Starting phenix.real_space_refine
on Sat Aug 3 13:21:01 2024 by dcliebschner
===============================================================================
Processing files:
-------------------------------------------------------------------------------
Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8twi_41668/08_2024/8twi_41668.cif
Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8twi_41668/08_2024/8twi_41668.map
Processing PHIL parameters:
-------------------------------------------------------------------------------
Adding command-line PHIL:
-------------------------
refinement.macro_cycles=10
scattering_table=electron
resolution=2.69
write_initial_geo_file=False
Final processed PHIL parameters:
-------------------------------------------------------------------------------
data_manager {
real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8twi_41668/08_2024/8twi_41668.map"
default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8twi_41668/08_2024/8twi_41668.map"
model {
file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8twi_41668/08_2024/8twi_41668.cif"
}
default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8twi_41668/08_2024/8twi_41668.cif"
}
resolution = 2.69
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: 7
Type Number sf(0) Gaussians
Fe 1 7.16 5
Zn 1 6.06 5
S 26 5.16 5
C 2584 2.51 5
N 696 2.21 5
O 765 1.98 5
H 4023 0.53 5
sf(0) = scattering factor at diffraction angle 0.
Process input model
Symmetric amino acids flipped
Residue "C TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Time to flip residues: 0.01s
Monomer Library directory:
"/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib"
Total number of atoms: 8096
Number of models: 1
Model: ""
Number of chains: 4
Chain: "A"
Number of atoms: 3096
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 194, 3096
Classifications: {'peptide': 194}
Modifications used: {'COO': 1}
Link IDs: {'PTRANS': 8, 'TRANS': 185}
Chain: "C"
Number of atoms: 4696
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 297, 4696
Classifications: {'peptide': 297}
Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 284}
Chain: "D"
Number of atoms: 302
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 19, 302
Classifications: {'peptide': 19}
Link IDs: {'TRANS': 18}
Chain: "C"
Number of atoms: 2
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 2, 2
Unusual residues: {' FE': 1, ' ZN': 1}
Classifications: {'undetermined': 2}
Link IDs: {None: 1}
Time building chain proxies: 7.14, per 1000 atoms: 0.88
Number of scatterers: 8096
At special positions: 0
Unit cell: (77.43, 72.624, 86.508, 90, 90, 90)
Space group: P 1 (No. 1)
Number of sites at special positions: 0
Number of scattering types: 7
Type Number sf(0)
Zn 1 29.99
Fe 1 26.01
S 26 16.00
O 765 8.00
N 696 7.00
C 2584 6.00
H 4023 1.00
sf(0) = scattering factor at diffraction angle 0.
Number of disulfides: simple=0, symmetry=0
Automatic linking
Parameters for automatic linking
Linking & cutoffs
Metal : Auto - 3.50
Amino acid : False - 1.90
Carbohydrate : True - 1.99
Ligands : True - 1.99
Small molecules : False - 1.98
Amino acid - RNA/DNA : False
Number of custom bonds: simple=0, symmetry=0
Time building additional restraints: 6.44
Conformation dependent library (CDL) restraints added in 948.0 milliseconds
Dynamic metal coordination
Zn2+ tetrahedral coordination
pdb=" ZN C 402 "
pdb="ZN ZN C 402 " - pdb=" NE2 HIS C 59 "
1008 Ramachandran restraints generated.
504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2.
Adding C-beta torsion restraints...
Number of C-beta restraints generated: 956
Finding SS restraints...
Secondary structure from input PDB file:
27 helices and 3 sheets defined
65.3% alpha, 7.8% beta
0 base pairs and 0 stacking pairs defined.
Time for finding SS restraints: 0.59
Creating SS restraints...
Processing helix chain 'A' and resid 396 through 413
removed outlier: 3.875A pdb=" N LEU A 400 " --> pdb=" O GLY A 396 " (cutoff:3.500A)
removed outlier: 4.445A pdb=" N GLN A 402 " --> pdb=" O ARG A 398 " (cutoff:3.500A)
removed outlier: 4.797A pdb=" N SER A 403 " --> pdb=" O GLN A 399 " (cutoff:3.500A)
Proline residue: A 406 - end of helix
Processing helix chain 'A' and resid 416 through 435
removed outlier: 3.587A pdb=" N TYR A 426 " --> pdb=" O ALA A 422 " (cutoff:3.500A)
Proline residue: A 428 - end of helix
Processing helix chain 'A' and resid 435 through 443
Processing helix chain 'A' and resid 443 through 452
removed outlier: 3.560A pdb=" N LEU A 451 " --> pdb=" O CYS A 447 " (cutoff:3.500A)
removed outlier: 3.805A pdb=" N VAL A 452 " --> pdb=" O MET A 448 " (cutoff:3.500A)
Processing helix chain 'A' and resid 455 through 482
removed outlier: 3.792A pdb=" N LYS A 467 " --> pdb=" O THR A 463 " (cutoff:3.500A)
removed outlier: 7.117A pdb=" N LYS A 475 " --> pdb=" O GLU A 471 " (cutoff:3.500A)
removed outlier: 8.804A pdb=" N GLU A 476 " --> pdb=" O LYS A 472 " (cutoff:3.500A)
removed outlier: 4.242A pdb=" N TRP A 477 " --> pdb=" O PHE A 473 " (cutoff:3.500A)
Processing helix chain 'A' and resid 482 through 489
removed outlier: 3.610A pdb=" N ALA A 488 " --> pdb=" O PRO A 484 " (cutoff:3.500A)
removed outlier: 3.797A pdb=" N MET A 489 " --> pdb=" O LYS A 485 " (cutoff:3.500A)
Processing helix chain 'A' and resid 490 through 492
No H-bonds generated for 'chain 'A' and resid 490 through 492'
Processing helix chain 'A' and resid 494 through 520
removed outlier: 3.502A pdb=" N THR A 501 " --> pdb=" O HIS A 497 " (cutoff:3.500A)
removed outlier: 3.680A pdb=" N LEU A 502 " --> pdb=" O ARG A 498 " (cutoff:3.500A)
removed outlier: 4.149A pdb=" N GLU A 510 " --> pdb=" O ASN A 506 " (cutoff:3.500A)
removed outlier: 4.063A pdb=" N VAL A 511 " --> pdb=" O VAL A 507 " (cutoff:3.500A)
removed outlier: 3.806A pdb=" N GLY A 513 " --> pdb=" O SER A 509 " (cutoff:3.500A)
removed outlier: 7.742A pdb=" N GLN A 514 " --> pdb=" O GLU A 510 " (cutoff:3.500A)
removed outlier: 8.220A pdb=" N ASP A 515 " --> pdb=" O VAL A 511 " (cutoff:3.500A)
removed outlier: 4.355A pdb=" N ILE A 516 " --> pdb=" O CYS A 512 " (cutoff:3.500A)
Processing helix chain 'A' and resid 521 through 528
Processing helix chain 'A' and resid 529 through 531
No H-bonds generated for 'chain 'A' and resid 529 through 531'
Processing helix chain 'A' and resid 533 through 548
Processing helix chain 'A' and resid 549 through 551
No H-bonds generated for 'chain 'A' and resid 549 through 551'
Processing helix chain 'A' and resid 552 through 559
Processing helix chain 'A' and resid 559 through 569
removed outlier: 3.658A pdb=" N ILE A 563 " --> pdb=" O GLU A 559 " (cutoff:3.500A)
removed outlier: 3.718A pdb=" N GLN A 569 " --> pdb=" O GLU A 565 " (cutoff:3.500A)
Processing helix chain 'A' and resid 572 through 586
Processing helix chain 'C' and resid 3 through 19
Processing helix chain 'C' and resid 24 through 40
Processing helix chain 'C' and resid 61 through 73
Processing helix chain 'C' and resid 92 through 107
Processing helix chain 'C' and resid 120 through 128
removed outlier: 3.627A pdb=" N VAL C 126 " --> pdb=" O GLN C 122 " (cutoff:3.500A)
removed outlier: 3.637A pdb=" N GLY C 128 " --> pdb=" O THR C 124 " (cutoff:3.500A)
Processing helix chain 'C' and resid 128 through 138
Processing helix chain 'C' and resid 140 through 151
removed outlier: 3.677A pdb=" N ASP C 151 " --> pdb=" O THR C 147 " (cutoff:3.500A)
Processing helix chain 'C' and resid 176 through 182
removed outlier: 3.600A pdb=" N ILE C 180 " --> pdb=" O THR C 176 " (cutoff:3.500A)
Processing helix chain 'C' and resid 193 through 201
removed outlier: 3.801A pdb=" N LEU C 199 " --> pdb=" O MET C 195 " (cutoff:3.500A)
Processing helix chain 'C' and resid 221 through 233
Processing helix chain 'C' and resid 264 through 268
Processing helix chain 'D' and resid 95 through 111
removed outlier: 3.664A pdb=" N GLU D 100 " --> pdb=" O LEU D 96 " (cutoff:3.500A)
removed outlier: 3.688A pdb=" N HIS D 103 " --> pdb=" O ARG D 99 " (cutoff:3.500A)
Processing sheet with id=AA1, first strand: chain 'C' and resid 45 through 48
removed outlier: 6.204A pdb=" N GLN C 46 " --> pdb=" O LEU C 158 " (cutoff:3.500A)
removed outlier: 6.157A pdb=" N PHE C 164 " --> pdb=" O SER C 238 " (cutoff:3.500A)
removed outlier: 6.434A pdb=" N VAL C 237 " --> pdb=" O VAL C 257 " (cutoff:3.500A)
removed outlier: 7.509A pdb=" N ILE C 259 " --> pdb=" O VAL C 237 " (cutoff:3.500A)
removed outlier: 6.260A pdb=" N ARG C 239 " --> pdb=" O ILE C 259 " (cutoff:3.500A)
Processing sheet with id=AA2, first strand: chain 'C' and resid 111 through 113
Processing sheet with id=AA3, first strand: chain 'C' and resid 202 through 203
220 hydrogen bonds defined for protein.
639 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: 2.81
Time building geometry restraints manager: 6.75 seconds
NOTE: a complete listing of the restraints can be obtained by requesting
output of .geo file.
Histogram of bond lengths:
0.84 - 1.03: 4010
1.03 - 1.23: 13
1.23 - 1.42: 1739
1.42 - 1.61: 2378
1.61 - 1.81: 39
Bond restraints: 8179
Sorted by residual:
bond pdb=" N GLY D 93 "
pdb=" CA GLY D 93 "
ideal model delta sigma weight residual
1.451 1.493 -0.042 1.60e-02 3.91e+03 6.75e+00
bond pdb=" N GLY A 396 "
pdb=" CA GLY A 396 "
ideal model delta sigma weight residual
1.451 1.491 -0.040 1.60e-02 3.91e+03 6.40e+00
bond pdb=" N ASP C 2 "
pdb=" CA ASP C 2 "
ideal model delta sigma weight residual
1.458 1.491 -0.033 1.90e-02 2.77e+03 2.93e+00
bond pdb=" N GLY D 93 "
pdb=" H GLY D 93 "
ideal model delta sigma weight residual
0.860 0.891 -0.031 2.00e-02 2.50e+03 2.34e+00
bond pdb=" N GLY A 396 "
pdb=" H GLY A 396 "
ideal model delta sigma weight residual
0.860 0.890 -0.030 2.00e-02 2.50e+03 2.21e+00
... (remaining 8174 not shown)
Histogram of bond angle deviations from ideal:
100.68 - 107.34: 269
107.34 - 113.99: 9654
113.99 - 120.65: 2792
120.65 - 127.30: 2010
127.30 - 133.96: 50
Bond angle restraints: 14775
Sorted by residual:
angle pdb=" N HIS C 241 "
pdb=" CA HIS C 241 "
pdb=" CB HIS C 241 "
ideal model delta sigma weight residual
114.27 108.67 5.60 1.64e+00 3.72e-01 1.17e+01
angle pdb=" C ARG C 239 "
pdb=" N ALA C 240 "
pdb=" CA ALA C 240 "
ideal model delta sigma weight residual
122.16 125.63 -3.47 1.32e+00 5.74e-01 6.91e+00
angle pdb=" N LEU C 282 "
pdb=" CA LEU C 282 "
pdb=" CB LEU C 282 "
ideal model delta sigma weight residual
113.65 110.06 3.59 1.47e+00 4.63e-01 5.97e+00
angle pdb=" C ALA C 240 "
pdb=" N HIS C 241 "
pdb=" CA HIS C 241 "
ideal model delta sigma weight residual
125.66 121.96 3.70 1.85e+00 2.92e-01 4.01e+00
angle pdb=" CA VAL C 58 "
pdb=" C VAL C 58 "
pdb=" N HIS C 59 "
ideal model delta sigma weight residual
116.60 119.10 -2.50 1.45e+00 4.76e-01 2.97e+00
... (remaining 14770 not shown)
Histogram of dihedral angle deviations from ideal:
0.00 - 16.80: 3569
16.80 - 33.60: 152
33.60 - 50.39: 72
50.39 - 67.19: 32
67.19 - 83.99: 12
Dihedral angle restraints: 3837
sinusoidal: 2094
harmonic: 1743
Sorted by residual:
dihedral pdb=" CA ALA C 240 "
pdb=" C ALA C 240 "
pdb=" N HIS C 241 "
pdb=" CA HIS C 241 "
ideal model delta harmonic sigma weight residual
180.00 160.47 19.53 0 5.00e+00 4.00e-02 1.53e+01
dihedral pdb=" CA TYR C 127 "
pdb=" C TYR C 127 "
pdb=" N GLY C 128 "
pdb=" CA GLY C 128 "
ideal model delta harmonic sigma weight residual
180.00 160.75 19.25 0 5.00e+00 4.00e-02 1.48e+01
dihedral pdb=" CA SER C 238 "
pdb=" C SER C 238 "
pdb=" N ARG C 239 "
pdb=" CA ARG C 239 "
ideal model delta harmonic sigma weight residual
-180.00 -161.60 -18.40 0 5.00e+00 4.00e-02 1.35e+01
... (remaining 3834 not shown)
Histogram of chiral volume deviations from ideal:
0.000 - 0.026: 418
0.026 - 0.052: 120
0.052 - 0.078: 55
0.078 - 0.104: 24
0.104 - 0.130: 12
Chirality restraints: 629
Sorted by residual:
chirality pdb=" CA VAL C 237 "
pdb=" N VAL C 237 "
pdb=" C VAL C 237 "
pdb=" CB VAL C 237 "
both_signs ideal model delta sigma weight residual
False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.21e-01
chirality pdb=" CA VAL C 45 "
pdb=" N VAL C 45 "
pdb=" C VAL C 45 "
pdb=" CB VAL C 45 "
both_signs ideal model delta sigma weight residual
False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.06e-01
chirality pdb=" CA ILE C 275 "
pdb=" N ILE C 275 "
pdb=" C ILE C 275 "
pdb=" CB ILE C 275 "
both_signs ideal model delta sigma weight residual
False 2.43 2.55 -0.11 2.00e-01 2.50e+01 3.26e-01
... (remaining 626 not shown)
Planarity restraints: 1215
Sorted by residual:
delta sigma weight rms_deltas residual
plane pdb=" CB PHE A 538 " -0.012 2.00e-02 2.50e+03 7.57e-03 1.72e+00
pdb=" CG PHE A 538 " 0.022 2.00e-02 2.50e+03
pdb=" CD1 PHE A 538 " -0.004 2.00e-02 2.50e+03
pdb=" CD2 PHE A 538 " -0.000 2.00e-02 2.50e+03
pdb=" CE1 PHE A 538 " 0.001 2.00e-02 2.50e+03
pdb=" CE2 PHE A 538 " -0.004 2.00e-02 2.50e+03
pdb=" CZ PHE A 538 " -0.001 2.00e-02 2.50e+03
pdb=" HD1 PHE A 538 " 0.000 2.00e-02 2.50e+03
pdb=" HD2 PHE A 538 " 0.001 2.00e-02 2.50e+03
pdb=" HE1 PHE A 538 " -0.001 2.00e-02 2.50e+03
pdb=" HE2 PHE A 538 " -0.002 2.00e-02 2.50e+03
pdb=" HZ PHE A 538 " 0.000 2.00e-02 2.50e+03
delta sigma weight rms_deltas residual
plane pdb=" C VAL C 189 " -0.020 5.00e-02 4.00e+02 3.00e-02 1.44e+00
pdb=" N PRO C 190 " 0.052 5.00e-02 4.00e+02
pdb=" CA PRO C 190 " -0.015 5.00e-02 4.00e+02
pdb=" CD PRO C 190 " -0.017 5.00e-02 4.00e+02
delta sigma weight rms_deltas residual
plane pdb=" CA ALA C 240 " 0.005 2.00e-02 2.50e+03 1.03e-02 1.05e+00
pdb=" C ALA C 240 " -0.018 2.00e-02 2.50e+03
pdb=" O ALA C 240 " 0.007 2.00e-02 2.50e+03
pdb=" N HIS C 241 " 0.006 2.00e-02 2.50e+03
... (remaining 1212 not shown)
Histogram of nonbonded interaction distances:
1.54 - 2.15: 264
2.15 - 2.76: 15414
2.76 - 3.37: 23905
3.37 - 3.99: 30526
3.99 - 4.60: 48717
Nonbonded interactions: 118826
Sorted by model distance:
nonbonded pdb=" HG SER C 120 "
pdb=" OE2 GLU C 188 "
model vdw
1.535 2.450
nonbonded pdb=" O VAL C 94 "
pdb=" HG1 THR C 98 "
model vdw
1.619 2.450
nonbonded pdb=" O GLY C 73 "
pdb=" HH TYR C 80 "
model vdw
1.619 2.450
nonbonded pdb=" O GLU A 565 "
pdb=" HG1 THR A 568 "
model vdw
1.637 2.450
nonbonded pdb=" OD1 ASP C 202 "
pdb="HH21 ARG C 239 "
model vdw
1.648 2.450
... (remaining 118821 not shown)
NOTE: a complete listing of the restraints can be obtained by requesting
output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============
No NCS relation were found !!!
================================
Found NCS groups:
found none.
Set up NCS constraints
No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
ADPs will be refined as 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: 11.450
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: 0.120
Extract box with map and model: 0.350
Check model and map are aligned: 0.060
Set scattering table: 0.070
Process input model: 34.800
Find NCS groups from input model: 0.220
Set up NCS constraints: 0.020
Set refine NCS operators: 0.000
Adjust number of macro_cycles: 0.000
Reset NCS operators: 0.000
Extract rigid body selections: 0.000
Check and reset occupancies: 0.000
Load rotamer database and sin/cos tables:12.950
Set ADP refinement strategy: 0.000
Make a string to write initial .geo file:0.000
Internal consistency checks: 0.000
Total: 60.040
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8076
moved from start: 0.0000
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.002 0.042 4156 Z= 0.141
Angle : 0.460 5.602 5633 Z= 0.255
Chirality : 0.036 0.130 629
Planarity : 0.003 0.030 728
Dihedral : 9.781 83.990 1539
Min Nonbonded Distance : 2.049
Molprobity Statistics.
All-atom Clashscore : 1.24
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 2.18 %
Favored : 97.82 %
Rotamer:
Outliers : 0.67 %
Allowed : 0.22 %
Favored : 99.11 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 10.00 %
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: 1.15 (0.38), residues: 504
helix: 1.17 (0.31), residues: 285
sheet: 0.20 (0.90), residues: 36
loop : 0.43 (0.48), residues: 183
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.005 0.001 TRP A 417
HIS 0.005 0.001 HIS C 63
PHE 0.022 0.001 PHE A 538
TYR 0.009 0.001 TYR C 127
ARG 0.002 0.000 ARG A 527
*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
1008 Ramachandran restraints generated.
504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
1008 Ramachandran restraints generated.
504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
88 residues out of total 447 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 3
poor density : 85
time to evaluate : 0.662
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: A 514 GLN cc_start: 0.9177 (tt0) cc_final: 0.8851 (tt0)
REVERT: A 555 THR cc_start: 0.9603 (m) cc_final: 0.9123 (p)
REVERT: A 558 SER cc_start: 0.9482 (t) cc_final: 0.9222 (p)
REVERT: C 197 ASP cc_start: 0.8834 (m-30) cc_final: 0.8421 (m-30)
REVERT: C 238 SER cc_start: 0.9108 (t) cc_final: 0.8734 (p)
outliers start: 3
outliers final: 1
residues processed: 87
average time/residue: 1.6605
time to fit residues: 151.8987
Evaluate side-chains
59 residues out of total 447 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 1
poor density : 58
time to evaluate : 0.637
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 515 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 49
random chunks:
chunk 41 optimal weight: 3.9990
chunk 37 optimal weight: 3.9990
chunk 20 optimal weight: 1.9990
chunk 12 optimal weight: 2.9990
chunk 25 optimal weight: 0.9980
chunk 19 optimal weight: 1.9990
chunk 38 optimal weight: 1.9990
chunk 14 optimal weight: 2.9990
chunk 23 optimal weight: 0.8980
chunk 28 optimal weight: 0.3980
chunk 44 optimal weight: 0.9980
overall best weight: 1.0582
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 465 ASN
Total number of N/Q/H flips: 1
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8126
moved from start: 0.2399
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.004 0.031 4156 Z= 0.256
Angle : 0.588 7.543 5633 Z= 0.315
Chirality : 0.040 0.133 629
Planarity : 0.005 0.058 728
Dihedral : 4.771 31.891 556
Min Nonbonded Distance : 1.901
Molprobity Statistics.
All-atom Clashscore : 4.70
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 2.38 %
Favored : 97.62 %
Rotamer:
Outliers : 0.22 %
Allowed : 9.62 %
Favored : 90.16 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 10.00 %
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: 1.21 (0.38), residues: 504
helix: 1.37 (0.31), residues: 291
sheet: -0.17 (0.94), residues: 37
loop : 0.23 (0.47), residues: 176
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.005 0.001 TRP A 417
HIS 0.003 0.001 HIS C 230
PHE 0.022 0.001 PHE A 538
TYR 0.011 0.001 TYR C 265
ARG 0.007 0.001 ARG C 49
*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
1008 Ramachandran restraints generated.
504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
1008 Ramachandran restraints generated.
504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
61 residues out of total 447 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 1
poor density : 60
time to evaluate : 0.675
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: A 512 CYS cc_start: 0.8765 (m) cc_final: 0.8494 (p)
REVERT: A 514 GLN cc_start: 0.9054 (tt0) cc_final: 0.8656 (tt0)
REVERT: A 517 THR cc_start: 0.9515 (m) cc_final: 0.9159 (p)
REVERT: A 558 SER cc_start: 0.9497 (t) cc_final: 0.9212 (p)
REVERT: A 570 ASP cc_start: 0.9030 (t0) cc_final: 0.8535 (t0)
outliers start: 1
outliers final: 0
residues processed: 61
average time/residue: 1.7321
time to fit residues: 111.1812
Evaluate side-chains
52 residues out of total 447 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 52
time to evaluate : 0.651
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 49
random chunks:
chunk 24 optimal weight: 0.9990
chunk 13 optimal weight: 2.9990
chunk 37 optimal weight: 0.9990
chunk 30 optimal weight: 0.9980
chunk 12 optimal weight: 0.6980
chunk 44 optimal weight: 1.9990
chunk 48 optimal weight: 8.9990
chunk 39 optimal weight: 1.9990
chunk 15 optimal weight: 0.5980
chunk 35 optimal weight: 0.9980
chunk 33 optimal weight: 0.9980
overall best weight: 0.8580
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8137
moved from start: 0.3094
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.025 4156 Z= 0.205
Angle : 0.532 6.066 5633 Z= 0.282
Chirality : 0.039 0.129 629
Planarity : 0.004 0.034 728
Dihedral : 4.301 19.629 554
Min Nonbonded Distance : 1.985
Molprobity Statistics.
All-atom Clashscore : 4.70
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 2.38 %
Favored : 97.62 %
Rotamer:
Outliers : 0.67 %
Allowed : 9.62 %
Favored : 89.71 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 10.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 1.31 (0.38), residues: 504
helix: 1.47 (0.31), residues: 299
sheet: -0.23 (0.90), residues: 37
loop : 0.21 (0.48), residues: 168
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.007 0.001 TRP A 417
HIS 0.004 0.001 HIS C 63
PHE 0.021 0.001 PHE A 538
TYR 0.008 0.001 TYR C 265
ARG 0.003 0.000 ARG C 49
*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
1008 Ramachandran restraints generated.
504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
1008 Ramachandran restraints generated.
504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
59 residues out of total 447 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 3
poor density : 56
time to evaluate : 0.659
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: A 512 CYS cc_start: 0.8708 (m) cc_final: 0.8453 (p)
REVERT: A 517 THR cc_start: 0.9508 (m) cc_final: 0.9188 (p)
REVERT: A 558 SER cc_start: 0.9538 (t) cc_final: 0.9257 (p)
REVERT: A 570 ASP cc_start: 0.8887 (t0) cc_final: 0.8658 (t0)
REVERT: C 238 SER cc_start: 0.9033 (OUTLIER) cc_final: 0.8137 (p)
REVERT: C 242 GLN cc_start: 0.8906 (tt0) cc_final: 0.8700 (tt0)
outliers start: 3
outliers final: 1
residues processed: 58
average time/residue: 1.9492
time to fit residues: 118.4166
Evaluate side-chains
53 residues out of total 447 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 2
poor density : 51
time to evaluate : 0.684
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 568 THR
Chi-restraints excluded: chain C residue 238 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 49
random chunks:
chunk 23 optimal weight: 1.9990
chunk 4 optimal weight: 0.9980
chunk 21 optimal weight: 0.7980
chunk 29 optimal weight: 1.9990
chunk 44 optimal weight: 1.9990
chunk 47 optimal weight: 0.5980
chunk 42 optimal weight: 0.6980
chunk 12 optimal weight: 2.9990
chunk 39 optimal weight: 1.9990
chunk 26 optimal weight: 0.6980
chunk 0 optimal weight: 3.9990
overall best weight: 0.7580
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 465 ASN
Total number of N/Q/H flips: 1
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8146
moved from start: 0.3385
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.032 4156 Z= 0.196
Angle : 0.529 6.247 5633 Z= 0.276
Chirality : 0.038 0.135 629
Planarity : 0.004 0.064 728
Dihedral : 4.159 19.334 554
Min Nonbonded Distance : 1.951
Molprobity Statistics.
All-atom Clashscore : 3.58
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 2.98 %
Favored : 97.02 %
Rotamer:
Outliers : 0.45 %
Allowed : 10.51 %
Favored : 89.04 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 10.00 %
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: 1.47 (0.38), residues: 504
helix: 1.62 (0.31), residues: 299
sheet: -0.09 (0.90), residues: 37
loop : 0.18 (0.48), residues: 168
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.007 0.001 TRP A 417
HIS 0.003 0.001 HIS C 63
PHE 0.022 0.001 PHE A 538
TYR 0.006 0.001 TYR C 265
ARG 0.005 0.000 ARG A 527
*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
1008 Ramachandran restraints generated.
504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
1008 Ramachandran restraints generated.
504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
55 residues out of total 447 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 2
poor density : 53
time to evaluate : 0.648
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: A 465 ASN cc_start: 0.8778 (t0) cc_final: 0.8520 (t0)
REVERT: A 512 CYS cc_start: 0.8827 (m) cc_final: 0.8487 (p)
REVERT: A 517 THR cc_start: 0.9499 (m) cc_final: 0.9218 (p)
REVERT: A 558 SER cc_start: 0.9548 (t) cc_final: 0.9259 (p)
REVERT: A 570 ASP cc_start: 0.8931 (t0) cc_final: 0.8674 (t0)
REVERT: C 197 ASP cc_start: 0.8821 (m-30) cc_final: 0.8447 (m-30)
REVERT: C 242 GLN cc_start: 0.8913 (tt0) cc_final: 0.8238 (mt0)
outliers start: 2
outliers final: 0
residues processed: 54
average time/residue: 2.0428
time to fit residues: 115.4052
Evaluate side-chains
50 residues out of total 447 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 50
time to evaluate : 0.638
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 49
random chunks:
chunk 35 optimal weight: 1.9990
chunk 19 optimal weight: 2.9990
chunk 40 optimal weight: 3.9990
chunk 32 optimal weight: 2.9990
chunk 0 optimal weight: 4.9990
chunk 24 optimal weight: 1.9990
chunk 42 optimal weight: 0.7980
chunk 11 optimal weight: 2.9990
chunk 15 optimal weight: 2.9990
chunk 9 optimal weight: 0.5980
chunk 27 optimal weight: 0.5980
overall best weight: 1.1984
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8174
moved from start: 0.3516
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.004 0.030 4156 Z= 0.266
Angle : 0.528 5.096 5633 Z= 0.282
Chirality : 0.039 0.135 629
Planarity : 0.004 0.045 728
Dihedral : 4.169 18.911 554
Min Nonbonded Distance : 1.940
Molprobity Statistics.
All-atom Clashscore : 4.08
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 2.98 %
Favored : 97.02 %
Rotamer:
Outliers : 0.22 %
Allowed : 11.19 %
Favored : 88.59 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 10.00 %
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: 1.43 (0.39), residues: 504
helix: 1.58 (0.31), residues: 300
sheet: -0.18 (0.89), residues: 37
loop : 0.22 (0.49), residues: 167
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.007 0.001 TRP A 417
HIS 0.004 0.001 HIS C 63
PHE 0.022 0.001 PHE A 538
TYR 0.006 0.001 TYR C 265
ARG 0.006 0.000 ARG A 527
*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
1008 Ramachandran restraints generated.
504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
1008 Ramachandran restraints generated.
504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
52 residues out of total 447 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 1
poor density : 51
time to evaluate : 0.614
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: A 512 CYS cc_start: 0.8797 (m) cc_final: 0.8541 (p)
REVERT: A 517 THR cc_start: 0.9498 (m) cc_final: 0.9245 (p)
REVERT: A 558 SER cc_start: 0.9552 (t) cc_final: 0.9264 (p)
REVERT: A 570 ASP cc_start: 0.8951 (t0) cc_final: 0.8600 (t0)
REVERT: C 197 ASP cc_start: 0.8827 (m-30) cc_final: 0.8443 (m-30)
REVERT: C 242 GLN cc_start: 0.8914 (tt0) cc_final: 0.8313 (mt0)
outliers start: 1
outliers final: 0
residues processed: 51
average time/residue: 2.1361
time to fit residues: 113.6973
Evaluate side-chains
47 residues out of total 447 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 47
time to evaluate : 0.661
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 49
random chunks:
chunk 11 optimal weight: 2.9990
chunk 47 optimal weight: 0.9990
chunk 39 optimal weight: 0.4980
chunk 21 optimal weight: 0.9980
chunk 3 optimal weight: 2.9990
chunk 15 optimal weight: 0.9990
chunk 24 optimal weight: 1.9990
chunk 45 optimal weight: 0.2980
chunk 5 optimal weight: 0.9980
chunk 27 optimal weight: 0.9980
chunk 34 optimal weight: 0.8980
overall best weight: 0.7380
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8161
moved from start: 0.3656
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.033 4156 Z= 0.189
Angle : 0.517 6.296 5633 Z= 0.271
Chirality : 0.038 0.126 629
Planarity : 0.004 0.050 728
Dihedral : 4.020 18.676 554
Min Nonbonded Distance : 1.976
Molprobity Statistics.
All-atom Clashscore : 4.70
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 2.78 %
Favored : 97.22 %
Rotamer:
Outliers : 0.22 %
Allowed : 12.53 %
Favored : 87.25 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 10.00 %
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: 1.51 (0.39), residues: 504
helix: 1.63 (0.31), residues: 300
sheet: -0.24 (0.87), residues: 37
loop : 0.30 (0.50), residues: 167
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.008 0.001 TRP A 477
HIS 0.003 0.001 HIS C 63
PHE 0.023 0.001 PHE A 538
TYR 0.006 0.001 TYR A 495
ARG 0.006 0.000 ARG A 527
*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
1008 Ramachandran restraints generated.
504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
1008 Ramachandran restraints generated.
504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
49 residues out of total 447 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 1
poor density : 48
time to evaluate : 0.651
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: A 512 CYS cc_start: 0.8839 (m) cc_final: 0.8570 (p)
REVERT: A 558 SER cc_start: 0.9552 (t) cc_final: 0.9268 (p)
REVERT: A 570 ASP cc_start: 0.8954 (t0) cc_final: 0.8639 (t0)
REVERT: C 197 ASP cc_start: 0.8818 (m-30) cc_final: 0.8435 (m-30)
REVERT: C 242 GLN cc_start: 0.8924 (tt0) cc_final: 0.8324 (mt0)
outliers start: 1
outliers final: 1
residues processed: 49
average time/residue: 2.2239
time to fit residues: 113.5483
Evaluate side-chains
48 residues out of total 447 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 1
poor density : 47
time to evaluate : 0.594
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue 120 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 49
random chunks:
chunk 26 optimal weight: 0.9980
chunk 39 optimal weight: 0.0770
chunk 47 optimal weight: 0.2980
chunk 29 optimal weight: 0.9980
chunk 28 optimal weight: 0.7980
chunk 21 optimal weight: 0.8980
chunk 18 optimal weight: 2.9990
chunk 14 optimal weight: 0.3980
chunk 9 optimal weight: 0.9990
chunk 30 optimal weight: 0.9990
chunk 32 optimal weight: 0.9990
overall best weight: 0.4938
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8153
moved from start: 0.3791
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.002 0.034 4156 Z= 0.160
Angle : 0.503 5.500 5633 Z= 0.264
Chirality : 0.037 0.125 629
Planarity : 0.004 0.050 728
Dihedral : 3.939 18.404 554
Min Nonbonded Distance : 1.975
Molprobity Statistics.
All-atom Clashscore : 5.07
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 2.78 %
Favored : 97.22 %
Rotamer:
Outliers : 0.45 %
Allowed : 12.75 %
Favored : 86.80 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 10.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 1.58 (0.39), residues: 504
helix: 1.67 (0.31), residues: 300
sheet: -0.18 (0.87), residues: 37
loop : 0.34 (0.50), residues: 167
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.008 0.001 TRP A 477
HIS 0.002 0.000 HIS C 63
PHE 0.021 0.001 PHE A 538
TYR 0.005 0.001 TYR C 265
ARG 0.007 0.000 ARG A 527
*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
1008 Ramachandran restraints generated.
504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
1008 Ramachandran restraints generated.
504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
52 residues out of total 447 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 2
poor density : 50
time to evaluate : 0.630
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: A 512 CYS cc_start: 0.8850 (m) cc_final: 0.8589 (p)
REVERT: A 558 SER cc_start: 0.9554 (t) cc_final: 0.9266 (p)
REVERT: A 570 ASP cc_start: 0.8935 (t0) cc_final: 0.8643 (t0)
REVERT: C 197 ASP cc_start: 0.8807 (m-30) cc_final: 0.8432 (m-30)
REVERT: C 242 GLN cc_start: 0.8920 (tt0) cc_final: 0.8280 (mt0)
outliers start: 2
outliers final: 1
residues processed: 51
average time/residue: 2.2484
time to fit residues: 119.6212
Evaluate side-chains
49 residues out of total 447 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 1
poor density : 48
time to evaluate : 0.659
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue 120 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 49
random chunks:
chunk 23 optimal weight: 1.9990
chunk 4 optimal weight: 2.9990
chunk 37 optimal weight: 0.6980
chunk 42 optimal weight: 1.9990
chunk 45 optimal weight: 0.0970
chunk 41 optimal weight: 0.7980
chunk 44 optimal weight: 0.7980
chunk 26 optimal weight: 0.8980
chunk 19 optimal weight: 2.9990
chunk 34 optimal weight: 0.3980
chunk 13 optimal weight: 1.9990
overall best weight: 0.5578
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
C 288 GLN
Total number of N/Q/H flips: 1
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8150
moved from start: 0.3921
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.038 4156 Z= 0.169
Angle : 0.522 6.013 5633 Z= 0.273
Chirality : 0.037 0.125 629
Planarity : 0.004 0.053 728
Dihedral : 3.964 17.998 554
Min Nonbonded Distance : 1.976
Molprobity Statistics.
All-atom Clashscore : 5.81
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 2.98 %
Favored : 97.02 %
Rotamer:
Outliers : 0.22 %
Allowed : 12.98 %
Favored : 86.80 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 10.00 %
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: 1.63 (0.39), residues: 504
helix: 1.68 (0.31), residues: 300
sheet: -0.06 (0.87), residues: 37
loop : 0.39 (0.51), residues: 167
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.009 0.001 TRP A 477
HIS 0.003 0.000 HIS C 63
PHE 0.021 0.001 PHE A 538
TYR 0.005 0.001 TYR A 495
ARG 0.006 0.000 ARG A 527
*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
1008 Ramachandran restraints generated.
504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
1008 Ramachandran restraints generated.
504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
48 residues out of total 447 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 1
poor density : 47
time to evaluate : 0.706
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: A 512 CYS cc_start: 0.8823 (m) cc_final: 0.8588 (p)
REVERT: A 558 SER cc_start: 0.9555 (t) cc_final: 0.9262 (p)
REVERT: A 570 ASP cc_start: 0.8940 (t0) cc_final: 0.8618 (t0)
REVERT: C 197 ASP cc_start: 0.8809 (m-30) cc_final: 0.8433 (m-30)
REVERT: C 242 GLN cc_start: 0.8925 (tt0) cc_final: 0.8298 (mt0)
outliers start: 1
outliers final: 1
residues processed: 48
average time/residue: 2.2547
time to fit residues: 113.0610
Evaluate side-chains
48 residues out of total 447 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 1
poor density : 47
time to evaluate : 0.705
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue 120 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 49
random chunks:
chunk 39 optimal weight: 0.5980
chunk 41 optimal weight: 0.9990
chunk 43 optimal weight: 0.7980
chunk 28 optimal weight: 0.6980
chunk 46 optimal weight: 0.9980
chunk 22 optimal weight: 1.9990
chunk 32 optimal weight: 0.8980
chunk 48 optimal weight: 5.9990
chunk 44 optimal weight: 0.5980
chunk 38 optimal weight: 0.9980
chunk 4 optimal weight: 0.5980
overall best weight: 0.6580
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8156
moved from start: 0.4006
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.039 4156 Z= 0.182
Angle : 0.530 6.249 5633 Z= 0.276
Chirality : 0.038 0.124 629
Planarity : 0.004 0.055 728
Dihedral : 3.914 17.903 554
Min Nonbonded Distance : 1.973
Molprobity Statistics.
All-atom Clashscore : 5.56
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 2.58 %
Favored : 97.42 %
Rotamer:
Outliers : 0.22 %
Allowed : 12.98 %
Favored : 86.80 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 10.00 %
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: 1.67 (0.39), residues: 504
helix: 1.71 (0.31), residues: 300
sheet: -0.08 (0.87), residues: 37
loop : 0.45 (0.51), residues: 167
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.010 0.001 TRP A 477
HIS 0.003 0.001 HIS C 63
PHE 0.021 0.001 PHE A 538
TYR 0.007 0.001 TYR C 265
ARG 0.007 0.000 ARG A 527
*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
1008 Ramachandran restraints generated.
504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
1008 Ramachandran restraints generated.
504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
47 residues out of total 447 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 1
poor density : 46
time to evaluate : 0.662
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: A 512 CYS cc_start: 0.8820 (m) cc_final: 0.8610 (p)
REVERT: A 558 SER cc_start: 0.9554 (t) cc_final: 0.9263 (p)
REVERT: A 570 ASP cc_start: 0.8946 (t0) cc_final: 0.8515 (t0)
REVERT: C 197 ASP cc_start: 0.8808 (m-30) cc_final: 0.8447 (m-30)
REVERT: C 242 GLN cc_start: 0.8920 (tt0) cc_final: 0.8331 (mt0)
outliers start: 1
outliers final: 1
residues processed: 47
average time/residue: 2.3000
time to fit residues: 112.6899
Evaluate side-chains
45 residues out of total 447 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 1
poor density : 44
time to evaluate : 0.640
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue 120 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 49
random chunks:
chunk 30 optimal weight: 1.9990
chunk 23 optimal weight: 2.9990
chunk 41 optimal weight: 2.9990
chunk 11 optimal weight: 1.9990
chunk 35 optimal weight: 0.9990
chunk 5 optimal weight: 1.9990
chunk 10 optimal weight: 0.9990
chunk 38 optimal weight: 1.9990
chunk 16 optimal weight: 1.9990
chunk 39 optimal weight: 0.0770
chunk 4 optimal weight: 0.9980
overall best weight: 1.0144
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8177
moved from start: 0.4022
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.004 0.033 4156 Z= 0.232
Angle : 0.534 6.407 5633 Z= 0.280
Chirality : 0.038 0.127 629
Planarity : 0.004 0.056 728
Dihedral : 3.981 17.921 554
Min Nonbonded Distance : 1.951
Molprobity Statistics.
All-atom Clashscore : 5.93
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 3.17 %
Favored : 96.83 %
Rotamer:
Outliers : 0.22 %
Allowed : 12.98 %
Favored : 86.80 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 10.00 %
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: 1.60 (0.39), residues: 504
helix: 1.67 (0.31), residues: 300
sheet: -0.07 (0.88), residues: 37
loop : 0.37 (0.51), residues: 167
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.009 0.001 TRP A 477
HIS 0.003 0.001 HIS C 63
PHE 0.021 0.001 PHE A 538
TYR 0.006 0.001 TYR C 265
ARG 0.006 0.000 ARG A 527
********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
1008 Ramachandran restraints generated.
504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
1008 Ramachandran restraints generated.
504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
46 residues out of total 447 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 1
poor density : 45
time to evaluate : 0.638
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: A 558 SER cc_start: 0.9553 (t) cc_final: 0.9265 (p)
REVERT: A 570 ASP cc_start: 0.8953 (t0) cc_final: 0.8537 (t0)
REVERT: C 197 ASP cc_start: 0.8818 (m-30) cc_final: 0.8446 (m-30)
REVERT: C 242 GLN cc_start: 0.8927 (tt0) cc_final: 0.8333 (mt0)
outliers start: 1
outliers final: 1
residues processed: 46
average time/residue: 2.2361
time to fit residues: 107.3172
Evaluate side-chains
43 residues out of total 447 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 1
poor density : 42
time to evaluate : 0.659
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue 120 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 49
random chunks:
chunk 7 optimal weight: 1.9990
chunk 34 optimal weight: 1.9990
chunk 2 optimal weight: 1.9990
chunk 28 optimal weight: 0.5980
chunk 44 optimal weight: 0.9990
chunk 26 optimal weight: 0.8980
chunk 33 optimal weight: 0.8980
chunk 1 optimal weight: 0.8980
chunk 31 optimal weight: 1.9990
chunk 29 optimal weight: 0.5980
chunk 19 optimal weight: 0.8980
overall best weight: 0.7780
-------------------------------------------------------------------------------
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 = 0.3451 r_free = 0.3451 target = 0.074840 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2955 r_free = 0.2955 target = 0.053523 restraints weight = 30905.712|
|-----------------------------------------------------------------------------|
r_work (start): 0.2914 rms_B_bonded: 3.38
r_work: 0.2754 rms_B_bonded: 3.68 restraints_weight: 0.5000
r_work (final): 0.2754
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8339
moved from start: 0.4096
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.034 4156 Z= 0.195
Angle : 0.520 5.556 5633 Z= 0.274
Chirality : 0.038 0.124 629
Planarity : 0.004 0.055 728
Dihedral : 3.969 17.869 554
Min Nonbonded Distance : 1.974
Molprobity Statistics.
All-atom Clashscore : 5.44
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 2.98 %
Favored : 97.02 %
Rotamer:
Outliers : 0.22 %
Allowed : 13.65 %
Favored : 86.13 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 10.00 %
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: 1.68 (0.39), residues: 504
helix: 1.73 (0.31), residues: 300
sheet: -0.07 (0.88), residues: 37
loop : 0.44 (0.52), residues: 167
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.009 0.001 TRP A 477
HIS 0.003 0.001 HIS C 63
PHE 0.021 0.001 PHE A 538
TYR 0.005 0.001 TYR A 495
ARG 0.007 0.000 ARG A 527
Origin is already at (0, 0, 0), no shifts will be applied
===============================================================================
Job complete
usr+sys time: 4094.89 seconds
wall clock time: 71 minutes 17.97 seconds (4277.97 seconds total)