Starting phenix.real_space_refine
on Fri Dec 8 03:56:51 2023 by dcliebschner
===============================================================================
Processing files:
-------------------------------------------------------------------------------
Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n9q_24259/12_2023/7n9q_24259.pdb
Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n9q_24259/12_2023/7n9q_24259.map
Processing PHIL parameters:
-------------------------------------------------------------------------------
Adding command-line PHIL:
-------------------------
refinement.macro_cycles=10
scattering_table=electron
resolution=4.6
write_initial_geo_file=False
Final processed PHIL parameters:
-------------------------------------------------------------------------------
data_manager {
real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n9q_24259/12_2023/7n9q_24259.map"
default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n9q_24259/12_2023/7n9q_24259.map"
model {
file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n9q_24259/12_2023/7n9q_24259.pdb"
}
default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n9q_24259/12_2023/7n9q_24259.pdb"
}
resolution = 4.6
write_initial_geo_file = False
refinement {
macro_cycles = 10
}
qi {
qm_restraints {
package {
program = *test
}
}
}
Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.
Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
Set to: 0
Set model cs if undefined
Decide on map wrapping
Map wrapping is set to: False
Normalize map: mean=0, sd=1
Input map: mean= 0.001 sd= 0.019
Set stop_for_unknowns flag
Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
Set to: electron
Number of scattering types: 2
Type Number sf(0) Gaussians
C 4630 2.51 5
N 2315 2.21 5
sf(0) = scattering factor at diffraction angle 0.
Process input model
Symmetric amino acids flipped
None
Time to flip residues: 0.01s
Monomer Library directory:
"/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib"
Total number of atoms: 6945
Number of models: 1
Model: ""
Number of chains: 1
Chain: "A"
Number of atoms: 6945
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 2315, 6945
Classifications: {'peptide': 2315}
Incomplete info: {'n_c_alpha_c_only': 2315}
Link IDs: {'PCIS': 1, 'PTRANS': 49, 'TRANS': 2264}
Chain breaks: 2
Unresolved chain link angles: 2364
Unresolved non-hydrogen bonds: 12079
Unresolved non-hydrogen angles: 16444
Unresolved non-hydrogen dihedrals: 6273
Unresolved non-hydrogen chiralities: 2840
Planarities with less than four sites: {'GLN:plan1': 58, 'HIS:plan': 23, 'TYR:plan': 134, 'ASN:plan1': 192, 'TRP:plan': 16, 'ASP:plan': 180, 'PHE:plan': 132, 'GLU:plan': 205, 'ARG:plan': 48}
Unresolved non-hydrogen planarities: 5074
Time building chain proxies: 5.24, per 1000 atoms: 0.75
Number of scatterers: 6945
At special positions: 0
Unit cell: (134.703, 146.37, 256.677, 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 2315 7.00
C 4630 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: 1.65
Conformation dependent library (CDL) restraints added in 2.5 seconds
4618 Ramachandran restraints generated.
2309 Oldfield, 0 Emsley, 2309 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: 2.67
Creating SS restraints...
No hydrogen bonds defined for protein.
Restraints generated for nucleic acids:
0 hydrogen bonds
0 hydrogen bond angles
0 basepair planarities
0 basepair parallelities
0 stacking parallelities
Total time for adding SS restraints: 0.00
Time building geometry restraints manager: 1.86 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: 2312
1.36 - 1.41: 0
1.41 - 1.45: 123
1.45 - 1.50: 2192
1.50 - 1.54: 2315
Bond restraints: 6942
Sorted by residual:
bond pdb=" CA VAL A1094 "
pdb=" C VAL A1094 "
ideal model delta sigma weight residual
1.525 1.540 -0.015 8.80e-03 1.29e+04 2.76e+00
bond pdb=" N ASP A 442 "
pdb=" CA ASP A 442 "
ideal model delta sigma weight residual
1.457 1.473 -0.016 1.29e-02 6.01e+03 1.54e+00
bond pdb=" CA ASP A1500 "
pdb=" C ASP A1500 "
ideal model delta sigma weight residual
1.523 1.532 -0.009 8.40e-03 1.42e+04 1.04e+00
bond pdb=" N ASN A1839 "
pdb=" CA ASN A1839 "
ideal model delta sigma weight residual
1.457 1.470 -0.013 1.29e-02 6.01e+03 9.99e-01
bond pdb=" N SER A1242 "
pdb=" CA SER A1242 "
ideal model delta sigma weight residual
1.457 1.470 -0.013 1.29e-02 6.01e+03 9.78e-01
... (remaining 6937 not shown)
Histogram of bond angle deviations from ideal:
105.27 - 110.81: 1225
110.81 - 116.35: 2113
116.35 - 121.89: 2570
121.89 - 127.43: 1022
127.43 - 132.97: 9
Bond angle restraints: 6939
Sorted by residual:
angle pdb=" C ALA A 441 "
pdb=" N ASP A 442 "
pdb=" CA ASP A 442 "
ideal model delta sigma weight residual
121.54 132.97 -11.43 1.91e+00 2.74e-01 3.58e+01
angle pdb=" C PHE A2069 "
pdb=" N ASP A2070 "
pdb=" CA ASP A2070 "
ideal model delta sigma weight residual
121.54 131.75 -10.21 1.91e+00 2.74e-01 2.86e+01
angle pdb=" C GLN A 193 "
pdb=" N ARG A 194 "
pdb=" CA ARG A 194 "
ideal model delta sigma weight residual
121.58 112.24 9.34 1.95e+00 2.63e-01 2.29e+01
angle pdb=" N TYR A2223 "
pdb=" CA TYR A2223 "
pdb=" C TYR A2223 "
ideal model delta sigma weight residual
114.75 109.14 5.61 1.26e+00 6.30e-01 1.98e+01
angle pdb=" C LYS A 76 "
pdb=" N GLU A 77 "
pdb=" CA GLU A 77 "
ideal model delta sigma weight residual
120.31 114.02 6.29 1.52e+00 4.33e-01 1.71e+01
... (remaining 6934 not shown)
Histogram of dihedral angle deviations from ideal:
0.00 - 5.68: 1687
5.68 - 11.36: 505
11.36 - 17.04: 98
17.04 - 22.71: 19
22.71 - 28.39: 3
Dihedral angle restraints: 2312
sinusoidal: 0
harmonic: 2312
Sorted by residual:
dihedral pdb=" CA TYR A2213 "
pdb=" C TYR A2213 "
pdb=" N ASP A2214 "
pdb=" CA ASP A2214 "
ideal model delta harmonic sigma weight residual
180.00 151.61 28.39 0 5.00e+00 4.00e-02 3.22e+01
dihedral pdb=" CA THR A1234 "
pdb=" C THR A1234 "
pdb=" N GLY A1235 "
pdb=" CA GLY A1235 "
ideal model delta harmonic sigma weight residual
180.00 154.19 25.81 0 5.00e+00 4.00e-02 2.67e+01
dihedral pdb=" CA GLU A1212 "
pdb=" C GLU A1212 "
pdb=" N LEU A1213 "
pdb=" CA LEU A1213 "
ideal model delta harmonic sigma weight residual
-180.00 -156.35 -23.65 0 5.00e+00 4.00e-02 2.24e+01
... (remaining 2309 not shown)
Chirality restraints: 0
Planarity restraints: 0
Histogram of nonbonded interaction distances:
2.60 - 3.06: 1995
3.06 - 3.52: 2446
3.52 - 3.98: 4853
3.98 - 4.44: 6241
4.44 - 4.90: 9761
Nonbonded interactions: 25296
Sorted by model distance:
nonbonded pdb=" N ASP A 442 "
pdb=" N ASN A 443 "
model vdw
2.600 2.560
nonbonded pdb=" N ASP A1812 "
pdb=" N LEU A1813 "
model vdw
2.603 2.560
nonbonded pdb=" N ILE A1809 "
pdb=" N GLY A1810 "
model vdw
2.606 2.560
nonbonded pdb=" N ASP A2214 "
pdb=" N MET A2215 "
model vdw
2.618 2.560
nonbonded pdb=" N GLY A1088 "
pdb=" N PHE A1089 "
model vdw
2.627 2.560
... (remaining 25291 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: 4.590
Set stop_for_unknowns flag: 0.000
Assert model is a single copy model: 0.000
Assert all atoms have isotropic ADPs: 0.000
Construct map_model_manager: 0.000
Extract box with map and model: 15.780
Check model and map are aligned: 0.110
Set scattering table: 0.070
Process input model: 20.760
Find NCS groups from input model: 0.570
Set up NCS constraints: 0.040
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:2.660
Set ADP refinement strategy: 0.000
Make a string to write initial .geo file:0.000
Internal consistency checks: 0.000
Total: 44.590
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6920
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 0.016 6942 Z= 0.171
Angle : 0.883 11.435 6939 Z= 0.561
Chirality : 0.000 0.000 0
Planarity : 0.000 0.000 0
Dihedral : 5.650 28.393 2312
Min Nonbonded Distance : 2.600
Molprobity Statistics.
All-atom Clashscore : 0.00
Ramachandran Plot:
Outliers : 0.78 %
Allowed : 8.92 %
Favored : 90.30 %
Rotamer:
Outliers : 0.00 %
Allowed : 0.00 %
Favored : 0.00 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 2.00 %
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: -1.59 (0.16), residues: 2309
helix: 0.26 (0.21), residues: 569
sheet: -0.42 (0.26), residues: 374
loop : -1.90 (0.16), residues: 1366
Max deviation from planes:
Type MaxDev MeanDev LineInFile
*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
4618 Ramachandran restraints generated.
2309 Oldfield, 0 Emsley, 2309 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
4618 Ramachandran restraints generated.
2309 Oldfield, 0 Emsley, 2309 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
44 residues out of total 2094 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 44
time to evaluate : 1.184
Fit side-chains
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: 44
average time/residue: 0.0544
time to fit residues: 5.9690
Evaluate side-chains
44 residues out of total 2094 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 44
time to evaluate : 0.986
Switching outliers to nearest non-outliers
outliers start: 0
outliers final: 0
residues processed: 0
time to fit residues: 1.3176
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 231
random chunks:
chunk 195 optimal weight: 6.9990
chunk 175 optimal weight: 0.7980
chunk 97 optimal weight: 10.0000
chunk 59 optimal weight: 4.9990
chunk 118 optimal weight: 0.4980
chunk 93 optimal weight: 0.0020
chunk 181 optimal weight: 3.9990
chunk 70 optimal weight: 0.0570
chunk 110 optimal weight: 5.9990
chunk 134 optimal weight: 2.9990
chunk 209 optimal weight: 3.9990
overall best weight: 0.8708
-------------------------------------------------------------------------------
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: 0.7364
moved from start: 0.3760
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.002 0.026 6942 Z= 0.126
Angle : 0.520 5.275 6939 Z= 0.326
Chirality : 0.000 0.000 0
Planarity : 0.000 0.000 0
Dihedral : 4.362 22.589 2312
Min Nonbonded Distance : 2.593
Molprobity Statistics.
All-atom Clashscore : 3.17
Ramachandran Plot:
Outliers : 0.69 %
Allowed : 7.49 %
Favored : 91.81 %
Rotamer:
Outliers : 0.00 %
Allowed : 0.00 %
Favored : 0.00 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 2.00 %
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: -1.07 (0.17), residues: 2309
helix: 1.51 (0.22), residues: 553
sheet: -0.54 (0.25), residues: 410
loop : -1.82 (0.16), residues: 1346
Max deviation from planes:
Type MaxDev MeanDev LineInFile
*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
4618 Ramachandran restraints generated.
2309 Oldfield, 0 Emsley, 2309 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
4618 Ramachandran restraints generated.
2309 Oldfield, 0 Emsley, 2309 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
44 residues out of total 2094 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 44
time to evaluate : 1.179
Fit side-chains
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: 44
average time/residue: 0.0599
time to fit residues: 6.7845
Evaluate side-chains
44 residues out of total 2094 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 44
time to evaluate : 1.085
Switching outliers to nearest non-outliers
outliers start: 0
outliers final: 0
residues processed: 0
time to fit residues: 1.4094
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 231
random chunks:
chunk 116 optimal weight: 4.9990
chunk 65 optimal weight: 10.0000
chunk 174 optimal weight: 0.8980
chunk 142 optimal weight: 0.0170
chunk 57 optimal weight: 9.9990
chunk 210 optimal weight: 4.9990
chunk 227 optimal weight: 20.0000
chunk 187 optimal weight: 10.0000
chunk 208 optimal weight: 6.9990
chunk 71 optimal weight: 0.4980
chunk 168 optimal weight: 2.9990
overall best weight: 1.8822
-------------------------------------------------------------------------------
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: 0.7666
moved from start: 0.7192
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.034 6942 Z= 0.231
Angle : 0.800 8.296 6939 Z= 0.503
Chirality : 0.000 0.000 0
Planarity : 0.000 0.000 0
Dihedral : 5.942 26.175 2312
Min Nonbonded Distance : 2.471
Molprobity Statistics.
All-atom Clashscore : 11.51
Ramachandran Plot:
Outliers : 0.69 %
Allowed : 10.18 %
Favored : 89.13 %
Rotamer:
Outliers : 0.00 %
Allowed : 0.00 %
Favored : 0.00 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 2.00 %
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: -1.88 (0.17), residues: 2309
helix: 0.40 (0.26), residues: 404
sheet: -1.13 (0.26), residues: 386
loop : -1.84 (0.15), residues: 1519
Max deviation from planes:
Type MaxDev MeanDev LineInFile
*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
4618 Ramachandran restraints generated.
2309 Oldfield, 0 Emsley, 2309 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
4618 Ramachandran restraints generated.
2309 Oldfield, 0 Emsley, 2309 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
44 residues out of total 2094 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 44
time to evaluate : 0.970
Fit side-chains
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: 44
average time/residue: 0.0581
time to fit residues: 6.5289
Evaluate side-chains
44 residues out of total 2094 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 44
time to evaluate : 0.973
Switching outliers to nearest non-outliers
outliers start: 0
outliers final: 0
residues processed: 0
time to fit residues: 1.3959
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 231
random chunks:
chunk 207 optimal weight: 5.9990
chunk 158 optimal weight: 0.0050
chunk 109 optimal weight: 7.9990
chunk 23 optimal weight: 3.9990
chunk 100 optimal weight: 0.7980
chunk 141 optimal weight: 7.9990
chunk 210 optimal weight: 4.9990
chunk 223 optimal weight: 4.9990
chunk 110 optimal weight: 0.8980
chunk 199 optimal weight: 6.9990
chunk 60 optimal weight: 10.0000
overall best weight: 2.1398
-------------------------------------------------------------------------------
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: 0.7772
moved from start: 0.9372
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.053 6942 Z= 0.255
Angle : 0.857 11.786 6939 Z= 0.531
Chirality : 0.000 0.000 0
Planarity : 0.000 0.000 0
Dihedral : 6.317 23.527 2312
Min Nonbonded Distance : 2.416
Molprobity Statistics.
All-atom Clashscore : 16.26
Ramachandran Plot:
Outliers : 0.87 %
Allowed : 12.13 %
Favored : 87.01 %
Rotamer:
Outliers : 0.00 %
Allowed : 0.00 %
Favored : 0.00 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 2.00 %
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: -2.64 (0.16), residues: 2309
helix: -0.85 (0.27), residues: 348
sheet: -1.14 (0.30), residues: 304
loop : -2.24 (0.14), residues: 1657
Max deviation from planes:
Type MaxDev MeanDev LineInFile
*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
4618 Ramachandran restraints generated.
2309 Oldfield, 0 Emsley, 2309 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
4618 Ramachandran restraints generated.
2309 Oldfield, 0 Emsley, 2309 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
44 residues out of total 2094 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 44
time to evaluate : 1.020
Fit side-chains
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: 44
average time/residue: 0.0707
time to fit residues: 7.8350
Evaluate side-chains
44 residues out of total 2094 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 44
time to evaluate : 1.029
Switching outliers to nearest non-outliers
outliers start: 0
outliers final: 0
residues processed: 0
time to fit residues: 1.4496
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 231
random chunks:
chunk 185 optimal weight: 3.9990
chunk 126 optimal weight: 8.9990
chunk 3 optimal weight: 0.7980
chunk 166 optimal weight: 3.9990
chunk 92 optimal weight: 9.9990
chunk 190 optimal weight: 10.0000
chunk 154 optimal weight: 10.0000
chunk 0 optimal weight: 2.9990
chunk 114 optimal weight: 9.9990
chunk 200 optimal weight: 10.0000
chunk 56 optimal weight: 9.9990
overall best weight: 4.1588
-------------------------------------------------------------------------------
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: 0.7957
moved from start: 1.2553
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.006 0.082 6942 Z= 0.466
Angle : 1.331 24.789 6939 Z= 0.825
Chirality : 0.000 0.000 0
Planarity : 0.000 0.000 0
Dihedral : 9.110 37.499 2312
Min Nonbonded Distance : 2.347
Molprobity Statistics.
All-atom Clashscore : 35.57
Ramachandran Plot:
Outliers : 1.00 %
Allowed : 18.93 %
Favored : 80.08 %
Rotamer:
Outliers : 0.00 %
Allowed : 0.00 %
Favored : 0.00 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 2.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.22 %
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: -3.75 (0.15), residues: 2309
helix: -2.78 (0.24), residues: 293
sheet: -1.56 (0.32), residues: 245
loop : -2.83 (0.13), residues: 1771
Max deviation from planes:
Type MaxDev MeanDev LineInFile
*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
4618 Ramachandran restraints generated.
2309 Oldfield, 0 Emsley, 2309 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
4618 Ramachandran restraints generated.
2309 Oldfield, 0 Emsley, 2309 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
44 residues out of total 2094 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 44
time to evaluate : 0.935
Fit side-chains
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: 44
average time/residue: 0.0611
time to fit residues: 6.8018
Evaluate side-chains
44 residues out of total 2094 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 44
time to evaluate : 1.060
Switching outliers to nearest non-outliers
outliers start: 0
outliers final: 0
residues processed: 0
time to fit residues: 1.5120
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 231
random chunks:
chunk 75 optimal weight: 10.0000
chunk 201 optimal weight: 10.0000
chunk 44 optimal weight: 0.0010
chunk 131 optimal weight: 20.0000
chunk 55 optimal weight: 10.0000
chunk 223 optimal weight: 4.9990
chunk 185 optimal weight: 4.9990
chunk 103 optimal weight: 9.9990
chunk 18 optimal weight: 8.9990
chunk 73 optimal weight: 8.9990
chunk 117 optimal weight: 9.9990
overall best weight: 5.5994
-------------------------------------------------------------------------------
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: 0.8061
moved from start: 1.4657
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.008 0.101 6942 Z= 0.588
Angle : 1.556 24.113 6939 Z= 0.979
Chirality : 0.000 0.000 0
Planarity : 0.000 0.000 0
Dihedral : 10.234 48.109 2312
Min Nonbonded Distance : 2.328
Molprobity Statistics.
All-atom Clashscore : 52.04
Ramachandran Plot:
Outliers : 1.08 %
Allowed : 24.73 %
Favored : 74.19 %
Rotamer:
Outliers : 0.00 %
Allowed : 0.00 %
Favored : 0.00 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 2.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.62 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: -4.61 (0.15), residues: 2309
helix: -3.77 (0.20), residues: 288
sheet: -1.86 (0.37), residues: 199
loop : -3.41 (0.12), residues: 1822
Max deviation from planes:
Type MaxDev MeanDev LineInFile
*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
4618 Ramachandran restraints generated.
2309 Oldfield, 0 Emsley, 2309 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
4618 Ramachandran restraints generated.
2309 Oldfield, 0 Emsley, 2309 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
44 residues out of total 2094 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 44
time to evaluate : 1.089
Fit side-chains
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: 44
average time/residue: 0.0613
time to fit residues: 6.9174
Evaluate side-chains
44 residues out of total 2094 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 44
time to evaluate : 1.021
Switching outliers to nearest non-outliers
outliers start: 0
outliers final: 0
residues processed: 0
time to fit residues: 1.4476
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 231
random chunks:
chunk 215 optimal weight: 10.0000
chunk 25 optimal weight: 6.9990
chunk 127 optimal weight: 5.9990
chunk 163 optimal weight: 4.9990
chunk 126 optimal weight: 0.9990
chunk 188 optimal weight: 7.9990
chunk 124 optimal weight: 2.9990
chunk 222 optimal weight: 4.9990
chunk 139 optimal weight: 0.0870
chunk 135 optimal weight: 0.9980
chunk 102 optimal weight: 3.9990
overall best weight: 1.8164
-------------------------------------------------------------------------------
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: 0.7977
moved from start: 1.4108
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.039 6942 Z= 0.217
Angle : 0.828 17.003 6939 Z= 0.512
Chirality : 0.000 0.000 0
Planarity : 0.000 0.000 0
Dihedral : 6.999 26.388 2312
Min Nonbonded Distance : 2.484
Molprobity Statistics.
All-atom Clashscore : 19.32
Ramachandran Plot:
Outliers : 0.87 %
Allowed : 17.54 %
Favored : 81.59 %
Rotamer:
Outliers : 0.00 %
Allowed : 0.00 %
Favored : 0.00 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 2.00 %
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: -4.35 (0.15), residues: 2309
helix: -3.26 (0.23), residues: 315
sheet: -2.26 (0.31), residues: 273
loop : -3.19 (0.13), residues: 1721
Max deviation from planes:
Type MaxDev MeanDev LineInFile
*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
4618 Ramachandran restraints generated.
2309 Oldfield, 0 Emsley, 2309 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
4618 Ramachandran restraints generated.
2309 Oldfield, 0 Emsley, 2309 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
44 residues out of total 2094 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 44
time to evaluate : 1.098
Fit side-chains
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: 44
average time/residue: 0.0602
time to fit residues: 6.7880
Evaluate side-chains
44 residues out of total 2094 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 44
time to evaluate : 0.943
Switching outliers to nearest non-outliers
outliers start: 0
outliers final: 0
residues processed: 0
time to fit residues: 1.4320
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 231
random chunks:
chunk 137 optimal weight: 6.9990
chunk 88 optimal weight: 0.8980
chunk 132 optimal weight: 0.0000
chunk 67 optimal weight: 2.9990
chunk 43 optimal weight: 3.9990
chunk 141 optimal weight: 1.9990
chunk 151 optimal weight: 4.9990
chunk 110 optimal weight: 3.9990
chunk 20 optimal weight: 8.9990
chunk 175 optimal weight: 7.9990
chunk 202 optimal weight: 8.9990
overall best weight: 1.9790
-------------------------------------------------------------------------------
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: 0.8000
moved from start: 1.4554
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.041 6942 Z= 0.232
Angle : 0.796 10.690 6939 Z= 0.506
Chirality : 0.000 0.000 0
Planarity : 0.000 0.000 0
Dihedral : 6.748 29.313 2312
Min Nonbonded Distance : 2.490
Molprobity Statistics.
All-atom Clashscore : 23.01
Ramachandran Plot:
Outliers : 0.87 %
Allowed : 23.39 %
Favored : 75.75 %
Rotamer:
Outliers : 0.00 %
Allowed : 0.00 %
Favored : 0.00 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 2.00 %
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: -4.33 (0.15), residues: 2309
helix: -2.81 (0.25), residues: 303
sheet: -2.02 (0.33), residues: 253
loop : -3.32 (0.13), residues: 1753
Max deviation from planes:
Type MaxDev MeanDev LineInFile
*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
4618 Ramachandran restraints generated.
2309 Oldfield, 0 Emsley, 2309 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
4618 Ramachandran restraints generated.
2309 Oldfield, 0 Emsley, 2309 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
44 residues out of total 2094 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 44
time to evaluate : 1.098
Fit side-chains
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: 44
average time/residue: 0.0601
time to fit residues: 6.8313
Evaluate side-chains
44 residues out of total 2094 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 44
time to evaluate : 1.032
Switching outliers to nearest non-outliers
outliers start: 0
outliers final: 0
residues processed: 0
time to fit residues: 1.3845
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 231
random chunks:
chunk 213 optimal weight: 7.9990
chunk 194 optimal weight: 20.0000
chunk 207 optimal weight: 7.9990
chunk 124 optimal weight: 0.6980
chunk 90 optimal weight: 30.0000
chunk 162 optimal weight: 6.9990
chunk 63 optimal weight: 4.9990
chunk 187 optimal weight: 9.9990
chunk 196 optimal weight: 10.0000
chunk 206 optimal weight: 4.9990
chunk 136 optimal weight: 9.9990
overall best weight: 5.1388
-------------------------------------------------------------------------------
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: 0.8091
moved from start: 1.5966
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.007 0.082 6942 Z= 0.538
Angle : 1.362 12.531 6939 Z= 0.881
Chirality : 0.000 0.000 0
Planarity : 0.000 0.000 0
Dihedral : 9.161 44.642 2312
Min Nonbonded Distance : 2.360
Molprobity Statistics.
All-atom Clashscore : 46.55
Ramachandran Plot:
Outliers : 0.95 %
Allowed : 28.58 %
Favored : 70.46 %
Rotamer:
Outliers : 0.00 %
Allowed : 0.00 %
Favored : 0.00 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 2.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.22 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: -4.86 (0.15), residues: 2309
helix: -3.40 (0.24), residues: 261
sheet: -2.12 (0.37), residues: 199
loop : -3.70 (0.12), residues: 1849
Max deviation from planes:
Type MaxDev MeanDev LineInFile
*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
4618 Ramachandran restraints generated.
2309 Oldfield, 0 Emsley, 2309 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
4618 Ramachandran restraints generated.
2309 Oldfield, 0 Emsley, 2309 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
44 residues out of total 2094 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 44
time to evaluate : 0.960
Fit side-chains
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: 44
average time/residue: 0.0629
time to fit residues: 6.9272
Evaluate side-chains
44 residues out of total 2094 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 44
time to evaluate : 1.004
Switching outliers to nearest non-outliers
outliers start: 0
outliers final: 0
residues processed: 0
time to fit residues: 1.4624
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 231
random chunks:
chunk 219 optimal weight: 6.9990
chunk 133 optimal weight: 6.9990
chunk 104 optimal weight: 9.9990
chunk 152 optimal weight: 5.9990
chunk 230 optimal weight: 7.9990
chunk 211 optimal weight: 4.9990
chunk 183 optimal weight: 7.9990
chunk 19 optimal weight: 1.9990
chunk 141 optimal weight: 7.9990
chunk 112 optimal weight: 1.9990
chunk 145 optimal weight: 8.9990
overall best weight: 4.3990
-------------------------------------------------------------------------------
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: 0.8091
moved from start: 1.6559
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.006 0.069 6942 Z= 0.464
Angle : 1.220 11.172 6939 Z= 0.793
Chirality : 0.000 0.000 0
Planarity : 0.000 0.000 0
Dihedral : 8.680 47.681 2312
Min Nonbonded Distance : 2.424
Molprobity Statistics.
All-atom Clashscore : 42.86
Ramachandran Plot:
Outliers : 1.00 %
Allowed : 28.41 %
Favored : 70.59 %
Rotamer:
Outliers : 0.00 %
Allowed : 0.00 %
Favored : 0.00 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 2.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.13 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: -4.98 (0.15), residues: 2309
helix: -3.53 (0.24), residues: 262
sheet: -2.14 (0.40), residues: 182
loop : -3.77 (0.12), residues: 1865
Max deviation from planes:
Type MaxDev MeanDev LineInFile
********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
4618 Ramachandran restraints generated.
2309 Oldfield, 0 Emsley, 2309 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
4618 Ramachandran restraints generated.
2309 Oldfield, 0 Emsley, 2309 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
44 residues out of total 2094 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 44
time to evaluate : 0.999
Fit side-chains
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: 44
average time/residue: 0.0600
time to fit residues: 6.7547
Evaluate side-chains
44 residues out of total 2094 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 44
time to evaluate : 1.004
Switching outliers to nearest non-outliers
outliers start: 0
outliers final: 0
residues processed: 0
time to fit residues: 1.4230
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 231
random chunks:
chunk 195 optimal weight: 0.0000
chunk 56 optimal weight: 0.8980
chunk 168 optimal weight: 7.9990
chunk 27 optimal weight: 2.9990
chunk 50 optimal weight: 2.9990
chunk 183 optimal weight: 4.9990
chunk 76 optimal weight: 2.9990
chunk 188 optimal weight: 0.6980
chunk 23 optimal weight: 4.9990
chunk 33 optimal weight: 0.1980
chunk 161 optimal weight: 0.0370
overall best weight: 0.3662
-------------------------------------------------------------------------------
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 = 0.3497 r_free = 0.3497 target = 0.106050 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2754 r_free = 0.2754 target = 0.061167 restraints weight = 18014.553|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.2733 r_free = 0.2733 target = 0.060214 restraints weight = 20298.453|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 18)----------------|
| r_work = 0.2733 r_free = 0.2733 target = 0.060209 restraints weight = 22467.072|
|-----------------------------------------------------------------------------|
r_work (final): 0.2616
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8117
moved from start: 1.5635
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.001 0.016 6942 Z= 0.081
Angle : 0.489 5.869 6939 Z= 0.313
Chirality : 0.000 0.000 0
Planarity : 0.000 0.000 0
Dihedral : 5.049 26.708 2312
Min Nonbonded Distance : 2.580
Molprobity Statistics.
All-atom Clashscore : 6.76
Ramachandran Plot:
Outliers : 0.91 %
Allowed : 12.30 %
Favored : 86.79 %
Rotamer:
Outliers : 0.00 %
Allowed : 0.00 %
Favored : 0.00 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 2.00 %
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: -4.51 (0.15), residues: 2309
helix: -2.74 (0.25), residues: 338
sheet: -2.23 (0.38), residues: 200
loop : -3.46 (0.13), residues: 1771
Max deviation from planes:
Type MaxDev MeanDev LineInFile
Origin is already at (0, 0, 0), no shifts will be applied
===============================================================================
Job complete
usr+sys time: 1549.14 seconds
wall clock time: 28 minutes 19.58 seconds (1699.58 seconds total)