Starting phenix.real_space_refine
on Wed Jan 22 06:11:29 2025 by dcliebschner
===============================================================================
Processing files:
-------------------------------------------------------------------------------
Found model, /net/cci-nas-00/data/ceres_data/9flx_50542/01_2025/9flx_50542.cif
Found real_map, /net/cci-nas-00/data/ceres_data/9flx_50542/01_2025/9flx_50542.map
Processing PHIL parameters:
-------------------------------------------------------------------------------
Adding command-line PHIL:
-------------------------
refinement.macro_cycles=10
scattering_table=electron
resolution=3.6
write_initial_geo_file=False
Final processed PHIL parameters:
-------------------------------------------------------------------------------
data_manager {
real_map_files = "/net/cci-nas-00/data/ceres_data/9flx_50542/01_2025/9flx_50542.map"
default_real_map = "/net/cci-nas-00/data/ceres_data/9flx_50542/01_2025/9flx_50542.map"
model {
file = "/net/cci-nas-00/data/ceres_data/9flx_50542/01_2025/9flx_50542.cif"
}
default_model = "/net/cci-nas-00/data/ceres_data/9flx_50542/01_2025/9flx_50542.cif"
}
resolution = 3.6
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= 0.137
Set stop_for_unknowns flag
Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
Set to: electron
Number of scattering types: 4
Type Number sf(0) Gaussians
S 77 5.16 5
C 11025 2.51 5
N 2842 2.21 5
O 3731 1.98 5
sf(0) = scattering factor at diffraction angle 0.
Process input model
Symmetric amino acids flipped. Time to flip 7 residue(s): 0.05s
Monomer Library directory:
"/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
Total number of atoms: 17675
Number of models: 1
Model: ""
Number of chains: 1
Chain: "A"
Number of atoms: 2525
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 348, 2525
Classifications: {'peptide': 348}
Link IDs: {'PTRANS': 26, 'TRANS': 321}
Restraints were copied for chains:
C, B, E, D, G, F
Time building chain proxies: 6.33, per 1000 atoms: 0.36
Number of scatterers: 17675
At special positions: 0
Unit cell: (101.175, 102.24, 202.35, 90, 90, 90)
Space group: P 1 (No. 1)
Number of sites at special positions: 0
Number of scattering types: 4
Type Number sf(0)
S 77 16.00
O 3731 8.00
N 2842 7.00
C 11025 6.00
sf(0) = scattering factor at diffraction angle 0.
Number of disulfides: simple=4, symmetry=0
Simple disulfide: pdb=" SG CYS B4092 " - pdb=" SG CYS B4243 " distance=2.03
Simple disulfide: pdb=" SG CYS B4173 " - pdb=" SG CYS B4325 " distance=2.05
Simple disulfide: pdb=" SG CYS B4186 " - pdb=" SG CYS B4236 " distance=2.03
Simple disulfide: pdb=" SG CYS B4270 " - pdb=" SG CYS B4406 " distance=2.04
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: 4.39
Conformation dependent library (CDL) restraints added in 2.5 seconds
4844 Ramachandran restraints generated.
2422 Oldfield, 0 Emsley, 2422 emsley8k and 0 Phi/Psi/2.
Adding C-beta torsion restraints...
Number of C-beta restraints generated: 4466
Finding SS restraints...
Secondary structure from input PDB file:
21 helices and 84 sheets defined
3.7% alpha, 35.3% beta
0 base pairs and 0 stacking pairs defined.
Time for finding SS restraints: 3.91
Creating SS restraints...
Processing helix chain 'B' and resid 4113 through 4115
No H-bonds generated for 'chain 'B' and resid 4113 through 4115'
Processing helix chain 'B' and resid 4129 through 4133
Processing helix chain 'B' and resid 4389 through 4393
Processing helix chain 'A' and resid 4113 through 4115
No H-bonds generated for 'chain 'A' and resid 4113 through 4115'
Processing helix chain 'A' and resid 4129 through 4133
Processing helix chain 'A' and resid 4389 through 4393
Processing helix chain 'C' and resid 4113 through 4115
No H-bonds generated for 'chain 'C' and resid 4113 through 4115'
Processing helix chain 'C' and resid 4129 through 4133
Processing helix chain 'C' and resid 4389 through 4393
Processing helix chain 'D' and resid 4113 through 4115
No H-bonds generated for 'chain 'D' and resid 4113 through 4115'
Processing helix chain 'D' and resid 4129 through 4133
Processing helix chain 'D' and resid 4389 through 4393
Processing helix chain 'E' and resid 4113 through 4115
No H-bonds generated for 'chain 'E' and resid 4113 through 4115'
Processing helix chain 'E' and resid 4129 through 4133
Processing helix chain 'E' and resid 4389 through 4393
Processing helix chain 'F' and resid 4113 through 4115
No H-bonds generated for 'chain 'F' and resid 4113 through 4115'
Processing helix chain 'F' and resid 4129 through 4133
Processing helix chain 'F' and resid 4389 through 4393
Processing helix chain 'G' and resid 4113 through 4115
No H-bonds generated for 'chain 'G' and resid 4113 through 4115'
Processing helix chain 'G' and resid 4129 through 4133
Processing helix chain 'G' and resid 4389 through 4393
Processing sheet with id=AA1, first strand: chain 'B' and resid 4091 through 4092
removed outlier: 6.804A pdb=" N VAL B4091 " --> pdb=" O ASN B4158 " (cutoff:3.500A)
No H-bonds generated for sheet with id=AA1
Processing sheet with id=AA2, first strand: chain 'B' and resid 4096 through 4097
Processing sheet with id=AA3, first strand: chain 'B' and resid 4117 through 4118
Processing sheet with id=AA4, first strand: chain 'B' and resid 4166 through 4168
Processing sheet with id=AA5, first strand: chain 'B' and resid 4171 through 4173
removed outlier: 7.064A pdb=" N ILE B4172 " --> pdb=" O ASN B4255 " (cutoff:3.500A)
Processing sheet with id=AA6, first strand: chain 'B' and resid 4171 through 4173
removed outlier: 7.064A pdb=" N ILE B4172 " --> pdb=" O ASN B4255 " (cutoff:3.500A)
Processing sheet with id=AA7, first strand: chain 'B' and resid 4263 through 4264
Processing sheet with id=AA8, first strand: chain 'B' and resid 4273 through 4276
removed outlier: 5.888A pdb=" N GLY B4273 " --> pdb=" O ASN B4309 " (cutoff:3.500A)
Processing sheet with id=AA9, first strand: chain 'B' and resid 4298 through 4300
removed outlier: 6.670A pdb=" N TRP B4289 " --> pdb=" O VAL B4299 " (cutoff:3.500A)
Processing sheet with id=AB1, first strand: chain 'B' and resid 4298 through 4300
removed outlier: 6.670A pdb=" N TRP B4289 " --> pdb=" O VAL B4299 " (cutoff:3.500A)
Processing sheet with id=AB2, first strand: chain 'B' and resid 4349 through 4352
removed outlier: 6.692A pdb=" N PHE B4349 " --> pdb=" O SER B4416 " (cutoff:3.500A)
removed outlier: 7.712A pdb=" N HIS B4418 " --> pdb=" O PHE B4349 " (cutoff:3.500A)
removed outlier: 6.960A pdb=" N VAL B4351 " --> pdb=" O HIS B4418 " (cutoff:3.500A)
Processing sheet with id=AB3, first strand: chain 'B' and resid 4356 through 4357
Processing sheet with id=AB4, first strand: chain 'A' and resid 4091 through 4092
removed outlier: 6.804A pdb=" N VAL A4091 " --> pdb=" O ASN A4158 " (cutoff:3.500A)
No H-bonds generated for sheet with id=AB4
Processing sheet with id=AB5, first strand: chain 'A' and resid 4096 through 4097
Processing sheet with id=AB6, first strand: chain 'A' and resid 4117 through 4118
Processing sheet with id=AB7, first strand: chain 'A' and resid 4166 through 4168
Processing sheet with id=AB8, first strand: chain 'A' and resid 4171 through 4173
removed outlier: 7.065A pdb=" N ILE A4172 " --> pdb=" O ASN A4255 " (cutoff:3.500A)
Processing sheet with id=AB9, first strand: chain 'A' and resid 4171 through 4173
removed outlier: 7.065A pdb=" N ILE A4172 " --> pdb=" O ASN A4255 " (cutoff:3.500A)
Processing sheet with id=AC1, first strand: chain 'A' and resid 4263 through 4264
Processing sheet with id=AC2, first strand: chain 'A' and resid 4273 through 4276
removed outlier: 5.888A pdb=" N GLY A4273 " --> pdb=" O ASN A4309 " (cutoff:3.500A)
Processing sheet with id=AC3, first strand: chain 'A' and resid 4298 through 4300
removed outlier: 6.669A pdb=" N TRP A4289 " --> pdb=" O VAL A4299 " (cutoff:3.500A)
Processing sheet with id=AC4, first strand: chain 'A' and resid 4298 through 4300
removed outlier: 6.669A pdb=" N TRP A4289 " --> pdb=" O VAL A4299 " (cutoff:3.500A)
Processing sheet with id=AC5, first strand: chain 'A' and resid 4349 through 4352
removed outlier: 6.692A pdb=" N PHE A4349 " --> pdb=" O SER A4416 " (cutoff:3.500A)
removed outlier: 7.713A pdb=" N HIS A4418 " --> pdb=" O PHE A4349 " (cutoff:3.500A)
removed outlier: 6.960A pdb=" N VAL A4351 " --> pdb=" O HIS A4418 " (cutoff:3.500A)
Processing sheet with id=AC6, first strand: chain 'A' and resid 4356 through 4357
Processing sheet with id=AC7, first strand: chain 'C' and resid 4091 through 4092
removed outlier: 6.804A pdb=" N VAL C4091 " --> pdb=" O ASN C4158 " (cutoff:3.500A)
No H-bonds generated for sheet with id=AC7
Processing sheet with id=AC8, first strand: chain 'C' and resid 4096 through 4097
Processing sheet with id=AC9, first strand: chain 'C' and resid 4117 through 4118
Processing sheet with id=AD1, first strand: chain 'C' and resid 4166 through 4168
Processing sheet with id=AD2, first strand: chain 'C' and resid 4171 through 4173
removed outlier: 7.064A pdb=" N ILE C4172 " --> pdb=" O ASN C4255 " (cutoff:3.500A)
Processing sheet with id=AD3, first strand: chain 'C' and resid 4171 through 4173
removed outlier: 7.064A pdb=" N ILE C4172 " --> pdb=" O ASN C4255 " (cutoff:3.500A)
Processing sheet with id=AD4, first strand: chain 'C' and resid 4263 through 4264
Processing sheet with id=AD5, first strand: chain 'C' and resid 4273 through 4276
removed outlier: 5.889A pdb=" N GLY C4273 " --> pdb=" O ASN C4309 " (cutoff:3.500A)
Processing sheet with id=AD6, first strand: chain 'C' and resid 4298 through 4300
removed outlier: 6.670A pdb=" N TRP C4289 " --> pdb=" O VAL C4299 " (cutoff:3.500A)
Processing sheet with id=AD7, first strand: chain 'C' and resid 4298 through 4300
removed outlier: 6.670A pdb=" N TRP C4289 " --> pdb=" O VAL C4299 " (cutoff:3.500A)
Processing sheet with id=AD8, first strand: chain 'C' and resid 4349 through 4352
removed outlier: 6.691A pdb=" N PHE C4349 " --> pdb=" O SER C4416 " (cutoff:3.500A)
removed outlier: 7.712A pdb=" N HIS C4418 " --> pdb=" O PHE C4349 " (cutoff:3.500A)
removed outlier: 6.959A pdb=" N VAL C4351 " --> pdb=" O HIS C4418 " (cutoff:3.500A)
Processing sheet with id=AD9, first strand: chain 'C' and resid 4356 through 4357
Processing sheet with id=AE1, first strand: chain 'D' and resid 4091 through 4092
removed outlier: 6.804A pdb=" N VAL D4091 " --> pdb=" O ASN D4158 " (cutoff:3.500A)
No H-bonds generated for sheet with id=AE1
Processing sheet with id=AE2, first strand: chain 'D' and resid 4096 through 4097
Processing sheet with id=AE3, first strand: chain 'D' and resid 4117 through 4118
Processing sheet with id=AE4, first strand: chain 'D' and resid 4166 through 4168
Processing sheet with id=AE5, first strand: chain 'D' and resid 4171 through 4173
removed outlier: 7.064A pdb=" N ILE D4172 " --> pdb=" O ASN D4255 " (cutoff:3.500A)
Processing sheet with id=AE6, first strand: chain 'D' and resid 4171 through 4173
removed outlier: 7.064A pdb=" N ILE D4172 " --> pdb=" O ASN D4255 " (cutoff:3.500A)
Processing sheet with id=AE7, first strand: chain 'D' and resid 4263 through 4264
Processing sheet with id=AE8, first strand: chain 'D' and resid 4273 through 4276
removed outlier: 5.888A pdb=" N GLY D4273 " --> pdb=" O ASN D4309 " (cutoff:3.500A)
Processing sheet with id=AE9, first strand: chain 'D' and resid 4298 through 4300
removed outlier: 6.669A pdb=" N TRP D4289 " --> pdb=" O VAL D4299 " (cutoff:3.500A)
Processing sheet with id=AF1, first strand: chain 'D' and resid 4298 through 4300
removed outlier: 6.669A pdb=" N TRP D4289 " --> pdb=" O VAL D4299 " (cutoff:3.500A)
Processing sheet with id=AF2, first strand: chain 'D' and resid 4349 through 4352
removed outlier: 6.691A pdb=" N PHE D4349 " --> pdb=" O SER D4416 " (cutoff:3.500A)
removed outlier: 7.711A pdb=" N HIS D4418 " --> pdb=" O PHE D4349 " (cutoff:3.500A)
removed outlier: 6.961A pdb=" N VAL D4351 " --> pdb=" O HIS D4418 " (cutoff:3.500A)
Processing sheet with id=AF3, first strand: chain 'D' and resid 4356 through 4357
Processing sheet with id=AF4, first strand: chain 'E' and resid 4091 through 4092
removed outlier: 6.804A pdb=" N VAL E4091 " --> pdb=" O ASN E4158 " (cutoff:3.500A)
No H-bonds generated for sheet with id=AF4
Processing sheet with id=AF5, first strand: chain 'E' and resid 4096 through 4097
Processing sheet with id=AF6, first strand: chain 'E' and resid 4117 through 4118
Processing sheet with id=AF7, first strand: chain 'E' and resid 4166 through 4168
Processing sheet with id=AF8, first strand: chain 'E' and resid 4171 through 4173
removed outlier: 7.065A pdb=" N ILE E4172 " --> pdb=" O ASN E4255 " (cutoff:3.500A)
Processing sheet with id=AF9, first strand: chain 'E' and resid 4171 through 4173
removed outlier: 7.065A pdb=" N ILE E4172 " --> pdb=" O ASN E4255 " (cutoff:3.500A)
Processing sheet with id=AG1, first strand: chain 'E' and resid 4263 through 4264
Processing sheet with id=AG2, first strand: chain 'E' and resid 4273 through 4276
removed outlier: 5.889A pdb=" N GLY E4273 " --> pdb=" O ASN E4309 " (cutoff:3.500A)
Processing sheet with id=AG3, first strand: chain 'E' and resid 4298 through 4300
removed outlier: 6.669A pdb=" N TRP E4289 " --> pdb=" O VAL E4299 " (cutoff:3.500A)
Processing sheet with id=AG4, first strand: chain 'E' and resid 4298 through 4300
removed outlier: 6.669A pdb=" N TRP E4289 " --> pdb=" O VAL E4299 " (cutoff:3.500A)
Processing sheet with id=AG5, first strand: chain 'E' and resid 4349 through 4352
removed outlier: 6.691A pdb=" N PHE E4349 " --> pdb=" O SER E4416 " (cutoff:3.500A)
removed outlier: 7.712A pdb=" N HIS E4418 " --> pdb=" O PHE E4349 " (cutoff:3.500A)
removed outlier: 6.960A pdb=" N VAL E4351 " --> pdb=" O HIS E4418 " (cutoff:3.500A)
Processing sheet with id=AG6, first strand: chain 'E' and resid 4356 through 4357
Processing sheet with id=AG7, first strand: chain 'F' and resid 4091 through 4092
removed outlier: 6.804A pdb=" N VAL F4091 " --> pdb=" O ASN F4158 " (cutoff:3.500A)
No H-bonds generated for sheet with id=AG7
Processing sheet with id=AG8, first strand: chain 'F' and resid 4096 through 4097
Processing sheet with id=AG9, first strand: chain 'F' and resid 4117 through 4118
Processing sheet with id=AH1, first strand: chain 'F' and resid 4166 through 4168
Processing sheet with id=AH2, first strand: chain 'F' and resid 4171 through 4173
removed outlier: 7.063A pdb=" N ILE F4172 " --> pdb=" O ASN F4255 " (cutoff:3.500A)
Processing sheet with id=AH3, first strand: chain 'F' and resid 4171 through 4173
removed outlier: 7.063A pdb=" N ILE F4172 " --> pdb=" O ASN F4255 " (cutoff:3.500A)
Processing sheet with id=AH4, first strand: chain 'F' and resid 4263 through 4264
Processing sheet with id=AH5, first strand: chain 'F' and resid 4273 through 4276
removed outlier: 5.889A pdb=" N GLY F4273 " --> pdb=" O ASN F4309 " (cutoff:3.500A)
Processing sheet with id=AH6, first strand: chain 'F' and resid 4298 through 4300
removed outlier: 6.670A pdb=" N TRP F4289 " --> pdb=" O VAL F4299 " (cutoff:3.500A)
Processing sheet with id=AH7, first strand: chain 'F' and resid 4298 through 4300
removed outlier: 6.670A pdb=" N TRP F4289 " --> pdb=" O VAL F4299 " (cutoff:3.500A)
Processing sheet with id=AH8, first strand: chain 'F' and resid 4349 through 4352
removed outlier: 6.691A pdb=" N PHE F4349 " --> pdb=" O SER F4416 " (cutoff:3.500A)
removed outlier: 7.712A pdb=" N HIS F4418 " --> pdb=" O PHE F4349 " (cutoff:3.500A)
removed outlier: 6.960A pdb=" N VAL F4351 " --> pdb=" O HIS F4418 " (cutoff:3.500A)
Processing sheet with id=AH9, first strand: chain 'F' and resid 4356 through 4357
Processing sheet with id=AI1, first strand: chain 'G' and resid 4091 through 4092
removed outlier: 6.804A pdb=" N VAL G4091 " --> pdb=" O ASN G4158 " (cutoff:3.500A)
No H-bonds generated for sheet with id=AI1
Processing sheet with id=AI2, first strand: chain 'G' and resid 4096 through 4097
Processing sheet with id=AI3, first strand: chain 'G' and resid 4117 through 4118
Processing sheet with id=AI4, first strand: chain 'G' and resid 4166 through 4168
Processing sheet with id=AI5, first strand: chain 'G' and resid 4171 through 4173
removed outlier: 7.065A pdb=" N ILE G4172 " --> pdb=" O ASN G4255 " (cutoff:3.500A)
Processing sheet with id=AI6, first strand: chain 'G' and resid 4171 through 4173
removed outlier: 7.065A pdb=" N ILE G4172 " --> pdb=" O ASN G4255 " (cutoff:3.500A)
Processing sheet with id=AI7, first strand: chain 'G' and resid 4263 through 4264
Processing sheet with id=AI8, first strand: chain 'G' and resid 4273 through 4276
removed outlier: 5.889A pdb=" N GLY G4273 " --> pdb=" O ASN G4309 " (cutoff:3.500A)
Processing sheet with id=AI9, first strand: chain 'G' and resid 4298 through 4300
removed outlier: 6.670A pdb=" N TRP G4289 " --> pdb=" O VAL G4299 " (cutoff:3.500A)
Processing sheet with id=AJ1, first strand: chain 'G' and resid 4298 through 4300
removed outlier: 6.670A pdb=" N TRP G4289 " --> pdb=" O VAL G4299 " (cutoff:3.500A)
Processing sheet with id=AJ2, first strand: chain 'G' and resid 4349 through 4352
removed outlier: 6.691A pdb=" N PHE G4349 " --> pdb=" O SER G4416 " (cutoff:3.500A)
removed outlier: 7.712A pdb=" N HIS G4418 " --> pdb=" O PHE G4349 " (cutoff:3.500A)
removed outlier: 6.960A pdb=" N VAL G4351 " --> pdb=" O HIS G4418 " (cutoff:3.500A)
Processing sheet with id=AJ3, first strand: chain 'G' and resid 4356 through 4357
567 hydrogen bonds defined for protein.
1260 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: 7.40
Time building geometry restraints manager: 5.08 seconds
NOTE: a complete listing of the restraints can be obtained by requesting
output of .geo file.
Histogram of bond lengths:
1.20 - 1.33: 4643
1.33 - 1.45: 4282
1.45 - 1.57: 9079
1.57 - 1.70: 21
1.70 - 1.82: 84
Bond restraints: 18109
Sorted by residual:
bond pdb=" CA SER C4135 "
pdb=" CB SER C4135 "
ideal model delta sigma weight residual
1.527 1.476 0.051 1.30e-02 5.92e+03 1.54e+01
bond pdb=" CA SER F4135 "
pdb=" CB SER F4135 "
ideal model delta sigma weight residual
1.527 1.477 0.051 1.30e-02 5.92e+03 1.52e+01
bond pdb=" CA SER B4135 "
pdb=" CB SER B4135 "
ideal model delta sigma weight residual
1.527 1.477 0.050 1.30e-02 5.92e+03 1.50e+01
bond pdb=" CA SER E4135 "
pdb=" CB SER E4135 "
ideal model delta sigma weight residual
1.527 1.477 0.050 1.30e-02 5.92e+03 1.50e+01
bond pdb=" CA SER G4135 "
pdb=" CB SER G4135 "
ideal model delta sigma weight residual
1.527 1.477 0.050 1.30e-02 5.92e+03 1.49e+01
... (remaining 18104 not shown)
Histogram of bond angle deviations from ideal:
0.00 - 2.36: 22435
2.36 - 4.71: 2340
4.71 - 7.07: 257
7.07 - 9.43: 42
9.43 - 11.78: 21
Bond angle restraints: 25095
Sorted by residual:
angle pdb=" C GLY D4372 "
pdb=" N PRO D4373 "
pdb=" CA PRO D4373 "
ideal model delta sigma weight residual
119.32 127.50 -8.18 1.14e+00 7.69e-01 5.15e+01
angle pdb=" C GLY F4372 "
pdb=" N PRO F4373 "
pdb=" CA PRO F4373 "
ideal model delta sigma weight residual
119.32 127.49 -8.17 1.14e+00 7.69e-01 5.13e+01
angle pdb=" C GLY G4372 "
pdb=" N PRO G4373 "
pdb=" CA PRO G4373 "
ideal model delta sigma weight residual
119.32 127.48 -8.16 1.14e+00 7.69e-01 5.12e+01
angle pdb=" C GLY B4372 "
pdb=" N PRO B4373 "
pdb=" CA PRO B4373 "
ideal model delta sigma weight residual
119.32 127.46 -8.14 1.14e+00 7.69e-01 5.09e+01
angle pdb=" C GLY E4372 "
pdb=" N PRO E4373 "
pdb=" CA PRO E4373 "
ideal model delta sigma weight residual
119.32 127.45 -8.13 1.14e+00 7.69e-01 5.09e+01
... (remaining 25090 not shown)
Histogram of dihedral angle deviations from ideal:
0.00 - 13.63: 9950
13.63 - 27.26: 445
27.26 - 40.89: 51
40.89 - 54.52: 30
54.52 - 68.15: 22
Dihedral angle restraints: 10498
sinusoidal: 3519
harmonic: 6979
Sorted by residual:
dihedral pdb=" CB CYS B4186 "
pdb=" SG CYS B4186 "
pdb=" SG CYS B4236 "
pdb=" CB CYS B4236 "
ideal model delta sinusoidal sigma weight residual
93.00 37.17 55.83 1 1.00e+01 1.00e-02 4.21e+01
dihedral pdb=" CB CYS B4092 "
pdb=" SG CYS B4092 "
pdb=" SG CYS B4243 "
pdb=" CB CYS B4243 "
ideal model delta sinusoidal sigma weight residual
93.00 136.74 -43.74 1 1.00e+01 1.00e-02 2.66e+01
dihedral pdb=" C PHE D4089 "
pdb=" N PHE D4089 "
pdb=" CA PHE D4089 "
pdb=" CB PHE D4089 "
ideal model delta harmonic sigma weight residual
-122.60 -109.81 -12.79 0 2.50e+00 1.60e-01 2.62e+01
... (remaining 10495 not shown)
Histogram of chiral volume deviations from ideal:
0.000 - 0.064: 1892
0.064 - 0.127: 942
0.127 - 0.191: 239
0.191 - 0.255: 13
0.255 - 0.318: 29
Chirality restraints: 3115
Sorted by residual:
chirality pdb=" CB VAL F4140 "
pdb=" CA VAL F4140 "
pdb=" CG1 VAL F4140 "
pdb=" CG2 VAL F4140 "
both_signs ideal model delta sigma weight residual
False -2.63 -2.31 -0.32 2.00e-01 2.50e+01 2.53e+00
chirality pdb=" CB VAL D4140 "
pdb=" CA VAL D4140 "
pdb=" CG1 VAL D4140 "
pdb=" CG2 VAL D4140 "
both_signs ideal model delta sigma weight residual
False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.46e+00
chirality pdb=" CB VAL A4140 "
pdb=" CA VAL A4140 "
pdb=" CG1 VAL A4140 "
pdb=" CG2 VAL A4140 "
both_signs ideal model delta sigma weight residual
False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.46e+00
... (remaining 3112 not shown)
Planarity restraints: 3255
Sorted by residual:
delta sigma weight rms_deltas residual
plane pdb=" CB TYR C4227 " 0.043 2.00e-02 2.50e+03 2.29e-02 1.05e+01
pdb=" CG TYR C4227 " -0.025 2.00e-02 2.50e+03
pdb=" CD1 TYR C4227 " -0.012 2.00e-02 2.50e+03
pdb=" CD2 TYR C4227 " -0.014 2.00e-02 2.50e+03
pdb=" CE1 TYR C4227 " -0.011 2.00e-02 2.50e+03
pdb=" CE2 TYR C4227 " -0.012 2.00e-02 2.50e+03
pdb=" CZ TYR C4227 " -0.002 2.00e-02 2.50e+03
pdb=" OH TYR C4227 " 0.033 2.00e-02 2.50e+03
delta sigma weight rms_deltas residual
plane pdb=" CB TYR D4227 " 0.043 2.00e-02 2.50e+03 2.29e-02 1.05e+01
pdb=" CG TYR D4227 " -0.025 2.00e-02 2.50e+03
pdb=" CD1 TYR D4227 " -0.012 2.00e-02 2.50e+03
pdb=" CD2 TYR D4227 " -0.014 2.00e-02 2.50e+03
pdb=" CE1 TYR D4227 " -0.010 2.00e-02 2.50e+03
pdb=" CE2 TYR D4227 " -0.013 2.00e-02 2.50e+03
pdb=" CZ TYR D4227 " -0.002 2.00e-02 2.50e+03
pdb=" OH TYR D4227 " 0.034 2.00e-02 2.50e+03
delta sigma weight rms_deltas residual
plane pdb=" CB TYR F4227 " -0.043 2.00e-02 2.50e+03 2.29e-02 1.05e+01
pdb=" CG TYR F4227 " 0.025 2.00e-02 2.50e+03
pdb=" CD1 TYR F4227 " 0.013 2.00e-02 2.50e+03
pdb=" CD2 TYR F4227 " 0.014 2.00e-02 2.50e+03
pdb=" CE1 TYR F4227 " 0.010 2.00e-02 2.50e+03
pdb=" CE2 TYR F4227 " 0.013 2.00e-02 2.50e+03
pdb=" CZ TYR F4227 " 0.002 2.00e-02 2.50e+03
pdb=" OH TYR F4227 " -0.033 2.00e-02 2.50e+03
... (remaining 3252 not shown)
Histogram of nonbonded interaction distances:
2.03 - 2.60: 248
2.60 - 3.18: 15714
3.18 - 3.75: 27019
3.75 - 4.33: 37417
4.33 - 4.90: 59623
Nonbonded interactions: 140021
Sorted by model distance:
nonbonded pdb=" SG CYS E4092 "
pdb=" SG CYS E4243 "
model vdw
2.030 3.760
nonbonded pdb=" SG CYS F4092 "
pdb=" SG CYS F4243 "
model vdw
2.030 3.760
nonbonded pdb=" SG CYS A4092 "
pdb=" SG CYS A4243 "
model vdw
2.030 3.760
nonbonded pdb=" SG CYS C4092 "
pdb=" SG CYS C4243 "
model vdw
2.031 3.760
nonbonded pdb=" SG CYS D4092 "
pdb=" SG CYS D4243 "
model vdw
2.031 3.760
... (remaining 140016 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: 0.17
Found NCS groups:
ncs_group {
reference = chain 'A'
selection = chain 'C'
selection = chain 'B'
selection = chain 'E'
selection = chain 'D'
selection = chain 'G'
selection = chain 'F'
}
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 group one per residue
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: 1.270
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: 0.020
Extract box with map and model: 0.600
Check model and map are aligned: 0.110
Set scattering table: 0.140
Process input model: 38.540
Find NCS groups from input model: 0.410
Set up NCS constraints: 0.050
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:2.780
Set ADP refinement strategy: 0.000
Make a string to write initial .geo file:0.000
Internal consistency checks: 0.000
Total: 43.930
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6265
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 : 0.017 0.087 18109 Z= 1.156
Angle : 1.518 11.783 25095 Z= 1.003
Chirality : 0.078 0.318 3115
Planarity : 0.008 0.028 3255
Dihedral : 9.300 68.146 6020
Min Nonbonded Distance : 2.030
Molprobity Statistics.
All-atom Clashscore : 6.30
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 2.02 %
Favored : 97.98 %
Rotamer:
Outliers : 0.00 %
Allowed : 2.29 %
Favored : 97.71 %
Cbeta Deviations : 0.63 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 0.42 (0.16), residues: 2422
helix: -2.03 (0.93), residues: 42
sheet: -0.24 (0.16), residues: 910
loop : 0.91 (0.15), residues: 1470
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.030 0.005 TRP C4370
HIS 0.009 0.003 HIS C4137
PHE 0.051 0.007 PHE F4399
TYR 0.046 0.008 TYR A4233
ARG 0.001 0.000 ARG F4075
*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
4844 Ramachandran restraints generated.
2422 Oldfield, 0 Emsley, 2422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
4844 Ramachandran restraints generated.
2422 Oldfield, 0 Emsley, 2422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
520 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 0
poor density : 520
time to evaluate : 1.893
Fit side-chains
revert: symmetry clash
REVERT: B 4154 GLN cc_start: 0.8055 (mm-40) cc_final: 0.7818 (tt0)
REVERT: B 4165 THR cc_start: 0.8203 (m) cc_final: 0.7968 (t)
REVERT: B 4176 ASP cc_start: 0.7709 (m-30) cc_final: 0.7391 (m-30)
REVERT: B 4216 SER cc_start: 0.8297 (m) cc_final: 0.7780 (p)
REVERT: B 4259 SER cc_start: 0.7101 (p) cc_final: 0.6871 (m)
REVERT: B 4278 SER cc_start: 0.8060 (p) cc_final: 0.7828 (t)
REVERT: B 4308 SER cc_start: 0.8145 (p) cc_final: 0.7919 (m)
REVERT: B 4402 ASP cc_start: 0.7294 (t0) cc_final: 0.6932 (m-30)
REVERT: A 4216 SER cc_start: 0.8260 (m) cc_final: 0.7782 (p)
REVERT: A 4278 SER cc_start: 0.8168 (p) cc_final: 0.7927 (t)
REVERT: C 4154 GLN cc_start: 0.7889 (mm-40) cc_final: 0.7630 (tt0)
REVERT: C 4216 SER cc_start: 0.8113 (m) cc_final: 0.7676 (p)
REVERT: C 4278 SER cc_start: 0.8244 (p) cc_final: 0.8024 (t)
REVERT: C 4302 ASN cc_start: 0.7446 (m-40) cc_final: 0.7058 (t0)
REVERT: D 4147 GLN cc_start: 0.7905 (mt0) cc_final: 0.7625 (mt0)
REVERT: D 4278 SER cc_start: 0.8171 (p) cc_final: 0.7925 (t)
REVERT: D 4302 ASN cc_start: 0.7722 (m-40) cc_final: 0.7270 (t0)
REVERT: D 4368 TYR cc_start: 0.7756 (m-80) cc_final: 0.7431 (m-80)
REVERT: D 4379 ASN cc_start: 0.7796 (p0) cc_final: 0.7578 (p0)
REVERT: E 4216 SER cc_start: 0.8163 (m) cc_final: 0.7596 (p)
REVERT: E 4278 SER cc_start: 0.8240 (p) cc_final: 0.7894 (t)
REVERT: E 4302 ASN cc_start: 0.7435 (m-40) cc_final: 0.6966 (t0)
REVERT: E 4379 ASN cc_start: 0.7566 (p0) cc_final: 0.7237 (p0)
REVERT: F 4165 THR cc_start: 0.7847 (m) cc_final: 0.7625 (t)
REVERT: F 4216 SER cc_start: 0.8384 (m) cc_final: 0.7735 (p)
REVERT: F 4259 SER cc_start: 0.7057 (p) cc_final: 0.6813 (m)
REVERT: F 4278 SER cc_start: 0.8136 (p) cc_final: 0.7825 (t)
REVERT: F 4302 ASN cc_start: 0.7278 (m-40) cc_final: 0.6830 (t0)
REVERT: F 4304 ASN cc_start: 0.7007 (m-40) cc_final: 0.6782 (m-40)
REVERT: F 4379 ASN cc_start: 0.7547 (p0) cc_final: 0.7163 (p0)
REVERT: F 4402 ASP cc_start: 0.7208 (t0) cc_final: 0.6629 (m-30)
REVERT: G 4165 THR cc_start: 0.8213 (m) cc_final: 0.7992 (t)
REVERT: G 4216 SER cc_start: 0.8566 (m) cc_final: 0.7998 (p)
REVERT: G 4259 SER cc_start: 0.7170 (p) cc_final: 0.6951 (m)
REVERT: G 4278 SER cc_start: 0.8100 (p) cc_final: 0.7855 (t)
REVERT: G 4308 SER cc_start: 0.8066 (p) cc_final: 0.7813 (m)
REVERT: G 4410 ASP cc_start: 0.8596 (p0) cc_final: 0.8331 (p0)
outliers start: 0
outliers final: 0
residues processed: 520
average time/residue: 0.2066
time to fit residues: 184.2147
Evaluate side-chains
260 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 0
poor density : 260
time to evaluate : 2.190
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 238
random chunks:
chunk 200 optimal weight: 1.9990
chunk 180 optimal weight: 0.7980
chunk 100 optimal weight: 0.8980
chunk 61 optimal weight: 0.8980
chunk 121 optimal weight: 2.9990
chunk 96 optimal weight: 4.9990
chunk 186 optimal weight: 1.9990
chunk 72 optimal weight: 0.9980
chunk 113 optimal weight: 0.8980
chunk 138 optimal weight: 0.9990
chunk 216 optimal weight: 0.9990
overall best weight: 0.8980
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
B4147 GLN
B4185 ASN
B4414 GLN
A4147 GLN
C4414 GLN
D4147 GLN
E4147 GLN
E4185 ASN
E4414 GLN
F4147 GLN
F4414 GLN
** G4142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G4414 GLN
Total number of N/Q/H flips: 12
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.113546 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2932 r_free = 0.2932 target = 0.096691 restraints weight = 22868.178|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2954 r_free = 0.2954 target = 0.098263 restraints weight = 14762.919|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2965 r_free = 0.2965 target = 0.099118 restraints weight = 9998.307|
|-----------------------------------------------------------------------------|
r_work (final): 0.2977
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8263
moved from start: 0.2598
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.030 18109 Z= 0.219
Angle : 0.588 6.907 25095 Z= 0.324
Chirality : 0.047 0.151 3115
Planarity : 0.005 0.052 3255
Dihedral : 5.268 19.112 2527
Min Nonbonded Distance : 2.139
Molprobity Statistics.
All-atom Clashscore : 5.16
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 0.62 %
Favored : 99.38 %
Rotamer:
Outliers : 3.17 %
Allowed : 10.48 %
Favored : 86.35 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 0.53 (0.16), residues: 2422
helix: -2.91 (0.61), residues: 42
sheet: 0.21 (0.16), residues: 875
loop : 0.70 (0.16), residues: 1505
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.016 0.002 TRP C4370
HIS 0.003 0.001 HIS D4137
PHE 0.017 0.002 PHE G4399
TYR 0.019 0.001 TYR D4233
ARG 0.001 0.000 ARG G4075
*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
4844 Ramachandran restraints generated.
2422 Oldfield, 0 Emsley, 2422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
4844 Ramachandran restraints generated.
2422 Oldfield, 0 Emsley, 2422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
382 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 65
poor density : 317
time to evaluate : 2.115
Fit side-chains
REVERT: B 4165 THR cc_start: 0.8346 (m) cc_final: 0.7849 (p)
REVERT: B 4259 SER cc_start: 0.8171 (p) cc_final: 0.7847 (m)
REVERT: B 4278 SER cc_start: 0.9020 (p) cc_final: 0.8660 (t)
REVERT: A 4278 SER cc_start: 0.9019 (p) cc_final: 0.8791 (t)
REVERT: A 4379 ASN cc_start: 0.8446 (p0) cc_final: 0.7900 (p0)
REVERT: A 4402 ASP cc_start: 0.8107 (t0) cc_final: 0.7822 (m-30)
REVERT: C 4308 SER cc_start: 0.8657 (OUTLIER) cc_final: 0.8440 (p)
REVERT: D 4139 TYR cc_start: 0.9273 (p90) cc_final: 0.9056 (p90)
REVERT: D 4176 ASP cc_start: 0.7770 (m-30) cc_final: 0.7522 (m-30)
REVERT: D 4278 SER cc_start: 0.8999 (p) cc_final: 0.8758 (t)
REVERT: D 4379 ASN cc_start: 0.8540 (p0) cc_final: 0.8108 (p0)
REVERT: E 4379 ASN cc_start: 0.8393 (p0) cc_final: 0.7922 (p0)
REVERT: F 4147 GLN cc_start: 0.8698 (mt0) cc_final: 0.8362 (mt0)
REVERT: F 4259 SER cc_start: 0.7999 (p) cc_final: 0.7675 (m)
REVERT: F 4402 ASP cc_start: 0.7908 (t0) cc_final: 0.7565 (m-30)
REVERT: G 4147 GLN cc_start: 0.8702 (mt0) cc_final: 0.8379 (mt0)
REVERT: G 4216 SER cc_start: 0.8650 (m) cc_final: 0.8284 (p)
REVERT: G 4238 ASP cc_start: 0.7643 (t0) cc_final: 0.7425 (t0)
REVERT: G 4259 SER cc_start: 0.8201 (p) cc_final: 0.7890 (m)
REVERT: G 4379 ASN cc_start: 0.8551 (p0) cc_final: 0.8091 (p0)
outliers start: 65
outliers final: 42
residues processed: 355
average time/residue: 0.2203
time to fit residues: 133.4132
Evaluate side-chains
256 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 43
poor density : 213
time to evaluate : 1.999
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue 4075 ARG
Chi-restraints excluded: chain B residue 4167 THR
Chi-restraints excluded: chain B residue 4239 THR
Chi-restraints excluded: chain B residue 4397 THR
Chi-restraints excluded: chain A residue 4075 ARG
Chi-restraints excluded: chain A residue 4099 LEU
Chi-restraints excluded: chain A residue 4107 SER
Chi-restraints excluded: chain A residue 4240 ILE
Chi-restraints excluded: chain A residue 4259 SER
Chi-restraints excluded: chain A residue 4308 SER
Chi-restraints excluded: chain A residue 4387 SER
Chi-restraints excluded: chain A residue 4400 ILE
Chi-restraints excluded: chain C residue 4075 ARG
Chi-restraints excluded: chain C residue 4082 THR
Chi-restraints excluded: chain C residue 4107 SER
Chi-restraints excluded: chain C residue 4167 THR
Chi-restraints excluded: chain C residue 4239 THR
Chi-restraints excluded: chain C residue 4257 ILE
Chi-restraints excluded: chain C residue 4259 SER
Chi-restraints excluded: chain C residue 4308 SER
Chi-restraints excluded: chain C residue 4397 THR
Chi-restraints excluded: chain D residue 4099 LEU
Chi-restraints excluded: chain D residue 4130 LEU
Chi-restraints excluded: chain D residue 4239 THR
Chi-restraints excluded: chain D residue 4259 SER
Chi-restraints excluded: chain D residue 4308 SER
Chi-restraints excluded: chain E residue 4107 SER
Chi-restraints excluded: chain E residue 4130 LEU
Chi-restraints excluded: chain E residue 4167 THR
Chi-restraints excluded: chain E residue 4286 THR
Chi-restraints excluded: chain E residue 4400 ILE
Chi-restraints excluded: chain F residue 4075 ARG
Chi-restraints excluded: chain F residue 4076 ILE
Chi-restraints excluded: chain F residue 4107 SER
Chi-restraints excluded: chain F residue 4167 THR
Chi-restraints excluded: chain F residue 4240 ILE
Chi-restraints excluded: chain F residue 4257 ILE
Chi-restraints excluded: chain F residue 4308 SER
Chi-restraints excluded: chain G residue 4106 THR
Chi-restraints excluded: chain G residue 4167 THR
Chi-restraints excluded: chain G residue 4286 THR
Chi-restraints excluded: chain G residue 4387 SER
Chi-restraints excluded: chain G residue 4395 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 238
random chunks:
chunk 89 optimal weight: 3.9990
chunk 214 optimal weight: 0.9990
chunk 130 optimal weight: 0.1980
chunk 165 optimal weight: 5.9990
chunk 35 optimal weight: 0.7980
chunk 102 optimal weight: 8.9990
chunk 88 optimal weight: 0.9990
chunk 153 optimal weight: 3.9990
chunk 84 optimal weight: 1.9990
chunk 196 optimal weight: 6.9990
chunk 116 optimal weight: 3.9990
overall best weight: 0.9986
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
B4142 ASN
B4185 ASN
A4142 ASN
D4142 ASN
E4142 ASN
E4185 ASN
F4142 ASN
G4142 ASN
Total number of N/Q/H flips: 8
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.118943 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3005 r_free = 0.3005 target = 0.100771 restraints weight = 22379.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3039 r_free = 0.3039 target = 0.103285 restraints weight = 12898.706|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3063 r_free = 0.3063 target = 0.104997 restraints weight = 8550.325|
|-----------------------------------------------------------------------------|
r_work (final): 0.2929
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8291
moved from start: 0.3254
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.050 18109 Z= 0.224
Angle : 0.556 6.188 25095 Z= 0.298
Chirality : 0.046 0.156 3115
Planarity : 0.005 0.040 3255
Dihedral : 4.846 19.268 2527
Min Nonbonded Distance : 2.217
Molprobity Statistics.
All-atom Clashscore : 4.87
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 1.36 %
Favored : 98.64 %
Rotamer:
Outliers : 3.71 %
Allowed : 12.19 %
Favored : 84.11 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 0.48 (0.17), residues: 2422
helix: -3.04 (0.56), residues: 42
sheet: 0.03 (0.17), residues: 903
loop : 0.80 (0.16), residues: 1477
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.014 0.002 TRP A4370
HIS 0.004 0.001 HIS B4137
PHE 0.014 0.001 PHE G4399
TYR 0.021 0.001 TYR A4139
ARG 0.001 0.000 ARG D4075
*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
4844 Ramachandran restraints generated.
2422 Oldfield, 0 Emsley, 2422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
4844 Ramachandran restraints generated.
2422 Oldfield, 0 Emsley, 2422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
329 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 76
poor density : 253
time to evaluate : 1.828
Fit side-chains
revert: symmetry clash
REVERT: B 4259 SER cc_start: 0.8079 (p) cc_final: 0.7717 (m)
REVERT: B 4278 SER cc_start: 0.9163 (p) cc_final: 0.8735 (t)
REVERT: A 4278 SER cc_start: 0.9153 (p) cc_final: 0.8778 (t)
REVERT: A 4379 ASN cc_start: 0.8547 (p0) cc_final: 0.8063 (p0)
REVERT: D 4176 ASP cc_start: 0.7722 (m-30) cc_final: 0.7464 (m-30)
REVERT: D 4278 SER cc_start: 0.9045 (p) cc_final: 0.8663 (t)
REVERT: D 4308 SER cc_start: 0.8663 (OUTLIER) cc_final: 0.8400 (p)
REVERT: D 4379 ASN cc_start: 0.8719 (p0) cc_final: 0.8269 (p0)
REVERT: E 4379 ASN cc_start: 0.8602 (p0) cc_final: 0.8198 (p0)
REVERT: F 4259 SER cc_start: 0.7950 (p) cc_final: 0.7629 (m)
REVERT: F 4308 SER cc_start: 0.8782 (OUTLIER) cc_final: 0.8503 (p)
REVERT: G 4147 GLN cc_start: 0.8754 (mt0) cc_final: 0.8416 (mt0)
REVERT: G 4259 SER cc_start: 0.8035 (p) cc_final: 0.7732 (m)
REVERT: G 4379 ASN cc_start: 0.8636 (p0) cc_final: 0.8174 (p0)
outliers start: 76
outliers final: 51
residues processed: 310
average time/residue: 0.2148
time to fit residues: 113.4894
Evaluate side-chains
257 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 53
poor density : 204
time to evaluate : 1.877
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue 4107 SER
Chi-restraints excluded: chain B residue 4167 THR
Chi-restraints excluded: chain B residue 4179 THR
Chi-restraints excluded: chain B residue 4239 THR
Chi-restraints excluded: chain B residue 4306 THR
Chi-restraints excluded: chain B residue 4311 THR
Chi-restraints excluded: chain B residue 4339 VAL
Chi-restraints excluded: chain B residue 4387 SER
Chi-restraints excluded: chain B residue 4400 ILE
Chi-restraints excluded: chain A residue 4167 THR
Chi-restraints excluded: chain A residue 4179 THR
Chi-restraints excluded: chain A residue 4240 ILE
Chi-restraints excluded: chain A residue 4306 THR
Chi-restraints excluded: chain A residue 4308 SER
Chi-restraints excluded: chain A residue 4400 ILE
Chi-restraints excluded: chain C residue 4082 THR
Chi-restraints excluded: chain C residue 4167 THR
Chi-restraints excluded: chain C residue 4234 MET
Chi-restraints excluded: chain C residue 4257 ILE
Chi-restraints excluded: chain C residue 4387 SER
Chi-restraints excluded: chain D residue 4075 ARG
Chi-restraints excluded: chain D residue 4107 SER
Chi-restraints excluded: chain D residue 4130 LEU
Chi-restraints excluded: chain D residue 4179 THR
Chi-restraints excluded: chain D residue 4270 CYS
Chi-restraints excluded: chain D residue 4308 SER
Chi-restraints excluded: chain D residue 4387 SER
Chi-restraints excluded: chain E residue 4075 ARG
Chi-restraints excluded: chain E residue 4167 THR
Chi-restraints excluded: chain E residue 4240 ILE
Chi-restraints excluded: chain E residue 4257 ILE
Chi-restraints excluded: chain E residue 4286 THR
Chi-restraints excluded: chain E residue 4306 THR
Chi-restraints excluded: chain F residue 4099 LEU
Chi-restraints excluded: chain F residue 4107 SER
Chi-restraints excluded: chain F residue 4167 THR
Chi-restraints excluded: chain F residue 4173 CYS
Chi-restraints excluded: chain F residue 4234 MET
Chi-restraints excluded: chain F residue 4240 ILE
Chi-restraints excluded: chain F residue 4257 ILE
Chi-restraints excluded: chain F residue 4270 CYS
Chi-restraints excluded: chain F residue 4286 THR
Chi-restraints excluded: chain F residue 4306 THR
Chi-restraints excluded: chain F residue 4308 SER
Chi-restraints excluded: chain F residue 4387 SER
Chi-restraints excluded: chain G residue 4075 ARG
Chi-restraints excluded: chain G residue 4107 SER
Chi-restraints excluded: chain G residue 4210 VAL
Chi-restraints excluded: chain G residue 4240 ILE
Chi-restraints excluded: chain G residue 4257 ILE
Chi-restraints excluded: chain G residue 4286 THR
Chi-restraints excluded: chain G residue 4387 SER
Chi-restraints excluded: chain G residue 4395 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 238
random chunks:
chunk 30 optimal weight: 3.9990
chunk 57 optimal weight: 4.9990
chunk 221 optimal weight: 0.9990
chunk 229 optimal weight: 0.2980
chunk 78 optimal weight: 4.9990
chunk 181 optimal weight: 1.9990
chunk 12 optimal weight: 0.0470
chunk 179 optimal weight: 3.9990
chunk 58 optimal weight: 0.6980
chunk 196 optimal weight: 6.9990
chunk 56 optimal weight: 1.9990
overall best weight: 0.8082
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** A4142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C4142 ASN
Total number of N/Q/H flips: 1
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.130828 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.115007 restraints weight = 21716.486|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.117049 restraints weight = 12832.952|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.118473 restraints weight = 8612.258|
|-----------------------------------------------------------------------------|
r_work (final): 0.2900
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8322
moved from start: 0.3615
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.036 18109 Z= 0.185
Angle : 0.516 6.502 25095 Z= 0.274
Chirality : 0.045 0.144 3115
Planarity : 0.005 0.045 3255
Dihedral : 4.586 16.988 2527
Min Nonbonded Distance : 2.412
Molprobity Statistics.
All-atom Clashscore : 4.47
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 1.45 %
Favored : 98.55 %
Rotamer:
Outliers : 3.32 %
Allowed : 14.48 %
Favored : 82.20 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 0.48 (0.17), residues: 2422
helix: -3.41 (0.44), residues: 42
sheet: 0.08 (0.17), residues: 938
loop : 0.79 (0.16), residues: 1442
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.011 0.001 TRP A4370
HIS 0.002 0.001 HIS D4137
PHE 0.019 0.001 PHE G4399
TYR 0.014 0.001 TYR F4139
ARG 0.001 0.000 ARG A4244
*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
4844 Ramachandran restraints generated.
2422 Oldfield, 0 Emsley, 2422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
4844 Ramachandran restraints generated.
2422 Oldfield, 0 Emsley, 2422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
322 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 68
poor density : 254
time to evaluate : 1.806
Fit side-chains
REVERT: B 4259 SER cc_start: 0.8060 (p) cc_final: 0.7665 (m)
REVERT: B 4278 SER cc_start: 0.9193 (p) cc_final: 0.8794 (t)
REVERT: A 4278 SER cc_start: 0.9177 (p) cc_final: 0.8738 (t)
REVERT: A 4379 ASN cc_start: 0.8631 (p0) cc_final: 0.8190 (p0)
REVERT: D 4185 ASN cc_start: 0.8455 (p0) cc_final: 0.8224 (p0)
REVERT: D 4278 SER cc_start: 0.9092 (p) cc_final: 0.8680 (t)
REVERT: D 4308 SER cc_start: 0.8711 (OUTLIER) cc_final: 0.8490 (p)
REVERT: D 4379 ASN cc_start: 0.8772 (p0) cc_final: 0.8326 (p0)
REVERT: E 4269 ILE cc_start: 0.7982 (mm) cc_final: 0.7487 (pt)
REVERT: E 4379 ASN cc_start: 0.8652 (p0) cc_final: 0.8307 (p0)
REVERT: F 4259 SER cc_start: 0.7900 (p) cc_final: 0.7499 (m)
REVERT: F 4308 SER cc_start: 0.8780 (OUTLIER) cc_final: 0.8550 (p)
REVERT: F 4309 ASN cc_start: 0.8899 (t0) cc_final: 0.8638 (t0)
REVERT: G 4259 SER cc_start: 0.7949 (p) cc_final: 0.7599 (m)
REVERT: G 4269 ILE cc_start: 0.7988 (mm) cc_final: 0.7562 (pt)
REVERT: G 4379 ASN cc_start: 0.8710 (p0) cc_final: 0.8349 (p0)
outliers start: 68
outliers final: 53
residues processed: 305
average time/residue: 0.2386
time to fit residues: 124.3982
Evaluate side-chains
263 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 55
poor density : 208
time to evaluate : 1.972
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue 4107 SER
Chi-restraints excluded: chain B residue 4167 THR
Chi-restraints excluded: chain B residue 4257 ILE
Chi-restraints excluded: chain B residue 4306 THR
Chi-restraints excluded: chain B residue 4308 SER
Chi-restraints excluded: chain B residue 4311 THR
Chi-restraints excluded: chain B residue 4339 VAL
Chi-restraints excluded: chain B residue 4387 SER
Chi-restraints excluded: chain A residue 4107 SER
Chi-restraints excluded: chain A residue 4167 THR
Chi-restraints excluded: chain A residue 4259 SER
Chi-restraints excluded: chain A residue 4306 THR
Chi-restraints excluded: chain A residue 4308 SER
Chi-restraints excluded: chain A residue 4387 SER
Chi-restraints excluded: chain A residue 4400 ILE
Chi-restraints excluded: chain C residue 4082 THR
Chi-restraints excluded: chain C residue 4107 SER
Chi-restraints excluded: chain C residue 4167 THR
Chi-restraints excluded: chain C residue 4179 THR
Chi-restraints excluded: chain C residue 4239 THR
Chi-restraints excluded: chain C residue 4259 SER
Chi-restraints excluded: chain C residue 4364 VAL
Chi-restraints excluded: chain C residue 4387 SER
Chi-restraints excluded: chain D residue 4075 ARG
Chi-restraints excluded: chain D residue 4107 SER
Chi-restraints excluded: chain D residue 4130 LEU
Chi-restraints excluded: chain D residue 4257 ILE
Chi-restraints excluded: chain D residue 4259 SER
Chi-restraints excluded: chain D residue 4308 SER
Chi-restraints excluded: chain D residue 4387 SER
Chi-restraints excluded: chain E residue 4075 ARG
Chi-restraints excluded: chain E residue 4130 LEU
Chi-restraints excluded: chain E residue 4167 THR
Chi-restraints excluded: chain E residue 4240 ILE
Chi-restraints excluded: chain E residue 4257 ILE
Chi-restraints excluded: chain E residue 4286 THR
Chi-restraints excluded: chain E residue 4308 SER
Chi-restraints excluded: chain F residue 4167 THR
Chi-restraints excluded: chain F residue 4173 CYS
Chi-restraints excluded: chain F residue 4179 THR
Chi-restraints excluded: chain F residue 4234 MET
Chi-restraints excluded: chain F residue 4240 ILE
Chi-restraints excluded: chain F residue 4286 THR
Chi-restraints excluded: chain F residue 4308 SER
Chi-restraints excluded: chain F residue 4387 SER
Chi-restraints excluded: chain G residue 4075 ARG
Chi-restraints excluded: chain G residue 4107 SER
Chi-restraints excluded: chain G residue 4179 THR
Chi-restraints excluded: chain G residue 4210 VAL
Chi-restraints excluded: chain G residue 4240 ILE
Chi-restraints excluded: chain G residue 4257 ILE
Chi-restraints excluded: chain G residue 4286 THR
Chi-restraints excluded: chain G residue 4302 ASN
Chi-restraints excluded: chain G residue 4306 THR
Chi-restraints excluded: chain G residue 4395 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 238
random chunks:
chunk 217 optimal weight: 4.9990
chunk 228 optimal weight: 3.9990
chunk 7 optimal weight: 5.9990
chunk 32 optimal weight: 0.9990
chunk 62 optimal weight: 0.9980
chunk 111 optimal weight: 0.8980
chunk 211 optimal weight: 9.9990
chunk 204 optimal weight: 7.9990
chunk 71 optimal weight: 7.9990
chunk 148 optimal weight: 2.9990
chunk 208 optimal weight: 5.9990
overall best weight: 1.9786
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
B4142 ASN
** A4142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E4185 ASN
F4142 ASN
** G4142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
Total number of N/Q/H flips: 3
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3014 r_free = 0.3014 target = 0.103626 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.2768 r_free = 0.2768 target = 0.086030 restraints weight = 23691.199|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2793 r_free = 0.2793 target = 0.087677 restraints weight = 15954.365|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2811 r_free = 0.2811 target = 0.088888 restraints weight = 11866.406|
|-----------------------------------------------------------------------------|
r_work (final): 0.2779
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8436
moved from start: 0.3897
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.006 0.040 18109 Z= 0.368
Angle : 0.609 6.729 25095 Z= 0.323
Chirality : 0.048 0.191 3115
Planarity : 0.005 0.056 3255
Dihedral : 5.045 18.256 2527
Min Nonbonded Distance : 2.244
Molprobity Statistics.
All-atom Clashscore : 5.66
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 2.68 %
Favored : 97.32 %
Rotamer:
Outliers : 4.29 %
Allowed : 14.82 %
Favored : 80.89 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 0.14 (0.17), residues: 2422
helix: -3.70 (0.38), residues: 42
sheet: -0.18 (0.17), residues: 896
loop : 0.56 (0.16), residues: 1484
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.011 0.002 TRP F4232
HIS 0.004 0.002 HIS B4137
PHE 0.017 0.002 PHE G4399
TYR 0.015 0.002 TYR F4337
ARG 0.001 0.000 ARG G4075
*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
4844 Ramachandran restraints generated.
2422 Oldfield, 0 Emsley, 2422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
4844 Ramachandran restraints generated.
2422 Oldfield, 0 Emsley, 2422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
313 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 88
poor density : 225
time to evaluate : 1.717
Fit side-chains
REVERT: B 4259 SER cc_start: 0.8226 (p) cc_final: 0.7774 (m)
REVERT: A 4368 TYR cc_start: 0.9082 (m-80) cc_final: 0.8599 (m-80)
REVERT: A 4379 ASN cc_start: 0.8849 (p0) cc_final: 0.8357 (p0)
REVERT: D 4117 GLN cc_start: 0.8587 (tm-30) cc_final: 0.8301 (tm-30)
REVERT: D 4308 SER cc_start: 0.8725 (OUTLIER) cc_final: 0.8445 (p)
REVERT: D 4379 ASN cc_start: 0.8931 (p0) cc_final: 0.8254 (p0)
REVERT: E 4269 ILE cc_start: 0.8105 (mm) cc_final: 0.7671 (pt)
REVERT: E 4379 ASN cc_start: 0.8900 (p0) cc_final: 0.8531 (p0)
REVERT: F 4117 GLN cc_start: 0.8533 (tm-30) cc_final: 0.8284 (tm-30)
REVERT: F 4259 SER cc_start: 0.8074 (p) cc_final: 0.7623 (m)
REVERT: G 4259 SER cc_start: 0.8148 (p) cc_final: 0.7734 (m)
REVERT: G 4269 ILE cc_start: 0.8079 (mm) cc_final: 0.7637 (pt)
REVERT: G 4379 ASN cc_start: 0.8856 (p0) cc_final: 0.8455 (p0)
outliers start: 88
outliers final: 63
residues processed: 291
average time/residue: 0.2158
time to fit residues: 106.2711
Evaluate side-chains
250 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 64
poor density : 186
time to evaluate : 1.750
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue 4091 VAL
Chi-restraints excluded: chain B residue 4167 THR
Chi-restraints excluded: chain B residue 4210 VAL
Chi-restraints excluded: chain B residue 4239 THR
Chi-restraints excluded: chain B residue 4240 ILE
Chi-restraints excluded: chain B residue 4257 ILE
Chi-restraints excluded: chain B residue 4260 THR
Chi-restraints excluded: chain B residue 4306 THR
Chi-restraints excluded: chain B residue 4308 SER
Chi-restraints excluded: chain B residue 4311 THR
Chi-restraints excluded: chain B residue 4339 VAL
Chi-restraints excluded: chain B residue 4387 SER
Chi-restraints excluded: chain A residue 4082 THR
Chi-restraints excluded: chain A residue 4107 SER
Chi-restraints excluded: chain A residue 4167 THR
Chi-restraints excluded: chain A residue 4222 SER
Chi-restraints excluded: chain A residue 4306 THR
Chi-restraints excluded: chain A residue 4308 SER
Chi-restraints excluded: chain A residue 4387 SER
Chi-restraints excluded: chain A residue 4400 ILE
Chi-restraints excluded: chain C residue 4082 THR
Chi-restraints excluded: chain C residue 4100 THR
Chi-restraints excluded: chain C residue 4107 SER
Chi-restraints excluded: chain C residue 4167 THR
Chi-restraints excluded: chain C residue 4234 MET
Chi-restraints excluded: chain C residue 4239 THR
Chi-restraints excluded: chain C residue 4257 ILE
Chi-restraints excluded: chain C residue 4308 SER
Chi-restraints excluded: chain C residue 4311 THR
Chi-restraints excluded: chain C residue 4387 SER
Chi-restraints excluded: chain D residue 4075 ARG
Chi-restraints excluded: chain D residue 4107 SER
Chi-restraints excluded: chain D residue 4130 LEU
Chi-restraints excluded: chain D residue 4173 CYS
Chi-restraints excluded: chain D residue 4306 THR
Chi-restraints excluded: chain D residue 4308 SER
Chi-restraints excluded: chain D residue 4387 SER
Chi-restraints excluded: chain E residue 4075 ARG
Chi-restraints excluded: chain E residue 4167 THR
Chi-restraints excluded: chain E residue 4240 ILE
Chi-restraints excluded: chain E residue 4257 ILE
Chi-restraints excluded: chain E residue 4286 THR
Chi-restraints excluded: chain E residue 4306 THR
Chi-restraints excluded: chain E residue 4308 SER
Chi-restraints excluded: chain E residue 4387 SER
Chi-restraints excluded: chain F residue 4107 SER
Chi-restraints excluded: chain F residue 4167 THR
Chi-restraints excluded: chain F residue 4173 CYS
Chi-restraints excluded: chain F residue 4234 MET
Chi-restraints excluded: chain F residue 4240 ILE
Chi-restraints excluded: chain F residue 4257 ILE
Chi-restraints excluded: chain F residue 4286 THR
Chi-restraints excluded: chain F residue 4306 THR
Chi-restraints excluded: chain F residue 4308 SER
Chi-restraints excluded: chain F residue 4387 SER
Chi-restraints excluded: chain G residue 4120 LEU
Chi-restraints excluded: chain G residue 4210 VAL
Chi-restraints excluded: chain G residue 4240 ILE
Chi-restraints excluded: chain G residue 4286 THR
Chi-restraints excluded: chain G residue 4306 THR
Chi-restraints excluded: chain G residue 4339 VAL
Chi-restraints excluded: chain G residue 4371 THR
Chi-restraints excluded: chain G residue 4387 SER
Chi-restraints excluded: chain G residue 4395 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 238
random chunks:
chunk 190 optimal weight: 1.9990
chunk 186 optimal weight: 0.9980
chunk 9 optimal weight: 3.9990
chunk 214 optimal weight: 2.9990
chunk 93 optimal weight: 5.9990
chunk 122 optimal weight: 0.9980
chunk 156 optimal weight: 0.9980
chunk 62 optimal weight: 1.9990
chunk 14 optimal weight: 0.4980
chunk 218 optimal weight: 0.8980
chunk 72 optimal weight: 0.9980
overall best weight: 0.8780
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** B4142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A4142 ASN
D4142 ASN
D4185 ASN
E4142 ASN
F4142 ASN
G4142 ASN
Total number of N/Q/H flips: 6
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.126718 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.109876 restraints weight = 22061.777|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3158 r_free = 0.3158 target = 0.112185 restraints weight = 12655.319|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.113727 restraints weight = 8429.531|
|-----------------------------------------------------------------------------|
r_work (final): 0.2854
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8320
moved from start: 0.4085
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.031 18109 Z= 0.191
Angle : 0.523 6.758 25095 Z= 0.275
Chirality : 0.045 0.146 3115
Planarity : 0.005 0.051 3255
Dihedral : 4.600 16.142 2527
Min Nonbonded Distance : 2.140
Molprobity Statistics.
All-atom Clashscore : 5.22
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 1.73 %
Favored : 98.27 %
Rotamer:
Outliers : 3.46 %
Allowed : 16.09 %
Favored : 80.45 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 0.23 (0.17), residues: 2422
helix: -3.81 (0.34), residues: 42
sheet: -0.10 (0.17), residues: 896
loop : 0.61 (0.16), residues: 1484
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.012 0.001 TRP A4370
HIS 0.002 0.001 HIS F4137
PHE 0.019 0.001 PHE E4399
TYR 0.017 0.001 TYR F4139
ARG 0.001 0.000 ARG A4244
*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
4844 Ramachandran restraints generated.
2422 Oldfield, 0 Emsley, 2422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
4844 Ramachandran restraints generated.
2422 Oldfield, 0 Emsley, 2422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
291 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 71
poor density : 220
time to evaluate : 1.787
Fit side-chains
REVERT: B 4259 SER cc_start: 0.8154 (p) cc_final: 0.7708 (m)
REVERT: A 4278 SER cc_start: 0.9241 (p) cc_final: 0.8724 (t)
REVERT: A 4368 TYR cc_start: 0.9036 (m-80) cc_final: 0.8527 (m-80)
REVERT: A 4379 ASN cc_start: 0.8865 (p0) cc_final: 0.8384 (p0)
REVERT: D 4117 GLN cc_start: 0.8653 (tm-30) cc_final: 0.8316 (tm-30)
REVERT: D 4308 SER cc_start: 0.8693 (OUTLIER) cc_final: 0.8424 (p)
REVERT: D 4379 ASN cc_start: 0.8948 (p0) cc_final: 0.8258 (p0)
REVERT: E 4269 ILE cc_start: 0.8231 (mm) cc_final: 0.7788 (pt)
REVERT: F 4117 GLN cc_start: 0.8594 (tm-30) cc_final: 0.8331 (tm-30)
REVERT: F 4259 SER cc_start: 0.7919 (p) cc_final: 0.7452 (m)
REVERT: F 4308 SER cc_start: 0.8754 (OUTLIER) cc_final: 0.8525 (p)
REVERT: G 4259 SER cc_start: 0.8047 (p) cc_final: 0.7619 (m)
REVERT: G 4379 ASN cc_start: 0.8831 (p0) cc_final: 0.8463 (p0)
outliers start: 71
outliers final: 51
residues processed: 273
average time/residue: 0.2202
time to fit residues: 102.5287
Evaluate side-chains
250 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 53
poor density : 197
time to evaluate : 1.793
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue 4167 THR
Chi-restraints excluded: chain B residue 4308 SER
Chi-restraints excluded: chain B residue 4311 THR
Chi-restraints excluded: chain B residue 4339 VAL
Chi-restraints excluded: chain B residue 4387 SER
Chi-restraints excluded: chain A residue 4107 SER
Chi-restraints excluded: chain A residue 4167 THR
Chi-restraints excluded: chain A residue 4222 SER
Chi-restraints excluded: chain A residue 4308 SER
Chi-restraints excluded: chain A residue 4387 SER
Chi-restraints excluded: chain A residue 4400 ILE
Chi-restraints excluded: chain C residue 4082 THR
Chi-restraints excluded: chain C residue 4107 SER
Chi-restraints excluded: chain C residue 4167 THR
Chi-restraints excluded: chain C residue 4234 MET
Chi-restraints excluded: chain C residue 4257 ILE
Chi-restraints excluded: chain C residue 4308 SER
Chi-restraints excluded: chain C residue 4339 VAL
Chi-restraints excluded: chain C residue 4364 VAL
Chi-restraints excluded: chain C residue 4387 SER
Chi-restraints excluded: chain D residue 4075 ARG
Chi-restraints excluded: chain D residue 4101 THR
Chi-restraints excluded: chain D residue 4107 SER
Chi-restraints excluded: chain D residue 4130 LEU
Chi-restraints excluded: chain D residue 4173 CYS
Chi-restraints excluded: chain D residue 4257 ILE
Chi-restraints excluded: chain D residue 4308 SER
Chi-restraints excluded: chain D residue 4339 VAL
Chi-restraints excluded: chain D residue 4387 SER
Chi-restraints excluded: chain E residue 4075 ARG
Chi-restraints excluded: chain E residue 4167 THR
Chi-restraints excluded: chain E residue 4240 ILE
Chi-restraints excluded: chain E residue 4257 ILE
Chi-restraints excluded: chain E residue 4308 SER
Chi-restraints excluded: chain E residue 4339 VAL
Chi-restraints excluded: chain E residue 4387 SER
Chi-restraints excluded: chain E residue 4400 ILE
Chi-restraints excluded: chain F residue 4167 THR
Chi-restraints excluded: chain F residue 4173 CYS
Chi-restraints excluded: chain F residue 4240 ILE
Chi-restraints excluded: chain F residue 4257 ILE
Chi-restraints excluded: chain F residue 4286 THR
Chi-restraints excluded: chain F residue 4308 SER
Chi-restraints excluded: chain F residue 4339 VAL
Chi-restraints excluded: chain F residue 4387 SER
Chi-restraints excluded: chain G residue 4100 THR
Chi-restraints excluded: chain G residue 4120 LEU
Chi-restraints excluded: chain G residue 4210 VAL
Chi-restraints excluded: chain G residue 4257 ILE
Chi-restraints excluded: chain G residue 4286 THR
Chi-restraints excluded: chain G residue 4387 SER
Chi-restraints excluded: chain G residue 4391 VAL
Chi-restraints excluded: chain G residue 4395 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 238
random chunks:
chunk 2 optimal weight: 3.9990
chunk 45 optimal weight: 0.0000
chunk 28 optimal weight: 5.9990
chunk 120 optimal weight: 3.9990
chunk 160 optimal weight: 0.8980
chunk 99 optimal weight: 0.9990
chunk 135 optimal weight: 6.9990
chunk 79 optimal weight: 4.9990
chunk 190 optimal weight: 0.9980
chunk 176 optimal weight: 3.9990
chunk 123 optimal weight: 5.9990
overall best weight: 1.3788
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** B4142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A4142 ASN
F4142 ASN
Total number of N/Q/H flips: 2
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3012 r_free = 0.3012 target = 0.103983 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2802 r_free = 0.2802 target = 0.088672 restraints weight = 23900.994|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.2793 r_free = 0.2793 target = 0.088100 restraints weight = 24313.476|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2800 r_free = 0.2800 target = 0.088579 restraints weight = 23846.567|
|-----------------------------------------------------------------------------|
r_work (final): 0.2863
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8409
moved from start: 0.4197
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.004 0.031 18109 Z= 0.265
Angle : 0.548 6.710 25095 Z= 0.291
Chirality : 0.046 0.166 3115
Planarity : 0.005 0.053 3255
Dihedral : 4.690 16.687 2527
Min Nonbonded Distance : 2.310
Molprobity Statistics.
All-atom Clashscore : 4.99
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 2.35 %
Favored : 97.65 %
Rotamer:
Outliers : 3.75 %
Allowed : 16.24 %
Favored : 80.01 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 0.19 (0.17), residues: 2422
helix: -3.88 (0.33), residues: 42
sheet: -0.09 (0.17), residues: 882
loop : 0.55 (0.16), residues: 1498
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.009 0.001 TRP A4370
HIS 0.003 0.001 HIS B4137
PHE 0.019 0.002 PHE E4399
TYR 0.017 0.001 TYR E4337
ARG 0.001 0.000 ARG B4075
*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
4844 Ramachandran restraints generated.
2422 Oldfield, 0 Emsley, 2422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
4844 Ramachandran restraints generated.
2422 Oldfield, 0 Emsley, 2422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
280 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 77
poor density : 203
time to evaluate : 1.997
Fit side-chains
REVERT: B 4259 SER cc_start: 0.8232 (p) cc_final: 0.7775 (m)
REVERT: B 4379 ASN cc_start: 0.8655 (p0) cc_final: 0.8385 (p0)
REVERT: A 4368 TYR cc_start: 0.9064 (m-80) cc_final: 0.8628 (m-80)
REVERT: A 4379 ASN cc_start: 0.8882 (p0) cc_final: 0.8385 (p0)
REVERT: D 4308 SER cc_start: 0.8713 (OUTLIER) cc_final: 0.8445 (p)
REVERT: E 4269 ILE cc_start: 0.8275 (mm) cc_final: 0.7782 (pt)
REVERT: F 4117 GLN cc_start: 0.8564 (tm-30) cc_final: 0.8335 (tm-30)
REVERT: F 4259 SER cc_start: 0.7971 (p) cc_final: 0.7476 (m)
REVERT: G 4216 SER cc_start: 0.8816 (m) cc_final: 0.8361 (p)
REVERT: G 4259 SER cc_start: 0.8138 (p) cc_final: 0.7674 (m)
REVERT: G 4379 ASN cc_start: 0.8864 (p0) cc_final: 0.8456 (p0)
outliers start: 77
outliers final: 67
residues processed: 259
average time/residue: 0.2205
time to fit residues: 97.6536
Evaluate side-chains
256 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 68
poor density : 188
time to evaluate : 1.830
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue 4149 LEU
Chi-restraints excluded: chain B residue 4167 THR
Chi-restraints excluded: chain B residue 4240 ILE
Chi-restraints excluded: chain B residue 4257 ILE
Chi-restraints excluded: chain B residue 4260 THR
Chi-restraints excluded: chain B residue 4278 SER
Chi-restraints excluded: chain B residue 4308 SER
Chi-restraints excluded: chain B residue 4311 THR
Chi-restraints excluded: chain B residue 4339 VAL
Chi-restraints excluded: chain B residue 4387 SER
Chi-restraints excluded: chain B residue 4391 VAL
Chi-restraints excluded: chain A residue 4100 THR
Chi-restraints excluded: chain A residue 4107 SER
Chi-restraints excluded: chain A residue 4167 THR
Chi-restraints excluded: chain A residue 4222 SER
Chi-restraints excluded: chain A residue 4259 SER
Chi-restraints excluded: chain A residue 4308 SER
Chi-restraints excluded: chain A residue 4339 VAL
Chi-restraints excluded: chain A residue 4387 SER
Chi-restraints excluded: chain A residue 4400 ILE
Chi-restraints excluded: chain C residue 4082 THR
Chi-restraints excluded: chain C residue 4107 SER
Chi-restraints excluded: chain C residue 4167 THR
Chi-restraints excluded: chain C residue 4239 THR
Chi-restraints excluded: chain C residue 4257 ILE
Chi-restraints excluded: chain C residue 4308 SER
Chi-restraints excluded: chain C residue 4311 THR
Chi-restraints excluded: chain C residue 4339 VAL
Chi-restraints excluded: chain C residue 4387 SER
Chi-restraints excluded: chain D residue 4075 ARG
Chi-restraints excluded: chain D residue 4101 THR
Chi-restraints excluded: chain D residue 4107 SER
Chi-restraints excluded: chain D residue 4130 LEU
Chi-restraints excluded: chain D residue 4173 CYS
Chi-restraints excluded: chain D residue 4257 ILE
Chi-restraints excluded: chain D residue 4306 THR
Chi-restraints excluded: chain D residue 4308 SER
Chi-restraints excluded: chain D residue 4339 VAL
Chi-restraints excluded: chain D residue 4387 SER
Chi-restraints excluded: chain E residue 4100 THR
Chi-restraints excluded: chain E residue 4167 THR
Chi-restraints excluded: chain E residue 4240 ILE
Chi-restraints excluded: chain E residue 4257 ILE
Chi-restraints excluded: chain E residue 4286 THR
Chi-restraints excluded: chain E residue 4308 SER
Chi-restraints excluded: chain E residue 4337 TYR
Chi-restraints excluded: chain E residue 4339 VAL
Chi-restraints excluded: chain E residue 4387 SER
Chi-restraints excluded: chain E residue 4400 ILE
Chi-restraints excluded: chain F residue 4107 SER
Chi-restraints excluded: chain F residue 4167 THR
Chi-restraints excluded: chain F residue 4173 CYS
Chi-restraints excluded: chain F residue 4240 ILE
Chi-restraints excluded: chain F residue 4257 ILE
Chi-restraints excluded: chain F residue 4286 THR
Chi-restraints excluded: chain F residue 4306 THR
Chi-restraints excluded: chain F residue 4308 SER
Chi-restraints excluded: chain F residue 4339 VAL
Chi-restraints excluded: chain F residue 4387 SER
Chi-restraints excluded: chain G residue 4100 THR
Chi-restraints excluded: chain G residue 4120 LEU
Chi-restraints excluded: chain G residue 4210 VAL
Chi-restraints excluded: chain G residue 4257 ILE
Chi-restraints excluded: chain G residue 4286 THR
Chi-restraints excluded: chain G residue 4306 THR
Chi-restraints excluded: chain G residue 4387 SER
Chi-restraints excluded: chain G residue 4391 VAL
Chi-restraints excluded: chain G residue 4395 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 238
random chunks:
chunk 56 optimal weight: 2.9990
chunk 146 optimal weight: 1.9990
chunk 176 optimal weight: 3.9990
chunk 77 optimal weight: 4.9990
chunk 197 optimal weight: 0.6980
chunk 100 optimal weight: 5.9990
chunk 71 optimal weight: 6.9990
chunk 19 optimal weight: 1.9990
chunk 90 optimal weight: 1.9990
chunk 183 optimal weight: 3.9990
chunk 166 optimal weight: 0.4980
overall best weight: 1.4386
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** B4142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A4142 ASN
A4185 ASN
C4084 ASN
F4142 ASN
G4185 ASN
Total number of N/Q/H flips: 5
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3007 r_free = 0.3007 target = 0.103626 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.2759 r_free = 0.2759 target = 0.085705 restraints weight = 23909.127|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2781 r_free = 0.2781 target = 0.087165 restraints weight = 16181.471|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.2801 r_free = 0.2801 target = 0.088485 restraints weight = 12157.246|
|-----------------------------------------------------------------------------|
r_work (final): 0.2874
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8404
moved from start: 0.4285
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.004 0.032 18109 Z= 0.273
Angle : 0.552 6.814 25095 Z= 0.292
Chirality : 0.046 0.144 3115
Planarity : 0.005 0.052 3255
Dihedral : 4.710 16.616 2527
Min Nonbonded Distance : 2.107
Molprobity Statistics.
All-atom Clashscore : 4.79
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 2.15 %
Favored : 97.85 %
Rotamer:
Outliers : 4.14 %
Allowed : 16.09 %
Favored : 79.77 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 0.31 (0.17), residues: 2422
helix: None (None), residues: 0
sheet: -0.16 (0.16), residues: 896
loop : 0.60 (0.16), residues: 1526
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.010 0.001 TRP A4370
HIS 0.003 0.001 HIS G4137
PHE 0.019 0.002 PHE E4399
TYR 0.018 0.001 TYR E4337
ARG 0.001 0.000 ARG B4075
*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
4844 Ramachandran restraints generated.
2422 Oldfield, 0 Emsley, 2422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
4844 Ramachandran restraints generated.
2422 Oldfield, 0 Emsley, 2422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
281 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 85
poor density : 196
time to evaluate : 1.846
Fit side-chains
REVERT: B 4259 SER cc_start: 0.8231 (p) cc_final: 0.7757 (m)
REVERT: B 4379 ASN cc_start: 0.8749 (p0) cc_final: 0.8504 (p0)
REVERT: A 4368 TYR cc_start: 0.9083 (m-80) cc_final: 0.8630 (m-80)
REVERT: D 4308 SER cc_start: 0.8713 (OUTLIER) cc_final: 0.8440 (p)
REVERT: E 4269 ILE cc_start: 0.8274 (mm) cc_final: 0.7793 (pt)
REVERT: F 4117 GLN cc_start: 0.8597 (tm-30) cc_final: 0.8350 (tm-30)
REVERT: F 4259 SER cc_start: 0.7952 (p) cc_final: 0.7439 (m)
REVERT: G 4163 ILE cc_start: 0.9090 (mm) cc_final: 0.8830 (mm)
REVERT: G 4216 SER cc_start: 0.8854 (m) cc_final: 0.8375 (p)
REVERT: G 4259 SER cc_start: 0.8157 (p) cc_final: 0.7667 (m)
REVERT: G 4379 ASN cc_start: 0.8945 (p0) cc_final: 0.8537 (p0)
outliers start: 85
outliers final: 77
residues processed: 260
average time/residue: 0.2145
time to fit residues: 95.2823
Evaluate side-chains
264 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 78
poor density : 186
time to evaluate : 1.938
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue 4149 LEU
Chi-restraints excluded: chain B residue 4167 THR
Chi-restraints excluded: chain B residue 4239 THR
Chi-restraints excluded: chain B residue 4240 ILE
Chi-restraints excluded: chain B residue 4257 ILE
Chi-restraints excluded: chain B residue 4260 THR
Chi-restraints excluded: chain B residue 4278 SER
Chi-restraints excluded: chain B residue 4306 THR
Chi-restraints excluded: chain B residue 4308 SER
Chi-restraints excluded: chain B residue 4311 THR
Chi-restraints excluded: chain B residue 4339 VAL
Chi-restraints excluded: chain B residue 4387 SER
Chi-restraints excluded: chain B residue 4391 VAL
Chi-restraints excluded: chain A residue 4100 THR
Chi-restraints excluded: chain A residue 4107 SER
Chi-restraints excluded: chain A residue 4167 THR
Chi-restraints excluded: chain A residue 4222 SER
Chi-restraints excluded: chain A residue 4306 THR
Chi-restraints excluded: chain A residue 4308 SER
Chi-restraints excluded: chain A residue 4339 VAL
Chi-restraints excluded: chain A residue 4387 SER
Chi-restraints excluded: chain A residue 4400 ILE
Chi-restraints excluded: chain C residue 4082 THR
Chi-restraints excluded: chain C residue 4107 SER
Chi-restraints excluded: chain C residue 4167 THR
Chi-restraints excluded: chain C residue 4239 THR
Chi-restraints excluded: chain C residue 4257 ILE
Chi-restraints excluded: chain C residue 4308 SER
Chi-restraints excluded: chain C residue 4311 THR
Chi-restraints excluded: chain C residue 4339 VAL
Chi-restraints excluded: chain C residue 4387 SER
Chi-restraints excluded: chain D residue 4075 ARG
Chi-restraints excluded: chain D residue 4101 THR
Chi-restraints excluded: chain D residue 4107 SER
Chi-restraints excluded: chain D residue 4130 LEU
Chi-restraints excluded: chain D residue 4173 CYS
Chi-restraints excluded: chain D residue 4257 ILE
Chi-restraints excluded: chain D residue 4259 SER
Chi-restraints excluded: chain D residue 4278 SER
Chi-restraints excluded: chain D residue 4306 THR
Chi-restraints excluded: chain D residue 4308 SER
Chi-restraints excluded: chain D residue 4339 VAL
Chi-restraints excluded: chain D residue 4387 SER
Chi-restraints excluded: chain E residue 4082 THR
Chi-restraints excluded: chain E residue 4100 THR
Chi-restraints excluded: chain E residue 4167 THR
Chi-restraints excluded: chain E residue 4240 ILE
Chi-restraints excluded: chain E residue 4257 ILE
Chi-restraints excluded: chain E residue 4286 THR
Chi-restraints excluded: chain E residue 4306 THR
Chi-restraints excluded: chain E residue 4308 SER
Chi-restraints excluded: chain E residue 4337 TYR
Chi-restraints excluded: chain E residue 4339 VAL
Chi-restraints excluded: chain E residue 4387 SER
Chi-restraints excluded: chain E residue 4400 ILE
Chi-restraints excluded: chain F residue 4107 SER
Chi-restraints excluded: chain F residue 4118 SER
Chi-restraints excluded: chain F residue 4167 THR
Chi-restraints excluded: chain F residue 4173 CYS
Chi-restraints excluded: chain F residue 4240 ILE
Chi-restraints excluded: chain F residue 4257 ILE
Chi-restraints excluded: chain F residue 4286 THR
Chi-restraints excluded: chain F residue 4306 THR
Chi-restraints excluded: chain F residue 4308 SER
Chi-restraints excluded: chain F residue 4339 VAL
Chi-restraints excluded: chain F residue 4387 SER
Chi-restraints excluded: chain G residue 4100 THR
Chi-restraints excluded: chain G residue 4120 LEU
Chi-restraints excluded: chain G residue 4210 VAL
Chi-restraints excluded: chain G residue 4240 ILE
Chi-restraints excluded: chain G residue 4257 ILE
Chi-restraints excluded: chain G residue 4286 THR
Chi-restraints excluded: chain G residue 4306 THR
Chi-restraints excluded: chain G residue 4339 VAL
Chi-restraints excluded: chain G residue 4387 SER
Chi-restraints excluded: chain G residue 4391 VAL
Chi-restraints excluded: chain G residue 4395 THR
Chi-restraints excluded: chain G residue 4400 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 238
random chunks:
chunk 32 optimal weight: 0.9990
chunk 87 optimal weight: 4.9990
chunk 97 optimal weight: 2.9990
chunk 189 optimal weight: 4.9990
chunk 81 optimal weight: 2.9990
chunk 138 optimal weight: 0.8980
chunk 39 optimal weight: 2.9990
chunk 137 optimal weight: 4.9990
chunk 78 optimal weight: 3.9990
chunk 45 optimal weight: 3.9990
chunk 192 optimal weight: 2.9990
overall best weight: 2.1788
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** B4142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C4084 ASN
F4142 ASN
G4185 ASN
Total number of N/Q/H flips: 3
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3078 r_free = 0.3078 target = 0.107033 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.2832 r_free = 0.2832 target = 0.089256 restraints weight = 23603.330|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.2859 r_free = 0.2859 target = 0.091051 restraints weight = 15373.507|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.2878 r_free = 0.2878 target = 0.092329 restraints weight = 11151.499|
|-----------------------------------------------------------------------------|
r_work (final): 0.2834
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8437
moved from start: 0.4338
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.006 0.043 18109 Z= 0.390
Angle : 0.605 6.865 25095 Z= 0.322
Chirality : 0.048 0.166 3115
Planarity : 0.005 0.057 3255
Dihedral : 5.034 17.549 2527
Min Nonbonded Distance : 2.194
Molprobity Statistics.
All-atom Clashscore : 4.67
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 3.43 %
Favored : 96.57 %
Rotamer:
Outliers : 4.34 %
Allowed : 16.14 %
Favored : 79.52 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 0.19 (0.17), residues: 2422
helix: None (None), residues: 0
sheet: -0.14 (0.17), residues: 868
loop : 0.43 (0.16), residues: 1554
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.010 0.002 TRP C4232
HIS 0.003 0.001 HIS B4137
PHE 0.020 0.002 PHE E4399
TYR 0.020 0.002 TYR E4337
ARG 0.001 0.000 ARG D4244
*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
4844 Ramachandran restraints generated.
2422 Oldfield, 0 Emsley, 2422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
4844 Ramachandran restraints generated.
2422 Oldfield, 0 Emsley, 2422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
271 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 89
poor density : 182
time to evaluate : 1.989
Fit side-chains
REVERT: B 4259 SER cc_start: 0.8317 (p) cc_final: 0.7737 (m)
REVERT: C 4368 TYR cc_start: 0.9105 (m-80) cc_final: 0.8643 (m-80)
REVERT: D 4379 ASN cc_start: 0.8909 (p0) cc_final: 0.8642 (p0)
REVERT: E 4269 ILE cc_start: 0.8314 (mm) cc_final: 0.7816 (pt)
REVERT: F 4117 GLN cc_start: 0.8628 (tm-30) cc_final: 0.8376 (tm-30)
REVERT: F 4259 SER cc_start: 0.7794 (p) cc_final: 0.7283 (m)
REVERT: G 4163 ILE cc_start: 0.9121 (mm) cc_final: 0.8887 (mm)
REVERT: G 4216 SER cc_start: 0.8877 (m) cc_final: 0.8418 (p)
REVERT: G 4259 SER cc_start: 0.8165 (p) cc_final: 0.7631 (m)
outliers start: 89
outliers final: 79
residues processed: 251
average time/residue: 0.2189
time to fit residues: 93.9367
Evaluate side-chains
255 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 79
poor density : 176
time to evaluate : 1.936
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue 4101 THR
Chi-restraints excluded: chain B residue 4107 SER
Chi-restraints excluded: chain B residue 4149 LEU
Chi-restraints excluded: chain B residue 4167 THR
Chi-restraints excluded: chain B residue 4239 THR
Chi-restraints excluded: chain B residue 4240 ILE
Chi-restraints excluded: chain B residue 4257 ILE
Chi-restraints excluded: chain B residue 4260 THR
Chi-restraints excluded: chain B residue 4278 SER
Chi-restraints excluded: chain B residue 4306 THR
Chi-restraints excluded: chain B residue 4308 SER
Chi-restraints excluded: chain B residue 4311 THR
Chi-restraints excluded: chain B residue 4377 THR
Chi-restraints excluded: chain B residue 4387 SER
Chi-restraints excluded: chain B residue 4391 VAL
Chi-restraints excluded: chain A residue 4100 THR
Chi-restraints excluded: chain A residue 4107 SER
Chi-restraints excluded: chain A residue 4167 THR
Chi-restraints excluded: chain A residue 4222 SER
Chi-restraints excluded: chain A residue 4306 THR
Chi-restraints excluded: chain A residue 4308 SER
Chi-restraints excluded: chain A residue 4339 VAL
Chi-restraints excluded: chain A residue 4387 SER
Chi-restraints excluded: chain A residue 4400 ILE
Chi-restraints excluded: chain C residue 4082 THR
Chi-restraints excluded: chain C residue 4107 SER
Chi-restraints excluded: chain C residue 4167 THR
Chi-restraints excluded: chain C residue 4239 THR
Chi-restraints excluded: chain C residue 4257 ILE
Chi-restraints excluded: chain C residue 4308 SER
Chi-restraints excluded: chain C residue 4311 THR
Chi-restraints excluded: chain C residue 4339 VAL
Chi-restraints excluded: chain C residue 4387 SER
Chi-restraints excluded: chain C residue 4391 VAL
Chi-restraints excluded: chain D residue 4075 ARG
Chi-restraints excluded: chain D residue 4101 THR
Chi-restraints excluded: chain D residue 4107 SER
Chi-restraints excluded: chain D residue 4130 LEU
Chi-restraints excluded: chain D residue 4153 VAL
Chi-restraints excluded: chain D residue 4173 CYS
Chi-restraints excluded: chain D residue 4259 SER
Chi-restraints excluded: chain D residue 4278 SER
Chi-restraints excluded: chain D residue 4306 THR
Chi-restraints excluded: chain D residue 4308 SER
Chi-restraints excluded: chain D residue 4339 VAL
Chi-restraints excluded: chain D residue 4387 SER
Chi-restraints excluded: chain E residue 4082 THR
Chi-restraints excluded: chain E residue 4100 THR
Chi-restraints excluded: chain E residue 4167 THR
Chi-restraints excluded: chain E residue 4240 ILE
Chi-restraints excluded: chain E residue 4257 ILE
Chi-restraints excluded: chain E residue 4286 THR
Chi-restraints excluded: chain E residue 4306 THR
Chi-restraints excluded: chain E residue 4308 SER
Chi-restraints excluded: chain E residue 4339 VAL
Chi-restraints excluded: chain E residue 4387 SER
Chi-restraints excluded: chain E residue 4400 ILE
Chi-restraints excluded: chain F residue 4107 SER
Chi-restraints excluded: chain F residue 4118 SER
Chi-restraints excluded: chain F residue 4167 THR
Chi-restraints excluded: chain F residue 4173 CYS
Chi-restraints excluded: chain F residue 4240 ILE
Chi-restraints excluded: chain F residue 4257 ILE
Chi-restraints excluded: chain F residue 4286 THR
Chi-restraints excluded: chain F residue 4306 THR
Chi-restraints excluded: chain F residue 4308 SER
Chi-restraints excluded: chain F residue 4339 VAL
Chi-restraints excluded: chain F residue 4387 SER
Chi-restraints excluded: chain G residue 4100 THR
Chi-restraints excluded: chain G residue 4101 THR
Chi-restraints excluded: chain G residue 4120 LEU
Chi-restraints excluded: chain G residue 4185 ASN
Chi-restraints excluded: chain G residue 4210 VAL
Chi-restraints excluded: chain G residue 4240 ILE
Chi-restraints excluded: chain G residue 4286 THR
Chi-restraints excluded: chain G residue 4306 THR
Chi-restraints excluded: chain G residue 4339 VAL
Chi-restraints excluded: chain G residue 4391 VAL
Chi-restraints excluded: chain G residue 4395 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 238
random chunks:
chunk 185 optimal weight: 0.6980
chunk 199 optimal weight: 3.9990
chunk 51 optimal weight: 2.9990
chunk 228 optimal weight: 0.9990
chunk 179 optimal weight: 2.9990
chunk 27 optimal weight: 0.9990
chunk 114 optimal weight: 3.9990
chunk 224 optimal weight: 1.9990
chunk 122 optimal weight: 0.8980
chunk 220 optimal weight: 0.9990
chunk 66 optimal weight: 0.9990
overall best weight: 0.9186
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** B4142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C4084 ASN
F4142 ASN
G4185 ASN
Total number of N/Q/H flips: 3
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3039 r_free = 0.3039 target = 0.105541 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.2798 r_free = 0.2798 target = 0.087987 restraints weight = 23557.897|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.2822 r_free = 0.2822 target = 0.089603 restraints weight = 15919.724|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.2839 r_free = 0.2839 target = 0.090770 restraints weight = 11887.694|
|-----------------------------------------------------------------------------|
r_work (final): 0.2896
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8380
moved from start: 0.4417
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.034 18109 Z= 0.200
Angle : 0.530 6.760 25095 Z= 0.279
Chirality : 0.045 0.144 3115
Planarity : 0.005 0.055 3255
Dihedral : 4.641 16.005 2527
Min Nonbonded Distance : 2.220
Molprobity Statistics.
All-atom Clashscore : 4.67
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 1.86 %
Favored : 98.14 %
Rotamer:
Outliers : 3.36 %
Allowed : 17.11 %
Favored : 79.52 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 0.33 (0.17), residues: 2422
helix: None (None), residues: 0
sheet: -0.07 (0.17), residues: 882
loop : 0.55 (0.16), residues: 1540
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.013 0.001 TRP A4370
HIS 0.002 0.001 HIS F4137
PHE 0.019 0.001 PHE E4399
TYR 0.018 0.001 TYR E4337
ARG 0.001 0.000 ARG B4075
********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
4844 Ramachandran restraints generated.
2422 Oldfield, 0 Emsley, 2422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
4844 Ramachandran restraints generated.
2422 Oldfield, 0 Emsley, 2422 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
260 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 69
poor density : 191
time to evaluate : 1.543
Fit side-chains
REVERT: B 4259 SER cc_start: 0.8222 (p) cc_final: 0.7656 (m)
REVERT: B 4379 ASN cc_start: 0.8785 (p0) cc_final: 0.8546 (p0)
REVERT: A 4368 TYR cc_start: 0.9075 (m-80) cc_final: 0.8687 (m-80)
REVERT: D 4308 SER cc_start: 0.8691 (OUTLIER) cc_final: 0.8429 (p)
REVERT: E 4269 ILE cc_start: 0.8281 (mm) cc_final: 0.7977 (pt)
REVERT: F 4117 GLN cc_start: 0.8611 (tm-30) cc_final: 0.8366 (tm-30)
REVERT: F 4259 SER cc_start: 0.7938 (p) cc_final: 0.7422 (m)
REVERT: F 4308 SER cc_start: 0.8770 (OUTLIER) cc_final: 0.8533 (p)
REVERT: G 4216 SER cc_start: 0.8863 (m) cc_final: 0.8298 (p)
REVERT: G 4259 SER cc_start: 0.8105 (p) cc_final: 0.7586 (m)
REVERT: G 4379 ASN cc_start: 0.8974 (p0) cc_final: 0.8506 (p0)
outliers start: 69
outliers final: 63
residues processed: 242
average time/residue: 0.2395
time to fit residues: 98.1182
Evaluate side-chains
239 residues out of total 2051 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 65
poor density : 174
time to evaluate : 1.771
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue 4107 SER
Chi-restraints excluded: chain B residue 4149 LEU
Chi-restraints excluded: chain B residue 4167 THR
Chi-restraints excluded: chain B residue 4240 ILE
Chi-restraints excluded: chain B residue 4257 ILE
Chi-restraints excluded: chain B residue 4260 THR
Chi-restraints excluded: chain B residue 4306 THR
Chi-restraints excluded: chain B residue 4377 THR
Chi-restraints excluded: chain B residue 4387 SER
Chi-restraints excluded: chain B residue 4391 VAL
Chi-restraints excluded: chain A residue 4107 SER
Chi-restraints excluded: chain A residue 4167 THR
Chi-restraints excluded: chain A residue 4308 SER
Chi-restraints excluded: chain A residue 4339 VAL
Chi-restraints excluded: chain A residue 4387 SER
Chi-restraints excluded: chain A residue 4400 ILE
Chi-restraints excluded: chain C residue 4082 THR
Chi-restraints excluded: chain C residue 4107 SER
Chi-restraints excluded: chain C residue 4167 THR
Chi-restraints excluded: chain C residue 4257 ILE
Chi-restraints excluded: chain C residue 4311 THR
Chi-restraints excluded: chain C residue 4339 VAL
Chi-restraints excluded: chain C residue 4387 SER
Chi-restraints excluded: chain C residue 4391 VAL
Chi-restraints excluded: chain D residue 4075 ARG
Chi-restraints excluded: chain D residue 4101 THR
Chi-restraints excluded: chain D residue 4107 SER
Chi-restraints excluded: chain D residue 4130 LEU
Chi-restraints excluded: chain D residue 4173 CYS
Chi-restraints excluded: chain D residue 4259 SER
Chi-restraints excluded: chain D residue 4278 SER
Chi-restraints excluded: chain D residue 4308 SER
Chi-restraints excluded: chain D residue 4339 VAL
Chi-restraints excluded: chain D residue 4387 SER
Chi-restraints excluded: chain E residue 4100 THR
Chi-restraints excluded: chain E residue 4167 THR
Chi-restraints excluded: chain E residue 4240 ILE
Chi-restraints excluded: chain E residue 4257 ILE
Chi-restraints excluded: chain E residue 4286 THR
Chi-restraints excluded: chain E residue 4306 THR
Chi-restraints excluded: chain E residue 4308 SER
Chi-restraints excluded: chain E residue 4337 TYR
Chi-restraints excluded: chain E residue 4339 VAL
Chi-restraints excluded: chain E residue 4387 SER
Chi-restraints excluded: chain E residue 4400 ILE
Chi-restraints excluded: chain F residue 4107 SER
Chi-restraints excluded: chain F residue 4118 SER
Chi-restraints excluded: chain F residue 4167 THR
Chi-restraints excluded: chain F residue 4173 CYS
Chi-restraints excluded: chain F residue 4240 ILE
Chi-restraints excluded: chain F residue 4257 ILE
Chi-restraints excluded: chain F residue 4286 THR
Chi-restraints excluded: chain F residue 4308 SER
Chi-restraints excluded: chain F residue 4339 VAL
Chi-restraints excluded: chain F residue 4387 SER
Chi-restraints excluded: chain G residue 4100 THR
Chi-restraints excluded: chain G residue 4101 THR
Chi-restraints excluded: chain G residue 4120 LEU
Chi-restraints excluded: chain G residue 4185 ASN
Chi-restraints excluded: chain G residue 4210 VAL
Chi-restraints excluded: chain G residue 4240 ILE
Chi-restraints excluded: chain G residue 4286 THR
Chi-restraints excluded: chain G residue 4339 VAL
Chi-restraints excluded: chain G residue 4391 VAL
Chi-restraints excluded: chain G residue 4395 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 238
random chunks:
chunk 55 optimal weight: 0.9990
chunk 99 optimal weight: 0.0970
chunk 188 optimal weight: 0.8980
chunk 176 optimal weight: 2.9990
chunk 76 optimal weight: 0.9980
chunk 110 optimal weight: 0.5980
chunk 229 optimal weight: 5.9990
chunk 212 optimal weight: 0.9990
chunk 45 optimal weight: 3.9990
chunk 46 optimal weight: 2.9990
chunk 134 optimal weight: 0.9980
overall best weight: 0.7178
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
B4142 ASN
A4142 ASN
C4084 ASN
F4142 ASN
G4185 ASN
Total number of N/Q/H flips: 5
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3040 r_free = 0.3040 target = 0.106047 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2839 r_free = 0.2839 target = 0.091117 restraints weight = 23753.335|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.2831 r_free = 0.2831 target = 0.090680 restraints weight = 23876.074|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2841 r_free = 0.2841 target = 0.091357 restraints weight = 23461.277|
|-----------------------------------------------------------------------------|
r_work (final): 0.2903
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8373
moved from start: 0.4490
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.035 18109 Z= 0.175
Angle : 0.514 6.765 25095 Z= 0.269
Chirality : 0.045 0.141 3115
Planarity : 0.005 0.052 3255
Dihedral : 4.449 16.108 2527
Min Nonbonded Distance : 2.197
Molprobity Statistics.
All-atom Clashscore : 4.87
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 2.11 %
Favored : 97.89 %
Rotamer:
Outliers : 3.22 %
Allowed : 17.50 %
Favored : 79.28 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 0.19 (0.17), residues: 2422
helix: -3.94 (0.32), residues: 42
sheet: -0.10 (0.17), residues: 910
loop : 0.58 (0.17), residues: 1470
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.012 0.001 TRP A4370
HIS 0.002 0.001 HIS B4137
PHE 0.018 0.001 PHE E4399
TYR 0.015 0.001 TYR E4337
ARG 0.001 0.000 ARG B4075
Origin is already at (0, 0, 0), no shifts will be applied
===============================================================================
Job complete
usr+sys time: 4670.86 seconds
wall clock time: 85 minutes 33.51 seconds (5133.51 seconds total)