Starting phenix.real_space_refine
on Fri Apr 5 20:33:00 2024 by dcliebschner
===============================================================================
Processing files:
-------------------------------------------------------------------------------
Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yw7_10960/04_2024/6yw7_10960_updated.pdb
Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yw7_10960/04_2024/6yw7_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_10960/04_2024/6yw7_10960.map"
default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yw7_10960/04_2024/6yw7_10960.map"
model {
file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yw7_10960/04_2024/6yw7_10960_updated.pdb"
}
default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yw7_10960/04_2024/6yw7_10960_updated.pdb"
}
resolution = 4.5
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= 0.003
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
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.
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-5288/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: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 333}
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: 4.44, per 1000 atoms: 0.82
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
Amino 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 1.9 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: 0.93
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: 1.71 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 - 16.28: 1758
16.28 - 32.56: 58
32.56 - 48.84: 17
48.84 - 65.12: 4
65.12 - 81.40: 4
Dihedral angle restraints: 1841
sinusoidal: 68
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 1838 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.
Find NCS groups from input model
========== WARNING! ============
No NCS relation were found !!!
================================
Found NCS groups:
found none.
Set up NCS constraints
No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
Set random seed: 0.000
Set model cs if undefined: 0.000
Decide on map wrapping: 0.000
Normalize map: mean=0, sd=1: 0.780
Set stop_for_unknowns flag: 0.000
Assert model is a single copy model: 0.000
Assert all atoms have isotropic ADPs: 0.000
Construct map_model_manager: 0.010
Extract box with map and model: 3.830
Check model and map are aligned: 0.090
Set scattering table: 0.050
Process input model: 18.640
Find NCS groups from input model: 0.320
Set up NCS constraints: 0.030
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: 0.010
Load rotamer database and sin/cos tables:2.690
Set ADP refinement strategy: 0.000
Make a string to write initial .geo file:0.000
Internal consistency checks: 0.000
Total: 26.450
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.3204
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 : 0.021 0.398 5415 Z= 1.606
Angle : 3.501 60.991 5438 Z= 2.353
Chirality : 0.091 0.173 8
Planarity : 0.011 0.016 2
Dihedral : 8.081 81.400 1841
Min Nonbonded Distance : 2.034
Molprobity Statistics.
All-atom Clashscore : 2.17
Ramachandran Plot:
Outliers : 0.85 %
Allowed : 4.49 %
Favored : 94.65 %
Rotamer:
Outliers : 0.00 %
Allowed : 0.00 %
Favored : 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 fitting.
rotamer outliers: 0
poor density : 41
time to evaluate : 0.777
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: 0.0455
time to fit residues: 4.7359
Evaluate side-chains
41 residues out of total 1567 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 41
time to evaluate : 0.812
-------------------------------------------------------------------------------
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: 0.3515
moved from start: 0.2761
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.001 0.037 5415 Z= 0.084
Angle : 0.445 7.990 5438 Z= 0.259
Chirality : 0.035 0.054 8
Planarity : 0.001 0.001 2
Dihedral : 5.084 79.122 1841
Min Nonbonded Distance : 2.447
Molprobity Statistics.
All-atom Clashscore : 0.27
Ramachandran Plot:
Outliers : 0.17 %
Allowed : 2.22 %
Favored : 97.61 %
Rotamer:
Outliers : 0.00 %
Allowed : 0.00 %
Favored : 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: 0.49 (0.20), residues: 1758
helix: 1.25 (0.21), residues: 634
sheet: 0.58 (0.28), residues: 316
loop : -0.47 (0.21), residues: 808
*********************** 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 fitting.
rotamer outliers: 0
poor density : 41
time to evaluate : 0.665
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: 0.0438
time to fit residues: 4.6348
Evaluate side-chains
41 residues out of total 1567 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 41
time to evaluate : 0.887
-------------------------------------------------------------------------------
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: 30.0000
chunk 49 optimal weight: 0.0770
chunk 132 optimal weight: 0.3980
chunk 108 optimal weight: 5.9990
chunk 43 optimal weight: 0.1980
chunk 159 optimal weight: 30.0000
chunk 171 optimal weight: 40.0000
chunk 141 optimal weight: 40.0000
chunk 157 optimal weight: 40.0000
chunk 54 optimal weight: 20.0000
chunk 127 optimal weight: 4.9990
overall best weight: 2.3342
-------------------------------------------------------------------------------
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: 0.4607
moved from start: 1.0006
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.002 0.035 5415 Z= 0.130
Angle : 0.617 5.836 5438 Z= 0.373
Chirality : 0.033 0.068 8
Planarity : 0.001 0.001 2
Dihedral : 6.122 88.858 1841
Min Nonbonded Distance : 2.357
Molprobity Statistics.
All-atom Clashscore : 5.57
Ramachandran Plot:
Outliers : 0.17 %
Allowed : 4.32 %
Favored : 95.51 %
Rotamer:
Outliers : 0.00 %
Allowed : 0.00 %
Favored : 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: 0.47 (0.20), residues: 1758
helix: 1.38 (0.21), residues: 563
sheet: 0.02 (0.31), residues: 262
loop : -0.20 (0.21), residues: 933
*********************** 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 fitting.
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: 0.0447
time to fit residues: 4.7576
Evaluate side-chains
41 residues out of total 1567 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 41
time to evaluate : 0.729
-------------------------------------------------------------------------------
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: 40.0000
chunk 119 optimal weight: 40.0000
chunk 82 optimal weight: 50.0000
chunk 17 optimal weight: 20.0000
chunk 75 optimal weight: 2.9990
chunk 106 optimal weight: 0.3980
chunk 159 optimal weight: 40.0000
chunk 169 optimal weight: 30.0000
chunk 83 optimal weight: 0.3980
chunk 151 optimal weight: 0.0670
chunk 45 optimal weight: 0.9980
overall best weight: 0.9720
-------------------------------------------------------------------------------
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: 0.4568
moved from start: 1.0195
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.001 0.015 5415 Z= 0.048
Angle : 0.267 3.264 5438 Z= 0.166
Chirality : 0.017 0.031 8
Planarity : 0.001 0.002 2
Dihedral : 4.472 89.403 1841
Min Nonbonded Distance : 2.417
Molprobity Statistics.
All-atom Clashscore : 1.22
Ramachandran Plot:
Outliers : 0.17 %
Allowed : 1.76 %
Favored : 98.07 %
Rotamer:
Outliers : 0.00 %
Allowed : 0.00 %
Favored : 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: 1.41 (0.21), residues: 1758
helix: 2.55 (0.22), residues: 597
sheet: 0.31 (0.32), residues: 271
loop : 0.07 (0.21), residues: 890
*********************** 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 fitting.
rotamer outliers: 0
poor density : 41
time to evaluate : 0.796
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: 0.0525
time to fit residues: 5.2440
Evaluate side-chains
41 residues out of total 1567 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 41
time to evaluate : 0.817
-------------------------------------------------------------------------------
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: 0.0770
chunk 96 optimal weight: 8.9990
chunk 2 optimal weight: 20.0000
chunk 125 optimal weight: 0.0970
chunk 69 optimal weight: 20.0000
chunk 144 optimal weight: 20.0000
chunk 116 optimal weight: 30.0000
chunk 0 optimal weight: 20.0000
chunk 86 optimal weight: 5.9990
chunk 151 optimal weight: 0.0020
chunk 42 optimal weight: 8.9990
overall best weight: 3.0348
-------------------------------------------------------------------------------
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: 0.5101
moved from start: 1.4028
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.002 0.042 5415 Z= 0.132
Angle : 0.522 4.800 5438 Z= 0.333
Chirality : 0.031 0.055 8
Planarity : 0.004 0.005 2
Dihedral : 5.919 85.626 1841
Min Nonbonded Distance : 2.461
Molprobity Statistics.
All-atom Clashscore : 5.84
Ramachandran Plot:
Outliers : 0.17 %
Allowed : 4.95 %
Favored : 94.88 %
Rotamer:
Outliers : 0.00 %
Allowed : 0.00 %
Favored : 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: 0.57 (0.20), residues: 1758
helix: 1.09 (0.22), residues: 529
sheet: 0.77 (0.32), residues: 262
loop : -0.06 (0.21), residues: 967
*********************** 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 fitting.
rotamer outliers: 0
poor density : 41
time to evaluate : 0.793
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: 0.0437
time to fit residues: 4.5986
Evaluate side-chains
41 residues out of total 1567 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 41
time to evaluate : 0.769
-------------------------------------------------------------------------------
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: 3.9990
chunk 152 optimal weight: 30.0000
chunk 33 optimal weight: 0.0370
chunk 99 optimal weight: 30.0000
chunk 41 optimal weight: 0.0040
chunk 169 optimal weight: 50.0000
chunk 140 optimal weight: 30.0000
chunk 78 optimal weight: 50.0000
chunk 14 optimal weight: 8.9990
chunk 88 optimal weight: 20.0000
chunk 163 optimal weight: 20.0000
overall best weight: 6.6078
-------------------------------------------------------------------------------
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: 0.5503
moved from start: 1.8296
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.038 5415 Z= 0.199
Angle : 0.686 7.930 5438 Z= 0.443
Chirality : 0.033 0.069 8
Planarity : 0.005 0.006 2
Dihedral : 7.274 82.520 1841
Min Nonbonded Distance : 2.438
Molprobity Statistics.
All-atom Clashscore : 13.45
Ramachandran Plot:
Outliers : 0.17 %
Allowed : 5.80 %
Favored : 94.03 %
Rotamer:
Outliers : 0.00 %
Allowed : 0.00 %
Favored : 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: -0.86 (0.20), residues: 1758
helix: -0.72 (0.23), residues: 447
sheet: -0.19 (0.32), residues: 246
loop : -0.53 (0.20), residues: 1065
*********************** 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 fitting.
rotamer outliers: 0
poor density : 41
time to evaluate : 0.849
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: 0.0489
time to fit residues: 4.9588
Evaluate side-chains
41 residues out of total 1567 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 41
time to evaluate : 0.785
-------------------------------------------------------------------------------
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: 20.0000
chunk 96 optimal weight: 0.0980
chunk 123 optimal weight: 40.0000
chunk 95 optimal weight: 20.0000
chunk 142 optimal weight: 10.0000
chunk 94 optimal weight: 0.0170
chunk 168 optimal weight: 30.0000
chunk 105 optimal weight: 20.0000
chunk 102 optimal weight: 40.0000
chunk 77 optimal weight: 0.8980
chunk 104 optimal weight: 10.0000
overall best weight: 4.2026
-------------------------------------------------------------------------------
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: 0.5473
moved from start: 1.8661
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.002 0.018 5415 Z= 0.113
Angle : 0.435 4.098 5438 Z= 0.279
Chirality : 0.023 0.049 8
Planarity : 0.002 0.003 2
Dihedral : 5.676 84.305 1841
Min Nonbonded Distance : 2.373
Molprobity Statistics.
All-atom Clashscore : 8.42
Ramachandran Plot:
Outliers : 0.17 %
Allowed : 5.69 %
Favored : 94.14 %
Rotamer:
Outliers : 0.00 %
Allowed : 0.00 %
Favored : 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: -0.71 (0.20), residues: 1758
helix: -0.43 (0.22), residues: 501
sheet: -0.20 (0.34), residues: 228
loop : -0.48 (0.20), residues: 1029
*********************** 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 fitting.
rotamer outliers: 0
poor density : 41
time to evaluate : 0.765
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: 0.0456
time to fit residues: 4.7048
Evaluate side-chains
41 residues out of total 1567 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 41
time to evaluate : 0.871
-------------------------------------------------------------------------------
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: 50.0000
chunk 100 optimal weight: 30.0000
chunk 50 optimal weight: 9.9990
chunk 33 optimal weight: 0.0020
chunk 32 optimal weight: 0.0870
chunk 107 optimal weight: 40.0000
chunk 114 optimal weight: 20.0000
chunk 83 optimal weight: 0.0670
chunk 15 optimal weight: 20.0000
chunk 132 optimal weight: 20.0000
chunk 153 optimal weight: 40.0000
overall best weight: 6.0310
-------------------------------------------------------------------------------
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: 0.5691
moved from start: 2.0416
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.002 0.036 5415 Z= 0.163
Angle : 0.583 5.242 5438 Z= 0.384
Chirality : 0.023 0.040 8
Planarity : 0.002 0.003 2
Dihedral : 6.879 86.506 1841
Min Nonbonded Distance : 2.430
Molprobity Statistics.
All-atom Clashscore : 16.17
Ramachandran Plot:
Outliers : 0.23 %
Allowed : 8.65 %
Favored : 91.13 %
Rotamer:
Outliers : 0.00 %
Allowed : 0.00 %
Favored : 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: -1.55 (0.19), residues: 1758
helix: -1.29 (0.22), residues: 442
sheet: -0.43 (0.35), residues: 206
loop : -1.03 (0.19), residues: 1110
*********************** 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 fitting.
rotamer outliers: 0
poor density : 41
time to evaluate : 0.822
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: 5.7224
Evaluate side-chains
41 residues out of total 1567 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 41
time to evaluate : 0.801
-------------------------------------------------------------------------------
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: 30.0000
chunk 157 optimal weight: 50.0000
chunk 94 optimal weight: 0.0040
chunk 68 optimal weight: 40.0000
chunk 123 optimal weight: 40.0000
chunk 48 optimal weight: 50.0000
chunk 142 optimal weight: 10.0000
chunk 148 optimal weight: 9.9990
chunk 156 optimal weight: 8.9990
chunk 103 optimal weight: 3.9990
overall best weight: 6.6002
-------------------------------------------------------------------------------
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: 0.5748
moved from start: 2.1471
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.002 0.027 5415 Z= 0.165
Angle : 0.559 6.527 5438 Z= 0.363
Chirality : 0.024 0.050 8
Planarity : 0.001 0.001 2
Dihedral : 6.368 81.539 1841
Min Nonbonded Distance : 2.314
Molprobity Statistics.
All-atom Clashscore : 14.26
Ramachandran Plot:
Outliers : 0.23 %
Allowed : 7.91 %
Favored : 91.87 %
Rotamer:
Outliers : 0.00 %
Allowed : 0.00 %
Favored : 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: -1.85 (0.19), residues: 1758
helix: -1.35 (0.23), residues: 434
sheet: -0.89 (0.38), residues: 184
loop : -1.26 (0.18), residues: 1140
*********************** 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 fitting.
rotamer outliers: 0
poor density : 41
time to evaluate : 0.838
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: 0.0449
time to fit residues: 4.7982
Evaluate side-chains
41 residues out of total 1567 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 41
time to evaluate : 0.854
-------------------------------------------------------------------------------
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: 40.0000
chunk 101 optimal weight: 30.0000
chunk 78 optimal weight: 20.0000
chunk 115 optimal weight: 30.0000
chunk 174 optimal weight: 30.0000
chunk 160 optimal weight: 9.9990
chunk 138 optimal weight: 0.0670
chunk 14 optimal weight: 30.0000
chunk 107 optimal weight: 50.0000
chunk 85 optimal weight: 50.0000
chunk 110 optimal weight: 50.0000
overall best weight: 18.0132
-------------------------------------------------------------------------------
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: 0.6082
moved from start: 2.3856
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.005 0.064 5415 Z= 0.383
Angle : 1.131 20.326 5438 Z= 0.708
Chirality : 0.024 0.040 8
Planarity : 0.005 0.005 2
Dihedral : 9.904 88.634 1841
Min Nonbonded Distance : 2.142
Molprobity Statistics.
All-atom Clashscore : 38.31
Ramachandran Plot:
Outliers : 0.57 %
Allowed : 17.18 %
Favored : 82.25 %
Rotamer:
Outliers : 0.00 %
Allowed : 0.00 %
Favored : 0.00 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 1.25 %
Cis-general : 0.06 %
Twisted Proline : 1.25 %
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: -3.69 (0.18), residues: 1758
helix: -3.56 (0.19), residues: 392
sheet: -1.22 (0.49), residues: 112
loop : -2.35 (0.17), residues: 1254
********************** 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 fitting.
rotamer outliers: 0
poor density : 41
time to evaluate : 0.832
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: 0.0454
time to fit residues: 4.7878
Evaluate side-chains
41 residues out of total 1567 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 41
time to evaluate : 0.784
-------------------------------------------------------------------------------
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: 20.0000
chunk 42 optimal weight: 20.0000
chunk 128 optimal weight: 40.0000
chunk 20 optimal weight: 6.9990
chunk 38 optimal weight: 0.0270
chunk 139 optimal weight: 9.9990
chunk 58 optimal weight: 50.0000
chunk 142 optimal weight: 10.0000
chunk 17 optimal weight: 30.0000
chunk 25 optimal weight: 20.0000
chunk 122 optimal weight: 0.3980
overall best weight: 5.4846
-------------------------------------------------------------------------------
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 = 0.2865 r_free = 0.2865 target = 0.046553 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2542 r_free = 0.2542 target = 0.034502 restraints weight = 66087.022|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.2533 r_free = 0.2533 target = 0.034257 restraints weight = 76800.105|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.2526 r_free = 0.2526 target = 0.034082 restraints weight = 86697.412|
|-----------------------------------------------------------------------------|
r_work (final): 0.2493
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6335
moved from start: 2.3521
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.002 0.023 5415 Z= 0.143
Angle : 0.577 11.202 5438 Z= 0.361
Chirality : 0.018 0.034 8
Planarity : 0.001 0.001 2
Dihedral : 6.663 85.242 1841
Min Nonbonded Distance : 2.224
Molprobity Statistics.
All-atom Clashscore : 16.71
Ramachandran Plot:
Outliers : 0.23 %
Allowed : 11.55 %
Favored : 88.23 %
Rotamer:
Outliers : 0.00 %
Allowed : 0.00 %
Favored : 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: -3.14 (0.19), residues: 1758
helix: -2.56 (0.22), residues: 411
sheet: -1.60 (0.42), residues: 158
loop : -2.08 (0.18), residues: 1189
Origin is already at (0, 0, 0), no shifts will be applied
===============================================================================
Job complete
usr+sys time: 1097.98 seconds
wall clock time: 20 minutes 17.44 seconds (1217.44 seconds total)