Starting phenix.real_space_refine
on Fri Jan 17 20:04:01 2025 by dcliebschner
===============================================================================
Processing files:
-------------------------------------------------------------------------------
Found model, /net/cci-nas-00/data/ceres_data/8xw0_38725/01_2025/8xw0_38725.cif
Found real_map, /net/cci-nas-00/data/ceres_data/8xw0_38725/01_2025/8xw0_38725.map
Processing PHIL parameters:
-------------------------------------------------------------------------------
Adding command-line PHIL:
-------------------------
refinement.macro_cycles=10
scattering_table=electron
resolution=3.11
write_initial_geo_file=False
Final processed PHIL parameters:
-------------------------------------------------------------------------------
data_manager {
real_map_files = "/net/cci-nas-00/data/ceres_data/8xw0_38725/01_2025/8xw0_38725.map"
default_real_map = "/net/cci-nas-00/data/ceres_data/8xw0_38725/01_2025/8xw0_38725.map"
model {
file = "/net/cci-nas-00/data/ceres_data/8xw0_38725/01_2025/8xw0_38725.cif"
}
default_model = "/net/cci-nas-00/data/ceres_data/8xw0_38725/01_2025/8xw0_38725.cif"
}
resolution = 3.11
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= 0.004 sd= 0.120
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: 5
Type Number sf(0) Gaussians
P 4 5.49 5
S 40 5.16 5
C 7508 2.51 5
N 1792 2.21 5
O 1976 1.98 5
sf(0) = scattering factor at diffraction angle 0.
Process input model
Symmetric amino acids flipped. Time to flip 42 residue(s): 0.04s
Monomer Library directory:
"/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
Total number of atoms: 11320
Number of models: 1
Model: ""
Number of chains: 4
Chain: "B"
Number of atoms: 5577
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 696, 5577
Classifications: {'peptide': 696}
Link IDs: {'CIS': 1, 'PTRANS': 31, 'TRANS': 663}
Chain: "A"
Number of atoms: 5577
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 696, 5577
Classifications: {'peptide': 696}
Link IDs: {'CIS': 1, 'PTRANS': 31, 'TRANS': 663}
Chain: "B"
Number of atoms: 83
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 2, 83
Classifications: {'peptide': 2}
Link IDs: {'TRANS': 1}
Chain breaks: 1
Unresolved non-hydrogen bonds: 25
Unresolved non-hydrogen angles: 25
Unresolved non-hydrogen dihedrals: 25
Chain: "A"
Number of atoms: 83
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 2, 83
Classifications: {'peptide': 2}
Link IDs: {'TRANS': 1}
Chain breaks: 1
Unresolved non-hydrogen bonds: 25
Unresolved non-hydrogen angles: 25
Unresolved non-hydrogen dihedrals: 25
Time building chain proxies: 7.01, per 1000 atoms: 0.62
Number of scatterers: 11320
At special positions: 0
Unit cell: (92.84, 140.315, 103.39, 90, 90, 90)
Space group: P 1 (No. 1)
Number of sites at special positions: 0
Number of scattering types: 5
Type Number sf(0)
S 40 16.00
P 4 15.00
O 1976 8.00
N 1792 7.00
C 7508 6.00
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 - 3.00
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: 3.02
Conformation dependent library (CDL) restraints added in 1.5 seconds
2776 Ramachandran restraints generated.
1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2.
Adding C-beta torsion restraints...
Number of C-beta restraints generated: 2668
Finding SS restraints...
Secondary structure from input PDB file:
62 helices and 4 sheets defined
69.3% alpha, 3.0% beta
0 base pairs and 0 stacking pairs defined.
Time for finding SS restraints: 1.51
Creating SS restraints...
Processing helix chain 'B' and resid 2 through 28
Processing helix chain 'B' and resid 30 through 32
No H-bonds generated for 'chain 'B' and resid 30 through 32'
Processing helix chain 'B' and resid 33 through 38
Processing helix chain 'B' and resid 38 through 43
Processing helix chain 'B' and resid 57 through 59
No H-bonds generated for 'chain 'B' and resid 57 through 59'
Processing helix chain 'B' and resid 60 through 67
Processing helix chain 'B' and resid 69 through 77
Processing helix chain 'B' and resid 80 through 113
removed outlier: 3.726A pdb=" N HIS B 84 " --> pdb=" O ASP B 80 " (cutoff:3.500A)
Proline residue: B 104 - end of helix
Proline residue: B 108 - end of helix
Processing helix chain 'B' and resid 118 through 123
removed outlier: 3.755A pdb=" N ALA B 122 " --> pdb=" O ASN B 118 " (cutoff:3.500A)
removed outlier: 3.525A pdb=" N THR B 123 " --> pdb=" O THR B 119 " (cutoff:3.500A)
No H-bonds generated for 'chain 'B' and resid 118 through 123'
Processing helix chain 'B' and resid 147 through 184
removed outlier: 3.854A pdb=" N ALA B 151 " --> pdb=" O SER B 147 " (cutoff:3.500A)
Processing helix chain 'B' and resid 188 through 191
Processing helix chain 'B' and resid 207 through 213
Processing helix chain 'B' and resid 215 through 220
Processing helix chain 'B' and resid 233 through 261
Processing helix chain 'B' and resid 269 through 273
removed outlier: 3.572A pdb=" N GLY B 272 " --> pdb=" O GLY B 269 " (cutoff:3.500A)
Processing helix chain 'B' and resid 280 through 302
Processing helix chain 'B' and resid 317 through 324
Processing helix chain 'B' and resid 355 through 389
Proline residue: B 380 - end of helix
removed outlier: 3.695A pdb=" N THR B 389 " --> pdb=" O SER B 385 " (cutoff:3.500A)
Processing helix chain 'B' and resid 391 through 395
removed outlier: 3.593A pdb=" N ARG B 395 " --> pdb=" O ASN B 392 " (cutoff:3.500A)
Processing helix chain 'B' and resid 397 through 401
Processing helix chain 'B' and resid 406 through 439
removed outlier: 3.588A pdb=" N ARG B 410 " --> pdb=" O ILE B 406 " (cutoff:3.500A)
Proline residue: B 418 - end of helix
Proline residue: B 430 - end of helix
Processing helix chain 'B' and resid 444 through 478
Processing helix chain 'B' and resid 485 through 523
removed outlier: 3.696A pdb=" N ILE B 490 " --> pdb=" O LYS B 486 " (cutoff:3.500A)
removed outlier: 4.680A pdb=" N ILE B 491 " --> pdb=" O LEU B 487 " (cutoff:3.500A)
Proline residue: B 499 - end of helix
Processing helix chain 'B' and resid 523 through 530
Processing helix chain 'B' and resid 543 through 549
removed outlier: 3.882A pdb=" N ALA B 547 " --> pdb=" O GLU B 543 " (cutoff:3.500A)
removed outlier: 3.807A pdb=" N TRP B 548 " --> pdb=" O VAL B 544 " (cutoff:3.500A)
Processing helix chain 'B' and resid 557 through 572
Processing helix chain 'B' and resid 578 through 601
removed outlier: 3.699A pdb=" N PHE B 582 " --> pdb=" O LEU B 578 " (cutoff:3.500A)
Processing helix chain 'B' and resid 612 through 635
Processing helix chain 'B' and resid 643 through 645
No H-bonds generated for 'chain 'B' and resid 643 through 645'
Processing helix chain 'B' and resid 646 through 664
Processing helix chain 'B' and resid 665 through 670
removed outlier: 3.757A pdb=" N GLU B 669 " --> pdb=" O TYR B 665 " (cutoff:3.500A)
removed outlier: 4.037A pdb=" N HIS B 670 " --> pdb=" O GLY B 666 " (cutoff:3.500A)
No H-bonds generated for 'chain 'B' and resid 665 through 670'
Processing helix chain 'A' and resid 2 through 28
Processing helix chain 'A' and resid 30 through 32
No H-bonds generated for 'chain 'A' and resid 30 through 32'
Processing helix chain 'A' and resid 33 through 38
Processing helix chain 'A' and resid 38 through 43
Processing helix chain 'A' and resid 57 through 59
No H-bonds generated for 'chain 'A' and resid 57 through 59'
Processing helix chain 'A' and resid 60 through 67
Processing helix chain 'A' and resid 69 through 77
Processing helix chain 'A' and resid 80 through 113
removed outlier: 3.727A pdb=" N HIS A 84 " --> pdb=" O ASP A 80 " (cutoff:3.500A)
Proline residue: A 104 - end of helix
Proline residue: A 108 - end of helix
Processing helix chain 'A' and resid 118 through 123
removed outlier: 3.756A pdb=" N ALA A 122 " --> pdb=" O ASN A 118 " (cutoff:3.500A)
removed outlier: 3.525A pdb=" N THR A 123 " --> pdb=" O THR A 119 " (cutoff:3.500A)
No H-bonds generated for 'chain 'A' and resid 118 through 123'
Processing helix chain 'A' and resid 147 through 184
removed outlier: 3.855A pdb=" N ALA A 151 " --> pdb=" O SER A 147 " (cutoff:3.500A)
Processing helix chain 'A' and resid 188 through 191
Processing helix chain 'A' and resid 207 through 213
Processing helix chain 'A' and resid 215 through 220
Processing helix chain 'A' and resid 233 through 261
Processing helix chain 'A' and resid 269 through 273
removed outlier: 3.572A pdb=" N GLY A 272 " --> pdb=" O GLY A 269 " (cutoff:3.500A)
Processing helix chain 'A' and resid 280 through 302
Processing helix chain 'A' and resid 317 through 324
Processing helix chain 'A' and resid 355 through 389
Proline residue: A 380 - end of helix
removed outlier: 3.695A pdb=" N THR A 389 " --> pdb=" O SER A 385 " (cutoff:3.500A)
Processing helix chain 'A' and resid 391 through 395
removed outlier: 3.592A pdb=" N ARG A 395 " --> pdb=" O ASN A 392 " (cutoff:3.500A)
Processing helix chain 'A' and resid 397 through 401
Processing helix chain 'A' and resid 406 through 439
removed outlier: 3.588A pdb=" N ARG A 410 " --> pdb=" O ILE A 406 " (cutoff:3.500A)
Proline residue: A 418 - end of helix
Proline residue: A 430 - end of helix
Processing helix chain 'A' and resid 444 through 478
Processing helix chain 'A' and resid 485 through 523
removed outlier: 3.696A pdb=" N ILE A 490 " --> pdb=" O LYS A 486 " (cutoff:3.500A)
removed outlier: 4.679A pdb=" N ILE A 491 " --> pdb=" O LEU A 487 " (cutoff:3.500A)
Proline residue: A 499 - end of helix
Processing helix chain 'A' and resid 523 through 530
Processing helix chain 'A' and resid 543 through 549
removed outlier: 3.881A pdb=" N ALA A 547 " --> pdb=" O GLU A 543 " (cutoff:3.500A)
removed outlier: 3.806A pdb=" N TRP A 548 " --> pdb=" O VAL A 544 " (cutoff:3.500A)
Processing helix chain 'A' and resid 557 through 572
Processing helix chain 'A' and resid 578 through 601
removed outlier: 3.700A pdb=" N PHE A 582 " --> pdb=" O LEU A 578 " (cutoff:3.500A)
Processing helix chain 'A' and resid 612 through 635
Processing helix chain 'A' and resid 643 through 645
No H-bonds generated for 'chain 'A' and resid 643 through 645'
Processing helix chain 'A' and resid 646 through 664
Processing helix chain 'A' and resid 665 through 670
removed outlier: 3.757A pdb=" N GLU A 669 " --> pdb=" O TYR A 665 " (cutoff:3.500A)
removed outlier: 4.036A pdb=" N HIS A 670 " --> pdb=" O GLY A 666 " (cutoff:3.500A)
No H-bonds generated for 'chain 'A' and resid 665 through 670'
Processing sheet with id=AA1, first strand: chain 'B' and resid 224 through 229
removed outlier: 6.825A pdb=" N PHE B 314 " --> pdb=" O TYR B 225 " (cutoff:3.500A)
removed outlier: 4.316A pdb=" N SER B 227 " --> pdb=" O VAL B 312 " (cutoff:3.500A)
removed outlier: 6.270A pdb=" N VAL B 312 " --> pdb=" O SER B 227 " (cutoff:3.500A)
removed outlier: 4.925A pdb=" N VAL B 229 " --> pdb=" O ALA B 310 " (cutoff:3.500A)
removed outlier: 7.189A pdb=" N ALA B 310 " --> pdb=" O VAL B 229 " (cutoff:3.500A)
Processing sheet with id=AA2, first strand: chain 'B' and resid 265 through 267
Processing sheet with id=AA3, first strand: chain 'A' and resid 224 through 229
removed outlier: 6.825A pdb=" N PHE A 314 " --> pdb=" O TYR A 225 " (cutoff:3.500A)
removed outlier: 4.315A pdb=" N SER A 227 " --> pdb=" O VAL A 312 " (cutoff:3.500A)
removed outlier: 6.269A pdb=" N VAL A 312 " --> pdb=" O SER A 227 " (cutoff:3.500A)
removed outlier: 4.925A pdb=" N VAL A 229 " --> pdb=" O ALA A 310 " (cutoff:3.500A)
removed outlier: 7.189A pdb=" N ALA A 310 " --> pdb=" O VAL A 229 " (cutoff:3.500A)
Processing sheet with id=AA4, first strand: chain 'A' and resid 265 through 267
686 hydrogen bonds defined for protein.
2022 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: 3.37
Time building geometry restraints manager: 3.36 seconds
NOTE: a complete listing of the restraints can be obtained by requesting
output of .geo file.
Histogram of bond lengths:
1.18 - 1.31: 1702
1.31 - 1.43: 3197
1.43 - 1.56: 6635
1.56 - 1.68: 8
1.68 - 1.81: 66
Bond restraints: 11608
Sorted by residual:
bond pdb=" C38 P5S B 801 "
pdb=" O37 P5S B 801 "
ideal model delta sigma weight residual
1.345 1.407 -0.062 2.00e-02 2.50e+03 9.64e+00
bond pdb=" C38 P5S A 801 "
pdb=" O37 P5S A 801 "
ideal model delta sigma weight residual
1.345 1.406 -0.061 2.00e-02 2.50e+03 9.40e+00
bond pdb=" C38 P5S B 802 "
pdb=" O37 P5S B 802 "
ideal model delta sigma weight residual
1.345 1.402 -0.057 2.00e-02 2.50e+03 8.10e+00
bond pdb=" C38 P5S A 802 "
pdb=" O37 P5S A 802 "
ideal model delta sigma weight residual
1.345 1.402 -0.057 2.00e-02 2.50e+03 8.06e+00
bond pdb=" C17 P5S A 802 "
pdb=" O19 P5S A 802 "
ideal model delta sigma weight residual
1.351 1.402 -0.051 2.00e-02 2.50e+03 6.54e+00
... (remaining 11603 not shown)
Histogram of bond angle deviations from ideal:
0.00 - 2.62: 15398
2.62 - 5.25: 272
5.25 - 7.87: 62
7.87 - 10.50: 12
10.50 - 13.12: 6
Bond angle restraints: 15750
Sorted by residual:
angle pdb=" C LEU B 54 "
pdb=" N THR B 55 "
pdb=" CA THR B 55 "
ideal model delta sigma weight residual
120.81 127.80 -6.99 1.63e+00 3.76e-01 1.84e+01
angle pdb=" C LEU A 54 "
pdb=" N THR A 55 "
pdb=" CA THR A 55 "
ideal model delta sigma weight residual
120.81 127.79 -6.98 1.63e+00 3.76e-01 1.83e+01
angle pdb=" C LEU B 626 "
pdb=" N PHE B 627 "
pdb=" CA PHE B 627 "
ideal model delta sigma weight residual
122.26 114.96 7.30 1.73e+00 3.34e-01 1.78e+01
angle pdb=" C LEU A 626 "
pdb=" N PHE A 627 "
pdb=" CA PHE A 627 "
ideal model delta sigma weight residual
122.26 114.99 7.27 1.73e+00 3.34e-01 1.77e+01
angle pdb=" O13 P5S B 802 "
pdb=" P12 P5S B 802 "
pdb=" O15 P5S B 802 "
ideal model delta sigma weight residual
121.25 109.04 12.21 3.00e+00 1.11e-01 1.66e+01
... (remaining 15745 not shown)
Histogram of dihedral angle deviations from ideal:
0.00 - 35.91: 6732
35.91 - 71.81: 165
71.81 - 107.72: 34
107.72 - 143.63: 15
143.63 - 179.54: 8
Dihedral angle restraints: 6954
sinusoidal: 2834
harmonic: 4120
Sorted by residual:
dihedral pdb=" CA PHE B 627 "
pdb=" C PHE B 627 "
pdb=" N GLN B 628 "
pdb=" CA GLN B 628 "
ideal model delta harmonic sigma weight residual
180.00 154.26 25.74 0 5.00e+00 4.00e-02 2.65e+01
dihedral pdb=" CA PHE A 627 "
pdb=" C PHE A 627 "
pdb=" N GLN A 628 "
pdb=" CA GLN A 628 "
ideal model delta harmonic sigma weight residual
180.00 154.27 25.73 0 5.00e+00 4.00e-02 2.65e+01
dihedral pdb=" CA ARG B 691 "
pdb=" C ARG B 691 "
pdb=" N ALA B 692 "
pdb=" CA ALA B 692 "
ideal model delta harmonic sigma weight residual
180.00 155.99 24.01 0 5.00e+00 4.00e-02 2.31e+01
... (remaining 6951 not shown)
Histogram of chiral volume deviations from ideal:
0.000 - 0.057: 1471
0.057 - 0.115: 299
0.115 - 0.172: 38
0.172 - 0.229: 3
0.229 - 0.286: 3
Chirality restraints: 1814
Sorted by residual:
chirality pdb=" C2 P5S A 801 "
pdb=" C1 P5S A 801 "
pdb=" C3 P5S A 801 "
pdb=" O37 P5S A 801 "
both_signs ideal model delta sigma weight residual
False 2.59 2.31 0.29 2.00e-01 2.50e+01 2.05e+00
chirality pdb=" C2 P5S B 801 "
pdb=" C1 P5S B 801 "
pdb=" C3 P5S B 801 "
pdb=" O37 P5S B 801 "
both_signs ideal model delta sigma weight residual
False 2.59 2.34 0.25 2.00e-01 2.50e+01 1.58e+00
chirality pdb=" CA PHE A 513 "
pdb=" N PHE A 513 "
pdb=" C PHE A 513 "
pdb=" CB PHE A 513 "
both_signs ideal model delta sigma weight residual
False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.38e+00
... (remaining 1811 not shown)
Planarity restraints: 1918
Sorted by residual:
delta sigma weight rms_deltas residual
plane pdb=" CB TYR B 171 " 0.036 2.00e-02 2.50e+03 2.82e-02 1.59e+01
pdb=" CG TYR B 171 " -0.069 2.00e-02 2.50e+03
pdb=" CD1 TYR B 171 " 0.013 2.00e-02 2.50e+03
pdb=" CD2 TYR B 171 " 0.006 2.00e-02 2.50e+03
pdb=" CE1 TYR B 171 " 0.001 2.00e-02 2.50e+03
pdb=" CE2 TYR B 171 " 0.007 2.00e-02 2.50e+03
pdb=" CZ TYR B 171 " 0.003 2.00e-02 2.50e+03
pdb=" OH TYR B 171 " 0.004 2.00e-02 2.50e+03
delta sigma weight rms_deltas residual
plane pdb=" CB TYR A 171 " 0.036 2.00e-02 2.50e+03 2.81e-02 1.58e+01
pdb=" CG TYR A 171 " -0.069 2.00e-02 2.50e+03
pdb=" CD1 TYR A 171 " 0.013 2.00e-02 2.50e+03
pdb=" CD2 TYR A 171 " 0.006 2.00e-02 2.50e+03
pdb=" CE1 TYR A 171 " 0.001 2.00e-02 2.50e+03
pdb=" CE2 TYR A 171 " 0.007 2.00e-02 2.50e+03
pdb=" CZ TYR A 171 " 0.003 2.00e-02 2.50e+03
pdb=" OH TYR A 171 " 0.004 2.00e-02 2.50e+03
delta sigma weight rms_deltas residual
plane pdb=" C ASN A 484 " 0.062 5.00e-02 4.00e+02 9.41e-02 1.42e+01
pdb=" N PRO A 485 " -0.163 5.00e-02 4.00e+02
pdb=" CA PRO A 485 " 0.049 5.00e-02 4.00e+02
pdb=" CD PRO A 485 " 0.052 5.00e-02 4.00e+02
... (remaining 1915 not shown)
Histogram of nonbonded interaction distances:
2.13 - 2.68: 194
2.68 - 3.24: 11524
3.24 - 3.79: 17752
3.79 - 4.35: 24272
4.35 - 4.90: 40247
Nonbonded interactions: 93989
Sorted by model distance:
nonbonded pdb=" O LEU B 493 "
pdb=" OG SER B 497 "
model vdw
2.126 3.040
nonbonded pdb=" O LEU A 493 "
pdb=" OG SER A 497 "
model vdw
2.126 3.040
nonbonded pdb=" OG1 THR A 125 "
pdb=" O SER A 127 "
model vdw
2.220 3.040
nonbonded pdb=" OG1 THR B 125 "
pdb=" O SER B 127 "
model vdw
2.221 3.040
nonbonded pdb=" O THR A 473 "
pdb=" OG1 THR A 477 "
model vdw
2.232 3.040
... (remaining 93984 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: 0.06
Found NCS groups:
ncs_group {
reference = chain 'A'
selection = chain 'B'
}
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: 0.010
Normalize map: mean=0, sd=1: 0.730
Set stop_for_unknowns flag: 0.000
Assert model is a single copy model: 0.000
Assert all atoms have isotropic ADPs: 0.000
Construct map_model_manager: 0.010
Extract box with map and model: 0.440
Check model and map are aligned: 0.080
Set scattering table: 0.120
Process input model: 27.830
Find NCS groups from input model: 0.200
Set up NCS constraints: 0.040
Set refine NCS operators: 0.000
Adjust number of macro_cycles: 0.000
Reset NCS operators: 0.000
Extract rigid body selections: 0.000
Check and reset occupancies: 0.010
Load rotamer database and sin/cos tables:2.790
Set ADP refinement strategy: 0.000
Make a string to write initial .geo file:0.000
Internal consistency checks: 0.000
Total: 32.260
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7743
moved from start: 0.0000
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.005 0.062 11608 Z= 0.290
Angle : 0.907 13.120 15750 Z= 0.457
Chirality : 0.047 0.286 1814
Planarity : 0.006 0.094 1918
Dihedral : 19.549 179.535 4286
Min Nonbonded Distance : 2.126
Molprobity Statistics.
All-atom Clashscore : 10.61
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 9.65 %
Favored : 90.35 %
Rotamer:
Outliers : 0.83 %
Allowed : 0.83 %
Favored : 98.34 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.15 %
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: -0.53 (0.24), residues: 1388
helix: 0.33 (0.18), residues: 906
sheet: -2.64 (0.97), residues: 30
loop : -1.45 (0.32), residues: 452
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.034 0.002 TRP B 613
HIS 0.004 0.001 HIS B 615
PHE 0.039 0.002 PHE B 513
TYR 0.069 0.002 TYR B 171
ARG 0.011 0.001 ARG B 29
*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
2776 Ramachandran restraints generated.
1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
2776 Ramachandran restraints generated.
1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
152 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 10
poor density : 142
time to evaluate : 1.277
Fit side-chains
revert: symmetry clash
revert: symmetry clash
REVERT: B 139 MET cc_start: 0.8452 (ttt) cc_final: 0.8217 (ttp)
REVERT: B 180 GLN cc_start: 0.7058 (mt0) cc_final: 0.6762 (mt0)
REVERT: B 242 LYS cc_start: 0.8139 (OUTLIER) cc_final: 0.7904 (tptt)
REVERT: B 465 PHE cc_start: 0.7502 (t80) cc_final: 0.7297 (t80)
REVERT: A 29 ARG cc_start: 0.8455 (OUTLIER) cc_final: 0.8217 (mtm180)
REVERT: A 180 GLN cc_start: 0.7251 (mt0) cc_final: 0.7030 (mt0)
REVERT: A 242 LYS cc_start: 0.8047 (OUTLIER) cc_final: 0.7775 (tttp)
REVERT: A 541 GLU cc_start: 0.8173 (pt0) cc_final: 0.7922 (pm20)
outliers start: 10
outliers final: 4
residues processed: 152
average time/residue: 0.2553
time to fit residues: 55.9975
Evaluate side-chains
122 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 7
poor density : 115
time to evaluate : 1.208
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue 242 LYS
Chi-restraints excluded: chain B residue 286 GLU
Chi-restraints excluded: chain B residue 460 SER
Chi-restraints excluded: chain A residue 29 ARG
Chi-restraints excluded: chain A residue 242 LYS
Chi-restraints excluded: chain A residue 286 GLU
Chi-restraints excluded: chain A residue 460 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 138
random chunks:
chunk 116 optimal weight: 5.9990
chunk 104 optimal weight: 2.9990
chunk 58 optimal weight: 1.9990
chunk 35 optimal weight: 0.0980
chunk 70 optimal weight: 1.9990
chunk 55 optimal weight: 2.9990
chunk 108 optimal weight: 2.9990
chunk 41 optimal weight: 1.9990
chunk 65 optimal weight: 2.9990
chunk 80 optimal weight: 0.0040
chunk 125 optimal weight: 0.8980
overall best weight: 0.9996
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
B 299 GLN
B 392 ASN
A 392 ASN
Total number of N/Q/H flips: 3
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.154036 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.118405 restraints weight = 13451.772|
|-----------------------------------------------------------------------------|
r_work (start): 0.3328 rms_B_bonded: 2.02
r_work: 0.3209 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.3075 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.3075
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8074
moved from start: 0.1097
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.004 0.047 11608 Z= 0.250
Angle : 0.667 10.129 15750 Z= 0.356
Chirality : 0.045 0.194 1814
Planarity : 0.006 0.080 1918
Dihedral : 19.009 168.303 1710
Min Nonbonded Distance : 2.518
Molprobity Statistics.
All-atom Clashscore : 8.00
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 8.21 %
Favored : 91.79 %
Rotamer:
Outliers : 0.91 %
Allowed : 7.04 %
Favored : 92.05 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.15 %
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: -0.29 (0.24), residues: 1388
helix: 0.57 (0.18), residues: 918
sheet: -3.23 (0.82), residues: 30
loop : -1.50 (0.32), residues: 440
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.032 0.002 TRP A 613
HIS 0.006 0.001 HIS B 615
PHE 0.059 0.002 PHE A 627
TYR 0.025 0.001 TYR B 171
ARG 0.004 0.000 ARG B 56
*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
2776 Ramachandran restraints generated.
1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
2776 Ramachandran restraints generated.
1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
151 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 11
poor density : 140
time to evaluate : 1.244
Fit side-chains
revert: symmetry clash
revert: symmetry clash
REVERT: B 139 MET cc_start: 0.9133 (ttt) cc_final: 0.8814 (ttp)
REVERT: B 180 GLN cc_start: 0.7729 (mt0) cc_final: 0.7406 (mt0)
REVERT: B 631 MET cc_start: 0.8977 (mmm) cc_final: 0.8762 (tpp)
REVERT: B 688 GLU cc_start: 0.7810 (mp0) cc_final: 0.7581 (mm-30)
REVERT: A 21 MET cc_start: 0.8291 (mmp) cc_final: 0.7953 (mmp)
REVERT: A 180 GLN cc_start: 0.7891 (mt0) cc_final: 0.7629 (mt0)
REVERT: A 541 GLU cc_start: 0.8294 (pt0) cc_final: 0.7843 (pm20)
outliers start: 11
outliers final: 4
residues processed: 147
average time/residue: 0.2237
time to fit residues: 48.5926
Evaluate side-chains
127 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 4
poor density : 123
time to evaluate : 1.282
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue 286 GLU
Chi-restraints excluded: chain B residue 460 SER
Chi-restraints excluded: chain A residue 42 ILE
Chi-restraints excluded: chain A residue 286 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 138
random chunks:
chunk 37 optimal weight: 1.9990
chunk 54 optimal weight: 1.9990
chunk 56 optimal weight: 0.9990
chunk 39 optimal weight: 5.9990
chunk 91 optimal weight: 4.9990
chunk 102 optimal weight: 0.0670
chunk 27 optimal weight: 0.5980
chunk 135 optimal weight: 2.9990
chunk 22 optimal weight: 0.9990
chunk 2 optimal weight: 3.9990
chunk 120 optimal weight: 2.9990
overall best weight: 0.9324
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
B 392 ASN
A 392 ASN
Total number of N/Q/H flips: 2
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.153814 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.118189 restraints weight = 13627.195|
|-----------------------------------------------------------------------------|
r_work (start): 0.3326 rms_B_bonded: 2.03
r_work: 0.3209 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.3074 rms_B_bonded: 4.42 restraints_weight: 0.2500
r_work (final): 0.3074
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8072
moved from start: 0.1435
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.004 0.045 11608 Z= 0.233
Angle : 0.619 8.070 15750 Z= 0.334
Chirality : 0.044 0.197 1814
Planarity : 0.005 0.065 1918
Dihedral : 17.342 174.751 1697
Min Nonbonded Distance : 2.450
Molprobity Statistics.
All-atom Clashscore : 8.09
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 8.50 %
Favored : 91.50 %
Rotamer:
Outliers : 1.82 %
Allowed : 11.26 %
Favored : 86.92 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.15 %
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 (0.24), residues: 1388
helix: 0.80 (0.18), residues: 918
sheet: -3.41 (0.75), residues: 30
loop : -1.51 (0.32), residues: 440
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.023 0.001 TRP B 613
HIS 0.006 0.001 HIS B 615
PHE 0.060 0.002 PHE A 627
TYR 0.013 0.001 TYR A 458
ARG 0.003 0.000 ARG B 56
*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
2776 Ramachandran restraints generated.
1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
2776 Ramachandran restraints generated.
1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
153 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 22
poor density : 131
time to evaluate : 1.366
Fit side-chains
revert: symmetry clash
REVERT: B 180 GLN cc_start: 0.7747 (mt0) cc_final: 0.7309 (mt0)
REVERT: B 254 GLU cc_start: 0.7425 (mm-30) cc_final: 0.7136 (mm-30)
REVERT: B 562 ASP cc_start: 0.8329 (m-30) cc_final: 0.7815 (m-30)
REVERT: B 688 GLU cc_start: 0.7988 (mp0) cc_final: 0.7742 (mm-30)
REVERT: A 180 GLN cc_start: 0.8012 (mt0) cc_final: 0.7690 (mt0)
REVERT: A 498 LEU cc_start: 0.6722 (OUTLIER) cc_final: 0.6480 (mp)
REVERT: A 541 GLU cc_start: 0.8309 (pt0) cc_final: 0.7857 (pm20)
outliers start: 22
outliers final: 11
residues processed: 144
average time/residue: 0.2509
time to fit residues: 53.4030
Evaluate side-chains
136 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 12
poor density : 124
time to evaluate : 1.251
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue 171 TYR
Chi-restraints excluded: chain B residue 286 GLU
Chi-restraints excluded: chain B residue 296 GLU
Chi-restraints excluded: chain B residue 563 MET
Chi-restraints excluded: chain B residue 566 LEU
Chi-restraints excluded: chain B residue 677 CYS
Chi-restraints excluded: chain A residue 42 ILE
Chi-restraints excluded: chain A residue 157 TYR
Chi-restraints excluded: chain A residue 243 LEU
Chi-restraints excluded: chain A residue 286 GLU
Chi-restraints excluded: chain A residue 357 PHE
Chi-restraints excluded: chain A residue 498 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 138
random chunks:
chunk 42 optimal weight: 3.9990
chunk 50 optimal weight: 0.5980
chunk 69 optimal weight: 5.9990
chunk 107 optimal weight: 3.9990
chunk 77 optimal weight: 0.7980
chunk 122 optimal weight: 4.9990
chunk 86 optimal weight: 0.6980
chunk 0 optimal weight: 0.6980
chunk 8 optimal weight: 0.9980
chunk 9 optimal weight: 0.7980
chunk 36 optimal weight: 0.8980
overall best weight: 0.7180
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
B 392 ASN
A 392 ASN
Total number of N/Q/H flips: 2
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.155395 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.119900 restraints weight = 13563.699|
|-----------------------------------------------------------------------------|
r_work (start): 0.3347 rms_B_bonded: 2.02
r_work: 0.3230 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.3095 rms_B_bonded: 4.46 restraints_weight: 0.2500
r_work (final): 0.3095
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8067
moved from start: 0.1650
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.042 11608 Z= 0.207
Angle : 0.599 8.784 15750 Z= 0.322
Chirality : 0.044 0.209 1814
Planarity : 0.005 0.058 1918
Dihedral : 16.450 175.580 1696
Min Nonbonded Distance : 2.437
Molprobity Statistics.
All-atom Clashscore : 8.13
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 8.14 %
Favored : 91.86 %
Rotamer:
Outliers : 2.15 %
Allowed : 13.41 %
Favored : 84.44 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.15 %
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 (0.24), residues: 1388
helix: 1.04 (0.18), residues: 906
sheet: -3.02 (0.75), residues: 34
loop : -1.66 (0.32), residues: 448
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.021 0.001 TRP A 613
HIS 0.004 0.001 HIS B 615
PHE 0.061 0.002 PHE A 627
TYR 0.010 0.001 TYR B 456
ARG 0.002 0.000 ARG B 56
*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
2776 Ramachandran restraints generated.
1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
2776 Ramachandran restraints generated.
1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
156 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 26
poor density : 130
time to evaluate : 1.312
Fit side-chains
revert: symmetry clash
REVERT: B 139 MET cc_start: 0.9061 (ttt) cc_final: 0.8833 (ttp)
REVERT: B 180 GLN cc_start: 0.7797 (mt0) cc_final: 0.7332 (mt0)
REVERT: B 254 GLU cc_start: 0.7438 (mm-30) cc_final: 0.7152 (mm-30)
REVERT: B 562 ASP cc_start: 0.8431 (m-30) cc_final: 0.8008 (m-30)
REVERT: B 688 GLU cc_start: 0.8062 (mp0) cc_final: 0.7839 (mm-30)
REVERT: A 56 ARG cc_start: 0.8320 (tpm170) cc_final: 0.7996 (tpt170)
REVERT: A 498 LEU cc_start: 0.6514 (OUTLIER) cc_final: 0.6272 (mp)
REVERT: A 541 GLU cc_start: 0.8390 (pt0) cc_final: 0.7946 (pm20)
outliers start: 26
outliers final: 17
residues processed: 145
average time/residue: 0.2250
time to fit residues: 48.9902
Evaluate side-chains
143 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 18
poor density : 125
time to evaluate : 1.296
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue 62 MET
Chi-restraints excluded: chain B residue 171 TYR
Chi-restraints excluded: chain B residue 286 GLU
Chi-restraints excluded: chain B residue 296 GLU
Chi-restraints excluded: chain B residue 374 ILE
Chi-restraints excluded: chain B residue 563 MET
Chi-restraints excluded: chain B residue 566 LEU
Chi-restraints excluded: chain B residue 579 ILE
Chi-restraints excluded: chain A residue 42 ILE
Chi-restraints excluded: chain A residue 157 TYR
Chi-restraints excluded: chain A residue 159 ILE
Chi-restraints excluded: chain A residue 171 TYR
Chi-restraints excluded: chain A residue 243 LEU
Chi-restraints excluded: chain A residue 286 GLU
Chi-restraints excluded: chain A residue 357 PHE
Chi-restraints excluded: chain A residue 498 LEU
Chi-restraints excluded: chain A residue 566 LEU
Chi-restraints excluded: chain A residue 579 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 138
random chunks:
chunk 58 optimal weight: 2.9990
chunk 116 optimal weight: 5.9990
chunk 119 optimal weight: 2.9990
chunk 41 optimal weight: 0.9980
chunk 84 optimal weight: 1.9990
chunk 18 optimal weight: 3.9990
chunk 131 optimal weight: 0.8980
chunk 11 optimal weight: 4.9990
chunk 26 optimal weight: 7.9990
chunk 47 optimal weight: 0.8980
chunk 93 optimal weight: 7.9990
overall best weight: 1.5584
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
B 299 GLN
A 299 GLN
A 392 ASN
Total number of N/Q/H flips: 3
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.151329 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.115351 restraints weight = 13531.931|
|-----------------------------------------------------------------------------|
r_work (start): 0.3288 rms_B_bonded: 2.01
r_work: 0.3169 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.3035 rms_B_bonded: 4.36 restraints_weight: 0.2500
r_work (final): 0.3035
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8114
moved from start: 0.1712
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.005 0.048 11608 Z= 0.310
Angle : 0.642 8.524 15750 Z= 0.346
Chirality : 0.046 0.208 1814
Planarity : 0.005 0.054 1918
Dihedral : 15.970 152.676 1696
Min Nonbonded Distance : 2.443
Molprobity Statistics.
All-atom Clashscore : 8.39
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 9.15 %
Favored : 90.85 %
Rotamer:
Outliers : 2.57 %
Allowed : 14.90 %
Favored : 82.53 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.15 %
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: 0.05 (0.24), residues: 1388
helix: 0.94 (0.18), residues: 916
sheet: -3.48 (0.72), residues: 30
loop : -1.60 (0.32), residues: 442
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.020 0.002 TRP B 613
HIS 0.007 0.001 HIS B 615
PHE 0.059 0.002 PHE A 627
TYR 0.016 0.001 TYR B 456
ARG 0.002 0.000 ARG A 56
*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
2776 Ramachandran restraints generated.
1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
2776 Ramachandran restraints generated.
1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
158 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 31
poor density : 127
time to evaluate : 1.210
Fit side-chains
revert: symmetry clash
REVERT: B 139 MET cc_start: 0.9093 (ttt) cc_final: 0.8840 (ttp)
REVERT: B 180 GLN cc_start: 0.7844 (mt0) cc_final: 0.7372 (mt0)
REVERT: B 254 GLU cc_start: 0.7436 (mm-30) cc_final: 0.7187 (mm-30)
REVERT: B 562 ASP cc_start: 0.8437 (m-30) cc_final: 0.8047 (m-30)
REVERT: B 691 ARG cc_start: 0.7814 (OUTLIER) cc_final: 0.7331 (ptm160)
REVERT: A 56 ARG cc_start: 0.8354 (tpm170) cc_final: 0.7921 (tpm170)
REVERT: A 76 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8344 (tt)
REVERT: A 405 GLU cc_start: 0.5440 (mt-10) cc_final: 0.5218 (mt-10)
REVERT: A 498 LEU cc_start: 0.6875 (OUTLIER) cc_final: 0.6630 (mp)
REVERT: A 541 GLU cc_start: 0.8413 (pt0) cc_final: 0.7873 (pm20)
outliers start: 31
outliers final: 24
residues processed: 141
average time/residue: 0.2302
time to fit residues: 48.0874
Evaluate side-chains
149 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 27
poor density : 122
time to evaluate : 1.359
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue 62 MET
Chi-restraints excluded: chain B residue 76 LEU
Chi-restraints excluded: chain B residue 157 TYR
Chi-restraints excluded: chain B residue 171 TYR
Chi-restraints excluded: chain B residue 286 GLU
Chi-restraints excluded: chain B residue 296 GLU
Chi-restraints excluded: chain B residue 374 ILE
Chi-restraints excluded: chain B residue 428 MET
Chi-restraints excluded: chain B residue 563 MET
Chi-restraints excluded: chain B residue 566 LEU
Chi-restraints excluded: chain B residue 579 ILE
Chi-restraints excluded: chain B residue 677 CYS
Chi-restraints excluded: chain B residue 691 ARG
Chi-restraints excluded: chain A residue 42 ILE
Chi-restraints excluded: chain A residue 76 LEU
Chi-restraints excluded: chain A residue 157 TYR
Chi-restraints excluded: chain A residue 171 TYR
Chi-restraints excluded: chain A residue 243 LEU
Chi-restraints excluded: chain A residue 286 GLU
Chi-restraints excluded: chain A residue 296 GLU
Chi-restraints excluded: chain A residue 357 PHE
Chi-restraints excluded: chain A residue 460 SER
Chi-restraints excluded: chain A residue 498 LEU
Chi-restraints excluded: chain A residue 566 LEU
Chi-restraints excluded: chain A residue 579 ILE
Chi-restraints excluded: chain A residue 677 CYS
Chi-restraints excluded: chain A residue 691 ARG
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 138
random chunks:
chunk 105 optimal weight: 0.9980
chunk 20 optimal weight: 0.9980
chunk 111 optimal weight: 0.7980
chunk 84 optimal weight: 1.9990
chunk 67 optimal weight: 0.8980
chunk 78 optimal weight: 1.9990
chunk 14 optimal weight: 0.9990
chunk 121 optimal weight: 0.8980
chunk 51 optimal weight: 2.9990
chunk 46 optimal weight: 0.9980
chunk 3 optimal weight: 0.7980
overall best weight: 0.8780
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 392 ASN
Total number of N/Q/H flips: 1
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.156123 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.119911 restraints weight = 13695.267|
|-----------------------------------------------------------------------------|
r_work (start): 0.3347 rms_B_bonded: 2.09
r_work: 0.3219 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.3080 rms_B_bonded: 4.60 restraints_weight: 0.2500
r_work (final): 0.3080
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7998
moved from start: 0.1830
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.041 11608 Z= 0.221
Angle : 0.600 8.983 15750 Z= 0.321
Chirality : 0.044 0.241 1814
Planarity : 0.005 0.050 1918
Dihedral : 15.205 150.140 1696
Min Nonbonded Distance : 2.388
Molprobity Statistics.
All-atom Clashscore : 8.22
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 8.07 %
Favored : 91.93 %
Rotamer:
Outliers : 2.07 %
Allowed : 15.73 %
Favored : 82.20 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.15 %
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: 0.18 (0.24), residues: 1388
helix: 1.06 (0.18), residues: 916
sheet: -3.41 (0.70), residues: 30
loop : -1.58 (0.32), residues: 442
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.020 0.001 TRP A 613
HIS 0.004 0.001 HIS B 615
PHE 0.034 0.002 PHE B 513
TYR 0.011 0.001 TYR B 456
ARG 0.002 0.000 ARG A 56
*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
2776 Ramachandran restraints generated.
1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
2776 Ramachandran restraints generated.
1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
157 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 25
poor density : 132
time to evaluate : 1.174
Fit side-chains
revert: symmetry clash
REVERT: B 139 MET cc_start: 0.9098 (ttt) cc_final: 0.8883 (ttt)
REVERT: B 157 TYR cc_start: 0.8343 (OUTLIER) cc_final: 0.7796 (t80)
REVERT: B 180 GLN cc_start: 0.7762 (mt0) cc_final: 0.7287 (mt0)
REVERT: B 254 GLU cc_start: 0.7448 (mm-30) cc_final: 0.7208 (mm-30)
REVERT: B 562 ASP cc_start: 0.8429 (m-30) cc_final: 0.7974 (m-30)
REVERT: B 691 ARG cc_start: 0.7628 (OUTLIER) cc_final: 0.7194 (ptm160)
REVERT: A 56 ARG cc_start: 0.8309 (tpm170) cc_final: 0.7749 (tpm170)
REVERT: A 76 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8347 (tt)
REVERT: A 498 LEU cc_start: 0.6585 (OUTLIER) cc_final: 0.6344 (mp)
REVERT: A 541 GLU cc_start: 0.8392 (pt0) cc_final: 0.7857 (pm20)
outliers start: 25
outliers final: 16
residues processed: 145
average time/residue: 0.2327
time to fit residues: 49.9996
Evaluate side-chains
144 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 20
poor density : 124
time to evaluate : 1.303
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue 62 MET
Chi-restraints excluded: chain B residue 76 LEU
Chi-restraints excluded: chain B residue 157 TYR
Chi-restraints excluded: chain B residue 171 TYR
Chi-restraints excluded: chain B residue 286 GLU
Chi-restraints excluded: chain B residue 296 GLU
Chi-restraints excluded: chain B residue 374 ILE
Chi-restraints excluded: chain B residue 409 ILE
Chi-restraints excluded: chain B residue 563 MET
Chi-restraints excluded: chain B residue 566 LEU
Chi-restraints excluded: chain B residue 579 ILE
Chi-restraints excluded: chain B residue 691 ARG
Chi-restraints excluded: chain A residue 76 LEU
Chi-restraints excluded: chain A residue 157 TYR
Chi-restraints excluded: chain A residue 159 ILE
Chi-restraints excluded: chain A residue 171 TYR
Chi-restraints excluded: chain A residue 286 GLU
Chi-restraints excluded: chain A residue 357 PHE
Chi-restraints excluded: chain A residue 498 LEU
Chi-restraints excluded: chain A residue 579 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 138
random chunks:
chunk 22 optimal weight: 1.9990
chunk 129 optimal weight: 0.9990
chunk 71 optimal weight: 2.9990
chunk 56 optimal weight: 0.8980
chunk 42 optimal weight: 0.7980
chunk 8 optimal weight: 0.5980
chunk 66 optimal weight: 0.0870
chunk 23 optimal weight: 2.9990
chunk 25 optimal weight: 5.9990
chunk 81 optimal weight: 0.2980
chunk 125 optimal weight: 2.9990
overall best weight: 0.5358
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
B 392 ASN
A 392 ASN
Total number of N/Q/H flips: 2
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.160501 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.126922 restraints weight = 13789.974|
|-----------------------------------------------------------------------------|
r_work (start): 0.3493 rms_B_bonded: 1.82
r_work: 0.3354 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.3222 rms_B_bonded: 4.34 restraints_weight: 0.2500
r_work (final): 0.3222
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8125
moved from start: 0.2016
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.039 11608 Z= 0.185
Angle : 0.584 8.303 15750 Z= 0.313
Chirality : 0.043 0.219 1814
Planarity : 0.005 0.049 1918
Dihedral : 14.774 148.543 1696
Min Nonbonded Distance : 2.428
Molprobity Statistics.
All-atom Clashscore : 8.48
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 8.00 %
Favored : 92.00 %
Rotamer:
Outliers : 2.15 %
Allowed : 16.23 %
Favored : 81.62 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.15 %
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: 0.32 (0.24), residues: 1388
helix: 1.17 (0.18), residues: 912
sheet: -3.37 (0.70), residues: 30
loop : -1.53 (0.32), residues: 446
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.020 0.001 TRP A 613
HIS 0.004 0.001 HIS A 617
PHE 0.031 0.001 PHE B 513
TYR 0.009 0.001 TYR B 456
ARG 0.001 0.000 ARG B 595
*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
2776 Ramachandran restraints generated.
1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
2776 Ramachandran restraints generated.
1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
163 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 26
poor density : 137
time to evaluate : 1.406
Fit side-chains
revert: symmetry clash
REVERT: B 139 MET cc_start: 0.8992 (ttt) cc_final: 0.8768 (ttt)
REVERT: B 157 TYR cc_start: 0.8386 (OUTLIER) cc_final: 0.7753 (t80)
REVERT: B 180 GLN cc_start: 0.7835 (mt0) cc_final: 0.7423 (mt0)
REVERT: B 254 GLU cc_start: 0.7478 (mm-30) cc_final: 0.7199 (mm-30)
REVERT: B 286 GLU cc_start: 0.7956 (OUTLIER) cc_final: 0.7574 (pp20)
REVERT: B 562 ASP cc_start: 0.8471 (m-30) cc_final: 0.8065 (m-30)
REVERT: B 691 ARG cc_start: 0.7481 (OUTLIER) cc_final: 0.7123 (ptm160)
REVERT: A 56 ARG cc_start: 0.8366 (tpm170) cc_final: 0.7849 (tpt170)
REVERT: A 76 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8303 (tt)
REVERT: A 286 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7756 (pp20)
REVERT: A 541 GLU cc_start: 0.8429 (pt0) cc_final: 0.7904 (pm20)
outliers start: 26
outliers final: 13
residues processed: 151
average time/residue: 0.2183
time to fit residues: 49.2975
Evaluate side-chains
147 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 18
poor density : 129
time to evaluate : 1.270
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue 62 MET
Chi-restraints excluded: chain B residue 157 TYR
Chi-restraints excluded: chain B residue 171 TYR
Chi-restraints excluded: chain B residue 286 GLU
Chi-restraints excluded: chain B residue 296 GLU
Chi-restraints excluded: chain B residue 409 ILE
Chi-restraints excluded: chain B residue 563 MET
Chi-restraints excluded: chain B residue 566 LEU
Chi-restraints excluded: chain B residue 579 ILE
Chi-restraints excluded: chain B residue 691 ARG
Chi-restraints excluded: chain A residue 76 LEU
Chi-restraints excluded: chain A residue 157 TYR
Chi-restraints excluded: chain A residue 159 ILE
Chi-restraints excluded: chain A residue 171 TYR
Chi-restraints excluded: chain A residue 286 GLU
Chi-restraints excluded: chain A residue 357 PHE
Chi-restraints excluded: chain A residue 566 LEU
Chi-restraints excluded: chain A residue 579 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 138
random chunks:
chunk 72 optimal weight: 0.8980
chunk 7 optimal weight: 1.9990
chunk 130 optimal weight: 0.9990
chunk 97 optimal weight: 2.9990
chunk 40 optimal weight: 4.9990
chunk 48 optimal weight: 0.4980
chunk 85 optimal weight: 2.9990
chunk 92 optimal weight: 5.9990
chunk 101 optimal weight: 6.9990
chunk 74 optimal weight: 4.9990
chunk 103 optimal weight: 2.9990
overall best weight: 1.4786
-------------------------------------------------------------------------------
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 = 0.3861 r_free = 0.3861 target = 0.159378 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.124620 restraints weight = 13754.375|
|-----------------------------------------------------------------------------|
r_work (start): 0.3419 rms_B_bonded: 1.85
r_work: 0.3275 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.3142 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.3142
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8217
moved from start: 0.1969
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.005 0.046 11608 Z= 0.302
Angle : 0.644 9.950 15750 Z= 0.345
Chirality : 0.046 0.243 1814
Planarity : 0.005 0.053 1918
Dihedral : 14.764 150.443 1696
Min Nonbonded Distance : 2.427
Molprobity Statistics.
All-atom Clashscore : 8.17
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 9.01 %
Favored : 90.99 %
Rotamer:
Outliers : 1.90 %
Allowed : 17.80 %
Favored : 80.30 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.15 %
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: 0.15 (0.24), residues: 1388
helix: 1.01 (0.18), residues: 918
sheet: -3.43 (0.68), residues: 30
loop : -1.55 (0.32), residues: 440
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.018 0.001 TRP A 613
HIS 0.007 0.001 HIS B 615
PHE 0.072 0.002 PHE B 627
TYR 0.016 0.001 TYR B 456
ARG 0.002 0.000 ARG B 197
*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
2776 Ramachandran restraints generated.
1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
2776 Ramachandran restraints generated.
1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
152 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 23
poor density : 129
time to evaluate : 1.206
Fit side-chains
REVERT: B 157 TYR cc_start: 0.8516 (OUTLIER) cc_final: 0.7913 (t80)
REVERT: B 180 GLN cc_start: 0.7940 (mt0) cc_final: 0.7524 (mt0)
REVERT: B 254 GLU cc_start: 0.7510 (mm-30) cc_final: 0.7259 (mm-30)
REVERT: B 286 GLU cc_start: 0.7973 (OUTLIER) cc_final: 0.7610 (pp20)
REVERT: B 562 ASP cc_start: 0.8459 (m-30) cc_final: 0.8109 (m-30)
REVERT: B 691 ARG cc_start: 0.7855 (OUTLIER) cc_final: 0.7536 (ptm160)
REVERT: A 76 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8325 (tt)
REVERT: A 141 ASN cc_start: 0.8589 (t0) cc_final: 0.8033 (t0)
REVERT: A 286 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7813 (pp20)
REVERT: A 541 GLU cc_start: 0.8473 (pt0) cc_final: 0.7914 (pm20)
outliers start: 23
outliers final: 15
residues processed: 140
average time/residue: 0.2301
time to fit residues: 47.8362
Evaluate side-chains
145 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 20
poor density : 125
time to evaluate : 1.340
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue 62 MET
Chi-restraints excluded: chain B residue 76 LEU
Chi-restraints excluded: chain B residue 157 TYR
Chi-restraints excluded: chain B residue 159 ILE
Chi-restraints excluded: chain B residue 171 TYR
Chi-restraints excluded: chain B residue 286 GLU
Chi-restraints excluded: chain B residue 563 MET
Chi-restraints excluded: chain B residue 566 LEU
Chi-restraints excluded: chain B residue 579 ILE
Chi-restraints excluded: chain B residue 677 CYS
Chi-restraints excluded: chain B residue 691 ARG
Chi-restraints excluded: chain A residue 76 LEU
Chi-restraints excluded: chain A residue 157 TYR
Chi-restraints excluded: chain A residue 159 ILE
Chi-restraints excluded: chain A residue 171 TYR
Chi-restraints excluded: chain A residue 286 GLU
Chi-restraints excluded: chain A residue 296 GLU
Chi-restraints excluded: chain A residue 357 PHE
Chi-restraints excluded: chain A residue 566 LEU
Chi-restraints excluded: chain A residue 579 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 138
random chunks:
chunk 116 optimal weight: 1.9990
chunk 109 optimal weight: 6.9990
chunk 56 optimal weight: 1.9990
chunk 123 optimal weight: 0.8980
chunk 11 optimal weight: 0.7980
chunk 114 optimal weight: 1.9990
chunk 137 optimal weight: 0.3980
chunk 95 optimal weight: 0.0270
chunk 117 optimal weight: 1.9990
chunk 46 optimal weight: 0.7980
chunk 40 optimal weight: 5.9990
overall best weight: 0.5838
-------------------------------------------------------------------------------
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 = 0.3909 r_free = 0.3909 target = 0.163881 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.129515 restraints weight = 13790.967|
|-----------------------------------------------------------------------------|
r_work (start): 0.3482 rms_B_bonded: 1.87
r_work: 0.3344 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.3211 rms_B_bonded: 4.43 restraints_weight: 0.2500
r_work (final): 0.3211
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8127
moved from start: 0.2135
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.046 11608 Z= 0.194
Angle : 0.595 8.884 15750 Z= 0.320
Chirality : 0.043 0.222 1814
Planarity : 0.005 0.049 1918
Dihedral : 14.377 151.669 1696
Min Nonbonded Distance : 2.443
Molprobity Statistics.
All-atom Clashscore : 8.26
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 8.14 %
Favored : 91.86 %
Rotamer:
Outliers : 1.82 %
Allowed : 18.21 %
Favored : 79.97 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.15 %
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: 0.26 (0.24), residues: 1388
helix: 1.14 (0.18), residues: 914
sheet: -3.38 (0.68), residues: 30
loop : -1.60 (0.31), residues: 444
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.020 0.001 TRP A 613
HIS 0.004 0.001 HIS A 617
PHE 0.055 0.001 PHE B 627
TYR 0.018 0.001 TYR A 572
ARG 0.001 0.000 ARG A 450
*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
2776 Ramachandran restraints generated.
1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
2776 Ramachandran restraints generated.
1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
151 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 22
poor density : 129
time to evaluate : 1.370
Fit side-chains
REVERT: B 157 TYR cc_start: 0.8450 (OUTLIER) cc_final: 0.7636 (t80)
REVERT: B 180 GLN cc_start: 0.7873 (mt0) cc_final: 0.7463 (mt0)
REVERT: B 254 GLU cc_start: 0.7493 (mm-30) cc_final: 0.7243 (mm-30)
REVERT: B 286 GLU cc_start: 0.8005 (OUTLIER) cc_final: 0.7697 (pp20)
REVERT: B 562 ASP cc_start: 0.8445 (m-30) cc_final: 0.8035 (m-30)
REVERT: B 691 ARG cc_start: 0.7502 (OUTLIER) cc_final: 0.7156 (ptm160)
REVERT: A 76 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8315 (tt)
REVERT: A 141 ASN cc_start: 0.8463 (t0) cc_final: 0.7890 (t0)
REVERT: A 286 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7794 (pp20)
REVERT: A 541 GLU cc_start: 0.8450 (pt0) cc_final: 0.7853 (pm20)
outliers start: 22
outliers final: 15
residues processed: 139
average time/residue: 0.2287
time to fit residues: 47.5539
Evaluate side-chains
147 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 20
poor density : 127
time to evaluate : 1.347
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue 62 MET
Chi-restraints excluded: chain B residue 76 LEU
Chi-restraints excluded: chain B residue 157 TYR
Chi-restraints excluded: chain B residue 159 ILE
Chi-restraints excluded: chain B residue 171 TYR
Chi-restraints excluded: chain B residue 286 GLU
Chi-restraints excluded: chain B residue 563 MET
Chi-restraints excluded: chain B residue 566 LEU
Chi-restraints excluded: chain B residue 579 ILE
Chi-restraints excluded: chain B residue 691 ARG
Chi-restraints excluded: chain A residue 76 LEU
Chi-restraints excluded: chain A residue 157 TYR
Chi-restraints excluded: chain A residue 159 ILE
Chi-restraints excluded: chain A residue 171 TYR
Chi-restraints excluded: chain A residue 286 GLU
Chi-restraints excluded: chain A residue 296 GLU
Chi-restraints excluded: chain A residue 357 PHE
Chi-restraints excluded: chain A residue 403 VAL
Chi-restraints excluded: chain A residue 566 LEU
Chi-restraints excluded: chain A residue 579 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 138
random chunks:
chunk 121 optimal weight: 3.9990
chunk 0 optimal weight: 5.9990
chunk 117 optimal weight: 1.9990
chunk 57 optimal weight: 0.9980
chunk 46 optimal weight: 0.6980
chunk 3 optimal weight: 0.5980
chunk 118 optimal weight: 0.7980
chunk 52 optimal weight: 0.9990
chunk 8 optimal weight: 0.3980
chunk 82 optimal weight: 0.8980
chunk 53 optimal weight: 0.6980
overall best weight: 0.6380
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
B 392 ASN
Total number of N/Q/H flips: 1
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3912 r_free = 0.3912 target = 0.164210 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.129951 restraints weight = 13698.099|
|-----------------------------------------------------------------------------|
r_work (start): 0.3486 rms_B_bonded: 1.86
r_work: 0.3345 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.3212 rms_B_bonded: 4.48 restraints_weight: 0.2500
r_work (final): 0.3212
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8133
moved from start: 0.2213
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.040 11608 Z= 0.198
Angle : 0.596 8.328 15750 Z= 0.319
Chirality : 0.044 0.240 1814
Planarity : 0.005 0.051 1918
Dihedral : 14.140 153.623 1696
Min Nonbonded Distance : 2.429
Molprobity Statistics.
All-atom Clashscore : 8.00
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 8.14 %
Favored : 91.86 %
Rotamer:
Outliers : 1.99 %
Allowed : 18.29 %
Favored : 79.72 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.15 %
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: 0.33 (0.24), residues: 1388
helix: 1.21 (0.18), residues: 910
sheet: -3.25 (0.70), residues: 30
loop : -1.59 (0.31), residues: 448
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.020 0.001 TRP A 613
HIS 0.004 0.001 HIS B 615
PHE 0.053 0.002 PHE B 627
TYR 0.026 0.001 TYR B 246
ARG 0.002 0.000 ARG A 691
********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
2776 Ramachandran restraints generated.
1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
2776 Ramachandran restraints generated.
1388 Oldfield, 0 Emsley, 1388 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
151 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 24
poor density : 127
time to evaluate : 1.302
Fit side-chains
REVERT: B 157 TYR cc_start: 0.8475 (OUTLIER) cc_final: 0.7649 (t80)
REVERT: B 180 GLN cc_start: 0.7896 (mt0) cc_final: 0.7489 (mt0)
REVERT: B 254 GLU cc_start: 0.7467 (mm-30) cc_final: 0.7216 (mm-30)
REVERT: B 286 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7645 (pp20)
REVERT: B 562 ASP cc_start: 0.8470 (m-30) cc_final: 0.8105 (m-30)
REVERT: B 691 ARG cc_start: 0.7526 (OUTLIER) cc_final: 0.7197 (ptm160)
REVERT: A 76 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.8302 (tt)
REVERT: A 141 ASN cc_start: 0.8454 (t0) cc_final: 0.7887 (t0)
REVERT: A 286 GLU cc_start: 0.8229 (OUTLIER) cc_final: 0.7922 (pp20)
REVERT: A 541 GLU cc_start: 0.8431 (pt0) cc_final: 0.7832 (pm20)
outliers start: 24
outliers final: 17
residues processed: 140
average time/residue: 0.2292
time to fit residues: 47.8705
Evaluate side-chains
145 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 22
poor density : 123
time to evaluate : 1.314
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue 62 MET
Chi-restraints excluded: chain B residue 76 LEU
Chi-restraints excluded: chain B residue 157 TYR
Chi-restraints excluded: chain B residue 159 ILE
Chi-restraints excluded: chain B residue 171 TYR
Chi-restraints excluded: chain B residue 286 GLU
Chi-restraints excluded: chain B residue 409 ILE
Chi-restraints excluded: chain B residue 563 MET
Chi-restraints excluded: chain B residue 566 LEU
Chi-restraints excluded: chain B residue 579 ILE
Chi-restraints excluded: chain B residue 691 ARG
Chi-restraints excluded: chain A residue 76 LEU
Chi-restraints excluded: chain A residue 137 LEU
Chi-restraints excluded: chain A residue 157 TYR
Chi-restraints excluded: chain A residue 159 ILE
Chi-restraints excluded: chain A residue 171 TYR
Chi-restraints excluded: chain A residue 286 GLU
Chi-restraints excluded: chain A residue 296 GLU
Chi-restraints excluded: chain A residue 357 PHE
Chi-restraints excluded: chain A residue 403 VAL
Chi-restraints excluded: chain A residue 566 LEU
Chi-restraints excluded: chain A residue 579 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 138
random chunks:
chunk 61 optimal weight: 0.9980
chunk 110 optimal weight: 0.7980
chunk 58 optimal weight: 2.9990
chunk 36 optimal weight: 0.8980
chunk 26 optimal weight: 7.9990
chunk 75 optimal weight: 0.2980
chunk 0 optimal weight: 5.9990
chunk 121 optimal weight: 0.6980
chunk 55 optimal weight: 0.7980
chunk 114 optimal weight: 3.9990
chunk 91 optimal weight: 0.7980
overall best weight: 0.6780
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
B 299 GLN
Total number of N/Q/H flips: 1
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3914 r_free = 0.3914 target = 0.164514 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.130306 restraints weight = 13703.202|
|-----------------------------------------------------------------------------|
r_work (start): 0.3492 rms_B_bonded: 1.86
r_work: 0.3353 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.3219 rms_B_bonded: 4.45 restraints_weight: 0.2500
r_work (final): 0.3219
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8116
moved from start: 0.2283
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.040 11608 Z= 0.199
Angle : 0.595 8.144 15750 Z= 0.319
Chirality : 0.043 0.211 1814
Planarity : 0.005 0.049 1918
Dihedral : 13.945 156.470 1696
Min Nonbonded Distance : 2.420
Molprobity Statistics.
All-atom Clashscore : 7.83
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 8.07 %
Favored : 91.93 %
Rotamer:
Outliers : 1.99 %
Allowed : 18.46 %
Favored : 79.55 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.15 %
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: 0.26 (0.24), residues: 1388
helix: 1.16 (0.18), residues: 922
sheet: -3.18 (0.70), residues: 30
loop : -1.73 (0.30), residues: 436
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.019 0.001 TRP A 613
HIS 0.004 0.001 HIS A 617
PHE 0.051 0.002 PHE B 627
TYR 0.041 0.001 TYR B 246
ARG 0.002 0.000 ARG A 691
Origin is already at (0, 0, 0), no shifts will be applied
===============================================================================
Job complete
usr+sys time: 5493.90 seconds
wall clock time: 99 minutes 29.27 seconds (5969.27 seconds total)