Starting phenix.real_space_refine
on Sun Dec 29 08:42:03 2024 by dcliebschner
===============================================================================
Processing files:
-------------------------------------------------------------------------------
Found model, /net/cci-nas-00/data/ceres_data/9c4o_45192/12_2024/9c4o_45192_trim.cif
Found real_map, /net/cci-nas-00/data/ceres_data/9c4o_45192/12_2024/9c4o_45192.map
Processing PHIL parameters:
-------------------------------------------------------------------------------
Adding command-line PHIL:
-------------------------
refinement.macro_cycles=10
scattering_table=electron
resolution=1.99
write_initial_geo_file=False
Final processed PHIL parameters:
-------------------------------------------------------------------------------
data_manager {
real_map_files = "/net/cci-nas-00/data/ceres_data/9c4o_45192/12_2024/9c4o_45192.map"
default_real_map = "/net/cci-nas-00/data/ceres_data/9c4o_45192/12_2024/9c4o_45192.map"
model {
file = "/net/cci-nas-00/data/ceres_data/9c4o_45192/12_2024/9c4o_45192_trim.cif"
}
default_model = "/net/cci-nas-00/data/ceres_data/9c4o_45192/12_2024/9c4o_45192_trim.cif"
}
resolution = 1.99
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= 0.064
Set stop_for_unknowns flag
Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
Set to: electron
Number of scattering types: 6
Type Number sf(0) Gaussians
Ca 1 9.91 5
S 19 5.16 5
C 3205 2.51 5
N 915 2.21 5
O 1143 1.98 5
H 4883 0.53 5
sf(0) = scattering factor at diffraction angle 0.
Process input model
Symmetric amino acids flipped. Time to flip 16 residue(s): 0.02s
Monomer Library directory:
"/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib"
Total number of atoms: 10166
Number of models: 1
Model: ""
Number of chains: 2
Chain: "A"
Number of atoms: 10030
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 661, 10030
Classifications: {'peptide': 661}
Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 633}
Unresolved non-hydrogen bonds: 1
Unresolved non-hydrogen angles: 1
Unresolved non-hydrogen dihedrals: 1
Chain: "A"
Number of atoms: 136
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 113, 136
Unusual residues: {' CA': 1, 'PQQ': 1}
Classifications: {'undetermined': 2, 'water': 111}
Link IDs: {None: 112}
Time building chain proxies: 6.01, per 1000 atoms: 0.59
Number of scatterers: 10166
At special positions: 0
Unit cell: (86.92, 62.32, 72.98, 90, 90, 90)
Space group: P 1 (No. 1)
Number of sites at special positions: 0
Number of scattering types: 6
Type Number sf(0)
Ca 1 19.99
S 19 16.00
O 1143 8.00
N 915 7.00
C 3205 6.00
H 4883 1.00
sf(0) = scattering factor at diffraction angle 0.
Number of disulfides: simple=1, symmetry=0
Simple disulfide: pdb=" SG CYS A 580 " - pdb=" SG CYS A 585 " 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: 3.11
Conformation dependent library (CDL) restraints added in 836.3 milliseconds
1318 Ramachandran restraints generated.
659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2.
Adding C-beta torsion restraints...
Number of C-beta restraints generated: 1178
Finding SS restraints...
Secondary structure from input PDB file:
7 helices and 6 sheets defined
6.5% alpha, 53.3% beta
0 base pairs and 0 stacking pairs defined.
Time for finding SS restraints: 0.82
Creating SS restraints...
Processing helix chain 'A' and resid 52 through 56
Processing helix chain 'A' and resid 64 through 69
removed outlier: 3.987A pdb=" N THR A 69 " --> pdb=" O SER A 65 " (cutoff:3.500A)
Processing helix chain 'A' and resid 126 through 128
No H-bonds generated for 'chain 'A' and resid 126 through 128'
Processing helix chain 'A' and resid 253 through 260
Processing helix chain 'A' and resid 264 through 271
Processing helix chain 'A' and resid 313 through 318
removed outlier: 3.861A pdb=" N GLN A 317 " --> pdb=" O PRO A 313 " (cutoff:3.500A)
Processing helix chain 'A' and resid 475 through 481
removed outlier: 4.264A pdb=" N TYR A 481 " --> pdb=" O ASN A 477 " (cutoff:3.500A)
Processing sheet with id=AA1, first strand: chain 'A' and resid 46 through 51
removed outlier: 4.284A pdb=" N ALA A 46 " --> pdb=" O ARG A 137 " (cutoff:3.500A)
removed outlier: 3.598A pdb=" N ASN A 132 " --> pdb=" O THR A 155 " (cutoff:3.500A)
removed outlier: 6.317A pdb=" N ARG A 105 " --> pdb=" O MET A 152 " (cutoff:3.500A)
removed outlier: 7.551A pdb=" N VAL A 154 " --> pdb=" O ARG A 105 " (cutoff:3.500A)
removed outlier: 6.445A pdb=" N TYR A 107 " --> pdb=" O VAL A 154 " (cutoff:3.500A)
removed outlier: 7.761A pdb=" N THR A 156 " --> pdb=" O TYR A 107 " (cutoff:3.500A)
Processing sheet with id=AA2, first strand: chain 'A' and resid 74 through 77
Processing sheet with id=AA3, first strand: chain 'A' and resid 164 through 172
removed outlier: 4.451A pdb=" N TRP A 405 " --> pdb=" O PRO A 349 " (cutoff:3.500A)
removed outlier: 6.503A pdb=" N THR A 351 " --> pdb=" O THR A 403 " (cutoff:3.500A)
removed outlier: 4.332A pdb=" N THR A 403 " --> pdb=" O THR A 351 " (cutoff:3.500A)
removed outlier: 6.571A pdb=" N THR A 353 " --> pdb=" O LEU A 401 " (cutoff:3.500A)
removed outlier: 4.302A pdb=" N LEU A 401 " --> pdb=" O THR A 353 " (cutoff:3.500A)
removed outlier: 6.674A pdb=" N GLY A 355 " --> pdb=" O PRO A 399 " (cutoff:3.500A)
removed outlier: 6.556A pdb=" N ASN A 357 " --> pdb=" O ILE A 397 " (cutoff:3.500A)
removed outlier: 4.174A pdb=" N ILE A 397 " --> pdb=" O ASN A 357 " (cutoff:3.500A)
removed outlier: 6.588A pdb=" N GLU A 359 " --> pdb=" O TRP A 395 " (cutoff:3.500A)
removed outlier: 4.282A pdb=" N TRP A 395 " --> pdb=" O GLU A 359 " (cutoff:3.500A)
removed outlier: 6.658A pdb=" N MET A 361 " --> pdb=" O LEU A 393 " (cutoff:3.500A)
removed outlier: 4.300A pdb=" N LEU A 393 " --> pdb=" O MET A 361 " (cutoff:3.500A)
removed outlier: 6.166A pdb=" N GLU A 363 " --> pdb=" O ARG A 391 " (cutoff:3.500A)
removed outlier: 4.067A pdb=" N ARG A 391 " --> pdb=" O GLU A 363 " (cutoff:3.500A)
removed outlier: 6.849A pdb=" N ARG A 365 " --> pdb=" O ASP A 389 " (cutoff:3.500A)
removed outlier: 3.948A pdb=" N ASP A 389 " --> pdb=" O ARG A 365 " (cutoff:3.500A)
removed outlier: 5.873A pdb=" N GLY A 367 " --> pdb=" O ARG A 387 " (cutoff:3.500A)
removed outlier: 9.712A pdb=" N TRP A 447 " --> pdb=" O PHE A 471 " (cutoff:3.500A)
removed outlier: 7.186A pdb=" N PHE A 471 " --> pdb=" O TRP A 447 " (cutoff:3.500A)
removed outlier: 7.464A pdb=" N LEU A 513 " --> pdb=" O GLN A 556 " (cutoff:3.500A)
removed outlier: 5.355A pdb=" N GLN A 556 " --> pdb=" O LEU A 513 " (cutoff:3.500A)
removed outlier: 7.450A pdb=" N SER A 515 " --> pdb=" O TRP A 554 " (cutoff:3.500A)
removed outlier: 5.373A pdb=" N TRP A 554 " --> pdb=" O SER A 515 " (cutoff:3.500A)
removed outlier: 7.180A pdb=" N ALA A 517 " --> pdb=" O LEU A 552 " (cutoff:3.500A)
removed outlier: 5.245A pdb=" N LEU A 552 " --> pdb=" O ALA A 517 " (cutoff:3.500A)
removed outlier: 7.142A pdb=" N PHE A 519 " --> pdb=" O ALA A 550 " (cutoff:3.500A)
removed outlier: 5.449A pdb=" N ALA A 550 " --> pdb=" O PHE A 519 " (cutoff:3.500A)
removed outlier: 7.324A pdb=" N THR A 521 " --> pdb=" O GLN A 548 " (cutoff:3.500A)
removed outlier: 5.456A pdb=" N GLN A 548 " --> pdb=" O THR A 521 " (cutoff:3.500A)
removed outlier: 7.026A pdb=" N THR A 523 " --> pdb=" O ARG A 546 " (cutoff:3.500A)
removed outlier: 5.439A pdb=" N ARG A 546 " --> pdb=" O THR A 523 " (cutoff:3.500A)
removed outlier: 6.773A pdb=" N ASP A 525 " --> pdb=" O LYS A 544 " (cutoff:3.500A)
removed outlier: 7.340A pdb=" N LYS A 544 " --> pdb=" O ASP A 525 " (cutoff:3.500A)
removed outlier: 5.594A pdb=" N ILE A 527 " --> pdb=" O ALA A 542 " (cutoff:3.500A)
removed outlier: 6.246A pdb=" N ALA A 542 " --> pdb=" O ILE A 527 " (cutoff:3.500A)
removed outlier: 5.287A pdb=" N VAL A 529 " --> pdb=" O LYS A 540 " (cutoff:3.500A)
removed outlier: 5.438A pdb=" N LYS A 540 " --> pdb=" O VAL A 529 " (cutoff:3.500A)
removed outlier: 3.528A pdb=" N PHE A 562 " --> pdb=" O PHE A 558 " (cutoff:3.500A)
Processing sheet with id=AA4, first strand: chain 'A' and resid 371 through 373
Processing sheet with id=AA5, first strand: chain 'A' and resid 622 through 623
Processing sheet with id=AA6, first strand: chain 'A' and resid 668 through 671
removed outlier: 3.561A pdb=" N SER A 670 " --> pdb=" O GLU A 682 " (cutoff:3.500A)
280 hydrogen bonds defined for protein.
795 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: 4.24
Time building geometry restraints manager: 3.49 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: 4883
1.03 - 1.23: 15
1.23 - 1.42: 2322
1.42 - 1.62: 2914
1.62 - 1.81: 36
Bond restraints: 10170
Sorted by residual:
bond pdb=" C PRO A 683 "
pdb=" N SER A 684 "
ideal model delta sigma weight residual
1.327 1.308 0.018 1.71e-02 3.42e+03 1.16e+00
bond pdb=" CA LYS A 277 "
pdb=" C LYS A 277 "
ideal model delta sigma weight residual
1.526 1.515 0.011 1.08e-02 8.57e+03 1.03e+00
bond pdb=" C ALA A 450 "
pdb=" N GLY A 451 "
ideal model delta sigma weight residual
1.330 1.317 0.013 1.32e-02 5.74e+03 9.14e-01
bond pdb=" C GLU A 363 "
pdb=" N ASN A 364 "
ideal model delta sigma weight residual
1.331 1.318 0.013 1.40e-02 5.10e+03 8.48e-01
bond pdb=" C ARG A 589 "
pdb=" N MET A 590 "
ideal model delta sigma weight residual
1.326 1.309 0.017 1.84e-02 2.95e+03 8.42e-01
... (remaining 10165 not shown)
Histogram of bond angle deviations from ideal:
0.00 - 1.29: 17527
1.29 - 2.58: 613
2.58 - 3.88: 50
3.88 - 5.17: 12
5.17 - 6.46: 2
Bond angle restraints: 18204
Sorted by residual:
angle pdb=" N GLY A 492 "
pdb=" CA GLY A 492 "
pdb=" C GLY A 492 "
ideal model delta sigma weight residual
114.67 111.15 3.52 1.10e+00 8.26e-01 1.02e+01
angle pdb=" N ASP A 530 "
pdb=" CA ASP A 530 "
pdb=" C ASP A 530 "
ideal model delta sigma weight residual
111.24 108.22 3.02 1.29e+00 6.01e-01 5.48e+00
angle pdb=" N SER A 375 "
pdb=" CA SER A 375 "
pdb=" C SER A 375 "
ideal model delta sigma weight residual
112.12 108.99 3.13 1.34e+00 5.57e-01 5.46e+00
angle pdb=" N PRO A 685 "
pdb=" CA PRO A 685 "
pdb=" C PRO A 685 "
ideal model delta sigma weight residual
112.47 116.85 -4.38 2.06e+00 2.36e-01 4.52e+00
angle pdb=" CA VAL A 348 "
pdb=" C VAL A 348 "
pdb=" N PRO A 349 "
ideal model delta sigma weight residual
117.33 119.30 -1.97 1.01e+00 9.80e-01 3.82e+00
... (remaining 18199 not shown)
Histogram of dihedral angle deviations from ideal:
0.00 - 17.76: 4301
17.76 - 35.52: 360
35.52 - 53.28: 114
53.28 - 71.04: 37
71.04 - 88.80: 16
Dihedral angle restraints: 4828
sinusoidal: 2618
harmonic: 2210
Sorted by residual:
dihedral pdb=" CA TYR A 680 "
pdb=" C TYR A 680 "
pdb=" N TYR A 681 "
pdb=" CA TYR A 681 "
ideal model delta harmonic sigma weight residual
-180.00 -154.89 -25.11 0 5.00e+00 4.00e-02 2.52e+01
dihedral pdb=" CA PRO A 685 "
pdb=" C PRO A 685 "
pdb=" N GLY A 686 "
pdb=" CA GLY A 686 "
ideal model delta harmonic sigma weight residual
-180.00 -155.22 -24.78 0 5.00e+00 4.00e-02 2.46e+01
dihedral pdb=" CA ASP A 398 "
pdb=" C ASP A 398 "
pdb=" N PRO A 399 "
pdb=" CA PRO A 399 "
ideal model delta harmonic sigma weight residual
180.00 155.87 24.13 0 5.00e+00 4.00e-02 2.33e+01
... (remaining 4825 not shown)
Histogram of chiral volume deviations from ideal:
0.000 - 0.034: 454
0.034 - 0.068: 216
0.068 - 0.102: 45
0.102 - 0.137: 29
0.137 - 0.171: 1
Chirality restraints: 745
Sorted by residual:
chirality pdb=" CA PRO A 685 "
pdb=" N PRO A 685 "
pdb=" C PRO A 685 "
pdb=" CB PRO A 685 "
both_signs ideal model delta sigma weight residual
False 2.72 2.55 0.17 2.00e-01 2.50e+01 7.29e-01
chirality pdb=" CA ILE A 501 "
pdb=" N ILE A 501 "
pdb=" C ILE A 501 "
pdb=" CB ILE A 501 "
both_signs ideal model delta sigma weight residual
False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.63e-01
chirality pdb=" CA ILE A 104 "
pdb=" N ILE A 104 "
pdb=" C ILE A 104 "
pdb=" CB ILE A 104 "
both_signs ideal model delta sigma weight residual
False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.43e-01
... (remaining 742 not shown)
Planarity restraints: 1591
Sorted by residual:
delta sigma weight rms_deltas residual
plane pdb=" C SER A 684 " 0.031 5.00e-02 4.00e+02 4.74e-02 3.59e+00
pdb=" N PRO A 685 " -0.082 5.00e-02 4.00e+02
pdb=" CA PRO A 685 " 0.024 5.00e-02 4.00e+02
pdb=" CD PRO A 685 " 0.026 5.00e-02 4.00e+02
delta sigma weight rms_deltas residual
plane pdb=" CD ARG A 91 " 0.114 9.50e-02 1.11e+02 3.82e-02 1.62e+00
pdb=" NE ARG A 91 " -0.007 2.00e-02 2.50e+03
pdb=" CZ ARG A 91 " -0.002 2.00e-02 2.50e+03
pdb=" NH1 ARG A 91 " 0.000 2.00e-02 2.50e+03
pdb=" NH2 ARG A 91 " 0.004 2.00e-02 2.50e+03
pdb="HH11 ARG A 91 " -0.001 2.00e-02 2.50e+03
pdb="HH12 ARG A 91 " -0.000 2.00e-02 2.50e+03
pdb="HH21 ARG A 91 " -0.000 2.00e-02 2.50e+03
pdb="HH22 ARG A 91 " 0.000 2.00e-02 2.50e+03
delta sigma weight rms_deltas residual
plane pdb=" C GLN A 192 " -0.021 5.00e-02 4.00e+02 3.12e-02 1.56e+00
pdb=" N PRO A 193 " 0.054 5.00e-02 4.00e+02
pdb=" CA PRO A 193 " -0.016 5.00e-02 4.00e+02
pdb=" CD PRO A 193 " -0.017 5.00e-02 4.00e+02
... (remaining 1588 not shown)
Histogram of nonbonded interaction distances:
1.58 - 2.18: 714
2.18 - 2.79: 21047
2.79 - 3.39: 30425
3.39 - 4.00: 43620
4.00 - 4.60: 63096
Nonbonded interactions: 158902
Sorted by model distance:
nonbonded pdb=" O LEU A 479 "
pdb=" H ASN A 490 "
model vdw
1.575 2.450
nonbonded pdb=" HH TYR A 481 "
pdb=" O2B PQQ A 802 "
model vdw
1.583 2.450
nonbonded pdb=" HH TYR A 464 "
pdb=" OE2 GLU A 502 "
model vdw
1.607 2.450
nonbonded pdb=" O VAL A 638 "
pdb=" H LEU A 662 "
model vdw
1.616 2.450
nonbonded pdb="HD21 ASN A 357 "
pdb=" OE2 GLU A 359 "
model vdw
1.627 2.450
... (remaining 158897 not shown)
NOTE: a complete listing of the restraints can be obtained by requesting
output of .geo file.
Find NCS groups from input model
========== WARNING! ============
No NCS relation were found !!!
================================
Found NCS groups:
found none.
Set up NCS constraints
No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
Set random seed: 0.000
Set model cs if undefined: 0.000
Decide on map wrapping: 0.000
Normalize map: mean=0, sd=1: 2.040
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: 0.220
Extract box with map and model: 0.380
Check model and map are aligned: 0.070
Set scattering table: 0.110
Process input model: 27.030
Find NCS groups from input model: 0.250
Set up NCS constraints: 0.030
Set refine NCS operators: 0.000
Adjust number of macro_cycles: 0.000
Reset NCS operators: 0.000
Extract rigid body selections: 0.000
Check and reset occupancies: 0.000
Load rotamer database and sin/cos tables:13.630
Set ADP refinement strategy: 0.000
Make a string to write initial .geo file:0.000
Internal consistency checks: 0.000
Total: 43.760
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8132
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 : 0.004 0.037 5287 Z= 0.277
Angle : 0.647 6.461 7177 Z= 0.367
Chirality : 0.044 0.171 745
Planarity : 0.005 0.051 958
Dihedral : 16.532 88.799 1925
Min Nonbonded Distance : 2.208
Molprobity Statistics.
All-atom Clashscore : 5.77
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 1.67 %
Favored : 98.33 %
Rotamer:
Outliers : 0.18 %
Allowed : 14.76 %
Favored : 85.06 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 3.70 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: -0.01 (0.32), residues: 659
helix: -1.84 (0.64), residues: 47
sheet: 0.18 (0.25), residues: 349
loop : 0.34 (0.40), residues: 263
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.009 0.001 TRP A 568
HIS 0.002 0.001 HIS A 445
PHE 0.016 0.002 PHE A 352
TYR 0.017 0.002 TYR A 681
ARG 0.004 0.001 ARG A 287
*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
1318 Ramachandran restraints generated.
659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
1318 Ramachandran restraints generated.
659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER 515 is missing expected H atoms. Skipping.
Evaluate side-chains
87 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 1
poor density : 86
time to evaluate : 0.921
Fit side-chains
revert: symmetry clash
revert: symmetry clash
REVERT: A 115 MET cc_start: 0.8545 (mmp) cc_final: 0.8331 (mmp)
outliers start: 1
outliers final: 1
residues processed: 87
average time/residue: 2.7528
time to fit residues: 249.8308
Evaluate side-chains
84 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 1
poor density : 83
time to evaluate : 0.660
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 363 GLU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 66
random chunks:
chunk 55 optimal weight: 0.6980
chunk 50 optimal weight: 1.9990
chunk 27 optimal weight: 0.5980
chunk 17 optimal weight: 2.9990
chunk 33 optimal weight: 0.8980
chunk 26 optimal weight: 0.9980
chunk 51 optimal weight: 3.9990
chunk 20 optimal weight: 0.6980
chunk 31 optimal weight: 0.9980
chunk 38 optimal weight: 2.9990
chunk 59 optimal weight: 1.9990
overall best weight: 0.7780
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 650 ASN
Total number of N/Q/H flips: 1
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8096
moved from start: 0.0623
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.004 0.035 5287 Z= 0.238
Angle : 0.580 6.422 7177 Z= 0.317
Chirality : 0.044 0.169 745
Planarity : 0.005 0.042 958
Dihedral : 6.778 74.239 746
Min Nonbonded Distance : 2.169
Molprobity Statistics.
All-atom Clashscore : 4.67
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 2.43 %
Favored : 97.57 %
Rotamer:
Outliers : 1.11 %
Allowed : 13.84 %
Favored : 85.06 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 3.70 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: -0.06 (0.32), residues: 659
helix: -1.82 (0.65), residues: 47
sheet: -0.01 (0.25), residues: 351
loop : 0.56 (0.42), residues: 261
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.009 0.001 TRP A 568
HIS 0.001 0.001 HIS A 649
PHE 0.017 0.002 PHE A 352
TYR 0.017 0.001 TYR A 681
ARG 0.005 0.000 ARG A 387
*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
1318 Ramachandran restraints generated.
659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
1318 Ramachandran restraints generated.
659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER 515 is missing expected H atoms. Skipping.
Evaluate side-chains
93 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 6
poor density : 87
time to evaluate : 0.741
Fit side-chains
revert: symmetry clash
revert: symmetry clash
REVERT: A 115 MET cc_start: 0.8598 (mmp) cc_final: 0.8172 (mmp)
REVERT: A 377 MET cc_start: 0.7191 (OUTLIER) cc_final: 0.6517 (mpt)
REVERT: A 379 GLU cc_start: 0.7178 (OUTLIER) cc_final: 0.6830 (tm-30)
REVERT: A 576 ARG cc_start: 0.7732 (mmp-170) cc_final: 0.7396 (mmp-170)
REVERT: A 595 ARG cc_start: 0.7741 (mtm180) cc_final: 0.7411 (ttp-170)
outliers start: 6
outliers final: 2
residues processed: 91
average time/residue: 2.5964
time to fit residues: 246.8611
Evaluate side-chains
86 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 4
poor density : 82
time to evaluate : 0.896
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 363 GLU
Chi-restraints excluded: chain A residue 377 MET
Chi-restraints excluded: chain A residue 379 GLU
Chi-restraints excluded: chain A residue 404 GLN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 66
random chunks:
chunk 33 optimal weight: 0.5980
chunk 18 optimal weight: 3.9990
chunk 49 optimal weight: 2.9990
chunk 40 optimal weight: 3.9990
chunk 16 optimal weight: 1.9990
chunk 60 optimal weight: 1.9990
chunk 64 optimal weight: 0.9980
chunk 53 optimal weight: 2.9990
chunk 59 optimal weight: 2.9990
chunk 20 optimal weight: 0.9980
chunk 48 optimal weight: 2.9990
overall best weight: 1.3184
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 146 ASN
** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 650 ASN
Total number of N/Q/H flips: 2
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8138
moved from start: 0.0726
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.005 0.057 5287 Z= 0.321
Angle : 0.626 6.321 7177 Z= 0.344
Chirality : 0.044 0.189 745
Planarity : 0.005 0.042 958
Dihedral : 7.056 75.124 746
Min Nonbonded Distance : 2.159
Molprobity Statistics.
All-atom Clashscore : 5.17
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 2.12 %
Favored : 97.88 %
Rotamer:
Outliers : 1.48 %
Allowed : 13.65 %
Favored : 84.87 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 3.70 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 0.02 (0.32), residues: 659
helix: -1.84 (0.63), residues: 47
sheet: 0.14 (0.26), residues: 345
loop : 0.46 (0.41), residues: 267
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.011 0.001 TRP A 568
HIS 0.002 0.001 HIS A 342
PHE 0.018 0.003 PHE A 352
TYR 0.018 0.002 TYR A 681
ARG 0.003 0.001 ARG A 658
*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
1318 Ramachandran restraints generated.
659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
1318 Ramachandran restraints generated.
659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER 515 is missing expected H atoms. Skipping.
Evaluate side-chains
93 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 8
poor density : 85
time to evaluate : 0.824
Fit side-chains
revert: symmetry clash
revert: symmetry clash
REVERT: A 115 MET cc_start: 0.8665 (mmp) cc_final: 0.8237 (mmp)
REVERT: A 377 MET cc_start: 0.7164 (OUTLIER) cc_final: 0.6496 (mpt)
REVERT: A 595 ARG cc_start: 0.7750 (mtm180) cc_final: 0.7429 (ttp-170)
outliers start: 8
outliers final: 3
residues processed: 88
average time/residue: 2.7857
time to fit residues: 255.6830
Evaluate side-chains
87 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 4
poor density : 83
time to evaluate : 0.732
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 363 GLU
Chi-restraints excluded: chain A residue 377 MET
Chi-restraints excluded: chain A residue 379 GLU
Chi-restraints excluded: chain A residue 404 GLN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 66
random chunks:
chunk 59 optimal weight: 2.9990
chunk 45 optimal weight: 2.9990
chunk 31 optimal weight: 0.6980
chunk 6 optimal weight: 2.9990
chunk 28 optimal weight: 1.9990
chunk 40 optimal weight: 1.9990
chunk 60 optimal weight: 0.7980
chunk 63 optimal weight: 1.9990
chunk 57 optimal weight: 0.8980
chunk 17 optimal weight: 2.9990
chunk 53 optimal weight: 2.9990
overall best weight: 1.2784
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 647 ASN
A 650 ASN
Total number of N/Q/H flips: 2
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8135
moved from start: 0.0803
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.005 0.053 5287 Z= 0.307
Angle : 0.617 6.942 7177 Z= 0.338
Chirality : 0.044 0.183 745
Planarity : 0.005 0.041 958
Dihedral : 7.069 75.550 746
Min Nonbonded Distance : 2.155
Molprobity Statistics.
All-atom Clashscore : 4.67
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 2.43 %
Favored : 97.57 %
Rotamer:
Outliers : 1.11 %
Allowed : 13.65 %
Favored : 85.24 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 3.70 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 0.03 (0.32), residues: 659
helix: -1.81 (0.62), residues: 47
sheet: 0.16 (0.26), residues: 345
loop : 0.43 (0.41), residues: 267
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.011 0.001 TRP A 568
HIS 0.002 0.001 HIS A 342
PHE 0.017 0.003 PHE A 352
TYR 0.018 0.002 TYR A 681
ARG 0.003 0.000 ARG A 287
*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
1318 Ramachandran restraints generated.
659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
1318 Ramachandran restraints generated.
659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER 515 is missing expected H atoms. Skipping.
Evaluate side-chains
88 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 6
poor density : 82
time to evaluate : 0.821
Fit side-chains
revert: symmetry clash
revert: symmetry clash
REVERT: A 115 MET cc_start: 0.8670 (mmp) cc_final: 0.8262 (mmp)
REVERT: A 377 MET cc_start: 0.7103 (OUTLIER) cc_final: 0.6440 (mpt)
REVERT: A 595 ARG cc_start: 0.7730 (mtm180) cc_final: 0.7412 (ttp-170)
outliers start: 6
outliers final: 3
residues processed: 85
average time/residue: 2.7945
time to fit residues: 247.9380
Evaluate side-chains
85 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 4
poor density : 81
time to evaluate : 1.103
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 363 GLU
Chi-restraints excluded: chain A residue 377 MET
Chi-restraints excluded: chain A residue 379 GLU
Chi-restraints excluded: chain A residue 404 GLN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 66
random chunks:
chunk 36 optimal weight: 1.9990
chunk 0 optimal weight: 5.9990
chunk 47 optimal weight: 0.5980
chunk 26 optimal weight: 1.9990
chunk 54 optimal weight: 3.9990
chunk 44 optimal weight: 1.9990
chunk 32 optimal weight: 1.9990
chunk 57 optimal weight: 3.9990
chunk 16 optimal weight: 2.9990
chunk 21 optimal weight: 0.5980
chunk 12 optimal weight: 0.8980
overall best weight: 1.2184
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 650 ASN
Total number of N/Q/H flips: 1
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8131
moved from start: 0.0868
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.005 0.044 5287 Z= 0.301
Angle : 0.613 7.071 7177 Z= 0.336
Chirality : 0.044 0.182 745
Planarity : 0.005 0.040 958
Dihedral : 7.069 74.843 746
Min Nonbonded Distance : 2.151
Molprobity Statistics.
All-atom Clashscore : 4.67
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 1.82 %
Favored : 98.18 %
Rotamer:
Outliers : 0.92 %
Allowed : 13.84 %
Favored : 85.24 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 3.70 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 0.02 (0.32), residues: 659
helix: -1.77 (0.63), residues: 47
sheet: 0.15 (0.26), residues: 345
loop : 0.43 (0.41), residues: 267
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.011 0.001 TRP A 568
HIS 0.002 0.001 HIS A 342
PHE 0.018 0.002 PHE A 352
TYR 0.017 0.002 TYR A 681
ARG 0.003 0.000 ARG A 287
*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
1318 Ramachandran restraints generated.
659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
1318 Ramachandran restraints generated.
659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER 515 is missing expected H atoms. Skipping.
Evaluate side-chains
86 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 5
poor density : 81
time to evaluate : 0.740
Fit side-chains
revert: symmetry clash
REVERT: A 115 MET cc_start: 0.8663 (mmp) cc_final: 0.8306 (mmp)
REVERT: A 377 MET cc_start: 0.7104 (OUTLIER) cc_final: 0.6314 (mpt)
REVERT: A 595 ARG cc_start: 0.7709 (mtm180) cc_final: 0.7392 (ttp-170)
REVERT: A 645 LYS cc_start: 0.8558 (mtmm) cc_final: 0.7967 (mtmp)
outliers start: 5
outliers final: 3
residues processed: 83
average time/residue: 2.7503
time to fit residues: 237.8253
Evaluate side-chains
83 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 4
poor density : 79
time to evaluate : 0.834
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 363 GLU
Chi-restraints excluded: chain A residue 377 MET
Chi-restraints excluded: chain A residue 379 GLU
Chi-restraints excluded: chain A residue 404 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 66
random chunks:
chunk 37 optimal weight: 1.9990
chunk 15 optimal weight: 1.9990
chunk 63 optimal weight: 3.9990
chunk 53 optimal weight: 2.9990
chunk 29 optimal weight: 1.9990
chunk 5 optimal weight: 3.9990
chunk 21 optimal weight: 0.0980
chunk 33 optimal weight: 0.4980
chunk 61 optimal weight: 0.6980
chunk 7 optimal weight: 0.5980
chunk 36 optimal weight: 0.6980
overall best weight: 0.5180
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 146 ASN
A 160 GLN
** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 650 ASN
Total number of N/Q/H flips: 3
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8066
moved from start: 0.1063
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.022 5287 Z= 0.193
Angle : 0.543 6.404 7177 Z= 0.295
Chirality : 0.044 0.153 745
Planarity : 0.004 0.036 958
Dihedral : 6.639 71.221 746
Min Nonbonded Distance : 2.144
Molprobity Statistics.
All-atom Clashscore : 4.28
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 3.03 %
Favored : 96.97 %
Rotamer:
Outliers : 0.92 %
Allowed : 13.47 %
Favored : 85.61 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 3.70 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: -0.02 (0.33), residues: 659
helix: -1.10 (0.73), residues: 41
sheet: -0.10 (0.26), residues: 352
loop : 0.60 (0.41), residues: 266
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.008 0.001 TRP A 568
HIS 0.002 0.000 HIS A 649
PHE 0.014 0.002 PHE A 352
TYR 0.015 0.001 TYR A 681
ARG 0.004 0.000 ARG A 96
*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
1318 Ramachandran restraints generated.
659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
1318 Ramachandran restraints generated.
659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER 515 is missing expected H atoms. Skipping.
Evaluate side-chains
93 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 5
poor density : 88
time to evaluate : 0.830
Fit side-chains
revert: symmetry clash
REVERT: A 115 MET cc_start: 0.8619 (mmp) cc_final: 0.8212 (mmp)
REVERT: A 379 GLU cc_start: 0.7178 (OUTLIER) cc_final: 0.6707 (tm-30)
REVERT: A 595 ARG cc_start: 0.7670 (mtm180) cc_final: 0.7384 (ttp-170)
REVERT: A 645 LYS cc_start: 0.8520 (mtmm) cc_final: 0.7928 (mtmp)
outliers start: 5
outliers final: 2
residues processed: 90
average time/residue: 2.7048
time to fit residues: 255.4319
Evaluate side-chains
82 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 3
poor density : 79
time to evaluate : 1.032
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 363 GLU
Chi-restraints excluded: chain A residue 379 GLU
Chi-restraints excluded: chain A residue 404 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 66
random chunks:
chunk 46 optimal weight: 1.9990
chunk 36 optimal weight: 2.9990
chunk 53 optimal weight: 2.9990
chunk 35 optimal weight: 2.9990
chunk 63 optimal weight: 2.9990
chunk 39 optimal weight: 0.5980
chunk 38 optimal weight: 0.6980
chunk 29 optimal weight: 2.9990
chunk 25 optimal weight: 3.9990
chunk 37 optimal weight: 0.9980
chunk 19 optimal weight: 0.9990
overall best weight: 1.0584
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 160 GLN
A 578 ASN
A 650 ASN
Total number of N/Q/H flips: 3
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8109
moved from start: 0.1031
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.004 0.042 5287 Z= 0.272
Angle : 0.588 6.959 7177 Z= 0.321
Chirality : 0.044 0.178 745
Planarity : 0.005 0.039 958
Dihedral : 6.885 73.356 746
Min Nonbonded Distance : 2.146
Molprobity Statistics.
All-atom Clashscore : 4.67
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 1.97 %
Favored : 98.03 %
Rotamer:
Outliers : 1.11 %
Allowed : 13.47 %
Favored : 85.42 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 3.70 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: -0.00 (0.33), residues: 659
helix: -1.59 (0.65), residues: 47
sheet: 0.05 (0.26), residues: 345
loop : 0.52 (0.41), residues: 267
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.010 0.001 TRP A 568
HIS 0.002 0.001 HIS A 649
PHE 0.017 0.002 PHE A 352
TYR 0.016 0.002 TYR A 681
ARG 0.003 0.000 ARG A 287
*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
1318 Ramachandran restraints generated.
659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
1318 Ramachandran restraints generated.
659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER 515 is missing expected H atoms. Skipping.
Evaluate side-chains
87 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 6
poor density : 81
time to evaluate : 1.012
Fit side-chains
revert: symmetry clash
REVERT: A 115 MET cc_start: 0.8657 (mmp) cc_final: 0.8226 (mmp)
REVERT: A 377 MET cc_start: 0.7068 (OUTLIER) cc_final: 0.6425 (mpt)
REVERT: A 595 ARG cc_start: 0.7672 (mtm180) cc_final: 0.7377 (ttp-170)
REVERT: A 645 LYS cc_start: 0.8555 (mtmm) cc_final: 0.7962 (mtmp)
outliers start: 6
outliers final: 3
residues processed: 83
average time/residue: 2.6993
time to fit residues: 234.0880
Evaluate side-chains
84 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 4
poor density : 80
time to evaluate : 0.894
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 363 GLU
Chi-restraints excluded: chain A residue 377 MET
Chi-restraints excluded: chain A residue 379 GLU
Chi-restraints excluded: chain A residue 404 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 66
random chunks:
chunk 12 optimal weight: 2.9990
chunk 40 optimal weight: 3.9990
chunk 43 optimal weight: 1.9990
chunk 31 optimal weight: 0.9980
chunk 5 optimal weight: 3.9990
chunk 50 optimal weight: 1.9990
chunk 57 optimal weight: 3.9990
chunk 60 optimal weight: 0.9980
chunk 55 optimal weight: 0.9980
chunk 59 optimal weight: 0.8980
chunk 35 optimal weight: 0.9990
overall best weight: 0.9782
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 556 GLN
A 578 ASN
A 650 ASN
Total number of N/Q/H flips: 3
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8104
moved from start: 0.1020
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.004 0.037 5287 Z= 0.258
Angle : 0.583 7.128 7177 Z= 0.317
Chirality : 0.044 0.171 745
Planarity : 0.005 0.039 958
Dihedral : 6.860 72.847 746
Min Nonbonded Distance : 2.145
Molprobity Statistics.
All-atom Clashscore : 4.38
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 2.58 %
Favored : 97.42 %
Rotamer:
Outliers : 0.74 %
Allowed : 13.65 %
Favored : 85.61 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 3.70 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: -0.08 (0.32), residues: 659
helix: -1.65 (0.64), residues: 47
sheet: 0.00 (0.26), residues: 350
loop : 0.46 (0.42), residues: 262
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.009 0.001 TRP A 568
HIS 0.002 0.001 HIS A 649
PHE 0.017 0.002 PHE A 352
TYR 0.016 0.002 TYR A 681
ARG 0.004 0.000 ARG A 287
*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
1318 Ramachandran restraints generated.
659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
1318 Ramachandran restraints generated.
659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER 515 is missing expected H atoms. Skipping.
Evaluate side-chains
85 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 4
poor density : 81
time to evaluate : 0.820
Fit side-chains
revert: symmetry clash
REVERT: A 115 MET cc_start: 0.8656 (mmp) cc_final: 0.8221 (mmp)
REVERT: A 377 MET cc_start: 0.7071 (OUTLIER) cc_final: 0.6423 (mpt)
REVERT: A 595 ARG cc_start: 0.7671 (mtm180) cc_final: 0.7375 (ttp-170)
REVERT: A 645 LYS cc_start: 0.8558 (mtmm) cc_final: 0.7968 (mtmp)
outliers start: 4
outliers final: 3
residues processed: 83
average time/residue: 2.7309
time to fit residues: 236.5829
Evaluate side-chains
82 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 4
poor density : 78
time to evaluate : 0.853
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 363 GLU
Chi-restraints excluded: chain A residue 377 MET
Chi-restraints excluded: chain A residue 379 GLU
Chi-restraints excluded: chain A residue 404 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 66
random chunks:
chunk 25 optimal weight: 2.9990
chunk 46 optimal weight: 3.9990
chunk 18 optimal weight: 3.9990
chunk 53 optimal weight: 2.9990
chunk 56 optimal weight: 0.8980
chunk 59 optimal weight: 1.9990
chunk 38 optimal weight: 0.7980
chunk 62 optimal weight: 0.9990
chunk 29 optimal weight: 1.9990
chunk 43 optimal weight: 0.9980
chunk 65 optimal weight: 2.9990
overall best weight: 1.1384
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 160 GLN
A 578 ASN
A 650 ASN
Total number of N/Q/H flips: 3
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8117
moved from start: 0.1028
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.004 0.048 5287 Z= 0.288
Angle : 0.603 7.282 7177 Z= 0.329
Chirality : 0.044 0.181 745
Planarity : 0.005 0.040 958
Dihedral : 6.972 73.662 746
Min Nonbonded Distance : 2.144
Molprobity Statistics.
All-atom Clashscore : 4.57
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 1.97 %
Favored : 98.03 %
Rotamer:
Outliers : 0.92 %
Allowed : 13.84 %
Favored : 85.24 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 3.70 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: -0.01 (0.32), residues: 659
helix: -1.71 (0.64), residues: 47
sheet: 0.08 (0.26), residues: 345
loop : 0.47 (0.41), residues: 267
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.010 0.001 TRP A 568
HIS 0.002 0.001 HIS A 649
PHE 0.018 0.002 PHE A 352
TYR 0.016 0.002 TYR A 681
ARG 0.004 0.000 ARG A 287
*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
1318 Ramachandran restraints generated.
659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
1318 Ramachandran restraints generated.
659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER 515 is missing expected H atoms. Skipping.
Evaluate side-chains
86 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 5
poor density : 81
time to evaluate : 0.881
Fit side-chains
revert: symmetry clash
REVERT: A 115 MET cc_start: 0.8668 (mmp) cc_final: 0.8225 (mmp)
REVERT: A 377 MET cc_start: 0.7104 (OUTLIER) cc_final: 0.6429 (mpt)
REVERT: A 595 ARG cc_start: 0.7662 (mtm180) cc_final: 0.7362 (ttp-170)
REVERT: A 645 LYS cc_start: 0.8573 (mtmm) cc_final: 0.7981 (mtmp)
outliers start: 5
outliers final: 3
residues processed: 83
average time/residue: 2.8988
time to fit residues: 250.4754
Evaluate side-chains
84 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 4
poor density : 80
time to evaluate : 0.889
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 363 GLU
Chi-restraints excluded: chain A residue 377 MET
Chi-restraints excluded: chain A residue 379 GLU
Chi-restraints excluded: chain A residue 404 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 66
random chunks:
chunk 60 optimal weight: 2.9990
chunk 52 optimal weight: 0.6980
chunk 5 optimal weight: 3.9990
chunk 40 optimal weight: 3.9990
chunk 32 optimal weight: 0.6980
chunk 41 optimal weight: 0.6980
chunk 55 optimal weight: 1.9990
chunk 16 optimal weight: 2.9990
chunk 48 optimal weight: 2.9990
chunk 7 optimal weight: 0.7980
chunk 14 optimal weight: 0.7980
overall best weight: 0.7380
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 160 GLN
A 556 GLN
A 578 ASN
A 650 ASN
Total number of N/Q/H flips: 4
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8084
moved from start: 0.1115
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.037 5287 Z= 0.225
Angle : 0.565 6.767 7177 Z= 0.307
Chirality : 0.044 0.162 745
Planarity : 0.004 0.038 958
Dihedral : 6.747 71.050 746
Min Nonbonded Distance : 2.138
Molprobity Statistics.
All-atom Clashscore : 4.18
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 2.58 %
Favored : 97.42 %
Rotamer:
Outliers : 0.92 %
Allowed : 13.84 %
Favored : 85.24 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 3.70 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: -0.11 (0.33), residues: 659
helix: -1.59 (0.65), residues: 47
sheet: -0.05 (0.26), residues: 350
loop : 0.49 (0.42), residues: 262
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.009 0.001 TRP A 568
HIS 0.004 0.001 HIS A 649
PHE 0.015 0.002 PHE A 352
TYR 0.015 0.001 TYR A 681
ARG 0.004 0.000 ARG A 287
********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
1318 Ramachandran restraints generated.
659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
1318 Ramachandran restraints generated.
659 Oldfield, 0 Emsley, 659 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER 515 is missing expected H atoms. Skipping.
Evaluate side-chains
84 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 5
poor density : 79
time to evaluate : 0.854
Fit side-chains
revert: symmetry clash
REVERT: A 115 MET cc_start: 0.8639 (mmp) cc_final: 0.8198 (mmp)
REVERT: A 377 MET cc_start: 0.7074 (OUTLIER) cc_final: 0.6415 (mpt)
REVERT: A 595 ARG cc_start: 0.7655 (mtm180) cc_final: 0.7369 (ttp-170)
REVERT: A 645 LYS cc_start: 0.8544 (mtmm) cc_final: 0.7954 (mtmp)
outliers start: 5
outliers final: 3
residues processed: 81
average time/residue: 2.6851
time to fit residues: 227.1719
Evaluate side-chains
85 residues out of total 543 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 4
poor density : 81
time to evaluate : 1.303
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 363 GLU
Chi-restraints excluded: chain A residue 377 MET
Chi-restraints excluded: chain A residue 379 GLU
Chi-restraints excluded: chain A residue 404 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 66
random chunks:
chunk 52 optimal weight: 2.9990
chunk 21 optimal weight: 0.7980
chunk 53 optimal weight: 2.9990
chunk 6 optimal weight: 0.0980
chunk 9 optimal weight: 5.9990
chunk 46 optimal weight: 2.9990
chunk 2 optimal weight: 1.9990
chunk 37 optimal weight: 2.9990
chunk 60 optimal weight: 1.9990
chunk 35 optimal weight: 2.9990
chunk 44 optimal weight: 0.7980
overall best weight: 1.1384
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 650 ASN
Total number of N/Q/H flips: 1
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.148617 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.135629 restraints weight = 11406.200|
|-----------------------------------------------------------------------------|
r_work (start): 0.3659 rms_B_bonded: 0.95
r_work: 0.3590 rms_B_bonded: 1.12 restraints_weight: 0.5000
r_work: 0.3507 rms_B_bonded: 1.97 restraints_weight: 0.2500
r_work (final): 0.3507
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8092
moved from start: 0.1034
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.004 0.050 5287 Z= 0.288
Angle : 0.606 7.202 7177 Z= 0.330
Chirality : 0.044 0.182 745
Planarity : 0.005 0.040 958
Dihedral : 6.976 73.300 746
Min Nonbonded Distance : 2.144
Molprobity Statistics.
All-atom Clashscore : 4.77
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 1.97 %
Favored : 98.03 %
Rotamer:
Outliers : 0.92 %
Allowed : 13.84 %
Favored : 85.24 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 3.70 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: -0.02 (0.33), residues: 659
helix: -1.72 (0.64), residues: 47
sheet: 0.06 (0.26), residues: 345
loop : 0.49 (0.41), residues: 267
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.010 0.001 TRP A 568
HIS 0.004 0.001 HIS A 649
PHE 0.018 0.002 PHE A 352
TYR 0.016 0.002 TYR A 681
ARG 0.004 0.000 ARG A 287
Origin is already at (0, 0, 0), no shifts will be applied
===============================================================================
Job complete
usr+sys time: 5208.62 seconds
wall clock time: 92 minutes 59.20 seconds (5579.20 seconds total)