Starting phenix.real_space_refine
on Fri Aug 2 21:04:16 2024 by dcliebschner
===============================================================================
Processing files:
-------------------------------------------------------------------------------
Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u1d_41810/08_2024/8u1d_41810.cif
Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u1d_41810/08_2024/8u1d_41810.map
Processing PHIL parameters:
-------------------------------------------------------------------------------
Adding command-line PHIL:
-------------------------
refinement.macro_cycles=10
scattering_table=electron
resolution=4.25
write_initial_geo_file=False
Final processed PHIL parameters:
-------------------------------------------------------------------------------
data_manager {
real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u1d_41810/08_2024/8u1d_41810.map"
default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u1d_41810/08_2024/8u1d_41810.map"
model {
file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u1d_41810/08_2024/8u1d_41810.cif"
}
default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u1d_41810/08_2024/8u1d_41810.cif"
}
resolution = 4.25
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= 0.012
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: 4
Type Number sf(0) Gaussians
S 35 5.16 5
C 3195 2.51 5
N 882 2.21 5
O 997 1.98 5
sf(0) = scattering factor at diffraction angle 0.
Process input model
Symmetric amino acids flipped
Residue "A ASP 57": "OD1" <-> "OD2"
Residue "A PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "A PHE 233": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "A GLU 275": "OE1" <-> "OE2"
Residue "A TYR 330": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "A ASP 368": "OD1" <-> "OD2"
Residue "A TYR 384": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "A TYR 435": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "I GLU 5": "OE1" <-> "OE2"
Residue "I TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "I TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "I TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "I GLU 61": "OE1" <-> "OE2"
Residue "I TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "I TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "J TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2"
Time to flip residues: 0.01s
Monomer Library directory:
"/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib"
Total number of atoms: 5109
Number of models: 1
Model: ""
Number of chains: 4
Chain: "A"
Number of atoms: 3310
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 421, 3310
Classifications: {'peptide': 421}
Link IDs: {'PTRANS': 18, 'TRANS': 402}
Chain breaks: 1
Chain: "I"
Number of atoms: 969
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 122, 969
Classifications: {'peptide': 122}
Link IDs: {'PTRANS': 3, 'TRANS': 118}
Chain: "J"
Number of atoms: 816
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 107, 816
Classifications: {'peptide': 107}
Link IDs: {'PTRANS': 6, 'TRANS': 100}
Chain: "A"
Number of atoms: 14
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 1, 14
Unusual residues: {'NAG': 1}
Classifications: {'undetermined': 1}
Unresolved non-hydrogen bonds: 1
Unresolved non-hydrogen angles: 2
Unresolved non-hydrogen dihedrals: 3
Unresolved non-hydrogen chiralities: 1
Time building chain proxies: 4.06, per 1000 atoms: 0.79
Number of scatterers: 5109
At special positions: 0
Unit cell: (89.64, 84.24, 85.32, 90, 90, 90)
Space group: P 1 (No. 1)
Number of sites at special positions: 0
Number of scattering types: 4
Type Number sf(0)
S 35 16.00
O 997 8.00
N 882 7.00
C 3195 6.00
sf(0) = scattering factor at diffraction angle 0.
Number of disulfides: simple=8, symmetry=0
Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03
Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.04
Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.04
Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.02
Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03
Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03
Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.04
Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.04
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
Links applied
NAG-ASN
" NAG A 701 " - " ASN A 386 "
Time building additional restraints: 1.97
Conformation dependent library (CDL) restraints added in 1.1 seconds
1284 Ramachandran restraints generated.
642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
Adding C-beta torsion restraints...
Number of C-beta restraints generated: 1212
Finding SS restraints...
Secondary structure from input PDB file:
13 helices and 14 sheets defined
13.8% alpha, 35.4% beta
0 base pairs and 0 stacking pairs defined.
Time for finding SS restraints: 0.66
Creating SS restraints...
Processing helix chain 'A' and resid 65 through 70
Processing helix chain 'A' and resid 71 through 73
No H-bonds generated for 'chain 'A' and resid 71 through 73'
Processing helix chain 'A' and resid 99 through 115
removed outlier: 4.125A pdb=" N GLN A 103 " --> pdb=" O ASP A 99 " (cutoff:3.500A)
Processing helix chain 'A' and resid 122 through 126
Processing helix chain 'A' and resid 138 through 142
removed outlier: 3.644A pdb=" N ILE A 141 " --> pdb=" O ASN A 138 " (cutoff:3.500A)
removed outlier: 4.053A pdb=" N ILE A 142 " --> pdb=" O SER A 139 " (cutoff:3.500A)
No H-bonds generated for 'chain 'A' and resid 138 through 142'
Processing helix chain 'A' and resid 205 through 209
removed outlier: 3.518A pdb=" N VAL A 208 " --> pdb=" O CYS A 205 " (cutoff:3.500A)
removed outlier: 3.688A pdb=" N SER A 209 " --> pdb=" O PRO A 206 " (cutoff:3.500A)
No H-bonds generated for 'chain 'A' and resid 205 through 209'
Processing helix chain 'A' and resid 334 through 350
Processing helix chain 'A' and resid 368 through 373
removed outlier: 3.826A pdb=" N THR A 372 " --> pdb=" O ASP A 368 " (cutoff:3.500A)
Processing helix chain 'A' and resid 388 through 392
removed outlier: 3.571A pdb=" N PHE A 391 " --> pdb=" O SER A 388 " (cutoff:3.500A)
removed outlier: 4.044A pdb=" N ASN A 392 " --> pdb=" O SER A 389 " (cutoff:3.500A)
No H-bonds generated for 'chain 'A' and resid 388 through 392'
Processing helix chain 'A' and resid 473 through 478
Processing helix chain 'I' and resid 28 through 32
removed outlier: 4.220A pdb=" N TYR I 32 " --> pdb=" O PHE I 29 " (cutoff:3.500A)
Processing helix chain 'I' and resid 83 through 87
removed outlier: 3.967A pdb=" N THR I 87 " --> pdb=" O SER I 84 " (cutoff:3.500A)
Processing helix chain 'J' and resid 79 through 83
Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 86
removed outlier: 3.637A pdb=" N SER A 243 " --> pdb=" O LYS A 227 " (cutoff:3.500A)
removed outlier: 4.186A pdb=" N VAL A 245 " --> pdb=" O ILE A 225 " (cutoff:3.500A)
removed outlier: 4.348A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A)
removed outlier: 3.504A pdb=" N ALA A 224 " --> pdb=" O VAL A 487 " (cutoff:3.500A)
Processing sheet with id=AA2, first strand: chain 'A' and resid 92 through 94
Processing sheet with id=AA3, first strand: chain 'A' and resid 170 through 174
Processing sheet with id=AA4, first strand: chain 'A' and resid 200 through 203
removed outlier: 6.377A pdb=" N VAL A 200 " --> pdb=" O ALA A 433 " (cutoff:3.500A)
removed outlier: 7.339A pdb=" N TYR A 435 " --> pdb=" O VAL A 200 " (cutoff:3.500A)
removed outlier: 6.597A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A)
Processing sheet with id=AA5, first strand: chain 'A' and resid 259 through 261
removed outlier: 6.556A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A)
removed outlier: 3.579A pdb=" N VAL A 292 " --> pdb=" O ILE A 449 " (cutoff:3.500A)
removed outlier: 7.690A pdb=" N GLY A 451 " --> pdb=" O GLU A 290 " (cutoff:3.500A)
removed outlier: 11.117A pdb=" N GLU A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A)
Processing sheet with id=AA6, first strand: chain 'A' and resid 259 through 261
removed outlier: 6.556A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A)
removed outlier: 3.579A pdb=" N VAL A 292 " --> pdb=" O ILE A 449 " (cutoff:3.500A)
removed outlier: 7.690A pdb=" N GLY A 451 " --> pdb=" O GLU A 290 " (cutoff:3.500A)
removed outlier: 11.117A pdb=" N GLU A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A)
removed outlier: 3.597A pdb=" N GLU A 295 " --> pdb=" O ASN A 332 " (cutoff:3.500A)
removed outlier: 3.904A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A)
Processing sheet with id=AA7, first strand: chain 'A' and resid 301 through 307
removed outlier: 6.898A pdb=" N ASN A 301 " --> pdb=" O VAL A 322 " (cutoff:3.500A)
removed outlier: 5.035A pdb=" N VAL A 322 " --> pdb=" O ASN A 301 " (cutoff:3.500A)
removed outlier: 5.546A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A)
Processing sheet with id=AA8, first strand: chain 'A' and resid 357 through 361
removed outlier: 6.928A pdb=" N ASN A 357 " --> pdb=" O GLU A 464 " (cutoff:3.500A)
removed outlier: 8.120A pdb=" N PHE A 466 " --> pdb=" O ASN A 357 " (cutoff:3.500A)
removed outlier: 6.600A pdb=" N THR A 359 " --> pdb=" O PHE A 466 " (cutoff:3.500A)
Processing sheet with id=AA9, first strand: chain 'I' and resid 3 through 6
removed outlier: 3.527A pdb=" N LEU I 82 " --> pdb=" O VAL I 18 " (cutoff:3.500A)
Processing sheet with id=AB1, first strand: chain 'I' and resid 57 through 58
removed outlier: 6.056A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A)
removed outlier: 6.871A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A)
removed outlier: 3.779A pdb=" N GLY I 49 " --> pdb=" O TRP I 36 " (cutoff:3.500A)
removed outlier: 3.983A pdb=" N SER I 102 " --> pdb=" O ARG I 94 " (cutoff:3.500A)
Processing sheet with id=AB2, first strand: chain 'I' and resid 57 through 58
removed outlier: 6.056A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A)
removed outlier: 6.871A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A)
removed outlier: 3.779A pdb=" N GLY I 49 " --> pdb=" O TRP I 36 " (cutoff:3.500A)
Processing sheet with id=AB3, first strand: chain 'J' and resid 5 through 6
removed outlier: 3.800A pdb=" N ASP J 70 " --> pdb=" O SER J 67 " (cutoff:3.500A)
removed outlier: 3.610A pdb=" N SER J 67 " --> pdb=" O ASP J 70 " (cutoff:3.500A)
Processing sheet with id=AB4, first strand: chain 'J' and resid 10 through 13
removed outlier: 6.064A pdb=" N LEU J 11 " --> pdb=" O ASP J 105 " (cutoff:3.500A)
No H-bonds generated for sheet with id=AB4
Processing sheet with id=AB5, first strand: chain 'J' and resid 53 through 54
removed outlier: 6.542A pdb=" N ALA J 46 " --> pdb=" O GLN J 37 " (cutoff:3.500A)
removed outlier: 6.471A pdb=" N GLN J 37 " --> pdb=" O ALA J 46 " (cutoff:3.500A)
removed outlier: 4.114A pdb=" N ILE J 48 " --> pdb=" O TRP J 35 " (cutoff:3.500A)
168 hydrogen bonds defined for protein.
420 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: 1.55
Time building geometry restraints manager: 2.18 seconds
NOTE: a complete listing of the restraints can be obtained by requesting
output of .geo file.
Histogram of bond lengths:
1.22 - 1.34: 1654
1.34 - 1.46: 1222
1.46 - 1.59: 2297
1.59 - 1.71: 0
1.71 - 1.83: 48
Bond restraints: 5221
Sorted by residual:
bond pdb=" N ASP A 78 "
pdb=" CA ASP A 78 "
ideal model delta sigma weight residual
1.460 1.487 -0.027 7.10e-03 1.98e+04 1.46e+01
bond pdb=" N ILE A 271 "
pdb=" CA ILE A 271 "
ideal model delta sigma weight residual
1.457 1.493 -0.036 1.11e-02 8.12e+03 1.02e+01
bond pdb=" N VAL A 281 "
pdb=" CA VAL A 281 "
ideal model delta sigma weight residual
1.457 1.495 -0.038 1.19e-02 7.06e+03 1.00e+01
bond pdb=" N VAL A 65 "
pdb=" CA VAL A 65 "
ideal model delta sigma weight residual
1.459 1.495 -0.036 1.25e-02 6.40e+03 8.12e+00
bond pdb=" N VAL A 286 "
pdb=" CA VAL A 286 "
ideal model delta sigma weight residual
1.459 1.494 -0.035 1.24e-02 6.50e+03 8.07e+00
... (remaining 5216 not shown)
Histogram of bond angle deviations from ideal:
99.20 - 106.21: 126
106.21 - 113.21: 2773
113.21 - 120.21: 1860
120.21 - 127.21: 2260
127.21 - 134.21: 66
Bond angle restraints: 7085
Sorted by residual:
angle pdb=" N LYS A 63 "
pdb=" CA LYS A 63 "
pdb=" C LYS A 63 "
ideal model delta sigma weight residual
113.28 107.17 6.11 1.22e+00 6.72e-01 2.50e+01
angle pdb=" N ILE J 29 "
pdb=" CA ILE J 29 "
pdb=" C ILE J 29 "
ideal model delta sigma weight residual
112.17 107.96 4.21 9.50e-01 1.11e+00 1.96e+01
angle pdb=" N VAL A 68 "
pdb=" CA VAL A 68 "
pdb=" C VAL A 68 "
ideal model delta sigma weight residual
113.16 106.66 6.50 1.49e+00 4.50e-01 1.90e+01
angle pdb=" C PRO I 41 "
pdb=" N ARG I 42 "
pdb=" CA ARG I 42 "
ideal model delta sigma weight residual
121.54 129.09 -7.55 1.91e+00 2.74e-01 1.56e+01
angle pdb=" CB GLN I 39 "
pdb=" CG GLN I 39 "
pdb=" CD GLN I 39 "
ideal model delta sigma weight residual
112.60 119.26 -6.66 1.70e+00 3.46e-01 1.54e+01
... (remaining 7080 not shown)
Histogram of dihedral angle deviations from ideal:
0.00 - 17.29: 2836
17.29 - 34.58: 248
34.58 - 51.87: 59
51.87 - 69.16: 6
69.16 - 86.46: 4
Dihedral angle restraints: 3153
sinusoidal: 1264
harmonic: 1889
Sorted by residual:
dihedral pdb=" CA GLU A 429 "
pdb=" C GLU A 429 "
pdb=" N VAL A 430 "
pdb=" CA VAL A 430 "
ideal model delta harmonic sigma weight residual
180.00 157.51 22.49 0 5.00e+00 4.00e-02 2.02e+01
dihedral pdb=" CB CYS J 23 "
pdb=" SG CYS J 23 "
pdb=" SG CYS J 88 "
pdb=" CB CYS J 88 "
ideal model delta sinusoidal sigma weight residual
93.00 130.77 -37.77 1 1.00e+01 1.00e-02 2.01e+01
dihedral pdb=" CA MET A 434 "
pdb=" C MET A 434 "
pdb=" N TYR A 435 "
pdb=" CA TYR A 435 "
ideal model delta harmonic sigma weight residual
180.00 157.78 22.22 0 5.00e+00 4.00e-02 1.97e+01
... (remaining 3150 not shown)
Histogram of chiral volume deviations from ideal:
0.000 - 0.071: 617
0.071 - 0.143: 138
0.143 - 0.214: 30
0.214 - 0.285: 3
0.285 - 0.357: 1
Chirality restraints: 789
Sorted by residual:
chirality pdb=" CB VAL A 208 "
pdb=" CA VAL A 208 "
pdb=" CG1 VAL A 208 "
pdb=" CG2 VAL A 208 "
both_signs ideal model delta sigma weight residual
False -2.63 -2.27 -0.36 2.00e-01 2.50e+01 3.18e+00
chirality pdb=" CB ILE A 326 "
pdb=" CA ILE A 326 "
pdb=" CG1 ILE A 326 "
pdb=" CG2 ILE A 326 "
both_signs ideal model delta sigma weight residual
False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.55e+00
chirality pdb=" CA GLU J 81 "
pdb=" N GLU J 81 "
pdb=" C GLU J 81 "
pdb=" CB GLU J 81 "
both_signs ideal model delta sigma weight residual
False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.34e+00
... (remaining 786 not shown)
Planarity restraints: 910
Sorted by residual:
delta sigma weight rms_deltas residual
plane pdb=" C SER J 94 " -0.047 5.00e-02 4.00e+02 7.11e-02 8.09e+00
pdb=" N PRO J 95 " 0.123 5.00e-02 4.00e+02
pdb=" CA PRO J 95 " -0.036 5.00e-02 4.00e+02
pdb=" CD PRO J 95 " -0.040 5.00e-02 4.00e+02
delta sigma weight rms_deltas residual
plane pdb=" CB TRP I 103 " -0.015 2.00e-02 2.50e+03 1.54e-02 5.92e+00
pdb=" CG TRP I 103 " 0.038 2.00e-02 2.50e+03
pdb=" CD1 TRP I 103 " -0.024 2.00e-02 2.50e+03
pdb=" CD2 TRP I 103 " 0.002 2.00e-02 2.50e+03
pdb=" NE1 TRP I 103 " 0.005 2.00e-02 2.50e+03
pdb=" CE2 TRP I 103 " 0.001 2.00e-02 2.50e+03
pdb=" CE3 TRP I 103 " 0.002 2.00e-02 2.50e+03
pdb=" CZ2 TRP I 103 " -0.001 2.00e-02 2.50e+03
pdb=" CZ3 TRP I 103 " -0.008 2.00e-02 2.50e+03
pdb=" CH2 TRP I 103 " -0.000 2.00e-02 2.50e+03
delta sigma weight rms_deltas residual
plane pdb=" C GLN J 79 " 0.037 5.00e-02 4.00e+02 5.55e-02 4.92e+00
pdb=" N PRO J 80 " -0.096 5.00e-02 4.00e+02
pdb=" CA PRO J 80 " 0.028 5.00e-02 4.00e+02
pdb=" CD PRO J 80 " 0.031 5.00e-02 4.00e+02
... (remaining 907 not shown)
Histogram of nonbonded interaction distances:
2.28 - 2.80: 1334
2.80 - 3.33: 4531
3.33 - 3.85: 8162
3.85 - 4.38: 8702
4.38 - 4.90: 15210
Nonbonded interactions: 37939
Sorted by model distance:
nonbonded pdb=" NE2 GLN A 103 "
pdb=" OD2 ASP A 107 "
model vdw
2.280 3.120
nonbonded pdb=" OG SER J 14 "
pdb=" OD2 ASP J 17 "
model vdw
2.304 3.040
nonbonded pdb=" OG SER A 479 "
pdb=" OE1 GLU A 480 "
model vdw
2.334 3.040
nonbonded pdb=" O PHE I 100E"
pdb=" OH TYR J 36 "
model vdw
2.334 3.040
nonbonded pdb=" O GLN J 3 "
pdb=" OG SER J 26 "
model vdw
2.347 3.040
... (remaining 37934 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
========== 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: 2.530
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: 0.200
Check model and map are aligned: 0.040
Set scattering table: 0.060
Process input model: 19.370
Find NCS groups from input model: 0.050
Set up NCS constraints: 0.020
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:2.600
Set ADP refinement strategy: 0.000
Make a string to write initial .geo file:0.000
Internal consistency checks: 0.000
Total: 24.880
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7300
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 : 0.006 0.056 5221 Z= 0.393
Angle : 1.055 9.252 7085 Z= 0.610
Chirality : 0.064 0.357 789
Planarity : 0.007 0.071 909
Dihedral : 13.613 86.455 1917
Min Nonbonded Distance : 2.280
Molprobity Statistics.
All-atom Clashscore : 9.04
Ramachandran Plot:
Outliers : 0.31 %
Allowed : 7.94 %
Favored : 91.74 %
Rotamer:
Outliers : 0.52 %
Allowed : 1.22 %
Favored : 98.25 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
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: -2.32 (0.30), residues: 642
helix: -2.35 (0.52), residues: 57
sheet: -0.76 (0.36), residues: 189
loop : -1.87 (0.28), residues: 396
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.038 0.003 TRP I 103
HIS 0.016 0.002 HIS I 35
PHE 0.012 0.002 PHE A 210
TYR 0.033 0.003 TYR A 330
ARG 0.014 0.001 ARG J 42
*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
1284 Ramachandran restraints generated.
642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
1284 Ramachandran restraints generated.
642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
140 residues out of total 573 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 3
poor density : 137
time to evaluate : 0.564
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: A 77 THR cc_start: 0.8241 (p) cc_final: 0.7914 (t)
REVERT: A 396 MET cc_start: 0.6848 (ppp) cc_final: 0.6360 (ppp)
REVERT: I 3 HIS cc_start: 0.8035 (t-90) cc_final: 0.7531 (t-90)
REVERT: I 12 LYS cc_start: 0.8432 (mptt) cc_final: 0.8214 (mmtt)
REVERT: I 80 MET cc_start: 0.8926 (ttt) cc_final: 0.8424 (ttp)
REVERT: J 2 ILE cc_start: 0.7936 (mp) cc_final: 0.7267 (mp)
REVERT: J 4 MET cc_start: 0.7089 (mpp) cc_final: 0.6819 (mpp)
REVERT: J 58 VAL cc_start: 0.8674 (t) cc_final: 0.8212 (t)
outliers start: 3
outliers final: 1
residues processed: 139
average time/residue: 0.1743
time to fit residues: 31.7200
Evaluate side-chains
97 residues out of total 573 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 1
poor density : 96
time to evaluate : 0.588
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 64
random chunks:
chunk 54 optimal weight: 0.5980
chunk 48 optimal weight: 1.9990
chunk 26 optimal weight: 0.9980
chunk 16 optimal weight: 0.4980
chunk 32 optimal weight: 1.9990
chunk 25 optimal weight: 4.9990
chunk 50 optimal weight: 0.5980
chunk 19 optimal weight: 0.7980
chunk 30 optimal weight: 0.0170
chunk 37 optimal weight: 2.9990
chunk 58 optimal weight: 0.0670
overall best weight: 0.3556
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 92 ASN
A 195 ASN
Total number of N/Q/H flips: 2
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7328
moved from start: 0.1412
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.002 0.027 5221 Z= 0.158
Angle : 0.581 6.716 7085 Z= 0.312
Chirality : 0.043 0.143 789
Planarity : 0.005 0.053 909
Dihedral : 6.048 52.951 725
Min Nonbonded Distance : 2.551
Molprobity Statistics.
All-atom Clashscore : 6.36
Ramachandran Plot:
Outliers : 0.16 %
Allowed : 4.67 %
Favored : 95.17 %
Rotamer:
Outliers : 0.00 %
Allowed : 3.66 %
Favored : 96.34 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
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: -1.58 (0.31), residues: 642
helix: -0.73 (0.68), residues: 52
sheet: -0.40 (0.38), residues: 169
loop : -1.43 (0.28), residues: 421
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.015 0.001 TRP I 50
HIS 0.005 0.001 HIS I 35
PHE 0.014 0.001 PHE A 233
TYR 0.014 0.001 TYR A 330
ARG 0.005 0.000 ARG J 42
*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
1284 Ramachandran restraints generated.
642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
1284 Ramachandran restraints generated.
642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
121 residues out of total 573 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 121
time to evaluate : 1.135
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: A 77 THR cc_start: 0.8526 (p) cc_final: 0.8210 (t)
REVERT: A 122 LEU cc_start: 0.9199 (tp) cc_final: 0.8944 (tp)
REVERT: A 145 MET cc_start: 0.1777 (mtt) cc_final: 0.1469 (mtt)
REVERT: A 396 MET cc_start: 0.6772 (ppp) cc_final: 0.6296 (ppp)
REVERT: A 426 MET cc_start: 0.7086 (tmm) cc_final: 0.6617 (tmm)
REVERT: I 3 HIS cc_start: 0.7994 (t-90) cc_final: 0.7502 (t-90)
REVERT: I 4 LEU cc_start: 0.8103 (mt) cc_final: 0.7877 (mt)
REVERT: I 80 MET cc_start: 0.8878 (ttt) cc_final: 0.8379 (ttp)
REVERT: J 2 ILE cc_start: 0.7931 (mp) cc_final: 0.7354 (mp)
REVERT: J 79 GLN cc_start: 0.8004 (pp30) cc_final: 0.7565 (pp30)
outliers start: 0
outliers final: 0
residues processed: 121
average time/residue: 0.1764
time to fit residues: 27.7798
Evaluate side-chains
91 residues out of total 573 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 91
time to evaluate : 0.676
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 64
random chunks:
chunk 32 optimal weight: 0.0970
chunk 18 optimal weight: 2.9990
chunk 48 optimal weight: 2.9990
chunk 39 optimal weight: 6.9990
chunk 16 optimal weight: 3.9990
chunk 58 optimal weight: 2.9990
chunk 62 optimal weight: 3.9990
chunk 51 optimal weight: 1.9990
chunk 57 optimal weight: 0.5980
chunk 19 optimal weight: 0.8980
chunk 46 optimal weight: 0.8980
overall best weight: 0.8980
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 92 ASN
A 195 ASN
Total number of N/Q/H flips: 2
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7436
moved from start: 0.1979
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.004 0.033 5221 Z= 0.247
Angle : 0.617 5.141 7085 Z= 0.333
Chirality : 0.043 0.156 789
Planarity : 0.005 0.056 909
Dihedral : 6.040 52.082 725
Min Nonbonded Distance : 2.536
Molprobity Statistics.
All-atom Clashscore : 10.34
Ramachandran Plot:
Outliers : 0.16 %
Allowed : 7.01 %
Favored : 92.83 %
Rotamer:
Outliers : 0.00 %
Allowed : 5.41 %
Favored : 94.59 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
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: -1.33 (0.32), residues: 642
helix: 0.27 (0.75), residues: 46
sheet: -0.21 (0.38), residues: 186
loop : -1.40 (0.29), residues: 410
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.016 0.002 TRP I 50
HIS 0.004 0.001 HIS A 216
PHE 0.027 0.002 PHE J 83
TYR 0.018 0.002 TYR I 32
ARG 0.005 0.001 ARG I 42
*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
1284 Ramachandran restraints generated.
642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
1284 Ramachandran restraints generated.
642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
113 residues out of total 573 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 113
time to evaluate : 0.601
Fit side-chains
revert: symmetry clash
REVERT: A 77 THR cc_start: 0.8522 (p) cc_final: 0.8198 (t)
REVERT: A 145 MET cc_start: 0.2090 (mtt) cc_final: 0.1797 (mtt)
REVERT: A 321 GLN cc_start: 0.8839 (mp-120) cc_final: 0.8108 (pm20)
REVERT: A 396 MET cc_start: 0.6910 (ppp) cc_final: 0.6491 (ppp)
REVERT: A 426 MET cc_start: 0.7034 (tmm) cc_final: 0.6472 (tmm)
REVERT: I 3 HIS cc_start: 0.8036 (t-90) cc_final: 0.7559 (t-90)
REVERT: I 4 LEU cc_start: 0.8250 (mt) cc_final: 0.7866 (mt)
REVERT: I 52 ASN cc_start: 0.9433 (t0) cc_final: 0.9191 (t0)
REVERT: I 71 ARG cc_start: 0.9015 (ppt170) cc_final: 0.8305 (ptt90)
REVERT: I 80 MET cc_start: 0.8877 (ttt) cc_final: 0.8480 (ttp)
REVERT: J 2 ILE cc_start: 0.8151 (mp) cc_final: 0.7710 (mp)
REVERT: J 79 GLN cc_start: 0.8067 (pp30) cc_final: 0.7781 (pp30)
outliers start: 0
outliers final: 0
residues processed: 113
average time/residue: 0.1853
time to fit residues: 28.1524
Evaluate side-chains
90 residues out of total 573 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 90
time to evaluate : 0.559
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 64
random chunks:
chunk 57 optimal weight: 0.9990
chunk 43 optimal weight: 0.9990
chunk 30 optimal weight: 2.9990
chunk 6 optimal weight: 0.5980
chunk 27 optimal weight: 0.9980
chunk 39 optimal weight: 0.9990
chunk 58 optimal weight: 0.6980
chunk 61 optimal weight: 0.6980
chunk 55 optimal weight: 0.9990
chunk 16 optimal weight: 0.6980
chunk 51 optimal weight: 3.9990
overall best weight: 0.7380
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 92 ASN
A 195 ASN
** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Total number of N/Q/H flips: 2
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7412
moved from start: 0.2223
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.054 5221 Z= 0.215
Angle : 0.584 5.562 7085 Z= 0.313
Chirality : 0.042 0.166 789
Planarity : 0.004 0.052 909
Dihedral : 6.144 59.774 725
Min Nonbonded Distance : 2.561
Molprobity Statistics.
All-atom Clashscore : 9.14
Ramachandran Plot:
Outliers : 0.16 %
Allowed : 6.85 %
Favored : 92.99 %
Rotamer:
Outliers : 0.00 %
Allowed : 3.32 %
Favored : 96.68 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
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: -1.19 (0.33), residues: 642
helix: 0.75 (0.77), residues: 46
sheet: -0.11 (0.38), residues: 191
loop : -1.37 (0.30), residues: 405
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.012 0.001 TRP I 50
HIS 0.004 0.001 HIS J 90
PHE 0.012 0.001 PHE A 233
TYR 0.012 0.002 TYR A 330
ARG 0.004 0.000 ARG J 42
*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
1284 Ramachandran restraints generated.
642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
1284 Ramachandran restraints generated.
642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
115 residues out of total 573 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 115
time to evaluate : 0.559
Fit side-chains
revert: symmetry clash
REVERT: A 77 THR cc_start: 0.8516 (p) cc_final: 0.8205 (t)
REVERT: A 396 MET cc_start: 0.6850 (ppp) cc_final: 0.6399 (ppp)
REVERT: A 426 MET cc_start: 0.6913 (tmm) cc_final: 0.6410 (tmm)
REVERT: A 434 MET cc_start: 0.8039 (ttm) cc_final: 0.7571 (tpp)
REVERT: I 3 HIS cc_start: 0.8084 (t-90) cc_final: 0.7610 (t-90)
REVERT: I 4 LEU cc_start: 0.8150 (mt) cc_final: 0.7789 (mt)
REVERT: I 71 ARG cc_start: 0.9011 (ppt170) cc_final: 0.8298 (ptt90)
REVERT: I 80 MET cc_start: 0.8923 (ttt) cc_final: 0.8297 (ttp)
REVERT: J 79 GLN cc_start: 0.8160 (pp30) cc_final: 0.7939 (pp30)
outliers start: 0
outliers final: 0
residues processed: 115
average time/residue: 0.1505
time to fit residues: 22.9697
Evaluate side-chains
88 residues out of total 573 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 88
time to evaluate : 0.601
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 64
random chunks:
chunk 35 optimal weight: 0.4980
chunk 0 optimal weight: 9.9990
chunk 46 optimal weight: 0.9980
chunk 25 optimal weight: 0.0020
chunk 52 optimal weight: 0.4980
chunk 42 optimal weight: 3.9990
chunk 31 optimal weight: 3.9990
chunk 55 optimal weight: 0.0040
chunk 15 optimal weight: 0.8980
chunk 20 optimal weight: 0.7980
chunk 12 optimal weight: 0.6980
overall best weight: 0.3400
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 92 ASN
A 195 ASN
Total number of N/Q/H flips: 2
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7357
moved from start: 0.2424
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.025 5221 Z= 0.161
Angle : 0.591 9.418 7085 Z= 0.308
Chirality : 0.042 0.140 789
Planarity : 0.004 0.054 909
Dihedral : 5.713 47.286 725
Min Nonbonded Distance : 2.558
Molprobity Statistics.
All-atom Clashscore : 7.65
Ramachandran Plot:
Outliers : 0.16 %
Allowed : 6.23 %
Favored : 93.61 %
Rotamer:
Outliers : 0.00 %
Allowed : 2.79 %
Favored : 97.21 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
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: -1.25 (0.32), residues: 642
helix: 0.25 (0.73), residues: 52
sheet: -0.05 (0.38), residues: 186
loop : -1.42 (0.30), residues: 404
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.013 0.001 TRP I 103
HIS 0.003 0.001 HIS A 249
PHE 0.029 0.001 PHE J 83
TYR 0.011 0.001 TYR J 91
ARG 0.006 0.000 ARG J 42
*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
1284 Ramachandran restraints generated.
642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
1284 Ramachandran restraints generated.
642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
112 residues out of total 573 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 112
time to evaluate : 0.616
Fit side-chains
revert: symmetry clash
REVERT: A 77 THR cc_start: 0.8559 (p) cc_final: 0.8245 (t)
REVERT: A 236 THR cc_start: 0.8029 (m) cc_final: 0.7798 (m)
REVERT: A 321 GLN cc_start: 0.8804 (mp-120) cc_final: 0.8139 (pm20)
REVERT: A 347 LYS cc_start: 0.8463 (pttt) cc_final: 0.8188 (tptp)
REVERT: A 396 MET cc_start: 0.6793 (ppp) cc_final: 0.6342 (ppp)
REVERT: A 426 MET cc_start: 0.6790 (tmm) cc_final: 0.6504 (tmm)
REVERT: A 434 MET cc_start: 0.7955 (ttm) cc_final: 0.7473 (tpp)
REVERT: I 3 HIS cc_start: 0.8053 (t-90) cc_final: 0.7619 (t-90)
REVERT: I 4 LEU cc_start: 0.8172 (mt) cc_final: 0.7827 (mt)
REVERT: I 71 ARG cc_start: 0.8981 (ppt170) cc_final: 0.8299 (ptt90)
REVERT: I 80 MET cc_start: 0.8968 (ttt) cc_final: 0.8320 (ttp)
REVERT: J 79 GLN cc_start: 0.7956 (pp30) cc_final: 0.7337 (pp30)
outliers start: 0
outliers final: 0
residues processed: 112
average time/residue: 0.2054
time to fit residues: 30.7566
Evaluate side-chains
87 residues out of total 573 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 87
time to evaluate : 0.451
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 64
random chunks:
chunk 36 optimal weight: 2.9990
chunk 15 optimal weight: 0.0670
chunk 61 optimal weight: 0.9990
chunk 51 optimal weight: 0.9990
chunk 28 optimal weight: 4.9990
chunk 5 optimal weight: 2.9990
chunk 20 optimal weight: 0.9990
chunk 32 optimal weight: 1.9990
chunk 59 optimal weight: 2.9990
chunk 6 optimal weight: 0.7980
chunk 35 optimal weight: 0.8980
overall best weight: 0.7522
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 92 ASN
A 195 ASN
** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Total number of N/Q/H flips: 2
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7418
moved from start: 0.2627
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.024 5221 Z= 0.215
Angle : 0.605 11.244 7085 Z= 0.315
Chirality : 0.042 0.149 789
Planarity : 0.004 0.050 909
Dihedral : 5.575 36.832 725
Min Nonbonded Distance : 2.586
Molprobity Statistics.
All-atom Clashscore : 9.44
Ramachandran Plot:
Outliers : 0.16 %
Allowed : 5.76 %
Favored : 94.08 %
Rotamer:
Outliers : 0.00 %
Allowed : 2.27 %
Favored : 97.73 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
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: -1.31 (0.32), residues: 642
helix: 0.31 (0.72), residues: 53
sheet: -0.22 (0.37), residues: 198
loop : -1.44 (0.30), residues: 391
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.019 0.002 TRP I 47
HIS 0.006 0.001 HIS I 35
PHE 0.011 0.001 PHE A 233
TYR 0.012 0.002 TYR A 435
ARG 0.006 0.001 ARG J 24
*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
1284 Ramachandran restraints generated.
642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
1284 Ramachandran restraints generated.
642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
113 residues out of total 573 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 113
time to evaluate : 0.620
Fit side-chains
revert: symmetry clash
REVERT: A 77 THR cc_start: 0.8574 (p) cc_final: 0.8266 (t)
REVERT: A 236 THR cc_start: 0.8062 (m) cc_final: 0.7815 (m)
REVERT: A 347 LYS cc_start: 0.8496 (pttt) cc_final: 0.8219 (tptp)
REVERT: A 426 MET cc_start: 0.6758 (tmm) cc_final: 0.6437 (tmm)
REVERT: A 434 MET cc_start: 0.7993 (ttm) cc_final: 0.7496 (tpp)
REVERT: I 3 HIS cc_start: 0.8036 (t-90) cc_final: 0.7545 (t-90)
REVERT: I 4 LEU cc_start: 0.8184 (mt) cc_final: 0.7824 (mt)
REVERT: I 71 ARG cc_start: 0.8973 (ppt170) cc_final: 0.8321 (ptt90)
REVERT: I 80 MET cc_start: 0.8911 (ttt) cc_final: 0.8267 (ttp)
REVERT: J 79 GLN cc_start: 0.8173 (pp30) cc_final: 0.7607 (pp30)
outliers start: 0
outliers final: 0
residues processed: 113
average time/residue: 0.1639
time to fit residues: 24.4221
Evaluate side-chains
89 residues out of total 573 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 89
time to evaluate : 0.567
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 64
random chunks:
chunk 45 optimal weight: 2.9990
chunk 35 optimal weight: 0.6980
chunk 52 optimal weight: 2.9990
chunk 34 optimal weight: 1.9990
chunk 61 optimal weight: 0.6980
chunk 38 optimal weight: 0.3980
chunk 37 optimal weight: 4.9990
chunk 28 optimal weight: 0.7980
chunk 24 optimal weight: 0.8980
chunk 36 optimal weight: 0.9980
chunk 18 optimal weight: 3.9990
overall best weight: 0.6980
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 92 ASN
A 195 ASN
** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Total number of N/Q/H flips: 2
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7418
moved from start: 0.2715
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.029 5221 Z= 0.204
Angle : 0.609 11.758 7085 Z= 0.316
Chirality : 0.042 0.148 789
Planarity : 0.004 0.048 909
Dihedral : 5.451 30.142 725
Min Nonbonded Distance : 2.559
Molprobity Statistics.
All-atom Clashscore : 9.24
Ramachandran Plot:
Outliers : 0.16 %
Allowed : 5.45 %
Favored : 94.39 %
Rotamer:
Outliers : 0.00 %
Allowed : 1.92 %
Favored : 98.08 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
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: -1.27 (0.32), residues: 642
helix: 0.29 (0.72), residues: 54
sheet: -0.14 (0.38), residues: 198
loop : -1.43 (0.30), residues: 390
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.013 0.001 TRP I 50
HIS 0.003 0.001 HIS A 249
PHE 0.011 0.001 PHE A 233
TYR 0.018 0.002 TYR A 435
ARG 0.007 0.001 ARG I 42
*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
1284 Ramachandran restraints generated.
642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
1284 Ramachandran restraints generated.
642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
111 residues out of total 573 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 111
time to evaluate : 0.568
Fit side-chains
revert: symmetry clash
REVERT: A 77 THR cc_start: 0.8587 (p) cc_final: 0.8281 (t)
REVERT: A 116 LEU cc_start: 0.9603 (mm) cc_final: 0.9215 (mp)
REVERT: A 236 THR cc_start: 0.8064 (m) cc_final: 0.7854 (m)
REVERT: A 347 LYS cc_start: 0.8491 (pttt) cc_final: 0.8226 (tptp)
REVERT: A 396 MET cc_start: 0.6757 (ppp) cc_final: 0.6324 (ppp)
REVERT: A 426 MET cc_start: 0.6663 (tmm) cc_final: 0.6329 (tmm)
REVERT: A 434 MET cc_start: 0.8027 (ttm) cc_final: 0.7435 (tpp)
REVERT: I 3 HIS cc_start: 0.8055 (t-90) cc_final: 0.7592 (t-90)
REVERT: I 4 LEU cc_start: 0.8209 (mt) cc_final: 0.7863 (mt)
REVERT: I 71 ARG cc_start: 0.8986 (ppt170) cc_final: 0.8368 (ptt90)
REVERT: I 80 MET cc_start: 0.8937 (ttt) cc_final: 0.8296 (ttp)
REVERT: J 79 GLN cc_start: 0.8148 (pp30) cc_final: 0.7483 (pp30)
outliers start: 0
outliers final: 0
residues processed: 111
average time/residue: 0.1697
time to fit residues: 25.1267
Evaluate side-chains
86 residues out of total 573 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 86
time to evaluate : 0.591
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 64
random chunks:
chunk 12 optimal weight: 0.6980
chunk 11 optimal weight: 2.9990
chunk 39 optimal weight: 6.9990
chunk 42 optimal weight: 3.9990
chunk 30 optimal weight: 0.0870
chunk 5 optimal weight: 2.9990
chunk 48 optimal weight: 1.9990
chunk 56 optimal weight: 0.4980
chunk 59 optimal weight: 0.7980
chunk 53 optimal weight: 0.9990
chunk 57 optimal weight: 1.9990
overall best weight: 0.6160
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 92 ASN
A 195 ASN
** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Total number of N/Q/H flips: 2
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7414
moved from start: 0.2849
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.040 5221 Z= 0.199
Angle : 0.624 11.338 7085 Z= 0.322
Chirality : 0.043 0.167 789
Planarity : 0.004 0.047 909
Dihedral : 5.338 28.583 725
Min Nonbonded Distance : 2.552
Molprobity Statistics.
All-atom Clashscore : 9.54
Ramachandran Plot:
Outliers : 0.16 %
Allowed : 5.92 %
Favored : 93.93 %
Rotamer:
Outliers : 0.00 %
Allowed : 1.40 %
Favored : 98.60 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
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: -1.38 (0.32), residues: 642
helix: 0.35 (0.72), residues: 54
sheet: -0.21 (0.37), residues: 198
loop : -1.53 (0.30), residues: 390
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.011 0.001 TRP I 50
HIS 0.004 0.001 HIS A 249
PHE 0.019 0.001 PHE J 62
TYR 0.012 0.001 TYR J 49
ARG 0.006 0.001 ARG J 42
*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
1284 Ramachandran restraints generated.
642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
1284 Ramachandran restraints generated.
642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
107 residues out of total 573 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 107
time to evaluate : 0.600
Fit side-chains
revert: symmetry clash
REVERT: A 77 THR cc_start: 0.8621 (p) cc_final: 0.8320 (t)
REVERT: A 116 LEU cc_start: 0.9625 (mm) cc_final: 0.9211 (mp)
REVERT: A 347 LYS cc_start: 0.8465 (pttt) cc_final: 0.8207 (tptp)
REVERT: A 396 MET cc_start: 0.6703 (ppp) cc_final: 0.6319 (ppp)
REVERT: A 426 MET cc_start: 0.6726 (tmm) cc_final: 0.6361 (tmm)
REVERT: A 434 MET cc_start: 0.8050 (ttm) cc_final: 0.7534 (tpp)
REVERT: I 4 LEU cc_start: 0.8218 (mt) cc_final: 0.7924 (mt)
REVERT: I 12 LYS cc_start: 0.8698 (mmtm) cc_final: 0.8188 (mmmm)
REVERT: I 71 ARG cc_start: 0.9007 (ppt170) cc_final: 0.8324 (ptt90)
REVERT: I 80 MET cc_start: 0.8948 (ttt) cc_final: 0.8325 (ttp)
REVERT: J 79 GLN cc_start: 0.8072 (pp30) cc_final: 0.7586 (pp30)
outliers start: 0
outliers final: 0
residues processed: 107
average time/residue: 0.1638
time to fit residues: 22.9313
Evaluate side-chains
85 residues out of total 573 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 85
time to evaluate : 0.605
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 64
random chunks:
chunk 59 optimal weight: 0.2980
chunk 34 optimal weight: 0.0050
chunk 25 optimal weight: 0.0970
chunk 45 optimal weight: 2.9990
chunk 17 optimal weight: 3.9990
chunk 51 optimal weight: 0.6980
chunk 54 optimal weight: 0.0980
chunk 57 optimal weight: 0.7980
chunk 37 optimal weight: 0.2980
chunk 60 optimal weight: 1.9990
chunk 28 optimal weight: 2.9990
overall best weight: 0.1592
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 92 ASN
A 195 ASN
** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
J 38 GLN
Total number of N/Q/H flips: 3
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7350
moved from start: 0.2961
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.002 0.032 5221 Z= 0.153
Angle : 0.599 11.586 7085 Z= 0.310
Chirality : 0.043 0.166 789
Planarity : 0.004 0.048 909
Dihedral : 4.978 28.567 725
Min Nonbonded Distance : 2.540
Molprobity Statistics.
All-atom Clashscore : 7.06
Ramachandran Plot:
Outliers : 0.16 %
Allowed : 4.52 %
Favored : 95.33 %
Rotamer:
Outliers : 0.00 %
Allowed : 0.70 %
Favored : 99.30 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
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: -1.33 (0.32), residues: 642
helix: 0.38 (0.73), residues: 54
sheet: -0.16 (0.37), residues: 196
loop : -1.51 (0.29), residues: 392
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.009 0.001 TRP I 50
HIS 0.003 0.001 HIS I 35
PHE 0.014 0.001 PHE J 62
TYR 0.017 0.001 TYR A 435
ARG 0.006 0.001 ARG J 42
*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
1284 Ramachandran restraints generated.
642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
1284 Ramachandran restraints generated.
642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
112 residues out of total 573 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 112
time to evaluate : 0.525
Fit side-chains
revert: symmetry clash
REVERT: A 77 THR cc_start: 0.8642 (p) cc_final: 0.8333 (t)
REVERT: A 116 LEU cc_start: 0.9615 (mm) cc_final: 0.9206 (mp)
REVERT: A 236 THR cc_start: 0.8046 (m) cc_final: 0.7835 (m)
REVERT: A 321 GLN cc_start: 0.8766 (mp10) cc_final: 0.8464 (pm20)
REVERT: A 347 LYS cc_start: 0.8447 (pttt) cc_final: 0.8223 (tptp)
REVERT: A 396 MET cc_start: 0.6651 (ppp) cc_final: 0.6277 (ppp)
REVERT: A 426 MET cc_start: 0.6561 (tmm) cc_final: 0.6264 (tmm)
REVERT: A 434 MET cc_start: 0.7981 (ttm) cc_final: 0.7679 (tpp)
REVERT: A 435 TYR cc_start: 0.8350 (t80) cc_final: 0.8083 (t80)
REVERT: I 4 LEU cc_start: 0.8132 (mt) cc_final: 0.7928 (mt)
REVERT: I 12 LYS cc_start: 0.8658 (mmtm) cc_final: 0.7454 (ttpt)
REVERT: I 13 GLU cc_start: 0.8428 (mp0) cc_final: 0.8128 (mp0)
REVERT: I 59 TYR cc_start: 0.9080 (m-10) cc_final: 0.8579 (m-10)
REVERT: I 71 ARG cc_start: 0.9011 (ppt170) cc_final: 0.8403 (ptt90)
REVERT: I 80 MET cc_start: 0.9004 (ttt) cc_final: 0.8617 (ttp)
outliers start: 0
outliers final: 0
residues processed: 112
average time/residue: 0.1628
time to fit residues: 24.3083
Evaluate side-chains
89 residues out of total 573 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 89
time to evaluate : 0.597
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 64
random chunks:
chunk 42 optimal weight: 3.9990
chunk 63 optimal weight: 0.9980
chunk 58 optimal weight: 0.5980
chunk 50 optimal weight: 3.9990
chunk 5 optimal weight: 0.7980
chunk 39 optimal weight: 5.9990
chunk 31 optimal weight: 0.5980
chunk 40 optimal weight: 0.6980
chunk 54 optimal weight: 0.9990
chunk 15 optimal weight: 3.9990
chunk 46 optimal weight: 1.9990
overall best weight: 0.7380
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 92 ASN
** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Total number of N/Q/H flips: 1
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7414
moved from start: 0.3068
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.030 5221 Z= 0.212
Angle : 0.623 11.244 7085 Z= 0.322
Chirality : 0.043 0.170 789
Planarity : 0.004 0.048 909
Dihedral : 5.174 30.989 725
Min Nonbonded Distance : 2.534
Molprobity Statistics.
All-atom Clashscore : 9.64
Ramachandran Plot:
Outliers : 0.16 %
Allowed : 6.54 %
Favored : 93.30 %
Rotamer:
Outliers : 0.00 %
Allowed : 0.17 %
Favored : 99.83 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 3.70 %
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: -1.38 (0.32), residues: 642
helix: 0.15 (0.72), residues: 54
sheet: -0.16 (0.37), residues: 198
loop : -1.54 (0.29), residues: 390
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.016 0.002 TRP I 103
HIS 0.003 0.001 HIS I 58
PHE 0.011 0.001 PHE A 233
TYR 0.013 0.002 TYR A 435
ARG 0.006 0.001 ARG J 42
********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
1284 Ramachandran restraints generated.
642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
1284 Ramachandran restraints generated.
642 Oldfield, 0 Emsley, 642 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
108 residues out of total 573 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 108
time to evaluate : 0.564
Fit side-chains
revert: symmetry clash
revert: symmetry clash
REVERT: A 77 THR cc_start: 0.8645 (p) cc_final: 0.8355 (t)
REVERT: A 116 LEU cc_start: 0.9631 (mm) cc_final: 0.9219 (mp)
REVERT: A 236 THR cc_start: 0.8118 (m) cc_final: 0.7839 (m)
REVERT: A 347 LYS cc_start: 0.8466 (pttt) cc_final: 0.8206 (tptp)
REVERT: A 396 MET cc_start: 0.6727 (ppp) cc_final: 0.6362 (ppp)
REVERT: A 426 MET cc_start: 0.6755 (tmm) cc_final: 0.6357 (tmm)
REVERT: A 434 MET cc_start: 0.8079 (ttm) cc_final: 0.7646 (tpp)
REVERT: I 3 HIS cc_start: 0.8110 (t-90) cc_final: 0.7644 (t-90)
REVERT: I 4 LEU cc_start: 0.8301 (mt) cc_final: 0.7956 (mt)
REVERT: I 12 LYS cc_start: 0.8721 (mmtm) cc_final: 0.8182 (mmmm)
REVERT: I 80 MET cc_start: 0.8989 (ttt) cc_final: 0.8386 (ttp)
outliers start: 0
outliers final: 0
residues processed: 108
average time/residue: 0.1543
time to fit residues: 22.1001
Evaluate side-chains
89 residues out of total 573 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 89
time to evaluate : 0.603
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 64
random chunks:
chunk 7 optimal weight: 0.6980
chunk 14 optimal weight: 0.7980
chunk 50 optimal weight: 3.9990
chunk 21 optimal weight: 0.7980
chunk 52 optimal weight: 0.7980
chunk 6 optimal weight: 0.9990
chunk 9 optimal weight: 2.9990
chunk 44 optimal weight: 0.8980
chunk 2 optimal weight: 3.9990
chunk 36 optimal weight: 0.7980
chunk 58 optimal weight: 3.9990
overall best weight: 0.7780
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 92 ASN
** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Total number of N/Q/H flips: 1
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.140164 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.115880 restraints weight = 11531.272|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.119303 restraints weight = 7438.792|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.121726 restraints weight = 5403.055|
|-----------------------------------------------------------------------------|
r_work (final): 0.3564
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7539
moved from start: 0.3240
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.038 5221 Z= 0.218
Angle : 0.613 10.668 7085 Z= 0.321
Chirality : 0.043 0.178 789
Planarity : 0.004 0.048 909
Dihedral : 5.257 31.295 725
Min Nonbonded Distance : 2.533
Molprobity Statistics.
All-atom Clashscore : 10.14
Ramachandran Plot:
Outliers : 0.16 %
Allowed : 6.39 %
Favored : 93.46 %
Rotamer:
Outliers : 0.00 %
Allowed : 0.52 %
Favored : 99.48 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 3.70 %
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: -1.48 (0.32), residues: 642
helix: -0.34 (0.70), residues: 59
sheet: -0.22 (0.37), residues: 198
loop : -1.55 (0.30), residues: 385
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.014 0.001 TRP I 50
HIS 0.003 0.001 HIS A 249
PHE 0.012 0.001 PHE A 233
TYR 0.015 0.002 TYR A 217
ARG 0.007 0.001 ARG J 42
Origin is already at (0, 0, 0), no shifts will be applied
===============================================================================
Job complete
usr+sys time: 1542.87 seconds
wall clock time: 28 minutes 15.15 seconds (1695.15 seconds total)