Starting phenix.real_space_refine
on Fri Jan 17 17:53:56 2025 by dcliebschner
===============================================================================
Processing files:
-------------------------------------------------------------------------------
Found model, /net/cci-nas-00/data/ceres_data/8z85_39838/01_2025/8z85_39838.cif
Found real_map, /net/cci-nas-00/data/ceres_data/8z85_39838/01_2025/8z85_39838.map
Processing PHIL parameters:
-------------------------------------------------------------------------------
Adding command-line PHIL:
-------------------------
refinement.macro_cycles=10
scattering_table=electron
resolution=2.3
write_initial_geo_file=False
Final processed PHIL parameters:
-------------------------------------------------------------------------------
data_manager {
real_map_files = "/net/cci-nas-00/data/ceres_data/8z85_39838/01_2025/8z85_39838.map"
default_real_map = "/net/cci-nas-00/data/ceres_data/8z85_39838/01_2025/8z85_39838.map"
model {
file = "/net/cci-nas-00/data/ceres_data/8z85_39838/01_2025/8z85_39838.cif"
}
default_model = "/net/cci-nas-00/data/ceres_data/8z85_39838/01_2025/8z85_39838.cif"
}
resolution = 2.3
write_initial_geo_file = False
refinement {
macro_cycles = 10
}
qi {
qm_restraints {
package {
program = *test
}
}
}
Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.
Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
Set to: 0
Set model cs if undefined
Decide on map wrapping
Map wrapping is set to: False
Normalize map: mean=0, sd=1
Input map: mean= 0.000 sd= 0.006
Set stop_for_unknowns flag
Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Anisotropic ADP refinement not supported. Converting 1075 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
Set to: electron
Number of scattering types: 5
Type Number sf(0) Gaussians
P 17 5.49 5
S 63 5.16 5
C 6585 2.51 5
N 1804 2.21 5
O 1998 1.98 5
sf(0) = scattering factor at diffraction angle 0.
Process input model
Symmetric amino acids flipped. Time to flip 8 residue(s): 0.03s
Monomer Library directory:
"/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
Total number of atoms: 10467
Number of models: 1
Model: ""
Number of chains: 5
Chain: "A"
Number of atoms: 4771
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 591, 4771
Classifications: {'peptide': 591}
Modifications used: {'COO': 1}
Link IDs: {'PTRANS': 29, 'TRANS': 561}
Chain breaks: 2
Chain: "B"
Number of atoms: 4702
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 590, 4702
Classifications: {'peptide': 590}
Link IDs: {'PTRANS': 31, 'TRANS': 558}
Chain breaks: 2
Chain: "C"
Number of atoms: 608
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 75, 608
Classifications: {'peptide': 75}
Link IDs: {'PTRANS': 6, 'TRANS': 68}
Chain breaks: 1
Chain: "D"
Number of atoms: 283
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 13, 283
Classifications: {'RNA': 13}
Modifications used: {'5*END': 1, 'rna2p_pur': 3, 'rna3p_pur': 8, 'rna3p_pyr': 2}
Link IDs: {'rna2p': 3, 'rna3p': 9}
Chain: "E"
Number of atoms: 103
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 5, 103
Classifications: {'RNA': 5}
Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 2, 'rna3p_pyr': 2}
Link IDs: {'rna2p': 2, 'rna3p': 2}
Time building chain proxies: 6.52, per 1000 atoms: 0.62
Number of scatterers: 10467
At special positions: 0
Unit cell: (92.402, 100.708, 126.663, 90, 90, 90)
Space group: P 1 (No. 1)
Number of sites at special positions: 0
Number of scattering types: 5
Type Number sf(0)
S 63 16.00
P 17 15.00
O 1998 8.00
N 1804 7.00
C 6585 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: 2.58
Conformation dependent library (CDL) restraints added in 1.3 seconds
2480 Ramachandran restraints generated.
1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2.
Adding C-beta torsion restraints...
Number of C-beta restraints generated: 2386
Finding SS restraints...
Secondary structure from input PDB file:
54 helices and 12 sheets defined
49.6% alpha, 11.6% beta
2 base pairs and 8 stacking pairs defined.
Time for finding SS restraints: 3.52
Creating SS restraints...
Processing helix chain 'A' and resid 9 through 16
Processing helix chain 'A' and resid 27 through 46
Processing helix chain 'A' and resid 103 through 107
Processing helix chain 'A' and resid 126 through 133
removed outlier: 3.752A pdb=" N LEU A 131 " --> pdb=" O GLU A 127 " (cutoff:3.500A)
removed outlier: 3.522A pdb=" N VAL A 132 " --> pdb=" O SER A 128 " (cutoff:3.500A)
Processing helix chain 'A' and resid 134 through 155
removed outlier: 4.745A pdb=" N GLY A 143 " --> pdb=" O GLN A 139 " (cutoff:3.500A)
removed outlier: 4.109A pdb=" N PHE A 144 " --> pdb=" O ASP A 140 " (cutoff:3.500A)
removed outlier: 5.856A pdb=" N CYS A 146 " --> pdb=" O LYS A 142 " (cutoff:3.500A)
Processing helix chain 'A' and resid 157 through 166
Processing helix chain 'A' and resid 176 through 184
Processing helix chain 'A' and resid 233 through 235
No H-bonds generated for 'chain 'A' and resid 233 through 235'
Processing helix chain 'A' and resid 246 through 257
removed outlier: 3.965A pdb=" N GLN A 257 " --> pdb=" O TRP A 253 " (cutoff:3.500A)
Processing helix chain 'A' and resid 270 through 272
No H-bonds generated for 'chain 'A' and resid 270 through 272'
Processing helix chain 'A' and resid 273 through 286
removed outlier: 3.526A pdb=" N LEU A 277 " --> pdb=" O VAL A 273 " (cutoff:3.500A)
Processing helix chain 'A' and resid 296 through 302
Processing helix chain 'A' and resid 304 through 316
Processing helix chain 'A' and resid 335 through 345
removed outlier: 3.999A pdb=" N GLU A 339 " --> pdb=" O PRO A 335 " (cutoff:3.500A)
Processing helix chain 'A' and resid 362 through 381
removed outlier: 4.433A pdb=" N ARG A 381 " --> pdb=" O GLU A 377 " (cutoff:3.500A)
Processing helix chain 'A' and resid 382 through 401
removed outlier: 3.710A pdb=" N GLN A 401 " --> pdb=" O ARG A 397 " (cutoff:3.500A)
Processing helix chain 'A' and resid 485 through 492
Processing helix chain 'A' and resid 493 through 497
Processing helix chain 'A' and resid 498 through 517
Processing helix chain 'A' and resid 540 through 557
Processing helix chain 'A' and resid 559 through 581
removed outlier: 4.810A pdb=" N ARG A 571 " --> pdb=" O ALA A 567 " (cutoff:3.500A)
removed outlier: 4.261A pdb=" N LEU A 572 " --> pdb=" O ASN A 568 " (cutoff:3.500A)
removed outlier: 3.707A pdb=" N GLU A 581 " --> pdb=" O HIS A 577 " (cutoff:3.500A)
Processing helix chain 'A' and resid 592 through 599
removed outlier: 4.014A pdb=" N LYS A 596 " --> pdb=" O ARG A 592 " (cutoff:3.500A)
removed outlier: 3.794A pdb=" N VAL A 597 " --> pdb=" O PRO A 593 " (cutoff:3.500A)
Processing helix chain 'A' and resid 604 through 617
Processing helix chain 'B' and resid 1 through 5
Processing helix chain 'B' and resid 13 through 20
removed outlier: 4.244A pdb=" N GLU B 17 " --> pdb=" O THR B 14 " (cutoff:3.500A)
removed outlier: 3.757A pdb=" N TYR B 20 " --> pdb=" O GLU B 17 " (cutoff:3.500A)
Processing helix chain 'B' and resid 33 through 47
Proline residue: B 44 - end of helix
Processing helix chain 'B' and resid 53 through 58
Processing helix chain 'B' and resid 66 through 70
Processing helix chain 'B' and resid 80 through 94
Processing helix chain 'B' and resid 95 through 108
removed outlier: 3.622A pdb=" N LYS B 101 " --> pdb=" O PRO B 97 " (cutoff:3.500A)
removed outlier: 3.927A pdb=" N LEU B 102 " --> pdb=" O ALA B 98 " (cutoff:3.500A)
Processing helix chain 'B' and resid 108 through 113
removed outlier: 3.713A pdb=" N LYS B 112 " --> pdb=" O VAL B 108 " (cutoff:3.500A)
Processing helix chain 'B' and resid 114 through 121
removed outlier: 3.652A pdb=" N GLU B 117 " --> pdb=" O LYS B 114 " (cutoff:3.500A)
Processing helix chain 'B' and resid 134 through 151
Processing helix chain 'B' and resid 157 through 169
removed outlier: 3.543A pdb=" N MET B 169 " --> pdb=" O ILE B 165 " (cutoff:3.500A)
Processing helix chain 'B' and resid 216 through 224
Processing helix chain 'B' and resid 247 through 266
removed outlier: 4.127A pdb=" N GLY B 252 " --> pdb=" O MET B 248 " (cutoff:3.500A)
removed outlier: 5.117A pdb=" N PHE B 253 " --> pdb=" O LEU B 249 " (cutoff:3.500A)
removed outlier: 3.539A pdb=" N ILE B 256 " --> pdb=" O GLY B 252 " (cutoff:3.500A)
Processing helix chain 'B' and resid 279 through 287
Processing helix chain 'B' and resid 310 through 326
removed outlier: 3.728A pdb=" N MET B 314 " --> pdb=" O ASP B 310 " (cutoff:3.500A)
Processing helix chain 'B' and resid 328 through 344
Proline residue: B 338 - end of helix
removed outlier: 3.557A pdb=" N SER B 344 " --> pdb=" O MET B 340 " (cutoff:3.500A)
Processing helix chain 'B' and resid 373 through 378
removed outlier: 4.429A pdb=" N ARG B 378 " --> pdb=" O ASP B 375 " (cutoff:3.500A)
Processing helix chain 'B' and resid 396 through 409
removed outlier: 3.618A pdb=" N SER B 400 " --> pdb=" O TYR B 396 " (cutoff:3.500A)
removed outlier: 3.850A pdb=" N SER B 407 " --> pdb=" O LEU B 403 " (cutoff:3.500A)
removed outlier: 3.676A pdb=" N ILE B 408 " --> pdb=" O ALA B 404 " (cutoff:3.500A)
removed outlier: 3.844A pdb=" N GLU B 409 " --> pdb=" O LEU B 405 " (cutoff:3.500A)
Processing helix chain 'B' and resid 432 through 449
removed outlier: 3.552A pdb=" N LYS B 448 " --> pdb=" O ARG B 444 " (cutoff:3.500A)
Processing helix chain 'B' and resid 456 through 459
removed outlier: 3.774A pdb=" N CYS B 459 " --> pdb=" O PRO B 456 " (cutoff:3.500A)
No H-bonds generated for 'chain 'B' and resid 456 through 459'
Processing helix chain 'B' and resid 496 through 514
Processing helix chain 'B' and resid 518 through 537
removed outlier: 3.674A pdb=" N TYR B 537 " --> pdb=" O TYR B 533 " (cutoff:3.500A)
Processing helix chain 'B' and resid 543 through 552
removed outlier: 3.594A pdb=" N MET B 549 " --> pdb=" O ARG B 545 " (cutoff:3.500A)
Processing helix chain 'B' and resid 558 through 562
Processing helix chain 'B' and resid 575 through 583
Processing helix chain 'B' and resid 587 through 595
Processing helix chain 'C' and resid 52 through 55
Processing helix chain 'C' and resid 56 through 62
Processing helix chain 'C' and resid 102 through 111
removed outlier: 3.921A pdb=" N LYS C 109 " --> pdb=" O ASP C 105 " (cutoff:3.500A)
Processing helix chain 'C' and resid 115 through 123
Processing helix chain 'C' and resid 124 through 136
removed outlier: 3.688A pdb=" N LYS C 129 " --> pdb=" O ALA C 125 " (cutoff:3.500A)
removed outlier: 3.613A pdb=" N VAL C 130 " --> pdb=" O GLU C 126 " (cutoff:3.500A)
removed outlier: 3.613A pdb=" N THR C 136 " --> pdb=" O ARG C 132 " (cutoff:3.500A)
Processing sheet with id=AA1, first strand: chain 'A' and resid 87 through 88
removed outlier: 3.782A pdb=" N LEU A 117 " --> pdb=" O LYS A 97 " (cutoff:3.500A)
Processing sheet with id=AA2, first strand: chain 'A' and resid 210 through 211
Processing sheet with id=AA3, first strand: chain 'A' and resid 210 through 211
removed outlier: 4.503A pdb=" N ASN B 453 " --> pdb=" O GLU B 303 " (cutoff:3.500A)
Processing sheet with id=AA4, first strand: chain 'A' and resid 237 through 238
removed outlier: 4.253A pdb=" N ILE A 450 " --> pdb=" O GLU A 238 " (cutoff:3.500A)
removed outlier: 7.141A pdb=" N TRP A 426 " --> pdb=" O ILE A 450 " (cutoff:3.500A)
WARNING: can't find start of bonding for strands!
previous: chain 'A' and resid 423 through 431
current: chain 'A' and resid 463 through 469
removed outlier: 6.757A pdb=" N VAL A 464 " --> pdb=" O ILE A 263 " (cutoff:3.500A)
Processing sheet with id=AA5, first strand: chain 'A' and resid 240 through 242
removed outlier: 7.141A pdb=" N TRP A 426 " --> pdb=" O ILE A 450 " (cutoff:3.500A)
WARNING: can't find start of bonding for strands!
previous: chain 'A' and resid 442 through 451
current: chain 'A' and resid 290 through 291
Processing sheet with id=AA6, first strand: chain 'A' and resid 322 through 323
Processing sheet with id=AA7, first strand: chain 'A' and resid 526 through 531
Processing sheet with id=AA8, first strand: chain 'B' and resid 124 through 125
Processing sheet with id=AA9, first strand: chain 'B' and resid 173 through 175
Processing sheet with id=AB1, first strand: chain 'B' and resid 242 through 245
removed outlier: 4.587A pdb=" N THR B 228 " --> pdb=" O ASP B 348 " (cutoff:3.500A)
Processing sheet with id=AB2, first strand: chain 'B' and resid 467 through 469
Processing sheet with id=AB3, first strand: chain 'B' and resid 633 through 634
removed outlier: 4.697A pdb=" N THR B 633 " --> pdb=" O SER C 68 " (cutoff:3.500A)
463 hydrogen bonds defined for protein.
1278 hydrogen bond angles defined for protein.
Restraints generated for nucleic acids:
5 hydrogen bonds
10 hydrogen bond angles
0 basepair planarities
2 basepair parallelities
8 stacking parallelities
Total time for adding SS restraints: 3.34
Time building geometry restraints manager: 2.97 seconds
NOTE: a complete listing of the restraints can be obtained by requesting
output of .geo file.
Histogram of bond lengths:
1.22 - 1.33: 2846
1.33 - 1.45: 1854
1.45 - 1.57: 5896
1.57 - 1.69: 33
1.69 - 1.81: 105
Bond restraints: 10734
Sorted by residual:
bond pdb=" CA LYS A 170 "
pdb=" CB LYS A 170 "
ideal model delta sigma weight residual
1.518 1.541 -0.023 2.08e-02 2.31e+03 1.27e+00
bond pdb=" C ALA A 169 "
pdb=" N LYS A 170 "
ideal model delta sigma weight residual
1.325 1.338 -0.013 1.14e-02 7.69e+03 1.25e+00
bond pdb=" CA VAL B 491 "
pdb=" CB VAL B 491 "
ideal model delta sigma weight residual
1.546 1.538 0.009 8.80e-03 1.29e+04 9.61e-01
bond pdb=" CA ILE A 414 "
pdb=" CB ILE A 414 "
ideal model delta sigma weight residual
1.540 1.528 0.012 1.36e-02 5.41e+03 8.37e-01
bond pdb=" CB MET B 526 "
pdb=" CG MET B 526 "
ideal model delta sigma weight residual
1.520 1.498 0.022 3.00e-02 1.11e+03 5.58e-01
... (remaining 10729 not shown)
Histogram of bond angle deviations from ideal:
0.00 - 1.38: 14303
1.38 - 2.76: 245
2.76 - 4.14: 59
4.14 - 5.51: 13
5.51 - 6.89: 3
Bond angle restraints: 14623
Sorted by residual:
angle pdb=" N GLY B 352 "
pdb=" CA GLY B 352 "
pdb=" C GLY B 352 "
ideal model delta sigma weight residual
112.04 116.98 -4.94 1.02e+00 9.61e-01 2.35e+01
angle pdb=" C LYS A 170 "
pdb=" CA LYS A 170 "
pdb=" CB LYS A 170 "
ideal model delta sigma weight residual
115.79 111.83 3.96 1.19e+00 7.06e-01 1.11e+01
angle pdb=" C SER B 8 "
pdb=" N GLU B 9 "
pdb=" CA GLU B 9 "
ideal model delta sigma weight residual
121.54 126.53 -4.99 1.91e+00 2.74e-01 6.82e+00
angle pdb=" C TYR B 210 "
pdb=" N THR B 211 "
pdb=" CA THR B 211 "
ideal model delta sigma weight residual
121.54 126.05 -4.51 1.91e+00 2.74e-01 5.58e+00
angle pdb=" CB MET A 546 "
pdb=" CG MET A 546 "
pdb=" SD MET A 546 "
ideal model delta sigma weight residual
112.70 105.81 6.89 3.00e+00 1.11e-01 5.28e+00
... (remaining 14618 not shown)
Histogram of dihedral angle deviations from ideal:
0.00 - 17.19: 5978
17.19 - 34.38: 428
34.38 - 51.58: 80
51.58 - 68.77: 29
68.77 - 85.96: 15
Dihedral angle restraints: 6530
sinusoidal: 2854
harmonic: 3676
Sorted by residual:
dihedral pdb=" CA MET A 546 "
pdb=" C MET A 546 "
pdb=" N ILE A 547 "
pdb=" CA ILE A 547 "
ideal model delta harmonic sigma weight residual
180.00 156.37 23.63 0 5.00e+00 4.00e-02 2.23e+01
dihedral pdb=" CA ILE B 212 "
pdb=" C ILE B 212 "
pdb=" N LYS B 213 "
pdb=" CA LYS B 213 "
ideal model delta harmonic sigma weight residual
-180.00 -162.49 -17.51 0 5.00e+00 4.00e-02 1.23e+01
dihedral pdb=" CG ARG A 570 "
pdb=" CD ARG A 570 "
pdb=" NE ARG A 570 "
pdb=" CZ ARG A 570 "
ideal model delta sinusoidal sigma weight residual
180.00 135.09 44.91 2 1.50e+01 4.44e-03 1.06e+01
... (remaining 6527 not shown)
Histogram of chiral volume deviations from ideal:
0.000 - 0.027: 1025
0.027 - 0.055: 390
0.055 - 0.082: 132
0.082 - 0.109: 73
0.109 - 0.136: 25
Chirality restraints: 1645
Sorted by residual:
chirality pdb=" CA ILE B 460 "
pdb=" N ILE B 460 "
pdb=" C ILE B 460 "
pdb=" CB ILE B 460 "
both_signs ideal model delta sigma weight residual
False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.64e-01
chirality pdb=" CA ILE A 480 "
pdb=" N ILE A 480 "
pdb=" C ILE A 480 "
pdb=" CB ILE A 480 "
both_signs ideal model delta sigma weight residual
False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.49e-01
chirality pdb=" CA ILE C 75 "
pdb=" N ILE C 75 "
pdb=" C ILE C 75 "
pdb=" CB ILE C 75 "
both_signs ideal model delta sigma weight residual
False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.32e-01
... (remaining 1642 not shown)
Planarity restraints: 1804
Sorted by residual:
delta sigma weight rms_deltas residual
plane pdb=" C THR B 555 " -0.029 5.00e-02 4.00e+02 4.37e-02 3.05e+00
pdb=" N PRO B 556 " 0.076 5.00e-02 4.00e+02
pdb=" CA PRO B 556 " -0.023 5.00e-02 4.00e+02
pdb=" CD PRO B 556 " -0.024 5.00e-02 4.00e+02
delta sigma weight rms_deltas residual
plane pdb=" C ASP A 418 " -0.028 5.00e-02 4.00e+02 4.30e-02 2.96e+00
pdb=" N PRO A 419 " 0.074 5.00e-02 4.00e+02
pdb=" CA PRO A 419 " -0.022 5.00e-02 4.00e+02
pdb=" CD PRO A 419 " -0.024 5.00e-02 4.00e+02
delta sigma weight rms_deltas residual
plane pdb=" C SER A 108 " 0.028 5.00e-02 4.00e+02 4.22e-02 2.85e+00
pdb=" N PRO A 109 " -0.073 5.00e-02 4.00e+02
pdb=" CA PRO A 109 " 0.022 5.00e-02 4.00e+02
pdb=" CD PRO A 109 " 0.023 5.00e-02 4.00e+02
... (remaining 1801 not shown)
Histogram of nonbonded interaction distances:
2.23 - 2.77: 1798
2.77 - 3.30: 10157
3.30 - 3.83: 18189
3.83 - 4.37: 22434
4.37 - 4.90: 36834
Nonbonded interactions: 89412
Sorted by model distance:
nonbonded pdb=" O SER A 482 "
pdb=" O2' A D 3 "
model vdw
2.234 3.040
nonbonded pdb=" OE2 GLU A 122 "
pdb=" NZ LYS B 109 "
model vdw
2.263 3.120
nonbonded pdb=" NH2 ARG A 264 "
pdb=" O TYR A 459 "
model vdw
2.292 3.120
nonbonded pdb=" OD2 ASP B 362 "
pdb=" NZ LYS B 364 "
model vdw
2.296 3.120
nonbonded pdb=" OD1 ASN B 11 "
pdb=" OG1 THR B 14 "
model vdw
2.298 3.040
... (remaining 89407 not shown)
NOTE: a complete listing of the restraints can be obtained by requesting
output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============
No NCS relation were found !!!
================================
Found NCS groups:
found none.
Set up NCS constraints
No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
Set random seed: 0.000
Set model cs if undefined: 0.000
Decide on map wrapping: 0.000
Normalize map: mean=0, sd=1: 0.410
Set stop_for_unknowns flag: 0.000
Assert model is a single copy model: 0.000
Assert all atoms have isotropic ADPs: 0.080
Construct map_model_manager: 0.010
Extract box with map and model: 0.450
Check model and map are aligned: 0.090
Set scattering table: 0.100
Process input model: 28.380
Find NCS groups from input model: 0.140
Set up NCS constraints: 0.040
Set refine NCS operators: 0.000
Adjust number of macro_cycles: 0.000
Reset NCS operators: 0.000
Extract rigid body selections: 0.000
Check and reset occupancies: 0.000
Load rotamer database and sin/cos tables:12.590
Set ADP refinement strategy: 0.000
Make a string to write initial .geo file:0.000
Internal consistency checks: 0.000
Total: 42.290
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8330
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 : 0.002 0.029 10734 Z= 0.136
Angle : 0.484 6.893 14623 Z= 0.249
Chirality : 0.038 0.136 1645
Planarity : 0.004 0.044 1804
Dihedral : 13.262 85.961 4144
Min Nonbonded Distance : 2.234
Molprobity Statistics.
All-atom Clashscore : 7.19
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 2.42 %
Favored : 97.58 %
Rotamer:
Outliers : 0.00 %
Allowed : 0.09 %
Favored : 99.91 %
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: 0.02 (0.23), residues: 1240
helix: 0.58 (0.22), residues: 543
sheet: 0.43 (0.46), residues: 123
loop : -0.55 (0.25), residues: 574
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.008 0.001 TRP C 65
HIS 0.006 0.001 HIS B 476
PHE 0.017 0.001 PHE A 483
TYR 0.015 0.001 TYR B 22
ARG 0.008 0.000 ARG B 131
*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
2480 Ramachandran restraints generated.
1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
2480 Ramachandran restraints generated.
1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
160 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 0
poor density : 160
time to evaluate : 1.333
Fit side-chains
revert: symmetry clash
REVERT: A 155 ASN cc_start: 0.7519 (m110) cc_final: 0.7080 (m110)
REVERT: B 422 ASP cc_start: 0.7675 (p0) cc_final: 0.7249 (p0)
REVERT: B 575 ASP cc_start: 0.8128 (t70) cc_final: 0.7884 (t70)
outliers start: 0
outliers final: 0
residues processed: 160
average time/residue: 1.6655
time to fit residues: 282.9072
Evaluate side-chains
130 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 0
poor density : 130
time to evaluate : 1.231
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 126
random chunks:
chunk 106 optimal weight: 6.9990
chunk 95 optimal weight: 4.9990
chunk 52 optimal weight: 1.9990
chunk 32 optimal weight: 0.0670
chunk 64 optimal weight: 4.9990
chunk 51 optimal weight: 0.5980
chunk 98 optimal weight: 3.9990
chunk 38 optimal weight: 6.9990
chunk 60 optimal weight: 3.9990
chunk 73 optimal weight: 6.9990
chunk 114 optimal weight: 0.4980
overall best weight: 1.4322
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 307 GLN
A 311 GLN
A 516 ASN
** A 577 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 123 GLN
B 132 ASN
B 148 GLN
** B 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
Total number of N/Q/H flips: 6
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.122058 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3045 r_free = 0.3045 target = 0.082927 restraints weight = 13926.512|
|-----------------------------------------------------------------------------|
r_work (start): 0.2985 rms_B_bonded: 2.09
r_work: 0.2844 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.2718 rms_B_bonded: 4.04 restraints_weight: 0.2500
r_work (final): 0.2718
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8528
moved from start: 0.1405
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.063 10734 Z= 0.230
Angle : 0.581 7.408 14623 Z= 0.299
Chirality : 0.043 0.182 1645
Planarity : 0.005 0.049 1804
Dihedral : 10.234 73.017 1629
Min Nonbonded Distance : 2.527
Molprobity Statistics.
All-atom Clashscore : 6.85
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 2.50 %
Favored : 97.50 %
Rotamer:
Outliers : 1.61 %
Allowed : 7.23 %
Favored : 91.17 %
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: 0.51 (0.24), residues: 1240
helix: 1.21 (0.22), residues: 559
sheet: -0.02 (0.45), residues: 128
loop : -0.40 (0.26), residues: 553
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.010 0.001 TRP A 426
HIS 0.005 0.001 HIS A 577
PHE 0.018 0.002 PHE A 483
TYR 0.018 0.002 TYR A 489
ARG 0.013 0.001 ARG A 536
*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
2480 Ramachandran restraints generated.
1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
2480 Ramachandran restraints generated.
1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
151 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 18
poor density : 133
time to evaluate : 1.260
Fit side-chains
revert: symmetry clash
REVERT: A 155 ASN cc_start: 0.8737 (m110) cc_final: 0.8520 (m110)
REVERT: B 93 ARG cc_start: 0.8264 (OUTLIER) cc_final: 0.7887 (mpp80)
REVERT: B 332 MET cc_start: 0.8813 (OUTLIER) cc_final: 0.8002 (mmm)
REVERT: C 68 SER cc_start: 0.8917 (OUTLIER) cc_final: 0.8490 (p)
outliers start: 18
outliers final: 5
residues processed: 138
average time/residue: 1.6615
time to fit residues: 243.6433
Evaluate side-chains
138 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 8
poor density : 130
time to evaluate : 1.180
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 438 ARG
Chi-restraints excluded: chain B residue 93 ARG
Chi-restraints excluded: chain B residue 153 LYS
Chi-restraints excluded: chain B residue 332 MET
Chi-restraints excluded: chain B residue 393 MET
Chi-restraints excluded: chain B residue 625 SER
Chi-restraints excluded: chain C residue 68 SER
Chi-restraints excluded: chain C residue 102 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 126
random chunks:
chunk 25 optimal weight: 0.0470
chunk 59 optimal weight: 4.9990
chunk 43 optimal weight: 1.9990
chunk 98 optimal weight: 1.9990
chunk 61 optimal weight: 4.9990
chunk 117 optimal weight: 2.9990
chunk 97 optimal weight: 1.9990
chunk 2 optimal weight: 40.0000
chunk 34 optimal weight: 3.9990
chunk 89 optimal weight: 0.2980
chunk 113 optimal weight: 5.9990
overall best weight: 1.2684
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 307 GLN
A 311 GLN
A 358 ASN
A 516 ASN
B 148 GLN
** B 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 131 GLN
Total number of N/Q/H flips: 6
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.120505 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3016 r_free = 0.3016 target = 0.081664 restraints weight = 14128.615|
|-----------------------------------------------------------------------------|
r_work (start): 0.2991 rms_B_bonded: 2.09
r_work: 0.2847 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.2719 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.2719
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8549
moved from start: 0.1721
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.032 10734 Z= 0.193
Angle : 0.525 7.808 14623 Z= 0.270
Chirality : 0.041 0.164 1645
Planarity : 0.004 0.038 1804
Dihedral : 10.214 73.146 1629
Min Nonbonded Distance : 2.544
Molprobity Statistics.
All-atom Clashscore : 6.51
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 2.18 %
Favored : 97.82 %
Rotamer:
Outliers : 2.05 %
Allowed : 8.74 %
Favored : 89.21 %
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: 0.71 (0.24), residues: 1240
helix: 1.51 (0.22), residues: 560
sheet: -0.24 (0.43), residues: 130
loop : -0.38 (0.26), residues: 550
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.010 0.001 TRP A 336
HIS 0.005 0.001 HIS B 476
PHE 0.015 0.001 PHE A 483
TYR 0.014 0.001 TYR B 533
ARG 0.006 0.000 ARG B 151
*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
2480 Ramachandran restraints generated.
1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
2480 Ramachandran restraints generated.
1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
156 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 23
poor density : 133
time to evaluate : 1.214
Fit side-chains
revert: symmetry clash
revert: symmetry clash
REVERT: A 468 LYS cc_start: 0.8912 (OUTLIER) cc_final: 0.8439 (mmmm)
REVERT: A 489 TYR cc_start: 0.9034 (t80) cc_final: 0.8833 (t80)
REVERT: A 546 MET cc_start: 0.8840 (OUTLIER) cc_final: 0.8634 (ptm)
REVERT: B 17 GLU cc_start: 0.8549 (pt0) cc_final: 0.8207 (pt0)
REVERT: B 131 ARG cc_start: 0.8555 (ptt90) cc_final: 0.8298 (ptt90)
REVERT: B 383 ASN cc_start: 0.8736 (t0) cc_final: 0.8302 (t0)
REVERT: B 436 MET cc_start: 0.9156 (ttp) cc_final: 0.8870 (ttp)
REVERT: B 588 GLU cc_start: 0.7772 (tp30) cc_final: 0.7490 (tp30)
outliers start: 23
outliers final: 11
residues processed: 143
average time/residue: 1.5983
time to fit residues: 242.7567
Evaluate side-chains
140 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 13
poor density : 127
time to evaluate : 1.268
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 325 GLU
Chi-restraints excluded: chain A residue 438 ARG
Chi-restraints excluded: chain A residue 468 LYS
Chi-restraints excluded: chain A residue 515 GLU
Chi-restraints excluded: chain A residue 546 MET
Chi-restraints excluded: chain B residue 22 TYR
Chi-restraints excluded: chain B residue 153 LYS
Chi-restraints excluded: chain B residue 625 SER
Chi-restraints excluded: chain C residue 67 ILE
Chi-restraints excluded: chain C residue 68 SER
Chi-restraints excluded: chain C residue 72 SER
Chi-restraints excluded: chain C residue 102 VAL
Chi-restraints excluded: chain C residue 108 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 126
random chunks:
chunk 78 optimal weight: 2.9990
chunk 85 optimal weight: 7.9990
chunk 30 optimal weight: 0.6980
chunk 38 optimal weight: 2.9990
chunk 77 optimal weight: 0.5980
chunk 24 optimal weight: 4.9990
chunk 112 optimal weight: 9.9990
chunk 117 optimal weight: 0.8980
chunk 14 optimal weight: 3.9990
chunk 2 optimal weight: 9.9990
chunk 48 optimal weight: 4.9990
overall best weight: 1.6384
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 516 ASN
** A 577 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 148 GLN
** B 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
Total number of N/Q/H flips: 2
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.119274 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2989 r_free = 0.2989 target = 0.080015 restraints weight = 13908.035|
|-----------------------------------------------------------------------------|
r_work (start): 0.2964 rms_B_bonded: 2.07
r_work: 0.2817 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.2687 rms_B_bonded: 4.01 restraints_weight: 0.2500
r_work (final): 0.2687
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8564
moved from start: 0.1947
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.029 10734 Z= 0.220
Angle : 0.530 7.773 14623 Z= 0.273
Chirality : 0.042 0.176 1645
Planarity : 0.004 0.038 1804
Dihedral : 10.240 73.101 1629
Min Nonbonded Distance : 2.529
Molprobity Statistics.
All-atom Clashscore : 5.88
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 2.66 %
Favored : 97.34 %
Rotamer:
Outliers : 2.68 %
Allowed : 8.92 %
Favored : 88.40 %
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: 0.71 (0.24), residues: 1240
helix: 1.57 (0.22), residues: 560
sheet: -0.39 (0.43), residues: 130
loop : -0.41 (0.26), residues: 550
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.011 0.001 TRP A 426
HIS 0.004 0.001 HIS B 476
PHE 0.013 0.001 PHE A 483
TYR 0.016 0.001 TYR B 533
ARG 0.008 0.000 ARG A 536
*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
2480 Ramachandran restraints generated.
1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
2480 Ramachandran restraints generated.
1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
162 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 30
poor density : 132
time to evaluate : 1.064
Fit side-chains
revert: symmetry clash
revert: symmetry clash
REVERT: A 468 LYS cc_start: 0.8912 (OUTLIER) cc_final: 0.8438 (mmmm)
REVERT: A 516 ASN cc_start: 0.8780 (m-40) cc_final: 0.8210 (m110)
REVERT: A 546 MET cc_start: 0.8906 (OUTLIER) cc_final: 0.8672 (ptm)
REVERT: B 17 GLU cc_start: 0.8612 (pt0) cc_final: 0.8292 (pt0)
REVERT: B 131 ARG cc_start: 0.8510 (ptt90) cc_final: 0.8248 (ptt90)
REVERT: B 383 ASN cc_start: 0.8855 (t0) cc_final: 0.8386 (t0)
outliers start: 30
outliers final: 12
residues processed: 145
average time/residue: 1.6053
time to fit residues: 247.6644
Evaluate side-chains
142 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 14
poor density : 128
time to evaluate : 1.198
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 197 VAL
Chi-restraints excluded: chain A residue 325 GLU
Chi-restraints excluded: chain A residue 438 ARG
Chi-restraints excluded: chain A residue 468 LYS
Chi-restraints excluded: chain A residue 546 MET
Chi-restraints excluded: chain B residue 22 TYR
Chi-restraints excluded: chain B residue 153 LYS
Chi-restraints excluded: chain B residue 211 THR
Chi-restraints excluded: chain B residue 625 SER
Chi-restraints excluded: chain C residue 67 ILE
Chi-restraints excluded: chain C residue 68 SER
Chi-restraints excluded: chain C residue 72 SER
Chi-restraints excluded: chain C residue 102 VAL
Chi-restraints excluded: chain C residue 108 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 126
random chunks:
chunk 65 optimal weight: 6.9990
chunk 108 optimal weight: 1.9990
chunk 61 optimal weight: 4.9990
chunk 7 optimal weight: 40.0000
chunk 105 optimal weight: 0.8980
chunk 117 optimal weight: 0.0970
chunk 25 optimal weight: 8.9990
chunk 95 optimal weight: 2.9990
chunk 107 optimal weight: 0.8980
chunk 109 optimal weight: 0.8980
chunk 122 optimal weight: 4.9990
overall best weight: 0.9580
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
B 148 GLN
Total number of N/Q/H flips: 1
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.120840 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3023 r_free = 0.3023 target = 0.081588 restraints weight = 13891.959|
|-----------------------------------------------------------------------------|
r_work (start): 0.2993 rms_B_bonded: 2.07
r_work: 0.2852 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.2725 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.2725
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8548
moved from start: 0.2056
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.033 10734 Z= 0.166
Angle : 0.505 7.025 14623 Z= 0.259
Chirality : 0.040 0.166 1645
Planarity : 0.004 0.042 1804
Dihedral : 10.181 73.190 1629
Min Nonbonded Distance : 2.550
Molprobity Statistics.
All-atom Clashscore : 6.03
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 2.50 %
Favored : 97.50 %
Rotamer:
Outliers : 2.32 %
Allowed : 9.81 %
Favored : 87.87 %
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: 0.80 (0.24), residues: 1240
helix: 1.70 (0.22), residues: 561
sheet: -0.44 (0.43), residues: 130
loop : -0.39 (0.26), residues: 549
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.010 0.001 TRP A 336
HIS 0.004 0.001 HIS B 476
PHE 0.012 0.001 PHE B 214
TYR 0.019 0.001 TYR A 489
ARG 0.010 0.000 ARG A 536
*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
2480 Ramachandran restraints generated.
1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
2480 Ramachandran restraints generated.
1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
158 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 26
poor density : 132
time to evaluate : 1.445
Fit side-chains
revert: symmetry clash
revert: symmetry clash
REVERT: A 468 LYS cc_start: 0.8901 (OUTLIER) cc_final: 0.8447 (mmmm)
REVERT: A 489 TYR cc_start: 0.9063 (t80) cc_final: 0.8851 (t80)
REVERT: A 546 MET cc_start: 0.8833 (OUTLIER) cc_final: 0.8604 (ptm)
REVERT: B 17 GLU cc_start: 0.8573 (pt0) cc_final: 0.8279 (pt0)
REVERT: B 131 ARG cc_start: 0.8449 (ptt90) cc_final: 0.8217 (ptt90)
REVERT: B 383 ASN cc_start: 0.8914 (t0) cc_final: 0.8430 (t0)
REVERT: B 588 GLU cc_start: 0.7640 (tp30) cc_final: 0.7315 (tp30)
outliers start: 26
outliers final: 9
residues processed: 144
average time/residue: 1.6435
time to fit residues: 251.3408
Evaluate side-chains
140 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 11
poor density : 129
time to evaluate : 1.293
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 438 ARG
Chi-restraints excluded: chain A residue 468 LYS
Chi-restraints excluded: chain A residue 546 MET
Chi-restraints excluded: chain B residue 22 TYR
Chi-restraints excluded: chain B residue 153 LYS
Chi-restraints excluded: chain B residue 211 THR
Chi-restraints excluded: chain B residue 393 MET
Chi-restraints excluded: chain C residue 68 SER
Chi-restraints excluded: chain C residue 72 SER
Chi-restraints excluded: chain C residue 74 GLU
Chi-restraints excluded: chain C residue 102 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 126
random chunks:
chunk 125 optimal weight: 7.9990
chunk 105 optimal weight: 1.9990
chunk 21 optimal weight: 0.6980
chunk 59 optimal weight: 6.9990
chunk 95 optimal weight: 0.9990
chunk 78 optimal weight: 0.9990
chunk 80 optimal weight: 0.8980
chunk 23 optimal weight: 4.9990
chunk 96 optimal weight: 1.9990
chunk 20 optimal weight: 7.9990
chunk 12 optimal weight: 1.9990
overall best weight: 1.1186
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 516 ASN
** A 577 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 148 GLN
B 567 HIS
Total number of N/Q/H flips: 3
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.120484 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3012 r_free = 0.3012 target = 0.081147 restraints weight = 13866.556|
|-----------------------------------------------------------------------------|
r_work (start): 0.2956 rms_B_bonded: 2.06
r_work: 0.2814 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.2689 rms_B_bonded: 3.99 restraints_weight: 0.2500
r_work (final): 0.2689
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8545
moved from start: 0.2166
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.028 10734 Z= 0.177
Angle : 0.505 7.215 14623 Z= 0.258
Chirality : 0.040 0.167 1645
Planarity : 0.004 0.042 1804
Dihedral : 10.166 73.184 1629
Min Nonbonded Distance : 2.543
Molprobity Statistics.
All-atom Clashscore : 5.79
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 2.58 %
Favored : 97.42 %
Rotamer:
Outliers : 1.96 %
Allowed : 10.79 %
Favored : 87.24 %
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: 0.84 (0.24), residues: 1240
helix: 1.75 (0.22), residues: 561
sheet: -0.48 (0.43), residues: 130
loop : -0.39 (0.26), residues: 549
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.010 0.001 TRP A 336
HIS 0.003 0.001 HIS B 476
PHE 0.011 0.001 PHE B 214
TYR 0.017 0.001 TYR A 489
ARG 0.012 0.000 ARG A 536
*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
2480 Ramachandran restraints generated.
1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
2480 Ramachandran restraints generated.
1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
150 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 22
poor density : 128
time to evaluate : 1.247
Fit side-chains
revert: symmetry clash
revert: symmetry clash
REVERT: A 468 LYS cc_start: 0.8887 (OUTLIER) cc_final: 0.8414 (mmmm)
REVERT: A 546 MET cc_start: 0.8856 (OUTLIER) cc_final: 0.8631 (ptm)
REVERT: B 17 GLU cc_start: 0.8588 (pt0) cc_final: 0.8276 (pt0)
REVERT: B 131 ARG cc_start: 0.8427 (ptt90) cc_final: 0.8122 (ptt90)
REVERT: B 151 ARG cc_start: 0.7786 (mmm160) cc_final: 0.7580 (mmm160)
REVERT: B 332 MET cc_start: 0.8777 (OUTLIER) cc_final: 0.8281 (mtm)
REVERT: B 383 ASN cc_start: 0.8917 (t0) cc_final: 0.8377 (t0)
REVERT: B 588 GLU cc_start: 0.7770 (tp30) cc_final: 0.7471 (tp30)
outliers start: 22
outliers final: 12
residues processed: 138
average time/residue: 1.7107
time to fit residues: 250.9011
Evaluate side-chains
138 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 15
poor density : 123
time to evaluate : 1.356
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 325 GLU
Chi-restraints excluded: chain A residue 438 ARG
Chi-restraints excluded: chain A residue 468 LYS
Chi-restraints excluded: chain A residue 546 MET
Chi-restraints excluded: chain A residue 581 GLU
Chi-restraints excluded: chain B residue 22 TYR
Chi-restraints excluded: chain B residue 153 LYS
Chi-restraints excluded: chain B residue 211 THR
Chi-restraints excluded: chain B residue 332 MET
Chi-restraints excluded: chain C residue 67 ILE
Chi-restraints excluded: chain C residue 68 SER
Chi-restraints excluded: chain C residue 72 SER
Chi-restraints excluded: chain C residue 74 GLU
Chi-restraints excluded: chain C residue 102 VAL
Chi-restraints excluded: chain C residue 108 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 126
random chunks:
chunk 13 optimal weight: 8.9990
chunk 57 optimal weight: 2.9990
chunk 72 optimal weight: 1.9990
chunk 97 optimal weight: 5.9990
chunk 27 optimal weight: 0.6980
chunk 91 optimal weight: 9.9990
chunk 108 optimal weight: 3.9990
chunk 25 optimal weight: 5.9990
chunk 73 optimal weight: 0.8980
chunk 43 optimal weight: 0.7980
chunk 53 optimal weight: 0.6980
overall best weight: 1.0182
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 516 ASN
** A 577 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 148 GLN
B 475 HIS
C 131 GLN
Total number of N/Q/H flips: 4
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.120722 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3018 r_free = 0.3018 target = 0.081455 restraints weight = 13974.845|
|-----------------------------------------------------------------------------|
r_work (start): 0.2995 rms_B_bonded: 2.06
r_work: 0.2853 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.2729 rms_B_bonded: 3.99 restraints_weight: 0.2500
r_work (final): 0.2729
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8573
moved from start: 0.2221
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.034 10734 Z= 0.164
Angle : 0.499 6.993 14623 Z= 0.255
Chirality : 0.040 0.164 1645
Planarity : 0.004 0.051 1804
Dihedral : 10.139 73.200 1629
Min Nonbonded Distance : 2.532
Molprobity Statistics.
All-atom Clashscore : 5.59
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 2.50 %
Favored : 97.50 %
Rotamer:
Outliers : 2.05 %
Allowed : 10.70 %
Favored : 87.24 %
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: 0.89 (0.24), residues: 1240
helix: 1.86 (0.22), residues: 553
sheet: -0.50 (0.43), residues: 130
loop : -0.39 (0.25), residues: 557
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.010 0.001 TRP A 336
HIS 0.003 0.001 HIS B 476
PHE 0.011 0.001 PHE B 214
TYR 0.016 0.001 TYR B 533
ARG 0.014 0.000 ARG A 536
*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
2480 Ramachandran restraints generated.
1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
2480 Ramachandran restraints generated.
1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
149 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 23
poor density : 126
time to evaluate : 1.158
Fit side-chains
revert: symmetry clash
revert: symmetry clash
REVERT: A 468 LYS cc_start: 0.8926 (OUTLIER) cc_final: 0.8448 (mmmm)
REVERT: A 546 MET cc_start: 0.8836 (OUTLIER) cc_final: 0.8617 (ptm)
REVERT: B 17 GLU cc_start: 0.8598 (pt0) cc_final: 0.8295 (pt0)
REVERT: B 131 ARG cc_start: 0.8441 (ptt90) cc_final: 0.8158 (ptt90)
REVERT: B 151 ARG cc_start: 0.7836 (mmm160) cc_final: 0.7615 (mmm160)
REVERT: B 383 ASN cc_start: 0.8885 (t0) cc_final: 0.8342 (t0)
REVERT: B 588 GLU cc_start: 0.7810 (tp30) cc_final: 0.7447 (tp30)
REVERT: C 72 SER cc_start: 0.9044 (OUTLIER) cc_final: 0.8741 (p)
outliers start: 23
outliers final: 9
residues processed: 138
average time/residue: 1.6277
time to fit residues: 238.7613
Evaluate side-chains
136 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 12
poor density : 124
time to evaluate : 1.370
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 438 ARG
Chi-restraints excluded: chain A residue 468 LYS
Chi-restraints excluded: chain A residue 546 MET
Chi-restraints excluded: chain A residue 581 GLU
Chi-restraints excluded: chain B residue 22 TYR
Chi-restraints excluded: chain B residue 153 LYS
Chi-restraints excluded: chain B residue 211 THR
Chi-restraints excluded: chain C residue 67 ILE
Chi-restraints excluded: chain C residue 68 SER
Chi-restraints excluded: chain C residue 72 SER
Chi-restraints excluded: chain C residue 102 VAL
Chi-restraints excluded: chain C residue 108 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 126
random chunks:
chunk 98 optimal weight: 5.9990
chunk 80 optimal weight: 0.9990
chunk 30 optimal weight: 0.0470
chunk 95 optimal weight: 2.9990
chunk 100 optimal weight: 3.9990
chunk 108 optimal weight: 3.9990
chunk 25 optimal weight: 3.9990
chunk 113 optimal weight: 7.9990
chunk 32 optimal weight: 3.9990
chunk 70 optimal weight: 3.9990
chunk 66 optimal weight: 3.9990
overall best weight: 2.4086
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 516 ASN
A 577 HIS
B 148 GLN
B 475 HIS
Total number of N/Q/H flips: 4
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.117721 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2959 r_free = 0.2959 target = 0.078110 restraints weight = 13780.826|
|-----------------------------------------------------------------------------|
r_work (start): 0.2902 rms_B_bonded: 2.05
r_work: 0.2757 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.2630 rms_B_bonded: 3.94 restraints_weight: 0.2500
r_work (final): 0.2630
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8587
moved from start: 0.2325
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.005 0.039 10734 Z= 0.298
Angle : 0.571 8.370 14623 Z= 0.293
Chirality : 0.043 0.190 1645
Planarity : 0.005 0.055 1804
Dihedral : 10.283 73.015 1629
Min Nonbonded Distance : 2.498
Molprobity Statistics.
All-atom Clashscore : 5.69
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 2.74 %
Favored : 97.26 %
Rotamer:
Outliers : 2.23 %
Allowed : 10.70 %
Favored : 87.07 %
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: 0.60 (0.23), residues: 1240
helix: 1.54 (0.22), residues: 567
sheet: -0.54 (0.43), residues: 130
loop : -0.55 (0.25), residues: 543
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.013 0.002 TRP A 426
HIS 0.004 0.001 HIS B 531
PHE 0.013 0.002 PHE B 48
TYR 0.018 0.002 TYR A 489
ARG 0.013 0.001 ARG A 536
*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
2480 Ramachandran restraints generated.
1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
2480 Ramachandran restraints generated.
1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
148 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 25
poor density : 123
time to evaluate : 1.278
Fit side-chains
revert: symmetry clash
revert: symmetry clash
REVERT: A 468 LYS cc_start: 0.8891 (OUTLIER) cc_final: 0.8402 (mmmm)
REVERT: A 472 LYS cc_start: 0.8512 (mtmp) cc_final: 0.8128 (mtpp)
REVERT: B 17 GLU cc_start: 0.8607 (pt0) cc_final: 0.8307 (pt0)
REVERT: B 93 ARG cc_start: 0.8286 (OUTLIER) cc_final: 0.8042 (mtp85)
REVERT: B 131 ARG cc_start: 0.8417 (ptt90) cc_final: 0.8167 (ptt90)
REVERT: B 151 ARG cc_start: 0.7852 (mmm160) cc_final: 0.7585 (mmm160)
REVERT: B 383 ASN cc_start: 0.9019 (t0) cc_final: 0.8734 (t0)
REVERT: C 98 ARG cc_start: 0.8483 (ptm-80) cc_final: 0.8038 (mtm-85)
outliers start: 25
outliers final: 11
residues processed: 139
average time/residue: 1.6352
time to fit residues: 241.3184
Evaluate side-chains
134 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 13
poor density : 121
time to evaluate : 1.270
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 177 THR
Chi-restraints excluded: chain A residue 197 VAL
Chi-restraints excluded: chain A residue 438 ARG
Chi-restraints excluded: chain A residue 468 LYS
Chi-restraints excluded: chain B residue 22 TYR
Chi-restraints excluded: chain B residue 93 ARG
Chi-restraints excluded: chain B residue 211 THR
Chi-restraints excluded: chain B residue 625 SER
Chi-restraints excluded: chain C residue 67 ILE
Chi-restraints excluded: chain C residue 68 SER
Chi-restraints excluded: chain C residue 72 SER
Chi-restraints excluded: chain C residue 102 VAL
Chi-restraints excluded: chain C residue 108 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 126
random chunks:
chunk 31 optimal weight: 5.9990
chunk 112 optimal weight: 8.9990
chunk 60 optimal weight: 1.9990
chunk 56 optimal weight: 0.8980
chunk 114 optimal weight: 0.9980
chunk 113 optimal weight: 0.5980
chunk 26 optimal weight: 7.9990
chunk 110 optimal weight: 2.9990
chunk 20 optimal weight: 0.9990
chunk 87 optimal weight: 0.8980
chunk 51 optimal weight: 0.9990
overall best weight: 0.8782
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 516 ASN
B 148 GLN
B 475 HIS
Total number of N/Q/H flips: 3
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.120264 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3010 r_free = 0.3010 target = 0.080900 restraints weight = 14004.622|
|-----------------------------------------------------------------------------|
r_work (start): 0.2987 rms_B_bonded: 2.08
r_work: 0.2843 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.2716 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.2716
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8584
moved from start: 0.2376
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.002 0.043 10734 Z= 0.161
Angle : 0.510 5.604 14623 Z= 0.261
Chirality : 0.040 0.158 1645
Planarity : 0.004 0.056 1804
Dihedral : 10.152 73.265 1629
Min Nonbonded Distance : 2.493
Molprobity Statistics.
All-atom Clashscore : 6.22
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 2.58 %
Favored : 97.42 %
Rotamer:
Outliers : 1.52 %
Allowed : 11.69 %
Favored : 86.80 %
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: 0.85 (0.24), residues: 1240
helix: 1.83 (0.22), residues: 553
sheet: -0.55 (0.43), residues: 130
loop : -0.40 (0.25), residues: 557
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.012 0.001 TRP B 330
HIS 0.003 0.001 HIS A 577
PHE 0.011 0.001 PHE B 214
TYR 0.017 0.001 TYR B 533
ARG 0.014 0.000 ARG A 536
*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
2480 Ramachandran restraints generated.
1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
2480 Ramachandran restraints generated.
1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
141 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 17
poor density : 124
time to evaluate : 1.342
Fit side-chains
revert: symmetry clash
revert: symmetry clash
REVERT: A 468 LYS cc_start: 0.8943 (OUTLIER) cc_final: 0.8470 (mmmm)
REVERT: B 17 GLU cc_start: 0.8598 (pt0) cc_final: 0.8299 (pt0)
REVERT: B 131 ARG cc_start: 0.8407 (ptt90) cc_final: 0.8203 (ptt90)
REVERT: B 151 ARG cc_start: 0.7824 (mmm160) cc_final: 0.7593 (mmm160)
REVERT: B 383 ASN cc_start: 0.8934 (t0) cc_final: 0.8631 (t0)
REVERT: B 588 GLU cc_start: 0.7385 (tm-30) cc_final: 0.7178 (tp30)
REVERT: C 72 SER cc_start: 0.9049 (OUTLIER) cc_final: 0.8758 (p)
REVERT: C 98 ARG cc_start: 0.8500 (ptm-80) cc_final: 0.8115 (mtm-85)
outliers start: 17
outliers final: 8
residues processed: 134
average time/residue: 1.6576
time to fit residues: 236.4499
Evaluate side-chains
133 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 10
poor density : 123
time to evaluate : 1.331
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 438 ARG
Chi-restraints excluded: chain A residue 468 LYS
Chi-restraints excluded: chain B residue 22 TYR
Chi-restraints excluded: chain B residue 153 LYS
Chi-restraints excluded: chain B residue 211 THR
Chi-restraints excluded: chain B residue 591 LEU
Chi-restraints excluded: chain C residue 68 SER
Chi-restraints excluded: chain C residue 72 SER
Chi-restraints excluded: chain C residue 102 VAL
Chi-restraints excluded: chain C residue 108 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 126
random chunks:
chunk 100 optimal weight: 4.9990
chunk 44 optimal weight: 1.9990
chunk 1 optimal weight: 20.0000
chunk 29 optimal weight: 1.9990
chunk 120 optimal weight: 0.3980
chunk 66 optimal weight: 10.0000
chunk 78 optimal weight: 0.0270
chunk 110 optimal weight: 4.9990
chunk 37 optimal weight: 4.9990
chunk 60 optimal weight: 3.9990
chunk 21 optimal weight: 0.5980
overall best weight: 1.0042
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 516 ASN
B 148 GLN
B 475 HIS
Total number of N/Q/H flips: 3
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.120214 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3011 r_free = 0.3011 target = 0.080920 restraints weight = 13917.194|
|-----------------------------------------------------------------------------|
r_work (start): 0.2987 rms_B_bonded: 2.06
r_work: 0.2844 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.2718 rms_B_bonded: 4.00 restraints_weight: 0.2500
r_work (final): 0.2718
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8581
moved from start: 0.2405
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.046 10734 Z= 0.170
Angle : 0.511 6.304 14623 Z= 0.260
Chirality : 0.040 0.152 1645
Planarity : 0.004 0.060 1804
Dihedral : 10.122 73.178 1629
Min Nonbonded Distance : 2.463
Molprobity Statistics.
All-atom Clashscore : 5.84
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 2.50 %
Favored : 97.50 %
Rotamer:
Outliers : 1.16 %
Allowed : 11.95 %
Favored : 86.89 %
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: 0.90 (0.24), residues: 1240
helix: 1.86 (0.22), residues: 553
sheet: -0.54 (0.43), residues: 130
loop : -0.36 (0.26), residues: 557
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.010 0.001 TRP A 336
HIS 0.003 0.001 HIS B 476
PHE 0.011 0.001 PHE B 214
TYR 0.016 0.001 TYR B 533
ARG 0.015 0.000 ARG A 536
********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
2480 Ramachandran restraints generated.
1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
2480 Ramachandran restraints generated.
1240 Oldfield, 0 Emsley, 1240 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
133 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 13
poor density : 120
time to evaluate : 1.121
Fit side-chains
revert: symmetry clash
revert: symmetry clash
REVERT: A 468 LYS cc_start: 0.8937 (OUTLIER) cc_final: 0.8468 (mmmm)
REVERT: B 17 GLU cc_start: 0.8579 (pt0) cc_final: 0.8274 (pt0)
REVERT: B 93 ARG cc_start: 0.8184 (OUTLIER) cc_final: 0.7942 (mtp85)
REVERT: B 131 ARG cc_start: 0.8413 (ptt90) cc_final: 0.8140 (ptt90)
REVERT: B 151 ARG cc_start: 0.7812 (mmm160) cc_final: 0.7583 (mmm160)
REVERT: B 383 ASN cc_start: 0.8953 (t0) cc_final: 0.8656 (t0)
REVERT: C 72 SER cc_start: 0.9059 (OUTLIER) cc_final: 0.8810 (p)
REVERT: C 98 ARG cc_start: 0.8469 (ptm-80) cc_final: 0.8099 (mtm-85)
outliers start: 13
outliers final: 6
residues processed: 129
average time/residue: 1.6633
time to fit residues: 228.0369
Evaluate side-chains
129 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 9
poor density : 120
time to evaluate : 1.309
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 438 ARG
Chi-restraints excluded: chain A residue 468 LYS
Chi-restraints excluded: chain B residue 22 TYR
Chi-restraints excluded: chain B residue 93 ARG
Chi-restraints excluded: chain B residue 211 THR
Chi-restraints excluded: chain B residue 591 LEU
Chi-restraints excluded: chain C residue 68 SER
Chi-restraints excluded: chain C residue 72 SER
Chi-restraints excluded: chain C residue 102 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 126
random chunks:
chunk 97 optimal weight: 6.9990
chunk 42 optimal weight: 2.9990
chunk 37 optimal weight: 4.9990
chunk 54 optimal weight: 7.9990
chunk 118 optimal weight: 2.9990
chunk 57 optimal weight: 2.9990
chunk 114 optimal weight: 1.9990
chunk 99 optimal weight: 4.9990
chunk 3 optimal weight: 20.0000
chunk 32 optimal weight: 6.9990
chunk 72 optimal weight: 1.9990
overall best weight: 2.5990
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 516 ASN
B 148 GLN
B 475 HIS
Total number of N/Q/H flips: 3
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.117708 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2959 r_free = 0.2959 target = 0.078110 restraints weight = 13726.960|
|-----------------------------------------------------------------------------|
r_work (start): 0.2902 rms_B_bonded: 2.04
r_work: 0.2759 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.2632 rms_B_bonded: 3.92 restraints_weight: 0.2500
r_work (final): 0.2632
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8585
moved from start: 0.2440
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.005 0.042 10734 Z= 0.306
Angle : 0.571 7.236 14623 Z= 0.293
Chirality : 0.043 0.169 1645
Planarity : 0.005 0.064 1804
Dihedral : 10.246 73.050 1629
Min Nonbonded Distance : 2.470
Molprobity Statistics.
All-atom Clashscore : 5.74
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 2.58 %
Favored : 97.42 %
Rotamer:
Outliers : 1.52 %
Allowed : 11.69 %
Favored : 86.80 %
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: 0.61 (0.24), residues: 1240
helix: 1.56 (0.22), residues: 567
sheet: -0.58 (0.44), residues: 133
loop : -0.52 (0.25), residues: 540
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.013 0.002 TRP A 426
HIS 0.006 0.001 HIS A 577
PHE 0.013 0.002 PHE B 48
TYR 0.018 0.002 TYR A 489
ARG 0.015 0.000 ARG A 536
Origin is already at (0, 0, 0), no shifts will be applied
===============================================================================
Job complete
usr+sys time: 10247.22 seconds
wall clock time: 183 minutes 27.47 seconds (11007.47 seconds total)