Starting phenix.real_space_refine
on Tue Jan 14 20:58:12 2025 by dcliebschner
===============================================================================
Processing files:
-------------------------------------------------------------------------------
Found model, /net/cci-nas-00/data/ceres_data/9etm_19944/01_2025/9etm_19944.cif
Found real_map, /net/cci-nas-00/data/ceres_data/9etm_19944/01_2025/9etm_19944.map
Processing PHIL parameters:
-------------------------------------------------------------------------------
Adding command-line PHIL:
-------------------------
refinement.macro_cycles=10
scattering_table=electron
resolution=3.35
write_initial_geo_file=False
Final processed PHIL parameters:
-------------------------------------------------------------------------------
data_manager {
real_map_files = "/net/cci-nas-00/data/ceres_data/9etm_19944/01_2025/9etm_19944.map"
default_real_map = "/net/cci-nas-00/data/ceres_data/9etm_19944/01_2025/9etm_19944.map"
model {
file = "/net/cci-nas-00/data/ceres_data/9etm_19944/01_2025/9etm_19944.cif"
}
default_model = "/net/cci-nas-00/data/ceres_data/9etm_19944/01_2025/9etm_19944.cif"
}
resolution = 3.35
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= 0.000 sd= 0.015
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: 5
Type Number sf(0) Gaussians
P 5 5.49 5
S 32 5.16 5
C 4810 2.51 5
N 1219 2.21 5
O 1338 1.98 5
sf(0) = scattering factor at diffraction angle 0.
Process input model
Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s
Monomer Library directory:
"/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
Total number of atoms: 7404
Number of models: 1
Model: ""
Number of chains: 15
Chain: "G"
Number of atoms: 344
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 42, 344
Classifications: {'peptide': 42}
Link IDs: {'PTRANS': 1, 'TRANS': 40}
Chain: "I"
Number of atoms: 304
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 39, 304
Classifications: {'peptide': 39}
Link IDs: {'PTRANS': 3, 'TRANS': 35}
Chain: "E"
Number of atoms: 365
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 46, 365
Classifications: {'peptide': 46}
Modifications used: {'COO': 1}
Link IDs: {'PTRANS': 4, 'TRANS': 41}
Chain: "C"
Number of atoms: 377
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 47, 377
Classifications: {'peptide': 47}
Link IDs: {'PTRANS': 1, 'TRANS': 45}
Chain: "A"
Number of atoms: 2207
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 290, 2207
Classifications: {'peptide': 290}
Modifications used: {'COO': 1}
Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 277}
Chain: "H"
Number of atoms: 344
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 42, 344
Classifications: {'peptide': 42}
Link IDs: {'PTRANS': 1, 'TRANS': 40}
Chain: "J"
Number of atoms: 304
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 39, 304
Classifications: {'peptide': 39}
Link IDs: {'PTRANS': 3, 'TRANS': 35}
Chain: "F"
Number of atoms: 365
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 46, 365
Classifications: {'peptide': 46}
Modifications used: {'COO': 1}
Link IDs: {'PTRANS': 4, 'TRANS': 41}
Chain: "D"
Number of atoms: 377
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 47, 377
Classifications: {'peptide': 47}
Link IDs: {'PTRANS': 1, 'TRANS': 45}
Chain: "B"
Number of atoms: 2207
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 290, 2207
Classifications: {'peptide': 290}
Modifications used: {'COO': 1}
Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 277}
Chain: "G"
Number of atoms: 42
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 1, 42
Unusual residues: {'PLC': 1}
Classifications: {'undetermined': 1}
Chain: "C"
Number of atoms: 42
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 1, 42
Unusual residues: {'PLC': 1}
Classifications: {'undetermined': 1}
Chain: "H"
Number of atoms: 42
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 1, 42
Unusual residues: {'PLC': 1}
Classifications: {'undetermined': 1}
Chain: "D"
Number of atoms: 42
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 1, 42
Unusual residues: {'PLC': 1}
Classifications: {'undetermined': 1}
Chain: "B"
Number of atoms: 42
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 1, 42
Unusual residues: {'PLC': 1}
Classifications: {'undetermined': 1}
Time building chain proxies: 5.10, per 1000 atoms: 0.69
Number of scatterers: 7404
At special positions: 0
Unit cell: (94.581, 133.083, 95.418, 90, 90, 90)
Space group: P 1 (No. 1)
Number of sites at special positions: 0
Number of scattering types: 5
Type Number sf(0)
S 32 16.00
P 5 15.00
O 1338 8.00
N 1219 7.00
C 4810 6.00
sf(0) = scattering factor at diffraction angle 0.
Number of disulfides: simple=2, symmetry=0
Simple disulfide: pdb=" SG CYS A 70 " - pdb=" SG CYS A 256 " distance=2.04
Simple disulfide: pdb=" SG CYS B 70 " - pdb=" SG CYS B 256 " distance=2.04
Automatic linking
Parameters for automatic linking
Linking & cutoffs
Metal : Auto - 3.00
Amino acid : True - 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: 1.94
Conformation dependent library (CDL) restraints added in 992.6 milliseconds
1816 Ramachandran restraints generated.
908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
Adding C-beta torsion restraints...
Number of C-beta restraints generated: 1700
Finding SS restraints...
Secondary structure from input PDB file:
18 helices and 2 sheets defined
34.8% alpha, 37.1% beta
0 base pairs and 0 stacking pairs defined.
Time for finding SS restraints: 0.75
Creating SS restraints...
Processing helix chain 'G' and resid 7 through 16
removed outlier: 4.078A pdb=" N SER G 13 " --> pdb=" O SER G 9 " (cutoff:3.500A)
removed outlier: 3.508A pdb=" N ILE G 14 " --> pdb=" O ILE G 10 " (cutoff:3.500A)
Processing helix chain 'G' and resid 17 through 41
Processing helix chain 'I' and resid 11 through 45
removed outlier: 4.114A pdb=" N GLN I 15 " --> pdb=" O PRO I 11 " (cutoff:3.500A)
Proline residue: I 40 - end of helix
Processing helix chain 'E' and resid 10 through 38
removed outlier: 4.304A pdb=" N GLY E 16 " --> pdb=" O GLY E 12 " (cutoff:3.500A)
removed outlier: 5.473A pdb=" N VAL E 27 " --> pdb=" O HIS E 23 " (cutoff:3.500A)
Proline residue: E 28 - end of helix
Processing helix chain 'E' and resid 48 through 53
Processing helix chain 'C' and resid 78 through 104
Processing helix chain 'C' and resid 104 through 123
Processing helix chain 'A' and resid 62 through 68
Processing helix chain 'A' and resid 291 through 293
No H-bonds generated for 'chain 'A' and resid 291 through 293'
Processing helix chain 'H' and resid 8 through 16
removed outlier: 3.989A pdb=" N SER H 13 " --> pdb=" O SER H 9 " (cutoff:3.500A)
removed outlier: 3.536A pdb=" N ILE H 14 " --> pdb=" O ILE H 10 " (cutoff:3.500A)
Processing helix chain 'H' and resid 17 through 41
Processing helix chain 'J' and resid 11 through 45
removed outlier: 4.133A pdb=" N GLN J 15 " --> pdb=" O PRO J 11 " (cutoff:3.500A)
Proline residue: J 40 - end of helix
Processing helix chain 'F' and resid 10 through 38
removed outlier: 4.321A pdb=" N GLY F 16 " --> pdb=" O GLY F 12 " (cutoff:3.500A)
removed outlier: 5.482A pdb=" N VAL F 27 " --> pdb=" O HIS F 23 " (cutoff:3.500A)
Proline residue: F 28 - end of helix
Processing helix chain 'F' and resid 47 through 52
Processing helix chain 'D' and resid 78 through 104
Processing helix chain 'D' and resid 104 through 123
Processing helix chain 'B' and resid 62 through 68
Processing helix chain 'B' and resid 291 through 293
No H-bonds generated for 'chain 'B' and resid 291 through 293'
Processing sheet with id=AA1, first strand: chain 'A' and resid 80 through 90
removed outlier: 6.144A pdb=" N PHE A 93 " --> pdb=" O LEU A 89 " (cutoff:3.500A)
removed outlier: 6.471A pdb=" N GLN A 161 " --> pdb=" O VAL A 165 " (cutoff:3.500A)
removed outlier: 4.918A pdb=" N VAL A 165 " --> pdb=" O GLN A 161 " (cutoff:3.500A)
removed outlier: 6.540A pdb=" N LEU A 209 " --> pdb=" O VAL A 205 " (cutoff:3.500A)
removed outlier: 6.358A pdb=" N LEU A 265 " --> pdb=" O ALA A 261 " (cutoff:3.500A)
removed outlier: 4.023A pdb=" N GLN A 306 " --> pdb=" O ASP A 302 " (cutoff:3.500A)
Processing sheet with id=AA2, first strand: chain 'B' and resid 80 through 90
removed outlier: 6.201A pdb=" N PHE B 93 " --> pdb=" O LEU B 89 " (cutoff:3.500A)
removed outlier: 6.449A pdb=" N GLN B 161 " --> pdb=" O VAL B 165 " (cutoff:3.500A)
removed outlier: 5.020A pdb=" N VAL B 165 " --> pdb=" O GLN B 161 " (cutoff:3.500A)
removed outlier: 6.572A pdb=" N LEU B 209 " --> pdb=" O VAL B 205 " (cutoff:3.500A)
removed outlier: 4.077A pdb=" N GLY B 252 " --> pdb=" O GLY B 249 " (cutoff:3.500A)
removed outlier: 6.363A pdb=" N LEU B 265 " --> pdb=" O ALA B 261 " (cutoff:3.500A)
removed outlier: 3.940A pdb=" N GLN B 306 " --> pdb=" O ASP B 302 " (cutoff:3.500A)
531 hydrogen bonds defined for protein.
1530 hydrogen bond angles 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: 2.10
Time building geometry restraints manager: 2.20 seconds
NOTE: a complete listing of the restraints can be obtained by requesting
output of .geo file.
Histogram of bond lengths:
1.20 - 1.33: 1388
1.33 - 1.45: 1907
1.45 - 1.58: 4206
1.58 - 1.70: 10
1.70 - 1.83: 54
Bond restraints: 7565
Sorted by residual:
bond pdb=" CG LEU A 295 "
pdb=" CD1 LEU A 295 "
ideal model delta sigma weight residual
1.521 1.495 0.026 3.30e-02 9.18e+02 6.38e-01
bond pdb=" CG LEU A 311 "
pdb=" CD2 LEU A 311 "
ideal model delta sigma weight residual
1.521 1.498 0.023 3.30e-02 9.18e+02 4.92e-01
bond pdb=" CG LEU B 295 "
pdb=" CD1 LEU B 295 "
ideal model delta sigma weight residual
1.521 1.498 0.023 3.30e-02 9.18e+02 4.70e-01
bond pdb=" CB GLU B 270 "
pdb=" CG GLU B 270 "
ideal model delta sigma weight residual
1.520 1.499 0.021 3.00e-02 1.11e+03 4.68e-01
bond pdb=" CG LEU B 311 "
pdb=" CD2 LEU B 311 "
ideal model delta sigma weight residual
1.521 1.499 0.022 3.30e-02 9.18e+02 4.46e-01
... (remaining 7560 not shown)
Histogram of bond angle deviations from ideal:
0.00 - 1.48: 9847
1.48 - 2.96: 312
2.96 - 4.44: 47
4.44 - 5.93: 14
5.93 - 7.41: 1
Bond angle restraints: 10221
Sorted by residual:
angle pdb=" N PHE G 40 "
pdb=" CA PHE G 40 "
pdb=" C PHE G 40 "
ideal model delta sigma weight residual
112.87 117.03 -4.16 1.20e+00 6.94e-01 1.20e+01
angle pdb=" N GLY A 309 "
pdb=" CA GLY A 309 "
pdb=" C GLY A 309 "
ideal model delta sigma weight residual
113.18 107.72 5.46 2.37e+00 1.78e-01 5.30e+00
angle pdb=" N TRP F 24 "
pdb=" CA TRP F 24 "
pdb=" C TRP F 24 "
ideal model delta sigma weight residual
112.23 115.12 -2.89 1.26e+00 6.30e-01 5.26e+00
angle pdb=" N SER B 122 "
pdb=" CA SER B 122 "
pdb=" C SER B 122 "
ideal model delta sigma weight residual
109.81 114.77 -4.96 2.21e+00 2.05e-01 5.04e+00
angle pdb=" CA CYS B 256 "
pdb=" CB CYS B 256 "
pdb=" SG CYS B 256 "
ideal model delta sigma weight residual
114.40 119.50 -5.10 2.30e+00 1.89e-01 4.92e+00
... (remaining 10216 not shown)
Histogram of dihedral angle deviations from ideal:
0.00 - 34.35: 4387
34.35 - 68.70: 109
68.70 - 103.04: 15
103.04 - 137.39: 10
137.39 - 171.74: 2
Dihedral angle restraints: 4523
sinusoidal: 1877
harmonic: 2646
Sorted by residual:
dihedral pdb=" CA LEU B 311 "
pdb=" C LEU B 311 "
pdb=" N GLU B 312 "
pdb=" CA GLU B 312 "
ideal model delta harmonic sigma weight residual
180.00 150.54 29.46 0 5.00e+00 4.00e-02 3.47e+01
dihedral pdb=" CA TRP A 305 "
pdb=" C TRP A 305 "
pdb=" N GLN A 306 "
pdb=" CA GLN A 306 "
ideal model delta harmonic sigma weight residual
180.00 151.17 28.83 0 5.00e+00 4.00e-02 3.32e+01
dihedral pdb=" CA LEU A 318 "
pdb=" C LEU A 318 "
pdb=" N PRO A 319 "
pdb=" CA PRO A 319 "
ideal model delta harmonic sigma weight residual
-180.00 -151.42 -28.58 0 5.00e+00 4.00e-02 3.27e+01
... (remaining 4520 not shown)
Histogram of chiral volume deviations from ideal:
0.000 - 0.072: 1016
0.072 - 0.143: 108
0.143 - 0.215: 2
0.215 - 0.286: 0
0.286 - 0.358: 1
Chirality restraints: 1127
Sorted by residual:
chirality pdb=" CA PHE G 40 "
pdb=" N PHE G 40 "
pdb=" C PHE G 40 "
pdb=" CB PHE G 40 "
both_signs ideal model delta sigma weight residual
False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.21e+00
chirality pdb=" CA ILE B 99 "
pdb=" N ILE B 99 "
pdb=" C ILE B 99 "
pdb=" CB ILE B 99 "
both_signs ideal model delta sigma weight residual
False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.91e-01
chirality pdb=" CA ILE A 99 "
pdb=" N ILE A 99 "
pdb=" C ILE A 99 "
pdb=" CB ILE A 99 "
both_signs ideal model delta sigma weight residual
False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.31e-01
... (remaining 1124 not shown)
Planarity restraints: 1286
Sorted by residual:
delta sigma weight rms_deltas residual
plane pdb=" CD ARG D 113 " -0.269 9.50e-02 1.11e+02 1.21e-01 1.04e+01
pdb=" NE ARG D 113 " 0.023 2.00e-02 2.50e+03
pdb=" CZ ARG D 113 " -0.018 2.00e-02 2.50e+03
pdb=" NH1 ARG D 113 " 0.010 2.00e-02 2.50e+03
pdb=" NH2 ARG D 113 " -0.003 2.00e-02 2.50e+03
delta sigma weight rms_deltas residual
plane pdb=" CD ARG C 113 " 0.246 9.50e-02 1.11e+02 1.10e-01 7.90e+00
pdb=" NE ARG C 113 " -0.019 2.00e-02 2.50e+03
pdb=" CZ ARG C 113 " 0.009 2.00e-02 2.50e+03
pdb=" NH1 ARG C 113 " -0.006 2.00e-02 2.50e+03
pdb=" NH2 ARG C 113 " 0.005 2.00e-02 2.50e+03
delta sigma weight rms_deltas residual
plane pdb=" CB TYR B 286 " -0.005 2.00e-02 2.50e+03 1.32e-02 3.49e+00
pdb=" CG TYR B 286 " 0.006 2.00e-02 2.50e+03
pdb=" CD1 TYR B 286 " -0.013 2.00e-02 2.50e+03
pdb=" CD2 TYR B 286 " -0.007 2.00e-02 2.50e+03
pdb=" CE1 TYR B 286 " 0.012 2.00e-02 2.50e+03
pdb=" CE2 TYR B 286 " 0.007 2.00e-02 2.50e+03
pdb=" CZ TYR B 286 " 0.021 2.00e-02 2.50e+03
pdb=" OH TYR B 286 " -0.022 2.00e-02 2.50e+03
... (remaining 1283 not shown)
Histogram of nonbonded interaction distances:
2.38 - 2.88: 2732
2.88 - 3.39: 7049
3.39 - 3.89: 11692
3.89 - 4.40: 13093
4.40 - 4.90: 23915
Nonbonded interactions: 58481
Sorted by model distance:
nonbonded pdb=" OH TYR A 257 "
pdb=" OE1 GLN A 259 "
model vdw
2.377 3.040
nonbonded pdb=" OH TYR B 257 "
pdb=" OE1 GLN B 259 "
model vdw
2.401 3.040
nonbonded pdb=" NH1 ARG B 110 "
pdb=" OD1 ASP B 133 "
model vdw
2.440 3.120
nonbonded pdb=" O VAL C 107 "
pdb=" OG1 THR C 111 "
model vdw
2.443 3.040
nonbonded pdb=" O2 PLC C 401 "
pdb=" O3 PLC C 401 "
model vdw
2.444 2.432
... (remaining 58476 not shown)
NOTE: a complete listing of the restraints can be obtained by requesting
output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
reference = chain 'A'
selection = (chain 'B' and resid 55 through 344)
}
ncs_group {
reference = chain 'C'
selection = chain 'D'
}
ncs_group {
reference = chain 'E'
selection = chain 'F'
}
ncs_group {
reference = chain 'G'
selection = chain 'H'
}
ncs_group {
reference = chain 'I'
selection = chain 'J'
}
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 individual isotropic
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: 2.960
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: 0.340
Check model and map are aligned: 0.050
Set scattering table: 0.070
Process input model: 19.920
Find NCS groups from input model: 0.270
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: 0.000
Load rotamer database and sin/cos tables:2.680
Set ADP refinement strategy: 0.000
Make a string to write initial .geo file:0.000
Internal consistency checks: 0.000
Total: 26.340
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7371
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 : 0.003 0.026 7565 Z= 0.174
Angle : 0.643 7.406 10221 Z= 0.359
Chirality : 0.044 0.358 1127
Planarity : 0.007 0.121 1286
Dihedral : 17.420 171.741 2817
Min Nonbonded Distance : 2.377
Molprobity Statistics.
All-atom Clashscore : 2.14
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 2.75 %
Favored : 97.25 %
Rotamer:
Outliers : 0.00 %
Allowed : 2.45 %
Favored : 97.55 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 4.76 %
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: -0.09 (0.27), residues: 908
helix: -0.30 (0.26), residues: 282
sheet: 0.55 (0.26), residues: 394
loop : -0.49 (0.46), residues: 232
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.026 0.004 TRP A 305
HIS 0.007 0.002 HIS B 330
PHE 0.016 0.003 PHE B 127
TYR 0.022 0.006 TYR B 286
ARG 0.021 0.003 ARG D 113
*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
1816 Ramachandran restraints generated.
908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
1816 Ramachandran restraints generated.
908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
191 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 0
poor density : 191
time to evaluate : 0.835
Fit side-chains
REVERT: C 115 GLN cc_start: 0.7925 (tm-30) cc_final: 0.7667 (tm-30)
REVERT: D 115 GLN cc_start: 0.7868 (tm-30) cc_final: 0.7620 (tm-30)
REVERT: B 155 LYS cc_start: 0.7458 (mttp) cc_final: 0.7038 (mtpt)
outliers start: 0
outliers final: 0
residues processed: 191
average time/residue: 0.1856
time to fit residues: 47.9643
Evaluate side-chains
130 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 0
poor density : 130
time to evaluate : 0.788
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 88
random chunks:
chunk 74 optimal weight: 3.9990
chunk 66 optimal weight: 3.9990
chunk 37 optimal weight: 0.9980
chunk 22 optimal weight: 4.9990
chunk 44 optimal weight: 10.0000
chunk 35 optimal weight: 0.0010
chunk 68 optimal weight: 0.9990
chunk 26 optimal weight: 3.9990
chunk 41 optimal weight: 0.4980
chunk 51 optimal weight: 4.9990
chunk 79 optimal weight: 1.9990
overall best weight: 0.8990
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 97 HIS
J 8 GLN
Total number of N/Q/H flips: 2
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4751 r_free = 0.4751 target = 0.220142 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4425 r_free = 0.4425 target = 0.184370 restraints weight = 9351.059|
|-----------------------------------------------------------------------------|
r_work (start): 0.4429 rms_B_bonded: 2.70
r_work: 0.4272 rms_B_bonded: 3.28 restraints_weight: 0.5000
r_work (final): 0.4272
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7335
moved from start: 0.2028
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.004 0.036 7565 Z= 0.248
Angle : 0.746 14.542 10221 Z= 0.387
Chirality : 0.048 0.197 1127
Planarity : 0.005 0.041 1286
Dihedral : 16.912 168.371 1171
Min Nonbonded Distance : 2.434
Molprobity Statistics.
All-atom Clashscore : 6.29
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 1.98 %
Favored : 98.02 %
Rotamer:
Outliers : 2.97 %
Allowed : 9.17 %
Favored : 87.86 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 4.76 %
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: 0.76 (0.28), residues: 908
helix: 1.24 (0.29), residues: 288
sheet: 0.37 (0.25), residues: 394
loop : 0.06 (0.48), residues: 226
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.009 0.001 TRP A 244
HIS 0.004 0.001 HIS B 254
PHE 0.022 0.002 PHE I 29
TYR 0.016 0.002 TYR F 32
ARG 0.003 0.000 ARG A 110
*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
1816 Ramachandran restraints generated.
908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
1816 Ramachandran restraints generated.
908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
166 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 23
poor density : 143
time to evaluate : 0.786
Fit side-chains
REVERT: C 108 ILE cc_start: 0.8031 (mt) cc_final: 0.7804 (tp)
REVERT: C 115 GLN cc_start: 0.8188 (tm-30) cc_final: 0.7897 (tm-30)
REVERT: A 141 ASN cc_start: 0.8768 (m110) cc_final: 0.8559 (m-40)
REVERT: A 298 ARG cc_start: 0.7808 (mtm-85) cc_final: 0.6722 (mtm-85)
REVERT: A 342 MET cc_start: 0.7645 (ttp) cc_final: 0.7390 (tpp)
REVERT: D 91 ASN cc_start: 0.6168 (m-40) cc_final: 0.5966 (t0)
REVERT: D 108 ILE cc_start: 0.8062 (mt) cc_final: 0.7801 (tp)
REVERT: D 115 GLN cc_start: 0.8096 (tm-30) cc_final: 0.7836 (tm-30)
REVERT: B 155 LYS cc_start: 0.7480 (mttp) cc_final: 0.6968 (mtpt)
REVERT: B 298 ARG cc_start: 0.7840 (mtm-85) cc_final: 0.6757 (mtm-85)
outliers start: 23
outliers final: 16
residues processed: 158
average time/residue: 0.1882
time to fit residues: 40.3935
Evaluate side-chains
144 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 16
poor density : 128
time to evaluate : 0.851
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue 7 SER
Chi-restraints excluded: chain E residue 36 MET
Chi-restraints excluded: chain A residue 100 ASN
Chi-restraints excluded: chain A residue 107 SER
Chi-restraints excluded: chain A residue 125 GLU
Chi-restraints excluded: chain A residue 172 THR
Chi-restraints excluded: chain A residue 259 GLN
Chi-restraints excluded: chain A residue 277 MET
Chi-restraints excluded: chain A residue 281 VAL
Chi-restraints excluded: chain A residue 325 SER
Chi-restraints excluded: chain J residue 7 SER
Chi-restraints excluded: chain F residue 36 MET
Chi-restraints excluded: chain D residue 93 SER
Chi-restraints excluded: chain B residue 125 GLU
Chi-restraints excluded: chain B residue 277 MET
Chi-restraints excluded: chain B residue 325 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 88
random chunks:
chunk 52 optimal weight: 3.9990
chunk 61 optimal weight: 0.5980
chunk 26 optimal weight: 3.9990
chunk 36 optimal weight: 0.9980
chunk 74 optimal weight: 0.8980
chunk 16 optimal weight: 0.7980
chunk 6 optimal weight: 0.8980
chunk 70 optimal weight: 0.0770
chunk 75 optimal weight: 2.9990
chunk 15 optimal weight: 1.9990
chunk 71 optimal weight: 1.9990
overall best weight: 0.6538
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
C 120 HIS
A 254 HIS
D 120 HIS
B 254 HIS
Total number of N/Q/H flips: 4
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4774 r_free = 0.4774 target = 0.220761 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4413 r_free = 0.4413 target = 0.182988 restraints weight = 9156.521|
|-----------------------------------------------------------------------------|
r_work (start): 0.4426 rms_B_bonded: 2.71
r_work: 0.4272 rms_B_bonded: 3.30 restraints_weight: 0.5000
r_work (final): 0.4272
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7342
moved from start: 0.2502
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.050 7565 Z= 0.223
Angle : 0.687 10.808 10221 Z= 0.353
Chirality : 0.046 0.193 1127
Planarity : 0.004 0.043 1286
Dihedral : 15.954 165.893 1171
Min Nonbonded Distance : 2.429
Molprobity Statistics.
All-atom Clashscore : 7.70
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 1.87 %
Favored : 98.13 %
Rotamer:
Outliers : 2.97 %
Allowed : 11.63 %
Favored : 85.40 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 4.76 %
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: 0.90 (0.28), residues: 908
helix: 1.45 (0.28), residues: 298
sheet: 0.40 (0.26), residues: 392
loop : 0.04 (0.47), residues: 218
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.010 0.001 TRP D 94
HIS 0.004 0.001 HIS C 120
PHE 0.015 0.002 PHE I 29
TYR 0.015 0.001 TYR B 115
ARG 0.002 0.000 ARG C 113
*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
1816 Ramachandran restraints generated.
908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
1816 Ramachandran restraints generated.
908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
158 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 23
poor density : 135
time to evaluate : 0.857
Fit side-chains
REVERT: I 7 SER cc_start: 0.8773 (OUTLIER) cc_final: 0.8388 (p)
REVERT: C 115 GLN cc_start: 0.8178 (tm-30) cc_final: 0.7861 (tm-30)
REVERT: J 7 SER cc_start: 0.8703 (OUTLIER) cc_final: 0.8334 (p)
REVERT: D 115 GLN cc_start: 0.8066 (tm-30) cc_final: 0.7725 (tm-30)
REVERT: B 231 MET cc_start: 0.7436 (tpt) cc_final: 0.7221 (tpt)
REVERT: B 298 ARG cc_start: 0.7782 (mtm-85) cc_final: 0.6622 (mtm-85)
outliers start: 23
outliers final: 16
residues processed: 145
average time/residue: 0.1901
time to fit residues: 37.5579
Evaluate side-chains
141 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 18
poor density : 123
time to evaluate : 0.844
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue 7 SER
Chi-restraints excluded: chain E residue 15 VAL
Chi-restraints excluded: chain E residue 36 MET
Chi-restraints excluded: chain A residue 100 ASN
Chi-restraints excluded: chain A residue 107 SER
Chi-restraints excluded: chain A residue 125 GLU
Chi-restraints excluded: chain A residue 144 VAL
Chi-restraints excluded: chain A residue 172 THR
Chi-restraints excluded: chain A residue 277 MET
Chi-restraints excluded: chain A residue 325 SER
Chi-restraints excluded: chain J residue 7 SER
Chi-restraints excluded: chain J residue 45 HIS
Chi-restraints excluded: chain F residue 36 MET
Chi-restraints excluded: chain B residue 125 GLU
Chi-restraints excluded: chain B residue 144 VAL
Chi-restraints excluded: chain B residue 277 MET
Chi-restraints excluded: chain B residue 321 THR
Chi-restraints excluded: chain B residue 325 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 88
random chunks:
chunk 5 optimal weight: 8.9990
chunk 4 optimal weight: 0.7980
chunk 81 optimal weight: 4.9990
chunk 86 optimal weight: 2.9990
chunk 54 optimal weight: 8.9990
chunk 24 optimal weight: 0.8980
chunk 0 optimal weight: 9.9990
chunk 87 optimal weight: 0.9990
chunk 15 optimal weight: 0.7980
chunk 56 optimal weight: 0.6980
chunk 45 optimal weight: 1.9990
overall best weight: 0.8382
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
B 97 HIS
B 146 HIS
Total number of N/Q/H flips: 2
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4765 r_free = 0.4765 target = 0.219508 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4400 r_free = 0.4400 target = 0.181428 restraints weight = 9086.611|
|-----------------------------------------------------------------------------|
r_work (start): 0.4411 rms_B_bonded: 2.71
r_work: 0.4258 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.4258
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7367
moved from start: 0.2894
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.042 7565 Z= 0.232
Angle : 0.678 10.914 10221 Z= 0.350
Chirality : 0.046 0.195 1127
Planarity : 0.004 0.045 1286
Dihedral : 15.461 164.720 1171
Min Nonbonded Distance : 2.420
Molprobity Statistics.
All-atom Clashscore : 8.17
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 1.87 %
Favored : 98.13 %
Rotamer:
Outliers : 2.71 %
Allowed : 13.70 %
Favored : 83.59 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 4.76 %
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: 1.04 (0.29), residues: 908
helix: 1.63 (0.29), residues: 298
sheet: 0.43 (0.26), residues: 392
loop : 0.11 (0.47), residues: 218
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.010 0.001 TRP C 94
HIS 0.005 0.001 HIS B 146
PHE 0.021 0.002 PHE D 109
TYR 0.017 0.002 TYR A 115
ARG 0.005 0.000 ARG A 336
*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
1816 Ramachandran restraints generated.
908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
1816 Ramachandran restraints generated.
908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
156 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 21
poor density : 135
time to evaluate : 0.706
Fit side-chains
REVERT: C 108 ILE cc_start: 0.7954 (mt) cc_final: 0.7725 (tp)
REVERT: C 115 GLN cc_start: 0.8133 (tm-30) cc_final: 0.7832 (tm-30)
REVERT: D 115 GLN cc_start: 0.8045 (tm-30) cc_final: 0.7788 (tm-30)
outliers start: 21
outliers final: 19
residues processed: 141
average time/residue: 0.1818
time to fit residues: 35.3509
Evaluate side-chains
145 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 19
poor density : 126
time to evaluate : 0.964
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue 15 VAL
Chi-restraints excluded: chain E residue 36 MET
Chi-restraints excluded: chain A residue 100 ASN
Chi-restraints excluded: chain A residue 107 SER
Chi-restraints excluded: chain A residue 125 GLU
Chi-restraints excluded: chain A residue 144 VAL
Chi-restraints excluded: chain A residue 172 THR
Chi-restraints excluded: chain A residue 277 MET
Chi-restraints excluded: chain A residue 325 SER
Chi-restraints excluded: chain J residue 26 PHE
Chi-restraints excluded: chain J residue 45 HIS
Chi-restraints excluded: chain F residue 36 MET
Chi-restraints excluded: chain B residue 125 GLU
Chi-restraints excluded: chain B residue 144 VAL
Chi-restraints excluded: chain B residue 172 THR
Chi-restraints excluded: chain B residue 223 VAL
Chi-restraints excluded: chain B residue 277 MET
Chi-restraints excluded: chain B residue 321 THR
Chi-restraints excluded: chain B residue 325 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 88
random chunks:
chunk 31 optimal weight: 6.9990
chunk 28 optimal weight: 7.9990
chunk 77 optimal weight: 5.9990
chunk 29 optimal weight: 1.9990
chunk 76 optimal weight: 0.9980
chunk 62 optimal weight: 1.9990
chunk 27 optimal weight: 0.8980
chunk 74 optimal weight: 0.9980
chunk 15 optimal weight: 0.0970
chunk 38 optimal weight: 1.9990
chunk 5 optimal weight: 2.9990
overall best weight: 0.9980
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 146 HIS
B 146 HIS
Total number of N/Q/H flips: 2
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4746 r_free = 0.4746 target = 0.217304 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4385 r_free = 0.4385 target = 0.179536 restraints weight = 9089.776|
|-----------------------------------------------------------------------------|
r_work (start): 0.4401 rms_B_bonded: 2.66
r_work: 0.4245 rms_B_bonded: 3.28 restraints_weight: 0.5000
r_work (final): 0.4245
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7402
moved from start: 0.3170
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.004 0.042 7565 Z= 0.253
Angle : 0.695 10.958 10221 Z= 0.352
Chirality : 0.045 0.171 1127
Planarity : 0.004 0.046 1286
Dihedral : 15.273 164.196 1171
Min Nonbonded Distance : 2.425
Molprobity Statistics.
All-atom Clashscore : 9.17
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 2.31 %
Favored : 97.69 %
Rotamer:
Outliers : 3.10 %
Allowed : 14.73 %
Favored : 82.17 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 4.76 %
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: 1.04 (0.29), residues: 908
helix: 1.63 (0.28), residues: 310
sheet: 0.43 (0.26), residues: 392
loop : 0.02 (0.48), residues: 206
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.010 0.001 TRP D 94
HIS 0.006 0.001 HIS A 146
PHE 0.022 0.002 PHE D 109
TYR 0.019 0.002 TYR B 115
ARG 0.003 0.000 ARG B 110
*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
1816 Ramachandran restraints generated.
908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
1816 Ramachandran restraints generated.
908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
150 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 24
poor density : 126
time to evaluate : 0.689
Fit side-chains
REVERT: I 7 SER cc_start: 0.8623 (OUTLIER) cc_final: 0.8369 (p)
REVERT: C 115 GLN cc_start: 0.8103 (tm-30) cc_final: 0.7770 (tm-30)
REVERT: A 155 LYS cc_start: 0.7415 (mttp) cc_final: 0.6967 (mtpt)
REVERT: J 7 SER cc_start: 0.8608 (OUTLIER) cc_final: 0.8394 (p)
outliers start: 24
outliers final: 19
residues processed: 137
average time/residue: 0.1789
time to fit residues: 33.5919
Evaluate side-chains
140 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 21
poor density : 119
time to evaluate : 0.796
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue 7 SER
Chi-restraints excluded: chain E residue 15 VAL
Chi-restraints excluded: chain E residue 36 MET
Chi-restraints excluded: chain A residue 100 ASN
Chi-restraints excluded: chain A residue 107 SER
Chi-restraints excluded: chain A residue 125 GLU
Chi-restraints excluded: chain A residue 144 VAL
Chi-restraints excluded: chain A residue 172 THR
Chi-restraints excluded: chain A residue 277 MET
Chi-restraints excluded: chain A residue 325 SER
Chi-restraints excluded: chain J residue 7 SER
Chi-restraints excluded: chain J residue 26 PHE
Chi-restraints excluded: chain J residue 45 HIS
Chi-restraints excluded: chain F residue 36 MET
Chi-restraints excluded: chain B residue 125 GLU
Chi-restraints excluded: chain B residue 144 VAL
Chi-restraints excluded: chain B residue 172 THR
Chi-restraints excluded: chain B residue 223 VAL
Chi-restraints excluded: chain B residue 277 MET
Chi-restraints excluded: chain B residue 321 THR
Chi-restraints excluded: chain B residue 325 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 88
random chunks:
chunk 32 optimal weight: 3.9990
chunk 51 optimal weight: 3.9990
chunk 75 optimal weight: 6.9990
chunk 60 optimal weight: 0.9990
chunk 66 optimal weight: 1.9990
chunk 62 optimal weight: 2.9990
chunk 24 optimal weight: 0.9980
chunk 36 optimal weight: 1.9990
chunk 34 optimal weight: 1.9990
chunk 9 optimal weight: 0.9980
chunk 42 optimal weight: 0.8980
overall best weight: 1.1784
-------------------------------------------------------------------------------
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 = 0.4735 r_free = 0.4735 target = 0.215818 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4367 r_free = 0.4367 target = 0.177982 restraints weight = 9115.327|
|-----------------------------------------------------------------------------|
r_work (start): 0.4382 rms_B_bonded: 2.65
r_work: 0.4224 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.4224
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7429
moved from start: 0.3391
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.004 0.044 7565 Z= 0.275
Angle : 0.722 11.343 10221 Z= 0.363
Chirality : 0.045 0.168 1127
Planarity : 0.004 0.045 1286
Dihedral : 15.324 163.939 1171
Min Nonbonded Distance : 2.421
Molprobity Statistics.
All-atom Clashscore : 8.90
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 2.31 %
Favored : 97.69 %
Rotamer:
Outliers : 3.88 %
Allowed : 15.63 %
Favored : 80.49 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 4.76 %
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: 0.98 (0.29), residues: 908
helix: 1.72 (0.28), residues: 310
sheet: 0.30 (0.26), residues: 394
loop : -0.02 (0.48), residues: 204
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.010 0.001 TRP D 94
HIS 0.004 0.001 HIS F 23
PHE 0.023 0.002 PHE D 109
TYR 0.020 0.002 TYR B 115
ARG 0.003 0.000 ARG B 336
*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
1816 Ramachandran restraints generated.
908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
1816 Ramachandran restraints generated.
908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
158 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 30
poor density : 128
time to evaluate : 0.860
Fit side-chains
REVERT: I 7 SER cc_start: 0.8622 (OUTLIER) cc_final: 0.8419 (p)
REVERT: A 155 LYS cc_start: 0.7418 (mttp) cc_final: 0.6955 (mtpt)
REVERT: A 342 MET cc_start: 0.7579 (OUTLIER) cc_final: 0.7286 (ttp)
REVERT: D 115 GLN cc_start: 0.7981 (tm-30) cc_final: 0.7674 (tm-30)
REVERT: B 231 MET cc_start: 0.7288 (tpt) cc_final: 0.6918 (tpt)
outliers start: 30
outliers final: 22
residues processed: 140
average time/residue: 0.1762
time to fit residues: 34.4485
Evaluate side-chains
147 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 24
poor density : 123
time to evaluate : 0.805
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue 7 SER
Chi-restraints excluded: chain I residue 26 PHE
Chi-restraints excluded: chain E residue 15 VAL
Chi-restraints excluded: chain E residue 36 MET
Chi-restraints excluded: chain C residue 119 LEU
Chi-restraints excluded: chain A residue 98 THR
Chi-restraints excluded: chain A residue 100 ASN
Chi-restraints excluded: chain A residue 107 SER
Chi-restraints excluded: chain A residue 125 GLU
Chi-restraints excluded: chain A residue 144 VAL
Chi-restraints excluded: chain A residue 172 THR
Chi-restraints excluded: chain A residue 247 THR
Chi-restraints excluded: chain A residue 277 MET
Chi-restraints excluded: chain A residue 325 SER
Chi-restraints excluded: chain A residue 342 MET
Chi-restraints excluded: chain J residue 26 PHE
Chi-restraints excluded: chain J residue 45 HIS
Chi-restraints excluded: chain F residue 36 MET
Chi-restraints excluded: chain B residue 125 GLU
Chi-restraints excluded: chain B residue 144 VAL
Chi-restraints excluded: chain B residue 172 THR
Chi-restraints excluded: chain B residue 277 MET
Chi-restraints excluded: chain B residue 321 THR
Chi-restraints excluded: chain B residue 325 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 88
random chunks:
chunk 1 optimal weight: 2.9990
chunk 12 optimal weight: 3.9990
chunk 79 optimal weight: 1.9990
chunk 7 optimal weight: 5.9990
chunk 82 optimal weight: 0.9980
chunk 33 optimal weight: 4.9990
chunk 0 optimal weight: 7.9990
chunk 78 optimal weight: 2.9990
chunk 83 optimal weight: 0.7980
chunk 31 optimal weight: 3.9990
chunk 28 optimal weight: 5.9990
overall best weight: 1.9586
-------------------------------------------------------------------------------
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 = 0.4702 r_free = 0.4702 target = 0.211510 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4314 r_free = 0.4314 target = 0.172955 restraints weight = 9192.723|
|-----------------------------------------------------------------------------|
r_work (start): 0.4330 rms_B_bonded: 2.70
r_work: 0.4171 rms_B_bonded: 3.30 restraints_weight: 0.5000
r_work (final): 0.4171
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7507
moved from start: 0.3540
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.006 0.055 7565 Z= 0.401
Angle : 0.811 12.043 10221 Z= 0.407
Chirality : 0.048 0.176 1127
Planarity : 0.005 0.045 1286
Dihedral : 15.452 163.728 1171
Min Nonbonded Distance : 2.502
Molprobity Statistics.
All-atom Clashscore : 10.71
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 2.86 %
Favored : 97.14 %
Rotamer:
Outliers : 3.75 %
Allowed : 17.31 %
Favored : 78.94 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 4.76 %
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: 0.65 (0.29), residues: 908
helix: 1.50 (0.28), residues: 310
sheet: 0.13 (0.26), residues: 388
loop : -0.32 (0.47), residues: 210
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.010 0.002 TRP E 53
HIS 0.004 0.002 HIS B 97
PHE 0.017 0.002 PHE B 148
TYR 0.021 0.003 TYR A 115
ARG 0.003 0.000 ARG B 336
*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
1816 Ramachandran restraints generated.
908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
1816 Ramachandran restraints generated.
908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
155 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 29
poor density : 126
time to evaluate : 0.780
Fit side-chains
REVERT: C 115 GLN cc_start: 0.8066 (tm-30) cc_final: 0.7771 (tm-30)
REVERT: A 155 LYS cc_start: 0.7483 (mttp) cc_final: 0.7003 (mtpt)
REVERT: A 342 MET cc_start: 0.7636 (OUTLIER) cc_final: 0.7352 (ttp)
REVERT: B 298 ARG cc_start: 0.7775 (mtm-85) cc_final: 0.6666 (mtm-85)
outliers start: 29
outliers final: 22
residues processed: 139
average time/residue: 0.1690
time to fit residues: 33.1691
Evaluate side-chains
146 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 23
poor density : 123
time to evaluate : 0.924
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue 26 PHE
Chi-restraints excluded: chain E residue 15 VAL
Chi-restraints excluded: chain E residue 36 MET
Chi-restraints excluded: chain A residue 98 THR
Chi-restraints excluded: chain A residue 100 ASN
Chi-restraints excluded: chain A residue 107 SER
Chi-restraints excluded: chain A residue 144 VAL
Chi-restraints excluded: chain A residue 172 THR
Chi-restraints excluded: chain A residue 247 THR
Chi-restraints excluded: chain A residue 277 MET
Chi-restraints excluded: chain A residue 325 SER
Chi-restraints excluded: chain A residue 342 MET
Chi-restraints excluded: chain J residue 26 PHE
Chi-restraints excluded: chain J residue 45 HIS
Chi-restraints excluded: chain F residue 36 MET
Chi-restraints excluded: chain B residue 144 VAL
Chi-restraints excluded: chain B residue 172 THR
Chi-restraints excluded: chain B residue 184 THR
Chi-restraints excluded: chain B residue 223 VAL
Chi-restraints excluded: chain B residue 247 THR
Chi-restraints excluded: chain B residue 277 MET
Chi-restraints excluded: chain B residue 321 THR
Chi-restraints excluded: chain B residue 325 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 88
random chunks:
chunk 54 optimal weight: 1.9990
chunk 45 optimal weight: 0.9980
chunk 43 optimal weight: 2.9990
chunk 47 optimal weight: 0.8980
chunk 85 optimal weight: 0.2980
chunk 41 optimal weight: 0.8980
chunk 73 optimal weight: 2.9990
chunk 53 optimal weight: 0.6980
chunk 52 optimal weight: 0.0000
chunk 9 optimal weight: 0.7980
chunk 79 optimal weight: 0.5980
overall best weight: 0.4784
-------------------------------------------------------------------------------
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 = 0.4772 r_free = 0.4772 target = 0.219079 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4409 r_free = 0.4409 target = 0.182057 restraints weight = 9188.743|
|-----------------------------------------------------------------------------|
r_work (start): 0.4415 rms_B_bonded: 2.68
r_work: 0.4257 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.4257
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7380
moved from start: 0.3792
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.039 7565 Z= 0.198
Angle : 0.696 12.439 10221 Z= 0.346
Chirality : 0.045 0.156 1127
Planarity : 0.004 0.046 1286
Dihedral : 14.764 164.744 1171
Min Nonbonded Distance : 2.437
Molprobity Statistics.
All-atom Clashscore : 9.17
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 2.20 %
Favored : 97.80 %
Rotamer:
Outliers : 2.84 %
Allowed : 17.96 %
Favored : 79.20 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 4.76 %
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: 1.06 (0.29), residues: 908
helix: 1.94 (0.29), residues: 310
sheet: 0.21 (0.27), residues: 394
loop : 0.04 (0.48), residues: 204
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.015 0.001 TRP D 94
HIS 0.006 0.001 HIS F 23
PHE 0.024 0.002 PHE C 109
TYR 0.024 0.001 TYR B 115
ARG 0.002 0.000 ARG B 110
*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
1816 Ramachandran restraints generated.
908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
1816 Ramachandran restraints generated.
908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
161 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 22
poor density : 139
time to evaluate : 0.863
Fit side-chains
REVERT: C 115 GLN cc_start: 0.8059 (tm-30) cc_final: 0.7756 (tm-30)
REVERT: A 342 MET cc_start: 0.7423 (OUTLIER) cc_final: 0.7161 (ttp)
REVERT: D 115 GLN cc_start: 0.7929 (tm-30) cc_final: 0.7644 (tm-30)
REVERT: D 116 MET cc_start: 0.7648 (tpp) cc_final: 0.7419 (tpp)
REVERT: B 64 GLU cc_start: 0.8002 (mm-30) cc_final: 0.7801 (mm-30)
REVERT: B 68 LYS cc_start: 0.6687 (ttpt) cc_final: 0.6429 (ttmm)
REVERT: B 231 MET cc_start: 0.7064 (tpt) cc_final: 0.6687 (tpt)
outliers start: 22
outliers final: 17
residues processed: 149
average time/residue: 0.1771
time to fit residues: 36.3679
Evaluate side-chains
141 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 18
poor density : 123
time to evaluate : 0.786
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue 15 VAL
Chi-restraints excluded: chain E residue 36 MET
Chi-restraints excluded: chain A residue 125 GLU
Chi-restraints excluded: chain A residue 144 VAL
Chi-restraints excluded: chain A residue 247 THR
Chi-restraints excluded: chain A residue 277 MET
Chi-restraints excluded: chain A residue 325 SER
Chi-restraints excluded: chain A residue 342 MET
Chi-restraints excluded: chain J residue 26 PHE
Chi-restraints excluded: chain J residue 45 HIS
Chi-restraints excluded: chain F residue 17 VAL
Chi-restraints excluded: chain F residue 36 MET
Chi-restraints excluded: chain B residue 125 GLU
Chi-restraints excluded: chain B residue 144 VAL
Chi-restraints excluded: chain B residue 223 VAL
Chi-restraints excluded: chain B residue 277 MET
Chi-restraints excluded: chain B residue 321 THR
Chi-restraints excluded: chain B residue 325 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 88
random chunks:
chunk 26 optimal weight: 3.9990
chunk 58 optimal weight: 0.7980
chunk 83 optimal weight: 0.6980
chunk 75 optimal weight: 2.9990
chunk 34 optimal weight: 3.9990
chunk 73 optimal weight: 1.9990
chunk 15 optimal weight: 1.9990
chunk 13 optimal weight: 2.9990
chunk 29 optimal weight: 1.9990
chunk 41 optimal weight: 0.1980
chunk 57 optimal weight: 0.8980
overall best weight: 0.9182
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 141 ASN
A 159 GLN
Total number of N/Q/H flips: 2
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4739 r_free = 0.4739 target = 0.215547 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4371 r_free = 0.4371 target = 0.177958 restraints weight = 9165.728|
|-----------------------------------------------------------------------------|
r_work (start): 0.4388 rms_B_bonded: 2.69
r_work: 0.4231 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.4231
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7417
moved from start: 0.3913
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.004 0.040 7565 Z= 0.249
Angle : 0.735 13.052 10221 Z= 0.366
Chirality : 0.045 0.168 1127
Planarity : 0.004 0.046 1286
Dihedral : 14.527 162.703 1171
Min Nonbonded Distance : 2.407
Molprobity Statistics.
All-atom Clashscore : 9.37
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 2.64 %
Favored : 97.36 %
Rotamer:
Outliers : 3.23 %
Allowed : 18.22 %
Favored : 78.55 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 4.76 %
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: 1.14 (0.29), residues: 908
helix: 2.00 (0.29), residues: 310
sheet: 0.34 (0.27), residues: 388
loop : -0.07 (0.47), residues: 210
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.010 0.001 TRP C 94
HIS 0.005 0.001 HIS F 23
PHE 0.019 0.002 PHE J 29
TYR 0.021 0.002 TYR B 115
ARG 0.003 0.000 ARG B 336
*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
1816 Ramachandran restraints generated.
908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
1816 Ramachandran restraints generated.
908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
152 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 25
poor density : 127
time to evaluate : 0.826
Fit side-chains
REVERT: C 115 GLN cc_start: 0.8017 (tm-30) cc_final: 0.7703 (tm-30)
REVERT: A 155 LYS cc_start: 0.7430 (mttp) cc_final: 0.6980 (mtpt)
REVERT: D 115 GLN cc_start: 0.7872 (tm-30) cc_final: 0.7557 (tm-30)
REVERT: D 116 MET cc_start: 0.7712 (tpp) cc_final: 0.7475 (tpp)
REVERT: B 68 LYS cc_start: 0.6630 (ttpt) cc_final: 0.6402 (ttmm)
REVERT: B 231 MET cc_start: 0.7299 (tpt) cc_final: 0.7003 (tpp)
outliers start: 25
outliers final: 21
residues processed: 137
average time/residue: 0.1718
time to fit residues: 32.7464
Evaluate side-chains
140 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 21
poor density : 119
time to evaluate : 0.810
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue 22 MET
Chi-restraints excluded: chain E residue 15 VAL
Chi-restraints excluded: chain E residue 36 MET
Chi-restraints excluded: chain A residue 125 GLU
Chi-restraints excluded: chain A residue 144 VAL
Chi-restraints excluded: chain A residue 172 THR
Chi-restraints excluded: chain A residue 198 VAL
Chi-restraints excluded: chain A residue 247 THR
Chi-restraints excluded: chain A residue 277 MET
Chi-restraints excluded: chain A residue 281 VAL
Chi-restraints excluded: chain A residue 321 THR
Chi-restraints excluded: chain A residue 325 SER
Chi-restraints excluded: chain J residue 45 HIS
Chi-restraints excluded: chain F residue 36 MET
Chi-restraints excluded: chain B residue 125 GLU
Chi-restraints excluded: chain B residue 144 VAL
Chi-restraints excluded: chain B residue 152 LEU
Chi-restraints excluded: chain B residue 223 VAL
Chi-restraints excluded: chain B residue 277 MET
Chi-restraints excluded: chain B residue 321 THR
Chi-restraints excluded: chain B residue 325 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 88
random chunks:
chunk 25 optimal weight: 4.9990
chunk 61 optimal weight: 0.8980
chunk 49 optimal weight: 0.9980
chunk 9 optimal weight: 0.9990
chunk 18 optimal weight: 2.9990
chunk 23 optimal weight: 0.9980
chunk 52 optimal weight: 1.9990
chunk 11 optimal weight: 2.9990
chunk 60 optimal weight: 0.3980
chunk 67 optimal weight: 0.4980
chunk 83 optimal weight: 1.9990
overall best weight: 0.7580
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 141 ASN
Total number of N/Q/H flips: 1
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4748 r_free = 0.4748 target = 0.216405 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4383 r_free = 0.4383 target = 0.178923 restraints weight = 9223.750|
|-----------------------------------------------------------------------------|
r_work (start): 0.4403 rms_B_bonded: 2.70
r_work: 0.4248 rms_B_bonded: 3.30 restraints_weight: 0.5000
r_work (final): 0.4248
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7399
moved from start: 0.4024
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.039 7565 Z= 0.227
Angle : 0.735 13.499 10221 Z= 0.363
Chirality : 0.045 0.165 1127
Planarity : 0.004 0.046 1286
Dihedral : 14.239 161.997 1171
Min Nonbonded Distance : 2.444
Molprobity Statistics.
All-atom Clashscore : 9.11
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 2.42 %
Favored : 97.58 %
Rotamer:
Outliers : 2.84 %
Allowed : 18.86 %
Favored : 78.29 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 4.76 %
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: 1.22 (0.29), residues: 908
helix: 2.11 (0.29), residues: 310
sheet: 0.31 (0.27), residues: 392
loop : 0.03 (0.48), residues: 206
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.012 0.001 TRP D 94
HIS 0.005 0.001 HIS F 23
PHE 0.027 0.002 PHE C 109
TYR 0.021 0.002 TYR B 115
ARG 0.003 0.000 ARG B 336
********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
1816 Ramachandran restraints generated.
908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
1816 Ramachandran restraints generated.
908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
145 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 22
poor density : 123
time to evaluate : 0.781
Fit side-chains
REVERT: G 46 MET cc_start: 0.7928 (ptm) cc_final: 0.7717 (ptp)
REVERT: C 115 GLN cc_start: 0.7987 (tm-30) cc_final: 0.7674 (tm-30)
REVERT: C 116 MET cc_start: 0.7675 (tpt) cc_final: 0.7473 (tpp)
REVERT: A 155 LYS cc_start: 0.7426 (mttp) cc_final: 0.6985 (mtpt)
REVERT: D 116 MET cc_start: 0.7693 (tpp) cc_final: 0.7492 (tpp)
REVERT: B 68 LYS cc_start: 0.6623 (ttpt) cc_final: 0.6392 (ttmm)
outliers start: 22
outliers final: 21
residues processed: 133
average time/residue: 0.1763
time to fit residues: 32.5677
Evaluate side-chains
142 residues out of total 774 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 21
poor density : 121
time to evaluate : 1.028
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue 22 MET
Chi-restraints excluded: chain E residue 15 VAL
Chi-restraints excluded: chain E residue 36 MET
Chi-restraints excluded: chain A residue 125 GLU
Chi-restraints excluded: chain A residue 144 VAL
Chi-restraints excluded: chain A residue 198 VAL
Chi-restraints excluded: chain A residue 247 THR
Chi-restraints excluded: chain A residue 277 MET
Chi-restraints excluded: chain A residue 281 VAL
Chi-restraints excluded: chain A residue 321 THR
Chi-restraints excluded: chain A residue 325 SER
Chi-restraints excluded: chain J residue 45 HIS
Chi-restraints excluded: chain F residue 36 MET
Chi-restraints excluded: chain B residue 125 GLU
Chi-restraints excluded: chain B residue 144 VAL
Chi-restraints excluded: chain B residue 223 VAL
Chi-restraints excluded: chain B residue 277 MET
Chi-restraints excluded: chain B residue 312 GLU
Chi-restraints excluded: chain B residue 321 THR
Chi-restraints excluded: chain B residue 325 SER
Chi-restraints excluded: chain B residue 342 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 88
random chunks:
chunk 5 optimal weight: 0.9980
chunk 81 optimal weight: 1.9990
chunk 57 optimal weight: 0.9980
chunk 37 optimal weight: 3.9990
chunk 30 optimal weight: 2.9990
chunk 73 optimal weight: 2.9990
chunk 61 optimal weight: 0.7980
chunk 36 optimal weight: 1.9990
chunk 14 optimal weight: 0.5980
chunk 27 optimal weight: 3.9990
chunk 59 optimal weight: 0.7980
overall best weight: 0.8380
-------------------------------------------------------------------------------
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 = 0.4751 r_free = 0.4751 target = 0.218216 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4386 r_free = 0.4386 target = 0.180420 restraints weight = 9126.823|
|-----------------------------------------------------------------------------|
r_work (start): 0.4396 rms_B_bonded: 2.68
r_work: 0.4240 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.4240
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7400
moved from start: 0.4127
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.004 0.039 7565 Z= 0.238
Angle : 0.741 13.194 10221 Z= 0.367
Chirality : 0.045 0.170 1127
Planarity : 0.004 0.045 1286
Dihedral : 14.024 161.001 1171
Min Nonbonded Distance : 2.442
Molprobity Statistics.
All-atom Clashscore : 9.91
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 2.53 %
Favored : 97.47 %
Rotamer:
Outliers : 3.10 %
Allowed : 18.60 %
Favored : 78.29 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 4.76 %
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: 1.24 (0.29), residues: 908
helix: 2.14 (0.29), residues: 310
sheet: 0.31 (0.27), residues: 392
loop : 0.03 (0.48), residues: 206
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.010 0.001 TRP C 94
HIS 0.005 0.001 HIS F 23
PHE 0.030 0.002 PHE D 109
TYR 0.020 0.002 TYR B 115
ARG 0.003 0.000 ARG B 336
Origin is already at (0, 0, 0), no shifts will be applied
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Job complete
usr+sys time: 3483.83 seconds
wall clock time: 62 minutes 55.64 seconds (3775.64 seconds total)