Starting phenix.real_space_refine
on Mon Jan 13 22:07:21 2025 by dcliebschner
===============================================================================
Processing files:
-------------------------------------------------------------------------------
Found model, /net/cci-nas-00/data/ceres_data/8y2e_38852/01_2025/8y2e_38852.cif
Found real_map, /net/cci-nas-00/data/ceres_data/8y2e_38852/01_2025/8y2e_38852.map
Processing PHIL parameters:
-------------------------------------------------------------------------------
Adding command-line PHIL:
-------------------------
refinement.macro_cycles=10
scattering_table=electron
resolution=3.03
write_initial_geo_file=False
Final processed PHIL parameters:
-------------------------------------------------------------------------------
data_manager {
real_map_files = "/net/cci-nas-00/data/ceres_data/8y2e_38852/01_2025/8y2e_38852.map"
default_real_map = "/net/cci-nas-00/data/ceres_data/8y2e_38852/01_2025/8y2e_38852.map"
model {
file = "/net/cci-nas-00/data/ceres_data/8y2e_38852/01_2025/8y2e_38852.cif"
}
default_model = "/net/cci-nas-00/data/ceres_data/8y2e_38852/01_2025/8y2e_38852.cif"
}
resolution = 3.03
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= 0.042
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 23 5.16 5
C 2813 2.51 5
N 659 2.21 5
O 719 1.98 5
sf(0) = scattering factor at diffraction angle 0.
Process input model
Symmetric amino acids flipped. Time to flip 5 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: 4214
Number of models: 1
Model: ""
Number of chains: 2
Chain: "A"
Number of atoms: 4163
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 528, 4163
Classifications: {'peptide': 528}
Modifications used: {'COO': 1}
Link IDs: {'PTRANS': 23, 'TRANS': 504}
Chain breaks: 2
Chain: "A"
Number of atoms: 51
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 3, 51
Unusual residues: {'CXQ': 1, 'NAG': 2}
Classifications: {'undetermined': 3}
Link IDs: {None: 2}
Unresolved non-hydrogen bonds: 2
Unresolved non-hydrogen angles: 4
Unresolved non-hydrogen dihedrals: 6
Unresolved non-hydrogen chiralities: 2
Time building chain proxies: 3.65, per 1000 atoms: 0.87
Number of scatterers: 4214
At special positions: 0
Unit cell: (74.8, 69.7, 91.8, 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 23 16.00
O 719 8.00
N 659 7.00
C 2813 6.00
sf(0) = scattering factor at diffraction angle 0.
Number of disulfides: simple=1, symmetry=0
Simple disulfide: pdb=" SG CYS A 180 " - pdb=" SG CYS A 189 " distance=2.04
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
Links applied
NAG-ASN
" NAG A 701 " - " ASN A 181 "
" NAG A 702 " - " ASN A 188 "
Time building additional restraints: 1.18
Conformation dependent library (CDL) restraints added in 565.6 milliseconds
1044 Ramachandran restraints generated.
522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
Adding C-beta torsion restraints...
Number of C-beta restraints generated: 972
Finding SS restraints...
Secondary structure from input PDB file:
32 helices and 1 sheets defined
79.4% alpha, 0.4% beta
0 base pairs and 0 stacking pairs defined.
Time for finding SS restraints: 0.41
Creating SS restraints...
Processing helix chain 'A' and resid 66 through 78
removed outlier: 3.780A pdb=" N PHE A 76 " --> pdb=" O SER A 72 " (cutoff:3.500A)
removed outlier: 3.973A pdb=" N VAL A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A)
Processing helix chain 'A' and resid 79 through 84
Processing helix chain 'A' and resid 84 through 94
removed outlier: 3.782A pdb=" N TYR A 88 " --> pdb=" O TRP A 84 " (cutoff:3.500A)
Processing helix chain 'A' and resid 98 through 110
removed outlier: 3.598A pdb=" N ILE A 108 " --> pdb=" O LEU A 104 " (cutoff:3.500A)
Processing helix chain 'A' and resid 110 through 125
Processing helix chain 'A' and resid 140 through 170
removed outlier: 3.610A pdb=" N VAL A 145 " --> pdb=" O VAL A 141 " (cutoff:3.500A)
removed outlier: 3.940A pdb=" N ILE A 146 " --> pdb=" O GLY A 142 " (cutoff:3.500A)
removed outlier: 3.822A pdb=" N PHE A 155 " --> pdb=" O TYR A 151 " (cutoff:3.500A)
removed outlier: 4.032A pdb=" N ASN A 157 " --> pdb=" O GLY A 153 " (cutoff:3.500A)
removed outlier: 5.120A pdb=" N VAL A 158 " --> pdb=" O PHE A 154 " (cutoff:3.500A)
removed outlier: 4.411A pdb=" N ILE A 159 " --> pdb=" O PHE A 155 " (cutoff:3.500A)
removed outlier: 4.300A pdb=" N ILE A 160 " --> pdb=" O TYR A 156 " (cutoff:3.500A)
Processing helix chain 'A' and resid 211 through 220
Processing helix chain 'A' and resid 223 through 227
Processing helix chain 'A' and resid 237 through 255
Processing helix chain 'A' and resid 271 through 286
Processing helix chain 'A' and resid 289 through 296
removed outlier: 3.874A pdb=" N GLY A 293 " --> pdb=" O GLY A 289 " (cutoff:3.500A)
Processing helix chain 'A' and resid 301 through 306
removed outlier: 3.830A pdb=" N LEU A 305 " --> pdb=" O ASP A 301 " (cutoff:3.500A)
removed outlier: 3.783A pdb=" N CYS A 306 " --> pdb=" O PHE A 302 " (cutoff:3.500A)
No H-bonds generated for 'chain 'A' and resid 301 through 306'
Processing helix chain 'A' and resid 308 through 323
removed outlier: 3.523A pdb=" N CYS A 319 " --> pdb=" O ALA A 315 " (cutoff:3.500A)
Processing helix chain 'A' and resid 327 through 334
removed outlier: 3.874A pdb=" N ALA A 331 " --> pdb=" O GLY A 327 " (cutoff:3.500A)
Processing helix chain 'A' and resid 342 through 376
Processing helix chain 'A' and resid 378 through 382
removed outlier: 3.685A pdb=" N VAL A 382 " --> pdb=" O ILE A 379 " (cutoff:3.500A)
Processing helix chain 'A' and resid 389 through 400
Proline residue: A 395 - end of helix
Processing helix chain 'A' and resid 403 through 438
removed outlier: 3.521A pdb=" N TRP A 407 " --> pdb=" O LEU A 403 " (cutoff:3.500A)
Processing helix chain 'A' and resid 445 through 461
Processing helix chain 'A' and resid 462 through 464
No H-bonds generated for 'chain 'A' and resid 462 through 464'
Processing helix chain 'A' and resid 467 through 479
removed outlier: 4.111A pdb=" N VAL A 471 " --> pdb=" O GLY A 467 " (cutoff:3.500A)
Processing helix chain 'A' and resid 481 through 498
Processing helix chain 'A' and resid 500 through 513
Processing helix chain 'A' and resid 517 through 526
Processing helix chain 'A' and resid 526 through 542
removed outlier: 3.506A pdb=" N PHE A 531 " --> pdb=" O VAL A 527 " (cutoff:3.500A)
Processing helix chain 'A' and resid 554 through 570
removed outlier: 3.544A pdb=" N ASN A 558 " --> pdb=" O PRO A 554 " (cutoff:3.500A)
removed outlier: 3.792A pdb=" N SER A 568 " --> pdb=" O ILE A 564 " (cutoff:3.500A)
Processing helix chain 'A' and resid 570 through 583
removed outlier: 4.293A pdb=" N ILE A 574 " --> pdb=" O ALA A 570 " (cutoff:3.500A)
removed outlier: 3.544A pdb=" N TYR A 575 " --> pdb=" O MET A 571 " (cutoff:3.500A)
Processing helix chain 'A' and resid 586 through 596
removed outlier: 3.593A pdb=" N TYR A 593 " --> pdb=" O GLU A 589 " (cutoff:3.500A)
removed outlier: 3.554A pdb=" N ILE A 595 " --> pdb=" O LEU A 591 " (cutoff:3.500A)
Processing helix chain 'A' and resid 597 through 599
No H-bonds generated for 'chain 'A' and resid 597 through 599'
Processing helix chain 'A' and resid 600 through 605
Processing helix chain 'A' and resid 609 through 612
Processing helix chain 'A' and resid 613 through 618
removed outlier: 3.898A pdb=" N TRP A 617 " --> pdb=" O THR A 613 " (cutoff:3.500A)
Processing sheet with id=AA1, first strand: chain 'A' and resid 547 through 548
268 hydrogen bonds defined for protein.
789 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: 1.15
Time building geometry restraints manager: 1.30 seconds
NOTE: a complete listing of the restraints can be obtained by requesting
output of .geo file.
Histogram of bond lengths:
1.21 - 1.34: 1101
1.34 - 1.46: 925
1.46 - 1.58: 2282
1.58 - 1.70: 3
1.70 - 1.82: 34
Bond restraints: 4345
Sorted by residual:
bond pdb=" C1 CXQ A 703 "
pdb=" C5 CXQ A 703 "
ideal model delta sigma weight residual
1.519 1.633 -0.114 2.00e-02 2.50e+03 3.26e+01
bond pdb=" C1 CXQ A 703 "
pdb=" C4 CXQ A 703 "
ideal model delta sigma weight residual
1.513 1.594 -0.081 2.00e-02 2.50e+03 1.63e+01
bond pdb=" C17 CXQ A 703 "
pdb=" N1 CXQ A 703 "
ideal model delta sigma weight residual
1.448 1.510 -0.062 2.00e-02 2.50e+03 9.70e+00
bond pdb=" C1 CXQ A 703 "
pdb=" O1 CXQ A 703 "
ideal model delta sigma weight residual
1.397 1.458 -0.061 2.00e-02 2.50e+03 9.41e+00
bond pdb=" N ILE A 268 "
pdb=" CA ILE A 268 "
ideal model delta sigma weight residual
1.459 1.491 -0.032 1.25e-02 6.40e+03 6.49e+00
... (remaining 4340 not shown)
Histogram of bond angle deviations from ideal:
0.00 - 1.86: 5799
1.86 - 3.71: 114
3.71 - 5.57: 15
5.57 - 7.43: 2
7.43 - 9.28: 1
Bond angle restraints: 5931
Sorted by residual:
angle pdb=" CA PRO A 584 "
pdb=" N PRO A 584 "
pdb=" CD PRO A 584 "
ideal model delta sigma weight residual
112.00 106.62 5.38 1.40e+00 5.10e-01 1.48e+01
angle pdb=" CA ASP A 191 "
pdb=" C ASP A 191 "
pdb=" O ASP A 191 "
ideal model delta sigma weight residual
120.92 117.41 3.51 1.04e+00 9.25e-01 1.14e+01
angle pdb=" CA PHE A 531 "
pdb=" CB PHE A 531 "
pdb=" CG PHE A 531 "
ideal model delta sigma weight residual
113.80 117.14 -3.34 1.00e+00 1.00e+00 1.12e+01
angle pdb=" CA ARG A 606 "
pdb=" CB ARG A 606 "
pdb=" CG ARG A 606 "
ideal model delta sigma weight residual
114.10 120.47 -6.37 2.00e+00 2.50e-01 1.02e+01
angle pdb=" CA LEU A 250 "
pdb=" CB LEU A 250 "
pdb=" CG LEU A 250 "
ideal model delta sigma weight residual
116.30 125.58 -9.28 3.50e+00 8.16e-02 7.04e+00
... (remaining 5926 not shown)
Histogram of dihedral angle deviations from ideal:
0.00 - 28.42: 2330
28.42 - 56.85: 151
56.85 - 85.27: 11
85.27 - 113.70: 0
113.70 - 142.12: 2
Dihedral angle restraints: 2494
sinusoidal: 973
harmonic: 1521
Sorted by residual:
dihedral pdb=" C1 CXQ A 703 "
pdb=" C6 CXQ A 703 "
pdb=" O1 CXQ A 703 "
pdb=" C8 CXQ A 703 "
ideal model delta sinusoidal sigma weight residual
158.12 16.00 142.12 1 3.00e+01 1.11e-03 1.91e+01
dihedral pdb=" C1 CXQ A 703 "
pdb=" C6 CXQ A 703 "
pdb=" O1 CXQ A 703 "
pdb=" C7 CXQ A 703 "
ideal model delta sinusoidal sigma weight residual
280.48 139.54 140.94 1 3.00e+01 1.11e-03 1.89e+01
dihedral pdb=" CA TRP A 132 "
pdb=" C TRP A 132 "
pdb=" N LYS A 133 "
pdb=" CA LYS A 133 "
ideal model delta harmonic sigma weight residual
180.00 162.14 17.86 0 5.00e+00 4.00e-02 1.28e+01
... (remaining 2491 not shown)
Histogram of chiral volume deviations from ideal:
0.000 - 0.046: 529
0.046 - 0.093: 116
0.093 - 0.139: 30
0.139 - 0.185: 2
0.185 - 0.231: 1
Chirality restraints: 678
Sorted by residual:
chirality pdb=" CA ILE A 268 "
pdb=" N ILE A 268 "
pdb=" C ILE A 268 "
pdb=" CB ILE A 268 "
both_signs ideal model delta sigma weight residual
False 2.43 2.66 -0.23 2.00e-01 2.50e+01 1.34e+00
chirality pdb=" C2 CXQ A 703 "
pdb=" C13 CXQ A 703 "
pdb=" C7 CXQ A 703 "
pdb=" N1 CXQ A 703 "
both_signs ideal model delta sigma weight residual
False 2.74 2.92 -0.18 2.00e-01 2.50e+01 8.16e-01
chirality pdb=" CA PRO A 584 "
pdb=" N PRO A 584 "
pdb=" C PRO A 584 "
pdb=" CB PRO A 584 "
both_signs ideal model delta sigma weight residual
False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.90e-01
... (remaining 675 not shown)
Planarity restraints: 725
Sorted by residual:
delta sigma weight rms_deltas residual
plane pdb=" C TYR A 394 " -0.039 5.00e-02 4.00e+02 5.89e-02 5.54e+00
pdb=" N PRO A 395 " 0.102 5.00e-02 4.00e+02
pdb=" CA PRO A 395 " -0.030 5.00e-02 4.00e+02
pdb=" CD PRO A 395 " -0.033 5.00e-02 4.00e+02
delta sigma weight rms_deltas residual
plane pdb=" CA CYS A 189 " -0.010 2.00e-02 2.50e+03 2.03e-02 4.11e+00
pdb=" C CYS A 189 " 0.035 2.00e-02 2.50e+03
pdb=" O CYS A 189 " -0.013 2.00e-02 2.50e+03
pdb=" N SER A 190 " -0.012 2.00e-02 2.50e+03
delta sigma weight rms_deltas residual
plane pdb=" CB ASN A 181 " -0.016 2.00e-02 2.50e+03 1.47e-02 2.71e+00
pdb=" CG ASN A 181 " 0.021 2.00e-02 2.50e+03
pdb=" OD1 ASN A 181 " -0.003 2.00e-02 2.50e+03
pdb=" ND2 ASN A 181 " 0.013 2.00e-02 2.50e+03
pdb=" C1 NAG A 701 " -0.015 2.00e-02 2.50e+03
... (remaining 722 not shown)
Histogram of nonbonded interaction distances:
2.28 - 2.81: 1154
2.81 - 3.33: 3834
3.33 - 3.85: 6643
3.85 - 4.38: 7416
4.38 - 4.90: 13745
Nonbonded interactions: 32792
Sorted by model distance:
nonbonded pdb=" NH1 ARG A 237 "
pdb=" OD1 ASN A 466 "
model vdw
2.283 3.120
nonbonded pdb=" O ARG A 237 "
pdb=" OG1 THR A 241 "
model vdw
2.312 3.040
nonbonded pdb=" OG SER A 186 "
pdb=" OE2 GLU A 215 "
model vdw
2.340 3.040
nonbonded pdb=" N ASP A 79 "
pdb=" OD1 ASP A 79 "
model vdw
2.409 3.120
nonbonded pdb=" O PHE A 498 "
pdb=" NE2 GLN A 611 "
model vdw
2.419 3.120
... (remaining 32787 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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
Set random seed: 0.000
Set model cs if undefined: 0.000
Decide on map wrapping: 0.000
Normalize map: mean=0, sd=1: 2.320
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: 0.000
Extract box with map and model: 0.160
Check model and map are aligned: 0.030
Set scattering table: 0.050
Process input model: 14.690
Find NCS groups from input model: 0.040
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:2.750
Set ADP refinement strategy: 0.000
Make a string to write initial .geo file:0.000
Internal consistency checks: 0.000
Total: 20.050
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8336
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 : 0.005 0.114 4345 Z= 0.299
Angle : 0.610 9.283 5931 Z= 0.317
Chirality : 0.041 0.231 678
Planarity : 0.005 0.059 723
Dihedral : 17.534 142.121 1519
Min Nonbonded Distance : 2.283
Molprobity Statistics.
All-atom Clashscore : 3.56
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 4.41 %
Favored : 95.59 %
Rotamer:
Outliers : 0.00 %
Allowed : 23.76 %
Favored : 76.24 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 1.57 (0.38), residues: 522
helix: 1.92 (0.28), residues: 360
sheet: None (None), residues: 0
loop : -1.00 (0.49), residues: 162
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.013 0.001 TRP A 132
HIS 0.002 0.001 HIS A 225
PHE 0.016 0.001 PHE A 451
TYR 0.010 0.001 TYR A 575
ARG 0.001 0.000 ARG A 125
*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
1044 Ramachandran restraints generated.
522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
1044 Ramachandran restraints generated.
522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
48 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 0
poor density : 48
time to evaluate : 0.481
Fit side-chains
REVERT: A 126 GLU cc_start: 0.7627 (mt-10) cc_final: 0.7415 (mt-10)
REVERT: A 531 PHE cc_start: 0.8123 (t80) cc_final: 0.7252 (t80)
outliers start: 0
outliers final: 0
residues processed: 48
average time/residue: 0.1709
time to fit residues: 10.6673
Evaluate side-chains
44 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 0
poor density : 44
time to evaluate : 0.445
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 52
random chunks:
chunk 43 optimal weight: 0.7980
chunk 39 optimal weight: 1.9990
chunk 21 optimal weight: 1.9990
chunk 13 optimal weight: 0.7980
chunk 26 optimal weight: 0.9980
chunk 40 optimal weight: 0.8980
chunk 15 optimal weight: 0.9980
chunk 24 optimal weight: 2.9990
chunk 30 optimal weight: 0.9980
chunk 47 optimal weight: 0.0070
chunk 14 optimal weight: 1.9990
overall best weight: 0.6998
-------------------------------------------------------------------------------
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 = 0.3413 r_free = 0.3413 target = 0.132835 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.112347 restraints weight = 5082.736|
|-----------------------------------------------------------------------------|
r_work (start): 0.3187 rms_B_bonded: 1.77
r_work: 0.3091 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.2973 rms_B_bonded: 3.91 restraints_weight: 0.2500
r_work (final): 0.2973
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8147
moved from start: 0.0635
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.057 4345 Z= 0.192
Angle : 0.533 7.487 5931 Z= 0.268
Chirality : 0.037 0.122 678
Planarity : 0.004 0.060 723
Dihedral : 8.790 116.403 636
Min Nonbonded Distance : 2.474
Molprobity Statistics.
All-atom Clashscore : 1.90
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 3.45 %
Favored : 96.55 %
Rotamer:
Outliers : 2.71 %
Allowed : 22.85 %
Favored : 74.43 %
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: 1.89 (0.39), residues: 522
helix: 2.18 (0.28), residues: 362
sheet: None (None), residues: 0
loop : -0.97 (0.52), residues: 160
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.009 0.001 TRP A 132
HIS 0.002 0.001 HIS A 179
PHE 0.012 0.001 PHE A 412
TYR 0.013 0.001 TYR A 548
ARG 0.002 0.000 ARG A 237
*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
1044 Ramachandran restraints generated.
522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
1044 Ramachandran restraints generated.
522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
58 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 12
poor density : 46
time to evaluate : 0.424
Fit side-chains
REVERT: A 126 GLU cc_start: 0.7767 (mt-10) cc_final: 0.7512 (mt-10)
REVERT: A 320 PHE cc_start: 0.8126 (OUTLIER) cc_final: 0.6073 (t80)
REVERT: A 424 MET cc_start: 0.6319 (mtp) cc_final: 0.5891 (mtt)
REVERT: A 514 GLN cc_start: 0.7062 (tp40) cc_final: 0.6093 (pt0)
outliers start: 12
outliers final: 8
residues processed: 57
average time/residue: 0.1504
time to fit residues: 11.2614
Evaluate side-chains
54 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 9
poor density : 45
time to evaluate : 0.415
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 107 VAL
Chi-restraints excluded: chain A residue 149 SER
Chi-restraints excluded: chain A residue 210 THR
Chi-restraints excluded: chain A residue 281 LEU
Chi-restraints excluded: chain A residue 320 PHE
Chi-restraints excluded: chain A residue 429 SER
Chi-restraints excluded: chain A residue 432 THR
Chi-restraints excluded: chain A residue 435 ILE
Chi-restraints excluded: chain A residue 517 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 52
random chunks:
chunk 0 optimal weight: 8.9990
chunk 32 optimal weight: 0.8980
chunk 43 optimal weight: 0.6980
chunk 39 optimal weight: 0.8980
chunk 1 optimal weight: 0.9980
chunk 30 optimal weight: 0.6980
chunk 21 optimal weight: 0.9990
chunk 14 optimal weight: 0.9990
chunk 5 optimal weight: 2.9990
chunk 6 optimal weight: 3.9990
chunk 8 optimal weight: 2.9990
overall best weight: 0.8380
-------------------------------------------------------------------------------
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 = 0.3388 r_free = 0.3388 target = 0.130423 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.109979 restraints weight = 5096.917|
|-----------------------------------------------------------------------------|
r_work (start): 0.3160 rms_B_bonded: 1.77
r_work: 0.3061 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.2939 rms_B_bonded: 3.91 restraints_weight: 0.2500
r_work (final): 0.2939
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8074
moved from start: 0.0790
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.045 4345 Z= 0.203
Angle : 0.515 6.356 5931 Z= 0.260
Chirality : 0.038 0.118 678
Planarity : 0.005 0.062 723
Dihedral : 7.886 105.069 636
Min Nonbonded Distance : 2.565
Molprobity Statistics.
All-atom Clashscore : 2.14
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 3.45 %
Favored : 96.55 %
Rotamer:
Outliers : 4.52 %
Allowed : 21.27 %
Favored : 74.21 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 1.76 (0.38), residues: 522
helix: 2.07 (0.28), residues: 370
sheet: None (None), residues: 0
loop : -1.18 (0.52), residues: 152
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.010 0.001 TRP A 132
HIS 0.002 0.001 HIS A 477
PHE 0.016 0.001 PHE A 451
TYR 0.010 0.001 TYR A 548
ARG 0.002 0.000 ARG A 606
*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
1044 Ramachandran restraints generated.
522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
1044 Ramachandran restraints generated.
522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
63 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 20
poor density : 43
time to evaluate : 0.359
Fit side-chains
REVERT: A 320 PHE cc_start: 0.8037 (OUTLIER) cc_final: 0.5845 (t80)
REVERT: A 514 GLN cc_start: 0.7035 (tp40) cc_final: 0.5873 (pt0)
outliers start: 20
outliers final: 14
residues processed: 59
average time/residue: 0.1524
time to fit residues: 11.7446
Evaluate side-chains
58 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 15
poor density : 43
time to evaluate : 0.428
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 104 LEU
Chi-restraints excluded: chain A residue 107 VAL
Chi-restraints excluded: chain A residue 108 ILE
Chi-restraints excluded: chain A residue 131 VAL
Chi-restraints excluded: chain A residue 210 THR
Chi-restraints excluded: chain A residue 281 LEU
Chi-restraints excluded: chain A residue 291 ILE
Chi-restraints excluded: chain A residue 320 PHE
Chi-restraints excluded: chain A residue 404 SER
Chi-restraints excluded: chain A residue 429 SER
Chi-restraints excluded: chain A residue 432 THR
Chi-restraints excluded: chain A residue 456 THR
Chi-restraints excluded: chain A residue 517 SER
Chi-restraints excluded: chain A residue 605 ASP
Chi-restraints excluded: chain A residue 614 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 52
random chunks:
chunk 21 optimal weight: 1.9990
chunk 43 optimal weight: 0.7980
chunk 12 optimal weight: 6.9990
chunk 48 optimal weight: 0.8980
chunk 41 optimal weight: 0.8980
chunk 26 optimal weight: 0.6980
chunk 28 optimal weight: 2.9990
chunk 37 optimal weight: 1.9990
chunk 33 optimal weight: 0.9990
chunk 42 optimal weight: 0.6980
chunk 27 optimal weight: 0.9980
overall best weight: 0.7980
-------------------------------------------------------------------------------
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 = 0.3379 r_free = 0.3379 target = 0.130017 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.109856 restraints weight = 5100.663|
|-----------------------------------------------------------------------------|
r_work (start): 0.3168 rms_B_bonded: 1.74
r_work: 0.3069 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.2948 rms_B_bonded: 3.89 restraints_weight: 0.2500
r_work (final): 0.2948
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8067
moved from start: 0.0912
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.043 4345 Z= 0.196
Angle : 0.505 6.220 5931 Z= 0.256
Chirality : 0.037 0.113 678
Planarity : 0.004 0.061 723
Dihedral : 7.380 96.658 636
Min Nonbonded Distance : 2.614
Molprobity Statistics.
All-atom Clashscore : 2.14
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 3.45 %
Favored : 96.55 %
Rotamer:
Outliers : 4.07 %
Allowed : 22.40 %
Favored : 73.53 %
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: 1.71 (0.38), residues: 522
helix: 2.07 (0.28), residues: 371
sheet: None (None), residues: 0
loop : -1.30 (0.51), residues: 151
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.010 0.001 TRP A 132
HIS 0.002 0.001 HIS A 179
PHE 0.015 0.001 PHE A 451
TYR 0.010 0.001 TYR A 548
ARG 0.002 0.000 ARG A 606
*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
1044 Ramachandran restraints generated.
522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
1044 Ramachandran restraints generated.
522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
61 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 18
poor density : 43
time to evaluate : 0.449
Fit side-chains
REVERT: A 156 TYR cc_start: 0.8706 (OUTLIER) cc_final: 0.8061 (t80)
REVERT: A 320 PHE cc_start: 0.8042 (OUTLIER) cc_final: 0.5835 (t80)
REVERT: A 514 GLN cc_start: 0.7025 (tp40) cc_final: 0.5813 (pt0)
outliers start: 18
outliers final: 13
residues processed: 57
average time/residue: 0.1520
time to fit residues: 11.4325
Evaluate side-chains
58 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 15
poor density : 43
time to evaluate : 0.445
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 104 LEU
Chi-restraints excluded: chain A residue 107 VAL
Chi-restraints excluded: chain A residue 131 VAL
Chi-restraints excluded: chain A residue 156 TYR
Chi-restraints excluded: chain A residue 210 THR
Chi-restraints excluded: chain A residue 281 LEU
Chi-restraints excluded: chain A residue 320 PHE
Chi-restraints excluded: chain A residue 404 SER
Chi-restraints excluded: chain A residue 429 SER
Chi-restraints excluded: chain A residue 432 THR
Chi-restraints excluded: chain A residue 456 THR
Chi-restraints excluded: chain A residue 483 SER
Chi-restraints excluded: chain A residue 517 SER
Chi-restraints excluded: chain A residue 605 ASP
Chi-restraints excluded: chain A residue 614 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 52
random chunks:
chunk 4 optimal weight: 2.9990
chunk 1 optimal weight: 2.9990
chunk 41 optimal weight: 2.9990
chunk 43 optimal weight: 0.6980
chunk 13 optimal weight: 0.5980
chunk 46 optimal weight: 0.5980
chunk 27 optimal weight: 0.8980
chunk 34 optimal weight: 1.9990
chunk 3 optimal weight: 0.0030
chunk 11 optimal weight: 0.6980
chunk 33 optimal weight: 2.9990
overall best weight: 0.5190
-------------------------------------------------------------------------------
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 = 0.3398 r_free = 0.3398 target = 0.131756 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.111564 restraints weight = 5135.728|
|-----------------------------------------------------------------------------|
r_work (start): 0.3193 rms_B_bonded: 1.73
r_work: 0.3098 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.2979 rms_B_bonded: 3.84 restraints_weight: 0.2500
r_work (final): 0.2979
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8029
moved from start: 0.1029
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.002 0.041 4345 Z= 0.153
Angle : 0.473 6.126 5931 Z= 0.240
Chirality : 0.036 0.115 678
Planarity : 0.004 0.059 723
Dihedral : 7.032 90.836 636
Min Nonbonded Distance : 2.637
Molprobity Statistics.
All-atom Clashscore : 2.37
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 3.26 %
Favored : 96.74 %
Rotamer:
Outliers : 4.52 %
Allowed : 21.72 %
Favored : 73.76 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 1.76 (0.38), residues: 522
helix: 2.04 (0.28), residues: 377
sheet: None (None), residues: 0
loop : -1.22 (0.52), residues: 145
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.008 0.001 TRP A 556
HIS 0.001 0.000 HIS A 179
PHE 0.015 0.001 PHE A 451
TYR 0.008 0.001 TYR A 575
ARG 0.004 0.000 ARG A 606
*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
1044 Ramachandran restraints generated.
522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
1044 Ramachandran restraints generated.
522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
60 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 20
poor density : 40
time to evaluate : 0.462
Fit side-chains
REVERT: A 156 TYR cc_start: 0.8706 (OUTLIER) cc_final: 0.8001 (t80)
REVERT: A 320 PHE cc_start: 0.8031 (OUTLIER) cc_final: 0.5889 (t80)
REVERT: A 416 LEU cc_start: 0.7934 (OUTLIER) cc_final: 0.7508 (tp)
REVERT: A 514 GLN cc_start: 0.6975 (tp40) cc_final: 0.5741 (pt0)
outliers start: 20
outliers final: 13
residues processed: 57
average time/residue: 0.1292
time to fit residues: 10.0385
Evaluate side-chains
57 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 16
poor density : 41
time to evaluate : 0.456
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 104 LEU
Chi-restraints excluded: chain A residue 107 VAL
Chi-restraints excluded: chain A residue 108 ILE
Chi-restraints excluded: chain A residue 131 VAL
Chi-restraints excluded: chain A residue 156 TYR
Chi-restraints excluded: chain A residue 210 THR
Chi-restraints excluded: chain A residue 281 LEU
Chi-restraints excluded: chain A residue 320 PHE
Chi-restraints excluded: chain A residue 342 CYS
Chi-restraints excluded: chain A residue 416 LEU
Chi-restraints excluded: chain A residue 429 SER
Chi-restraints excluded: chain A residue 483 SER
Chi-restraints excluded: chain A residue 501 VAL
Chi-restraints excluded: chain A residue 517 SER
Chi-restraints excluded: chain A residue 605 ASP
Chi-restraints excluded: chain A residue 614 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 52
random chunks:
chunk 21 optimal weight: 0.5980
chunk 20 optimal weight: 1.9990
chunk 44 optimal weight: 2.9990
chunk 26 optimal weight: 0.8980
chunk 25 optimal weight: 0.9990
chunk 31 optimal weight: 0.6980
chunk 22 optimal weight: 2.9990
chunk 39 optimal weight: 0.7980
chunk 23 optimal weight: 0.5980
chunk 4 optimal weight: 0.9990
chunk 36 optimal weight: 2.9990
overall best weight: 0.7180
-------------------------------------------------------------------------------
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 = 0.3388 r_free = 0.3388 target = 0.130421 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.110081 restraints weight = 5092.842|
|-----------------------------------------------------------------------------|
r_work (start): 0.3160 rms_B_bonded: 1.75
r_work: 0.3063 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.2941 rms_B_bonded: 3.92 restraints_weight: 0.2500
r_work (final): 0.2941
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8061
moved from start: 0.1052
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.040 4345 Z= 0.181
Angle : 0.493 6.260 5931 Z= 0.249
Chirality : 0.037 0.113 678
Planarity : 0.004 0.061 723
Dihedral : 6.853 87.161 636
Min Nonbonded Distance : 2.627
Molprobity Statistics.
All-atom Clashscore : 2.26
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 3.45 %
Favored : 96.55 %
Rotamer:
Outliers : 4.07 %
Allowed : 22.17 %
Favored : 73.76 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 1.69 (0.38), residues: 522
helix: 1.98 (0.28), residues: 377
sheet: None (None), residues: 0
loop : -1.24 (0.51), residues: 145
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.010 0.001 TRP A 132
HIS 0.002 0.001 HIS A 477
PHE 0.015 0.001 PHE A 451
TYR 0.010 0.001 TYR A 575
ARG 0.001 0.000 ARG A 606
*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
1044 Ramachandran restraints generated.
522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
1044 Ramachandran restraints generated.
522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
59 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 18
poor density : 41
time to evaluate : 0.428
Fit side-chains
REVERT: A 156 TYR cc_start: 0.8756 (OUTLIER) cc_final: 0.7983 (t80)
REVERT: A 320 PHE cc_start: 0.8069 (OUTLIER) cc_final: 0.5860 (t80)
REVERT: A 416 LEU cc_start: 0.7953 (OUTLIER) cc_final: 0.7533 (tp)
REVERT: A 514 GLN cc_start: 0.6990 (tp40) cc_final: 0.5734 (pt0)
outliers start: 18
outliers final: 14
residues processed: 56
average time/residue: 0.1442
time to fit residues: 10.7369
Evaluate side-chains
59 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 17
poor density : 42
time to evaluate : 0.416
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 104 LEU
Chi-restraints excluded: chain A residue 107 VAL
Chi-restraints excluded: chain A residue 108 ILE
Chi-restraints excluded: chain A residue 131 VAL
Chi-restraints excluded: chain A residue 156 TYR
Chi-restraints excluded: chain A residue 210 THR
Chi-restraints excluded: chain A residue 281 LEU
Chi-restraints excluded: chain A residue 320 PHE
Chi-restraints excluded: chain A residue 342 CYS
Chi-restraints excluded: chain A residue 404 SER
Chi-restraints excluded: chain A residue 416 LEU
Chi-restraints excluded: chain A residue 424 MET
Chi-restraints excluded: chain A residue 429 SER
Chi-restraints excluded: chain A residue 483 SER
Chi-restraints excluded: chain A residue 517 SER
Chi-restraints excluded: chain A residue 605 ASP
Chi-restraints excluded: chain A residue 614 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 52
random chunks:
chunk 47 optimal weight: 1.9990
chunk 37 optimal weight: 2.9990
chunk 26 optimal weight: 0.6980
chunk 16 optimal weight: 0.7980
chunk 15 optimal weight: 0.5980
chunk 5 optimal weight: 3.9990
chunk 36 optimal weight: 0.9980
chunk 50 optimal weight: 0.8980
chunk 18 optimal weight: 0.6980
chunk 46 optimal weight: 0.2980
chunk 33 optimal weight: 5.9990
overall best weight: 0.6180
-------------------------------------------------------------------------------
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 = 0.3388 r_free = 0.3388 target = 0.130989 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.110877 restraints weight = 5070.985|
|-----------------------------------------------------------------------------|
r_work (start): 0.3175 rms_B_bonded: 1.72
r_work: 0.3080 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.2960 rms_B_bonded: 3.83 restraints_weight: 0.2500
r_work (final): 0.2960
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8033
moved from start: 0.1146
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.040 4345 Z= 0.166
Angle : 0.481 6.593 5931 Z= 0.244
Chirality : 0.037 0.114 678
Planarity : 0.004 0.059 723
Dihedral : 6.718 84.436 636
Min Nonbonded Distance : 2.632
Molprobity Statistics.
All-atom Clashscore : 2.49
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 3.26 %
Favored : 96.74 %
Rotamer:
Outliers : 4.52 %
Allowed : 21.72 %
Favored : 73.76 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 1.74 (0.38), residues: 522
helix: 2.06 (0.27), residues: 375
sheet: None (None), residues: 0
loop : -1.31 (0.51), residues: 147
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.008 0.001 TRP A 132
HIS 0.002 0.001 HIS A 179
PHE 0.016 0.001 PHE A 451
TYR 0.011 0.001 TYR A 575
ARG 0.001 0.000 ARG A 606
*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
1044 Ramachandran restraints generated.
522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
1044 Ramachandran restraints generated.
522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
60 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 20
poor density : 40
time to evaluate : 0.517
Fit side-chains
REVERT: A 156 TYR cc_start: 0.8761 (OUTLIER) cc_final: 0.7990 (t80)
REVERT: A 320 PHE cc_start: 0.8040 (OUTLIER) cc_final: 0.5830 (t80)
REVERT: A 416 LEU cc_start: 0.7923 (OUTLIER) cc_final: 0.7504 (tp)
REVERT: A 514 GLN cc_start: 0.6962 (tp40) cc_final: 0.5695 (pt0)
outliers start: 20
outliers final: 16
residues processed: 56
average time/residue: 0.1378
time to fit residues: 10.4424
Evaluate side-chains
59 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 19
poor density : 40
time to evaluate : 0.436
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 104 LEU
Chi-restraints excluded: chain A residue 107 VAL
Chi-restraints excluded: chain A residue 108 ILE
Chi-restraints excluded: chain A residue 131 VAL
Chi-restraints excluded: chain A residue 156 TYR
Chi-restraints excluded: chain A residue 210 THR
Chi-restraints excluded: chain A residue 281 LEU
Chi-restraints excluded: chain A residue 320 PHE
Chi-restraints excluded: chain A residue 342 CYS
Chi-restraints excluded: chain A residue 404 SER
Chi-restraints excluded: chain A residue 416 LEU
Chi-restraints excluded: chain A residue 424 MET
Chi-restraints excluded: chain A residue 429 SER
Chi-restraints excluded: chain A residue 441 LEU
Chi-restraints excluded: chain A residue 456 THR
Chi-restraints excluded: chain A residue 483 SER
Chi-restraints excluded: chain A residue 517 SER
Chi-restraints excluded: chain A residue 605 ASP
Chi-restraints excluded: chain A residue 614 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 52
random chunks:
chunk 50 optimal weight: 1.9990
chunk 16 optimal weight: 0.9980
chunk 29 optimal weight: 0.8980
chunk 4 optimal weight: 0.2980
chunk 42 optimal weight: 0.8980
chunk 10 optimal weight: 0.3980
chunk 33 optimal weight: 0.8980
chunk 36 optimal weight: 1.9990
chunk 39 optimal weight: 0.5980
chunk 30 optimal weight: 0.6980
chunk 9 optimal weight: 0.9980
overall best weight: 0.5780
-------------------------------------------------------------------------------
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 = 0.3401 r_free = 0.3401 target = 0.131742 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.111536 restraints weight = 5006.327|
|-----------------------------------------------------------------------------|
r_work (start): 0.3178 rms_B_bonded: 1.73
r_work: 0.3083 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.2962 rms_B_bonded: 3.86 restraints_weight: 0.2500
r_work (final): 0.2962
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8035
moved from start: 0.1167
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.002 0.040 4345 Z= 0.161
Angle : 0.479 6.855 5931 Z= 0.242
Chirality : 0.037 0.113 678
Planarity : 0.004 0.059 723
Dihedral : 6.565 81.645 636
Min Nonbonded Distance : 2.631
Molprobity Statistics.
All-atom Clashscore : 2.26
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 3.26 %
Favored : 96.74 %
Rotamer:
Outliers : 4.52 %
Allowed : 21.72 %
Favored : 73.76 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 1.77 (0.38), residues: 522
helix: 2.08 (0.27), residues: 375
sheet: None (None), residues: 0
loop : -1.29 (0.51), residues: 147
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.008 0.001 TRP A 132
HIS 0.002 0.001 HIS A 179
PHE 0.016 0.001 PHE A 451
TYR 0.009 0.001 TYR A 575
ARG 0.001 0.000 ARG A 588
*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
1044 Ramachandran restraints generated.
522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
1044 Ramachandran restraints generated.
522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
61 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 20
poor density : 41
time to evaluate : 0.459
Fit side-chains
REVERT: A 156 TYR cc_start: 0.8763 (OUTLIER) cc_final: 0.7990 (t80)
REVERT: A 320 PHE cc_start: 0.8050 (OUTLIER) cc_final: 0.5852 (t80)
REVERT: A 416 LEU cc_start: 0.7932 (OUTLIER) cc_final: 0.7512 (tp)
REVERT: A 514 GLN cc_start: 0.6985 (tp40) cc_final: 0.5695 (pt0)
outliers start: 20
outliers final: 16
residues processed: 58
average time/residue: 0.1524
time to fit residues: 11.5842
Evaluate side-chains
60 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 19
poor density : 41
time to evaluate : 0.426
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 104 LEU
Chi-restraints excluded: chain A residue 107 VAL
Chi-restraints excluded: chain A residue 108 ILE
Chi-restraints excluded: chain A residue 131 VAL
Chi-restraints excluded: chain A residue 156 TYR
Chi-restraints excluded: chain A residue 210 THR
Chi-restraints excluded: chain A residue 277 LEU
Chi-restraints excluded: chain A residue 320 PHE
Chi-restraints excluded: chain A residue 342 CYS
Chi-restraints excluded: chain A residue 404 SER
Chi-restraints excluded: chain A residue 416 LEU
Chi-restraints excluded: chain A residue 424 MET
Chi-restraints excluded: chain A residue 429 SER
Chi-restraints excluded: chain A residue 441 LEU
Chi-restraints excluded: chain A residue 454 LEU
Chi-restraints excluded: chain A residue 456 THR
Chi-restraints excluded: chain A residue 483 SER
Chi-restraints excluded: chain A residue 517 SER
Chi-restraints excluded: chain A residue 605 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 52
random chunks:
chunk 7 optimal weight: 0.3980
chunk 36 optimal weight: 3.9990
chunk 46 optimal weight: 0.8980
chunk 4 optimal weight: 0.8980
chunk 43 optimal weight: 0.9990
chunk 34 optimal weight: 0.0870
chunk 16 optimal weight: 0.7980
chunk 18 optimal weight: 0.7980
chunk 29 optimal weight: 0.5980
chunk 32 optimal weight: 0.5980
chunk 17 optimal weight: 0.8980
overall best weight: 0.4958
-------------------------------------------------------------------------------
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 = 0.3409 r_free = 0.3409 target = 0.132374 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3173 r_free = 0.3173 target = 0.112084 restraints weight = 5041.598|
|-----------------------------------------------------------------------------|
r_work (start): 0.3187 rms_B_bonded: 1.75
r_work: 0.3091 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.2971 rms_B_bonded: 3.89 restraints_weight: 0.2500
r_work (final): 0.2971
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8035
moved from start: 0.1231
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.002 0.039 4345 Z= 0.151
Angle : 0.472 6.612 5931 Z= 0.239
Chirality : 0.036 0.113 678
Planarity : 0.004 0.059 723
Dihedral : 6.458 79.626 636
Min Nonbonded Distance : 2.634
Molprobity Statistics.
All-atom Clashscore : 2.26
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 3.26 %
Favored : 96.74 %
Rotamer:
Outliers : 4.30 %
Allowed : 21.95 %
Favored : 73.76 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 1.82 (0.38), residues: 522
helix: 2.12 (0.27), residues: 375
sheet: None (None), residues: 0
loop : -1.27 (0.51), residues: 147
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.008 0.001 TRP A 556
HIS 0.001 0.001 HIS A 179
PHE 0.016 0.001 PHE A 451
TYR 0.009 0.001 TYR A 575
ARG 0.001 0.000 ARG A 606
*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
1044 Ramachandran restraints generated.
522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
1044 Ramachandran restraints generated.
522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
61 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 19
poor density : 42
time to evaluate : 0.519
Fit side-chains
REVERT: A 156 TYR cc_start: 0.8754 (OUTLIER) cc_final: 0.7989 (t80)
REVERT: A 320 PHE cc_start: 0.8055 (OUTLIER) cc_final: 0.5921 (t80)
REVERT: A 416 LEU cc_start: 0.7952 (OUTLIER) cc_final: 0.7518 (tp)
outliers start: 19
outliers final: 15
residues processed: 57
average time/residue: 0.1351
time to fit residues: 10.6872
Evaluate side-chains
59 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 18
poor density : 41
time to evaluate : 0.455
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 104 LEU
Chi-restraints excluded: chain A residue 107 VAL
Chi-restraints excluded: chain A residue 108 ILE
Chi-restraints excluded: chain A residue 131 VAL
Chi-restraints excluded: chain A residue 156 TYR
Chi-restraints excluded: chain A residue 210 THR
Chi-restraints excluded: chain A residue 277 LEU
Chi-restraints excluded: chain A residue 320 PHE
Chi-restraints excluded: chain A residue 342 CYS
Chi-restraints excluded: chain A residue 404 SER
Chi-restraints excluded: chain A residue 416 LEU
Chi-restraints excluded: chain A residue 424 MET
Chi-restraints excluded: chain A residue 429 SER
Chi-restraints excluded: chain A residue 441 LEU
Chi-restraints excluded: chain A residue 454 LEU
Chi-restraints excluded: chain A residue 483 SER
Chi-restraints excluded: chain A residue 517 SER
Chi-restraints excluded: chain A residue 605 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 52
random chunks:
chunk 40 optimal weight: 1.9990
chunk 7 optimal weight: 0.7980
chunk 16 optimal weight: 0.6980
chunk 22 optimal weight: 0.9990
chunk 43 optimal weight: 0.9980
chunk 9 optimal weight: 0.7980
chunk 2 optimal weight: 0.5980
chunk 19 optimal weight: 1.9990
chunk 10 optimal weight: 2.9990
chunk 30 optimal weight: 0.8980
chunk 15 optimal weight: 3.9990
overall best weight: 0.7580
-------------------------------------------------------------------------------
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 = 0.3393 r_free = 0.3393 target = 0.130677 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3155 r_free = 0.3155 target = 0.110457 restraints weight = 5052.409|
|-----------------------------------------------------------------------------|
r_work (start): 0.3165 rms_B_bonded: 1.74
r_work: 0.3069 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.2948 rms_B_bonded: 3.89 restraints_weight: 0.2500
r_work (final): 0.2948
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8067
moved from start: 0.1185
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.038 4345 Z= 0.186
Angle : 0.497 7.290 5931 Z= 0.252
Chirality : 0.037 0.112 678
Planarity : 0.004 0.060 723
Dihedral : 6.464 78.926 636
Min Nonbonded Distance : 2.627
Molprobity Statistics.
All-atom Clashscore : 2.26
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 3.45 %
Favored : 96.55 %
Rotamer:
Outliers : 4.07 %
Allowed : 22.17 %
Favored : 73.76 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 1.76 (0.38), residues: 522
helix: 2.15 (0.28), residues: 369
sheet: None (None), residues: 0
loop : -1.38 (0.49), residues: 153
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.010 0.001 TRP A 132
HIS 0.002 0.001 HIS A 179
PHE 0.016 0.001 PHE A 451
TYR 0.010 0.001 TYR A 575
ARG 0.001 0.000 ARG A 125
********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
1044 Ramachandran restraints generated.
522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
1044 Ramachandran restraints generated.
522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
59 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 18
poor density : 41
time to evaluate : 0.479
Fit side-chains
REVERT: A 156 TYR cc_start: 0.8800 (OUTLIER) cc_final: 0.8040 (t80)
REVERT: A 320 PHE cc_start: 0.8102 (OUTLIER) cc_final: 0.5921 (t80)
REVERT: A 416 LEU cc_start: 0.7968 (OUTLIER) cc_final: 0.7548 (tp)
REVERT: A 514 GLN cc_start: 0.7047 (tp40) cc_final: 0.5683 (pt0)
outliers start: 18
outliers final: 14
residues processed: 57
average time/residue: 0.1379
time to fit residues: 10.3873
Evaluate side-chains
58 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 17
poor density : 41
time to evaluate : 0.457
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 104 LEU
Chi-restraints excluded: chain A residue 107 VAL
Chi-restraints excluded: chain A residue 108 ILE
Chi-restraints excluded: chain A residue 131 VAL
Chi-restraints excluded: chain A residue 156 TYR
Chi-restraints excluded: chain A residue 277 LEU
Chi-restraints excluded: chain A residue 320 PHE
Chi-restraints excluded: chain A residue 342 CYS
Chi-restraints excluded: chain A residue 404 SER
Chi-restraints excluded: chain A residue 416 LEU
Chi-restraints excluded: chain A residue 424 MET
Chi-restraints excluded: chain A residue 429 SER
Chi-restraints excluded: chain A residue 441 LEU
Chi-restraints excluded: chain A residue 454 LEU
Chi-restraints excluded: chain A residue 483 SER
Chi-restraints excluded: chain A residue 517 SER
Chi-restraints excluded: chain A residue 605 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 52
random chunks:
chunk 14 optimal weight: 0.8980
chunk 47 optimal weight: 2.9990
chunk 8 optimal weight: 0.4980
chunk 48 optimal weight: 0.9980
chunk 32 optimal weight: 1.9990
chunk 11 optimal weight: 0.5980
chunk 20 optimal weight: 2.9990
chunk 10 optimal weight: 0.3980
chunk 12 optimal weight: 0.9980
chunk 34 optimal weight: 3.9990
chunk 49 optimal weight: 0.9990
overall best weight: 0.6780
-------------------------------------------------------------------------------
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 = 0.3387 r_free = 0.3387 target = 0.130557 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3148 r_free = 0.3148 target = 0.110329 restraints weight = 5062.525|
|-----------------------------------------------------------------------------|
r_work (start): 0.3171 rms_B_bonded: 1.74
r_work: 0.3074 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.2953 rms_B_bonded: 3.89 restraints_weight: 0.2500
r_work (final): 0.2953
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8064
moved from start: 0.1235
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.038 4345 Z= 0.175
Angle : 0.495 7.687 5931 Z= 0.250
Chirality : 0.037 0.112 678
Planarity : 0.004 0.060 723
Dihedral : 6.414 77.645 636
Min Nonbonded Distance : 2.629
Molprobity Statistics.
All-atom Clashscore : 2.37
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 3.26 %
Favored : 96.74 %
Rotamer:
Outliers : 4.30 %
Allowed : 21.95 %
Favored : 73.76 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 1.78 (0.38), residues: 522
helix: 2.17 (0.27), residues: 369
sheet: None (None), residues: 0
loop : -1.38 (0.49), residues: 153
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.009 0.001 TRP A 132
HIS 0.002 0.001 HIS A 179
PHE 0.016 0.001 PHE A 451
TYR 0.009 0.001 TYR A 575
ARG 0.001 0.000 ARG A 606
Origin is already at (0, 0, 0), no shifts will be applied
===============================================================================
Job complete
usr+sys time: 2278.45 seconds
wall clock time: 41 minutes 23.98 seconds (2483.98 seconds total)