Starting phenix.real_space_refine (version: dev)
on Sat Feb 18 06:05:24 2023 by dcliebschner
===============================================================================
Processing files:
-------------------------------------------------------------------------------
Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n9y_24264/02_2023/7n9y_24264.pdb
Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n9y_24264/02_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_24264/02_2023/7n9y_24264.map"
default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n9y_24264/02_2023/7n9y_24264.map"
model {
file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n9y_24264/02_2023/7n9y_24264.pdb"
}
default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n9y_24264/02_2023/7n9y_24264.pdb"
}
resolution = 4.8
write_initial_geo_file = False
refinement {
macro_cycles = 10
}
Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.
Validating inputs
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
Set to: 0
Set model cs if undefined
Decide on map wrapping
Map wrapping is set to: False
Normalize map: mean=0, sd=1
Input map: mean= 0.001 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
Process input model
Symmetric amino acids flipped
None
Time to flip residues: 0.02s
Monomer Library directory:
"/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/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: 5.86, per 1000 atoms: 0.78
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: 1.98
Conformation dependent library (CDL) restraints added in 2.5 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: 2.77
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: 2.21 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
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.
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: 3.860
Set stop_for_unknowns flag: 0.000
Assert model is a single copy model: 0.000
Assert all atoms have isotropic ADPs: 0.000
Construct map_model_manager: 0.000
Extract box with map and model: 12.960
Check model and map are aligned: 0.110
Process input model: 22.310
Find NCS groups from input model: 0.450
Set up NCS constraints: 0.060
Set refine NCS operators: 0.000
Set scattering table: 0.070
Adjust number of macro_cycles: 0.000
Reset NCS operators: 0.000
Extract rigid body selections: 0.000
Check and reset occupancies: 0.000
Load rotamer database and sin/cos tables:2.810
Set ADP refinement strategy: 0.000
Make a string to write initial .geo file:0.000
Internal consistency checks: 0.000
Total: 42.630
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.3255
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 : 1.072 26.844 7497 Z= 0.723
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 %
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 : 1.285
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: 0.0628
time to fit residues: 7.3841
Evaluate side-chains
47 residues out of total 2259 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 47
time to evaluate : 0.993
Switching outliers to nearest non-outliers
outliers start: 0
outliers final: 0
residues processed: 0
time to fit residues: 1.4764
-------------------------------------------------------------------------------
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: 0.3452
moved from start: 0.6349
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
Bond : 0.003 0.054 7506 Z= 0.277
Angle : 0.794 10.551 7497 Z= 0.504
Chirality : 0.000 0.000 0
Planarity : 0.000 0.000 0
Dihedral : 6.221 30.254 2496
Min Nonbonded Distance : 2.458
Molprobity Statistics.
All-atom Clashscore : 6.24
Ramachandran Plot:
Outliers : 0.36 %
Allowed : 9.09 %
Favored : 90.55 %
Rotamer Outliers : 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: -2.18 (0.16), residues: 2487
helix: -0.47 (0.23), residues: 467
sheet: -0.93 (0.33), residues: 249
loop : -1.94 (0.14), residues: 1771
*********************** 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 : 0.951
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: 0.0635
time to fit residues: 7.3250
Evaluate side-chains
47 residues out of total 2259 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 47
time to evaluate : 0.947
Switching outliers to nearest non-outliers
outliers start: 0
outliers final: 0
residues processed: 0
time to fit residues: 1.3904
-------------------------------------------------------------------------------
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: 9.9990
chunk 70 optimal weight: 4.9990
chunk 188 optimal weight: 7.9990
chunk 154 optimal weight: 7.9990
chunk 62 optimal weight: 3.9990
chunk 227 optimal weight: 6.9990
chunk 245 optimal weight: 20.0000
chunk 202 optimal weight: 5.9990
chunk 225 optimal weight: 7.9990
chunk 77 optimal weight: 5.9990
chunk 182 optimal weight: 0.0270
overall best weight: 4.2046
-------------------------------------------------------------------------------
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: 0.3460
moved from start: 1.2485
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
Bond : 0.007 0.083 7506 Z= 0.531
Angle : 1.380 15.021 7497 Z= 0.884
Chirality : 0.000 0.000 0
Planarity : 0.000 0.000 0
Dihedral : 9.593 36.607 2496
Min Nonbonded Distance : 2.286
Molprobity Statistics.
All-atom Clashscore : 24.67
Ramachandran Plot:
Outliers : 1.01 %
Allowed : 15.68 %
Favored : 83.31 %
Rotamer Outliers : 0.00 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.25 %
Twisted Proline : 0.00 %
Twisted General : 0.45 %
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: -3.82 (0.15), residues: 2487
helix: -3.48 (0.18), residues: 365
sheet: -2.10 (0.33), residues: 213
loop : -2.61 (0.13), residues: 1909
*********************** 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 : 1.139
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: 0.0679
time to fit residues: 7.9650
Evaluate side-chains
47 residues out of total 2259 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 47
time to evaluate : 1.110
Switching outliers to nearest non-outliers
outliers start: 0
outliers final: 0
residues processed: 0
time to fit residues: 1.5752
-------------------------------------------------------------------------------
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: 6.9990
chunk 170 optimal weight: 0.0870
chunk 118 optimal weight: 7.9990
chunk 25 optimal weight: 0.9990
chunk 108 optimal weight: 30.0000
chunk 152 optimal weight: 10.0000
chunk 228 optimal weight: 10.0000
chunk 241 optimal weight: 7.9990
chunk 119 optimal weight: 2.9990
chunk 216 optimal weight: 9.9990
chunk 65 optimal weight: 0.0170
overall best weight: 2.2202
-------------------------------------------------------------------------------
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: 0.3394
moved from start: 1.2996
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
Bond : 0.004 0.043 7506 Z= 0.288
Angle : 0.848 10.376 7497 Z= 0.542
Chirality : 0.000 0.000 0
Planarity : 0.000 0.000 0
Dihedral : 6.686 33.215 2496
Min Nonbonded Distance : 2.401
Molprobity Statistics.
All-atom Clashscore : 13.08
Ramachandran Plot:
Outliers : 0.36 %
Allowed : 16.20 %
Favored : 83.43 %
Rotamer Outliers : 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: -3.89 (0.15), residues: 2487
helix: -3.38 (0.18), residues: 415
sheet: -2.25 (0.33), residues: 208
loop : -2.64 (0.13), residues: 1864
*********************** 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 : 1.187
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: 0.0663
time to fit residues: 7.8911
Evaluate side-chains
47 residues out of total 2259 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 47
time to evaluate : 1.035
Switching outliers to nearest non-outliers
outliers start: 0
outliers final: 0
residues processed: 0
time to fit residues: 1.6134
-------------------------------------------------------------------------------
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: 6.9990
chunk 137 optimal weight: 8.9990
chunk 3 optimal weight: 0.0070
chunk 179 optimal weight: 10.0000
chunk 99 optimal weight: 10.0000
chunk 206 optimal weight: 10.0000
chunk 167 optimal weight: 3.9990
chunk 0 optimal weight: 5.9990
chunk 123 optimal weight: 10.0000
chunk 216 optimal weight: 9.9990
chunk 60 optimal weight: 0.0060
overall best weight: 3.4020
-------------------------------------------------------------------------------
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: 0.3397
moved from start: 1.5675
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
Bond : 0.006 0.071 7506 Z= 0.434
Angle : 1.134 10.979 7497 Z= 0.725
Chirality : 0.000 0.000 0
Planarity : 0.000 0.000 0
Dihedral : 8.506 34.667 2496
Min Nonbonded Distance : 2.359
Molprobity Statistics.
All-atom Clashscore : 24.37
Ramachandran Plot:
Outliers : 0.72 %
Allowed : 22.16 %
Favored : 77.12 %
Rotamer Outliers : 0.00 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.25 %
Twisted Proline : 0.00 %
Twisted General : 0.25 %
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: -4.48 (0.14), residues: 2487
helix: -3.92 (0.17), residues: 350
sheet: -2.42 (0.36), residues: 191
loop : -3.14 (0.12), residues: 1946
*********************** 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 : 1.213
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: 0.0699
time to fit residues: 8.3226
Evaluate side-chains
47 residues out of total 2259 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 47
time to evaluate : 1.109
Switching outliers to nearest non-outliers
outliers start: 0
outliers final: 0
residues processed: 0
time to fit residues: 1.5794
-------------------------------------------------------------------------------
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: 0.0010
chunk 217 optimal weight: 10.0000
chunk 47 optimal weight: 0.0370
chunk 141 optimal weight: 7.9990
chunk 59 optimal weight: 0.0970
chunk 241 optimal weight: 2.9990
chunk 200 optimal weight: 0.3980
chunk 111 optimal weight: 0.5980
chunk 20 optimal weight: 4.9990
chunk 80 optimal weight: 3.9990
chunk 126 optimal weight: 9.9990
overall best weight: 0.2262
-------------------------------------------------------------------------------
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: 0.3271
moved from start: 1.4746
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
Bond : 0.001 0.011 7506 Z= 0.067
Angle : 0.443 6.428 7497 Z= 0.271
Chirality : 0.000 0.000 0
Planarity : 0.000 0.000 0
Dihedral : 4.084 23.192 2496
Min Nonbonded Distance : 2.514
Molprobity Statistics.
All-atom Clashscore : 1.49
Ramachandran Plot:
Outliers : 0.40 %
Allowed : 9.77 %
Favored : 89.83 %
Rotamer Outliers : 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: -3.71 (0.15), residues: 2487
helix: -2.50 (0.21), residues: 411
sheet: -1.92 (0.38), residues: 208
loop : -2.75 (0.13), residues: 1868
*********************** 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 : 1.092
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: 0.0662
time to fit residues: 7.5765
Evaluate side-chains
47 residues out of total 2259 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 47
time to evaluate : 1.018
Switching outliers to nearest non-outliers
outliers start: 0
outliers final: 0
residues processed: 0
time to fit residues: 1.4638
-------------------------------------------------------------------------------
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: 10.0000
chunk 27 optimal weight: 2.9990
chunk 137 optimal weight: 8.9990
chunk 176 optimal weight: 9.9990
chunk 136 optimal weight: 10.0000
chunk 203 optimal weight: 5.9990
chunk 135 optimal weight: 8.9990
chunk 240 optimal weight: 2.9990
chunk 150 optimal weight: 9.9990
chunk 146 optimal weight: 9.9990
chunk 111 optimal weight: 40.0000
overall best weight: 5.9990
-------------------------------------------------------------------------------
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: 0.3433
moved from start: 1.7360
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
Bond : 0.009 0.100 7506 Z= 0.658
Angle : 1.511 11.423 7497 Z= 0.988
Chirality : 0.000 0.000 0
Planarity : 0.000 0.000 0
Dihedral : 9.874 36.731 2496
Min Nonbonded Distance : 2.260
Molprobity Statistics.
All-atom Clashscore : 46.66
Ramachandran Plot:
Outliers : 2.17 %
Allowed : 26.34 %
Favored : 71.49 %
Rotamer Outliers : 0.00 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.25 %
Twisted Proline : 1.54 %
Twisted General : 0.58 %
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: -4.98 (0.14), residues: 2487
helix: -4.30 (0.16), residues: 335
sheet: -2.64 (0.42), residues: 145
loop : -3.52 (0.12), residues: 2007
*********************** 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 : 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: 0.0632
time to fit residues: 7.3493
Evaluate side-chains
47 residues out of total 2259 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 47
time to evaluate : 1.008
Switching outliers to nearest non-outliers
outliers start: 0
outliers final: 0
residues processed: 0
time to fit residues: 1.4603
-------------------------------------------------------------------------------
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: 10.0000
chunk 96 optimal weight: 0.9990
chunk 143 optimal weight: 0.9990
chunk 72 optimal weight: 0.0020
chunk 47 optimal weight: 0.9990
chunk 46 optimal weight: 0.7980
chunk 153 optimal weight: 4.9990
chunk 164 optimal weight: 10.0000
chunk 119 optimal weight: 0.0270
chunk 22 optimal weight: 0.4980
chunk 189 optimal weight: 10.0000
overall best weight: 0.4648
-------------------------------------------------------------------------------
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: 0.3272
moved from start: 1.6315
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
Bond : 0.001 0.017 7506 Z= 0.092
Angle : 0.509 5.034 7497 Z= 0.317
Chirality : 0.000 0.000 0
Planarity : 0.000 0.000 0
Dihedral : 4.762 24.882 2496
Min Nonbonded Distance : 2.516
Molprobity Statistics.
All-atom Clashscore : 2.08
Ramachandran Plot:
Outliers : 0.36 %
Allowed : 12.63 %
Favored : 87.01 %
Rotamer Outliers : 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: -4.30 (0.15), residues: 2487
helix: -3.04 (0.21), residues: 382
sheet: -2.31 (0.39), residues: 192
loop : -3.16 (0.13), residues: 1913
*********************** 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 : 1.062
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: 0.0666
time to fit residues: 7.6730
Evaluate side-chains
47 residues out of total 2259 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 47
time to evaluate : 1.126
Switching outliers to nearest non-outliers
outliers start: 0
outliers final: 0
residues processed: 0
time to fit residues: 1.5263
-------------------------------------------------------------------------------
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: 20.0000
chunk 230 optimal weight: 9.9990
chunk 210 optimal weight: 8.9990
chunk 224 optimal weight: 10.0000
chunk 135 optimal weight: 7.9990
chunk 97 optimal weight: 0.0000
chunk 176 optimal weight: 4.9990
chunk 68 optimal weight: 2.9990
chunk 202 optimal weight: 4.9990
chunk 212 optimal weight: 5.9990
chunk 223 optimal weight: 8.9990
overall best weight: 3.7992
-------------------------------------------------------------------------------
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: 0.3385
moved from start: 1.7753
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
Bond : 0.006 0.076 7506 Z= 0.437
Angle : 1.116 8.654 7497 Z= 0.725
Chirality : 0.000 0.000 0
Planarity : 0.000 0.000 0
Dihedral : 8.180 32.573 2496
Min Nonbonded Distance : 2.408
Molprobity Statistics.
All-atom Clashscore : 28.53
Ramachandran Plot:
Outliers : 0.76 %
Allowed : 27.18 %
Favored : 72.05 %
Rotamer Outliers : 0.00 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.25 %
Twisted Proline : 0.00 %
Twisted General : 0.16 %
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: -4.72 (0.15), residues: 2487
helix: -4.02 (0.18), residues: 312
sheet: -2.41 (0.41), residues: 171
loop : -3.38 (0.12), residues: 2004
*********************** 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 : 1.118
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: 0.0690
time to fit residues: 8.1425
Evaluate side-chains
47 residues out of total 2259 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 47
time to evaluate : 1.152
Switching outliers to nearest non-outliers
outliers start: 0
outliers final: 0
residues processed: 0
time to fit residues: 1.5178
-------------------------------------------------------------------------------
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: 10.0000
chunk 144 optimal weight: 2.9990
chunk 112 optimal weight: 0.0670
chunk 165 optimal weight: 10.0000
chunk 249 optimal weight: 0.0470
chunk 229 optimal weight: 0.0030
chunk 198 optimal weight: 4.9990
chunk 20 optimal weight: 4.9990
chunk 153 optimal weight: 2.9990
chunk 121 optimal weight: 0.0670
overall best weight: 0.6366
-------------------------------------------------------------------------------
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: 0.3274
moved from start: 1.7058
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
Bond : 0.001 0.023 7506 Z= 0.104
Angle : 0.496 4.834 7497 Z= 0.311
Chirality : 0.000 0.000 0
Planarity : 0.000 0.000 0
Dihedral : 4.678 25.441 2496
Min Nonbonded Distance : 2.558
Molprobity Statistics.
All-atom Clashscore : 3.86
Ramachandran Plot:
Outliers : 0.40 %
Allowed : 12.99 %
Favored : 86.61 %
Rotamer Outliers : 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: -4.27 (0.15), residues: 2487
helix: -2.77 (0.22), residues: 393
sheet: -2.03 (0.41), residues: 181
loop : -3.22 (0.13), residues: 1913
********************** 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 : 0.992
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: 0.0637
time to fit residues: 7.2966
Evaluate side-chains
47 residues out of total 2259 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 47
time to evaluate : 1.001
Switching outliers to nearest non-outliers
outliers start: 0
outliers final: 0
residues processed: 0
time to fit residues: 1.4345
-------------------------------------------------------------------------------
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: 0.0970
chunk 211 optimal weight: 3.9990
chunk 60 optimal weight: 2.9990
chunk 182 optimal weight: 5.9990
chunk 29 optimal weight: 0.9980
chunk 55 optimal weight: 5.9990
chunk 198 optimal weight: 3.9990
chunk 83 optimal weight: 0.0470
chunk 203 optimal weight: 9.9990
chunk 25 optimal weight: 0.0270
chunk 36 optimal weight: 5.9990
overall best weight: 0.8336
-------------------------------------------------------------------------------
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 = 0.4802 r_free = 0.4802 target = 0.276509 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.4662 r_free = 0.4662 target = 0.262438 restraints weight = 36579.049|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.4662 r_free = 0.4662 target = 0.262438 restraints weight = 37377.775|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.4662 r_free = 0.4662 target = 0.262438 restraints weight = 37378.732|
|-----------------------------------------------------------------------------|
r_work (final): 0.4602
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.3064
moved from start: 1.7179
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= 0.120
Angle : 0.481 4.747 7497 Z= 0.304
Chirality : 0.000 0.000 0
Planarity : 0.000 0.000 0
Dihedral : 4.449 25.596 2496
Min Nonbonded Distance : 2.547
Molprobity Statistics.
All-atom Clashscore : 7.13
Ramachandran Plot:
Outliers : 0.36 %
Allowed : 19.38 %
Favored : 80.26 %
Rotamer Outliers : 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: -4.00 (0.15), residues: 2487
helix: -2.33 (0.24), residues: 379
sheet: -2.04 (0.40), residues: 189
loop : -3.07 (0.13), residues: 1919
===============================================================================
Job complete
usr+sys time: 1457.89 seconds
wall clock time: 26 minutes 51.87 seconds (1611.87 seconds total)