Starting phenix.real_space_refine
on Wed Jan 15 17:32:53 2025 by dcliebschner
===============================================================================
Processing files:
-------------------------------------------------------------------------------
Found model, /net/cci-nas-00/data/ceres_data/8ykw_39374/01_2025/8ykw_39374_neut.cif
Found real_map, /net/cci-nas-00/data/ceres_data/8ykw_39374/01_2025/8ykw_39374.map
Processing PHIL parameters:
-------------------------------------------------------------------------------
Adding command-line PHIL:
-------------------------
refinement.macro_cycles=10
scattering_table=electron
resolution=2.75
write_initial_geo_file=False
Final processed PHIL parameters:
-------------------------------------------------------------------------------
data_manager {
real_map_files = "/net/cci-nas-00/data/ceres_data/8ykw_39374/01_2025/8ykw_39374.map"
default_real_map = "/net/cci-nas-00/data/ceres_data/8ykw_39374/01_2025/8ykw_39374.map"
model {
file = "/net/cci-nas-00/data/ceres_data/8ykw_39374/01_2025/8ykw_39374_neut.cif"
}
default_model = "/net/cci-nas-00/data/ceres_data/8ykw_39374/01_2025/8ykw_39374_neut.cif"
}
resolution = 2.75
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= 0.081
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 55 5.16 5
C 5574 2.51 5
N 1481 2.21 5
O 1608 1.98 5
sf(0) = scattering factor at diffraction angle 0.
Process input model
Symmetric amino acids flipped. Time to flip 13 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: 8718
Number of models: 1
Model: ""
Number of chains: 6
Chain: "A"
Number of atoms: 1713
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 213, 1713
Classifications: {'peptide': 213}
Modifications used: {'COO': 1}
Incomplete info: {'truncation_to_alanine': 2}
Link IDs: {'PTRANS': 2, 'TRANS': 210}
Chain breaks: 3
Unresolved non-hydrogen bonds: 9
Unresolved non-hydrogen angles: 11
Unresolved non-hydrogen dihedrals: 7
Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1}
Unresolved non-hydrogen planarities: 8
Chain: "B"
Number of atoms: 2560
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 337, 2560
Classifications: {'peptide': 337}
Incomplete info: {'truncation_to_alanine': 9}
Link IDs: {'PTRANS': 5, 'TRANS': 331}
Unresolved non-hydrogen bonds: 33
Unresolved non-hydrogen angles: 42
Unresolved non-hydrogen dihedrals: 29
Unresolved non-hydrogen chiralities: 2
Planarities with less than four sites: {'TYR:plan': 1, 'PHE:plan': 1, 'ASP:plan': 2}
Unresolved non-hydrogen planarities: 19
Chain: "E"
Number of atoms: 1719
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 232, 1719
Classifications: {'peptide': 232}
Incomplete info: {'truncation_to_alanine': 20}
Link IDs: {'PTRANS': 10, 'TRANS': 221}
Chain breaks: 1
Unresolved non-hydrogen bonds: 66
Unresolved non-hydrogen angles: 82
Unresolved non-hydrogen dihedrals: 55
Unresolved non-hydrogen chiralities: 2
Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 6, 'TYR:plan': 1, 'ASP:plan': 3}
Unresolved non-hydrogen planarities: 46
Chain: "G"
Number of atoms: 440
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 58, 440
Classifications: {'peptide': 58}
Incomplete info: {'truncation_to_alanine': 2}
Link IDs: {'PTRANS': 4, 'TRANS': 53}
Unresolved non-hydrogen bonds: 7
Unresolved non-hydrogen angles: 8
Unresolved non-hydrogen dihedrals: 6
Planarities with less than four sites: {'ASP:plan': 1}
Unresolved non-hydrogen planarities: 3
Chain: "R"
Number of atoms: 2278
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 284, 2278
Classifications: {'peptide': 284}
Incomplete info: {'truncation_to_alanine': 10}
Link IDs: {'PTRANS': 12, 'TRANS': 271}
Chain breaks: 3
Unresolved non-hydrogen bonds: 33
Unresolved non-hydrogen angles: 44
Unresolved non-hydrogen dihedrals: 24
Unresolved non-hydrogen chiralities: 5
Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'GLN:plan1': 2}
Unresolved non-hydrogen planarities: 21
Chain: "R"
Number of atoms: 8
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 1, 8
Unusual residues: {'SIN': 1}
Classifications: {'undetermined': 1}
Time building chain proxies: 5.19, per 1000 atoms: 0.60
Number of scatterers: 8718
At special positions: 0
Unit cell: (86.1, 119.72, 135.3, 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 55 16.00
O 1608 8.00
N 1481 7.00
C 5574 6.00
sf(0) = scattering factor at diffraction angle 0.
Number of disulfides: simple=1, symmetry=0
Simple disulfide: pdb=" SG CYS R 11 " - pdb=" SG CYS R 268 " distance=2.30
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: 2.47
Conformation dependent library (CDL) restraints added in 1.1 seconds
2200 Ramachandran restraints generated.
1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
Adding C-beta torsion restraints...
Number of C-beta restraints generated: 2108
Finding SS restraints...
Secondary structure from input PDB file:
30 helices and 14 sheets defined
39.2% alpha, 24.1% beta
0 base pairs and 0 stacking pairs defined.
Time for finding SS restraints: 1.01
Creating SS restraints...
Processing helix chain 'A' and resid 6 through 32
removed outlier: 3.746A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A)
Processing helix chain 'A' and resid 45 through 53
Processing helix chain 'A' and resid 207 through 216
removed outlier: 4.407A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A)
removed outlier: 5.469A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A)
Processing helix chain 'A' and resid 242 through 255
Processing helix chain 'A' and resid 256 through 260
removed outlier: 4.161A pdb=" N THR A 260 " --> pdb=" O LYS A 257 " (cutoff:3.500A)
Processing helix chain 'A' and resid 270 through 279
removed outlier: 3.951A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A)
Processing helix chain 'A' and resid 282 through 286
removed outlier: 3.701A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A)
Processing helix chain 'A' and resid 295 through 309
Processing helix chain 'A' and resid 330 through 351
Processing helix chain 'B' and resid 5 through 25
Processing helix chain 'B' and resid 29 through 35
Processing helix chain 'E' and resid 28 through 32
Processing helix chain 'E' and resid 87 through 91
Processing helix chain 'G' and resid 8 through 24
Processing helix chain 'G' and resid 29 through 44
Processing helix chain 'G' and resid 45 through 48
Processing helix chain 'R' and resid 11 through 24
Processing helix chain 'R' and resid 24 through 49
Processing helix chain 'R' and resid 56 through 74
Processing helix chain 'R' and resid 75 through 86
removed outlier: 4.008A pdb=" N LEU R 79 " --> pdb=" O THR R 75 " (cutoff:3.500A)
Processing helix chain 'R' and resid 91 through 126
removed outlier: 3.664A pdb=" N ILE R 124 " --> pdb=" O ARG R 120 " (cutoff:3.500A)
Processing helix chain 'R' and resid 131 through 134
Processing helix chain 'R' and resid 135 through 155
Processing helix chain 'R' and resid 156 through 158
No H-bonds generated for 'chain 'R' and resid 156 through 158'
Processing helix chain 'R' and resid 180 through 196
removed outlier: 3.603A pdb=" N ILE R 186 " --> pdb=" O ASN R 182 " (cutoff:3.500A)
Processing helix chain 'R' and resid 196 through 217
Processing helix chain 'R' and resid 227 through 260
removed outlier: 3.563A pdb=" N VAL R 238 " --> pdb=" O VAL R 234 " (cutoff:3.500A)
Proline residue: R 247 - end of helix
Processing helix chain 'R' and resid 269 through 286
removed outlier: 3.534A pdb=" N ILE R 273 " --> pdb=" O THR R 269 " (cutoff:3.500A)
removed outlier: 3.558A pdb=" N VAL R 279 " --> pdb=" O SER R 275 " (cutoff:3.500A)
Proline residue: R 282 - end of helix
Processing helix chain 'R' and resid 286 through 297
Proline residue: R 292 - end of helix
Processing helix chain 'R' and resid 299 through 309
Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191
removed outlier: 6.082A pdb=" N VAL A 34 " --> pdb=" O LYS A 197 " (cutoff:3.500A)
removed outlier: 7.418A pdb=" N PHE A 199 " --> pdb=" O VAL A 34 " (cutoff:3.500A)
removed outlier: 6.948A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A)
removed outlier: 3.703A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A)
removed outlier: 6.171A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A)
removed outlier: 7.137A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A)
removed outlier: 6.325A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A)
removed outlier: 7.092A pdb=" N ASN A 269 " --> pdb=" O PHE A 223 " (cutoff:3.500A)
removed outlier: 6.631A pdb=" N VAL A 225 " --> pdb=" O ASN A 269 " (cutoff:3.500A)
Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 52
removed outlier: 5.664A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A)
removed outlier: 6.814A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A)
removed outlier: 3.773A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A)
Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
removed outlier: 3.690A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A)
removed outlier: 6.451A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A)
removed outlier: 6.107A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A)
Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
removed outlier: 6.746A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A)
removed outlier: 4.277A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A)
removed outlier: 6.370A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A)
removed outlier: 4.821A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A)
removed outlier: 7.031A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A)
removed outlier: 6.305A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A)
removed outlier: 4.576A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A)
removed outlier: 6.647A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A)
removed outlier: 3.603A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A)
Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
removed outlier: 6.257A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A)
removed outlier: 5.947A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A)
Processing sheet with id=AA6, first strand: chain 'B' and resid 191 through 192
removed outlier: 3.545A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A)
removed outlier: 6.403A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A)
removed outlier: 6.337A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A)
Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
removed outlier: 6.421A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A)
removed outlier: 4.272A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A)
removed outlier: 6.589A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A)
removed outlier: 4.902A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A)
removed outlier: 7.024A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A)
removed outlier: 6.417A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A)
removed outlier: 4.449A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A)
removed outlier: 6.639A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A)
removed outlier: 3.538A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A)
Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
removed outlier: 3.725A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A)
removed outlier: 6.342A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A)
removed outlier: 4.470A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A)
removed outlier: 6.433A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A)
Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7
Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12
removed outlier: 5.938A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A)
removed outlier: 5.224A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A)
Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 12
removed outlier: 4.416A pdb=" N PHE E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A)
Processing sheet with id=AB3, first strand: chain 'E' and resid 140 through 141
Processing sheet with id=AB4, first strand: chain 'E' and resid 146 through 148
removed outlier: 6.375A pdb=" N LEU E 174 " --> pdb=" O TYR E 190 " (cutoff:3.500A)
removed outlier: 4.594A pdb=" N TYR E 190 " --> pdb=" O LEU E 174 " (cutoff:3.500A)
removed outlier: 6.549A pdb=" N TRP E 176 " --> pdb=" O LEU E 188 " (cutoff:3.500A)
Processing sheet with id=AB5, first strand: chain 'E' and resid 146 through 148
removed outlier: 3.869A pdb=" N THR E 238 " --> pdb=" O GLN E 231 " (cutoff:3.500A)
470 hydrogen bonds defined for protein.
1308 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: 2.69
Time building geometry restraints manager: 2.81 seconds
NOTE: a complete listing of the restraints can be obtained by requesting
output of .geo file.
Histogram of bond lengths:
1.19 - 1.31: 1410
1.31 - 1.44: 2459
1.44 - 1.57: 4948
1.57 - 1.69: 2
1.69 - 1.82: 78
Bond restraints: 8897
Sorted by residual:
bond pdb=" CA LEU E 233 "
pdb=" C LEU E 233 "
ideal model delta sigma weight residual
1.524 1.451 0.073 1.32e-02 5.74e+03 3.05e+01
bond pdb=" CA LEU E 237 "
pdb=" C LEU E 237 "
ideal model delta sigma weight residual
1.523 1.460 0.063 1.30e-02 5.92e+03 2.37e+01
bond pdb=" CA VAL A 233 "
pdb=" C VAL A 233 "
ideal model delta sigma weight residual
1.524 1.473 0.051 1.08e-02 8.57e+03 2.21e+01
bond pdb=" CA THR R 246 "
pdb=" C THR R 246 "
ideal model delta sigma weight residual
1.521 1.571 -0.049 1.17e-02 7.31e+03 1.77e+01
bond pdb=" C LEU E 237 "
pdb=" O LEU E 237 "
ideal model delta sigma weight residual
1.234 1.186 0.048 1.23e-02 6.61e+03 1.53e+01
... (remaining 8892 not shown)
Histogram of bond angle deviations from ideal:
0.00 - 2.25: 11888
2.25 - 4.50: 145
4.50 - 6.74: 20
6.74 - 8.99: 7
8.99 - 11.24: 1
Bond angle restraints: 12061
Sorted by residual:
angle pdb=" C LYS R 229 "
pdb=" N PRO R 230 "
pdb=" CA PRO R 230 "
ideal model delta sigma weight residual
119.05 111.98 7.07 1.11e+00 8.12e-01 4.06e+01
angle pdb=" N GLN R 270 "
pdb=" CA GLN R 270 "
pdb=" C GLN R 270 "
ideal model delta sigma weight residual
112.23 104.57 7.66 1.26e+00 6.30e-01 3.70e+01
angle pdb=" N LEU A 232 "
pdb=" CA LEU A 232 "
pdb=" C LEU A 232 "
ideal model delta sigma weight residual
110.55 102.91 7.64 1.35e+00 5.49e-01 3.20e+01
angle pdb=" O LYS R 229 "
pdb=" C LYS R 229 "
pdb=" N PRO R 230 "
ideal model delta sigma weight residual
120.48 124.76 -4.28 8.90e-01 1.26e+00 2.31e+01
angle pdb=" CA LYS R 229 "
pdb=" C LYS R 229 "
pdb=" N PRO R 230 "
ideal model delta sigma weight residual
120.77 116.60 4.17 9.70e-01 1.06e+00 1.85e+01
... (remaining 12056 not shown)
Histogram of dihedral angle deviations from ideal:
0.00 - 17.91: 4725
17.91 - 35.82: 410
35.82 - 53.73: 107
53.73 - 71.63: 14
71.63 - 89.54: 8
Dihedral angle restraints: 5264
sinusoidal: 1998
harmonic: 3266
Sorted by residual:
dihedral pdb=" CA LYS B 78 "
pdb=" C LYS B 78 "
pdb=" N LEU B 79 "
pdb=" CA LEU B 79 "
ideal model delta harmonic sigma weight residual
180.00 158.58 21.42 0 5.00e+00 4.00e-02 1.83e+01
dihedral pdb=" CA GLN B 75 "
pdb=" C GLN B 75 "
pdb=" N ASP B 76 "
pdb=" CA ASP B 76 "
ideal model delta harmonic sigma weight residual
180.00 160.72 19.28 0 5.00e+00 4.00e-02 1.49e+01
dihedral pdb=" CA ARG E 191 "
pdb=" C ARG E 191 "
pdb=" N MET E 192 "
pdb=" CA MET E 192 "
ideal model delta harmonic sigma weight residual
180.00 163.21 16.79 0 5.00e+00 4.00e-02 1.13e+01
... (remaining 5261 not shown)
Histogram of chiral volume deviations from ideal:
0.000 - 0.055: 1182
0.055 - 0.109: 156
0.109 - 0.164: 37
0.164 - 0.219: 1
0.219 - 0.273: 4
Chirality restraints: 1380
Sorted by residual:
chirality pdb=" CA TYR E 235 "
pdb=" N TYR E 235 "
pdb=" C TYR E 235 "
pdb=" CB TYR E 235 "
both_signs ideal model delta sigma weight residual
False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.87e+00
chirality pdb=" CA ILE R 278 "
pdb=" N ILE R 278 "
pdb=" C ILE R 278 "
pdb=" CB ILE R 278 "
both_signs ideal model delta sigma weight residual
False 2.43 2.68 -0.25 2.00e-01 2.50e+01 1.54e+00
chirality pdb=" CA THR E 238 "
pdb=" N THR E 238 "
pdb=" C THR E 238 "
pdb=" CB THR E 238 "
both_signs ideal model delta sigma weight residual
False 2.53 2.28 0.25 2.00e-01 2.50e+01 1.53e+00
... (remaining 1377 not shown)
Planarity restraints: 1523
Sorted by residual:
delta sigma weight rms_deltas residual
plane pdb=" C THR E 150 " 0.042 5.00e-02 4.00e+02 6.43e-02 6.61e+00
pdb=" N PRO E 151 " -0.111 5.00e-02 4.00e+02
pdb=" CA PRO E 151 " 0.033 5.00e-02 4.00e+02
pdb=" CD PRO E 151 " 0.036 5.00e-02 4.00e+02
delta sigma weight rms_deltas residual
plane pdb=" CA PHE R 245 " 0.012 2.00e-02 2.50e+03 2.32e-02 5.40e+00
pdb=" C PHE R 245 " -0.040 2.00e-02 2.50e+03
pdb=" O PHE R 245 " 0.015 2.00e-02 2.50e+03
pdb=" N THR R 246 " 0.014 2.00e-02 2.50e+03
delta sigma weight rms_deltas residual
plane pdb=" C ASN R 291 " -0.037 5.00e-02 4.00e+02 5.59e-02 4.99e+00
pdb=" N PRO R 292 " 0.097 5.00e-02 4.00e+02
pdb=" CA PRO R 292 " -0.028 5.00e-02 4.00e+02
pdb=" CD PRO R 292 " -0.031 5.00e-02 4.00e+02
... (remaining 1520 not shown)
Histogram of nonbonded interaction distances:
2.24 - 2.77: 1688
2.77 - 3.30: 8501
3.30 - 3.84: 14751
3.84 - 4.37: 18209
4.37 - 4.90: 31450
Nonbonded interactions: 74599
Sorted by model distance:
nonbonded pdb=" O THR B 86 "
pdb=" OG1 THR B 87 "
model vdw
2.239 3.040
nonbonded pdb=" O ASP B 195 "
pdb=" OG1 THR B 196 "
model vdw
2.248 3.040
nonbonded pdb=" OD1 ASP B 247 "
pdb=" OG1 THR B 249 "
model vdw
2.277 3.040
nonbonded pdb=" O ASP B 333 "
pdb=" OG SER B 334 "
model vdw
2.284 3.040
nonbonded pdb=" O ASN R 274 "
pdb=" N TYR R 277 "
model vdw
2.313 3.120
... (remaining 74594 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 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: 0.810
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: 0.320
Check model and map are aligned: 0.050
Set scattering table: 0.080
Process input model: 22.840
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: 0.010
Load rotamer database and sin/cos tables:11.900
Set ADP refinement strategy: 0.000
Make a string to write initial .geo file:0.000
Internal consistency checks: 0.000
Total: 36.150
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8329
moved from start: 0.0000
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.004 0.073 8897 Z= 0.252
Angle : 0.652 11.238 12061 Z= 0.374
Chirality : 0.043 0.273 1380
Planarity : 0.005 0.068 1523
Dihedral : 14.747 89.543 3153
Min Nonbonded Distance : 2.239
Molprobity Statistics.
All-atom Clashscore : 3.36
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 2.91 %
Favored : 97.09 %
Rotamer:
Outliers : 0.54 %
Allowed : 15.09 %
Favored : 84.38 %
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: 1.10 (0.26), residues: 1100
helix: 1.71 (0.27), residues: 383
sheet: 0.32 (0.29), residues: 307
loop : 0.27 (0.32), residues: 410
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.011 0.001 TRP R 88
HIS 0.005 0.001 HIS A 188
PHE 0.013 0.001 PHE R 34
TYR 0.016 0.001 TYR R 83
ARG 0.014 0.001 ARG E 160
*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
2200 Ramachandran restraints generated.
1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
2200 Ramachandran restraints generated.
1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
148 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 5
poor density : 143
time to evaluate : 0.988
Fit side-chains
REVERT: A 33 GLU cc_start: 0.7893 (mm-30) cc_final: 0.7386 (mm-30)
REVERT: B 46 ARG cc_start: 0.8073 (ptm160) cc_final: 0.7854 (ptm160)
REVERT: B 219 ARG cc_start: 0.7946 (mmm160) cc_final: 0.7352 (mmt-90)
REVERT: E 46 GLU cc_start: 0.8026 (tt0) cc_final: 0.7812 (tt0)
REVERT: R 189 MET cc_start: 0.8267 (mmm) cc_final: 0.8018 (mmm)
outliers start: 5
outliers final: 2
residues processed: 146
average time/residue: 1.4089
time to fit residues: 217.9052
Evaluate side-chains
121 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 2
poor density : 119
time to evaluate : 1.029
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 261 ASP
Chi-restraints excluded: chain E residue 193 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 110
random chunks:
chunk 92 optimal weight: 2.9990
chunk 83 optimal weight: 0.0980
chunk 46 optimal weight: 0.9990
chunk 28 optimal weight: 4.9990
chunk 56 optimal weight: 4.9990
chunk 44 optimal weight: 1.9990
chunk 86 optimal weight: 0.7980
chunk 33 optimal weight: 2.9990
chunk 52 optimal weight: 2.9990
chunk 64 optimal weight: 0.9990
chunk 99 optimal weight: 3.9990
overall best weight: 0.9786
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 188 HIS
A 255 ASN
A 269 ASN
A 331 ASN
A 333 GLN
B 75 GLN
B 259 GLN
E 77 ASN
E 179 GLN
** R 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Total number of N/Q/H flips: 9
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3959 r_free = 0.3959 target = 0.162346 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.113136 restraints weight = 9909.421|
|-----------------------------------------------------------------------------|
r_work (start): 0.3373 rms_B_bonded: 2.32
r_work: 0.3217 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.3075 rms_B_bonded: 4.49 restraints_weight: 0.2500
r_work (final): 0.3075
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8337
moved from start: 0.1376
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.034 8897 Z= 0.213
Angle : 0.558 9.305 12061 Z= 0.300
Chirality : 0.043 0.153 1380
Planarity : 0.004 0.039 1523
Dihedral : 4.602 37.606 1221
Min Nonbonded Distance : 2.520
Molprobity Statistics.
All-atom Clashscore : 3.82
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 2.27 %
Favored : 97.73 %
Rotamer:
Outliers : 2.59 %
Allowed : 14.66 %
Favored : 82.76 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 1.60 (0.26), residues: 1100
helix: 2.31 (0.25), residues: 388
sheet: 0.43 (0.31), residues: 293
loop : 0.47 (0.32), residues: 419
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.021 0.002 TRP B 82
HIS 0.004 0.001 HIS B 91
PHE 0.014 0.001 PHE A 274
TYR 0.022 0.001 TYR R 48
ARG 0.007 0.001 ARG E 160
*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
2200 Ramachandran restraints generated.
1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
2200 Ramachandran restraints generated.
1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
167 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 24
poor density : 143
time to evaluate : 0.943
Fit side-chains
REVERT: A 243 MET cc_start: 0.8326 (tpp) cc_final: 0.8123 (ttm)
REVERT: A 298 GLU cc_start: 0.8377 (tt0) cc_final: 0.7931 (tt0)
REVERT: B 214 ARG cc_start: 0.8243 (mmt-90) cc_final: 0.7990 (mmp80)
REVERT: B 219 ARG cc_start: 0.8242 (OUTLIER) cc_final: 0.7408 (mmt-90)
REVERT: B 267 ASP cc_start: 0.8163 (m-30) cc_final: 0.7800 (m-30)
REVERT: E 46 GLU cc_start: 0.8383 (tt0) cc_final: 0.8091 (tt0)
REVERT: E 229 CYS cc_start: 0.8737 (p) cc_final: 0.8509 (p)
REVERT: R 189 MET cc_start: 0.8420 (mmm) cc_final: 0.8019 (mmm)
REVERT: R 193 LEU cc_start: 0.7640 (OUTLIER) cc_final: 0.7437 (tt)
REVERT: R 253 ASN cc_start: 0.8774 (m-40) cc_final: 0.8448 (m-40)
outliers start: 24
outliers final: 9
residues processed: 151
average time/residue: 1.3196
time to fit residues: 211.4426
Evaluate side-chains
129 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 11
poor density : 118
time to evaluate : 0.988
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 313 ARG
Chi-restraints excluded: chain A residue 332 VAL
Chi-restraints excluded: chain B residue 96 ARG
Chi-restraints excluded: chain B residue 219 ARG
Chi-restraints excluded: chain B residue 270 ILE
Chi-restraints excluded: chain E residue 6 GLU
Chi-restraints excluded: chain E residue 12 VAL
Chi-restraints excluded: chain E residue 69 THR
Chi-restraints excluded: chain G residue 16 VAL
Chi-restraints excluded: chain R residue 149 LEU
Chi-restraints excluded: chain R residue 193 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 110
random chunks:
chunk 48 optimal weight: 4.9990
chunk 79 optimal weight: 5.9990
chunk 73 optimal weight: 8.9990
chunk 71 optimal weight: 2.9990
chunk 51 optimal weight: 8.9990
chunk 7 optimal weight: 0.0770
chunk 93 optimal weight: 3.9990
chunk 30 optimal weight: 0.9990
chunk 5 optimal weight: 2.9990
chunk 59 optimal weight: 0.7980
chunk 55 optimal weight: 8.9990
overall best weight: 1.5744
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 269 ASN
A 311 ASN
A 331 ASN
B 75 GLN
B 259 GLN
E 39 GLN
E 77 ASN
** R 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Total number of N/Q/H flips: 7
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3937 r_free = 0.3937 target = 0.160374 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.110743 restraints weight = 10110.379|
|-----------------------------------------------------------------------------|
r_work (start): 0.3341 rms_B_bonded: 2.33
r_work: 0.3185 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.3043 rms_B_bonded: 4.50 restraints_weight: 0.2500
r_work (final): 0.3043
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8370
moved from start: 0.1572
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.004 0.038 8897 Z= 0.266
Angle : 0.557 9.593 12061 Z= 0.297
Chirality : 0.044 0.145 1380
Planarity : 0.004 0.038 1523
Dihedral : 4.356 22.463 1218
Min Nonbonded Distance : 2.539
Molprobity Statistics.
All-atom Clashscore : 3.94
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 2.55 %
Favored : 97.45 %
Rotamer:
Outliers : 3.45 %
Allowed : 15.73 %
Favored : 80.82 %
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: 1.66 (0.25), residues: 1100
helix: 2.48 (0.25), residues: 388
sheet: 0.48 (0.30), residues: 293
loop : 0.36 (0.31), residues: 419
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.017 0.002 TRP B 82
HIS 0.005 0.001 HIS G 44
PHE 0.013 0.001 PHE R 115
TYR 0.022 0.001 TYR R 48
ARG 0.005 0.001 ARG B 314
*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
2200 Ramachandran restraints generated.
1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
2200 Ramachandran restraints generated.
1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
169 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 32
poor density : 137
time to evaluate : 0.862
Fit side-chains
REVERT: A 243 MET cc_start: 0.8325 (tpp) cc_final: 0.7895 (ttm)
REVERT: A 298 GLU cc_start: 0.8395 (tt0) cc_final: 0.7944 (tt0)
REVERT: B 219 ARG cc_start: 0.8297 (OUTLIER) cc_final: 0.7484 (mmt-90)
REVERT: B 267 ASP cc_start: 0.8202 (m-30) cc_final: 0.7859 (m-30)
REVERT: E 38 ARG cc_start: 0.8891 (ptt180) cc_final: 0.8685 (ptt-90)
REVERT: E 46 GLU cc_start: 0.8446 (tt0) cc_final: 0.8147 (tt0)
REVERT: E 183 GLN cc_start: 0.8482 (OUTLIER) cc_final: 0.8165 (mt0)
REVERT: E 202 ARG cc_start: 0.7659 (ptt-90) cc_final: 0.7453 (ptt-90)
REVERT: R 189 MET cc_start: 0.8475 (mmm) cc_final: 0.8065 (mmm)
REVERT: R 193 LEU cc_start: 0.7835 (OUTLIER) cc_final: 0.7624 (tt)
REVERT: R 217 ARG cc_start: 0.7699 (tpp-160) cc_final: 0.7454 (tpp-160)
REVERT: R 253 ASN cc_start: 0.8761 (m-40) cc_final: 0.8447 (m-40)
outliers start: 32
outliers final: 17
residues processed: 151
average time/residue: 1.2201
time to fit residues: 196.5676
Evaluate side-chains
143 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 20
poor density : 123
time to evaluate : 1.082
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 246 SER
Chi-restraints excluded: chain A residue 313 ARG
Chi-restraints excluded: chain A residue 332 VAL
Chi-restraints excluded: chain B residue 96 ARG
Chi-restraints excluded: chain B residue 153 ASP
Chi-restraints excluded: chain B residue 219 ARG
Chi-restraints excluded: chain B residue 263 THR
Chi-restraints excluded: chain B residue 270 ILE
Chi-restraints excluded: chain E residue 6 GLU
Chi-restraints excluded: chain E residue 12 VAL
Chi-restraints excluded: chain E residue 69 THR
Chi-restraints excluded: chain E residue 86 LEU
Chi-restraints excluded: chain E residue 155 VAL
Chi-restraints excluded: chain E residue 183 GLN
Chi-restraints excluded: chain G residue 16 VAL
Chi-restraints excluded: chain R residue 93 VAL
Chi-restraints excluded: chain R residue 149 LEU
Chi-restraints excluded: chain R residue 186 ILE
Chi-restraints excluded: chain R residue 193 LEU
Chi-restraints excluded: chain R residue 234 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 110
random chunks:
chunk 54 optimal weight: 9.9990
chunk 99 optimal weight: 0.0060
chunk 85 optimal weight: 0.8980
chunk 88 optimal weight: 0.0030
chunk 13 optimal weight: 0.7980
chunk 48 optimal weight: 2.9990
chunk 10 optimal weight: 8.9990
chunk 57 optimal weight: 0.9990
chunk 90 optimal weight: 0.9990
chunk 67 optimal weight: 7.9990
chunk 7 optimal weight: 7.9990
overall best weight: 0.5408
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 255 ASN
A 269 ASN
A 311 ASN
A 331 ASN
B 75 GLN
B 237 ASN
B 239 ASN
** R 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Total number of N/Q/H flips: 7
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3970 r_free = 0.3970 target = 0.163329 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.115328 restraints weight = 10078.598|
|-----------------------------------------------------------------------------|
r_work (start): 0.3401 rms_B_bonded: 2.27
r_work: 0.3247 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.3107 rms_B_bonded: 4.49 restraints_weight: 0.2500
r_work (final): 0.3107
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8346
moved from start: 0.1900
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.002 0.030 8897 Z= 0.156
Angle : 0.516 9.052 12061 Z= 0.272
Chirality : 0.041 0.166 1380
Planarity : 0.004 0.043 1523
Dihedral : 4.050 20.802 1218
Min Nonbonded Distance : 2.560
Molprobity Statistics.
All-atom Clashscore : 4.57
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 2.36 %
Favored : 97.64 %
Rotamer:
Outliers : 2.69 %
Allowed : 17.24 %
Favored : 80.06 %
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: 1.79 (0.26), residues: 1100
helix: 2.71 (0.25), residues: 388
sheet: 0.52 (0.30), residues: 291
loop : 0.32 (0.31), residues: 421
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.020 0.001 TRP B 82
HIS 0.007 0.001 HIS B 266
PHE 0.009 0.001 PHE R 115
TYR 0.025 0.001 TYR R 48
ARG 0.004 0.000 ARG E 160
*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
2200 Ramachandran restraints generated.
1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
2200 Ramachandran restraints generated.
1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
166 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 25
poor density : 141
time to evaluate : 0.987
Fit side-chains
REVERT: A 297 GLU cc_start: 0.8384 (mm-30) cc_final: 0.8078 (tt0)
REVERT: B 175 GLN cc_start: 0.8007 (mm-40) cc_final: 0.7647 (pp30)
REVERT: B 219 ARG cc_start: 0.8283 (OUTLIER) cc_final: 0.7482 (mmt-90)
REVERT: B 267 ASP cc_start: 0.8264 (m-30) cc_final: 0.7899 (m-30)
REVERT: E 46 GLU cc_start: 0.8409 (tt0) cc_final: 0.8142 (tt0)
REVERT: E 202 ARG cc_start: 0.7678 (ptt-90) cc_final: 0.7435 (ptt-90)
REVERT: E 229 CYS cc_start: 0.8745 (p) cc_final: 0.8544 (p)
REVERT: E 244 LYS cc_start: 0.8120 (ttpp) cc_final: 0.7897 (tttm)
REVERT: R 189 MET cc_start: 0.8505 (mmm) cc_final: 0.8057 (mmm)
REVERT: R 253 ASN cc_start: 0.8752 (m-40) cc_final: 0.8432 (m-40)
outliers start: 25
outliers final: 13
residues processed: 152
average time/residue: 1.2154
time to fit residues: 197.3789
Evaluate side-chains
142 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 14
poor density : 128
time to evaluate : 1.035
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 246 SER
Chi-restraints excluded: chain A residue 313 ARG
Chi-restraints excluded: chain A residue 332 VAL
Chi-restraints excluded: chain B residue 96 ARG
Chi-restraints excluded: chain B residue 153 ASP
Chi-restraints excluded: chain B residue 219 ARG
Chi-restraints excluded: chain B residue 263 THR
Chi-restraints excluded: chain B residue 270 ILE
Chi-restraints excluded: chain E residue 65 LYS
Chi-restraints excluded: chain E residue 69 THR
Chi-restraints excluded: chain E residue 86 LEU
Chi-restraints excluded: chain E residue 155 VAL
Chi-restraints excluded: chain G residue 16 VAL
Chi-restraints excluded: chain R residue 149 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 110
random chunks:
chunk 39 optimal weight: 3.9990
chunk 73 optimal weight: 10.0000
chunk 54 optimal weight: 10.0000
chunk 42 optimal weight: 5.9990
chunk 86 optimal weight: 0.9990
chunk 100 optimal weight: 2.9990
chunk 24 optimal weight: 6.9990
chunk 44 optimal weight: 0.8980
chunk 105 optimal weight: 3.9990
chunk 106 optimal weight: 6.9990
chunk 56 optimal weight: 0.7980
overall best weight: 1.9386
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 255 ASN
A 269 ASN
A 311 ASN
B 75 GLN
B 237 ASN
B 239 ASN
E 39 GLN
E 77 ASN
** R 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Total number of N/Q/H flips: 8
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.158470 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.107527 restraints weight = 10100.401|
|-----------------------------------------------------------------------------|
r_work (start): 0.3261 rms_B_bonded: 2.42
r_work: 0.3111 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.2967 rms_B_bonded: 4.56 restraints_weight: 0.2500
r_work (final): 0.2967
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8354
moved from start: 0.1877
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.005 0.040 8897 Z= 0.311
Angle : 0.569 8.779 12061 Z= 0.302
Chirality : 0.044 0.162 1380
Planarity : 0.004 0.041 1523
Dihedral : 4.265 20.557 1218
Min Nonbonded Distance : 2.451
Molprobity Statistics.
All-atom Clashscore : 4.17
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 2.55 %
Favored : 97.45 %
Rotamer:
Outliers : 3.56 %
Allowed : 17.56 %
Favored : 78.88 %
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: 1.62 (0.25), residues: 1100
helix: 2.54 (0.25), residues: 388
sheet: 0.46 (0.30), residues: 293
loop : 0.22 (0.31), residues: 419
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.014 0.001 TRP B 169
HIS 0.007 0.001 HIS B 266
PHE 0.014 0.002 PHE A 196
TYR 0.022 0.002 TYR R 48
ARG 0.006 0.001 ARG R 255
*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
2200 Ramachandran restraints generated.
1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
2200 Ramachandran restraints generated.
1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
169 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 33
poor density : 136
time to evaluate : 0.953
Fit side-chains
REVERT: A 297 GLU cc_start: 0.8374 (mm-30) cc_final: 0.8073 (tt0)
REVERT: A 298 GLU cc_start: 0.8407 (tt0) cc_final: 0.8021 (tt0)
REVERT: B 175 GLN cc_start: 0.8021 (mm-40) cc_final: 0.7528 (pp30)
REVERT: B 219 ARG cc_start: 0.8281 (OUTLIER) cc_final: 0.7241 (mmt180)
REVERT: B 267 ASP cc_start: 0.8298 (m-30) cc_final: 0.7991 (m-30)
REVERT: E 46 GLU cc_start: 0.8435 (tt0) cc_final: 0.8170 (tt0)
REVERT: E 160 ARG cc_start: 0.7962 (ttm110) cc_final: 0.7644 (tpp-160)
REVERT: E 183 GLN cc_start: 0.8460 (OUTLIER) cc_final: 0.8136 (mt0)
REVERT: E 244 LYS cc_start: 0.8059 (ttpp) cc_final: 0.7825 (tttm)
REVERT: R 253 ASN cc_start: 0.8818 (m-40) cc_final: 0.8562 (m-40)
outliers start: 33
outliers final: 20
residues processed: 150
average time/residue: 1.1998
time to fit residues: 192.2973
Evaluate side-chains
147 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 22
poor density : 125
time to evaluate : 1.032
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 246 SER
Chi-restraints excluded: chain A residue 313 ARG
Chi-restraints excluded: chain A residue 332 VAL
Chi-restraints excluded: chain B residue 96 ARG
Chi-restraints excluded: chain B residue 135 VAL
Chi-restraints excluded: chain B residue 153 ASP
Chi-restraints excluded: chain B residue 176 GLN
Chi-restraints excluded: chain B residue 219 ARG
Chi-restraints excluded: chain B residue 263 THR
Chi-restraints excluded: chain B residue 270 ILE
Chi-restraints excluded: chain B residue 279 SER
Chi-restraints excluded: chain E residue 11 LEU
Chi-restraints excluded: chain E residue 69 THR
Chi-restraints excluded: chain E residue 86 LEU
Chi-restraints excluded: chain E residue 155 VAL
Chi-restraints excluded: chain E residue 183 GLN
Chi-restraints excluded: chain E residue 184 SER
Chi-restraints excluded: chain E residue 193 SER
Chi-restraints excluded: chain G residue 16 VAL
Chi-restraints excluded: chain R residue 79 LEU
Chi-restraints excluded: chain R residue 149 LEU
Chi-restraints excluded: chain R residue 234 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 110
random chunks:
chunk 28 optimal weight: 0.9980
chunk 24 optimal weight: 6.9990
chunk 50 optimal weight: 0.9990
chunk 29 optimal weight: 0.7980
chunk 11 optimal weight: 2.9990
chunk 47 optimal weight: 0.0030
chunk 84 optimal weight: 1.9990
chunk 57 optimal weight: 3.9990
chunk 20 optimal weight: 0.6980
chunk 4 optimal weight: 0.9990
chunk 94 optimal weight: 1.9990
overall best weight: 0.6992
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 269 ASN
A 311 ASN
B 75 GLN
B 237 ASN
B 239 ASN
R 134 GLN
Total number of N/Q/H flips: 6
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3959 r_free = 0.3959 target = 0.162448 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.113904 restraints weight = 10013.615|
|-----------------------------------------------------------------------------|
r_work (start): 0.3386 rms_B_bonded: 2.29
r_work: 0.3232 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.3089 rms_B_bonded: 4.51 restraints_weight: 0.2500
r_work (final): 0.3089
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8359
moved from start: 0.2094
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.046 8897 Z= 0.173
Angle : 0.533 9.458 12061 Z= 0.277
Chirality : 0.041 0.159 1380
Planarity : 0.004 0.048 1523
Dihedral : 4.042 20.698 1218
Min Nonbonded Distance : 2.547
Molprobity Statistics.
All-atom Clashscore : 4.17
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 2.00 %
Favored : 98.00 %
Rotamer:
Outliers : 2.48 %
Allowed : 19.07 %
Favored : 78.45 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 1.68 (0.26), residues: 1100
helix: 2.69 (0.25), residues: 388
sheet: 0.40 (0.30), residues: 291
loop : 0.23 (0.31), residues: 421
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.019 0.001 TRP B 82
HIS 0.007 0.001 HIS B 266
PHE 0.019 0.001 PHE A 274
TYR 0.028 0.001 TYR R 48
ARG 0.004 0.000 ARG R 255
*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
2200 Ramachandran restraints generated.
1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
2200 Ramachandran restraints generated.
1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
162 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 23
poor density : 139
time to evaluate : 1.845
Fit side-chains
REVERT: A 297 GLU cc_start: 0.8330 (mm-30) cc_final: 0.8063 (tt0)
REVERT: A 298 GLU cc_start: 0.8397 (tt0) cc_final: 0.8012 (tt0)
REVERT: B 175 GLN cc_start: 0.8070 (mm-40) cc_final: 0.7656 (pp30)
REVERT: B 219 ARG cc_start: 0.8295 (OUTLIER) cc_final: 0.7374 (mmt-90)
REVERT: B 267 ASP cc_start: 0.8261 (m-30) cc_final: 0.7933 (m-30)
REVERT: E 46 GLU cc_start: 0.8415 (tt0) cc_final: 0.8176 (tt0)
REVERT: E 160 ARG cc_start: 0.7991 (ttm110) cc_final: 0.7582 (tpp-160)
REVERT: E 244 LYS cc_start: 0.8173 (ttpp) cc_final: 0.7948 (tttm)
REVERT: R 253 ASN cc_start: 0.8830 (m-40) cc_final: 0.8572 (m-40)
outliers start: 23
outliers final: 15
residues processed: 150
average time/residue: 1.3022
time to fit residues: 208.2352
Evaluate side-chains
143 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 16
poor density : 127
time to evaluate : 1.054
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 246 SER
Chi-restraints excluded: chain A residue 313 ARG
Chi-restraints excluded: chain A residue 332 VAL
Chi-restraints excluded: chain B residue 96 ARG
Chi-restraints excluded: chain B residue 153 ASP
Chi-restraints excluded: chain B residue 219 ARG
Chi-restraints excluded: chain B residue 263 THR
Chi-restraints excluded: chain B residue 270 ILE
Chi-restraints excluded: chain B residue 279 SER
Chi-restraints excluded: chain E residue 65 LYS
Chi-restraints excluded: chain E residue 69 THR
Chi-restraints excluded: chain E residue 86 LEU
Chi-restraints excluded: chain E residue 155 VAL
Chi-restraints excluded: chain G residue 16 VAL
Chi-restraints excluded: chain R residue 79 LEU
Chi-restraints excluded: chain R residue 149 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 110
random chunks:
chunk 41 optimal weight: 4.9990
chunk 21 optimal weight: 20.0000
chunk 0 optimal weight: 7.9990
chunk 83 optimal weight: 2.9990
chunk 33 optimal weight: 3.9990
chunk 75 optimal weight: 4.9990
chunk 1 optimal weight: 0.6980
chunk 56 optimal weight: 0.9990
chunk 44 optimal weight: 0.6980
chunk 65 optimal weight: 2.9990
chunk 9 optimal weight: 0.4980
overall best weight: 1.1784
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 255 ASN
A 269 ASN
B 75 GLN
E 39 GLN
E 77 ASN
Total number of N/Q/H flips: 5
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3946 r_free = 0.3946 target = 0.161425 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.111984 restraints weight = 10068.365|
|-----------------------------------------------------------------------------|
r_work (start): 0.3362 rms_B_bonded: 2.34
r_work: 0.3206 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.3064 rms_B_bonded: 4.52 restraints_weight: 0.2500
r_work (final): 0.3064
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8352
moved from start: 0.2109
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.061 8897 Z= 0.223
Angle : 0.543 8.246 12061 Z= 0.285
Chirality : 0.042 0.171 1380
Planarity : 0.004 0.048 1523
Dihedral : 4.065 20.744 1218
Min Nonbonded Distance : 2.463
Molprobity Statistics.
All-atom Clashscore : 4.17
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 2.55 %
Favored : 97.45 %
Rotamer:
Outliers : 2.80 %
Allowed : 19.83 %
Favored : 77.37 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 1.67 (0.26), residues: 1100
helix: 2.69 (0.25), residues: 388
sheet: 0.35 (0.30), residues: 285
loop : 0.25 (0.31), residues: 427
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.015 0.001 TRP B 82
HIS 0.006 0.001 HIS B 266
PHE 0.021 0.001 PHE A 274
TYR 0.027 0.001 TYR R 48
ARG 0.006 0.000 ARG R 255
*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
2200 Ramachandran restraints generated.
1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
2200 Ramachandran restraints generated.
1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
158 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 26
poor density : 132
time to evaluate : 1.075
Fit side-chains
REVERT: A 297 GLU cc_start: 0.8307 (mm-30) cc_final: 0.8040 (tt0)
REVERT: A 298 GLU cc_start: 0.8410 (tt0) cc_final: 0.8060 (tt0)
REVERT: B 175 GLN cc_start: 0.8038 (mm-40) cc_final: 0.7606 (pp30)
REVERT: B 219 ARG cc_start: 0.8274 (OUTLIER) cc_final: 0.7343 (mmt-90)
REVERT: B 267 ASP cc_start: 0.8266 (m-30) cc_final: 0.7937 (m-30)
REVERT: E 46 GLU cc_start: 0.8411 (tt0) cc_final: 0.8162 (tt0)
REVERT: E 160 ARG cc_start: 0.7963 (ttm110) cc_final: 0.7642 (tpp-160)
REVERT: E 244 LYS cc_start: 0.8125 (ttpp) cc_final: 0.7901 (tttm)
REVERT: R 193 LEU cc_start: 0.8017 (OUTLIER) cc_final: 0.7803 (tt)
REVERT: R 253 ASN cc_start: 0.8821 (m-40) cc_final: 0.8554 (m-40)
outliers start: 26
outliers final: 15
residues processed: 147
average time/residue: 1.2521
time to fit residues: 196.2334
Evaluate side-chains
142 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 17
poor density : 125
time to evaluate : 0.923
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 246 SER
Chi-restraints excluded: chain A residue 313 ARG
Chi-restraints excluded: chain A residue 332 VAL
Chi-restraints excluded: chain B residue 96 ARG
Chi-restraints excluded: chain B residue 153 ASP
Chi-restraints excluded: chain B residue 219 ARG
Chi-restraints excluded: chain B residue 263 THR
Chi-restraints excluded: chain B residue 270 ILE
Chi-restraints excluded: chain B residue 279 SER
Chi-restraints excluded: chain E residue 11 LEU
Chi-restraints excluded: chain E residue 65 LYS
Chi-restraints excluded: chain E residue 86 LEU
Chi-restraints excluded: chain E residue 155 VAL
Chi-restraints excluded: chain E residue 184 SER
Chi-restraints excluded: chain G residue 16 VAL
Chi-restraints excluded: chain R residue 79 LEU
Chi-restraints excluded: chain R residue 193 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 110
random chunks:
chunk 25 optimal weight: 3.9990
chunk 72 optimal weight: 0.9980
chunk 82 optimal weight: 2.9990
chunk 95 optimal weight: 0.9980
chunk 35 optimal weight: 1.9990
chunk 2 optimal weight: 0.0570
chunk 99 optimal weight: 0.9980
chunk 64 optimal weight: 0.7980
chunk 42 optimal weight: 5.9990
chunk 49 optimal weight: 2.9990
chunk 36 optimal weight: 0.8980
overall best weight: 0.7498
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 255 ASN
A 269 ASN
A 311 ASN
B 75 GLN
E 77 ASN
Total number of N/Q/H flips: 5
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.161552 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.111170 restraints weight = 10159.473|
|-----------------------------------------------------------------------------|
r_work (start): 0.3315 rms_B_bonded: 2.41
r_work: 0.3164 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work: 0.3021 rms_B_bonded: 4.59 restraints_weight: 0.2500
r_work (final): 0.3021
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8277
moved from start: 0.2214
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.066 8897 Z= 0.185
Angle : 0.541 8.637 12061 Z= 0.282
Chirality : 0.042 0.170 1380
Planarity : 0.004 0.039 1523
Dihedral : 4.007 21.191 1218
Min Nonbonded Distance : 2.455
Molprobity Statistics.
All-atom Clashscore : 4.34
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 2.18 %
Favored : 97.82 %
Rotamer:
Outliers : 2.16 %
Allowed : 20.91 %
Favored : 76.94 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 1.68 (0.26), residues: 1100
helix: 2.73 (0.26), residues: 388
sheet: 0.38 (0.30), residues: 283
loop : 0.20 (0.31), residues: 429
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.017 0.001 TRP B 82
HIS 0.006 0.001 HIS B 266
PHE 0.010 0.001 PHE R 115
TYR 0.030 0.001 TYR R 48
ARG 0.007 0.000 ARG R 255
*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
2200 Ramachandran restraints generated.
1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
2200 Ramachandran restraints generated.
1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
152 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 20
poor density : 132
time to evaluate : 0.992
Fit side-chains
REVERT: A 297 GLU cc_start: 0.8285 (mm-30) cc_final: 0.8017 (tt0)
REVERT: A 298 GLU cc_start: 0.8383 (tt0) cc_final: 0.8040 (tt0)
REVERT: B 175 GLN cc_start: 0.7933 (mm-40) cc_final: 0.7487 (pp30)
REVERT: B 219 ARG cc_start: 0.8219 (mmm160) cc_final: 0.7219 (mmt-90)
REVERT: B 267 ASP cc_start: 0.8245 (m-30) cc_final: 0.7920 (m-30)
REVERT: E 46 GLU cc_start: 0.8369 (tt0) cc_final: 0.8111 (tt0)
REVERT: E 82 GLN cc_start: 0.8168 (tp40) cc_final: 0.7944 (tp40)
REVERT: E 160 ARG cc_start: 0.7922 (ttm110) cc_final: 0.7613 (tpp-160)
REVERT: E 244 LYS cc_start: 0.7988 (ttpp) cc_final: 0.7772 (tttm)
REVERT: R 253 ASN cc_start: 0.8803 (m-40) cc_final: 0.8562 (m-40)
outliers start: 20
outliers final: 18
residues processed: 144
average time/residue: 1.2836
time to fit residues: 196.4408
Evaluate side-chains
140 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 18
poor density : 122
time to evaluate : 1.048
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 246 SER
Chi-restraints excluded: chain A residue 313 ARG
Chi-restraints excluded: chain A residue 332 VAL
Chi-restraints excluded: chain B residue 38 ASP
Chi-restraints excluded: chain B residue 96 ARG
Chi-restraints excluded: chain B residue 153 ASP
Chi-restraints excluded: chain B residue 263 THR
Chi-restraints excluded: chain B residue 270 ILE
Chi-restraints excluded: chain B residue 279 SER
Chi-restraints excluded: chain E residue 11 LEU
Chi-restraints excluded: chain E residue 65 LYS
Chi-restraints excluded: chain E residue 86 LEU
Chi-restraints excluded: chain E residue 155 VAL
Chi-restraints excluded: chain E residue 184 SER
Chi-restraints excluded: chain E residue 193 SER
Chi-restraints excluded: chain G residue 9 ILE
Chi-restraints excluded: chain G residue 16 VAL
Chi-restraints excluded: chain R residue 79 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 110
random chunks:
chunk 13 optimal weight: 0.8980
chunk 94 optimal weight: 3.9990
chunk 84 optimal weight: 0.9980
chunk 109 optimal weight: 6.9990
chunk 61 optimal weight: 2.9990
chunk 99 optimal weight: 0.9980
chunk 76 optimal weight: 3.9990
chunk 66 optimal weight: 2.9990
chunk 69 optimal weight: 0.9990
chunk 87 optimal weight: 0.9990
chunk 6 optimal weight: 5.9990
overall best weight: 0.9784
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 255 ASN
A 269 ASN
A 311 ASN
A 331 ASN
B 75 GLN
Total number of N/Q/H flips: 5
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.161240 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.110639 restraints weight = 10082.973|
|-----------------------------------------------------------------------------|
r_work (start): 0.3308 rms_B_bonded: 2.42
r_work: 0.3156 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work: 0.3013 rms_B_bonded: 4.60 restraints_weight: 0.2500
r_work (final): 0.3013
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8314
moved from start: 0.2241
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.071 8897 Z= 0.204
Angle : 0.540 8.228 12061 Z= 0.285
Chirality : 0.042 0.214 1380
Planarity : 0.004 0.039 1523
Dihedral : 4.046 21.804 1218
Min Nonbonded Distance : 2.464
Molprobity Statistics.
All-atom Clashscore : 4.52
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 2.36 %
Favored : 97.64 %
Rotamer:
Outliers : 2.26 %
Allowed : 20.69 %
Favored : 77.05 %
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: 1.68 (0.26), residues: 1100
helix: 2.73 (0.25), residues: 387
sheet: 0.36 (0.30), residues: 285
loop : 0.22 (0.31), residues: 428
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.015 0.001 TRP B 82
HIS 0.006 0.001 HIS B 266
PHE 0.011 0.001 PHE A 196
TYR 0.032 0.001 TYR R 48
ARG 0.007 0.000 ARG R 255
*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
2200 Ramachandran restraints generated.
1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
2200 Ramachandran restraints generated.
1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
148 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 21
poor density : 127
time to evaluate : 1.032
Fit side-chains
REVERT: A 297 GLU cc_start: 0.8300 (mm-30) cc_final: 0.8041 (tt0)
REVERT: A 298 GLU cc_start: 0.8419 (tt0) cc_final: 0.8079 (tt0)
REVERT: B 175 GLN cc_start: 0.7970 (mm-40) cc_final: 0.7542 (pp30)
REVERT: B 219 ARG cc_start: 0.8229 (OUTLIER) cc_final: 0.7250 (mmt-90)
REVERT: B 267 ASP cc_start: 0.8250 (m-30) cc_final: 0.7921 (m-30)
REVERT: E 46 GLU cc_start: 0.8390 (tt0) cc_final: 0.8135 (tt0)
REVERT: E 82 GLN cc_start: 0.8153 (tp40) cc_final: 0.7950 (tp40)
REVERT: E 160 ARG cc_start: 0.7926 (ttm110) cc_final: 0.7612 (tpp-160)
REVERT: E 244 LYS cc_start: 0.8037 (ttpp) cc_final: 0.7821 (tttm)
REVERT: R 64 ASN cc_start: 0.7954 (m110) cc_final: 0.7544 (m-40)
REVERT: R 253 ASN cc_start: 0.8803 (m-40) cc_final: 0.8549 (m-40)
outliers start: 21
outliers final: 18
residues processed: 139
average time/residue: 1.3018
time to fit residues: 192.3192
Evaluate side-chains
142 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 19
poor density : 123
time to evaluate : 0.929
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 246 SER
Chi-restraints excluded: chain A residue 313 ARG
Chi-restraints excluded: chain A residue 332 VAL
Chi-restraints excluded: chain B residue 96 ARG
Chi-restraints excluded: chain B residue 153 ASP
Chi-restraints excluded: chain B residue 219 ARG
Chi-restraints excluded: chain B residue 263 THR
Chi-restraints excluded: chain B residue 270 ILE
Chi-restraints excluded: chain B residue 279 SER
Chi-restraints excluded: chain E residue 11 LEU
Chi-restraints excluded: chain E residue 65 LYS
Chi-restraints excluded: chain E residue 86 LEU
Chi-restraints excluded: chain E residue 155 VAL
Chi-restraints excluded: chain E residue 184 SER
Chi-restraints excluded: chain E residue 193 SER
Chi-restraints excluded: chain G residue 9 ILE
Chi-restraints excluded: chain G residue 16 VAL
Chi-restraints excluded: chain R residue 79 LEU
Chi-restraints excluded: chain R residue 186 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 110
random chunks:
chunk 102 optimal weight: 5.9990
chunk 91 optimal weight: 0.5980
chunk 75 optimal weight: 3.9990
chunk 34 optimal weight: 6.9990
chunk 31 optimal weight: 0.0370
chunk 89 optimal weight: 20.0000
chunk 65 optimal weight: 4.9990
chunk 6 optimal weight: 1.9990
chunk 98 optimal weight: 2.9990
chunk 17 optimal weight: 2.9990
chunk 13 optimal weight: 0.8980
overall best weight: 1.3062
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 255 ASN
A 269 ASN
A 311 ASN
A 331 ASN
B 75 GLN
B 259 GLN
E 77 ASN
Total number of N/Q/H flips: 7
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3903 r_free = 0.3903 target = 0.160370 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.109622 restraints weight = 10106.121|
|-----------------------------------------------------------------------------|
r_work (start): 0.3292 rms_B_bonded: 2.43
r_work: 0.3139 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.2997 rms_B_bonded: 4.60 restraints_weight: 0.2500
r_work (final): 0.2997
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8329
moved from start: 0.2219
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.004 0.079 8897 Z= 0.244
Angle : 0.567 8.699 12061 Z= 0.296
Chirality : 0.043 0.187 1380
Planarity : 0.004 0.038 1523
Dihedral : 4.130 22.091 1218
Min Nonbonded Distance : 2.457
Molprobity Statistics.
All-atom Clashscore : 4.57
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 2.36 %
Favored : 97.64 %
Rotamer:
Outliers : 2.26 %
Allowed : 20.80 %
Favored : 76.94 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 1.64 (0.26), residues: 1100
helix: 2.67 (0.26), residues: 387
sheet: 0.34 (0.30), residues: 285
loop : 0.22 (0.31), residues: 428
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.014 0.001 TRP B 82
HIS 0.006 0.001 HIS B 266
PHE 0.012 0.001 PHE A 196
TYR 0.030 0.001 TYR R 48
ARG 0.007 0.000 ARG R 255
********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
2200 Ramachandran restraints generated.
1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
2200 Ramachandran restraints generated.
1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
148 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 21
poor density : 127
time to evaluate : 0.946
Fit side-chains
REVERT: A 297 GLU cc_start: 0.8296 (mm-30) cc_final: 0.8044 (tt0)
REVERT: A 298 GLU cc_start: 0.8402 (tt0) cc_final: 0.8044 (tt0)
REVERT: B 175 GLN cc_start: 0.7989 (mm-40) cc_final: 0.7546 (pp30)
REVERT: B 219 ARG cc_start: 0.8250 (OUTLIER) cc_final: 0.7296 (mmt-90)
REVERT: B 267 ASP cc_start: 0.8265 (m-30) cc_final: 0.7929 (m-30)
REVERT: E 46 GLU cc_start: 0.8398 (tt0) cc_final: 0.8157 (tt0)
REVERT: E 76 LYS cc_start: 0.8159 (mtmm) cc_final: 0.7941 (ptpp)
REVERT: E 160 ARG cc_start: 0.7948 (ttm110) cc_final: 0.7531 (mmm-85)
REVERT: E 244 LYS cc_start: 0.8058 (ttpp) cc_final: 0.7836 (tttm)
REVERT: R 64 ASN cc_start: 0.7979 (m110) cc_final: 0.7630 (m-40)
REVERT: R 253 ASN cc_start: 0.8808 (m-40) cc_final: 0.8559 (m-40)
outliers start: 21
outliers final: 18
residues processed: 139
average time/residue: 1.2869
time to fit residues: 191.0096
Evaluate side-chains
143 residues out of total 971 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 19
poor density : 124
time to evaluate : 1.085
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 246 SER
Chi-restraints excluded: chain A residue 313 ARG
Chi-restraints excluded: chain A residue 332 VAL
Chi-restraints excluded: chain B residue 96 ARG
Chi-restraints excluded: chain B residue 153 ASP
Chi-restraints excluded: chain B residue 219 ARG
Chi-restraints excluded: chain B residue 263 THR
Chi-restraints excluded: chain B residue 270 ILE
Chi-restraints excluded: chain B residue 279 SER
Chi-restraints excluded: chain E residue 11 LEU
Chi-restraints excluded: chain E residue 65 LYS
Chi-restraints excluded: chain E residue 86 LEU
Chi-restraints excluded: chain E residue 155 VAL
Chi-restraints excluded: chain E residue 184 SER
Chi-restraints excluded: chain E residue 193 SER
Chi-restraints excluded: chain G residue 9 ILE
Chi-restraints excluded: chain G residue 16 VAL
Chi-restraints excluded: chain R residue 79 LEU
Chi-restraints excluded: chain R residue 186 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 110
random chunks:
chunk 32 optimal weight: 1.9990
chunk 28 optimal weight: 1.9990
chunk 86 optimal weight: 3.9990
chunk 34 optimal weight: 4.9990
chunk 67 optimal weight: 7.9990
chunk 94 optimal weight: 5.9990
chunk 40 optimal weight: 0.0970
chunk 15 optimal weight: 0.0010
chunk 52 optimal weight: 1.9990
chunk 85 optimal weight: 5.9990
chunk 71 optimal weight: 3.9990
overall best weight: 1.2190
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 255 ASN
A 269 ASN
A 311 ASN
B 75 GLN
Total number of N/Q/H flips: 4
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3904 r_free = 0.3904 target = 0.160467 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.109754 restraints weight = 10101.958|
|-----------------------------------------------------------------------------|
r_work (start): 0.3296 rms_B_bonded: 2.42
r_work: 0.3144 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.3000 rms_B_bonded: 4.59 restraints_weight: 0.2500
r_work (final): 0.3000
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8293
moved from start: 0.2267
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.076 8897 Z= 0.234
Angle : 0.570 8.776 12061 Z= 0.296
Chirality : 0.043 0.183 1380
Planarity : 0.004 0.038 1523
Dihedral : 4.134 22.290 1218
Min Nonbonded Distance : 2.457
Molprobity Statistics.
All-atom Clashscore : 4.81
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 2.45 %
Favored : 97.55 %
Rotamer:
Outliers : 2.37 %
Allowed : 20.69 %
Favored : 76.94 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 1.64 (0.26), residues: 1100
helix: 2.67 (0.26), residues: 387
sheet: 0.31 (0.30), residues: 285
loop : 0.24 (0.31), residues: 428
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.014 0.001 TRP B 82
HIS 0.007 0.001 HIS B 266
PHE 0.012 0.001 PHE A 196
TYR 0.032 0.001 TYR R 48
ARG 0.008 0.001 ARG E 180
Origin is already at (0, 0, 0), no shifts will be applied
===============================================================================
Job complete
usr+sys time: 7881.56 seconds
wall clock time: 139 minutes 49.41 seconds (8389.41 seconds total)