
poor density : 109
time to evaluate : 0.924
Fit side-chains
revert: symmetry clash
revert: symmetry clash
REVERT: A 58 GLN cc_start: 0.7732 (mm110) cc_final: 0.6828 (tm-30)
REVERT: A 212 GLN cc_start: 0.8902 (OUTLIER) cc_final: 0.8658 (tt0)
REVERT: A 316 ARG cc_start: 0.7301 (OUTLIER) cc_final: 0.6871 (ptt90)
REVERT: B 247 PHE cc_start: 0.9140 (OUTLIER) cc_final: 0.8202 (t80)
REVERT: R 193 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8283 (mm)
outliers start: 31
outliers final: 18
residues processed: 129
average time/residue: 1.1225
time to fit residues: 154.5387
Evaluate side-chains
130 residues out of total 899 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 22
poor density : 108
time to evaluate : 0.834
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 212 GLN
Chi-restraints excluded: chain A residue 299 LYS
Chi-restraints excluded: chain A residue 316 ARG
Chi-restraints excluded: chain A residue 366 VAL
Chi-restraints excluded: chain B residue 53 VAL
Chi-restraints excluded: chain B residue 72 TYR
Chi-restraints excluded: chain B residue 111 SER
Chi-restraints excluded: chain B residue 114 MET
Chi-restraints excluded: chain B residue 116 CYS
Chi-restraints excluded: chain B residue 159 LEU
Chi-restraints excluded: chain B residue 177 THR
Chi-restraints excluded: chain B residue 191 THR
Chi-restraints excluded: chain B residue 236 THR
Chi-restraints excluded: chain B residue 247 PHE
Chi-restraints excluded: chain B residue 275 MET
Chi-restraints excluded: chain B residue 287 THR
Chi-restraints excluded: chain N residue 105 THR
Chi-restraints excluded: chain N residue 109 PHE
Chi-restraints excluded: chain N residue 115 THR
Chi-restraints excluded: chain R residue 193 LEU
Chi-restraints excluded: chain R residue 209 VAL
Chi-restraints excluded: chain R residue 229 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 101
random chunks:
chunk 11 optimal weight: 0.9990
chunk 55 optimal weight: 0.6980
chunk 71 optimal weight: 0.4980
chunk 82 optimal weight: 0.9990
chunk 54 optimal weight: 1.9990
chunk 97 optimal weight: 3.9990
chunk 60 optimal weight: 0.8980
chunk 59 optimal weight: 5.9990
chunk 44 optimal weight: 6.9990
chunk 38 optimal weight: 0.8980
chunk 58 optimal weight: 4.9990
overall best weight: 0.7982
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** A 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 272 GLN
N 4 GLN
N 6 GLN
N 78 ASN
Total number of N/Q/H flips: 4
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8328
moved from start: 0.2012
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.036 8494 Z= 0.169
Angle : 0.490 8.067 11518 Z= 0.263
Chirality : 0.041 0.130 1295
Planarity : 0.004 0.062 1446
Dihedral : 4.812 59.881 1342
Min Nonbonded Distance : 2.443
Molprobity Statistics.
All-atom Clashscore : 4.78
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 2.05 %
Favored : 97.95 %
Rotamer:
Outliers : 3.02 %
Allowed : 16.44 %
Favored : 80.54 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 1.29 (0.26), residues: 1023
helix: 2.50 (0.25), residues: 413
sheet: -0.26 (0.32), residues: 223
loop : -0.20 (0.31), residues: 387
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.020 0.002 TRP R 291
HIS 0.003 0.001 HIS R 63
PHE 0.011 0.001 PHE B 164
TYR 0.013 0.001 TYR R 79
ARG 0.006 0.000 ARG A 264
*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
2046 Ramachandran restraints generated.
1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
2046 Ramachandran restraints generated.
1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
144 residues out of total 899 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 27
poor density : 117
time to evaluate : 0.927
Fit side-chains
revert: symmetry clash
revert: symmetry clash
REVERT: A 212 GLN cc_start: 0.8830 (OUTLIER) cc_final: 0.8590 (tt0)
REVERT: A 316 ARG cc_start: 0.7230 (OUTLIER) cc_final: 0.6818 (ptt90)
REVERT: B 247 PHE cc_start: 0.9118 (OUTLIER) cc_final: 0.8303 (t80)
REVERT: N 107 ASP cc_start: 0.7823 (p0) cc_final: 0.7245 (p0)
REVERT: R 193 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8298 (mm)
outliers start: 27
outliers final: 17
residues processed: 134
average time/residue: 1.1391
time to fit residues: 163.0618
Evaluate side-chains
134 residues out of total 899 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 21
poor density : 113
time to evaluate : 0.827
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 212 GLN
Chi-restraints excluded: chain A residue 299 LYS
Chi-restraints excluded: chain A residue 316 ARG
Chi-restraints excluded: chain A residue 366 VAL
Chi-restraints excluded: chain B residue 53 VAL
Chi-restraints excluded: chain B residue 72 TYR
Chi-restraints excluded: chain B residue 111 SER
Chi-restraints excluded: chain B residue 114 MET
Chi-restraints excluded: chain B residue 159 LEU
Chi-restraints excluded: chain B residue 177 THR
Chi-restraints excluded: chain B residue 191 THR
Chi-restraints excluded: chain B residue 247 PHE
Chi-restraints excluded: chain B residue 275 MET
Chi-restraints excluded: chain B residue 287 THR
Chi-restraints excluded: chain B residue 330 CYS
Chi-restraints excluded: chain N residue 105 THR
Chi-restraints excluded: chain N residue 109 PHE
Chi-restraints excluded: chain N residue 115 THR
Chi-restraints excluded: chain R residue 193 LEU
Chi-restraints excluded: chain R residue 209 VAL
Chi-restraints excluded: chain R residue 229 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 101
random chunks:
chunk 29 optimal weight: 0.8980
chunk 19 optimal weight: 0.8980
chunk 18 optimal weight: 0.9980
chunk 61 optimal weight: 0.0060
chunk 66 optimal weight: 0.1980
chunk 48 optimal weight: 1.9990
chunk 9 optimal weight: 0.4980
chunk 76 optimal weight: 3.9990
chunk 88 optimal weight: 0.9990
chunk 93 optimal weight: 2.9990
chunk 85 optimal weight: 0.7980
overall best weight: 0.4796
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** A 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 272 GLN
N 4 GLN
N 6 GLN
N 78 ASN
Total number of N/Q/H flips: 4
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8289
moved from start: 0.2227
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.002 0.032 8494 Z= 0.137
Angle : 0.469 7.864 11518 Z= 0.251
Chirality : 0.041 0.128 1295
Planarity : 0.004 0.061 1446
Dihedral : 4.587 57.909 1342
Min Nonbonded Distance : 2.457
Molprobity Statistics.
All-atom Clashscore : 4.84
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 1.86 %
Favored : 98.14 %
Rotamer:
Outliers : 2.46 %
Allowed : 17.45 %
Favored : 80.09 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 1.41 (0.26), residues: 1023
helix: 2.63 (0.25), residues: 414
sheet: -0.28 (0.32), residues: 229
loop : -0.12 (0.32), residues: 380
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.019 0.002 TRP R 291
HIS 0.002 0.000 HIS R 63
PHE 0.010 0.001 PHE R 95
TYR 0.013 0.001 TYR R 79
ARG 0.006 0.000 ARG A 264
*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
2046 Ramachandran restraints generated.
1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
2046 Ramachandran restraints generated.
1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
150 residues out of total 899 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 22
poor density : 128
time to evaluate : 0.966
Fit side-chains
revert: symmetry clash
revert: symmetry clash
REVERT: A 58 GLN cc_start: 0.7709 (mm110) cc_final: 0.6851 (tm-30)
REVERT: A 212 GLN cc_start: 0.8783 (OUTLIER) cc_final: 0.8525 (tt0)
REVERT: A 316 ARG cc_start: 0.7202 (OUTLIER) cc_final: 0.6907 (ptt90)
REVERT: B 247 PHE cc_start: 0.9096 (OUTLIER) cc_final: 0.8300 (t80)
REVERT: N 107 ASP cc_start: 0.7745 (p0) cc_final: 0.7085 (p0)
REVERT: R 193 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.8300 (mm)
outliers start: 22
outliers final: 15
residues processed: 141
average time/residue: 1.1392
time to fit residues: 171.6656
Evaluate side-chains
144 residues out of total 899 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 19
poor density : 125
time to evaluate : 0.945
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 212 GLN
Chi-restraints excluded: chain A residue 299 LYS
Chi-restraints excluded: chain A residue 316 ARG
Chi-restraints excluded: chain A residue 366 VAL
Chi-restraints excluded: chain B residue 72 TYR
Chi-restraints excluded: chain B residue 111 SER
Chi-restraints excluded: chain B residue 114 MET
Chi-restraints excluded: chain B residue 159 LEU
Chi-restraints excluded: chain B residue 191 THR
Chi-restraints excluded: chain B residue 247 PHE
Chi-restraints excluded: chain B residue 275 MET
Chi-restraints excluded: chain B residue 287 THR
Chi-restraints excluded: chain B residue 330 CYS
Chi-restraints excluded: chain N residue 105 THR
Chi-restraints excluded: chain N residue 109 PHE
Chi-restraints excluded: chain N residue 115 THR
Chi-restraints excluded: chain R residue 193 LEU
Chi-restraints excluded: chain R residue 209 VAL
Chi-restraints excluded: chain R residue 229 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 101
random chunks:
chunk 90 optimal weight: 0.9980
chunk 93 optimal weight: 1.9990
chunk 54 optimal weight: 0.8980
chunk 39 optimal weight: 0.7980
chunk 71 optimal weight: 1.9990
chunk 27 optimal weight: 6.9990
chunk 81 optimal weight: 2.9990
chunk 85 optimal weight: 2.9990
chunk 59 optimal weight: 3.9990
chunk 95 optimal weight: 2.9990
chunk 58 optimal weight: 5.9990
overall best weight: 1.3384
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** A 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 233 GLN
B 272 GLN
N 4 GLN
N 6 GLN
N 78 ASN
Total number of N/Q/H flips: 5
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8350
moved from start: 0.2069
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.004 0.040 8494 Z= 0.236
Angle : 0.535 7.480 11518 Z= 0.285
Chirality : 0.043 0.187 1295
Planarity : 0.004 0.062 1446
Dihedral : 4.829 59.856 1342
Min Nonbonded Distance : 2.398
Molprobity Statistics.
All-atom Clashscore : 4.54
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 2.35 %
Favored : 97.65 %
Rotamer:
Outliers : 2.68 %
Allowed : 17.79 %
Favored : 79.53 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 1.37 (0.26), residues: 1023
helix: 2.57 (0.25), residues: 413
sheet: -0.26 (0.32), residues: 223
loop : -0.15 (0.31), residues: 387
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.019 0.002 TRP R 291
HIS 0.005 0.001 HIS R 63
PHE 0.012 0.001 PHE B 164
TYR 0.016 0.001 TYR R 79
ARG 0.007 0.000 ARG B 147
*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
2046 Ramachandran restraints generated.
1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
2046 Ramachandran restraints generated.
1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
140 residues out of total 899 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 24
poor density : 116
time to evaluate : 0.944
Fit side-chains
revert: symmetry clash
REVERT: A 212 GLN cc_start: 0.8822 (OUTLIER) cc_final: 0.8577 (tt0)
REVERT: A 316 ARG cc_start: 0.7248 (OUTLIER) cc_final: 0.6852 (ptt90)
REVERT: B 247 PHE cc_start: 0.9134 (OUTLIER) cc_final: 0.8295 (t80)
REVERT: N 107 ASP cc_start: 0.7805 (p0) cc_final: 0.7263 (p0)
REVERT: R 193 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8295 (mm)
outliers start: 24
outliers final: 16
residues processed: 131
average time/residue: 1.1771
time to fit residues: 165.0817
Evaluate side-chains
132 residues out of total 899 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 20
poor density : 112
time to evaluate : 0.892
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 212 GLN
Chi-restraints excluded: chain A residue 299 LYS
Chi-restraints excluded: chain A residue 316 ARG
Chi-restraints excluded: chain A residue 366 VAL
Chi-restraints excluded: chain B residue 53 VAL
Chi-restraints excluded: chain B residue 72 TYR
Chi-restraints excluded: chain B residue 111 SER
Chi-restraints excluded: chain B residue 114 MET
Chi-restraints excluded: chain B residue 159 LEU
Chi-restraints excluded: chain B residue 191 THR
Chi-restraints excluded: chain B residue 236 THR
Chi-restraints excluded: chain B residue 247 PHE
Chi-restraints excluded: chain B residue 287 THR
Chi-restraints excluded: chain B residue 330 CYS
Chi-restraints excluded: chain N residue 105 THR
Chi-restraints excluded: chain N residue 109 PHE
Chi-restraints excluded: chain N residue 115 THR
Chi-restraints excluded: chain R residue 193 LEU
Chi-restraints excluded: chain R residue 209 VAL
Chi-restraints excluded: chain R residue 229 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 101
random chunks:
chunk 45 optimal weight: 4.9990
chunk 66 optimal weight: 0.4980
chunk 100 optimal weight: 1.9990
chunk 92 optimal weight: 1.9990
chunk 80 optimal weight: 2.9990
chunk 8 optimal weight: 0.5980
chunk 61 optimal weight: 3.9990
chunk 49 optimal weight: 4.9990
chunk 63 optimal weight: 0.9990
chunk 85 optimal weight: 0.9980
chunk 24 optimal weight: 0.9980
overall best weight: 0.8182
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** A 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 233 GLN
B 272 GLN
N 4 GLN
N 6 GLN
N 78 ASN
Total number of N/Q/H flips: 5
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8321
moved from start: 0.2223
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.037 8494 Z= 0.177
Angle : 0.504 7.520 11518 Z= 0.269
Chirality : 0.042 0.178 1295
Planarity : 0.004 0.061 1446
Dihedral : 4.671 58.815 1342
Min Nonbonded Distance : 2.399
Molprobity Statistics.
All-atom Clashscore : 4.78
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 1.96 %
Favored : 98.04 %
Rotamer:
Outliers : 2.24 %
Allowed : 19.13 %
Favored : 78.64 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 1.41 (0.26), residues: 1023
helix: 2.58 (0.25), residues: 413
sheet: -0.25 (0.31), residues: 227
loop : -0.08 (0.32), residues: 383
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.019 0.002 TRP R 291
HIS 0.003 0.001 HIS R 63
PHE 0.012 0.001 PHE R 95
TYR 0.015 0.001 TYR N 96
ARG 0.007 0.000 ARG A 264
********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
2046 Ramachandran restraints generated.
1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
2046 Ramachandran restraints generated.
1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
139 residues out of total 899 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 20
poor density : 119
time to evaluate : 0.923
Fit side-chains
revert: symmetry clash
revert: symmetry clash
REVERT: A 58 GLN cc_start: 0.7710 (mm110) cc_final: 0.6851 (tm-30)
REVERT: A 212 GLN cc_start: 0.8807 (OUTLIER) cc_final: 0.8540 (tt0)
REVERT: A 316 ARG cc_start: 0.7222 (OUTLIER) cc_final: 0.6827 (ptt90)
REVERT: B 247 PHE cc_start: 0.9109 (OUTLIER) cc_final: 0.8298 (t80)
REVERT: N 107 ASP cc_start: 0.7779 (p0) cc_final: 0.7188 (p0)
REVERT: R 193 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8290 (mm)
outliers start: 20
outliers final: 14
residues processed: 131
average time/residue: 1.1054
time to fit residues: 154.9146
Evaluate side-chains
136 residues out of total 899 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 18
poor density : 118
time to evaluate : 0.950
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 212 GLN
Chi-restraints excluded: chain A residue 299 LYS
Chi-restraints excluded: chain A residue 316 ARG
Chi-restraints excluded: chain A residue 366 VAL
Chi-restraints excluded: chain B residue 53 VAL
Chi-restraints excluded: chain B residue 72 TYR
Chi-restraints excluded: chain B residue 111 SER
Chi-restraints excluded: chain B residue 114 MET
Chi-restraints excluded: chain B residue 159 LEU
Chi-restraints excluded: chain B residue 191 THR
Chi-restraints excluded: chain B residue 247 PHE
Chi-restraints excluded: chain B residue 330 CYS
Chi-restraints excluded: chain N residue 105 THR
Chi-restraints excluded: chain N residue 109 PHE
Chi-restraints excluded: chain N residue 115 THR
Chi-restraints excluded: chain R residue 193 LEU
Chi-restraints excluded: chain R residue 209 VAL
Chi-restraints excluded: chain R residue 229 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 101
random chunks:
chunk 73 optimal weight: 9.9990
chunk 11 optimal weight: 0.9990
chunk 22 optimal weight: 0.9990
chunk 80 optimal weight: 0.6980
chunk 33 optimal weight: 3.9990
chunk 82 optimal weight: 1.9990
chunk 10 optimal weight: 0.9980
chunk 14 optimal weight: 0.8980
chunk 70 optimal weight: 4.9990
chunk 4 optimal weight: 3.9990
chunk 57 optimal weight: 9.9990
overall best weight: 0.9184
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** A 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 233 GLN
B 272 GLN
N 4 GLN
N 6 GLN
N 78 ASN
Total number of N/Q/H flips: 5
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3930 r_free = 0.3930 target = 0.155892 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.120306 restraints weight = 9472.074|
|-----------------------------------------------------------------------------|
r_work (start): 0.3545 rms_B_bonded: 1.90
r_work: 0.3449 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.3352 rms_B_bonded: 4.04 restraints_weight: 0.2500
r_work (final): 0.3352
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3347
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3347 r_free = 0.3347 target_work(ls_wunit_k1) = 0.112 |
| occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 47 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3301 r_free = 0.3301 target_work(ls_wunit_k1) = 0.109 |
| occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 81 |
|-----------------------------------------------------------------------------|
r_final: 0.3301
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8263
moved from start: 0.2197
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.036 8494 Z= 0.186
Angle : 0.511 7.372 11518 Z= 0.272
Chirality : 0.042 0.180 1295
Planarity : 0.004 0.061 1446
Dihedral : 4.645 58.927 1341
Min Nonbonded Distance : 2.412
Molprobity Statistics.
All-atom Clashscore : 4.50
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 2.15 %
Favored : 97.85 %
Rotamer:
Outliers : 2.68 %
Allowed : 18.34 %
Favored : 78.97 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 1.41 (0.26), residues: 1023
helix: 2.58 (0.25), residues: 414
sheet: -0.30 (0.31), residues: 229
loop : -0.05 (0.32), residues: 380
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.019 0.002 TRP R 291
HIS 0.003 0.001 HIS R 63
PHE 0.012 0.001 PHE R 95
TYR 0.016 0.001 TYR N 96
ARG 0.007 0.000 ARG A 264
Origin is already at (0, 0, 0), no shifts will be applied
===============================================================================
Job complete
usr+sys time: 3452.96 seconds
wall clock time: 61 minutes 8.81 seconds (3668.81 seconds total)