Starting phenix.real_space_refine
on Mon Jan 13 15:41:28 2025 by dcliebschner
===============================================================================
Processing files:
-------------------------------------------------------------------------------
Found model, /net/cci-nas-00/data/ceres_data/8xv2_38691/01_2025/8xv2_38691.cif
Found real_map, /net/cci-nas-00/data/ceres_data/8xv2_38691/01_2025/8xv2_38691.map
Processing PHIL parameters:
-------------------------------------------------------------------------------
Adding command-line PHIL:
-------------------------
refinement.macro_cycles=10
scattering_table=electron
resolution=3.7
write_initial_geo_file=False
Final processed PHIL parameters:
-------------------------------------------------------------------------------
data_manager {
real_map_files = "/net/cci-nas-00/data/ceres_data/8xv2_38691/01_2025/8xv2_38691.map"
default_real_map = "/net/cci-nas-00/data/ceres_data/8xv2_38691/01_2025/8xv2_38691.map"
model {
file = "/net/cci-nas-00/data/ceres_data/8xv2_38691/01_2025/8xv2_38691.cif"
}
default_model = "/net/cci-nas-00/data/ceres_data/8xv2_38691/01_2025/8xv2_38691.cif"
}
resolution = 3.7
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= 0.017
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 17 5.16 5
C 2112 2.51 5
N 470 2.21 5
O 529 1.98 5
sf(0) = scattering factor at diffraction angle 0.
Process input model
Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s
Monomer Library directory:
"/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
Total number of atoms: 3128
Number of models: 1
Model: ""
Number of chains: 2
Chain: "A"
Number of atoms: 3110
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 388, 3110
Classifications: {'peptide': 388}
Link IDs: {'PTRANS': 14, 'TRANS': 373}
Chain breaks: 1
Chain: "A"
Number of atoms: 18
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 1, 18
Unusual residues: {'VIB': 1}
Classifications: {'undetermined': 1}
Time building chain proxies: 2.73, per 1000 atoms: 0.87
Number of scatterers: 3128
At special positions: 0
Unit cell: (69.55, 58.85, 79.18, 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 17 16.00
O 529 8.00
N 470 7.00
C 2112 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: 0.86
Conformation dependent library (CDL) restraints added in 371.2 milliseconds
768 Ramachandran restraints generated.
384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2.
Adding C-beta torsion restraints...
Number of C-beta restraints generated: 736
Finding SS restraints...
Secondary structure from input PDB file:
18 helices and 0 sheets defined
84.5% alpha, 0.0% beta
0 base pairs and 0 stacking pairs defined.
Time for finding SS restraints: 0.30
Creating SS restraints...
Processing helix chain 'A' and resid 12 through 28
Processing helix chain 'A' and resid 34 through 40
Processing helix chain 'A' and resid 47 through 55
removed outlier: 3.880A pdb=" N ILE A 55 " --> pdb=" O ILE A 51 " (cutoff:3.500A)
Processing helix chain 'A' and resid 56 through 66
removed outlier: 4.013A pdb=" N THR A 60 " --> pdb=" O PHE A 56 " (cutoff:3.500A)
removed outlier: 3.604A pdb=" N LEU A 66 " --> pdb=" O SER A 62 " (cutoff:3.500A)
Processing helix chain 'A' and resid 67 through 76
removed outlier: 3.532A pdb=" N PHE A 71 " --> pdb=" O LEU A 67 " (cutoff:3.500A)
removed outlier: 3.619A pdb=" N VAL A 72 " --> pdb=" O LEU A 68 " (cutoff:3.500A)
removed outlier: 3.766A pdb=" N TYR A 76 " --> pdb=" O VAL A 72 " (cutoff:3.500A)
Processing helix chain 'A' and resid 80 through 100
Processing helix chain 'A' and resid 104 through 126
removed outlier: 3.540A pdb=" N VAL A 108 " --> pdb=" O LYS A 104 " (cutoff:3.500A)
removed outlier: 4.508A pdb=" N VAL A 121 " --> pdb=" O THR A 117 " (cutoff:3.500A)
removed outlier: 4.377A pdb=" N ALA A 122 " --> pdb=" O ALA A 118 " (cutoff:3.500A)
Processing helix chain 'A' and resid 126 through 131
Processing helix chain 'A' and resid 132 through 134
No H-bonds generated for 'chain 'A' and resid 132 through 134'
Processing helix chain 'A' and resid 135 through 166
removed outlier: 4.002A pdb=" N SER A 140 " --> pdb=" O TYR A 136 " (cutoff:3.500A)
removed outlier: 3.849A pdb=" N ASN A 166 " --> pdb=" O VAL A 162 " (cutoff:3.500A)
Processing helix chain 'A' and resid 168 through 188
removed outlier: 3.644A pdb=" N LEU A 172 " --> pdb=" O SER A 168 " (cutoff:3.500A)
removed outlier: 3.670A pdb=" N LEU A 188 " --> pdb=" O PHE A 184 " (cutoff:3.500A)
Processing helix chain 'A' and resid 268 through 273
removed outlier: 3.587A pdb=" N CYS A 272 " --> pdb=" O ASP A 268 " (cutoff:3.500A)
removed outlier: 4.015A pdb=" N TYR A 273 " --> pdb=" O LEU A 269 " (cutoff:3.500A)
No H-bonds generated for 'chain 'A' and resid 268 through 273'
Processing helix chain 'A' and resid 275 through 307
removed outlier: 4.500A pdb=" N TYR A 280 " --> pdb=" O LYS A 276 " (cutoff:3.500A)
removed outlier: 5.411A pdb=" N TRP A 281 " --> pdb=" O ARG A 277 " (cutoff:3.500A)
removed outlier: 3.748A pdb=" N SER A 282 " --> pdb=" O LEU A 278 " (cutoff:3.500A)
removed outlier: 5.408A pdb=" N GLN A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A)
removed outlier: 4.930A pdb=" N ILE A 301 " --> pdb=" O ASN A 297 " (cutoff:3.500A)
Processing helix chain 'A' and resid 315 through 335
removed outlier: 3.993A pdb=" N GLY A 335 " --> pdb=" O ALA A 331 " (cutoff:3.500A)
Processing helix chain 'A' and resid 340 through 366
removed outlier: 4.167A pdb=" N GLU A 346 " --> pdb=" O ASP A 342 " (cutoff:3.500A)
removed outlier: 4.434A pdb=" N LEU A 347 " --> pdb=" O LEU A 343 " (cutoff:3.500A)
removed outlier: 3.627A pdb=" N LEU A 349 " --> pdb=" O GLY A 345 " (cutoff:3.500A)
removed outlier: 5.008A pdb=" N VAL A 350 " --> pdb=" O GLU A 346 " (cutoff:3.500A)
removed outlier: 3.783A pdb=" N PHE A 352 " --> pdb=" O ALA A 348 " (cutoff:3.500A)
Processing helix chain 'A' and resid 368 through 396
removed outlier: 3.914A pdb=" N VAL A 396 " --> pdb=" O PHE A 392 " (cutoff:3.500A)
Processing helix chain 'A' and resid 400 through 426
removed outlier: 3.571A pdb=" N ALA A 404 " --> pdb=" O VAL A 400 " (cutoff:3.500A)
removed outlier: 3.829A pdb=" N LEU A 405 " --> pdb=" O GLU A 401 " (cutoff:3.500A)
Processing helix chain 'A' and resid 434 through 458
removed outlier: 3.621A pdb=" N GLN A 438 " --> pdb=" O PRO A 434 " (cutoff:3.500A)
removed outlier: 3.944A pdb=" N PHE A 439 " --> pdb=" O VAL A 435 " (cutoff:3.500A)
removed outlier: 3.891A pdb=" N LEU A 440 " --> pdb=" O SER A 436 " (cutoff:3.500A)
225 hydrogen bonds defined for protein.
675 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: 0.78
Time building geometry restraints manager: 0.93 seconds
NOTE: a complete listing of the restraints can be obtained by requesting
output of .geo file.
Histogram of bond lengths:
1.23 - 1.34: 885
1.34 - 1.46: 853
1.46 - 1.58: 1459
1.58 - 1.69: 0
1.69 - 1.81: 28
Bond restraints: 3225
Sorted by residual:
bond pdb=" C5 VIB A 501 "
pdb=" S1 VIB A 501 "
ideal model delta sigma weight residual
1.721 1.507 0.214 2.00e-02 2.50e+03 1.14e+02
bond pdb=" C2 VIB A 501 "
pdb=" S1 VIB A 501 "
ideal model delta sigma weight residual
1.670 1.541 0.129 2.00e-02 2.50e+03 4.16e+01
bond pdb=" C2 VIB A 501 "
pdb=" N3 VIB A 501 "
ideal model delta sigma weight residual
1.315 1.420 -0.105 2.00e-02 2.50e+03 2.78e+01
bond pdb=" C4A VIB A 501 "
pdb=" N4A VIB A 501 "
ideal model delta sigma weight residual
1.347 1.449 -0.102 2.00e-02 2.50e+03 2.60e+01
bond pdb=" C4 VIB A 501 "
pdb=" C5 VIB A 501 "
ideal model delta sigma weight residual
1.358 1.446 -0.088 2.00e-02 2.50e+03 1.92e+01
... (remaining 3220 not shown)
Histogram of bond angle deviations from ideal:
0.00 - 2.49: 4279
2.49 - 4.98: 102
4.98 - 7.47: 18
7.47 - 9.95: 4
9.95 - 12.44: 3
Bond angle restraints: 4406
Sorted by residual:
angle pdb=" C2 VIB A 501 "
pdb=" S1 VIB A 501 "
pdb=" C5 VIB A 501 "
ideal model delta sigma weight residual
91.25 103.69 -12.44 3.00e+00 1.11e-01 1.72e+01
angle pdb=" C VAL A 77 "
pdb=" N ARG A 78 "
pdb=" CA ARG A 78 "
ideal model delta sigma weight residual
122.46 127.56 -5.10 1.41e+00 5.03e-01 1.31e+01
angle pdb=" C6A VIB A 501 "
pdb=" C5A VIB A 501 "
pdb=" C7A VIB A 501 "
ideal model delta sigma weight residual
121.49 111.43 10.06 3.00e+00 1.11e-01 1.13e+01
angle pdb=" CA TRP A 284 "
pdb=" CB TRP A 284 "
pdb=" CG TRP A 284 "
ideal model delta sigma weight residual
113.60 107.61 5.99 1.90e+00 2.77e-01 9.96e+00
angle pdb=" N PHE A 56 "
pdb=" CA PHE A 56 "
pdb=" C PHE A 56 "
ideal model delta sigma weight residual
113.16 117.60 -4.44 1.42e+00 4.96e-01 9.77e+00
... (remaining 4401 not shown)
Histogram of dihedral angle deviations from ideal:
0.00 - 14.74: 1716
14.74 - 29.47: 87
29.47 - 44.20: 16
44.20 - 58.94: 0
58.94 - 73.67: 2
Dihedral angle restraints: 1821
sinusoidal: 669
harmonic: 1152
Sorted by residual:
dihedral pdb=" CA ARG A 78 "
pdb=" C ARG A 78 "
pdb=" N TYR A 79 "
pdb=" CA TYR A 79 "
ideal model delta harmonic sigma weight residual
180.00 156.93 23.07 0 5.00e+00 4.00e-02 2.13e+01
dihedral pdb=" CA TRP A 12 "
pdb=" C TRP A 12 "
pdb=" N ILE A 13 "
pdb=" CA ILE A 13 "
ideal model delta harmonic sigma weight residual
-180.00 -159.74 -20.26 0 5.00e+00 4.00e-02 1.64e+01
dihedral pdb=" CA VAL A 426 "
pdb=" C VAL A 426 "
pdb=" N ASP A 427 "
pdb=" CA ASP A 427 "
ideal model delta harmonic sigma weight residual
-180.00 -160.73 -19.27 0 5.00e+00 4.00e-02 1.48e+01
... (remaining 1818 not shown)
Histogram of chiral volume deviations from ideal:
0.000 - 0.040: 285
0.040 - 0.081: 156
0.081 - 0.121: 42
0.121 - 0.161: 12
0.161 - 0.202: 7
Chirality restraints: 502
Sorted by residual:
chirality pdb=" CA PHE A 56 "
pdb=" N PHE A 56 "
pdb=" C PHE A 56 "
pdb=" CB PHE A 56 "
both_signs ideal model delta sigma weight residual
False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.02e+00
chirality pdb=" CB VAL A 435 "
pdb=" CA VAL A 435 "
pdb=" CG1 VAL A 435 "
pdb=" CG2 VAL A 435 "
both_signs ideal model delta sigma weight residual
False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 9.56e-01
chirality pdb=" CA TRP A 94 "
pdb=" N TRP A 94 "
pdb=" C TRP A 94 "
pdb=" CB TRP A 94 "
both_signs ideal model delta sigma weight residual
False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.39e-01
... (remaining 499 not shown)
Planarity restraints: 528
Sorted by residual:
delta sigma weight rms_deltas residual
plane pdb=" CB TYR A 63 " 0.020 2.00e-02 2.50e+03 2.31e-02 1.07e+01
pdb=" CG TYR A 63 " -0.057 2.00e-02 2.50e+03
pdb=" CD1 TYR A 63 " 0.022 2.00e-02 2.50e+03
pdb=" CD2 TYR A 63 " 0.011 2.00e-02 2.50e+03
pdb=" CE1 TYR A 63 " -0.003 2.00e-02 2.50e+03
pdb=" CE2 TYR A 63 " 0.007 2.00e-02 2.50e+03
pdb=" CZ TYR A 63 " 0.000 2.00e-02 2.50e+03
pdb=" OH TYR A 63 " -0.000 2.00e-02 2.50e+03
delta sigma weight rms_deltas residual
plane pdb=" CB TYR A 373 " 0.025 2.00e-02 2.50e+03 2.04e-02 8.35e+00
pdb=" CG TYR A 373 " -0.050 2.00e-02 2.50e+03
pdb=" CD1 TYR A 373 " 0.010 2.00e-02 2.50e+03
pdb=" CD2 TYR A 373 " 0.004 2.00e-02 2.50e+03
pdb=" CE1 TYR A 373 " 0.002 2.00e-02 2.50e+03
pdb=" CE2 TYR A 373 " 0.007 2.00e-02 2.50e+03
pdb=" CZ TYR A 373 " 0.002 2.00e-02 2.50e+03
pdb=" OH TYR A 373 " 0.001 2.00e-02 2.50e+03
delta sigma weight rms_deltas residual
plane pdb=" CA TYR A 61 " 0.013 2.00e-02 2.50e+03 2.54e-02 6.43e+00
pdb=" C TYR A 61 " -0.044 2.00e-02 2.50e+03
pdb=" O TYR A 61 " 0.016 2.00e-02 2.50e+03
pdb=" N SER A 62 " 0.015 2.00e-02 2.50e+03
... (remaining 525 not shown)
Histogram of nonbonded interaction distances:
2.32 - 2.83: 1027
2.83 - 3.35: 3005
3.35 - 3.87: 5221
3.87 - 4.38: 5967
4.38 - 4.90: 10133
Nonbonded interactions: 25353
Sorted by model distance:
nonbonded pdb=" OH TYR A 151 "
pdb=" OE2 GLU A 320 "
model vdw
2.318 3.040
nonbonded pdb=" O GLN A 418 "
pdb=" OG1 THR A 422 "
model vdw
2.371 3.040
nonbonded pdb=" OE2 GLU A 54 "
pdb=" NE2 GLN A 428 "
model vdw
2.382 3.120
nonbonded pdb=" NE2 GLN A 294 "
pdb=" OG1 THR A 422 "
model vdw
2.386 3.120
nonbonded pdb=" ND2 ASN A 53 "
pdb=" O LEU A 433 "
model vdw
2.414 3.120
... (remaining 25348 not shown)
NOTE: a complete listing of the restraints can be obtained by requesting
output of .geo file.
Find NCS groups from input model
========== 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 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: 0.830
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: 0.130
Check model and map are aligned: 0.030
Set scattering table: 0.030
Process input model: 12.450
Find NCS groups from input model: 0.030
Set up NCS constraints: 0.010
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:2.840
Set ADP refinement strategy: 0.000
Make a string to write initial .geo file:0.000
Internal consistency checks: 0.000
Total: 16.360
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7224
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 : 0.009 0.214 3225 Z= 0.539
Angle : 0.986 12.443 4406 Z= 0.506
Chirality : 0.056 0.202 502
Planarity : 0.008 0.053 528
Dihedral : 9.841 73.672 1085
Min Nonbonded Distance : 2.318
Molprobity Statistics.
All-atom Clashscore : 2.55
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 5.21 %
Favored : 94.79 %
Rotamer:
Outliers : 0.00 %
Allowed : 2.10 %
Favored : 97.90 %
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: -3.54 (0.33), residues: 384
helix: -1.92 (0.23), residues: 282
sheet: None (None), residues: 0
loop : -3.09 (0.54), residues: 102
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.040 0.003 TRP A 284
HIS 0.003 0.001 HIS A 200
PHE 0.028 0.003 PHE A 439
TYR 0.057 0.004 TYR A 63
ARG 0.001 0.000 ARG A 29
*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
768 Ramachandran restraints generated.
384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
768 Ramachandran restraints generated.
384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
122 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 0
poor density : 122
time to evaluate : 0.377
Fit side-chains
revert: symmetry clash
REVERT: A 34 PHE cc_start: 0.7993 (m-80) cc_final: 0.7793 (m-10)
REVERT: A 61 TYR cc_start: 0.7845 (m-10) cc_final: 0.7555 (m-80)
REVERT: A 73 LEU cc_start: 0.7463 (tp) cc_final: 0.7263 (tp)
REVERT: A 91 ILE cc_start: 0.8298 (mt) cc_final: 0.8070 (mm)
REVERT: A 98 LEU cc_start: 0.8166 (mt) cc_final: 0.7797 (mm)
REVERT: A 105 THR cc_start: 0.7228 (p) cc_final: 0.6995 (p)
REVERT: A 113 TYR cc_start: 0.7811 (t80) cc_final: 0.7598 (t80)
REVERT: A 159 GLN cc_start: 0.6641 (tm-30) cc_final: 0.6208 (tm-30)
REVERT: A 160 LEU cc_start: 0.7459 (mt) cc_final: 0.7219 (tp)
REVERT: A 161 LEU cc_start: 0.7954 (mt) cc_final: 0.7639 (tp)
REVERT: A 167 MET cc_start: 0.6672 (ttm) cc_final: 0.6041 (ttm)
REVERT: A 175 ILE cc_start: 0.8539 (mt) cc_final: 0.8178 (mp)
REVERT: A 176 SER cc_start: 0.8290 (m) cc_final: 0.7665 (p)
REVERT: A 198 PHE cc_start: 0.8204 (m-80) cc_final: 0.7754 (m-80)
REVERT: A 283 LEU cc_start: 0.7909 (tp) cc_final: 0.7682 (tp)
REVERT: A 300 GLN cc_start: 0.8328 (mt0) cc_final: 0.8091 (mt0)
REVERT: A 325 PHE cc_start: 0.8449 (t80) cc_final: 0.8103 (t80)
REVERT: A 361 PHE cc_start: 0.7886 (m-10) cc_final: 0.7586 (m-80)
REVERT: A 363 MET cc_start: 0.6951 (mtm) cc_final: 0.6643 (mtm)
REVERT: A 384 MET cc_start: 0.7864 (tpp) cc_final: 0.7482 (tpt)
REVERT: A 387 ILE cc_start: 0.8227 (tp) cc_final: 0.7806 (tp)
REVERT: A 403 TYR cc_start: 0.7903 (t80) cc_final: 0.7683 (t80)
REVERT: A 406 VAL cc_start: 0.7813 (t) cc_final: 0.6833 (p)
REVERT: A 410 ASN cc_start: 0.7593 (m-40) cc_final: 0.7231 (m-40)
REVERT: A 418 GLN cc_start: 0.8140 (tt0) cc_final: 0.7904 (tt0)
REVERT: A 425 VAL cc_start: 0.8383 (t) cc_final: 0.8162 (p)
REVERT: A 432 ASN cc_start: 0.7278 (t0) cc_final: 0.7034 (t0)
REVERT: A 438 GLN cc_start: 0.7665 (mt0) cc_final: 0.7374 (mt0)
outliers start: 0
outliers final: 0
residues processed: 122
average time/residue: 0.1059
time to fit residues: 16.8060
Evaluate side-chains
104 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 0
poor density : 104
time to evaluate : 0.316
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 38
random chunks:
chunk 32 optimal weight: 0.0170
chunk 28 optimal weight: 1.9990
chunk 15 optimal weight: 0.3980
chunk 9 optimal weight: 0.8980
chunk 19 optimal weight: 0.6980
chunk 29 optimal weight: 0.0980
chunk 11 optimal weight: 0.5980
chunk 18 optimal weight: 0.3980
chunk 22 optimal weight: 0.5980
chunk 34 optimal weight: 0.5980
chunk 10 optimal weight: 0.6980
overall best weight: 0.3018
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 86 GLN
A 200 HIS
A 397 ASN
Total number of N/Q/H flips: 3
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.115963 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.101306 restraints weight = 5717.355|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.104781 restraints weight = 2799.586|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.107022 restraints weight = 1660.694|
|-----------------------------------------------------------------------------|
r_work (final): 0.3370
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7228
moved from start: 0.1953
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.021 3225 Z= 0.169
Angle : 0.599 6.685 4406 Z= 0.315
Chirality : 0.042 0.137 502
Planarity : 0.005 0.042 528
Dihedral : 6.900 68.489 428
Min Nonbonded Distance : 2.527
Molprobity Statistics.
All-atom Clashscore : 8.76
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 2.08 %
Favored : 97.92 %
Rotamer:
Outliers : 1.80 %
Allowed : 12.91 %
Favored : 85.29 %
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: -0.58 (0.39), residues: 384
helix: 0.34 (0.28), residues: 285
sheet: None (None), residues: 0
loop : -2.40 (0.56), residues: 99
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.024 0.001 TRP A 284
HIS 0.007 0.002 HIS A 364
PHE 0.016 0.002 PHE A 439
TYR 0.019 0.002 TYR A 373
ARG 0.001 0.000 ARG A 78
*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
768 Ramachandran restraints generated.
384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
768 Ramachandran restraints generated.
384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
120 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 6
poor density : 114
time to evaluate : 0.299
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: A 34 PHE cc_start: 0.7941 (m-80) cc_final: 0.7699 (m-10)
REVERT: A 52 THR cc_start: 0.7846 (m) cc_final: 0.7478 (p)
REVERT: A 73 LEU cc_start: 0.7775 (tp) cc_final: 0.7330 (tp)
REVERT: A 86 GLN cc_start: 0.8188 (tt0) cc_final: 0.7674 (tt0)
REVERT: A 89 SER cc_start: 0.8111 (m) cc_final: 0.7799 (p)
REVERT: A 156 VAL cc_start: 0.8111 (OUTLIER) cc_final: 0.7907 (m)
REVERT: A 161 LEU cc_start: 0.8070 (mt) cc_final: 0.7831 (mt)
REVERT: A 198 PHE cc_start: 0.8100 (m-80) cc_final: 0.7896 (m-80)
REVERT: A 283 LEU cc_start: 0.7929 (tp) cc_final: 0.7718 (tp)
REVERT: A 325 PHE cc_start: 0.8460 (t80) cc_final: 0.8247 (t80)
REVERT: A 361 PHE cc_start: 0.7812 (m-10) cc_final: 0.7524 (m-10)
REVERT: A 387 ILE cc_start: 0.8067 (tp) cc_final: 0.7751 (tp)
REVERT: A 406 VAL cc_start: 0.7851 (t) cc_final: 0.6914 (p)
REVERT: A 410 ASN cc_start: 0.7577 (m-40) cc_final: 0.7250 (m-40)
REVERT: A 431 LEU cc_start: 0.7582 (mt) cc_final: 0.7354 (mt)
REVERT: A 432 ASN cc_start: 0.7434 (t0) cc_final: 0.7088 (t0)
REVERT: A 433 LEU cc_start: 0.8269 (mt) cc_final: 0.7916 (mt)
outliers start: 6
outliers final: 2
residues processed: 117
average time/residue: 0.1007
time to fit residues: 15.3351
Evaluate side-chains
118 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 3
poor density : 115
time to evaluate : 0.371
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 88 ILE
Chi-restraints excluded: chain A residue 156 VAL
Chi-restraints excluded: chain A residue 449 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 38
random chunks:
chunk 35 optimal weight: 0.9990
chunk 2 optimal weight: 0.6980
chunk 34 optimal weight: 0.6980
chunk 16 optimal weight: 0.6980
chunk 3 optimal weight: 0.4980
chunk 28 optimal weight: 0.9990
chunk 4 optimal weight: 0.9990
chunk 5 optimal weight: 0.5980
chunk 9 optimal weight: 0.9980
chunk 20 optimal weight: 0.9990
chunk 25 optimal weight: 0.6980
overall best weight: 0.6380
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 300 GLN
** A 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 418 GLN
Total number of N/Q/H flips: 2
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.113594 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.099517 restraints weight = 5609.252|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.102796 restraints weight = 2774.812|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.105008 restraints weight = 1654.915|
|-----------------------------------------------------------------------------|
r_work (final): 0.3333
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7265
moved from start: 0.2617
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.004 0.036 3225 Z= 0.251
Angle : 0.614 7.092 4406 Z= 0.328
Chirality : 0.044 0.157 502
Planarity : 0.004 0.042 528
Dihedral : 6.651 69.205 428
Min Nonbonded Distance : 2.488
Molprobity Statistics.
All-atom Clashscore : 10.51
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 3.91 %
Favored : 96.09 %
Rotamer:
Outliers : 3.60 %
Allowed : 15.62 %
Favored : 80.78 %
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: 0.55 (0.42), residues: 384
helix: 1.09 (0.29), residues: 289
sheet: None (None), residues: 0
loop : -1.86 (0.63), residues: 95
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.023 0.002 TRP A 284
HIS 0.005 0.001 HIS A 364
PHE 0.016 0.002 PHE A 99
TYR 0.022 0.002 TYR A 63
ARG 0.001 0.000 ARG A 78
*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
768 Ramachandran restraints generated.
384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
768 Ramachandran restraints generated.
384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
127 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 12
poor density : 115
time to evaluate : 0.289
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: A 34 PHE cc_start: 0.8099 (m-80) cc_final: 0.7814 (m-10)
REVERT: A 52 THR cc_start: 0.8020 (m) cc_final: 0.7602 (p)
REVERT: A 73 LEU cc_start: 0.7837 (tp) cc_final: 0.7577 (tp)
REVERT: A 86 GLN cc_start: 0.8175 (tt0) cc_final: 0.7677 (tt0)
REVERT: A 89 SER cc_start: 0.8105 (m) cc_final: 0.7797 (p)
REVERT: A 101 GLN cc_start: 0.6837 (mm110) cc_final: 0.6543 (mm110)
REVERT: A 152 THR cc_start: 0.8303 (OUTLIER) cc_final: 0.8020 (t)
REVERT: A 156 VAL cc_start: 0.8239 (OUTLIER) cc_final: 0.7959 (m)
REVERT: A 161 LEU cc_start: 0.8172 (mt) cc_final: 0.7663 (tp)
REVERT: A 197 MET cc_start: 0.8206 (tpp) cc_final: 0.7714 (tpp)
REVERT: A 283 LEU cc_start: 0.7925 (tp) cc_final: 0.7689 (tp)
REVERT: A 325 PHE cc_start: 0.8415 (t80) cc_final: 0.8111 (t80)
REVERT: A 361 PHE cc_start: 0.7889 (m-10) cc_final: 0.7619 (m-80)
REVERT: A 384 MET cc_start: 0.7962 (mmm) cc_final: 0.7719 (mmm)
REVERT: A 385 LEU cc_start: 0.8074 (tt) cc_final: 0.7780 (tp)
REVERT: A 387 ILE cc_start: 0.8042 (tp) cc_final: 0.7692 (tp)
REVERT: A 406 VAL cc_start: 0.7868 (t) cc_final: 0.7045 (p)
REVERT: A 407 PHE cc_start: 0.7872 (OUTLIER) cc_final: 0.7621 (m-80)
REVERT: A 410 ASN cc_start: 0.7696 (m-40) cc_final: 0.7321 (m-40)
REVERT: A 431 LEU cc_start: 0.7649 (mt) cc_final: 0.7406 (mt)
REVERT: A 432 ASN cc_start: 0.7622 (t0) cc_final: 0.7274 (t0)
REVERT: A 433 LEU cc_start: 0.8264 (mt) cc_final: 0.7858 (mt)
outliers start: 12
outliers final: 6
residues processed: 118
average time/residue: 0.1046
time to fit residues: 15.8539
Evaluate side-chains
122 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 9
poor density : 113
time to evaluate : 0.309
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 43 ASP
Chi-restraints excluded: chain A residue 152 THR
Chi-restraints excluded: chain A residue 156 VAL
Chi-restraints excluded: chain A residue 167 MET
Chi-restraints excluded: chain A residue 176 SER
Chi-restraints excluded: chain A residue 188 LEU
Chi-restraints excluded: chain A residue 401 GLU
Chi-restraints excluded: chain A residue 407 PHE
Chi-restraints excluded: chain A residue 458 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 38
random chunks:
chunk 31 optimal weight: 0.6980
chunk 18 optimal weight: 0.9990
chunk 23 optimal weight: 0.9980
chunk 30 optimal weight: 0.7980
chunk 27 optimal weight: 0.5980
chunk 22 optimal weight: 0.3980
chunk 15 optimal weight: 0.5980
chunk 2 optimal weight: 0.4980
chunk 7 optimal weight: 0.6980
chunk 21 optimal weight: 0.2980
chunk 8 optimal weight: 0.7980
overall best weight: 0.4780
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 173 ASN
Total number of N/Q/H flips: 1
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.113771 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.099322 restraints weight = 5736.941|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.102720 restraints weight = 2839.977|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.104902 restraints weight = 1685.100|
|-----------------------------------------------------------------------------|
r_work (final): 0.3339
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7258
moved from start: 0.3011
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.028 3225 Z= 0.213
Angle : 0.584 6.758 4406 Z= 0.311
Chirality : 0.042 0.144 502
Planarity : 0.004 0.040 528
Dihedral : 6.436 64.542 428
Min Nonbonded Distance : 2.484
Molprobity Statistics.
All-atom Clashscore : 9.72
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 3.12 %
Favored : 96.88 %
Rotamer:
Outliers : 3.00 %
Allowed : 18.92 %
Favored : 78.08 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 1.10 (0.42), residues: 384
helix: 1.47 (0.29), residues: 291
sheet: None (None), residues: 0
loop : -1.62 (0.64), residues: 93
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.020 0.001 TRP A 284
HIS 0.005 0.001 HIS A 364
PHE 0.019 0.002 PHE A 99
TYR 0.015 0.002 TYR A 383
ARG 0.002 0.000 ARG A 78
*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
768 Ramachandran restraints generated.
384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
768 Ramachandran restraints generated.
384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
125 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 10
poor density : 115
time to evaluate : 0.330
Fit side-chains
revert: symmetry clash
revert: symmetry clash
REVERT: A 33 PRO cc_start: 0.8415 (Cg_exo) cc_final: 0.8155 (Cg_endo)
REVERT: A 34 PHE cc_start: 0.8117 (m-80) cc_final: 0.7906 (m-10)
REVERT: A 52 THR cc_start: 0.7955 (m) cc_final: 0.7536 (p)
REVERT: A 73 LEU cc_start: 0.7973 (tp) cc_final: 0.7708 (tp)
REVERT: A 81 PRO cc_start: 0.8336 (Cg_exo) cc_final: 0.8056 (Cg_endo)
REVERT: A 89 SER cc_start: 0.8075 (m) cc_final: 0.7795 (p)
REVERT: A 101 GLN cc_start: 0.6925 (mm110) cc_final: 0.6620 (mm110)
REVERT: A 161 LEU cc_start: 0.8134 (mt) cc_final: 0.7679 (tp)
REVERT: A 175 ILE cc_start: 0.8457 (mt) cc_final: 0.8194 (mp)
REVERT: A 197 MET cc_start: 0.8262 (tpp) cc_final: 0.7849 (tpp)
REVERT: A 283 LEU cc_start: 0.7900 (tp) cc_final: 0.7689 (tp)
REVERT: A 325 PHE cc_start: 0.8441 (t80) cc_final: 0.8202 (t80)
REVERT: A 361 PHE cc_start: 0.7868 (m-10) cc_final: 0.7640 (m-80)
REVERT: A 363 MET cc_start: 0.7262 (mtm) cc_final: 0.6966 (mtm)
REVERT: A 376 TYR cc_start: 0.8720 (t80) cc_final: 0.8256 (t80)
REVERT: A 380 LYS cc_start: 0.8400 (tttt) cc_final: 0.8155 (ttmm)
REVERT: A 384 MET cc_start: 0.7968 (mmm) cc_final: 0.7722 (mmm)
REVERT: A 387 ILE cc_start: 0.8012 (tp) cc_final: 0.7695 (tp)
REVERT: A 406 VAL cc_start: 0.7886 (t) cc_final: 0.6838 (p)
REVERT: A 407 PHE cc_start: 0.7883 (OUTLIER) cc_final: 0.7578 (m-80)
REVERT: A 410 ASN cc_start: 0.7635 (m-40) cc_final: 0.7213 (m-40)
REVERT: A 418 GLN cc_start: 0.7905 (tt0) cc_final: 0.7644 (tt0)
REVERT: A 419 THR cc_start: 0.8296 (OUTLIER) cc_final: 0.7853 (p)
REVERT: A 431 LEU cc_start: 0.7585 (mt) cc_final: 0.7331 (mt)
REVERT: A 432 ASN cc_start: 0.7637 (t0) cc_final: 0.7288 (t0)
REVERT: A 433 LEU cc_start: 0.8231 (mt) cc_final: 0.7885 (mt)
outliers start: 10
outliers final: 7
residues processed: 117
average time/residue: 0.1012
time to fit residues: 15.3594
Evaluate side-chains
122 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 9
poor density : 113
time to evaluate : 0.317
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 43 ASP
Chi-restraints excluded: chain A residue 103 VAL
Chi-restraints excluded: chain A residue 167 MET
Chi-restraints excluded: chain A residue 173 ASN
Chi-restraints excluded: chain A residue 188 LEU
Chi-restraints excluded: chain A residue 300 GLN
Chi-restraints excluded: chain A residue 407 PHE
Chi-restraints excluded: chain A residue 419 THR
Chi-restraints excluded: chain A residue 458 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 38
random chunks:
chunk 16 optimal weight: 0.9980
chunk 15 optimal weight: 0.6980
chunk 11 optimal weight: 1.9990
chunk 33 optimal weight: 1.9990
chunk 0 optimal weight: 0.9990
chunk 30 optimal weight: 0.9980
chunk 13 optimal weight: 0.6980
chunk 6 optimal weight: 0.9980
chunk 12 optimal weight: 0.7980
chunk 20 optimal weight: 0.4980
chunk 28 optimal weight: 1.9990
overall best weight: 0.7380
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 173 ASN
Total number of N/Q/H flips: 1
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.112965 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.098501 restraints weight = 5666.586|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.101798 restraints weight = 2823.186|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.104006 restraints weight = 1699.991|
|-----------------------------------------------------------------------------|
r_work (final): 0.3331
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7289
moved from start: 0.3183
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.005 0.036 3225 Z= 0.287
Angle : 0.661 12.462 4406 Z= 0.343
Chirality : 0.046 0.170 502
Planarity : 0.004 0.043 528
Dihedral : 6.298 62.278 428
Min Nonbonded Distance : 2.468
Molprobity Statistics.
All-atom Clashscore : 10.36
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 3.12 %
Favored : 96.88 %
Rotamer:
Outliers : 3.30 %
Allowed : 18.92 %
Favored : 77.78 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 1.19 (0.42), residues: 384
helix: 1.57 (0.29), residues: 292
sheet: None (None), residues: 0
loop : -1.78 (0.65), residues: 92
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.021 0.001 TRP A 284
HIS 0.003 0.001 HIS A 364
PHE 0.023 0.002 PHE A 99
TYR 0.016 0.002 TYR A 383
ARG 0.002 0.000 ARG A 78
*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
768 Ramachandran restraints generated.
384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
768 Ramachandran restraints generated.
384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
124 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 11
poor density : 113
time to evaluate : 0.302
Fit side-chains
revert: symmetry clash
revert: symmetry clash
REVERT: A 33 PRO cc_start: 0.8383 (Cg_exo) cc_final: 0.8116 (Cg_endo)
REVERT: A 52 THR cc_start: 0.8070 (m) cc_final: 0.7625 (p)
REVERT: A 73 LEU cc_start: 0.8195 (tp) cc_final: 0.7985 (tp)
REVERT: A 79 TYR cc_start: 0.7684 (m-80) cc_final: 0.7324 (m-80)
REVERT: A 89 SER cc_start: 0.8058 (m) cc_final: 0.7809 (p)
REVERT: A 101 GLN cc_start: 0.6905 (mm110) cc_final: 0.6615 (mm110)
REVERT: A 161 LEU cc_start: 0.8142 (mt) cc_final: 0.7679 (tp)
REVERT: A 175 ILE cc_start: 0.8432 (mt) cc_final: 0.8160 (mp)
REVERT: A 197 MET cc_start: 0.8318 (tpp) cc_final: 0.7957 (tpp)
REVERT: A 283 LEU cc_start: 0.7886 (tp) cc_final: 0.7660 (tp)
REVERT: A 325 PHE cc_start: 0.8467 (t80) cc_final: 0.8236 (t80)
REVERT: A 361 PHE cc_start: 0.7901 (m-10) cc_final: 0.7674 (m-80)
REVERT: A 363 MET cc_start: 0.7300 (mtm) cc_final: 0.7013 (mtm)
REVERT: A 376 TYR cc_start: 0.8697 (t80) cc_final: 0.8239 (t80)
REVERT: A 380 LYS cc_start: 0.8440 (tttt) cc_final: 0.8217 (ttmm)
REVERT: A 387 ILE cc_start: 0.8061 (tp) cc_final: 0.7745 (tp)
REVERT: A 388 THR cc_start: 0.7941 (t) cc_final: 0.7718 (p)
REVERT: A 406 VAL cc_start: 0.7886 (t) cc_final: 0.7096 (p)
REVERT: A 407 PHE cc_start: 0.7883 (OUTLIER) cc_final: 0.7633 (m-80)
REVERT: A 410 ASN cc_start: 0.7745 (m-40) cc_final: 0.7405 (m-40)
REVERT: A 419 THR cc_start: 0.8218 (OUTLIER) cc_final: 0.7847 (p)
REVERT: A 431 LEU cc_start: 0.7624 (mt) cc_final: 0.7378 (mt)
REVERT: A 432 ASN cc_start: 0.7693 (t0) cc_final: 0.7364 (t0)
REVERT: A 433 LEU cc_start: 0.8287 (mt) cc_final: 0.7886 (mt)
outliers start: 11
outliers final: 5
residues processed: 116
average time/residue: 0.1111
time to fit residues: 16.5936
Evaluate side-chains
116 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 7
poor density : 109
time to evaluate : 0.321
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 43 ASP
Chi-restraints excluded: chain A residue 160 LEU
Chi-restraints excluded: chain A residue 167 MET
Chi-restraints excluded: chain A residue 188 LEU
Chi-restraints excluded: chain A residue 300 GLN
Chi-restraints excluded: chain A residue 407 PHE
Chi-restraints excluded: chain A residue 419 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 38
random chunks:
chunk 16 optimal weight: 0.5980
chunk 27 optimal weight: 0.7980
chunk 1 optimal weight: 0.5980
chunk 37 optimal weight: 1.9990
chunk 0 optimal weight: 0.9990
chunk 2 optimal weight: 0.0270
chunk 14 optimal weight: 0.6980
chunk 9 optimal weight: 0.8980
chunk 34 optimal weight: 0.6980
chunk 29 optimal weight: 0.9990
chunk 31 optimal weight: 0.5980
overall best weight: 0.5038
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.113722 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.098926 restraints weight = 5791.148|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.102336 restraints weight = 2862.856|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.104527 restraints weight = 1717.449|
|-----------------------------------------------------------------------------|
r_work (final): 0.3346
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7277
moved from start: 0.3408
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.004 0.072 3225 Z= 0.239
Angle : 0.622 9.531 4406 Z= 0.324
Chirality : 0.043 0.151 502
Planarity : 0.004 0.043 528
Dihedral : 6.107 58.266 428
Min Nonbonded Distance : 2.475
Molprobity Statistics.
All-atom Clashscore : 10.36
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 3.12 %
Favored : 96.88 %
Rotamer:
Outliers : 2.10 %
Allowed : 21.62 %
Favored : 76.28 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 1.41 (0.42), residues: 384
helix: 1.73 (0.29), residues: 289
sheet: None (None), residues: 0
loop : -1.58 (0.62), residues: 95
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.019 0.001 TRP A 284
HIS 0.004 0.002 HIS A 364
PHE 0.021 0.002 PHE A 99
TYR 0.016 0.002 TYR A 383
ARG 0.002 0.000 ARG A 78
*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
768 Ramachandran restraints generated.
384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
768 Ramachandran restraints generated.
384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
121 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 7
poor density : 114
time to evaluate : 0.339
Fit side-chains
revert: symmetry clash
revert: symmetry clash
REVERT: A 48 SER cc_start: 0.8210 (m) cc_final: 0.7864 (t)
REVERT: A 52 THR cc_start: 0.8062 (m) cc_final: 0.7680 (p)
REVERT: A 59 TRP cc_start: 0.8399 (t60) cc_final: 0.7642 (t60)
REVERT: A 79 TYR cc_start: 0.7603 (m-80) cc_final: 0.7236 (m-80)
REVERT: A 89 SER cc_start: 0.8135 (m) cc_final: 0.7903 (p)
REVERT: A 101 GLN cc_start: 0.6895 (mm110) cc_final: 0.6656 (mm110)
REVERT: A 161 LEU cc_start: 0.8166 (mt) cc_final: 0.7701 (tp)
REVERT: A 171 TYR cc_start: 0.8066 (m-10) cc_final: 0.7698 (m-10)
REVERT: A 175 ILE cc_start: 0.8457 (mt) cc_final: 0.8157 (mp)
REVERT: A 320 GLU cc_start: 0.7297 (tp30) cc_final: 0.7089 (tp30)
REVERT: A 325 PHE cc_start: 0.8417 (t80) cc_final: 0.8191 (t80)
REVERT: A 361 PHE cc_start: 0.7877 (m-10) cc_final: 0.7637 (m-80)
REVERT: A 363 MET cc_start: 0.7262 (mtm) cc_final: 0.6985 (mtm)
REVERT: A 376 TYR cc_start: 0.8634 (t80) cc_final: 0.8033 (t80)
REVERT: A 380 LYS cc_start: 0.8441 (tttt) cc_final: 0.8213 (ttmm)
REVERT: A 384 MET cc_start: 0.8000 (mmm) cc_final: 0.7694 (tpp)
REVERT: A 387 ILE cc_start: 0.8068 (tp) cc_final: 0.7727 (tp)
REVERT: A 406 VAL cc_start: 0.7899 (t) cc_final: 0.6985 (p)
REVERT: A 407 PHE cc_start: 0.7858 (OUTLIER) cc_final: 0.7496 (m-80)
REVERT: A 410 ASN cc_start: 0.7592 (m-40) cc_final: 0.7193 (m-40)
REVERT: A 419 THR cc_start: 0.8216 (OUTLIER) cc_final: 0.7841 (p)
REVERT: A 431 LEU cc_start: 0.7583 (mt) cc_final: 0.7343 (mt)
REVERT: A 432 ASN cc_start: 0.7643 (t0) cc_final: 0.7329 (t0)
REVERT: A 433 LEU cc_start: 0.8276 (mt) cc_final: 0.7915 (mt)
outliers start: 7
outliers final: 4
residues processed: 115
average time/residue: 0.1088
time to fit residues: 16.1310
Evaluate side-chains
120 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 6
poor density : 114
time to evaluate : 0.306
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 43 ASP
Chi-restraints excluded: chain A residue 160 LEU
Chi-restraints excluded: chain A residue 167 MET
Chi-restraints excluded: chain A residue 300 GLN
Chi-restraints excluded: chain A residue 407 PHE
Chi-restraints excluded: chain A residue 419 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 38
random chunks:
chunk 33 optimal weight: 0.5980
chunk 2 optimal weight: 0.7980
chunk 6 optimal weight: 0.6980
chunk 25 optimal weight: 0.5980
chunk 8 optimal weight: 0.5980
chunk 32 optimal weight: 2.9990
chunk 5 optimal weight: 0.9980
chunk 12 optimal weight: 6.9990
chunk 28 optimal weight: 0.9990
chunk 21 optimal weight: 0.8980
chunk 7 optimal weight: 0.5980
overall best weight: 0.6180
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 173 ASN
Total number of N/Q/H flips: 1
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.112888 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.098574 restraints weight = 5714.746|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.101873 restraints weight = 2829.413|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.104081 restraints weight = 1699.121|
|-----------------------------------------------------------------------------|
r_work (final): 0.3332
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7286
moved from start: 0.3657
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.004 0.075 3225 Z= 0.274
Angle : 0.647 8.793 4406 Z= 0.337
Chirality : 0.045 0.149 502
Planarity : 0.004 0.043 528
Dihedral : 6.061 57.418 428
Min Nonbonded Distance : 2.405
Molprobity Statistics.
All-atom Clashscore : 9.88
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 3.65 %
Favored : 96.35 %
Rotamer:
Outliers : 1.80 %
Allowed : 24.02 %
Favored : 74.17 %
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: 1.50 (0.42), residues: 384
helix: 1.69 (0.29), residues: 297
sheet: None (None), residues: 0
loop : -1.46 (0.68), residues: 87
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.021 0.001 TRP A 284
HIS 0.003 0.001 HIS A 364
PHE 0.024 0.002 PHE A 99
TYR 0.016 0.002 TYR A 136
ARG 0.001 0.000 ARG A 78
*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
768 Ramachandran restraints generated.
384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
768 Ramachandran restraints generated.
384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
118 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 6
poor density : 112
time to evaluate : 0.308
Fit side-chains
revert: symmetry clash
revert: symmetry clash
REVERT: A 48 SER cc_start: 0.8203 (m) cc_final: 0.7864 (t)
REVERT: A 52 THR cc_start: 0.8084 (m) cc_final: 0.7699 (p)
REVERT: A 67 LEU cc_start: 0.8452 (tp) cc_final: 0.8173 (tt)
REVERT: A 79 TYR cc_start: 0.7640 (m-80) cc_final: 0.7230 (m-80)
REVERT: A 89 SER cc_start: 0.8083 (m) cc_final: 0.7860 (p)
REVERT: A 101 GLN cc_start: 0.6864 (mm110) cc_final: 0.6608 (mm110)
REVERT: A 161 LEU cc_start: 0.8225 (mt) cc_final: 0.7742 (tp)
REVERT: A 171 TYR cc_start: 0.8086 (m-10) cc_final: 0.7679 (m-10)
REVERT: A 175 ILE cc_start: 0.8453 (mt) cc_final: 0.8200 (mp)
REVERT: A 320 GLU cc_start: 0.7294 (tp30) cc_final: 0.7002 (tp30)
REVERT: A 361 PHE cc_start: 0.7893 (m-10) cc_final: 0.7670 (m-80)
REVERT: A 363 MET cc_start: 0.7276 (mtm) cc_final: 0.7001 (mtm)
REVERT: A 380 LYS cc_start: 0.8457 (tttt) cc_final: 0.8144 (ttmm)
REVERT: A 387 ILE cc_start: 0.8041 (tp) cc_final: 0.7718 (tp)
REVERT: A 406 VAL cc_start: 0.7941 (t) cc_final: 0.7016 (p)
REVERT: A 407 PHE cc_start: 0.7861 (OUTLIER) cc_final: 0.7549 (m-80)
REVERT: A 410 ASN cc_start: 0.7659 (m-40) cc_final: 0.7289 (m-40)
REVERT: A 419 THR cc_start: 0.8208 (OUTLIER) cc_final: 0.7833 (p)
REVERT: A 431 LEU cc_start: 0.7593 (mt) cc_final: 0.7354 (mt)
REVERT: A 432 ASN cc_start: 0.7658 (t0) cc_final: 0.7353 (t0)
REVERT: A 433 LEU cc_start: 0.8287 (mt) cc_final: 0.7928 (mt)
outliers start: 6
outliers final: 3
residues processed: 114
average time/residue: 0.1112
time to fit residues: 16.4749
Evaluate side-chains
111 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 5
poor density : 106
time to evaluate : 0.316
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 43 ASP
Chi-restraints excluded: chain A residue 188 LEU
Chi-restraints excluded: chain A residue 300 GLN
Chi-restraints excluded: chain A residue 407 PHE
Chi-restraints excluded: chain A residue 419 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 38
random chunks:
chunk 21 optimal weight: 0.7980
chunk 30 optimal weight: 0.5980
chunk 20 optimal weight: 0.9990
chunk 6 optimal weight: 0.8980
chunk 13 optimal weight: 0.3980
chunk 24 optimal weight: 0.8980
chunk 19 optimal weight: 2.9990
chunk 12 optimal weight: 3.9990
chunk 10 optimal weight: 0.9990
chunk 26 optimal weight: 1.9990
chunk 15 optimal weight: 0.0770
overall best weight: 0.5538
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 173 ASN
Total number of N/Q/H flips: 1
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.113148 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.098680 restraints weight = 5712.882|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.102029 restraints weight = 2820.523|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.104086 restraints weight = 1682.598|
|-----------------------------------------------------------------------------|
r_work (final): 0.3333
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7278
moved from start: 0.3768
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.004 0.068 3225 Z= 0.251
Angle : 0.638 8.977 4406 Z= 0.332
Chirality : 0.044 0.145 502
Planarity : 0.004 0.043 528
Dihedral : 5.992 56.012 428
Min Nonbonded Distance : 2.526
Molprobity Statistics.
All-atom Clashscore : 9.56
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 3.65 %
Favored : 96.35 %
Rotamer:
Outliers : 1.80 %
Allowed : 24.32 %
Favored : 73.87 %
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: 1.63 (0.42), residues: 384
helix: 1.84 (0.29), residues: 291
sheet: None (None), residues: 0
loop : -1.41 (0.65), residues: 93
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.020 0.001 TRP A 284
HIS 0.004 0.001 HIS A 364
PHE 0.025 0.002 PHE A 99
TYR 0.016 0.002 TYR A 383
ARG 0.001 0.000 ARG A 78
*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
768 Ramachandran restraints generated.
384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
768 Ramachandran restraints generated.
384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
116 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 6
poor density : 110
time to evaluate : 0.306
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: A 52 THR cc_start: 0.8097 (m) cc_final: 0.7744 (t)
REVERT: A 59 TRP cc_start: 0.8346 (t60) cc_final: 0.7691 (t60)
REVERT: A 67 LEU cc_start: 0.8455 (tp) cc_final: 0.8171 (tt)
REVERT: A 79 TYR cc_start: 0.7615 (m-80) cc_final: 0.7188 (m-80)
REVERT: A 86 GLN cc_start: 0.8255 (tt0) cc_final: 0.7872 (tt0)
REVERT: A 89 SER cc_start: 0.8145 (m) cc_final: 0.7908 (p)
REVERT: A 101 GLN cc_start: 0.6938 (mm110) cc_final: 0.6669 (mm-40)
REVERT: A 161 LEU cc_start: 0.8192 (mt) cc_final: 0.7793 (tp)
REVERT: A 171 TYR cc_start: 0.8088 (m-10) cc_final: 0.7846 (m-10)
REVERT: A 314 ILE cc_start: 0.8123 (pt) cc_final: 0.7876 (pt)
REVERT: A 320 GLU cc_start: 0.7327 (tp30) cc_final: 0.7030 (tp30)
REVERT: A 361 PHE cc_start: 0.7908 (m-10) cc_final: 0.7690 (m-80)
REVERT: A 363 MET cc_start: 0.7316 (mtm) cc_final: 0.7045 (mtm)
REVERT: A 387 ILE cc_start: 0.7992 (tp) cc_final: 0.7651 (tp)
REVERT: A 406 VAL cc_start: 0.7896 (t) cc_final: 0.6963 (p)
REVERT: A 407 PHE cc_start: 0.7879 (OUTLIER) cc_final: 0.7529 (m-80)
REVERT: A 410 ASN cc_start: 0.7541 (m-40) cc_final: 0.7157 (m-40)
REVERT: A 419 THR cc_start: 0.8221 (OUTLIER) cc_final: 0.7842 (p)
REVERT: A 431 LEU cc_start: 0.7585 (mt) cc_final: 0.7344 (mt)
REVERT: A 432 ASN cc_start: 0.7659 (t0) cc_final: 0.7368 (t0)
REVERT: A 433 LEU cc_start: 0.8276 (mt) cc_final: 0.7903 (mt)
outliers start: 6
outliers final: 4
residues processed: 112
average time/residue: 0.1039
time to fit residues: 14.9913
Evaluate side-chains
116 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 6
poor density : 110
time to evaluate : 0.344
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 43 ASP
Chi-restraints excluded: chain A residue 173 ASN
Chi-restraints excluded: chain A residue 188 LEU
Chi-restraints excluded: chain A residue 300 GLN
Chi-restraints excluded: chain A residue 407 PHE
Chi-restraints excluded: chain A residue 419 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 38
random chunks:
chunk 30 optimal weight: 0.5980
chunk 31 optimal weight: 0.7980
chunk 0 optimal weight: 0.9990
chunk 15 optimal weight: 0.5980
chunk 23 optimal weight: 0.9980
chunk 21 optimal weight: 0.5980
chunk 36 optimal weight: 0.4980
chunk 32 optimal weight: 1.9990
chunk 3 optimal weight: 0.9980
chunk 19 optimal weight: 0.9980
chunk 10 optimal weight: 0.6980
overall best weight: 0.5980
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 173 ASN
Total number of N/Q/H flips: 1
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.113531 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.099128 restraints weight = 5649.176|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.102458 restraints weight = 2824.942|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.104616 restraints weight = 1697.755|
|-----------------------------------------------------------------------------|
r_work (final): 0.3337
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7286
moved from start: 0.3828
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.004 0.069 3225 Z= 0.264
Angle : 0.647 8.206 4406 Z= 0.339
Chirality : 0.044 0.146 502
Planarity : 0.004 0.043 528
Dihedral : 5.993 55.679 428
Min Nonbonded Distance : 2.437
Molprobity Statistics.
All-atom Clashscore : 9.72
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 3.65 %
Favored : 96.35 %
Rotamer:
Outliers : 1.80 %
Allowed : 25.83 %
Favored : 72.37 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 1.62 (0.42), residues: 384
helix: 1.83 (0.29), residues: 291
sheet: None (None), residues: 0
loop : -1.40 (0.66), residues: 93
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.021 0.001 TRP A 284
HIS 0.004 0.001 HIS A 364
PHE 0.027 0.002 PHE A 99
TYR 0.015 0.002 TYR A 383
ARG 0.001 0.000 ARG A 78
*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
768 Ramachandran restraints generated.
384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
768 Ramachandran restraints generated.
384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
115 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 6
poor density : 109
time to evaluate : 0.316
Fit side-chains
revert: symmetry clash
revert: symmetry clash
REVERT: A 52 THR cc_start: 0.8130 (m) cc_final: 0.7757 (t)
REVERT: A 59 TRP cc_start: 0.8415 (t60) cc_final: 0.7751 (t60)
REVERT: A 67 LEU cc_start: 0.8443 (tp) cc_final: 0.8148 (tt)
REVERT: A 79 TYR cc_start: 0.7613 (m-80) cc_final: 0.7192 (m-80)
REVERT: A 86 GLN cc_start: 0.8270 (tt0) cc_final: 0.7874 (tt0)
REVERT: A 89 SER cc_start: 0.8151 (m) cc_final: 0.7932 (p)
REVERT: A 101 GLN cc_start: 0.6906 (mm110) cc_final: 0.6633 (mm110)
REVERT: A 161 LEU cc_start: 0.8081 (mt) cc_final: 0.7755 (tp)
REVERT: A 314 ILE cc_start: 0.8142 (pt) cc_final: 0.7903 (pt)
REVERT: A 320 GLU cc_start: 0.7299 (tp30) cc_final: 0.7044 (tp30)
REVERT: A 361 PHE cc_start: 0.7895 (m-10) cc_final: 0.7678 (m-80)
REVERT: A 363 MET cc_start: 0.7278 (mtm) cc_final: 0.7017 (mtm)
REVERT: A 380 LYS cc_start: 0.8457 (tttt) cc_final: 0.8115 (ttmm)
REVERT: A 387 ILE cc_start: 0.8040 (tp) cc_final: 0.7691 (tp)
REVERT: A 406 VAL cc_start: 0.7929 (t) cc_final: 0.7012 (p)
REVERT: A 407 PHE cc_start: 0.7859 (OUTLIER) cc_final: 0.7516 (m-80)
REVERT: A 410 ASN cc_start: 0.7528 (m-40) cc_final: 0.7160 (m-40)
REVERT: A 419 THR cc_start: 0.8206 (OUTLIER) cc_final: 0.7835 (p)
REVERT: A 431 LEU cc_start: 0.7586 (mt) cc_final: 0.7343 (mt)
REVERT: A 432 ASN cc_start: 0.7654 (t0) cc_final: 0.7351 (t0)
REVERT: A 433 LEU cc_start: 0.8279 (mt) cc_final: 0.7922 (mt)
outliers start: 6
outliers final: 3
residues processed: 111
average time/residue: 0.1065
time to fit residues: 15.3785
Evaluate side-chains
114 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 5
poor density : 109
time to evaluate : 0.321
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 43 ASP
Chi-restraints excluded: chain A residue 188 LEU
Chi-restraints excluded: chain A residue 300 GLN
Chi-restraints excluded: chain A residue 407 PHE
Chi-restraints excluded: chain A residue 419 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 38
random chunks:
chunk 20 optimal weight: 0.9980
chunk 11 optimal weight: 0.9980
chunk 9 optimal weight: 0.9990
chunk 26 optimal weight: 0.0570
chunk 0 optimal weight: 0.9980
chunk 30 optimal weight: 0.3980
chunk 8 optimal weight: 0.7980
chunk 13 optimal weight: 0.8980
chunk 19 optimal weight: 0.4980
chunk 35 optimal weight: 0.7980
chunk 27 optimal weight: 2.9990
overall best weight: 0.5098
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 173 ASN
Total number of N/Q/H flips: 1
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.113777 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.099334 restraints weight = 5639.297|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.102700 restraints weight = 2816.479|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.104834 restraints weight = 1686.759|
|-----------------------------------------------------------------------------|
r_work (final): 0.3341
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7275
moved from start: 0.3872
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.004 0.064 3225 Z= 0.244
Angle : 0.644 8.429 4406 Z= 0.338
Chirality : 0.044 0.141 502
Planarity : 0.004 0.042 528
Dihedral : 5.942 54.489 428
Min Nonbonded Distance : 2.398
Molprobity Statistics.
All-atom Clashscore : 10.36
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 3.39 %
Favored : 96.61 %
Rotamer:
Outliers : 1.80 %
Allowed : 25.83 %
Favored : 72.37 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 1.76 (0.43), residues: 384
helix: 1.90 (0.29), residues: 291
sheet: None (None), residues: 0
loop : -1.24 (0.67), residues: 93
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.020 0.001 TRP A 284
HIS 0.004 0.001 HIS A 364
PHE 0.030 0.002 PHE A 99
TYR 0.015 0.002 TYR A 383
ARG 0.001 0.000 ARG A 78
********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
768 Ramachandran restraints generated.
384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
768 Ramachandran restraints generated.
384 Oldfield, 0 Emsley, 384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
116 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 6
poor density : 110
time to evaluate : 0.341
Fit side-chains
revert: symmetry clash
revert: symmetry clash
REVERT: A 52 THR cc_start: 0.8126 (m) cc_final: 0.7766 (t)
REVERT: A 67 LEU cc_start: 0.8513 (tp) cc_final: 0.8246 (tt)
REVERT: A 86 GLN cc_start: 0.8253 (tt0) cc_final: 0.7874 (tt0)
REVERT: A 89 SER cc_start: 0.8144 (m) cc_final: 0.7929 (p)
REVERT: A 101 GLN cc_start: 0.6887 (mm110) cc_final: 0.6622 (mm110)
REVERT: A 161 LEU cc_start: 0.8077 (mt) cc_final: 0.7763 (tp)
REVERT: A 314 ILE cc_start: 0.8136 (pt) cc_final: 0.7886 (pt)
REVERT: A 320 GLU cc_start: 0.7294 (tp30) cc_final: 0.7032 (tp30)
REVERT: A 361 PHE cc_start: 0.7892 (m-10) cc_final: 0.7673 (m-80)
REVERT: A 363 MET cc_start: 0.7276 (mtm) cc_final: 0.7015 (mtm)
REVERT: A 380 LYS cc_start: 0.8453 (tttt) cc_final: 0.8111 (ttmm)
REVERT: A 387 ILE cc_start: 0.8037 (tp) cc_final: 0.7684 (tp)
REVERT: A 406 VAL cc_start: 0.7926 (t) cc_final: 0.6999 (p)
REVERT: A 407 PHE cc_start: 0.7847 (OUTLIER) cc_final: 0.7480 (m-80)
REVERT: A 410 ASN cc_start: 0.7522 (m-40) cc_final: 0.7170 (m-40)
REVERT: A 419 THR cc_start: 0.8202 (OUTLIER) cc_final: 0.7825 (p)
REVERT: A 431 LEU cc_start: 0.7569 (mt) cc_final: 0.7334 (mt)
REVERT: A 432 ASN cc_start: 0.7639 (t0) cc_final: 0.7343 (t0)
REVERT: A 433 LEU cc_start: 0.8216 (mt) cc_final: 0.7862 (mt)
outliers start: 6
outliers final: 4
residues processed: 112
average time/residue: 0.1051
time to fit residues: 15.2532
Evaluate side-chains
115 residues out of total 333 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 6
poor density : 109
time to evaluate : 0.300
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 43 ASP
Chi-restraints excluded: chain A residue 173 ASN
Chi-restraints excluded: chain A residue 188 LEU
Chi-restraints excluded: chain A residue 300 GLN
Chi-restraints excluded: chain A residue 407 PHE
Chi-restraints excluded: chain A residue 419 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 38
random chunks:
chunk 35 optimal weight: 0.6980
chunk 15 optimal weight: 0.5980
chunk 12 optimal weight: 1.9990
chunk 31 optimal weight: 0.6980
chunk 10 optimal weight: 0.9980
chunk 9 optimal weight: 0.6980
chunk 22 optimal weight: 0.6980
chunk 24 optimal weight: 1.9990
chunk 14 optimal weight: 0.9990
chunk 13 optimal weight: 0.9980
chunk 16 optimal weight: 0.5980
overall best weight: 0.6580
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.113870 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.099506 restraints weight = 5724.955|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.102751 restraints weight = 2827.784|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.104865 restraints weight = 1700.308|
|-----------------------------------------------------------------------------|
r_work (final): 0.3350
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7281
moved from start: 0.3910
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.005 0.107 3225 Z= 0.358
Angle : 1.351 59.200 4406 Z= 0.823
Chirality : 0.045 0.183 502
Planarity : 0.004 0.043 528
Dihedral : 5.988 54.511 428
Min Nonbonded Distance : 2.351
Molprobity Statistics.
All-atom Clashscore : 11.63
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 3.65 %
Favored : 96.35 %
Rotamer:
Outliers : 1.50 %
Allowed : 25.83 %
Favored : 72.67 %
Cbeta Deviations : 0.27 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 1.69 (0.43), residues: 384
helix: 1.85 (0.29), residues: 291
sheet: None (None), residues: 0
loop : -1.26 (0.67), residues: 93
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.019 0.001 TRP A 284
HIS 0.004 0.001 HIS A 364
PHE 0.030 0.002 PHE A 186
TYR 0.015 0.002 TYR A 383
ARG 0.001 0.000 ARG A 78
Origin is already at (0, 0, 0), no shifts will be applied
===============================================================================
Job complete
usr+sys time: 1283.79 seconds
wall clock time: 23 minutes 59.70 seconds (1439.70 seconds total)