Starting phenix.real_space_refine (version: 1.21rc1)
on Thu Sep 28 15:24:35 2023 by dcliebschner
===============================================================================
Processing files:
-------------------------------------------------------------------------------
Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n9y_24264/09_2023/7n9y_24264.pdb
Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n9y_24264/09_2023/7n9y_24264.map
Processing PHIL parameters:
-------------------------------------------------------------------------------
Adding command-line PHIL:
-------------------------
refinement.macro_cycles=10
scattering_table=electron
resolution=4.8
write_initial_geo_file=False
Final processed PHIL parameters:
-------------------------------------------------------------------------------
data_manager {
real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n9y_24264/09_2023/7n9y_24264.map"
default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n9y_24264/09_2023/7n9y_24264.map"
model {
file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n9y_24264/09_2023/7n9y_24264.pdb"
}
default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n9y_24264/09_2023/7n9y_24264.pdb"
}
resolution = 4.8
write_initial_geo_file = False
refinement {
macro_cycles = 10
}
qi {
qm_restraints {
package {
program = *test
}
}
}
Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.
Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
Set to: 0
Set model cs if undefined
Decide on map wrapping
Map wrapping is set to: False
Normalize map: mean=0, sd=1
Input map: mean= 0.001 sd= 0.019
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: 2
Type Number sf(0) Gaussians
C 5010 2.51 5
N 2505 2.21 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-1.21rc1-5097/modules/chem_data/mon_lib"
Total number of atoms: 7515
Number of models: 1
Model: ""
Number of chains: 2
Chain: "B"
Number of atoms: 420
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 140, 420
Classifications: {'peptide': 140}
Incomplete info: {'n_c_alpha_c_only': 140}
Link IDs: {'PTRANS': 13, 'TRANS': 126}
Unresolved chain link angles: 152
Unresolved non-hydrogen bonds: 699
Unresolved non-hydrogen angles: 957
Unresolved non-hydrogen dihedrals: 347
Unresolved non-hydrogen chiralities: 179
Planarities with less than four sites: {'GLN:plan1': 7, 'ASP:plan': 6, 'TYR:plan': 1, 'ASN:plan1': 4, 'TRP:plan': 2, 'HIS:plan': 3, 'PHE:plan': 5, 'GLU:plan': 10, 'ARG:plan': 10}
Unresolved non-hydrogen planarities: 239
Chain: "A"
Number of atoms: 7095
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 2365, 7095
Classifications: {'peptide': 2365}
Incomplete info: {'n_c_alpha_c_only': 2365}
Link IDs: {'CIS': 6, 'PTRANS': 52, 'TRANS': 2306}
Chain breaks: 7
Unresolved chain link angles: 2416
Unresolved non-hydrogen bonds: 12299
Unresolved non-hydrogen angles: 16744
Unresolved non-hydrogen dihedrals: 6365
Unresolved non-hydrogen chiralities: 2907
Planarities with less than four sites: {'GLN:plan1': 59, 'HIS:plan': 23, 'TYR:plan': 134, 'ASN:plan1': 194, 'TRP:plan': 16, 'ASP:plan': 182, 'PHE:plan': 132, 'GLU:plan': 210, 'ARG:plan': 49}
Unresolved non-hydrogen planarities: 5119
Residues with excluded nonbonded symmetry interactions: 1674
residue:
pdb=" N SER A 2 " occ=0.00
pdb=" CA SER A 2 " occ=0.00
pdb=" C SER A 2 " occ=0.00
residue:
pdb=" N LEU A 3 " occ=0.00
pdb=" CA LEU A 3 " occ=0.00
pdb=" C LEU A 3 " occ=0.00
residue:
pdb=" N VAL A 4 " occ=0.00
pdb=" CA VAL A 4 " occ=0.00
pdb=" C VAL A 4 " occ=0.00
residue:
pdb=" N ASN A 5 " occ=0.00
pdb=" CA ASN A 5 " occ=0.00
pdb=" C ASN A 5 " occ=0.00
residue:
pdb=" N ARG A 6 " occ=0.00
pdb=" CA ARG A 6 " occ=0.00
pdb=" C ARG A 6 " occ=0.00
residue:
pdb=" N LYS A 7 " occ=0.00
pdb=" CA LYS A 7 " occ=0.00
pdb=" C LYS A 7 " occ=0.00
residue:
pdb=" N GLN A 8 " occ=0.00
pdb=" CA GLN A 8 " occ=0.00
pdb=" C GLN A 8 " occ=0.00
residue:
pdb=" N LEU A 9 " occ=0.00
pdb=" CA LEU A 9 " occ=0.00
pdb=" C LEU A 9 " occ=0.00
residue:
pdb=" N GLU A 10 " occ=0.00
pdb=" CA GLU A 10 " occ=0.00
pdb=" C GLU A 10 " occ=0.00
residue:
pdb=" N LYS A 11 " occ=0.00
pdb=" CA LYS A 11 " occ=0.00
pdb=" C LYS A 11 " occ=0.00
residue:
pdb=" N MET A 12 " occ=0.00
pdb=" CA MET A 12 " occ=0.00
pdb=" C MET A 12 " occ=0.00
residue:
pdb=" N ALA A 13 " occ=0.00
pdb=" CA ALA A 13 " occ=0.00
pdb=" C ALA A 13 " occ=0.00
... (remaining 1662 not shown)
Time building chain proxies: 5.64, per 1000 atoms: 0.75
Number of scatterers: 7515
At special positions: 0
Unit cell: (144.64, 136.73, 241.82, 90, 90, 90)
Space group: P 1 (No. 1)
Number of sites at special positions: 0
Number of scattering types: 2
Type Number sf(0)
N 2505 7.00
C 5010 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: 1.93
Conformation dependent library (CDL) restraints added in 2.4 seconds
4970 Ramachandran restraints generated.
2485 Oldfield, 0 Emsley, 2485 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: 2.85
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: 2.18 seconds
NOTE: a complete listing of the restraints can be obtained by requesting
output of .geo file.
Histogram of bond lengths:
1.32 - 1.64: 7504
1.64 - 1.96: 1
1.96 - 2.28: 0
2.28 - 2.60: 0
2.60 - 2.92: 1
Bond restraints: 7506
Sorted by residual:
bond pdb=" C TRP A1742 "
pdb=" N SER A1743 "
ideal model delta sigma weight residual
1.332 2.920 -1.587 1.40e-02 5.10e+03 1.29e+04
bond pdb=" CA ASN A 422 "
pdb=" C ASN A 422 "
ideal model delta sigma weight residual
1.526 1.865 -0.338 1.03e-02 9.43e+03 1.08e+03
bond pdb=" C ASN A 422 "
pdb=" N ASP A 423 "
ideal model delta sigma weight residual
1.331 1.398 -0.067 1.36e-02 5.41e+03 2.42e+01
bond pdb=" N ASN A 422 "
pdb=" CA ASN A 422 "
ideal model delta sigma weight residual
1.463 1.492 -0.029 1.27e-02 6.20e+03 5.21e+00
bond pdb=" N ASP A 614 "
pdb=" CA ASP A 614 "
ideal model delta sigma weight residual
1.457 1.475 -0.018 1.29e-02 6.01e+03 1.86e+00
... (remaining 7501 not shown)
Histogram of bond angle deviations from ideal:
89.45 - 97.44: 1
97.44 - 105.43: 2
105.43 - 113.42: 2364
113.42 - 121.41: 3713
121.41 - 129.40: 1417
Bond angle restraints: 7497
Sorted by residual:
angle pdb=" CA TRP A1742 "
pdb=" C TRP A1742 "
pdb=" N SER A1743 "
ideal model delta sigma weight residual
116.29 89.45 26.84 1.30e+00 5.92e-01 4.26e+02
angle pdb=" C TRP A1742 "
pdb=" N SER A1743 "
pdb=" CA SER A1743 "
ideal model delta sigma weight residual
121.54 97.82 23.72 1.91e+00 2.74e-01 1.54e+02
angle pdb=" CA ASN A 422 "
pdb=" C ASN A 422 "
pdb=" N ASP A 423 "
ideal model delta sigma weight residual
116.26 126.63 -10.37 1.27e+00 6.20e-01 6.67e+01
angle pdb=" N ASN A 422 "
pdb=" CA ASN A 422 "
pdb=" C ASN A 422 "
ideal model delta sigma weight residual
107.23 119.24 -12.01 1.67e+00 3.59e-01 5.17e+01
angle pdb=" N ILE A1085 "
pdb=" CA ILE A1085 "
pdb=" C ILE A1085 "
ideal model delta sigma weight residual
113.71 108.66 5.05 9.50e-01 1.11e+00 2.83e+01
... (remaining 7492 not shown)
Histogram of dihedral angle deviations from ideal:
0.00 - 6.23: 1836
6.23 - 12.46: 536
12.46 - 18.69: 106
18.69 - 24.92: 16
24.92 - 31.15: 2
Dihedral angle restraints: 2496
sinusoidal: 0
harmonic: 2496
Sorted by residual:
dihedral pdb=" CA ASP A 421 "
pdb=" C ASP A 421 "
pdb=" N ASN A 422 "
pdb=" CA ASN A 422 "
ideal model delta harmonic sigma weight residual
180.00 148.85 31.15 0 5.00e+00 4.00e-02 3.88e+01
dihedral pdb=" CA THR A1713 "
pdb=" C THR A1713 "
pdb=" N TYR A1714 "
pdb=" CA TYR A1714 "
ideal model delta harmonic sigma weight residual
180.00 -150.44 -29.56 0 5.00e+00 4.00e-02 3.50e+01
dihedral pdb=" CA GLU A1947 "
pdb=" C GLU A1947 "
pdb=" N TRP A1948 "
pdb=" CA TRP A1948 "
ideal model delta harmonic sigma weight residual
180.00 156.23 23.77 0 5.00e+00 4.00e-02 2.26e+01
... (remaining 2493 not shown)
Chirality restraints: 0
Planarity restraints: 0
Histogram of nonbonded interaction distances:
2.54 - 3.01: 1577
3.01 - 3.48: 2974
3.48 - 3.96: 5393
3.96 - 4.43: 6288
4.43 - 4.90: 10995
Nonbonded interactions: 27227
Sorted by model distance:
nonbonded pdb=" N ARG A 165 "
pdb=" N PHE A 166 "
model vdw
2.538 2.560
nonbonded pdb=" N GLU A 904 "
pdb=" N THR A 905 "
model vdw
2.562 2.560
nonbonded pdb=" N ASN A1941 "
pdb=" N TYR A1942 "
model vdw
2.571 2.560
nonbonded pdb=" N SER A 881 "
pdb=" N HIS A 882 "
model vdw
2.577 2.560
nonbonded pdb=" N ILE A1193 "
pdb=" N THR A1194 "
model vdw
2.577 2.560
... (remaining 27222 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=0.00 max=1.00 mean=0.33
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: 2.660
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: 13.040
Check model and map are aligned: 0.110
Set scattering table: 0.070
Process input model: 22.370
Find NCS groups from input model: 0.440
Set up NCS constraints: 0.050
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:2.650
Set ADP refinement strategy: 0.000
Make a string to write initial .geo file:0.000
Internal consistency checks: 0.000
Total: 41.410
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.3280
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 : 0.019 1.587 7506 Z= 1.377
Angle : 1.073 26.844 7497 Z= 0.724
Chirality : 0.000 0.000 0
Planarity : 0.000 0.000 0
Dihedral : 6.040 31.146 2496
Min Nonbonded Distance : 2.538
Molprobity Statistics.
All-atom Clashscore : 0.59
Ramachandran Plot:
Outliers : 0.32 %
Allowed : 8.53 %
Favored : 91.15 %
Rotamer:
Outliers : 0.00 %
Allowed : 0.00 %
Favored : 0.00 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.25 %
Twisted Proline : 0.00 %
Twisted General : 0.04 %
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 (0.16), residues: 2485
helix: -0.12 (0.21), residues: 558
sheet: -1.32 (0.27), residues: 354
loop : -1.84 (0.15), residues: 1573
*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
4970 Ramachandran restraints generated.
2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
4970 Ramachandran restraints generated.
2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
47 residues out of total 2259 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 47
time to evaluate : 1.063
Fit side-chains
TARDY: cannot create tardy model for: "MET B 459 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 493 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 530 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 12 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 37 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 176 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 283 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 289 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 314 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 321 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 337 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 366 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 436 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 447 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 448 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 483 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 489 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 516 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 700 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 727 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 820 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 985 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1067 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1144 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1145 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1172 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1220 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1332 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1437 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1499 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1569 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1582 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1588 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1655 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1752 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1830 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1831 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1955 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1985 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2005 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2025 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2117 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2215 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2251 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2271 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2282 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2291 " (corrupted residue). Skipping it.
outliers start: 0
outliers final: 0
residues processed: 47
average time/residue: 0.0688
time to fit residues: 7.9039
Evaluate side-chains
47 residues out of total 2259 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 47
time to evaluate : 1.100
Switching outliers to nearest non-outliers
outliers start: 0
outliers final: 0
residues processed: 0
time to fit residues: 1.5312
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 250
random chunks:
chunk 211 optimal weight: 20.0000
chunk 189 optimal weight: 6.9990
chunk 105 optimal weight: 0.4980
chunk 64 optimal weight: 9.9990
chunk 127 optimal weight: 0.3980
chunk 101 optimal weight: 0.8980
chunk 195 optimal weight: 10.0000
chunk 75 optimal weight: 10.0000
chunk 119 optimal weight: 0.0470
chunk 145 optimal weight: 5.9990
chunk 227 optimal weight: 9.9990
overall best weight: 1.5680
-------------------------------------------------------------------------------
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: 0.3476
moved from start: 0.6023
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.024 7506 Z= 0.218
Angle : 0.787 11.928 7497 Z= 0.498
Chirality : 0.000 0.000 0
Planarity : 0.000 0.000 0
Dihedral : 6.090 29.069 2496
Min Nonbonded Distance : 2.457
Molprobity Statistics.
All-atom Clashscore : 4.75
Ramachandran Plot:
Outliers : 0.36 %
Allowed : 8.97 %
Favored : 90.67 %
Rotamer:
Outliers : 0.00 %
Allowed : 0.00 %
Favored : 0.00 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.25 %
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: -2.14 (0.16), residues: 2487
helix: -0.45 (0.23), residues: 478
sheet: -0.89 (0.34), residues: 255
loop : -1.91 (0.14), residues: 1754
*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
4974 Ramachandran restraints generated.
2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
4974 Ramachandran restraints generated.
2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
47 residues out of total 2259 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 47
time to evaluate : 1.072
Fit side-chains
TARDY: cannot create tardy model for: "MET B 459 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 493 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 530 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 12 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 37 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 176 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 283 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 289 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 314 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 321 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 337 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 366 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 436 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 447 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 448 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 483 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 489 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 516 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 700 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 727 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 820 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 985 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1067 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1144 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1145 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1172 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1220 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1332 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1437 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1499 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1569 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1582 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1588 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1655 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1752 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1830 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1831 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1955 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1985 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2005 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2025 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2117 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2215 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2251 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2271 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2282 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2291 " (corrupted residue). Skipping it.
outliers start: 0
outliers final: 0
residues processed: 47
average time/residue: 0.0687
time to fit residues: 8.3074
Evaluate side-chains
47 residues out of total 2259 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 47
time to evaluate : 1.069
Switching outliers to nearest non-outliers
outliers start: 0
outliers final: 0
residues processed: 0
time to fit residues: 1.5260
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 250
random chunks:
chunk 126 optimal weight: 10.0000
chunk 70 optimal weight: 0.9980
chunk 188 optimal weight: 5.9990
chunk 154 optimal weight: 7.9990
chunk 62 optimal weight: 3.9990
chunk 227 optimal weight: 5.9990
chunk 245 optimal weight: 3.9990
chunk 202 optimal weight: 5.9990
chunk 225 optimal weight: 8.9990
chunk 77 optimal weight: 1.9990
chunk 182 optimal weight: 0.0170
overall best weight: 2.2024
-------------------------------------------------------------------------------
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: 0.3447
moved from start: 1.0401
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.004 0.038 7506 Z= 0.288
Angle : 0.908 8.799 7497 Z= 0.584
Chirality : 0.000 0.000 0
Planarity : 0.000 0.000 0
Dihedral : 7.025 34.321 2496
Min Nonbonded Distance : 2.397
Molprobity Statistics.
All-atom Clashscore : 14.56
Ramachandran Plot:
Outliers : 0.44 %
Allowed : 11.78 %
Favored : 87.78 %
Rotamer:
Outliers : 0.00 %
Allowed : 0.00 %
Favored : 0.00 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.25 %
Twisted Proline : 0.00 %
Twisted General : 0.08 %
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 (0.15), residues: 2487
helix: -1.84 (0.22), residues: 429
sheet: -1.48 (0.30), residues: 273
loop : -2.22 (0.14), residues: 1785
*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
4974 Ramachandran restraints generated.
2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
4974 Ramachandran restraints generated.
2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
47 residues out of total 2259 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 47
time to evaluate : 1.009
Fit side-chains
TARDY: cannot create tardy model for: "MET B 459 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 493 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 530 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 12 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 37 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 176 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 283 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 289 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 314 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 321 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 337 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 366 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 436 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 447 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 448 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 483 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 489 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 516 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 700 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 727 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 820 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 985 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1067 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1144 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1145 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1172 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1220 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1332 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1437 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1499 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1569 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1582 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1588 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1655 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1752 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1830 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1831 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1955 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1985 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2005 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2025 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2117 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2215 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2251 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2271 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2282 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2291 " (corrupted residue). Skipping it.
outliers start: 0
outliers final: 0
residues processed: 47
average time/residue: 0.0627
time to fit residues: 7.3099
Evaluate side-chains
47 residues out of total 2259 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 47
time to evaluate : 1.028
Switching outliers to nearest non-outliers
outliers start: 0
outliers final: 0
residues processed: 0
time to fit residues: 1.4849
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 250
random chunks:
chunk 224 optimal weight: 3.9990
chunk 170 optimal weight: 2.9990
chunk 118 optimal weight: 20.0000
chunk 25 optimal weight: 0.3980
chunk 108 optimal weight: 30.0000
chunk 152 optimal weight: 5.9990
chunk 228 optimal weight: 0.1980
chunk 241 optimal weight: 4.9990
chunk 119 optimal weight: 0.0040
chunk 216 optimal weight: 10.0000
chunk 65 optimal weight: 3.9990
overall best weight: 1.5196
-------------------------------------------------------------------------------
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: 0.3407
moved from start: 1.1526
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.021 7506 Z= 0.196
Angle : 0.656 8.803 7497 Z= 0.417
Chirality : 0.000 0.000 0
Planarity : 0.000 0.000 0
Dihedral : 5.389 24.448 2496
Min Nonbonded Distance : 2.477
Molprobity Statistics.
All-atom Clashscore : 8.92
Ramachandran Plot:
Outliers : 0.36 %
Allowed : 11.18 %
Favored : 88.46 %
Rotamer:
Outliers : 0.00 %
Allowed : 0.00 %
Favored : 0.00 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.25 %
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: -2.97 (0.15), residues: 2487
helix: -1.77 (0.22), residues: 457
sheet: -1.36 (0.32), residues: 253
loop : -2.28 (0.14), residues: 1777
*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
4974 Ramachandran restraints generated.
2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
4974 Ramachandran restraints generated.
2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
47 residues out of total 2259 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 47
time to evaluate : 1.055
Fit side-chains
TARDY: cannot create tardy model for: "MET B 459 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 493 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 530 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 12 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 37 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 176 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 283 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 289 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 314 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 321 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 337 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 366 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 436 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 447 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 448 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 483 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 489 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 516 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 700 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 727 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 820 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 985 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1067 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1144 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1145 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1172 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1220 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1332 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1437 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1499 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1569 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1582 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1588 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1655 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1752 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1830 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1831 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1955 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1985 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2005 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2025 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2117 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2215 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2251 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2271 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2282 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2291 " (corrupted residue). Skipping it.
outliers start: 0
outliers final: 0
residues processed: 47
average time/residue: 0.0689
time to fit residues: 8.0727
Evaluate side-chains
47 residues out of total 2259 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 47
time to evaluate : 1.145
Switching outliers to nearest non-outliers
outliers start: 0
outliers final: 0
residues processed: 0
time to fit residues: 1.5199
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 250
random chunks:
chunk 201 optimal weight: 10.0000
chunk 137 optimal weight: 9.9990
chunk 3 optimal weight: 0.0980
chunk 179 optimal weight: 9.9990
chunk 99 optimal weight: 4.9990
chunk 206 optimal weight: 0.0670
chunk 167 optimal weight: 2.9990
chunk 0 optimal weight: 6.9990
chunk 123 optimal weight: 2.9990
chunk 216 optimal weight: 5.9990
chunk 60 optimal weight: 2.9990
overall best weight: 1.8324
-------------------------------------------------------------------------------
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: 0.3402
moved from start: 1.3316
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.038 7506 Z= 0.243
Angle : 0.747 8.658 7497 Z= 0.477
Chirality : 0.000 0.000 0
Planarity : 0.000 0.000 0
Dihedral : 6.159 27.516 2496
Min Nonbonded Distance : 2.451
Molprobity Statistics.
All-atom Clashscore : 13.08
Ramachandran Plot:
Outliers : 0.32 %
Allowed : 14.72 %
Favored : 84.96 %
Rotamer:
Outliers : 0.00 %
Allowed : 0.00 %
Favored : 0.00 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.25 %
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: -3.39 (0.15), residues: 2487
helix: -2.52 (0.21), residues: 429
sheet: -1.83 (0.37), residues: 192
loop : -2.42 (0.13), residues: 1866
*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
4974 Ramachandran restraints generated.
2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
4974 Ramachandran restraints generated.
2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
47 residues out of total 2259 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 47
time to evaluate : 1.090
Fit side-chains
TARDY: cannot create tardy model for: "MET B 459 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 493 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 530 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 12 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 37 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 176 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 283 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 289 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 314 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 321 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 337 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 366 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 436 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 447 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 448 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 483 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 489 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 516 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 700 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 727 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 820 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 985 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1067 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1144 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1145 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1172 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1220 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1332 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1437 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1499 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1569 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1582 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1588 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1655 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1752 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1830 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1831 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1955 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1985 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2005 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2025 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2117 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2215 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2251 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2271 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2282 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2291 " (corrupted residue). Skipping it.
outliers start: 0
outliers final: 0
residues processed: 47
average time/residue: 0.0652
time to fit residues: 7.5957
Evaluate side-chains
47 residues out of total 2259 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 47
time to evaluate : 1.120
Switching outliers to nearest non-outliers
outliers start: 0
outliers final: 0
residues processed: 0
time to fit residues: 1.6219
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 250
random chunks:
chunk 81 optimal weight: 0.0470
chunk 217 optimal weight: 9.9990
chunk 47 optimal weight: 0.0050
chunk 141 optimal weight: 8.9990
chunk 59 optimal weight: 0.0770
chunk 241 optimal weight: 7.9990
chunk 200 optimal weight: 3.9990
chunk 111 optimal weight: 20.0000
chunk 20 optimal weight: 5.9990
chunk 80 optimal weight: 0.0060
chunk 126 optimal weight: 4.9990
overall best weight: 0.8268
-------------------------------------------------------------------------------
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: 0.3360
moved from start: 1.3237
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.002 0.019 7506 Z= 0.114
Angle : 0.466 7.402 7497 Z= 0.293
Chirality : 0.000 0.000 0
Planarity : 0.000 0.000 0
Dihedral : 4.226 22.366 2496
Min Nonbonded Distance : 2.513
Molprobity Statistics.
All-atom Clashscore : 6.24
Ramachandran Plot:
Outliers : 0.28 %
Allowed : 10.82 %
Favored : 88.90 %
Rotamer:
Outliers : 0.00 %
Allowed : 0.00 %
Favored : 0.00 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.25 %
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: -3.05 (0.16), residues: 2487
helix: -1.65 (0.23), residues: 462
sheet: -1.72 (0.36), residues: 230
loop : -2.34 (0.14), residues: 1795
*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
4974 Ramachandran restraints generated.
2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
4974 Ramachandran restraints generated.
2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
47 residues out of total 2259 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 47
time to evaluate : 0.973
Fit side-chains
TARDY: cannot create tardy model for: "MET B 459 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 493 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 530 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 12 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 37 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 176 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 283 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 289 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 314 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 321 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 337 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 366 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 436 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 447 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 448 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 483 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 489 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 516 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 700 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 727 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 820 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 985 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1067 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1144 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1145 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1172 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1220 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1332 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1437 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1499 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1569 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1582 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1588 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1655 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1752 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1830 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1831 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1955 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1985 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2005 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2025 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2117 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2215 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2251 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2271 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2282 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2291 " (corrupted residue). Skipping it.
outliers start: 0
outliers final: 0
residues processed: 47
average time/residue: 0.0644
time to fit residues: 7.4914
Evaluate side-chains
47 residues out of total 2259 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 47
time to evaluate : 0.960
Switching outliers to nearest non-outliers
outliers start: 0
outliers final: 0
residues processed: 0
time to fit residues: 1.4731
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 250
random chunks:
chunk 233 optimal weight: 6.9990
chunk 27 optimal weight: 3.9990
chunk 137 optimal weight: 9.9990
chunk 176 optimal weight: 9.9990
chunk 136 optimal weight: 10.0000
chunk 203 optimal weight: 4.9990
chunk 135 optimal weight: 3.9990
chunk 240 optimal weight: 4.9990
chunk 150 optimal weight: 9.9990
chunk 146 optimal weight: 9.9990
chunk 111 optimal weight: 50.0000
overall best weight: 4.9990
-------------------------------------------------------------------------------
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: 0.3448
moved from start: 1.6526
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.008 0.093 7506 Z= 0.566
Angle : 1.380 15.889 7497 Z= 0.894
Chirality : 0.000 0.000 0
Planarity : 0.000 0.000 0
Dihedral : 9.419 35.578 2496
Min Nonbonded Distance : 2.319
Molprobity Statistics.
All-atom Clashscore : 38.63
Ramachandran Plot:
Outliers : 1.69 %
Allowed : 22.40 %
Favored : 75.91 %
Rotamer:
Outliers : 0.00 %
Allowed : 0.00 %
Favored : 0.00 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.25 %
Twisted Proline : 0.00 %
Twisted General : 0.33 %
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: -4.50 (0.14), residues: 2487
helix: -3.99 (0.18), residues: 333
sheet: -2.13 (0.43), residues: 142
loop : -3.18 (0.12), residues: 2012
*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
4974 Ramachandran restraints generated.
2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
4974 Ramachandran restraints generated.
2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
47 residues out of total 2259 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 47
time to evaluate : 0.985
Fit side-chains
TARDY: cannot create tardy model for: "MET B 459 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 493 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 530 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 12 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 37 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 176 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 283 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 289 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 314 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 321 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 337 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 366 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 436 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 447 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 448 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 483 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 489 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 516 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 700 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 727 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 820 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 985 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1067 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1144 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1145 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1172 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1220 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1332 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1437 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1499 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1569 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1582 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1588 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1655 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1752 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1830 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1831 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1955 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1985 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2005 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2025 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2117 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2215 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2251 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2271 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2282 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2291 " (corrupted residue). Skipping it.
outliers start: 0
outliers final: 0
residues processed: 47
average time/residue: 0.0634
time to fit residues: 7.4755
Evaluate side-chains
47 residues out of total 2259 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 47
time to evaluate : 1.041
Switching outliers to nearest non-outliers
outliers start: 0
outliers final: 0
residues processed: 0
time to fit residues: 1.5319
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 250
random chunks:
chunk 149 optimal weight: 8.9990
chunk 96 optimal weight: 0.7980
chunk 143 optimal weight: 9.9990
chunk 72 optimal weight: 5.9990
chunk 47 optimal weight: 0.0870
chunk 46 optimal weight: 0.9980
chunk 153 optimal weight: 2.9990
chunk 164 optimal weight: 9.9990
chunk 119 optimal weight: 0.0040
chunk 22 optimal weight: 1.9990
chunk 189 optimal weight: 0.5980
overall best weight: 0.4970
-------------------------------------------------------------------------------
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: 0.3321
moved from start: 1.5629
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.001 0.018 7506 Z= 0.090
Angle : 0.515 7.531 7497 Z= 0.317
Chirality : 0.000 0.000 0
Planarity : 0.000 0.000 0
Dihedral : 4.691 21.212 2496
Min Nonbonded Distance : 2.487
Molprobity Statistics.
All-atom Clashscore : 4.16
Ramachandran Plot:
Outliers : 0.40 %
Allowed : 11.42 %
Favored : 88.18 %
Rotamer:
Outliers : 0.00 %
Allowed : 0.00 %
Favored : 0.00 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.25 %
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: -3.87 (0.15), residues: 2487
helix: -3.02 (0.21), residues: 385
sheet: -2.02 (0.38), residues: 199
loop : -2.77 (0.13), residues: 1903
*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
4974 Ramachandran restraints generated.
2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
4974 Ramachandran restraints generated.
2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
47 residues out of total 2259 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 47
time to evaluate : 1.141
Fit side-chains
TARDY: cannot create tardy model for: "MET B 459 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 493 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 530 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 12 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 37 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 176 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 283 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 289 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 314 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 321 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 337 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 366 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 436 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 447 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 448 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 483 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 489 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 516 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 700 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 727 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 820 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 985 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1067 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1144 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1145 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1172 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1220 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1332 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1437 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1499 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1569 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1582 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1588 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1655 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1752 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1830 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1831 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1955 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1985 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2005 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2025 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2117 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2215 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2251 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2271 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2282 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2291 " (corrupted residue). Skipping it.
outliers start: 0
outliers final: 0
residues processed: 47
average time/residue: 0.0633
time to fit residues: 7.3827
Evaluate side-chains
47 residues out of total 2259 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 47
time to evaluate : 1.164
Switching outliers to nearest non-outliers
outliers start: 0
outliers final: 0
residues processed: 0
time to fit residues: 1.6491
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 250
random chunks:
chunk 219 optimal weight: 10.0000
chunk 230 optimal weight: 9.9990
chunk 210 optimal weight: 8.9990
chunk 224 optimal weight: 6.9990
chunk 135 optimal weight: 7.9990
chunk 97 optimal weight: 0.0030
chunk 176 optimal weight: 0.9990
chunk 68 optimal weight: 3.9990
chunk 202 optimal weight: 4.9990
chunk 212 optimal weight: 6.9990
chunk 223 optimal weight: 7.9990
overall best weight: 3.3998
-------------------------------------------------------------------------------
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: 0.3408
moved from start: 1.6977
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.005 0.068 7506 Z= 0.393
Angle : 1.037 10.909 7497 Z= 0.672
Chirality : 0.000 0.000 0
Planarity : 0.000 0.000 0
Dihedral : 7.638 29.297 2496
Min Nonbonded Distance : 2.422
Molprobity Statistics.
All-atom Clashscore : 24.07
Ramachandran Plot:
Outliers : 0.56 %
Allowed : 24.45 %
Favored : 74.99 %
Rotamer:
Outliers : 0.00 %
Allowed : 0.00 %
Favored : 0.00 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.25 %
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: -4.46 (0.14), residues: 2487
helix: -3.82 (0.19), residues: 359
sheet: -2.40 (0.41), residues: 166
loop : -3.14 (0.12), residues: 1962
*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
4974 Ramachandran restraints generated.
2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
4974 Ramachandran restraints generated.
2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
47 residues out of total 2259 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 47
time to evaluate : 1.135
Fit side-chains
TARDY: cannot create tardy model for: "MET B 459 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 493 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 530 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 12 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 37 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 176 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 283 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 289 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 314 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 321 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 337 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 366 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 436 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 447 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 448 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 483 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 489 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 516 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 700 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 727 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 820 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 985 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1067 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1144 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1145 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1172 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1220 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1332 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1437 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1499 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1569 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1582 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1588 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1655 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1752 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1830 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1831 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1955 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1985 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2005 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2025 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2117 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2215 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2251 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2271 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2282 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2291 " (corrupted residue). Skipping it.
outliers start: 0
outliers final: 0
residues processed: 47
average time/residue: 0.0673
time to fit residues: 7.8671
Evaluate side-chains
47 residues out of total 2259 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 47
time to evaluate : 1.043
Switching outliers to nearest non-outliers
outliers start: 0
outliers final: 0
residues processed: 0
time to fit residues: 1.4471
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 250
random chunks:
chunk 147 optimal weight: 4.9990
chunk 237 optimal weight: 8.9990
chunk 144 optimal weight: 3.9990
chunk 112 optimal weight: 0.2980
chunk 165 optimal weight: 20.0000
chunk 249 optimal weight: 3.9990
chunk 229 optimal weight: 3.9990
chunk 198 optimal weight: 4.9990
chunk 20 optimal weight: 4.9990
chunk 153 optimal weight: 4.9990
chunk 121 optimal weight: 0.0770
overall best weight: 2.4744
-------------------------------------------------------------------------------
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: 0.3366
moved from start: 1.7324
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.004 0.057 7506 Z= 0.299
Angle : 0.833 7.679 7497 Z= 0.539
Chirality : 0.000 0.000 0
Planarity : 0.000 0.000 0
Dihedral : 6.588 27.140 2496
Min Nonbonded Distance : 2.457
Molprobity Statistics.
All-atom Clashscore : 16.05
Ramachandran Plot:
Outliers : 0.48 %
Allowed : 20.39 %
Favored : 79.13 %
Rotamer:
Outliers : 0.00 %
Allowed : 0.00 %
Favored : 0.00 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.25 %
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: -4.52 (0.14), residues: 2487
helix: -3.82 (0.18), residues: 366
sheet: -2.18 (0.40), residues: 168
loop : -3.20 (0.12), residues: 1953
********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
4974 Ramachandran restraints generated.
2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
4974 Ramachandran restraints generated.
2487 Oldfield, 0 Emsley, 2487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
47 residues out of total 2259 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 47
time to evaluate : 1.083
Fit side-chains
TARDY: cannot create tardy model for: "MET B 459 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 493 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 530 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 12 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 37 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 176 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 283 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 289 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 314 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 321 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 337 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 366 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 436 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 447 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 448 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 483 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 489 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 516 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 700 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 727 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 820 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A 985 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1067 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1144 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1145 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1172 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1220 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1332 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1437 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1499 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1569 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1582 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1588 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1655 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1752 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1830 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1831 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1955 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A1985 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2005 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2025 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2117 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2215 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2251 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2271 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2282 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET A2291 " (corrupted residue). Skipping it.
outliers start: 0
outliers final: 0
residues processed: 47
average time/residue: 0.0697
time to fit residues: 7.9244
Evaluate side-chains
47 residues out of total 2259 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 47
time to evaluate : 0.982
Switching outliers to nearest non-outliers
outliers start: 0
outliers final: 0
residues processed: 0
time to fit residues: 1.6041
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 250
random chunks:
chunk 157 optimal weight: 0.8980
chunk 211 optimal weight: 2.9990
chunk 60 optimal weight: 0.0370
chunk 182 optimal weight: 4.9990
chunk 29 optimal weight: 7.9990
chunk 55 optimal weight: 0.0980
chunk 198 optimal weight: 6.9990
chunk 83 optimal weight: 6.9990
chunk 203 optimal weight: 0.7980
chunk 25 optimal weight: 4.9990
chunk 36 optimal weight: 5.9990
overall best weight: 0.9660
-------------------------------------------------------------------------------
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 = 0.4797 r_free = 0.4797 target = 0.276224 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4656 r_free = 0.4656 target = 0.262375 restraints weight = 36717.602|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 17)----------------|
| r_work = 0.4656 r_free = 0.4656 target = 0.262375 restraints weight = 37299.321|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.4656 r_free = 0.4656 target = 0.262375 restraints weight = 37300.746|
|-----------------------------------------------------------------------------|
r_work (final): 0.4599
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.3078
moved from start: 1.7161
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.002 0.029 7506 Z= 0.132
Angle : 0.528 4.624 7497 Z= 0.336
Chirality : 0.000 0.000 0
Planarity : 0.000 0.000 0
Dihedral : 4.811 20.911 2496
Min Nonbonded Distance : 2.550
Molprobity Statistics.
All-atom Clashscore : 7.43
Ramachandran Plot:
Outliers : 0.48 %
Allowed : 18.17 %
Favored : 81.34 %
Rotamer:
Outliers : 0.00 %
Allowed : 0.00 %
Favored : 0.00 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.25 %
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: -4.24 (0.15), residues: 2487
helix: -3.10 (0.20), residues: 411
sheet: -1.90 (0.41), residues: 183
loop : -3.12 (0.13), residues: 1893
Origin is already at (0, 0, 0), no shifts will be applied
===============================================================================
Job complete
usr+sys time: 1439.91 seconds
wall clock time: 26 minutes 1.81 seconds (1561.81 seconds total)