Starting phenix.real_space_refine (version: 1.21rc1)
on Thu Apr 20 12:21:05 2023 by dcliebschner
===============================================================================
Processing files:
-------------------------------------------------------------------------------
Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n95_24250/04_2023/7n95_24250.pdb
Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n95_24250/04_2023/7n95_24250.map
Processing PHIL parameters:
-------------------------------------------------------------------------------
Adding command-line PHIL:
-------------------------
refinement.macro_cycles=10
scattering_table=electron
resolution=4.1
write_initial_geo_file=False
Final processed PHIL parameters:
-------------------------------------------------------------------------------
data_manager {
real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n95_24250/04_2023/7n95_24250.map"
default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n95_24250/04_2023/7n95_24250.map"
model {
file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n95_24250/04_2023/7n95_24250.pdb"
}
default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n95_24250/04_2023/7n95_24250.pdb"
}
resolution = 4.1
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= 0.018
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 4866 2.51 5
N 2433 2.21 5
sf(0) = scattering factor at diffraction angle 0.
Process input model
Symmetric amino acids flipped
None
Time to flip residues: 0.02s
Monomer Library directory:
"/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib"
Total number of atoms: 7299
Number of models: 1
Model: ""
Number of chains: 2
Chain: "B"
Number of atoms: 363
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 121, 363
Classifications: {'peptide': 121}
Incomplete info: {'n_c_alpha_c_only': 121}
Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 110}
Unresolved chain link angles: 130
Unresolved non-hydrogen bonds: 629
Unresolved non-hydrogen angles: 854
Unresolved non-hydrogen dihedrals: 335
Unresolved non-hydrogen chiralities: 141
Planarities with less than four sites: {'GLN:plan1': 10, 'ARG:plan': 7, 'TYR:plan': 3, 'ASN:plan1': 5, 'TRP:plan': 1, 'HIS:plan': 6, 'PHE:plan': 7, 'GLU:plan': 9, 'ASP:plan': 3}
Unresolved non-hydrogen planarities: 262
Chain: "A"
Number of atoms: 6936
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 2312, 6936
Classifications: {'peptide': 2312}
Incomplete info: {'n_c_alpha_c_only': 2312}
Link IDs: {'PCIS': 1, 'PTRANS': 48, 'TRANS': 2262}
Chain breaks: 2
Unresolved chain link angles: 2360
Unresolved non-hydrogen bonds: 12070
Unresolved non-hydrogen angles: 16430
Unresolved non-hydrogen dihedrals: 6269
Unresolved non-hydrogen chiralities: 2838
Planarities with less than four sites: {'GLN:plan1': 58, 'HIS:plan': 23, 'TYR:plan': 134, 'ASN:plan1': 192, 'TRP:plan': 16, 'ASP:plan': 179, 'PHE:plan': 131, 'GLU:plan': 207, 'ARG:plan': 47}
Unresolved non-hydrogen planarities: 5066
Time building chain proxies: 5.49, per 1000 atoms: 0.75
Number of scatterers: 7299
At special positions: 0
Unit cell: (132.581, 145.309, 255.617, 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 2433 7.00
C 4866 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: 1.86
Conformation dependent library (CDL) restraints added in 2.4 seconds
4850 Ramachandran restraints generated.
2425 Oldfield, 0 Emsley, 2425 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: 2.23
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: 2.09 seconds
NOTE: a complete listing of the restraints can be obtained by requesting
output of .geo file.
Histogram of bond lengths:
1.32 - 1.36: 2429
1.36 - 1.41: 0
1.41 - 1.45: 256
1.45 - 1.50: 2177
1.50 - 1.54: 2433
Bond restraints: 7295
Sorted by residual:
bond pdb=" CA THR A2204 "
pdb=" C THR A2204 "
ideal model delta sigma weight residual
1.523 1.545 -0.022 1.56e-02 4.11e+03 1.91e+00
bond pdb=" N ASP A2145 "
pdb=" CA ASP A2145 "
ideal model delta sigma weight residual
1.457 1.472 -0.015 1.29e-02 6.01e+03 1.37e+00
bond pdb=" C ASP A 181 "
pdb=" N LYS A 182 "
ideal model delta sigma weight residual
1.335 1.348 -0.014 1.31e-02 5.83e+03 1.07e+00
bond pdb=" N GLU A1369 "
pdb=" CA GLU A1369 "
ideal model delta sigma weight residual
1.457 1.470 -0.013 1.29e-02 6.01e+03 9.72e-01
bond pdb=" N GLU A 329 "
pdb=" CA GLU A 329 "
ideal model delta sigma weight residual
1.457 1.470 -0.013 1.29e-02 6.01e+03 9.52e-01
... (remaining 7290 not shown)
Histogram of bond angle deviations from ideal:
105.08 - 109.87: 753
109.87 - 114.67: 1679
114.67 - 119.47: 2528
119.47 - 124.26: 2275
124.26 - 129.06: 56
Bond angle restraints: 7291
Sorted by residual:
angle pdb=" N ILE A1684 "
pdb=" CA ILE A1684 "
pdb=" C ILE A1684 "
ideal model delta sigma weight residual
113.20 108.21 4.99 9.60e-01 1.09e+00 2.71e+01
angle pdb=" N GLU A1947 "
pdb=" CA GLU A1947 "
pdb=" C GLU A1947 "
ideal model delta sigma weight residual
110.91 116.95 -6.04 1.17e+00 7.31e-01 2.67e+01
angle pdb=" C ILE A 403 "
pdb=" N GLU A 404 "
pdb=" CA GLU A 404 "
ideal model delta sigma weight residual
120.31 113.31 7.00 1.52e+00 4.33e-01 2.12e+01
angle pdb=" N ASP A2126 "
pdb=" CA ASP A2126 "
pdb=" C ASP A2126 "
ideal model delta sigma weight residual
114.62 109.75 4.87 1.14e+00 7.69e-01 1.82e+01
angle pdb=" N ILE A1809 "
pdb=" CA ILE A1809 "
pdb=" C ILE A1809 "
ideal model delta sigma weight residual
113.53 109.48 4.05 9.80e-01 1.04e+00 1.71e+01
... (remaining 7286 not shown)
Histogram of dihedral angle deviations from ideal:
0.00 - 6.18: 1953
6.18 - 12.35: 414
12.35 - 18.53: 56
18.53 - 24.70: 5
24.70 - 30.88: 1
Dihedral angle restraints: 2429
sinusoidal: 0
harmonic: 2429
Sorted by residual:
dihedral pdb=" CA GLU A1947 "
pdb=" C GLU A1947 "
pdb=" N TRP A1948 "
pdb=" CA TRP A1948 "
ideal model delta harmonic sigma weight residual
180.00 149.12 30.88 0 5.00e+00 4.00e-02 3.81e+01
dihedral pdb=" CA ILE A 813 "
pdb=" C ILE A 813 "
pdb=" N GLU A 814 "
pdb=" CA GLU A 814 "
ideal model delta harmonic sigma weight residual
-180.00 -156.10 -23.90 0 5.00e+00 4.00e-02 2.29e+01
dihedral pdb=" CA LEU A1404 "
pdb=" C LEU A1404 "
pdb=" N THR A1405 "
pdb=" CA THR A1405 "
ideal model delta harmonic sigma weight residual
-180.00 -158.36 -21.64 0 5.00e+00 4.00e-02 1.87e+01
... (remaining 2426 not shown)
Chirality restraints: 0
Planarity restraints: 0
Histogram of nonbonded interaction distances:
2.57 - 3.04: 1925
3.04 - 3.50: 2617
3.50 - 3.97: 4896
3.97 - 4.43: 5866
4.43 - 4.90: 10075
Nonbonded interactions: 25379
Sorted by model distance:
nonbonded pdb=" N ILE A1684 "
pdb=" N ASP A1685 "
model vdw
2.573 2.560
nonbonded pdb=" N ILE A1031 "
pdb=" N ILE A1032 "
model vdw
2.599 2.560
nonbonded pdb=" N ILE A1590 "
pdb=" N LYS A1591 "
model vdw
2.606 2.560
nonbonded pdb=" N GLY A1667 "
pdb=" N ASP A1668 "
model vdw
2.661 2.560
nonbonded pdb=" N VAL A1352 "
pdb=" N ARG A1353 "
model vdw
2.662 2.560
... (remaining 25374 not shown)
NOTE: a complete listing of the restraints can be obtained by requesting
output of .geo file.
Find NCS groups from input model
========== WARNING! ============
No NCS relation were found !!!
================================
Found NCS groups:
found none.
Set up NCS constraints
No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
Set random seed: 0.000
Set model cs if undefined: 0.000
Decide on map wrapping: 0.000
Normalize map: mean=0, sd=1: 3.360
Set stop_for_unknowns flag: 0.000
Assert model is a single copy model: 0.000
Assert all atoms have isotropic ADPs: 0.010
Construct map_model_manager: 0.000
Extract box with map and model: 15.740
Check model and map are aligned: 0.110
Set scattering table: 0.080
Process input model: 21.520
Find NCS groups from input model: 0.420
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:2.750
Set ADP refinement strategy: 0.000
Make a string to write initial .geo file:0.000
Internal consistency checks: 0.000
Total: 44.050
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6999
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 : 0.002 0.022 7295 Z= 0.153
Angle : 0.742 7.522 7291 Z= 0.486
Chirality : 0.000 0.000 0
Planarity : 0.000 0.000 0
Dihedral : 5.054 30.879 2429
Min Nonbonded Distance : 2.573
Molprobity Statistics.
All-atom Clashscore : 0.10
Ramachandran Plot:
Outliers : 0.58 %
Allowed : 7.09 %
Favored : 92.33 %
Rotamer Outliers : 0.00 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 3.39 %
Cis-general : 0.00 %
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: -1.14 (0.17), residues: 2425
helix: 0.47 (0.21), residues: 597
sheet: -0.38 (0.30), residues: 308
loop : -1.40 (0.16), residues: 1520
*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
4850 Ramachandran restraints generated.
2425 Oldfield, 0 Emsley, 2425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
4850 Ramachandran restraints generated.
2425 Oldfield, 0 Emsley, 2425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
47 residues out of total 2199 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 47
time to evaluate : 1.105
Fit side-chains
TARDY: cannot create tardy model for: "MET B 57 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 95 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 125 " (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: 0.0656
time to fit residues: 8.0453
Evaluate side-chains
47 residues out of total 2199 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 47
time to evaluate : 1.086
Switching outliers to nearest non-outliers
outliers start: 0
outliers final: 0
residues processed: 0
time to fit residues: 1.5773
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 243
random chunks:
chunk 205 optimal weight: 3.9990
chunk 184 optimal weight: 0.5980
chunk 102 optimal weight: 2.9990
chunk 62 optimal weight: 0.5980
chunk 124 optimal weight: 9.9990
chunk 98 optimal weight: 2.9990
chunk 190 optimal weight: 4.9990
chunk 73 optimal weight: 9.9990
chunk 115 optimal weight: 50.0000
chunk 141 optimal weight: 0.9980
chunk 220 optimal weight: 8.9990
overall best weight: 1.6384
-------------------------------------------------------------------------------
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: 0.7484
moved from start: 0.4909
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
Bond : 0.003 0.044 7295 Z= 0.258
Angle : 0.684 8.109 7291 Z= 0.442
Chirality : 0.000 0.000 0
Planarity : 0.000 0.000 0
Dihedral : 5.224 23.556 2429
Min Nonbonded Distance : 2.613
Molprobity Statistics.
All-atom Clashscore : 3.82
Ramachandran Plot:
Outliers : 0.54 %
Allowed : 8.16 %
Favored : 91.30 %
Rotamer Outliers : 0.00 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 3.39 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: -1.43 (0.17), residues: 2425
helix: -0.09 (0.21), residues: 535
sheet: -0.57 (0.27), residues: 364
loop : -1.42 (0.16), residues: 1526
*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
4850 Ramachandran restraints generated.
2425 Oldfield, 0 Emsley, 2425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
4850 Ramachandran restraints generated.
2425 Oldfield, 0 Emsley, 2425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
47 residues out of total 2199 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 47
time to evaluate : 1.116
Fit side-chains
TARDY: cannot create tardy model for: "MET B 57 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 95 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 125 " (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: 0.0590
time to fit residues: 7.0998
Evaluate side-chains
47 residues out of total 2199 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: 2.0230
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 243
random chunks:
chunk 122 optimal weight: 0.0040
chunk 68 optimal weight: 3.9990
chunk 183 optimal weight: 9.9990
chunk 150 optimal weight: 0.0370
chunk 60 optimal weight: 5.9990
chunk 221 optimal weight: 10.0000
chunk 238 optimal weight: 8.9990
chunk 196 optimal weight: 4.9990
chunk 219 optimal weight: 7.9990
chunk 75 optimal weight: 5.9990
chunk 177 optimal weight: 2.9990
overall best weight: 2.4076
-------------------------------------------------------------------------------
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: 0.7609
moved from start: 0.7609
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
Bond : 0.005 0.090 7295 Z= 0.338
Angle : 0.847 6.744 7291 Z= 0.548
Chirality : 0.000 0.000 0
Planarity : 0.000 0.000 0
Dihedral : 6.171 26.790 2429
Min Nonbonded Distance : 2.565
Molprobity Statistics.
All-atom Clashscore : 6.43
Ramachandran Plot:
Outliers : 0.41 %
Allowed : 11.34 %
Favored : 88.25 %
Rotamer Outliers : 0.00 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 3.39 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: -2.35 (0.16), residues: 2425
helix: -1.34 (0.21), residues: 496
sheet: -0.98 (0.28), residues: 343
loop : -1.85 (0.15), residues: 1586
*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
4850 Ramachandran restraints generated.
2425 Oldfield, 0 Emsley, 2425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
4850 Ramachandran restraints generated.
2425 Oldfield, 0 Emsley, 2425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
47 residues out of total 2199 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 47
time to evaluate : 1.161
Fit side-chains
TARDY: cannot create tardy model for: "MET B 57 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 95 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 125 " (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: 7.5785
Evaluate side-chains
47 residues out of total 2199 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 47
time to evaluate : 1.074
Switching outliers to nearest non-outliers
outliers start: 0
outliers final: 0
residues processed: 0
time to fit residues: 1.5039
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 243
random chunks:
chunk 218 optimal weight: 10.0000
chunk 166 optimal weight: 9.9990
chunk 114 optimal weight: 2.9990
chunk 24 optimal weight: 0.0060
chunk 105 optimal weight: 3.9990
chunk 148 optimal weight: 10.0000
chunk 221 optimal weight: 9.9990
chunk 234 optimal weight: 9.9990
chunk 115 optimal weight: 40.0000
chunk 210 optimal weight: 4.9990
chunk 63 optimal weight: 3.9990
overall best weight: 3.2004
-------------------------------------------------------------------------------
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: 0.7699
moved from start: 0.9641
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
Bond : 0.006 0.105 7295 Z= 0.433
Angle : 1.013 10.066 7291 Z= 0.655
Chirality : 0.000 0.000 0
Planarity : 0.000 0.000 0
Dihedral : 7.166 33.200 2429
Min Nonbonded Distance : 2.471
Molprobity Statistics.
All-atom Clashscore : 8.55
Ramachandran Plot:
Outliers : 0.33 %
Allowed : 14.93 %
Favored : 84.74 %
Rotamer Outliers : 0.00 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 3.39 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.17 %
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: -3.34 (0.15), residues: 2425
helix: -2.44 (0.20), residues: 460
sheet: -1.43 (0.31), residues: 274
loop : -2.46 (0.14), residues: 1691
*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
4850 Ramachandran restraints generated.
2425 Oldfield, 0 Emsley, 2425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
4850 Ramachandran restraints generated.
2425 Oldfield, 0 Emsley, 2425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
47 residues out of total 2199 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 47
time to evaluate : 1.099
Fit side-chains
TARDY: cannot create tardy model for: "MET B 57 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 95 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 125 " (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: 0.0646
time to fit residues: 8.0750
Evaluate side-chains
47 residues out of total 2199 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 47
time to evaluate : 1.099
Switching outliers to nearest non-outliers
outliers start: 0
outliers final: 0
residues processed: 0
time to fit residues: 1.5894
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 243
random chunks:
chunk 195 optimal weight: 3.9990
chunk 133 optimal weight: 10.0000
chunk 3 optimal weight: 6.9990
chunk 174 optimal weight: 0.1980
chunk 96 optimal weight: 0.9990
chunk 200 optimal weight: 3.9990
chunk 162 optimal weight: 4.9990
chunk 0 optimal weight: 10.0000
chunk 119 optimal weight: 3.9990
chunk 210 optimal weight: 9.9990
chunk 59 optimal weight: 1.9990
overall best weight: 2.2388
-------------------------------------------------------------------------------
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: 0.7688
moved from start: 0.9915
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
Bond : 0.004 0.083 7295 Z= 0.298
Angle : 0.754 5.845 7291 Z= 0.484
Chirality : 0.000 0.000 0
Planarity : 0.000 0.000 0
Dihedral : 5.726 30.513 2429
Min Nonbonded Distance : 2.536
Molprobity Statistics.
All-atom Clashscore : 5.73
Ramachandran Plot:
Outliers : 0.21 %
Allowed : 13.86 %
Favored : 85.94 %
Rotamer Outliers : 0.00 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 3.39 %
Cis-general : 0.00 %
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: -3.24 (0.16), residues: 2425
helix: -2.17 (0.21), residues: 445
sheet: -1.51 (0.32), residues: 260
loop : -2.41 (0.14), residues: 1720
*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
4850 Ramachandran restraints generated.
2425 Oldfield, 0 Emsley, 2425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
4850 Ramachandran restraints generated.
2425 Oldfield, 0 Emsley, 2425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
47 residues out of total 2199 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 47
time to evaluate : 1.120
Fit side-chains
TARDY: cannot create tardy model for: "MET B 57 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 95 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 125 " (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: 0.0617
time to fit residues: 7.3810
Evaluate side-chains
47 residues out of total 2199 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 47
time to evaluate : 1.096
Switching outliers to nearest non-outliers
outliers start: 0
outliers final: 0
residues processed: 0
time to fit residues: 1.5747
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 243
random chunks:
chunk 79 optimal weight: 3.9990
chunk 211 optimal weight: 6.9990
chunk 46 optimal weight: 0.2980
chunk 137 optimal weight: 8.9990
chunk 57 optimal weight: 0.0270
chunk 235 optimal weight: 8.9990
chunk 195 optimal weight: 3.9990
chunk 108 optimal weight: 1.9990
chunk 19 optimal weight: 2.9990
chunk 77 optimal weight: 3.9990
chunk 123 optimal weight: 20.0000
overall best weight: 1.8644
-------------------------------------------------------------------------------
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: 0.7688
moved from start: 1.0479
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
Bond : 0.003 0.075 7295 Z= 0.249
Angle : 0.674 5.368 7291 Z= 0.430
Chirality : 0.000 0.000 0
Planarity : 0.000 0.000 0
Dihedral : 5.284 23.320 2429
Min Nonbonded Distance : 2.554
Molprobity Statistics.
All-atom Clashscore : 5.93
Ramachandran Plot:
Outliers : 0.21 %
Allowed : 15.96 %
Favored : 83.84 %
Rotamer Outliers : 0.00 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 3.39 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: -3.26 (0.16), residues: 2425
helix: -2.08 (0.22), residues: 427
sheet: -1.34 (0.34), residues: 228
loop : -2.49 (0.14), residues: 1770
*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
4850 Ramachandran restraints generated.
2425 Oldfield, 0 Emsley, 2425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
4850 Ramachandran restraints generated.
2425 Oldfield, 0 Emsley, 2425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
47 residues out of total 2199 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 47
time to evaluate : 1.077
Fit side-chains
TARDY: cannot create tardy model for: "MET B 57 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 95 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 125 " (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: 0.0606
time to fit residues: 7.1085
Evaluate side-chains
47 residues out of total 2199 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 47
time to evaluate : 1.059
Switching outliers to nearest non-outliers
outliers start: 0
outliers final: 0
residues processed: 0
time to fit residues: 1.5415
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 243
random chunks:
chunk 226 optimal weight: 10.0000
chunk 26 optimal weight: 3.9990
chunk 133 optimal weight: 7.9990
chunk 171 optimal weight: 2.9990
chunk 197 optimal weight: 9.9990
chunk 131 optimal weight: 0.0670
chunk 234 optimal weight: 10.0000
chunk 146 optimal weight: 5.9990
chunk 142 optimal weight: 2.9990
chunk 108 optimal weight: 2.9990
chunk 144 optimal weight: 0.0970
overall best weight: 1.8322
-------------------------------------------------------------------------------
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: 0.7691
moved from start: 1.0834
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
Bond : 0.003 0.074 7295 Z= 0.247
Angle : 0.655 5.834 7291 Z= 0.418
Chirality : 0.000 0.000 0
Planarity : 0.000 0.000 0
Dihedral : 5.116 29.226 2429
Min Nonbonded Distance : 2.526
Molprobity Statistics.
All-atom Clashscore : 6.43
Ramachandran Plot:
Outliers : 0.16 %
Allowed : 15.46 %
Favored : 84.37 %
Rotamer Outliers : 0.00 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 3.39 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: -3.25 (0.16), residues: 2425
helix: -1.87 (0.23), residues: 435
sheet: -1.48 (0.34), residues: 230
loop : -2.52 (0.14), residues: 1760
*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
4850 Ramachandran restraints generated.
2425 Oldfield, 0 Emsley, 2425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
4850 Ramachandran restraints generated.
2425 Oldfield, 0 Emsley, 2425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
47 residues out of total 2199 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 47
time to evaluate : 1.096
Fit side-chains
TARDY: cannot create tardy model for: "MET B 57 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 95 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 125 " (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: 0.0609
time to fit residues: 7.2683
Evaluate side-chains
47 residues out of total 2199 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 47
time to evaluate : 1.078
Switching outliers to nearest non-outliers
outliers start: 0
outliers final: 0
residues processed: 0
time to fit residues: 1.5307
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 243
random chunks:
chunk 93 optimal weight: 0.7980
chunk 139 optimal weight: 10.0000
chunk 70 optimal weight: 0.0050
chunk 46 optimal weight: 0.0470
chunk 45 optimal weight: 0.0570
chunk 148 optimal weight: 5.9990
chunk 159 optimal weight: 5.9990
chunk 115 optimal weight: 0.0670
chunk 21 optimal weight: 1.9990
chunk 184 optimal weight: 1.9990
chunk 213 optimal weight: 10.0000
overall best weight: 0.1948
-------------------------------------------------------------------------------
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: 0.7595
moved from start: 1.0496
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
Bond : 0.001 0.012 7295 Z= 0.042
Angle : 0.311 2.845 7291 Z= 0.191
Chirality : 0.000 0.000 0
Planarity : 0.000 0.000 0
Dihedral : 2.805 14.652 2429
Min Nonbonded Distance : 2.592
Molprobity Statistics.
All-atom Clashscore : 0.90
Ramachandran Plot:
Outliers : 0.16 %
Allowed : 7.96 %
Favored : 91.88 %
Rotamer Outliers : 0.00 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 3.39 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: -2.59 (0.17), residues: 2425
helix: -0.62 (0.24), residues: 479
sheet: -1.28 (0.32), residues: 269
loop : -2.29 (0.15), residues: 1677
*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
4850 Ramachandran restraints generated.
2425 Oldfield, 0 Emsley, 2425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
4850 Ramachandran restraints generated.
2425 Oldfield, 0 Emsley, 2425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
47 residues out of total 2199 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 47
time to evaluate : 1.137
Fit side-chains
TARDY: cannot create tardy model for: "MET B 57 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 95 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 125 " (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: 8.0212
Evaluate side-chains
47 residues out of total 2199 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 47
time to evaluate : 1.124
Switching outliers to nearest non-outliers
outliers start: 0
outliers final: 0
residues processed: 0
time to fit residues: 1.6552
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 243
random chunks:
chunk 224 optimal weight: 8.9990
chunk 204 optimal weight: 1.9990
chunk 218 optimal weight: 9.9990
chunk 131 optimal weight: 5.9990
chunk 95 optimal weight: 3.9990
chunk 171 optimal weight: 0.9980
chunk 66 optimal weight: 6.9990
chunk 197 optimal weight: 0.0470
chunk 206 optimal weight: 9.9990
chunk 217 optimal weight: 9.9990
chunk 143 optimal weight: 4.9990
overall best weight: 2.4084
-------------------------------------------------------------------------------
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: 0.7711
moved from start: 1.1167
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
Bond : 0.004 0.083 7295 Z= 0.320
Angle : 0.731 8.904 7291 Z= 0.474
Chirality : 0.000 0.000 0
Planarity : 0.000 0.000 0
Dihedral : 5.266 27.090 2429
Min Nonbonded Distance : 2.478
Molprobity Statistics.
All-atom Clashscore : 7.64
Ramachandran Plot:
Outliers : 0.21 %
Allowed : 18.10 %
Favored : 81.69 %
Rotamer Outliers : 0.00 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 3.39 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: -3.09 (0.16), residues: 2425
helix: -1.59 (0.24), residues: 432
sheet: -1.38 (0.35), residues: 243
loop : -2.46 (0.14), residues: 1750
*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
4850 Ramachandran restraints generated.
2425 Oldfield, 0 Emsley, 2425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
4850 Ramachandran restraints generated.
2425 Oldfield, 0 Emsley, 2425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
47 residues out of total 2199 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 47
time to evaluate : 1.110
Fit side-chains
TARDY: cannot create tardy model for: "MET B 57 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 95 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 125 " (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: 0.0626
time to fit residues: 8.0437
Evaluate side-chains
47 residues out of total 2199 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 47
time to evaluate : 1.099
Switching outliers to nearest non-outliers
outliers start: 0
outliers final: 0
residues processed: 0
time to fit residues: 1.6757
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 243
random chunks:
chunk 230 optimal weight: 20.0000
chunk 140 optimal weight: 10.0000
chunk 109 optimal weight: 0.7980
chunk 160 optimal weight: 0.9990
chunk 242 optimal weight: 10.0000
chunk 222 optimal weight: 10.0000
chunk 192 optimal weight: 6.9990
chunk 20 optimal weight: 1.9990
chunk 148 optimal weight: 5.9990
chunk 118 optimal weight: 8.9990
chunk 153 optimal weight: 0.0970
overall best weight: 1.9784
-------------------------------------------------------------------------------
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: 0.7700
moved from start: 1.1441
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
Bond : 0.004 0.081 7295 Z= 0.264
Angle : 0.655 6.154 7291 Z= 0.422
Chirality : 0.000 0.000 0
Planarity : 0.000 0.000 0
Dihedral : 4.985 23.450 2429
Min Nonbonded Distance : 2.513
Molprobity Statistics.
All-atom Clashscore : 6.43
Ramachandran Plot:
Outliers : 0.21 %
Allowed : 15.18 %
Favored : 84.62 %
Rotamer Outliers : 0.00 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 3.39 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: -3.18 (0.16), residues: 2425
helix: -1.60 (0.24), residues: 435
sheet: -1.20 (0.35), residues: 228
loop : -2.57 (0.14), residues: 1762
********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
4850 Ramachandran restraints generated.
2425 Oldfield, 0 Emsley, 2425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
4850 Ramachandran restraints generated.
2425 Oldfield, 0 Emsley, 2425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
47 residues out of total 2199 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 47
time to evaluate : 1.154
Fit side-chains
TARDY: cannot create tardy model for: "MET B 57 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 95 " (corrupted residue). Skipping it.
TARDY: cannot create tardy model for: "MET B 125 " (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: 0.0613
time to fit residues: 7.4796
Evaluate side-chains
47 residues out of total 2199 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 47
time to evaluate : 1.150
Switching outliers to nearest non-outliers
outliers start: 0
outliers final: 0
residues processed: 0
time to fit residues: 1.6495
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 243
random chunks:
chunk 205 optimal weight: 9.9990
chunk 59 optimal weight: 0.0980
chunk 177 optimal weight: 9.9990
chunk 28 optimal weight: 1.9990
chunk 53 optimal weight: 2.9990
chunk 193 optimal weight: 5.9990
chunk 80 optimal weight: 0.0470
chunk 198 optimal weight: 10.0000
chunk 24 optimal weight: 3.9990
chunk 35 optimal weight: 6.9990
chunk 169 optimal weight: 6.9990
overall best weight: 1.8284
-------------------------------------------------------------------------------
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 = 0.3659 r_free = 0.3659 target = 0.127126 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2856 r_free = 0.2856 target = 0.078821 restraints weight = 20962.731|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2861 r_free = 0.2861 target = 0.077701 restraints weight = 23250.907|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2838 r_free = 0.2838 target = 0.077328 restraints weight = 24228.154|
|-----------------------------------------------------------------------------|
r_work (final): 0.2654
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8328
moved from start: 1.1743
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
Bond : 0.003 0.078 7295 Z= 0.246
Angle : 0.647 8.934 7291 Z= 0.411
Chirality : 0.000 0.000 0
Planarity : 0.000 0.000 0
Dihedral : 4.970 26.193 2429
Min Nonbonded Distance : 2.503
Molprobity Statistics.
All-atom Clashscore : 6.53
Ramachandran Plot:
Outliers : 0.21 %
Allowed : 18.10 %
Favored : 81.69 %
Rotamer Outliers : 0.00 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 3.39 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: -3.26 (0.16), residues: 2425
helix: -1.62 (0.24), residues: 430
sheet: -1.32 (0.35), residues: 226
loop : -2.63 (0.14), residues: 1769
===============================================================================
Job complete
usr+sys time: 1740.46 seconds
wall clock time: 31 minutes 24.84 seconds (1884.84 seconds total)