Starting phenix.real_space_refine
on Sun Jan 19 01:22:14 2025 by dcliebschner
===============================================================================
Processing files:
-------------------------------------------------------------------------------
Found model, /net/cci-nas-00/data/ceres_data/8yx8_39650/01_2025/8yx8_39650.cif
Found real_map, /net/cci-nas-00/data/ceres_data/8yx8_39650/01_2025/8yx8_39650.map
Processing PHIL parameters:
-------------------------------------------------------------------------------
Adding command-line PHIL:
-------------------------
refinement.macro_cycles=10
scattering_table=electron
resolution=2.8
write_initial_geo_file=False
Final processed PHIL parameters:
-------------------------------------------------------------------------------
data_manager {
real_map_files = "/net/cci-nas-00/data/ceres_data/8yx8_39650/01_2025/8yx8_39650.map"
default_real_map = "/net/cci-nas-00/data/ceres_data/8yx8_39650/01_2025/8yx8_39650.map"
model {
file = "/net/cci-nas-00/data/ceres_data/8yx8_39650/01_2025/8yx8_39650.cif"
}
default_model = "/net/cci-nas-00/data/ceres_data/8yx8_39650/01_2025/8yx8_39650.cif"
}
resolution = 2.8
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= 0.001 sd= 0.024
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 55 5.16 5
C 8485 2.51 5
N 2190 2.21 5
O 2340 1.98 5
sf(0) = scattering factor at diffraction angle 0.
Process input model
Monomer Library directory:
"/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
Total number of atoms: 13070
Number of models: 1
Model: ""
Number of chains: 15
Chain: "A"
Number of atoms: 2572
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 324, 2572
Classifications: {'peptide': 324}
Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 306}
Chain breaks: 1
Chain: "B"
Number of atoms: 2572
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 324, 2572
Classifications: {'peptide': 324}
Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 306}
Chain breaks: 1
Chain: "C"
Number of atoms: 2572
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 324, 2572
Classifications: {'peptide': 324}
Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 306}
Chain breaks: 1
Chain: "D"
Number of atoms: 2572
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 324, 2572
Classifications: {'peptide': 324}
Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 306}
Chain breaks: 1
Chain: "E"
Number of atoms: 2572
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 324, 2572
Classifications: {'peptide': 324}
Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 306}
Chain breaks: 1
Chain: "F"
Number of atoms: 28
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 2, 28
Unusual residues: {'NAG': 2}
Classifications: {'undetermined': 2}
Link IDs: {None: 1}
Unresolved non-hydrogen bonds: 2
Unresolved non-hydrogen angles: 4
Unresolved non-hydrogen dihedrals: 6
Unresolved non-hydrogen chiralities: 2
Chain: "G"
Number of atoms: 28
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 2, 28
Unusual residues: {'NAG': 2}
Classifications: {'undetermined': 2}
Link IDs: {None: 1}
Unresolved non-hydrogen bonds: 2
Unresolved non-hydrogen angles: 4
Unresolved non-hydrogen dihedrals: 6
Unresolved non-hydrogen chiralities: 2
Chain: "H"
Number of atoms: 28
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 2, 28
Unusual residues: {'NAG': 2}
Classifications: {'undetermined': 2}
Link IDs: {None: 1}
Unresolved non-hydrogen bonds: 2
Unresolved non-hydrogen angles: 4
Unresolved non-hydrogen dihedrals: 6
Unresolved non-hydrogen chiralities: 2
Chain: "I"
Number of atoms: 28
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 2, 28
Unusual residues: {'NAG': 2}
Classifications: {'undetermined': 2}
Link IDs: {None: 1}
Unresolved non-hydrogen bonds: 2
Unresolved non-hydrogen angles: 4
Unresolved non-hydrogen dihedrals: 6
Unresolved non-hydrogen chiralities: 2
Chain: "J"
Number of atoms: 28
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 2, 28
Unusual residues: {'NAG': 2}
Classifications: {'undetermined': 2}
Link IDs: {None: 1}
Unresolved non-hydrogen bonds: 2
Unresolved non-hydrogen angles: 4
Unresolved non-hydrogen dihedrals: 6
Unresolved non-hydrogen chiralities: 2
Chain: "A"
Number of atoms: 14
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 1, 14
Unusual residues: {'NAG': 1}
Classifications: {'undetermined': 1}
Unresolved non-hydrogen bonds: 1
Unresolved non-hydrogen angles: 2
Unresolved non-hydrogen dihedrals: 3
Unresolved non-hydrogen chiralities: 1
Chain: "B"
Number of atoms: 14
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 1, 14
Unusual residues: {'NAG': 1}
Classifications: {'undetermined': 1}
Unresolved non-hydrogen bonds: 1
Unresolved non-hydrogen angles: 2
Unresolved non-hydrogen dihedrals: 3
Unresolved non-hydrogen chiralities: 1
Chain: "C"
Number of atoms: 14
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 1, 14
Unusual residues: {'NAG': 1}
Classifications: {'undetermined': 1}
Unresolved non-hydrogen bonds: 1
Unresolved non-hydrogen angles: 2
Unresolved non-hydrogen dihedrals: 3
Unresolved non-hydrogen chiralities: 1
Chain: "D"
Number of atoms: 14
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 1, 14
Unusual residues: {'NAG': 1}
Classifications: {'undetermined': 1}
Unresolved non-hydrogen bonds: 1
Unresolved non-hydrogen angles: 2
Unresolved non-hydrogen dihedrals: 3
Unresolved non-hydrogen chiralities: 1
Chain: "E"
Number of atoms: 14
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 1, 14
Unusual residues: {'NAG': 1}
Classifications: {'undetermined': 1}
Unresolved non-hydrogen bonds: 1
Unresolved non-hydrogen angles: 2
Unresolved non-hydrogen dihedrals: 3
Unresolved non-hydrogen chiralities: 1
Residues with excluded nonbonded symmetry interactions: 5
residue:
pdb=" C1 NAG F 2 " occ=0.60
... (12 atoms not shown)
pdb=" O7 NAG F 2 " occ=0.60
residue:
pdb=" C1 NAG G 2 " occ=0.60
... (12 atoms not shown)
pdb=" O7 NAG G 2 " occ=0.60
residue:
pdb=" C1 NAG H 2 " occ=0.60
... (12 atoms not shown)
pdb=" O7 NAG H 2 " occ=0.60
residue:
pdb=" C1 NAG I 2 " occ=0.60
... (12 atoms not shown)
pdb=" O7 NAG I 2 " occ=0.60
residue:
pdb=" C1 NAG J 2 " occ=0.60
... (12 atoms not shown)
pdb=" O7 NAG J 2 " occ=0.60
Time building chain proxies: 7.81, per 1000 atoms: 0.60
Number of scatterers: 13070
At special positions: 0
Unit cell: (93, 93, 121.83, 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 55 16.00
O 2340 8.00
N 2190 7.00
C 8485 6.00
sf(0) = scattering factor at diffraction angle 0.
Number of disulfides: simple=10, symmetry=0
Simple disulfide: pdb=" SG CYS A 157 " - pdb=" SG CYS A 171 " distance=2.03
Simple disulfide: pdb=" SG CYS A 289 " - pdb=" SG CYS A 394 " distance=2.03
Simple disulfide: pdb=" SG CYS B 157 " - pdb=" SG CYS B 171 " distance=2.03
Simple disulfide: pdb=" SG CYS B 289 " - pdb=" SG CYS B 394 " distance=2.03
Simple disulfide: pdb=" SG CYS C 157 " - pdb=" SG CYS C 171 " distance=2.03
Simple disulfide: pdb=" SG CYS C 289 " - pdb=" SG CYS C 394 " distance=2.03
Simple disulfide: pdb=" SG CYS D 157 " - pdb=" SG CYS D 171 " distance=2.03
Simple disulfide: pdb=" SG CYS D 289 " - pdb=" SG CYS D 394 " distance=2.03
Simple disulfide: pdb=" SG CYS E 157 " - pdb=" SG CYS E 171 " distance=2.03
Simple disulfide: pdb=" SG CYS E 289 " - pdb=" SG CYS E 394 " distance=2.03
Automatic linking
Parameters for automatic linking
Linking & cutoffs
Metal : Auto - 3.00
Amino acid : True - 1.90
Carbohydrate : True - 1.99
Ligands : True - 1.99
Small molecules : False - 1.98
Amino acid - RNA/DNA : False
Number of custom bonds: simple=0, symmetry=0
Links applied
BETA1-4
" NAG F 1 " - " NAG F 2 "
" NAG G 1 " - " NAG G 2 "
" NAG H 1 " - " NAG H 2 "
" NAG I 1 " - " NAG I 2 "
" NAG J 1 " - " NAG J 2 "
NAG-ASN
" NAG A 501 " - " ASN A 170 "
" NAG B 501 " - " ASN B 170 "
" NAG C 501 " - " ASN C 170 "
" NAG D 501 " - " ASN D 170 "
" NAG E 501 " - " ASN E 170 "
" NAG F 1 " - " ASN A 55 "
" NAG G 1 " - " ASN B 55 "
" NAG H 1 " - " ASN C 55 "
" NAG I 1 " - " ASN D 55 "
" NAG J 1 " - " ASN E 55 "
Time building additional restraints: 3.21
Conformation dependent library (CDL) restraints added in 1.7 seconds
3200 Ramachandran restraints generated.
1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2.
Adding C-beta torsion restraints...
Number of C-beta restraints generated: 3140
Finding SS restraints...
Secondary structure from input PDB file:
30 helices and 15 sheets defined
36.7% alpha, 32.7% beta
0 base pairs and 0 stacking pairs defined.
Time for finding SS restraints: 1.41
Creating SS restraints...
Processing helix chain 'A' and resid 94 through 97
Processing helix chain 'A' and resid 231 through 252
removed outlier: 4.465A pdb=" N VAL A 239 " --> pdb=" O ILE A 235 " (cutoff:3.500A)
Proline residue: A 240 - end of helix
Processing helix chain 'A' and resid 259 through 283
removed outlier: 4.175A pdb=" N GLY A 263 " --> pdb=" O ILE A 259 " (cutoff:3.500A)
Processing helix chain 'A' and resid 291 through 320
removed outlier: 3.998A pdb=" N TYR A 295 " --> pdb=" O PRO A 291 " (cutoff:3.500A)
Processing helix chain 'A' and resid 361 through 392
Processing helix chain 'A' and resid 399 through 404
Processing helix chain 'B' and resid 94 through 97
Processing helix chain 'B' and resid 231 through 252
removed outlier: 4.463A pdb=" N VAL B 239 " --> pdb=" O ILE B 235 " (cutoff:3.500A)
Proline residue: B 240 - end of helix
Processing helix chain 'B' and resid 259 through 283
removed outlier: 4.175A pdb=" N GLY B 263 " --> pdb=" O ILE B 259 " (cutoff:3.500A)
Processing helix chain 'B' and resid 291 through 320
removed outlier: 3.998A pdb=" N TYR B 295 " --> pdb=" O PRO B 291 " (cutoff:3.500A)
Processing helix chain 'B' and resid 361 through 392
Processing helix chain 'B' and resid 399 through 404
Processing helix chain 'C' and resid 94 through 97
Processing helix chain 'C' and resid 231 through 252
removed outlier: 4.463A pdb=" N VAL C 239 " --> pdb=" O ILE C 235 " (cutoff:3.500A)
Proline residue: C 240 - end of helix
Processing helix chain 'C' and resid 259 through 283
removed outlier: 4.175A pdb=" N GLY C 263 " --> pdb=" O ILE C 259 " (cutoff:3.500A)
Processing helix chain 'C' and resid 291 through 320
removed outlier: 3.998A pdb=" N TYR C 295 " --> pdb=" O PRO C 291 " (cutoff:3.500A)
Processing helix chain 'C' and resid 361 through 392
Processing helix chain 'C' and resid 399 through 404
Processing helix chain 'D' and resid 94 through 97
Processing helix chain 'D' and resid 231 through 252
removed outlier: 4.465A pdb=" N VAL D 239 " --> pdb=" O ILE D 235 " (cutoff:3.500A)
Proline residue: D 240 - end of helix
Processing helix chain 'D' and resid 259 through 283
removed outlier: 4.175A pdb=" N GLY D 263 " --> pdb=" O ILE D 259 " (cutoff:3.500A)
Processing helix chain 'D' and resid 291 through 320
removed outlier: 3.998A pdb=" N TYR D 295 " --> pdb=" O PRO D 291 " (cutoff:3.500A)
Processing helix chain 'D' and resid 361 through 392
Processing helix chain 'D' and resid 399 through 404
Processing helix chain 'E' and resid 94 through 97
Processing helix chain 'E' and resid 231 through 252
removed outlier: 4.464A pdb=" N VAL E 239 " --> pdb=" O ILE E 235 " (cutoff:3.500A)
Proline residue: E 240 - end of helix
Processing helix chain 'E' and resid 259 through 283
removed outlier: 4.175A pdb=" N GLY E 263 " --> pdb=" O ILE E 259 " (cutoff:3.500A)
Processing helix chain 'E' and resid 291 through 320
removed outlier: 3.998A pdb=" N TYR E 295 " --> pdb=" O PRO E 291 " (cutoff:3.500A)
Processing helix chain 'E' and resid 361 through 392
Processing helix chain 'E' and resid 399 through 404
Processing sheet with id=AA1, first strand: chain 'A' and resid 107 through 111
removed outlier: 5.688A pdb=" N GLN A 136 " --> pdb=" O ASN A 148 " (cutoff:3.500A)
removed outlier: 4.913A pdb=" N ASN A 148 " --> pdb=" O GLN A 136 " (cutoff:3.500A)
removed outlier: 4.382A pdb=" N HIS A 144 " --> pdb=" O ASP A 140 " (cutoff:3.500A)
removed outlier: 7.117A pdb=" N ALA A 150 " --> pdb=" O TRP A 130 " (cutoff:3.500A)
removed outlier: 4.665A pdb=" N TRP A 130 " --> pdb=" O ALA A 150 " (cutoff:3.500A)
removed outlier: 6.564A pdb=" N ALA A 152 " --> pdb=" O VAL A 128 " (cutoff:3.500A)
removed outlier: 4.474A pdb=" N VAL A 128 " --> pdb=" O ALA A 152 " (cutoff:3.500A)
removed outlier: 6.649A pdb=" N GLU A 154 " --> pdb=" O LEU A 126 " (cutoff:3.500A)
Processing sheet with id=AA2, first strand: chain 'A' and resid 107 through 111
removed outlier: 5.688A pdb=" N GLN A 136 " --> pdb=" O ASN A 148 " (cutoff:3.500A)
removed outlier: 4.913A pdb=" N ASN A 148 " --> pdb=" O GLN A 136 " (cutoff:3.500A)
removed outlier: 4.382A pdb=" N HIS A 144 " --> pdb=" O ASP A 140 " (cutoff:3.500A)
removed outlier: 3.775A pdb=" N ASN A 73 " --> pdb=" O SER A 82 " (cutoff:3.500A)
removed outlier: 7.335A pdb=" N MET A 84 " --> pdb=" O VAL A 71 " (cutoff:3.500A)
removed outlier: 5.881A pdb=" N VAL A 71 " --> pdb=" O MET A 84 " (cutoff:3.500A)
removed outlier: 8.577A pdb=" N LEU A 86 " --> pdb=" O SER A 69 " (cutoff:3.500A)
removed outlier: 7.093A pdb=" N SER A 69 " --> pdb=" O LEU A 86 " (cutoff:3.500A)
removed outlier: 7.835A pdb=" N ARG A 88 " --> pdb=" O PHE A 67 " (cutoff:3.500A)
removed outlier: 7.926A pdb=" N PHE A 67 " --> pdb=" O ARG A 88 " (cutoff:3.500A)
removed outlier: 7.853A pdb=" N SER A 90 " --> pdb=" O ARG A 65 " (cutoff:3.500A)
removed outlier: 7.785A pdb=" N ARG A 65 " --> pdb=" O SER A 90 " (cutoff:3.500A)
removed outlier: 8.768A pdb=" N LEU A 92 " --> pdb=" O ASP A 63 " (cutoff:3.500A)
removed outlier: 9.645A pdb=" N ASP A 63 " --> pdb=" O LEU A 92 " (cutoff:3.500A)
Processing sheet with id=AA3, first strand: chain 'A' and resid 121 through 122
removed outlier: 4.115A pdb=" N ASP A 206 " --> pdb=" O ARG A 225 " (cutoff:3.500A)
removed outlier: 7.023A pdb=" N LYS A 227 " --> pdb=" O VAL A 204 " (cutoff:3.500A)
removed outlier: 5.484A pdb=" N VAL A 204 " --> pdb=" O LYS A 227 " (cutoff:3.500A)
Processing sheet with id=AA4, first strand: chain 'B' and resid 107 through 111
removed outlier: 5.687A pdb=" N GLN B 136 " --> pdb=" O ASN B 148 " (cutoff:3.500A)
removed outlier: 4.913A pdb=" N ASN B 148 " --> pdb=" O GLN B 136 " (cutoff:3.500A)
removed outlier: 4.381A pdb=" N HIS B 144 " --> pdb=" O ASP B 140 " (cutoff:3.500A)
removed outlier: 7.118A pdb=" N ALA B 150 " --> pdb=" O TRP B 130 " (cutoff:3.500A)
removed outlier: 4.667A pdb=" N TRP B 130 " --> pdb=" O ALA B 150 " (cutoff:3.500A)
removed outlier: 6.564A pdb=" N ALA B 152 " --> pdb=" O VAL B 128 " (cutoff:3.500A)
removed outlier: 4.475A pdb=" N VAL B 128 " --> pdb=" O ALA B 152 " (cutoff:3.500A)
removed outlier: 6.650A pdb=" N GLU B 154 " --> pdb=" O LEU B 126 " (cutoff:3.500A)
Processing sheet with id=AA5, first strand: chain 'B' and resid 107 through 111
removed outlier: 5.687A pdb=" N GLN B 136 " --> pdb=" O ASN B 148 " (cutoff:3.500A)
removed outlier: 4.913A pdb=" N ASN B 148 " --> pdb=" O GLN B 136 " (cutoff:3.500A)
removed outlier: 4.381A pdb=" N HIS B 144 " --> pdb=" O ASP B 140 " (cutoff:3.500A)
removed outlier: 3.775A pdb=" N ASN B 73 " --> pdb=" O SER B 82 " (cutoff:3.500A)
removed outlier: 7.335A pdb=" N MET B 84 " --> pdb=" O VAL B 71 " (cutoff:3.500A)
removed outlier: 5.881A pdb=" N VAL B 71 " --> pdb=" O MET B 84 " (cutoff:3.500A)
removed outlier: 8.578A pdb=" N LEU B 86 " --> pdb=" O SER B 69 " (cutoff:3.500A)
removed outlier: 7.093A pdb=" N SER B 69 " --> pdb=" O LEU B 86 " (cutoff:3.500A)
removed outlier: 7.835A pdb=" N ARG B 88 " --> pdb=" O PHE B 67 " (cutoff:3.500A)
removed outlier: 7.926A pdb=" N PHE B 67 " --> pdb=" O ARG B 88 " (cutoff:3.500A)
removed outlier: 7.853A pdb=" N SER B 90 " --> pdb=" O ARG B 65 " (cutoff:3.500A)
removed outlier: 7.784A pdb=" N ARG B 65 " --> pdb=" O SER B 90 " (cutoff:3.500A)
removed outlier: 8.768A pdb=" N LEU B 92 " --> pdb=" O ASP B 63 " (cutoff:3.500A)
removed outlier: 9.645A pdb=" N ASP B 63 " --> pdb=" O LEU B 92 " (cutoff:3.500A)
Processing sheet with id=AA6, first strand: chain 'B' and resid 121 through 122
removed outlier: 4.115A pdb=" N ASP B 206 " --> pdb=" O ARG B 225 " (cutoff:3.500A)
removed outlier: 7.024A pdb=" N LYS B 227 " --> pdb=" O VAL B 204 " (cutoff:3.500A)
removed outlier: 5.484A pdb=" N VAL B 204 " --> pdb=" O LYS B 227 " (cutoff:3.500A)
Processing sheet with id=AA7, first strand: chain 'C' and resid 107 through 111
removed outlier: 5.687A pdb=" N GLN C 136 " --> pdb=" O ASN C 148 " (cutoff:3.500A)
removed outlier: 4.913A pdb=" N ASN C 148 " --> pdb=" O GLN C 136 " (cutoff:3.500A)
removed outlier: 4.381A pdb=" N HIS C 144 " --> pdb=" O ASP C 140 " (cutoff:3.500A)
removed outlier: 7.117A pdb=" N ALA C 150 " --> pdb=" O TRP C 130 " (cutoff:3.500A)
removed outlier: 4.666A pdb=" N TRP C 130 " --> pdb=" O ALA C 150 " (cutoff:3.500A)
removed outlier: 6.564A pdb=" N ALA C 152 " --> pdb=" O VAL C 128 " (cutoff:3.500A)
removed outlier: 4.474A pdb=" N VAL C 128 " --> pdb=" O ALA C 152 " (cutoff:3.500A)
removed outlier: 6.649A pdb=" N GLU C 154 " --> pdb=" O LEU C 126 " (cutoff:3.500A)
Processing sheet with id=AA8, first strand: chain 'C' and resid 107 through 111
removed outlier: 5.687A pdb=" N GLN C 136 " --> pdb=" O ASN C 148 " (cutoff:3.500A)
removed outlier: 4.913A pdb=" N ASN C 148 " --> pdb=" O GLN C 136 " (cutoff:3.500A)
removed outlier: 4.381A pdb=" N HIS C 144 " --> pdb=" O ASP C 140 " (cutoff:3.500A)
removed outlier: 3.775A pdb=" N ASN C 73 " --> pdb=" O SER C 82 " (cutoff:3.500A)
removed outlier: 7.335A pdb=" N MET C 84 " --> pdb=" O VAL C 71 " (cutoff:3.500A)
removed outlier: 5.881A pdb=" N VAL C 71 " --> pdb=" O MET C 84 " (cutoff:3.500A)
removed outlier: 8.577A pdb=" N LEU C 86 " --> pdb=" O SER C 69 " (cutoff:3.500A)
removed outlier: 7.093A pdb=" N SER C 69 " --> pdb=" O LEU C 86 " (cutoff:3.500A)
removed outlier: 7.835A pdb=" N ARG C 88 " --> pdb=" O PHE C 67 " (cutoff:3.500A)
removed outlier: 7.926A pdb=" N PHE C 67 " --> pdb=" O ARG C 88 " (cutoff:3.500A)
removed outlier: 7.853A pdb=" N SER C 90 " --> pdb=" O ARG C 65 " (cutoff:3.500A)
removed outlier: 7.784A pdb=" N ARG C 65 " --> pdb=" O SER C 90 " (cutoff:3.500A)
removed outlier: 8.768A pdb=" N LEU C 92 " --> pdb=" O ASP C 63 " (cutoff:3.500A)
removed outlier: 9.645A pdb=" N ASP C 63 " --> pdb=" O LEU C 92 " (cutoff:3.500A)
Processing sheet with id=AA9, first strand: chain 'C' and resid 121 through 122
removed outlier: 4.114A pdb=" N ASP C 206 " --> pdb=" O ARG C 225 " (cutoff:3.500A)
removed outlier: 7.023A pdb=" N LYS C 227 " --> pdb=" O VAL C 204 " (cutoff:3.500A)
removed outlier: 5.484A pdb=" N VAL C 204 " --> pdb=" O LYS C 227 " (cutoff:3.500A)
Processing sheet with id=AB1, first strand: chain 'D' and resid 107 through 111
removed outlier: 5.688A pdb=" N GLN D 136 " --> pdb=" O ASN D 148 " (cutoff:3.500A)
removed outlier: 4.913A pdb=" N ASN D 148 " --> pdb=" O GLN D 136 " (cutoff:3.500A)
removed outlier: 4.382A pdb=" N HIS D 144 " --> pdb=" O ASP D 140 " (cutoff:3.500A)
removed outlier: 7.118A pdb=" N ALA D 150 " --> pdb=" O TRP D 130 " (cutoff:3.500A)
removed outlier: 4.667A pdb=" N TRP D 130 " --> pdb=" O ALA D 150 " (cutoff:3.500A)
removed outlier: 6.563A pdb=" N ALA D 152 " --> pdb=" O VAL D 128 " (cutoff:3.500A)
removed outlier: 4.475A pdb=" N VAL D 128 " --> pdb=" O ALA D 152 " (cutoff:3.500A)
removed outlier: 6.650A pdb=" N GLU D 154 " --> pdb=" O LEU D 126 " (cutoff:3.500A)
Processing sheet with id=AB2, first strand: chain 'D' and resid 107 through 111
removed outlier: 5.688A pdb=" N GLN D 136 " --> pdb=" O ASN D 148 " (cutoff:3.500A)
removed outlier: 4.913A pdb=" N ASN D 148 " --> pdb=" O GLN D 136 " (cutoff:3.500A)
removed outlier: 4.382A pdb=" N HIS D 144 " --> pdb=" O ASP D 140 " (cutoff:3.500A)
removed outlier: 3.775A pdb=" N ASN D 73 " --> pdb=" O SER D 82 " (cutoff:3.500A)
removed outlier: 7.335A pdb=" N MET D 84 " --> pdb=" O VAL D 71 " (cutoff:3.500A)
removed outlier: 5.881A pdb=" N VAL D 71 " --> pdb=" O MET D 84 " (cutoff:3.500A)
removed outlier: 8.578A pdb=" N LEU D 86 " --> pdb=" O SER D 69 " (cutoff:3.500A)
removed outlier: 7.093A pdb=" N SER D 69 " --> pdb=" O LEU D 86 " (cutoff:3.500A)
removed outlier: 7.835A pdb=" N ARG D 88 " --> pdb=" O PHE D 67 " (cutoff:3.500A)
removed outlier: 7.926A pdb=" N PHE D 67 " --> pdb=" O ARG D 88 " (cutoff:3.500A)
removed outlier: 7.853A pdb=" N SER D 90 " --> pdb=" O ARG D 65 " (cutoff:3.500A)
removed outlier: 7.785A pdb=" N ARG D 65 " --> pdb=" O SER D 90 " (cutoff:3.500A)
removed outlier: 8.768A pdb=" N LEU D 92 " --> pdb=" O ASP D 63 " (cutoff:3.500A)
removed outlier: 9.645A pdb=" N ASP D 63 " --> pdb=" O LEU D 92 " (cutoff:3.500A)
Processing sheet with id=AB3, first strand: chain 'D' and resid 121 through 122
removed outlier: 4.115A pdb=" N ASP D 206 " --> pdb=" O ARG D 225 " (cutoff:3.500A)
removed outlier: 7.023A pdb=" N LYS D 227 " --> pdb=" O VAL D 204 " (cutoff:3.500A)
removed outlier: 5.484A pdb=" N VAL D 204 " --> pdb=" O LYS D 227 " (cutoff:3.500A)
Processing sheet with id=AB4, first strand: chain 'E' and resid 107 through 111
removed outlier: 5.687A pdb=" N GLN E 136 " --> pdb=" O ASN E 148 " (cutoff:3.500A)
removed outlier: 4.913A pdb=" N ASN E 148 " --> pdb=" O GLN E 136 " (cutoff:3.500A)
removed outlier: 4.381A pdb=" N HIS E 144 " --> pdb=" O ASP E 140 " (cutoff:3.500A)
removed outlier: 7.118A pdb=" N ALA E 150 " --> pdb=" O TRP E 130 " (cutoff:3.500A)
removed outlier: 4.666A pdb=" N TRP E 130 " --> pdb=" O ALA E 150 " (cutoff:3.500A)
removed outlier: 6.564A pdb=" N ALA E 152 " --> pdb=" O VAL E 128 " (cutoff:3.500A)
removed outlier: 4.474A pdb=" N VAL E 128 " --> pdb=" O ALA E 152 " (cutoff:3.500A)
removed outlier: 6.649A pdb=" N GLU E 154 " --> pdb=" O LEU E 126 " (cutoff:3.500A)
Processing sheet with id=AB5, first strand: chain 'E' and resid 107 through 111
removed outlier: 5.687A pdb=" N GLN E 136 " --> pdb=" O ASN E 148 " (cutoff:3.500A)
removed outlier: 4.913A pdb=" N ASN E 148 " --> pdb=" O GLN E 136 " (cutoff:3.500A)
removed outlier: 4.381A pdb=" N HIS E 144 " --> pdb=" O ASP E 140 " (cutoff:3.500A)
removed outlier: 3.775A pdb=" N ASN E 73 " --> pdb=" O SER E 82 " (cutoff:3.500A)
removed outlier: 7.334A pdb=" N MET E 84 " --> pdb=" O VAL E 71 " (cutoff:3.500A)
removed outlier: 5.881A pdb=" N VAL E 71 " --> pdb=" O MET E 84 " (cutoff:3.500A)
removed outlier: 8.577A pdb=" N LEU E 86 " --> pdb=" O SER E 69 " (cutoff:3.500A)
removed outlier: 7.093A pdb=" N SER E 69 " --> pdb=" O LEU E 86 " (cutoff:3.500A)
removed outlier: 7.835A pdb=" N ARG E 88 " --> pdb=" O PHE E 67 " (cutoff:3.500A)
removed outlier: 7.926A pdb=" N PHE E 67 " --> pdb=" O ARG E 88 " (cutoff:3.500A)
removed outlier: 7.853A pdb=" N SER E 90 " --> pdb=" O ARG E 65 " (cutoff:3.500A)
removed outlier: 7.785A pdb=" N ARG E 65 " --> pdb=" O SER E 90 " (cutoff:3.500A)
removed outlier: 8.768A pdb=" N LEU E 92 " --> pdb=" O ASP E 63 " (cutoff:3.500A)
removed outlier: 9.645A pdb=" N ASP E 63 " --> pdb=" O LEU E 92 " (cutoff:3.500A)
Processing sheet with id=AB6, first strand: chain 'E' and resid 121 through 122
removed outlier: 4.114A pdb=" N ASP E 206 " --> pdb=" O ARG E 225 " (cutoff:3.500A)
removed outlier: 7.023A pdb=" N LYS E 227 " --> pdb=" O VAL E 204 " (cutoff:3.500A)
removed outlier: 5.484A pdb=" N VAL E 204 " --> pdb=" O LYS E 227 " (cutoff:3.500A)
715 hydrogen bonds defined for protein.
2100 hydrogen bond angles defined for protein.
Restraints generated for nucleic acids:
0 hydrogen bonds
0 hydrogen bond angles
0 basepair planarities
0 basepair parallelities
0 stacking parallelities
Total time for adding SS restraints: 4.13
Time building geometry restraints manager: 3.72 seconds
NOTE: a complete listing of the restraints can be obtained by requesting
output of .geo file.
Histogram of bond lengths:
1.18 - 1.31: 2020
1.31 - 1.44: 3605
1.44 - 1.56: 7685
1.56 - 1.69: 0
1.69 - 1.81: 75
Bond restraints: 13385
Sorted by residual:
bond pdb=" C7 NAG J 1 "
pdb=" N2 NAG J 1 "
ideal model delta sigma weight residual
1.346 1.463 -0.117 2.00e-02 2.50e+03 3.42e+01
bond pdb=" C7 NAG H 2 "
pdb=" N2 NAG H 2 "
ideal model delta sigma weight residual
1.346 1.463 -0.117 2.00e-02 2.50e+03 3.40e+01
bond pdb=" C7 NAG H 1 "
pdb=" N2 NAG H 1 "
ideal model delta sigma weight residual
1.346 1.463 -0.117 2.00e-02 2.50e+03 3.40e+01
bond pdb=" C7 NAG J 2 "
pdb=" N2 NAG J 2 "
ideal model delta sigma weight residual
1.346 1.462 -0.116 2.00e-02 2.50e+03 3.39e+01
bond pdb=" C7 NAG F 2 "
pdb=" N2 NAG F 2 "
ideal model delta sigma weight residual
1.346 1.462 -0.116 2.00e-02 2.50e+03 3.39e+01
... (remaining 13380 not shown)
Histogram of bond angle deviations from ideal:
0.00 - 1.10: 17547
1.10 - 2.20: 461
2.20 - 3.30: 169
3.30 - 4.40: 81
4.40 - 5.50: 47
Bond angle restraints: 18305
Sorted by residual:
angle pdb=" C4 NAG H 2 "
pdb=" C5 NAG H 2 "
pdb=" C6 NAG H 2 "
ideal model delta sigma weight residual
113.89 108.79 5.10 3.00e+00 1.11e-01 2.89e+00
angle pdb=" C4 NAG G 2 "
pdb=" C5 NAG G 2 "
pdb=" C6 NAG G 2 "
ideal model delta sigma weight residual
113.89 108.81 5.08 3.00e+00 1.11e-01 2.87e+00
angle pdb=" C4 NAG F 2 "
pdb=" C5 NAG F 2 "
pdb=" C6 NAG F 2 "
ideal model delta sigma weight residual
113.89 108.81 5.08 3.00e+00 1.11e-01 2.87e+00
angle pdb=" C4 NAG I 2 "
pdb=" C5 NAG I 2 "
pdb=" C6 NAG I 2 "
ideal model delta sigma weight residual
113.89 108.82 5.07 3.00e+00 1.11e-01 2.86e+00
angle pdb=" C4 NAG J 2 "
pdb=" C5 NAG J 2 "
pdb=" C6 NAG J 2 "
ideal model delta sigma weight residual
113.89 108.84 5.05 3.00e+00 1.11e-01 2.84e+00
... (remaining 18300 not shown)
Histogram of dihedral angle deviations from ideal:
0.00 - 17.97: 7582
17.97 - 35.94: 523
35.94 - 53.91: 60
53.91 - 71.87: 5
71.87 - 89.84: 10
Dihedral angle restraints: 8180
sinusoidal: 3385
harmonic: 4795
Sorted by residual:
dihedral pdb=" CA VAL B 71 "
pdb=" C VAL B 71 "
pdb=" N PHE B 72 "
pdb=" CA PHE B 72 "
ideal model delta harmonic sigma weight residual
-180.00 -165.58 -14.42 0 5.00e+00 4.00e-02 8.31e+00
dihedral pdb=" CA VAL D 71 "
pdb=" C VAL D 71 "
pdb=" N PHE D 72 "
pdb=" CA PHE D 72 "
ideal model delta harmonic sigma weight residual
-180.00 -165.60 -14.40 0 5.00e+00 4.00e-02 8.29e+00
dihedral pdb=" CA VAL A 71 "
pdb=" C VAL A 71 "
pdb=" N PHE A 72 "
pdb=" CA PHE A 72 "
ideal model delta harmonic sigma weight residual
180.00 -165.62 -14.38 0 5.00e+00 4.00e-02 8.27e+00
... (remaining 8177 not shown)
Histogram of chiral volume deviations from ideal:
0.000 - 0.031: 1462
0.031 - 0.063: 539
0.063 - 0.094: 129
0.094 - 0.126: 80
0.126 - 0.157: 25
Chirality restraints: 2235
Sorted by residual:
chirality pdb=" CA PHE A 72 "
pdb=" N PHE A 72 "
pdb=" C PHE A 72 "
pdb=" CB PHE A 72 "
both_signs ideal model delta sigma weight residual
False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.16e-01
chirality pdb=" CA PHE E 72 "
pdb=" N PHE E 72 "
pdb=" C PHE E 72 "
pdb=" CB PHE E 72 "
both_signs ideal model delta sigma weight residual
False 2.51 2.36 0.16 2.00e-01 2.50e+01 6.01e-01
chirality pdb=" CA PHE B 72 "
pdb=" N PHE B 72 "
pdb=" C PHE B 72 "
pdb=" CB PHE B 72 "
both_signs ideal model delta sigma weight residual
False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.96e-01
... (remaining 2232 not shown)
Planarity restraints: 2260
Sorted by residual:
delta sigma weight rms_deltas residual
plane pdb=" CB PHE B 72 " -0.010 2.00e-02 2.50e+03 8.91e-03 1.39e+00
pdb=" CG PHE B 72 " 0.021 2.00e-02 2.50e+03
pdb=" CD1 PHE B 72 " -0.004 2.00e-02 2.50e+03
pdb=" CD2 PHE B 72 " -0.002 2.00e-02 2.50e+03
pdb=" CE1 PHE B 72 " 0.000 2.00e-02 2.50e+03
pdb=" CE2 PHE B 72 " -0.002 2.00e-02 2.50e+03
pdb=" CZ PHE B 72 " -0.003 2.00e-02 2.50e+03
delta sigma weight rms_deltas residual
plane pdb=" CB PHE C 72 " 0.010 2.00e-02 2.50e+03 8.88e-03 1.38e+00
pdb=" CG PHE C 72 " -0.021 2.00e-02 2.50e+03
pdb=" CD1 PHE C 72 " 0.004 2.00e-02 2.50e+03
pdb=" CD2 PHE C 72 " 0.002 2.00e-02 2.50e+03
pdb=" CE1 PHE C 72 " 0.000 2.00e-02 2.50e+03
pdb=" CE2 PHE C 72 " 0.002 2.00e-02 2.50e+03
pdb=" CZ PHE C 72 " 0.002 2.00e-02 2.50e+03
delta sigma weight rms_deltas residual
plane pdb=" CB PHE D 72 " 0.010 2.00e-02 2.50e+03 8.72e-03 1.33e+00
pdb=" CG PHE D 72 " -0.020 2.00e-02 2.50e+03
pdb=" CD1 PHE D 72 " 0.004 2.00e-02 2.50e+03
pdb=" CD2 PHE D 72 " 0.002 2.00e-02 2.50e+03
pdb=" CE1 PHE D 72 " -0.000 2.00e-02 2.50e+03
pdb=" CE2 PHE D 72 " 0.002 2.00e-02 2.50e+03
pdb=" CZ PHE D 72 " 0.003 2.00e-02 2.50e+03
... (remaining 2257 not shown)
Histogram of nonbonded interaction distances:
2.28 - 2.80: 2871
2.80 - 3.33: 11982
3.33 - 3.85: 22222
3.85 - 4.38: 25474
4.38 - 4.90: 44314
Nonbonded interactions: 106863
Sorted by model distance:
nonbonded pdb=" OE2 GLU D 242 "
pdb=" OH TYR D 296 "
model vdw
2.281 3.040
nonbonded pdb=" OE2 GLU B 242 "
pdb=" OH TYR B 296 "
model vdw
2.281 3.040
nonbonded pdb=" OE2 GLU A 242 "
pdb=" OH TYR A 296 "
model vdw
2.281 3.040
nonbonded pdb=" OE2 GLU C 242 "
pdb=" OH TYR C 296 "
model vdw
2.281 3.040
nonbonded pdb=" NE1 TRP B 127 "
pdb=" OE1 GLU B 154 "
model vdw
2.282 3.120
... (remaining 106858 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: 0.10
Found NCS groups:
ncs_group {
reference = chain 'A'
selection = chain 'C'
selection = chain 'B'
selection = chain 'E'
selection = chain 'D'
}
ncs_group {
reference = chain 'G'
selection = chain 'F'
selection = chain 'I'
selection = chain 'H'
selection = chain 'J'
}
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=0.60 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
Set random seed: 0.000
Set model cs if undefined: 0.000
Decide on map wrapping: 0.000
Normalize map: mean=0, sd=1: 1.280
Set stop_for_unknowns flag: 0.000
Assert model is a single copy model: 0.000
Assert all atoms have isotropic ADPs: 0.000
Construct map_model_manager: 0.010
Extract box with map and model: 0.520
Check model and map are aligned: 0.110
Set scattering table: 0.140
Process input model: 30.690
Find NCS groups from input model: 0.250
Set up NCS constraints: 0.060
Set refine NCS operators: 0.000
Adjust number of macro_cycles: 0.000
Reset NCS operators: 0.000
Extract rigid body selections: 0.000
Check and reset occupancies: 0.000
Load rotamer database and sin/cos tables:12.330
Set ADP refinement strategy: 0.000
Make a string to write initial .geo file:0.000
Internal consistency checks: 0.000
Total: 45.390
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7932
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 : 0.007 0.117 13385 Z= 0.429
Angle : 0.578 5.495 18305 Z= 0.265
Chirality : 0.040 0.157 2235
Planarity : 0.003 0.029 2250
Dihedral : 12.018 89.842 5010
Min Nonbonded Distance : 2.281
Molprobity Statistics.
All-atom Clashscore : 8.00
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 0.00 %
Favored : 100.00 %
Rotamer:
Outliers : 0.00 %
Allowed : 0.00 %
Favored : 100.00 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 5.88 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 2.24 (0.21), residues: 1600
helix: 3.04 (0.20), residues: 530
sheet: 1.44 (0.25), residues: 495
loop : 0.04 (0.26), residues: 575
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.009 0.001 TRP D 91
HIS 0.001 0.000 HIS B 276
PHE 0.021 0.001 PHE C 72
TYR 0.009 0.001 TYR A 272
ARG 0.002 0.000 ARG A 200
*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
3200 Ramachandran restraints generated.
1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
3200 Ramachandran restraints generated.
1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
491 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 0
poor density : 491
time to evaluate : 1.484
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: A 124 GLU cc_start: 0.8389 (mp0) cc_final: 0.8073 (mp0)
REVERT: A 176 TYR cc_start: 0.8727 (m-80) cc_final: 0.8425 (m-80)
REVERT: A 184 GLU cc_start: 0.8121 (mt-10) cc_final: 0.7873 (mt-10)
REVERT: A 206 ASP cc_start: 0.8188 (t0) cc_final: 0.7831 (t0)
REVERT: A 208 LYS cc_start: 0.8308 (ptpt) cc_final: 0.8039 (mtmm)
REVERT: A 259 ILE cc_start: 0.9299 (pt) cc_final: 0.9050 (pp)
REVERT: A 272 TYR cc_start: 0.8625 (t80) cc_final: 0.8103 (t80)
REVERT: A 283 LEU cc_start: 0.8421 (mt) cc_final: 0.7824 (mp)
REVERT: A 297 PHE cc_start: 0.8570 (m-80) cc_final: 0.8119 (m-80)
REVERT: A 364 GLU cc_start: 0.7934 (mt-10) cc_final: 0.7640 (mt-10)
REVERT: B 75 ASP cc_start: 0.7925 (t0) cc_final: 0.7045 (t0)
REVERT: B 129 ASP cc_start: 0.8050 (t0) cc_final: 0.7833 (t0)
REVERT: B 206 ASP cc_start: 0.8133 (t0) cc_final: 0.7629 (t0)
REVERT: B 208 LYS cc_start: 0.8348 (ptpt) cc_final: 0.8081 (mtmm)
REVERT: B 259 ILE cc_start: 0.9220 (pt) cc_final: 0.8798 (pp)
REVERT: B 281 GLN cc_start: 0.8557 (mm110) cc_final: 0.8330 (pt0)
REVERT: B 283 LEU cc_start: 0.8378 (mt) cc_final: 0.7797 (mp)
REVERT: B 310 GLU cc_start: 0.8661 (tm-30) cc_final: 0.8341 (pp20)
REVERT: B 361 SER cc_start: 0.8191 (m) cc_final: 0.7662 (p)
REVERT: C 75 ASP cc_start: 0.8016 (t0) cc_final: 0.7206 (t0)
REVERT: C 77 LEU cc_start: 0.9344 (mt) cc_final: 0.9128 (mm)
REVERT: C 124 GLU cc_start: 0.8371 (mp0) cc_final: 0.7991 (mp0)
REVERT: C 129 ASP cc_start: 0.8026 (t0) cc_final: 0.7814 (t0)
REVERT: C 208 LYS cc_start: 0.8453 (ptpt) cc_final: 0.8157 (mtmm)
REVERT: C 279 LEU cc_start: 0.8964 (tp) cc_final: 0.8611 (tp)
REVERT: C 281 GLN cc_start: 0.8559 (mm110) cc_final: 0.8328 (tt0)
REVERT: C 283 LEU cc_start: 0.8597 (mt) cc_final: 0.8058 (mp)
REVERT: C 297 PHE cc_start: 0.8595 (m-80) cc_final: 0.8258 (m-10)
REVERT: C 361 SER cc_start: 0.8129 (m) cc_final: 0.7926 (p)
REVERT: D 75 ASP cc_start: 0.8025 (t0) cc_final: 0.7304 (t0)
REVERT: D 77 LEU cc_start: 0.9336 (mt) cc_final: 0.9082 (mm)
REVERT: D 124 GLU cc_start: 0.8357 (mp0) cc_final: 0.8040 (mp0)
REVERT: D 206 ASP cc_start: 0.8104 (t0) cc_final: 0.7884 (t0)
REVERT: D 259 ILE cc_start: 0.9437 (pt) cc_final: 0.9156 (pp)
REVERT: D 272 TYR cc_start: 0.8495 (t80) cc_final: 0.7830 (t80)
REVERT: D 279 LEU cc_start: 0.9006 (tp) cc_final: 0.8733 (tp)
REVERT: D 283 LEU cc_start: 0.8620 (mt) cc_final: 0.8066 (mp)
REVERT: D 297 PHE cc_start: 0.8572 (m-80) cc_final: 0.7882 (m-10)
REVERT: E 75 ASP cc_start: 0.8068 (t0) cc_final: 0.7406 (t0)
REVERT: E 77 LEU cc_start: 0.9319 (mt) cc_final: 0.9075 (mm)
REVERT: E 206 ASP cc_start: 0.8133 (t0) cc_final: 0.7782 (t0)
REVERT: E 208 LYS cc_start: 0.8310 (ptpt) cc_final: 0.7910 (mtmm)
REVERT: E 227 LYS cc_start: 0.8278 (ptmt) cc_final: 0.8042 (ptmt)
REVERT: E 272 TYR cc_start: 0.8636 (t80) cc_final: 0.8185 (t80)
REVERT: E 283 LEU cc_start: 0.8482 (mt) cc_final: 0.7935 (mp)
REVERT: E 297 PHE cc_start: 0.8564 (m-80) cc_final: 0.7960 (m-10)
outliers start: 0
outliers final: 1
residues processed: 491
average time/residue: 1.0779
time to fit residues: 583.3206
Evaluate side-chains
353 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 1
poor density : 352
time to evaluate : 1.624
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue 142 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 160
random chunks:
chunk 135 optimal weight: 0.0870
chunk 121 optimal weight: 1.9990
chunk 67 optimal weight: 3.9990
chunk 41 optimal weight: 6.9990
chunk 81 optimal weight: 0.6980
chunk 64 optimal weight: 0.6980
chunk 125 optimal weight: 0.8980
chunk 48 optimal weight: 5.9990
chunk 76 optimal weight: 2.9990
chunk 93 optimal weight: 0.6980
chunk 145 optimal weight: 0.8980
overall best weight: 0.6158
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 221 GLN
B 215 GLN
B 221 GLN
C 214 GLN
C 221 GLN
D 221 GLN
E 221 GLN
Total number of N/Q/H flips: 7
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.097080 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3042 r_free = 0.3042 target = 0.084023 restraints weight = 20225.952|
|-----------------------------------------------------------------------------|
r_work (start): 0.3042 rms_B_bonded: 2.50
r_work: 0.2905 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.2758 rms_B_bonded: 4.82 restraints_weight: 0.2500
r_work (final): 0.2758
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2783
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2783 r_free = 0.2783 target_work(ls_wunit_k1) = 0.069 |
| occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2779 r_free = 0.2779 target_work(ls_wunit_k1) = 0.068 |
| occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 |
|-----------------------------------------------------------------------------|
r_final: 0.2779
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8198
moved from start: 0.1720
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.025 13385 Z= 0.178
Angle : 0.514 7.656 18305 Z= 0.253
Chirality : 0.039 0.142 2235
Planarity : 0.004 0.031 2250
Dihedral : 5.852 59.449 2062
Min Nonbonded Distance : 2.462
Molprobity Statistics.
All-atom Clashscore : 8.84
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 0.69 %
Favored : 99.31 %
Rotamer:
Outliers : 2.52 %
Allowed : 14.20 %
Favored : 83.29 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 5.88 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 2.28 (0.21), residues: 1600
helix: 3.21 (0.20), residues: 530
sheet: 1.35 (0.24), residues: 465
loop : 0.10 (0.26), residues: 605
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.006 0.001 TRP E 91
HIS 0.002 0.000 HIS C 276
PHE 0.020 0.002 PHE A 72
TYR 0.019 0.002 TYR D 176
ARG 0.007 0.001 ARG C 257
*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
3200 Ramachandran restraints generated.
1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
3200 Ramachandran restraints generated.
1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
407 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 36
poor density : 371
time to evaluate : 1.610
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: A 48 GLU cc_start: 0.8478 (tp30) cc_final: 0.8058 (mm-30)
REVERT: A 75 ASP cc_start: 0.8382 (t0) cc_final: 0.8053 (t0)
REVERT: A 78 ARG cc_start: 0.8789 (mtp85) cc_final: 0.8568 (mtp85)
REVERT: A 160 GLU cc_start: 0.8536 (tt0) cc_final: 0.7778 (tm-30)
REVERT: A 176 TYR cc_start: 0.8805 (m-80) cc_final: 0.8529 (m-80)
REVERT: A 201 GLU cc_start: 0.8699 (mt-10) cc_final: 0.8307 (mp0)
REVERT: A 206 ASP cc_start: 0.8461 (t0) cc_final: 0.8088 (t0)
REVERT: A 208 LYS cc_start: 0.8479 (ptpt) cc_final: 0.8247 (mtmm)
REVERT: A 221 GLN cc_start: 0.8721 (tt0) cc_final: 0.8404 (tt0)
REVERT: A 272 TYR cc_start: 0.8852 (t80) cc_final: 0.8319 (t80)
REVERT: A 283 LEU cc_start: 0.8531 (mt) cc_final: 0.8029 (mp)
REVERT: A 297 PHE cc_start: 0.8772 (m-80) cc_final: 0.8404 (m-10)
REVERT: A 364 GLU cc_start: 0.8435 (mt-10) cc_final: 0.8121 (mt-10)
REVERT: B 48 GLU cc_start: 0.8539 (tp30) cc_final: 0.8234 (mm-30)
REVERT: B 54 ASN cc_start: 0.9000 (OUTLIER) cc_final: 0.8493 (m-40)
REVERT: B 75 ASP cc_start: 0.8231 (t0) cc_final: 0.7682 (t0)
REVERT: B 113 GLU cc_start: 0.8470 (OUTLIER) cc_final: 0.8013 (mp0)
REVERT: B 129 ASP cc_start: 0.8567 (t0) cc_final: 0.8217 (t0)
REVERT: B 154 GLU cc_start: 0.8670 (tt0) cc_final: 0.8412 (tt0)
REVERT: B 160 GLU cc_start: 0.8587 (tt0) cc_final: 0.7927 (tm-30)
REVERT: B 201 GLU cc_start: 0.8593 (mt-10) cc_final: 0.8242 (mp0)
REVERT: B 206 ASP cc_start: 0.8360 (t0) cc_final: 0.7816 (t0)
REVERT: B 259 ILE cc_start: 0.9351 (pt) cc_final: 0.9018 (mt)
REVERT: B 281 GLN cc_start: 0.8720 (mm110) cc_final: 0.8286 (pt0)
REVERT: B 283 LEU cc_start: 0.8450 (mt) cc_final: 0.8067 (mp)
REVERT: B 310 GLU cc_start: 0.8957 (tm-30) cc_final: 0.8660 (pp20)
REVERT: C 48 GLU cc_start: 0.8383 (tp30) cc_final: 0.8098 (mm-30)
REVERT: C 75 ASP cc_start: 0.8267 (t0) cc_final: 0.7707 (t0)
REVERT: C 77 LEU cc_start: 0.9267 (mt) cc_final: 0.9050 (mm)
REVERT: C 124 GLU cc_start: 0.8976 (mp0) cc_final: 0.8695 (mp0)
REVERT: C 129 ASP cc_start: 0.8568 (t0) cc_final: 0.8236 (t0)
REVERT: C 160 GLU cc_start: 0.8589 (tt0) cc_final: 0.7982 (tp30)
REVERT: C 201 GLU cc_start: 0.8586 (mt-10) cc_final: 0.8273 (mp0)
REVERT: C 208 LYS cc_start: 0.8598 (ptpt) cc_final: 0.8299 (mtmm)
REVERT: C 281 GLN cc_start: 0.8751 (mm110) cc_final: 0.8267 (pt0)
REVERT: C 283 LEU cc_start: 0.8711 (mt) cc_final: 0.8310 (mp)
REVERT: C 402 GLU cc_start: 0.8635 (mm-30) cc_final: 0.8373 (mt-10)
REVERT: D 75 ASP cc_start: 0.8394 (t0) cc_final: 0.7866 (t0)
REVERT: D 77 LEU cc_start: 0.9267 (mt) cc_final: 0.9036 (mm)
REVERT: D 124 GLU cc_start: 0.8847 (mp0) cc_final: 0.8342 (mp0)
REVERT: D 141 GLN cc_start: 0.8661 (OUTLIER) cc_final: 0.8060 (pm20)
REVERT: D 160 GLU cc_start: 0.8717 (tt0) cc_final: 0.8179 (tp30)
REVERT: D 188 GLN cc_start: 0.8323 (mt0) cc_final: 0.8115 (tt0)
REVERT: D 201 GLU cc_start: 0.8587 (mt-10) cc_final: 0.8346 (mp0)
REVERT: D 206 ASP cc_start: 0.8376 (t0) cc_final: 0.8083 (t0)
REVERT: D 208 LYS cc_start: 0.8661 (mtmm) cc_final: 0.8441 (mtmm)
REVERT: D 283 LEU cc_start: 0.8654 (mt) cc_final: 0.8235 (mp)
REVERT: D 402 GLU cc_start: 0.8535 (mm-30) cc_final: 0.8238 (mt-10)
REVERT: E 75 ASP cc_start: 0.8352 (t0) cc_final: 0.7893 (t0)
REVERT: E 77 LEU cc_start: 0.9219 (mt) cc_final: 0.8988 (mm)
REVERT: E 78 ARG cc_start: 0.8842 (mtp85) cc_final: 0.8625 (mtm110)
REVERT: E 113 GLU cc_start: 0.8578 (OUTLIER) cc_final: 0.8186 (mp0)
REVERT: E 160 GLU cc_start: 0.8741 (tt0) cc_final: 0.7894 (tm-30)
REVERT: E 201 GLU cc_start: 0.8626 (mt-10) cc_final: 0.8288 (mp0)
REVERT: E 206 ASP cc_start: 0.8392 (t0) cc_final: 0.8027 (t0)
REVERT: E 208 LYS cc_start: 0.8546 (ptpt) cc_final: 0.8190 (mtmm)
REVERT: E 272 TYR cc_start: 0.8862 (t80) cc_final: 0.8362 (t80)
REVERT: E 283 LEU cc_start: 0.8550 (mt) cc_final: 0.8077 (mp)
REVERT: E 297 PHE cc_start: 0.8818 (m-80) cc_final: 0.8382 (m-10)
REVERT: E 370 PHE cc_start: 0.8726 (t80) cc_final: 0.8500 (t80)
REVERT: E 390 MET cc_start: 0.8043 (mmt) cc_final: 0.7825 (mmt)
REVERT: E 402 GLU cc_start: 0.8487 (mm-30) cc_final: 0.8247 (mt-10)
outliers start: 36
outliers final: 14
residues processed: 388
average time/residue: 1.2167
time to fit residues: 516.6186
Evaluate side-chains
355 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 18
poor density : 337
time to evaluate : 1.479
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 117 THR
Chi-restraints excluded: chain A residue 179 SER
Chi-restraints excluded: chain A residue 183 MET
Chi-restraints excluded: chain A residue 211 VAL
Chi-restraints excluded: chain A residue 302 LEU
Chi-restraints excluded: chain B residue 54 ASN
Chi-restraints excluded: chain B residue 113 GLU
Chi-restraints excluded: chain B residue 179 SER
Chi-restraints excluded: chain B residue 235 ILE
Chi-restraints excluded: chain C residue 179 SER
Chi-restraints excluded: chain C residue 304 LEU
Chi-restraints excluded: chain D residue 141 GLN
Chi-restraints excluded: chain D residue 153 THR
Chi-restraints excluded: chain D residue 179 SER
Chi-restraints excluded: chain D residue 304 LEU
Chi-restraints excluded: chain E residue 113 GLU
Chi-restraints excluded: chain E residue 142 ASP
Chi-restraints excluded: chain E residue 198 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 160
random chunks:
chunk 107 optimal weight: 0.9990
chunk 88 optimal weight: 3.9990
chunk 65 optimal weight: 7.9990
chunk 98 optimal weight: 4.9990
chunk 63 optimal weight: 9.9990
chunk 114 optimal weight: 0.9980
chunk 42 optimal weight: 0.9980
chunk 53 optimal weight: 2.9990
chunk 105 optimal weight: 4.9990
chunk 92 optimal weight: 4.9990
chunk 102 optimal weight: 2.9990
overall best weight: 1.7986
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 156 ASN
B 221 GLN
** C 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 221 GLN
** D 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 221 GLN
E 156 ASN
E 382 GLN
Total number of N/Q/H flips: 6
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.094348 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2985 r_free = 0.2985 target = 0.080267 restraints weight = 20461.817|
|-----------------------------------------------------------------------------|
r_work (start): 0.2974 rms_B_bonded: 2.79
r_work: 0.2808 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work (final): 0.2808
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2804
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2804 r_free = 0.2804 target_work(ls_wunit_k1) = 0.070 |
| occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2803 r_free = 0.2803 target_work(ls_wunit_k1) = 0.070 |
| occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 |
|-----------------------------------------------------------------------------|
r_final: 0.2803
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8048
moved from start: 0.2385
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.005 0.031 13385 Z= 0.326
Angle : 0.555 8.406 18305 Z= 0.273
Chirality : 0.041 0.217 2235
Planarity : 0.004 0.036 2250
Dihedral : 5.556 55.683 2062
Min Nonbonded Distance : 2.426
Molprobity Statistics.
All-atom Clashscore : 8.99
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 0.88 %
Favored : 99.12 %
Rotamer:
Outliers : 3.71 %
Allowed : 14.90 %
Favored : 81.40 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 5.88 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 1.90 (0.21), residues: 1600
helix: 2.85 (0.20), residues: 530
sheet: 1.28 (0.25), residues: 430
loop : -0.12 (0.25), residues: 640
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.011 0.001 TRP A 112
HIS 0.003 0.001 HIS E 103
PHE 0.021 0.002 PHE A 72
TYR 0.019 0.002 TYR E 176
ARG 0.007 0.001 ARG B 78
*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
3200 Ramachandran restraints generated.
1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
3200 Ramachandran restraints generated.
1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
399 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 53
poor density : 346
time to evaluate : 1.530
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: A 48 GLU cc_start: 0.8375 (tp30) cc_final: 0.7938 (mm-30)
REVERT: A 75 ASP cc_start: 0.8169 (t0) cc_final: 0.7777 (t0)
REVERT: A 78 ARG cc_start: 0.8700 (mtp85) cc_final: 0.8454 (mtp85)
REVERT: A 132 ASP cc_start: 0.8230 (m-30) cc_final: 0.7954 (t0)
REVERT: A 160 GLU cc_start: 0.8403 (tt0) cc_final: 0.7553 (tm-30)
REVERT: A 176 TYR cc_start: 0.8741 (m-80) cc_final: 0.8227 (m-80)
REVERT: A 201 GLU cc_start: 0.8662 (mt-10) cc_final: 0.8330 (mp0)
REVERT: A 206 ASP cc_start: 0.8339 (t0) cc_final: 0.7892 (t0)
REVERT: A 208 LYS cc_start: 0.8448 (ptpt) cc_final: 0.8125 (mtmm)
REVERT: A 272 TYR cc_start: 0.8782 (t80) cc_final: 0.8167 (t80)
REVERT: A 281 GLN cc_start: 0.8703 (mm110) cc_final: 0.8279 (pt0)
REVERT: A 283 LEU cc_start: 0.8682 (mt) cc_final: 0.8270 (mp)
REVERT: A 297 PHE cc_start: 0.8688 (m-80) cc_final: 0.8302 (m-10)
REVERT: A 364 GLU cc_start: 0.8247 (mt-10) cc_final: 0.7767 (mt-10)
REVERT: B 75 ASP cc_start: 0.7913 (t0) cc_final: 0.7394 (t0)
REVERT: B 129 ASP cc_start: 0.8529 (t0) cc_final: 0.8047 (t0)
REVERT: B 146 LYS cc_start: 0.8451 (OUTLIER) cc_final: 0.7639 (mttp)
REVERT: B 199 LYS cc_start: 0.8185 (ptpt) cc_final: 0.7742 (ptmm)
REVERT: B 201 GLU cc_start: 0.8512 (mt-10) cc_final: 0.8163 (mp0)
REVERT: B 206 ASP cc_start: 0.8288 (t0) cc_final: 0.7648 (t0)
REVERT: B 208 LYS cc_start: 0.8422 (mtmm) cc_final: 0.8149 (mtmm)
REVERT: B 233 SER cc_start: 0.8669 (OUTLIER) cc_final: 0.8469 (p)
REVERT: B 281 GLN cc_start: 0.8731 (mm110) cc_final: 0.8324 (pt0)
REVERT: B 283 LEU cc_start: 0.8566 (mt) cc_final: 0.8155 (mp)
REVERT: C 75 ASP cc_start: 0.8070 (t0) cc_final: 0.7419 (t0)
REVERT: C 113 GLU cc_start: 0.8997 (mp0) cc_final: 0.8734 (mp0)
REVERT: C 129 ASP cc_start: 0.8623 (t0) cc_final: 0.8180 (t0)
REVERT: C 146 LYS cc_start: 0.8431 (mtpt) cc_final: 0.7741 (mtmp)
REVERT: C 160 GLU cc_start: 0.8536 (tt0) cc_final: 0.7986 (mm-30)
REVERT: C 184 GLU cc_start: 0.8417 (mt-10) cc_final: 0.7907 (pt0)
REVERT: C 201 GLU cc_start: 0.8631 (mt-10) cc_final: 0.8334 (mp0)
REVERT: C 208 LYS cc_start: 0.8460 (ptpt) cc_final: 0.8179 (mtmm)
REVERT: C 232 LYS cc_start: 0.8623 (ttmt) cc_final: 0.8347 (ttmt)
REVERT: C 233 SER cc_start: 0.8712 (m) cc_final: 0.8485 (p)
REVERT: C 281 GLN cc_start: 0.8803 (mm110) cc_final: 0.8265 (pt0)
REVERT: C 283 LEU cc_start: 0.8764 (mt) cc_final: 0.8376 (mp)
REVERT: C 402 GLU cc_start: 0.8531 (mm-30) cc_final: 0.8278 (mt-10)
REVERT: D 48 GLU cc_start: 0.8312 (tp30) cc_final: 0.8028 (mm-30)
REVERT: D 75 ASP cc_start: 0.8164 (t0) cc_final: 0.7530 (t0)
REVERT: D 77 LEU cc_start: 0.9243 (mt) cc_final: 0.9004 (mm)
REVERT: D 124 GLU cc_start: 0.8723 (mp0) cc_final: 0.8326 (mp0)
REVERT: D 154 GLU cc_start: 0.8860 (tt0) cc_final: 0.8632 (tt0)
REVERT: D 184 GLU cc_start: 0.8298 (mt-10) cc_final: 0.7769 (pt0)
REVERT: D 201 GLU cc_start: 0.8491 (mt-10) cc_final: 0.8262 (mp0)
REVERT: D 206 ASP cc_start: 0.8272 (t0) cc_final: 0.7849 (t0)
REVERT: D 208 LYS cc_start: 0.8493 (mtmm) cc_final: 0.8182 (mtmm)
REVERT: D 214 GLN cc_start: 0.8189 (mm-40) cc_final: 0.7989 (mm-40)
REVERT: D 272 TYR cc_start: 0.8786 (t80) cc_final: 0.7828 (t80)
REVERT: D 281 GLN cc_start: 0.8688 (mm110) cc_final: 0.8385 (mm-40)
REVERT: D 283 LEU cc_start: 0.8734 (mt) cc_final: 0.8364 (mp)
REVERT: D 402 GLU cc_start: 0.8445 (mm-30) cc_final: 0.8169 (mt-10)
REVERT: E 75 ASP cc_start: 0.8124 (t0) cc_final: 0.7544 (t0)
REVERT: E 77 LEU cc_start: 0.9198 (mt) cc_final: 0.8915 (mm)
REVERT: E 78 ARG cc_start: 0.8733 (mtp85) cc_final: 0.8487 (mtp85)
REVERT: E 146 LYS cc_start: 0.8482 (mtpt) cc_final: 0.7732 (mtmp)
REVERT: E 160 GLU cc_start: 0.8653 (tt0) cc_final: 0.8167 (mm-30)
REVERT: E 198 VAL cc_start: 0.9302 (OUTLIER) cc_final: 0.9002 (m)
REVERT: E 201 GLU cc_start: 0.8579 (mt-10) cc_final: 0.8259 (mp0)
REVERT: E 206 ASP cc_start: 0.8264 (t0) cc_final: 0.7827 (t0)
REVERT: E 208 LYS cc_start: 0.8369 (ptpt) cc_final: 0.7962 (mtmm)
REVERT: E 283 LEU cc_start: 0.8660 (mt) cc_final: 0.8322 (mp)
outliers start: 53
outliers final: 20
residues processed: 370
average time/residue: 1.1006
time to fit residues: 449.1876
Evaluate side-chains
344 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 23
poor density : 321
time to evaluate : 1.660
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 117 THR
Chi-restraints excluded: chain A residue 179 SER
Chi-restraints excluded: chain A residue 211 VAL
Chi-restraints excluded: chain A residue 302 LEU
Chi-restraints excluded: chain A residue 372 LEU
Chi-restraints excluded: chain B residue 54 ASN
Chi-restraints excluded: chain B residue 113 GLU
Chi-restraints excluded: chain B residue 146 LYS
Chi-restraints excluded: chain B residue 179 SER
Chi-restraints excluded: chain B residue 210 GLN
Chi-restraints excluded: chain B residue 233 SER
Chi-restraints excluded: chain B residue 253 LEU
Chi-restraints excluded: chain C residue 179 SER
Chi-restraints excluded: chain C residue 198 VAL
Chi-restraints excluded: chain C residue 235 ILE
Chi-restraints excluded: chain D residue 153 THR
Chi-restraints excluded: chain D residue 179 SER
Chi-restraints excluded: chain D residue 183 MET
Chi-restraints excluded: chain D residue 235 ILE
Chi-restraints excluded: chain E residue 142 ASP
Chi-restraints excluded: chain E residue 198 VAL
Chi-restraints excluded: chain E residue 237 LEU
Chi-restraints excluded: chain E residue 372 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 160
random chunks:
chunk 88 optimal weight: 3.9990
chunk 83 optimal weight: 0.0970
chunk 135 optimal weight: 0.9980
chunk 5 optimal weight: 0.0870
chunk 138 optimal weight: 0.9980
chunk 15 optimal weight: 0.9990
chunk 106 optimal weight: 0.9980
chunk 113 optimal weight: 0.9990
chunk 46 optimal weight: 0.9990
chunk 148 optimal weight: 4.9990
chunk 98 optimal weight: 1.9990
overall best weight: 0.6356
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** A 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 221 GLN
** C 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 221 GLN
** D 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 156 ASN
Total number of N/Q/H flips: 3
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.096203 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3005 r_free = 0.3005 target = 0.081618 restraints weight = 20037.920|
|-----------------------------------------------------------------------------|
r_work (start): 0.3024 rms_B_bonded: 2.89
r_work: 0.2863 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.2863
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2839
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2839 r_free = 0.2839 target_work(ls_wunit_k1) = 0.072 |
| occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2839 r_free = 0.2839 target_work(ls_wunit_k1) = 0.072 |
| occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 |
|-----------------------------------------------------------------------------|
r_final: 0.2839
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7937
moved from start: 0.2436
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.026 13385 Z= 0.167
Angle : 0.510 8.431 18305 Z= 0.249
Chirality : 0.039 0.180 2235
Planarity : 0.004 0.030 2250
Dihedral : 5.414 55.686 2062
Min Nonbonded Distance : 2.448
Molprobity Statistics.
All-atom Clashscore : 8.19
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 0.94 %
Favored : 99.06 %
Rotamer:
Outliers : 3.15 %
Allowed : 16.99 %
Favored : 79.86 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 5.88 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 1.97 (0.21), residues: 1600
helix: 2.95 (0.20), residues: 530
sheet: 0.84 (0.24), residues: 475
loop : 0.25 (0.27), residues: 595
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.009 0.001 TRP E 112
HIS 0.001 0.000 HIS C 276
PHE 0.017 0.002 PHE B 385
TYR 0.015 0.002 TYR E 176
ARG 0.008 0.000 ARG C 257
*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
3200 Ramachandran restraints generated.
1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
3200 Ramachandran restraints generated.
1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
378 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 45
poor density : 333
time to evaluate : 1.519
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: A 75 ASP cc_start: 0.8093 (t0) cc_final: 0.7645 (t0)
REVERT: A 78 ARG cc_start: 0.8573 (mtp85) cc_final: 0.8332 (mtp85)
REVERT: A 141 GLN cc_start: 0.8501 (OUTLIER) cc_final: 0.7927 (pm20)
REVERT: A 153 THR cc_start: 0.9120 (p) cc_final: 0.8861 (t)
REVERT: A 201 GLU cc_start: 0.8546 (mt-10) cc_final: 0.8174 (mp0)
REVERT: A 206 ASP cc_start: 0.8289 (t0) cc_final: 0.7850 (t0)
REVERT: A 208 LYS cc_start: 0.8340 (ptpt) cc_final: 0.8034 (mtmm)
REVERT: A 232 LYS cc_start: 0.8485 (ttmt) cc_final: 0.8063 (ttmm)
REVERT: A 272 TYR cc_start: 0.8686 (t80) cc_final: 0.8033 (t80)
REVERT: A 281 GLN cc_start: 0.8679 (mm110) cc_final: 0.8258 (pt0)
REVERT: A 283 LEU cc_start: 0.8496 (mt) cc_final: 0.8167 (mp)
REVERT: A 297 PHE cc_start: 0.8544 (m-80) cc_final: 0.8136 (m-10)
REVERT: A 364 GLU cc_start: 0.8175 (mt-10) cc_final: 0.7685 (mt-10)
REVERT: B 75 ASP cc_start: 0.7825 (t0) cc_final: 0.7272 (t0)
REVERT: B 129 ASP cc_start: 0.8542 (t0) cc_final: 0.8027 (t0)
REVERT: B 146 LYS cc_start: 0.8398 (mtmt) cc_final: 0.7583 (mttp)
REVERT: B 160 GLU cc_start: 0.8389 (mm-30) cc_final: 0.8041 (mm-30)
REVERT: B 199 LYS cc_start: 0.8011 (ptpt) cc_final: 0.7762 (ptmt)
REVERT: B 201 GLU cc_start: 0.8395 (mt-10) cc_final: 0.8060 (mp0)
REVERT: B 206 ASP cc_start: 0.8246 (t0) cc_final: 0.7649 (t0)
REVERT: B 279 LEU cc_start: 0.8922 (tp) cc_final: 0.8690 (tt)
REVERT: B 281 GLN cc_start: 0.8722 (mm110) cc_final: 0.8332 (pt0)
REVERT: B 283 LEU cc_start: 0.8525 (mt) cc_final: 0.8153 (mp)
REVERT: B 296 TYR cc_start: 0.8317 (t80) cc_final: 0.8076 (t80)
REVERT: C 75 ASP cc_start: 0.7972 (t0) cc_final: 0.7283 (t0)
REVERT: C 77 LEU cc_start: 0.9185 (mt) cc_final: 0.8949 (mm)
REVERT: C 113 GLU cc_start: 0.9046 (mp0) cc_final: 0.8583 (mp0)
REVERT: C 129 ASP cc_start: 0.8588 (t0) cc_final: 0.8110 (t0)
REVERT: C 146 LYS cc_start: 0.8372 (mtpt) cc_final: 0.7685 (mtmp)
REVERT: C 160 GLU cc_start: 0.8509 (tt0) cc_final: 0.7912 (mm-30)
REVERT: C 184 GLU cc_start: 0.8301 (mt-10) cc_final: 0.7713 (pt0)
REVERT: C 201 GLU cc_start: 0.8574 (mt-10) cc_final: 0.8262 (mp0)
REVERT: C 208 LYS cc_start: 0.8372 (ptpt) cc_final: 0.8087 (mtmm)
REVERT: C 232 LYS cc_start: 0.8544 (ttmt) cc_final: 0.8311 (ttmt)
REVERT: C 233 SER cc_start: 0.8682 (m) cc_final: 0.8388 (p)
REVERT: C 281 GLN cc_start: 0.8711 (mm110) cc_final: 0.8162 (pt0)
REVERT: C 283 LEU cc_start: 0.8688 (mt) cc_final: 0.8369 (mp)
REVERT: C 402 GLU cc_start: 0.8486 (mm-30) cc_final: 0.8237 (mt-10)
REVERT: D 75 ASP cc_start: 0.8090 (t0) cc_final: 0.7387 (t0)
REVERT: D 77 LEU cc_start: 0.9167 (mt) cc_final: 0.8925 (mm)
REVERT: D 78 ARG cc_start: 0.8763 (mtp85) cc_final: 0.8452 (mtp85)
REVERT: D 160 GLU cc_start: 0.8690 (OUTLIER) cc_final: 0.8318 (mm-30)
REVERT: D 184 GLU cc_start: 0.8284 (mt-10) cc_final: 0.7723 (pt0)
REVERT: D 201 GLU cc_start: 0.8441 (mt-10) cc_final: 0.8178 (mp0)
REVERT: D 206 ASP cc_start: 0.8224 (t0) cc_final: 0.7821 (t0)
REVERT: D 208 LYS cc_start: 0.8458 (mtmm) cc_final: 0.8128 (mtmm)
REVERT: D 281 GLN cc_start: 0.8644 (mm110) cc_final: 0.8109 (pt0)
REVERT: D 283 LEU cc_start: 0.8628 (mt) cc_final: 0.8065 (mp)
REVERT: D 402 GLU cc_start: 0.8436 (mm-30) cc_final: 0.8144 (mt-10)
REVERT: E 75 ASP cc_start: 0.8034 (t0) cc_final: 0.7392 (t0)
REVERT: E 77 LEU cc_start: 0.9071 (mt) cc_final: 0.8836 (mm)
REVERT: E 78 ARG cc_start: 0.8646 (mtp85) cc_final: 0.8428 (mtp85)
REVERT: E 113 GLU cc_start: 0.9010 (mp0) cc_final: 0.8557 (mp0)
REVERT: E 146 LYS cc_start: 0.8385 (mtpt) cc_final: 0.7646 (mtmp)
REVERT: E 160 GLU cc_start: 0.8621 (tt0) cc_final: 0.8125 (mm-30)
REVERT: E 184 GLU cc_start: 0.8116 (mt-10) cc_final: 0.7902 (mt-10)
REVERT: E 188 GLN cc_start: 0.7994 (mt0) cc_final: 0.7683 (tt0)
REVERT: E 198 VAL cc_start: 0.9255 (OUTLIER) cc_final: 0.8950 (m)
REVERT: E 201 GLU cc_start: 0.8502 (mt-10) cc_final: 0.8158 (mp0)
REVERT: E 206 ASP cc_start: 0.8209 (t0) cc_final: 0.7772 (t0)
REVERT: E 208 LYS cc_start: 0.8289 (ptpt) cc_final: 0.7852 (mtmm)
REVERT: E 279 LEU cc_start: 0.8904 (tp) cc_final: 0.8692 (tt)
REVERT: E 283 LEU cc_start: 0.8510 (mt) cc_final: 0.8060 (mp)
outliers start: 45
outliers final: 20
residues processed: 356
average time/residue: 1.0504
time to fit residues: 413.7145
Evaluate side-chains
343 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 23
poor density : 320
time to evaluate : 1.546
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 141 GLN
Chi-restraints excluded: chain A residue 179 SER
Chi-restraints excluded: chain A residue 211 VAL
Chi-restraints excluded: chain A residue 253 LEU
Chi-restraints excluded: chain A residue 302 LEU
Chi-restraints excluded: chain B residue 54 ASN
Chi-restraints excluded: chain B residue 179 SER
Chi-restraints excluded: chain B residue 246 LEU
Chi-restraints excluded: chain B residue 253 LEU
Chi-restraints excluded: chain B residue 277 SER
Chi-restraints excluded: chain C residue 54 ASN
Chi-restraints excluded: chain C residue 179 SER
Chi-restraints excluded: chain C residue 198 VAL
Chi-restraints excluded: chain C residue 304 LEU
Chi-restraints excluded: chain D residue 153 THR
Chi-restraints excluded: chain D residue 160 GLU
Chi-restraints excluded: chain D residue 179 SER
Chi-restraints excluded: chain D residue 235 ILE
Chi-restraints excluded: chain E residue 156 ASN
Chi-restraints excluded: chain E residue 198 VAL
Chi-restraints excluded: chain E residue 233 SER
Chi-restraints excluded: chain E residue 237 LEU
Chi-restraints excluded: chain E residue 277 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 160
random chunks:
chunk 124 optimal weight: 4.9990
chunk 0 optimal weight: 5.9990
chunk 98 optimal weight: 0.7980
chunk 151 optimal weight: 6.9990
chunk 114 optimal weight: 1.9990
chunk 122 optimal weight: 2.9990
chunk 34 optimal weight: 0.5980
chunk 111 optimal weight: 0.7980
chunk 35 optimal weight: 5.9990
chunk 102 optimal weight: 3.9990
chunk 127 optimal weight: 10.0000
overall best weight: 1.4384
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** A 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 221 GLN
B 221 GLN
C 156 ASN
C 221 GLN
D 156 ASN
D 221 GLN
D 382 GLN
E 156 ASN
Total number of N/Q/H flips: 8
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.091204 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.2945 r_free = 0.2945 target = 0.078105 restraints weight = 20677.675|
|-----------------------------------------------------------------------------|
r_work (start): 0.2934 rms_B_bonded: 2.45
r_work: 0.2793 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.2644 rms_B_bonded: 4.69 restraints_weight: 0.2500
r_work (final): 0.2644
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2667
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2667 r_free = 0.2667 target_work(ls_wunit_k1) = 0.063 |
| occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2667 r_free = 0.2667 target_work(ls_wunit_k1) = 0.063 |
| occupancies: max = 1.00 min = 0.90 number of occupancies < 0.1: 0 |
|-----------------------------------------------------------------------------|
r_final: 0.2667
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8342
moved from start: 0.2667
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.004 0.029 13385 Z= 0.265
Angle : 0.528 8.791 18305 Z= 0.257
Chirality : 0.040 0.139 2235
Planarity : 0.004 0.034 2250
Dihedral : 5.124 52.376 2060
Min Nonbonded Distance : 2.441
Molprobity Statistics.
All-atom Clashscore : 8.23
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 1.00 %
Favored : 99.00 %
Rotamer:
Outliers : 3.36 %
Allowed : 17.69 %
Favored : 78.95 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 5.88 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 1.85 (0.21), residues: 1600
helix: 2.87 (0.20), residues: 530
sheet: 0.72 (0.24), residues: 475
loop : 0.20 (0.27), residues: 595
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.009 0.001 TRP E 112
HIS 0.002 0.000 HIS E 103
PHE 0.019 0.002 PHE D 72
TYR 0.019 0.002 TYR D 176
ARG 0.011 0.000 ARG C 257
*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
3200 Ramachandran restraints generated.
1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
3200 Ramachandran restraints generated.
1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
390 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 48
poor density : 342
time to evaluate : 1.641
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: A 75 ASP cc_start: 0.8449 (t0) cc_final: 0.8079 (t0)
REVERT: A 201 GLU cc_start: 0.8809 (mt-10) cc_final: 0.8473 (mp0)
REVERT: A 206 ASP cc_start: 0.8475 (t0) cc_final: 0.8113 (t0)
REVERT: A 207 LEU cc_start: 0.9341 (OUTLIER) cc_final: 0.9140 (mp)
REVERT: A 208 LYS cc_start: 0.8616 (ptpt) cc_final: 0.8334 (mtmm)
REVERT: A 272 TYR cc_start: 0.8970 (t80) cc_final: 0.8417 (t80)
REVERT: A 281 GLN cc_start: 0.8727 (mm110) cc_final: 0.8328 (pt0)
REVERT: A 283 LEU cc_start: 0.8590 (mt) cc_final: 0.8254 (mp)
REVERT: A 297 PHE cc_start: 0.8913 (m-80) cc_final: 0.8580 (m-10)
REVERT: A 364 GLU cc_start: 0.8512 (mt-10) cc_final: 0.8118 (mt-10)
REVERT: B 75 ASP cc_start: 0.8292 (t0) cc_final: 0.7802 (t0)
REVERT: B 129 ASP cc_start: 0.8824 (t0) cc_final: 0.8334 (t0)
REVERT: B 146 LYS cc_start: 0.8791 (mtmt) cc_final: 0.8092 (mttp)
REVERT: B 160 GLU cc_start: 0.8769 (mm-30) cc_final: 0.8381 (mm-30)
REVERT: B 201 GLU cc_start: 0.8671 (mt-10) cc_final: 0.8332 (mp0)
REVERT: B 206 ASP cc_start: 0.8414 (t0) cc_final: 0.7918 (t0)
REVERT: B 279 LEU cc_start: 0.9057 (tp) cc_final: 0.8788 (tt)
REVERT: B 281 GLN cc_start: 0.8777 (mm110) cc_final: 0.8390 (pt0)
REVERT: B 283 LEU cc_start: 0.8546 (mt) cc_final: 0.8209 (mp)
REVERT: B 296 TYR cc_start: 0.8615 (t80) cc_final: 0.8400 (t80)
REVERT: C 75 ASP cc_start: 0.8392 (t0) cc_final: 0.7790 (t0)
REVERT: C 77 LEU cc_start: 0.9409 (mt) cc_final: 0.9204 (mm)
REVERT: C 113 GLU cc_start: 0.9073 (mp0) cc_final: 0.8702 (mp0)
REVERT: C 129 ASP cc_start: 0.8825 (t0) cc_final: 0.8350 (t0)
REVERT: C 146 LYS cc_start: 0.8709 (mtpt) cc_final: 0.8108 (mtmp)
REVERT: C 160 GLU cc_start: 0.8580 (tt0) cc_final: 0.8159 (mm-30)
REVERT: C 184 GLU cc_start: 0.8644 (mt-10) cc_final: 0.8171 (pt0)
REVERT: C 199 LYS cc_start: 0.8339 (OUTLIER) cc_final: 0.7631 (ptmm)
REVERT: C 201 GLU cc_start: 0.8806 (mt-10) cc_final: 0.8514 (mp0)
REVERT: C 233 SER cc_start: 0.8837 (m) cc_final: 0.8623 (p)
REVERT: C 281 GLN cc_start: 0.8750 (mm110) cc_final: 0.8252 (pt0)
REVERT: C 283 LEU cc_start: 0.8671 (mt) cc_final: 0.8359 (mp)
REVERT: C 402 GLU cc_start: 0.8653 (mm-30) cc_final: 0.8413 (mt-10)
REVERT: D 48 GLU cc_start: 0.8575 (tp30) cc_final: 0.8289 (mm-30)
REVERT: D 75 ASP cc_start: 0.8451 (t0) cc_final: 0.7821 (t0)
REVERT: D 78 ARG cc_start: 0.8994 (mtp85) cc_final: 0.8625 (mtp85)
REVERT: D 124 GLU cc_start: 0.8949 (mp0) cc_final: 0.8593 (mp0)
REVERT: D 146 LYS cc_start: 0.8664 (OUTLIER) cc_final: 0.8075 (mttp)
REVERT: D 160 GLU cc_start: 0.8803 (OUTLIER) cc_final: 0.8309 (tp30)
REVERT: D 199 LYS cc_start: 0.8413 (ptpt) cc_final: 0.8142 (ptmm)
REVERT: D 201 GLU cc_start: 0.8734 (mt-10) cc_final: 0.8469 (mp0)
REVERT: D 206 ASP cc_start: 0.8465 (t0) cc_final: 0.8133 (t0)
REVERT: D 208 LYS cc_start: 0.8744 (mtmm) cc_final: 0.8525 (mtmm)
REVERT: D 272 TYR cc_start: 0.8952 (t80) cc_final: 0.8101 (t80)
REVERT: D 281 GLN cc_start: 0.8663 (mm110) cc_final: 0.8184 (pt0)
REVERT: D 283 LEU cc_start: 0.8727 (mt) cc_final: 0.8419 (mp)
REVERT: D 402 GLU cc_start: 0.8572 (mm-30) cc_final: 0.8333 (mt-10)
REVERT: E 75 ASP cc_start: 0.8414 (t0) cc_final: 0.7810 (t0)
REVERT: E 77 LEU cc_start: 0.9323 (mt) cc_final: 0.9106 (mm)
REVERT: E 78 ARG cc_start: 0.8885 (mtp85) cc_final: 0.8680 (mtp85)
REVERT: E 113 GLU cc_start: 0.9107 (mp0) cc_final: 0.8677 (mp0)
REVERT: E 146 LYS cc_start: 0.8742 (mtpt) cc_final: 0.8080 (mtmp)
REVERT: E 160 GLU cc_start: 0.8722 (OUTLIER) cc_final: 0.8345 (mm-30)
REVERT: E 198 VAL cc_start: 0.9357 (OUTLIER) cc_final: 0.9045 (m)
REVERT: E 201 GLU cc_start: 0.8738 (mt-10) cc_final: 0.8420 (mp0)
REVERT: E 206 ASP cc_start: 0.8435 (t0) cc_final: 0.8097 (t0)
REVERT: E 208 LYS cc_start: 0.8610 (ptpt) cc_final: 0.8187 (mtmm)
REVERT: E 279 LEU cc_start: 0.9089 (tp) cc_final: 0.8873 (tt)
REVERT: E 283 LEU cc_start: 0.8649 (mt) cc_final: 0.8318 (mp)
outliers start: 48
outliers final: 27
residues processed: 372
average time/residue: 1.1139
time to fit residues: 457.9235
Evaluate side-chains
364 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 33
poor density : 331
time to evaluate : 1.636
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 179 SER
Chi-restraints excluded: chain A residue 207 LEU
Chi-restraints excluded: chain A residue 211 VAL
Chi-restraints excluded: chain A residue 253 LEU
Chi-restraints excluded: chain A residue 302 LEU
Chi-restraints excluded: chain A residue 372 LEU
Chi-restraints excluded: chain B residue 54 ASN
Chi-restraints excluded: chain B residue 179 SER
Chi-restraints excluded: chain B residue 246 LEU
Chi-restraints excluded: chain B residue 253 LEU
Chi-restraints excluded: chain C residue 54 ASN
Chi-restraints excluded: chain C residue 179 SER
Chi-restraints excluded: chain C residue 198 VAL
Chi-restraints excluded: chain C residue 199 LYS
Chi-restraints excluded: chain C residue 235 ILE
Chi-restraints excluded: chain C residue 237 LEU
Chi-restraints excluded: chain C residue 304 LEU
Chi-restraints excluded: chain D residue 146 LYS
Chi-restraints excluded: chain D residue 153 THR
Chi-restraints excluded: chain D residue 160 GLU
Chi-restraints excluded: chain D residue 179 SER
Chi-restraints excluded: chain D residue 235 ILE
Chi-restraints excluded: chain D residue 277 SER
Chi-restraints excluded: chain D residue 304 LEU
Chi-restraints excluded: chain E residue 123 LEU
Chi-restraints excluded: chain E residue 155 THR
Chi-restraints excluded: chain E residue 160 GLU
Chi-restraints excluded: chain E residue 198 VAL
Chi-restraints excluded: chain E residue 233 SER
Chi-restraints excluded: chain E residue 237 LEU
Chi-restraints excluded: chain E residue 253 LEU
Chi-restraints excluded: chain E residue 277 SER
Chi-restraints excluded: chain E residue 379 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 160
random chunks:
chunk 107 optimal weight: 4.9990
chunk 72 optimal weight: 1.9990
chunk 125 optimal weight: 1.9990
chunk 39 optimal weight: 3.9990
chunk 151 optimal weight: 2.9990
chunk 101 optimal weight: 2.9990
chunk 89 optimal weight: 3.9990
chunk 124 optimal weight: 2.9990
chunk 20 optimal weight: 0.5980
chunk 155 optimal weight: 2.9990
chunk 75 optimal weight: 4.9990
overall best weight: 2.1188
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 156 ASN
A 221 GLN
C 156 ASN
** D 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 221 GLN
** E 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
Total number of N/Q/H flips: 4
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3120 r_free = 0.3120 target = 0.089233 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2908 r_free = 0.2908 target = 0.075928 restraints weight = 20910.256|
|-----------------------------------------------------------------------------|
r_work (start): 0.2901 rms_B_bonded: 2.50
r_work: 0.2755 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.2605 rms_B_bonded: 4.73 restraints_weight: 0.2500
r_work (final): 0.2605
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2626
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2626 r_free = 0.2626 target_work(ls_wunit_k1) = 0.061 |
| occupancies: max = 1.00 min = 0.90 number of occupancies < 0.1: 0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2626 r_free = 0.2626 target_work(ls_wunit_k1) = 0.061 |
| occupancies: max = 1.00 min = 0.90 number of occupancies < 0.1: 0 |
|-----------------------------------------------------------------------------|
r_final: 0.2626
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8292
moved from start: 0.2844
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.005 0.042 13385 Z= 0.360
Angle : 0.569 8.963 18305 Z= 0.278
Chirality : 0.041 0.144 2235
Planarity : 0.004 0.033 2250
Dihedral : 5.024 48.926 2060
Min Nonbonded Distance : 2.444
Molprobity Statistics.
All-atom Clashscore : 8.95
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 1.31 %
Favored : 98.69 %
Rotamer:
Outliers : 3.64 %
Allowed : 18.53 %
Favored : 77.83 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 5.88 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 1.66 (0.21), residues: 1600
helix: 2.71 (0.20), residues: 530
sheet: 0.58 (0.24), residues: 475
loop : 0.13 (0.26), residues: 595
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.009 0.001 TRP E 112
HIS 0.002 0.001 HIS E 103
PHE 0.022 0.002 PHE A 72
TYR 0.021 0.002 TYR D 176
ARG 0.009 0.000 ARG C 257
*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
3200 Ramachandran restraints generated.
1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
3200 Ramachandran restraints generated.
1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
375 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 52
poor density : 323
time to evaluate : 1.604
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: A 48 GLU cc_start: 0.8569 (tp30) cc_final: 0.8144 (mm-30)
REVERT: A 75 ASP cc_start: 0.8393 (t0) cc_final: 0.7983 (t0)
REVERT: A 132 ASP cc_start: 0.8405 (m-30) cc_final: 0.8134 (t0)
REVERT: A 146 LYS cc_start: 0.8680 (mtpt) cc_final: 0.8092 (mttp)
REVERT: A 176 TYR cc_start: 0.9313 (m-80) cc_final: 0.8643 (m-80)
REVERT: A 201 GLU cc_start: 0.8792 (mt-10) cc_final: 0.8425 (mp0)
REVERT: A 206 ASP cc_start: 0.8516 (t0) cc_final: 0.8148 (t0)
REVERT: A 208 LYS cc_start: 0.8561 (ptpt) cc_final: 0.8246 (mtmm)
REVERT: A 232 LYS cc_start: 0.8651 (ttmt) cc_final: 0.8268 (ttmm)
REVERT: A 272 TYR cc_start: 0.8959 (t80) cc_final: 0.8291 (t80)
REVERT: A 281 GLN cc_start: 0.8797 (mm110) cc_final: 0.8352 (pt0)
REVERT: A 283 LEU cc_start: 0.8610 (mt) cc_final: 0.8294 (mp)
REVERT: A 297 PHE cc_start: 0.8877 (m-80) cc_final: 0.8506 (m-10)
REVERT: A 364 GLU cc_start: 0.8489 (mt-10) cc_final: 0.8064 (mt-10)
REVERT: B 75 ASP cc_start: 0.8239 (t0) cc_final: 0.7704 (t0)
REVERT: B 129 ASP cc_start: 0.8786 (t0) cc_final: 0.8258 (t0)
REVERT: B 146 LYS cc_start: 0.8727 (OUTLIER) cc_final: 0.8014 (mttp)
REVERT: B 201 GLU cc_start: 0.8708 (mt-10) cc_final: 0.8323 (mp0)
REVERT: B 206 ASP cc_start: 0.8406 (t0) cc_final: 0.7896 (t0)
REVERT: B 279 LEU cc_start: 0.9034 (tp) cc_final: 0.8765 (tt)
REVERT: B 281 GLN cc_start: 0.8759 (mm110) cc_final: 0.8318 (pt0)
REVERT: B 283 LEU cc_start: 0.8545 (mt) cc_final: 0.8201 (mp)
REVERT: C 75 ASP cc_start: 0.8336 (t0) cc_final: 0.7722 (t0)
REVERT: C 77 LEU cc_start: 0.9373 (mt) cc_final: 0.9117 (mm)
REVERT: C 113 GLU cc_start: 0.9125 (mp0) cc_final: 0.8731 (mp0)
REVERT: C 129 ASP cc_start: 0.8788 (t0) cc_final: 0.8253 (t0)
REVERT: C 146 LYS cc_start: 0.8656 (mtpt) cc_final: 0.8032 (mtmp)
REVERT: C 160 GLU cc_start: 0.8597 (tt0) cc_final: 0.8149 (mm-30)
REVERT: C 201 GLU cc_start: 0.8821 (mt-10) cc_final: 0.8489 (mp0)
REVERT: C 208 LYS cc_start: 0.8655 (mtmm) cc_final: 0.8375 (mtmm)
REVERT: C 281 GLN cc_start: 0.8763 (mm110) cc_final: 0.8278 (pt0)
REVERT: C 283 LEU cc_start: 0.8670 (mt) cc_final: 0.8335 (mp)
REVERT: C 402 GLU cc_start: 0.8647 (mm-30) cc_final: 0.8387 (mt-10)
REVERT: D 75 ASP cc_start: 0.8371 (t0) cc_final: 0.7746 (t0)
REVERT: D 146 LYS cc_start: 0.8591 (OUTLIER) cc_final: 0.7967 (mttp)
REVERT: D 160 GLU cc_start: 0.8824 (OUTLIER) cc_final: 0.8487 (mm-30)
REVERT: D 184 GLU cc_start: 0.8708 (mt-10) cc_final: 0.8244 (pt0)
REVERT: D 199 LYS cc_start: 0.8471 (ptpt) cc_final: 0.8137 (ptmm)
REVERT: D 201 GLU cc_start: 0.8737 (mt-10) cc_final: 0.8435 (mp0)
REVERT: D 206 ASP cc_start: 0.8487 (t0) cc_final: 0.8076 (t0)
REVERT: D 208 LYS cc_start: 0.8686 (mtmm) cc_final: 0.8438 (mtmm)
REVERT: D 272 TYR cc_start: 0.8971 (t80) cc_final: 0.8139 (t80)
REVERT: D 281 GLN cc_start: 0.8734 (mm110) cc_final: 0.8423 (mm-40)
REVERT: D 283 LEU cc_start: 0.8702 (mt) cc_final: 0.8319 (mp)
REVERT: D 402 GLU cc_start: 0.8546 (mm-30) cc_final: 0.8274 (mt-10)
REVERT: E 75 ASP cc_start: 0.8358 (t0) cc_final: 0.7695 (t0)
REVERT: E 77 LEU cc_start: 0.9285 (mt) cc_final: 0.9062 (mm)
REVERT: E 113 GLU cc_start: 0.9175 (mp0) cc_final: 0.8905 (mp0)
REVERT: E 132 ASP cc_start: 0.7913 (t0) cc_final: 0.7629 (t0)
REVERT: E 146 LYS cc_start: 0.8679 (mtpt) cc_final: 0.7996 (mtmp)
REVERT: E 160 GLU cc_start: 0.8777 (OUTLIER) cc_final: 0.8372 (mm-30)
REVERT: E 167 ASP cc_start: 0.9416 (p0) cc_final: 0.9059 (p0)
REVERT: E 201 GLU cc_start: 0.8724 (mt-10) cc_final: 0.8408 (mp0)
REVERT: E 206 ASP cc_start: 0.8439 (t0) cc_final: 0.8153 (t0)
REVERT: E 279 LEU cc_start: 0.9078 (tp) cc_final: 0.8864 (tt)
REVERT: E 283 LEU cc_start: 0.8694 (mt) cc_final: 0.8296 (mp)
outliers start: 52
outliers final: 24
residues processed: 351
average time/residue: 1.1170
time to fit residues: 432.0866
Evaluate side-chains
337 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 28
poor density : 309
time to evaluate : 1.535
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 179 SER
Chi-restraints excluded: chain A residue 253 LEU
Chi-restraints excluded: chain A residue 302 LEU
Chi-restraints excluded: chain A residue 372 LEU
Chi-restraints excluded: chain B residue 54 ASN
Chi-restraints excluded: chain B residue 146 LYS
Chi-restraints excluded: chain B residue 179 SER
Chi-restraints excluded: chain B residue 233 SER
Chi-restraints excluded: chain B residue 246 LEU
Chi-restraints excluded: chain B residue 253 LEU
Chi-restraints excluded: chain C residue 179 SER
Chi-restraints excluded: chain C residue 198 VAL
Chi-restraints excluded: chain C residue 235 ILE
Chi-restraints excluded: chain C residue 304 LEU
Chi-restraints excluded: chain D residue 146 LYS
Chi-restraints excluded: chain D residue 153 THR
Chi-restraints excluded: chain D residue 160 GLU
Chi-restraints excluded: chain D residue 179 SER
Chi-restraints excluded: chain D residue 235 ILE
Chi-restraints excluded: chain E residue 123 LEU
Chi-restraints excluded: chain E residue 155 THR
Chi-restraints excluded: chain E residue 160 GLU
Chi-restraints excluded: chain E residue 198 VAL
Chi-restraints excluded: chain E residue 233 SER
Chi-restraints excluded: chain E residue 237 LEU
Chi-restraints excluded: chain E residue 253 LEU
Chi-restraints excluded: chain E residue 372 LEU
Chi-restraints excluded: chain E residue 379 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 160
random chunks:
chunk 95 optimal weight: 9.9990
chunk 28 optimal weight: 3.9990
chunk 122 optimal weight: 3.9990
chunk 136 optimal weight: 4.9990
chunk 157 optimal weight: 0.6980
chunk 135 optimal weight: 0.6980
chunk 3 optimal weight: 1.9990
chunk 71 optimal weight: 0.9980
chunk 100 optimal weight: 0.8980
chunk 105 optimal weight: 0.9990
chunk 108 optimal weight: 3.9990
overall best weight: 0.8582
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 156 ASN
A 221 GLN
C 156 ASN
C 221 GLN
** D 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
Total number of N/Q/H flips: 4
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3150 r_free = 0.3150 target = 0.091167 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2942 r_free = 0.2942 target = 0.078044 restraints weight = 20544.680|
|-----------------------------------------------------------------------------|
r_work (start): 0.2937 rms_B_bonded: 2.43
r_work: 0.2796 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.2647 rms_B_bonded: 4.68 restraints_weight: 0.2500
r_work (final): 0.2647
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2685
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2685 r_free = 0.2685 target_work(ls_wunit_k1) = 0.064 |
| occupancies: max = 1.00 min = 0.90 number of occupancies < 0.1: 0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2685 r_free = 0.2685 target_work(ls_wunit_k1) = 0.064 |
| occupancies: max = 1.00 min = 0.90 number of occupancies < 0.1: 0 |
|-----------------------------------------------------------------------------|
r_final: 0.2685
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8333
moved from start: 0.2880
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.029 13385 Z= 0.191
Angle : 0.533 9.299 18305 Z= 0.259
Chirality : 0.039 0.186 2235
Planarity : 0.004 0.027 2250
Dihedral : 4.734 44.639 2060
Min Nonbonded Distance : 2.479
Molprobity Statistics.
All-atom Clashscore : 7.97
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 1.12 %
Favored : 98.88 %
Rotamer:
Outliers : 2.80 %
Allowed : 20.00 %
Favored : 77.20 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 5.88 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 1.76 (0.21), residues: 1600
helix: 2.85 (0.20), residues: 530
sheet: 0.56 (0.24), residues: 475
loop : 0.21 (0.27), residues: 595
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.008 0.001 TRP A 112
HIS 0.001 0.000 HIS E 276
PHE 0.020 0.002 PHE A 385
TYR 0.020 0.002 TYR D 176
ARG 0.010 0.000 ARG C 257
*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
3200 Ramachandran restraints generated.
1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
3200 Ramachandran restraints generated.
1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
371 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 40
poor density : 331
time to evaluate : 1.439
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: A 75 ASP cc_start: 0.8382 (t0) cc_final: 0.8034 (t0)
REVERT: A 81 MET cc_start: 0.9017 (ttp) cc_final: 0.8695 (ptt)
REVERT: A 132 ASP cc_start: 0.8331 (m-30) cc_final: 0.8117 (t0)
REVERT: A 153 THR cc_start: 0.9347 (p) cc_final: 0.9052 (t)
REVERT: A 201 GLU cc_start: 0.8764 (mt-10) cc_final: 0.8426 (mp0)
REVERT: A 206 ASP cc_start: 0.8475 (t0) cc_final: 0.8143 (t0)
REVERT: A 208 LYS cc_start: 0.8606 (ptpt) cc_final: 0.8265 (mtmm)
REVERT: A 232 LYS cc_start: 0.8709 (ttmt) cc_final: 0.8343 (ttmm)
REVERT: A 272 TYR cc_start: 0.8942 (t80) cc_final: 0.8289 (t80)
REVERT: A 281 GLN cc_start: 0.8728 (mm110) cc_final: 0.8327 (pt0)
REVERT: A 283 LEU cc_start: 0.8608 (mt) cc_final: 0.8200 (mp)
REVERT: A 296 TYR cc_start: 0.8454 (t80) cc_final: 0.8236 (t80)
REVERT: A 297 PHE cc_start: 0.8893 (m-80) cc_final: 0.8494 (m-10)
REVERT: A 364 GLU cc_start: 0.8530 (mt-10) cc_final: 0.8118 (mt-10)
REVERT: B 75 ASP cc_start: 0.8302 (t0) cc_final: 0.7789 (t0)
REVERT: B 78 ARG cc_start: 0.8767 (mtp85) cc_final: 0.8562 (mtp85)
REVERT: B 129 ASP cc_start: 0.8839 (t0) cc_final: 0.8341 (t0)
REVERT: B 146 LYS cc_start: 0.8794 (mtmt) cc_final: 0.8120 (mttp)
REVERT: B 201 GLU cc_start: 0.8647 (mt-10) cc_final: 0.8262 (mp0)
REVERT: B 206 ASP cc_start: 0.8377 (t0) cc_final: 0.7910 (t0)
REVERT: B 232 LYS cc_start: 0.8706 (ttmt) cc_final: 0.8386 (ttmm)
REVERT: B 260 GLU cc_start: 0.8927 (pm20) cc_final: 0.8397 (pm20)
REVERT: B 281 GLN cc_start: 0.8705 (mm110) cc_final: 0.8316 (pt0)
REVERT: B 283 LEU cc_start: 0.8555 (mt) cc_final: 0.8210 (mp)
REVERT: C 75 ASP cc_start: 0.8407 (t0) cc_final: 0.7970 (t0)
REVERT: C 77 LEU cc_start: 0.9374 (mt) cc_final: 0.9156 (mm)
REVERT: C 113 GLU cc_start: 0.9103 (mp0) cc_final: 0.8744 (mp0)
REVERT: C 129 ASP cc_start: 0.8833 (t0) cc_final: 0.8231 (t0)
REVERT: C 146 LYS cc_start: 0.8718 (mtpt) cc_final: 0.8128 (mtmp)
REVERT: C 160 GLU cc_start: 0.8572 (tt0) cc_final: 0.8148 (mm-30)
REVERT: C 184 GLU cc_start: 0.8736 (mt-10) cc_final: 0.8329 (pt0)
REVERT: C 201 GLU cc_start: 0.8773 (mt-10) cc_final: 0.8475 (mp0)
REVERT: C 208 LYS cc_start: 0.8727 (mtmm) cc_final: 0.8428 (mtmm)
REVERT: C 238 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8486 (mm)
REVERT: C 281 GLN cc_start: 0.8717 (mm110) cc_final: 0.8218 (pt0)
REVERT: C 402 GLU cc_start: 0.8650 (mm-30) cc_final: 0.8437 (mt-10)
REVERT: D 75 ASP cc_start: 0.8438 (t0) cc_final: 0.7816 (t0)
REVERT: D 160 GLU cc_start: 0.8797 (OUTLIER) cc_final: 0.8546 (mm-30)
REVERT: D 184 GLU cc_start: 0.8647 (mt-10) cc_final: 0.8281 (pt0)
REVERT: D 199 LYS cc_start: 0.8416 (ptpt) cc_final: 0.8122 (ptmm)
REVERT: D 201 GLU cc_start: 0.8740 (mt-10) cc_final: 0.8458 (mp0)
REVERT: D 206 ASP cc_start: 0.8473 (t0) cc_final: 0.8113 (t0)
REVERT: D 208 LYS cc_start: 0.8727 (mtmm) cc_final: 0.8493 (mtmm)
REVERT: D 272 TYR cc_start: 0.8951 (t80) cc_final: 0.8056 (t80)
REVERT: D 281 GLN cc_start: 0.8664 (mm110) cc_final: 0.8247 (pt0)
REVERT: D 283 LEU cc_start: 0.8736 (mt) cc_final: 0.8237 (mp)
REVERT: D 402 GLU cc_start: 0.8580 (mm-30) cc_final: 0.8312 (mt-10)
REVERT: E 75 ASP cc_start: 0.8393 (t0) cc_final: 0.7937 (t0)
REVERT: E 113 GLU cc_start: 0.9140 (mp0) cc_final: 0.8912 (mp0)
REVERT: E 146 LYS cc_start: 0.8760 (mtpt) cc_final: 0.8085 (mttp)
REVERT: E 160 GLU cc_start: 0.8775 (OUTLIER) cc_final: 0.8411 (mm-30)
REVERT: E 167 ASP cc_start: 0.9425 (p0) cc_final: 0.9085 (p0)
REVERT: E 198 VAL cc_start: 0.9374 (OUTLIER) cc_final: 0.9011 (m)
REVERT: E 201 GLU cc_start: 0.8691 (mt-10) cc_final: 0.8371 (mp0)
REVERT: E 206 ASP cc_start: 0.8429 (t0) cc_final: 0.8078 (t0)
REVERT: E 208 LYS cc_start: 0.8750 (mtmm) cc_final: 0.8235 (mtmm)
REVERT: E 227 LYS cc_start: 0.8836 (ptmt) cc_final: 0.8530 (ptpp)
REVERT: E 232 LYS cc_start: 0.8797 (ttmt) cc_final: 0.8418 (ttmm)
REVERT: E 272 TYR cc_start: 0.8957 (t80) cc_final: 0.8222 (t80)
REVERT: E 283 LEU cc_start: 0.8637 (mt) cc_final: 0.8184 (mp)
outliers start: 40
outliers final: 20
residues processed: 354
average time/residue: 1.0805
time to fit residues: 422.6135
Evaluate side-chains
353 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 24
poor density : 329
time to evaluate : 1.393
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 179 SER
Chi-restraints excluded: chain A residue 253 LEU
Chi-restraints excluded: chain A residue 302 LEU
Chi-restraints excluded: chain B residue 54 ASN
Chi-restraints excluded: chain B residue 179 SER
Chi-restraints excluded: chain B residue 246 LEU
Chi-restraints excluded: chain B residue 253 LEU
Chi-restraints excluded: chain C residue 179 SER
Chi-restraints excluded: chain C residue 198 VAL
Chi-restraints excluded: chain C residue 238 LEU
Chi-restraints excluded: chain C residue 304 LEU
Chi-restraints excluded: chain D residue 153 THR
Chi-restraints excluded: chain D residue 160 GLU
Chi-restraints excluded: chain D residue 179 SER
Chi-restraints excluded: chain D residue 235 ILE
Chi-restraints excluded: chain D residue 253 LEU
Chi-restraints excluded: chain D residue 277 SER
Chi-restraints excluded: chain E residue 123 LEU
Chi-restraints excluded: chain E residue 142 ASP
Chi-restraints excluded: chain E residue 155 THR
Chi-restraints excluded: chain E residue 160 GLU
Chi-restraints excluded: chain E residue 198 VAL
Chi-restraints excluded: chain E residue 237 LEU
Chi-restraints excluded: chain E residue 253 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 160
random chunks:
chunk 32 optimal weight: 5.9990
chunk 10 optimal weight: 1.9990
chunk 153 optimal weight: 4.9990
chunk 89 optimal weight: 4.9990
chunk 101 optimal weight: 0.0270
chunk 27 optimal weight: 2.9990
chunk 28 optimal weight: 2.9990
chunk 8 optimal weight: 1.9990
chunk 116 optimal weight: 2.9990
chunk 50 optimal weight: 1.9990
chunk 71 optimal weight: 4.9990
overall best weight: 1.8046
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 156 ASN
A 221 GLN
C 156 ASN
** D 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 156 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 = 0.3122 r_free = 0.3122 target = 0.089387 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2908 r_free = 0.2908 target = 0.076043 restraints weight = 20856.863|
|-----------------------------------------------------------------------------|
r_work (start): 0.2914 rms_B_bonded: 2.49
r_work: 0.2773 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.2627 rms_B_bonded: 4.71 restraints_weight: 0.2500
r_work (final): 0.2627
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2628
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2628 r_free = 0.2628 target_work(ls_wunit_k1) = 0.061 |
| occupancies: max = 1.00 min = 0.90 number of occupancies < 0.1: 0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2628 r_free = 0.2628 target_work(ls_wunit_k1) = 0.061 |
| occupancies: max = 1.00 min = 0.90 number of occupancies < 0.1: 0 |
|-----------------------------------------------------------------------------|
r_final: 0.2628
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8288
moved from start: 0.3057
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.005 0.046 13385 Z= 0.322
Angle : 0.577 9.445 18305 Z= 0.281
Chirality : 0.041 0.174 2235
Planarity : 0.004 0.035 2250
Dihedral : 4.534 37.029 2060
Min Nonbonded Distance : 2.501
Molprobity Statistics.
All-atom Clashscore : 8.80
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 1.25 %
Favored : 98.75 %
Rotamer:
Outliers : 2.80 %
Allowed : 20.49 %
Favored : 76.71 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 5.88 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 1.58 (0.21), residues: 1600
helix: 2.77 (0.20), residues: 525
sheet: 0.73 (0.24), residues: 430
loop : -0.14 (0.26), residues: 645
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.009 0.001 TRP E 112
HIS 0.002 0.001 HIS E 103
PHE 0.025 0.002 PHE A 385
TYR 0.025 0.002 TYR B 176
ARG 0.014 0.000 ARG C 257
*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
3200 Ramachandran restraints generated.
1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
3200 Ramachandran restraints generated.
1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
374 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 40
poor density : 334
time to evaluate : 1.644
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: A 48 GLU cc_start: 0.8584 (tp30) cc_final: 0.8155 (mm-30)
REVERT: A 75 ASP cc_start: 0.8367 (t0) cc_final: 0.7962 (t0)
REVERT: A 81 MET cc_start: 0.9062 (ttp) cc_final: 0.8773 (ptt)
REVERT: A 132 ASP cc_start: 0.8395 (m-30) cc_final: 0.8099 (t0)
REVERT: A 146 LYS cc_start: 0.8688 (mtpt) cc_final: 0.8103 (mttp)
REVERT: A 201 GLU cc_start: 0.8768 (mt-10) cc_final: 0.8405 (mp0)
REVERT: A 206 ASP cc_start: 0.8495 (t0) cc_final: 0.8142 (t0)
REVERT: A 208 LYS cc_start: 0.8567 (ptpt) cc_final: 0.8217 (mtmm)
REVERT: A 272 TYR cc_start: 0.8939 (t80) cc_final: 0.8278 (t80)
REVERT: A 281 GLN cc_start: 0.8792 (mm110) cc_final: 0.8330 (pt0)
REVERT: A 283 LEU cc_start: 0.8584 (mt) cc_final: 0.8266 (mp)
REVERT: A 296 TYR cc_start: 0.8439 (t80) cc_final: 0.8238 (t80)
REVERT: A 297 PHE cc_start: 0.8881 (m-80) cc_final: 0.8574 (m-80)
REVERT: A 364 GLU cc_start: 0.8517 (mt-10) cc_final: 0.8094 (mt-10)
REVERT: B 75 ASP cc_start: 0.8216 (t0) cc_final: 0.7686 (t0)
REVERT: B 129 ASP cc_start: 0.8776 (t0) cc_final: 0.8226 (t0)
REVERT: B 201 GLU cc_start: 0.8671 (mt-10) cc_final: 0.8267 (mp0)
REVERT: B 206 ASP cc_start: 0.8394 (t0) cc_final: 0.7944 (t0)
REVERT: B 260 GLU cc_start: 0.8909 (pm20) cc_final: 0.8361 (pm20)
REVERT: B 281 GLN cc_start: 0.8720 (mm110) cc_final: 0.8358 (pt0)
REVERT: C 48 GLU cc_start: 0.8493 (tp30) cc_final: 0.8229 (mm-30)
REVERT: C 75 ASP cc_start: 0.8342 (t0) cc_final: 0.8036 (t0)
REVERT: C 77 LEU cc_start: 0.9403 (mt) cc_final: 0.9176 (mm)
REVERT: C 113 GLU cc_start: 0.9130 (mp0) cc_final: 0.8785 (mp0)
REVERT: C 124 GLU cc_start: 0.8977 (mp0) cc_final: 0.8646 (mp0)
REVERT: C 129 ASP cc_start: 0.8771 (t0) cc_final: 0.8172 (t0)
REVERT: C 146 LYS cc_start: 0.8645 (mtpt) cc_final: 0.8014 (mtmp)
REVERT: C 160 GLU cc_start: 0.8589 (tt0) cc_final: 0.8062 (tp30)
REVERT: C 184 GLU cc_start: 0.8751 (mt-10) cc_final: 0.8283 (pt0)
REVERT: C 201 GLU cc_start: 0.8793 (mt-10) cc_final: 0.8446 (mp0)
REVERT: C 208 LYS cc_start: 0.8654 (mtmm) cc_final: 0.8400 (mtmm)
REVERT: C 232 LYS cc_start: 0.8632 (ttmt) cc_final: 0.8333 (tppp)
REVERT: C 281 GLN cc_start: 0.8770 (mm110) cc_final: 0.8282 (pt0)
REVERT: C 364 GLU cc_start: 0.8619 (mp0) cc_final: 0.8366 (mt-10)
REVERT: C 402 GLU cc_start: 0.8646 (mm-30) cc_final: 0.8408 (mt-10)
REVERT: D 48 GLU cc_start: 0.8542 (tp30) cc_final: 0.8253 (mm-30)
REVERT: D 75 ASP cc_start: 0.8383 (t0) cc_final: 0.7704 (t0)
REVERT: D 160 GLU cc_start: 0.8830 (OUTLIER) cc_final: 0.8297 (tp30)
REVERT: D 184 GLU cc_start: 0.8689 (mt-10) cc_final: 0.8218 (pt0)
REVERT: D 199 LYS cc_start: 0.8493 (ptpt) cc_final: 0.8196 (ptmm)
REVERT: D 201 GLU cc_start: 0.8747 (mt-10) cc_final: 0.8425 (mp0)
REVERT: D 206 ASP cc_start: 0.8481 (t0) cc_final: 0.8074 (t0)
REVERT: D 208 LYS cc_start: 0.8676 (mtmm) cc_final: 0.8421 (mtmm)
REVERT: D 272 TYR cc_start: 0.8961 (t80) cc_final: 0.8092 (t80)
REVERT: D 281 GLN cc_start: 0.8723 (mm110) cc_final: 0.8403 (mm-40)
REVERT: D 283 LEU cc_start: 0.8726 (mt) cc_final: 0.8310 (mp)
REVERT: D 402 GLU cc_start: 0.8572 (mm-30) cc_final: 0.8313 (mt-10)
REVERT: E 75 ASP cc_start: 0.8305 (t0) cc_final: 0.7963 (t0)
REVERT: E 113 GLU cc_start: 0.9178 (mp0) cc_final: 0.8930 (mp0)
REVERT: E 132 ASP cc_start: 0.7933 (t0) cc_final: 0.7626 (t0)
REVERT: E 146 LYS cc_start: 0.8664 (mtpt) cc_final: 0.7990 (mtmp)
REVERT: E 160 GLU cc_start: 0.8788 (OUTLIER) cc_final: 0.8397 (mm-30)
REVERT: E 167 ASP cc_start: 0.9426 (p0) cc_final: 0.9084 (p0)
REVERT: E 201 GLU cc_start: 0.8716 (mt-10) cc_final: 0.8410 (mp0)
REVERT: E 206 ASP cc_start: 0.8434 (t0) cc_final: 0.8062 (t0)
REVERT: E 208 LYS cc_start: 0.8757 (mtmm) cc_final: 0.8279 (mtmm)
REVERT: E 283 LEU cc_start: 0.8696 (mt) cc_final: 0.8469 (mp)
outliers start: 40
outliers final: 21
residues processed: 357
average time/residue: 1.2326
time to fit residues: 482.0141
Evaluate side-chains
344 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 23
poor density : 321
time to evaluate : 1.497
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 179 SER
Chi-restraints excluded: chain A residue 253 LEU
Chi-restraints excluded: chain A residue 302 LEU
Chi-restraints excluded: chain A residue 372 LEU
Chi-restraints excluded: chain B residue 54 ASN
Chi-restraints excluded: chain B residue 179 SER
Chi-restraints excluded: chain B residue 233 SER
Chi-restraints excluded: chain B residue 246 LEU
Chi-restraints excluded: chain B residue 253 LEU
Chi-restraints excluded: chain C residue 179 SER
Chi-restraints excluded: chain C residue 198 VAL
Chi-restraints excluded: chain C residue 235 ILE
Chi-restraints excluded: chain C residue 304 LEU
Chi-restraints excluded: chain D residue 153 THR
Chi-restraints excluded: chain D residue 160 GLU
Chi-restraints excluded: chain D residue 179 SER
Chi-restraints excluded: chain D residue 235 ILE
Chi-restraints excluded: chain E residue 123 LEU
Chi-restraints excluded: chain E residue 155 THR
Chi-restraints excluded: chain E residue 160 GLU
Chi-restraints excluded: chain E residue 237 LEU
Chi-restraints excluded: chain E residue 277 SER
Chi-restraints excluded: chain E residue 372 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 160
random chunks:
chunk 92 optimal weight: 3.9990
chunk 23 optimal weight: 4.9990
chunk 128 optimal weight: 3.9990
chunk 81 optimal weight: 0.9980
chunk 25 optimal weight: 3.9990
chunk 43 optimal weight: 0.8980
chunk 106 optimal weight: 4.9990
chunk 112 optimal weight: 3.9990
chunk 75 optimal weight: 0.8980
chunk 137 optimal weight: 3.9990
chunk 13 optimal weight: 0.7980
overall best weight: 1.5182
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 156 ASN
A 221 GLN
C 156 ASN
** D 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 382 GLN
** E 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
Total number of N/Q/H flips: 4
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3125 r_free = 0.3125 target = 0.089609 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2910 r_free = 0.2910 target = 0.076341 restraints weight = 20486.806|
|-----------------------------------------------------------------------------|
r_work (start): 0.2912 rms_B_bonded: 2.43
r_work: 0.2770 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.2623 rms_B_bonded: 4.64 restraints_weight: 0.2500
r_work (final): 0.2623
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2658
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2658 r_free = 0.2658 target_work(ls_wunit_k1) = 0.062 |
| occupancies: max = 1.00 min = 0.90 number of occupancies < 0.1: 0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2658 r_free = 0.2658 target_work(ls_wunit_k1) = 0.062 |
| occupancies: max = 1.00 min = 0.91 number of occupancies < 0.1: 0 |
|-----------------------------------------------------------------------------|
r_final: 0.2658
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8353
moved from start: 0.3088
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.004 0.043 13385 Z= 0.280
Angle : 0.568 9.623 18305 Z= 0.277
Chirality : 0.040 0.142 2235
Planarity : 0.004 0.039 2250
Dihedral : 4.412 31.631 2060
Min Nonbonded Distance : 2.543
Molprobity Statistics.
All-atom Clashscore : 9.18
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 1.50 %
Favored : 98.50 %
Rotamer:
Outliers : 2.52 %
Allowed : 20.84 %
Favored : 76.64 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 5.88 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 1.59 (0.21), residues: 1600
helix: 2.72 (0.20), residues: 530
sheet: 0.68 (0.24), residues: 430
loop : -0.06 (0.26), residues: 640
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.009 0.001 TRP E 112
HIS 0.002 0.000 HIS E 276
PHE 0.022 0.002 PHE A 385
TYR 0.020 0.002 TYR D 176
ARG 0.017 0.001 ARG C 257
*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
3200 Ramachandran restraints generated.
1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
3200 Ramachandran restraints generated.
1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
367 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 36
poor density : 331
time to evaluate : 1.557
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: A 75 ASP cc_start: 0.8382 (t0) cc_final: 0.7997 (t0)
REVERT: A 81 MET cc_start: 0.9041 (ttp) cc_final: 0.8754 (ptt)
REVERT: A 146 LYS cc_start: 0.8755 (mtpt) cc_final: 0.8191 (mttp)
REVERT: A 201 GLU cc_start: 0.8807 (mt-10) cc_final: 0.8440 (mp0)
REVERT: A 206 ASP cc_start: 0.8512 (t0) cc_final: 0.8192 (t0)
REVERT: A 232 LYS cc_start: 0.8706 (ttmt) cc_final: 0.8282 (ttmm)
REVERT: A 272 TYR cc_start: 0.8973 (t80) cc_final: 0.8335 (t80)
REVERT: A 281 GLN cc_start: 0.8795 (mm110) cc_final: 0.8395 (pt0)
REVERT: A 283 LEU cc_start: 0.8590 (mt) cc_final: 0.8200 (mp)
REVERT: A 297 PHE cc_start: 0.8930 (m-80) cc_final: 0.8571 (m-10)
REVERT: A 364 GLU cc_start: 0.8558 (mt-10) cc_final: 0.8118 (mt-10)
REVERT: B 48 GLU cc_start: 0.8652 (tp30) cc_final: 0.8421 (tp30)
REVERT: B 75 ASP cc_start: 0.8308 (t0) cc_final: 0.7795 (t0)
REVERT: B 129 ASP cc_start: 0.8807 (t0) cc_final: 0.8402 (t0)
REVERT: B 146 LYS cc_start: 0.8797 (mtmt) cc_final: 0.8132 (mttp)
REVERT: B 201 GLU cc_start: 0.8707 (mt-10) cc_final: 0.8312 (mp0)
REVERT: B 206 ASP cc_start: 0.8396 (t0) cc_final: 0.7979 (t0)
REVERT: B 232 LYS cc_start: 0.8708 (ttmt) cc_final: 0.8383 (ttmm)
REVERT: B 260 GLU cc_start: 0.8927 (pm20) cc_final: 0.8385 (pm20)
REVERT: B 281 GLN cc_start: 0.8717 (mm110) cc_final: 0.8358 (pt0)
REVERT: B 364 GLU cc_start: 0.8724 (mt-10) cc_final: 0.8473 (mt-10)
REVERT: C 48 GLU cc_start: 0.8544 (tp30) cc_final: 0.8284 (mm-30)
REVERT: C 75 ASP cc_start: 0.8414 (t0) cc_final: 0.7950 (t0)
REVERT: C 77 LEU cc_start: 0.9434 (mt) cc_final: 0.9221 (mm)
REVERT: C 81 MET cc_start: 0.9126 (ttp) cc_final: 0.8856 (ptm)
REVERT: C 113 GLU cc_start: 0.9123 (mp0) cc_final: 0.8815 (mp0)
REVERT: C 124 GLU cc_start: 0.8994 (mp0) cc_final: 0.8686 (mp0)
REVERT: C 129 ASP cc_start: 0.8827 (t0) cc_final: 0.8278 (t0)
REVERT: C 146 LYS cc_start: 0.8733 (mtpt) cc_final: 0.8140 (mtmp)
REVERT: C 160 GLU cc_start: 0.8572 (tt0) cc_final: 0.8091 (tp30)
REVERT: C 201 GLU cc_start: 0.8794 (mt-10) cc_final: 0.8466 (mp0)
REVERT: C 232 LYS cc_start: 0.8692 (ttmt) cc_final: 0.8365 (tppp)
REVERT: C 281 GLN cc_start: 0.8738 (mm110) cc_final: 0.8266 (pt0)
REVERT: C 364 GLU cc_start: 0.8668 (mp0) cc_final: 0.8435 (mt-10)
REVERT: C 402 GLU cc_start: 0.8666 (mm-30) cc_final: 0.8443 (mt-10)
REVERT: D 75 ASP cc_start: 0.8443 (t0) cc_final: 0.7789 (t0)
REVERT: D 146 LYS cc_start: 0.8700 (mtmt) cc_final: 0.8130 (mttp)
REVERT: D 160 GLU cc_start: 0.8833 (OUTLIER) cc_final: 0.8600 (mm-30)
REVERT: D 184 GLU cc_start: 0.8695 (mt-10) cc_final: 0.8266 (pt0)
REVERT: D 199 LYS cc_start: 0.8509 (ptpt) cc_final: 0.8221 (ptmm)
REVERT: D 201 GLU cc_start: 0.8768 (mt-10) cc_final: 0.8454 (mp0)
REVERT: D 206 ASP cc_start: 0.8492 (t0) cc_final: 0.8115 (t0)
REVERT: D 208 LYS cc_start: 0.8722 (mtmm) cc_final: 0.8465 (mtmm)
REVERT: D 232 LYS cc_start: 0.8563 (ttmt) cc_final: 0.8330 (tppp)
REVERT: D 281 GLN cc_start: 0.8772 (mm110) cc_final: 0.8473 (mm-40)
REVERT: D 283 LEU cc_start: 0.8693 (mt) cc_final: 0.8159 (mp)
REVERT: D 402 GLU cc_start: 0.8615 (mm-30) cc_final: 0.8368 (mt-10)
REVERT: E 75 ASP cc_start: 0.8397 (t0) cc_final: 0.7942 (t0)
REVERT: E 113 GLU cc_start: 0.9164 (mp0) cc_final: 0.8630 (mp0)
REVERT: E 132 ASP cc_start: 0.7922 (t0) cc_final: 0.7633 (t0)
REVERT: E 146 LYS cc_start: 0.8749 (mtpt) cc_final: 0.8093 (mtmp)
REVERT: E 160 GLU cc_start: 0.8785 (OUTLIER) cc_final: 0.8443 (mm-30)
REVERT: E 167 ASP cc_start: 0.9449 (p0) cc_final: 0.9097 (p0)
REVERT: E 201 GLU cc_start: 0.8721 (mt-10) cc_final: 0.8422 (mp0)
REVERT: E 206 ASP cc_start: 0.8454 (t0) cc_final: 0.8106 (t0)
REVERT: E 208 LYS cc_start: 0.8838 (mtmm) cc_final: 0.8395 (mtmm)
REVERT: E 232 LYS cc_start: 0.8784 (ttmt) cc_final: 0.8414 (ttmm)
REVERT: E 283 LEU cc_start: 0.8701 (mt) cc_final: 0.8360 (mp)
outliers start: 36
outliers final: 23
residues processed: 355
average time/residue: 1.1649
time to fit residues: 454.1455
Evaluate side-chains
334 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 25
poor density : 309
time to evaluate : 1.585
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 156 ASN
Chi-restraints excluded: chain A residue 179 SER
Chi-restraints excluded: chain A residue 253 LEU
Chi-restraints excluded: chain A residue 302 LEU
Chi-restraints excluded: chain A residue 372 LEU
Chi-restraints excluded: chain B residue 54 ASN
Chi-restraints excluded: chain B residue 179 SER
Chi-restraints excluded: chain B residue 246 LEU
Chi-restraints excluded: chain B residue 253 LEU
Chi-restraints excluded: chain C residue 179 SER
Chi-restraints excluded: chain C residue 198 VAL
Chi-restraints excluded: chain C residue 235 ILE
Chi-restraints excluded: chain C residue 304 LEU
Chi-restraints excluded: chain D residue 153 THR
Chi-restraints excluded: chain D residue 160 GLU
Chi-restraints excluded: chain D residue 179 SER
Chi-restraints excluded: chain D residue 235 ILE
Chi-restraints excluded: chain D residue 277 SER
Chi-restraints excluded: chain E residue 123 LEU
Chi-restraints excluded: chain E residue 155 THR
Chi-restraints excluded: chain E residue 160 GLU
Chi-restraints excluded: chain E residue 233 SER
Chi-restraints excluded: chain E residue 253 LEU
Chi-restraints excluded: chain E residue 277 SER
Chi-restraints excluded: chain E residue 372 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 160
random chunks:
chunk 49 optimal weight: 0.5980
chunk 23 optimal weight: 0.4980
chunk 85 optimal weight: 2.9990
chunk 1 optimal weight: 0.9980
chunk 127 optimal weight: 4.9990
chunk 73 optimal weight: 2.9990
chunk 106 optimal weight: 4.9990
chunk 136 optimal weight: 0.4980
chunk 81 optimal weight: 0.5980
chunk 22 optimal weight: 0.5980
chunk 8 optimal weight: 2.9990
overall best weight: 0.5580
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 156 ASN
A 221 GLN
C 156 ASN
C 221 GLN
** D 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 156 ASN
Total number of N/Q/H flips: 5
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.091845 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2951 r_free = 0.2951 target = 0.078609 restraints weight = 20436.293|
|-----------------------------------------------------------------------------|
r_work (start): 0.2951 rms_B_bonded: 2.43
r_work: 0.2810 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.2663 rms_B_bonded: 4.68 restraints_weight: 0.2500
r_work (final): 0.2663
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2678
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2678 r_free = 0.2678 target_work(ls_wunit_k1) = 0.064 |
| occupancies: max = 1.00 min = 0.91 number of occupancies < 0.1: 0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2678 r_free = 0.2678 target_work(ls_wunit_k1) = 0.064 |
| occupancies: max = 1.00 min = 0.91 number of occupancies < 0.1: 0 |
|-----------------------------------------------------------------------------|
r_final: 0.2678
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8324
moved from start: 0.3064
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.036 13385 Z= 0.176
Angle : 0.562 9.682 18305 Z= 0.271
Chirality : 0.039 0.142 2235
Planarity : 0.004 0.026 2250
Dihedral : 4.182 25.415 2060
Min Nonbonded Distance : 2.599
Molprobity Statistics.
All-atom Clashscore : 8.65
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 1.31 %
Favored : 98.69 %
Rotamer:
Outliers : 1.89 %
Allowed : 21.61 %
Favored : 76.50 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 5.88 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 1.75 (0.21), residues: 1600
helix: 2.96 (0.20), residues: 525
sheet: 0.72 (0.25), residues: 430
loop : -0.02 (0.26), residues: 645
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.010 0.001 TRP D 362
HIS 0.001 0.000 HIS A 276
PHE 0.020 0.002 PHE A 385
TYR 0.032 0.002 TYR D 176
ARG 0.011 0.000 ARG C 257
********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
3200 Ramachandran restraints generated.
1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
3200 Ramachandran restraints generated.
1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
354 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 27
poor density : 327
time to evaluate : 1.645
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: A 48 GLU cc_start: 0.8647 (tp30) cc_final: 0.8220 (mm-30)
REVERT: A 75 ASP cc_start: 0.8381 (t0) cc_final: 0.8008 (t0)
REVERT: A 81 MET cc_start: 0.8973 (ttp) cc_final: 0.8668 (ptt)
REVERT: A 146 LYS cc_start: 0.8738 (mtpt) cc_final: 0.8177 (mttp)
REVERT: A 153 THR cc_start: 0.9341 (p) cc_final: 0.9038 (t)
REVERT: A 184 GLU cc_start: 0.8626 (mt-10) cc_final: 0.8425 (mt-10)
REVERT: A 201 GLU cc_start: 0.8763 (mt-10) cc_final: 0.8408 (mp0)
REVERT: A 206 ASP cc_start: 0.8433 (t0) cc_final: 0.8128 (t0)
REVERT: A 208 LYS cc_start: 0.8730 (ptpp) cc_final: 0.8209 (mtmm)
REVERT: A 232 LYS cc_start: 0.8696 (ttmt) cc_final: 0.8274 (ttmm)
REVERT: A 272 TYR cc_start: 0.8909 (t80) cc_final: 0.8271 (t80)
REVERT: A 283 LEU cc_start: 0.8641 (mt) cc_final: 0.8278 (mp)
REVERT: A 297 PHE cc_start: 0.8876 (m-80) cc_final: 0.8506 (m-10)
REVERT: A 364 GLU cc_start: 0.8543 (mt-10) cc_final: 0.8218 (mp0)
REVERT: B 75 ASP cc_start: 0.8257 (t0) cc_final: 0.7793 (t0)
REVERT: B 129 ASP cc_start: 0.8823 (t0) cc_final: 0.8415 (t0)
REVERT: B 146 LYS cc_start: 0.8786 (mtmt) cc_final: 0.8138 (mttp)
REVERT: B 160 GLU cc_start: 0.8938 (mm-30) cc_final: 0.8458 (mm-30)
REVERT: B 201 GLU cc_start: 0.8662 (mt-10) cc_final: 0.8274 (mp0)
REVERT: B 206 ASP cc_start: 0.8364 (t0) cc_final: 0.7916 (t0)
REVERT: B 232 LYS cc_start: 0.8706 (ttmt) cc_final: 0.8388 (ttmm)
REVERT: B 260 GLU cc_start: 0.8876 (pm20) cc_final: 0.8360 (pm20)
REVERT: C 75 ASP cc_start: 0.8407 (t0) cc_final: 0.7937 (t0)
REVERT: C 77 LEU cc_start: 0.9405 (mt) cc_final: 0.9204 (mm)
REVERT: C 81 MET cc_start: 0.9106 (ttp) cc_final: 0.8854 (ptm)
REVERT: C 129 ASP cc_start: 0.8834 (t0) cc_final: 0.8208 (t0)
REVERT: C 146 LYS cc_start: 0.8717 (mtpt) cc_final: 0.8128 (mtmp)
REVERT: C 160 GLU cc_start: 0.8574 (tt0) cc_final: 0.8147 (mm-30)
REVERT: C 184 GLU cc_start: 0.8720 (mt-10) cc_final: 0.8342 (pt0)
REVERT: C 201 GLU cc_start: 0.8728 (mt-10) cc_final: 0.8398 (mp0)
REVERT: C 232 LYS cc_start: 0.8714 (ttmt) cc_final: 0.8412 (tppp)
REVERT: C 260 GLU cc_start: 0.8882 (pm20) cc_final: 0.8400 (pm20)
REVERT: C 402 GLU cc_start: 0.8668 (mm-30) cc_final: 0.8458 (mt-10)
REVERT: D 75 ASP cc_start: 0.8460 (t0) cc_final: 0.7826 (t0)
REVERT: D 146 LYS cc_start: 0.8679 (mtmt) cc_final: 0.8104 (mttp)
REVERT: D 184 GLU cc_start: 0.8646 (mt-10) cc_final: 0.8280 (pt0)
REVERT: D 199 LYS cc_start: 0.8448 (ptpt) cc_final: 0.8127 (ptmm)
REVERT: D 201 GLU cc_start: 0.8744 (mt-10) cc_final: 0.8446 (mp0)
REVERT: D 206 ASP cc_start: 0.8462 (t0) cc_final: 0.8118 (t0)
REVERT: D 208 LYS cc_start: 0.8693 (mtmm) cc_final: 0.8446 (mtmm)
REVERT: D 232 LYS cc_start: 0.8533 (ttmt) cc_final: 0.8310 (tppp)
REVERT: D 272 TYR cc_start: 0.8952 (t80) cc_final: 0.8101 (t80)
REVERT: D 281 GLN cc_start: 0.8711 (mm110) cc_final: 0.8337 (pt0)
REVERT: D 283 LEU cc_start: 0.8682 (mt) cc_final: 0.8159 (mp)
REVERT: D 402 GLU cc_start: 0.8587 (mm-30) cc_final: 0.8338 (mt-10)
REVERT: E 75 ASP cc_start: 0.8381 (t0) cc_final: 0.7986 (t0)
REVERT: E 113 GLU cc_start: 0.9126 (mp0) cc_final: 0.8751 (mp0)
REVERT: E 132 ASP cc_start: 0.7815 (t0) cc_final: 0.7556 (t0)
REVERT: E 146 LYS cc_start: 0.8756 (mtpt) cc_final: 0.8080 (mttp)
REVERT: E 160 GLU cc_start: 0.8764 (OUTLIER) cc_final: 0.8435 (mm-30)
REVERT: E 167 ASP cc_start: 0.9440 (p0) cc_final: 0.9112 (p0)
REVERT: E 201 GLU cc_start: 0.8693 (mt-10) cc_final: 0.8405 (mp0)
REVERT: E 206 ASP cc_start: 0.8423 (t0) cc_final: 0.8100 (t0)
REVERT: E 208 LYS cc_start: 0.8805 (mtmm) cc_final: 0.8394 (mtmm)
REVERT: E 227 LYS cc_start: 0.8841 (ptmt) cc_final: 0.8533 (ptpp)
REVERT: E 232 LYS cc_start: 0.8780 (ttmt) cc_final: 0.8400 (ttmm)
REVERT: E 283 LEU cc_start: 0.8664 (mt) cc_final: 0.8349 (mp)
outliers start: 27
outliers final: 19
residues processed: 345
average time/residue: 1.1109
time to fit residues: 422.9326
Evaluate side-chains
336 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 20
poor density : 316
time to evaluate : 1.484
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 179 SER
Chi-restraints excluded: chain A residue 253 LEU
Chi-restraints excluded: chain A residue 302 LEU
Chi-restraints excluded: chain B residue 54 ASN
Chi-restraints excluded: chain B residue 179 SER
Chi-restraints excluded: chain B residue 246 LEU
Chi-restraints excluded: chain B residue 253 LEU
Chi-restraints excluded: chain C residue 179 SER
Chi-restraints excluded: chain C residue 198 VAL
Chi-restraints excluded: chain C residue 235 ILE
Chi-restraints excluded: chain C residue 304 LEU
Chi-restraints excluded: chain D residue 142 ASP
Chi-restraints excluded: chain D residue 153 THR
Chi-restraints excluded: chain D residue 179 SER
Chi-restraints excluded: chain D residue 235 ILE
Chi-restraints excluded: chain D residue 277 SER
Chi-restraints excluded: chain E residue 155 THR
Chi-restraints excluded: chain E residue 160 GLU
Chi-restraints excluded: chain E residue 277 SER
Chi-restraints excluded: chain E residue 305 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 160
random chunks:
chunk 74 optimal weight: 5.9990
chunk 1 optimal weight: 5.9990
chunk 88 optimal weight: 0.8980
chunk 126 optimal weight: 2.9990
chunk 111 optimal weight: 2.9990
chunk 10 optimal weight: 3.9990
chunk 56 optimal weight: 0.2980
chunk 154 optimal weight: 5.9990
chunk 36 optimal weight: 3.9990
chunk 83 optimal weight: 4.9990
chunk 127 optimal weight: 10.0000
overall best weight: 2.2386
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 156 ASN
A 221 GLN
C 156 ASN
C 382 GLN
** D 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 382 GLN
E 156 ASN
Total number of N/Q/H flips: 6
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.089105 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2902 r_free = 0.2902 target = 0.075772 restraints weight = 20573.992|
|-----------------------------------------------------------------------------|
r_work (start): 0.2900 rms_B_bonded: 2.43
r_work: 0.2757 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.2610 rms_B_bonded: 4.62 restraints_weight: 0.2500
r_work (final): 0.2610
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2628
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2628 r_free = 0.2628 target_work(ls_wunit_k1) = 0.061 |
| occupancies: max = 1.00 min = 0.91 number of occupancies < 0.1: 0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2628 r_free = 0.2628 target_work(ls_wunit_k1) = 0.061 |
| occupancies: max = 1.00 min = 0.92 number of occupancies < 0.1: 0 |
|-----------------------------------------------------------------------------|
r_final: 0.2628
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8367
moved from start: 0.3225
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.006 0.062 13385 Z= 0.381
Angle : 0.608 9.724 18305 Z= 0.300
Chirality : 0.042 0.248 2235
Planarity : 0.004 0.027 2250
Dihedral : 4.278 23.308 2060
Min Nonbonded Distance : 2.584
Molprobity Statistics.
All-atom Clashscore : 10.20
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 1.50 %
Favored : 98.50 %
Rotamer:
Outliers : 2.24 %
Allowed : 21.12 %
Favored : 76.64 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 5.88 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 1.49 (0.21), residues: 1600
helix: 2.68 (0.20), residues: 525
sheet: 0.61 (0.24), residues: 430
loop : -0.11 (0.26), residues: 645
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.011 0.001 TRP E 112
HIS 0.002 0.001 HIS E 103
PHE 0.023 0.002 PHE A 385
TYR 0.059 0.003 TYR D 176
ARG 0.015 0.001 ARG C 257
Origin is already at (0, 0, 0), no shifts will be applied
===============================================================================
Job complete
usr+sys time: 9567.40 seconds
wall clock time: 170 minutes 21.58 seconds (10221.58 seconds total)