Starting phenix.real_space_refine (version: dev)
on Mon May 3 16:01:32 2021 by dcliebschner
===============================================================================
Processing files:
-------------------------------------------------------------------------------
Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yw7_10960/05_2021/6yw7_10960_updated.pdb
Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yw7_10960/05_2021/6yw7_10960.map
Processing PHIL parameters:
-------------------------------------------------------------------------------
Adding command-line PHIL:
-------------------------
refinement.macro_cycles=10
scattering_table=electron
resolution=4.5
write_initial_geo_file=False
Final processed PHIL parameters:
-------------------------------------------------------------------------------
data_manager {
real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yw7_10960/05_2021/6yw7_10960.map"
default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yw7_10960/05_2021/6yw7_10960.map"
model {
file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yw7_10960/05_2021/6yw7_10960_updated.pdb"
}
default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yw7_10960/05_2021/6yw7_10960_updated.pdb"
}
resolution = 4.5
write_initial_geo_file = False
refinement {
macro_cycles = 10
}
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
-------------------------------------------------------------------------------
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= 0.003
Set model interpretation parameters
Set stop_for_unknowns flag
Set to: True
Assert model is a single copy model
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Convert atoms to be neutral
Process input model
Symmetric amino acids flipped
None
Time to flip residues: 0.01s
Monomer Library directory:
"/net/cci-filer2/raid1/xp/phenix/phenix-dev-4223/modules/chem_data/mon_lib"
Total number of atoms: 5426
Number of models: 1
Model: ""
Number of chains: 9
Chain: "A"
Number of atoms: 1188
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 396, 1188
Classifications: {'peptide': 396}
Incomplete info: {'n_c_alpha_c_only': 396}
Link IDs: {'PTRANS': 26, 'TRANS': 369}
Chain breaks: 2
Unresolved chain link angles: 421
Unresolved non-hydrogen bonds: 2072
Unresolved non-hydrogen angles: 2818
Unresolved non-hydrogen dihedrals: 1103
Unresolved non-hydrogen chiralities: 481
Planarities with less than four sites: {'GLN:plan1': 14, 'HIS:plan': 9, 'TYR:plan': 18, 'ASN:plan1': 10, 'TRP:plan': 5, 'ASP:plan': 24, 'PHE:plan': 20, 'GLU:plan': 32, 'ARG:plan': 22}
Unresolved non-hydrogen planarities: 818
Chain: "D"
Number of atoms: 852
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 284, 852
Classifications: {'peptide': 284}
Incomplete info: {'n_c_alpha_c_only': 284}
Link IDs: {'PTRANS': 9, 'TRANS': 274}
Unresolved chain link angles: 292
Unresolved non-hydrogen bonds: 1489
Unresolved non-hydrogen angles: 2017
Unresolved non-hydrogen dihedrals: 780
Unresolved non-hydrogen chiralities: 346
Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 11, 'TYR:plan': 12, 'ASN:plan1': 16, 'ASP:plan': 20, 'PHE:plan': 18, 'GLU:plan': 21, 'ARG:plan': 16}
Unresolved non-hydrogen planarities: 620
Chain: "E"
Number of atoms: 510
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 170, 510
Classifications: {'peptide': 170}
Incomplete info: {'n_c_alpha_c_only': 170}
Link IDs: {'PTRANS': 11, 'TRANS': 158}
Chain breaks: 1
Unresolved chain link angles: 180
Unresolved non-hydrogen bonds: 903
Unresolved non-hydrogen angles: 1215
Unresolved non-hydrogen dihedrals: 488
Unresolved non-hydrogen chiralities: 202
Planarities with less than four sites: {'GLN:plan1': 9, 'TYR:plan': 8, 'ASN:plan1': 10, 'TRP:plan': 2, 'ASP:plan': 9, 'PHE:plan': 9, 'GLU:plan': 12, 'ARG:plan': 7}
Unresolved non-hydrogen planarities: 342
Chain: "B"
Number of atoms: 858
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 286, 858
Classifications: {'peptide': 286}
Incomplete info: {'n_c_alpha_c_only': 286}
Link IDs: {'PTRANS': 14, 'TRANS': 271}
Chain breaks: 3
Unresolved chain link angles: 299
Unresolved non-hydrogen bonds: 1467
Unresolved non-hydrogen angles: 1992
Unresolved non-hydrogen dihedrals: 764
Unresolved non-hydrogen chiralities: 353
Planarities with less than four sites: {'GLN:plan1': 8, 'ARG:plan': 16, 'TYR:plan': 12, 'ASN:plan1': 7, 'TRP:plan': 2, 'HIS:plan': 8, 'PHE:plan': 14, 'GLU:plan': 20, 'ASP:plan': 17}
Unresolved non-hydrogen planarities: 550
Chain: "F"
Number of atoms: 495
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 165, 495
Classifications: {'peptide': 165}
Incomplete info: {'n_c_alpha_c_only': 165}
Link IDs: {'PTRANS': 4, 'TRANS': 160}
Unresolved chain link angles: 168
Unresolved non-hydrogen bonds: 886
Unresolved non-hydrogen angles: 1190
Unresolved non-hydrogen dihedrals: 462
Unresolved non-hydrogen chiralities: 211
Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 4, 'TYR:plan': 3, 'ASN:plan1': 8, 'HIS:plan': 5, 'PHE:plan': 11, 'GLU:plan': 19, 'ARG:plan': 12}
Unresolved non-hydrogen planarities: 335
Chain: "G"
Number of atoms: 417
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 139, 417
Classifications: {'peptide': 139}
Incomplete info: {'n_c_alpha_c_only': 139}
Link IDs: {'PTRANS': 4, 'TRANS': 134}
Chain breaks: 1
Unresolved chain link angles: 142
Unresolved non-hydrogen bonds: 658
Unresolved non-hydrogen angles: 889
Unresolved non-hydrogen dihedrals: 318
Unresolved non-hydrogen chiralities: 164
Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 7, 'TRP:plan': 1, 'ASP:plan': 12, 'PHE:plan': 4, 'GLU:plan': 9, 'ARG:plan': 6}
Unresolved non-hydrogen planarities: 230
Chain: "C"
Number of atoms: 1044
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 348, 1044
Classifications: {'peptide': 348}
Incomplete info: {'n_c_alpha_c_only': 348}
Link IDs: {'PTRANS': 12, 'CIS': 1, 'TRANS': 333, 'PCIS': 1}
Chain breaks: 1
Unresolved chain link angles: 360
Unresolved non-hydrogen bonds: 1764
Unresolved non-hydrogen angles: 2409
Unresolved non-hydrogen dihedrals: 949
Unresolved non-hydrogen chiralities: 420
Planarities with less than four sites: {'GLN:plan1': 12, 'ASP:plan': 19, 'TYR:plan': 6, 'ASN:plan1': 14, 'TRP:plan': 13, 'HIS:plan': 13, 'PHE:plan': 15, 'GLU:plan': 15, 'ARG:plan': 13}
Unresolved non-hydrogen planarities: 666
Chain: "A"
Number of atoms: 31
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 1, 31
Unusual residues: {'ATP': 1}
Classifications: {'undetermined': 1}
Chain: "B"
Number of atoms: 31
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 1, 31
Unusual residues: {'ATP': 1}
Classifications: {'undetermined': 1}
Time building chain proxies: 4.08, per 1000 atoms: 0.75
========== WARNING! ============
No NCS relation were found !!!
================================
Found NCS groups:
found none.
Number of scatterers: 5426
At special positions: 0
Unit cell: (138.43, 91.56, 136.25, 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)
P 6 15.00
O 26 8.00
N 1798 7.00
C 3596 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 - 3.50
Amimo acid : False - 1.90
Carbohydrate : True - 1.99
Ligands : True - 1.99
Small molecules : False - 1.98
Amino acid - RNA/DNA : False
Number of custom bonds: simple=0, symmetry=0
Time building additional restraints: 1.56
Conformation dependent library (CDL) restraints added in 1.7 seconds
3516 Ramachandran restraints generated.
1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2.
Adding C-beta torsion restraints...
Number of C-beta restraints generated: 0
Finding SS restraints...
running ksdssp...
Secondary structure from input PDB file:
0 helices and 0 sheets defined
0.0% alpha, 0.0% beta
0 base pairs and 0 stacking pairs defined.
Time for finding SS restraints: 0.41
Creating SS restraints...
No hydrogen bonds 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: 0.00
Time building geometry restraints manager: 1.68 seconds
NOTE: a complete listing of the restraints can be obtained by requesting
output of .geo file.
Histogram of bond lengths:
1.15 - 1.27: 6
1.27 - 1.39: 1767
1.39 - 1.50: 2102
1.50 - 1.62: 1530
1.62 - 1.73: 10
Bond restraints: 5415
Sorted by residual:
bond pdb=" C VAL A 83 "
pdb=" N GLU A 84 "
ideal model delta sigma weight residual
1.334 1.733 -0.398 1.27e-02 6.20e+03 9.84e+02
bond pdb=" C GLU A 280 "
pdb=" N ILE A 281 "
ideal model delta sigma weight residual
1.335 1.155 0.181 1.05e-02 9.07e+03 2.96e+02
bond pdb=" C ILE B 184 "
pdb=" N ALA B 185 "
ideal model delta sigma weight residual
1.331 1.535 -0.204 1.29e-02 6.01e+03 2.50e+02
bond pdb=" CA ALA B 261 "
pdb=" C ALA B 261 "
ideal model delta sigma weight residual
1.524 1.707 -0.183 1.26e-02 6.30e+03 2.11e+02
bond pdb=" C TYR B 310 "
pdb=" N PRO B 311 "
ideal model delta sigma weight residual
1.330 1.501 -0.171 1.19e-02 7.06e+03 2.07e+02
... (remaining 5410 not shown)
Histogram of bond angle deviations from ideal:
50.01 - 69.36: 1
69.36 - 88.71: 3
88.71 - 108.05: 367
108.05 - 127.40: 4986
127.40 - 146.75: 81
Bond angle restraints: 5438
Sorted by residual:
angle pdb=" CA GLN B 267 "
pdb=" C GLN B 267 "
pdb=" N PRO B 268 "
ideal model delta sigma weight residual
118.87 93.23 25.64 9.00e-01 1.23e+00 8.11e+02
angle pdb=" N GLU A 39 "
pdb=" CA GLU A 39 "
pdb=" C GLU A 39 "
ideal model delta sigma weight residual
111.00 50.01 60.99 2.80e+00 1.28e-01 4.74e+02
angle pdb=" CA PHE D 83 "
pdb=" C PHE D 83 "
pdb=" N LEU D 84 "
ideal model delta sigma weight residual
118.38 90.25 28.13 1.30e+00 5.92e-01 4.68e+02
angle pdb=" CA LEU B 240 "
pdb=" C LEU B 240 "
pdb=" N VAL B 241 "
ideal model delta sigma weight residual
117.39 92.00 25.39 1.24e+00 6.50e-01 4.19e+02
angle pdb=" CA GLN A 366 "
pdb=" C GLN A 366 "
pdb=" N VAL A 367 "
ideal model delta sigma weight residual
116.01 85.37 30.64 1.51e+00 4.39e-01 4.12e+02
... (remaining 5433 not shown)
Histogram of dihedral angle deviations from ideal:
0.00 - 14.18: 1708
14.18 - 28.35: 52
28.35 - 42.53: 11
42.53 - 56.70: 6
56.70 - 70.88: 2
Dihedral angle restraints: 1779
sinusoidal: 6
harmonic: 1773
Sorted by residual:
dihedral pdb=" CA LYS A 38 "
pdb=" C LYS A 38 "
pdb=" N GLU A 39 "
pdb=" CA GLU A 39 "
ideal model delta harmonic sigma weight residual
-180.00 -109.12 -70.88 0 5.00e+00 4.00e-02 2.01e+02
dihedral pdb=" CA PHE D 63 "
pdb=" C PHE D 63 "
pdb=" N TYR D 64 "
pdb=" CA TYR D 64 "
ideal model delta harmonic sigma weight residual
-180.00 -133.67 -46.33 0 5.00e+00 4.00e-02 8.59e+01
dihedral pdb=" CA ASP A 57 "
pdb=" C ASP A 57 "
pdb=" N LEU A 58 "
pdb=" CA LEU A 58 "
ideal model delta harmonic sigma weight residual
180.00 -134.14 -45.86 0 5.00e+00 4.00e-02 8.41e+01
... (remaining 1776 not shown)
Histogram of chiral volume deviations from ideal:
0.008 - 0.041: 3
0.041 - 0.074: 1
0.074 - 0.107: 2
0.107 - 0.140: 1
0.140 - 0.173: 1
Chirality restraints: 8
Sorted by residual:
chirality pdb=" C1' ATP A 501 "
pdb=" C2' ATP A 501 "
pdb=" N9 ATP A 501 "
pdb=" O4' ATP A 501 "
both_signs ideal model delta sigma weight residual
False 2.41 2.24 0.17 2.00e-01 2.50e+01 7.44e-01
chirality pdb=" C2' ATP B 401 "
pdb=" C1' ATP B 401 "
pdb=" C3' ATP B 401 "
pdb=" O2' ATP B 401 "
both_signs ideal model delta sigma weight residual
False -2.68 -2.54 -0.14 2.00e-01 2.50e+01 4.61e-01
chirality pdb=" C1' ATP B 401 "
pdb=" C2' ATP B 401 "
pdb=" N9 ATP B 401 "
pdb=" O4' ATP B 401 "
both_signs ideal model delta sigma weight residual
False 2.41 2.50 -0.09 2.00e-01 2.50e+01 2.03e-01
... (remaining 5 not shown)
Planarity restraints: 2
Sorted by residual:
delta sigma weight rms_deltas residual
plane pdb=" C1' ATP A 501 " 0.023 2.00e-02 2.50e+03 1.59e-02 6.92e+00
pdb=" C2 ATP A 501 " 0.001 2.00e-02 2.50e+03
pdb=" C4 ATP A 501 " -0.000 2.00e-02 2.50e+03
pdb=" C5 ATP A 501 " 0.000 2.00e-02 2.50e+03
pdb=" C6 ATP A 501 " 0.002 2.00e-02 2.50e+03
pdb=" C8 ATP A 501 " 0.015 2.00e-02 2.50e+03
pdb=" N1 ATP A 501 " 0.000 2.00e-02 2.50e+03
pdb=" N3 ATP A 501 " 0.001 2.00e-02 2.50e+03
pdb=" N6 ATP A 501 " 0.003 2.00e-02 2.50e+03
pdb=" N7 ATP A 501 " -0.001 2.00e-02 2.50e+03
pdb=" N9 ATP A 501 " -0.045 2.00e-02 2.50e+03
delta sigma weight rms_deltas residual
plane pdb=" C1' ATP B 401 " 0.001 2.00e-02 2.50e+03 7.78e-04 1.66e-02
pdb=" C2 ATP B 401 " -0.000 2.00e-02 2.50e+03
pdb=" C4 ATP B 401 " 0.002 2.00e-02 2.50e+03
pdb=" C5 ATP B 401 " 0.001 2.00e-02 2.50e+03
pdb=" C6 ATP B 401 " -0.000 2.00e-02 2.50e+03
pdb=" C8 ATP B 401 " -0.000 2.00e-02 2.50e+03
pdb=" N1 ATP B 401 " -0.000 2.00e-02 2.50e+03
pdb=" N3 ATP B 401 " -0.001 2.00e-02 2.50e+03
pdb=" N6 ATP B 401 " 0.000 2.00e-02 2.50e+03
pdb=" N7 ATP B 401 " -0.000 2.00e-02 2.50e+03
pdb=" N9 ATP B 401 " -0.002 2.00e-02 2.50e+03
Histogram of nonbonded interaction distances:
2.03 - 2.61: 44
2.61 - 3.18: 2284
3.18 - 3.75: 2819
3.75 - 4.33: 5699
4.33 - 4.90: 10226
Nonbonded interactions: 21072
Sorted by model distance:
nonbonded pdb=" N LEU B 240 "
pdb=" N VAL B 241 "
model vdw
2.034 2.560
nonbonded pdb=" N PHE D 83 "
pdb=" N LEU D 84 "
model vdw
2.040 2.560
nonbonded pdb=" N LEU A 58 "
pdb=" N ASP A 59 "
model vdw
2.065 2.560
nonbonded pdb=" N SER C 196 "
pdb=" N GLU C 197 "
model vdw
2.166 2.560
nonbonded pdb=" C LYS A 38 "
pdb=" C GLU A 39 "
model vdw
2.190 2.800
... (remaining 21067 not shown)
NOTE: a complete listing of the restraints can be obtained by requesting
output of .geo file.
Set up NCS constraints
No NCS constraints will be used in refinement.
Set refine NCS operators
Set scattering table
Set to: electron
Number of scattering types: 4
Type Number sf(0) Gaussians
P 6 5.49 5
C 3596 2.51 5
N 1798 2.21 5
O 26 1.98 5
sf(0) = scattering factor at diffraction angle 0.
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
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: 0.620
Set model interpretation parameters: 0.210
Set stop_for_unknowns flag: 0.000
Assert model is a single copy model: 0.000
Construct map_model_manager: 0.010
Extract box with map and model: 4.250
Check model and map are aligned: 0.070
Convert atoms to be neutral: 0.050
Process input model: 17.480
Set up NCS constraints: 0.050
Set refine NCS operators: 0.000
Set scattering table: 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:2.340
Set ADP refinement strategy: 0.000
Internal consistency checks: 0.000
Total: 25.080
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.3197
moved from start: 0.0000
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values.
Bond : 0.021 0.398 5415
Angle : 3.503 60.991 5438
Chirality : 0.091 0.173 8
Planarity : 0.011 0.016 2
Dihedral : 6.696 70.879 1779
Min Nonbonded Distance : 2.034
Molprobity Statistics.
All-atom Clashscore : 1.63
Ramachandran Plot:
Outliers : 0.85 %
Allowed : 4.49 %
Favored : 94.65 %
Rotamer Outliers : 0.00 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 1.25 %
Cis-general : 0.06 %
Twisted Proline : 0.00 %
Twisted General : 0.89 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: -1.45 (0.18), residues: 1758
helix: -0.92 (0.18), residues: 641
sheet: -0.01 (0.26), residues: 340
loop : -1.34 (0.21), residues: 777
*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
3516 Ramachandran restraints generated.
1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
3516 Ramachandran restraints generated.
1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
41 residues out of total 1567 (non-ALA, GLY, PRO) need a fit.
rotamer outliers: 0
poor density : 41
time to evaluate : 0.833
Fit side-chains
TARDY: cannot create tardy model for: "MET A 52 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 89 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 93 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 130 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 327 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 372 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 383 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET D 1 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET D 56 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET D 115 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET D 152 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET D 182 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET D 266 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET E 9 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET E 19 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET E 95 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET E 129 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET E 169 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 85 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 114 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 215 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 309 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 353 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 365 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 373 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET F 91 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET F 94 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET F 95 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET F 96 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET F 126 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET F 139 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET F 149 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET G 51 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET G 107 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET G 124 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET C 1 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET C 189 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET C 195 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET C 270 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET C 352 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET C 370 " (corrupted residue). Skipping it.
outliers start: 0
outliers final: 0
residues processed: 41
average time/residue: 0.0532
time to fit residues: 3.5057
Evaluate side-chains
41 residues out of total 1567 (non-ALA, GLY, PRO) need a fit.
rotamer outliers: 0
poor density : 41
time to evaluate : 0.840
Switching outliers to nearest non-outliers
outliers start: 0
outliers final: 0
residues processed: 0
time to fit residues: 1.1200
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 175
random chunks:
chunk 147 optimal weight: 5.9990
chunk 132 optimal weight: 0.1980
chunk 73 optimal weight: 40.0000
chunk 45 optimal weight: 0.1980
chunk 89 optimal weight: 4.9990
chunk 70 optimal weight: 10.0000
chunk 137 optimal weight: 20.0000
chunk 53 optimal weight: 40.0000
chunk 83 optimal weight: 0.0570
chunk 102 optimal weight: 5.9990
chunk 158 optimal weight: 0.7980
overall best weight: 1.2500
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.3914
moved from start: 0.5366
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values.
Bond : 0.001 0.017 5415
Angle : 0.463 6.209 5438
Chirality : 0.026 0.051 8
Planarity : 0.003 0.003 2
Dihedral : 3.626 43.955 1779
Min Nonbonded Distance : 2.305
Molprobity Statistics.
All-atom Clashscore : 0.68
Ramachandran Plot:
Outliers : 0.23 %
Allowed : 2.67 %
Favored : 97.10 %
Rotamer Outliers : 0.00 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 1.25 %
Cis-general : 0.06 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 0.51 (0.20), residues: 1758
helix: 1.23 (0.21), residues: 622
sheet: 0.63 (0.28), residues: 303
loop : -0.39 (0.21), residues: 833
*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
3516 Ramachandran restraints generated.
1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
3516 Ramachandran restraints generated.
1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
41 residues out of total 1567 (non-ALA, GLY, PRO) need a fit.
rotamer outliers: 0
poor density : 41
time to evaluate : 0.805
Fit side-chains
TARDY: cannot create tardy model for: "MET A 52 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 89 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 93 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 130 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 327 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 372 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 383 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET D 1 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET D 56 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET D 115 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET D 152 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET D 182 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET D 266 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET E 9 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET E 19 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET E 95 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET E 129 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET E 169 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 85 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 114 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 215 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 309 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 353 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 365 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 373 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET F 91 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET F 94 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET F 95 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET F 96 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET F 126 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET F 139 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET F 149 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET G 51 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET G 107 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET G 124 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET C 1 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET C 189 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET C 195 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET C 270 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET C 352 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET C 370 " (corrupted residue). Skipping it.
outliers start: 0
outliers final: 0
residues processed: 41
average time/residue: 0.0521
time to fit residues: 3.5136
Evaluate side-chains
41 residues out of total 1567 (non-ALA, GLY, PRO) need a fit.
rotamer outliers: 0
poor density : 41
time to evaluate : 0.877
Switching outliers to nearest non-outliers
outliers start: 0
outliers final: 0
residues processed: 0
time to fit residues: 1.0788
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 175
random chunks:
chunk 88 optimal weight: 40.0000
chunk 49 optimal weight: 3.9990
chunk 132 optimal weight: 5.9990
chunk 108 optimal weight: 0.9980
chunk 43 optimal weight: 20.0000
chunk 159 optimal weight: 0.1980
chunk 171 optimal weight: 8.9990
chunk 141 optimal weight: 50.0000
chunk 157 optimal weight: 50.0000
chunk 54 optimal weight: 30.0000
chunk 127 optimal weight: 0.0270
overall best weight: 2.2442
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4852
moved from start: 1.2923
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values.
Bond : 0.001 0.018 5415
Angle : 0.456 6.920 5438
Chirality : 0.015 0.026 8
Planarity : 0.002 0.003 2
Dihedral : 4.609 63.967 1779
Min Nonbonded Distance : 2.476
Molprobity Statistics.
All-atom Clashscore : 2.04
Ramachandran Plot:
Outliers : 0.17 %
Allowed : 3.30 %
Favored : 96.53 %
Rotamer Outliers : 0.00 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 1.25 %
Cis-general : 0.06 %
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: 0.83 (0.20), residues: 1758
helix: 1.82 (0.22), residues: 581
sheet: 0.53 (0.33), residues: 224
loop : -0.20 (0.20), residues: 953
*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
3516 Ramachandran restraints generated.
1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
3516 Ramachandran restraints generated.
1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
41 residues out of total 1567 (non-ALA, GLY, PRO) need a fit.
rotamer outliers: 0
poor density : 41
time to evaluate : 0.836
Fit side-chains
TARDY: cannot create tardy model for: "MET A 52 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 89 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 93 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 130 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 327 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 372 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 383 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET D 1 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET D 56 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET D 115 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET D 152 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET D 182 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET D 266 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET E 9 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET E 19 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET E 95 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET E 129 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET E 169 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 85 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 114 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 215 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 309 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 353 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 365 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 373 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET F 91 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET F 94 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET F 95 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET F 96 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET F 126 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET F 139 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET F 149 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET G 51 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET G 107 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET G 124 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET C 1 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET C 189 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET C 195 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET C 270 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET C 352 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET C 370 " (corrupted residue). Skipping it.
outliers start: 0
outliers final: 0
residues processed: 41
average time/residue: 0.0500
time to fit residues: 3.3172
Evaluate side-chains
41 residues out of total 1567 (non-ALA, GLY, PRO) need a fit.
rotamer outliers: 0
poor density : 41
time to evaluate : 0.811
Switching outliers to nearest non-outliers
outliers start: 0
outliers final: 0
residues processed: 0
time to fit residues: 1.0639
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 175
random chunks:
chunk 157 optimal weight: 30.0000
chunk 119 optimal weight: 50.0000
chunk 82 optimal weight: 0.0870
chunk 17 optimal weight: 50.0000
chunk 75 optimal weight: 50.0000
chunk 106 optimal weight: 40.0000
chunk 159 optimal weight: 40.0000
chunk 169 optimal weight: 9.9990
chunk 83 optimal weight: 20.0000
chunk 151 optimal weight: 10.0000
chunk 45 optimal weight: 0.0030
overall best weight: 8.0178
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5595
moved from start: 1.9824
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values.
Bond : 0.003 0.040 5415
Angle : 0.771 9.328 5438
Chirality : 0.027 0.059 8
Planarity : 0.004 0.004 2
Dihedral : 7.169 77.109 1779
Min Nonbonded Distance : 2.201
Molprobity Statistics.
All-atom Clashscore : 12.77
Ramachandran Plot:
Outliers : 0.28 %
Allowed : 6.48 %
Favored : 93.23 %
Rotamer Outliers : 0.00 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 1.25 %
Cis-general : 0.06 %
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: -0.91 (0.20), residues: 1758
helix: -0.94 (0.23), residues: 423
sheet: -0.02 (0.31), residues: 259
loop : -0.56 (0.19), residues: 1076
*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
3516 Ramachandran restraints generated.
1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
3516 Ramachandran restraints generated.
1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
41 residues out of total 1567 (non-ALA, GLY, PRO) need a fit.
rotamer outliers: 0
poor density : 41
time to evaluate : 0.810
Fit side-chains
TARDY: cannot create tardy model for: "MET A 52 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 89 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 93 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 130 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 327 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 372 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 383 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET D 1 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET D 56 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET D 115 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET D 152 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET D 182 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET D 266 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET E 9 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET E 19 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET E 95 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET E 129 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET E 169 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 85 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 114 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 215 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 309 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 353 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 365 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 373 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET F 91 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET F 94 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET F 95 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET F 96 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET F 126 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET F 139 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET F 149 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET G 51 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET G 107 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET G 124 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET C 1 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET C 189 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET C 195 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET C 270 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET C 352 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET C 370 " (corrupted residue). Skipping it.
outliers start: 0
outliers final: 0
residues processed: 41
average time/residue: 0.0524
time to fit residues: 3.5234
Evaluate side-chains
41 residues out of total 1567 (non-ALA, GLY, PRO) need a fit.
rotamer outliers: 0
poor density : 41
time to evaluate : 0.810
Switching outliers to nearest non-outliers
outliers start: 0
outliers final: 0
residues processed: 0
time to fit residues: 1.1360
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 175
random chunks:
chunk 140 optimal weight: 20.0000
chunk 96 optimal weight: 3.9990
chunk 2 optimal weight: 20.0000
chunk 125 optimal weight: 2.9990
chunk 69 optimal weight: 40.0000
chunk 144 optimal weight: 8.9990
chunk 116 optimal weight: 40.0000
chunk 0 optimal weight: 30.0000
chunk 86 optimal weight: 50.0000
chunk 151 optimal weight: 9.9990
chunk 42 optimal weight: 50.0000
overall best weight: 9.1992
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5850
moved from start: 2.2374
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values.
Bond : 0.003 0.057 5415
Angle : 0.771 14.208 5438
Chirality : 0.027 0.057 8
Planarity : 0.001 0.001 2
Dihedral : 7.059 56.195 1779
Min Nonbonded Distance : 2.218
Molprobity Statistics.
All-atom Clashscore : 16.30
Ramachandran Plot:
Outliers : 0.28 %
Allowed : 8.99 %
Favored : 90.73 %
Rotamer Outliers : 0.00 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 1.25 %
Cis-general : 0.06 %
Twisted Proline : 0.00 %
Twisted General : 0.06 %
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: -1.98 (0.20), residues: 1758
helix: -1.97 (0.22), residues: 434
sheet: -1.01 (0.33), residues: 220
loop : -1.07 (0.20), residues: 1104
*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
3516 Ramachandran restraints generated.
1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
3516 Ramachandran restraints generated.
1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
41 residues out of total 1567 (non-ALA, GLY, PRO) need a fit.
rotamer outliers: 0
poor density : 41
time to evaluate : 0.808
Fit side-chains
TARDY: cannot create tardy model for: "MET A 52 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 89 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 93 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 130 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 327 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 372 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 383 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET D 1 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET D 56 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET D 115 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET D 152 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET D 182 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET D 266 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET E 9 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET E 19 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET E 95 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET E 129 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET E 169 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 85 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 114 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 215 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 309 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 353 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 365 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 373 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET F 91 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET F 94 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET F 95 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET F 96 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET F 126 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET F 139 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET F 149 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET G 51 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET G 107 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET G 124 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET C 1 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET C 189 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET C 195 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET C 270 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET C 352 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET C 370 " (corrupted residue). Skipping it.
outliers start: 0
outliers final: 0
residues processed: 41
average time/residue: 0.0539
time to fit residues: 3.5230
Evaluate side-chains
41 residues out of total 1567 (non-ALA, GLY, PRO) need a fit.
rotamer outliers: 0
poor density : 41
time to evaluate : 0.807
Switching outliers to nearest non-outliers
outliers start: 0
outliers final: 0
residues processed: 0
time to fit residues: 1.0823
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 175
random chunks:
chunk 56 optimal weight: 8.9990
chunk 152 optimal weight: 50.0000
chunk 33 optimal weight: 40.0000
chunk 99 optimal weight: 30.0000
chunk 41 optimal weight: 50.0000
chunk 169 optimal weight: 50.0000
chunk 140 optimal weight: 0.3980
chunk 78 optimal weight: 9.9990
chunk 14 optimal weight: 7.9990
chunk 88 optimal weight: 20.0000
chunk 163 optimal weight: 9.9990
overall best weight: 7.4788
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5929
moved from start: 2.3882
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values.
Bond : 0.003 0.073 5415
Angle : 0.705 16.790 5438
Chirality : 0.019 0.039 8
Planarity : 0.003 0.003 2
Dihedral : 6.184 54.170 1779
Min Nonbonded Distance : 2.223
Molprobity Statistics.
All-atom Clashscore : 14.67
Ramachandran Plot:
Outliers : 0.17 %
Allowed : 10.98 %
Favored : 88.85 %
Rotamer Outliers : 0.00 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 1.25 %
Cis-general : 0.06 %
Twisted Proline : 0.00 %
Twisted General : 0.06 %
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: -2.30 (0.20), residues: 1758
helix: -2.12 (0.22), residues: 430
sheet: -1.28 (0.36), residues: 201
loop : -1.34 (0.19), residues: 1127
*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
3516 Ramachandran restraints generated.
1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
3516 Ramachandran restraints generated.
1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
41 residues out of total 1567 (non-ALA, GLY, PRO) need a fit.
rotamer outliers: 0
poor density : 41
time to evaluate : 0.791
Fit side-chains
TARDY: cannot create tardy model for: "MET A 52 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 89 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 93 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 130 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 327 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 372 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 383 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET D 1 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET D 56 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET D 115 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET D 152 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET D 182 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET D 266 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET E 9 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET E 19 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET E 95 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET E 129 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET E 169 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 85 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 114 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 215 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 309 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 353 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 365 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 373 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET F 91 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET F 94 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET F 95 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET F 96 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET F 126 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET F 139 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET F 149 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET G 51 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET G 107 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET G 124 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET C 1 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET C 189 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET C 195 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET C 270 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET C 352 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET C 370 " (corrupted residue). Skipping it.
outliers start: 0
outliers final: 0
residues processed: 41
average time/residue: 0.0514
time to fit residues: 3.4102
Evaluate side-chains
41 residues out of total 1567 (non-ALA, GLY, PRO) need a fit.
rotamer outliers: 0
poor density : 41
time to evaluate : 0.849
Switching outliers to nearest non-outliers
outliers start: 0
outliers final: 0
residues processed: 0
time to fit residues: 1.1277
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 175
random chunks:
chunk 19 optimal weight: 3.9990
chunk 96 optimal weight: 0.0020
chunk 123 optimal weight: 40.0000
chunk 95 optimal weight: 40.0000
chunk 142 optimal weight: 20.0000
chunk 94 optimal weight: 0.9980
chunk 168 optimal weight: 40.0000
chunk 105 optimal weight: 40.0000
chunk 102 optimal weight: 50.0000
chunk 77 optimal weight: 20.0000
chunk 104 optimal weight: 20.0000
overall best weight: 8.9998
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6064
moved from start: 2.5305
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values.
Bond : 0.003 0.031 5415
Angle : 0.761 15.244 5438
Chirality : 0.028 0.058 8
Planarity : 0.001 0.002 2
Dihedral : 6.947 76.358 1779
Min Nonbonded Distance : 2.240
Molprobity Statistics.
All-atom Clashscore : 19.02
Ramachandran Plot:
Outliers : 0.23 %
Allowed : 13.77 %
Favored : 86.01 %
Rotamer Outliers : 0.00 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 1.25 %
Cis-general : 0.06 %
Twisted Proline : 0.00 %
Twisted General : 0.06 %
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: -2.95 (0.19), residues: 1758
helix: -2.52 (0.22), residues: 416
sheet: -1.69 (0.39), residues: 171
loop : -1.86 (0.18), residues: 1171
*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
3516 Ramachandran restraints generated.
1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
3516 Ramachandran restraints generated.
1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
41 residues out of total 1567 (non-ALA, GLY, PRO) need a fit.
rotamer outliers: 0
poor density : 41
time to evaluate : 0.841
Fit side-chains
TARDY: cannot create tardy model for: "MET A 52 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 89 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 93 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 130 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 327 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 372 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 383 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET D 1 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET D 56 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET D 115 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET D 152 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET D 182 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET D 266 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET E 9 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET E 19 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET E 95 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET E 129 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET E 169 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 85 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 114 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 215 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 309 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 353 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 365 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 373 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET F 91 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET F 94 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET F 95 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET F 96 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET F 126 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET F 139 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET F 149 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET G 51 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET G 107 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET G 124 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET C 1 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET C 189 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET C 195 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET C 270 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET C 352 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET C 370 " (corrupted residue). Skipping it.
outliers start: 0
outliers final: 0
residues processed: 41
average time/residue: 0.0519
time to fit residues: 3.4684
Evaluate side-chains
41 residues out of total 1567 (non-ALA, GLY, PRO) need a fit.
rotamer outliers: 0
poor density : 41
time to evaluate : 0.799
Switching outliers to nearest non-outliers
outliers start: 0
outliers final: 0
residues processed: 0
time to fit residues: 1.0482
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 175
random chunks:
chunk 67 optimal weight: 40.0000
chunk 100 optimal weight: 0.0980
chunk 50 optimal weight: 0.9990
chunk 33 optimal weight: 50.0000
chunk 32 optimal weight: 7.9990
chunk 107 optimal weight: 0.2980
chunk 114 optimal weight: 6.9990
chunk 83 optimal weight: 40.0000
chunk 15 optimal weight: 10.0000
chunk 132 optimal weight: 20.0000
chunk 153 optimal weight: 40.0000
overall best weight: 3.2786
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5907
moved from start: 2.5002
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values.
Bond : 0.001 0.010 5415
Angle : 0.439 10.346 5438
Chirality : 0.012 0.016 8
Planarity : 0.001 0.001 2
Dihedral : 4.679 69.765 1779
Min Nonbonded Distance : 2.314
Molprobity Statistics.
All-atom Clashscore : 6.66
Ramachandran Plot:
Outliers : 0.11 %
Allowed : 8.65 %
Favored : 91.24 %
Rotamer Outliers : 0.00 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 1.25 %
Cis-general : 0.06 %
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: -2.52 (0.20), residues: 1758
helix: -2.00 (0.23), residues: 430
sheet: -1.67 (0.41), residues: 157
loop : -1.59 (0.19), residues: 1171
*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
3516 Ramachandran restraints generated.
1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
3516 Ramachandran restraints generated.
1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
41 residues out of total 1567 (non-ALA, GLY, PRO) need a fit.
rotamer outliers: 0
poor density : 41
time to evaluate : 0.972
Fit side-chains
TARDY: cannot create tardy model for: "MET A 52 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 89 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 93 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 130 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 327 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 372 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 383 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET D 1 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET D 56 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET D 115 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET D 152 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET D 182 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET D 266 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET E 9 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET E 19 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET E 95 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET E 129 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET E 169 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 85 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 114 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 215 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 309 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 353 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 365 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 373 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET F 91 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET F 94 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET F 95 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET F 96 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET F 126 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET F 139 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET F 149 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET G 51 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET G 107 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET G 124 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET C 1 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET C 189 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET C 195 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET C 270 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET C 352 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET C 370 " (corrupted residue). Skipping it.
outliers start: 0
outliers final: 0
residues processed: 41
average time/residue: 0.0528
time to fit residues: 3.5492
Evaluate side-chains
41 residues out of total 1567 (non-ALA, GLY, PRO) need a fit.
rotamer outliers: 0
poor density : 41
time to evaluate : 0.843
Switching outliers to nearest non-outliers
outliers start: 0
outliers final: 0
residues processed: 0
time to fit residues: 1.1921
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 175
random chunks:
chunk 161 optimal weight: 20.0000
chunk 147 optimal weight: 20.0000
chunk 157 optimal weight: 20.0000
chunk 94 optimal weight: 5.9990
chunk 68 optimal weight: 40.0000
chunk 123 optimal weight: 40.0000
chunk 48 optimal weight: 50.0000
chunk 142 optimal weight: 20.0000
chunk 148 optimal weight: 4.9990
chunk 156 optimal weight: 0.0060
chunk 103 optimal weight: 30.0000
overall best weight: 10.2008
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6171
moved from start: 2.6555
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values.
Bond : 0.004 0.080 5415
Angle : 0.807 15.474 5438
Chirality : 0.021 0.046 8
Planarity : 0.003 0.003 2
Dihedral : 7.146 83.877 1779
Min Nonbonded Distance : 2.271
Molprobity Statistics.
All-atom Clashscore : 21.19
Ramachandran Plot:
Outliers : 0.34 %
Allowed : 17.69 %
Favored : 81.97 %
Rotamer Outliers : 0.00 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 1.25 %
Cis-general : 0.06 %
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: -3.33 (0.19), residues: 1758
helix: -2.79 (0.21), residues: 409
sheet: -2.17 (0.45), residues: 114
loop : -2.14 (0.18), residues: 1235
*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
3516 Ramachandran restraints generated.
1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
3516 Ramachandran restraints generated.
1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
41 residues out of total 1567 (non-ALA, GLY, PRO) need a fit.
rotamer outliers: 0
poor density : 41
time to evaluate : 0.771
Fit side-chains
TARDY: cannot create tardy model for: "MET A 52 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 89 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 93 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 130 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 327 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 372 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 383 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET D 1 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET D 56 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET D 115 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET D 152 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET D 182 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET D 266 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET E 9 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET E 19 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET E 95 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET E 129 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET E 169 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 85 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 114 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 215 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 309 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 353 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 365 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 373 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET F 91 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET F 94 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET F 95 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET F 96 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET F 126 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET F 139 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET F 149 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET G 51 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET G 107 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET G 124 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET C 1 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET C 189 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET C 195 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET C 270 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET C 352 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET C 370 " (corrupted residue). Skipping it.
outliers start: 0
outliers final: 0
residues processed: 41
average time/residue: 0.0507
time to fit residues: 3.3544
Evaluate side-chains
41 residues out of total 1567 (non-ALA, GLY, PRO) need a fit.
rotamer outliers: 0
poor density : 41
time to evaluate : 0.844
Switching outliers to nearest non-outliers
outliers start: 0
outliers final: 0
residues processed: 0
time to fit residues: 1.1668
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 175
random chunks:
chunk 166 optimal weight: 50.0000
chunk 101 optimal weight: 20.0000
chunk 78 optimal weight: 50.0000
chunk 115 optimal weight: 0.2980
chunk 174 optimal weight: 20.0000
chunk 160 optimal weight: 8.9990
chunk 138 optimal weight: 0.6980
chunk 14 optimal weight: 40.0000
chunk 107 optimal weight: 0.0050
chunk 85 optimal weight: 50.0000
chunk 110 optimal weight: 40.0000
overall best weight: 6.0000
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6098
moved from start: 2.6470
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values.
Bond : 0.002 0.020 5415
Angle : 0.596 14.391 5438
Chirality : 0.017 0.026 8
Planarity : 0.001 0.002 2
Dihedral : 5.835 87.067 1779
Min Nonbonded Distance : 2.307
Molprobity Statistics.
All-atom Clashscore : 12.77
Ramachandran Plot:
Outliers : 0.17 %
Allowed : 12.80 %
Favored : 87.03 %
Rotamer Outliers : 0.00 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 1.25 %
Cis-general : 0.06 %
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: -3.20 (0.19), residues: 1758
helix: -2.59 (0.22), residues: 410
sheet: -1.85 (0.42), residues: 143
loop : -2.10 (0.18), residues: 1205
********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
3516 Ramachandran restraints generated.
1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
3516 Ramachandran restraints generated.
1758 Oldfield, 0 Emsley, 1758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
41 residues out of total 1567 (non-ALA, GLY, PRO) need a fit.
rotamer outliers: 0
poor density : 41
time to evaluate : 0.847
Fit side-chains
TARDY: cannot create tardy model for: "MET A 52 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 89 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 93 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 130 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 327 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 372 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 383 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET D 1 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET D 56 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET D 115 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET D 152 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET D 182 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET D 266 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET E 9 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET E 19 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET E 95 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET E 129 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET E 169 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 85 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 114 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 215 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 309 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 353 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 365 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 373 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET F 91 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET F 94 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET F 95 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET F 96 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET F 126 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET F 139 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET F 149 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET G 51 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET G 107 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET G 124 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET C 1 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET C 189 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET C 195 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET C 270 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET C 352 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET C 370 " (corrupted residue). Skipping it.
outliers start: 0
outliers final: 0
residues processed: 41
average time/residue: 0.0523
time to fit residues: 3.5824
Evaluate side-chains
41 residues out of total 1567 (non-ALA, GLY, PRO) need a fit.
rotamer outliers: 0
poor density : 41
time to evaluate : 0.846
Switching outliers to nearest non-outliers
outliers start: 0
outliers final: 0
residues processed: 0
time to fit residues: 1.1261
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 175
random chunks:
chunk 147 optimal weight: 30.0000
chunk 42 optimal weight: 40.0000
chunk 128 optimal weight: 40.0000
chunk 20 optimal weight: 0.0040
chunk 38 optimal weight: 1.9990
chunk 139 optimal weight: 0.0270
chunk 58 optimal weight: 2.9990
chunk 142 optimal weight: 20.0000
chunk 17 optimal weight: 20.0000
chunk 25 optimal weight: 50.0000
chunk 122 optimal weight: 50.0000
overall best weight: 5.0058
-------------------------------------------------------------------------------
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 = 0.2843 r_free = 0.2843 target = 0.045964 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2423 r_free = 0.2423 target = 0.032168 restraints weight = 33763.184|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.2416 r_free = 0.2416 target = 0.031981 restraints weight = 36833.561|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.2416 r_free = 0.2416 target = 0.031981 restraints weight = 39748.297|
|-----------------------------------------------------------------------------|
GEOMETRY RESTRAINTS LIBRARY: GEOSTD + MONOMER LIBRARY + CDL V1.2
DEVIATIONS FROM IDEAL VALUES.
BOND : 0.002 0.022 5415
ANGLE : 0.513 10.836 5438
CHIRALITY : 0.014 0.020 8
PLANARITY : 0.002 0.002 2
DIHEDRAL : 5.296 81.650 1779
MIN NONBONDED DISTANCE : 2.335
MOLPROBITY STATISTICS.
ALL-ATOM CLASHSCORE : 9.92
RAMACHANDRAN PLOT:
OUTLIERS : 0.17 %
ALLOWED : 16.78 %
FAVORED : 83.05 %
ROTAMER OUTLIERS : 0.00 %
CBETA DEVIATIONS : 0.00 %
PEPTIDE PLANE:
CIS-PROLINE : 1.25 %
CIS-GENERAL : 0.06 %
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: -3.04 (0.20), RESIDUES: 1758
HELIX: -2.36 (0.23), RESIDUES: 410
SHEET: -1.84 (0.43), RESIDUES: 138
LOOP : -2.02 (0.19), RESIDUES: 1210
-------------------------------------------------------------------------------
Occupancy refinement
********************
GEOMETRY RESTRAINTS LIBRARY: GEOSTD + MONOMER LIBRARY + CDL V1.2
DEVIATIONS FROM IDEAL VALUES.
BOND : 0.002 0.022 5415
ANGLE : 0.513 10.836 5438
CHIRALITY : 0.014 0.020 8
PLANARITY : 0.002 0.002 2
DIHEDRAL : 5.296 81.650 1779
MIN NONBONDED DISTANCE : 2.335
MOLPROBITY STATISTICS.
ALL-ATOM CLASHSCORE : 9.92
RAMACHANDRAN PLOT:
OUTLIERS : 0.17 %
ALLOWED : 16.78 %
FAVORED : 83.05 %
ROTAMER OUTLIERS : 0.00 %
CBETA DEVIATIONS : 0.00 %
PEPTIDE PLANE:
CIS-PROLINE : 1.25 %
CIS-GENERAL : 0.06 %
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: -3.04 (0.20), RESIDUES: 1758
HELIX: -2.36 (0.23), RESIDUES: 410
SHEET: -1.84 (0.43), RESIDUES: 138
LOOP : -2.02 (0.19), RESIDUES: 1210
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7370
moved from start: 2.6830
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values.
Bond : 0.002 0.022 5415
Angle : 0.513 10.836 5438
Chirality : 0.014 0.020 8
Planarity : 0.002 0.002 2
Dihedral : 5.296 81.650 1779
Min Nonbonded Distance : 2.335
Molprobity Statistics.
All-atom Clashscore : 9.92
Ramachandran Plot:
Outliers : 0.17 %
Allowed : 16.78 %
Favored : 83.05 %
Rotamer Outliers : 0.00 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 1.25 %
Cis-general : 0.06 %
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: -3.04 (0.20), residues: 1758
helix: -2.36 (0.23), residues: 410
sheet: -1.84 (0.43), residues: 138
loop : -2.02 (0.19), residues: 1210
===============================================================================
Job complete
usr+sys time: 1078.69 seconds
wall clock time: 19 minutes 55.16 seconds (1195.16 seconds total)