Starting phenix.real_space_refine
on Tue Jan 21 14:43:22 2025 by dcliebschner
===============================================================================
Processing files:
-------------------------------------------------------------------------------
Found model, /net/cci-nas-00/data/ceres_data/9c5b_45213/01_2025/9c5b_45213.cif
Found real_map, /net/cci-nas-00/data/ceres_data/9c5b_45213/01_2025/9c5b_45213.map
Processing PHIL parameters:
-------------------------------------------------------------------------------
Adding command-line PHIL:
-------------------------
refinement.macro_cycles=10
scattering_table=electron
resolution=4.5
write_initial_geo_file=False
Final processed PHIL parameters:
-------------------------------------------------------------------------------
data_manager {
real_map_files = "/net/cci-nas-00/data/ceres_data/9c5b_45213/01_2025/9c5b_45213.map"
default_real_map = "/net/cci-nas-00/data/ceres_data/9c5b_45213/01_2025/9c5b_45213.map"
model {
file = "/net/cci-nas-00/data/ceres_data/9c5b_45213/01_2025/9c5b_45213.cif"
}
default_model = "/net/cci-nas-00/data/ceres_data/9c5b_45213/01_2025/9c5b_45213.cif"
}
resolution = 4.5
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= 0.019
Set stop_for_unknowns flag
Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
Set to: electron
Number of scattering types: 6
Type Number sf(0) Gaussians
P 6 5.49 5
Mg 2 5.21 5
S 88 5.16 5
C 10770 2.51 5
N 2876 2.21 5
O 3132 1.98 5
sf(0) = scattering factor at diffraction angle 0.
Process input model
Symmetric amino acids flipped. Time to flip 57 residue(s): 0.06s
Monomer Library directory:
"/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
Total number of atoms: 16874
Number of models: 1
Model: ""
Number of chains: 9
Chain: "A"
Number of atoms: 1330
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 165, 1330
Classifications: {'peptide': 165}
Link IDs: {'PTRANS': 3, 'TRANS': 161}
Chain: "C"
Number of atoms: 1447
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 180, 1447
Classifications: {'peptide': 180}
Link IDs: {'PTRANS': 3, 'TRANS': 176}
Chain: "D"
Number of atoms: 4770
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 605, 4770
Classifications: {'peptide': 605}
Link IDs: {'PTRANS': 20, 'TRANS': 584}
Chain: "M"
Number of atoms: 3309
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 418, 3309
Classifications: {'peptide': 418}
Modifications used: {'COO': 1}
Link IDs: {'PTRANS': 26, 'TRANS': 391}
Chain: "S"
Number of atoms: 1219
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 151, 1219
Classifications: {'peptide': 151}
Link IDs: {'PTRANS': 2, 'TRANS': 148}
Chain: "Y"
Number of atoms: 62
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 8, 62
Classifications: {'peptide': 8}
Modifications used: {'COO': 1}
Link IDs: {'TRANS': 7}
Chain: "B"
Number of atoms: 4671
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 587, 4671
Classifications: {'peptide': 587}
Link IDs: {'PTRANS': 25, 'TRANS': 561}
Chain breaks: 1
Chain: "A"
Number of atoms: 33
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 2, 33
Unusual residues: {' MG': 1, 'GTP': 1}
Classifications: {'undetermined': 2}
Link IDs: {None: 1}
Chain: "C"
Number of atoms: 33
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 2, 33
Unusual residues: {' MG': 1, 'GTP': 1}
Classifications: {'undetermined': 2}
Link IDs: {None: 1}
Time building chain proxies: 10.06, per 1000 atoms: 0.60
Number of scatterers: 16874
At special positions: 0
Unit cell: (128.018, 142.83, 154.468, 90, 90, 90)
Space group: P 1 (No. 1)
Number of sites at special positions: 0
Number of scattering types: 6
Type Number sf(0)
S 88 16.00
P 6 15.00
Mg 2 11.99
O 3132 8.00
N 2876 7.00
C 10770 6.00
sf(0) = scattering factor at diffraction angle 0.
Number of disulfides: simple=0, symmetry=0
Automatic linking
Parameters for automatic linking
Linking & cutoffs
Metal : Auto - 3.00
Amino acid : True - 1.90
Carbohydrate : True - 1.99
Ligands : True - 1.99
Small molecules : False - 1.98
Amino acid - RNA/DNA : False
Number of custom bonds: simple=0, symmetry=0
Time building additional restraints: 4.51
Conformation dependent library (CDL) restraints added in 2.1 seconds
4196 Ramachandran restraints generated.
2098 Oldfield, 0 Emsley, 2098 emsley8k and 0 Phi/Psi/2.
Adding C-beta torsion restraints...
Number of C-beta restraints generated: 4038
Finding SS restraints...
Secondary structure from input PDB file:
112 helices and 10 sheets defined
63.4% alpha, 14.5% beta
0 base pairs and 0 stacking pairs defined.
Time for finding SS restraints: 1.78
Creating SS restraints...
Processing helix chain 'A' and resid 29 through 40
Processing helix chain 'A' and resid 71 through 82
Proline residue: A 76 - end of helix
removed outlier: 3.645A pdb=" N ARG A 79 " --> pdb=" O PRO A 76 " (cutoff:3.500A)
Processing helix chain 'A' and resid 96 through 98
No H-bonds generated for 'chain 'A' and resid 96 through 98'
Processing helix chain 'A' and resid 99 through 112
Processing helix chain 'A' and resid 113 through 117
Processing helix chain 'A' and resid 135 through 144
Processing helix chain 'A' and resid 145 through 148
removed outlier: 3.557A pdb=" N LEU A 148 " --> pdb=" O LEU A 145 " (cutoff:3.500A)
No H-bonds generated for 'chain 'A' and resid 145 through 148'
Processing helix chain 'A' and resid 165 through 178
Processing helix chain 'C' and resid 4 through 14
removed outlier: 3.755A pdb=" N PHE C 13 " --> pdb=" O PHE C 9 " (cutoff:3.500A)
Processing helix chain 'C' and resid 29 through 39
Processing helix chain 'C' and resid 74 through 82
Processing helix chain 'C' and resid 99 through 112
Processing helix chain 'C' and resid 135 through 144
Processing helix chain 'C' and resid 145 through 148
Processing helix chain 'C' and resid 165 through 177
Processing helix chain 'D' and resid 2 through 14
Processing helix chain 'D' and resid 17 through 28
Processing helix chain 'D' and resid 31 through 47
Processing helix chain 'D' and resid 51 through 68
Processing helix chain 'D' and resid 72 through 74
No H-bonds generated for 'chain 'D' and resid 72 through 74'
Processing helix chain 'D' and resid 75 through 84
Processing helix chain 'D' and resid 87 through 102
removed outlier: 4.556A pdb=" N ILE D 93 " --> pdb=" O THR D 89 " (cutoff:3.500A)
removed outlier: 3.622A pdb=" N GLN D 100 " --> pdb=" O LEU D 96 " (cutoff:3.500A)
Processing helix chain 'D' and resid 107 through 112
Processing helix chain 'D' and resid 112 through 122
Processing helix chain 'D' and resid 124 through 138
removed outlier: 3.704A pdb=" N CYS D 137 " --> pdb=" O THR D 133 " (cutoff:3.500A)
Processing helix chain 'D' and resid 140 through 155
removed outlier: 4.488A pdb=" N ASN D 149 " --> pdb=" O ARG D 145 " (cutoff:3.500A)
removed outlier: 4.392A pdb=" N ASP D 150 " --> pdb=" O ASP D 146 " (cutoff:3.500A)
removed outlier: 4.394A pdb=" N THR D 153 " --> pdb=" O ASN D 149 " (cutoff:3.500A)
Processing helix chain 'D' and resid 159 through 177
removed outlier: 3.685A pdb=" N LYS D 172 " --> pdb=" O LEU D 168 " (cutoff:3.500A)
Processing helix chain 'D' and resid 177 through 192
removed outlier: 3.644A pdb=" N LEU D 181 " --> pdb=" O TYR D 177 " (cutoff:3.500A)
Proline residue: D 183 - end of helix
Proline residue: D 186 - end of helix
Processing helix chain 'D' and resid 196 through 214
Processing helix chain 'D' and resid 215 through 218
Processing helix chain 'D' and resid 221 through 232
Processing helix chain 'D' and resid 234 through 249
Processing helix chain 'D' and resid 252 through 270
removed outlier: 3.630A pdb=" N GLY D 256 " --> pdb=" O GLU D 252 " (cutoff:3.500A)
removed outlier: 4.905A pdb=" N GLU D 261 " --> pdb=" O LYS D 257 " (cutoff:3.500A)
Proline residue: D 262 - end of helix
Processing helix chain 'D' and resid 272 through 292
removed outlier: 3.509A pdb=" N GLU D 278 " --> pdb=" O SER D 274 " (cutoff:3.500A)
removed outlier: 4.318A pdb=" N SER D 292 " --> pdb=" O ILE D 288 " (cutoff:3.500A)
Processing helix chain 'D' and resid 296 through 314
Processing helix chain 'D' and resid 316 through 332
Processing helix chain 'D' and resid 334 through 339
Processing helix chain 'D' and resid 341 through 349
removed outlier: 3.695A pdb=" N LEU D 349 " --> pdb=" O ILE D 345 " (cutoff:3.500A)
Processing helix chain 'D' and resid 353 through 368
Processing helix chain 'D' and resid 372 through 387
Processing helix chain 'D' and resid 389 through 410
removed outlier: 6.709A pdb=" N SER D 407 " --> pdb=" O ILE D 403 " (cutoff:3.500A)
removed outlier: 6.389A pdb=" N ASN D 408 " --> pdb=" O CYS D 404 " (cutoff:3.500A)
Processing helix chain 'D' and resid 414 through 426
Processing helix chain 'D' and resid 433 through 448
Processing helix chain 'D' and resid 451 through 465
Processing helix chain 'D' and resid 465 through 470
Processing helix chain 'D' and resid 479 through 492
removed outlier: 3.614A pdb=" N TYR D 483 " --> pdb=" O CYS D 479 " (cutoff:3.500A)
Processing helix chain 'D' and resid 493 through 496
Processing helix chain 'D' and resid 498 through 507
Processing helix chain 'D' and resid 508 through 514
Processing helix chain 'D' and resid 515 through 541
Processing helix chain 'D' and resid 542 through 555
Processing helix chain 'D' and resid 556 through 561
removed outlier: 3.537A pdb=" N PHE D 560 " --> pdb=" O ARG D 556 " (cutoff:3.500A)
Processing helix chain 'D' and resid 565 through 588
Processing helix chain 'D' and resid 592 through 602
removed outlier: 3.806A pdb=" N LEU D 599 " --> pdb=" O GLU D 595 " (cutoff:3.500A)
removed outlier: 4.204A pdb=" N PHE D 600 " --> pdb=" O VAL D 596 " (cutoff:3.500A)
removed outlier: 3.932A pdb=" N GLY D 602 " --> pdb=" O ALA D 598 " (cutoff:3.500A)
Processing helix chain 'M' and resid 25 through 27
No H-bonds generated for 'chain 'M' and resid 25 through 27'
Processing helix chain 'M' and resid 28 through 39
removed outlier: 4.023A pdb=" N PHE M 32 " --> pdb=" O VAL M 28 " (cutoff:3.500A)
Processing helix chain 'M' and resid 41 through 45
Processing helix chain 'M' and resid 75 through 95
Processing helix chain 'M' and resid 98 through 105
Processing helix chain 'M' and resid 105 through 116
Processing helix chain 'M' and resid 126 through 134
removed outlier: 3.669A pdb=" N GLU M 132 " --> pdb=" O ASN M 128 " (cutoff:3.500A)
Processing helix chain 'M' and resid 138 through 149
Processing helix chain 'M' and resid 158 through 163
Processing helix chain 'M' and resid 224 through 228
Processing helix chain 'M' and resid 238 through 245
Processing helix chain 'S' and resid 24 through 41
removed outlier: 3.801A pdb=" N LYS S 41 " --> pdb=" O HIS S 37 " (cutoff:3.500A)
Processing helix chain 'S' and resid 82 through 102
Processing helix chain 'S' and resid 105 through 112
Processing helix chain 'S' and resid 112 through 123
Processing helix chain 'S' and resid 133 through 151
Processing helix chain 'B' and resid 39 through 53
Processing helix chain 'B' and resid 55 through 72
Processing helix chain 'B' and resid 76 through 78
No H-bonds generated for 'chain 'B' and resid 76 through 78'
Processing helix chain 'B' and resid 79 through 84
Processing helix chain 'B' and resid 85 through 89
removed outlier: 4.342A pdb=" N ALA B 88 " --> pdb=" O LYS B 85 " (cutoff:3.500A)
Processing helix chain 'B' and resid 91 through 106
Processing helix chain 'B' and resid 109 through 114
removed outlier: 3.715A pdb=" N LEU B 114 " --> pdb=" O GLN B 110 " (cutoff:3.500A)
Processing helix chain 'B' and resid 116 through 124
Processing helix chain 'B' and resid 128 through 142
Processing helix chain 'B' and resid 144 through 146
No H-bonds generated for 'chain 'B' and resid 144 through 146'
Processing helix chain 'B' and resid 147 through 160
Processing helix chain 'B' and resid 163 through 181
Processing helix chain 'B' and resid 184 through 196
Processing helix chain 'B' and resid 200 through 215
removed outlier: 4.349A pdb=" N GLY B 205 " --> pdb=" O THR B 201 " (cutoff:3.500A)
removed outlier: 5.512A pdb=" N SER B 206 " --> pdb=" O LEU B 202 " (cutoff:3.500A)
Processing helix chain 'B' and resid 218 through 224
removed outlier: 4.273A pdb=" N HIS B 223 " --> pdb=" O ASP B 220 " (cutoff:3.500A)
removed outlier: 5.295A pdb=" N LYS B 224 " --> pdb=" O LEU B 221 " (cutoff:3.500A)
Processing helix chain 'B' and resid 225 through 233
Processing helix chain 'B' and resid 234 through 236
No H-bonds generated for 'chain 'B' and resid 234 through 236'
Processing helix chain 'B' and resid 237 through 256
removed outlier: 4.282A pdb=" N THR B 254 " --> pdb=" O ARG B 250 " (cutoff:3.500A)
Processing helix chain 'B' and resid 294 through 305
Processing helix chain 'B' and resid 306 through 310
Processing helix chain 'B' and resid 312 through 326
Processing helix chain 'B' and resid 331 through 333
No H-bonds generated for 'chain 'B' and resid 331 through 333'
Processing helix chain 'B' and resid 334 through 343
removed outlier: 4.015A pdb=" N SER B 338 " --> pdb=" O ILE B 334 " (cutoff:3.500A)
removed outlier: 3.772A pdb=" N LEU B 343 " --> pdb=" O LEU B 339 " (cutoff:3.500A)
Processing helix chain 'B' and resid 346 through 362
removed outlier: 3.656A pdb=" N ILE B 352 " --> pdb=" O GLU B 348 " (cutoff:3.500A)
Processing helix chain 'B' and resid 364 through 376
removed outlier: 3.868A pdb=" N GLU B 369 " --> pdb=" O GLY B 366 " (cutoff:3.500A)
Proline residue: B 370 - end of helix
removed outlier: 5.601A pdb=" N LYS B 373 " --> pdb=" O PRO B 370 " (cutoff:3.500A)
Processing helix chain 'B' and resid 382 through 397
Processing helix chain 'B' and resid 401 through 414
removed outlier: 3.756A pdb=" N LYS B 414 " --> pdb=" O GLN B 410 " (cutoff:3.500A)
Processing helix chain 'B' and resid 417 through 435
Processing helix chain 'B' and resid 438 through 449
Processing helix chain 'B' and resid 450 through 452
No H-bonds generated for 'chain 'B' and resid 450 through 452'
Processing helix chain 'B' and resid 454 through 472
Processing helix chain 'B' and resid 476 through 487
Processing helix chain 'B' and resid 492 through 506
Processing helix chain 'B' and resid 513 through 525
Processing helix chain 'B' and resid 526 through 528
No H-bonds generated for 'chain 'B' and resid 526 through 528'
Processing helix chain 'B' and resid 529 through 565
removed outlier: 7.343A pdb=" N LYS B 549 " --> pdb=" O LEU B 545 " (cutoff:3.500A)
removed outlier: 7.295A pdb=" N GLN B 550 " --> pdb=" O THR B 546 " (cutoff:3.500A)
removed outlier: 6.912A pdb=" N LEU B 553 " --> pdb=" O LYS B 549 " (cutoff:3.500A)
removed outlier: 5.746A pdb=" N LEU B 554 " --> pdb=" O GLN B 550 " (cutoff:3.500A)
removed outlier: 3.554A pdb=" N TYR B 564 " --> pdb=" O ASN B 560 " (cutoff:3.500A)
Processing helix chain 'B' and resid 567 through 582
Processing helix chain 'B' and resid 590 through 592
No H-bonds generated for 'chain 'B' and resid 590 through 592'
Processing helix chain 'B' and resid 593 through 599
Processing helix chain 'B' and resid 609 through 615
removed outlier: 3.991A pdb=" N ASP B 615 " --> pdb=" O LYS B 612 " (cutoff:3.500A)
Processing helix chain 'B' and resid 621 through 627
removed outlier: 3.512A pdb=" N THR B 625 " --> pdb=" O THR B 621 " (cutoff:3.500A)
Processing helix chain 'B' and resid 645 through 650
Processing sheet with id=AA1, first strand: chain 'A' and resid 51 through 58
removed outlier: 3.806A pdb=" N VAL A 68 " --> pdb=" O MET A 22 " (cutoff:3.500A)
Processing sheet with id=AA2, first strand: chain 'C' and resid 51 through 58
removed outlier: 5.173A pdb=" N GLY C 24 " --> pdb=" O VAL C 68 " (cutoff:3.500A)
removed outlier: 6.561A pdb=" N ARG C 19 " --> pdb=" O GLY C 87 " (cutoff:3.500A)
removed outlier: 7.680A pdb=" N ILE C 89 " --> pdb=" O ARG C 19 " (cutoff:3.500A)
removed outlier: 6.375A pdb=" N LEU C 21 " --> pdb=" O ILE C 89 " (cutoff:3.500A)
removed outlier: 7.508A pdb=" N VAL C 91 " --> pdb=" O LEU C 21 " (cutoff:3.500A)
removed outlier: 7.179A pdb=" N VAL C 23 " --> pdb=" O VAL C 91 " (cutoff:3.500A)
removed outlier: 8.628A pdb=" N ASP C 93 " --> pdb=" O VAL C 23 " (cutoff:3.500A)
removed outlier: 6.559A pdb=" N LEU C 121 " --> pdb=" O TYR C 154 " (cutoff:3.500A)
removed outlier: 7.555A pdb=" N GLN C 156 " --> pdb=" O LEU C 121 " (cutoff:3.500A)
removed outlier: 6.086A pdb=" N VAL C 123 " --> pdb=" O GLN C 156 " (cutoff:3.500A)
Processing sheet with id=AA3, first strand: chain 'M' and resid 14 through 19
removed outlier: 6.499A pdb=" N LEU M 7 " --> pdb=" O PHE M 15 " (cutoff:3.500A)
removed outlier: 4.549A pdb=" N GLU M 17 " --> pdb=" O LEU M 5 " (cutoff:3.500A)
removed outlier: 6.807A pdb=" N LEU M 5 " --> pdb=" O GLU M 17 " (cutoff:3.500A)
Processing sheet with id=AA4, first strand: chain 'M' and resid 117 through 118
Processing sheet with id=AA5, first strand: chain 'M' and resid 229 through 233
removed outlier: 5.089A pdb=" N ASP M 230 " --> pdb=" O ARG M 263 " (cutoff:3.500A)
removed outlier: 4.135A pdb=" N ARG M 263 " --> pdb=" O ASP M 230 " (cutoff:3.500A)
removed outlier: 5.825A pdb=" N ASN M 256 " --> pdb=" O ILE M 210 " (cutoff:3.500A)
removed outlier: 6.626A pdb=" N ILE M 210 " --> pdb=" O ASN M 256 " (cutoff:3.500A)
removed outlier: 5.063A pdb=" N ARG M 258 " --> pdb=" O ALA M 208 " (cutoff:3.500A)
removed outlier: 6.514A pdb=" N ALA M 208 " --> pdb=" O ARG M 258 " (cutoff:3.500A)
removed outlier: 3.893A pdb=" N ILE M 202 " --> pdb=" O VAL M 264 " (cutoff:3.500A)
removed outlier: 6.523A pdb=" N ILE M 190 " --> pdb=" O VAL M 198 " (cutoff:3.500A)
removed outlier: 4.251A pdb=" N ALA M 200 " --> pdb=" O ASP M 188 " (cutoff:3.500A)
removed outlier: 6.933A pdb=" N ASP M 188 " --> pdb=" O ALA M 200 " (cutoff:3.500A)
removed outlier: 4.701A pdb=" N ILE M 202 " --> pdb=" O GLU M 186 " (cutoff:3.500A)
removed outlier: 6.313A pdb=" N GLU M 186 " --> pdb=" O ILE M 202 " (cutoff:3.500A)
removed outlier: 4.480A pdb=" N GLY M 204 " --> pdb=" O VAL M 184 " (cutoff:3.500A)
removed outlier: 6.804A pdb=" N VAL M 184 " --> pdb=" O GLY M 204 " (cutoff:3.500A)
removed outlier: 4.361A pdb=" N ILE M 206 " --> pdb=" O ASP M 182 " (cutoff:3.500A)
removed outlier: 6.267A pdb=" N ASP M 182 " --> pdb=" O ILE M 206 " (cutoff:3.500A)
removed outlier: 4.253A pdb=" N ALA M 208 " --> pdb=" O TYR M 180 " (cutoff:3.500A)
removed outlier: 6.405A pdb=" N TYR M 180 " --> pdb=" O ALA M 208 " (cutoff:3.500A)
removed outlier: 5.158A pdb=" N ILE M 210 " --> pdb=" O GLU M 178 " (cutoff:3.500A)
removed outlier: 7.182A pdb=" N GLU M 178 " --> pdb=" O ILE M 210 " (cutoff:3.500A)
removed outlier: 11.065A pdb=" N ALA M 179 " --> pdb=" O VAL M 405 " (cutoff:3.500A)
removed outlier: 11.780A pdb=" N TYR M 407 " --> pdb=" O ALA M 179 " (cutoff:3.500A)
removed outlier: 11.123A pdb=" N PHE M 181 " --> pdb=" O TYR M 407 " (cutoff:3.500A)
removed outlier: 11.398A pdb=" N THR M 409 " --> pdb=" O PHE M 181 " (cutoff:3.500A)
removed outlier: 10.777A pdb=" N VAL M 183 " --> pdb=" O THR M 409 " (cutoff:3.500A)
removed outlier: 10.960A pdb=" N ALA M 411 " --> pdb=" O VAL M 183 " (cutoff:3.500A)
removed outlier: 8.332A pdb=" N GLU M 185 " --> pdb=" O ALA M 411 " (cutoff:3.500A)
removed outlier: 8.713A pdb=" N LYS M 413 " --> pdb=" O GLU M 185 " (cutoff:3.500A)
removed outlier: 6.912A pdb=" N ILE M 187 " --> pdb=" O LYS M 413 " (cutoff:3.500A)
removed outlier: 6.523A pdb=" N GLN M 415 " --> pdb=" O ILE M 187 " (cutoff:3.500A)
removed outlier: 6.249A pdb=" N ALA M 189 " --> pdb=" O GLN M 415 " (cutoff:3.500A)
removed outlier: 7.637A pdb=" N ARG M 417 " --> pdb=" O ALA M 189 " (cutoff:3.500A)
removed outlier: 7.004A pdb=" N ILE M 191 " --> pdb=" O ARG M 417 " (cutoff:3.500A)
removed outlier: 5.813A pdb=" N PHE M 377 " --> pdb=" O ALA M 411 " (cutoff:3.500A)
removed outlier: 7.093A pdb=" N LYS M 413 " --> pdb=" O ILE M 375 " (cutoff:3.500A)
removed outlier: 7.871A pdb=" N ILE M 375 " --> pdb=" O LYS M 413 " (cutoff:3.500A)
removed outlier: 4.264A pdb=" N GLN M 415 " --> pdb=" O LEU M 373 " (cutoff:3.500A)
removed outlier: 6.115A pdb=" N LEU M 373 " --> pdb=" O GLN M 415 " (cutoff:3.500A)
removed outlier: 6.440A pdb=" N ARG M 417 " --> pdb=" O PRO M 371 " (cutoff:3.500A)
removed outlier: 5.714A pdb=" N SER M 372 " --> pdb=" O HIS M 313 " (cutoff:3.500A)
removed outlier: 4.760A pdb=" N HIS M 313 " --> pdb=" O SER M 372 " (cutoff:3.500A)
removed outlier: 4.389A pdb=" N LYS M 378 " --> pdb=" O GLY M 307 " (cutoff:3.500A)
removed outlier: 5.147A pdb=" N GLY M 307 " --> pdb=" O LYS M 378 " (cutoff:3.500A)
removed outlier: 6.095A pdb=" N ILE M 308 " --> pdb=" O VAL M 343 " (cutoff:3.500A)
Processing sheet with id=AA6, first strand: chain 'M' and resid 229 through 233
removed outlier: 5.089A pdb=" N ASP M 230 " --> pdb=" O ARG M 263 " (cutoff:3.500A)
removed outlier: 4.135A pdb=" N ARG M 263 " --> pdb=" O ASP M 230 " (cutoff:3.500A)
removed outlier: 5.825A pdb=" N ASN M 256 " --> pdb=" O ILE M 210 " (cutoff:3.500A)
removed outlier: 6.626A pdb=" N ILE M 210 " --> pdb=" O ASN M 256 " (cutoff:3.500A)
removed outlier: 5.063A pdb=" N ARG M 258 " --> pdb=" O ALA M 208 " (cutoff:3.500A)
removed outlier: 6.514A pdb=" N ALA M 208 " --> pdb=" O ARG M 258 " (cutoff:3.500A)
removed outlier: 3.893A pdb=" N ILE M 202 " --> pdb=" O VAL M 264 " (cutoff:3.500A)
removed outlier: 6.523A pdb=" N ILE M 190 " --> pdb=" O VAL M 198 " (cutoff:3.500A)
removed outlier: 4.251A pdb=" N ALA M 200 " --> pdb=" O ASP M 188 " (cutoff:3.500A)
removed outlier: 6.933A pdb=" N ASP M 188 " --> pdb=" O ALA M 200 " (cutoff:3.500A)
removed outlier: 4.701A pdb=" N ILE M 202 " --> pdb=" O GLU M 186 " (cutoff:3.500A)
removed outlier: 6.313A pdb=" N GLU M 186 " --> pdb=" O ILE M 202 " (cutoff:3.500A)
removed outlier: 4.480A pdb=" N GLY M 204 " --> pdb=" O VAL M 184 " (cutoff:3.500A)
removed outlier: 6.804A pdb=" N VAL M 184 " --> pdb=" O GLY M 204 " (cutoff:3.500A)
removed outlier: 4.361A pdb=" N ILE M 206 " --> pdb=" O ASP M 182 " (cutoff:3.500A)
removed outlier: 6.267A pdb=" N ASP M 182 " --> pdb=" O ILE M 206 " (cutoff:3.500A)
removed outlier: 4.253A pdb=" N ALA M 208 " --> pdb=" O TYR M 180 " (cutoff:3.500A)
removed outlier: 6.405A pdb=" N TYR M 180 " --> pdb=" O ALA M 208 " (cutoff:3.500A)
removed outlier: 5.158A pdb=" N ILE M 210 " --> pdb=" O GLU M 178 " (cutoff:3.500A)
removed outlier: 7.182A pdb=" N GLU M 178 " --> pdb=" O ILE M 210 " (cutoff:3.500A)
removed outlier: 11.065A pdb=" N ALA M 179 " --> pdb=" O VAL M 405 " (cutoff:3.500A)
removed outlier: 11.780A pdb=" N TYR M 407 " --> pdb=" O ALA M 179 " (cutoff:3.500A)
removed outlier: 11.123A pdb=" N PHE M 181 " --> pdb=" O TYR M 407 " (cutoff:3.500A)
removed outlier: 11.398A pdb=" N THR M 409 " --> pdb=" O PHE M 181 " (cutoff:3.500A)
removed outlier: 10.777A pdb=" N VAL M 183 " --> pdb=" O THR M 409 " (cutoff:3.500A)
removed outlier: 10.960A pdb=" N ALA M 411 " --> pdb=" O VAL M 183 " (cutoff:3.500A)
removed outlier: 8.332A pdb=" N GLU M 185 " --> pdb=" O ALA M 411 " (cutoff:3.500A)
removed outlier: 8.713A pdb=" N LYS M 413 " --> pdb=" O GLU M 185 " (cutoff:3.500A)
removed outlier: 6.912A pdb=" N ILE M 187 " --> pdb=" O LYS M 413 " (cutoff:3.500A)
removed outlier: 6.523A pdb=" N GLN M 415 " --> pdb=" O ILE M 187 " (cutoff:3.500A)
removed outlier: 6.249A pdb=" N ALA M 189 " --> pdb=" O GLN M 415 " (cutoff:3.500A)
removed outlier: 7.637A pdb=" N ARG M 417 " --> pdb=" O ALA M 189 " (cutoff:3.500A)
removed outlier: 7.004A pdb=" N ILE M 191 " --> pdb=" O ARG M 417 " (cutoff:3.500A)
Processing sheet with id=AA7, first strand: chain 'M' and resid 248 through 250
Processing sheet with id=AA8, first strand: chain 'M' and resid 274 through 281
removed outlier: 6.898A pdb=" N SER M 353 " --> pdb=" O PRO M 325 " (cutoff:3.500A)
removed outlier: 6.187A pdb=" N LYS M 355 " --> pdb=" O LEU M 323 " (cutoff:3.500A)
removed outlier: 4.914A pdb=" N LEU M 323 " --> pdb=" O LYS M 355 " (cutoff:3.500A)
removed outlier: 6.783A pdb=" N LEU M 357 " --> pdb=" O MET M 321 " (cutoff:3.500A)
removed outlier: 5.125A pdb=" N MET M 321 " --> pdb=" O LEU M 357 " (cutoff:3.500A)
removed outlier: 6.794A pdb=" N ASN M 359 " --> pdb=" O LEU M 319 " (cutoff:3.500A)
Processing sheet with id=AA9, first strand: chain 'S' and resid 14 through 19
removed outlier: 6.167A pdb=" N ILE S 7 " --> pdb=" O ARG S 15 " (cutoff:3.500A)
removed outlier: 4.358A pdb=" N SER S 17 " --> pdb=" O ILE S 5 " (cutoff:3.500A)
removed outlier: 6.882A pdb=" N ILE S 5 " --> pdb=" O SER S 17 " (cutoff:3.500A)
removed outlier: 5.059A pdb=" N PHE S 19 " --> pdb=" O LYS S 3 " (cutoff:3.500A)
removed outlier: 7.807A pdb=" N LYS S 3 " --> pdb=" O PHE S 19 " (cutoff:3.500A)
Processing sheet with id=AB1, first strand: chain 'S' and resid 124 through 125
1004 hydrogen bonds defined for protein.
2835 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: 5.69
Time building geometry restraints manager: 5.17 seconds
NOTE: a complete listing of the restraints can be obtained by requesting
output of .geo file.
Histogram of bond lengths:
1.20 - 1.32: 3852
1.32 - 1.45: 3874
1.45 - 1.57: 9294
1.57 - 1.69: 10
1.69 - 1.81: 147
Bond restraints: 17177
Sorted by residual:
bond pdb=" CA ILE C 89 "
pdb=" C ILE C 89 "
ideal model delta sigma weight residual
1.522 1.474 0.048 1.21e-02 6.83e+03 1.59e+01
bond pdb=" CA ILE S 86 "
pdb=" C ILE S 86 "
ideal model delta sigma weight residual
1.524 1.480 0.044 1.22e-02 6.72e+03 1.30e+01
bond pdb=" CA LEU D 373 "
pdb=" C LEU D 373 "
ideal model delta sigma weight residual
1.524 1.481 0.043 1.24e-02 6.50e+03 1.22e+01
bond pdb=" CA ILE D 162 "
pdb=" C ILE D 162 "
ideal model delta sigma weight residual
1.524 1.476 0.047 1.39e-02 5.18e+03 1.16e+01
bond pdb=" CA ASP C 67 "
pdb=" C ASP C 67 "
ideal model delta sigma weight residual
1.526 1.487 0.039 1.20e-02 6.94e+03 1.04e+01
... (remaining 17172 not shown)
Histogram of bond angle deviations from ideal:
0.00 - 1.98: 20649
1.98 - 3.96: 2214
3.96 - 5.94: 287
5.94 - 7.92: 66
7.92 - 9.90: 37
Bond angle restraints: 23253
Sorted by residual:
angle pdb=" C LYS M 135 "
pdb=" N PRO M 136 "
pdb=" CA PRO M 136 "
ideal model delta sigma weight residual
119.66 126.73 -7.07 7.30e-01 1.88e+00 9.39e+01
angle pdb=" C ASN M 224 "
pdb=" N PRO M 225 "
pdb=" CA PRO M 225 "
ideal model delta sigma weight residual
119.56 129.17 -9.61 1.02e+00 9.61e-01 8.88e+01
angle pdb=" C ASN D 214 "
pdb=" N PRO D 215 "
pdb=" CA PRO D 215 "
ideal model delta sigma weight residual
119.56 129.10 -9.54 1.02e+00 9.61e-01 8.74e+01
angle pdb=" C SER B 609 "
pdb=" N PRO B 610 "
pdb=" CA PRO B 610 "
ideal model delta sigma weight residual
119.56 128.94 -9.38 1.02e+00 9.61e-01 8.45e+01
angle pdb=" C ILE M 165 "
pdb=" N PRO M 166 "
pdb=" CA PRO M 166 "
ideal model delta sigma weight residual
119.56 128.84 -9.28 1.02e+00 9.61e-01 8.28e+01
... (remaining 23248 not shown)
Histogram of dihedral angle deviations from ideal:
0.00 - 35.80: 10376
35.80 - 71.60: 119
71.60 - 107.40: 15
107.40 - 143.20: 4
143.20 - 179.00: 4
Dihedral angle restraints: 10518
sinusoidal: 4307
harmonic: 6211
Sorted by residual:
dihedral pdb=" O3B GTP A 202 "
pdb=" O3A GTP A 202 "
pdb=" PB GTP A 202 "
pdb=" PA GTP A 202 "
ideal model delta sinusoidal sigma weight residual
-68.92 110.08 -179.00 1 2.00e+01 2.50e-03 4.80e+01
dihedral pdb=" O3B GTP C 202 "
pdb=" O3A GTP C 202 "
pdb=" PB GTP C 202 "
pdb=" PA GTP C 202 "
ideal model delta sinusoidal sigma weight residual
-68.92 110.08 -179.00 1 2.00e+01 2.50e-03 4.80e+01
dihedral pdb=" C8 GTP C 202 "
pdb=" C1' GTP C 202 "
pdb=" N9 GTP C 202 "
pdb=" O4' GTP C 202 "
ideal model delta sinusoidal sigma weight residual
104.59 -70.89 175.48 1 2.00e+01 2.50e-03 4.79e+01
... (remaining 10515 not shown)
Histogram of chiral volume deviations from ideal:
0.000 - 0.059: 1675
0.059 - 0.118: 841
0.118 - 0.177: 168
0.177 - 0.237: 20
0.237 - 0.296: 1
Chirality restraints: 2705
Sorted by residual:
chirality pdb=" CA TYR C 35 "
pdb=" N TYR C 35 "
pdb=" C TYR C 35 "
pdb=" CB TYR C 35 "
both_signs ideal model delta sigma weight residual
False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.19e+00
chirality pdb=" CA ILE C 46 "
pdb=" N ILE C 46 "
pdb=" C ILE C 46 "
pdb=" CB ILE C 46 "
both_signs ideal model delta sigma weight residual
False 2.43 2.66 -0.22 2.00e-01 2.50e+01 1.24e+00
chirality pdb=" CA MET D 459 "
pdb=" N MET D 459 "
pdb=" C MET D 459 "
pdb=" CB MET D 459 "
both_signs ideal model delta sigma weight residual
False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.14e+00
... (remaining 2702 not shown)
Planarity restraints: 2931
Sorted by residual:
delta sigma weight rms_deltas residual
plane pdb=" CB TYR M 110 " -0.064 2.00e-02 2.50e+03 3.62e-02 2.62e+01
pdb=" CG TYR M 110 " 0.024 2.00e-02 2.50e+03
pdb=" CD1 TYR M 110 " 0.027 2.00e-02 2.50e+03
pdb=" CD2 TYR M 110 " 0.019 2.00e-02 2.50e+03
pdb=" CE1 TYR M 110 " 0.017 2.00e-02 2.50e+03
pdb=" CE2 TYR M 110 " 0.025 2.00e-02 2.50e+03
pdb=" CZ TYR M 110 " 0.012 2.00e-02 2.50e+03
pdb=" OH TYR M 110 " -0.060 2.00e-02 2.50e+03
delta sigma weight rms_deltas residual
plane pdb=" CB TRP B 639 " -0.045 2.00e-02 2.50e+03 2.41e-02 1.46e+01
pdb=" CG TRP B 639 " 0.001 2.00e-02 2.50e+03
pdb=" CD1 TRP B 639 " 0.018 2.00e-02 2.50e+03
pdb=" CD2 TRP B 639 " 0.021 2.00e-02 2.50e+03
pdb=" NE1 TRP B 639 " 0.012 2.00e-02 2.50e+03
pdb=" CE2 TRP B 639 " 0.003 2.00e-02 2.50e+03
pdb=" CE3 TRP B 639 " 0.036 2.00e-02 2.50e+03
pdb=" CZ2 TRP B 639 " -0.027 2.00e-02 2.50e+03
pdb=" CZ3 TRP B 639 " 0.010 2.00e-02 2.50e+03
pdb=" CH2 TRP B 639 " -0.028 2.00e-02 2.50e+03
delta sigma weight rms_deltas residual
plane pdb=" CB TRP M 341 " 0.040 2.00e-02 2.50e+03 2.05e-02 1.05e+01
pdb=" CG TRP M 341 " -0.007 2.00e-02 2.50e+03
pdb=" CD1 TRP M 341 " -0.012 2.00e-02 2.50e+03
pdb=" CD2 TRP M 341 " -0.020 2.00e-02 2.50e+03
pdb=" NE1 TRP M 341 " -0.006 2.00e-02 2.50e+03
pdb=" CE2 TRP M 341 " -0.005 2.00e-02 2.50e+03
pdb=" CE3 TRP M 341 " -0.028 2.00e-02 2.50e+03
pdb=" CZ2 TRP M 341 " 0.019 2.00e-02 2.50e+03
pdb=" CZ3 TRP M 341 " -0.008 2.00e-02 2.50e+03
pdb=" CH2 TRP M 341 " 0.027 2.00e-02 2.50e+03
... (remaining 2928 not shown)
Histogram of nonbonded interaction distances:
1.94 - 2.53: 58
2.53 - 3.12: 15004
3.12 - 3.72: 26819
3.72 - 4.31: 40425
4.31 - 4.90: 62295
Nonbonded interactions: 144601
Sorted by model distance:
nonbonded pdb="MG MG C 201 "
pdb=" O2G GTP C 202 "
model vdw
1.940 2.170
nonbonded pdb="MG MG A 201 "
pdb=" O2G GTP A 202 "
model vdw
1.940 2.170
nonbonded pdb=" OG1 THR C 48 "
pdb="MG MG C 201 "
model vdw
1.960 2.170
nonbonded pdb=" OG1 THR C 31 "
pdb="MG MG C 201 "
model vdw
2.055 2.170
nonbonded pdb=" OG1 THR A 31 "
pdb="MG MG A 201 "
model vdw
2.077 2.170
... (remaining 144596 not shown)
NOTE: a complete listing of the restraints can be obtained by requesting
output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
reference = chain 'A'
selection = (chain 'C' and (resid 17 through 181 or resid 201 through 202))
}
Set up NCS constraints
No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
Set random seed: 0.000
Set model cs if undefined: 0.000
Decide on map wrapping: 0.000
Normalize map: mean=0, sd=1: 5.230
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: 0.020
Extract box with map and model: 0.660
Check model and map are aligned: 0.110
Set scattering table: 0.140
Process input model: 37.930
Find NCS groups from input model: 0.320
Set up NCS constraints: 0.080
Set refine NCS operators: 0.000
Adjust number of macro_cycles: 0.000
Reset NCS operators: 0.000
Extract rigid body selections: 0.000
Check and reset occupancies: 0.010
Load rotamer database and sin/cos tables:2.870
Set ADP refinement strategy: 0.000
Make a string to write initial .geo file:0.000
Internal consistency checks: 0.000
Total: 47.370
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6455
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 : 0.013 0.055 17177 Z= 0.831
Angle : 1.359 9.905 23253 Z= 0.959
Chirality : 0.067 0.296 2705
Planarity : 0.006 0.037 2931
Dihedral : 12.252 179.004 6480
Min Nonbonded Distance : 1.940
Molprobity Statistics.
All-atom Clashscore : 5.09
Ramachandran Plot:
Outliers : 0.19 %
Allowed : 2.10 %
Favored : 97.71 %
Rotamer:
Outliers : 0.11 %
Allowed : 0.32 %
Favored : 99.57 %
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: 0.47 (0.18), residues: 2098
helix: 0.06 (0.14), residues: 1111
sheet: -0.01 (0.33), residues: 240
loop : 1.23 (0.26), residues: 747
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.045 0.006 TRP B 639
HIS 0.010 0.002 HIS M 3
PHE 0.024 0.004 PHE B 80
TYR 0.064 0.006 TYR M 110
ARG 0.008 0.001 ARG B 227
*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
4196 Ramachandran restraints generated.
2098 Oldfield, 0 Emsley, 2098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
4196 Ramachandran restraints generated.
2098 Oldfield, 0 Emsley, 2098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
636 residues out of total 1879 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 2
poor density : 634
time to evaluate : 1.698
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: A 38 LYS cc_start: 0.8348 (tttt) cc_final: 0.8023 (mttt)
REVERT: A 41 GLU cc_start: 0.7422 (mm-30) cc_final: 0.7079 (mm-30)
REVERT: A 84 ASN cc_start: 0.6426 (m-40) cc_final: 0.6219 (m-40)
REVERT: C 22 MET cc_start: 0.7979 (ttp) cc_final: 0.6970 (tmm)
REVERT: C 86 GLN cc_start: 0.7139 (mt0) cc_final: 0.6116 (mt0)
REVERT: C 110 MET cc_start: 0.8134 (mtm) cc_final: 0.7849 (ttm)
REVERT: C 143 LEU cc_start: 0.7670 (mt) cc_final: 0.7421 (mm)
REVERT: C 173 LEU cc_start: 0.8091 (mt) cc_final: 0.7830 (mt)
REVERT: D 1 MET cc_start: 0.4789 (ttp) cc_final: 0.4551 (ttp)
REVERT: D 66 GLN cc_start: 0.7264 (tp40) cc_final: 0.6993 (tp40)
REVERT: D 67 MET cc_start: 0.7768 (ttp) cc_final: 0.6508 (tmm)
REVERT: D 110 MET cc_start: 0.6335 (mmm) cc_final: 0.5945 (mmm)
REVERT: D 117 ARG cc_start: 0.8110 (mtp-110) cc_final: 0.7901 (ttm-80)
REVERT: D 118 LYS cc_start: 0.8707 (tttt) cc_final: 0.8360 (tptm)
REVERT: D 126 TYR cc_start: 0.7925 (m-80) cc_final: 0.7664 (m-80)
REVERT: D 128 THR cc_start: 0.7586 (m) cc_final: 0.7132 (p)
REVERT: D 146 ASP cc_start: 0.7939 (m-30) cc_final: 0.7674 (p0)
REVERT: D 155 MET cc_start: 0.7937 (mtm) cc_final: 0.7662 (mtm)
REVERT: D 157 HIS cc_start: 0.7635 (t-90) cc_final: 0.7099 (t-90)
REVERT: D 169 ILE cc_start: 0.6505 (tt) cc_final: 0.6021 (pt)
REVERT: D 189 LYS cc_start: 0.7575 (mtmt) cc_final: 0.7335 (mttt)
REVERT: D 200 GLN cc_start: 0.6976 (tt0) cc_final: 0.6684 (mt0)
REVERT: D 201 SER cc_start: 0.8136 (m) cc_final: 0.7857 (p)
REVERT: D 221 LEU cc_start: 0.7865 (mp) cc_final: 0.6488 (tp)
REVERT: D 223 PRO cc_start: 0.7494 (Cg_exo) cc_final: 0.6820 (Cg_endo)
REVERT: D 225 PHE cc_start: 0.6101 (m-80) cc_final: 0.5398 (m-80)
REVERT: D 239 ILE cc_start: 0.8446 (mt) cc_final: 0.8198 (mt)
REVERT: D 240 LYS cc_start: 0.8419 (mmtt) cc_final: 0.7895 (mmtp)
REVERT: D 265 ASN cc_start: 0.8207 (m-40) cc_final: 0.7858 (m-40)
REVERT: D 268 HIS cc_start: 0.8800 (m-70) cc_final: 0.8598 (m-70)
REVERT: D 275 LEU cc_start: 0.8767 (tp) cc_final: 0.8518 (tp)
REVERT: D 302 GLN cc_start: 0.8764 (tt0) cc_final: 0.8489 (tt0)
REVERT: D 307 LYS cc_start: 0.8019 (mmtt) cc_final: 0.7726 (mmtt)
REVERT: D 314 ASP cc_start: 0.5087 (t0) cc_final: 0.4663 (t0)
REVERT: D 327 MET cc_start: 0.7803 (tpp) cc_final: 0.7326 (tpp)
REVERT: D 339 GLN cc_start: 0.7928 (pt0) cc_final: 0.7395 (pp30)
REVERT: D 354 GLU cc_start: 0.8393 (pm20) cc_final: 0.7688 (pm20)
REVERT: D 362 ASP cc_start: 0.8723 (m-30) cc_final: 0.8051 (m-30)
REVERT: D 367 MET cc_start: 0.7187 (mtm) cc_final: 0.6758 (mtm)
REVERT: D 374 MET cc_start: 0.8060 (mtt) cc_final: 0.6912 (mtt)
REVERT: D 378 LYS cc_start: 0.8780 (mttt) cc_final: 0.8407 (mttt)
REVERT: D 380 LEU cc_start: 0.8172 (mt) cc_final: 0.7853 (mt)
REVERT: D 393 ARG cc_start: 0.7926 (mtt180) cc_final: 0.7521 (ptp-110)
REVERT: D 400 ILE cc_start: 0.8994 (mt) cc_final: 0.8716 (mm)
REVERT: D 403 ILE cc_start: 0.8276 (mt) cc_final: 0.8066 (mt)
REVERT: D 406 GLN cc_start: 0.7856 (pt0) cc_final: 0.7508 (pt0)
REVERT: D 419 ILE cc_start: 0.8670 (mt) cc_final: 0.8398 (pt)
REVERT: D 429 GLU cc_start: 0.8457 (tt0) cc_final: 0.7877 (tm-30)
REVERT: D 433 HIS cc_start: 0.7438 (m90) cc_final: 0.7228 (m90)
REVERT: D 440 GLN cc_start: 0.7468 (mm-40) cc_final: 0.6912 (tp40)
REVERT: D 488 ILE cc_start: 0.8029 (mm) cc_final: 0.7739 (mt)
REVERT: D 530 TYR cc_start: 0.7783 (m-80) cc_final: 0.7454 (m-80)
REVERT: D 534 LEU cc_start: 0.7974 (mt) cc_final: 0.7660 (tp)
REVERT: D 559 GLN cc_start: 0.7116 (tt0) cc_final: 0.6863 (tt0)
REVERT: D 573 SER cc_start: 0.8466 (m) cc_final: 0.8210 (p)
REVERT: M 6 PHE cc_start: 0.7505 (m-80) cc_final: 0.7039 (m-80)
REVERT: M 15 PHE cc_start: 0.6110 (m-80) cc_final: 0.5550 (m-80)
REVERT: M 16 LEU cc_start: 0.7210 (tp) cc_final: 0.6994 (tp)
REVERT: M 62 ASP cc_start: 0.7911 (m-30) cc_final: 0.7047 (m-30)
REVERT: M 67 VAL cc_start: 0.7528 (t) cc_final: 0.7180 (m)
REVERT: M 111 GLU cc_start: 0.8136 (tp30) cc_final: 0.7901 (tp30)
REVERT: M 156 THR cc_start: 0.8102 (m) cc_final: 0.7629 (p)
REVERT: M 157 LEU cc_start: 0.8116 (tp) cc_final: 0.7290 (pt)
REVERT: M 196 SER cc_start: 0.6927 (m) cc_final: 0.6581 (p)
REVERT: M 201 GLU cc_start: 0.7855 (pt0) cc_final: 0.7565 (pt0)
REVERT: M 203 GLN cc_start: 0.7447 (tp40) cc_final: 0.6951 (tm-30)
REVERT: M 210 ILE cc_start: 0.6957 (mm) cc_final: 0.6551 (mt)
REVERT: M 227 LEU cc_start: 0.7251 (mt) cc_final: 0.6905 (mt)
REVERT: M 228 LEU cc_start: 0.8309 (mt) cc_final: 0.8062 (mt)
REVERT: M 229 ASP cc_start: 0.6953 (t0) cc_final: 0.6670 (t0)
REVERT: M 250 PHE cc_start: 0.7030 (p90) cc_final: 0.6411 (p90)
REVERT: M 298 LYS cc_start: 0.7625 (tttt) cc_final: 0.7393 (ttmm)
REVERT: M 300 ASN cc_start: 0.6967 (p0) cc_final: 0.6692 (p0)
REVERT: M 303 LYS cc_start: 0.7003 (mmtt) cc_final: 0.6555 (mmmt)
REVERT: M 332 PHE cc_start: 0.5418 (t80) cc_final: 0.4545 (t80)
REVERT: M 333 ASP cc_start: 0.5346 (t0) cc_final: 0.5073 (t0)
REVERT: M 345 LYS cc_start: 0.6417 (pttt) cc_final: 0.6007 (pttp)
REVERT: M 359 ASN cc_start: 0.6923 (m-40) cc_final: 0.6596 (m-40)
REVERT: M 380 GLN cc_start: 0.7261 (mt0) cc_final: 0.6764 (mt0)
REVERT: M 397 GLU cc_start: 0.6587 (mm-30) cc_final: 0.6316 (mp0)
REVERT: M 409 THR cc_start: 0.6869 (m) cc_final: 0.6580 (p)
REVERT: M 410 LYS cc_start: 0.7576 (mttt) cc_final: 0.7301 (mttt)
REVERT: S 6 LEU cc_start: 0.7763 (mt) cc_final: 0.7538 (mt)
REVERT: S 7 ILE cc_start: 0.7528 (mt) cc_final: 0.7278 (mt)
REVERT: S 8 PHE cc_start: 0.7140 (p90) cc_final: 0.6886 (p90)
REVERT: S 17 SER cc_start: 0.7778 (t) cc_final: 0.7066 (p)
REVERT: S 18 LYS cc_start: 0.7545 (tttp) cc_final: 0.6915 (tttp)
REVERT: S 77 VAL cc_start: 0.6796 (m) cc_final: 0.6531 (p)
REVERT: S 117 HIS cc_start: 0.8814 (m-70) cc_final: 0.8413 (m-70)
REVERT: S 122 GLU cc_start: 0.7832 (mm-30) cc_final: 0.7625 (mm-30)
REVERT: S 123 MET cc_start: 0.8072 (tpt) cc_final: 0.7607 (tpt)
REVERT: S 125 MET cc_start: 0.8432 (ttt) cc_final: 0.7919 (ttm)
REVERT: S 128 MET cc_start: 0.7028 (mtp) cc_final: 0.6560 (mtp)
REVERT: B 41 LEU cc_start: 0.7736 (tp) cc_final: 0.7215 (pp)
REVERT: B 45 GLU cc_start: 0.7646 (mm-30) cc_final: 0.7242 (mm-30)
REVERT: B 63 MET cc_start: 0.6337 (mmm) cc_final: 0.5671 (mmm)
REVERT: B 90 LYS cc_start: 0.7998 (mmtt) cc_final: 0.7649 (mtmm)
REVERT: B 96 LYS cc_start: 0.7769 (mmmt) cc_final: 0.7413 (tttp)
REVERT: B 97 LEU cc_start: 0.7433 (mt) cc_final: 0.7086 (mt)
REVERT: B 151 MET cc_start: 0.7715 (mtm) cc_final: 0.7420 (mtt)
REVERT: B 152 MET cc_start: 0.6872 (tmm) cc_final: 0.6620 (tmm)
REVERT: B 169 ASN cc_start: 0.8251 (m-40) cc_final: 0.7976 (t0)
REVERT: B 187 MET cc_start: 0.8459 (mtp) cc_final: 0.8174 (mtp)
REVERT: B 241 GLN cc_start: 0.7360 (mt0) cc_final: 0.6994 (mt0)
REVERT: B 255 GLN cc_start: 0.8228 (mm-40) cc_final: 0.7397 (mm-40)
REVERT: B 307 LEU cc_start: 0.8553 (mt) cc_final: 0.8181 (tp)
REVERT: B 335 ILE cc_start: 0.8368 (pt) cc_final: 0.7914 (pt)
REVERT: B 342 LEU cc_start: 0.8433 (mt) cc_final: 0.8209 (mm)
REVERT: B 346 ASN cc_start: 0.6218 (t0) cc_final: 0.5928 (t0)
REVERT: B 372 LEU cc_start: 0.7693 (tp) cc_final: 0.7462 (tp)
REVERT: B 389 LYS cc_start: 0.8018 (mttt) cc_final: 0.7745 (mmtp)
REVERT: B 390 LEU cc_start: 0.8116 (tp) cc_final: 0.7868 (tt)
REVERT: B 391 GLU cc_start: 0.7827 (tp30) cc_final: 0.7413 (tp30)
REVERT: B 440 ASP cc_start: 0.7783 (m-30) cc_final: 0.7476 (p0)
REVERT: B 442 CYS cc_start: 0.8001 (m) cc_final: 0.7726 (m)
REVERT: B 447 VAL cc_start: 0.8000 (t) cc_final: 0.7756 (t)
REVERT: B 468 LEU cc_start: 0.8052 (mt) cc_final: 0.7714 (tt)
REVERT: B 472 GLN cc_start: 0.7694 (tp40) cc_final: 0.7363 (tp40)
REVERT: B 481 LYS cc_start: 0.8837 (mttt) cc_final: 0.8363 (mttp)
REVERT: B 483 MET cc_start: 0.8410 (mmt) cc_final: 0.8024 (mmm)
REVERT: B 486 LEU cc_start: 0.7984 (mt) cc_final: 0.7643 (mt)
REVERT: B 521 MET cc_start: 0.6627 (mmp) cc_final: 0.6231 (mmm)
REVERT: B 539 LEU cc_start: 0.8320 (tp) cc_final: 0.8066 (tp)
REVERT: B 569 ASP cc_start: 0.7608 (t70) cc_final: 0.7404 (t70)
REVERT: B 577 ILE cc_start: 0.8190 (mt) cc_final: 0.7894 (tp)
REVERT: B 578 ARG cc_start: 0.7952 (ttp80) cc_final: 0.7652 (ttp80)
outliers start: 2
outliers final: 2
residues processed: 635
average time/residue: 0.3276
time to fit residues: 299.9206
Evaluate side-chains
546 residues out of total 1879 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 2
poor density : 544
time to evaluate : 1.886
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 208
random chunks:
chunk 175 optimal weight: 0.5980
chunk 157 optimal weight: 0.7980
chunk 87 optimal weight: 0.8980
chunk 53 optimal weight: 2.9990
chunk 106 optimal weight: 1.9990
chunk 84 optimal weight: 0.6980
chunk 163 optimal weight: 0.5980
chunk 63 optimal weight: 4.9990
chunk 99 optimal weight: 0.6980
chunk 121 optimal weight: 0.6980
chunk 188 optimal weight: 0.8980
overall best weight: 0.6580
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** C 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 205 ASN
M 177 ASN
M 278 HIS
M 322 ASN
M 359 ASN
M 374 ASN
** B 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 303 ASN
Total number of N/Q/H flips: 7
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3982 r_free = 0.3982 target = 0.148131 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.128395 restraints weight = 36286.354|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.132320 restraints weight = 21889.974|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.135030 restraints weight = 14338.727|
|-----------------------------------------------------------------------------|
r_work (final): 0.3784
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6651
moved from start: 0.2327
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.004 0.046 17177 Z= 0.251
Angle : 0.649 12.298 23253 Z= 0.352
Chirality : 0.045 0.166 2705
Planarity : 0.004 0.036 2931
Dihedral : 10.522 172.018 2299
Min Nonbonded Distance : 1.932
Molprobity Statistics.
All-atom Clashscore : 8.73
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 1.33 %
Favored : 98.67 %
Rotamer:
Outliers : 0.00 %
Allowed : 1.86 %
Favored : 98.14 %
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: 1.34 (0.19), residues: 2098
helix: 1.01 (0.15), residues: 1135
sheet: -0.12 (0.33), residues: 235
loop : 1.41 (0.26), residues: 728
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.021 0.002 TRP D 74
HIS 0.022 0.002 HIS B 223
PHE 0.027 0.002 PHE D 245
TYR 0.028 0.002 TYR M 180
ARG 0.014 0.001 ARG B 649
*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
4196 Ramachandran restraints generated.
2098 Oldfield, 0 Emsley, 2098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
4196 Ramachandran restraints generated.
2098 Oldfield, 0 Emsley, 2098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
587 residues out of total 1879 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 0
poor density : 587
time to evaluate : 1.734
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: A 38 LYS cc_start: 0.8205 (tttt) cc_final: 0.7812 (tttt)
REVERT: A 61 ILE cc_start: 0.8422 (mm) cc_final: 0.8185 (mm)
REVERT: A 84 ASN cc_start: 0.6971 (m-40) cc_final: 0.6402 (m-40)
REVERT: C 81 TYR cc_start: 0.7866 (m-80) cc_final: 0.7565 (m-80)
REVERT: C 86 GLN cc_start: 0.7371 (mt0) cc_final: 0.6715 (mt0)
REVERT: C 110 MET cc_start: 0.7957 (mtm) cc_final: 0.7705 (mtp)
REVERT: C 120 VAL cc_start: 0.7791 (t) cc_final: 0.7527 (t)
REVERT: C 138 GLU cc_start: 0.7325 (tt0) cc_final: 0.6553 (tt0)
REVERT: C 173 LEU cc_start: 0.7939 (mt) cc_final: 0.7715 (mt)
REVERT: C 176 GLN cc_start: 0.6808 (mm-40) cc_final: 0.6423 (mm-40)
REVERT: D 1 MET cc_start: 0.4095 (ttp) cc_final: 0.3801 (ttp)
REVERT: D 59 VAL cc_start: 0.8091 (t) cc_final: 0.7862 (t)
REVERT: D 66 GLN cc_start: 0.7691 (tp40) cc_final: 0.7485 (tp40)
REVERT: D 67 MET cc_start: 0.7560 (ttp) cc_final: 0.6597 (tmm)
REVERT: D 74 TRP cc_start: 0.8413 (p-90) cc_final: 0.8145 (p-90)
REVERT: D 120 LEU cc_start: 0.7597 (mt) cc_final: 0.7343 (mt)
REVERT: D 126 TYR cc_start: 0.8222 (m-80) cc_final: 0.7922 (m-80)
REVERT: D 128 THR cc_start: 0.7548 (m) cc_final: 0.7190 (p)
REVERT: D 132 LEU cc_start: 0.7773 (mt) cc_final: 0.7564 (mt)
REVERT: D 151 ILE cc_start: 0.7425 (mt) cc_final: 0.7096 (tp)
REVERT: D 155 MET cc_start: 0.8046 (mtm) cc_final: 0.7741 (mtm)
REVERT: D 157 HIS cc_start: 0.8220 (t-90) cc_final: 0.7952 (t-90)
REVERT: D 177 TYR cc_start: 0.7453 (t80) cc_final: 0.6780 (t80)
REVERT: D 179 GLU cc_start: 0.8319 (mp0) cc_final: 0.6927 (mp0)
REVERT: D 201 SER cc_start: 0.7818 (m) cc_final: 0.7441 (p)
REVERT: D 221 LEU cc_start: 0.8050 (mp) cc_final: 0.6999 (mp)
REVERT: D 240 LYS cc_start: 0.8321 (mmtt) cc_final: 0.8005 (mmtt)
REVERT: D 252 GLU cc_start: 0.6656 (tp30) cc_final: 0.6419 (tp30)
REVERT: D 257 LYS cc_start: 0.8143 (tttt) cc_final: 0.7644 (tttm)
REVERT: D 273 MET cc_start: 0.8083 (pmm) cc_final: 0.7809 (pmm)
REVERT: D 302 GLN cc_start: 0.8753 (tt0) cc_final: 0.8427 (tt0)
REVERT: D 307 LYS cc_start: 0.8194 (mmtt) cc_final: 0.7568 (mmtt)
REVERT: D 309 ARG cc_start: 0.7921 (ttp-110) cc_final: 0.7164 (ttp-110)
REVERT: D 324 LEU cc_start: 0.8480 (mt) cc_final: 0.8095 (mt)
REVERT: D 327 MET cc_start: 0.7247 (tpp) cc_final: 0.6472 (tpp)
REVERT: D 329 LYS cc_start: 0.9043 (mttt) cc_final: 0.8753 (mttt)
REVERT: D 339 GLN cc_start: 0.8215 (pt0) cc_final: 0.7624 (pm20)
REVERT: D 362 ASP cc_start: 0.8498 (m-30) cc_final: 0.8297 (m-30)
REVERT: D 367 MET cc_start: 0.6984 (mtm) cc_final: 0.6437 (mtm)
REVERT: D 374 MET cc_start: 0.7434 (mtt) cc_final: 0.5842 (mtt)
REVERT: D 376 ILE cc_start: 0.8197 (mt) cc_final: 0.7861 (mt)
REVERT: D 378 LYS cc_start: 0.8819 (mttt) cc_final: 0.8251 (mtmm)
REVERT: D 393 ARG cc_start: 0.7758 (mtt180) cc_final: 0.7555 (ttm-80)
REVERT: D 394 ASP cc_start: 0.8498 (m-30) cc_final: 0.7879 (m-30)
REVERT: D 396 LEU cc_start: 0.8613 (mt) cc_final: 0.8258 (mt)
REVERT: D 398 THR cc_start: 0.8098 (p) cc_final: 0.7658 (t)
REVERT: D 400 ILE cc_start: 0.8897 (mt) cc_final: 0.8585 (mt)
REVERT: D 403 ILE cc_start: 0.8212 (mt) cc_final: 0.7942 (mt)
REVERT: D 422 LEU cc_start: 0.9096 (tp) cc_final: 0.8831 (tp)
REVERT: D 488 ILE cc_start: 0.7565 (mm) cc_final: 0.7296 (mm)
REVERT: D 514 LEU cc_start: 0.6954 (mt) cc_final: 0.6655 (mt)
REVERT: D 534 LEU cc_start: 0.8239 (mt) cc_final: 0.7633 (tp)
REVERT: D 536 GLN cc_start: 0.8143 (tm-30) cc_final: 0.7902 (tm-30)
REVERT: D 559 GLN cc_start: 0.7826 (tt0) cc_final: 0.7610 (tt0)
REVERT: D 571 ARG cc_start: 0.8496 (mtt-85) cc_final: 0.8095 (mtt-85)
REVERT: D 573 SER cc_start: 0.8134 (m) cc_final: 0.7816 (p)
REVERT: M 25 SER cc_start: 0.7848 (t) cc_final: 0.7528 (p)
REVERT: M 62 ASP cc_start: 0.8290 (m-30) cc_final: 0.7676 (m-30)
REVERT: M 67 VAL cc_start: 0.7957 (t) cc_final: 0.7621 (m)
REVERT: M 111 GLU cc_start: 0.8192 (tp30) cc_final: 0.7651 (tp30)
REVERT: M 156 THR cc_start: 0.8069 (m) cc_final: 0.7861 (p)
REVERT: M 157 LEU cc_start: 0.8388 (tp) cc_final: 0.7578 (pt)
REVERT: M 177 ASN cc_start: 0.6769 (m-40) cc_final: 0.6087 (m-40)
REVERT: M 196 SER cc_start: 0.6741 (m) cc_final: 0.6356 (p)
REVERT: M 201 GLU cc_start: 0.8056 (pt0) cc_final: 0.7224 (pm20)
REVERT: M 210 ILE cc_start: 0.7736 (mm) cc_final: 0.7307 (mp)
REVERT: M 212 LEU cc_start: 0.7475 (mt) cc_final: 0.6897 (mt)
REVERT: M 239 PHE cc_start: 0.8028 (t80) cc_final: 0.7609 (t80)
REVERT: M 256 ASN cc_start: 0.7874 (t0) cc_final: 0.7530 (t0)
REVERT: M 263 ARG cc_start: 0.6739 (mtp180) cc_final: 0.6111 (mtp180)
REVERT: M 303 LYS cc_start: 0.8203 (mmtt) cc_final: 0.7343 (mmtt)
REVERT: M 316 LYS cc_start: 0.7913 (mmtm) cc_final: 0.7612 (mmtm)
REVERT: M 329 SER cc_start: 0.7414 (t) cc_final: 0.6986 (p)
REVERT: M 352 PRO cc_start: 0.8351 (Cg_endo) cc_final: 0.8008 (Cg_exo)
REVERT: M 376 GLN cc_start: 0.5999 (mm-40) cc_final: 0.5689 (mp10)
REVERT: M 380 GLN cc_start: 0.7600 (mt0) cc_final: 0.7347 (mt0)
REVERT: M 399 TYR cc_start: 0.7868 (p90) cc_final: 0.6475 (p90)
REVERT: M 409 THR cc_start: 0.7908 (m) cc_final: 0.7521 (p)
REVERT: M 410 LYS cc_start: 0.8159 (mttt) cc_final: 0.7829 (mttt)
REVERT: S 7 ILE cc_start: 0.8290 (mt) cc_final: 0.8077 (mt)
REVERT: S 8 PHE cc_start: 0.7152 (p90) cc_final: 0.6933 (p90)
REVERT: S 17 SER cc_start: 0.7812 (t) cc_final: 0.7238 (p)
REVERT: S 18 LYS cc_start: 0.8303 (tttp) cc_final: 0.7579 (tttp)
REVERT: S 29 GLN cc_start: 0.8475 (mt0) cc_final: 0.8171 (mm-40)
REVERT: S 77 VAL cc_start: 0.7359 (m) cc_final: 0.7064 (p)
REVERT: S 82 SER cc_start: 0.6967 (t) cc_final: 0.6532 (t)
REVERT: S 89 LEU cc_start: 0.7606 (mt) cc_final: 0.7083 (mt)
REVERT: S 116 VAL cc_start: 0.7769 (t) cc_final: 0.7466 (t)
REVERT: S 117 HIS cc_start: 0.8365 (m-70) cc_final: 0.7978 (m-70)
REVERT: S 123 MET cc_start: 0.7320 (tpt) cc_final: 0.6771 (tpt)
REVERT: S 125 MET cc_start: 0.8353 (ttt) cc_final: 0.7896 (ttm)
REVERT: S 128 MET cc_start: 0.7549 (mtp) cc_final: 0.6699 (mtp)
REVERT: B 41 LEU cc_start: 0.7823 (tp) cc_final: 0.7487 (pp)
REVERT: B 45 GLU cc_start: 0.7462 (mm-30) cc_final: 0.7144 (mm-30)
REVERT: B 63 MET cc_start: 0.6675 (mmm) cc_final: 0.5782 (mmm)
REVERT: B 69 MET cc_start: 0.7543 (mtm) cc_final: 0.7251 (mtm)
REVERT: B 75 ASN cc_start: 0.8192 (m110) cc_final: 0.7477 (m-40)
REVERT: B 78 GLU cc_start: 0.7700 (pm20) cc_final: 0.7481 (pm20)
REVERT: B 97 LEU cc_start: 0.7575 (mt) cc_final: 0.7186 (mt)
REVERT: B 98 VAL cc_start: 0.8062 (t) cc_final: 0.7844 (p)
REVERT: B 151 MET cc_start: 0.7999 (mtm) cc_final: 0.7718 (mtt)
REVERT: B 152 MET cc_start: 0.6883 (tmm) cc_final: 0.6625 (tmm)
REVERT: B 153 LEU cc_start: 0.7941 (mt) cc_final: 0.7381 (mp)
REVERT: B 187 MET cc_start: 0.8185 (mtp) cc_final: 0.7468 (mtp)
REVERT: B 213 GLU cc_start: 0.7483 (mm-30) cc_final: 0.6969 (tp30)
REVERT: B 241 GLN cc_start: 0.7664 (mt0) cc_final: 0.7054 (mt0)
REVERT: B 293 MET cc_start: 0.6582 (ttm) cc_final: 0.5933 (ttm)
REVERT: B 307 LEU cc_start: 0.8741 (mt) cc_final: 0.8311 (tp)
REVERT: B 323 TYR cc_start: 0.7674 (m-10) cc_final: 0.7451 (m-80)
REVERT: B 360 MET cc_start: 0.7882 (mtp) cc_final: 0.7480 (mtm)
REVERT: B 368 PHE cc_start: 0.7510 (m-80) cc_final: 0.7241 (m-80)
REVERT: B 386 LYS cc_start: 0.8081 (mttt) cc_final: 0.7619 (mttt)
REVERT: B 389 LYS cc_start: 0.8445 (mttt) cc_final: 0.8207 (mmmm)
REVERT: B 390 LEU cc_start: 0.8162 (tp) cc_final: 0.7918 (tt)
REVERT: B 391 GLU cc_start: 0.7741 (tp30) cc_final: 0.7323 (tp30)
REVERT: B 426 GLN cc_start: 0.8485 (mt0) cc_final: 0.7829 (mm-40)
REVERT: B 437 GLU cc_start: 0.7702 (tm-30) cc_final: 0.7497 (pp20)
REVERT: B 440 ASP cc_start: 0.8024 (m-30) cc_final: 0.7746 (m-30)
REVERT: B 462 VAL cc_start: 0.8674 (t) cc_final: 0.8424 (t)
REVERT: B 465 ILE cc_start: 0.8810 (mt) cc_final: 0.8609 (mt)
REVERT: B 481 LYS cc_start: 0.8913 (mttt) cc_final: 0.8473 (tptt)
REVERT: B 486 LEU cc_start: 0.8279 (mt) cc_final: 0.7803 (mt)
REVERT: B 521 MET cc_start: 0.6789 (mmp) cc_final: 0.6321 (mmm)
REVERT: B 539 LEU cc_start: 0.8480 (tp) cc_final: 0.8248 (tp)
REVERT: B 543 LEU cc_start: 0.7535 (mt) cc_final: 0.7315 (mt)
REVERT: B 545 LEU cc_start: 0.8714 (mt) cc_final: 0.8489 (mt)
REVERT: B 577 ILE cc_start: 0.8589 (mt) cc_final: 0.7888 (tp)
REVERT: B 578 ARG cc_start: 0.7872 (ttp80) cc_final: 0.7655 (ttp80)
REVERT: B 635 GLU cc_start: 0.7781 (mt-10) cc_final: 0.7308 (mp0)
REVERT: B 645 ASP cc_start: 0.7153 (p0) cc_final: 0.6881 (p0)
REVERT: B 647 SER cc_start: 0.7403 (t) cc_final: 0.7080 (m)
outliers start: 0
outliers final: 0
residues processed: 587
average time/residue: 0.3155
time to fit residues: 269.8949
Evaluate side-chains
528 residues out of total 1879 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 0
poor density : 528
time to evaluate : 1.974
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 208
random chunks:
chunk 21 optimal weight: 1.9990
chunk 134 optimal weight: 0.9990
chunk 35 optimal weight: 8.9990
chunk 193 optimal weight: 1.9990
chunk 78 optimal weight: 0.7980
chunk 173 optimal weight: 0.5980
chunk 36 optimal weight: 0.9990
chunk 100 optimal weight: 1.9990
chunk 44 optimal weight: 0.0050
chunk 46 optimal weight: 0.7980
chunk 58 optimal weight: 0.4980
overall best weight: 0.5394
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
C 150 HIS
D 78 ASN
D 214 ASN
D 268 HIS
** M 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
M 359 ASN
M 370 ASN
M 374 ASN
** B 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 346 ASN
Total number of N/Q/H flips: 8
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3982 r_free = 0.3982 target = 0.148514 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.127889 restraints weight = 36082.740|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.131929 restraints weight = 21693.184|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.134737 restraints weight = 14253.944|
|-----------------------------------------------------------------------------|
r_work (final): 0.3766
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6669
moved from start: 0.3186
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.070 17177 Z= 0.213
Angle : 0.597 11.394 23253 Z= 0.318
Chirality : 0.044 0.157 2705
Planarity : 0.004 0.041 2931
Dihedral : 9.969 169.968 2299
Min Nonbonded Distance : 1.966
Molprobity Statistics.
All-atom Clashscore : 9.60
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 1.62 %
Favored : 98.38 %
Rotamer:
Outliers : 0.00 %
Allowed : 1.38 %
Favored : 98.62 %
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 (0.19), residues: 2098
helix: 1.16 (0.15), residues: 1151
sheet: -0.08 (0.34), residues: 227
loop : 1.14 (0.26), residues: 720
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.016 0.002 TRP D 236
HIS 0.014 0.001 HIS B 223
PHE 0.027 0.002 PHE M 15
TYR 0.017 0.002 TYR B 105
ARG 0.007 0.001 ARG C 75
*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
4196 Ramachandran restraints generated.
2098 Oldfield, 0 Emsley, 2098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
4196 Ramachandran restraints generated.
2098 Oldfield, 0 Emsley, 2098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
574 residues out of total 1879 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 0
poor density : 574
time to evaluate : 1.896
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: A 38 LYS cc_start: 0.8313 (tttt) cc_final: 0.7833 (tttt)
REVERT: A 61 ILE cc_start: 0.8544 (mm) cc_final: 0.8305 (mm)
REVERT: A 84 ASN cc_start: 0.7080 (m-40) cc_final: 0.6451 (m-40)
REVERT: C 81 TYR cc_start: 0.7886 (m-80) cc_final: 0.7627 (m-80)
REVERT: C 86 GLN cc_start: 0.7252 (mt0) cc_final: 0.6333 (mt0)
REVERT: C 110 MET cc_start: 0.8067 (mtm) cc_final: 0.7685 (mtp)
REVERT: C 138 GLU cc_start: 0.7390 (tt0) cc_final: 0.6754 (tt0)
REVERT: C 172 TRP cc_start: 0.8155 (t60) cc_final: 0.7662 (t60)
REVERT: C 173 LEU cc_start: 0.8089 (mt) cc_final: 0.7825 (mt)
REVERT: C 175 ASN cc_start: 0.7756 (m-40) cc_final: 0.7212 (t0)
REVERT: C 176 GLN cc_start: 0.7002 (mm-40) cc_final: 0.6143 (mm-40)
REVERT: D 1 MET cc_start: 0.4038 (ttp) cc_final: 0.3714 (ttp)
REVERT: D 66 GLN cc_start: 0.7693 (tp40) cc_final: 0.7492 (tp40)
REVERT: D 74 TRP cc_start: 0.8432 (p-90) cc_final: 0.8224 (p-90)
REVERT: D 126 TYR cc_start: 0.8132 (m-80) cc_final: 0.7841 (m-80)
REVERT: D 128 THR cc_start: 0.7541 (m) cc_final: 0.7186 (p)
REVERT: D 132 LEU cc_start: 0.7743 (mt) cc_final: 0.7389 (mt)
REVERT: D 155 MET cc_start: 0.8071 (mtm) cc_final: 0.7727 (mtm)
REVERT: D 157 HIS cc_start: 0.8234 (t-90) cc_final: 0.7938 (t70)
REVERT: D 189 LYS cc_start: 0.7824 (mtmt) cc_final: 0.7496 (mtmm)
REVERT: D 200 GLN cc_start: 0.7129 (mm110) cc_final: 0.6704 (mm-40)
REVERT: D 201 SER cc_start: 0.7723 (m) cc_final: 0.7499 (p)
REVERT: D 221 LEU cc_start: 0.7885 (mp) cc_final: 0.7180 (mp)
REVERT: D 257 LYS cc_start: 0.8160 (tttt) cc_final: 0.7697 (tttm)
REVERT: D 265 ASN cc_start: 0.8033 (m-40) cc_final: 0.7776 (m-40)
REVERT: D 268 HIS cc_start: 0.8649 (m90) cc_final: 0.8379 (m90)
REVERT: D 273 MET cc_start: 0.8176 (pmm) cc_final: 0.7916 (pmm)
REVERT: D 307 LYS cc_start: 0.8169 (mmtt) cc_final: 0.7801 (mmtt)
REVERT: D 320 LYS cc_start: 0.7953 (mtpt) cc_final: 0.7263 (mtpt)
REVERT: D 324 LEU cc_start: 0.8576 (mt) cc_final: 0.8264 (mt)
REVERT: D 327 MET cc_start: 0.7315 (tpp) cc_final: 0.6442 (tpp)
REVERT: D 329 LYS cc_start: 0.8961 (mttt) cc_final: 0.8671 (mttt)
REVERT: D 362 ASP cc_start: 0.8667 (m-30) cc_final: 0.8422 (m-30)
REVERT: D 367 MET cc_start: 0.6993 (mtm) cc_final: 0.6404 (mtm)
REVERT: D 372 ASN cc_start: 0.7230 (p0) cc_final: 0.6977 (p0)
REVERT: D 382 THR cc_start: 0.8548 (m) cc_final: 0.8310 (p)
REVERT: D 393 ARG cc_start: 0.7785 (mtt180) cc_final: 0.7508 (ttm-80)
REVERT: D 394 ASP cc_start: 0.8278 (m-30) cc_final: 0.7849 (m-30)
REVERT: D 396 LEU cc_start: 0.8621 (mt) cc_final: 0.8344 (mt)
REVERT: D 403 ILE cc_start: 0.8352 (mt) cc_final: 0.7839 (mm)
REVERT: D 415 PHE cc_start: 0.6658 (m-80) cc_final: 0.6399 (m-80)
REVERT: D 422 LEU cc_start: 0.9114 (tp) cc_final: 0.8699 (mt)
REVERT: D 499 PRO cc_start: 0.7878 (Cg_endo) cc_final: 0.7644 (Cg_exo)
REVERT: D 503 LEU cc_start: 0.8251 (mt) cc_final: 0.7970 (mm)
REVERT: D 514 LEU cc_start: 0.6697 (mt) cc_final: 0.6389 (mt)
REVERT: D 521 VAL cc_start: 0.8454 (p) cc_final: 0.7839 (t)
REVERT: D 530 TYR cc_start: 0.7496 (m-80) cc_final: 0.7128 (m-80)
REVERT: D 532 SER cc_start: 0.7557 (m) cc_final: 0.7077 (p)
REVERT: D 534 LEU cc_start: 0.8105 (mt) cc_final: 0.7479 (tp)
REVERT: D 553 MET cc_start: 0.7323 (mtm) cc_final: 0.6898 (mtm)
REVERT: D 571 ARG cc_start: 0.8505 (mtt-85) cc_final: 0.8210 (mtt-85)
REVERT: D 573 SER cc_start: 0.8117 (m) cc_final: 0.7794 (p)
REVERT: M 34 GLU cc_start: 0.7205 (tt0) cc_final: 0.6965 (tt0)
REVERT: M 45 VAL cc_start: 0.8577 (t) cc_final: 0.8366 (p)
REVERT: M 60 TYR cc_start: 0.7370 (t80) cc_final: 0.6995 (t80)
REVERT: M 62 ASP cc_start: 0.8273 (m-30) cc_final: 0.7972 (m-30)
REVERT: M 67 VAL cc_start: 0.7983 (t) cc_final: 0.7643 (m)
REVERT: M 111 GLU cc_start: 0.8085 (tp30) cc_final: 0.7572 (tp30)
REVERT: M 156 THR cc_start: 0.8027 (m) cc_final: 0.7797 (p)
REVERT: M 157 LEU cc_start: 0.8393 (tp) cc_final: 0.8122 (tp)
REVERT: M 177 ASN cc_start: 0.6980 (m-40) cc_final: 0.6334 (t0)
REVERT: M 178 GLU cc_start: 0.6436 (pt0) cc_final: 0.5932 (pt0)
REVERT: M 196 SER cc_start: 0.6908 (m) cc_final: 0.6537 (p)
REVERT: M 198 VAL cc_start: 0.7527 (t) cc_final: 0.7304 (t)
REVERT: M 201 GLU cc_start: 0.8083 (pt0) cc_final: 0.7427 (pm20)
REVERT: M 212 LEU cc_start: 0.7420 (mt) cc_final: 0.7118 (mm)
REVERT: M 230 ASP cc_start: 0.7364 (t0) cc_final: 0.6988 (t0)
REVERT: M 233 PHE cc_start: 0.7493 (m-80) cc_final: 0.7218 (m-80)
REVERT: M 239 PHE cc_start: 0.8025 (t80) cc_final: 0.7657 (t80)
REVERT: M 250 PHE cc_start: 0.7799 (p90) cc_final: 0.7559 (p90)
REVERT: M 256 ASN cc_start: 0.7842 (t0) cc_final: 0.7480 (t0)
REVERT: M 333 ASP cc_start: 0.7612 (t0) cc_final: 0.7322 (t0)
REVERT: M 376 GLN cc_start: 0.6030 (mm-40) cc_final: 0.5752 (mp10)
REVERT: M 380 GLN cc_start: 0.7832 (mt0) cc_final: 0.7484 (mt0)
REVERT: M 381 GLN cc_start: 0.7928 (tm-30) cc_final: 0.7538 (tm-30)
REVERT: M 394 MET cc_start: 0.7218 (tmm) cc_final: 0.6846 (tmm)
REVERT: M 397 GLU cc_start: 0.6281 (mp0) cc_final: 0.5924 (mp0)
REVERT: M 409 THR cc_start: 0.7947 (m) cc_final: 0.7414 (p)
REVERT: M 410 LYS cc_start: 0.8166 (mttt) cc_final: 0.7826 (mttt)
REVERT: S 8 PHE cc_start: 0.7129 (p90) cc_final: 0.6867 (p90)
REVERT: S 17 SER cc_start: 0.7872 (t) cc_final: 0.7464 (p)
REVERT: S 18 LYS cc_start: 0.8199 (tttp) cc_final: 0.7406 (tttp)
REVERT: S 29 GLN cc_start: 0.8553 (mt0) cc_final: 0.8243 (mm-40)
REVERT: S 77 VAL cc_start: 0.7435 (m) cc_final: 0.7131 (p)
REVERT: S 86 ILE cc_start: 0.8081 (mm) cc_final: 0.7807 (mm)
REVERT: S 116 VAL cc_start: 0.7714 (t) cc_final: 0.7479 (t)
REVERT: S 117 HIS cc_start: 0.8464 (m-70) cc_final: 0.8122 (m-70)
REVERT: S 123 MET cc_start: 0.7498 (tpt) cc_final: 0.6903 (tpt)
REVERT: S 125 MET cc_start: 0.8383 (ttt) cc_final: 0.7898 (ttm)
REVERT: S 128 MET cc_start: 0.7565 (mtp) cc_final: 0.6929 (mtp)
REVERT: B 41 LEU cc_start: 0.7900 (tp) cc_final: 0.7434 (pp)
REVERT: B 45 GLU cc_start: 0.7462 (mm-30) cc_final: 0.7113 (mm-30)
REVERT: B 72 LYS cc_start: 0.7955 (mmmt) cc_final: 0.7727 (mtpp)
REVERT: B 96 LYS cc_start: 0.8121 (mmtp) cc_final: 0.7183 (mmmm)
REVERT: B 152 MET cc_start: 0.6958 (tmm) cc_final: 0.6657 (tmm)
REVERT: B 153 LEU cc_start: 0.7970 (mt) cc_final: 0.7664 (mt)
REVERT: B 156 LYS cc_start: 0.8212 (mtpt) cc_final: 0.7943 (mttm)
REVERT: B 169 ASN cc_start: 0.8543 (m-40) cc_final: 0.8250 (t0)
REVERT: B 187 MET cc_start: 0.8057 (mtp) cc_final: 0.7691 (mtp)
REVERT: B 192 ILE cc_start: 0.7866 (mm) cc_final: 0.7646 (mt)
REVERT: B 199 LYS cc_start: 0.8328 (tmtt) cc_final: 0.8022 (tmtt)
REVERT: B 213 GLU cc_start: 0.7696 (mm-30) cc_final: 0.7127 (tp30)
REVERT: B 239 TRP cc_start: 0.7759 (m100) cc_final: 0.7217 (m100)
REVERT: B 241 GLN cc_start: 0.7752 (mt0) cc_final: 0.7020 (mt0)
REVERT: B 293 MET cc_start: 0.6616 (ttm) cc_final: 0.6258 (ttm)
REVERT: B 297 HIS cc_start: 0.7766 (t-90) cc_final: 0.7463 (t70)
REVERT: B 307 LEU cc_start: 0.8735 (mt) cc_final: 0.8377 (tp)
REVERT: B 322 LEU cc_start: 0.8043 (tp) cc_final: 0.7718 (tp)
REVERT: B 323 TYR cc_start: 0.7645 (m-10) cc_final: 0.7380 (m-80)
REVERT: B 346 ASN cc_start: 0.7149 (t0) cc_final: 0.6807 (t0)
REVERT: B 365 LYS cc_start: 0.7666 (mttt) cc_final: 0.7142 (mtpp)
REVERT: B 375 PHE cc_start: 0.7589 (m-80) cc_final: 0.7239 (m-80)
REVERT: B 389 LYS cc_start: 0.8495 (mttt) cc_final: 0.7861 (mtpp)
REVERT: B 390 LEU cc_start: 0.8261 (tp) cc_final: 0.7998 (tt)
REVERT: B 391 GLU cc_start: 0.7705 (tp30) cc_final: 0.7298 (tp30)
REVERT: B 414 LYS cc_start: 0.8335 (mtpp) cc_final: 0.7862 (mtpp)
REVERT: B 416 GLN cc_start: 0.7392 (pt0) cc_final: 0.6753 (pt0)
REVERT: B 418 LYS cc_start: 0.7197 (mtmm) cc_final: 0.6937 (mppt)
REVERT: B 426 GLN cc_start: 0.8553 (mt0) cc_final: 0.7953 (mm-40)
REVERT: B 433 THR cc_start: 0.8259 (t) cc_final: 0.7999 (t)
REVERT: B 440 ASP cc_start: 0.7937 (m-30) cc_final: 0.7458 (p0)
REVERT: B 462 VAL cc_start: 0.8581 (t) cc_final: 0.8379 (t)
REVERT: B 465 ILE cc_start: 0.8791 (mt) cc_final: 0.8539 (mt)
REVERT: B 479 ILE cc_start: 0.8670 (mm) cc_final: 0.8318 (mm)
REVERT: B 481 LYS cc_start: 0.8880 (mttt) cc_final: 0.8207 (mttt)
REVERT: B 483 MET cc_start: 0.8481 (mmm) cc_final: 0.7474 (mmm)
REVERT: B 486 LEU cc_start: 0.8284 (mt) cc_final: 0.7725 (mt)
REVERT: B 499 ILE cc_start: 0.8475 (mm) cc_final: 0.7867 (tp)
REVERT: B 521 MET cc_start: 0.6676 (mmp) cc_final: 0.6263 (mmm)
REVERT: B 539 LEU cc_start: 0.8492 (tp) cc_final: 0.8283 (tt)
REVERT: B 545 LEU cc_start: 0.8708 (mt) cc_final: 0.8503 (mt)
REVERT: B 556 GLN cc_start: 0.8061 (mt0) cc_final: 0.7785 (mt0)
REVERT: B 577 ILE cc_start: 0.8686 (mt) cc_final: 0.7981 (tp)
REVERT: B 578 ARG cc_start: 0.7835 (ttp80) cc_final: 0.7565 (ttp80)
REVERT: B 635 GLU cc_start: 0.7763 (mt-10) cc_final: 0.7421 (mp0)
REVERT: B 650 ASN cc_start: 0.7740 (t0) cc_final: 0.7485 (t0)
outliers start: 0
outliers final: 0
residues processed: 574
average time/residue: 0.3362
time to fit residues: 276.6633
Evaluate side-chains
524 residues out of total 1879 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 0
poor density : 524
time to evaluate : 1.783
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 208
random chunks:
chunk 37 optimal weight: 8.9990
chunk 89 optimal weight: 2.9990
chunk 28 optimal weight: 1.9990
chunk 151 optimal weight: 0.7980
chunk 180 optimal weight: 0.9980
chunk 83 optimal weight: 0.2980
chunk 205 optimal weight: 2.9990
chunk 168 optimal weight: 0.9990
chunk 207 optimal weight: 1.9990
chunk 54 optimal weight: 0.9990
chunk 201 optimal weight: 2.9990
overall best weight: 0.8184
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
D 66 GLN
D 78 ASN
** D 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 214 ASN
M 71 GLN
** M 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
M 359 ASN
M 370 ASN
** M 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
S 117 HIS
** S 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 321 GLN
B 482 HIS
Total number of N/Q/H flips: 9
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3955 r_free = 0.3955 target = 0.146262 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.125107 restraints weight = 35952.574|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.129206 restraints weight = 21709.851|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.132011 restraints weight = 14258.030|
|-----------------------------------------------------------------------------|
r_work (final): 0.3718
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6736
moved from start: 0.3993
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.004 0.048 17177 Z= 0.262
Angle : 0.630 14.478 23253 Z= 0.333
Chirality : 0.044 0.157 2705
Planarity : 0.005 0.062 2931
Dihedral : 9.539 173.829 2299
Min Nonbonded Distance : 1.908
Molprobity Statistics.
All-atom Clashscore : 9.81
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 2.38 %
Favored : 97.62 %
Rotamer:
Outliers : 0.05 %
Allowed : 1.44 %
Favored : 98.51 %
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: 1.26 (0.19), residues: 2098
helix: 1.23 (0.15), residues: 1144
sheet: -0.16 (0.36), residues: 228
loop : 0.81 (0.25), residues: 726
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.025 0.002 TRP D 417
HIS 0.007 0.001 HIS B 476
PHE 0.025 0.002 PHE D 245
TYR 0.022 0.002 TYR B 105
ARG 0.016 0.001 ARG B 649
*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
4196 Ramachandran restraints generated.
2098 Oldfield, 0 Emsley, 2098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
4196 Ramachandran restraints generated.
2098 Oldfield, 0 Emsley, 2098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
565 residues out of total 1879 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 1
poor density : 564
time to evaluate : 1.759
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: A 41 GLU cc_start: 0.5733 (mm-30) cc_final: 0.5389 (mm-30)
REVERT: A 61 ILE cc_start: 0.8585 (mm) cc_final: 0.8356 (mm)
REVERT: A 84 ASN cc_start: 0.7165 (m-40) cc_final: 0.6541 (m-40)
REVERT: C 81 TYR cc_start: 0.7800 (m-80) cc_final: 0.7504 (m-80)
REVERT: C 104 ARG cc_start: 0.8550 (ttp80) cc_final: 0.8127 (ttm-80)
REVERT: C 110 MET cc_start: 0.8078 (mtm) cc_final: 0.7747 (mtp)
REVERT: C 138 GLU cc_start: 0.7623 (tt0) cc_final: 0.6865 (tt0)
REVERT: C 149 ARG cc_start: 0.7013 (ttm-80) cc_final: 0.6403 (mtp85)
REVERT: C 173 LEU cc_start: 0.8251 (mt) cc_final: 0.7967 (mt)
REVERT: C 175 ASN cc_start: 0.7958 (m-40) cc_final: 0.7376 (t0)
REVERT: C 176 GLN cc_start: 0.6934 (mm-40) cc_final: 0.6382 (mm-40)
REVERT: D 1 MET cc_start: 0.3996 (ttp) cc_final: 0.3635 (ttp)
REVERT: D 20 ASP cc_start: 0.7147 (t0) cc_final: 0.6744 (t0)
REVERT: D 74 TRP cc_start: 0.8479 (p-90) cc_final: 0.8263 (p-90)
REVERT: D 116 ILE cc_start: 0.8409 (mm) cc_final: 0.8160 (mm)
REVERT: D 126 TYR cc_start: 0.8114 (m-80) cc_final: 0.7838 (m-80)
REVERT: D 128 THR cc_start: 0.7523 (m) cc_final: 0.7159 (p)
REVERT: D 132 LEU cc_start: 0.7823 (mt) cc_final: 0.7429 (mt)
REVERT: D 154 LEU cc_start: 0.8429 (mt) cc_final: 0.8215 (mp)
REVERT: D 155 MET cc_start: 0.7897 (mtm) cc_final: 0.7678 (mtm)
REVERT: D 157 HIS cc_start: 0.8319 (t-90) cc_final: 0.7943 (t-170)
REVERT: D 221 LEU cc_start: 0.7913 (mp) cc_final: 0.7088 (mp)
REVERT: D 236 TRP cc_start: 0.8021 (t-100) cc_final: 0.7714 (t-100)
REVERT: D 240 LYS cc_start: 0.8120 (mmtp) cc_final: 0.7734 (mttt)
REVERT: D 257 LYS cc_start: 0.8223 (tttt) cc_final: 0.7745 (tttm)
REVERT: D 273 MET cc_start: 0.8230 (pmm) cc_final: 0.8009 (pmm)
REVERT: D 305 VAL cc_start: 0.8525 (m) cc_final: 0.8252 (m)
REVERT: D 307 LYS cc_start: 0.8226 (mmtt) cc_final: 0.7821 (mmtt)
REVERT: D 320 LYS cc_start: 0.8041 (mtpt) cc_final: 0.7365 (mtpt)
REVERT: D 324 LEU cc_start: 0.8584 (mt) cc_final: 0.8298 (mt)
REVERT: D 327 MET cc_start: 0.7403 (tpp) cc_final: 0.6848 (tpp)
REVERT: D 329 LYS cc_start: 0.8945 (mttt) cc_final: 0.8717 (mttt)
REVERT: D 336 LYS cc_start: 0.8215 (ptpp) cc_final: 0.7814 (ptpp)
REVERT: D 342 LYS cc_start: 0.7874 (tmmt) cc_final: 0.7601 (tmmt)
REVERT: D 362 ASP cc_start: 0.8663 (m-30) cc_final: 0.8249 (m-30)
REVERT: D 367 MET cc_start: 0.7136 (mtm) cc_final: 0.6418 (mtm)
REVERT: D 374 MET cc_start: 0.7564 (mtt) cc_final: 0.5665 (mtt)
REVERT: D 378 LYS cc_start: 0.8910 (mttt) cc_final: 0.8430 (mttt)
REVERT: D 381 MET cc_start: 0.7884 (mtp) cc_final: 0.7675 (mtp)
REVERT: D 393 ARG cc_start: 0.7763 (mtt180) cc_final: 0.7551 (ttm-80)
REVERT: D 394 ASP cc_start: 0.8162 (m-30) cc_final: 0.7858 (m-30)
REVERT: D 396 LEU cc_start: 0.8665 (mt) cc_final: 0.8430 (mt)
REVERT: D 399 LYS cc_start: 0.8092 (mmmt) cc_final: 0.7124 (mmmt)
REVERT: D 400 ILE cc_start: 0.9051 (tt) cc_final: 0.8571 (tp)
REVERT: D 403 ILE cc_start: 0.8373 (mt) cc_final: 0.8053 (pt)
REVERT: D 406 GLN cc_start: 0.7735 (mt0) cc_final: 0.7459 (mt0)
REVERT: D 422 LEU cc_start: 0.8995 (tp) cc_final: 0.8733 (tp)
REVERT: D 479 CYS cc_start: 0.8568 (m) cc_final: 0.7983 (p)
REVERT: D 514 LEU cc_start: 0.6763 (mt) cc_final: 0.6520 (mt)
REVERT: D 521 VAL cc_start: 0.8355 (p) cc_final: 0.7952 (t)
REVERT: D 530 TYR cc_start: 0.7620 (m-80) cc_final: 0.7251 (m-80)
REVERT: D 532 SER cc_start: 0.7708 (m) cc_final: 0.7330 (p)
REVERT: D 534 LEU cc_start: 0.8229 (mt) cc_final: 0.7616 (tp)
REVERT: D 553 MET cc_start: 0.7410 (mtm) cc_final: 0.6987 (mtm)
REVERT: D 571 ARG cc_start: 0.8473 (mtt-85) cc_final: 0.8217 (mtt-85)
REVERT: M 62 ASP cc_start: 0.8336 (m-30) cc_final: 0.8098 (m-30)
REVERT: M 63 LYS cc_start: 0.8665 (mttt) cc_final: 0.8116 (mttt)
REVERT: M 67 VAL cc_start: 0.8054 (t) cc_final: 0.7695 (m)
REVERT: M 111 GLU cc_start: 0.8087 (tp30) cc_final: 0.7557 (tp30)
REVERT: M 176 ASN cc_start: 0.6601 (m-40) cc_final: 0.5708 (m-40)
REVERT: M 196 SER cc_start: 0.6604 (m) cc_final: 0.6218 (p)
REVERT: M 201 GLU cc_start: 0.8084 (pt0) cc_final: 0.7717 (pt0)
REVERT: M 212 LEU cc_start: 0.7527 (mt) cc_final: 0.7306 (mm)
REVERT: M 228 LEU cc_start: 0.8645 (mt) cc_final: 0.8400 (tp)
REVERT: M 230 ASP cc_start: 0.7445 (t0) cc_final: 0.7018 (t0)
REVERT: M 239 PHE cc_start: 0.8141 (t80) cc_final: 0.7588 (t80)
REVERT: M 250 PHE cc_start: 0.7837 (p90) cc_final: 0.6673 (p90)
REVERT: M 256 ASN cc_start: 0.7741 (t0) cc_final: 0.7357 (t0)
REVERT: M 263 ARG cc_start: 0.6923 (mtp180) cc_final: 0.6691 (mtp-110)
REVERT: M 333 ASP cc_start: 0.7967 (t0) cc_final: 0.7722 (t0)
REVERT: M 359 ASN cc_start: 0.6793 (m110) cc_final: 0.6565 (m110)
REVERT: M 376 GLN cc_start: 0.6051 (mm-40) cc_final: 0.5718 (mp10)
REVERT: M 381 GLN cc_start: 0.7773 (tm-30) cc_final: 0.7267 (tm-30)
REVERT: M 394 MET cc_start: 0.7137 (tmm) cc_final: 0.6864 (tmm)
REVERT: M 406 LYS cc_start: 0.8225 (mtpt) cc_final: 0.7957 (mtmt)
REVERT: M 409 THR cc_start: 0.7929 (m) cc_final: 0.7470 (p)
REVERT: M 410 LYS cc_start: 0.8171 (mttt) cc_final: 0.7966 (mttt)
REVERT: S 17 SER cc_start: 0.8237 (t) cc_final: 0.7942 (p)
REVERT: S 18 LYS cc_start: 0.8200 (tttp) cc_final: 0.7423 (tttp)
REVERT: S 29 GLN cc_start: 0.8574 (mt0) cc_final: 0.8258 (mm-40)
REVERT: S 77 VAL cc_start: 0.7410 (m) cc_final: 0.7094 (p)
REVERT: S 82 SER cc_start: 0.7635 (t) cc_final: 0.6917 (p)
REVERT: S 86 ILE cc_start: 0.8071 (mm) cc_final: 0.7759 (mm)
REVERT: S 89 LEU cc_start: 0.7729 (mt) cc_final: 0.6969 (mt)
REVERT: S 117 HIS cc_start: 0.8387 (m90) cc_final: 0.8118 (m90)
REVERT: S 123 MET cc_start: 0.7494 (tpt) cc_final: 0.6797 (tpt)
REVERT: S 125 MET cc_start: 0.8425 (ttt) cc_final: 0.7818 (ttm)
REVERT: S 128 MET cc_start: 0.7601 (mtp) cc_final: 0.6834 (mtp)
REVERT: B 41 LEU cc_start: 0.7980 (tp) cc_final: 0.7437 (pp)
REVERT: B 45 GLU cc_start: 0.7683 (mm-30) cc_final: 0.7272 (mm-30)
REVERT: B 63 MET cc_start: 0.6628 (mmm) cc_final: 0.5883 (mmm)
REVERT: B 75 ASN cc_start: 0.8195 (m110) cc_final: 0.7477 (m110)
REVERT: B 78 GLU cc_start: 0.8132 (pm20) cc_final: 0.7921 (pm20)
REVERT: B 96 LYS cc_start: 0.7889 (mmmt) cc_final: 0.7564 (tptt)
REVERT: B 97 LEU cc_start: 0.7837 (mt) cc_final: 0.7519 (mt)
REVERT: B 129 GLN cc_start: 0.8496 (pm20) cc_final: 0.7989 (pt0)
REVERT: B 152 MET cc_start: 0.6894 (tmm) cc_final: 0.6682 (tmm)
REVERT: B 153 LEU cc_start: 0.8107 (mt) cc_final: 0.7382 (mp)
REVERT: B 156 LYS cc_start: 0.8246 (mtpt) cc_final: 0.7717 (mtpp)
REVERT: B 169 ASN cc_start: 0.8564 (m-40) cc_final: 0.8280 (t0)
REVERT: B 187 MET cc_start: 0.8016 (mtp) cc_final: 0.7690 (mtp)
REVERT: B 192 ILE cc_start: 0.7966 (mm) cc_final: 0.7696 (mt)
REVERT: B 197 LYS cc_start: 0.8856 (mttp) cc_final: 0.8427 (mtmm)
REVERT: B 199 LYS cc_start: 0.8455 (tmtt) cc_final: 0.8085 (tmtt)
REVERT: B 213 GLU cc_start: 0.7909 (mm-30) cc_final: 0.7376 (tp30)
REVERT: B 239 TRP cc_start: 0.7686 (m100) cc_final: 0.7226 (m100)
REVERT: B 241 GLN cc_start: 0.7793 (mt0) cc_final: 0.6965 (mt0)
REVERT: B 293 MET cc_start: 0.6774 (ttm) cc_final: 0.6294 (ttm)
REVERT: B 307 LEU cc_start: 0.8584 (mt) cc_final: 0.8260 (tp)
REVERT: B 323 TYR cc_start: 0.7697 (m-10) cc_final: 0.7467 (m-80)
REVERT: B 331 GLU cc_start: 0.7694 (mm-30) cc_final: 0.7455 (mm-30)
REVERT: B 346 ASN cc_start: 0.7358 (t0) cc_final: 0.7084 (t0)
REVERT: B 365 LYS cc_start: 0.8026 (mttt) cc_final: 0.7509 (mtpp)
REVERT: B 371 TYR cc_start: 0.7438 (m-10) cc_final: 0.7123 (m-80)
REVERT: B 384 MET cc_start: 0.7811 (ptt) cc_final: 0.7603 (ptp)
REVERT: B 386 LYS cc_start: 0.8163 (mttt) cc_final: 0.7723 (mttt)
REVERT: B 389 LYS cc_start: 0.8507 (mttt) cc_final: 0.8151 (mtpp)
REVERT: B 390 LEU cc_start: 0.8131 (tp) cc_final: 0.7748 (tt)
REVERT: B 391 GLU cc_start: 0.7572 (tp30) cc_final: 0.7077 (tp30)
REVERT: B 399 GLU cc_start: 0.8045 (pm20) cc_final: 0.7365 (pp20)
REVERT: B 426 GLN cc_start: 0.8547 (mt0) cc_final: 0.7907 (mm-40)
REVERT: B 433 THR cc_start: 0.8247 (t) cc_final: 0.8035 (t)
REVERT: B 437 GLU cc_start: 0.7771 (tm-30) cc_final: 0.7504 (tp30)
REVERT: B 440 ASP cc_start: 0.7840 (m-30) cc_final: 0.7409 (p0)
REVERT: B 465 ILE cc_start: 0.8769 (mt) cc_final: 0.8448 (tp)
REVERT: B 481 LYS cc_start: 0.8914 (mttt) cc_final: 0.8329 (tptp)
REVERT: B 483 MET cc_start: 0.8573 (mmm) cc_final: 0.7794 (mmm)
REVERT: B 486 LEU cc_start: 0.8325 (mt) cc_final: 0.7750 (mt)
REVERT: B 498 SER cc_start: 0.8628 (m) cc_final: 0.8173 (p)
REVERT: B 499 ILE cc_start: 0.8446 (mm) cc_final: 0.7873 (tp)
REVERT: B 521 MET cc_start: 0.6975 (mmp) cc_final: 0.6501 (mmm)
REVERT: B 539 LEU cc_start: 0.8325 (tp) cc_final: 0.7822 (tp)
REVERT: B 543 LEU cc_start: 0.7686 (mt) cc_final: 0.7356 (mt)
REVERT: B 577 ILE cc_start: 0.8825 (mt) cc_final: 0.8115 (tp)
REVERT: B 578 ARG cc_start: 0.7816 (ttp80) cc_final: 0.7429 (ttp80)
REVERT: B 635 GLU cc_start: 0.8037 (mt-10) cc_final: 0.7481 (mp0)
outliers start: 1
outliers final: 1
residues processed: 565
average time/residue: 0.3312
time to fit residues: 267.7824
Evaluate side-chains
527 residues out of total 1879 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 1
poor density : 526
time to evaluate : 1.807
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 208
random chunks:
chunk 22 optimal weight: 3.9990
chunk 82 optimal weight: 0.9980
chunk 109 optimal weight: 1.9990
chunk 199 optimal weight: 0.9990
chunk 61 optimal weight: 0.7980
chunk 176 optimal weight: 0.0570
chunk 27 optimal weight: 0.0060
chunk 113 optimal weight: 0.0060
chunk 180 optimal weight: 0.0570
chunk 204 optimal weight: 0.8980
chunk 149 optimal weight: 0.9980
overall best weight: 0.1848
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** D 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 214 ASN
D 265 ASN
** D 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 559 GLN
M 54 HIS
** M 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
M 370 ASN
M 374 ASN
S 29 GLN
** B 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 303 ASN
Total number of N/Q/H flips: 8
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4005 r_free = 0.4005 target = 0.150008 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.128674 restraints weight = 36137.348|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.132890 restraints weight = 21518.984|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.135831 restraints weight = 14003.141|
|-----------------------------------------------------------------------------|
r_work (final): 0.3784
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6651
moved from start: 0.4260
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.002 0.037 17177 Z= 0.158
Angle : 0.546 9.393 23253 Z= 0.285
Chirality : 0.042 0.219 2705
Planarity : 0.004 0.045 2931
Dihedral : 9.042 166.484 2299
Min Nonbonded Distance : 2.037
Molprobity Statistics.
All-atom Clashscore : 9.16
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 1.81 %
Favored : 98.19 %
Rotamer:
Outliers : 0.00 %
Allowed : 1.12 %
Favored : 98.88 %
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: 1.52 (0.19), residues: 2098
helix: 1.46 (0.15), residues: 1148
sheet: -0.03 (0.36), residues: 223
loop : 0.84 (0.25), residues: 727
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.021 0.001 TRP D 417
HIS 0.014 0.001 HIS D 268
PHE 0.029 0.002 PHE B 211
TYR 0.022 0.002 TYR M 174
ARG 0.008 0.001 ARG D 432
*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
4196 Ramachandran restraints generated.
2098 Oldfield, 0 Emsley, 2098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
4196 Ramachandran restraints generated.
2098 Oldfield, 0 Emsley, 2098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
550 residues out of total 1879 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 0
poor density : 550
time to evaluate : 1.928
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: A 38 LYS cc_start: 0.8316 (tttt) cc_final: 0.7809 (tttt)
REVERT: A 41 GLU cc_start: 0.5312 (mm-30) cc_final: 0.5085 (mm-30)
REVERT: A 61 ILE cc_start: 0.8542 (mm) cc_final: 0.8328 (mm)
REVERT: A 84 ASN cc_start: 0.6916 (m-40) cc_final: 0.6370 (m-40)
REVERT: C 86 GLN cc_start: 0.6864 (mt0) cc_final: 0.6129 (mt0)
REVERT: C 110 MET cc_start: 0.8086 (mtm) cc_final: 0.7819 (mtp)
REVERT: C 149 ARG cc_start: 0.6896 (ttm-80) cc_final: 0.6454 (mtp85)
REVERT: C 173 LEU cc_start: 0.8243 (mt) cc_final: 0.8027 (mt)
REVERT: C 175 ASN cc_start: 0.7817 (m-40) cc_final: 0.7335 (t0)
REVERT: C 176 GLN cc_start: 0.6919 (mm-40) cc_final: 0.6487 (mm-40)
REVERT: C 178 ARG cc_start: 0.7167 (ttt180) cc_final: 0.6961 (ttt180)
REVERT: D 1 MET cc_start: 0.4023 (ttp) cc_final: 0.3687 (ttp)
REVERT: D 20 ASP cc_start: 0.7102 (t0) cc_final: 0.6666 (t0)
REVERT: D 67 MET cc_start: 0.7401 (ttt) cc_final: 0.7124 (ttt)
REVERT: D 91 LYS cc_start: 0.7301 (mtmt) cc_final: 0.6886 (mtmt)
REVERT: D 118 LYS cc_start: 0.8401 (ttmt) cc_final: 0.8177 (tptm)
REVERT: D 126 TYR cc_start: 0.8068 (m-80) cc_final: 0.7710 (m-80)
REVERT: D 128 THR cc_start: 0.7387 (m) cc_final: 0.6949 (p)
REVERT: D 132 LEU cc_start: 0.7761 (mt) cc_final: 0.7429 (mt)
REVERT: D 154 LEU cc_start: 0.8250 (mt) cc_final: 0.7965 (mp)
REVERT: D 157 HIS cc_start: 0.8265 (t-90) cc_final: 0.7976 (t70)
REVERT: D 176 LYS cc_start: 0.8126 (mmpt) cc_final: 0.7604 (mmtm)
REVERT: D 189 LYS cc_start: 0.7952 (mtmt) cc_final: 0.7673 (mtmt)
REVERT: D 221 LEU cc_start: 0.7835 (mp) cc_final: 0.7082 (mp)
REVERT: D 257 LYS cc_start: 0.8091 (tttt) cc_final: 0.7571 (tttm)
REVERT: D 307 LYS cc_start: 0.8174 (mmtt) cc_final: 0.7744 (mmtt)
REVERT: D 320 LYS cc_start: 0.7967 (mtpt) cc_final: 0.7246 (mtmm)
REVERT: D 324 LEU cc_start: 0.8544 (mt) cc_final: 0.8288 (mt)
REVERT: D 327 MET cc_start: 0.7215 (tpp) cc_final: 0.6515 (tpp)
REVERT: D 329 LYS cc_start: 0.8890 (mttt) cc_final: 0.8620 (mttt)
REVERT: D 336 LYS cc_start: 0.8091 (ptpp) cc_final: 0.7646 (ptpp)
REVERT: D 358 LEU cc_start: 0.8531 (mt) cc_final: 0.8303 (mt)
REVERT: D 367 MET cc_start: 0.7161 (mtm) cc_final: 0.6579 (mtm)
REVERT: D 377 VAL cc_start: 0.8770 (t) cc_final: 0.8512 (p)
REVERT: D 378 LYS cc_start: 0.8845 (mttt) cc_final: 0.8325 (mttt)
REVERT: D 393 ARG cc_start: 0.7817 (mtt180) cc_final: 0.7392 (ttm-80)
REVERT: D 394 ASP cc_start: 0.8126 (m-30) cc_final: 0.7779 (m-30)
REVERT: D 399 LYS cc_start: 0.8102 (mmmt) cc_final: 0.7743 (mmmt)
REVERT: D 400 ILE cc_start: 0.9015 (tt) cc_final: 0.8799 (tt)
REVERT: D 403 ILE cc_start: 0.8344 (mt) cc_final: 0.8099 (pt)
REVERT: D 406 GLN cc_start: 0.7672 (mt0) cc_final: 0.7330 (mt0)
REVERT: D 422 LEU cc_start: 0.8983 (tp) cc_final: 0.8720 (tp)
REVERT: D 479 CYS cc_start: 0.8569 (m) cc_final: 0.8056 (p)
REVERT: D 530 TYR cc_start: 0.7460 (m-80) cc_final: 0.7125 (m-80)
REVERT: D 534 LEU cc_start: 0.8115 (mt) cc_final: 0.7452 (tt)
REVERT: D 535 GLN cc_start: 0.7992 (pp30) cc_final: 0.7649 (pp30)
REVERT: D 547 GLN cc_start: 0.7352 (mm-40) cc_final: 0.7121 (tp40)
REVERT: D 553 MET cc_start: 0.7367 (mtm) cc_final: 0.6923 (mtm)
REVERT: D 571 ARG cc_start: 0.8462 (mtt-85) cc_final: 0.8165 (mtt-85)
REVERT: M 17 GLU cc_start: 0.7898 (tt0) cc_final: 0.7652 (tt0)
REVERT: M 63 LYS cc_start: 0.8478 (mttt) cc_final: 0.7912 (mttt)
REVERT: M 67 VAL cc_start: 0.7988 (t) cc_final: 0.7640 (m)
REVERT: M 111 GLU cc_start: 0.7957 (tp30) cc_final: 0.7368 (tp30)
REVERT: M 176 ASN cc_start: 0.6527 (m-40) cc_final: 0.5573 (m-40)
REVERT: M 196 SER cc_start: 0.6821 (m) cc_final: 0.6417 (p)
REVERT: M 198 VAL cc_start: 0.7728 (t) cc_final: 0.7464 (t)
REVERT: M 212 LEU cc_start: 0.7447 (mt) cc_final: 0.7245 (mm)
REVERT: M 228 LEU cc_start: 0.8622 (mt) cc_final: 0.8399 (mt)
REVERT: M 230 ASP cc_start: 0.7435 (t0) cc_final: 0.6963 (t0)
REVERT: M 233 PHE cc_start: 0.7731 (m-80) cc_final: 0.7249 (m-80)
REVERT: M 239 PHE cc_start: 0.7935 (t80) cc_final: 0.7568 (t80)
REVERT: M 250 PHE cc_start: 0.7786 (p90) cc_final: 0.6579 (p90)
REVERT: M 256 ASN cc_start: 0.7679 (t0) cc_final: 0.7368 (t0)
REVERT: M 332 PHE cc_start: 0.5924 (t80) cc_final: 0.5594 (t80)
REVERT: M 333 ASP cc_start: 0.7841 (t0) cc_final: 0.7362 (t0)
REVERT: M 376 GLN cc_start: 0.5874 (mm-40) cc_final: 0.5632 (mp10)
REVERT: M 380 GLN cc_start: 0.7683 (mt0) cc_final: 0.7273 (mt0)
REVERT: M 381 GLN cc_start: 0.7789 (tm-30) cc_final: 0.7323 (tm-30)
REVERT: M 394 MET cc_start: 0.7072 (tmm) cc_final: 0.6785 (tmm)
REVERT: M 406 LYS cc_start: 0.8181 (mtpt) cc_final: 0.7770 (mtmt)
REVERT: M 409 THR cc_start: 0.7933 (m) cc_final: 0.7453 (p)
REVERT: M 410 LYS cc_start: 0.8179 (mttt) cc_final: 0.7957 (mttt)
REVERT: S 17 SER cc_start: 0.8067 (t) cc_final: 0.7513 (p)
REVERT: S 18 LYS cc_start: 0.8216 (tttp) cc_final: 0.7457 (tttp)
REVERT: S 29 GLN cc_start: 0.8527 (mt0) cc_final: 0.8055 (mm-40)
REVERT: S 77 VAL cc_start: 0.7386 (m) cc_final: 0.7084 (p)
REVERT: S 82 SER cc_start: 0.7386 (t) cc_final: 0.6844 (t)
REVERT: S 86 ILE cc_start: 0.8028 (mm) cc_final: 0.7694 (mm)
REVERT: S 117 HIS cc_start: 0.8387 (m90) cc_final: 0.8118 (m90)
REVERT: S 123 MET cc_start: 0.7418 (tpt) cc_final: 0.6901 (tpt)
REVERT: S 128 MET cc_start: 0.7490 (mtp) cc_final: 0.6667 (mtp)
REVERT: B 41 LEU cc_start: 0.7930 (tp) cc_final: 0.7345 (pp)
REVERT: B 45 GLU cc_start: 0.7660 (mm-30) cc_final: 0.7213 (mm-30)
REVERT: B 50 MET cc_start: 0.7163 (mtm) cc_final: 0.6958 (mtm)
REVERT: B 75 ASN cc_start: 0.8055 (m110) cc_final: 0.7333 (m110)
REVERT: B 96 LYS cc_start: 0.7769 (mmmt) cc_final: 0.7568 (tttp)
REVERT: B 129 GLN cc_start: 0.8471 (pm20) cc_final: 0.8051 (pt0)
REVERT: B 143 ARG cc_start: 0.7555 (ptp90) cc_final: 0.7330 (ptp-170)
REVERT: B 153 LEU cc_start: 0.8055 (mt) cc_final: 0.7322 (mp)
REVERT: B 156 LYS cc_start: 0.8175 (mtpt) cc_final: 0.7917 (mttm)
REVERT: B 169 ASN cc_start: 0.8375 (m-40) cc_final: 0.8074 (t0)
REVERT: B 187 MET cc_start: 0.7875 (mtp) cc_final: 0.7649 (mtp)
REVERT: B 197 LYS cc_start: 0.8736 (mttp) cc_final: 0.8253 (mtmm)
REVERT: B 199 LYS cc_start: 0.8341 (tmtt) cc_final: 0.8091 (ttpp)
REVERT: B 213 GLU cc_start: 0.7885 (mm-30) cc_final: 0.7504 (tp30)
REVERT: B 227 ARG cc_start: 0.7932 (mtt-85) cc_final: 0.7671 (mtt-85)
REVERT: B 241 GLN cc_start: 0.7881 (mt0) cc_final: 0.7087 (mt0)
REVERT: B 297 HIS cc_start: 0.7682 (t-90) cc_final: 0.7333 (t-90)
REVERT: B 307 LEU cc_start: 0.8534 (mt) cc_final: 0.8141 (tp)
REVERT: B 323 TYR cc_start: 0.7561 (m-10) cc_final: 0.7218 (m-80)
REVERT: B 331 GLU cc_start: 0.7552 (mm-30) cc_final: 0.7280 (mm-30)
REVERT: B 360 MET cc_start: 0.7475 (ttm) cc_final: 0.7100 (mmm)
REVERT: B 365 LYS cc_start: 0.8048 (mttt) cc_final: 0.7450 (mtpp)
REVERT: B 375 PHE cc_start: 0.7696 (m-80) cc_final: 0.6869 (m-80)
REVERT: B 376 TYR cc_start: 0.8696 (m-80) cc_final: 0.8349 (m-80)
REVERT: B 384 MET cc_start: 0.7798 (ptt) cc_final: 0.7559 (ptp)
REVERT: B 386 LYS cc_start: 0.8129 (mttt) cc_final: 0.7604 (mttt)
REVERT: B 389 LYS cc_start: 0.8392 (mttt) cc_final: 0.7955 (mttt)
REVERT: B 390 LEU cc_start: 0.8088 (tp) cc_final: 0.7755 (tt)
REVERT: B 391 GLU cc_start: 0.7451 (tp30) cc_final: 0.6944 (tp30)
REVERT: B 399 GLU cc_start: 0.8042 (pm20) cc_final: 0.7460 (pp20)
REVERT: B 426 GLN cc_start: 0.8604 (mt0) cc_final: 0.7964 (mm-40)
REVERT: B 428 ILE cc_start: 0.7456 (mt) cc_final: 0.7072 (pt)
REVERT: B 433 THR cc_start: 0.7881 (t) cc_final: 0.7621 (t)
REVERT: B 437 GLU cc_start: 0.7747 (tm-30) cc_final: 0.7440 (tp30)
REVERT: B 440 ASP cc_start: 0.7850 (m-30) cc_final: 0.7261 (p0)
REVERT: B 465 ILE cc_start: 0.8667 (mt) cc_final: 0.8174 (tp)
REVERT: B 481 LYS cc_start: 0.8864 (mttt) cc_final: 0.8245 (mttt)
REVERT: B 483 MET cc_start: 0.8564 (mmm) cc_final: 0.7776 (mmm)
REVERT: B 486 LEU cc_start: 0.8221 (mt) cc_final: 0.7716 (mt)
REVERT: B 498 SER cc_start: 0.8604 (m) cc_final: 0.8176 (p)
REVERT: B 499 ILE cc_start: 0.8511 (mm) cc_final: 0.7863 (tp)
REVERT: B 521 MET cc_start: 0.6730 (mmp) cc_final: 0.6328 (mmm)
REVERT: B 539 LEU cc_start: 0.8323 (tp) cc_final: 0.7887 (tp)
REVERT: B 543 LEU cc_start: 0.7557 (mt) cc_final: 0.7342 (mt)
REVERT: B 577 ILE cc_start: 0.8787 (mt) cc_final: 0.8071 (tp)
outliers start: 0
outliers final: 0
residues processed: 550
average time/residue: 0.3425
time to fit residues: 269.7676
Evaluate side-chains
511 residues out of total 1879 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 0
poor density : 511
time to evaluate : 1.810
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 208
random chunks:
chunk 69 optimal weight: 0.0980
chunk 146 optimal weight: 0.9980
chunk 105 optimal weight: 1.9990
chunk 43 optimal weight: 0.3980
chunk 20 optimal weight: 0.8980
chunk 27 optimal weight: 0.0770
chunk 21 optimal weight: 0.8980
chunk 119 optimal weight: 0.8980
chunk 109 optimal weight: 1.9990
chunk 75 optimal weight: 0.6980
chunk 0 optimal weight: 6.9990
overall best weight: 0.4338
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
D 78 ASN
** D 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 214 ASN
** M 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
M 359 ASN
** M 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
S 118 ASN
** B 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Total number of N/Q/H flips: 4
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3990 r_free = 0.3990 target = 0.149145 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.127718 restraints weight = 36129.924|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.131946 restraints weight = 21541.765|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.134909 restraints weight = 14079.734|
|-----------------------------------------------------------------------------|
r_work (final): 0.3762
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6680
moved from start: 0.4581
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.040 17177 Z= 0.191
Angle : 0.559 10.004 23253 Z= 0.294
Chirality : 0.043 0.193 2705
Planarity : 0.004 0.046 2931
Dihedral : 8.816 166.742 2299
Min Nonbonded Distance : 1.998
Molprobity Statistics.
All-atom Clashscore : 9.54
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 2.05 %
Favored : 97.95 %
Rotamer:
Outliers : 0.00 %
Allowed : 0.90 %
Favored : 99.10 %
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: 1.48 (0.19), residues: 2098
helix: 1.46 (0.15), residues: 1149
sheet: 0.14 (0.36), residues: 217
loop : 0.70 (0.25), residues: 732
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.027 0.002 TRP D 74
HIS 0.011 0.001 HIS D 268
PHE 0.023 0.002 PHE S 49
TYR 0.023 0.002 TYR M 174
ARG 0.015 0.001 ARG D 432
*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
4196 Ramachandran restraints generated.
2098 Oldfield, 0 Emsley, 2098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
4196 Ramachandran restraints generated.
2098 Oldfield, 0 Emsley, 2098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
552 residues out of total 1879 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 0
poor density : 552
time to evaluate : 1.934
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: A 38 LYS cc_start: 0.8348 (tttt) cc_final: 0.7848 (tttt)
REVERT: A 41 GLU cc_start: 0.5430 (mm-30) cc_final: 0.5043 (mm-30)
REVERT: A 61 ILE cc_start: 0.8577 (mm) cc_final: 0.8351 (mm)
REVERT: A 84 ASN cc_start: 0.6983 (m-40) cc_final: 0.6437 (m-40)
REVERT: C 37 LEU cc_start: 0.8171 (mt) cc_final: 0.7623 (tt)
REVERT: C 86 GLN cc_start: 0.6936 (mt0) cc_final: 0.6254 (mt0)
REVERT: C 97 ARG cc_start: 0.8537 (ptp-110) cc_final: 0.8112 (mtp85)
REVERT: C 104 ARG cc_start: 0.8504 (ttp80) cc_final: 0.8103 (ttm-80)
REVERT: C 110 MET cc_start: 0.8142 (mtm) cc_final: 0.7844 (mtp)
REVERT: C 149 ARG cc_start: 0.7002 (ttm-80) cc_final: 0.6794 (mmm160)
REVERT: C 173 LEU cc_start: 0.8324 (mt) cc_final: 0.8059 (mt)
REVERT: C 175 ASN cc_start: 0.7931 (m-40) cc_final: 0.7388 (t0)
REVERT: C 176 GLN cc_start: 0.6972 (mm-40) cc_final: 0.6557 (mm-40)
REVERT: D 1 MET cc_start: 0.4007 (ttp) cc_final: 0.3660 (ttp)
REVERT: D 20 ASP cc_start: 0.7134 (t0) cc_final: 0.6834 (t0)
REVERT: D 77 PHE cc_start: 0.7277 (t80) cc_final: 0.7053 (t80)
REVERT: D 95 TYR cc_start: 0.7746 (m-80) cc_final: 0.7388 (m-80)
REVERT: D 110 MET cc_start: 0.6703 (mmt) cc_final: 0.6398 (mmt)
REVERT: D 126 TYR cc_start: 0.8004 (m-80) cc_final: 0.7682 (m-80)
REVERT: D 128 THR cc_start: 0.7318 (m) cc_final: 0.6948 (p)
REVERT: D 132 LEU cc_start: 0.7776 (mt) cc_final: 0.7478 (mt)
REVERT: D 154 LEU cc_start: 0.8303 (mt) cc_final: 0.8036 (mp)
REVERT: D 155 MET cc_start: 0.7923 (mtm) cc_final: 0.7612 (mtm)
REVERT: D 157 HIS cc_start: 0.8308 (t-90) cc_final: 0.8049 (t70)
REVERT: D 169 ILE cc_start: 0.7343 (tt) cc_final: 0.6745 (pt)
REVERT: D 176 LYS cc_start: 0.8181 (mmpt) cc_final: 0.7485 (mmtm)
REVERT: D 189 LYS cc_start: 0.8045 (mtmt) cc_final: 0.7826 (mtmt)
REVERT: D 221 LEU cc_start: 0.7562 (mp) cc_final: 0.7058 (mp)
REVERT: D 236 TRP cc_start: 0.7934 (t-100) cc_final: 0.7360 (t-100)
REVERT: D 240 LYS cc_start: 0.8019 (mmtp) cc_final: 0.7671 (mtpt)
REVERT: D 257 LYS cc_start: 0.8087 (tttt) cc_final: 0.7566 (tttm)
REVERT: D 265 ASN cc_start: 0.7962 (m110) cc_final: 0.7729 (m110)
REVERT: D 306 GLN cc_start: 0.7561 (mm-40) cc_final: 0.6955 (mm-40)
REVERT: D 307 LYS cc_start: 0.8229 (mmtt) cc_final: 0.7787 (mmtt)
REVERT: D 320 LYS cc_start: 0.8016 (mtpt) cc_final: 0.7300 (mtmm)
REVERT: D 324 LEU cc_start: 0.8589 (mt) cc_final: 0.8308 (mt)
REVERT: D 327 MET cc_start: 0.7234 (tpp) cc_final: 0.6640 (tpp)
REVERT: D 329 LYS cc_start: 0.8914 (mttt) cc_final: 0.8631 (mttt)
REVERT: D 336 LYS cc_start: 0.8097 (ptpp) cc_final: 0.7644 (ptpp)
REVERT: D 339 GLN cc_start: 0.8308 (pt0) cc_final: 0.7749 (pp30)
REVERT: D 342 LYS cc_start: 0.8057 (pptt) cc_final: 0.7723 (pptt)
REVERT: D 346 LEU cc_start: 0.8626 (mt) cc_final: 0.8404 (mt)
REVERT: D 358 LEU cc_start: 0.8577 (mt) cc_final: 0.8368 (mt)
REVERT: D 367 MET cc_start: 0.7227 (mtm) cc_final: 0.6627 (mtm)
REVERT: D 374 MET cc_start: 0.7448 (mtt) cc_final: 0.6276 (mtt)
REVERT: D 377 VAL cc_start: 0.8779 (t) cc_final: 0.8489 (p)
REVERT: D 378 LYS cc_start: 0.8859 (mttt) cc_final: 0.8340 (mttt)
REVERT: D 392 TYR cc_start: 0.7553 (t80) cc_final: 0.7336 (t80)
REVERT: D 393 ARG cc_start: 0.7689 (mtt180) cc_final: 0.7346 (ttm-80)
REVERT: D 394 ASP cc_start: 0.8025 (m-30) cc_final: 0.7776 (m-30)
REVERT: D 396 LEU cc_start: 0.8802 (pp) cc_final: 0.8591 (pp)
REVERT: D 399 LYS cc_start: 0.8080 (mmmt) cc_final: 0.7622 (mmmt)
REVERT: D 406 GLN cc_start: 0.7617 (mt0) cc_final: 0.7324 (mt0)
REVERT: D 413 THR cc_start: 0.7492 (p) cc_final: 0.7219 (p)
REVERT: D 422 LEU cc_start: 0.8930 (tp) cc_final: 0.8642 (tp)
REVERT: D 521 VAL cc_start: 0.8255 (p) cc_final: 0.7739 (t)
REVERT: D 530 TYR cc_start: 0.7445 (m-80) cc_final: 0.7063 (m-80)
REVERT: D 534 LEU cc_start: 0.8146 (mt) cc_final: 0.7452 (tt)
REVERT: D 535 GLN cc_start: 0.8022 (pp30) cc_final: 0.7641 (pp30)
REVERT: D 547 GLN cc_start: 0.7406 (mm-40) cc_final: 0.7107 (tp40)
REVERT: D 553 MET cc_start: 0.7315 (mtm) cc_final: 0.6745 (mtm)
REVERT: D 571 ARG cc_start: 0.8464 (mtt-85) cc_final: 0.8104 (mtt-85)
REVERT: M 63 LYS cc_start: 0.8488 (mttt) cc_final: 0.7991 (mttt)
REVERT: M 67 VAL cc_start: 0.8030 (t) cc_final: 0.7691 (m)
REVERT: M 111 GLU cc_start: 0.8047 (tp30) cc_final: 0.7576 (tp30)
REVERT: M 176 ASN cc_start: 0.6508 (m-40) cc_final: 0.6298 (m-40)
REVERT: M 178 GLU cc_start: 0.6431 (pt0) cc_final: 0.6176 (pt0)
REVERT: M 196 SER cc_start: 0.6710 (m) cc_final: 0.6326 (p)
REVERT: M 198 VAL cc_start: 0.7750 (t) cc_final: 0.7491 (t)
REVERT: M 212 LEU cc_start: 0.7505 (mt) cc_final: 0.7266 (mm)
REVERT: M 228 LEU cc_start: 0.8637 (mt) cc_final: 0.8417 (mt)
REVERT: M 230 ASP cc_start: 0.7458 (t0) cc_final: 0.7044 (t0)
REVERT: M 233 PHE cc_start: 0.7774 (m-80) cc_final: 0.7398 (m-80)
REVERT: M 239 PHE cc_start: 0.8005 (t80) cc_final: 0.7652 (t80)
REVERT: M 250 PHE cc_start: 0.7821 (p90) cc_final: 0.6700 (p90)
REVERT: M 256 ASN cc_start: 0.7709 (t0) cc_final: 0.7402 (t0)
REVERT: M 333 ASP cc_start: 0.7935 (t0) cc_final: 0.7494 (t0)
REVERT: M 376 GLN cc_start: 0.5980 (mm-40) cc_final: 0.5676 (mp10)
REVERT: M 380 GLN cc_start: 0.7706 (mt0) cc_final: 0.7233 (mt0)
REVERT: M 381 GLN cc_start: 0.7791 (tm-30) cc_final: 0.7302 (tm-30)
REVERT: M 394 MET cc_start: 0.7089 (tmm) cc_final: 0.6781 (tmm)
REVERT: M 406 LYS cc_start: 0.8135 (mtpt) cc_final: 0.7642 (mtmt)
REVERT: M 409 THR cc_start: 0.7919 (m) cc_final: 0.7426 (p)
REVERT: M 410 LYS cc_start: 0.8128 (mttt) cc_final: 0.7894 (mttt)
REVERT: S 17 SER cc_start: 0.8127 (t) cc_final: 0.7620 (p)
REVERT: S 18 LYS cc_start: 0.8190 (tttp) cc_final: 0.7440 (tttp)
REVERT: S 29 GLN cc_start: 0.8642 (mt0) cc_final: 0.8360 (mt0)
REVERT: S 77 VAL cc_start: 0.7399 (m) cc_final: 0.7112 (p)
REVERT: S 82 SER cc_start: 0.7317 (t) cc_final: 0.6927 (t)
REVERT: S 89 LEU cc_start: 0.7578 (mt) cc_final: 0.6710 (mt)
REVERT: S 97 LEU cc_start: 0.7951 (mt) cc_final: 0.7350 (mt)
REVERT: S 123 MET cc_start: 0.7502 (tpt) cc_final: 0.6891 (tpt)
REVERT: S 128 MET cc_start: 0.7631 (mtp) cc_final: 0.6830 (mtp)
REVERT: B 50 MET cc_start: 0.7317 (mtm) cc_final: 0.7014 (mtm)
REVERT: B 63 MET cc_start: 0.6358 (mmm) cc_final: 0.5546 (mmm)
REVERT: B 75 ASN cc_start: 0.7838 (m110) cc_final: 0.7411 (m110)
REVERT: B 86 ASN cc_start: 0.7947 (t0) cc_final: 0.7680 (t0)
REVERT: B 97 LEU cc_start: 0.7939 (mt) cc_final: 0.7701 (mt)
REVERT: B 129 GLN cc_start: 0.8508 (pm20) cc_final: 0.8202 (pt0)
REVERT: B 152 MET cc_start: 0.7005 (tmm) cc_final: 0.6558 (tmm)
REVERT: B 156 LYS cc_start: 0.8202 (mtpt) cc_final: 0.7676 (mtpp)
REVERT: B 169 ASN cc_start: 0.8432 (m-40) cc_final: 0.8108 (t0)
REVERT: B 187 MET cc_start: 0.7943 (mtp) cc_final: 0.7691 (mtp)
REVERT: B 197 LYS cc_start: 0.8709 (mttp) cc_final: 0.8217 (mtmm)
REVERT: B 199 LYS cc_start: 0.8368 (tmtt) cc_final: 0.8127 (ttpp)
REVERT: B 213 GLU cc_start: 0.7943 (mm-30) cc_final: 0.7453 (tp30)
REVERT: B 227 ARG cc_start: 0.7941 (mtt-85) cc_final: 0.7605 (mmt90)
REVERT: B 241 GLN cc_start: 0.7929 (mt0) cc_final: 0.7137 (mt0)
REVERT: B 307 LEU cc_start: 0.8610 (mt) cc_final: 0.8207 (tp)
REVERT: B 323 TYR cc_start: 0.7518 (m-10) cc_final: 0.7237 (m-80)
REVERT: B 330 SER cc_start: 0.7723 (t) cc_final: 0.7231 (t)
REVERT: B 331 GLU cc_start: 0.7438 (mm-30) cc_final: 0.6793 (mm-30)
REVERT: B 342 LEU cc_start: 0.8638 (mm) cc_final: 0.8301 (mt)
REVERT: B 345 SER cc_start: 0.8245 (t) cc_final: 0.8006 (t)
REVERT: B 360 MET cc_start: 0.7453 (ttm) cc_final: 0.7045 (mmm)
REVERT: B 365 LYS cc_start: 0.8156 (mttt) cc_final: 0.7522 (mtpp)
REVERT: B 384 MET cc_start: 0.7747 (ptt) cc_final: 0.7519 (ptp)
REVERT: B 386 LYS cc_start: 0.8090 (mttt) cc_final: 0.7576 (mttt)
REVERT: B 389 LYS cc_start: 0.8409 (mttt) cc_final: 0.8001 (mtpp)
REVERT: B 390 LEU cc_start: 0.8020 (tp) cc_final: 0.7684 (tt)
REVERT: B 391 GLU cc_start: 0.7482 (tp30) cc_final: 0.6998 (tp30)
REVERT: B 399 GLU cc_start: 0.8095 (pm20) cc_final: 0.7721 (pp20)
REVERT: B 426 GLN cc_start: 0.8607 (mt0) cc_final: 0.7938 (mm-40)
REVERT: B 428 ILE cc_start: 0.7546 (mt) cc_final: 0.7137 (pt)
REVERT: B 433 THR cc_start: 0.7924 (t) cc_final: 0.7659 (t)
REVERT: B 437 GLU cc_start: 0.7744 (tm-30) cc_final: 0.7445 (tp30)
REVERT: B 462 VAL cc_start: 0.8627 (t) cc_final: 0.8379 (t)
REVERT: B 465 ILE cc_start: 0.8731 (mt) cc_final: 0.8179 (tp)
REVERT: B 481 LYS cc_start: 0.8856 (mttt) cc_final: 0.8185 (mttt)
REVERT: B 483 MET cc_start: 0.8542 (mmm) cc_final: 0.7656 (mmm)
REVERT: B 486 LEU cc_start: 0.8229 (mt) cc_final: 0.7865 (mt)
REVERT: B 498 SER cc_start: 0.8609 (m) cc_final: 0.8207 (p)
REVERT: B 499 ILE cc_start: 0.8513 (mm) cc_final: 0.7860 (tp)
REVERT: B 521 MET cc_start: 0.6743 (mmp) cc_final: 0.6341 (mmm)
REVERT: B 539 LEU cc_start: 0.8322 (tp) cc_final: 0.7918 (tp)
REVERT: B 578 ARG cc_start: 0.7917 (tmm160) cc_final: 0.7550 (tmm160)
outliers start: 0
outliers final: 0
residues processed: 552
average time/residue: 0.3402
time to fit residues: 269.0724
Evaluate side-chains
516 residues out of total 1879 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 0
poor density : 516
time to evaluate : 1.864
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 208
random chunks:
chunk 126 optimal weight: 0.0870
chunk 179 optimal weight: 0.4980
chunk 10 optimal weight: 3.9990
chunk 171 optimal weight: 0.8980
chunk 188 optimal weight: 0.0070
chunk 5 optimal weight: 5.9990
chunk 173 optimal weight: 1.9990
chunk 41 optimal weight: 0.2980
chunk 194 optimal weight: 0.0970
chunk 163 optimal weight: 0.3980
chunk 206 optimal weight: 0.1980
overall best weight: 0.1374
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
D 78 ASN
D 125 GLN
D 214 ASN
** D 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 246 HIS
B 321 GLN
Total number of N/Q/H flips: 5
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4031 r_free = 0.4031 target = 0.151975 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.130498 restraints weight = 35805.490|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.134799 restraints weight = 21233.071|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.137786 restraints weight = 13775.182|
|-----------------------------------------------------------------------------|
r_work (final): 0.3799
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6633
moved from start: 0.4807
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.002 0.034 17177 Z= 0.152
Angle : 0.547 7.249 23253 Z= 0.282
Chirality : 0.042 0.298 2705
Planarity : 0.004 0.048 2931
Dihedral : 8.511 161.748 2299
Min Nonbonded Distance : 1.989
Molprobity Statistics.
All-atom Clashscore : 9.37
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 1.86 %
Favored : 98.14 %
Rotamer:
Outliers : 0.05 %
Allowed : 0.48 %
Favored : 99.47 %
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: 1.53 (0.19), residues: 2098
helix: 1.50 (0.15), residues: 1149
sheet: 0.20 (0.35), residues: 221
loop : 0.70 (0.24), residues: 728
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.027 0.001 TRP D 74
HIS 0.021 0.001 HIS D 268
PHE 0.016 0.001 PHE B 211
TYR 0.016 0.002 TYR M 174
ARG 0.012 0.001 ARG B 167
*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
4196 Ramachandran restraints generated.
2098 Oldfield, 0 Emsley, 2098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
4196 Ramachandran restraints generated.
2098 Oldfield, 0 Emsley, 2098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
554 residues out of total 1879 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 1
poor density : 553
time to evaluate : 1.766
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: A 38 LYS cc_start: 0.8372 (tttt) cc_final: 0.7855 (tttt)
REVERT: A 41 GLU cc_start: 0.5272 (mm-30) cc_final: 0.5016 (mm-30)
REVERT: A 61 ILE cc_start: 0.8472 (mm) cc_final: 0.8241 (mm)
REVERT: A 84 ASN cc_start: 0.6865 (m-40) cc_final: 0.6271 (m-40)
REVERT: A 110 MET cc_start: 0.7709 (ttp) cc_final: 0.7434 (ttp)
REVERT: C 86 GLN cc_start: 0.6947 (mt0) cc_final: 0.6144 (mt0)
REVERT: C 88 LEU cc_start: 0.8088 (tt) cc_final: 0.7819 (tt)
REVERT: C 104 ARG cc_start: 0.8502 (ttp80) cc_final: 0.8067 (ttm-80)
REVERT: C 110 MET cc_start: 0.8163 (mtm) cc_final: 0.7802 (mtp)
REVERT: C 138 GLU cc_start: 0.7208 (tm-30) cc_final: 0.6969 (tm-30)
REVERT: C 173 LEU cc_start: 0.8330 (mt) cc_final: 0.8047 (mt)
REVERT: C 176 GLN cc_start: 0.6853 (mm-40) cc_final: 0.6419 (mm-40)
REVERT: C 178 ARG cc_start: 0.7060 (ttt-90) cc_final: 0.6812 (ttt-90)
REVERT: D 1 MET cc_start: 0.4090 (ttp) cc_final: 0.3711 (ttp)
REVERT: D 77 PHE cc_start: 0.7256 (t80) cc_final: 0.7002 (t80)
REVERT: D 91 LYS cc_start: 0.7402 (mtmt) cc_final: 0.6921 (mtmt)
REVERT: D 95 TYR cc_start: 0.7564 (m-80) cc_final: 0.7126 (m-80)
REVERT: D 110 MET cc_start: 0.6643 (mmt) cc_final: 0.6301 (mmt)
REVERT: D 126 TYR cc_start: 0.7968 (m-80) cc_final: 0.7664 (m-80)
REVERT: D 128 THR cc_start: 0.7429 (m) cc_final: 0.7002 (p)
REVERT: D 132 LEU cc_start: 0.7720 (mt) cc_final: 0.7355 (mt)
REVERT: D 155 MET cc_start: 0.7807 (mtm) cc_final: 0.7430 (mtm)
REVERT: D 157 HIS cc_start: 0.8289 (t-90) cc_final: 0.8048 (t70)
REVERT: D 169 ILE cc_start: 0.7332 (tt) cc_final: 0.6701 (pt)
REVERT: D 176 LYS cc_start: 0.8204 (mmpt) cc_final: 0.7545 (mmtm)
REVERT: D 200 GLN cc_start: 0.7025 (mm110) cc_final: 0.6794 (mm110)
REVERT: D 221 LEU cc_start: 0.7729 (mp) cc_final: 0.6944 (mp)
REVERT: D 236 TRP cc_start: 0.7796 (t-100) cc_final: 0.7405 (t-100)
REVERT: D 240 LYS cc_start: 0.7967 (mmtp) cc_final: 0.7612 (mmmm)
REVERT: D 257 LYS cc_start: 0.8042 (tttt) cc_final: 0.7420 (tmtt)
REVERT: D 275 LEU cc_start: 0.7920 (tp) cc_final: 0.7558 (tp)
REVERT: D 307 LYS cc_start: 0.8224 (mmtt) cc_final: 0.7822 (mmtt)
REVERT: D 324 LEU cc_start: 0.8546 (mt) cc_final: 0.8226 (mt)
REVERT: D 327 MET cc_start: 0.7172 (tpp) cc_final: 0.6464 (tpp)
REVERT: D 329 LYS cc_start: 0.8887 (mttt) cc_final: 0.8624 (mttt)
REVERT: D 336 LYS cc_start: 0.7984 (ptpp) cc_final: 0.7556 (ptpp)
REVERT: D 358 LEU cc_start: 0.8574 (mt) cc_final: 0.8322 (mt)
REVERT: D 364 LEU cc_start: 0.8781 (mm) cc_final: 0.8226 (pp)
REVERT: D 367 MET cc_start: 0.7182 (mtm) cc_final: 0.6650 (mtm)
REVERT: D 374 MET cc_start: 0.7437 (mtt) cc_final: 0.6208 (mtt)
REVERT: D 378 LYS cc_start: 0.8850 (mttt) cc_final: 0.8343 (mttt)
REVERT: D 393 ARG cc_start: 0.7823 (mtt180) cc_final: 0.7473 (ttm-80)
REVERT: D 394 ASP cc_start: 0.8053 (m-30) cc_final: 0.7790 (m-30)
REVERT: D 399 LYS cc_start: 0.7885 (mmmt) cc_final: 0.7387 (mmmt)
REVERT: D 403 ILE cc_start: 0.8407 (pt) cc_final: 0.7994 (pt)
REVERT: D 406 GLN cc_start: 0.7489 (mt0) cc_final: 0.7268 (mt0)
REVERT: D 413 THR cc_start: 0.7481 (p) cc_final: 0.7223 (p)
REVERT: D 422 LEU cc_start: 0.8976 (tp) cc_final: 0.8693 (mt)
REVERT: D 521 VAL cc_start: 0.8218 (p) cc_final: 0.7770 (t)
REVERT: D 530 TYR cc_start: 0.7382 (m-80) cc_final: 0.6990 (m-80)
REVERT: D 534 LEU cc_start: 0.8243 (mt) cc_final: 0.7576 (tt)
REVERT: D 535 GLN cc_start: 0.7984 (pp30) cc_final: 0.7642 (pp30)
REVERT: D 547 GLN cc_start: 0.7405 (mm-40) cc_final: 0.7073 (tp40)
REVERT: D 553 MET cc_start: 0.7302 (mtm) cc_final: 0.6693 (mtm)
REVERT: D 567 GLU cc_start: 0.7571 (tp30) cc_final: 0.7260 (tp30)
REVERT: D 571 ARG cc_start: 0.8483 (mtt-85) cc_final: 0.8192 (mtt-85)
REVERT: D 573 SER cc_start: 0.7996 (m) cc_final: 0.7642 (p)
REVERT: M 18 LYS cc_start: 0.8611 (tptm) cc_final: 0.8284 (tptp)
REVERT: M 63 LYS cc_start: 0.8454 (mttt) cc_final: 0.7964 (mttt)
REVERT: M 67 VAL cc_start: 0.7975 (t) cc_final: 0.7608 (m)
REVERT: M 111 GLU cc_start: 0.7749 (tp30) cc_final: 0.7310 (tp30)
REVERT: M 178 GLU cc_start: 0.6358 (pt0) cc_final: 0.6111 (pt0)
REVERT: M 196 SER cc_start: 0.6653 (m) cc_final: 0.6277 (p)
REVERT: M 198 VAL cc_start: 0.7578 (t) cc_final: 0.7356 (t)
REVERT: M 201 GLU cc_start: 0.8170 (pt0) cc_final: 0.7468 (pm20)
REVERT: M 228 LEU cc_start: 0.8621 (mt) cc_final: 0.8396 (mt)
REVERT: M 230 ASP cc_start: 0.7428 (t0) cc_final: 0.6991 (t0)
REVERT: M 233 PHE cc_start: 0.7710 (m-80) cc_final: 0.7380 (m-80)
REVERT: M 239 PHE cc_start: 0.7868 (t80) cc_final: 0.7478 (t80)
REVERT: M 240 LYS cc_start: 0.7465 (tttm) cc_final: 0.7202 (mmtm)
REVERT: M 250 PHE cc_start: 0.7781 (p90) cc_final: 0.6565 (p90)
REVERT: M 256 ASN cc_start: 0.7655 (t0) cc_final: 0.7360 (t0)
REVERT: M 333 ASP cc_start: 0.8031 (t0) cc_final: 0.7537 (t0)
REVERT: M 350 LYS cc_start: 0.7873 (mppt) cc_final: 0.7296 (tptm)
REVERT: M 376 GLN cc_start: 0.5897 (mm-40) cc_final: 0.5619 (mp10)
REVERT: M 380 GLN cc_start: 0.7739 (mt0) cc_final: 0.7212 (mt0)
REVERT: M 381 GLN cc_start: 0.7818 (tm-30) cc_final: 0.7276 (tm-30)
REVERT: M 394 MET cc_start: 0.6996 (tmm) cc_final: 0.6701 (tmm)
REVERT: M 398 LYS cc_start: 0.8352 (mmmt) cc_final: 0.8074 (mmtm)
REVERT: M 406 LYS cc_start: 0.8038 (mtpt) cc_final: 0.7655 (ttmt)
REVERT: M 409 THR cc_start: 0.7901 (m) cc_final: 0.7382 (p)
REVERT: M 410 LYS cc_start: 0.8118 (mttt) cc_final: 0.7864 (mttt)
REVERT: S 17 SER cc_start: 0.8020 (t) cc_final: 0.7781 (p)
REVERT: S 18 LYS cc_start: 0.8211 (tttp) cc_final: 0.7477 (tttp)
REVERT: S 29 GLN cc_start: 0.8580 (mt0) cc_final: 0.8050 (mm-40)
REVERT: S 77 VAL cc_start: 0.7416 (m) cc_final: 0.7095 (p)
REVERT: S 82 SER cc_start: 0.7139 (t) cc_final: 0.6312 (p)
REVERT: S 86 ILE cc_start: 0.7933 (mm) cc_final: 0.7691 (mm)
REVERT: S 89 LEU cc_start: 0.7846 (mt) cc_final: 0.6870 (mt)
REVERT: S 97 LEU cc_start: 0.7925 (mt) cc_final: 0.7385 (mt)
REVERT: S 123 MET cc_start: 0.7452 (tpt) cc_final: 0.6858 (tpt)
REVERT: S 128 MET cc_start: 0.7469 (mtp) cc_final: 0.6590 (mtp)
REVERT: B 50 MET cc_start: 0.7199 (mtm) cc_final: 0.6850 (mtm)
REVERT: B 63 MET cc_start: 0.6338 (mmm) cc_final: 0.5492 (mmm)
REVERT: B 75 ASN cc_start: 0.7745 (m110) cc_final: 0.7522 (m110)
REVERT: B 96 LYS cc_start: 0.7844 (tptt) cc_final: 0.7535 (tttt)
REVERT: B 97 LEU cc_start: 0.7782 (mt) cc_final: 0.7542 (mt)
REVERT: B 129 GLN cc_start: 0.8477 (pm20) cc_final: 0.8172 (pt0)
REVERT: B 152 MET cc_start: 0.7119 (tmm) cc_final: 0.6758 (tmm)
REVERT: B 156 LYS cc_start: 0.7976 (mtpt) cc_final: 0.7616 (mttm)
REVERT: B 187 MET cc_start: 0.7824 (mtp) cc_final: 0.7595 (mtp)
REVERT: B 197 LYS cc_start: 0.8681 (mttp) cc_final: 0.8139 (mtmm)
REVERT: B 199 LYS cc_start: 0.8314 (tmtt) cc_final: 0.8082 (ttpp)
REVERT: B 213 GLU cc_start: 0.7837 (mm-30) cc_final: 0.7457 (tp30)
REVERT: B 227 ARG cc_start: 0.7888 (mtt-85) cc_final: 0.7667 (mtt90)
REVERT: B 241 GLN cc_start: 0.7886 (mt0) cc_final: 0.7013 (mt0)
REVERT: B 307 LEU cc_start: 0.8363 (mt) cc_final: 0.7973 (tp)
REVERT: B 323 TYR cc_start: 0.7528 (m-10) cc_final: 0.7282 (m-80)
REVERT: B 330 SER cc_start: 0.7667 (t) cc_final: 0.6699 (t)
REVERT: B 331 GLU cc_start: 0.7371 (mm-30) cc_final: 0.6560 (mm-30)
REVERT: B 345 SER cc_start: 0.8082 (t) cc_final: 0.7816 (t)
REVERT: B 360 MET cc_start: 0.7296 (ttm) cc_final: 0.6722 (mmm)
REVERT: B 365 LYS cc_start: 0.8067 (mttt) cc_final: 0.7427 (mtpp)
REVERT: B 386 LYS cc_start: 0.8001 (mttt) cc_final: 0.7518 (mttt)
REVERT: B 389 LYS cc_start: 0.8408 (mttt) cc_final: 0.8018 (mtpp)
REVERT: B 390 LEU cc_start: 0.7970 (tp) cc_final: 0.7691 (tt)
REVERT: B 391 GLU cc_start: 0.7386 (tp30) cc_final: 0.6889 (tp30)
REVERT: B 426 GLN cc_start: 0.8572 (mt0) cc_final: 0.7980 (mm-40)
REVERT: B 433 THR cc_start: 0.7788 (t) cc_final: 0.7532 (t)
REVERT: B 437 GLU cc_start: 0.7688 (tm-30) cc_final: 0.7416 (tp30)
REVERT: B 465 ILE cc_start: 0.8654 (mt) cc_final: 0.8138 (tp)
REVERT: B 481 LYS cc_start: 0.8821 (mttt) cc_final: 0.8219 (mttt)
REVERT: B 483 MET cc_start: 0.8487 (mmm) cc_final: 0.7699 (mmm)
REVERT: B 486 LEU cc_start: 0.8253 (mt) cc_final: 0.7720 (mt)
REVERT: B 498 SER cc_start: 0.8595 (m) cc_final: 0.8191 (p)
REVERT: B 499 ILE cc_start: 0.8531 (mm) cc_final: 0.7888 (tp)
REVERT: B 520 LYS cc_start: 0.7479 (mtpt) cc_final: 0.7206 (ptpt)
REVERT: B 521 MET cc_start: 0.6630 (mmp) cc_final: 0.6225 (mmm)
REVERT: B 539 LEU cc_start: 0.8235 (tp) cc_final: 0.7890 (tp)
REVERT: B 578 ARG cc_start: 0.7901 (tmm160) cc_final: 0.7475 (tmm160)
outliers start: 1
outliers final: 0
residues processed: 553
average time/residue: 0.3346
time to fit residues: 266.0881
Evaluate side-chains
520 residues out of total 1879 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 0
poor density : 520
time to evaluate : 1.983
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 208
random chunks:
chunk 102 optimal weight: 0.5980
chunk 53 optimal weight: 0.9980
chunk 154 optimal weight: 0.8980
chunk 182 optimal weight: 0.9980
chunk 156 optimal weight: 0.7980
chunk 90 optimal weight: 0.9980
chunk 157 optimal weight: 0.0980
chunk 184 optimal weight: 0.6980
chunk 173 optimal weight: 0.7980
chunk 73 optimal weight: 0.9980
chunk 56 optimal weight: 0.9980
overall best weight: 0.5980
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
D 78 ASN
D 214 ASN
** D 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 562 GLN
M 145 ASN
** M 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 246 HIS
B 321 GLN
Total number of N/Q/H flips: 6
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3985 r_free = 0.3985 target = 0.148778 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.126896 restraints weight = 35523.546|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.131161 restraints weight = 21396.175|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.134130 restraints weight = 14015.220|
|-----------------------------------------------------------------------------|
r_work (final): 0.3744
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6709
moved from start: 0.5093
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.038 17177 Z= 0.213
Angle : 0.577 10.537 23253 Z= 0.305
Chirality : 0.044 0.269 2705
Planarity : 0.004 0.045 2931
Dihedral : 8.485 166.344 2299
Min Nonbonded Distance : 1.920
Molprobity Statistics.
All-atom Clashscore : 10.34
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 2.67 %
Favored : 97.33 %
Rotamer:
Outliers : 0.05 %
Allowed : 0.69 %
Favored : 99.25 %
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: 1.45 (0.19), residues: 2098
helix: 1.50 (0.15), residues: 1144
sheet: 0.23 (0.35), residues: 229
loop : 0.54 (0.25), residues: 725
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.020 0.002 TRP D 74
HIS 0.020 0.001 HIS D 268
PHE 0.043 0.002 PHE D 245
TYR 0.024 0.002 TYR M 174
ARG 0.010 0.001 ARG B 167
*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
4196 Ramachandran restraints generated.
2098 Oldfield, 0 Emsley, 2098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
4196 Ramachandran restraints generated.
2098 Oldfield, 0 Emsley, 2098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
534 residues out of total 1879 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 1
poor density : 533
time to evaluate : 1.805
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: A 38 LYS cc_start: 0.8376 (tttt) cc_final: 0.7915 (tttt)
REVERT: A 41 GLU cc_start: 0.5526 (mm-30) cc_final: 0.5149 (mm-30)
REVERT: A 84 ASN cc_start: 0.6957 (m-40) cc_final: 0.6326 (m-40)
REVERT: A 110 MET cc_start: 0.7709 (ttp) cc_final: 0.7451 (ttp)
REVERT: C 86 GLN cc_start: 0.7164 (mt0) cc_final: 0.6311 (mt0)
REVERT: C 104 ARG cc_start: 0.8570 (ttp80) cc_final: 0.8154 (ttm-80)
REVERT: C 110 MET cc_start: 0.8205 (mtm) cc_final: 0.7901 (mtp)
REVERT: C 173 LEU cc_start: 0.8430 (mt) cc_final: 0.8130 (mt)
REVERT: C 175 ASN cc_start: 0.8000 (m-40) cc_final: 0.7509 (t0)
REVERT: C 176 GLN cc_start: 0.6952 (mm-40) cc_final: 0.6616 (mm-40)
REVERT: D 1 MET cc_start: 0.4065 (ttp) cc_final: 0.3683 (ttp)
REVERT: D 116 ILE cc_start: 0.8464 (mm) cc_final: 0.8137 (mm)
REVERT: D 117 ARG cc_start: 0.8268 (ttm170) cc_final: 0.7959 (mtm-85)
REVERT: D 118 LYS cc_start: 0.8300 (tttt) cc_final: 0.8002 (mtpt)
REVERT: D 126 TYR cc_start: 0.7996 (m-80) cc_final: 0.7719 (m-80)
REVERT: D 128 THR cc_start: 0.7455 (m) cc_final: 0.7033 (p)
REVERT: D 132 LEU cc_start: 0.7788 (mt) cc_final: 0.7413 (mt)
REVERT: D 154 LEU cc_start: 0.8317 (mt) cc_final: 0.8041 (mp)
REVERT: D 155 MET cc_start: 0.7845 (mtm) cc_final: 0.7551 (mtm)
REVERT: D 157 HIS cc_start: 0.8342 (t-90) cc_final: 0.8085 (t70)
REVERT: D 169 ILE cc_start: 0.7385 (tt) cc_final: 0.6818 (pt)
REVERT: D 176 LYS cc_start: 0.8335 (mmpt) cc_final: 0.7679 (mmtm)
REVERT: D 200 GLN cc_start: 0.7168 (mm110) cc_final: 0.6790 (mm-40)
REVERT: D 221 LEU cc_start: 0.7544 (mp) cc_final: 0.7123 (mp)
REVERT: D 236 TRP cc_start: 0.7870 (t-100) cc_final: 0.7551 (t-100)
REVERT: D 257 LYS cc_start: 0.8114 (tttt) cc_final: 0.7477 (tmtt)
REVERT: D 275 LEU cc_start: 0.7989 (tp) cc_final: 0.7693 (tp)
REVERT: D 307 LYS cc_start: 0.8230 (mmtt) cc_final: 0.7832 (mmtt)
REVERT: D 320 LYS cc_start: 0.8039 (mtpt) cc_final: 0.7304 (mtmm)
REVERT: D 324 LEU cc_start: 0.8588 (mt) cc_final: 0.8289 (mt)
REVERT: D 327 MET cc_start: 0.7267 (tpp) cc_final: 0.6731 (tpp)
REVERT: D 329 LYS cc_start: 0.8931 (mttt) cc_final: 0.8636 (mttt)
REVERT: D 336 LYS cc_start: 0.8077 (ptpp) cc_final: 0.7591 (ptpp)
REVERT: D 346 LEU cc_start: 0.8693 (mt) cc_final: 0.8437 (mt)
REVERT: D 358 LEU cc_start: 0.8551 (mt) cc_final: 0.8282 (mt)
REVERT: D 367 MET cc_start: 0.7205 (mtm) cc_final: 0.6850 (mtm)
REVERT: D 374 MET cc_start: 0.7186 (mtt) cc_final: 0.6173 (mtt)
REVERT: D 378 LYS cc_start: 0.8874 (mttt) cc_final: 0.8378 (mttt)
REVERT: D 381 MET cc_start: 0.7984 (mtp) cc_final: 0.7701 (mtp)
REVERT: D 393 ARG cc_start: 0.7954 (mtt180) cc_final: 0.7548 (ptp-110)
REVERT: D 394 ASP cc_start: 0.8145 (m-30) cc_final: 0.7938 (m-30)
REVERT: D 399 LYS cc_start: 0.8006 (mmmt) cc_final: 0.7489 (mmmt)
REVERT: D 403 ILE cc_start: 0.8506 (pt) cc_final: 0.8106 (pt)
REVERT: D 406 GLN cc_start: 0.7552 (mt0) cc_final: 0.7349 (mt0)
REVERT: D 421 ILE cc_start: 0.8529 (mm) cc_final: 0.8236 (mm)
REVERT: D 422 LEU cc_start: 0.8995 (tp) cc_final: 0.8793 (tp)
REVERT: D 459 MET cc_start: 0.8107 (mtm) cc_final: 0.7852 (ptm)
REVERT: D 530 TYR cc_start: 0.7505 (m-80) cc_final: 0.7045 (m-80)
REVERT: D 532 SER cc_start: 0.7793 (p) cc_final: 0.7543 (p)
REVERT: D 534 LEU cc_start: 0.8284 (mt) cc_final: 0.7683 (tt)
REVERT: D 547 GLN cc_start: 0.7580 (mm-40) cc_final: 0.7208 (tp40)
REVERT: D 553 MET cc_start: 0.7497 (mtm) cc_final: 0.6852 (mtm)
REVERT: D 567 GLU cc_start: 0.7681 (tp30) cc_final: 0.7419 (tp30)
REVERT: D 571 ARG cc_start: 0.8523 (mtt-85) cc_final: 0.8189 (mtt-85)
REVERT: M 6 PHE cc_start: 0.7859 (m-80) cc_final: 0.7545 (m-10)
REVERT: M 43 GLU cc_start: 0.8439 (mm-30) cc_final: 0.7779 (mm-30)
REVERT: M 63 LYS cc_start: 0.8520 (mttt) cc_final: 0.8031 (mttt)
REVERT: M 67 VAL cc_start: 0.8063 (t) cc_final: 0.7694 (m)
REVERT: M 111 GLU cc_start: 0.8086 (tp30) cc_final: 0.7053 (tp30)
REVERT: M 167 TRP cc_start: 0.7948 (p90) cc_final: 0.6944 (p90)
REVERT: M 176 ASN cc_start: 0.6413 (m-40) cc_final: 0.5603 (m-40)
REVERT: M 196 SER cc_start: 0.6415 (m) cc_final: 0.6038 (p)
REVERT: M 228 LEU cc_start: 0.8590 (mt) cc_final: 0.8386 (mt)
REVERT: M 230 ASP cc_start: 0.7573 (t0) cc_final: 0.7098 (t0)
REVERT: M 233 PHE cc_start: 0.7806 (m-80) cc_final: 0.7499 (m-80)
REVERT: M 239 PHE cc_start: 0.7942 (t80) cc_final: 0.7653 (t80)
REVERT: M 250 PHE cc_start: 0.7894 (p90) cc_final: 0.7630 (p90)
REVERT: M 256 ASN cc_start: 0.7631 (t0) cc_final: 0.7430 (t0)
REVERT: M 333 ASP cc_start: 0.8168 (t0) cc_final: 0.7686 (t0)
REVERT: M 376 GLN cc_start: 0.5955 (mm-40) cc_final: 0.5657 (mp10)
REVERT: M 380 GLN cc_start: 0.7687 (mt0) cc_final: 0.7165 (mt0)
REVERT: M 381 GLN cc_start: 0.7848 (tm-30) cc_final: 0.7324 (tm-30)
REVERT: M 394 MET cc_start: 0.7028 (tmm) cc_final: 0.6718 (tmm)
REVERT: M 406 LYS cc_start: 0.8072 (mtpt) cc_final: 0.7687 (ttmt)
REVERT: M 409 THR cc_start: 0.7837 (m) cc_final: 0.7380 (p)
REVERT: S 17 SER cc_start: 0.8136 (t) cc_final: 0.7801 (p)
REVERT: S 18 LYS cc_start: 0.8225 (tttp) cc_final: 0.7391 (tttp)
REVERT: S 29 GLN cc_start: 0.8661 (mt0) cc_final: 0.8372 (mt0)
REVERT: S 77 VAL cc_start: 0.7188 (m) cc_final: 0.6960 (p)
REVERT: S 89 LEU cc_start: 0.7550 (mt) cc_final: 0.6759 (mt)
REVERT: S 97 LEU cc_start: 0.7970 (mt) cc_final: 0.7377 (mt)
REVERT: S 123 MET cc_start: 0.7504 (tpt) cc_final: 0.6886 (tpt)
REVERT: S 124 VAL cc_start: 0.8123 (t) cc_final: 0.7877 (t)
REVERT: S 128 MET cc_start: 0.7293 (mtp) cc_final: 0.6408 (mtp)
REVERT: B 50 MET cc_start: 0.7305 (mtm) cc_final: 0.6994 (mtm)
REVERT: B 63 MET cc_start: 0.6717 (mmm) cc_final: 0.5783 (mmm)
REVERT: B 75 ASN cc_start: 0.7811 (m110) cc_final: 0.7512 (m110)
REVERT: B 86 ASN cc_start: 0.8326 (t0) cc_final: 0.8044 (t0)
REVERT: B 89 SER cc_start: 0.8676 (m) cc_final: 0.8431 (t)
REVERT: B 96 LYS cc_start: 0.7901 (mmmt) cc_final: 0.7546 (tptm)
REVERT: B 97 LEU cc_start: 0.7854 (mt) cc_final: 0.7505 (mt)
REVERT: B 126 ASP cc_start: 0.7523 (t70) cc_final: 0.7242 (t70)
REVERT: B 129 GLN cc_start: 0.8512 (pm20) cc_final: 0.8094 (mt0)
REVERT: B 142 ILE cc_start: 0.7872 (tp) cc_final: 0.7373 (mm)
REVERT: B 152 MET cc_start: 0.7182 (tmm) cc_final: 0.6789 (tmm)
REVERT: B 156 LYS cc_start: 0.8012 (mtpt) cc_final: 0.7551 (mtpp)
REVERT: B 187 MET cc_start: 0.7935 (mtp) cc_final: 0.7689 (mtp)
REVERT: B 197 LYS cc_start: 0.8663 (mttp) cc_final: 0.8183 (mtmm)
REVERT: B 199 LYS cc_start: 0.8403 (tmtt) cc_final: 0.7961 (tmtt)
REVERT: B 207 VAL cc_start: 0.8085 (p) cc_final: 0.7818 (m)
REVERT: B 213 GLU cc_start: 0.7852 (mm-30) cc_final: 0.7627 (tp30)
REVERT: B 227 ARG cc_start: 0.7918 (mtt-85) cc_final: 0.7532 (mmt90)
REVERT: B 241 GLN cc_start: 0.8003 (mt0) cc_final: 0.7155 (mt0)
REVERT: B 297 HIS cc_start: 0.8017 (t-90) cc_final: 0.7750 (t-90)
REVERT: B 307 LEU cc_start: 0.8521 (mt) cc_final: 0.8141 (tp)
REVERT: B 323 TYR cc_start: 0.7608 (m-10) cc_final: 0.7375 (m-80)
REVERT: B 330 SER cc_start: 0.7605 (t) cc_final: 0.6555 (t)
REVERT: B 331 GLU cc_start: 0.7298 (mm-30) cc_final: 0.6422 (mm-30)
REVERT: B 345 SER cc_start: 0.8291 (t) cc_final: 0.8023 (t)
REVERT: B 360 MET cc_start: 0.7443 (ttm) cc_final: 0.6888 (mmm)
REVERT: B 365 LYS cc_start: 0.8181 (mttt) cc_final: 0.7485 (mtpp)
REVERT: B 375 PHE cc_start: 0.7679 (m-80) cc_final: 0.7388 (m-80)
REVERT: B 378 ARG cc_start: 0.7625 (mtt90) cc_final: 0.7354 (mtm180)
REVERT: B 386 LYS cc_start: 0.8080 (mttt) cc_final: 0.7593 (mttt)
REVERT: B 389 LYS cc_start: 0.8495 (mttt) cc_final: 0.8107 (mtpt)
REVERT: B 390 LEU cc_start: 0.8044 (tp) cc_final: 0.7723 (tt)
REVERT: B 391 GLU cc_start: 0.7374 (tp30) cc_final: 0.6699 (tp30)
REVERT: B 426 GLN cc_start: 0.8541 (mt0) cc_final: 0.7957 (mm-40)
REVERT: B 433 THR cc_start: 0.7935 (t) cc_final: 0.7667 (t)
REVERT: B 440 ASP cc_start: 0.7767 (m-30) cc_final: 0.7276 (p0)
REVERT: B 462 VAL cc_start: 0.8658 (t) cc_final: 0.8444 (t)
REVERT: B 465 ILE cc_start: 0.8693 (mt) cc_final: 0.8199 (tp)
REVERT: B 481 LYS cc_start: 0.8832 (mttt) cc_final: 0.8241 (mttt)
REVERT: B 483 MET cc_start: 0.8549 (mmm) cc_final: 0.8292 (mmm)
REVERT: B 486 LEU cc_start: 0.8271 (mt) cc_final: 0.7939 (mt)
REVERT: B 498 SER cc_start: 0.8613 (m) cc_final: 0.8155 (p)
REVERT: B 499 ILE cc_start: 0.8523 (mm) cc_final: 0.7888 (tp)
REVERT: B 520 LYS cc_start: 0.7667 (mtpt) cc_final: 0.7420 (ptpt)
REVERT: B 521 MET cc_start: 0.6845 (mmp) cc_final: 0.6415 (mmm)
REVERT: B 539 LEU cc_start: 0.8213 (tp) cc_final: 0.7835 (tp)
REVERT: B 543 LEU cc_start: 0.7624 (mt) cc_final: 0.7392 (mt)
REVERT: B 578 ARG cc_start: 0.7930 (tmm160) cc_final: 0.7450 (tmm160)
outliers start: 1
outliers final: 0
residues processed: 533
average time/residue: 0.3450
time to fit residues: 263.5828
Evaluate side-chains
525 residues out of total 1879 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 0
poor density : 525
time to evaluate : 2.096
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 208
random chunks:
chunk 25 optimal weight: 0.9980
chunk 167 optimal weight: 0.9980
chunk 165 optimal weight: 1.9990
chunk 154 optimal weight: 0.6980
chunk 107 optimal weight: 0.8980
chunk 113 optimal weight: 0.0970
chunk 18 optimal weight: 0.7980
chunk 145 optimal weight: 0.0770
chunk 40 optimal weight: 0.8980
chunk 171 optimal weight: 0.6980
chunk 65 optimal weight: 4.9990
overall best weight: 0.4736
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
D 78 ASN
D 214 ASN
** M 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
M 145 ASN
** M 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 246 HIS
B 321 GLN
Total number of N/Q/H flips: 5
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3994 r_free = 0.3994 target = 0.149344 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.127488 restraints weight = 35665.668|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.131676 restraints weight = 21464.685|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.134607 restraints weight = 14105.418|
|-----------------------------------------------------------------------------|
r_work (final): 0.3761
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6697
moved from start: 0.5263
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.041 17177 Z= 0.188
Angle : 0.562 9.940 23253 Z= 0.296
Chirality : 0.043 0.229 2705
Planarity : 0.004 0.048 2931
Dihedral : 8.371 165.452 2299
Min Nonbonded Distance : 1.903
Molprobity Statistics.
All-atom Clashscore : 10.60
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 2.34 %
Favored : 97.66 %
Rotamer:
Outliers : 0.05 %
Allowed : 0.21 %
Favored : 99.73 %
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: 1.45 (0.19), residues: 2098
helix: 1.49 (0.15), residues: 1149
sheet: 0.25 (0.35), residues: 228
loop : 0.53 (0.24), residues: 721
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.015 0.002 TRP D 74
HIS 0.018 0.001 HIS D 268
PHE 0.036 0.002 PHE D 245
TYR 0.022 0.002 TYR M 174
ARG 0.010 0.001 ARG M 61
*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
4196 Ramachandran restraints generated.
2098 Oldfield, 0 Emsley, 2098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
4196 Ramachandran restraints generated.
2098 Oldfield, 0 Emsley, 2098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
548 residues out of total 1879 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 1
poor density : 547
time to evaluate : 2.046
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: A 38 LYS cc_start: 0.8377 (tttt) cc_final: 0.7911 (tttt)
REVERT: A 41 GLU cc_start: 0.5504 (mm-30) cc_final: 0.5162 (mm-30)
REVERT: A 84 ASN cc_start: 0.6946 (m-40) cc_final: 0.6312 (m-40)
REVERT: A 110 MET cc_start: 0.7737 (ttp) cc_final: 0.7488 (ttp)
REVERT: C 86 GLN cc_start: 0.7134 (mt0) cc_final: 0.6346 (mt0)
REVERT: C 104 ARG cc_start: 0.8582 (ttp80) cc_final: 0.8129 (ttm-80)
REVERT: C 110 MET cc_start: 0.8212 (mtm) cc_final: 0.7901 (mtp)
REVERT: C 173 LEU cc_start: 0.8431 (mt) cc_final: 0.8149 (mt)
REVERT: C 175 ASN cc_start: 0.7923 (m-40) cc_final: 0.7388 (t0)
REVERT: C 176 GLN cc_start: 0.6927 (mm-40) cc_final: 0.6569 (mm-40)
REVERT: D 1 MET cc_start: 0.4130 (ttp) cc_final: 0.3751 (ttp)
REVERT: D 91 LYS cc_start: 0.7513 (mtmt) cc_final: 0.7168 (mtmt)
REVERT: D 95 TYR cc_start: 0.7017 (m-10) cc_final: 0.6816 (m-10)
REVERT: D 116 ILE cc_start: 0.8446 (mm) cc_final: 0.8179 (mm)
REVERT: D 117 ARG cc_start: 0.8310 (ttm170) cc_final: 0.7955 (mtm-85)
REVERT: D 118 LYS cc_start: 0.8284 (tttt) cc_final: 0.8015 (mtpt)
REVERT: D 126 TYR cc_start: 0.8006 (m-80) cc_final: 0.7702 (m-80)
REVERT: D 128 THR cc_start: 0.7383 (m) cc_final: 0.7164 (p)
REVERT: D 155 MET cc_start: 0.7961 (mtm) cc_final: 0.7658 (mtm)
REVERT: D 157 HIS cc_start: 0.8355 (t-90) cc_final: 0.8106 (t70)
REVERT: D 169 ILE cc_start: 0.7384 (tt) cc_final: 0.7009 (mm)
REVERT: D 176 LYS cc_start: 0.8369 (mmpt) cc_final: 0.7244 (tppt)
REVERT: D 221 LEU cc_start: 0.7714 (mp) cc_final: 0.7053 (mp)
REVERT: D 236 TRP cc_start: 0.7822 (t-100) cc_final: 0.7472 (t-100)
REVERT: D 273 MET cc_start: 0.8174 (pmm) cc_final: 0.7969 (pmm)
REVERT: D 275 LEU cc_start: 0.7963 (tp) cc_final: 0.7664 (tp)
REVERT: D 302 GLN cc_start: 0.8570 (tt0) cc_final: 0.7669 (tm-30)
REVERT: D 307 LYS cc_start: 0.8218 (mmtt) cc_final: 0.7830 (mmtt)
REVERT: D 320 LYS cc_start: 0.7950 (mtpt) cc_final: 0.7192 (mtpt)
REVERT: D 324 LEU cc_start: 0.8574 (mt) cc_final: 0.8255 (mt)
REVERT: D 327 MET cc_start: 0.7212 (tpp) cc_final: 0.6710 (tpp)
REVERT: D 329 LYS cc_start: 0.8920 (mttt) cc_final: 0.8616 (mttt)
REVERT: D 336 LYS cc_start: 0.7857 (ptpp) cc_final: 0.7405 (ptpp)
REVERT: D 339 GLN cc_start: 0.8415 (pt0) cc_final: 0.7974 (pp30)
REVERT: D 346 LEU cc_start: 0.8634 (mt) cc_final: 0.8372 (mt)
REVERT: D 362 ASP cc_start: 0.8637 (m-30) cc_final: 0.8332 (m-30)
REVERT: D 367 MET cc_start: 0.7195 (mtm) cc_final: 0.6861 (mtm)
REVERT: D 373 LEU cc_start: 0.8673 (tp) cc_final: 0.8334 (pp)
REVERT: D 374 MET cc_start: 0.7174 (mtt) cc_final: 0.5890 (mtt)
REVERT: D 378 LYS cc_start: 0.8887 (mttt) cc_final: 0.8369 (mttt)
REVERT: D 381 MET cc_start: 0.7980 (mtp) cc_final: 0.7678 (mtp)
REVERT: D 393 ARG cc_start: 0.7821 (mtt180) cc_final: 0.7469 (ttm-80)
REVERT: D 394 ASP cc_start: 0.8115 (m-30) cc_final: 0.7908 (m-30)
REVERT: D 399 LYS cc_start: 0.8002 (mmmt) cc_final: 0.7455 (mmmt)
REVERT: D 403 ILE cc_start: 0.8465 (pt) cc_final: 0.8079 (pt)
REVERT: D 421 ILE cc_start: 0.8567 (mm) cc_final: 0.8207 (mm)
REVERT: D 422 LEU cc_start: 0.9045 (tp) cc_final: 0.8627 (mt)
REVERT: D 440 GLN cc_start: 0.7615 (mm-40) cc_final: 0.6941 (mm-40)
REVERT: D 530 TYR cc_start: 0.7481 (m-80) cc_final: 0.7044 (m-80)
REVERT: D 534 LEU cc_start: 0.8272 (mt) cc_final: 0.7624 (tt)
REVERT: D 535 GLN cc_start: 0.8022 (pp30) cc_final: 0.7708 (pp30)
REVERT: D 547 GLN cc_start: 0.7670 (mm-40) cc_final: 0.7280 (tp40)
REVERT: D 553 MET cc_start: 0.7568 (mtm) cc_final: 0.6919 (mtm)
REVERT: D 567 GLU cc_start: 0.7662 (tp30) cc_final: 0.7395 (tp30)
REVERT: D 571 ARG cc_start: 0.8497 (mtt-85) cc_final: 0.8187 (mtt-85)
REVERT: M 43 GLU cc_start: 0.8434 (mm-30) cc_final: 0.7703 (mm-30)
REVERT: M 67 VAL cc_start: 0.8049 (t) cc_final: 0.7634 (m)
REVERT: M 85 ARG cc_start: 0.8413 (tpp80) cc_final: 0.8133 (tpp80)
REVERT: M 111 GLU cc_start: 0.8072 (tp30) cc_final: 0.7129 (tp30)
REVERT: M 167 TRP cc_start: 0.7921 (p90) cc_final: 0.6946 (p90)
REVERT: M 176 ASN cc_start: 0.6373 (m-40) cc_final: 0.5580 (m-40)
REVERT: M 196 SER cc_start: 0.6589 (m) cc_final: 0.6191 (p)
REVERT: M 201 GLU cc_start: 0.8255 (pt0) cc_final: 0.7718 (pt0)
REVERT: M 230 ASP cc_start: 0.7535 (t0) cc_final: 0.7129 (t0)
REVERT: M 233 PHE cc_start: 0.7772 (m-80) cc_final: 0.7397 (m-80)
REVERT: M 239 PHE cc_start: 0.7869 (t80) cc_final: 0.7564 (t80)
REVERT: M 250 PHE cc_start: 0.7926 (p90) cc_final: 0.6775 (p90)
REVERT: M 256 ASN cc_start: 0.7698 (t0) cc_final: 0.7467 (m110)
REVERT: M 316 LYS cc_start: 0.7919 (mmtm) cc_final: 0.7667 (mmtm)
REVERT: M 333 ASP cc_start: 0.8187 (t0) cc_final: 0.7722 (t0)
REVERT: M 376 GLN cc_start: 0.5990 (mm-40) cc_final: 0.5715 (mp10)
REVERT: M 380 GLN cc_start: 0.7568 (mt0) cc_final: 0.7019 (mt0)
REVERT: M 381 GLN cc_start: 0.7819 (tm-30) cc_final: 0.7236 (tm-30)
REVERT: M 394 MET cc_start: 0.6945 (tmm) cc_final: 0.6694 (tmm)
REVERT: M 406 LYS cc_start: 0.8060 (mtpt) cc_final: 0.7711 (ttmt)
REVERT: M 409 THR cc_start: 0.7813 (m) cc_final: 0.7473 (p)
REVERT: S 17 SER cc_start: 0.8130 (t) cc_final: 0.7839 (p)
REVERT: S 18 LYS cc_start: 0.8151 (tttp) cc_final: 0.7299 (tttp)
REVERT: S 29 GLN cc_start: 0.8626 (mt0) cc_final: 0.8357 (mt0)
REVERT: S 89 LEU cc_start: 0.7581 (mt) cc_final: 0.6767 (mt)
REVERT: S 97 LEU cc_start: 0.7959 (mt) cc_final: 0.7381 (mt)
REVERT: S 123 MET cc_start: 0.7469 (tpt) cc_final: 0.6928 (tpt)
REVERT: S 124 VAL cc_start: 0.8102 (t) cc_final: 0.7901 (t)
REVERT: S 128 MET cc_start: 0.7450 (mtp) cc_final: 0.6674 (mtp)
REVERT: B 50 MET cc_start: 0.7319 (mtm) cc_final: 0.6929 (mtm)
REVERT: B 63 MET cc_start: 0.6559 (mmm) cc_final: 0.5682 (mmm)
REVERT: B 75 ASN cc_start: 0.7765 (m110) cc_final: 0.7447 (m110)
REVERT: B 85 LYS cc_start: 0.7701 (mttt) cc_final: 0.7357 (tppt)
REVERT: B 86 ASN cc_start: 0.8329 (t0) cc_final: 0.8006 (t0)
REVERT: B 89 SER cc_start: 0.8643 (m) cc_final: 0.8396 (t)
REVERT: B 96 LYS cc_start: 0.7832 (mmmt) cc_final: 0.7520 (tptm)
REVERT: B 97 LEU cc_start: 0.7781 (mt) cc_final: 0.7453 (mt)
REVERT: B 129 GLN cc_start: 0.8460 (pm20) cc_final: 0.8111 (mt0)
REVERT: B 142 ILE cc_start: 0.7857 (tp) cc_final: 0.7312 (mm)
REVERT: B 152 MET cc_start: 0.7208 (tmm) cc_final: 0.6786 (tmm)
REVERT: B 156 LYS cc_start: 0.8002 (mtpt) cc_final: 0.7657 (mtpt)
REVERT: B 185 LYS cc_start: 0.7836 (mtpt) cc_final: 0.7393 (mmmt)
REVERT: B 187 MET cc_start: 0.7837 (mtp) cc_final: 0.7627 (mtp)
REVERT: B 197 LYS cc_start: 0.8695 (mttp) cc_final: 0.8214 (mtmm)
REVERT: B 199 LYS cc_start: 0.8398 (tmtt) cc_final: 0.7941 (tmtt)
REVERT: B 207 VAL cc_start: 0.8061 (p) cc_final: 0.7796 (m)
REVERT: B 213 GLU cc_start: 0.7844 (mm-30) cc_final: 0.7581 (tp30)
REVERT: B 227 ARG cc_start: 0.7901 (mtt-85) cc_final: 0.7697 (mtt-85)
REVERT: B 241 GLN cc_start: 0.7986 (mt0) cc_final: 0.7159 (mt0)
REVERT: B 297 HIS cc_start: 0.8011 (t-90) cc_final: 0.7712 (t-90)
REVERT: B 307 LEU cc_start: 0.8487 (mt) cc_final: 0.8152 (tp)
REVERT: B 323 TYR cc_start: 0.7598 (m-10) cc_final: 0.7351 (m-80)
REVERT: B 330 SER cc_start: 0.7578 (t) cc_final: 0.7353 (t)
REVERT: B 331 GLU cc_start: 0.7239 (mm-30) cc_final: 0.6791 (mm-30)
REVERT: B 345 SER cc_start: 0.8243 (t) cc_final: 0.7965 (t)
REVERT: B 348 GLU cc_start: 0.8118 (mm-30) cc_final: 0.7628 (mm-30)
REVERT: B 360 MET cc_start: 0.7286 (ttm) cc_final: 0.6934 (mmm)
REVERT: B 365 LYS cc_start: 0.8219 (mttt) cc_final: 0.7512 (mtpp)
REVERT: B 378 ARG cc_start: 0.7687 (mtt90) cc_final: 0.7417 (mtm180)
REVERT: B 386 LYS cc_start: 0.8069 (mttt) cc_final: 0.7393 (mttt)
REVERT: B 389 LYS cc_start: 0.8468 (mttt) cc_final: 0.8067 (mtpt)
REVERT: B 390 LEU cc_start: 0.8041 (tp) cc_final: 0.7796 (tt)
REVERT: B 391 GLU cc_start: 0.7348 (tp30) cc_final: 0.6792 (tp30)
REVERT: B 399 GLU cc_start: 0.8006 (pp20) cc_final: 0.7656 (pp20)
REVERT: B 426 GLN cc_start: 0.8508 (mt0) cc_final: 0.7922 (mm-40)
REVERT: B 433 THR cc_start: 0.7844 (t) cc_final: 0.7583 (t)
REVERT: B 465 ILE cc_start: 0.8658 (mt) cc_final: 0.8301 (tp)
REVERT: B 481 LYS cc_start: 0.8828 (mttt) cc_final: 0.8207 (mttt)
REVERT: B 483 MET cc_start: 0.8540 (mmm) cc_final: 0.8235 (mmm)
REVERT: B 486 LEU cc_start: 0.8259 (mt) cc_final: 0.7905 (mt)
REVERT: B 498 SER cc_start: 0.8604 (m) cc_final: 0.8151 (p)
REVERT: B 499 ILE cc_start: 0.8518 (mm) cc_final: 0.7862 (tp)
REVERT: B 521 MET cc_start: 0.6812 (mmp) cc_final: 0.6381 (mmm)
REVERT: B 539 LEU cc_start: 0.8188 (tp) cc_final: 0.7927 (tt)
REVERT: B 578 ARG cc_start: 0.7878 (tmm160) cc_final: 0.7435 (tmm160)
outliers start: 1
outliers final: 0
residues processed: 547
average time/residue: 0.3438
time to fit residues: 268.2910
Evaluate side-chains
539 residues out of total 1879 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 0
poor density : 539
time to evaluate : 2.057
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 208
random chunks:
chunk 68 optimal weight: 1.9990
chunk 31 optimal weight: 0.4980
chunk 32 optimal weight: 0.6980
chunk 94 optimal weight: 0.9990
chunk 183 optimal weight: 1.9990
chunk 137 optimal weight: 0.2980
chunk 170 optimal weight: 0.8980
chunk 190 optimal weight: 0.9990
chunk 77 optimal weight: 0.1980
chunk 133 optimal weight: 0.6980
chunk 58 optimal weight: 0.7980
overall best weight: 0.4780
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
D 214 ASN
** M 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
M 145 ASN
** M 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 246 HIS
B 321 GLN
Total number of N/Q/H flips: 4
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3990 r_free = 0.3990 target = 0.149220 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.127568 restraints weight = 35261.912|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.131837 restraints weight = 21247.108|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.134717 restraints weight = 13927.664|
|-----------------------------------------------------------------------------|
r_work (final): 0.3762
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6694
moved from start: 0.5475
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.047 17177 Z= 0.188
Angle : 0.582 12.031 23253 Z= 0.303
Chirality : 0.044 0.225 2705
Planarity : 0.004 0.049 2931
Dihedral : 8.272 165.616 2299
Min Nonbonded Distance : 1.876
Molprobity Statistics.
All-atom Clashscore : 10.31
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 2.67 %
Favored : 97.33 %
Rotamer:
Outliers : 0.05 %
Allowed : 0.27 %
Favored : 99.68 %
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 (0.19), residues: 2098
helix: 1.42 (0.15), residues: 1158
sheet: 0.25 (0.34), residues: 228
loop : 0.43 (0.25), residues: 712
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.016 0.002 TRP D 74
HIS 0.017 0.001 HIS D 268
PHE 0.032 0.002 PHE D 245
TYR 0.018 0.002 TYR B 412
ARG 0.009 0.001 ARG B 167
********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
4196 Ramachandran restraints generated.
2098 Oldfield, 0 Emsley, 2098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
4196 Ramachandran restraints generated.
2098 Oldfield, 0 Emsley, 2098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
535 residues out of total 1879 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 1
poor density : 534
time to evaluate : 2.086
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: A 38 LYS cc_start: 0.8365 (tttt) cc_final: 0.7877 (tttt)
REVERT: A 41 GLU cc_start: 0.5482 (mm-30) cc_final: 0.5164 (mm-30)
REVERT: A 84 ASN cc_start: 0.6921 (m-40) cc_final: 0.6294 (m-40)
REVERT: A 110 MET cc_start: 0.7718 (ttp) cc_final: 0.7462 (ttp)
REVERT: C 38 LYS cc_start: 0.8471 (tmtt) cc_final: 0.8195 (tmtt)
REVERT: C 39 LEU cc_start: 0.8569 (mp) cc_final: 0.7691 (mp)
REVERT: C 57 GLU cc_start: 0.6779 (mt-10) cc_final: 0.6567 (mt-10)
REVERT: C 86 GLN cc_start: 0.7091 (mt0) cc_final: 0.6371 (mt0)
REVERT: C 104 ARG cc_start: 0.8584 (ttp80) cc_final: 0.8099 (mtp85)
REVERT: C 173 LEU cc_start: 0.8460 (mt) cc_final: 0.8155 (mt)
REVERT: C 175 ASN cc_start: 0.7948 (m-40) cc_final: 0.7515 (t0)
REVERT: C 176 GLN cc_start: 0.6959 (mm-40) cc_final: 0.6625 (mm-40)
REVERT: D 1 MET cc_start: 0.4039 (ttp) cc_final: 0.3640 (ttp)
REVERT: D 83 MET cc_start: 0.8053 (mtt) cc_final: 0.7474 (mtt)
REVERT: D 91 LYS cc_start: 0.7452 (mtmt) cc_final: 0.7121 (mtmt)
REVERT: D 110 MET cc_start: 0.6608 (mmt) cc_final: 0.6301 (mmt)
REVERT: D 118 LYS cc_start: 0.8298 (tttt) cc_final: 0.7986 (mtpt)
REVERT: D 126 TYR cc_start: 0.8018 (m-80) cc_final: 0.7739 (m-80)
REVERT: D 155 MET cc_start: 0.7931 (mtm) cc_final: 0.7593 (mtm)
REVERT: D 157 HIS cc_start: 0.8341 (t-90) cc_final: 0.8123 (t70)
REVERT: D 176 LYS cc_start: 0.8432 (mmpt) cc_final: 0.7363 (tppt)
REVERT: D 221 LEU cc_start: 0.7487 (mp) cc_final: 0.7108 (mp)
REVERT: D 236 TRP cc_start: 0.7786 (t-100) cc_final: 0.7359 (t-100)
REVERT: D 273 MET cc_start: 0.8240 (pmm) cc_final: 0.7991 (pmm)
REVERT: D 275 LEU cc_start: 0.7955 (tp) cc_final: 0.7650 (tp)
REVERT: D 302 GLN cc_start: 0.8574 (tt0) cc_final: 0.7684 (tm-30)
REVERT: D 307 LYS cc_start: 0.8215 (mmtt) cc_final: 0.7828 (mmtt)
REVERT: D 324 LEU cc_start: 0.8565 (mt) cc_final: 0.8239 (mt)
REVERT: D 327 MET cc_start: 0.7148 (tpp) cc_final: 0.6496 (tpp)
REVERT: D 329 LYS cc_start: 0.8902 (mttt) cc_final: 0.8579 (mttt)
REVERT: D 336 LYS cc_start: 0.7810 (ptpp) cc_final: 0.7372 (ptpp)
REVERT: D 346 LEU cc_start: 0.8621 (mt) cc_final: 0.8394 (mt)
REVERT: D 362 ASP cc_start: 0.8633 (m-30) cc_final: 0.8341 (m-30)
REVERT: D 367 MET cc_start: 0.7031 (mtm) cc_final: 0.6785 (mtm)
REVERT: D 373 LEU cc_start: 0.8681 (tp) cc_final: 0.8286 (pp)
REVERT: D 374 MET cc_start: 0.7091 (mtt) cc_final: 0.5791 (mtt)
REVERT: D 378 LYS cc_start: 0.8870 (mttt) cc_final: 0.8367 (mttt)
REVERT: D 381 MET cc_start: 0.8012 (mtp) cc_final: 0.7743 (mtp)
REVERT: D 392 TYR cc_start: 0.7533 (t80) cc_final: 0.7043 (t80)
REVERT: D 393 ARG cc_start: 0.7778 (mtt180) cc_final: 0.7336 (mmm-85)
REVERT: D 399 LYS cc_start: 0.8018 (mmmt) cc_final: 0.7427 (mmmt)
REVERT: D 403 ILE cc_start: 0.8524 (pt) cc_final: 0.8112 (pt)
REVERT: D 406 GLN cc_start: 0.7562 (mt0) cc_final: 0.7333 (mt0)
REVERT: D 421 ILE cc_start: 0.8559 (mm) cc_final: 0.8243 (mm)
REVERT: D 429 GLU cc_start: 0.7639 (tm-30) cc_final: 0.7202 (tm-30)
REVERT: D 479 CYS cc_start: 0.8584 (m) cc_final: 0.8263 (m)
REVERT: D 530 TYR cc_start: 0.7481 (m-80) cc_final: 0.7036 (m-80)
REVERT: D 534 LEU cc_start: 0.8277 (mt) cc_final: 0.7633 (tt)
REVERT: D 535 GLN cc_start: 0.8001 (pp30) cc_final: 0.7693 (pp30)
REVERT: D 547 GLN cc_start: 0.7698 (mm-40) cc_final: 0.7308 (tp40)
REVERT: D 553 MET cc_start: 0.7570 (mtm) cc_final: 0.7009 (mtm)
REVERT: D 571 ARG cc_start: 0.8513 (mtt-85) cc_final: 0.8245 (mtt-85)
REVERT: M 43 GLU cc_start: 0.8442 (mm-30) cc_final: 0.7775 (mm-30)
REVERT: M 59 ILE cc_start: 0.8163 (mp) cc_final: 0.7797 (mm)
REVERT: M 67 VAL cc_start: 0.8056 (t) cc_final: 0.7581 (m)
REVERT: M 85 ARG cc_start: 0.8430 (tpp80) cc_final: 0.7770 (tpp80)
REVERT: M 111 GLU cc_start: 0.8102 (tp30) cc_final: 0.7097 (tp30)
REVERT: M 167 TRP cc_start: 0.7894 (p90) cc_final: 0.6898 (p90)
REVERT: M 176 ASN cc_start: 0.6457 (m-40) cc_final: 0.5653 (m-40)
REVERT: M 196 SER cc_start: 0.6567 (m) cc_final: 0.6203 (p)
REVERT: M 201 GLU cc_start: 0.8235 (pt0) cc_final: 0.7704 (pt0)
REVERT: M 250 PHE cc_start: 0.7851 (p90) cc_final: 0.6744 (p90)
REVERT: M 301 MET cc_start: 0.7261 (tpt) cc_final: 0.6578 (tpt)
REVERT: M 303 LYS cc_start: 0.8234 (mmtt) cc_final: 0.7879 (mmtt)
REVERT: M 333 ASP cc_start: 0.8246 (t0) cc_final: 0.7845 (t0)
REVERT: M 376 GLN cc_start: 0.5997 (mm-40) cc_final: 0.5736 (mp10)
REVERT: M 380 GLN cc_start: 0.7550 (mt0) cc_final: 0.6974 (mt0)
REVERT: M 381 GLN cc_start: 0.7798 (tm-30) cc_final: 0.7345 (tm-30)
REVERT: M 394 MET cc_start: 0.6924 (tmm) cc_final: 0.6629 (tmm)
REVERT: M 406 LYS cc_start: 0.8065 (mtpt) cc_final: 0.7740 (ttmt)
REVERT: M 409 THR cc_start: 0.7745 (m) cc_final: 0.7300 (p)
REVERT: S 17 SER cc_start: 0.8134 (t) cc_final: 0.7827 (p)
REVERT: S 18 LYS cc_start: 0.8049 (tttp) cc_final: 0.7242 (tttp)
REVERT: S 29 GLN cc_start: 0.8605 (mt0) cc_final: 0.8322 (mt0)
REVERT: S 89 LEU cc_start: 0.7580 (mt) cc_final: 0.6618 (mt)
REVERT: S 97 LEU cc_start: 0.7982 (mt) cc_final: 0.7389 (mt)
REVERT: S 123 MET cc_start: 0.7488 (tpt) cc_final: 0.6820 (tpt)
REVERT: S 124 VAL cc_start: 0.8011 (t) cc_final: 0.7708 (t)
REVERT: S 128 MET cc_start: 0.7390 (mtp) cc_final: 0.7018 (mtp)
REVERT: B 50 MET cc_start: 0.7276 (mtm) cc_final: 0.6941 (mtm)
REVERT: B 63 MET cc_start: 0.6553 (mmm) cc_final: 0.5788 (mmm)
REVERT: B 74 LYS cc_start: 0.8602 (mmmm) cc_final: 0.8387 (mmmm)
REVERT: B 85 LYS cc_start: 0.7693 (mttt) cc_final: 0.7384 (tppt)
REVERT: B 86 ASN cc_start: 0.8293 (t0) cc_final: 0.7933 (t0)
REVERT: B 89 SER cc_start: 0.8576 (m) cc_final: 0.8250 (t)
REVERT: B 96 LYS cc_start: 0.7864 (mmmt) cc_final: 0.7553 (tptm)
REVERT: B 97 LEU cc_start: 0.7781 (mt) cc_final: 0.7497 (mt)
REVERT: B 152 MET cc_start: 0.7236 (tmm) cc_final: 0.6823 (tmm)
REVERT: B 156 LYS cc_start: 0.8008 (mtpt) cc_final: 0.7501 (mtpp)
REVERT: B 185 LYS cc_start: 0.7832 (mtpt) cc_final: 0.7394 (mmmt)
REVERT: B 187 MET cc_start: 0.7892 (mtp) cc_final: 0.7603 (mtp)
REVERT: B 197 LYS cc_start: 0.8694 (mttp) cc_final: 0.8224 (mtmm)
REVERT: B 199 LYS cc_start: 0.8423 (tmtt) cc_final: 0.7908 (tmtt)
REVERT: B 207 VAL cc_start: 0.8062 (p) cc_final: 0.7814 (m)
REVERT: B 213 GLU cc_start: 0.7884 (mm-30) cc_final: 0.7665 (tp30)
REVERT: B 227 ARG cc_start: 0.7875 (mtt-85) cc_final: 0.7657 (mtt-85)
REVERT: B 241 GLN cc_start: 0.7976 (mt0) cc_final: 0.7154 (mt0)
REVERT: B 297 HIS cc_start: 0.8066 (t-90) cc_final: 0.7631 (t-90)
REVERT: B 307 LEU cc_start: 0.8517 (mt) cc_final: 0.8193 (tp)
REVERT: B 331 GLU cc_start: 0.7123 (mm-30) cc_final: 0.6790 (mm-30)
REVERT: B 342 LEU cc_start: 0.8504 (mt) cc_final: 0.8208 (mt)
REVERT: B 345 SER cc_start: 0.8254 (t) cc_final: 0.7732 (p)
REVERT: B 360 MET cc_start: 0.7492 (ttm) cc_final: 0.6966 (mmm)
REVERT: B 365 LYS cc_start: 0.8252 (mttt) cc_final: 0.7534 (mtpp)
REVERT: B 378 ARG cc_start: 0.7706 (mtt90) cc_final: 0.7392 (mtm180)
REVERT: B 386 LYS cc_start: 0.8126 (mttt) cc_final: 0.7393 (mttt)
REVERT: B 389 LYS cc_start: 0.8473 (mttt) cc_final: 0.8124 (mttm)
REVERT: B 390 LEU cc_start: 0.7911 (tp) cc_final: 0.7571 (tt)
REVERT: B 391 GLU cc_start: 0.7407 (tp30) cc_final: 0.6738 (tp30)
REVERT: B 426 GLN cc_start: 0.8473 (mt0) cc_final: 0.7913 (mm-40)
REVERT: B 462 VAL cc_start: 0.8618 (t) cc_final: 0.8400 (t)
REVERT: B 465 ILE cc_start: 0.8645 (mt) cc_final: 0.8194 (tp)
REVERT: B 481 LYS cc_start: 0.8826 (mttt) cc_final: 0.8238 (mttt)
REVERT: B 483 MET cc_start: 0.8557 (mmm) cc_final: 0.7871 (mmm)
REVERT: B 486 LEU cc_start: 0.8205 (mt) cc_final: 0.7975 (mt)
REVERT: B 498 SER cc_start: 0.8597 (m) cc_final: 0.8354 (p)
REVERT: B 499 ILE cc_start: 0.8523 (mm) cc_final: 0.7960 (tp)
REVERT: B 521 MET cc_start: 0.6835 (mmp) cc_final: 0.6375 (mmm)
REVERT: B 539 LEU cc_start: 0.8214 (tp) cc_final: 0.7942 (tt)
REVERT: B 578 ARG cc_start: 0.7899 (tmm160) cc_final: 0.7410 (tmm160)
outliers start: 1
outliers final: 0
residues processed: 534
average time/residue: 0.3333
time to fit residues: 254.9200
Evaluate side-chains
522 residues out of total 1879 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 0
poor density : 522
time to evaluate : 1.753
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 208
random chunks:
chunk 200 optimal weight: 0.7980
chunk 37 optimal weight: 0.9990
chunk 51 optimal weight: 0.5980
chunk 127 optimal weight: 0.7980
chunk 118 optimal weight: 0.4980
chunk 111 optimal weight: 0.6980
chunk 117 optimal weight: 0.5980
chunk 155 optimal weight: 0.0170
chunk 65 optimal weight: 3.9990
chunk 70 optimal weight: 2.9990
chunk 158 optimal weight: 0.7980
overall best weight: 0.4818
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
D 214 ASN
** M 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 246 HIS
B 321 GLN
Total number of N/Q/H flips: 3
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3986 r_free = 0.3986 target = 0.148843 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.127245 restraints weight = 35197.247|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.131459 restraints weight = 21194.818|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.134370 restraints weight = 13913.251|
|-----------------------------------------------------------------------------|
r_work (final): 0.3754
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6701
moved from start: 0.5625
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.039 17177 Z= 0.194
Angle : 0.582 9.562 23253 Z= 0.302
Chirality : 0.044 0.258 2705
Planarity : 0.004 0.050 2931
Dihedral : 8.178 165.745 2299
Min Nonbonded Distance : 1.864
Molprobity Statistics.
All-atom Clashscore : 10.45
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 2.86 %
Favored : 97.14 %
Rotamer:
Outliers : 0.05 %
Allowed : 0.21 %
Favored : 99.73 %
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: 1.39 (0.19), residues: 2098
helix: 1.47 (0.15), residues: 1152
sheet: 0.19 (0.35), residues: 228
loop : 0.46 (0.25), residues: 718
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.016 0.002 TRP C 78
HIS 0.015 0.001 HIS D 268
PHE 0.033 0.002 PHE B 409
TYR 0.017 0.002 TYR D 392
ARG 0.010 0.001 ARG B 167
Origin is already at (0, 0, 0), no shifts will be applied
===============================================================================
Job complete
usr+sys time: 6141.71 seconds
wall clock time: 111 minutes 30.55 seconds (6690.55 seconds total)