Starting phenix.real_space_refine
on Tue Jan 14 06:05:33 2025 by dcliebschner
===============================================================================
Processing files:
-------------------------------------------------------------------------------
Found model, /net/cci-nas-00/data/ceres_data/9epo_19881/01_2025/9epo_19881.cif
Found real_map, /net/cci-nas-00/data/ceres_data/9epo_19881/01_2025/9epo_19881.map
Processing PHIL parameters:
-------------------------------------------------------------------------------
Adding command-line PHIL:
-------------------------
refinement.macro_cycles=10
scattering_table=electron
resolution=1.9
write_initial_geo_file=False
Final processed PHIL parameters:
-------------------------------------------------------------------------------
data_manager {
real_map_files = "/net/cci-nas-00/data/ceres_data/9epo_19881/01_2025/9epo_19881.map"
default_real_map = "/net/cci-nas-00/data/ceres_data/9epo_19881/01_2025/9epo_19881.map"
model {
file = "/net/cci-nas-00/data/ceres_data/9epo_19881/01_2025/9epo_19881.cif"
}
default_model = "/net/cci-nas-00/data/ceres_data/9epo_19881/01_2025/9epo_19881.cif"
}
resolution = 1.9
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= 0.010
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 48 5.16 5
C 3870 2.51 5
N 910 2.21 5
O 1032 1.98 5
sf(0) = scattering factor at diffraction angle 0.
Process input model
Monomer Library directory:
"/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
Total number of atoms: 5860
Number of models: 1
Model: ""
Number of chains: 6
Chain: "A"
Number of atoms: 2795
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 346, 2795
Classifications: {'peptide': 346}
Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 328}
Chain breaks: 1
Chain: "D"
Number of atoms: 2795
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 346, 2795
Classifications: {'peptide': 346}
Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 328}
Chain breaks: 1
Chain: "A"
Number of atoms: 88
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 3, 88
Unusual residues: {'PLM': 1, 'Y01': 2}
Classifications: {'undetermined': 3}
Link IDs: {None: 2}
Chain: "D"
Number of atoms: 88
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 3, 88
Unusual residues: {'PLM': 1, 'Y01': 2}
Classifications: {'undetermined': 3}
Link IDs: {None: 2}
Chain: "A"
Number of atoms: 47
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 47, 47
Classifications: {'water': 47}
Link IDs: {None: 46}
Chain: "D"
Number of atoms: 47
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 47, 47
Classifications: {'water': 47}
Link IDs: {None: 46}
Time building chain proxies: 4.82, per 1000 atoms: 0.82
Number of scatterers: 5860
At special positions: 0
Unit cell: (91.368, 98.136, 59.5584, 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 48 16.00
O 1032 8.00
N 910 7.00
C 3870 6.00
sf(0) = scattering factor at diffraction angle 0.
Number of disulfides: simple=8, symmetry=0
Simple disulfide: pdb=" SG CYS A 210 " - pdb=" SG CYS A 230 " distance=2.03
Simple disulfide: pdb=" SG CYS A 234 " - pdb=" SG CYS A 315 " distance=2.02
Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 411 " distance=2.03
Simple disulfide: pdb=" SG CYS A 508 " - pdb=" SG CYS A 515 " distance=2.03
Simple disulfide: pdb=" SG CYS D 210 " - pdb=" SG CYS D 230 " distance=2.03
Simple disulfide: pdb=" SG CYS D 234 " - pdb=" SG CYS D 315 " distance=2.02
Simple disulfide: pdb=" SG CYS D 336 " - pdb=" SG CYS D 411 " distance=2.03
Simple disulfide: pdb=" SG CYS D 508 " - pdb=" SG CYS D 515 " distance=2.03
Automatic linking
Parameters for automatic linking
Linking & cutoffs
Metal : Auto - 3.00
Amino acid : True - 1.90
Carbohydrate : True - 1.99
Ligands : True - 1.99
Small molecules : False - 1.98
Amino acid - RNA/DNA : False
Number of custom bonds: simple=0, symmetry=0
Time building additional restraints: 1.52
Conformation dependent library (CDL) restraints added in 821.7 milliseconds
1368 Ramachandran restraints generated.
684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2.
Adding C-beta torsion restraints...
Number of C-beta restraints generated: 1280
Finding SS restraints...
Secondary structure from input PDB file:
26 helices and 6 sheets defined
72.3% alpha, 2.3% beta
0 base pairs and 0 stacking pairs defined.
Time for finding SS restraints: 0.52
Creating SS restraints...
Processing helix chain 'A' and resid 211 through 215
Processing helix chain 'A' and resid 217 through 221
Processing helix chain 'A' and resid 246 through 277
Processing helix chain 'A' and resid 286 through 310
removed outlier: 3.828A pdb=" N ILE A 290 " --> pdb=" O GLU A 286 " (cutoff:3.500A)
Processing helix chain 'A' and resid 333 through 366
Processing helix chain 'A' and resid 370 through 376
Processing helix chain 'A' and resid 377 through 399
Proline residue: A 389 - end of helix
Processing helix chain 'A' and resid 417 through 425
Processing helix chain 'A' and resid 425 through 451
Processing helix chain 'A' and resid 465 through 508
removed outlier: 3.781A pdb=" N THR A 479 " --> pdb=" O SER A 475 " (cutoff:3.500A)
removed outlier: 4.080A pdb=" N VAL A 480 " --> pdb=" O VAL A 476 " (cutoff:3.500A)
Proline residue: A 481 - end of helix
removed outlier: 5.340A pdb=" N GLU A 497 " --> pdb=" O GLN A 493 " (cutoff:3.500A)
removed outlier: 5.527A pdb=" N HIS A 498 " --> pdb=" O ALA A 494 " (cutoff:3.500A)
Processing helix chain 'A' and resid 526 through 543
removed outlier: 4.653A pdb=" N VAL A 540 " --> pdb=" O MET A 536 " (cutoff:3.500A)
removed outlier: 5.494A pdb=" N GLY A 541 " --> pdb=" O THR A 537 " (cutoff:3.500A)
Processing helix chain 'A' and resid 543 through 549
Processing helix chain 'A' and resid 550 through 563
Processing helix chain 'D' and resid 211 through 215
Processing helix chain 'D' and resid 217 through 221
Processing helix chain 'D' and resid 246 through 277
Processing helix chain 'D' and resid 286 through 310
removed outlier: 3.828A pdb=" N ILE D 290 " --> pdb=" O GLU D 286 " (cutoff:3.500A)
Processing helix chain 'D' and resid 333 through 366
Processing helix chain 'D' and resid 370 through 376
Processing helix chain 'D' and resid 377 through 399
Proline residue: D 389 - end of helix
Processing helix chain 'D' and resid 417 through 425
Processing helix chain 'D' and resid 425 through 451
Processing helix chain 'D' and resid 465 through 508
removed outlier: 3.782A pdb=" N THR D 479 " --> pdb=" O SER D 475 " (cutoff:3.500A)
removed outlier: 4.080A pdb=" N VAL D 480 " --> pdb=" O VAL D 476 " (cutoff:3.500A)
Proline residue: D 481 - end of helix
removed outlier: 5.341A pdb=" N GLU D 497 " --> pdb=" O GLN D 493 " (cutoff:3.500A)
removed outlier: 5.528A pdb=" N HIS D 498 " --> pdb=" O ALA D 494 " (cutoff:3.500A)
Processing helix chain 'D' and resid 526 through 543
removed outlier: 4.653A pdb=" N VAL D 540 " --> pdb=" O MET D 536 " (cutoff:3.500A)
removed outlier: 5.494A pdb=" N GLY D 541 " --> pdb=" O THR D 537 " (cutoff:3.500A)
Processing helix chain 'D' and resid 543 through 549
Processing helix chain 'D' and resid 550 through 563
Processing sheet with id=AA1, first strand: chain 'A' and resid 223 through 224
Processing sheet with id=AA2, first strand: chain 'A' and resid 315 through 316
removed outlier: 3.631A pdb=" N THR A 326 " --> pdb=" O VAL A 316 " (cutoff:3.500A)
Processing sheet with id=AA3, first strand: chain 'A' and resid 402 through 404
Processing sheet with id=AA4, first strand: chain 'D' and resid 223 through 224
Processing sheet with id=AA5, first strand: chain 'D' and resid 315 through 316
removed outlier: 3.631A pdb=" N THR D 326 " --> pdb=" O VAL D 316 " (cutoff:3.500A)
Processing sheet with id=AA6, first strand: chain 'D' and resid 402 through 404
384 hydrogen bonds defined for protein.
1122 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: 1.77
Time building geometry restraints manager: 1.75 seconds
NOTE: a complete listing of the restraints can be obtained by requesting
output of .geo file.
Histogram of bond lengths:
1.20 - 1.32: 907
1.32 - 1.45: 1766
1.45 - 1.58: 3215
1.58 - 1.70: 0
1.70 - 1.83: 72
Bond restraints: 5960
Sorted by residual:
bond pdb=" CA VAL A 388 "
pdb=" C VAL A 388 "
ideal model delta sigma weight residual
1.523 1.543 -0.020 9.20e-03 1.18e+04 4.81e+00
bond pdb=" CA VAL D 388 "
pdb=" C VAL D 388 "
ideal model delta sigma weight residual
1.523 1.542 -0.019 9.20e-03 1.18e+04 4.12e+00
bond pdb=" C VAL A 388 "
pdb=" O VAL A 388 "
ideal model delta sigma weight residual
1.242 1.226 0.016 8.60e-03 1.35e+04 3.62e+00
bond pdb=" C VAL D 388 "
pdb=" O VAL D 388 "
ideal model delta sigma weight residual
1.242 1.226 0.016 8.60e-03 1.35e+04 3.46e+00
bond pdb=" CA VAL D 388 "
pdb=" CB VAL D 388 "
ideal model delta sigma weight residual
1.539 1.530 0.009 5.40e-03 3.43e+04 2.88e+00
... (remaining 5955 not shown)
Histogram of bond angle deviations from ideal:
0.00 - 1.79: 7726
1.79 - 3.58: 303
3.58 - 5.37: 61
5.37 - 7.16: 18
7.16 - 8.95: 2
Bond angle restraints: 8110
Sorted by residual:
angle pdb=" C GLU D 248 "
pdb=" N GLU D 249 "
pdb=" CA GLU D 249 "
ideal model delta sigma weight residual
120.31 114.65 5.66 1.52e+00 4.33e-01 1.39e+01
angle pdb=" C GLU A 248 "
pdb=" N GLU A 249 "
pdb=" CA GLU A 249 "
ideal model delta sigma weight residual
120.31 114.67 5.64 1.52e+00 4.33e-01 1.38e+01
angle pdb=" C ILE D 290 "
pdb=" N PHE D 291 "
pdb=" CA PHE D 291 "
ideal model delta sigma weight residual
120.31 114.80 5.51 1.52e+00 4.33e-01 1.31e+01
angle pdb=" C ILE A 290 "
pdb=" N PHE A 291 "
pdb=" CA PHE A 291 "
ideal model delta sigma weight residual
120.31 114.84 5.47 1.52e+00 4.33e-01 1.29e+01
angle pdb=" C TYR A 489 "
pdb=" N PHE A 490 "
pdb=" CA PHE A 490 "
ideal model delta sigma weight residual
120.28 125.05 -4.77 1.34e+00 5.57e-01 1.27e+01
... (remaining 8105 not shown)
Histogram of dihedral angle deviations from ideal:
0.00 - 17.91: 3463
17.91 - 35.83: 127
35.83 - 53.74: 27
53.74 - 71.66: 5
71.66 - 89.57: 2
Dihedral angle restraints: 3624
sinusoidal: 1622
harmonic: 2002
Sorted by residual:
dihedral pdb=" CA TYR A 324 "
pdb=" C TYR A 324 "
pdb=" N ARG A 325 "
pdb=" CA ARG A 325 "
ideal model delta harmonic sigma weight residual
180.00 157.47 22.53 0 5.00e+00 4.00e-02 2.03e+01
dihedral pdb=" CA TYR D 324 "
pdb=" C TYR D 324 "
pdb=" N ARG D 325 "
pdb=" CA ARG D 325 "
ideal model delta harmonic sigma weight residual
180.00 157.52 22.48 0 5.00e+00 4.00e-02 2.02e+01
dihedral pdb=" CA TYR D 244 "
pdb=" C TYR D 244 "
pdb=" N PHE D 245 "
pdb=" CA PHE D 245 "
ideal model delta harmonic sigma weight residual
-180.00 -165.13 -14.87 0 5.00e+00 4.00e-02 8.84e+00
... (remaining 3621 not shown)
Histogram of chiral volume deviations from ideal:
0.000 - 0.087: 800
0.087 - 0.173: 56
0.173 - 0.260: 14
0.260 - 0.346: 4
0.346 - 0.433: 4
Chirality restraints: 878
Sorted by residual:
chirality pdb=" CB VAL A 473 "
pdb=" CA VAL A 473 "
pdb=" CG1 VAL A 473 "
pdb=" CG2 VAL A 473 "
both_signs ideal model delta sigma weight residual
False -2.63 -2.20 -0.43 2.00e-01 2.50e+01 4.68e+00
chirality pdb=" CB VAL D 473 "
pdb=" CA VAL D 473 "
pdb=" CG1 VAL D 473 "
pdb=" CG2 VAL D 473 "
both_signs ideal model delta sigma weight residual
False -2.63 -2.20 -0.43 2.00e-01 2.50e+01 4.68e+00
chirality pdb=" CG LEU A 383 "
pdb=" CB LEU A 383 "
pdb=" CD1 LEU A 383 "
pdb=" CD2 LEU A 383 "
both_signs ideal model delta sigma weight residual
False -2.59 -2.19 -0.40 2.00e-01 2.50e+01 3.92e+00
... (remaining 875 not shown)
Planarity restraints: 972
Sorted by residual:
delta sigma weight rms_deltas residual
plane pdb=" CB TYR A 491 " -0.024 2.00e-02 2.50e+03 4.47e-02 4.00e+01
pdb=" CG TYR A 491 " 0.004 2.00e-02 2.50e+03
pdb=" CD1 TYR A 491 " 0.003 2.00e-02 2.50e+03
pdb=" CD2 TYR A 491 " -0.002 2.00e-02 2.50e+03
pdb=" CE1 TYR A 491 " -0.011 2.00e-02 2.50e+03
pdb=" CE2 TYR A 491 " -0.001 2.00e-02 2.50e+03
pdb=" CZ TYR A 491 " 0.101 2.00e-02 2.50e+03
pdb=" OH TYR A 491 " -0.071 2.00e-02 2.50e+03
delta sigma weight rms_deltas residual
plane pdb=" CB TYR D 491 " -0.024 2.00e-02 2.50e+03 4.47e-02 3.99e+01
pdb=" CG TYR D 491 " 0.004 2.00e-02 2.50e+03
pdb=" CD1 TYR D 491 " 0.003 2.00e-02 2.50e+03
pdb=" CD2 TYR D 491 " -0.003 2.00e-02 2.50e+03
pdb=" CE1 TYR D 491 " -0.011 2.00e-02 2.50e+03
pdb=" CE2 TYR D 491 " -0.000 2.00e-02 2.50e+03
pdb=" CZ TYR D 491 " 0.101 2.00e-02 2.50e+03
pdb=" OH TYR D 491 " -0.071 2.00e-02 2.50e+03
delta sigma weight rms_deltas residual
plane pdb=" CB TRP D 354 " -0.005 2.00e-02 2.50e+03 3.92e-02 3.83e+01
pdb=" CG TRP D 354 " 0.011 2.00e-02 2.50e+03
pdb=" CD1 TRP D 354 " 0.015 2.00e-02 2.50e+03
pdb=" CD2 TRP D 354 " 0.000 2.00e-02 2.50e+03
pdb=" NE1 TRP D 354 " -0.001 2.00e-02 2.50e+03
pdb=" CE2 TRP D 354 " -0.004 2.00e-02 2.50e+03
pdb=" CE3 TRP D 354 " -0.002 2.00e-02 2.50e+03
pdb=" CZ2 TRP D 354 " -0.067 2.00e-02 2.50e+03
pdb=" CZ3 TRP D 354 " -0.042 2.00e-02 2.50e+03
pdb=" CH2 TRP D 354 " 0.093 2.00e-02 2.50e+03
... (remaining 969 not shown)
Histogram of nonbonded interaction distances:
2.14 - 2.69: 148
2.69 - 3.24: 5979
3.24 - 3.80: 9782
3.80 - 4.35: 13043
4.35 - 4.90: 21642
Nonbonded interactions: 50594
Sorted by model distance:
nonbonded pdb=" O HOH D 843 "
pdb=" O HOH D 845 "
model vdw
2.140 3.040
nonbonded pdb=" O HOH A 842 "
pdb=" O HOH A 845 "
model vdw
2.141 3.040
nonbonded pdb=" OH TYR D 489 "
pdb=" O HOH D 801 "
model vdw
2.292 3.040
nonbonded pdb=" OH TYR A 489 "
pdb=" O HOH A 801 "
model vdw
2.293 3.040
nonbonded pdb=" O HOH A 816 "
pdb=" O HOH A 841 "
model vdw
2.301 3.040
... (remaining 50589 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: 0.03
Found NCS groups:
ncs_group {
reference = (chain 'A' and (resid 206 through 563 or resid 701))
selection = (chain 'D' and (resid 206 through 563 or resid 701))
}
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: 0.010
Set model cs if undefined: 0.000
Decide on map wrapping: 0.000
Normalize map: mean=0, sd=1: 4.690
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: 0.240
Check model and map are aligned: 0.040
Set scattering table: 0.060
Process input model: 17.960
Find NCS groups from input model: 0.270
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: 0.010
Load rotamer database and sin/cos tables:11.640
Set ADP refinement strategy: 0.000
Make a string to write initial .geo file:0.000
Internal consistency checks: 0.000
Total: 34.940
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5703
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 0.049 5960 Z= 0.325
Angle : 0.859 8.950 8110 Z= 0.500
Chirality : 0.063 0.433 878
Planarity : 0.010 0.077 972
Dihedral : 10.139 89.573 2320
Min Nonbonded Distance : 2.140
Molprobity Statistics.
All-atom Clashscore : 1.04
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 0.29 %
Favored : 99.71 %
Rotamer:
Outliers : 0.00 %
Allowed : 1.02 %
Favored : 98.98 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 5.88 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 1.04 (0.31), residues: 684
helix: 1.37 (0.23), residues: 474
sheet: -4.83 (0.46), residues: 20
loop : -0.23 (0.44), residues: 190
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.093 0.010 TRP D 354
HIS 0.022 0.004 HIS D 371
PHE 0.079 0.004 PHE A 439
TYR 0.101 0.012 TYR A 491
ARG 0.051 0.002 ARG A 223
*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
1368 Ramachandran restraints generated.
684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
1368 Ramachandran restraints generated.
684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
126 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 0
poor density : 126
time to evaluate : 0.705
Fit side-chains
REVERT: A 372 GLU cc_start: 0.5997 (mp0) cc_final: 0.5706 (mt-10)
REVERT: A 379 GLN cc_start: 0.5239 (mt0) cc_final: 0.4620 (pt0)
REVERT: A 380 TYR cc_start: 0.5769 (m-80) cc_final: 0.5076 (m-80)
REVERT: A 418 VAL cc_start: 0.6116 (t) cc_final: 0.5710 (p)
REVERT: A 466 LYS cc_start: 0.6705 (tttt) cc_final: 0.6329 (tttm)
REVERT: A 497 GLU cc_start: 0.6049 (mt-10) cc_final: 0.5760 (pm20)
REVERT: D 372 GLU cc_start: 0.6013 (mp0) cc_final: 0.5730 (mt-10)
REVERT: D 379 GLN cc_start: 0.5249 (mt0) cc_final: 0.4626 (pt0)
REVERT: D 380 TYR cc_start: 0.5775 (m-80) cc_final: 0.5081 (m-80)
REVERT: D 418 VAL cc_start: 0.6116 (t) cc_final: 0.5710 (p)
REVERT: D 466 LYS cc_start: 0.6701 (tttt) cc_final: 0.6326 (tttm)
REVERT: D 497 GLU cc_start: 0.6058 (mt-10) cc_final: 0.5733 (pm20)
outliers start: 0
outliers final: 0
residues processed: 126
average time/residue: 2.0019
time to fit residues: 259.4717
Evaluate side-chains
101 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 0
poor density : 101
time to evaluate : 0.793
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 68
random chunks:
chunk 57 optimal weight: 2.9990
chunk 51 optimal weight: 2.9990
chunk 28 optimal weight: 4.9990
chunk 17 optimal weight: 0.9980
chunk 34 optimal weight: 8.9990
chunk 27 optimal weight: 0.9990
chunk 53 optimal weight: 0.9980
chunk 20 optimal weight: 0.8980
chunk 32 optimal weight: 0.7980
chunk 39 optimal weight: 0.6980
chunk 61 optimal weight: 3.9990
overall best weight: 0.8780
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 329 GLN
D 329 GLN
Total number of N/Q/H flips: 2
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4032 r_free = 0.4032 target = 0.166664 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.136906 restraints weight = 4633.129|
|-----------------------------------------------------------------------------|
r_work (start): 0.3699 rms_B_bonded: 1.00
r_work: 0.3594 rms_B_bonded: 1.53 restraints_weight: 0.5000
r_work: 0.3506 rms_B_bonded: 2.46 restraints_weight: 0.2500
r_work (final): 0.3506
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8214
moved from start: 0.2067
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.056 5960 Z= 0.195
Angle : 0.550 5.965 8110 Z= 0.293
Chirality : 0.040 0.126 878
Planarity : 0.005 0.029 972
Dihedral : 6.984 54.279 1078
Min Nonbonded Distance : 2.554
Molprobity Statistics.
All-atom Clashscore : 3.72
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 0.88 %
Favored : 99.12 %
Rotamer:
Outliers : 1.53 %
Allowed : 7.82 %
Favored : 90.65 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 5.88 %
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: 2.10 (0.31), residues: 684
helix: 2.40 (0.23), residues: 454
sheet: -4.53 (0.46), residues: 20
loop : -0.24 (0.37), residues: 210
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.014 0.002 TRP A 354
HIS 0.003 0.001 HIS D 498
PHE 0.016 0.002 PHE A 340
TYR 0.012 0.002 TYR A 491
ARG 0.005 0.001 ARG D 212
*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
1368 Ramachandran restraints generated.
684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
1368 Ramachandran restraints generated.
684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
119 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 9
poor density : 110
time to evaluate : 0.663
Fit side-chains
REVERT: A 212 ARG cc_start: 0.7165 (ttp80) cc_final: 0.6923 (ptt-90)
REVERT: A 215 LYS cc_start: 0.8209 (mtpm) cc_final: 0.7561 (mtmm)
REVERT: A 248 GLU cc_start: 0.7691 (pm20) cc_final: 0.7177 (tm-30)
REVERT: A 279 MET cc_start: 0.7680 (mtm) cc_final: 0.7352 (mtp)
REVERT: A 379 GLN cc_start: 0.7657 (mt0) cc_final: 0.7430 (pt0)
REVERT: A 466 LYS cc_start: 0.8279 (tttt) cc_final: 0.8063 (tttm)
REVERT: D 212 ARG cc_start: 0.7172 (ttp80) cc_final: 0.6925 (ptt-90)
REVERT: D 215 LYS cc_start: 0.8207 (mtpm) cc_final: 0.7554 (mtmm)
REVERT: D 248 GLU cc_start: 0.7710 (pm20) cc_final: 0.7214 (tm-30)
REVERT: D 279 MET cc_start: 0.7664 (mtm) cc_final: 0.7347 (mtp)
REVERT: D 379 GLN cc_start: 0.7673 (mt0) cc_final: 0.7432 (pt0)
REVERT: D 466 LYS cc_start: 0.8262 (tttt) cc_final: 0.8052 (tttm)
outliers start: 9
outliers final: 2
residues processed: 114
average time/residue: 2.0731
time to fit residues: 243.0790
Evaluate side-chains
104 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 2
poor density : 102
time to evaluate : 0.660
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 505 LEU
Chi-restraints excluded: chain D residue 505 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 68
random chunks:
chunk 65 optimal weight: 0.8980
chunk 26 optimal weight: 0.9990
chunk 10 optimal weight: 0.9980
chunk 8 optimal weight: 1.9990
chunk 4 optimal weight: 2.9990
chunk 2 optimal weight: 2.9990
chunk 59 optimal weight: 3.9990
chunk 24 optimal weight: 0.9980
chunk 31 optimal weight: 2.9990
chunk 29 optimal weight: 0.0980
chunk 54 optimal weight: 0.9990
overall best weight: 0.7982
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 329 GLN
D 329 GLN
Total number of N/Q/H flips: 2
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4047 r_free = 0.4047 target = 0.166949 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.136914 restraints weight = 4657.698|
|-----------------------------------------------------------------------------|
r_work (start): 0.3679 rms_B_bonded: 1.02
r_work: 0.3575 rms_B_bonded: 1.56 restraints_weight: 0.5000
r_work: 0.3487 rms_B_bonded: 2.51 restraints_weight: 0.2500
r_work (final): 0.3487
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8237
moved from start: 0.2468
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.050 5960 Z= 0.178
Angle : 0.526 5.981 8110 Z= 0.280
Chirality : 0.038 0.121 878
Planarity : 0.004 0.030 972
Dihedral : 7.140 55.761 1078
Min Nonbonded Distance : 2.562
Molprobity Statistics.
All-atom Clashscore : 3.97
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 0.88 %
Favored : 99.12 %
Rotamer:
Outliers : 1.87 %
Allowed : 10.03 %
Favored : 88.10 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 5.88 %
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 (0.30), residues: 684
helix: 2.46 (0.23), residues: 454
sheet: -4.27 (0.48), residues: 20
loop : -0.21 (0.37), residues: 210
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.014 0.001 TRP D 256
HIS 0.002 0.001 HIS D 562
PHE 0.015 0.001 PHE A 340
TYR 0.014 0.001 TYR D 491
ARG 0.006 0.001 ARG A 281
*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
1368 Ramachandran restraints generated.
684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
1368 Ramachandran restraints generated.
684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
111 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 11
poor density : 100
time to evaluate : 0.664
Fit side-chains
REVERT: A 248 GLU cc_start: 0.7663 (pm20) cc_final: 0.7210 (tm-30)
REVERT: A 279 MET cc_start: 0.7719 (mtm) cc_final: 0.7394 (mtp)
REVERT: A 379 GLN cc_start: 0.7743 (mt0) cc_final: 0.7487 (pt0)
REVERT: A 466 LYS cc_start: 0.8330 (tttt) cc_final: 0.8117 (tttm)
REVERT: D 248 GLU cc_start: 0.7658 (pm20) cc_final: 0.7207 (tm-30)
REVERT: D 279 MET cc_start: 0.7724 (mtm) cc_final: 0.7413 (mtp)
REVERT: D 379 GLN cc_start: 0.7745 (mt0) cc_final: 0.7481 (pt0)
REVERT: D 466 LYS cc_start: 0.8318 (tttt) cc_final: 0.8107 (tttm)
REVERT: D 559 ARG cc_start: 0.6788 (ttp-110) cc_final: 0.6489 (mtm-85)
outliers start: 11
outliers final: 4
residues processed: 104
average time/residue: 2.0969
time to fit residues: 224.4389
Evaluate side-chains
102 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 4
poor density : 98
time to evaluate : 0.661
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 375 GLU
Chi-restraints excluded: chain A residue 505 LEU
Chi-restraints excluded: chain D residue 375 GLU
Chi-restraints excluded: chain D residue 505 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 68
random chunks:
chunk 22 optimal weight: 0.6980
chunk 16 optimal weight: 8.9990
chunk 14 optimal weight: 0.7980
chunk 64 optimal weight: 2.9990
chunk 29 optimal weight: 1.9990
chunk 63 optimal weight: 2.9990
chunk 12 optimal weight: 0.9990
chunk 5 optimal weight: 4.9990
chunk 3 optimal weight: 0.0770
chunk 4 optimal weight: 0.9980
chunk 6 optimal weight: 2.9990
overall best weight: 0.7140
-------------------------------------------------------------------------------
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 = 0.4051 r_free = 0.4051 target = 0.167385 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.137544 restraints weight = 4762.703|
|-----------------------------------------------------------------------------|
r_work (start): 0.3686 rms_B_bonded: 1.02
r_work: 0.3582 rms_B_bonded: 1.57 restraints_weight: 0.5000
r_work: 0.3494 rms_B_bonded: 2.53 restraints_weight: 0.2500
r_work (final): 0.3494
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8231
moved from start: 0.2705
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.048 5960 Z= 0.165
Angle : 0.511 5.964 8110 Z= 0.269
Chirality : 0.038 0.118 878
Planarity : 0.004 0.028 972
Dihedral : 7.282 56.141 1078
Min Nonbonded Distance : 2.577
Molprobity Statistics.
All-atom Clashscore : 4.23
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 1.17 %
Favored : 98.83 %
Rotamer:
Outliers : 1.36 %
Allowed : 11.05 %
Favored : 87.59 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 5.88 %
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: 2.37 (0.31), residues: 684
helix: 2.56 (0.23), residues: 456
sheet: -4.21 (0.48), residues: 20
loop : -0.05 (0.38), residues: 208
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.015 0.001 TRP A 256
HIS 0.001 0.001 HIS D 382
PHE 0.014 0.001 PHE A 340
TYR 0.014 0.001 TYR D 491
ARG 0.008 0.001 ARG A 501
*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
1368 Ramachandran restraints generated.
684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
1368 Ramachandran restraints generated.
684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
105 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 8
poor density : 97
time to evaluate : 0.679
Fit side-chains
REVERT: A 247 GLU cc_start: 0.7174 (OUTLIER) cc_final: 0.6365 (mm-30)
REVERT: A 279 MET cc_start: 0.7762 (OUTLIER) cc_final: 0.7466 (mtp)
REVERT: A 379 GLN cc_start: 0.7737 (mt0) cc_final: 0.7511 (pt0)
REVERT: A 466 LYS cc_start: 0.8312 (tttt) cc_final: 0.8044 (tttm)
REVERT: D 247 GLU cc_start: 0.7178 (OUTLIER) cc_final: 0.6371 (mm-30)
REVERT: D 279 MET cc_start: 0.7770 (OUTLIER) cc_final: 0.7497 (mtp)
REVERT: D 379 GLN cc_start: 0.7726 (mt0) cc_final: 0.7500 (pt0)
REVERT: D 466 LYS cc_start: 0.8300 (tttt) cc_final: 0.8033 (tttm)
REVERT: D 559 ARG cc_start: 0.6906 (ttp-110) cc_final: 0.6653 (mtm-85)
outliers start: 8
outliers final: 2
residues processed: 99
average time/residue: 2.0888
time to fit residues: 212.6755
Evaluate side-chains
102 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 6
poor density : 96
time to evaluate : 0.632
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 247 GLU
Chi-restraints excluded: chain A residue 279 MET
Chi-restraints excluded: chain A residue 505 LEU
Chi-restraints excluded: chain D residue 247 GLU
Chi-restraints excluded: chain D residue 279 MET
Chi-restraints excluded: chain D residue 505 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 68
random chunks:
chunk 24 optimal weight: 4.9990
chunk 57 optimal weight: 0.7980
chunk 23 optimal weight: 0.7980
chunk 29 optimal weight: 0.9990
chunk 27 optimal weight: 2.9990
chunk 54 optimal weight: 0.9990
chunk 1 optimal weight: 4.9990
chunk 67 optimal weight: 0.0570
chunk 28 optimal weight: 0.8980
chunk 39 optimal weight: 0.7980
chunk 59 optimal weight: 3.9990
overall best weight: 0.6698
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 371 HIS
D 371 HIS
Total number of N/Q/H flips: 2
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4077 r_free = 0.4077 target = 0.168359 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.139914 restraints weight = 4696.895|
|-----------------------------------------------------------------------------|
r_work (start): 0.3736 rms_B_bonded: 0.97
r_work: 0.3635 rms_B_bonded: 1.50 restraints_weight: 0.5000
r_work: 0.3549 rms_B_bonded: 2.42 restraints_weight: 0.2500
r_work (final): 0.3549
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8237
moved from start: 0.2863
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.047 5960 Z= 0.161
Angle : 0.512 7.479 8110 Z= 0.268
Chirality : 0.037 0.118 878
Planarity : 0.004 0.029 972
Dihedral : 7.331 57.745 1078
Min Nonbonded Distance : 2.577
Molprobity Statistics.
All-atom Clashscore : 4.23
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 1.17 %
Favored : 98.83 %
Rotamer:
Outliers : 2.04 %
Allowed : 11.05 %
Favored : 86.90 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 5.88 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 2.40 (0.31), residues: 684
helix: 2.59 (0.23), residues: 456
sheet: -4.19 (0.48), residues: 20
loop : -0.07 (0.37), residues: 208
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.016 0.001 TRP A 256
HIS 0.001 0.001 HIS A 498
PHE 0.015 0.001 PHE D 340
TYR 0.014 0.001 TYR D 491
ARG 0.005 0.001 ARG D 501
*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
1368 Ramachandran restraints generated.
684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
1368 Ramachandran restraints generated.
684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
112 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 12
poor density : 100
time to evaluate : 0.681
Fit side-chains
REVERT: A 247 GLU cc_start: 0.7218 (OUTLIER) cc_final: 0.6332 (mm-30)
REVERT: A 248 GLU cc_start: 0.7652 (pm20) cc_final: 0.7278 (tm-30)
REVERT: A 279 MET cc_start: 0.7771 (OUTLIER) cc_final: 0.7485 (mtp)
REVERT: A 466 LYS cc_start: 0.8322 (tttt) cc_final: 0.8057 (tttm)
REVERT: D 247 GLU cc_start: 0.7217 (OUTLIER) cc_final: 0.6328 (mm-30)
REVERT: D 248 GLU cc_start: 0.7643 (pm20) cc_final: 0.7269 (tm-30)
REVERT: D 279 MET cc_start: 0.7759 (OUTLIER) cc_final: 0.7455 (mtp)
REVERT: D 379 GLN cc_start: 0.7750 (mt0) cc_final: 0.7548 (pt0)
REVERT: D 466 LYS cc_start: 0.8306 (tttt) cc_final: 0.8044 (tttm)
REVERT: D 559 ARG cc_start: 0.7001 (ttp-110) cc_final: 0.6724 (mtm-85)
outliers start: 12
outliers final: 5
residues processed: 106
average time/residue: 2.0215
time to fit residues: 220.4477
Evaluate side-chains
106 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 9
poor density : 97
time to evaluate : 0.599
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 216 VAL
Chi-restraints excluded: chain A residue 247 GLU
Chi-restraints excluded: chain A residue 279 MET
Chi-restraints excluded: chain A residue 316 VAL
Chi-restraints excluded: chain A residue 505 LEU
Chi-restraints excluded: chain D residue 216 VAL
Chi-restraints excluded: chain D residue 247 GLU
Chi-restraints excluded: chain D residue 279 MET
Chi-restraints excluded: chain D residue 505 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 68
random chunks:
chunk 35 optimal weight: 4.9990
chunk 39 optimal weight: 0.9990
chunk 18 optimal weight: 0.9980
chunk 4 optimal weight: 0.2980
chunk 46 optimal weight: 5.9990
chunk 28 optimal weight: 2.9990
chunk 3 optimal weight: 0.9980
chunk 49 optimal weight: 4.9990
chunk 45 optimal weight: 0.6980
chunk 14 optimal weight: 0.5980
chunk 26 optimal weight: 1.9990
overall best weight: 0.7180
-------------------------------------------------------------------------------
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 = 0.4077 r_free = 0.4077 target = 0.168178 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.139684 restraints weight = 4734.402|
|-----------------------------------------------------------------------------|
r_work (start): 0.3736 rms_B_bonded: 0.98
r_work: 0.3631 rms_B_bonded: 1.52 restraints_weight: 0.5000
r_work: 0.3545 rms_B_bonded: 2.45 restraints_weight: 0.2500
r_work (final): 0.3545
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8247
moved from start: 0.2991
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.047 5960 Z= 0.164
Angle : 0.523 7.718 8110 Z= 0.273
Chirality : 0.037 0.118 878
Planarity : 0.004 0.028 972
Dihedral : 7.506 59.883 1078
Min Nonbonded Distance : 2.574
Molprobity Statistics.
All-atom Clashscore : 3.97
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 1.17 %
Favored : 98.83 %
Rotamer:
Outliers : 2.72 %
Allowed : 11.05 %
Favored : 86.22 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 5.88 %
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: 2.38 (0.31), residues: 684
helix: 2.59 (0.23), residues: 456
sheet: -4.12 (0.49), residues: 20
loop : -0.12 (0.37), residues: 208
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.017 0.001 TRP D 256
HIS 0.001 0.001 HIS A 562
PHE 0.015 0.001 PHE D 340
TYR 0.014 0.001 TYR A 491
ARG 0.006 0.001 ARG A 501
*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
1368 Ramachandran restraints generated.
684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
1368 Ramachandran restraints generated.
684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
116 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 16
poor density : 100
time to evaluate : 0.706
Fit side-chains
REVERT: A 247 GLU cc_start: 0.7199 (OUTLIER) cc_final: 0.6312 (mm-30)
REVERT: A 248 GLU cc_start: 0.7627 (pm20) cc_final: 0.7257 (tm-30)
REVERT: A 279 MET cc_start: 0.7815 (OUTLIER) cc_final: 0.7529 (mtp)
REVERT: A 466 LYS cc_start: 0.8316 (tttt) cc_final: 0.7960 (tttp)
REVERT: D 247 GLU cc_start: 0.7200 (OUTLIER) cc_final: 0.6309 (mm-30)
REVERT: D 248 GLU cc_start: 0.7619 (pm20) cc_final: 0.7244 (tm-30)
REVERT: D 279 MET cc_start: 0.7784 (OUTLIER) cc_final: 0.7514 (mtp)
REVERT: D 466 LYS cc_start: 0.8312 (tttt) cc_final: 0.7976 (tttp)
REVERT: D 559 ARG cc_start: 0.7054 (ttp-110) cc_final: 0.6841 (mtm-85)
outliers start: 16
outliers final: 4
residues processed: 108
average time/residue: 2.0696
time to fit residues: 230.0278
Evaluate side-chains
107 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 8
poor density : 99
time to evaluate : 0.694
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 216 VAL
Chi-restraints excluded: chain A residue 247 GLU
Chi-restraints excluded: chain A residue 279 MET
Chi-restraints excluded: chain A residue 316 VAL
Chi-restraints excluded: chain A residue 379 GLN
Chi-restraints excluded: chain D residue 216 VAL
Chi-restraints excluded: chain D residue 247 GLU
Chi-restraints excluded: chain D residue 279 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 68
random chunks:
chunk 59 optimal weight: 4.9990
chunk 39 optimal weight: 0.8980
chunk 6 optimal weight: 0.9990
chunk 27 optimal weight: 3.9990
chunk 7 optimal weight: 0.6980
chunk 54 optimal weight: 2.9990
chunk 20 optimal weight: 2.9990
chunk 16 optimal weight: 5.9990
chunk 37 optimal weight: 3.9990
chunk 8 optimal weight: 0.9990
chunk 41 optimal weight: 0.8980
overall best weight: 0.8984
-------------------------------------------------------------------------------
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 = 0.4071 r_free = 0.4071 target = 0.167500 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.138778 restraints weight = 4742.326|
|-----------------------------------------------------------------------------|
r_work (start): 0.3723 rms_B_bonded: 0.99
r_work: 0.3619 rms_B_bonded: 1.52 restraints_weight: 0.5000
r_work: 0.3532 rms_B_bonded: 2.46 restraints_weight: 0.2500
r_work (final): 0.3532
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8261
moved from start: 0.3052
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.052 5960 Z= 0.181
Angle : 0.545 9.233 8110 Z= 0.284
Chirality : 0.038 0.120 878
Planarity : 0.004 0.028 972
Dihedral : 7.660 59.649 1078
Min Nonbonded Distance : 2.568
Molprobity Statistics.
All-atom Clashscore : 4.15
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 0.88 %
Favored : 99.12 %
Rotamer:
Outliers : 3.74 %
Allowed : 10.54 %
Favored : 85.71 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 5.88 %
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: 2.27 (0.30), residues: 684
helix: 2.51 (0.23), residues: 454
sheet: -3.99 (0.51), residues: 20
loop : -0.18 (0.36), residues: 210
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.016 0.002 TRP A 256
HIS 0.002 0.001 HIS D 498
PHE 0.017 0.001 PHE D 340
TYR 0.015 0.001 TYR D 491
ARG 0.006 0.001 ARG D 501
*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
1368 Ramachandran restraints generated.
684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
1368 Ramachandran restraints generated.
684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
124 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 22
poor density : 102
time to evaluate : 0.681
Fit side-chains
REVERT: A 247 GLU cc_start: 0.7247 (OUTLIER) cc_final: 0.6438 (mm-30)
REVERT: A 279 MET cc_start: 0.7811 (OUTLIER) cc_final: 0.7527 (mtp)
REVERT: A 466 LYS cc_start: 0.8338 (tttt) cc_final: 0.7993 (tttp)
REVERT: D 247 GLU cc_start: 0.7248 (OUTLIER) cc_final: 0.6436 (mm-30)
REVERT: D 279 MET cc_start: 0.7808 (OUTLIER) cc_final: 0.7522 (mtp)
REVERT: D 466 LYS cc_start: 0.8321 (tttt) cc_final: 0.7978 (tttp)
REVERT: D 559 ARG cc_start: 0.7086 (ttp-110) cc_final: 0.6868 (mtm-85)
outliers start: 22
outliers final: 14
residues processed: 110
average time/residue: 2.0491
time to fit residues: 232.0271
Evaluate side-chains
114 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 18
poor density : 96
time to evaluate : 0.619
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 216 VAL
Chi-restraints excluded: chain A residue 247 GLU
Chi-restraints excluded: chain A residue 263 LEU
Chi-restraints excluded: chain A residue 279 MET
Chi-restraints excluded: chain A residue 316 VAL
Chi-restraints excluded: chain A residue 372 GLU
Chi-restraints excluded: chain A residue 375 GLU
Chi-restraints excluded: chain A residue 379 GLN
Chi-restraints excluded: chain A residue 505 LEU
Chi-restraints excluded: chain D residue 216 VAL
Chi-restraints excluded: chain D residue 247 GLU
Chi-restraints excluded: chain D residue 263 LEU
Chi-restraints excluded: chain D residue 279 MET
Chi-restraints excluded: chain D residue 316 VAL
Chi-restraints excluded: chain D residue 372 GLU
Chi-restraints excluded: chain D residue 375 GLU
Chi-restraints excluded: chain D residue 379 GLN
Chi-restraints excluded: chain D residue 505 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 68
random chunks:
chunk 62 optimal weight: 2.9990
chunk 19 optimal weight: 0.0060
chunk 12 optimal weight: 3.9990
chunk 10 optimal weight: 3.9990
chunk 18 optimal weight: 0.9980
chunk 24 optimal weight: 9.9990
chunk 48 optimal weight: 0.5980
chunk 40 optimal weight: 5.9990
chunk 3 optimal weight: 3.9990
chunk 61 optimal weight: 1.9990
chunk 65 optimal weight: 1.9990
overall best weight: 1.1200
-------------------------------------------------------------------------------
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 = 0.4061 r_free = 0.4061 target = 0.166505 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.137882 restraints weight = 4689.093|
|-----------------------------------------------------------------------------|
r_work (start): 0.3711 rms_B_bonded: 0.97
r_work: 0.3607 rms_B_bonded: 1.50 restraints_weight: 0.5000
r_work: 0.3519 rms_B_bonded: 2.42 restraints_weight: 0.2500
r_work (final): 0.3519
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8271
moved from start: 0.3093
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.057 5960 Z= 0.206
Angle : 0.580 10.461 8110 Z= 0.302
Chirality : 0.039 0.120 878
Planarity : 0.004 0.028 972
Dihedral : 7.915 59.162 1078
Min Nonbonded Distance : 2.564
Molprobity Statistics.
All-atom Clashscore : 4.49
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 0.88 %
Favored : 99.12 %
Rotamer:
Outliers : 3.74 %
Allowed : 10.03 %
Favored : 86.22 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 5.88 %
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: 2.35 (0.30), residues: 684
helix: 2.44 (0.23), residues: 454
sheet: None (None), residues: 0
loop : -0.24 (0.34), residues: 230
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.014 0.002 TRP D 354
HIS 0.002 0.001 HIS A 562
PHE 0.019 0.002 PHE D 340
TYR 0.015 0.002 TYR D 491
ARG 0.007 0.001 ARG A 281
*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
1368 Ramachandran restraints generated.
684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
1368 Ramachandran restraints generated.
684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
122 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 22
poor density : 100
time to evaluate : 0.618
Fit side-chains
REVERT: A 247 GLU cc_start: 0.7278 (OUTLIER) cc_final: 0.6338 (mm-30)
REVERT: A 248 GLU cc_start: 0.7719 (pm20) cc_final: 0.7269 (tm-30)
REVERT: A 279 MET cc_start: 0.7836 (OUTLIER) cc_final: 0.7558 (mtp)
REVERT: A 466 LYS cc_start: 0.8356 (tttt) cc_final: 0.8010 (tttp)
REVERT: A 497 GLU cc_start: 0.7537 (OUTLIER) cc_final: 0.6814 (mp0)
REVERT: D 247 GLU cc_start: 0.7275 (OUTLIER) cc_final: 0.6336 (mm-30)
REVERT: D 248 GLU cc_start: 0.7705 (pm20) cc_final: 0.7261 (tm-30)
REVERT: D 279 MET cc_start: 0.7820 (OUTLIER) cc_final: 0.7519 (mtp)
REVERT: D 466 LYS cc_start: 0.8328 (tttt) cc_final: 0.7986 (tttp)
REVERT: D 497 GLU cc_start: 0.7541 (OUTLIER) cc_final: 0.6820 (mp0)
outliers start: 22
outliers final: 12
residues processed: 108
average time/residue: 1.8508
time to fit residues: 206.1941
Evaluate side-chains
116 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 18
poor density : 98
time to evaluate : 1.144
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 216 VAL
Chi-restraints excluded: chain A residue 247 GLU
Chi-restraints excluded: chain A residue 263 LEU
Chi-restraints excluded: chain A residue 279 MET
Chi-restraints excluded: chain A residue 316 VAL
Chi-restraints excluded: chain A residue 372 GLU
Chi-restraints excluded: chain A residue 379 GLN
Chi-restraints excluded: chain A residue 497 GLU
Chi-restraints excluded: chain A residue 505 LEU
Chi-restraints excluded: chain D residue 216 VAL
Chi-restraints excluded: chain D residue 247 GLU
Chi-restraints excluded: chain D residue 263 LEU
Chi-restraints excluded: chain D residue 279 MET
Chi-restraints excluded: chain D residue 316 VAL
Chi-restraints excluded: chain D residue 372 GLU
Chi-restraints excluded: chain D residue 379 GLN
Chi-restraints excluded: chain D residue 497 GLU
Chi-restraints excluded: chain D residue 505 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 68
random chunks:
chunk 61 optimal weight: 3.9990
chunk 23 optimal weight: 0.6980
chunk 51 optimal weight: 2.9990
chunk 40 optimal weight: 3.9990
chunk 43 optimal weight: 1.9990
chunk 21 optimal weight: 3.9990
chunk 49 optimal weight: 4.9990
chunk 36 optimal weight: 1.9990
chunk 62 optimal weight: 0.5980
chunk 32 optimal weight: 2.9990
chunk 12 optimal weight: 5.9990
overall best weight: 1.6586
-------------------------------------------------------------------------------
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 = 0.4046 r_free = 0.4046 target = 0.164996 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.136110 restraints weight = 4719.038|
|-----------------------------------------------------------------------------|
r_work (start): 0.3690 rms_B_bonded: 0.99
r_work: 0.3585 rms_B_bonded: 1.51 restraints_weight: 0.5000
r_work: 0.3497 rms_B_bonded: 2.43 restraints_weight: 0.2500
r_work (final): 0.3497
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8294
moved from start: 0.3139
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.004 0.068 5960 Z= 0.263
Angle : 0.631 11.558 8110 Z= 0.328
Chirality : 0.041 0.128 878
Planarity : 0.005 0.058 972
Dihedral : 8.495 59.888 1078
Min Nonbonded Distance : 2.551
Molprobity Statistics.
All-atom Clashscore : 4.49
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 0.58 %
Favored : 99.42 %
Rotamer:
Outliers : 3.74 %
Allowed : 10.54 %
Favored : 85.71 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 5.88 %
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: 2.10 (0.30), residues: 684
helix: 2.25 (0.23), residues: 454
sheet: None (None), residues: 0
loop : -0.35 (0.34), residues: 230
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.014 0.002 TRP D 354
HIS 0.003 0.001 HIS A 562
PHE 0.023 0.002 PHE D 340
TYR 0.014 0.002 TYR D 491
ARG 0.007 0.001 ARG D 281
*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
1368 Ramachandran restraints generated.
684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
1368 Ramachandran restraints generated.
684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
122 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 22
poor density : 100
time to evaluate : 0.626
Fit side-chains
REVERT: A 247 GLU cc_start: 0.7243 (OUTLIER) cc_final: 0.6286 (mm-30)
REVERT: A 248 GLU cc_start: 0.7682 (pm20) cc_final: 0.7236 (tm-30)
REVERT: A 279 MET cc_start: 0.7876 (OUTLIER) cc_final: 0.7585 (mtp)
REVERT: A 466 LYS cc_start: 0.8353 (tttt) cc_final: 0.8003 (tttp)
REVERT: A 497 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.6841 (mp0)
REVERT: D 247 GLU cc_start: 0.7242 (OUTLIER) cc_final: 0.6283 (mm-30)
REVERT: D 248 GLU cc_start: 0.7709 (pm20) cc_final: 0.7242 (tm-30)
REVERT: D 279 MET cc_start: 0.7874 (OUTLIER) cc_final: 0.7593 (mtp)
REVERT: D 466 LYS cc_start: 0.8339 (tttt) cc_final: 0.7997 (tttp)
REVERT: D 497 GLU cc_start: 0.7612 (OUTLIER) cc_final: 0.6853 (mp0)
REVERT: D 559 ARG cc_start: 0.7157 (mtm-85) cc_final: 0.6801 (mtm-85)
outliers start: 22
outliers final: 11
residues processed: 108
average time/residue: 1.9135
time to fit residues: 212.9013
Evaluate side-chains
114 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 17
poor density : 97
time to evaluate : 0.662
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 216 VAL
Chi-restraints excluded: chain A residue 247 GLU
Chi-restraints excluded: chain A residue 263 LEU
Chi-restraints excluded: chain A residue 279 MET
Chi-restraints excluded: chain A residue 316 VAL
Chi-restraints excluded: chain A residue 372 GLU
Chi-restraints excluded: chain A residue 477 LEU
Chi-restraints excluded: chain A residue 497 GLU
Chi-restraints excluded: chain A residue 505 LEU
Chi-restraints excluded: chain D residue 216 VAL
Chi-restraints excluded: chain D residue 247 GLU
Chi-restraints excluded: chain D residue 263 LEU
Chi-restraints excluded: chain D residue 279 MET
Chi-restraints excluded: chain D residue 316 VAL
Chi-restraints excluded: chain D residue 372 GLU
Chi-restraints excluded: chain D residue 497 GLU
Chi-restraints excluded: chain D residue 505 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 68
random chunks:
chunk 58 optimal weight: 7.9990
chunk 16 optimal weight: 3.9990
chunk 44 optimal weight: 4.9990
chunk 28 optimal weight: 0.8980
chunk 38 optimal weight: 2.9990
chunk 29 optimal weight: 0.9990
chunk 62 optimal weight: 2.9990
chunk 22 optimal weight: 0.8980
chunk 4 optimal weight: 0.1980
chunk 9 optimal weight: 2.9990
chunk 37 optimal weight: 0.6980
overall best weight: 0.7382
-------------------------------------------------------------------------------
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 = 0.4072 r_free = 0.4072 target = 0.167451 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.138947 restraints weight = 4797.441|
|-----------------------------------------------------------------------------|
r_work (start): 0.3726 rms_B_bonded: 1.00
r_work: 0.3622 rms_B_bonded: 1.53 restraints_weight: 0.5000
r_work: 0.3535 rms_B_bonded: 2.46 restraints_weight: 0.2500
r_work (final): 0.3535
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8256
moved from start: 0.3180
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.050 5960 Z= 0.173
Angle : 0.564 12.111 8110 Z= 0.289
Chirality : 0.038 0.117 878
Planarity : 0.004 0.037 972
Dihedral : 8.251 58.681 1078
Min Nonbonded Distance : 2.578
Molprobity Statistics.
All-atom Clashscore : 3.97
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 1.17 %
Favored : 98.83 %
Rotamer:
Outliers : 2.55 %
Allowed : 11.56 %
Favored : 85.88 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 5.88 %
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: 2.37 (0.30), residues: 684
helix: 2.47 (0.23), residues: 454
sheet: None (None), residues: 0
loop : -0.28 (0.35), residues: 230
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.017 0.001 TRP D 256
HIS 0.002 0.001 HIS D 498
PHE 0.015 0.001 PHE D 340
TYR 0.015 0.001 TYR D 491
ARG 0.007 0.001 ARG D 559
********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
1368 Ramachandran restraints generated.
684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
1368 Ramachandran restraints generated.
684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
118 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 15
poor density : 103
time to evaluate : 0.632
Fit side-chains
REVERT: A 247 GLU cc_start: 0.7218 (OUTLIER) cc_final: 0.6301 (mm-30)
REVERT: A 248 GLU cc_start: 0.7659 (pm20) cc_final: 0.7261 (tm-30)
REVERT: A 279 MET cc_start: 0.7824 (OUTLIER) cc_final: 0.7537 (mtp)
REVERT: A 466 LYS cc_start: 0.8347 (tttt) cc_final: 0.8005 (tttp)
REVERT: D 247 GLU cc_start: 0.7217 (OUTLIER) cc_final: 0.6301 (mm-30)
REVERT: D 248 GLU cc_start: 0.7652 (pm20) cc_final: 0.7259 (tm-30)
REVERT: D 279 MET cc_start: 0.7829 (OUTLIER) cc_final: 0.7552 (mtp)
REVERT: D 466 LYS cc_start: 0.8333 (tttt) cc_final: 0.7990 (tttp)
outliers start: 15
outliers final: 9
residues processed: 111
average time/residue: 1.9808
time to fit residues: 226.1374
Evaluate side-chains
113 residues out of total 588 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 13
poor density : 100
time to evaluate : 0.612
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 216 VAL
Chi-restraints excluded: chain A residue 247 GLU
Chi-restraints excluded: chain A residue 279 MET
Chi-restraints excluded: chain A residue 316 VAL
Chi-restraints excluded: chain A residue 372 GLU
Chi-restraints excluded: chain A residue 477 LEU
Chi-restraints excluded: chain A residue 505 LEU
Chi-restraints excluded: chain D residue 216 VAL
Chi-restraints excluded: chain D residue 247 GLU
Chi-restraints excluded: chain D residue 279 MET
Chi-restraints excluded: chain D residue 316 VAL
Chi-restraints excluded: chain D residue 372 GLU
Chi-restraints excluded: chain D residue 505 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 68
random chunks:
chunk 1 optimal weight: 0.5980
chunk 32 optimal weight: 2.9990
chunk 17 optimal weight: 6.9990
chunk 6 optimal weight: 0.8980
chunk 38 optimal weight: 2.9990
chunk 57 optimal weight: 0.7980
chunk 41 optimal weight: 3.9990
chunk 40 optimal weight: 0.8980
chunk 34 optimal weight: 9.9990
chunk 11 optimal weight: 8.9990
chunk 52 optimal weight: 2.9990
overall best weight: 1.2382
-------------------------------------------------------------------------------
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 = 0.4057 r_free = 0.4057 target = 0.166038 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.137221 restraints weight = 4758.429|
|-----------------------------------------------------------------------------|
r_work (start): 0.3704 rms_B_bonded: 0.99
r_work: 0.3598 rms_B_bonded: 1.53 restraints_weight: 0.5000
r_work: 0.3510 rms_B_bonded: 2.46 restraints_weight: 0.2500
r_work (final): 0.3510
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8282
moved from start: 0.3156
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.004 0.060 5960 Z= 0.220
Angle : 0.606 12.089 8110 Z= 0.313
Chirality : 0.040 0.122 878
Planarity : 0.004 0.053 972
Dihedral : 8.542 59.759 1078
Min Nonbonded Distance : 2.561
Molprobity Statistics.
All-atom Clashscore : 4.23
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 0.58 %
Favored : 99.42 %
Rotamer:
Outliers : 2.55 %
Allowed : 11.73 %
Favored : 85.71 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 5.88 %
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 (0.30), residues: 684
helix: 2.30 (0.23), residues: 454
sheet: None (None), residues: 0
loop : -0.32 (0.35), residues: 230
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.016 0.002 TRP D 256
HIS 0.002 0.001 HIS A 498
PHE 0.020 0.002 PHE D 340
TYR 0.015 0.002 TYR D 491
ARG 0.012 0.001 ARG D 559
Origin is already at (0, 0, 0), no shifts will be applied
===============================================================================
Job complete
usr+sys time: 6944.05 seconds
wall clock time: 123 minutes 15.01 seconds (7395.01 seconds total)