Starting phenix.real_space_refine
on Tue Jan 14 23:18:39 2025 by dcliebschner
===============================================================================
Processing files:
-------------------------------------------------------------------------------
Found model, /net/cci-nas-00/data/ceres_data/9b91_44365/01_2025/9b91_44365.cif
Found real_map, /net/cci-nas-00/data/ceres_data/9b91_44365/01_2025/9b91_44365.map
Processing PHIL parameters:
-------------------------------------------------------------------------------
Adding command-line PHIL:
-------------------------
refinement.macro_cycles=10
scattering_table=electron
resolution=3.3
write_initial_geo_file=False
Final processed PHIL parameters:
-------------------------------------------------------------------------------
data_manager {
real_map_files = "/net/cci-nas-00/data/ceres_data/9b91_44365/01_2025/9b91_44365.map"
default_real_map = "/net/cci-nas-00/data/ceres_data/9b91_44365/01_2025/9b91_44365.map"
model {
file = "/net/cci-nas-00/data/ceres_data/9b91_44365/01_2025/9b91_44365.cif"
}
default_model = "/net/cci-nas-00/data/ceres_data/9b91_44365/01_2025/9b91_44365.cif"
}
resolution = 3.3
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= 0.000
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: 6
Type Number sf(0) Gaussians
Ca 2 9.91 5
P 3 5.49 5
S 38 5.16 5
C 4854 2.51 5
N 1327 2.21 5
O 1287 1.98 5
sf(0) = scattering factor at diffraction angle 0.
Process input model
Symmetric amino acids flipped. Time to flip 2 residue(s): 0.03s
Monomer Library directory:
"/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
Total number of atoms: 7511
Number of models: 1
Model: ""
Number of chains: 2
Chain: "A"
Number of atoms: 7478
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 993, 7478
Classifications: {'peptide': 993}
Incomplete info: {'truncation_to_alanine': 108}
Link IDs: {'PTRANS': 43, 'TRANS': 949}
Chain breaks: 8
Unresolved chain link angles: 3
Unresolved non-hydrogen bonds: 411
Unresolved non-hydrogen angles: 510
Unresolved non-hydrogen dihedrals: 333
Unresolved non-hydrogen chiralities: 18
Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 19, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 3, 'PHE:plan': 4, 'GLU:plan': 19, 'ARG:plan': 15}
Unresolved non-hydrogen planarities: 285
Chain: "A"
Number of atoms: 33
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 3, 33
Unusual residues: {' CA': 2, 'ATP': 1}
Classifications: {'undetermined': 3}
Link IDs: {None: 2}
Time building chain proxies: 5.42, per 1000 atoms: 0.72
Number of scatterers: 7511
At special positions: 0
Unit cell: (87.768, 120.06, 153.18, 90, 90, 90)
Space group: P 1 (No. 1)
Number of sites at special positions: 0
Number of scattering types: 6
Type Number sf(0)
Ca 2 19.99
S 38 16.00
P 3 15.00
O 1287 8.00
N 1327 7.00
C 4854 6.00
sf(0) = scattering factor at diffraction angle 0.
Number of disulfides: simple=1, symmetry=0
Simple disulfide: pdb=" SG CYS A 993 " - pdb=" SG CYS A1011 " distance=2.59
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: 2.72
Conformation dependent library (CDL) restraints added in 976.5 milliseconds
1950 Ramachandran restraints generated.
975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2.
Adding C-beta torsion restraints...
Number of C-beta restraints generated: 1840
Finding SS restraints...
Secondary structure from input PDB file:
48 helices and 4 sheets defined
67.7% alpha, 4.5% beta
0 base pairs and 0 stacking pairs defined.
Time for finding SS restraints: 0.92
Creating SS restraints...
Processing helix chain 'A' and resid 7 through 9
No H-bonds generated for 'chain 'A' and resid 7 through 9'
Processing helix chain 'A' and resid 10 through 15
removed outlier: 3.650A pdb=" N ILE A 14 " --> pdb=" O TRP A 10 " (cutoff:3.500A)
Processing helix chain 'A' and resid 98 through 109
removed outlier: 3.884A pdb=" N VAL A 102 " --> pdb=" O ASP A 98 " (cutoff:3.500A)
Processing helix chain 'A' and resid 131 through 150
removed outlier: 3.724A pdb=" N VAL A 143 " --> pdb=" O ARG A 139 " (cutoff:3.500A)
Processing helix chain 'A' and resid 160 through 176
Processing helix chain 'A' and resid 246 through 259
Processing helix chain 'A' and resid 264 through 268
removed outlier: 3.951A pdb=" N GLY A 268 " --> pdb=" O GLY A 265 " (cutoff:3.500A)
Processing helix chain 'A' and resid 281 through 294
Processing helix chain 'A' and resid 308 through 318
Processing helix chain 'A' and resid 327 through 336
Processing helix chain 'A' and resid 344 through 357
removed outlier: 4.294A pdb=" N GLN A 348 " --> pdb=" O LEU A 344 " (cutoff:3.500A)
removed outlier: 3.609A pdb=" N ARG A 357 " --> pdb=" O ARG A 353 " (cutoff:3.500A)
Processing helix chain 'A' and resid 373 through 386
removed outlier: 3.508A pdb=" N GLY A 386 " --> pdb=" O VAL A 382 " (cutoff:3.500A)
Processing helix chain 'A' and resid 393 through 403
Processing helix chain 'A' and resid 406 through 413
Processing helix chain 'A' and resid 421 through 435
removed outlier: 4.076A pdb=" N ALA A 427 " --> pdb=" O PHE A 423 " (cutoff:3.500A)
removed outlier: 4.340A pdb=" N SER A 428 " --> pdb=" O HIS A 424 " (cutoff:3.500A)
Processing helix chain 'A' and resid 437 through 447
Processing helix chain 'A' and resid 450 through 455
Processing helix chain 'A' and resid 456 through 466
Processing helix chain 'A' and resid 471 through 480
Processing helix chain 'A' and resid 502 through 512
removed outlier: 3.589A pdb=" N VAL A 506 " --> pdb=" O ASP A 502 " (cutoff:3.500A)
Processing helix chain 'A' and resid 558 through 570
Processing helix chain 'A' and resid 571 through 582
Processing helix chain 'A' and resid 584 through 603
Processing helix chain 'A' and resid 607 through 634
removed outlier: 3.645A pdb=" N ARG A 611 " --> pdb=" O GLU A 607 " (cutoff:3.500A)
Processing helix chain 'A' and resid 634 through 645
removed outlier: 3.541A pdb=" N LEU A 643 " --> pdb=" O ALA A 639 " (cutoff:3.500A)
Processing helix chain 'A' and resid 653 through 662
Processing helix chain 'A' and resid 663 through 668
Processing helix chain 'A' and resid 669 through 681
Processing helix chain 'A' and resid 689 through 699
Processing helix chain 'A' and resid 700 through 705
removed outlier: 3.557A pdb=" N THR A 705 " --> pdb=" O LEU A 702 " (cutoff:3.500A)
Processing helix chain 'A' and resid 767 through 778
removed outlier: 3.526A pdb=" N ALA A 778 " --> pdb=" O HIS A 774 " (cutoff:3.500A)
Processing helix chain 'A' and resid 778 through 803
Processing helix chain 'A' and resid 811 through 834
Processing helix chain 'A' and resid 852 through 862
removed outlier: 3.847A pdb=" N ASP A 862 " --> pdb=" O LEU A 858 " (cutoff:3.500A)
Processing helix chain 'A' and resid 862 through 884
Processing helix chain 'A' and resid 887 through 905
Processing helix chain 'A' and resid 906 through 912
Processing helix chain 'A' and resid 916 through 926
Processing helix chain 'A' and resid 926 through 953
Processing helix chain 'A' and resid 958 through 967
Processing helix chain 'A' and resid 967 through 974
removed outlier: 3.624A pdb=" N ILE A 974 " --> pdb=" O PRO A 970 " (cutoff:3.500A)
Processing helix chain 'A' and resid 979 through 983
Processing helix chain 'A' and resid 984 through 988
Processing helix chain 'A' and resid 1016 through 1033
removed outlier: 3.883A pdb=" N VAL A1020 " --> pdb=" O ALA A1016 " (cutoff:3.500A)
Processing helix chain 'A' and resid 1033 through 1071
removed outlier: 4.877A pdb=" N GLY A1052 " --> pdb=" O GLY A1048 " (cutoff:3.500A)
removed outlier: 5.017A pdb=" N ASN A1053 " --> pdb=" O LYS A1049 " (cutoff:3.500A)
removed outlier: 4.081A pdb=" N TYR A1063 " --> pdb=" O LYS A1059 " (cutoff:3.500A)
removed outlier: 4.215A pdb=" N ARG A1064 " --> pdb=" O ALA A1060 " (cutoff:3.500A)
Processing helix chain 'A' and resid 1079 through 1088
removed outlier: 4.267A pdb=" N SER A1083 " --> pdb=" O PHE A1079 " (cutoff:3.500A)
Processing helix chain 'A' and resid 1116 through 1143
Processing helix chain 'A' and resid 1143 through 1176
Processing sheet with id=AA1, first strand: chain 'A' and resid 16 through 19
Processing sheet with id=AA2, first strand: chain 'A' and resid 155 through 156
removed outlier: 6.165A pdb=" N THR A 155 " --> pdb=" O VAL A 188 " (cutoff:3.500A)
removed outlier: 7.086A pdb=" N GLY A 187 " --> pdb=" O PHE A 233 " (cutoff:3.500A)
removed outlier: 7.155A pdb=" N VAL A 235 " --> pdb=" O GLY A 187 " (cutoff:3.500A)
removed outlier: 6.450A pdb=" N ALA A 189 " --> pdb=" O VAL A 235 " (cutoff:3.500A)
removed outlier: 6.655A pdb=" N ASN A 89 " --> pdb=" O PHE A 232 " (cutoff:3.500A)
removed outlier: 7.253A pdb=" N LEU A 234 " --> pdb=" O ASN A 89 " (cutoff:3.500A)
removed outlier: 6.574A pdb=" N LEU A 91 " --> pdb=" O LEU A 234 " (cutoff:3.500A)
removed outlier: 7.006A pdb=" N ASP A 236 " --> pdb=" O LEU A 91 " (cutoff:3.500A)
removed outlier: 6.183A pdb=" N LEU A 93 " --> pdb=" O ASP A 236 " (cutoff:3.500A)
removed outlier: 7.680A pdb=" N TYR A 211 " --> pdb=" O GLU A 77 " (cutoff:3.500A)
removed outlier: 7.147A pdb=" N ASP A 79 " --> pdb=" O TYR A 211 " (cutoff:3.500A)
Processing sheet with id=AA3, first strand: chain 'A' and resid 118 through 122
removed outlier: 6.550A pdb=" N VAL A 118 " --> pdb=" O LEU A 274 " (cutoff:3.500A)
removed outlier: 7.565A pdb=" N LEU A 276 " --> pdb=" O VAL A 118 " (cutoff:3.500A)
removed outlier: 6.077A pdb=" N SER A 120 " --> pdb=" O LEU A 276 " (cutoff:3.500A)
removed outlier: 7.878A pdb=" N LEU A 299 " --> pdb=" O VAL A 273 " (cutoff:3.500A)
removed outlier: 6.121A pdb=" N LEU A 275 " --> pdb=" O LEU A 299 " (cutoff:3.500A)
removed outlier: 7.423A pdb=" N VAL A 301 " --> pdb=" O LEU A 275 " (cutoff:3.500A)
removed outlier: 7.351A pdb=" N LEU A 277 " --> pdb=" O VAL A 301 " (cutoff:3.500A)
removed outlier: 6.947A pdb=" N CYS A 298 " --> pdb=" O THR A 362 " (cutoff:3.500A)
removed outlier: 7.431A pdb=" N TYR A 364 " --> pdb=" O CYS A 298 " (cutoff:3.500A)
removed outlier: 6.196A pdb=" N LEU A 300 " --> pdb=" O TYR A 364 " (cutoff:3.500A)
No H-bonds generated for sheet with id=AA3
Processing sheet with id=AA4, first strand: chain 'A' and resid 989 through 991
removed outlier: 4.062A pdb=" N GLU A 989 " --> pdb=" O HIS A1002 " (cutoff:3.500A)
removed outlier: 4.228A pdb=" N TRP A1000 " --> pdb=" O SER A 991 " (cutoff:3.500A)
476 hydrogen bonds defined for protein.
1383 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: 2.46
Time building geometry restraints manager: 2.74 seconds
NOTE: a complete listing of the restraints can be obtained by requesting
output of .geo file.
Histogram of bond lengths:
1.23 - 1.34: 2433
1.34 - 1.46: 1693
1.46 - 1.57: 3494
1.57 - 1.69: 5
1.69 - 1.81: 57
Bond restraints: 7682
Sorted by residual:
bond pdb=" CB THR A 823 "
pdb=" CG2 THR A 823 "
ideal model delta sigma weight residual
1.521 1.481 0.040 3.30e-02 9.18e+02 1.45e+00
bond pdb=" CB TRP A1124 "
pdb=" CG TRP A1124 "
ideal model delta sigma weight residual
1.498 1.462 0.036 3.10e-02 1.04e+03 1.34e+00
bond pdb=" CB GLN A 669 "
pdb=" CG GLN A 669 "
ideal model delta sigma weight residual
1.520 1.489 0.031 3.00e-02 1.11e+03 1.07e+00
bond pdb=" CB TRP A 681 "
pdb=" CG TRP A 681 "
ideal model delta sigma weight residual
1.498 1.468 0.030 3.10e-02 1.04e+03 9.61e-01
bond pdb=" CB CYS A1011 "
pdb=" SG CYS A1011 "
ideal model delta sigma weight residual
1.808 1.776 0.032 3.30e-02 9.18e+02 9.17e-01
... (remaining 7677 not shown)
Histogram of bond angle deviations from ideal:
0.00 - 1.27: 10227
1.27 - 2.55: 171
2.55 - 3.82: 45
3.82 - 5.10: 12
5.10 - 6.37: 4
Bond angle restraints: 10459
Sorted by residual:
angle pdb=" C3' ATP A2003 "
pdb=" C4' ATP A2003 "
pdb=" C5' ATP A2003 "
ideal model delta sigma weight residual
115.19 110.95 4.24 1.76e+00 3.23e-01 5.81e+00
angle pdb=" C2' ATP A2003 "
pdb=" C3' ATP A2003 "
pdb=" O3' ATP A2003 "
ideal model delta sigma weight residual
111.83 105.58 6.25 2.67e+00 1.40e-01 5.48e+00
angle pdb=" N GLY A 220 "
pdb=" CA GLY A 220 "
pdb=" C GLY A 220 "
ideal model delta sigma weight residual
110.77 115.28 -4.51 1.93e+00 2.68e-01 5.46e+00
angle pdb=" C1' ATP A2003 "
pdb=" C2' ATP A2003 "
pdb=" O2' ATP A2003 "
ideal model delta sigma weight residual
110.58 104.21 6.37 2.79e+00 1.28e-01 5.20e+00
angle pdb=" C3' ATP A2003 "
pdb=" C2' ATP A2003 "
pdb=" O2' ATP A2003 "
ideal model delta sigma weight residual
111.83 106.09 5.74 2.67e+00 1.40e-01 4.62e+00
... (remaining 10454 not shown)
Histogram of dihedral angle deviations from ideal:
0.00 - 16.86: 4256
16.86 - 33.72: 205
33.72 - 50.59: 41
50.59 - 67.45: 19
67.45 - 84.31: 5
Dihedral angle restraints: 4526
sinusoidal: 1679
harmonic: 2847
Sorted by residual:
dihedral pdb=" CB CYS A 993 "
pdb=" SG CYS A 993 "
pdb=" SG CYS A1011 "
pdb=" CB CYS A1011 "
ideal model delta sinusoidal sigma weight residual
-86.00 -146.15 60.15 1 1.00e+01 1.00e-02 4.82e+01
dihedral pdb=" CA PHE A 207 "
pdb=" C PHE A 207 "
pdb=" N PRO A 208 "
pdb=" CA PRO A 208 "
ideal model delta harmonic sigma weight residual
180.00 160.30 19.70 0 5.00e+00 4.00e-02 1.55e+01
dihedral pdb=" CA ARG A 139 "
pdb=" CB ARG A 139 "
pdb=" CG ARG A 139 "
pdb=" CD ARG A 139 "
ideal model delta sinusoidal sigma weight residual
-60.00 -118.74 58.74 3 1.50e+01 4.44e-03 9.47e+00
... (remaining 4523 not shown)
Histogram of chiral volume deviations from ideal:
0.000 - 0.059: 1097
0.059 - 0.117: 101
0.117 - 0.176: 5
0.176 - 0.235: 0
0.235 - 0.294: 3
Chirality restraints: 1206
Sorted by residual:
chirality pdb=" C2' ATP A2003 "
pdb=" C1' ATP A2003 "
pdb=" C3' ATP A2003 "
pdb=" O2' ATP A2003 "
both_signs ideal model delta sigma weight residual
False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.16e+00
chirality pdb=" C3' ATP A2003 "
pdb=" C2' ATP A2003 "
pdb=" C4' ATP A2003 "
pdb=" O3' ATP A2003 "
both_signs ideal model delta sigma weight residual
False -2.63 -2.92 0.28 2.00e-01 2.50e+01 2.01e+00
chirality pdb=" C4' ATP A2003 "
pdb=" C3' ATP A2003 "
pdb=" C5' ATP A2003 "
pdb=" O4' ATP A2003 "
both_signs ideal model delta sigma weight residual
False -2.49 -2.73 0.24 2.00e-01 2.50e+01 1.43e+00
... (remaining 1203 not shown)
Planarity restraints: 1315
Sorted by residual:
delta sigma weight rms_deltas residual
plane pdb=" C CYS A 699 " -0.027 5.00e-02 4.00e+02 4.06e-02 2.64e+00
pdb=" N PRO A 700 " 0.070 5.00e-02 4.00e+02
pdb=" CA PRO A 700 " -0.021 5.00e-02 4.00e+02
pdb=" CD PRO A 700 " -0.022 5.00e-02 4.00e+02
delta sigma weight rms_deltas residual
plane pdb=" C ALA A1076 " 0.016 5.00e-02 4.00e+02 2.34e-02 8.79e-01
pdb=" N PRO A1077 " -0.041 5.00e-02 4.00e+02
pdb=" CA PRO A1077 " 0.012 5.00e-02 4.00e+02
pdb=" CD PRO A1077 " 0.013 5.00e-02 4.00e+02
delta sigma weight rms_deltas residual
plane pdb=" C THR A 456 " -0.013 5.00e-02 4.00e+02 1.94e-02 6.05e-01
pdb=" N PRO A 457 " 0.034 5.00e-02 4.00e+02
pdb=" CA PRO A 457 " -0.010 5.00e-02 4.00e+02
pdb=" CD PRO A 457 " -0.011 5.00e-02 4.00e+02
... (remaining 1312 not shown)
Histogram of nonbonded interaction distances:
2.12 - 2.67: 143
2.67 - 3.23: 8232
3.23 - 3.79: 11978
3.79 - 4.34: 14841
4.34 - 4.90: 24713
Nonbonded interactions: 59907
Sorted by model distance:
nonbonded pdb=" OE2 GLU A 828 "
pdb="CA CA A2001 "
model vdw
2.119 2.510
nonbonded pdb=" OE1 GLN A 831 "
pdb="CA CA A2001 "
model vdw
2.170 2.510
nonbonded pdb=" N GLU A 374 "
pdb=" OE1 GLU A 374 "
model vdw
2.204 3.120
nonbonded pdb=" O PHE A 454 "
pdb=" NH1 ARG A 459 "
model vdw
2.236 3.120
nonbonded pdb=" N GLU A 389 "
pdb=" OE1 GLU A 389 "
model vdw
2.238 3.120
... (remaining 59902 not shown)
NOTE: a complete listing of the restraints can be obtained by requesting
output of .geo file.
Find NCS groups from input model
========== WARNING! ============
No NCS relation were found !!!
================================
Found NCS groups:
found none.
Set up NCS constraints
No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
ADPs will be refined as 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: 11.210
Set stop_for_unknowns flag: 0.000
Assert model is a single copy model: 0.000
Assert all atoms have isotropic ADPs: 0.000
Construct map_model_manager: 0.000
Extract box with map and model: 0.000
Check model and map are aligned: 0.000
Set scattering table: 0.000
Process input model: 21.780
Find NCS groups from input model: 0.070
Set up NCS constraints: 0.030
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:2.940
Set ADP refinement strategy: 0.000
Make a string to write initial .geo file:0.000
Internal consistency checks: 0.000
Total: 36.030
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8341
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 : 0.005 0.040 7682 Z= 0.334
Angle : 0.499 6.369 10459 Z= 0.270
Chirality : 0.036 0.294 1206
Planarity : 0.003 0.041 1315
Dihedral : 11.380 84.310 2683
Min Nonbonded Distance : 2.119
Molprobity Statistics.
All-atom Clashscore : 6.47
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 3.90 %
Favored : 96.10 %
Rotamer:
Outliers : 0.28 %
Allowed : 5.79 %
Favored : 93.93 %
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: 1.45 (0.27), residues: 975
helix: 2.00 (0.21), residues: 605
sheet: -2.01 (0.59), residues: 59
loop : -0.46 (0.37), residues: 311
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.007 0.001 TRP A 213
HIS 0.003 0.001 HIS A 173
PHE 0.007 0.001 PHE A 223
TYR 0.007 0.001 TYR A1015
ARG 0.003 0.000 ARG A1062
*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
1950 Ramachandran restraints generated.
975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
1950 Ramachandran restraints generated.
975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
110 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 2
poor density : 108
time to evaluate : 0.842
Fit side-chains
revert: symmetry clash
revert: symmetry clash
REVERT: A 1037 ASN cc_start: 0.8974 (m-40) cc_final: 0.8671 (m110)
REVERT: A 1038 LEU cc_start: 0.9535 (tp) cc_final: 0.9307 (tt)
outliers start: 2
outliers final: 2
residues processed: 110
average time/residue: 0.2000
time to fit residues: 30.1241
Evaluate side-chains
66 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 2
poor density : 64
time to evaluate : 0.919
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 119 VAL
Chi-restraints excluded: chain A residue 373 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 99
random chunks:
chunk 83 optimal weight: 1.9990
chunk 75 optimal weight: 4.9990
chunk 41 optimal weight: 0.6980
chunk 25 optimal weight: 3.9990
chunk 50 optimal weight: 0.8980
chunk 40 optimal weight: 0.9990
chunk 77 optimal weight: 2.9990
chunk 30 optimal weight: 10.0000
chunk 47 optimal weight: 0.7980
chunk 57 optimal weight: 0.9980
chunk 89 optimal weight: 0.9990
overall best weight: 0.8782
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 44 HIS
A1032 ASN
Total number of N/Q/H flips: 2
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.077004 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3184 r_free = 0.3184 target = 0.060616 restraints weight = 29018.777|
|-----------------------------------------------------------------------------|
r_work (start): 0.3119 rms_B_bonded: 4.05
r_work: 0.2982 rms_B_bonded: 4.47 restraints_weight: 0.5000
r_work (final): 0.2982
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8556
moved from start: 0.1943
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.044 7682 Z= 0.205
Angle : 0.582 10.997 10459 Z= 0.296
Chirality : 0.038 0.160 1206
Planarity : 0.004 0.041 1315
Dihedral : 6.966 69.036 1108
Min Nonbonded Distance : 2.307
Molprobity Statistics.
All-atom Clashscore : 6.07
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 3.38 %
Favored : 96.62 %
Rotamer:
Outliers : 2.07 %
Allowed : 8.83 %
Favored : 89.10 %
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: 2.25 (0.28), residues: 975
helix: 2.61 (0.21), residues: 621
sheet: -1.21 (0.64), residues: 64
loop : -0.34 (0.38), residues: 290
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.011 0.001 TRP A 772
HIS 0.002 0.001 HIS A 159
PHE 0.022 0.002 PHE A 249
TYR 0.010 0.001 TYR A 227
ARG 0.010 0.001 ARG A 601
*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
1950 Ramachandran restraints generated.
975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
1950 Ramachandran restraints generated.
975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
99 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 15
poor density : 84
time to evaluate : 0.924
Fit side-chains
revert: symmetry clash
revert: symmetry clash
REVERT: A 784 MET cc_start: 0.9283 (ttm) cc_final: 0.9008 (tmm)
REVERT: A 1034 LEU cc_start: 0.9185 (mp) cc_final: 0.8772 (tt)
REVERT: A 1037 ASN cc_start: 0.9415 (m-40) cc_final: 0.9097 (m110)
REVERT: A 1051 GLN cc_start: 0.8760 (tm-30) cc_final: 0.8418 (tm-30)
outliers start: 15
outliers final: 7
residues processed: 92
average time/residue: 0.1790
time to fit residues: 23.5712
Evaluate side-chains
73 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 7
poor density : 66
time to evaluate : 0.924
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 102 VAL
Chi-restraints excluded: chain A residue 119 VAL
Chi-restraints excluded: chain A residue 184 VAL
Chi-restraints excluded: chain A residue 194 VAL
Chi-restraints excluded: chain A residue 240 HIS
Chi-restraints excluded: chain A residue 373 PHE
Chi-restraints excluded: chain A residue 904 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 99
random chunks:
chunk 84 optimal weight: 4.9990
chunk 48 optimal weight: 0.9990
chunk 26 optimal weight: 7.9990
chunk 91 optimal weight: 0.8980
chunk 55 optimal weight: 0.9980
chunk 77 optimal weight: 3.9990
chunk 41 optimal weight: 0.7980
chunk 32 optimal weight: 2.9990
chunk 86 optimal weight: 0.8980
chunk 17 optimal weight: 9.9990
chunk 64 optimal weight: 0.6980
overall best weight: 0.8580
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 165 HIS
A 505 HIS
A 973 GLN
A1032 ASN
Total number of N/Q/H flips: 4
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.076407 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.060054 restraints weight = 29312.492|
|-----------------------------------------------------------------------------|
r_work (start): 0.3126 rms_B_bonded: 4.01
r_work: 0.2994 rms_B_bonded: 4.46 restraints_weight: 0.5000
r_work (final): 0.2994
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8600
moved from start: 0.2500
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.026 7682 Z= 0.186
Angle : 0.533 9.320 10459 Z= 0.272
Chirality : 0.036 0.178 1206
Planarity : 0.004 0.049 1315
Dihedral : 6.587 79.120 1108
Min Nonbonded Distance : 2.323
Molprobity Statistics.
All-atom Clashscore : 5.06
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 2.97 %
Favored : 97.03 %
Rotamer:
Outliers : 2.21 %
Allowed : 11.31 %
Favored : 86.48 %
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: 2.13 (0.28), residues: 975
helix: 2.52 (0.21), residues: 623
sheet: -1.22 (0.64), residues: 64
loop : -0.44 (0.38), residues: 288
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.013 0.001 TRP A 61
HIS 0.003 0.001 HIS A 505
PHE 0.021 0.001 PHE A 697
TYR 0.009 0.001 TYR A 227
ARG 0.007 0.000 ARG A 327
*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
1950 Ramachandran restraints generated.
975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
1950 Ramachandran restraints generated.
975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
88 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 16
poor density : 72
time to evaluate : 0.833
Fit side-chains
revert: symmetry clash
revert: symmetry clash
REVERT: A 186 MET cc_start: 0.8970 (ptp) cc_final: 0.8591 (ptp)
REVERT: A 629 GLU cc_start: 0.8519 (tm-30) cc_final: 0.8246 (tm-30)
REVERT: A 1034 LEU cc_start: 0.9185 (mp) cc_final: 0.8751 (tt)
REVERT: A 1037 ASN cc_start: 0.9369 (m-40) cc_final: 0.9060 (m110)
REVERT: A 1051 GLN cc_start: 0.8707 (tm-30) cc_final: 0.8218 (tm-30)
outliers start: 16
outliers final: 10
residues processed: 82
average time/residue: 0.1618
time to fit residues: 19.6456
Evaluate side-chains
74 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 10
poor density : 64
time to evaluate : 0.843
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 102 VAL
Chi-restraints excluded: chain A residue 119 VAL
Chi-restraints excluded: chain A residue 184 VAL
Chi-restraints excluded: chain A residue 194 VAL
Chi-restraints excluded: chain A residue 240 HIS
Chi-restraints excluded: chain A residue 373 PHE
Chi-restraints excluded: chain A residue 657 LEU
Chi-restraints excluded: chain A residue 869 LEU
Chi-restraints excluded: chain A residue 904 VAL
Chi-restraints excluded: chain A residue 988 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 99
random chunks:
chunk 75 optimal weight: 4.9990
chunk 8 optimal weight: 0.9990
chunk 11 optimal weight: 0.7980
chunk 10 optimal weight: 2.9990
chunk 69 optimal weight: 7.9990
chunk 39 optimal weight: 3.9990
chunk 80 optimal weight: 0.9990
chunk 12 optimal weight: 2.9990
chunk 81 optimal weight: 0.7980
chunk 20 optimal weight: 4.9990
chunk 60 optimal weight: 2.9990
overall best weight: 1.3186
-------------------------------------------------------------------------------
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 = 0.3524 r_free = 0.3524 target = 0.075292 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.058962 restraints weight = 29260.902|
|-----------------------------------------------------------------------------|
r_work (start): 0.3074 rms_B_bonded: 4.05
r_work: 0.2930 rms_B_bonded: 4.53 restraints_weight: 0.5000
r_work (final): 0.2930
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8623
moved from start: 0.2821
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.033 7682 Z= 0.232
Angle : 0.527 7.671 10459 Z= 0.268
Chirality : 0.036 0.148 1206
Planarity : 0.004 0.042 1315
Dihedral : 6.261 86.739 1108
Min Nonbonded Distance : 2.292
Molprobity Statistics.
All-atom Clashscore : 6.00
Ramachandran Plot:
Outliers : 0.10 %
Allowed : 2.87 %
Favored : 97.03 %
Rotamer:
Outliers : 2.76 %
Allowed : 12.83 %
Favored : 84.41 %
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: 2.11 (0.28), residues: 975
helix: 2.54 (0.21), residues: 625
sheet: -1.30 (0.62), residues: 64
loop : -0.55 (0.38), residues: 286
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.010 0.001 TRP A 680
HIS 0.005 0.001 HIS A 505
PHE 0.025 0.001 PHE A 697
TYR 0.009 0.001 TYR A 227
ARG 0.005 0.000 ARG A1138
*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
1950 Ramachandran restraints generated.
975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
1950 Ramachandran restraints generated.
975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
85 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 20
poor density : 65
time to evaluate : 1.052
Fit side-chains
revert: symmetry clash
revert: symmetry clash
REVERT: A 186 MET cc_start: 0.9145 (ptp) cc_final: 0.8767 (ptp)
REVERT: A 430 MET cc_start: 0.9607 (tpp) cc_final: 0.9407 (mmm)
REVERT: A 669 GLN cc_start: 0.8952 (mm-40) cc_final: 0.8647 (mm110)
REVERT: A 1034 LEU cc_start: 0.9212 (mp) cc_final: 0.8736 (tt)
REVERT: A 1037 ASN cc_start: 0.9372 (m-40) cc_final: 0.9065 (m110)
REVERT: A 1051 GLN cc_start: 0.8690 (tm-30) cc_final: 0.8266 (tm-30)
outliers start: 20
outliers final: 11
residues processed: 79
average time/residue: 0.1683
time to fit residues: 19.5774
Evaluate side-chains
72 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 11
poor density : 61
time to evaluate : 0.847
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 102 VAL
Chi-restraints excluded: chain A residue 184 VAL
Chi-restraints excluded: chain A residue 194 VAL
Chi-restraints excluded: chain A residue 599 MET
Chi-restraints excluded: chain A residue 636 VAL
Chi-restraints excluded: chain A residue 823 THR
Chi-restraints excluded: chain A residue 829 LEU
Chi-restraints excluded: chain A residue 869 LEU
Chi-restraints excluded: chain A residue 904 VAL
Chi-restraints excluded: chain A residue 988 MET
Chi-restraints excluded: chain A residue 1032 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 99
random chunks:
chunk 13 optimal weight: 6.9990
chunk 3 optimal weight: 4.9990
chunk 80 optimal weight: 0.8980
chunk 19 optimal weight: 0.2980
chunk 48 optimal weight: 5.9990
chunk 44 optimal weight: 5.9990
chunk 88 optimal weight: 0.2980
chunk 76 optimal weight: 3.9990
chunk 42 optimal weight: 0.7980
chunk 5 optimal weight: 10.0000
chunk 20 optimal weight: 0.9990
overall best weight: 0.6582
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 505 HIS
Total number of N/Q/H flips: 1
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.076316 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3182 r_free = 0.3182 target = 0.060207 restraints weight = 28738.359|
|-----------------------------------------------------------------------------|
r_work (start): 0.3106 rms_B_bonded: 3.98
r_work: 0.2972 rms_B_bonded: 4.42 restraints_weight: 0.5000
r_work (final): 0.2972
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8584
moved from start: 0.3071
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.002 0.034 7682 Z= 0.167
Angle : 0.514 7.069 10459 Z= 0.259
Chirality : 0.035 0.152 1206
Planarity : 0.004 0.038 1315
Dihedral : 5.871 87.902 1105
Min Nonbonded Distance : 2.351
Molprobity Statistics.
All-atom Clashscore : 5.87
Ramachandran Plot:
Outliers : 0.10 %
Allowed : 2.36 %
Favored : 97.54 %
Rotamer:
Outliers : 2.34 %
Allowed : 14.21 %
Favored : 83.45 %
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: 2.04 (0.28), residues: 975
helix: 2.50 (0.21), residues: 633
sheet: -1.51 (0.60), residues: 70
loop : -0.62 (0.38), residues: 272
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.009 0.001 TRP A 680
HIS 0.005 0.001 HIS A 505
PHE 0.025 0.001 PHE A 373
TYR 0.008 0.001 TYR A 227
ARG 0.005 0.000 ARG A1138
*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
1950 Ramachandran restraints generated.
975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
1950 Ramachandran restraints generated.
975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
85 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 17
poor density : 68
time to evaluate : 0.859
Fit side-chains
revert: symmetry clash
revert: symmetry clash
REVERT: A 186 MET cc_start: 0.9125 (ptp) cc_final: 0.8742 (ptp)
REVERT: A 327 ARG cc_start: 0.9199 (tpt170) cc_final: 0.8929 (tmm160)
REVERT: A 574 MET cc_start: 0.9086 (mmt) cc_final: 0.8878 (mmt)
REVERT: A 669 GLN cc_start: 0.8906 (mm-40) cc_final: 0.8643 (mm110)
REVERT: A 1034 LEU cc_start: 0.9186 (mp) cc_final: 0.8719 (tt)
REVERT: A 1037 ASN cc_start: 0.9329 (m-40) cc_final: 0.9030 (m110)
REVERT: A 1051 GLN cc_start: 0.8627 (tm-30) cc_final: 0.8119 (tm-30)
outliers start: 17
outliers final: 14
residues processed: 79
average time/residue: 0.1595
time to fit residues: 18.7252
Evaluate side-chains
73 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 14
poor density : 59
time to evaluate : 0.895
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 102 VAL
Chi-restraints excluded: chain A residue 119 VAL
Chi-restraints excluded: chain A residue 184 VAL
Chi-restraints excluded: chain A residue 194 VAL
Chi-restraints excluded: chain A residue 240 HIS
Chi-restraints excluded: chain A residue 361 LEU
Chi-restraints excluded: chain A residue 599 MET
Chi-restraints excluded: chain A residue 636 VAL
Chi-restraints excluded: chain A residue 695 LEU
Chi-restraints excluded: chain A residue 823 THR
Chi-restraints excluded: chain A residue 824 LEU
Chi-restraints excluded: chain A residue 869 LEU
Chi-restraints excluded: chain A residue 988 MET
Chi-restraints excluded: chain A residue 1032 ASN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 99
random chunks:
chunk 74 optimal weight: 0.7980
chunk 45 optimal weight: 10.0000
chunk 52 optimal weight: 6.9990
chunk 27 optimal weight: 4.9990
chunk 34 optimal weight: 1.9990
chunk 23 optimal weight: 6.9990
chunk 72 optimal weight: 2.9990
chunk 43 optimal weight: 4.9990
chunk 83 optimal weight: 8.9990
chunk 87 optimal weight: 1.9990
chunk 2 optimal weight: 7.9990
overall best weight: 2.5588
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 44 HIS
A 89 ASN
A 240 HIS
A 908 HIS
Total number of N/Q/H flips: 4
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.072147 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3052 r_free = 0.3052 target = 0.055642 restraints weight = 29555.870|
|-----------------------------------------------------------------------------|
r_work (start): 0.2997 rms_B_bonded: 4.02
r_work: 0.2858 rms_B_bonded: 4.47 restraints_weight: 0.5000
r_work (final): 0.2858
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8686
moved from start: 0.3313
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.006 0.054 7682 Z= 0.389
Angle : 0.606 6.735 10459 Z= 0.310
Chirality : 0.039 0.157 1206
Planarity : 0.004 0.043 1315
Dihedral : 5.763 86.135 1105
Min Nonbonded Distance : 2.214
Molprobity Statistics.
All-atom Clashscore : 7.22
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 3.59 %
Favored : 96.41 %
Rotamer:
Outliers : 2.90 %
Allowed : 14.76 %
Favored : 82.34 %
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: 1.89 (0.28), residues: 975
helix: 2.34 (0.21), residues: 636
sheet: -1.51 (0.59), residues: 69
loop : -0.62 (0.38), residues: 270
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.011 0.001 TRP A 680
HIS 0.004 0.001 HIS A 173
PHE 0.022 0.002 PHE A 697
TYR 0.012 0.001 TYR A 227
ARG 0.004 0.000 ARG A1138
*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
1950 Ramachandran restraints generated.
975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
1950 Ramachandran restraints generated.
975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
75 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 21
poor density : 54
time to evaluate : 0.892
Fit side-chains
revert: symmetry clash
revert: symmetry clash
REVERT: A 186 MET cc_start: 0.9244 (ptp) cc_final: 0.8842 (ptp)
REVERT: A 784 MET cc_start: 0.9235 (ttm) cc_final: 0.8951 (tmm)
REVERT: A 1037 ASN cc_start: 0.9428 (m-40) cc_final: 0.9145 (m110)
REVERT: A 1051 GLN cc_start: 0.8723 (tm-30) cc_final: 0.8287 (tm-30)
REVERT: A 1138 ARG cc_start: 0.9369 (ttp80) cc_final: 0.9130 (ttp80)
outliers start: 21
outliers final: 15
residues processed: 70
average time/residue: 0.1555
time to fit residues: 16.6286
Evaluate side-chains
68 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 15
poor density : 53
time to evaluate : 0.860
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 102 VAL
Chi-restraints excluded: chain A residue 119 VAL
Chi-restraints excluded: chain A residue 184 VAL
Chi-restraints excluded: chain A residue 194 VAL
Chi-restraints excluded: chain A residue 262 THR
Chi-restraints excluded: chain A residue 510 LEU
Chi-restraints excluded: chain A residue 599 MET
Chi-restraints excluded: chain A residue 636 VAL
Chi-restraints excluded: chain A residue 695 LEU
Chi-restraints excluded: chain A residue 823 THR
Chi-restraints excluded: chain A residue 824 LEU
Chi-restraints excluded: chain A residue 829 LEU
Chi-restraints excluded: chain A residue 869 LEU
Chi-restraints excluded: chain A residue 904 VAL
Chi-restraints excluded: chain A residue 1032 ASN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 99
random chunks:
chunk 0 optimal weight: 7.9990
chunk 55 optimal weight: 5.9990
chunk 12 optimal weight: 4.9990
chunk 65 optimal weight: 0.6980
chunk 64 optimal weight: 0.9980
chunk 88 optimal weight: 0.7980
chunk 61 optimal weight: 0.9990
chunk 62 optimal weight: 0.7980
chunk 44 optimal weight: 3.9990
chunk 17 optimal weight: 4.9990
chunk 2 optimal weight: 8.9990
overall best weight: 0.8582
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 240 HIS
Total number of N/Q/H flips: 1
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.073959 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3109 r_free = 0.3109 target = 0.057689 restraints weight = 29081.270|
|-----------------------------------------------------------------------------|
r_work (start): 0.3063 rms_B_bonded: 3.98
r_work: 0.2930 rms_B_bonded: 4.39 restraints_weight: 0.5000
r_work (final): 0.2930
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8639
moved from start: 0.3484
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.036 7682 Z= 0.182
Angle : 0.521 7.983 10459 Z= 0.265
Chirality : 0.036 0.165 1206
Planarity : 0.004 0.040 1315
Dihedral : 5.559 81.875 1105
Min Nonbonded Distance : 2.341
Molprobity Statistics.
All-atom Clashscore : 6.54
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 2.67 %
Favored : 97.33 %
Rotamer:
Outliers : 3.31 %
Allowed : 15.17 %
Favored : 81.52 %
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: 2.11 (0.28), residues: 975
helix: 2.59 (0.21), residues: 628
sheet: -1.93 (0.60), residues: 65
loop : -0.55 (0.36), residues: 282
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.010 0.001 TRP A 649
HIS 0.003 0.000 HIS A 66
PHE 0.017 0.001 PHE A 697
TYR 0.008 0.001 TYR A 227
ARG 0.009 0.000 ARG A 327
*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
1950 Ramachandran restraints generated.
975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
1950 Ramachandran restraints generated.
975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
85 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 24
poor density : 61
time to evaluate : 0.940
Fit side-chains
revert: symmetry clash
revert: symmetry clash
REVERT: A 135 GLN cc_start: 0.9162 (tm-30) cc_final: 0.8948 (tm-30)
REVERT: A 186 MET cc_start: 0.9191 (ptp) cc_final: 0.8805 (ptp)
REVERT: A 430 MET cc_start: 0.9640 (mmm) cc_final: 0.9275 (tpp)
REVERT: A 669 GLN cc_start: 0.8973 (mm-40) cc_final: 0.8697 (mm110)
REVERT: A 784 MET cc_start: 0.9192 (ttm) cc_final: 0.8913 (tmm)
REVERT: A 1034 LEU cc_start: 0.9229 (mp) cc_final: 0.8727 (tt)
REVERT: A 1037 ASN cc_start: 0.9390 (m-40) cc_final: 0.9090 (m110)
REVERT: A 1051 GLN cc_start: 0.8659 (tm-30) cc_final: 0.8212 (tm-30)
REVERT: A 1138 ARG cc_start: 0.9352 (ttp80) cc_final: 0.8807 (ttp80)
outliers start: 24
outliers final: 18
residues processed: 78
average time/residue: 0.1575
time to fit residues: 18.5317
Evaluate side-chains
78 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 18
poor density : 60
time to evaluate : 0.871
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 102 VAL
Chi-restraints excluded: chain A residue 119 VAL
Chi-restraints excluded: chain A residue 132 THR
Chi-restraints excluded: chain A residue 184 VAL
Chi-restraints excluded: chain A residue 194 VAL
Chi-restraints excluded: chain A residue 262 THR
Chi-restraints excluded: chain A residue 361 LEU
Chi-restraints excluded: chain A residue 510 LEU
Chi-restraints excluded: chain A residue 564 LEU
Chi-restraints excluded: chain A residue 599 MET
Chi-restraints excluded: chain A residue 636 VAL
Chi-restraints excluded: chain A residue 695 LEU
Chi-restraints excluded: chain A residue 823 THR
Chi-restraints excluded: chain A residue 824 LEU
Chi-restraints excluded: chain A residue 829 LEU
Chi-restraints excluded: chain A residue 869 LEU
Chi-restraints excluded: chain A residue 904 VAL
Chi-restraints excluded: chain A residue 1032 ASN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 99
random chunks:
chunk 50 optimal weight: 0.9980
chunk 91 optimal weight: 1.9990
chunk 25 optimal weight: 0.9980
chunk 4 optimal weight: 9.9990
chunk 75 optimal weight: 4.9990
chunk 76 optimal weight: 0.8980
chunk 0 optimal weight: 6.9990
chunk 93 optimal weight: 6.9990
chunk 38 optimal weight: 5.9990
chunk 84 optimal weight: 0.1980
chunk 8 optimal weight: 4.9990
overall best weight: 1.0182
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 240 HIS
Total number of N/Q/H flips: 1
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.074169 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.057932 restraints weight = 29407.372|
|-----------------------------------------------------------------------------|
r_work (start): 0.3071 rms_B_bonded: 4.03
r_work: 0.2934 rms_B_bonded: 4.49 restraints_weight: 0.5000
r_work (final): 0.2934
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8662
moved from start: 0.3646
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.033 7682 Z= 0.194
Angle : 0.513 7.720 10459 Z= 0.262
Chirality : 0.036 0.166 1206
Planarity : 0.004 0.040 1315
Dihedral : 5.400 79.176 1105
Min Nonbonded Distance : 2.316
Molprobity Statistics.
All-atom Clashscore : 6.41
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 2.97 %
Favored : 97.03 %
Rotamer:
Outliers : 2.90 %
Allowed : 16.00 %
Favored : 81.10 %
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: 2.16 (0.28), residues: 975
helix: 2.62 (0.21), residues: 629
sheet: -1.89 (0.61), residues: 65
loop : -0.53 (0.36), residues: 281
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.009 0.001 TRP A 772
HIS 0.002 0.001 HIS A 66
PHE 0.017 0.001 PHE A 697
TYR 0.007 0.001 TYR A 818
ARG 0.006 0.000 ARG A 327
*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
1950 Ramachandran restraints generated.
975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
1950 Ramachandran restraints generated.
975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
83 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 21
poor density : 62
time to evaluate : 0.746
Fit side-chains
revert: symmetry clash
revert: symmetry clash
REVERT: A 135 GLN cc_start: 0.9160 (tm-30) cc_final: 0.8943 (tm-30)
REVERT: A 186 MET cc_start: 0.9169 (ptp) cc_final: 0.8864 (ptp)
REVERT: A 327 ARG cc_start: 0.8732 (tmm160) cc_final: 0.8467 (ttp80)
REVERT: A 629 GLU cc_start: 0.8513 (tm-30) cc_final: 0.8159 (tm-30)
REVERT: A 669 GLN cc_start: 0.8944 (mm-40) cc_final: 0.8717 (mm110)
REVERT: A 784 MET cc_start: 0.9181 (ttm) cc_final: 0.8912 (tmm)
REVERT: A 983 MET cc_start: 0.9011 (mtt) cc_final: 0.8738 (mtt)
REVERT: A 1034 LEU cc_start: 0.9236 (mp) cc_final: 0.8729 (tt)
REVERT: A 1037 ASN cc_start: 0.9368 (m-40) cc_final: 0.9095 (m110)
REVERT: A 1051 GLN cc_start: 0.8671 (tm-30) cc_final: 0.8228 (tm-30)
REVERT: A 1138 ARG cc_start: 0.9369 (ttp80) cc_final: 0.8852 (ttp80)
outliers start: 21
outliers final: 14
residues processed: 76
average time/residue: 0.1572
time to fit residues: 17.8009
Evaluate side-chains
74 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 14
poor density : 60
time to evaluate : 0.830
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 102 VAL
Chi-restraints excluded: chain A residue 119 VAL
Chi-restraints excluded: chain A residue 184 VAL
Chi-restraints excluded: chain A residue 194 VAL
Chi-restraints excluded: chain A residue 262 THR
Chi-restraints excluded: chain A residue 510 LEU
Chi-restraints excluded: chain A residue 599 MET
Chi-restraints excluded: chain A residue 636 VAL
Chi-restraints excluded: chain A residue 695 LEU
Chi-restraints excluded: chain A residue 823 THR
Chi-restraints excluded: chain A residue 824 LEU
Chi-restraints excluded: chain A residue 829 LEU
Chi-restraints excluded: chain A residue 869 LEU
Chi-restraints excluded: chain A residue 904 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 99
random chunks:
chunk 8 optimal weight: 4.9990
chunk 88 optimal weight: 1.9990
chunk 38 optimal weight: 4.9990
chunk 31 optimal weight: 4.9990
chunk 64 optimal weight: 0.7980
chunk 36 optimal weight: 0.4980
chunk 60 optimal weight: 0.2980
chunk 83 optimal weight: 0.4980
chunk 59 optimal weight: 1.9990
chunk 33 optimal weight: 7.9990
chunk 72 optimal weight: 0.2980
overall best weight: 0.4780
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 240 HIS
A1032 ASN
Total number of N/Q/H flips: 2
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.075929 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3120 r_free = 0.3120 target = 0.059295 restraints weight = 29732.233|
|-----------------------------------------------------------------------------|
r_work (start): 0.3085 rms_B_bonded: 4.22
r_work: 0.2945 rms_B_bonded: 4.63 restraints_weight: 0.5000
r_work (final): 0.2945
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8524
moved from start: 0.3790
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.002 0.034 7682 Z= 0.151
Angle : 0.504 7.283 10459 Z= 0.258
Chirality : 0.036 0.186 1206
Planarity : 0.004 0.039 1315
Dihedral : 5.308 76.901 1105
Min Nonbonded Distance : 2.381
Molprobity Statistics.
All-atom Clashscore : 6.68
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 2.36 %
Favored : 97.64 %
Rotamer:
Outliers : 2.76 %
Allowed : 15.59 %
Favored : 81.66 %
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: 2.18 (0.28), residues: 975
helix: 2.63 (0.21), residues: 630
sheet: -1.39 (0.60), residues: 70
loop : -0.62 (0.37), residues: 275
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.009 0.001 TRP A 772
HIS 0.002 0.000 HIS A 66
PHE 0.016 0.001 PHE A 697
TYR 0.014 0.001 TYR A 818
ARG 0.004 0.000 ARG A1138
*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
1950 Ramachandran restraints generated.
975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
1950 Ramachandran restraints generated.
975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
85 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 20
poor density : 65
time to evaluate : 0.880
Fit side-chains
revert: symmetry clash
REVERT: A 77 GLU cc_start: 0.8220 (mt-10) cc_final: 0.7856 (tm-30)
REVERT: A 135 GLN cc_start: 0.9119 (tm-30) cc_final: 0.8900 (tm-30)
REVERT: A 186 MET cc_start: 0.9166 (ptp) cc_final: 0.8728 (ptp)
REVERT: A 430 MET cc_start: 0.9693 (tpp) cc_final: 0.9481 (mmm)
REVERT: A 629 GLU cc_start: 0.8504 (tm-30) cc_final: 0.8141 (tm-30)
REVERT: A 784 MET cc_start: 0.9141 (ttm) cc_final: 0.8819 (tmm)
REVERT: A 983 MET cc_start: 0.8990 (mtt) cc_final: 0.8706 (mtt)
REVERT: A 1034 LEU cc_start: 0.9182 (mp) cc_final: 0.8673 (tt)
REVERT: A 1051 GLN cc_start: 0.8507 (tm-30) cc_final: 0.7987 (tm-30)
REVERT: A 1138 ARG cc_start: 0.9334 (ttp80) cc_final: 0.9104 (ttp80)
outliers start: 20
outliers final: 17
residues processed: 78
average time/residue: 0.1615
time to fit residues: 18.8820
Evaluate side-chains
81 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 17
poor density : 64
time to evaluate : 1.076
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 102 VAL
Chi-restraints excluded: chain A residue 119 VAL
Chi-restraints excluded: chain A residue 184 VAL
Chi-restraints excluded: chain A residue 194 VAL
Chi-restraints excluded: chain A residue 240 HIS
Chi-restraints excluded: chain A residue 262 THR
Chi-restraints excluded: chain A residue 564 LEU
Chi-restraints excluded: chain A residue 599 MET
Chi-restraints excluded: chain A residue 636 VAL
Chi-restraints excluded: chain A residue 695 LEU
Chi-restraints excluded: chain A residue 789 SER
Chi-restraints excluded: chain A residue 823 THR
Chi-restraints excluded: chain A residue 824 LEU
Chi-restraints excluded: chain A residue 829 LEU
Chi-restraints excluded: chain A residue 869 LEU
Chi-restraints excluded: chain A residue 904 VAL
Chi-restraints excluded: chain A residue 1032 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 99
random chunks:
chunk 35 optimal weight: 5.9990
chunk 12 optimal weight: 2.9990
chunk 23 optimal weight: 6.9990
chunk 39 optimal weight: 0.8980
chunk 42 optimal weight: 1.9990
chunk 67 optimal weight: 2.9990
chunk 9 optimal weight: 2.9990
chunk 31 optimal weight: 5.9990
chunk 57 optimal weight: 4.9990
chunk 15 optimal weight: 3.9990
chunk 61 optimal weight: 0.3980
overall best weight: 1.8586
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 240 HIS
A1032 ASN
A1037 ASN
Total number of N/Q/H flips: 3
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.074161 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3135 r_free = 0.3135 target = 0.057891 restraints weight = 29951.368|
|-----------------------------------------------------------------------------|
r_work (start): 0.3045 rms_B_bonded: 4.02
r_work: 0.2902 rms_B_bonded: 4.47 restraints_weight: 0.5000
r_work (final): 0.2902
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8665
moved from start: 0.3817
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.004 0.043 7682 Z= 0.286
Angle : 0.546 8.710 10459 Z= 0.280
Chirality : 0.037 0.184 1206
Planarity : 0.004 0.041 1315
Dihedral : 5.304 76.693 1105
Min Nonbonded Distance : 2.275
Molprobity Statistics.
All-atom Clashscore : 6.74
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 3.08 %
Favored : 96.92 %
Rotamer:
Outliers : 2.76 %
Allowed : 16.00 %
Favored : 81.24 %
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: 2.18 (0.28), residues: 975
helix: 2.66 (0.21), residues: 629
sheet: -1.68 (0.63), residues: 64
loop : -0.65 (0.36), residues: 282
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.009 0.001 TRP A 680
HIS 0.006 0.001 HIS A 240
PHE 0.016 0.001 PHE A 697
TYR 0.007 0.001 TYR A 227
ARG 0.005 0.000 ARG A 327
********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
1950 Ramachandran restraints generated.
975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
1950 Ramachandran restraints generated.
975 Oldfield, 0 Emsley, 975 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
81 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 20
poor density : 61
time to evaluate : 0.893
Fit side-chains
revert: symmetry clash
REVERT: A 135 GLN cc_start: 0.9176 (tm-30) cc_final: 0.8955 (tm-30)
REVERT: A 186 MET cc_start: 0.9191 (ptp) cc_final: 0.8740 (ptp)
REVERT: A 430 MET cc_start: 0.9667 (tpp) cc_final: 0.9421 (mmm)
REVERT: A 784 MET cc_start: 0.9206 (ttm) cc_final: 0.8925 (tmm)
REVERT: A 1034 LEU cc_start: 0.9262 (mp) cc_final: 0.8739 (tt)
REVERT: A 1051 GLN cc_start: 0.8662 (tm-30) cc_final: 0.8203 (tm-30)
REVERT: A 1138 ARG cc_start: 0.9375 (ttp80) cc_final: 0.9143 (ttp80)
outliers start: 20
outliers final: 18
residues processed: 74
average time/residue: 0.1586
time to fit residues: 17.8059
Evaluate side-chains
77 residues out of total 835 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 18
poor density : 59
time to evaluate : 0.894
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 102 VAL
Chi-restraints excluded: chain A residue 119 VAL
Chi-restraints excluded: chain A residue 184 VAL
Chi-restraints excluded: chain A residue 194 VAL
Chi-restraints excluded: chain A residue 240 HIS
Chi-restraints excluded: chain A residue 262 THR
Chi-restraints excluded: chain A residue 510 LEU
Chi-restraints excluded: chain A residue 564 LEU
Chi-restraints excluded: chain A residue 599 MET
Chi-restraints excluded: chain A residue 636 VAL
Chi-restraints excluded: chain A residue 695 LEU
Chi-restraints excluded: chain A residue 789 SER
Chi-restraints excluded: chain A residue 823 THR
Chi-restraints excluded: chain A residue 824 LEU
Chi-restraints excluded: chain A residue 829 LEU
Chi-restraints excluded: chain A residue 869 LEU
Chi-restraints excluded: chain A residue 904 VAL
Chi-restraints excluded: chain A residue 1032 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 99
random chunks:
chunk 18 optimal weight: 4.9990
chunk 57 optimal weight: 3.9990
chunk 52 optimal weight: 3.9990
chunk 87 optimal weight: 2.9990
chunk 66 optimal weight: 0.0070
chunk 58 optimal weight: 5.9990
chunk 29 optimal weight: 0.8980
chunk 38 optimal weight: 4.9990
chunk 88 optimal weight: 0.8980
chunk 69 optimal weight: 7.9990
chunk 2 optimal weight: 10.0000
overall best weight: 1.7602
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 240 HIS
A1037 ASN
Total number of N/Q/H flips: 2
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.074695 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.058477 restraints weight = 29819.432|
|-----------------------------------------------------------------------------|
r_work (start): 0.3044 rms_B_bonded: 4.04
r_work: 0.2906 rms_B_bonded: 4.44 restraints_weight: 0.5000
r_work (final): 0.2906
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8648
moved from start: 0.3837
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.004 0.040 7682 Z= 0.274
Angle : 0.544 8.427 10459 Z= 0.280
Chirality : 0.037 0.191 1206
Planarity : 0.004 0.042 1315
Dihedral : 5.319 75.983 1105
Min Nonbonded Distance : 2.289
Molprobity Statistics.
All-atom Clashscore : 6.68
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 3.49 %
Favored : 96.51 %
Rotamer:
Outliers : 2.76 %
Allowed : 15.72 %
Favored : 81.52 %
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: 2.14 (0.28), residues: 975
helix: 2.63 (0.21), residues: 628
sheet: -1.64 (0.63), residues: 64
loop : -0.66 (0.36), residues: 283
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.010 0.001 TRP A 680
HIS 0.005 0.001 HIS A 240
PHE 0.016 0.001 PHE A 697
TYR 0.007 0.001 TYR A 227
ARG 0.004 0.000 ARG A 327
Origin is already at (0, 0, 0), no shifts will be applied
===============================================================================
Job complete
usr+sys time: 3611.43 seconds
wall clock time: 65 minutes 9.36 seconds (3909.36 seconds total)