Starting phenix.real_space_refine
on Sun Jan 19 01:42:10 2025 by dcliebschner
===============================================================================
Processing files:
-------------------------------------------------------------------------------
Found model, /net/cci-nas-00/data/ceres_data/8vsz_43512/01_2025/8vsz_43512.cif
Found real_map, /net/cci-nas-00/data/ceres_data/8vsz_43512/01_2025/8vsz_43512.map
Processing PHIL parameters:
-------------------------------------------------------------------------------
Adding command-line PHIL:
-------------------------
refinement.macro_cycles=10
scattering_table=electron
resolution=3.07
write_initial_geo_file=False
Final processed PHIL parameters:
-------------------------------------------------------------------------------
data_manager {
real_map_files = "/net/cci-nas-00/data/ceres_data/8vsz_43512/01_2025/8vsz_43512.map"
default_real_map = "/net/cci-nas-00/data/ceres_data/8vsz_43512/01_2025/8vsz_43512.map"
model {
file = "/net/cci-nas-00/data/ceres_data/8vsz_43512/01_2025/8vsz_43512.cif"
}
default_model = "/net/cci-nas-00/data/ceres_data/8vsz_43512/01_2025/8vsz_43512.cif"
}
resolution = 3.07
write_initial_geo_file = False
refinement {
macro_cycles = 10
}
qi {
qm_restraints {
package {
program = *test
}
}
}
Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.
Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
Set to: 0
Set model cs if undefined
Decide on map wrapping
Map wrapping is set to: False
Normalize map: mean=0, sd=1
Input map: mean= 0.004 sd= 0.039
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 65 5.16 5
C 8590 2.51 5
N 2100 2.21 5
O 2465 1.98 5
sf(0) = scattering factor at diffraction angle 0.
Process input model
Symmetric amino acids flipped. Time to flip 30 residue(s): 0.05s
Monomer Library directory:
"/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
Total number of atoms: 13220
Number of models: 1
Model: ""
Number of chains: 3
Chain: "A"
Number of atoms: 2580
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 316, 2580
Classifications: {'peptide': 316}
Modifications used: {'COO': 1}
Link IDs: {'PTRANS': 8, 'TRANS': 307}
Chain breaks: 1
Chain: "G"
Number of atoms: 50
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 4, 50
Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2}
Classifications: {'undetermined': 4}
Link IDs: {None: 3}
Unresolved non-hydrogen bonds: 4
Unresolved non-hydrogen angles: 8
Unresolved non-hydrogen dihedrals: 12
Unresolved non-hydrogen chiralities: 4
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
Restraints were copied for chains:
C, B, E, D, F, I, H, J
Time building chain proxies: 5.55, per 1000 atoms: 0.42
Number of scatterers: 13220
At special positions: 0
Unit cell: (93.225, 91.575, 120.45, 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 65 16.00
O 2465 8.00
N 2100 7.00
C 8590 6.00
sf(0) = scattering factor at diffraction angle 0.
Number of disulfides: simple=1, symmetry=0
Simple disulfide: pdb=" SG CYS A 160 " - pdb=" SG CYS A 174 " 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=5, symmetry=0
Links applied
ALPHA1-4
" BMA F 3 " - " MAN F 4 "
" BMA G 3 " - " MAN G 4 "
" BMA H 3 " - " MAN H 4 "
" BMA I 3 " - " MAN I 4 "
" BMA J 3 " - " MAN J 4 "
BETA1-4
" NAG F 1 " - " NAG F 2 "
" NAG F 2 " - " BMA F 3 "
" NAG G 1 " - " NAG G 2 "
" NAG G 2 " - " BMA G 3 "
" NAG H 1 " - " NAG H 2 "
" NAG H 2 " - " BMA H 3 "
" NAG I 1 " - " NAG I 2 "
" NAG I 2 " - " BMA I 3 "
" NAG J 1 " - " NAG J 2 "
" NAG J 2 " - " BMA J 3 "
NAG-ASN
" NAG A 501 " - " ASN A 196 "
" NAG B 501 " - " ASN B 196 "
" NAG C 501 " - " ASN C 196 "
" NAG D 501 " - " ASN D 196 "
" NAG E 501 " - " ASN E 196 "
" NAG F 1 " - " ASN A 145 "
" NAG G 1 " - " ASN B 145 "
" NAG H 1 " - " ASN C 145 "
" NAG I 1 " - " ASN D 145 "
" NAG J 1 " - " ASN E 145 "
Number of additional bonds: simple=5, symmetry=0
Coordination:
Other bonds:
Time building additional restraints: 3.67
Conformation dependent library (CDL) restraints added in 1.6 seconds
3120 Ramachandran restraints generated.
1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2.
Adding C-beta torsion restraints...
Number of C-beta restraints generated: 3010
Finding SS restraints...
Secondary structure from input PDB file:
45 helices and 20 sheets defined
36.4% alpha, 43.0% beta
0 base pairs and 0 stacking pairs defined.
Time for finding SS restraints: 1.82
Creating SS restraints...
Processing helix chain 'A' and resid 194 through 197
Processing helix chain 'A' and resid 201 through 205
Processing helix chain 'A' and resid 241 through 249
removed outlier: 4.050A pdb=" N PHE A 245 " --> pdb=" O ASN A 241 " (cutoff:3.500A)
Processing helix chain 'A' and resid 249 through 263
Processing helix chain 'A' and resid 264 through 266
No H-bonds generated for 'chain 'A' and resid 264 through 266'
Processing helix chain 'A' and resid 270 through 296
removed outlier: 3.684A pdb=" N LEU A 296 " --> pdb=" O SER A 292 " (cutoff:3.500A)
Processing helix chain 'A' and resid 304 through 332
removed outlier: 3.609A pdb=" N VAL A 308 " --> pdb=" O LYS A 304 " (cutoff:3.500A)
Processing helix chain 'A' and resid 415 through 420
removed outlier: 4.334A pdb=" N LEU A 420 " --> pdb=" O HIS A 416 " (cutoff:3.500A)
Processing helix chain 'A' and resid 421 through 437
Processing helix chain 'B' and resid 194 through 197
Processing helix chain 'B' and resid 201 through 205
Processing helix chain 'B' and resid 241 through 249
removed outlier: 4.050A pdb=" N PHE B 245 " --> pdb=" O ASN B 241 " (cutoff:3.500A)
Processing helix chain 'B' and resid 249 through 263
Processing helix chain 'B' and resid 264 through 266
No H-bonds generated for 'chain 'B' and resid 264 through 266'
Processing helix chain 'B' and resid 270 through 296
removed outlier: 3.684A pdb=" N LEU B 296 " --> pdb=" O SER B 292 " (cutoff:3.500A)
Processing helix chain 'B' and resid 304 through 332
removed outlier: 3.608A pdb=" N VAL B 308 " --> pdb=" O LYS B 304 " (cutoff:3.500A)
Processing helix chain 'B' and resid 415 through 420
removed outlier: 4.334A pdb=" N LEU B 420 " --> pdb=" O HIS B 416 " (cutoff:3.500A)
Processing helix chain 'B' and resid 421 through 437
Processing helix chain 'C' and resid 194 through 197
Processing helix chain 'C' and resid 201 through 205
Processing helix chain 'C' and resid 241 through 249
removed outlier: 4.049A pdb=" N PHE C 245 " --> pdb=" O ASN C 241 " (cutoff:3.500A)
Processing helix chain 'C' and resid 249 through 263
Processing helix chain 'C' and resid 264 through 266
No H-bonds generated for 'chain 'C' and resid 264 through 266'
Processing helix chain 'C' and resid 270 through 296
removed outlier: 3.684A pdb=" N LEU C 296 " --> pdb=" O SER C 292 " (cutoff:3.500A)
Processing helix chain 'C' and resid 304 through 332
removed outlier: 3.608A pdb=" N VAL C 308 " --> pdb=" O LYS C 304 " (cutoff:3.500A)
Processing helix chain 'C' and resid 415 through 420
removed outlier: 4.334A pdb=" N LEU C 420 " --> pdb=" O HIS C 416 " (cutoff:3.500A)
Processing helix chain 'C' and resid 421 through 437
Processing helix chain 'D' and resid 194 through 197
Processing helix chain 'D' and resid 201 through 205
Processing helix chain 'D' and resid 241 through 249
removed outlier: 4.050A pdb=" N PHE D 245 " --> pdb=" O ASN D 241 " (cutoff:3.500A)
Processing helix chain 'D' and resid 249 through 263
Processing helix chain 'D' and resid 264 through 266
No H-bonds generated for 'chain 'D' and resid 264 through 266'
Processing helix chain 'D' and resid 270 through 296
removed outlier: 3.684A pdb=" N LEU D 296 " --> pdb=" O SER D 292 " (cutoff:3.500A)
Processing helix chain 'D' and resid 304 through 332
removed outlier: 3.608A pdb=" N VAL D 308 " --> pdb=" O LYS D 304 " (cutoff:3.500A)
Processing helix chain 'D' and resid 415 through 420
removed outlier: 4.334A pdb=" N LEU D 420 " --> pdb=" O HIS D 416 " (cutoff:3.500A)
Processing helix chain 'D' and resid 421 through 437
Processing helix chain 'E' and resid 194 through 197
Processing helix chain 'E' and resid 201 through 205
Processing helix chain 'E' and resid 241 through 249
removed outlier: 4.050A pdb=" N PHE E 245 " --> pdb=" O ASN E 241 " (cutoff:3.500A)
Processing helix chain 'E' and resid 249 through 263
Processing helix chain 'E' and resid 264 through 266
No H-bonds generated for 'chain 'E' and resid 264 through 266'
Processing helix chain 'E' and resid 270 through 296
removed outlier: 3.684A pdb=" N LEU E 296 " --> pdb=" O SER E 292 " (cutoff:3.500A)
Processing helix chain 'E' and resid 304 through 332
removed outlier: 3.608A pdb=" N VAL E 308 " --> pdb=" O LYS E 304 " (cutoff:3.500A)
Processing helix chain 'E' and resid 415 through 420
removed outlier: 4.333A pdb=" N LEU E 420 " --> pdb=" O HIS E 416 " (cutoff:3.500A)
Processing helix chain 'E' and resid 421 through 437
Processing sheet with id=AA1, first strand: chain 'A' and resid 105 through 107
removed outlier: 3.790A pdb=" N ILE A 140 " --> pdb=" O LEU A 107 " (cutoff:3.500A)
removed outlier: 5.930A pdb=" N ASP A 81 " --> pdb=" O SER A 74 " (cutoff:3.500A)
removed outlier: 6.830A pdb=" N SER A 74 " --> pdb=" O ASP A 81 " (cutoff:3.500A)
removed outlier: 6.825A pdb=" N THR A 83 " --> pdb=" O ILE A 72 " (cutoff:3.500A)
removed outlier: 4.445A pdb=" N ILE A 72 " --> pdb=" O THR A 83 " (cutoff:3.500A)
removed outlier: 6.501A pdb=" N THR A 85 " --> pdb=" O ALA A 70 " (cutoff:3.500A)
removed outlier: 4.348A pdb=" N MET A 93 " --> pdb=" O GLN A 62 " (cutoff:3.500A)
removed outlier: 6.156A pdb=" N GLN A 62 " --> pdb=" O MET A 93 " (cutoff:3.500A)
Processing sheet with id=AA2, first strand: chain 'A' and resid 125 through 130
removed outlier: 6.939A pdb=" N THR A 157 " --> pdb=" O LYS A 126 " (cutoff:3.500A)
removed outlier: 4.506A pdb=" N SER A 128 " --> pdb=" O THR A 155 " (cutoff:3.500A)
removed outlier: 6.941A pdb=" N THR A 155 " --> pdb=" O SER A 128 " (cutoff:3.500A)
removed outlier: 4.800A pdb=" N LEU A 130 " --> pdb=" O ARG A 153 " (cutoff:3.500A)
removed outlier: 7.461A pdb=" N ARG A 153 " --> pdb=" O LEU A 130 " (cutoff:3.500A)
removed outlier: 5.930A pdb=" N ASP A 81 " --> pdb=" O SER A 74 " (cutoff:3.500A)
removed outlier: 6.830A pdb=" N SER A 74 " --> pdb=" O ASP A 81 " (cutoff:3.500A)
removed outlier: 6.825A pdb=" N THR A 83 " --> pdb=" O ILE A 72 " (cutoff:3.500A)
removed outlier: 4.445A pdb=" N ILE A 72 " --> pdb=" O THR A 83 " (cutoff:3.500A)
removed outlier: 6.501A pdb=" N THR A 85 " --> pdb=" O ALA A 70 " (cutoff:3.500A)
removed outlier: 4.348A pdb=" N MET A 93 " --> pdb=" O GLN A 62 " (cutoff:3.500A)
removed outlier: 6.156A pdb=" N GLN A 62 " --> pdb=" O MET A 93 " (cutoff:3.500A)
removed outlier: 8.665A pdb=" N ARG A 200 " --> pdb=" O LEU A 65 " (cutoff:3.500A)
removed outlier: 6.514A pdb=" N LEU A 67 " --> pdb=" O ARG A 200 " (cutoff:3.500A)
Processing sheet with id=AA3, first strand: chain 'A' and resid 120 through 122
Processing sheet with id=AA4, first strand: chain 'A' and resid 120 through 122
Processing sheet with id=AA5, first strand: chain 'B' and resid 105 through 107
removed outlier: 3.790A pdb=" N ILE B 140 " --> pdb=" O LEU B 107 " (cutoff:3.500A)
removed outlier: 5.930A pdb=" N ASP B 81 " --> pdb=" O SER B 74 " (cutoff:3.500A)
removed outlier: 6.829A pdb=" N SER B 74 " --> pdb=" O ASP B 81 " (cutoff:3.500A)
removed outlier: 6.825A pdb=" N THR B 83 " --> pdb=" O ILE B 72 " (cutoff:3.500A)
removed outlier: 4.445A pdb=" N ILE B 72 " --> pdb=" O THR B 83 " (cutoff:3.500A)
removed outlier: 6.502A pdb=" N THR B 85 " --> pdb=" O ALA B 70 " (cutoff:3.500A)
removed outlier: 4.347A pdb=" N MET B 93 " --> pdb=" O GLN B 62 " (cutoff:3.500A)
removed outlier: 6.155A pdb=" N GLN B 62 " --> pdb=" O MET B 93 " (cutoff:3.500A)
Processing sheet with id=AA6, first strand: chain 'B' and resid 125 through 130
removed outlier: 6.939A pdb=" N THR B 157 " --> pdb=" O LYS B 126 " (cutoff:3.500A)
removed outlier: 4.505A pdb=" N SER B 128 " --> pdb=" O THR B 155 " (cutoff:3.500A)
removed outlier: 6.942A pdb=" N THR B 155 " --> pdb=" O SER B 128 " (cutoff:3.500A)
removed outlier: 4.801A pdb=" N LEU B 130 " --> pdb=" O ARG B 153 " (cutoff:3.500A)
removed outlier: 7.461A pdb=" N ARG B 153 " --> pdb=" O LEU B 130 " (cutoff:3.500A)
removed outlier: 5.930A pdb=" N ASP B 81 " --> pdb=" O SER B 74 " (cutoff:3.500A)
removed outlier: 6.829A pdb=" N SER B 74 " --> pdb=" O ASP B 81 " (cutoff:3.500A)
removed outlier: 6.825A pdb=" N THR B 83 " --> pdb=" O ILE B 72 " (cutoff:3.500A)
removed outlier: 4.445A pdb=" N ILE B 72 " --> pdb=" O THR B 83 " (cutoff:3.500A)
removed outlier: 6.502A pdb=" N THR B 85 " --> pdb=" O ALA B 70 " (cutoff:3.500A)
removed outlier: 4.347A pdb=" N MET B 93 " --> pdb=" O GLN B 62 " (cutoff:3.500A)
removed outlier: 6.155A pdb=" N GLN B 62 " --> pdb=" O MET B 93 " (cutoff:3.500A)
removed outlier: 8.665A pdb=" N ARG B 200 " --> pdb=" O LEU B 65 " (cutoff:3.500A)
removed outlier: 6.513A pdb=" N LEU B 67 " --> pdb=" O ARG B 200 " (cutoff:3.500A)
Processing sheet with id=AA7, first strand: chain 'B' and resid 120 through 122
Processing sheet with id=AA8, first strand: chain 'B' and resid 120 through 122
Processing sheet with id=AA9, first strand: chain 'C' and resid 105 through 107
removed outlier: 3.790A pdb=" N ILE C 140 " --> pdb=" O LEU C 107 " (cutoff:3.500A)
removed outlier: 5.929A pdb=" N ASP C 81 " --> pdb=" O SER C 74 " (cutoff:3.500A)
removed outlier: 6.830A pdb=" N SER C 74 " --> pdb=" O ASP C 81 " (cutoff:3.500A)
removed outlier: 6.825A pdb=" N THR C 83 " --> pdb=" O ILE C 72 " (cutoff:3.500A)
removed outlier: 4.445A pdb=" N ILE C 72 " --> pdb=" O THR C 83 " (cutoff:3.500A)
removed outlier: 6.501A pdb=" N THR C 85 " --> pdb=" O ALA C 70 " (cutoff:3.500A)
removed outlier: 4.348A pdb=" N MET C 93 " --> pdb=" O GLN C 62 " (cutoff:3.500A)
removed outlier: 6.155A pdb=" N GLN C 62 " --> pdb=" O MET C 93 " (cutoff:3.500A)
Processing sheet with id=AB1, first strand: chain 'C' and resid 125 through 130
removed outlier: 6.939A pdb=" N THR C 157 " --> pdb=" O LYS C 126 " (cutoff:3.500A)
removed outlier: 4.505A pdb=" N SER C 128 " --> pdb=" O THR C 155 " (cutoff:3.500A)
removed outlier: 6.942A pdb=" N THR C 155 " --> pdb=" O SER C 128 " (cutoff:3.500A)
removed outlier: 4.800A pdb=" N LEU C 130 " --> pdb=" O ARG C 153 " (cutoff:3.500A)
removed outlier: 7.462A pdb=" N ARG C 153 " --> pdb=" O LEU C 130 " (cutoff:3.500A)
removed outlier: 5.929A pdb=" N ASP C 81 " --> pdb=" O SER C 74 " (cutoff:3.500A)
removed outlier: 6.830A pdb=" N SER C 74 " --> pdb=" O ASP C 81 " (cutoff:3.500A)
removed outlier: 6.825A pdb=" N THR C 83 " --> pdb=" O ILE C 72 " (cutoff:3.500A)
removed outlier: 4.445A pdb=" N ILE C 72 " --> pdb=" O THR C 83 " (cutoff:3.500A)
removed outlier: 6.501A pdb=" N THR C 85 " --> pdb=" O ALA C 70 " (cutoff:3.500A)
removed outlier: 4.348A pdb=" N MET C 93 " --> pdb=" O GLN C 62 " (cutoff:3.500A)
removed outlier: 6.155A pdb=" N GLN C 62 " --> pdb=" O MET C 93 " (cutoff:3.500A)
removed outlier: 8.665A pdb=" N ARG C 200 " --> pdb=" O LEU C 65 " (cutoff:3.500A)
removed outlier: 6.513A pdb=" N LEU C 67 " --> pdb=" O ARG C 200 " (cutoff:3.500A)
Processing sheet with id=AB2, first strand: chain 'C' and resid 120 through 122
Processing sheet with id=AB3, first strand: chain 'C' and resid 120 through 122
Processing sheet with id=AB4, first strand: chain 'D' and resid 105 through 107
removed outlier: 3.790A pdb=" N ILE D 140 " --> pdb=" O LEU D 107 " (cutoff:3.500A)
removed outlier: 5.929A pdb=" N ASP D 81 " --> pdb=" O SER D 74 " (cutoff:3.500A)
removed outlier: 6.830A pdb=" N SER D 74 " --> pdb=" O ASP D 81 " (cutoff:3.500A)
removed outlier: 6.825A pdb=" N THR D 83 " --> pdb=" O ILE D 72 " (cutoff:3.500A)
removed outlier: 4.445A pdb=" N ILE D 72 " --> pdb=" O THR D 83 " (cutoff:3.500A)
removed outlier: 6.501A pdb=" N THR D 85 " --> pdb=" O ALA D 70 " (cutoff:3.500A)
removed outlier: 4.347A pdb=" N MET D 93 " --> pdb=" O GLN D 62 " (cutoff:3.500A)
removed outlier: 6.156A pdb=" N GLN D 62 " --> pdb=" O MET D 93 " (cutoff:3.500A)
Processing sheet with id=AB5, first strand: chain 'D' and resid 125 through 130
removed outlier: 6.939A pdb=" N THR D 157 " --> pdb=" O LYS D 126 " (cutoff:3.500A)
removed outlier: 4.505A pdb=" N SER D 128 " --> pdb=" O THR D 155 " (cutoff:3.500A)
removed outlier: 6.942A pdb=" N THR D 155 " --> pdb=" O SER D 128 " (cutoff:3.500A)
removed outlier: 4.800A pdb=" N LEU D 130 " --> pdb=" O ARG D 153 " (cutoff:3.500A)
removed outlier: 7.460A pdb=" N ARG D 153 " --> pdb=" O LEU D 130 " (cutoff:3.500A)
removed outlier: 5.929A pdb=" N ASP D 81 " --> pdb=" O SER D 74 " (cutoff:3.500A)
removed outlier: 6.830A pdb=" N SER D 74 " --> pdb=" O ASP D 81 " (cutoff:3.500A)
removed outlier: 6.825A pdb=" N THR D 83 " --> pdb=" O ILE D 72 " (cutoff:3.500A)
removed outlier: 4.445A pdb=" N ILE D 72 " --> pdb=" O THR D 83 " (cutoff:3.500A)
removed outlier: 6.501A pdb=" N THR D 85 " --> pdb=" O ALA D 70 " (cutoff:3.500A)
removed outlier: 4.347A pdb=" N MET D 93 " --> pdb=" O GLN D 62 " (cutoff:3.500A)
removed outlier: 6.156A pdb=" N GLN D 62 " --> pdb=" O MET D 93 " (cutoff:3.500A)
removed outlier: 8.665A pdb=" N ARG D 200 " --> pdb=" O LEU D 65 " (cutoff:3.500A)
removed outlier: 6.513A pdb=" N LEU D 67 " --> pdb=" O ARG D 200 " (cutoff:3.500A)
Processing sheet with id=AB6, first strand: chain 'D' and resid 120 through 122
Processing sheet with id=AB7, first strand: chain 'D' and resid 120 through 122
Processing sheet with id=AB8, first strand: chain 'E' and resid 105 through 107
removed outlier: 3.791A pdb=" N ILE E 140 " --> pdb=" O LEU E 107 " (cutoff:3.500A)
removed outlier: 5.929A pdb=" N ASP E 81 " --> pdb=" O SER E 74 " (cutoff:3.500A)
removed outlier: 6.830A pdb=" N SER E 74 " --> pdb=" O ASP E 81 " (cutoff:3.500A)
removed outlier: 6.825A pdb=" N THR E 83 " --> pdb=" O ILE E 72 " (cutoff:3.500A)
removed outlier: 4.445A pdb=" N ILE E 72 " --> pdb=" O THR E 83 " (cutoff:3.500A)
removed outlier: 6.501A pdb=" N THR E 85 " --> pdb=" O ALA E 70 " (cutoff:3.500A)
removed outlier: 4.347A pdb=" N MET E 93 " --> pdb=" O GLN E 62 " (cutoff:3.500A)
removed outlier: 6.155A pdb=" N GLN E 62 " --> pdb=" O MET E 93 " (cutoff:3.500A)
Processing sheet with id=AB9, first strand: chain 'E' and resid 125 through 130
removed outlier: 6.938A pdb=" N THR E 157 " --> pdb=" O LYS E 126 " (cutoff:3.500A)
removed outlier: 4.506A pdb=" N SER E 128 " --> pdb=" O THR E 155 " (cutoff:3.500A)
removed outlier: 6.943A pdb=" N THR E 155 " --> pdb=" O SER E 128 " (cutoff:3.500A)
removed outlier: 4.800A pdb=" N LEU E 130 " --> pdb=" O ARG E 153 " (cutoff:3.500A)
removed outlier: 7.461A pdb=" N ARG E 153 " --> pdb=" O LEU E 130 " (cutoff:3.500A)
removed outlier: 5.929A pdb=" N ASP E 81 " --> pdb=" O SER E 74 " (cutoff:3.500A)
removed outlier: 6.830A pdb=" N SER E 74 " --> pdb=" O ASP E 81 " (cutoff:3.500A)
removed outlier: 6.825A pdb=" N THR E 83 " --> pdb=" O ILE E 72 " (cutoff:3.500A)
removed outlier: 4.445A pdb=" N ILE E 72 " --> pdb=" O THR E 83 " (cutoff:3.500A)
removed outlier: 6.501A pdb=" N THR E 85 " --> pdb=" O ALA E 70 " (cutoff:3.500A)
removed outlier: 4.347A pdb=" N MET E 93 " --> pdb=" O GLN E 62 " (cutoff:3.500A)
removed outlier: 6.155A pdb=" N GLN E 62 " --> pdb=" O MET E 93 " (cutoff:3.500A)
removed outlier: 8.665A pdb=" N ARG E 200 " --> pdb=" O LEU E 65 " (cutoff:3.500A)
removed outlier: 6.514A pdb=" N LEU E 67 " --> pdb=" O ARG E 200 " (cutoff:3.500A)
Processing sheet with id=AC1, first strand: chain 'E' and resid 120 through 122
Processing sheet with id=AC2, first strand: chain 'E' and resid 120 through 122
770 hydrogen bonds defined for protein.
2220 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: 4.04
Time building geometry restraints manager: 4.17 seconds
NOTE: a complete listing of the restraints can be obtained by requesting
output of .geo file.
Histogram of bond lengths:
1.23 - 1.34: 3999
1.34 - 1.46: 3293
1.46 - 1.58: 6148
1.58 - 1.69: 0
1.69 - 1.81: 105
Bond restraints: 13545
Sorted by residual:
bond pdb=" C1 MAN J 4 "
pdb=" C2 MAN J 4 "
ideal model delta sigma weight residual
1.526 1.558 -0.032 2.00e-02 2.50e+03 2.54e+00
bond pdb=" C1 MAN I 4 "
pdb=" C2 MAN I 4 "
ideal model delta sigma weight residual
1.526 1.557 -0.031 2.00e-02 2.50e+03 2.45e+00
bond pdb=" C1 MAN F 4 "
pdb=" C2 MAN F 4 "
ideal model delta sigma weight residual
1.526 1.557 -0.031 2.00e-02 2.50e+03 2.43e+00
bond pdb=" C1 MAN G 4 "
pdb=" C2 MAN G 4 "
ideal model delta sigma weight residual
1.526 1.557 -0.031 2.00e-02 2.50e+03 2.41e+00
bond pdb=" C1 MAN H 4 "
pdb=" C2 MAN H 4 "
ideal model delta sigma weight residual
1.526 1.557 -0.031 2.00e-02 2.50e+03 2.41e+00
... (remaining 13540 not shown)
Histogram of bond angle deviations from ideal:
0.00 - 1.58: 17932
1.58 - 3.15: 366
3.15 - 4.73: 87
4.73 - 6.30: 40
6.30 - 7.88: 10
Bond angle restraints: 18435
Sorted by residual:
angle pdb=" C LEU E 420 "
pdb=" N LEU E 421 "
pdb=" CA LEU E 421 "
ideal model delta sigma weight residual
122.17 115.67 6.50 1.54e+00 4.22e-01 1.78e+01
angle pdb=" C LEU B 420 "
pdb=" N LEU B 421 "
pdb=" CA LEU B 421 "
ideal model delta sigma weight residual
122.17 115.70 6.47 1.54e+00 4.22e-01 1.76e+01
angle pdb=" C LEU A 420 "
pdb=" N LEU A 421 "
pdb=" CA LEU A 421 "
ideal model delta sigma weight residual
122.17 115.71 6.46 1.54e+00 4.22e-01 1.76e+01
angle pdb=" C LEU D 420 "
pdb=" N LEU D 421 "
pdb=" CA LEU D 421 "
ideal model delta sigma weight residual
122.17 115.71 6.46 1.54e+00 4.22e-01 1.76e+01
angle pdb=" C LEU C 420 "
pdb=" N LEU C 421 "
pdb=" CA LEU C 421 "
ideal model delta sigma weight residual
122.17 115.72 6.45 1.54e+00 4.22e-01 1.75e+01
... (remaining 18430 not shown)
Histogram of dihedral angle deviations from ideal:
0.00 - 21.90: 7084
21.90 - 43.80: 907
43.80 - 65.69: 117
65.69 - 87.59: 45
87.59 - 109.49: 25
Dihedral angle restraints: 8178
sinusoidal: 3498
harmonic: 4680
Sorted by residual:
dihedral pdb=" CB CYS A 160 "
pdb=" SG CYS A 160 "
pdb=" SG CYS A 174 "
pdb=" CB CYS A 174 "
ideal model delta sinusoidal sigma weight residual
93.00 49.50 43.50 1 1.00e+01 1.00e-02 2.64e+01
dihedral pdb=" O4 BMA G 3 "
pdb=" C4 BMA G 3 "
pdb=" C5 BMA G 3 "
pdb=" O5 BMA G 3 "
ideal model delta sinusoidal sigma weight residual
288.71 179.22 109.49 1 3.00e+01 1.11e-03 1.42e+01
dihedral pdb=" O4 BMA F 3 "
pdb=" C4 BMA F 3 "
pdb=" C5 BMA F 3 "
pdb=" O5 BMA F 3 "
ideal model delta sinusoidal sigma weight residual
288.71 179.24 109.47 1 3.00e+01 1.11e-03 1.42e+01
... (remaining 8175 not shown)
Histogram of chiral volume deviations from ideal:
0.000 - 0.059: 1871
0.059 - 0.118: 274
0.118 - 0.178: 25
0.178 - 0.237: 5
0.237 - 0.296: 10
Chirality restraints: 2185
Sorted by residual:
chirality pdb=" C1 NAG C 501 "
pdb=" ND2 ASN C 196 "
pdb=" C2 NAG C 501 "
pdb=" O5 NAG C 501 "
both_signs ideal model delta sigma weight residual
False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.19e+00
chirality pdb=" C1 NAG D 501 "
pdb=" ND2 ASN D 196 "
pdb=" C2 NAG D 501 "
pdb=" O5 NAG D 501 "
both_signs ideal model delta sigma weight residual
False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.17e+00
chirality pdb=" C1 NAG A 501 "
pdb=" ND2 ASN A 196 "
pdb=" C2 NAG A 501 "
pdb=" O5 NAG A 501 "
both_signs ideal model delta sigma weight residual
False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.17e+00
... (remaining 2182 not shown)
Planarity restraints: 2245
Sorted by residual:
delta sigma weight rms_deltas residual
plane pdb=" CB TRP B 261 " 0.007 2.00e-02 2.50e+03 6.16e-03 9.49e-01
pdb=" CG TRP B 261 " -0.017 2.00e-02 2.50e+03
pdb=" CD1 TRP B 261 " 0.005 2.00e-02 2.50e+03
pdb=" CD2 TRP B 261 " 0.001 2.00e-02 2.50e+03
pdb=" NE1 TRP B 261 " 0.003 2.00e-02 2.50e+03
pdb=" CE2 TRP B 261 " -0.000 2.00e-02 2.50e+03
pdb=" CE3 TRP B 261 " 0.003 2.00e-02 2.50e+03
pdb=" CZ2 TRP B 261 " -0.000 2.00e-02 2.50e+03
pdb=" CZ3 TRP B 261 " 0.000 2.00e-02 2.50e+03
pdb=" CH2 TRP B 261 " -0.000 2.00e-02 2.50e+03
delta sigma weight rms_deltas residual
plane pdb=" CB TRP A 261 " 0.007 2.00e-02 2.50e+03 6.12e-03 9.36e-01
pdb=" CG TRP A 261 " -0.017 2.00e-02 2.50e+03
pdb=" CD1 TRP A 261 " 0.004 2.00e-02 2.50e+03
pdb=" CD2 TRP A 261 " 0.000 2.00e-02 2.50e+03
pdb=" NE1 TRP A 261 " 0.003 2.00e-02 2.50e+03
pdb=" CE2 TRP A 261 " 0.000 2.00e-02 2.50e+03
pdb=" CE3 TRP A 261 " 0.003 2.00e-02 2.50e+03
pdb=" CZ2 TRP A 261 " -0.000 2.00e-02 2.50e+03
pdb=" CZ3 TRP A 261 " 0.001 2.00e-02 2.50e+03
pdb=" CH2 TRP A 261 " -0.001 2.00e-02 2.50e+03
delta sigma weight rms_deltas residual
plane pdb=" CB TRP D 261 " -0.007 2.00e-02 2.50e+03 6.06e-03 9.18e-01
pdb=" CG TRP D 261 " 0.017 2.00e-02 2.50e+03
pdb=" CD1 TRP D 261 " -0.005 2.00e-02 2.50e+03
pdb=" CD2 TRP D 261 " -0.001 2.00e-02 2.50e+03
pdb=" NE1 TRP D 261 " -0.002 2.00e-02 2.50e+03
pdb=" CE2 TRP D 261 " -0.000 2.00e-02 2.50e+03
pdb=" CE3 TRP D 261 " -0.003 2.00e-02 2.50e+03
pdb=" CZ2 TRP D 261 " 0.000 2.00e-02 2.50e+03
pdb=" CZ3 TRP D 261 " -0.000 2.00e-02 2.50e+03
pdb=" CH2 TRP D 261 " 0.000 2.00e-02 2.50e+03
... (remaining 2242 not shown)
Histogram of nonbonded interaction distances:
2.03 - 2.61: 153
2.61 - 3.18: 11176
3.18 - 3.75: 20408
3.75 - 4.33: 28642
4.33 - 4.90: 47152
Nonbonded interactions: 107531
Sorted by model distance:
nonbonded pdb=" SG CYS D 160 "
pdb=" SG CYS D 174 "
model vdw
2.032 3.760
nonbonded pdb=" SG CYS C 160 "
pdb=" SG CYS C 174 "
model vdw
2.032 3.760
nonbonded pdb=" SG CYS B 160 "
pdb=" SG CYS B 174 "
model vdw
2.033 3.760
nonbonded pdb=" SG CYS E 160 "
pdb=" SG CYS E 174 "
model vdw
2.033 3.760
nonbonded pdb=" OG SER B 180 "
pdb=" O TYR B 183 "
model vdw
2.233 3.040
... (remaining 107526 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=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
Set random seed: 0.000
Set model cs if undefined: 0.000
Decide on map wrapping: 0.000
Normalize map: mean=0, sd=1: 1.620
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: 0.470
Check model and map are aligned: 0.090
Set scattering table: 0.130
Process input model: 29.620
Find NCS groups from input model: 0.250
Set up NCS constraints: 0.030
Set refine NCS operators: 0.000
Adjust number of macro_cycles: 0.000
Reset NCS operators: 0.000
Extract rigid body selections: 0.000
Check and reset occupancies: 0.000
Load rotamer database and sin/cos tables:2.820
Set ADP refinement strategy: 0.000
Make a string to write initial .geo file:0.000
Internal consistency checks: 0.010
Total: 35.050
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7228
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 : 0.003 0.032 13545 Z= 0.202
Angle : 0.650 7.879 18435 Z= 0.321
Chirality : 0.047 0.296 2185
Planarity : 0.002 0.023 2235
Dihedral : 19.650 109.487 5165
Min Nonbonded Distance : 2.032
Molprobity Statistics.
All-atom Clashscore : 10.74
Ramachandran Plot:
Outliers : 0.32 %
Allowed : 2.88 %
Favored : 96.79 %
Rotamer:
Outliers : 0.00 %
Allowed : 34.97 %
Favored : 65.03 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: -0.47 (0.22), residues: 1560
helix: 2.25 (0.24), residues: 490
sheet: -1.25 (0.28), residues: 320
loop : -1.69 (0.22), residues: 750
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.017 0.002 TRP B 261
HIS 0.004 0.001 HIS C 204
PHE 0.014 0.001 PHE E 318
TYR 0.011 0.001 TYR D 433
ARG 0.002 0.000 ARG C 53
*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
3120 Ramachandran restraints generated.
1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
3120 Ramachandran restraints generated.
1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
126 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 0
poor density : 126
time to evaluate : 1.448
Fit side-chains
REVERT: B 285 MET cc_start: 0.7070 (tpt) cc_final: 0.6792 (tpt)
REVERT: D 304 LYS cc_start: 0.7626 (mtmm) cc_final: 0.7370 (mtmm)
REVERT: E 304 LYS cc_start: 0.7541 (mtmm) cc_final: 0.7315 (mtmm)
outliers start: 0
outliers final: 0
residues processed: 126
average time/residue: 0.2383
time to fit residues: 45.4410
Evaluate side-chains
118 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 0
poor density : 118
time to evaluate : 1.518
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 155
random chunks:
chunk 130 optimal weight: 9.9990
chunk 117 optimal weight: 20.0000
chunk 65 optimal weight: 1.9990
chunk 40 optimal weight: 0.7980
chunk 79 optimal weight: 7.9990
chunk 62 optimal weight: 2.9990
chunk 121 optimal weight: 40.0000
chunk 47 optimal weight: 2.9990
chunk 73 optimal weight: 0.9990
chunk 90 optimal weight: 5.9990
chunk 140 optimal weight: 6.9990
overall best weight: 1.9588
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 204 HIS
B 204 HIS
C 204 HIS
D 204 HIS
E 204 HIS
Total number of N/Q/H flips: 5
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4509 r_free = 0.4509 target = 0.237975 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.4209 r_free = 0.4209 target = 0.204638 restraints weight = 13191.123|
|-----------------------------------------------------------------------------|
r_work (start): 0.4212 rms_B_bonded: 1.18
r_work: 0.3830 rms_B_bonded: 2.08 restraints_weight: 0.5000
r_work: 0.3549 rms_B_bonded: 4.27 restraints_weight: 0.2500
r_work (final): 0.3549
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7845
moved from start: 0.1411
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.005 0.066 13545 Z= 0.323
Angle : 0.686 6.814 18435 Z= 0.342
Chirality : 0.048 0.335 2185
Planarity : 0.004 0.027 2235
Dihedral : 11.677 80.491 2270
Min Nonbonded Distance : 2.240
Molprobity Statistics.
All-atom Clashscore : 9.14
Ramachandran Plot:
Outliers : 0.32 %
Allowed : 3.53 %
Favored : 96.15 %
Rotamer:
Outliers : 3.71 %
Allowed : 32.31 %
Favored : 63.99 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: -0.35 (0.22), residues: 1560
helix: 2.48 (0.24), residues: 495
sheet: -0.99 (0.26), residues: 315
loop : -1.84 (0.23), residues: 750
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.018 0.002 TRP B 261
HIS 0.005 0.002 HIS B 204
PHE 0.023 0.002 PHE D 316
TYR 0.016 0.002 TYR E 121
ARG 0.003 0.000 ARG B 153
*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
3120 Ramachandran restraints generated.
1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
3120 Ramachandran restraints generated.
1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
203 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 53
poor density : 150
time to evaluate : 1.461
Fit side-chains
REVERT: A 93 MET cc_start: 0.7745 (tpp) cc_final: 0.7542 (tpp)
REVERT: A 234 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.8087 (tp)
REVERT: A 318 PHE cc_start: 0.7776 (OUTLIER) cc_final: 0.6975 (p90)
REVERT: C 295 SER cc_start: 0.6162 (OUTLIER) cc_final: 0.5167 (t)
REVERT: C 304 LYS cc_start: 0.7519 (mtmm) cc_final: 0.6975 (mtmt)
REVERT: D 318 PHE cc_start: 0.7571 (OUTLIER) cc_final: 0.7118 (p90)
REVERT: E 304 LYS cc_start: 0.7685 (mtmm) cc_final: 0.7167 (mtmt)
outliers start: 53
outliers final: 27
residues processed: 193
average time/residue: 0.2167
time to fit residues: 64.5489
Evaluate side-chains
158 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 31
poor density : 127
time to evaluate : 1.357
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 61 VAL
Chi-restraints excluded: chain A residue 104 SER
Chi-restraints excluded: chain A residue 181 TRP
Chi-restraints excluded: chain A residue 211 THR
Chi-restraints excluded: chain A residue 218 LEU
Chi-restraints excluded: chain A residue 234 LEU
Chi-restraints excluded: chain A residue 318 PHE
Chi-restraints excluded: chain B residue 140 ILE
Chi-restraints excluded: chain B residue 181 TRP
Chi-restraints excluded: chain B residue 211 THR
Chi-restraints excluded: chain B residue 218 LEU
Chi-restraints excluded: chain B residue 234 LEU
Chi-restraints excluded: chain B residue 432 PHE
Chi-restraints excluded: chain C residue 61 VAL
Chi-restraints excluded: chain C residue 181 TRP
Chi-restraints excluded: chain C residue 211 THR
Chi-restraints excluded: chain C residue 242 VAL
Chi-restraints excluded: chain C residue 282 VAL
Chi-restraints excluded: chain C residue 295 SER
Chi-restraints excluded: chain C residue 432 PHE
Chi-restraints excluded: chain D residue 104 SER
Chi-restraints excluded: chain D residue 181 TRP
Chi-restraints excluded: chain D residue 211 THR
Chi-restraints excluded: chain D residue 218 LEU
Chi-restraints excluded: chain D residue 234 LEU
Chi-restraints excluded: chain D residue 318 PHE
Chi-restraints excluded: chain E residue 140 ILE
Chi-restraints excluded: chain E residue 181 TRP
Chi-restraints excluded: chain E residue 211 THR
Chi-restraints excluded: chain E residue 218 LEU
Chi-restraints excluded: chain E residue 432 PHE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 155
random chunks:
chunk 63 optimal weight: 0.1980
chunk 55 optimal weight: 6.9990
chunk 52 optimal weight: 0.6980
chunk 96 optimal weight: 0.9990
chunk 81 optimal weight: 2.9990
chunk 78 optimal weight: 6.9990
chunk 69 optimal weight: 0.6980
chunk 6 optimal weight: 7.9990
chunk 1 optimal weight: 0.1980
chunk 149 optimal weight: 9.9990
chunk 121 optimal weight: 30.0000
overall best weight: 0.5582
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 204 HIS
Total number of N/Q/H flips: 1
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4535 r_free = 0.4535 target = 0.241180 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.4233 r_free = 0.4233 target = 0.207156 restraints weight = 13334.273|
|-----------------------------------------------------------------------------|
r_work (start): 0.4224 rms_B_bonded: 1.22
r_work: 0.3859 rms_B_bonded: 2.12 restraints_weight: 0.5000
r_work: 0.3587 rms_B_bonded: 4.29 restraints_weight: 0.2500
r_work (final): 0.3587
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7760
moved from start: 0.1568
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.033 13545 Z= 0.172
Angle : 0.607 11.311 18435 Z= 0.294
Chirality : 0.044 0.274 2185
Planarity : 0.003 0.024 2235
Dihedral : 10.522 69.940 2270
Min Nonbonded Distance : 2.267
Molprobity Statistics.
All-atom Clashscore : 6.70
Ramachandran Plot:
Outliers : 0.32 %
Allowed : 2.95 %
Favored : 96.73 %
Rotamer:
Outliers : 4.55 %
Allowed : 31.40 %
Favored : 64.06 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: -0.04 (0.22), residues: 1560
helix: 2.53 (0.23), residues: 495
sheet: -0.88 (0.25), residues: 340
loop : -1.47 (0.23), residues: 725
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.018 0.002 TRP A 261
HIS 0.005 0.001 HIS A 204
PHE 0.019 0.001 PHE B 316
TYR 0.012 0.001 TYR D 121
ARG 0.002 0.000 ARG E 89
*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
3120 Ramachandran restraints generated.
1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
3120 Ramachandran restraints generated.
1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
207 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 65
poor density : 142
time to evaluate : 1.456
Fit side-chains
REVERT: A 247 LEU cc_start: 0.7274 (OUTLIER) cc_final: 0.6953 (tt)
REVERT: A 295 SER cc_start: 0.5650 (OUTLIER) cc_final: 0.4975 (t)
REVERT: A 318 PHE cc_start: 0.7797 (OUTLIER) cc_final: 0.7002 (p90)
REVERT: B 48 TYR cc_start: -0.0681 (OUTLIER) cc_final: -0.1678 (m-10)
REVERT: B 110 ARG cc_start: 0.7432 (OUTLIER) cc_final: 0.7035 (mtm180)
REVERT: B 285 MET cc_start: 0.6905 (tpt) cc_final: 0.6682 (tpt)
REVERT: B 304 LYS cc_start: 0.7001 (mtmt) cc_final: 0.6667 (mtmm)
REVERT: C 110 ARG cc_start: 0.7423 (OUTLIER) cc_final: 0.7054 (mtm180)
REVERT: C 250 TYR cc_start: 0.6538 (m-80) cc_final: 0.6055 (m-80)
REVERT: C 304 LYS cc_start: 0.7442 (mtmm) cc_final: 0.6896 (mtmt)
REVERT: D 110 ARG cc_start: 0.7457 (OUTLIER) cc_final: 0.7059 (mtm180)
REVERT: D 295 SER cc_start: 0.6110 (OUTLIER) cc_final: 0.5282 (t)
REVERT: D 318 PHE cc_start: 0.7574 (OUTLIER) cc_final: 0.7142 (p90)
REVERT: E 110 ARG cc_start: 0.7337 (OUTLIER) cc_final: 0.7014 (mtt180)
REVERT: E 295 SER cc_start: 0.6242 (OUTLIER) cc_final: 0.5454 (t)
REVERT: E 304 LYS cc_start: 0.7656 (mtmm) cc_final: 0.7113 (mtmt)
outliers start: 65
outliers final: 31
residues processed: 194
average time/residue: 0.2763
time to fit residues: 76.6743
Evaluate side-chains
178 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 42
poor density : 136
time to evaluate : 1.407
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 61 VAL
Chi-restraints excluded: chain A residue 128 SER
Chi-restraints excluded: chain A residue 181 TRP
Chi-restraints excluded: chain A residue 215 TYR
Chi-restraints excluded: chain A residue 247 LEU
Chi-restraints excluded: chain A residue 295 SER
Chi-restraints excluded: chain A residue 318 PHE
Chi-restraints excluded: chain B residue 48 TYR
Chi-restraints excluded: chain B residue 110 ARG
Chi-restraints excluded: chain B residue 128 SER
Chi-restraints excluded: chain B residue 133 VAL
Chi-restraints excluded: chain B residue 181 TRP
Chi-restraints excluded: chain B residue 191 THR
Chi-restraints excluded: chain B residue 306 ILE
Chi-restraints excluded: chain B residue 432 PHE
Chi-restraints excluded: chain C residue 61 VAL
Chi-restraints excluded: chain C residue 104 SER
Chi-restraints excluded: chain C residue 110 ARG
Chi-restraints excluded: chain C residue 128 SER
Chi-restraints excluded: chain C residue 133 VAL
Chi-restraints excluded: chain C residue 181 TRP
Chi-restraints excluded: chain C residue 215 TYR
Chi-restraints excluded: chain C residue 234 LEU
Chi-restraints excluded: chain C residue 242 VAL
Chi-restraints excluded: chain C residue 306 ILE
Chi-restraints excluded: chain C residue 316 PHE
Chi-restraints excluded: chain C residue 432 PHE
Chi-restraints excluded: chain D residue 110 ARG
Chi-restraints excluded: chain D residue 128 SER
Chi-restraints excluded: chain D residue 181 TRP
Chi-restraints excluded: chain D residue 215 TYR
Chi-restraints excluded: chain D residue 295 SER
Chi-restraints excluded: chain D residue 306 ILE
Chi-restraints excluded: chain D residue 318 PHE
Chi-restraints excluded: chain E residue 110 ARG
Chi-restraints excluded: chain E residue 128 SER
Chi-restraints excluded: chain E residue 181 TRP
Chi-restraints excluded: chain E residue 215 TYR
Chi-restraints excluded: chain E residue 242 VAL
Chi-restraints excluded: chain E residue 295 SER
Chi-restraints excluded: chain E residue 316 PHE
Chi-restraints excluded: chain E residue 432 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 155
random chunks:
chunk 99 optimal weight: 1.9990
chunk 146 optimal weight: 20.0000
chunk 134 optimal weight: 0.3980
chunk 65 optimal weight: 2.9990
chunk 71 optimal weight: 2.9990
chunk 63 optimal weight: 0.0670
chunk 95 optimal weight: 3.9990
chunk 154 optimal weight: 8.9990
chunk 101 optimal weight: 3.9990
chunk 72 optimal weight: 0.9980
chunk 1 optimal weight: 0.9990
overall best weight: 0.8922
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4530 r_free = 0.4530 target = 0.240412 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.4206 r_free = 0.4206 target = 0.204024 restraints weight = 13084.490|
|-----------------------------------------------------------------------------|
r_work (start): 0.4188 rms_B_bonded: 1.26
r_work: 0.3819 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.3568 rms_B_bonded: 4.49 restraints_weight: 0.2500
r_work (final): 0.3568
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7813
moved from start: 0.1909
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.035 13545 Z= 0.198
Angle : 0.628 10.820 18435 Z= 0.302
Chirality : 0.045 0.244 2185
Planarity : 0.003 0.025 2235
Dihedral : 9.555 61.523 2270
Min Nonbonded Distance : 2.245
Molprobity Statistics.
All-atom Clashscore : 7.20
Ramachandran Plot:
Outliers : 0.32 %
Allowed : 3.27 %
Favored : 96.41 %
Rotamer:
Outliers : 5.66 %
Allowed : 30.63 %
Favored : 63.71 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 0.12 (0.22), residues: 1560
helix: 2.56 (0.23), residues: 500
sheet: -0.70 (0.26), residues: 340
loop : -1.37 (0.24), residues: 720
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.018 0.002 TRP B 261
HIS 0.003 0.001 HIS B 131
PHE 0.018 0.002 PHE B 316
TYR 0.010 0.001 TYR A 121
ARG 0.004 0.000 ARG D 221
*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
3120 Ramachandran restraints generated.
1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
3120 Ramachandran restraints generated.
1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
216 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 81
poor density : 135
time to evaluate : 1.442
Fit side-chains
REVERT: A 48 TYR cc_start: -0.0304 (OUTLIER) cc_final: -0.2342 (m-80)
REVERT: A 234 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.8080 (tp)
REVERT: A 247 LEU cc_start: 0.7307 (OUTLIER) cc_final: 0.7059 (tt)
REVERT: A 318 PHE cc_start: 0.7820 (OUTLIER) cc_final: 0.7045 (p90)
REVERT: B 48 TYR cc_start: -0.0399 (OUTLIER) cc_final: -0.1626 (m-10)
REVERT: B 105 PHE cc_start: 0.5576 (OUTLIER) cc_final: 0.5363 (m-80)
REVERT: B 110 ARG cc_start: 0.7448 (OUTLIER) cc_final: 0.7063 (mtm180)
REVERT: B 255 PHE cc_start: 0.5497 (OUTLIER) cc_final: 0.4709 (m-80)
REVERT: B 304 LYS cc_start: 0.7279 (mtmt) cc_final: 0.6922 (mtmm)
REVERT: C 48 TYR cc_start: -0.0045 (OUTLIER) cc_final: -0.2419 (m-80)
REVERT: C 110 ARG cc_start: 0.7490 (OUTLIER) cc_final: 0.7101 (mtm180)
REVERT: C 304 LYS cc_start: 0.7488 (mtmm) cc_final: 0.6839 (mtmt)
REVERT: D 48 TYR cc_start: -0.0127 (OUTLIER) cc_final: -0.1207 (m-10)
REVERT: D 110 ARG cc_start: 0.7458 (OUTLIER) cc_final: 0.7034 (mtm180)
REVERT: D 255 PHE cc_start: 0.5680 (OUTLIER) cc_final: 0.4894 (m-80)
REVERT: D 318 PHE cc_start: 0.7586 (OUTLIER) cc_final: 0.7148 (p90)
REVERT: E 48 TYR cc_start: 0.0034 (OUTLIER) cc_final: -0.2749 (m-80)
REVERT: E 110 ARG cc_start: 0.7482 (OUTLIER) cc_final: 0.7187 (mtt180)
REVERT: E 304 LYS cc_start: 0.7640 (mtmm) cc_final: 0.7194 (mtmt)
outliers start: 81
outliers final: 41
residues processed: 205
average time/residue: 0.2826
time to fit residues: 81.8982
Evaluate side-chains
189 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 57
poor density : 132
time to evaluate : 1.445
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 48 TYR
Chi-restraints excluded: chain A residue 61 VAL
Chi-restraints excluded: chain A residue 128 SER
Chi-restraints excluded: chain A residue 181 TRP
Chi-restraints excluded: chain A residue 211 THR
Chi-restraints excluded: chain A residue 218 LEU
Chi-restraints excluded: chain A residue 234 LEU
Chi-restraints excluded: chain A residue 247 LEU
Chi-restraints excluded: chain A residue 306 ILE
Chi-restraints excluded: chain A residue 318 PHE
Chi-restraints excluded: chain B residue 48 TYR
Chi-restraints excluded: chain B residue 105 PHE
Chi-restraints excluded: chain B residue 110 ARG
Chi-restraints excluded: chain B residue 128 SER
Chi-restraints excluded: chain B residue 133 VAL
Chi-restraints excluded: chain B residue 181 TRP
Chi-restraints excluded: chain B residue 191 THR
Chi-restraints excluded: chain B residue 211 THR
Chi-restraints excluded: chain B residue 234 LEU
Chi-restraints excluded: chain B residue 255 PHE
Chi-restraints excluded: chain B residue 316 PHE
Chi-restraints excluded: chain B residue 432 PHE
Chi-restraints excluded: chain C residue 48 TYR
Chi-restraints excluded: chain C residue 61 VAL
Chi-restraints excluded: chain C residue 104 SER
Chi-restraints excluded: chain C residue 110 ARG
Chi-restraints excluded: chain C residue 128 SER
Chi-restraints excluded: chain C residue 133 VAL
Chi-restraints excluded: chain C residue 181 TRP
Chi-restraints excluded: chain C residue 234 LEU
Chi-restraints excluded: chain C residue 242 VAL
Chi-restraints excluded: chain C residue 306 ILE
Chi-restraints excluded: chain C residue 316 PHE
Chi-restraints excluded: chain C residue 432 PHE
Chi-restraints excluded: chain D residue 48 TYR
Chi-restraints excluded: chain D residue 104 SER
Chi-restraints excluded: chain D residue 110 ARG
Chi-restraints excluded: chain D residue 128 SER
Chi-restraints excluded: chain D residue 181 TRP
Chi-restraints excluded: chain D residue 191 THR
Chi-restraints excluded: chain D residue 211 THR
Chi-restraints excluded: chain D residue 234 LEU
Chi-restraints excluded: chain D residue 255 PHE
Chi-restraints excluded: chain D residue 306 ILE
Chi-restraints excluded: chain D residue 318 PHE
Chi-restraints excluded: chain E residue 48 TYR
Chi-restraints excluded: chain E residue 65 LEU
Chi-restraints excluded: chain E residue 104 SER
Chi-restraints excluded: chain E residue 110 ARG
Chi-restraints excluded: chain E residue 128 SER
Chi-restraints excluded: chain E residue 181 TRP
Chi-restraints excluded: chain E residue 191 THR
Chi-restraints excluded: chain E residue 211 THR
Chi-restraints excluded: chain E residue 218 LEU
Chi-restraints excluded: chain E residue 242 VAL
Chi-restraints excluded: chain E residue 316 PHE
Chi-restraints excluded: chain E residue 432 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 155
random chunks:
chunk 80 optimal weight: 4.9990
chunk 58 optimal weight: 0.9990
chunk 134 optimal weight: 0.5980
chunk 25 optimal weight: 3.9990
chunk 141 optimal weight: 7.9990
chunk 79 optimal weight: 2.9990
chunk 91 optimal weight: 20.0000
chunk 66 optimal weight: 0.5980
chunk 89 optimal weight: 1.9990
chunk 131 optimal weight: 2.9990
chunk 55 optimal weight: 20.0000
overall best weight: 1.4386
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4890 r_free = 0.4890 target = 0.269829 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4729 r_free = 0.4729 target = 0.251130 restraints weight = 13610.167|
|-----------------------------------------------------------------------------|
r_work (start): 0.4671 rms_B_bonded: 0.66
r_work: 0.4427 rms_B_bonded: 1.60 restraints_weight: 0.5000
r_work: 0.4143 rms_B_bonded: 3.50 restraints_weight: 0.2500
r_work (final): 0.4143
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7531
moved from start: 0.2226
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.004 0.037 13545 Z= 0.257
Angle : 0.675 10.997 18435 Z= 0.323
Chirality : 0.046 0.250 2185
Planarity : 0.003 0.026 2235
Dihedral : 9.186 56.036 2270
Min Nonbonded Distance : 2.235
Molprobity Statistics.
All-atom Clashscore : 7.46
Ramachandran Plot:
Outliers : 0.32 %
Allowed : 3.53 %
Favored : 96.15 %
Rotamer:
Outliers : 6.15 %
Allowed : 30.70 %
Favored : 63.15 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 0.07 (0.22), residues: 1560
helix: 2.61 (0.24), residues: 500
sheet: -0.76 (0.25), residues: 340
loop : -1.46 (0.24), residues: 720
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.017 0.002 TRP D 261
HIS 0.005 0.001 HIS B 131
PHE 0.028 0.002 PHE A 426
TYR 0.010 0.001 TYR A 309
ARG 0.007 0.001 ARG C 91
*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
3120 Ramachandran restraints generated.
1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
3120 Ramachandran restraints generated.
1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
235 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 88
poor density : 147
time to evaluate : 1.331
Fit side-chains
REVERT: A 48 TYR cc_start: 0.0620 (OUTLIER) cc_final: -0.1787 (m-80)
REVERT: A 234 LEU cc_start: 0.8257 (OUTLIER) cc_final: 0.7928 (tp)
REVERT: A 318 PHE cc_start: 0.7084 (OUTLIER) cc_final: 0.6418 (p90)
REVERT: B 48 TYR cc_start: 0.0476 (OUTLIER) cc_final: -0.0994 (m-10)
REVERT: B 110 ARG cc_start: 0.7450 (OUTLIER) cc_final: 0.7043 (mtm180)
REVERT: B 255 PHE cc_start: 0.5758 (OUTLIER) cc_final: 0.4830 (m-80)
REVERT: C 48 TYR cc_start: 0.1260 (OUTLIER) cc_final: -0.1853 (m-80)
REVERT: C 110 ARG cc_start: 0.7506 (OUTLIER) cc_final: 0.7133 (mtm180)
REVERT: C 255 PHE cc_start: 0.5602 (OUTLIER) cc_final: 0.4975 (m-80)
REVERT: C 304 LYS cc_start: 0.7716 (mtmm) cc_final: 0.7267 (mtmt)
REVERT: D 48 TYR cc_start: 0.0807 (OUTLIER) cc_final: -0.0640 (m-10)
REVERT: D 110 ARG cc_start: 0.7561 (OUTLIER) cc_final: 0.7107 (mtm180)
REVERT: D 255 PHE cc_start: 0.5999 (OUTLIER) cc_final: 0.5037 (m-80)
REVERT: D 318 PHE cc_start: 0.6892 (OUTLIER) cc_final: 0.6588 (p90)
REVERT: E 48 TYR cc_start: 0.0772 (OUTLIER) cc_final: -0.2278 (m-80)
REVERT: E 110 ARG cc_start: 0.7532 (OUTLIER) cc_final: 0.7181 (mtt180)
REVERT: E 304 LYS cc_start: 0.7827 (mtmm) cc_final: 0.7610 (mtmm)
outliers start: 88
outliers final: 49
residues processed: 220
average time/residue: 0.2494
time to fit residues: 80.4296
Evaluate side-chains
198 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 64
poor density : 134
time to evaluate : 1.477
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 48 TYR
Chi-restraints excluded: chain A residue 61 VAL
Chi-restraints excluded: chain A residue 104 SER
Chi-restraints excluded: chain A residue 106 THR
Chi-restraints excluded: chain A residue 128 SER
Chi-restraints excluded: chain A residue 181 TRP
Chi-restraints excluded: chain A residue 211 THR
Chi-restraints excluded: chain A residue 218 LEU
Chi-restraints excluded: chain A residue 234 LEU
Chi-restraints excluded: chain A residue 242 VAL
Chi-restraints excluded: chain A residue 255 PHE
Chi-restraints excluded: chain A residue 318 PHE
Chi-restraints excluded: chain B residue 48 TYR
Chi-restraints excluded: chain B residue 104 SER
Chi-restraints excluded: chain B residue 110 ARG
Chi-restraints excluded: chain B residue 128 SER
Chi-restraints excluded: chain B residue 133 VAL
Chi-restraints excluded: chain B residue 181 TRP
Chi-restraints excluded: chain B residue 191 THR
Chi-restraints excluded: chain B residue 205 LEU
Chi-restraints excluded: chain B residue 211 THR
Chi-restraints excluded: chain B residue 234 LEU
Chi-restraints excluded: chain B residue 242 VAL
Chi-restraints excluded: chain B residue 255 PHE
Chi-restraints excluded: chain B residue 306 ILE
Chi-restraints excluded: chain B residue 316 PHE
Chi-restraints excluded: chain B residue 432 PHE
Chi-restraints excluded: chain C residue 48 TYR
Chi-restraints excluded: chain C residue 61 VAL
Chi-restraints excluded: chain C residue 104 SER
Chi-restraints excluded: chain C residue 110 ARG
Chi-restraints excluded: chain C residue 128 SER
Chi-restraints excluded: chain C residue 133 VAL
Chi-restraints excluded: chain C residue 181 TRP
Chi-restraints excluded: chain C residue 211 THR
Chi-restraints excluded: chain C residue 255 PHE
Chi-restraints excluded: chain C residue 306 ILE
Chi-restraints excluded: chain C residue 316 PHE
Chi-restraints excluded: chain C residue 432 PHE
Chi-restraints excluded: chain D residue 48 TYR
Chi-restraints excluded: chain D residue 65 LEU
Chi-restraints excluded: chain D residue 104 SER
Chi-restraints excluded: chain D residue 110 ARG
Chi-restraints excluded: chain D residue 128 SER
Chi-restraints excluded: chain D residue 181 TRP
Chi-restraints excluded: chain D residue 205 LEU
Chi-restraints excluded: chain D residue 218 LEU
Chi-restraints excluded: chain D residue 234 LEU
Chi-restraints excluded: chain D residue 255 PHE
Chi-restraints excluded: chain D residue 306 ILE
Chi-restraints excluded: chain D residue 316 PHE
Chi-restraints excluded: chain D residue 318 PHE
Chi-restraints excluded: chain E residue 48 TYR
Chi-restraints excluded: chain E residue 65 LEU
Chi-restraints excluded: chain E residue 104 SER
Chi-restraints excluded: chain E residue 110 ARG
Chi-restraints excluded: chain E residue 128 SER
Chi-restraints excluded: chain E residue 181 TRP
Chi-restraints excluded: chain E residue 205 LEU
Chi-restraints excluded: chain E residue 211 THR
Chi-restraints excluded: chain E residue 218 LEU
Chi-restraints excluded: chain E residue 242 VAL
Chi-restraints excluded: chain E residue 316 PHE
Chi-restraints excluded: chain E residue 432 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 155
random chunks:
chunk 18 optimal weight: 3.9990
chunk 80 optimal weight: 2.9990
chunk 113 optimal weight: 9.9990
chunk 17 optimal weight: 0.8980
chunk 28 optimal weight: 50.0000
chunk 103 optimal weight: 2.9990
chunk 112 optimal weight: 2.9990
chunk 141 optimal weight: 6.9990
chunk 140 optimal weight: 5.9990
chunk 68 optimal weight: 2.9990
chunk 79 optimal weight: 0.9990
overall best weight: 2.1788
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4490 r_free = 0.4490 target = 0.235561 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4222 r_free = 0.4222 target = 0.205590 restraints weight = 13272.336|
|-----------------------------------------------------------------------------|
r_work (start): 0.4224 rms_B_bonded: 1.02
r_work: 0.3877 rms_B_bonded: 1.78 restraints_weight: 0.5000
r_work: 0.3584 rms_B_bonded: 3.63 restraints_weight: 0.2500
r_work (final): 0.3584
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7847
moved from start: 0.2676
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.005 0.044 13545 Z= 0.348
Angle : 0.730 10.837 18435 Z= 0.352
Chirality : 0.048 0.248 2185
Planarity : 0.004 0.027 2235
Dihedral : 8.975 53.214 2270
Min Nonbonded Distance : 2.193
Molprobity Statistics.
All-atom Clashscore : 8.72
Ramachandran Plot:
Outliers : 0.32 %
Allowed : 4.29 %
Favored : 95.38 %
Rotamer:
Outliers : 6.64 %
Allowed : 30.35 %
Favored : 63.01 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: -0.15 (0.22), residues: 1560
helix: 2.57 (0.24), residues: 500
sheet: -0.57 (0.26), residues: 310
loop : -1.86 (0.23), residues: 750
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.017 0.002 TRP E 261
HIS 0.006 0.001 HIS B 131
PHE 0.020 0.002 PHE A 426
TYR 0.012 0.002 TYR A 309
ARG 0.006 0.001 ARG B 91
*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
3120 Ramachandran restraints generated.
1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
3120 Ramachandran restraints generated.
1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
235 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 95
poor density : 140
time to evaluate : 1.389
Fit side-chains
REVERT: A 48 TYR cc_start: 0.0084 (OUTLIER) cc_final: -0.2051 (m-80)
REVERT: A 234 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.8023 (tp)
REVERT: A 318 PHE cc_start: 0.7764 (OUTLIER) cc_final: 0.6967 (p90)
REVERT: B 48 TYR cc_start: -0.0070 (OUTLIER) cc_final: -0.1440 (m-10)
REVERT: B 102 ASN cc_start: 0.5922 (p0) cc_final: 0.5435 (p0)
REVERT: B 110 ARG cc_start: 0.7582 (OUTLIER) cc_final: 0.7275 (mtm180)
REVERT: C 48 TYR cc_start: 0.0182 (OUTLIER) cc_final: -0.2298 (m-80)
REVERT: C 102 ASN cc_start: 0.5952 (p0) cc_final: 0.5527 (p0)
REVERT: C 110 ARG cc_start: 0.7693 (OUTLIER) cc_final: 0.7406 (mtm180)
REVERT: C 255 PHE cc_start: 0.5669 (OUTLIER) cc_final: 0.4760 (m-80)
REVERT: C 304 LYS cc_start: 0.7670 (mtmm) cc_final: 0.7138 (mtmt)
REVERT: D 48 TYR cc_start: -0.0005 (OUTLIER) cc_final: -0.1154 (m-10)
REVERT: D 110 ARG cc_start: 0.7629 (OUTLIER) cc_final: 0.7309 (mtm180)
REVERT: D 318 PHE cc_start: 0.7560 (OUTLIER) cc_final: 0.7195 (p90)
REVERT: E 48 TYR cc_start: -0.0018 (OUTLIER) cc_final: -0.1337 (m-10)
REVERT: E 110 ARG cc_start: 0.7591 (OUTLIER) cc_final: 0.7285 (mtt180)
REVERT: E 255 PHE cc_start: 0.5874 (OUTLIER) cc_final: 0.4835 (m-80)
REVERT: E 304 LYS cc_start: 0.7719 (mtmm) cc_final: 0.7457 (mtmm)
outliers start: 95
outliers final: 67
residues processed: 215
average time/residue: 0.2456
time to fit residues: 77.5525
Evaluate side-chains
213 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 81
poor density : 132
time to evaluate : 1.539
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 48 TYR
Chi-restraints excluded: chain A residue 61 VAL
Chi-restraints excluded: chain A residue 65 LEU
Chi-restraints excluded: chain A residue 68 ASP
Chi-restraints excluded: chain A residue 104 SER
Chi-restraints excluded: chain A residue 106 THR
Chi-restraints excluded: chain A residue 128 SER
Chi-restraints excluded: chain A residue 142 LEU
Chi-restraints excluded: chain A residue 161 ASN
Chi-restraints excluded: chain A residue 181 TRP
Chi-restraints excluded: chain A residue 211 THR
Chi-restraints excluded: chain A residue 218 LEU
Chi-restraints excluded: chain A residue 234 LEU
Chi-restraints excluded: chain A residue 242 VAL
Chi-restraints excluded: chain A residue 255 PHE
Chi-restraints excluded: chain A residue 258 VAL
Chi-restraints excluded: chain A residue 318 PHE
Chi-restraints excluded: chain B residue 48 TYR
Chi-restraints excluded: chain B residue 65 LEU
Chi-restraints excluded: chain B residue 104 SER
Chi-restraints excluded: chain B residue 110 ARG
Chi-restraints excluded: chain B residue 128 SER
Chi-restraints excluded: chain B residue 133 VAL
Chi-restraints excluded: chain B residue 140 ILE
Chi-restraints excluded: chain B residue 181 TRP
Chi-restraints excluded: chain B residue 191 THR
Chi-restraints excluded: chain B residue 205 LEU
Chi-restraints excluded: chain B residue 211 THR
Chi-restraints excluded: chain B residue 218 LEU
Chi-restraints excluded: chain B residue 234 LEU
Chi-restraints excluded: chain B residue 242 VAL
Chi-restraints excluded: chain B residue 306 ILE
Chi-restraints excluded: chain B residue 316 PHE
Chi-restraints excluded: chain B residue 432 PHE
Chi-restraints excluded: chain C residue 48 TYR
Chi-restraints excluded: chain C residue 61 VAL
Chi-restraints excluded: chain C residue 65 LEU
Chi-restraints excluded: chain C residue 68 ASP
Chi-restraints excluded: chain C residue 104 SER
Chi-restraints excluded: chain C residue 110 ARG
Chi-restraints excluded: chain C residue 128 SER
Chi-restraints excluded: chain C residue 133 VAL
Chi-restraints excluded: chain C residue 181 TRP
Chi-restraints excluded: chain C residue 211 THR
Chi-restraints excluded: chain C residue 255 PHE
Chi-restraints excluded: chain C residue 306 ILE
Chi-restraints excluded: chain C residue 316 PHE
Chi-restraints excluded: chain C residue 432 PHE
Chi-restraints excluded: chain D residue 48 TYR
Chi-restraints excluded: chain D residue 65 LEU
Chi-restraints excluded: chain D residue 104 SER
Chi-restraints excluded: chain D residue 110 ARG
Chi-restraints excluded: chain D residue 128 SER
Chi-restraints excluded: chain D residue 161 ASN
Chi-restraints excluded: chain D residue 181 TRP
Chi-restraints excluded: chain D residue 205 LEU
Chi-restraints excluded: chain D residue 211 THR
Chi-restraints excluded: chain D residue 218 LEU
Chi-restraints excluded: chain D residue 234 LEU
Chi-restraints excluded: chain D residue 242 VAL
Chi-restraints excluded: chain D residue 306 ILE
Chi-restraints excluded: chain D residue 312 ILE
Chi-restraints excluded: chain D residue 316 PHE
Chi-restraints excluded: chain D residue 318 PHE
Chi-restraints excluded: chain E residue 48 TYR
Chi-restraints excluded: chain E residue 65 LEU
Chi-restraints excluded: chain E residue 104 SER
Chi-restraints excluded: chain E residue 110 ARG
Chi-restraints excluded: chain E residue 128 SER
Chi-restraints excluded: chain E residue 133 VAL
Chi-restraints excluded: chain E residue 140 ILE
Chi-restraints excluded: chain E residue 161 ASN
Chi-restraints excluded: chain E residue 181 TRP
Chi-restraints excluded: chain E residue 205 LEU
Chi-restraints excluded: chain E residue 211 THR
Chi-restraints excluded: chain E residue 218 LEU
Chi-restraints excluded: chain E residue 219 VAL
Chi-restraints excluded: chain E residue 220 THR
Chi-restraints excluded: chain E residue 255 PHE
Chi-restraints excluded: chain E residue 316 PHE
Chi-restraints excluded: chain E residue 432 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 155
random chunks:
chunk 43 optimal weight: 0.9980
chunk 8 optimal weight: 0.8980
chunk 130 optimal weight: 0.0270
chunk 69 optimal weight: 0.7980
chunk 79 optimal weight: 0.9990
chunk 78 optimal weight: 0.7980
chunk 34 optimal weight: 3.9990
chunk 113 optimal weight: 9.9990
chunk 38 optimal weight: 0.9980
chunk 5 optimal weight: 3.9990
chunk 125 optimal weight: 0.8980
overall best weight: 0.6838
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 204 HIS
Total number of N/Q/H flips: 1
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4519 r_free = 0.4519 target = 0.239567 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.4259 r_free = 0.4259 target = 0.210035 restraints weight = 13211.527|
|-----------------------------------------------------------------------------|
r_work (start): 0.4263 rms_B_bonded: 1.00
r_work: 0.3938 rms_B_bonded: 1.75 restraints_weight: 0.5000
r_work: 0.3629 rms_B_bonded: 4.02 restraints_weight: 0.2500
r_work (final): 0.3629
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7771
moved from start: 0.2629
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.025 13545 Z= 0.184
Angle : 0.645 11.156 18435 Z= 0.309
Chirality : 0.044 0.232 2185
Planarity : 0.003 0.030 2235
Dihedral : 8.428 50.690 2270
Min Nonbonded Distance : 2.253
Molprobity Statistics.
All-atom Clashscore : 8.45
Ramachandran Plot:
Outliers : 0.32 %
Allowed : 3.53 %
Favored : 96.15 %
Rotamer:
Outliers : 4.41 %
Allowed : 32.52 %
Favored : 63.08 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: -0.05 (0.22), residues: 1560
helix: 2.60 (0.24), residues: 500
sheet: -0.88 (0.24), residues: 385
loop : -1.60 (0.25), residues: 675
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.019 0.002 TRP D 261
HIS 0.005 0.001 HIS E 204
PHE 0.017 0.001 PHE D 316
TYR 0.015 0.001 TYR D 121
ARG 0.006 0.000 ARG E 91
*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
3120 Ramachandran restraints generated.
1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
3120 Ramachandran restraints generated.
1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
209 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 63
poor density : 146
time to evaluate : 1.506
Fit side-chains
REVERT: A 48 TYR cc_start: -0.0005 (OUTLIER) cc_final: -0.2123 (m-80)
REVERT: A 102 ASN cc_start: 0.6079 (p0) cc_final: 0.5568 (p0)
REVERT: A 108 ASP cc_start: 0.8096 (m-30) cc_final: 0.7872 (m-30)
REVERT: A 234 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.7978 (tp)
REVERT: A 318 PHE cc_start: 0.7714 (OUTLIER) cc_final: 0.7011 (p90)
REVERT: B 48 TYR cc_start: 0.0071 (OUTLIER) cc_final: -0.1417 (m-10)
REVERT: B 102 ASN cc_start: 0.5936 (p0) cc_final: 0.5412 (p0)
REVERT: B 110 ARG cc_start: 0.7472 (OUTLIER) cc_final: 0.7117 (mtm180)
REVERT: C 48 TYR cc_start: 0.0188 (OUTLIER) cc_final: -0.2317 (m-80)
REVERT: C 102 ASN cc_start: 0.5902 (p0) cc_final: 0.5508 (p0)
REVERT: C 108 ASP cc_start: 0.8008 (m-30) cc_final: 0.7775 (m-30)
REVERT: C 110 ARG cc_start: 0.7729 (OUTLIER) cc_final: 0.7435 (mtm180)
REVERT: D 48 TYR cc_start: 0.0048 (OUTLIER) cc_final: -0.1221 (m-10)
REVERT: D 102 ASN cc_start: 0.5824 (p0) cc_final: 0.5402 (p0)
REVERT: D 255 PHE cc_start: 0.6052 (OUTLIER) cc_final: 0.5556 (m-80)
REVERT: D 318 PHE cc_start: 0.7500 (OUTLIER) cc_final: 0.7081 (p90)
REVERT: E 48 TYR cc_start: 0.0158 (OUTLIER) cc_final: -0.1491 (m-80)
REVERT: E 108 ASP cc_start: 0.8166 (m-30) cc_final: 0.7889 (m-30)
REVERT: E 110 ARG cc_start: 0.7507 (OUTLIER) cc_final: 0.7168 (mtt180)
REVERT: E 255 PHE cc_start: 0.5827 (OUTLIER) cc_final: 0.5074 (m-80)
REVERT: E 304 LYS cc_start: 0.7717 (mtmm) cc_final: 0.7451 (mtmm)
outliers start: 63
outliers final: 40
residues processed: 193
average time/residue: 0.2335
time to fit residues: 68.1316
Evaluate side-chains
196 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 53
poor density : 143
time to evaluate : 1.372
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 48 TYR
Chi-restraints excluded: chain A residue 61 VAL
Chi-restraints excluded: chain A residue 104 SER
Chi-restraints excluded: chain A residue 128 SER
Chi-restraints excluded: chain A residue 142 LEU
Chi-restraints excluded: chain A residue 181 TRP
Chi-restraints excluded: chain A residue 234 LEU
Chi-restraints excluded: chain A residue 242 VAL
Chi-restraints excluded: chain A residue 255 PHE
Chi-restraints excluded: chain A residue 258 VAL
Chi-restraints excluded: chain A residue 318 PHE
Chi-restraints excluded: chain B residue 48 TYR
Chi-restraints excluded: chain B residue 110 ARG
Chi-restraints excluded: chain B residue 128 SER
Chi-restraints excluded: chain B residue 133 VAL
Chi-restraints excluded: chain B residue 181 TRP
Chi-restraints excluded: chain B residue 191 THR
Chi-restraints excluded: chain B residue 205 LEU
Chi-restraints excluded: chain B residue 215 TYR
Chi-restraints excluded: chain B residue 234 LEU
Chi-restraints excluded: chain B residue 242 VAL
Chi-restraints excluded: chain B residue 306 ILE
Chi-restraints excluded: chain B residue 316 PHE
Chi-restraints excluded: chain B residue 432 PHE
Chi-restraints excluded: chain C residue 48 TYR
Chi-restraints excluded: chain C residue 61 VAL
Chi-restraints excluded: chain C residue 104 SER
Chi-restraints excluded: chain C residue 110 ARG
Chi-restraints excluded: chain C residue 128 SER
Chi-restraints excluded: chain C residue 133 VAL
Chi-restraints excluded: chain C residue 181 TRP
Chi-restraints excluded: chain C residue 316 PHE
Chi-restraints excluded: chain C residue 432 PHE
Chi-restraints excluded: chain D residue 48 TYR
Chi-restraints excluded: chain D residue 104 SER
Chi-restraints excluded: chain D residue 128 SER
Chi-restraints excluded: chain D residue 181 TRP
Chi-restraints excluded: chain D residue 205 LEU
Chi-restraints excluded: chain D residue 215 TYR
Chi-restraints excluded: chain D residue 234 LEU
Chi-restraints excluded: chain D residue 255 PHE
Chi-restraints excluded: chain D residue 306 ILE
Chi-restraints excluded: chain D residue 316 PHE
Chi-restraints excluded: chain D residue 318 PHE
Chi-restraints excluded: chain E residue 48 TYR
Chi-restraints excluded: chain E residue 110 ARG
Chi-restraints excluded: chain E residue 128 SER
Chi-restraints excluded: chain E residue 181 TRP
Chi-restraints excluded: chain E residue 205 LEU
Chi-restraints excluded: chain E residue 220 THR
Chi-restraints excluded: chain E residue 255 PHE
Chi-restraints excluded: chain E residue 316 PHE
Chi-restraints excluded: chain E residue 432 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 155
random chunks:
chunk 104 optimal weight: 1.9990
chunk 58 optimal weight: 0.8980
chunk 131 optimal weight: 3.9990
chunk 65 optimal weight: 5.9990
chunk 22 optimal weight: 10.0000
chunk 95 optimal weight: 3.9990
chunk 29 optimal weight: 20.0000
chunk 20 optimal weight: 9.9990
chunk 116 optimal weight: 9.9990
chunk 35 optimal weight: 0.9990
chunk 13 optimal weight: 0.9990
overall best weight: 1.7788
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 204 HIS
Total number of N/Q/H flips: 1
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4498 r_free = 0.4498 target = 0.236881 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4217 r_free = 0.4217 target = 0.205138 restraints weight = 13228.707|
|-----------------------------------------------------------------------------|
r_work (start): 0.4219 rms_B_bonded: 1.09
r_work: 0.3866 rms_B_bonded: 1.90 restraints_weight: 0.5000
r_work: 0.3570 rms_B_bonded: 4.00 restraints_weight: 0.2500
r_work (final): 0.3570
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7864
moved from start: 0.2849
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.005 0.039 13545 Z= 0.302
Angle : 0.695 10.950 18435 Z= 0.334
Chirality : 0.047 0.236 2185
Planarity : 0.004 0.029 2235
Dihedral : 8.319 48.014 2270
Min Nonbonded Distance : 2.261
Molprobity Statistics.
All-atom Clashscore : 8.84
Ramachandran Plot:
Outliers : 0.32 %
Allowed : 3.97 %
Favored : 95.71 %
Rotamer:
Outliers : 4.97 %
Allowed : 31.89 %
Favored : 63.15 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: -0.03 (0.22), residues: 1560
helix: 2.61 (0.24), residues: 500
sheet: -0.71 (0.24), residues: 335
loop : -1.65 (0.23), residues: 725
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.018 0.002 TRP B 261
HIS 0.004 0.001 HIS E 204
PHE 0.017 0.002 PHE D 316
TYR 0.010 0.001 TYR C 433
ARG 0.004 0.000 ARG C 91
*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
3120 Ramachandran restraints generated.
1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
3120 Ramachandran restraints generated.
1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
212 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 71
poor density : 141
time to evaluate : 1.532
Fit side-chains
REVERT: A 48 TYR cc_start: -0.0170 (OUTLIER) cc_final: -0.2091 (m-80)
REVERT: A 102 ASN cc_start: 0.6201 (p0) cc_final: 0.5665 (p0)
REVERT: A 234 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.8027 (tp)
REVERT: A 318 PHE cc_start: 0.7773 (OUTLIER) cc_final: 0.7182 (p90)
REVERT: B 48 TYR cc_start: -0.0282 (OUTLIER) cc_final: -0.1765 (m-80)
REVERT: B 102 ASN cc_start: 0.6032 (p0) cc_final: 0.5512 (p0)
REVERT: B 105 PHE cc_start: 0.6010 (OUTLIER) cc_final: 0.5727 (m-80)
REVERT: B 110 ARG cc_start: 0.7587 (OUTLIER) cc_final: 0.7273 (mtm180)
REVERT: B 255 PHE cc_start: 0.6125 (OUTLIER) cc_final: 0.5483 (m-80)
REVERT: C 48 TYR cc_start: 0.0161 (OUTLIER) cc_final: -0.2272 (m-80)
REVERT: C 102 ASN cc_start: 0.6078 (p0) cc_final: 0.5633 (p0)
REVERT: C 110 ARG cc_start: 0.7720 (OUTLIER) cc_final: 0.7431 (mtm180)
REVERT: C 255 PHE cc_start: 0.5686 (OUTLIER) cc_final: 0.4948 (m-80)
REVERT: D 48 TYR cc_start: -0.0088 (OUTLIER) cc_final: -0.1367 (m-10)
REVERT: D 102 ASN cc_start: 0.5872 (p0) cc_final: 0.5435 (p0)
REVERT: D 110 ARG cc_start: 0.7637 (OUTLIER) cc_final: 0.7331 (mtm180)
REVERT: D 255 PHE cc_start: 0.6011 (OUTLIER) cc_final: 0.5573 (m-80)
REVERT: D 318 PHE cc_start: 0.7660 (OUTLIER) cc_final: 0.7387 (p90)
REVERT: E 48 TYR cc_start: 0.0004 (OUTLIER) cc_final: -0.1462 (m-10)
REVERT: E 110 ARG cc_start: 0.7571 (OUTLIER) cc_final: 0.7289 (mtt180)
REVERT: E 255 PHE cc_start: 0.5982 (OUTLIER) cc_final: 0.5259 (m-80)
outliers start: 71
outliers final: 48
residues processed: 200
average time/residue: 0.2565
time to fit residues: 75.5456
Evaluate side-chains
201 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 65
poor density : 136
time to evaluate : 1.435
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 48 TYR
Chi-restraints excluded: chain A residue 53 ARG
Chi-restraints excluded: chain A residue 61 VAL
Chi-restraints excluded: chain A residue 104 SER
Chi-restraints excluded: chain A residue 110 ARG
Chi-restraints excluded: chain A residue 128 SER
Chi-restraints excluded: chain A residue 142 LEU
Chi-restraints excluded: chain A residue 161 ASN
Chi-restraints excluded: chain A residue 181 TRP
Chi-restraints excluded: chain A residue 218 LEU
Chi-restraints excluded: chain A residue 234 LEU
Chi-restraints excluded: chain A residue 255 PHE
Chi-restraints excluded: chain A residue 258 VAL
Chi-restraints excluded: chain A residue 318 PHE
Chi-restraints excluded: chain B residue 48 TYR
Chi-restraints excluded: chain B residue 65 LEU
Chi-restraints excluded: chain B residue 104 SER
Chi-restraints excluded: chain B residue 105 PHE
Chi-restraints excluded: chain B residue 110 ARG
Chi-restraints excluded: chain B residue 128 SER
Chi-restraints excluded: chain B residue 133 VAL
Chi-restraints excluded: chain B residue 181 TRP
Chi-restraints excluded: chain B residue 191 THR
Chi-restraints excluded: chain B residue 205 LEU
Chi-restraints excluded: chain B residue 234 LEU
Chi-restraints excluded: chain B residue 242 VAL
Chi-restraints excluded: chain B residue 255 PHE
Chi-restraints excluded: chain B residue 306 ILE
Chi-restraints excluded: chain B residue 316 PHE
Chi-restraints excluded: chain B residue 432 PHE
Chi-restraints excluded: chain C residue 48 TYR
Chi-restraints excluded: chain C residue 61 VAL
Chi-restraints excluded: chain C residue 104 SER
Chi-restraints excluded: chain C residue 110 ARG
Chi-restraints excluded: chain C residue 128 SER
Chi-restraints excluded: chain C residue 133 VAL
Chi-restraints excluded: chain C residue 181 TRP
Chi-restraints excluded: chain C residue 255 PHE
Chi-restraints excluded: chain C residue 316 PHE
Chi-restraints excluded: chain C residue 432 PHE
Chi-restraints excluded: chain D residue 48 TYR
Chi-restraints excluded: chain D residue 65 LEU
Chi-restraints excluded: chain D residue 110 ARG
Chi-restraints excluded: chain D residue 128 SER
Chi-restraints excluded: chain D residue 181 TRP
Chi-restraints excluded: chain D residue 205 LEU
Chi-restraints excluded: chain D residue 211 THR
Chi-restraints excluded: chain D residue 220 THR
Chi-restraints excluded: chain D residue 230 THR
Chi-restraints excluded: chain D residue 234 LEU
Chi-restraints excluded: chain D residue 255 PHE
Chi-restraints excluded: chain D residue 312 ILE
Chi-restraints excluded: chain D residue 316 PHE
Chi-restraints excluded: chain D residue 318 PHE
Chi-restraints excluded: chain E residue 48 TYR
Chi-restraints excluded: chain E residue 65 LEU
Chi-restraints excluded: chain E residue 104 SER
Chi-restraints excluded: chain E residue 110 ARG
Chi-restraints excluded: chain E residue 128 SER
Chi-restraints excluded: chain E residue 181 TRP
Chi-restraints excluded: chain E residue 205 LEU
Chi-restraints excluded: chain E residue 220 THR
Chi-restraints excluded: chain E residue 255 PHE
Chi-restraints excluded: chain E residue 316 PHE
Chi-restraints excluded: chain E residue 432 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 155
random chunks:
chunk 133 optimal weight: 0.8980
chunk 145 optimal weight: 7.9990
chunk 56 optimal weight: 9.9990
chunk 33 optimal weight: 2.9990
chunk 134 optimal weight: 0.7980
chunk 27 optimal weight: 5.9990
chunk 0 optimal weight: 10.0000
chunk 29 optimal weight: 20.0000
chunk 99 optimal weight: 0.0470
chunk 124 optimal weight: 7.9990
chunk 69 optimal weight: 0.7980
overall best weight: 1.1080
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
E 204 HIS
Total number of N/Q/H flips: 1
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4511 r_free = 0.4511 target = 0.238668 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 80)----------------|
| r_work = 0.4236 r_free = 0.4236 target = 0.207421 restraints weight = 13167.010|
|-----------------------------------------------------------------------------|
r_work (start): 0.4236 rms_B_bonded: 1.17
r_work: 0.3868 rms_B_bonded: 2.13 restraints_weight: 0.5000
r_work: 0.3554 rms_B_bonded: 4.69 restraints_weight: 0.2500
r_work (final): 0.3554
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7859
moved from start: 0.2868
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.031 13545 Z= 0.220
Angle : 0.661 11.099 18435 Z= 0.317
Chirality : 0.045 0.234 2185
Planarity : 0.003 0.030 2235
Dihedral : 8.008 45.854 2270
Min Nonbonded Distance : 2.298
Molprobity Statistics.
All-atom Clashscore : 8.91
Ramachandran Plot:
Outliers : 0.32 %
Allowed : 2.95 %
Favored : 96.73 %
Rotamer:
Outliers : 4.41 %
Allowed : 32.24 %
Favored : 63.36 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 0.05 (0.22), residues: 1560
helix: 2.62 (0.24), residues: 500
sheet: -0.62 (0.25), residues: 335
loop : -1.57 (0.23), residues: 725
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.019 0.002 TRP B 261
HIS 0.004 0.001 HIS E 204
PHE 0.017 0.002 PHE D 316
TYR 0.013 0.001 TYR C 433
ARG 0.004 0.000 ARG E 91
*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
3120 Ramachandran restraints generated.
1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
3120 Ramachandran restraints generated.
1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
209 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 63
poor density : 146
time to evaluate : 1.446
Fit side-chains
REVERT: A 48 TYR cc_start: -0.0150 (OUTLIER) cc_final: -0.2002 (m-80)
REVERT: A 102 ASN cc_start: 0.6192 (p0) cc_final: 0.5682 (p0)
REVERT: A 108 ASP cc_start: 0.8222 (m-30) cc_final: 0.8002 (m-30)
REVERT: A 234 LEU cc_start: 0.8348 (OUTLIER) cc_final: 0.8034 (tp)
REVERT: A 318 PHE cc_start: 0.7766 (OUTLIER) cc_final: 0.7234 (p90)
REVERT: B 48 TYR cc_start: -0.0176 (OUTLIER) cc_final: -0.1735 (m-80)
REVERT: B 102 ASN cc_start: 0.6074 (p0) cc_final: 0.5563 (p0)
REVERT: B 105 PHE cc_start: 0.6028 (OUTLIER) cc_final: 0.5764 (m-80)
REVERT: B 110 ARG cc_start: 0.7575 (OUTLIER) cc_final: 0.7257 (mtm180)
REVERT: B 255 PHE cc_start: 0.6109 (OUTLIER) cc_final: 0.5507 (m-80)
REVERT: C 48 TYR cc_start: 0.0242 (OUTLIER) cc_final: -0.2305 (m-80)
REVERT: C 102 ASN cc_start: 0.6063 (p0) cc_final: 0.5618 (p0)
REVERT: C 110 ARG cc_start: 0.7698 (OUTLIER) cc_final: 0.7402 (mtm180)
REVERT: C 255 PHE cc_start: 0.5647 (OUTLIER) cc_final: 0.4927 (m-80)
REVERT: D 48 TYR cc_start: -0.0020 (OUTLIER) cc_final: -0.1343 (m-10)
REVERT: D 102 ASN cc_start: 0.5924 (p0) cc_final: 0.5457 (p0)
REVERT: D 110 ARG cc_start: 0.7608 (OUTLIER) cc_final: 0.7293 (mtm180)
REVERT: D 255 PHE cc_start: 0.6046 (OUTLIER) cc_final: 0.5606 (m-80)
REVERT: D 318 PHE cc_start: 0.7707 (OUTLIER) cc_final: 0.7350 (p90)
REVERT: E 48 TYR cc_start: -0.0033 (OUTLIER) cc_final: -0.1574 (m-80)
REVERT: E 102 ASN cc_start: 0.6217 (p0) cc_final: 0.5700 (p0)
REVERT: E 110 ARG cc_start: 0.7555 (OUTLIER) cc_final: 0.7263 (mtt180)
REVERT: E 255 PHE cc_start: 0.5971 (OUTLIER) cc_final: 0.5274 (m-80)
REVERT: E 304 LYS cc_start: 0.7664 (mtmm) cc_final: 0.7402 (mtmm)
outliers start: 63
outliers final: 40
residues processed: 196
average time/residue: 0.2608
time to fit residues: 74.6176
Evaluate side-chains
203 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 57
poor density : 146
time to evaluate : 1.386
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 48 TYR
Chi-restraints excluded: chain A residue 53 ARG
Chi-restraints excluded: chain A residue 61 VAL
Chi-restraints excluded: chain A residue 104 SER
Chi-restraints excluded: chain A residue 128 SER
Chi-restraints excluded: chain A residue 142 LEU
Chi-restraints excluded: chain A residue 181 TRP
Chi-restraints excluded: chain A residue 234 LEU
Chi-restraints excluded: chain A residue 258 VAL
Chi-restraints excluded: chain A residue 318 PHE
Chi-restraints excluded: chain B residue 48 TYR
Chi-restraints excluded: chain B residue 53 ARG
Chi-restraints excluded: chain B residue 104 SER
Chi-restraints excluded: chain B residue 105 PHE
Chi-restraints excluded: chain B residue 110 ARG
Chi-restraints excluded: chain B residue 128 SER
Chi-restraints excluded: chain B residue 133 VAL
Chi-restraints excluded: chain B residue 181 TRP
Chi-restraints excluded: chain B residue 191 THR
Chi-restraints excluded: chain B residue 205 LEU
Chi-restraints excluded: chain B residue 215 TYR
Chi-restraints excluded: chain B residue 234 LEU
Chi-restraints excluded: chain B residue 242 VAL
Chi-restraints excluded: chain B residue 255 PHE
Chi-restraints excluded: chain B residue 316 PHE
Chi-restraints excluded: chain B residue 432 PHE
Chi-restraints excluded: chain C residue 48 TYR
Chi-restraints excluded: chain C residue 61 VAL
Chi-restraints excluded: chain C residue 104 SER
Chi-restraints excluded: chain C residue 110 ARG
Chi-restraints excluded: chain C residue 128 SER
Chi-restraints excluded: chain C residue 133 VAL
Chi-restraints excluded: chain C residue 181 TRP
Chi-restraints excluded: chain C residue 255 PHE
Chi-restraints excluded: chain C residue 316 PHE
Chi-restraints excluded: chain C residue 432 PHE
Chi-restraints excluded: chain D residue 48 TYR
Chi-restraints excluded: chain D residue 110 ARG
Chi-restraints excluded: chain D residue 128 SER
Chi-restraints excluded: chain D residue 181 TRP
Chi-restraints excluded: chain D residue 205 LEU
Chi-restraints excluded: chain D residue 211 THR
Chi-restraints excluded: chain D residue 220 THR
Chi-restraints excluded: chain D residue 234 LEU
Chi-restraints excluded: chain D residue 255 PHE
Chi-restraints excluded: chain D residue 312 ILE
Chi-restraints excluded: chain D residue 316 PHE
Chi-restraints excluded: chain D residue 318 PHE
Chi-restraints excluded: chain E residue 48 TYR
Chi-restraints excluded: chain E residue 104 SER
Chi-restraints excluded: chain E residue 110 ARG
Chi-restraints excluded: chain E residue 128 SER
Chi-restraints excluded: chain E residue 181 TRP
Chi-restraints excluded: chain E residue 205 LEU
Chi-restraints excluded: chain E residue 255 PHE
Chi-restraints excluded: chain E residue 316 PHE
Chi-restraints excluded: chain E residue 432 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 155
random chunks:
chunk 77 optimal weight: 1.9990
chunk 59 optimal weight: 20.0000
chunk 1 optimal weight: 0.9990
chunk 98 optimal weight: 9.9990
chunk 17 optimal weight: 0.7980
chunk 12 optimal weight: 5.9990
chunk 148 optimal weight: 9.9990
chunk 141 optimal weight: 2.9990
chunk 62 optimal weight: 9.9990
chunk 71 optimal weight: 0.9980
chunk 123 optimal weight: 6.9990
overall best weight: 1.5586
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 102 ASN
E 204 HIS
Total number of N/Q/H flips: 2
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4501 r_free = 0.4501 target = 0.237415 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.4218 r_free = 0.4218 target = 0.205402 restraints weight = 13196.348|
|-----------------------------------------------------------------------------|
r_work (start): 0.4219 rms_B_bonded: 1.11
r_work: 0.3860 rms_B_bonded: 1.98 restraints_weight: 0.5000
r_work: 0.3556 rms_B_bonded: 4.28 restraints_weight: 0.2500
r_work (final): 0.3556
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7873
moved from start: 0.3000
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.004 0.046 13545 Z= 0.276
Angle : 0.688 10.991 18435 Z= 0.330
Chirality : 0.046 0.237 2185
Planarity : 0.003 0.030 2235
Dihedral : 7.887 45.536 2270
Min Nonbonded Distance : 2.304
Molprobity Statistics.
All-atom Clashscore : 8.76
Ramachandran Plot:
Outliers : 0.32 %
Allowed : 4.04 %
Favored : 95.64 %
Rotamer:
Outliers : 4.41 %
Allowed : 32.52 %
Favored : 63.08 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: -0.04 (0.22), residues: 1560
helix: 2.58 (0.24), residues: 500
sheet: -0.70 (0.24), residues: 335
loop : -1.65 (0.23), residues: 725
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.019 0.002 TRP B 261
HIS 0.005 0.001 HIS E 204
PHE 0.029 0.002 PHE C 99
TYR 0.011 0.001 TYR C 433
ARG 0.004 0.000 ARG C 91
********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
3120 Ramachandran restraints generated.
1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
3120 Ramachandran restraints generated.
1560 Oldfield, 0 Emsley, 1560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
205 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 63
poor density : 142
time to evaluate : 1.352
Fit side-chains
REVERT: A 48 TYR cc_start: -0.0065 (OUTLIER) cc_final: -0.1886 (m-80)
REVERT: A 102 ASN cc_start: 0.6259 (p0) cc_final: 0.5730 (p0)
REVERT: A 108 ASP cc_start: 0.8190 (m-30) cc_final: 0.7952 (m-30)
REVERT: A 234 LEU cc_start: 0.8366 (OUTLIER) cc_final: 0.8039 (tp)
REVERT: A 255 PHE cc_start: 0.6418 (OUTLIER) cc_final: 0.5952 (m-80)
REVERT: A 318 PHE cc_start: 0.7773 (OUTLIER) cc_final: 0.7305 (p90)
REVERT: B 48 TYR cc_start: -0.0284 (OUTLIER) cc_final: -0.1896 (m-80)
REVERT: B 102 ASN cc_start: 0.6212 (p0) cc_final: 0.5670 (p0)
REVERT: B 105 PHE cc_start: 0.5983 (OUTLIER) cc_final: 0.5711 (m-80)
REVERT: B 110 ARG cc_start: 0.7582 (OUTLIER) cc_final: 0.7243 (mtm180)
REVERT: B 255 PHE cc_start: 0.6133 (OUTLIER) cc_final: 0.5563 (m-80)
REVERT: C 48 TYR cc_start: 0.0203 (OUTLIER) cc_final: -0.2297 (m-80)
REVERT: C 102 ASN cc_start: 0.5993 (p0) cc_final: 0.5619 (p0)
REVERT: C 110 ARG cc_start: 0.7727 (OUTLIER) cc_final: 0.7442 (mtm180)
REVERT: C 255 PHE cc_start: 0.5686 (OUTLIER) cc_final: 0.4951 (m-80)
REVERT: D 48 TYR cc_start: -0.0083 (OUTLIER) cc_final: -0.1548 (m-80)
REVERT: D 102 ASN cc_start: 0.5935 (p0) cc_final: 0.5475 (p0)
REVERT: D 110 ARG cc_start: 0.7628 (OUTLIER) cc_final: 0.7280 (mtm180)
REVERT: D 255 PHE cc_start: 0.6161 (OUTLIER) cc_final: 0.5864 (m-80)
REVERT: E 48 TYR cc_start: 0.0029 (OUTLIER) cc_final: -0.1657 (m-80)
REVERT: E 102 ASN cc_start: 0.6222 (p0) cc_final: 0.5702 (p0)
REVERT: E 110 ARG cc_start: 0.7577 (OUTLIER) cc_final: 0.7267 (mtt180)
REVERT: E 255 PHE cc_start: 0.6006 (OUTLIER) cc_final: 0.5345 (m-80)
REVERT: E 304 LYS cc_start: 0.7558 (mtmm) cc_final: 0.7301 (mtmm)
outliers start: 63
outliers final: 45
residues processed: 194
average time/residue: 0.2508
time to fit residues: 71.3699
Evaluate side-chains
203 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 62
poor density : 141
time to evaluate : 1.491
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 48 TYR
Chi-restraints excluded: chain A residue 53 ARG
Chi-restraints excluded: chain A residue 61 VAL
Chi-restraints excluded: chain A residue 65 LEU
Chi-restraints excluded: chain A residue 104 SER
Chi-restraints excluded: chain A residue 110 ARG
Chi-restraints excluded: chain A residue 128 SER
Chi-restraints excluded: chain A residue 142 LEU
Chi-restraints excluded: chain A residue 181 TRP
Chi-restraints excluded: chain A residue 218 LEU
Chi-restraints excluded: chain A residue 234 LEU
Chi-restraints excluded: chain A residue 255 PHE
Chi-restraints excluded: chain A residue 258 VAL
Chi-restraints excluded: chain A residue 318 PHE
Chi-restraints excluded: chain B residue 48 TYR
Chi-restraints excluded: chain B residue 104 SER
Chi-restraints excluded: chain B residue 105 PHE
Chi-restraints excluded: chain B residue 110 ARG
Chi-restraints excluded: chain B residue 128 SER
Chi-restraints excluded: chain B residue 133 VAL
Chi-restraints excluded: chain B residue 140 ILE
Chi-restraints excluded: chain B residue 181 TRP
Chi-restraints excluded: chain B residue 191 THR
Chi-restraints excluded: chain B residue 205 LEU
Chi-restraints excluded: chain B residue 234 LEU
Chi-restraints excluded: chain B residue 242 VAL
Chi-restraints excluded: chain B residue 255 PHE
Chi-restraints excluded: chain B residue 316 PHE
Chi-restraints excluded: chain B residue 432 PHE
Chi-restraints excluded: chain C residue 48 TYR
Chi-restraints excluded: chain C residue 61 VAL
Chi-restraints excluded: chain C residue 104 SER
Chi-restraints excluded: chain C residue 110 ARG
Chi-restraints excluded: chain C residue 128 SER
Chi-restraints excluded: chain C residue 133 VAL
Chi-restraints excluded: chain C residue 181 TRP
Chi-restraints excluded: chain C residue 255 PHE
Chi-restraints excluded: chain C residue 316 PHE
Chi-restraints excluded: chain C residue 432 PHE
Chi-restraints excluded: chain D residue 48 TYR
Chi-restraints excluded: chain D residue 110 ARG
Chi-restraints excluded: chain D residue 128 SER
Chi-restraints excluded: chain D residue 181 TRP
Chi-restraints excluded: chain D residue 205 LEU
Chi-restraints excluded: chain D residue 211 THR
Chi-restraints excluded: chain D residue 220 THR
Chi-restraints excluded: chain D residue 234 LEU
Chi-restraints excluded: chain D residue 255 PHE
Chi-restraints excluded: chain D residue 312 ILE
Chi-restraints excluded: chain D residue 316 PHE
Chi-restraints excluded: chain E residue 48 TYR
Chi-restraints excluded: chain E residue 65 LEU
Chi-restraints excluded: chain E residue 104 SER
Chi-restraints excluded: chain E residue 110 ARG
Chi-restraints excluded: chain E residue 128 SER
Chi-restraints excluded: chain E residue 181 TRP
Chi-restraints excluded: chain E residue 205 LEU
Chi-restraints excluded: chain E residue 218 LEU
Chi-restraints excluded: chain E residue 220 THR
Chi-restraints excluded: chain E residue 255 PHE
Chi-restraints excluded: chain E residue 316 PHE
Chi-restraints excluded: chain E residue 432 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 155
random chunks:
chunk 124 optimal weight: 7.9990
chunk 99 optimal weight: 0.7980
chunk 29 optimal weight: 20.0000
chunk 44 optimal weight: 2.9990
chunk 144 optimal weight: 0.9990
chunk 28 optimal weight: 20.0000
chunk 39 optimal weight: 0.9980
chunk 145 optimal weight: 3.9990
chunk 38 optimal weight: 0.7980
chunk 57 optimal weight: 9.9990
chunk 142 optimal weight: 3.9990
overall best weight: 1.3184
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 102 ASN
E 204 HIS
Total number of N/Q/H flips: 2
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4505 r_free = 0.4505 target = 0.238018 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.4225 r_free = 0.4225 target = 0.206286 restraints weight = 13266.536|
|-----------------------------------------------------------------------------|
r_work (start): 0.4223 rms_B_bonded: 1.11
r_work: 0.3860 rms_B_bonded: 1.99 restraints_weight: 0.5000
r_work: 0.3563 rms_B_bonded: 4.50 restraints_weight: 0.2500
r_work (final): 0.3563
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7853
moved from start: 0.3083
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.004 0.036 13545 Z= 0.243
Angle : 0.672 11.077 18435 Z= 0.322
Chirality : 0.046 0.231 2185
Planarity : 0.003 0.030 2235
Dihedral : 7.629 45.250 2270
Min Nonbonded Distance : 2.329
Molprobity Statistics.
All-atom Clashscore : 9.03
Ramachandran Plot:
Outliers : 0.32 %
Allowed : 3.27 %
Favored : 96.41 %
Rotamer:
Outliers : 4.69 %
Allowed : 32.31 %
Favored : 63.01 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: -0.01 (0.22), residues: 1560
helix: 2.53 (0.24), residues: 500
sheet: -0.66 (0.24), residues: 335
loop : -1.58 (0.23), residues: 725
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.019 0.002 TRP D 261
HIS 0.004 0.001 HIS E 204
PHE 0.027 0.002 PHE C 99
TYR 0.012 0.001 TYR C 433
ARG 0.004 0.000 ARG E 91
Origin is already at (0, 0, 0), no shifts will be applied
===============================================================================
Job complete
usr+sys time: 6839.42 seconds
wall clock time: 122 minutes 49.44 seconds (7369.44 seconds total)