Starting phenix.real_space_refine
on Tue Jan 14 11:45:28 2025 by dcliebschner
===============================================================================
Processing files:
-------------------------------------------------------------------------------
Found model, /net/cci-nas-00/data/ceres_data/8yfd_39220/01_2025/8yfd_39220.cif
Found real_map, /net/cci-nas-00/data/ceres_data/8yfd_39220/01_2025/8yfd_39220.map
Processing PHIL parameters:
-------------------------------------------------------------------------------
Adding command-line PHIL:
-------------------------
refinement.macro_cycles=10
scattering_table=electron
resolution=3.57
write_initial_geo_file=False
Final processed PHIL parameters:
-------------------------------------------------------------------------------
data_manager {
real_map_files = "/net/cci-nas-00/data/ceres_data/8yfd_39220/01_2025/8yfd_39220.map"
default_real_map = "/net/cci-nas-00/data/ceres_data/8yfd_39220/01_2025/8yfd_39220.map"
model {
file = "/net/cci-nas-00/data/ceres_data/8yfd_39220/01_2025/8yfd_39220.cif"
}
default_model = "/net/cci-nas-00/data/ceres_data/8yfd_39220/01_2025/8yfd_39220.cif"
}
resolution = 3.57
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= 0.082
Set stop_for_unknowns flag
Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
Set to: electron
Number of scattering types: 4
Type Number sf(0) Gaussians
S 32 5.16 5
C 4414 2.51 5
N 1054 2.21 5
O 1088 1.98 5
sf(0) = scattering factor at diffraction angle 0.
Process input model
Symmetric amino acids flipped. Time to flip 19 residue(s): 0.02s
Monomer Library directory:
"/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
Total number of atoms: 6588
Number of models: 1
Model: ""
Number of chains: 2
Chain: "A"
Number of atoms: 3294
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 396, 3294
Classifications: {'peptide': 396}
Link IDs: {'PTRANS': 15, 'TRANS': 380}
Chain: "B"
Number of atoms: 3294
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 396, 3294
Classifications: {'peptide': 396}
Link IDs: {'PTRANS': 15, 'TRANS': 380}
Time building chain proxies: 4.53, per 1000 atoms: 0.69
Number of scatterers: 6588
At special positions: 0
Unit cell: (79.2, 67.1, 125.4, 90, 90, 90)
Space group: P 1 (No. 1)
Number of sites at special positions: 0
Number of scattering types: 4
Type Number sf(0)
S 32 16.00
O 1088 8.00
N 1054 7.00
C 4414 6.00
sf(0) = scattering factor at diffraction angle 0.
Number of disulfides: simple=2, symmetry=0
Simple disulfide: pdb=" SG CYS A 415 " - pdb=" SG CYS A 440 " distance=2.03
Simple disulfide: pdb=" SG CYS B 415 " - pdb=" SG CYS B 440 " distance=2.03
Automatic linking
Parameters for automatic linking
Linking & cutoffs
Metal : Auto - 3.00
Amino acid : True - 1.90
Carbohydrate : True - 1.99
Ligands : True - 1.99
Small molecules : False - 1.98
Amino acid - RNA/DNA : False
Number of custom bonds: simple=0, symmetry=0
Time building additional restraints: 1.77
Conformation dependent library (CDL) restraints added in 924.2 milliseconds
1576 Ramachandran restraints generated.
788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
Adding C-beta torsion restraints...
Number of C-beta restraints generated: 1504
Finding SS restraints...
Secondary structure from input PDB file:
28 helices and 0 sheets defined
73.7% alpha, 0.0% beta
0 base pairs and 0 stacking pairs defined.
Time for finding SS restraints: 0.62
Creating SS restraints...
Processing helix chain 'A' and resid 230 through 258
removed outlier: 3.619A pdb=" N THR A 234 " --> pdb=" O PRO A 230 " (cutoff:3.500A)
Processing helix chain 'A' and resid 265 through 296
removed outlier: 4.856A pdb=" N GLY A 274 " --> pdb=" O ARG A 270 " (cutoff:3.500A)
removed outlier: 4.620A pdb=" N GLY A 275 " --> pdb=" O ILE A 271 " (cutoff:3.500A)
Processing helix chain 'A' and resid 312 through 337
removed outlier: 3.629A pdb=" N LEU A 316 " --> pdb=" O SER A 312 " (cutoff:3.500A)
Processing helix chain 'A' and resid 345 through 360
removed outlier: 3.948A pdb=" N LEU A 349 " --> pdb=" O TYR A 345 " (cutoff:3.500A)
Processing helix chain 'A' and resid 367 through 383
Processing helix chain 'A' and resid 390 through 402
removed outlier: 3.637A pdb=" N PHE A 394 " --> pdb=" O GLY A 390 " (cutoff:3.500A)
removed outlier: 3.655A pdb=" N SER A 402 " --> pdb=" O ASP A 398 " (cutoff:3.500A)
Processing helix chain 'A' and resid 403 through 419
removed outlier: 3.920A pdb=" N LEU A 407 " --> pdb=" O LEU A 403 " (cutoff:3.500A)
Processing helix chain 'A' and resid 447 through 471
Proline residue: A 455 - end of helix
Processing helix chain 'A' and resid 476 through 501
removed outlier: 4.326A pdb=" N THR A 486 " --> pdb=" O LYS A 482 " (cutoff:3.500A)
removed outlier: 4.654A pdb=" N PHE A 487 " --> pdb=" O TYR A 483 " (cutoff:3.500A)
removed outlier: 3.782A pdb=" N PHE A 488 " --> pdb=" O SER A 484 " (cutoff:3.500A)
removed outlier: 4.362A pdb=" N GLU A 501 " --> pdb=" O SER A 497 " (cutoff:3.500A)
Processing helix chain 'A' and resid 506 through 532
removed outlier: 3.559A pdb=" N ILE A 520 " --> pdb=" O VAL A 516 " (cutoff:3.500A)
removed outlier: 4.054A pdb=" N LEU A 526 " --> pdb=" O SER A 522 " (cutoff:3.500A)
removed outlier: 3.614A pdb=" N ILE A 527 " --> pdb=" O CYS A 523 " (cutoff:3.500A)
removed outlier: 3.508A pdb=" N MET A 532 " --> pdb=" O TRP A 528 " (cutoff:3.500A)
Processing helix chain 'A' and resid 555 through 571
removed outlier: 4.026A pdb=" N TYR A 559 " --> pdb=" O GLN A 555 " (cutoff:3.500A)
Processing helix chain 'A' and resid 572 through 583
removed outlier: 3.713A pdb=" N GLN A 576 " --> pdb=" O ALA A 572 " (cutoff:3.500A)
Processing helix chain 'A' and resid 588 through 622
Proline residue: A 598 - end of helix
removed outlier: 4.225A pdb=" N VAL A 601 " --> pdb=" O ALA A 597 " (cutoff:3.500A)
removed outlier: 4.750A pdb=" N PHE A 602 " --> pdb=" O PRO A 598 " (cutoff:3.500A)
removed outlier: 3.900A pdb=" N PHE A 609 " --> pdb=" O PHE A 605 " (cutoff:3.500A)
removed outlier: 3.987A pdb=" N PHE A 610 " --> pdb=" O VAL A 606 " (cutoff:3.500A)
Processing helix chain 'B' and resid 230 through 258
Processing helix chain 'B' and resid 265 through 296
removed outlier: 3.673A pdb=" N ILE B 269 " --> pdb=" O ILE B 265 " (cutoff:3.500A)
removed outlier: 5.207A pdb=" N GLY B 274 " --> pdb=" O ARG B 270 " (cutoff:3.500A)
removed outlier: 4.601A pdb=" N GLY B 275 " --> pdb=" O ILE B 271 " (cutoff:3.500A)
Processing helix chain 'B' and resid 298 through 303
removed outlier: 3.743A pdb=" N ILE B 302 " --> pdb=" O ASN B 298 " (cutoff:3.500A)
Processing helix chain 'B' and resid 312 through 337
removed outlier: 3.555A pdb=" N LEU B 316 " --> pdb=" O SER B 312 " (cutoff:3.500A)
Processing helix chain 'B' and resid 343 through 345
No H-bonds generated for 'chain 'B' and resid 343 through 345'
Processing helix chain 'B' and resid 346 through 360
removed outlier: 3.759A pdb=" N LEU B 359 " --> pdb=" O MET B 355 " (cutoff:3.500A)
Processing helix chain 'B' and resid 369 through 382
removed outlier: 3.513A pdb=" N PHE B 379 " --> pdb=" O LEU B 375 " (cutoff:3.500A)
Processing helix chain 'B' and resid 390 through 399
Processing helix chain 'B' and resid 404 through 420
removed outlier: 3.518A pdb=" N LEU B 410 " --> pdb=" O ILE B 406 " (cutoff:3.500A)
removed outlier: 3.871A pdb=" N GLU B 411 " --> pdb=" O LEU B 407 " (cutoff:3.500A)
removed outlier: 3.812A pdb=" N TYR B 412 " --> pdb=" O MET B 408 " (cutoff:3.500A)
removed outlier: 3.529A pdb=" N GLU B 420 " --> pdb=" O PHE B 416 " (cutoff:3.500A)
Processing helix chain 'B' and resid 448 through 471
Proline residue: B 455 - end of helix
Processing helix chain 'B' and resid 473 through 501
removed outlier: 4.112A pdb=" N GLY B 481 " --> pdb=" O LEU B 477 " (cutoff:3.500A)
removed outlier: 4.735A pdb=" N THR B 486 " --> pdb=" O LYS B 482 " (cutoff:3.500A)
removed outlier: 3.696A pdb=" N PHE B 487 " --> pdb=" O TYR B 483 " (cutoff:3.500A)
Processing helix chain 'B' and resid 506 through 532
removed outlier: 3.638A pdb=" N PHE B 511 " --> pdb=" O THR B 507 " (cutoff:3.500A)
removed outlier: 4.585A pdb=" N TYR B 512 " --> pdb=" O MET B 508 " (cutoff:3.500A)
removed outlier: 3.681A pdb=" N LEU B 513 " --> pdb=" O VAL B 509 " (cutoff:3.500A)
removed outlier: 4.236A pdb=" N VAL B 516 " --> pdb=" O TYR B 512 " (cutoff:3.500A)
removed outlier: 3.519A pdb=" N SER B 521 " --> pdb=" O PHE B 517 " (cutoff:3.500A)
removed outlier: 4.256A pdb=" N ILE B 527 " --> pdb=" O CYS B 523 " (cutoff:3.500A)
Processing helix chain 'B' and resid 555 through 571
removed outlier: 4.180A pdb=" N TYR B 559 " --> pdb=" O GLN B 555 " (cutoff:3.500A)
removed outlier: 3.783A pdb=" N PHE B 571 " --> pdb=" O VAL B 567 " (cutoff:3.500A)
Processing helix chain 'B' and resid 573 through 580
Processing helix chain 'B' and resid 588 through 622
removed outlier: 4.247A pdb=" N ILE B 592 " --> pdb=" O SER B 588 " (cutoff:3.500A)
removed outlier: 4.073A pdb=" N ALA B 593 " --> pdb=" O GLY B 589 " (cutoff:3.500A)
removed outlier: 3.651A pdb=" N VAL B 595 " --> pdb=" O ILE B 591 " (cutoff:3.500A)
Proline residue: B 598 - end of helix
removed outlier: 4.040A pdb=" N VAL B 601 " --> pdb=" O ALA B 597 " (cutoff:3.500A)
removed outlier: 3.534A pdb=" N PHE B 602 " --> pdb=" O PRO B 598 " (cutoff:3.500A)
removed outlier: 3.943A pdb=" N PHE B 609 " --> pdb=" O PHE B 605 " (cutoff:3.500A)
removed outlier: 4.023A pdb=" N PHE B 610 " --> pdb=" O VAL B 606 " (cutoff:3.500A)
410 hydrogen bonds defined for protein.
1230 hydrogen bond angles defined for protein.
Restraints generated for nucleic acids:
0 hydrogen bonds
0 hydrogen bond angles
0 basepair planarities
0 basepair parallelities
0 stacking parallelities
Total time for adding SS restraints: 1.85
Time building geometry restraints manager: 2.01 seconds
NOTE: a complete listing of the restraints can be obtained by requesting
output of .geo file.
Histogram of bond lengths:
1.23 - 1.35: 1955
1.35 - 1.46: 1935
1.46 - 1.58: 2874
1.58 - 1.70: 0
1.70 - 1.82: 44
Bond restraints: 6808
Sorted by residual:
bond pdb=" CA THR A 261 "
pdb=" CB THR A 261 "
ideal model delta sigma weight residual
1.526 1.547 -0.021 1.53e-02 4.27e+03 1.88e+00
bond pdb=" N PRO A 475 "
pdb=" CA PRO A 475 "
ideal model delta sigma weight residual
1.474 1.465 0.009 7.40e-03 1.83e+04 1.40e+00
bond pdb=" CA HIS A 504 "
pdb=" C HIS A 504 "
ideal model delta sigma weight residual
1.532 1.522 0.011 9.60e-03 1.09e+04 1.21e+00
bond pdb=" CA ILE B 339 "
pdb=" CB ILE B 339 "
ideal model delta sigma weight residual
1.527 1.540 -0.013 1.31e-02 5.83e+03 1.04e+00
bond pdb=" CA TYR B 367 "
pdb=" C TYR B 367 "
ideal model delta sigma weight residual
1.532 1.523 0.010 9.60e-03 1.09e+04 1.01e+00
... (remaining 6803 not shown)
Histogram of bond angle deviations from ideal:
0.00 - 2.12: 9087
2.12 - 4.25: 152
4.25 - 6.37: 23
6.37 - 8.50: 4
8.50 - 10.62: 2
Bond angle restraints: 9268
Sorted by residual:
angle pdb=" N ASP A 262 "
pdb=" CA ASP A 262 "
pdb=" C ASP A 262 "
ideal model delta sigma weight residual
114.64 107.72 6.92 1.52e+00 4.33e-01 2.07e+01
angle pdb=" C THR B 383 "
pdb=" N ALA B 384 "
pdb=" CA ALA B 384 "
ideal model delta sigma weight residual
121.80 130.88 -9.08 2.44e+00 1.68e-01 1.39e+01
angle pdb=" C ARG B 308 "
pdb=" N SER B 309 "
pdb=" CA SER B 309 "
ideal model delta sigma weight residual
121.54 127.58 -6.04 1.91e+00 2.74e-01 9.99e+00
angle pdb=" CA TRP B 395 "
pdb=" CB TRP B 395 "
pdb=" CG TRP B 395 "
ideal model delta sigma weight residual
113.60 119.47 -5.87 1.90e+00 2.77e-01 9.53e+00
angle pdb=" CA TYR B 290 "
pdb=" CB TYR B 290 "
pdb=" CG TYR B 290 "
ideal model delta sigma weight residual
113.90 119.46 -5.56 1.80e+00 3.09e-01 9.53e+00
... (remaining 9263 not shown)
Histogram of dihedral angle deviations from ideal:
0.00 - 16.45: 3194
16.45 - 32.91: 458
32.91 - 49.36: 179
49.36 - 65.81: 34
65.81 - 82.26: 3
Dihedral angle restraints: 3868
sinusoidal: 1532
harmonic: 2336
Sorted by residual:
dihedral pdb=" CA GLN B 399 "
pdb=" C GLN B 399 "
pdb=" N LEU B 400 "
pdb=" CA LEU B 400 "
ideal model delta harmonic sigma weight residual
180.00 155.83 24.17 0 5.00e+00 4.00e-02 2.34e+01
dihedral pdb=" CA ALA B 384 "
pdb=" C ALA B 384 "
pdb=" N PRO B 385 "
pdb=" CA PRO B 385 "
ideal model delta harmonic sigma weight residual
180.00 -158.86 -21.14 0 5.00e+00 4.00e-02 1.79e+01
dihedral pdb=" CA ILE A 342 "
pdb=" C ILE A 342 "
pdb=" N PRO A 343 "
pdb=" CA PRO A 343 "
ideal model delta harmonic sigma weight residual
-180.00 -160.24 -19.76 0 5.00e+00 4.00e-02 1.56e+01
... (remaining 3865 not shown)
Histogram of chiral volume deviations from ideal:
0.000 - 0.034: 653
0.034 - 0.067: 264
0.067 - 0.101: 75
0.101 - 0.135: 17
0.135 - 0.168: 3
Chirality restraints: 1012
Sorted by residual:
chirality pdb=" CA GLN B 399 "
pdb=" N GLN B 399 "
pdb=" C GLN B 399 "
pdb=" CB GLN B 399 "
both_signs ideal model delta sigma weight residual
False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.09e-01
chirality pdb=" CG LEU B 311 "
pdb=" CB LEU B 311 "
pdb=" CD1 LEU B 311 "
pdb=" CD2 LEU B 311 "
both_signs ideal model delta sigma weight residual
False -2.59 -2.45 -0.14 2.00e-01 2.50e+01 5.19e-01
chirality pdb=" CB THR A 507 "
pdb=" CA THR A 507 "
pdb=" OG1 THR A 507 "
pdb=" CG2 THR A 507 "
both_signs ideal model delta sigma weight residual
False 2.55 2.41 0.14 2.00e-01 2.50e+01 4.88e-01
... (remaining 1009 not shown)
Planarity restraints: 1134
Sorted by residual:
delta sigma weight rms_deltas residual
plane pdb=" CB TRP B 395 " -0.021 2.00e-02 2.50e+03 1.62e-02 6.59e+00
pdb=" CG TRP B 395 " 0.044 2.00e-02 2.50e+03
pdb=" CD1 TRP B 395 " -0.011 2.00e-02 2.50e+03
pdb=" CD2 TRP B 395 " -0.001 2.00e-02 2.50e+03
pdb=" NE1 TRP B 395 " 0.002 2.00e-02 2.50e+03
pdb=" CE2 TRP B 395 " -0.012 2.00e-02 2.50e+03
pdb=" CE3 TRP B 395 " -0.000 2.00e-02 2.50e+03
pdb=" CZ2 TRP B 395 " 0.000 2.00e-02 2.50e+03
pdb=" CZ3 TRP B 395 " -0.001 2.00e-02 2.50e+03
pdb=" CH2 TRP B 395 " 0.001 2.00e-02 2.50e+03
delta sigma weight rms_deltas residual
plane pdb=" CA ASN B 310 " -0.010 2.00e-02 2.50e+03 1.95e-02 3.82e+00
pdb=" C ASN B 310 " 0.034 2.00e-02 2.50e+03
pdb=" O ASN B 310 " -0.013 2.00e-02 2.50e+03
pdb=" N LEU B 311 " -0.011 2.00e-02 2.50e+03
delta sigma weight rms_deltas residual
plane pdb=" C ALA B 384 " 0.031 5.00e-02 4.00e+02 4.69e-02 3.52e+00
pdb=" N PRO B 385 " -0.081 5.00e-02 4.00e+02
pdb=" CA PRO B 385 " 0.024 5.00e-02 4.00e+02
pdb=" CD PRO B 385 " 0.026 5.00e-02 4.00e+02
... (remaining 1131 not shown)
Histogram of nonbonded interaction distances:
2.19 - 2.74: 431
2.74 - 3.28: 6891
3.28 - 3.82: 10931
3.82 - 4.36: 11858
4.36 - 4.90: 20548
Nonbonded interactions: 50659
Sorted by model distance:
nonbonded pdb=" O ILE A 579 "
pdb=" OG1 THR A 583 "
model vdw
2.195 3.040
nonbonded pdb=" O SER A 578 "
pdb=" OG1 THR A 582 "
model vdw
2.231 3.040
nonbonded pdb=" O ARG B 308 "
pdb=" OG SER B 309 "
model vdw
2.241 3.040
nonbonded pdb=" O ARG A 466 "
pdb=" OG1 THR A 470 "
model vdw
2.274 3.040
nonbonded pdb=" O ILE A 271 "
pdb=" OH TYR A 352 "
model vdw
2.278 3.040
... (remaining 50654 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: 0.03
Found NCS groups:
ncs_group {
reference = chain 'A'
selection = chain 'B'
}
Set up NCS constraints
No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
Set random seed: 0.000
Set model cs if undefined: 0.000
Decide on map wrapping: 0.000
Normalize map: mean=0, sd=1: 0.890
Set stop_for_unknowns flag: 0.000
Assert model is a single copy model: 0.000
Assert all atoms have isotropic ADPs: 0.000
Construct map_model_manager: 0.010
Extract box with map and model: 0.280
Check model and map are aligned: 0.050
Set scattering table: 0.080
Process input model: 19.090
Find NCS groups from input model: 0.210
Set up NCS constraints: 0.020
Set refine NCS operators: 0.000
Adjust number of macro_cycles: 0.000
Reset NCS operators: 0.000
Extract rigid body selections: 0.000
Check and reset occupancies: 0.000
Load rotamer database and sin/cos tables:2.830
Set ADP refinement strategy: 0.000
Make a string to write initial .geo file:0.000
Internal consistency checks: 0.000
Total: 23.460
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7575
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 : 0.003 0.032 6808 Z= 0.186
Angle : 0.678 10.623 9268 Z= 0.384
Chirality : 0.040 0.168 1012
Planarity : 0.004 0.047 1134
Dihedral : 17.761 82.263 2358
Min Nonbonded Distance : 2.195
Molprobity Statistics.
All-atom Clashscore : 9.97
Ramachandran Plot:
Outliers : 0.38 %
Allowed : 6.09 %
Favored : 93.53 %
Rotamer:
Outliers : 0.57 %
Allowed : 29.97 %
Favored : 69.46 %
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: 0.20 (0.32), residues: 788
helix: 1.21 (0.22), residues: 566
sheet: None (None), residues: 0
loop : -2.80 (0.42), residues: 222
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.044 0.002 TRP B 395
HIS 0.004 0.001 HIS B 441
PHE 0.012 0.001 PHE A 394
TYR 0.015 0.001 TYR A 518
ARG 0.004 0.000 ARG A 472
*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
1576 Ramachandran restraints generated.
788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
1576 Ramachandran restraints generated.
788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
144 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 4
poor density : 140
time to evaluate : 0.730
Fit side-chains
REVERT: A 489 MET cc_start: 0.7149 (tmm) cc_final: 0.6595 (tmm)
outliers start: 4
outliers final: 4
residues processed: 142
average time/residue: 0.1667
time to fit residues: 32.1523
Evaluate side-chains
129 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 4
poor density : 125
time to evaluate : 0.751
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 426 SER
Chi-restraints excluded: chain A residue 441 HIS
Chi-restraints excluded: chain B residue 310 ASN
Chi-restraints excluded: chain B residue 398 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 78
random chunks:
chunk 65 optimal weight: 0.9980
chunk 59 optimal weight: 0.0370
chunk 32 optimal weight: 0.0670
chunk 20 optimal weight: 5.9990
chunk 39 optimal weight: 2.9990
chunk 31 optimal weight: 0.4980
chunk 61 optimal weight: 0.9980
chunk 23 optimal weight: 2.9990
chunk 37 optimal weight: 0.7980
chunk 45 optimal weight: 0.7980
chunk 70 optimal weight: 5.9990
overall best weight: 0.4396
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
B 310 ASN
B 479 ASN
Total number of N/Q/H flips: 2
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4066 r_free = 0.4066 target = 0.177516 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.143537 restraints weight = 9667.086|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.147103 restraints weight = 6079.238|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.149139 restraints weight = 4606.696|
|-----------------------------------------------------------------------------|
r_work (final): 0.3662
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7559
moved from start: 0.0801
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.036 6808 Z= 0.163
Angle : 0.572 9.126 9268 Z= 0.298
Chirality : 0.040 0.142 1012
Planarity : 0.005 0.065 1134
Dihedral : 5.756 59.523 879
Min Nonbonded Distance : 2.488
Molprobity Statistics.
All-atom Clashscore : 6.93
Ramachandran Plot:
Outliers : 0.25 %
Allowed : 6.35 %
Favored : 93.40 %
Rotamer:
Outliers : 4.55 %
Allowed : 25.57 %
Favored : 69.89 %
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: 0.61 (0.31), residues: 788
helix: 1.60 (0.22), residues: 564
sheet: None (None), residues: 0
loop : -2.88 (0.42), residues: 224
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.037 0.001 TRP B 395
HIS 0.005 0.001 HIS B 441
PHE 0.015 0.001 PHE A 394
TYR 0.013 0.001 TYR A 518
ARG 0.004 0.000 ARG A 448
*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
1576 Ramachandran restraints generated.
788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
1576 Ramachandran restraints generated.
788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
169 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 32
poor density : 137
time to evaluate : 0.745
Fit side-chains
REVERT: A 263 ARG cc_start: 0.5709 (tpt170) cc_final: 0.5469 (ttt90)
REVERT: A 497 SER cc_start: 0.8416 (m) cc_final: 0.8085 (p)
REVERT: A 518 TYR cc_start: 0.8280 (OUTLIER) cc_final: 0.7369 (m-80)
REVERT: B 245 ILE cc_start: 0.7280 (mm) cc_final: 0.7065 (mm)
REVERT: B 452 GLN cc_start: 0.8030 (tp40) cc_final: 0.7743 (tp40)
REVERT: B 508 MET cc_start: 0.7617 (mtm) cc_final: 0.7225 (mpp)
REVERT: B 613 GLU cc_start: 0.7013 (OUTLIER) cc_final: 0.6775 (pp20)
outliers start: 32
outliers final: 15
residues processed: 157
average time/residue: 0.1669
time to fit residues: 36.2159
Evaluate side-chains
137 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 17
poor density : 120
time to evaluate : 0.752
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 341 VAL
Chi-restraints excluded: chain A residue 378 LEU
Chi-restraints excluded: chain A residue 419 LEU
Chi-restraints excluded: chain A residue 423 TRP
Chi-restraints excluded: chain A residue 424 ASP
Chi-restraints excluded: chain A residue 487 PHE
Chi-restraints excluded: chain A residue 495 LEU
Chi-restraints excluded: chain A residue 510 PHE
Chi-restraints excluded: chain A residue 518 TYR
Chi-restraints excluded: chain B residue 310 ASN
Chi-restraints excluded: chain B residue 398 ASP
Chi-restraints excluded: chain B residue 406 ILE
Chi-restraints excluded: chain B residue 410 LEU
Chi-restraints excluded: chain B residue 453 CYS
Chi-restraints excluded: chain B residue 463 CYS
Chi-restraints excluded: chain B residue 544 ASN
Chi-restraints excluded: chain B residue 613 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 78
random chunks:
chunk 48 optimal weight: 0.9990
chunk 31 optimal weight: 10.0000
chunk 46 optimal weight: 1.9990
chunk 24 optimal weight: 6.9990
chunk 12 optimal weight: 0.9990
chunk 49 optimal weight: 0.7980
chunk 13 optimal weight: 0.0870
chunk 66 optimal weight: 0.7980
chunk 60 optimal weight: 4.9990
chunk 7 optimal weight: 3.9990
chunk 57 optimal weight: 0.9990
overall best weight: 0.7362
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 441 HIS
Total number of N/Q/H flips: 1
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4039 r_free = 0.4039 target = 0.174958 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.140526 restraints weight = 9921.554|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.144029 restraints weight = 6253.144|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.146349 restraints weight = 4758.499|
|-----------------------------------------------------------------------------|
r_work (final): 0.3715
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7580
moved from start: 0.1151
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.042 6808 Z= 0.182
Angle : 0.558 9.134 9268 Z= 0.288
Chirality : 0.040 0.134 1012
Planarity : 0.004 0.065 1134
Dihedral : 5.129 57.079 876
Min Nonbonded Distance : 2.485
Molprobity Statistics.
All-atom Clashscore : 7.69
Ramachandran Plot:
Outliers : 0.25 %
Allowed : 5.58 %
Favored : 94.16 %
Rotamer:
Outliers : 5.97 %
Allowed : 25.28 %
Favored : 68.75 %
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 (0.31), residues: 788
helix: 1.76 (0.22), residues: 564
sheet: None (None), residues: 0
loop : -2.87 (0.42), residues: 224
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.029 0.001 TRP B 395
HIS 0.005 0.001 HIS B 441
PHE 0.017 0.001 PHE A 394
TYR 0.016 0.001 TYR A 496
ARG 0.003 0.000 ARG A 448
*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
1576 Ramachandran restraints generated.
788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
1576 Ramachandran restraints generated.
788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
174 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 42
poor density : 132
time to evaluate : 0.711
Fit side-chains
revert: symmetry clash
REVERT: A 263 ARG cc_start: 0.5501 (tpt170) cc_final: 0.5263 (ttt90)
REVERT: A 345 TYR cc_start: 0.7000 (OUTLIER) cc_final: 0.6298 (m-80)
REVERT: A 497 SER cc_start: 0.8374 (m) cc_final: 0.8065 (p)
REVERT: B 245 ILE cc_start: 0.7293 (mm) cc_final: 0.6981 (mm)
REVERT: B 502 ARG cc_start: 0.7973 (tmm-80) cc_final: 0.7615 (ttm-80)
REVERT: B 613 GLU cc_start: 0.7114 (OUTLIER) cc_final: 0.6297 (tm-30)
outliers start: 42
outliers final: 23
residues processed: 163
average time/residue: 0.1727
time to fit residues: 38.7920
Evaluate side-chains
143 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 25
poor density : 118
time to evaluate : 0.795
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 253 LEU
Chi-restraints excluded: chain A residue 326 LEU
Chi-restraints excluded: chain A residue 341 VAL
Chi-restraints excluded: chain A residue 345 TYR
Chi-restraints excluded: chain A residue 377 LEU
Chi-restraints excluded: chain A residue 378 LEU
Chi-restraints excluded: chain A residue 417 TYR
Chi-restraints excluded: chain A residue 419 LEU
Chi-restraints excluded: chain A residue 423 TRP
Chi-restraints excluded: chain A residue 425 GLU
Chi-restraints excluded: chain A residue 441 HIS
Chi-restraints excluded: chain A residue 487 PHE
Chi-restraints excluded: chain A residue 495 LEU
Chi-restraints excluded: chain A residue 510 PHE
Chi-restraints excluded: chain B residue 310 ASN
Chi-restraints excluded: chain B residue 389 VAL
Chi-restraints excluded: chain B residue 396 LEU
Chi-restraints excluded: chain B residue 403 LEU
Chi-restraints excluded: chain B residue 410 LEU
Chi-restraints excluded: chain B residue 463 CYS
Chi-restraints excluded: chain B residue 519 ILE
Chi-restraints excluded: chain B residue 530 LEU
Chi-restraints excluded: chain B residue 544 ASN
Chi-restraints excluded: chain B residue 592 ILE
Chi-restraints excluded: chain B residue 613 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 78
random chunks:
chunk 11 optimal weight: 5.9990
chunk 43 optimal weight: 0.8980
chunk 15 optimal weight: 0.8980
chunk 53 optimal weight: 2.9990
chunk 47 optimal weight: 0.9980
chunk 32 optimal weight: 0.4980
chunk 68 optimal weight: 1.9990
chunk 24 optimal weight: 0.6980
chunk 77 optimal weight: 1.9990
chunk 45 optimal weight: 0.9980
chunk 70 optimal weight: 6.9990
overall best weight: 0.7980
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 441 HIS
B 399 GLN
Total number of N/Q/H flips: 2
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4028 r_free = 0.4028 target = 0.173962 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.139463 restraints weight = 9942.184|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.143123 restraints weight = 6174.186|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.145431 restraints weight = 4635.425|
|-----------------------------------------------------------------------------|
r_work (final): 0.3627
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7600
moved from start: 0.1371
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.055 6808 Z= 0.197
Angle : 0.576 9.273 9268 Z= 0.296
Chirality : 0.040 0.187 1012
Planarity : 0.004 0.063 1134
Dihedral : 4.699 52.744 874
Min Nonbonded Distance : 2.489
Molprobity Statistics.
All-atom Clashscore : 8.07
Ramachandran Plot:
Outliers : 0.25 %
Allowed : 6.47 %
Favored : 93.27 %
Rotamer:
Outliers : 5.54 %
Allowed : 25.57 %
Favored : 68.89 %
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: 0.82 (0.31), residues: 788
helix: 1.77 (0.22), residues: 566
sheet: None (None), residues: 0
loop : -2.89 (0.42), residues: 222
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.032 0.001 TRP B 395
HIS 0.005 0.001 HIS B 441
PHE 0.018 0.001 PHE A 394
TYR 0.012 0.001 TYR A 496
ARG 0.002 0.000 ARG A 448
*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
1576 Ramachandran restraints generated.
788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
1576 Ramachandran restraints generated.
788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
164 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 39
poor density : 125
time to evaluate : 0.718
Fit side-chains
revert: symmetry clash
REVERT: A 345 TYR cc_start: 0.7035 (OUTLIER) cc_final: 0.6312 (m-80)
REVERT: A 497 SER cc_start: 0.8351 (m) cc_final: 0.8045 (p)
REVERT: B 245 ILE cc_start: 0.7313 (mm) cc_final: 0.7022 (mm)
REVERT: B 502 ARG cc_start: 0.7948 (tmm-80) cc_final: 0.7635 (ttm-80)
REVERT: B 587 HIS cc_start: 0.6385 (OUTLIER) cc_final: 0.6142 (t-90)
REVERT: B 613 GLU cc_start: 0.7178 (OUTLIER) cc_final: 0.6381 (tm-30)
outliers start: 39
outliers final: 25
residues processed: 152
average time/residue: 0.1640
time to fit residues: 33.9788
Evaluate side-chains
147 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 28
poor density : 119
time to evaluate : 0.732
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 253 LEU
Chi-restraints excluded: chain A residue 326 LEU
Chi-restraints excluded: chain A residue 341 VAL
Chi-restraints excluded: chain A residue 345 TYR
Chi-restraints excluded: chain A residue 377 LEU
Chi-restraints excluded: chain A residue 378 LEU
Chi-restraints excluded: chain A residue 408 MET
Chi-restraints excluded: chain A residue 417 TYR
Chi-restraints excluded: chain A residue 419 LEU
Chi-restraints excluded: chain A residue 423 TRP
Chi-restraints excluded: chain A residue 425 GLU
Chi-restraints excluded: chain A residue 429 LEU
Chi-restraints excluded: chain A residue 487 PHE
Chi-restraints excluded: chain A residue 495 LEU
Chi-restraints excluded: chain A residue 510 PHE
Chi-restraints excluded: chain A residue 518 TYR
Chi-restraints excluded: chain B residue 310 ASN
Chi-restraints excluded: chain B residue 389 VAL
Chi-restraints excluded: chain B residue 396 LEU
Chi-restraints excluded: chain B residue 403 LEU
Chi-restraints excluded: chain B residue 463 CYS
Chi-restraints excluded: chain B residue 519 ILE
Chi-restraints excluded: chain B residue 530 LEU
Chi-restraints excluded: chain B residue 544 ASN
Chi-restraints excluded: chain B residue 551 ILE
Chi-restraints excluded: chain B residue 582 THR
Chi-restraints excluded: chain B residue 587 HIS
Chi-restraints excluded: chain B residue 613 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 78
random chunks:
chunk 12 optimal weight: 0.9980
chunk 64 optimal weight: 1.9990
chunk 63 optimal weight: 0.8980
chunk 52 optimal weight: 8.9990
chunk 2 optimal weight: 0.9980
chunk 3 optimal weight: 0.9980
chunk 7 optimal weight: 3.9990
chunk 54 optimal weight: 2.9990
chunk 48 optimal weight: 0.7980
chunk 21 optimal weight: 5.9990
chunk 31 optimal weight: 9.9990
overall best weight: 0.9380
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
B 462 GLN
Total number of N/Q/H flips: 1
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4026 r_free = 0.4026 target = 0.173580 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.139010 restraints weight = 9812.094|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.142528 restraints weight = 6181.961|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.144828 restraints weight = 4668.387|
|-----------------------------------------------------------------------------|
r_work (final): 0.3673
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7624
moved from start: 0.1582
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.043 6808 Z= 0.210
Angle : 0.577 9.239 9268 Z= 0.300
Chirality : 0.041 0.207 1012
Planarity : 0.004 0.060 1134
Dihedral : 4.675 50.400 874
Min Nonbonded Distance : 2.495
Molprobity Statistics.
All-atom Clashscore : 7.53
Ramachandran Plot:
Outliers : 0.25 %
Allowed : 5.58 %
Favored : 94.16 %
Rotamer:
Outliers : 5.40 %
Allowed : 26.85 %
Favored : 67.76 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 0.79 (0.31), residues: 788
helix: 1.77 (0.22), residues: 565
sheet: None (None), residues: 0
loop : -2.95 (0.41), residues: 223
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.033 0.001 TRP B 395
HIS 0.005 0.001 HIS A 504
PHE 0.019 0.001 PHE A 394
TYR 0.011 0.001 TYR A 496
ARG 0.002 0.000 ARG A 448
*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
1576 Ramachandran restraints generated.
788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
1576 Ramachandran restraints generated.
788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
161 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 38
poor density : 123
time to evaluate : 0.776
Fit side-chains
revert: symmetry clash
REVERT: A 345 TYR cc_start: 0.7105 (OUTLIER) cc_final: 0.6317 (m-80)
REVERT: A 497 SER cc_start: 0.8347 (m) cc_final: 0.8053 (p)
REVERT: A 512 TYR cc_start: 0.7908 (m-10) cc_final: 0.7549 (m-80)
REVERT: B 245 ILE cc_start: 0.7316 (mm) cc_final: 0.7021 (mm)
REVERT: B 331 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.8154 (tt)
REVERT: B 335 PHE cc_start: 0.7176 (OUTLIER) cc_final: 0.6958 (m-80)
REVERT: B 502 ARG cc_start: 0.7882 (tmm-80) cc_final: 0.7675 (tmm-80)
REVERT: B 587 HIS cc_start: 0.6167 (OUTLIER) cc_final: 0.5903 (t-90)
REVERT: B 613 GLU cc_start: 0.7247 (OUTLIER) cc_final: 0.6472 (tm-30)
outliers start: 38
outliers final: 24
residues processed: 148
average time/residue: 0.1644
time to fit residues: 33.2804
Evaluate side-chains
146 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 29
poor density : 117
time to evaluate : 0.781
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 253 LEU
Chi-restraints excluded: chain A residue 326 LEU
Chi-restraints excluded: chain A residue 339 ILE
Chi-restraints excluded: chain A residue 341 VAL
Chi-restraints excluded: chain A residue 345 TYR
Chi-restraints excluded: chain A residue 378 LEU
Chi-restraints excluded: chain A residue 417 TYR
Chi-restraints excluded: chain A residue 419 LEU
Chi-restraints excluded: chain A residue 423 TRP
Chi-restraints excluded: chain A residue 425 GLU
Chi-restraints excluded: chain A residue 429 LEU
Chi-restraints excluded: chain A residue 487 PHE
Chi-restraints excluded: chain A residue 495 LEU
Chi-restraints excluded: chain A residue 510 PHE
Chi-restraints excluded: chain A residue 518 TYR
Chi-restraints excluded: chain A residue 547 LEU
Chi-restraints excluded: chain B residue 310 ASN
Chi-restraints excluded: chain B residue 331 LEU
Chi-restraints excluded: chain B residue 335 PHE
Chi-restraints excluded: chain B residue 389 VAL
Chi-restraints excluded: chain B residue 396 LEU
Chi-restraints excluded: chain B residue 403 LEU
Chi-restraints excluded: chain B residue 463 CYS
Chi-restraints excluded: chain B residue 530 LEU
Chi-restraints excluded: chain B residue 544 ASN
Chi-restraints excluded: chain B residue 551 ILE
Chi-restraints excluded: chain B residue 582 THR
Chi-restraints excluded: chain B residue 587 HIS
Chi-restraints excluded: chain B residue 613 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 78
random chunks:
chunk 9 optimal weight: 0.9990
chunk 17 optimal weight: 0.9990
chunk 12 optimal weight: 0.9980
chunk 52 optimal weight: 3.9990
chunk 62 optimal weight: 0.4980
chunk 2 optimal weight: 0.6980
chunk 64 optimal weight: 0.6980
chunk 19 optimal weight: 1.9990
chunk 29 optimal weight: 2.9990
chunk 46 optimal weight: 0.0770
chunk 30 optimal weight: 0.3980
overall best weight: 0.4738
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 608 ASN
Total number of N/Q/H flips: 1
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4040 r_free = 0.4040 target = 0.175047 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.141048 restraints weight = 9696.295|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.144621 restraints weight = 6036.187|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.146920 restraints weight = 4535.564|
|-----------------------------------------------------------------------------|
r_work (final): 0.3683
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7574
moved from start: 0.1664
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.042 6808 Z= 0.165
Angle : 0.552 9.431 9268 Z= 0.285
Chirality : 0.040 0.180 1012
Planarity : 0.004 0.057 1134
Dihedral : 4.549 48.606 874
Min Nonbonded Distance : 2.507
Molprobity Statistics.
All-atom Clashscore : 7.15
Ramachandran Plot:
Outliers : 0.25 %
Allowed : 5.84 %
Favored : 93.91 %
Rotamer:
Outliers : 5.82 %
Allowed : 26.42 %
Favored : 67.76 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 0.99 (0.31), residues: 788
helix: 1.95 (0.22), residues: 565
sheet: None (None), residues: 0
loop : -2.97 (0.41), residues: 223
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.026 0.001 TRP B 395
HIS 0.005 0.001 HIS B 441
PHE 0.015 0.001 PHE A 394
TYR 0.010 0.001 TYR A 496
ARG 0.002 0.000 ARG A 570
*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
1576 Ramachandran restraints generated.
788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
1576 Ramachandran restraints generated.
788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
175 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 41
poor density : 134
time to evaluate : 0.754
Fit side-chains
revert: symmetry clash
REVERT: A 345 TYR cc_start: 0.7031 (OUTLIER) cc_final: 0.6338 (m-80)
REVERT: A 497 SER cc_start: 0.8325 (m) cc_final: 0.8049 (p)
REVERT: B 245 ILE cc_start: 0.7297 (mm) cc_final: 0.6984 (mm)
REVERT: B 331 LEU cc_start: 0.8350 (OUTLIER) cc_final: 0.8135 (tt)
REVERT: B 335 PHE cc_start: 0.7151 (OUTLIER) cc_final: 0.6920 (m-80)
REVERT: B 508 MET cc_start: 0.7022 (mtm) cc_final: 0.6766 (mpp)
REVERT: B 613 GLU cc_start: 0.7265 (OUTLIER) cc_final: 0.6456 (tm-30)
outliers start: 41
outliers final: 28
residues processed: 162
average time/residue: 0.1592
time to fit residues: 35.6953
Evaluate side-chains
160 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 32
poor density : 128
time to evaluate : 0.717
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 253 LEU
Chi-restraints excluded: chain A residue 265 ILE
Chi-restraints excluded: chain A residue 326 LEU
Chi-restraints excluded: chain A residue 339 ILE
Chi-restraints excluded: chain A residue 341 VAL
Chi-restraints excluded: chain A residue 345 TYR
Chi-restraints excluded: chain A residue 377 LEU
Chi-restraints excluded: chain A residue 417 TYR
Chi-restraints excluded: chain A residue 419 LEU
Chi-restraints excluded: chain A residue 423 TRP
Chi-restraints excluded: chain A residue 425 GLU
Chi-restraints excluded: chain A residue 429 LEU
Chi-restraints excluded: chain A residue 487 PHE
Chi-restraints excluded: chain A residue 495 LEU
Chi-restraints excluded: chain A residue 510 PHE
Chi-restraints excluded: chain A residue 518 TYR
Chi-restraints excluded: chain A residue 547 LEU
Chi-restraints excluded: chain A residue 608 ASN
Chi-restraints excluded: chain B residue 310 ASN
Chi-restraints excluded: chain B residue 311 LEU
Chi-restraints excluded: chain B residue 331 LEU
Chi-restraints excluded: chain B residue 335 PHE
Chi-restraints excluded: chain B residue 389 VAL
Chi-restraints excluded: chain B residue 396 LEU
Chi-restraints excluded: chain B residue 403 LEU
Chi-restraints excluded: chain B residue 463 CYS
Chi-restraints excluded: chain B residue 530 LEU
Chi-restraints excluded: chain B residue 544 ASN
Chi-restraints excluded: chain B residue 551 ILE
Chi-restraints excluded: chain B residue 582 THR
Chi-restraints excluded: chain B residue 592 ILE
Chi-restraints excluded: chain B residue 613 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 78
random chunks:
chunk 10 optimal weight: 0.7980
chunk 13 optimal weight: 0.0970
chunk 42 optimal weight: 6.9990
chunk 57 optimal weight: 0.8980
chunk 62 optimal weight: 0.0980
chunk 52 optimal weight: 3.9990
chunk 51 optimal weight: 0.6980
chunk 61 optimal weight: 0.9990
chunk 75 optimal weight: 5.9990
chunk 2 optimal weight: 0.6980
chunk 41 optimal weight: 0.8980
overall best weight: 0.4778
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 608 ASN
Total number of N/Q/H flips: 1
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4037 r_free = 0.4037 target = 0.175185 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.141384 restraints weight = 9865.680|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.144890 restraints weight = 6169.267|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.147130 restraints weight = 4657.123|
|-----------------------------------------------------------------------------|
r_work (final): 0.3682
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7582
moved from start: 0.1749
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.053 6808 Z= 0.175
Angle : 0.573 9.506 9268 Z= 0.294
Chirality : 0.040 0.171 1012
Planarity : 0.004 0.055 1134
Dihedral : 4.517 47.350 874
Min Nonbonded Distance : 2.511
Molprobity Statistics.
All-atom Clashscore : 7.84
Ramachandran Plot:
Outliers : 0.25 %
Allowed : 5.58 %
Favored : 94.16 %
Rotamer:
Outliers : 5.82 %
Allowed : 27.27 %
Favored : 66.90 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 0.96 (0.31), residues: 788
helix: 1.93 (0.22), residues: 565
sheet: None (None), residues: 0
loop : -2.99 (0.41), residues: 223
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.023 0.001 TRP B 395
HIS 0.005 0.001 HIS B 441
PHE 0.013 0.001 PHE A 394
TYR 0.009 0.001 TYR A 496
ARG 0.002 0.000 ARG A 570
*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
1576 Ramachandran restraints generated.
788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
1576 Ramachandran restraints generated.
788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
166 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 41
poor density : 125
time to evaluate : 0.786
Fit side-chains
revert: symmetry clash
REVERT: A 345 TYR cc_start: 0.7003 (OUTLIER) cc_final: 0.6287 (m-80)
REVERT: A 497 SER cc_start: 0.8372 (m) cc_final: 0.8093 (p)
REVERT: A 518 TYR cc_start: 0.8429 (OUTLIER) cc_final: 0.7446 (m-80)
REVERT: B 245 ILE cc_start: 0.7226 (mm) cc_final: 0.6935 (mm)
REVERT: B 283 PHE cc_start: 0.7955 (m-10) cc_final: 0.7725 (m-10)
REVERT: B 331 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.8205 (tt)
REVERT: B 335 PHE cc_start: 0.7152 (OUTLIER) cc_final: 0.6914 (m-80)
REVERT: B 452 GLN cc_start: 0.8628 (mm-40) cc_final: 0.8423 (tp40)
REVERT: B 508 MET cc_start: 0.6912 (mtm) cc_final: 0.6699 (mpp)
REVERT: B 613 GLU cc_start: 0.7248 (OUTLIER) cc_final: 0.6448 (tm-30)
outliers start: 41
outliers final: 28
residues processed: 151
average time/residue: 0.1566
time to fit residues: 32.8121
Evaluate side-chains
155 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 33
poor density : 122
time to evaluate : 0.820
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 253 LEU
Chi-restraints excluded: chain A residue 265 ILE
Chi-restraints excluded: chain A residue 299 HIS
Chi-restraints excluded: chain A residue 326 LEU
Chi-restraints excluded: chain A residue 339 ILE
Chi-restraints excluded: chain A residue 341 VAL
Chi-restraints excluded: chain A residue 345 TYR
Chi-restraints excluded: chain A residue 377 LEU
Chi-restraints excluded: chain A residue 417 TYR
Chi-restraints excluded: chain A residue 419 LEU
Chi-restraints excluded: chain A residue 423 TRP
Chi-restraints excluded: chain A residue 425 GLU
Chi-restraints excluded: chain A residue 429 LEU
Chi-restraints excluded: chain A residue 482 LYS
Chi-restraints excluded: chain A residue 487 PHE
Chi-restraints excluded: chain A residue 495 LEU
Chi-restraints excluded: chain A residue 510 PHE
Chi-restraints excluded: chain A residue 518 TYR
Chi-restraints excluded: chain A residue 547 LEU
Chi-restraints excluded: chain B residue 310 ASN
Chi-restraints excluded: chain B residue 311 LEU
Chi-restraints excluded: chain B residue 331 LEU
Chi-restraints excluded: chain B residue 335 PHE
Chi-restraints excluded: chain B residue 389 VAL
Chi-restraints excluded: chain B residue 396 LEU
Chi-restraints excluded: chain B residue 403 LEU
Chi-restraints excluded: chain B residue 463 CYS
Chi-restraints excluded: chain B residue 530 LEU
Chi-restraints excluded: chain B residue 544 ASN
Chi-restraints excluded: chain B residue 551 ILE
Chi-restraints excluded: chain B residue 582 THR
Chi-restraints excluded: chain B residue 592 ILE
Chi-restraints excluded: chain B residue 613 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 78
random chunks:
chunk 57 optimal weight: 0.6980
chunk 35 optimal weight: 0.9980
chunk 17 optimal weight: 2.9990
chunk 40 optimal weight: 2.9990
chunk 34 optimal weight: 4.9990
chunk 37 optimal weight: 0.5980
chunk 32 optimal weight: 0.6980
chunk 58 optimal weight: 0.9990
chunk 16 optimal weight: 0.9980
chunk 71 optimal weight: 1.9990
chunk 11 optimal weight: 4.9990
overall best weight: 0.7980
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 608 ASN
** B 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Total number of N/Q/H flips: 1
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4019 r_free = 0.4019 target = 0.173525 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.139650 restraints weight = 9901.941|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.143084 restraints weight = 6235.263|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.144989 restraints weight = 4726.582|
|-----------------------------------------------------------------------------|
r_work (final): 0.3654
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7613
moved from start: 0.1934
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.061 6808 Z= 0.202
Angle : 0.586 9.462 9268 Z= 0.300
Chirality : 0.041 0.163 1012
Planarity : 0.004 0.051 1134
Dihedral : 4.507 45.083 874
Min Nonbonded Distance : 2.514
Molprobity Statistics.
All-atom Clashscore : 7.38
Ramachandran Plot:
Outliers : 0.25 %
Allowed : 6.60 %
Favored : 93.15 %
Rotamer:
Outliers : 5.82 %
Allowed : 27.41 %
Favored : 66.76 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 0.87 (0.31), residues: 788
helix: 1.86 (0.22), residues: 565
sheet: None (None), residues: 0
loop : -3.01 (0.41), residues: 223
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.036 0.002 TRP B 395
HIS 0.005 0.001 HIS B 441
PHE 0.016 0.001 PHE A 394
TYR 0.009 0.001 TYR A 496
ARG 0.003 0.000 ARG B 502
*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
1576 Ramachandran restraints generated.
788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
1576 Ramachandran restraints generated.
788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
168 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 41
poor density : 127
time to evaluate : 0.754
Fit side-chains
revert: symmetry clash
REVERT: A 345 TYR cc_start: 0.7070 (OUTLIER) cc_final: 0.6344 (m-80)
REVERT: A 497 SER cc_start: 0.8382 (m) cc_final: 0.8126 (p)
REVERT: B 245 ILE cc_start: 0.7188 (mm) cc_final: 0.6936 (mm)
REVERT: B 269 ILE cc_start: 0.6066 (OUTLIER) cc_final: 0.5641 (tp)
REVERT: B 283 PHE cc_start: 0.8017 (m-10) cc_final: 0.7790 (m-10)
REVERT: B 335 PHE cc_start: 0.7085 (OUTLIER) cc_final: 0.6883 (m-80)
REVERT: B 508 MET cc_start: 0.7030 (mtm) cc_final: 0.6820 (mpp)
REVERT: B 613 GLU cc_start: 0.7180 (OUTLIER) cc_final: 0.6384 (tm-30)
outliers start: 41
outliers final: 29
residues processed: 155
average time/residue: 0.1536
time to fit residues: 33.0336
Evaluate side-chains
159 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 33
poor density : 126
time to evaluate : 0.793
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 253 LEU
Chi-restraints excluded: chain A residue 265 ILE
Chi-restraints excluded: chain A residue 299 HIS
Chi-restraints excluded: chain A residue 326 LEU
Chi-restraints excluded: chain A residue 339 ILE
Chi-restraints excluded: chain A residue 341 VAL
Chi-restraints excluded: chain A residue 345 TYR
Chi-restraints excluded: chain A residue 377 LEU
Chi-restraints excluded: chain A residue 417 TYR
Chi-restraints excluded: chain A residue 419 LEU
Chi-restraints excluded: chain A residue 423 TRP
Chi-restraints excluded: chain A residue 425 GLU
Chi-restraints excluded: chain A residue 429 LEU
Chi-restraints excluded: chain A residue 487 PHE
Chi-restraints excluded: chain A residue 495 LEU
Chi-restraints excluded: chain A residue 510 PHE
Chi-restraints excluded: chain A residue 518 TYR
Chi-restraints excluded: chain A residue 547 LEU
Chi-restraints excluded: chain A residue 608 ASN
Chi-restraints excluded: chain B residue 269 ILE
Chi-restraints excluded: chain B residue 310 ASN
Chi-restraints excluded: chain B residue 311 LEU
Chi-restraints excluded: chain B residue 335 PHE
Chi-restraints excluded: chain B residue 389 VAL
Chi-restraints excluded: chain B residue 396 LEU
Chi-restraints excluded: chain B residue 403 LEU
Chi-restraints excluded: chain B residue 463 CYS
Chi-restraints excluded: chain B residue 530 LEU
Chi-restraints excluded: chain B residue 544 ASN
Chi-restraints excluded: chain B residue 551 ILE
Chi-restraints excluded: chain B residue 582 THR
Chi-restraints excluded: chain B residue 592 ILE
Chi-restraints excluded: chain B residue 613 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 78
random chunks:
chunk 22 optimal weight: 0.8980
chunk 50 optimal weight: 0.2980
chunk 1 optimal weight: 1.9990
chunk 20 optimal weight: 0.0770
chunk 0 optimal weight: 3.9990
chunk 69 optimal weight: 0.3980
chunk 57 optimal weight: 2.9990
chunk 35 optimal weight: 0.6980
chunk 36 optimal weight: 4.9990
chunk 64 optimal weight: 0.8980
chunk 15 optimal weight: 0.9980
overall best weight: 0.4738
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 608 ASN
B 399 GLN
Total number of N/Q/H flips: 2
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4038 r_free = 0.4038 target = 0.175223 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.140873 restraints weight = 9846.694|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.144459 restraints weight = 6132.752|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.146787 restraints weight = 4612.293|
|-----------------------------------------------------------------------------|
r_work (final): 0.3687
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7575
moved from start: 0.1973
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.055 6808 Z= 0.180
Angle : 0.588 9.613 9268 Z= 0.302
Chirality : 0.040 0.166 1012
Planarity : 0.004 0.050 1134
Dihedral : 4.474 43.743 874
Min Nonbonded Distance : 2.495
Molprobity Statistics.
All-atom Clashscore : 7.84
Ramachandran Plot:
Outliers : 0.25 %
Allowed : 6.35 %
Favored : 93.40 %
Rotamer:
Outliers : 4.97 %
Allowed : 27.98 %
Favored : 67.05 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 0.94 (0.31), residues: 788
helix: 1.91 (0.22), residues: 566
sheet: None (None), residues: 0
loop : -3.00 (0.41), residues: 222
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.041 0.002 TRP B 395
HIS 0.005 0.001 HIS B 441
PHE 0.013 0.001 PHE A 394
TYR 0.009 0.001 TYR A 496
ARG 0.003 0.000 ARG B 502
*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
1576 Ramachandran restraints generated.
788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
1576 Ramachandran restraints generated.
788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
163 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 35
poor density : 128
time to evaluate : 0.932
Fit side-chains
revert: symmetry clash
REVERT: A 345 TYR cc_start: 0.7031 (OUTLIER) cc_final: 0.6305 (m-80)
REVERT: A 352 TYR cc_start: 0.7331 (m-80) cc_final: 0.7083 (m-80)
REVERT: A 497 SER cc_start: 0.8319 (m) cc_final: 0.8097 (p)
REVERT: A 518 TYR cc_start: 0.8348 (OUTLIER) cc_final: 0.7257 (m-80)
REVERT: B 245 ILE cc_start: 0.7175 (mm) cc_final: 0.6921 (mm)
REVERT: B 283 PHE cc_start: 0.7984 (m-10) cc_final: 0.7754 (m-10)
REVERT: B 408 MET cc_start: 0.7582 (mmm) cc_final: 0.7176 (mmm)
REVERT: B 613 GLU cc_start: 0.7176 (OUTLIER) cc_final: 0.6378 (tm-30)
outliers start: 35
outliers final: 29
residues processed: 151
average time/residue: 0.1592
time to fit residues: 33.6722
Evaluate side-chains
157 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 32
poor density : 125
time to evaluate : 0.744
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 253 LEU
Chi-restraints excluded: chain A residue 265 ILE
Chi-restraints excluded: chain A residue 299 HIS
Chi-restraints excluded: chain A residue 326 LEU
Chi-restraints excluded: chain A residue 339 ILE
Chi-restraints excluded: chain A residue 341 VAL
Chi-restraints excluded: chain A residue 345 TYR
Chi-restraints excluded: chain A residue 377 LEU
Chi-restraints excluded: chain A residue 417 TYR
Chi-restraints excluded: chain A residue 419 LEU
Chi-restraints excluded: chain A residue 423 TRP
Chi-restraints excluded: chain A residue 425 GLU
Chi-restraints excluded: chain A residue 429 LEU
Chi-restraints excluded: chain A residue 487 PHE
Chi-restraints excluded: chain A residue 495 LEU
Chi-restraints excluded: chain A residue 510 PHE
Chi-restraints excluded: chain A residue 518 TYR
Chi-restraints excluded: chain A residue 547 LEU
Chi-restraints excluded: chain A residue 608 ASN
Chi-restraints excluded: chain B residue 310 ASN
Chi-restraints excluded: chain B residue 311 LEU
Chi-restraints excluded: chain B residue 389 VAL
Chi-restraints excluded: chain B residue 396 LEU
Chi-restraints excluded: chain B residue 398 ASP
Chi-restraints excluded: chain B residue 403 LEU
Chi-restraints excluded: chain B residue 463 CYS
Chi-restraints excluded: chain B residue 530 LEU
Chi-restraints excluded: chain B residue 544 ASN
Chi-restraints excluded: chain B residue 551 ILE
Chi-restraints excluded: chain B residue 582 THR
Chi-restraints excluded: chain B residue 592 ILE
Chi-restraints excluded: chain B residue 613 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 78
random chunks:
chunk 64 optimal weight: 0.9990
chunk 0 optimal weight: 4.9990
chunk 34 optimal weight: 0.3980
chunk 44 optimal weight: 1.9990
chunk 65 optimal weight: 0.7980
chunk 9 optimal weight: 1.9990
chunk 47 optimal weight: 0.0370
chunk 30 optimal weight: 0.9990
chunk 71 optimal weight: 0.0980
chunk 6 optimal weight: 0.7980
chunk 55 optimal weight: 0.6980
overall best weight: 0.4058
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 608 ASN
B 452 GLN
Total number of N/Q/H flips: 2
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4044 r_free = 0.4044 target = 0.175712 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.141163 restraints weight = 9968.841|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.144821 restraints weight = 6211.269|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.147130 restraints weight = 4703.531|
|-----------------------------------------------------------------------------|
r_work (final): 0.3702
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7570
moved from start: 0.2019
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.061 6808 Z= 0.175
Angle : 0.586 9.628 9268 Z= 0.298
Chirality : 0.040 0.160 1012
Planarity : 0.004 0.050 1134
Dihedral : 4.454 42.322 874
Min Nonbonded Distance : 2.518
Molprobity Statistics.
All-atom Clashscore : 7.61
Ramachandran Plot:
Outliers : 0.25 %
Allowed : 6.60 %
Favored : 93.15 %
Rotamer:
Outliers : 4.97 %
Allowed : 27.70 %
Favored : 67.33 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 0.99 (0.31), residues: 788
helix: 1.92 (0.22), residues: 569
sheet: None (None), residues: 0
loop : -2.95 (0.41), residues: 219
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.043 0.001 TRP B 395
HIS 0.005 0.001 HIS B 441
PHE 0.013 0.001 PHE A 391
TYR 0.009 0.001 TYR A 496
ARG 0.003 0.000 ARG B 502
********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
1576 Ramachandran restraints generated.
788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
1576 Ramachandran restraints generated.
788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
161 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 35
poor density : 126
time to evaluate : 0.736
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: A 345 TYR cc_start: 0.7106 (OUTLIER) cc_final: 0.6431 (m-80)
REVERT: A 497 SER cc_start: 0.8314 (m) cc_final: 0.8094 (p)
REVERT: A 512 TYR cc_start: 0.7959 (m-10) cc_final: 0.7576 (m-10)
REVERT: A 518 TYR cc_start: 0.8368 (OUTLIER) cc_final: 0.7350 (m-80)
REVERT: B 245 ILE cc_start: 0.7158 (mm) cc_final: 0.6881 (mm)
REVERT: B 283 PHE cc_start: 0.7964 (m-10) cc_final: 0.7717 (m-10)
REVERT: B 331 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.8207 (tt)
REVERT: B 613 GLU cc_start: 0.7116 (OUTLIER) cc_final: 0.6296 (tm-30)
outliers start: 35
outliers final: 28
residues processed: 148
average time/residue: 0.1557
time to fit residues: 32.0583
Evaluate side-chains
156 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 32
poor density : 124
time to evaluate : 0.744
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 253 LEU
Chi-restraints excluded: chain A residue 265 ILE
Chi-restraints excluded: chain A residue 299 HIS
Chi-restraints excluded: chain A residue 326 LEU
Chi-restraints excluded: chain A residue 339 ILE
Chi-restraints excluded: chain A residue 341 VAL
Chi-restraints excluded: chain A residue 345 TYR
Chi-restraints excluded: chain A residue 377 LEU
Chi-restraints excluded: chain A residue 417 TYR
Chi-restraints excluded: chain A residue 419 LEU
Chi-restraints excluded: chain A residue 423 TRP
Chi-restraints excluded: chain A residue 425 GLU
Chi-restraints excluded: chain A residue 429 LEU
Chi-restraints excluded: chain A residue 487 PHE
Chi-restraints excluded: chain A residue 495 LEU
Chi-restraints excluded: chain A residue 510 PHE
Chi-restraints excluded: chain A residue 518 TYR
Chi-restraints excluded: chain A residue 547 LEU
Chi-restraints excluded: chain A residue 608 ASN
Chi-restraints excluded: chain B residue 310 ASN
Chi-restraints excluded: chain B residue 311 LEU
Chi-restraints excluded: chain B residue 331 LEU
Chi-restraints excluded: chain B residue 389 VAL
Chi-restraints excluded: chain B residue 396 LEU
Chi-restraints excluded: chain B residue 398 ASP
Chi-restraints excluded: chain B residue 403 LEU
Chi-restraints excluded: chain B residue 463 CYS
Chi-restraints excluded: chain B residue 544 ASN
Chi-restraints excluded: chain B residue 551 ILE
Chi-restraints excluded: chain B residue 582 THR
Chi-restraints excluded: chain B residue 592 ILE
Chi-restraints excluded: chain B residue 613 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 78
random chunks:
chunk 11 optimal weight: 5.9990
chunk 6 optimal weight: 0.6980
chunk 8 optimal weight: 0.0010
chunk 4 optimal weight: 0.9980
chunk 36 optimal weight: 0.9980
chunk 32 optimal weight: 4.9990
chunk 62 optimal weight: 0.9990
chunk 10 optimal weight: 0.5980
chunk 74 optimal weight: 9.9990
chunk 64 optimal weight: 1.9990
chunk 0 optimal weight: 4.9990
overall best weight: 0.6586
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 608 ASN
Total number of N/Q/H flips: 1
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4036 r_free = 0.4036 target = 0.174739 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.140516 restraints weight = 9945.250|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.144073 restraints weight = 6189.813|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.146388 restraints weight = 4686.064|
|-----------------------------------------------------------------------------|
r_work (final): 0.3623
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7593
moved from start: 0.2072
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.065 6808 Z= 0.193
Angle : 0.592 9.641 9268 Z= 0.306
Chirality : 0.040 0.165 1012
Planarity : 0.004 0.050 1134
Dihedral : 4.439 40.879 874
Min Nonbonded Distance : 2.521
Molprobity Statistics.
All-atom Clashscore : 7.61
Ramachandran Plot:
Outliers : 0.25 %
Allowed : 6.35 %
Favored : 93.40 %
Rotamer:
Outliers : 4.97 %
Allowed : 27.84 %
Favored : 67.19 %
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: 0.94 (0.31), residues: 788
helix: 1.87 (0.22), residues: 570
sheet: None (None), residues: 0
loop : -2.97 (0.41), residues: 218
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.044 0.001 TRP B 395
HIS 0.005 0.001 HIS B 441
PHE 0.014 0.001 PHE A 394
TYR 0.009 0.001 TYR A 496
ARG 0.003 0.000 ARG B 502
Origin is already at (0, 0, 0), no shifts will be applied
===============================================================================
Job complete
usr+sys time: 2159.32 seconds
wall clock time: 39 minutes 29.58 seconds (2369.58 seconds total)