Starting phenix.real_space_refine (version: dev)
on Thu May 12 18:24:49 2022 by dcliebschner
===============================================================================
Processing files:
-------------------------------------------------------------------------------
Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n95_24250/05_2022/7n95_24250.pdb
Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n95_24250/05_2022/7n95_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_24250/05_2022/7n95_24250.map"
default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n95_24250/05_2022/7n95_24250.map"
model {
file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n95_24250/05_2022/7n95_24250.pdb"
}
default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n95_24250/05_2022/7n95_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
Convert atoms to be neutral
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-4597/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: {'PTRANS': 9, 'TRANS': 110, 'PCIS': 1}
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: {'PTRANS': 48, 'TRANS': 2262, 'PCIS': 1}
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: 5.99, per 1000 atoms: 0.82
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: 2.35
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: 2.13 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
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.
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: 2.770
Set stop_for_unknowns flag: 0.000
Assert model is a single copy model: 0.000
Assert all atoms have isotropic ADPs: 0.000
Construct map_model_manager: 0.010
Extract box with map and model: 16.920
Check model and map are aligned: 0.100
Convert atoms to be neutral: 0.050
Process input model: 22.220
Find NCS groups from input model: 0.580
Set up NCS constraints: 0.050
Set refine NCS operators: 0.000
Set scattering table: 0.010
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:2.690
Set ADP refinement strategy: 0.000
Make a string to write initial .geo file:0.000
Internal consistency checks: 0.000
Total: 45.400
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7009
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 : 1.041
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: 0.0629
time to fit residues: 7.3662
Evaluate side-chains
47 residues out of total 2199 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 47
time to evaluate : 1.036
Switching outliers to nearest non-outliers
outliers start: 0
outliers final: 0
residues processed: 0
time to fit residues: 1.4997
-------------------------------------------------------------------------------
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: 0.7495
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 : 1.159
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: 0.0614
time to fit residues: 7.3773
Evaluate side-chains
47 residues out of total 2199 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 47
time to evaluate : 1.082
Switching outliers to nearest non-outliers
outliers start: 0
outliers final: 0
residues processed: 0
time to fit residues: 1.5613
-------------------------------------------------------------------------------
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: 0.8980
chunk 68 optimal weight: 0.0770
chunk 183 optimal weight: 9.9990
chunk 150 optimal weight: 0.9990
chunk 60 optimal weight: 6.9990
chunk 221 optimal weight: 0.0060
chunk 238 optimal weight: 9.9990
chunk 196 optimal weight: 4.9990
chunk 219 optimal weight: 0.2980
chunk 75 optimal weight: 5.9990
chunk 177 optimal weight: 2.9990
overall best weight: 0.4556
-------------------------------------------------------------------------------
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: 0.7436
moved from start: 0.4838
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
Bond : 0.001 0.010 7295 Z= 0.072
Angle : 0.347 3.612 7291 Z= 0.216
Chirality : 0.000 0.000 0
Planarity : 0.000 0.000 0
Dihedral : 3.065 16.590 2429
Min Nonbonded Distance : 2.615
Molprobity Statistics.
All-atom Clashscore : 1.01
Ramachandran Plot:
Outliers : 0.45 %
Allowed : 5.03 %
Favored : 94.52 %
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: -0.77 (0.17), residues: 2425
helix: 1.10 (0.22), residues: 545
sheet: -0.53 (0.28), residues: 379
loop : -1.16 (0.16), residues: 1501
*********************** 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 : 1.156
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: 0.0586
time to fit residues: 7.0825
Evaluate side-chains
47 residues out of total 2199 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 47
time to evaluate : 1.163
Switching outliers to nearest non-outliers
outliers start: 0
outliers final: 0
residues processed: 0
time to fit residues: 1.6682
-------------------------------------------------------------------------------
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: 9.9990
chunk 166 optimal weight: 9.9990
chunk 114 optimal weight: 0.0980
chunk 24 optimal weight: 0.0060
chunk 105 optimal weight: 3.9990
chunk 148 optimal weight: 10.0000
chunk 221 optimal weight: 8.9990
chunk 234 optimal weight: 10.0000
chunk 115 optimal weight: 9.9990
chunk 210 optimal weight: 8.9990
chunk 63 optimal weight: 2.9990
overall best weight: 3.2202
-------------------------------------------------------------------------------
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: 0.7664
moved from start: 0.8158
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
Bond : 0.006 0.121 7295 Z= 0.430
Angle : 1.005 8.948 7291 Z= 0.652
Chirality : 0.000 0.000 0
Planarity : 0.000 0.000 0
Dihedral : 6.987 29.841 2429
Min Nonbonded Distance : 2.532
Molprobity Statistics.
All-atom Clashscore : 8.04
Ramachandran Plot:
Outliers : 0.37 %
Allowed : 13.20 %
Favored : 86.43 %
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: -2.55 (0.16), residues: 2425
helix: -1.59 (0.21), residues: 487
sheet: -0.64 (0.29), residues: 309
loop : -2.05 (0.14), residues: 1629
*********************** 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: 0.0639
time to fit residues: 7.5692
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
Switching outliers to nearest non-outliers
outliers start: 0
outliers final: 0
residues processed: 0
time to fit residues: 1.6480
-------------------------------------------------------------------------------
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: 0.9980
chunk 174 optimal weight: 1.9990
chunk 96 optimal weight: 5.9990
chunk 200 optimal weight: 4.9990
chunk 162 optimal weight: 2.9990
chunk 0 optimal weight: 9.9990
chunk 119 optimal weight: 3.9990
chunk 210 optimal weight: 4.9990
chunk 59 optimal weight: 0.4980
overall best weight: 2.0986
-------------------------------------------------------------------------------
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: 0.7656
moved from start: 0.8622
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
Bond : 0.004 0.070 7295 Z= 0.282
Angle : 0.716 6.468 7291 Z= 0.460
Chirality : 0.000 0.000 0
Planarity : 0.000 0.000 0
Dihedral : 5.388 22.445 2429
Min Nonbonded Distance : 2.579
Molprobity Statistics.
All-atom Clashscore : 4.32
Ramachandran Plot:
Outliers : 0.21 %
Allowed : 11.46 %
Favored : 88.33 %
Rotamer Outliers : 0.00 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 3.39 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
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: -2.73 (0.16), residues: 2425
helix: -1.58 (0.21), residues: 486
sheet: -1.03 (0.29), residues: 325
loop : -2.18 (0.15), residues: 1614
*********************** 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 : 1.236
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: 0.0654
time to fit residues: 7.9181
Evaluate side-chains
47 residues out of total 2199 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 47
time to evaluate : 1.071
Switching outliers to nearest non-outliers
outliers start: 0
outliers final: 0
residues processed: 0
time to fit residues: 1.5038
-------------------------------------------------------------------------------
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: 7.9990
chunk 46 optimal weight: 0.6980
chunk 137 optimal weight: 9.9990
chunk 57 optimal weight: 0.0020
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: 0.4980
overall best weight: 1.2392
-------------------------------------------------------------------------------
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: 0.7644
moved from start: 0.9029
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
Bond : 0.002 0.052 7295 Z= 0.171
Angle : 0.521 4.901 7291 Z= 0.330
Chirality : 0.000 0.000 0
Planarity : 0.000 0.000 0
Dihedral : 4.279 19.714 2429
Min Nonbonded Distance : 2.592
Molprobity Statistics.
All-atom Clashscore : 3.52
Ramachandran Plot:
Outliers : 0.21 %
Allowed : 12.04 %
Favored : 87.75 %
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: -2.40 (0.16), residues: 2425
helix: -1.01 (0.23), residues: 488
sheet: -0.81 (0.31), residues: 300
loop : -2.05 (0.15), residues: 1637
*********************** 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 : 1.024
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: 0.0637
time to fit residues: 7.4987
Evaluate side-chains
47 residues out of total 2199 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 47
time to evaluate : 1.126
Switching outliers to nearest non-outliers
outliers start: 0
outliers final: 0
residues processed: 0
time to fit residues: 1.5555
-------------------------------------------------------------------------------
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: 8.9990
chunk 171 optimal weight: 0.0980
chunk 197 optimal weight: 4.9990
chunk 131 optimal weight: 4.9990
chunk 234 optimal weight: 9.9990
chunk 146 optimal weight: 10.0000
chunk 142 optimal weight: 4.9990
chunk 108 optimal weight: 0.8980
chunk 144 optimal weight: 0.0000
overall best weight: 1.9988
-------------------------------------------------------------------------------
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: 0.7693
moved from start: 0.9956
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
Bond : 0.004 0.065 7295 Z= 0.267
Angle : 0.696 5.165 7291 Z= 0.448
Chirality : 0.000 0.000 0
Planarity : 0.000 0.000 0
Dihedral : 5.331 21.596 2429
Min Nonbonded Distance : 2.581
Molprobity Statistics.
All-atom Clashscore : 5.73
Ramachandran Plot:
Outliers : 0.25 %
Allowed : 14.23 %
Favored : 85.53 %
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: -2.76 (0.16), residues: 2425
helix: -1.44 (0.23), residues: 429
sheet: -1.21 (0.32), residues: 268
loop : -2.20 (0.14), residues: 1728
*********************** 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 : 1.014
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: 7.5919
Evaluate side-chains
47 residues out of total 2199 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 47
time to evaluate : 0.991
Switching outliers to nearest non-outliers
outliers start: 0
outliers final: 0
residues processed: 0
time to fit residues: 1.6146
-------------------------------------------------------------------------------
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: 0.0370
chunk 139 optimal weight: 10.0000
chunk 70 optimal weight: 1.9990
chunk 46 optimal weight: 0.0020
chunk 45 optimal weight: 0.8980
chunk 148 optimal weight: 9.9990
chunk 159 optimal weight: 9.9990
chunk 115 optimal weight: 0.9990
chunk 21 optimal weight: 1.9990
chunk 184 optimal weight: 3.9990
chunk 213 optimal weight: 8.9990
overall best weight: 0.7870
-------------------------------------------------------------------------------
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: 0.7641
moved from start: 0.9792
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
Bond : 0.002 0.032 7295 Z= 0.113
Angle : 0.416 3.605 7291 Z= 0.262
Chirality : 0.000 0.000 0
Planarity : 0.000 0.000 0
Dihedral : 3.631 20.078 2429
Min Nonbonded Distance : 2.595
Molprobity Statistics.
All-atom Clashscore : 2.31
Ramachandran Plot:
Outliers : 0.16 %
Allowed : 9.53 %
Favored : 90.31 %
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: -2.36 (0.17), residues: 2425
helix: -0.77 (0.24), residues: 476
sheet: -0.83 (0.34), residues: 254
loop : -2.07 (0.15), residues: 1695
*********************** 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 : 1.034
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: 0.0603
time to fit residues: 7.1565
Evaluate side-chains
47 residues out of total 2199 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 47
time to evaluate : 1.060
Switching outliers to nearest non-outliers
outliers start: 0
outliers final: 0
residues processed: 0
time to fit residues: 1.5708
-------------------------------------------------------------------------------
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: 6.9990
chunk 204 optimal weight: 0.0570
chunk 218 optimal weight: 9.9990
chunk 131 optimal weight: 6.9990
chunk 95 optimal weight: 3.9990
chunk 171 optimal weight: 0.9980
chunk 66 optimal weight: 6.9990
chunk 197 optimal weight: 5.9990
chunk 206 optimal weight: 10.0000
chunk 217 optimal weight: 10.0000
chunk 143 optimal weight: 4.9990
overall best weight: 3.2104
-------------------------------------------------------------------------------
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: 0.7746
moved from start: 1.0913
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
Bond : 0.006 0.119 7295 Z= 0.420
Angle : 0.930 12.162 7291 Z= 0.602
Chirality : 0.000 0.000 0
Planarity : 0.000 0.000 0
Dihedral : 6.392 29.991 2429
Min Nonbonded Distance : 2.470
Molprobity Statistics.
All-atom Clashscore : 10.86
Ramachandran Plot:
Outliers : 0.29 %
Allowed : 18.39 %
Favored : 81.32 %
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: -3.24 (0.16), residues: 2425
helix: -1.95 (0.23), residues: 404
sheet: -1.31 (0.35), residues: 222
loop : -2.52 (0.14), residues: 1799
*********************** 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 : 1.077
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: 0.0634
time to fit residues: 7.5382
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
Switching outliers to nearest non-outliers
outliers start: 0
outliers final: 0
residues processed: 0
time to fit residues: 1.5846
-------------------------------------------------------------------------------
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: 9.9990
chunk 109 optimal weight: 4.9990
chunk 160 optimal weight: 0.9980
chunk 242 optimal weight: 10.0000
chunk 222 optimal weight: 0.0050
chunk 192 optimal weight: 6.9990
chunk 20 optimal weight: 2.9990
chunk 148 optimal weight: 6.9990
chunk 118 optimal weight: 10.0000
chunk 153 optimal weight: 0.7980
overall best weight: 1.9598
-------------------------------------------------------------------------------
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: 0.7706
moved from start: 1.0930
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
Bond : 0.004 0.075 7295 Z= 0.260
Angle : 0.658 6.221 7291 Z= 0.422
Chirality : 0.000 0.000 0
Planarity : 0.000 0.000 0
Dihedral : 5.104 27.723 2429
Min Nonbonded Distance : 2.515
Molprobity Statistics.
All-atom Clashscore : 5.93
Ramachandran Plot:
Outliers : 0.16 %
Allowed : 13.90 %
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 : 0.00 %
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: -1.73 (0.24), residues: 427
sheet: -1.26 (0.36), residues: 220
loop : -2.43 (0.14), residues: 1778
********************** 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 : 1.095
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: 0.0629
time to fit residues: 7.5316
Evaluate side-chains
47 residues out of total 2199 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 47
time to evaluate : 1.072
Switching outliers to nearest non-outliers
outliers start: 0
outliers final: 0
residues processed: 0
time to fit residues: 1.5419
-------------------------------------------------------------------------------
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: 10.0000
chunk 59 optimal weight: 0.0170
chunk 177 optimal weight: 10.0000
chunk 28 optimal weight: 1.9990
chunk 53 optimal weight: 0.0070
chunk 193 optimal weight: 5.9990
chunk 80 optimal weight: 0.2980
chunk 198 optimal weight: 9.9990
chunk 24 optimal weight: 9.9990
chunk 35 optimal weight: 2.9990
chunk 169 optimal weight: 5.9990
overall best weight: 1.0640
-------------------------------------------------------------------------------
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 = 0.3700 r_free = 0.3700 target = 0.129794 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3073 r_free = 0.3073 target = 0.088620 restraints weight = 20950.571|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2947 r_free = 0.2947 target = 0.083973 restraints weight = 22172.302|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.2941 r_free = 0.2941 target = 0.083558 restraints weight = 24946.234|
|-----------------------------------------------------------------------------|
r_work (final): 0.2743
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8136
moved from start: 1.0924
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
Bond : 0.002 0.042 7295 Z= 0.145
Angle : 0.472 5.617 7291 Z= 0.297
Chirality : 0.000 0.000 0
Planarity : 0.000 0.000 0
Dihedral : 3.970 22.205 2429
Min Nonbonded Distance : 2.551
Molprobity Statistics.
All-atom Clashscore : 3.52
Ramachandran Plot:
Outliers : 0.16 %
Allowed : 14.43 %
Favored : 85.40 %
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: -2.80 (0.17), residues: 2425
helix: -1.16 (0.25), residues: 438
sheet: -1.10 (0.37), residues: 219
loop : -2.33 (0.14), residues: 1768
===============================================================================
Job complete
usr+sys time: 1715.54 seconds
wall clock time: 30 minutes 55.01 seconds (1855.01 seconds total)