Starting phenix.real_space_refine
on Wed Jan 15 14:54:04 2025 by dcliebschner
===============================================================================
Processing files:
-------------------------------------------------------------------------------
Found model, /net/cci-nas-00/data/ceres_data/9bbc_44417/01_2025/9bbc_44417.cif
Found real_map, /net/cci-nas-00/data/ceres_data/9bbc_44417/01_2025/9bbc_44417.map
Processing PHIL parameters:
-------------------------------------------------------------------------------
Adding command-line PHIL:
-------------------------
refinement.macro_cycles=10
scattering_table=electron
resolution=3.3
write_initial_geo_file=False
Final processed PHIL parameters:
-------------------------------------------------------------------------------
data_manager {
real_map_files = "/net/cci-nas-00/data/ceres_data/9bbc_44417/01_2025/9bbc_44417.map"
default_real_map = "/net/cci-nas-00/data/ceres_data/9bbc_44417/01_2025/9bbc_44417.map"
model {
file = "/net/cci-nas-00/data/ceres_data/9bbc_44417/01_2025/9bbc_44417.cif"
}
default_model = "/net/cci-nas-00/data/ceres_data/9bbc_44417/01_2025/9bbc_44417.cif"
}
resolution = 3.3
write_initial_geo_file = False
refinement {
macro_cycles = 10
}
qi {
qm_restraints {
package {
program = *test
}
}
}
Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.
Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
Set to: 0
Set model cs if undefined
Decide on map wrapping
Map wrapping is set to: False
Normalize map: mean=0, sd=1
Input map: mean= -0.001 sd= 0.034
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 50 5.16 5
C 5385 2.51 5
N 1347 2.21 5
O 1658 1.98 5
sf(0) = scattering factor at diffraction angle 0.
Process input model
Symmetric amino acids flipped. Time to flip 25 residue(s): 0.03s
Monomer Library directory:
"/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
Total number of atoms: 8440
Number of models: 1
Model: ""
Number of chains: 16
Chain: "A"
Number of atoms: 1932
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 253, 1932
Classifications: {'peptide': 253}
Incomplete info: {'truncation_to_alanine': 8}
Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 240}
Unresolved non-hydrogen bonds: 33
Unresolved non-hydrogen angles: 41
Unresolved non-hydrogen dihedrals: 28
Unresolved non-hydrogen chiralities: 2
Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1}
Unresolved non-hydrogen planarities: 20
Chain: "B"
Number of atoms: 2206
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 284, 2206
Classifications: {'peptide': 284}
Incomplete info: {'truncation_to_alanine': 6}
Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 12, 'TRANS': 268}
Unresolved non-hydrogen bonds: 16
Unresolved non-hydrogen angles: 19
Unresolved non-hydrogen dihedrals: 13
Unresolved non-hydrogen chiralities: 1
Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1}
Unresolved non-hydrogen planarities: 8
Chain: "D"
Number of atoms: 810
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 105, 810
Classifications: {'peptide': 105}
Incomplete info: {'truncation_to_alanine': 2}
Link IDs: {'CIS': 1, 'PTRANS': 3, 'TRANS': 100}
Unresolved non-hydrogen bonds: 7
Unresolved non-hydrogen angles: 8
Unresolved non-hydrogen dihedrals: 6
Planarities with less than four sites: {'ASP:plan': 1}
Unresolved non-hydrogen planarities: 3
Chain: "E"
Number of atoms: 930
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 119, 930
Classifications: {'peptide': 119}
Incomplete info: {'truncation_to_alanine': 5}
Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 113}
Unresolved non-hydrogen bonds: 14
Unresolved non-hydrogen angles: 17
Unresolved non-hydrogen dihedrals: 11
Planarities with less than four sites: {'ASP:plan': 3}
Unresolved non-hydrogen planarities: 9
Chain: "F"
Number of atoms: 936
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 119, 936
Classifications: {'peptide': 119}
Incomplete info: {'truncation_to_alanine': 2}
Link IDs: {'PTRANS': 5, 'TRANS': 113}
Unresolved non-hydrogen bonds: 8
Unresolved non-hydrogen angles: 9
Unresolved non-hydrogen dihedrals: 7
Planarities with less than four sites: {'GLN:plan1': 1}
Unresolved non-hydrogen planarities: 4
Chain: "G"
Number of atoms: 888
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 114, 888
Classifications: {'peptide': 114}
Incomplete info: {'truncation_to_alanine': 5}
Link IDs: {'PTRANS': 2, 'TRANS': 111}
Unresolved non-hydrogen bonds: 12
Unresolved non-hydrogen angles: 13
Unresolved non-hydrogen dihedrals: 11
Unresolved non-hydrogen chiralities: 1
Chain: "X"
Number of atoms: 219
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 30, 219
Classifications: {'peptide': 30}
Incomplete info: {'truncation_to_alanine': 5}
Link IDs: {'PTRANS': 1, 'TRANS': 28}
Unresolved non-hydrogen bonds: 19
Unresolved non-hydrogen angles: 26
Unresolved non-hydrogen dihedrals: 15
Unresolved non-hydrogen chiralities: 4
Planarities with less than four sites: {'TYR:plan': 1}
Unresolved non-hydrogen planarities: 7
Chain: "Y"
Number of atoms: 220
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 28, 220
Classifications: {'peptide': 28}
Incomplete info: {'truncation_to_alanine': 3}
Link IDs: {'PTRANS': 1, 'TRANS': 26}
Unresolved non-hydrogen bonds: 9
Unresolved non-hydrogen angles: 12
Unresolved non-hydrogen dihedrals: 6
Unresolved non-hydrogen chiralities: 2
Planarities with less than four sites: {'ASP:plan': 1}
Unresolved non-hydrogen planarities: 3
Chain: "I"
Number of atoms: 28
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 2, 28
Unusual residues: {'NAG': 2}
Classifications: {'undetermined': 2}
Link IDs: {None: 1}
Unresolved non-hydrogen bonds: 2
Unresolved non-hydrogen angles: 4
Unresolved non-hydrogen dihedrals: 6
Unresolved non-hydrogen chiralities: 2
Chain: "O"
Number of atoms: 39
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 3, 39
Unusual residues: {'BMA': 1, 'NAG': 2}
Classifications: {'undetermined': 3}
Link IDs: {None: 2}
Unresolved non-hydrogen bonds: 3
Unresolved non-hydrogen angles: 6
Unresolved non-hydrogen dihedrals: 9
Unresolved non-hydrogen chiralities: 3
Chain: "R"
Number of atoms: 28
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 2, 28
Unusual residues: {'NAG': 2}
Classifications: {'undetermined': 2}
Link IDs: {None: 1}
Unresolved non-hydrogen bonds: 2
Unresolved non-hydrogen angles: 4
Unresolved non-hydrogen dihedrals: 6
Unresolved non-hydrogen chiralities: 2
Chain: "C"
Number of atoms: 39
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 3, 39
Unusual residues: {'BMA': 1, 'NAG': 2}
Classifications: {'undetermined': 3}
Link IDs: {None: 2}
Unresolved non-hydrogen bonds: 3
Unresolved non-hydrogen angles: 6
Unresolved non-hydrogen dihedrals: 9
Unresolved non-hydrogen chiralities: 3
Chain: "H"
Number of atoms: 39
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 3, 39
Unusual residues: {'BMA': 1, 'NAG': 2}
Classifications: {'undetermined': 3}
Link IDs: {None: 2}
Unresolved non-hydrogen bonds: 3
Unresolved non-hydrogen angles: 6
Unresolved non-hydrogen dihedrals: 9
Unresolved non-hydrogen chiralities: 3
Chain: "A"
Number of atoms: 84
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 5, 84
Unusual residues: {'CLR': 1, 'NAG': 4}
Classifications: {'undetermined': 5}
Link IDs: {None: 4}
Unresolved non-hydrogen bonds: 4
Unresolved non-hydrogen angles: 8
Unresolved non-hydrogen dihedrals: 12
Unresolved non-hydrogen chiralities: 4
Chain: "G"
Number of atoms: 14
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 1, 14
Unusual residues: {'NAG': 1}
Classifications: {'undetermined': 1}
Unresolved non-hydrogen bonds: 1
Unresolved non-hydrogen angles: 2
Unresolved non-hydrogen dihedrals: 3
Unresolved non-hydrogen chiralities: 1
Chain: "Y"
Number of atoms: 28
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 1, 28
Unusual residues: {'CLR': 1}
Classifications: {'undetermined': 1}
Time building chain proxies: 5.53, per 1000 atoms: 0.66
Number of scatterers: 8440
At special positions: 0
Unit cell: (88.56, 101.52, 138.24, 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 50 16.00
O 1658 8.00
N 1347 7.00
C 5385 6.00
sf(0) = scattering factor at diffraction angle 0.
Number of disulfides: simple=14, symmetry=0
Simple disulfide: pdb=" SG CYS A 42 " - pdb=" SG CYS A 109 " distance=2.03
Simple disulfide: pdb=" SG CYS A 156 " - pdb=" SG CYS A 206 " distance=2.03
Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS B 263 " distance=2.04
Simple disulfide: pdb=" SG CYS B 42 " - pdb=" SG CYS B 110 " distance=2.03
Simple disulfide: pdb=" SG CYS B 163 " - pdb=" SG CYS B 228 " distance=2.03
Simple disulfide: pdb=" SG CYS D 37 " - pdb=" SG CYS D 73 " distance=2.03
Simple disulfide: pdb=" SG CYS D 93 " - pdb=" SG CYS D 96 " distance=2.03
Simple disulfide: pdb=" SG CYS E 49 " - pdb=" SG CYS E 98 " distance=2.03
Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 122 " distance=2.03
Simple disulfide: pdb=" SG CYS F 49 " - pdb=" SG CYS F 98 " distance=2.03
Simple disulfide: pdb=" SG CYS F 119 " - pdb=" SG CYS F 122 " distance=2.03
Simple disulfide: pdb=" SG CYS G 46 " - pdb=" SG CYS G 87 " distance=2.04
Simple disulfide: pdb=" SG CYS G 104 " - pdb=" SG CYS G 107 " distance=2.03
Simple disulfide: pdb=" SG CYS X 32 " - pdb=" SG CYS Y 32 " distance=2.03
Automatic linking
Parameters for automatic linking
Linking & cutoffs
Metal : Auto - 3.00
Amino acid : True - 1.90
Carbohydrate : True - 1.99
Ligands : True - 1.99
Small molecules : False - 1.98
Amino acid - RNA/DNA : False
Number of custom bonds: simple=0, symmetry=0
Links applied
BETA1-4
" NAG C 1 " - " NAG C 2 "
" NAG C 2 " - " BMA C 3 "
" NAG H 1 " - " NAG H 2 "
" NAG H 2 " - " BMA H 3 "
" NAG I 1 " - " NAG I 2 "
" NAG O 1 " - " NAG O 2 "
" NAG O 2 " - " BMA O 3 "
" NAG R 1 " - " NAG R 2 "
NAG-ASN
" NAG A 301 " - " ASN A 82 "
" NAG A 302 " - " ASN A 166 "
" NAG A 303 " - " ASN A 200 "
" NAG A 304 " - " ASN A 211 "
" NAG C 1 " - " ASN D 38 "
" NAG G 201 " - " ASN G 92 "
" NAG H 1 " - " ASN D 74 "
" NAG I 1 " - " ASN A 41 "
" NAG O 1 " - " ASN B 84 "
" NAG R 1 " - " ASN G 52 "
Time building additional restraints: 2.51
Conformation dependent library (CDL) restraints added in 1.1 seconds
2072 Ramachandran restraints generated.
1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
Adding C-beta torsion restraints...
Number of C-beta restraints generated: 1962
Finding SS restraints...
Secondary structure from input PDB file:
23 helices and 17 sheets defined
28.1% alpha, 31.1% beta
0 base pairs and 0 stacking pairs defined.
Time for finding SS restraints: 1.10
Creating SS restraints...
Processing helix chain 'A' and resid 100 through 104
Processing helix chain 'A' and resid 205 through 210
removed outlier: 3.685A pdb=" N ALA A 209 " --> pdb=" O ALA A 205 " (cutoff:3.500A)
removed outlier: 4.329A pdb=" N PHE A 210 " --> pdb=" O CYS A 206 " (cutoff:3.500A)
No H-bonds generated for 'chain 'A' and resid 205 through 210'
Processing helix chain 'A' and resid 229 through 235
removed outlier: 3.661A pdb=" N VAL A 233 " --> pdb=" O ASP A 229 " (cutoff:3.500A)
removed outlier: 3.582A pdb=" N LYS A 235 " --> pdb=" O LYS A 231 " (cutoff:3.500A)
Processing helix chain 'A' and resid 240 through 273
Processing helix chain 'B' and resid 101 through 105
removed outlier: 3.503A pdb=" N THR B 105 " --> pdb=" O PRO B 102 " (cutoff:3.500A)
Processing helix chain 'B' and resid 134 through 138
removed outlier: 3.980A pdb=" N ASN B 137 " --> pdb=" O ASP B 134 " (cutoff:3.500A)
Processing helix chain 'B' and resid 149 through 156
removed outlier: 3.517A pdb=" N ILE B 153 " --> pdb=" O SER B 149 " (cutoff:3.500A)
Processing helix chain 'B' and resid 216 through 220
Processing helix chain 'B' and resid 266 through 305
Processing helix chain 'D' and resid 64 through 66
No H-bonds generated for 'chain 'D' and resid 64 through 66'
Processing helix chain 'D' and resid 100 through 126
Processing helix chain 'E' and resid 88 through 93
removed outlier: 3.653A pdb=" N SER E 93 " --> pdb=" O GLU E 89 " (cutoff:3.500A)
Processing helix chain 'E' and resid 126 through 149
removed outlier: 3.957A pdb=" N ILE E 133 " --> pdb=" O SER E 129 " (cutoff:3.500A)
removed outlier: 4.124A pdb=" N VAL E 134 " --> pdb=" O VAL E 130 " (cutoff:3.500A)
removed outlier: 3.655A pdb=" N ILE E 135 " --> pdb=" O ALA E 131 " (cutoff:3.500A)
removed outlier: 3.818A pdb=" N LEU E 147 " --> pdb=" O GLY E 143 " (cutoff:3.500A)
Processing helix chain 'F' and resid 88 through 93
removed outlier: 3.587A pdb=" N SER F 93 " --> pdb=" O GLU F 89 " (cutoff:3.500A)
Processing helix chain 'F' and resid 104 through 108
Processing helix chain 'F' and resid 126 through 151
removed outlier: 3.636A pdb=" N ALA F 131 " --> pdb=" O VAL F 127 " (cutoff:3.500A)
removed outlier: 3.863A pdb=" N THR F 132 " --> pdb=" O MET F 128 " (cutoff:3.500A)
removed outlier: 3.895A pdb=" N ILE F 133 " --> pdb=" O SER F 129 " (cutoff:3.500A)
removed outlier: 3.863A pdb=" N VAL F 134 " --> pdb=" O VAL F 130 " (cutoff:3.500A)
removed outlier: 3.549A pdb=" N ILE F 135 " --> pdb=" O ALA F 131 " (cutoff:3.500A)
removed outlier: 3.648A pdb=" N ILE F 138 " --> pdb=" O VAL F 134 " (cutoff:3.500A)
removed outlier: 3.596A pdb=" N GLY F 143 " --> pdb=" O CYS F 139 " (cutoff:3.500A)
removed outlier: 3.693A pdb=" N LEU F 144 " --> pdb=" O ILE F 140 " (cutoff:3.500A)
removed outlier: 4.226A pdb=" N LEU F 146 " --> pdb=" O GLY F 142 " (cutoff:3.500A)
removed outlier: 3.754A pdb=" N LEU F 147 " --> pdb=" O GLY F 143 " (cutoff:3.500A)
removed outlier: 3.696A pdb=" N VAL F 148 " --> pdb=" O LEU F 144 " (cutoff:3.500A)
Processing helix chain 'G' and resid 24 through 28
Processing helix chain 'G' and resid 78 through 80
No H-bonds generated for 'chain 'G' and resid 78 through 80'
Processing helix chain 'G' and resid 111 through 137
Processing helix chain 'X' and resid 28 through 33
removed outlier: 3.947A pdb=" N CYS X 32 " --> pdb=" O ASP X 28 " (cutoff:3.500A)
Processing helix chain 'X' and resid 36 through 47
removed outlier: 4.388A pdb=" N TYR X 42 " --> pdb=" O ILE X 38 " (cutoff:3.500A)
removed outlier: 3.731A pdb=" N ILE X 45 " --> pdb=" O ILE X 41 " (cutoff:3.500A)
Processing helix chain 'X' and resid 48 through 51
Processing helix chain 'Y' and resid 29 through 55
Processing sheet with id=AA1, first strand: chain 'A' and resid 23 through 26
removed outlier: 3.601A pdb=" N ASN A 41 " --> pdb=" O ILE A 26 " (cutoff:3.500A)
Processing sheet with id=AA2, first strand: chain 'A' and resid 29 through 33
removed outlier: 6.441A pdb=" N LEU A 30 " --> pdb=" O ILE A 130 " (cutoff:3.500A)
removed outlier: 7.748A pdb=" N HIS A 132 " --> pdb=" O LEU A 30 " (cutoff:3.500A)
removed outlier: 6.963A pdb=" N VAL A 32 " --> pdb=" O HIS A 132 " (cutoff:3.500A)
Processing sheet with id=AA3, first strand: chain 'A' and resid 141 through 145
removed outlier: 4.407A pdb=" N VAL A 155 " --> pdb=" O LEU A 145 " (cutoff:3.500A)
Processing sheet with id=AA4, first strand: chain 'A' and resid 141 through 145
removed outlier: 4.407A pdb=" N VAL A 155 " --> pdb=" O LEU A 145 " (cutoff:3.500A)
Processing sheet with id=AA5, first strand: chain 'B' and resid 23 through 26
Processing sheet with id=AA6, first strand: chain 'B' and resid 29 through 33
removed outlier: 3.531A pdb=" N VAL B 107 " --> pdb=" O GLN B 56 " (cutoff:3.500A)
removed outlier: 3.731A pdb=" N TRP B 53 " --> pdb=" O HIS B 66 " (cutoff:3.500A)
removed outlier: 4.900A pdb=" N HIS B 66 " --> pdb=" O TRP B 53 " (cutoff:3.500A)
removed outlier: 6.260A pdb=" N ARG B 55 " --> pdb=" O LEU B 64 " (cutoff:3.500A)
removed outlier: 5.367A pdb=" N LEU B 64 " --> pdb=" O ARG B 55 " (cutoff:3.500A)
removed outlier: 7.494A pdb=" N ASP B 57 " --> pdb=" O LEU B 62 " (cutoff:3.500A)
removed outlier: 5.761A pdb=" N LEU B 62 " --> pdb=" O ASP B 57 " (cutoff:3.500A)
Processing sheet with id=AA7, first strand: chain 'B' and resid 29 through 33
Processing sheet with id=AA8, first strand: chain 'B' and resid 142 through 146
removed outlier: 5.723A pdb=" N TYR B 206 " --> pdb=" O GLY B 167 " (cutoff:3.500A)
Processing sheet with id=AA9, first strand: chain 'B' and resid 142 through 146
removed outlier: 5.723A pdb=" N TYR B 206 " --> pdb=" O GLY B 167 " (cutoff:3.500A)
Processing sheet with id=AB1, first strand: chain 'B' and resid 182 through 183
Processing sheet with id=AB2, first strand: chain 'D' and resid 26 through 27
removed outlier: 5.670A pdb=" N VAL D 33 " --> pdb=" O LEU D 60 " (cutoff:3.500A)
Processing sheet with id=AB3, first strand: chain 'D' and resid 42 through 46
removed outlier: 4.121A pdb=" N ILE D 70 " --> pdb=" O VAL D 44 " (cutoff:3.500A)
removed outlier: 4.779A pdb=" N GLY D 46 " --> pdb=" O ARG D 68 " (cutoff:3.500A)
removed outlier: 7.201A pdb=" N ARG D 68 " --> pdb=" O GLY D 46 " (cutoff:3.500A)
removed outlier: 6.916A pdb=" N THR D 85 " --> pdb=" O TYR E 111 " (cutoff:3.500A)
removed outlier: 8.125A pdb=" N TYR E 113 " --> pdb=" O THR D 85 " (cutoff:3.500A)
removed outlier: 6.606A pdb=" N GLN D 87 " --> pdb=" O TYR E 113 " (cutoff:3.500A)
removed outlier: 8.149A pdb=" N ARG E 115 " --> pdb=" O GLN D 87 " (cutoff:3.500A)
removed outlier: 7.033A pdb=" N HIS D 89 " --> pdb=" O ARG E 115 " (cutoff:3.500A)
removed outlier: 7.275A pdb=" N PHE E 110 " --> pdb=" O CYS E 98 " (cutoff:3.500A)
removed outlier: 5.589A pdb=" N CYS E 98 " --> pdb=" O PHE E 110 " (cutoff:3.500A)
Processing sheet with id=AB4, first strand: chain 'D' and resid 96 through 98
removed outlier: 3.961A pdb=" N VAL D 97 " --> pdb=" O MET E 123 " (cutoff:3.500A)
removed outlier: 4.200A pdb=" N MET E 123 " --> pdb=" O VAL D 97 " (cutoff:3.500A)
No H-bonds generated for sheet with id=AB4
Processing sheet with id=AB5, first strand: chain 'E' and resid 37 through 41
Processing sheet with id=AB6, first strand: chain 'F' and resid 37 through 41
Processing sheet with id=AB7, first strand: chain 'F' and resid 64 through 66
removed outlier: 3.952A pdb=" N TRP F 59 " --> pdb=" O ILE F 66 " (cutoff:3.500A)
removed outlier: 6.873A pdb=" N TYR F 111 " --> pdb=" O GLN G 98 " (cutoff:3.500A)
removed outlier: 8.041A pdb=" N TYR G 100 " --> pdb=" O TYR F 111 " (cutoff:3.500A)
removed outlier: 6.317A pdb=" N TYR F 113 " --> pdb=" O TYR G 100 " (cutoff:3.500A)
removed outlier: 7.749A pdb=" N ARG G 102 " --> pdb=" O TYR F 113 " (cutoff:3.500A)
removed outlier: 6.902A pdb=" N ARG F 115 " --> pdb=" O ARG G 102 " (cutoff:3.500A)
removed outlier: 3.875A pdb=" N THR G 54 " --> pdb=" O LYS G 88 " (cutoff:3.500A)
removed outlier: 3.696A pdb=" N ILE G 53 " --> pdb=" O LEU G 65 " (cutoff:3.500A)
removed outlier: 3.610A pdb=" N GLY G 63 " --> pdb=" O TRP G 55 " (cutoff:3.500A)
removed outlier: 6.124A pdb=" N LYS G 57 " --> pdb=" O MET G 61 " (cutoff:3.500A)
removed outlier: 5.612A pdb=" N MET G 61 " --> pdb=" O LYS G 57 " (cutoff:3.500A)
Processing sheet with id=AB8, first strand: chain 'G' and resid 31 through 34
removed outlier: 5.784A pdb=" N VAL G 42 " --> pdb=" O LEU G 74 " (cutoff:3.500A)
402 hydrogen bonds defined for protein.
1065 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: 2.50
Time building geometry restraints manager: 2.83 seconds
NOTE: a complete listing of the restraints can be obtained by requesting
output of .geo file.
Histogram of bond lengths:
1.22 - 1.34: 2645
1.34 - 1.46: 2087
1.46 - 1.58: 3821
1.58 - 1.71: 0
1.71 - 1.83: 68
Bond restraints: 8621
Sorted by residual:
bond pdb=" CA ASP D 31 "
pdb=" CB ASP D 31 "
ideal model delta sigma weight residual
1.530 1.558 -0.027 1.69e-02 3.50e+03 2.63e+00
bond pdb=" CG1 ILE B 283 "
pdb=" CD1 ILE B 283 "
ideal model delta sigma weight residual
1.513 1.452 0.061 3.90e-02 6.57e+02 2.43e+00
bond pdb=" CG1 ILE D 108 "
pdb=" CD1 ILE D 108 "
ideal model delta sigma weight residual
1.513 1.454 0.059 3.90e-02 6.57e+02 2.28e+00
bond pdb=" C TYR F 52 "
pdb=" O TYR F 52 "
ideal model delta sigma weight residual
1.235 1.228 0.007 4.70e-03 4.53e+04 2.26e+00
bond pdb=" CB CYS G 104 "
pdb=" SG CYS G 104 "
ideal model delta sigma weight residual
1.808 1.761 0.047 3.30e-02 9.18e+02 2.02e+00
... (remaining 8616 not shown)
Histogram of bond angle deviations from ideal:
0.00 - 2.41: 11398
2.41 - 4.82: 251
4.82 - 7.23: 60
7.23 - 9.64: 17
9.64 - 12.05: 8
Bond angle restraints: 11734
Sorted by residual:
angle pdb=" C GLU D 30 "
pdb=" N ASP D 31 "
pdb=" CA ASP D 31 "
ideal model delta sigma weight residual
121.54 133.59 -12.05 1.91e+00 2.74e-01 3.98e+01
angle pdb=" CB LYS A 149 "
pdb=" CG LYS A 149 "
pdb=" CD LYS A 149 "
ideal model delta sigma weight residual
111.30 120.54 -9.24 2.30e+00 1.89e-01 1.61e+01
angle pdb=" N PHE Y 50 "
pdb=" CA PHE Y 50 "
pdb=" CB PHE Y 50 "
ideal model delta sigma weight residual
110.40 116.78 -6.38 1.63e+00 3.76e-01 1.53e+01
angle pdb=" C LEU Y 49 "
pdb=" N PHE Y 50 "
pdb=" CA PHE Y 50 "
ideal model delta sigma weight residual
121.14 114.35 6.79 1.75e+00 3.27e-01 1.51e+01
angle pdb=" N ILE D 107 "
pdb=" CA ILE D 107 "
pdb=" CB ILE D 107 "
ideal model delta sigma weight residual
110.57 115.53 -4.96 1.28e+00 6.10e-01 1.50e+01
... (remaining 11729 not shown)
Histogram of dihedral angle deviations from ideal:
0.00 - 17.68: 4807
17.68 - 35.35: 506
35.35 - 53.03: 127
53.03 - 70.71: 23
70.71 - 88.38: 7
Dihedral angle restraints: 5470
sinusoidal: 2415
harmonic: 3055
Sorted by residual:
dihedral pdb=" CA CYS G 104 "
pdb=" C CYS G 104 "
pdb=" N GLN G 105 "
pdb=" CA GLN G 105 "
ideal model delta harmonic sigma weight residual
180.00 144.55 35.45 0 5.00e+00 4.00e-02 5.03e+01
dihedral pdb=" CA GLN G 91 "
pdb=" C GLN G 91 "
pdb=" N ASN G 92 "
pdb=" CA ASN G 92 "
ideal model delta harmonic sigma weight residual
180.00 153.53 26.47 0 5.00e+00 4.00e-02 2.80e+01
dihedral pdb=" CA LYS A 201 "
pdb=" C LYS A 201 "
pdb=" N SER A 202 "
pdb=" CA SER A 202 "
ideal model delta harmonic sigma weight residual
180.00 153.59 26.41 0 5.00e+00 4.00e-02 2.79e+01
... (remaining 5467 not shown)
Histogram of chiral volume deviations from ideal:
0.000 - 0.084: 1248
0.084 - 0.169: 135
0.169 - 0.253: 6
0.253 - 0.337: 3
0.337 - 0.421: 1
Chirality restraints: 1393
Sorted by residual:
chirality pdb=" C2 NAG G 201 "
pdb=" C1 NAG G 201 "
pdb=" C3 NAG G 201 "
pdb=" N2 NAG G 201 "
both_signs ideal model delta sigma weight residual
False -2.49 -2.07 -0.42 2.00e-01 2.50e+01 4.44e+00
chirality pdb=" C1 NAG O 1 "
pdb=" ND2 ASN B 84 "
pdb=" C2 NAG O 1 "
pdb=" O5 NAG O 1 "
both_signs ideal model delta sigma weight residual
False -2.40 -2.07 -0.33 2.00e-01 2.50e+01 2.75e+00
chirality pdb=" CG LEU G 129 "
pdb=" CB LEU G 129 "
pdb=" CD1 LEU G 129 "
pdb=" CD2 LEU G 129 "
both_signs ideal model delta sigma weight residual
False -2.59 -2.32 -0.27 2.00e-01 2.50e+01 1.85e+00
... (remaining 1390 not shown)
Planarity restraints: 1474
Sorted by residual:
delta sigma weight rms_deltas residual
plane pdb=" CA GLU D 30 " -0.015 2.00e-02 2.50e+03 3.06e-02 9.38e+00
pdb=" C GLU D 30 " 0.053 2.00e-02 2.50e+03
pdb=" O GLU D 30 " -0.021 2.00e-02 2.50e+03
pdb=" N ASP D 31 " -0.017 2.00e-02 2.50e+03
delta sigma weight rms_deltas residual
plane pdb=" CB PHE X 40 " 0.009 2.00e-02 2.50e+03 1.51e-02 4.01e+00
pdb=" CG PHE X 40 " -0.034 2.00e-02 2.50e+03
pdb=" CD1 PHE X 40 " 0.014 2.00e-02 2.50e+03
pdb=" CD2 PHE X 40 " 0.013 2.00e-02 2.50e+03
pdb=" CE1 PHE X 40 " -0.001 2.00e-02 2.50e+03
pdb=" CE2 PHE X 40 " -0.001 2.00e-02 2.50e+03
pdb=" CZ PHE X 40 " -0.001 2.00e-02 2.50e+03
delta sigma weight rms_deltas residual
plane pdb=" CB ASN D 74 " -0.019 2.00e-02 2.50e+03 1.75e-02 3.85e+00
pdb=" CG ASN D 74 " 0.022 2.00e-02 2.50e+03
pdb=" OD1 ASN D 74 " -0.002 2.00e-02 2.50e+03
pdb=" ND2 ASN D 74 " 0.018 2.00e-02 2.50e+03
pdb=" C1 NAG H 1 " -0.019 2.00e-02 2.50e+03
... (remaining 1471 not shown)
Histogram of nonbonded interaction distances:
2.21 - 2.74: 847
2.74 - 3.28: 8677
3.28 - 3.82: 13853
3.82 - 4.36: 15506
4.36 - 4.90: 26845
Nonbonded interactions: 65728
Sorted by model distance:
nonbonded pdb=" N GLU E 91 "
pdb=" OE1 GLU E 91 "
model vdw
2.206 3.120
nonbonded pdb=" O THR D 47 "
pdb=" OH TYR D 71 "
model vdw
2.211 3.040
nonbonded pdb=" O ASP D 100 "
pdb=" OG1 THR D 103 "
model vdw
2.218 3.040
nonbonded pdb=" O ASP F 137 "
pdb=" OG1 THR F 141 "
model vdw
2.228 3.040
nonbonded pdb=" OE1 GLU E 120 "
pdb=" ND2 ASN E 121 "
model vdw
2.230 3.120
... (remaining 65723 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: 0.00
Found NCS groups:
ncs_group {
reference = chain 'C'
selection = chain 'H'
selection = chain 'O'
}
ncs_group {
reference = (chain 'E' and ((resid 33 and (name N or name CA or name C or name O or name CB \
)) or resid 34 through 151))
selection = (chain 'F' and (resid 33 through 54 or (resid 55 and (name N or name CA or name \
C or name O or name CB )) or resid 56 through 62 or (resid 63 and (name N or nam \
e CA or name C or name O or name CB )) or resid 64 through 68 or (resid 69 and ( \
name N or name CA or name C or name O or name CB )) or resid 70 or (resid 71 and \
(name N or name CA or name C or name O or name CB )) or resid 72 through 151))
}
ncs_group {
reference = chain 'I'
selection = chain 'R'
}
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: 1.540
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: 0.340
Check model and map are aligned: 0.060
Set scattering table: 0.090
Process input model: 22.920
Find NCS groups from input model: 0.170
Set up NCS constraints: 0.040
Set refine NCS operators: 0.000
Adjust number of macro_cycles: 0.000
Reset NCS operators: 0.000
Extract rigid body selections: 0.000
Check and reset occupancies: 0.000
Load rotamer database and sin/cos tables:2.860
Set ADP refinement strategy: 0.000
Make a string to write initial .geo file:0.000
Internal consistency checks: 0.000
Total: 28.030
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8289
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 0.061 8621 Z= 0.215
Angle : 0.923 12.048 11734 Z= 0.438
Chirality : 0.051 0.421 1393
Planarity : 0.004 0.067 1464
Dihedral : 15.190 88.382 3466
Min Nonbonded Distance : 2.206
Molprobity Statistics.
All-atom Clashscore : 13.57
Ramachandran Plot:
Outliers : 0.10 %
Allowed : 3.67 %
Favored : 96.24 %
Rotamer:
Outliers : 0.56 %
Allowed : 25.65 %
Favored : 73.79 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 11.63 %
Cis-general : 0.20 %
Twisted Proline : 0.00 %
Twisted General : 0.10 %
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: 0.51 (0.26), residues: 1036
helix: 0.63 (0.34), residues: 214
sheet: 1.85 (0.32), residues: 286
loop : -0.64 (0.26), residues: 536
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.014 0.001 TRP E 59
HIS 0.006 0.001 HIS B 225
PHE 0.034 0.002 PHE X 40
TYR 0.022 0.001 TYR A 119
ARG 0.012 0.001 ARG E 115
*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
2072 Ramachandran restraints generated.
1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
2072 Ramachandran restraints generated.
1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
192 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 5
poor density : 187
time to evaluate : 0.991
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: A 267 MET cc_start: 0.8676 (mmp) cc_final: 0.8091 (mmp)
REVERT: B 169 TYR cc_start: 0.8760 (t80) cc_final: 0.8537 (t80)
REVERT: D 30 GLU cc_start: 0.8565 (pt0) cc_final: 0.8169 (pp20)
REVERT: E 91 GLU cc_start: 0.8624 (pm20) cc_final: 0.8311 (pm20)
REVERT: X 30 LYS cc_start: 0.9520 (mtmt) cc_final: 0.8992 (mmmt)
REVERT: X 46 LEU cc_start: 0.7927 (pp) cc_final: 0.7703 (pt)
outliers start: 5
outliers final: 4
residues processed: 190
average time/residue: 0.2063
time to fit residues: 53.6419
Evaluate side-chains
172 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 4
poor density : 168
time to evaluate : 0.956
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue 73 CYS
Chi-restraints excluded: chain D residue 93 CYS
Chi-restraints excluded: chain G residue 47 ASP
Chi-restraints excluded: chain Y residue 30 LYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 101
random chunks:
chunk 85 optimal weight: 0.6980
chunk 76 optimal weight: 5.9990
chunk 42 optimal weight: 1.9990
chunk 26 optimal weight: 6.9990
chunk 51 optimal weight: 0.6980
chunk 40 optimal weight: 2.9990
chunk 79 optimal weight: 3.9990
chunk 30 optimal weight: 5.9990
chunk 48 optimal weight: 5.9990
chunk 58 optimal weight: 7.9990
chunk 91 optimal weight: 2.9990
overall best weight: 1.8786
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
B 48 HIS
F 74 ASN
Total number of N/Q/H flips: 2
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.061086 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3087 r_free = 0.3087 target = 0.048661 restraints weight = 39968.655|
|-----------------------------------------------------------------------------|
r_work (start): 0.3046 rms_B_bonded: 5.23
r_work (final): 0.3046
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8366
moved from start: 0.1362
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.005 0.052 8621 Z= 0.296
Angle : 0.804 9.174 11734 Z= 0.389
Chirality : 0.049 0.368 1393
Planarity : 0.004 0.033 1464
Dihedral : 9.015 59.365 1638
Min Nonbonded Distance : 2.507
Molprobity Statistics.
All-atom Clashscore : 11.04
Ramachandran Plot:
Outliers : 0.10 %
Allowed : 3.67 %
Favored : 96.24 %
Rotamer:
Outliers : 4.16 %
Allowed : 18.34 %
Favored : 77.50 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 11.63 %
Cis-general : 0.20 %
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: 0.44 (0.25), residues: 1036
helix: 0.91 (0.33), residues: 228
sheet: 1.68 (0.32), residues: 269
loop : -0.72 (0.26), residues: 539
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.013 0.001 TRP A 198
HIS 0.005 0.001 HIS B 225
PHE 0.045 0.002 PHE Y 50
TYR 0.028 0.002 TYR Y 33
ARG 0.003 0.000 ARG E 115
*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
2072 Ramachandran restraints generated.
1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
2072 Ramachandran restraints generated.
1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
212 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 37
poor density : 175
time to evaluate : 0.996
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: A 134 TYR cc_start: 0.8802 (t80) cc_final: 0.8553 (t80)
REVERT: A 267 MET cc_start: 0.8739 (mmp) cc_final: 0.8526 (mmm)
REVERT: B 46 MET cc_start: 0.9149 (OUTLIER) cc_final: 0.8673 (ptm)
REVERT: G 38 GLU cc_start: 0.9012 (pm20) cc_final: 0.8665 (pm20)
REVERT: X 30 LYS cc_start: 0.9577 (mtmt) cc_final: 0.9046 (mmmt)
outliers start: 37
outliers final: 22
residues processed: 198
average time/residue: 0.2103
time to fit residues: 57.1000
Evaluate side-chains
184 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 23
poor density : 161
time to evaluate : 0.902
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 173 SER
Chi-restraints excluded: chain A residue 206 CYS
Chi-restraints excluded: chain A residue 271 LEU
Chi-restraints excluded: chain B residue 46 MET
Chi-restraints excluded: chain B residue 293 VAL
Chi-restraints excluded: chain D residue 73 CYS
Chi-restraints excluded: chain D residue 83 GLU
Chi-restraints excluded: chain D residue 93 CYS
Chi-restraints excluded: chain D residue 110 THR
Chi-restraints excluded: chain D residue 118 LEU
Chi-restraints excluded: chain E residue 48 THR
Chi-restraints excluded: chain E residue 112 LEU
Chi-restraints excluded: chain E residue 119 CYS
Chi-restraints excluded: chain E residue 122 CYS
Chi-restraints excluded: chain E residue 134 VAL
Chi-restraints excluded: chain E residue 146 LEU
Chi-restraints excluded: chain F residue 126 ASP
Chi-restraints excluded: chain F residue 133 ILE
Chi-restraints excluded: chain F residue 134 VAL
Chi-restraints excluded: chain F residue 140 ILE
Chi-restraints excluded: chain G residue 25 ILE
Chi-restraints excluded: chain G residue 129 LEU
Chi-restraints excluded: chain X residue 23 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 101
random chunks:
chunk 65 optimal weight: 1.9990
chunk 23 optimal weight: 2.9990
chunk 40 optimal weight: 0.9990
chunk 85 optimal weight: 9.9990
chunk 24 optimal weight: 0.9980
chunk 94 optimal weight: 0.8980
chunk 81 optimal weight: 0.8980
chunk 51 optimal weight: 0.9980
chunk 54 optimal weight: 5.9990
chunk 72 optimal weight: 5.9990
chunk 64 optimal weight: 1.9990
overall best weight: 0.9582
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** A 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Total number of N/Q/H flips: 0
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.061477 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3100 r_free = 0.3100 target = 0.048999 restraints weight = 40040.221|
|-----------------------------------------------------------------------------|
r_work (start): 0.3060 rms_B_bonded: 5.28
r_work (final): 0.3060
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8350
moved from start: 0.1645
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.051 8621 Z= 0.198
Angle : 0.766 12.101 11734 Z= 0.365
Chirality : 0.047 0.337 1393
Planarity : 0.003 0.034 1464
Dihedral : 8.536 59.568 1632
Min Nonbonded Distance : 2.535
Molprobity Statistics.
All-atom Clashscore : 9.77
Ramachandran Plot:
Outliers : 0.10 %
Allowed : 3.86 %
Favored : 96.04 %
Rotamer:
Outliers : 3.37 %
Allowed : 19.69 %
Favored : 76.94 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 11.63 %
Cis-general : 0.20 %
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: 0.40 (0.26), residues: 1036
helix: 0.89 (0.33), residues: 228
sheet: 1.62 (0.32), residues: 269
loop : -0.74 (0.25), residues: 539
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.010 0.001 TRP A 198
HIS 0.003 0.001 HIS B 225
PHE 0.013 0.001 PHE A 263
TYR 0.013 0.001 TYR D 79
ARG 0.003 0.000 ARG A 186
*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
2072 Ramachandran restraints generated.
1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
2072 Ramachandran restraints generated.
1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
205 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 30
poor density : 175
time to evaluate : 0.921
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: A 134 TYR cc_start: 0.8786 (t80) cc_final: 0.8543 (t80)
REVERT: A 267 MET cc_start: 0.8747 (mmp) cc_final: 0.8534 (mmm)
REVERT: B 46 MET cc_start: 0.9154 (mtp) cc_final: 0.8728 (ptm)
REVERT: B 301 MET cc_start: 0.9065 (ppp) cc_final: 0.8860 (ppp)
REVERT: E 120 GLU cc_start: 0.9145 (pp20) cc_final: 0.8896 (tm-30)
REVERT: G 37 GLN cc_start: 0.7013 (tm-30) cc_final: 0.6716 (tm-30)
REVERT: X 30 LYS cc_start: 0.9558 (mtmt) cc_final: 0.9088 (mmmt)
outliers start: 30
outliers final: 20
residues processed: 193
average time/residue: 0.2068
time to fit residues: 54.7540
Evaluate side-chains
183 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 20
poor density : 163
time to evaluate : 0.945
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 111 VAL
Chi-restraints excluded: chain A residue 135 ILE
Chi-restraints excluded: chain A residue 173 SER
Chi-restraints excluded: chain A residue 206 CYS
Chi-restraints excluded: chain A residue 271 LEU
Chi-restraints excluded: chain B residue 121 LEU
Chi-restraints excluded: chain B residue 285 LEU
Chi-restraints excluded: chain B residue 293 VAL
Chi-restraints excluded: chain D residue 83 GLU
Chi-restraints excluded: chain D residue 93 CYS
Chi-restraints excluded: chain D residue 118 LEU
Chi-restraints excluded: chain E residue 48 THR
Chi-restraints excluded: chain E residue 112 LEU
Chi-restraints excluded: chain E residue 122 CYS
Chi-restraints excluded: chain E residue 134 VAL
Chi-restraints excluded: chain E residue 146 LEU
Chi-restraints excluded: chain F residue 126 ASP
Chi-restraints excluded: chain G residue 25 ILE
Chi-restraints excluded: chain G residue 129 LEU
Chi-restraints excluded: chain X residue 23 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 101
random chunks:
chunk 88 optimal weight: 5.9990
chunk 75 optimal weight: 7.9990
chunk 56 optimal weight: 4.9990
chunk 41 optimal weight: 6.9990
chunk 38 optimal weight: 3.9990
chunk 86 optimal weight: 2.9990
chunk 39 optimal weight: 0.9980
chunk 51 optimal weight: 2.9990
chunk 49 optimal weight: 0.9990
chunk 60 optimal weight: 3.9990
chunk 43 optimal weight: 0.9980
overall best weight: 1.7986
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** A 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Total number of N/Q/H flips: 0
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.060271 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3064 r_free = 0.3064 target = 0.047882 restraints weight = 39759.423|
|-----------------------------------------------------------------------------|
r_work (start): 0.3025 rms_B_bonded: 5.23
r_work (final): 0.3025
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8387
moved from start: 0.2013
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.005 0.055 8621 Z= 0.284
Angle : 0.766 10.970 11734 Z= 0.369
Chirality : 0.049 0.404 1393
Planarity : 0.004 0.032 1464
Dihedral : 8.381 59.823 1631
Min Nonbonded Distance : 2.551
Molprobity Statistics.
All-atom Clashscore : 10.61
Ramachandran Plot:
Outliers : 0.10 %
Allowed : 4.34 %
Favored : 95.56 %
Rotamer:
Outliers : 3.60 %
Allowed : 21.48 %
Favored : 74.92 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 11.63 %
Cis-general : 0.20 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 0.32 (0.26), residues: 1036
helix: 0.76 (0.33), residues: 230
sheet: 1.59 (0.32), residues: 269
loop : -0.77 (0.26), residues: 537
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.010 0.001 TRP A 198
HIS 0.003 0.001 HIS B 225
PHE 0.037 0.002 PHE Y 50
TYR 0.015 0.001 TYR D 79
ARG 0.003 0.000 ARG E 115
*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
2072 Ramachandran restraints generated.
1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
2072 Ramachandran restraints generated.
1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
198 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 32
poor density : 166
time to evaluate : 0.924
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: A 213 SER cc_start: 0.8644 (OUTLIER) cc_final: 0.8239 (m)
REVERT: A 267 MET cc_start: 0.8757 (mmp) cc_final: 0.8323 (mmp)
REVERT: E 120 GLU cc_start: 0.9020 (pp20) cc_final: 0.8672 (tm-30)
REVERT: G 37 GLN cc_start: 0.6909 (tm-30) cc_final: 0.6655 (tm-30)
REVERT: X 30 LYS cc_start: 0.9572 (mtmt) cc_final: 0.9119 (mmmt)
outliers start: 32
outliers final: 26
residues processed: 187
average time/residue: 0.1949
time to fit residues: 50.8729
Evaluate side-chains
185 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 27
poor density : 158
time to evaluate : 0.972
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 32 VAL
Chi-restraints excluded: chain A residue 135 ILE
Chi-restraints excluded: chain A residue 173 SER
Chi-restraints excluded: chain A residue 185 MET
Chi-restraints excluded: chain A residue 206 CYS
Chi-restraints excluded: chain A residue 213 SER
Chi-restraints excluded: chain A residue 228 CYS
Chi-restraints excluded: chain A residue 271 LEU
Chi-restraints excluded: chain B residue 46 MET
Chi-restraints excluded: chain B residue 84 ASN
Chi-restraints excluded: chain B residue 252 ILE
Chi-restraints excluded: chain B residue 285 LEU
Chi-restraints excluded: chain B residue 293 VAL
Chi-restraints excluded: chain D residue 83 GLU
Chi-restraints excluded: chain D residue 93 CYS
Chi-restraints excluded: chain D residue 118 LEU
Chi-restraints excluded: chain E residue 48 THR
Chi-restraints excluded: chain E residue 98 CYS
Chi-restraints excluded: chain E residue 112 LEU
Chi-restraints excluded: chain E residue 119 CYS
Chi-restraints excluded: chain E residue 145 LEU
Chi-restraints excluded: chain E residue 146 LEU
Chi-restraints excluded: chain F residue 126 ASP
Chi-restraints excluded: chain G residue 25 ILE
Chi-restraints excluded: chain G residue 33 VAL
Chi-restraints excluded: chain G residue 129 LEU
Chi-restraints excluded: chain X residue 23 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 101
random chunks:
chunk 1 optimal weight: 2.9990
chunk 67 optimal weight: 9.9990
chunk 44 optimal weight: 0.8980
chunk 61 optimal weight: 2.9990
chunk 21 optimal weight: 1.9990
chunk 46 optimal weight: 1.9990
chunk 97 optimal weight: 7.9990
chunk 31 optimal weight: 0.7980
chunk 57 optimal weight: 5.9990
chunk 8 optimal weight: 1.9990
chunk 82 optimal weight: 4.9990
overall best weight: 1.5386
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** A 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
Total number of N/Q/H flips: 0
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.060206 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3065 r_free = 0.3065 target = 0.047911 restraints weight = 39651.531|
|-----------------------------------------------------------------------------|
r_work (start): 0.3024 rms_B_bonded: 5.19
r_work (final): 0.3024
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8384
moved from start: 0.2198
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.004 0.064 8621 Z= 0.254
Angle : 0.762 12.292 11734 Z= 0.367
Chirality : 0.048 0.388 1393
Planarity : 0.003 0.033 1464
Dihedral : 8.237 58.975 1631
Min Nonbonded Distance : 2.537
Molprobity Statistics.
All-atom Clashscore : 10.61
Ramachandran Plot:
Outliers : 0.10 %
Allowed : 4.34 %
Favored : 95.56 %
Rotamer:
Outliers : 3.82 %
Allowed : 22.27 %
Favored : 73.90 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 11.63 %
Cis-general : 0.20 %
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: 0.28 (0.26), residues: 1036
helix: 0.64 (0.33), residues: 233
sheet: 1.58 (0.32), residues: 269
loop : -0.78 (0.26), residues: 534
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.009 0.001 TRP A 198
HIS 0.002 0.001 HIS F 61
PHE 0.020 0.001 PHE Y 50
TYR 0.014 0.001 TYR D 79
ARG 0.003 0.000 ARG A 186
*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
2072 Ramachandran restraints generated.
1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
2072 Ramachandran restraints generated.
1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
197 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 34
poor density : 163
time to evaluate : 0.890
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: A 213 SER cc_start: 0.8664 (OUTLIER) cc_final: 0.8253 (m)
REVERT: A 267 MET cc_start: 0.8715 (mmp) cc_final: 0.8318 (mmp)
REVERT: E 91 GLU cc_start: 0.8642 (pm20) cc_final: 0.8309 (pm20)
REVERT: X 30 LYS cc_start: 0.9560 (mtmt) cc_final: 0.9123 (mmmt)
outliers start: 34
outliers final: 28
residues processed: 186
average time/residue: 0.1957
time to fit residues: 50.4965
Evaluate side-chains
182 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 29
poor density : 153
time to evaluate : 1.044
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 32 VAL
Chi-restraints excluded: chain A residue 111 VAL
Chi-restraints excluded: chain A residue 135 ILE
Chi-restraints excluded: chain A residue 173 SER
Chi-restraints excluded: chain A residue 185 MET
Chi-restraints excluded: chain A residue 206 CYS
Chi-restraints excluded: chain A residue 213 SER
Chi-restraints excluded: chain A residue 228 CYS
Chi-restraints excluded: chain A residue 271 LEU
Chi-restraints excluded: chain B residue 46 MET
Chi-restraints excluded: chain B residue 84 ASN
Chi-restraints excluded: chain B residue 121 LEU
Chi-restraints excluded: chain B residue 252 ILE
Chi-restraints excluded: chain B residue 285 LEU
Chi-restraints excluded: chain B residue 293 VAL
Chi-restraints excluded: chain D residue 26 ILE
Chi-restraints excluded: chain D residue 83 GLU
Chi-restraints excluded: chain D residue 93 CYS
Chi-restraints excluded: chain E residue 48 THR
Chi-restraints excluded: chain E residue 98 CYS
Chi-restraints excluded: chain E residue 112 LEU
Chi-restraints excluded: chain E residue 119 CYS
Chi-restraints excluded: chain E residue 122 CYS
Chi-restraints excluded: chain E residue 134 VAL
Chi-restraints excluded: chain E residue 146 LEU
Chi-restraints excluded: chain F residue 126 ASP
Chi-restraints excluded: chain G residue 33 VAL
Chi-restraints excluded: chain G residue 129 LEU
Chi-restraints excluded: chain X residue 23 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 101
random chunks:
chunk 89 optimal weight: 0.7980
chunk 86 optimal weight: 7.9990
chunk 90 optimal weight: 1.9990
chunk 82 optimal weight: 3.9990
chunk 15 optimal weight: 2.9990
chunk 56 optimal weight: 1.9990
chunk 78 optimal weight: 3.9990
chunk 14 optimal weight: 3.9990
chunk 32 optimal weight: 6.9990
chunk 44 optimal weight: 1.9990
chunk 85 optimal weight: 9.9990
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 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
Total number of N/Q/H flips: 0
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.059548 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3044 r_free = 0.3044 target = 0.047201 restraints weight = 40298.274|
|-----------------------------------------------------------------------------|
r_work (start): 0.3006 rms_B_bonded: 5.19
r_work (final): 0.3006
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8405
moved from start: 0.2423
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.005 0.064 8621 Z= 0.307
Angle : 0.785 13.456 11734 Z= 0.381
Chirality : 0.048 0.388 1393
Planarity : 0.004 0.037 1464
Dihedral : 8.282 58.626 1631
Min Nonbonded Distance : 2.380
Molprobity Statistics.
All-atom Clashscore : 11.16
Ramachandran Plot:
Outliers : 0.10 %
Allowed : 4.34 %
Favored : 95.56 %
Rotamer:
Outliers : 4.16 %
Allowed : 23.28 %
Favored : 72.55 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 11.63 %
Cis-general : 0.20 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 0.23 (0.26), residues: 1036
helix: 0.64 (0.33), residues: 233
sheet: 1.50 (0.32), residues: 267
loop : -0.79 (0.26), residues: 536
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.010 0.001 TRP A 198
HIS 0.003 0.001 HIS B 66
PHE 0.037 0.002 PHE Y 50
TYR 0.016 0.001 TYR D 79
ARG 0.008 0.000 ARG E 115
*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
2072 Ramachandran restraints generated.
1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
2072 Ramachandran restraints generated.
1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
196 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 37
poor density : 159
time to evaluate : 0.934
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: A 213 SER cc_start: 0.8675 (OUTLIER) cc_final: 0.8259 (m)
REVERT: D 92 MET cc_start: 0.9300 (mmp) cc_final: 0.8816 (mmp)
REVERT: E 86 GLU cc_start: 0.8596 (mp0) cc_final: 0.8308 (pm20)
REVERT: F 147 LEU cc_start: 0.8546 (tp) cc_final: 0.8158 (mm)
REVERT: X 30 LYS cc_start: 0.9562 (mtmt) cc_final: 0.9134 (mmmt)
outliers start: 37
outliers final: 31
residues processed: 183
average time/residue: 0.1843
time to fit residues: 47.0666
Evaluate side-chains
184 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 32
poor density : 152
time to evaluate : 0.994
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 32 VAL
Chi-restraints excluded: chain A residue 111 VAL
Chi-restraints excluded: chain A residue 135 ILE
Chi-restraints excluded: chain A residue 173 SER
Chi-restraints excluded: chain A residue 185 MET
Chi-restraints excluded: chain A residue 206 CYS
Chi-restraints excluded: chain A residue 213 SER
Chi-restraints excluded: chain A residue 228 CYS
Chi-restraints excluded: chain A residue 271 LEU
Chi-restraints excluded: chain B residue 46 MET
Chi-restraints excluded: chain B residue 60 MET
Chi-restraints excluded: chain B residue 65 ILE
Chi-restraints excluded: chain B residue 84 ASN
Chi-restraints excluded: chain B residue 121 LEU
Chi-restraints excluded: chain B residue 252 ILE
Chi-restraints excluded: chain B residue 285 LEU
Chi-restraints excluded: chain B residue 293 VAL
Chi-restraints excluded: chain D residue 26 ILE
Chi-restraints excluded: chain D residue 83 GLU
Chi-restraints excluded: chain D residue 93 CYS
Chi-restraints excluded: chain D residue 110 THR
Chi-restraints excluded: chain E residue 48 THR
Chi-restraints excluded: chain E residue 98 CYS
Chi-restraints excluded: chain E residue 112 LEU
Chi-restraints excluded: chain E residue 119 CYS
Chi-restraints excluded: chain E residue 145 LEU
Chi-restraints excluded: chain E residue 146 LEU
Chi-restraints excluded: chain F residue 126 ASP
Chi-restraints excluded: chain F residue 133 ILE
Chi-restraints excluded: chain G residue 33 VAL
Chi-restraints excluded: chain G residue 129 LEU
Chi-restraints excluded: chain X residue 23 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 101
random chunks:
chunk 17 optimal weight: 4.9990
chunk 26 optimal weight: 0.0980
chunk 50 optimal weight: 1.9990
chunk 28 optimal weight: 0.9980
chunk 32 optimal weight: 0.0670
chunk 69 optimal weight: 2.9990
chunk 71 optimal weight: 2.9990
chunk 67 optimal weight: 7.9990
chunk 73 optimal weight: 0.9980
chunk 47 optimal weight: 3.9990
chunk 95 optimal weight: 0.8980
overall best weight: 0.6118
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 25 GLN
** A 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
Total number of N/Q/H flips: 1
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.060835 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3083 r_free = 0.3083 target = 0.048485 restraints weight = 39566.954|
|-----------------------------------------------------------------------------|
r_work (start): 0.3044 rms_B_bonded: 5.19
r_work (final): 0.3044
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8360
moved from start: 0.2444
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.059 8621 Z= 0.191
Angle : 0.800 15.847 11734 Z= 0.382
Chirality : 0.048 0.380 1393
Planarity : 0.003 0.047 1464
Dihedral : 8.132 57.520 1631
Min Nonbonded Distance : 2.485
Molprobity Statistics.
All-atom Clashscore : 10.01
Ramachandran Plot:
Outliers : 0.10 %
Allowed : 4.44 %
Favored : 95.46 %
Rotamer:
Outliers : 4.05 %
Allowed : 23.28 %
Favored : 72.67 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 11.63 %
Cis-general : 0.20 %
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: 0.30 (0.26), residues: 1036
helix: 0.67 (0.33), residues: 233
sheet: 1.55 (0.32), residues: 269
loop : -0.74 (0.26), residues: 534
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.008 0.001 TRP D 43
HIS 0.002 0.000 HIS B 66
PHE 0.020 0.001 PHE Y 50
TYR 0.015 0.001 TYR D 79
ARG 0.009 0.000 ARG E 115
*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
2072 Ramachandran restraints generated.
1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
2072 Ramachandran restraints generated.
1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
201 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 36
poor density : 165
time to evaluate : 0.960
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: A 134 TYR cc_start: 0.8792 (t80) cc_final: 0.8383 (t80)
REVERT: A 213 SER cc_start: 0.8628 (OUTLIER) cc_final: 0.8226 (m)
REVERT: A 238 GLU cc_start: 0.7582 (pp20) cc_final: 0.7184 (pp20)
REVERT: A 254 ARG cc_start: 0.9078 (mtp180) cc_final: 0.8800 (mtp180)
REVERT: A 263 PHE cc_start: 0.8736 (t80) cc_final: 0.8364 (t80)
REVERT: A 266 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.7998 (tt)
REVERT: A 267 MET cc_start: 0.8337 (mmp) cc_final: 0.7586 (mmp)
REVERT: D 28 GLU cc_start: 0.8198 (mt-10) cc_final: 0.7870 (mt-10)
REVERT: F 147 LEU cc_start: 0.8555 (tp) cc_final: 0.8177 (mm)
REVERT: X 30 LYS cc_start: 0.9553 (mtmt) cc_final: 0.9115 (mmmt)
outliers start: 36
outliers final: 26
residues processed: 187
average time/residue: 0.1839
time to fit residues: 48.1953
Evaluate side-chains
187 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 28
poor density : 159
time to evaluate : 1.236
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 85 LEU
Chi-restraints excluded: chain A residue 111 VAL
Chi-restraints excluded: chain A residue 135 ILE
Chi-restraints excluded: chain A residue 173 SER
Chi-restraints excluded: chain A residue 185 MET
Chi-restraints excluded: chain A residue 206 CYS
Chi-restraints excluded: chain A residue 213 SER
Chi-restraints excluded: chain A residue 266 LEU
Chi-restraints excluded: chain A residue 271 LEU
Chi-restraints excluded: chain B residue 46 MET
Chi-restraints excluded: chain B residue 60 MET
Chi-restraints excluded: chain B residue 84 ASN
Chi-restraints excluded: chain B residue 121 LEU
Chi-restraints excluded: chain B residue 252 ILE
Chi-restraints excluded: chain B residue 285 LEU
Chi-restraints excluded: chain B residue 293 VAL
Chi-restraints excluded: chain D residue 83 GLU
Chi-restraints excluded: chain D residue 93 CYS
Chi-restraints excluded: chain D residue 110 THR
Chi-restraints excluded: chain E residue 98 CYS
Chi-restraints excluded: chain E residue 112 LEU
Chi-restraints excluded: chain E residue 119 CYS
Chi-restraints excluded: chain E residue 122 CYS
Chi-restraints excluded: chain E residue 134 VAL
Chi-restraints excluded: chain E residue 145 LEU
Chi-restraints excluded: chain E residue 146 LEU
Chi-restraints excluded: chain G residue 129 LEU
Chi-restraints excluded: chain X residue 23 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 101
random chunks:
chunk 31 optimal weight: 4.9990
chunk 78 optimal weight: 3.9990
chunk 72 optimal weight: 6.9990
chunk 44 optimal weight: 3.9990
chunk 84 optimal weight: 0.0980
chunk 4 optimal weight: 0.0980
chunk 33 optimal weight: 0.9990
chunk 11 optimal weight: 4.9990
chunk 1 optimal weight: 0.0980
chunk 35 optimal weight: 4.9990
chunk 64 optimal weight: 0.7980
overall best weight: 0.4182
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** A 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
Total number of N/Q/H flips: 0
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.061199 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3091 r_free = 0.3091 target = 0.048810 restraints weight = 39672.381|
|-----------------------------------------------------------------------------|
r_work (start): 0.3057 rms_B_bonded: 5.23
r_work (final): 0.3057
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8355
moved from start: 0.2529
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.067 8621 Z= 0.198
Angle : 0.840 15.415 11734 Z= 0.397
Chirality : 0.050 0.384 1393
Planarity : 0.003 0.031 1464
Dihedral : 8.123 57.392 1631
Min Nonbonded Distance : 2.486
Molprobity Statistics.
All-atom Clashscore : 10.67
Ramachandran Plot:
Outliers : 0.10 %
Allowed : 4.15 %
Favored : 95.75 %
Rotamer:
Outliers : 3.71 %
Allowed : 23.96 %
Favored : 72.33 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 11.63 %
Cis-general : 0.20 %
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: 0.27 (0.26), residues: 1036
helix: 0.60 (0.33), residues: 235
sheet: 1.58 (0.32), residues: 269
loop : -0.77 (0.26), residues: 532
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.008 0.001 TRP D 43
HIS 0.002 0.000 HIS F 61
PHE 0.041 0.001 PHE Y 50
TYR 0.015 0.001 TYR D 79
ARG 0.006 0.000 ARG E 115
*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
2072 Ramachandran restraints generated.
1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
2072 Ramachandran restraints generated.
1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
197 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 33
poor density : 164
time to evaluate : 0.923
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: A 134 TYR cc_start: 0.8769 (t80) cc_final: 0.8332 (t80)
REVERT: A 213 SER cc_start: 0.8608 (OUTLIER) cc_final: 0.8217 (m)
REVERT: A 254 ARG cc_start: 0.9024 (mtp180) cc_final: 0.8749 (mtp180)
REVERT: A 266 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8052 (tt)
REVERT: A 267 MET cc_start: 0.8269 (mmp) cc_final: 0.7927 (mmm)
REVERT: B 46 MET cc_start: 0.9096 (OUTLIER) cc_final: 0.8614 (ptm)
REVERT: E 86 GLU cc_start: 0.8633 (mp0) cc_final: 0.8260 (pm20)
REVERT: F 147 LEU cc_start: 0.8526 (tp) cc_final: 0.8193 (mm)
REVERT: X 30 LYS cc_start: 0.9556 (mtmt) cc_final: 0.9104 (mmmt)
outliers start: 33
outliers final: 23
residues processed: 185
average time/residue: 0.1941
time to fit residues: 50.0325
Evaluate side-chains
184 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 26
poor density : 158
time to evaluate : 0.950
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 32 VAL
Chi-restraints excluded: chain A residue 111 VAL
Chi-restraints excluded: chain A residue 173 SER
Chi-restraints excluded: chain A residue 206 CYS
Chi-restraints excluded: chain A residue 213 SER
Chi-restraints excluded: chain A residue 228 CYS
Chi-restraints excluded: chain A residue 266 LEU
Chi-restraints excluded: chain A residue 271 LEU
Chi-restraints excluded: chain B residue 46 MET
Chi-restraints excluded: chain B residue 60 MET
Chi-restraints excluded: chain B residue 121 LEU
Chi-restraints excluded: chain B residue 252 ILE
Chi-restraints excluded: chain B residue 293 VAL
Chi-restraints excluded: chain D residue 83 GLU
Chi-restraints excluded: chain D residue 93 CYS
Chi-restraints excluded: chain D residue 110 THR
Chi-restraints excluded: chain E residue 98 CYS
Chi-restraints excluded: chain E residue 112 LEU
Chi-restraints excluded: chain E residue 119 CYS
Chi-restraints excluded: chain E residue 122 CYS
Chi-restraints excluded: chain E residue 134 VAL
Chi-restraints excluded: chain E residue 146 LEU
Chi-restraints excluded: chain G residue 33 VAL
Chi-restraints excluded: chain G residue 129 LEU
Chi-restraints excluded: chain X residue 23 SER
Chi-restraints excluded: chain X residue 31 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 101
random chunks:
chunk 18 optimal weight: 0.6980
chunk 23 optimal weight: 3.9990
chunk 33 optimal weight: 0.7980
chunk 53 optimal weight: 3.9990
chunk 0 optimal weight: 7.9990
chunk 92 optimal weight: 6.9990
chunk 30 optimal weight: 4.9990
chunk 66 optimal weight: 10.0000
chunk 79 optimal weight: 0.6980
chunk 7 optimal weight: 0.9980
chunk 54 optimal weight: 2.9990
overall best weight: 1.2382
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** A 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 212 ASN
** G 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
Total number of N/Q/H flips: 1
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.060129 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3064 r_free = 0.3064 target = 0.047939 restraints weight = 40832.217|
|-----------------------------------------------------------------------------|
r_work (start): 0.3028 rms_B_bonded: 5.21
r_work (final): 0.3028
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8374
moved from start: 0.2587
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.004 0.080 8621 Z= 0.250
Angle : 0.842 14.167 11734 Z= 0.403
Chirality : 0.051 0.451 1393
Planarity : 0.003 0.032 1464
Dihedral : 8.201 57.270 1631
Min Nonbonded Distance : 2.437
Molprobity Statistics.
All-atom Clashscore : 11.04
Ramachandran Plot:
Outliers : 0.10 %
Allowed : 4.34 %
Favored : 95.56 %
Rotamer:
Outliers : 3.82 %
Allowed : 23.51 %
Favored : 72.67 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 11.63 %
Cis-general : 0.20 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 0.26 (0.26), residues: 1036
helix: 0.55 (0.33), residues: 235
sheet: 1.58 (0.32), residues: 269
loop : -0.76 (0.27), residues: 532
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.010 0.001 TRP A 198
HIS 0.002 0.001 HIS F 61
PHE 0.021 0.001 PHE Y 50
TYR 0.015 0.001 TYR D 79
ARG 0.006 0.000 ARG E 115
*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
2072 Ramachandran restraints generated.
1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
2072 Ramachandran restraints generated.
1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
192 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 34
poor density : 158
time to evaluate : 1.005
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: A 213 SER cc_start: 0.8619 (OUTLIER) cc_final: 0.8218 (m)
REVERT: A 254 ARG cc_start: 0.9102 (mtp180) cc_final: 0.8798 (mtp180)
REVERT: A 263 PHE cc_start: 0.8771 (t80) cc_final: 0.8448 (t80)
REVERT: A 267 MET cc_start: 0.8298 (mmp) cc_final: 0.8007 (mmp)
REVERT: B 46 MET cc_start: 0.9107 (OUTLIER) cc_final: 0.8616 (ptm)
REVERT: D 28 GLU cc_start: 0.8136 (mt-10) cc_final: 0.7911 (mt-10)
REVERT: E 86 GLU cc_start: 0.8641 (mp0) cc_final: 0.8256 (pm20)
REVERT: F 147 LEU cc_start: 0.8523 (tp) cc_final: 0.8181 (mm)
REVERT: X 30 LYS cc_start: 0.9555 (mtmt) cc_final: 0.9107 (mmmt)
outliers start: 34
outliers final: 28
residues processed: 180
average time/residue: 0.1949
time to fit residues: 49.0365
Evaluate side-chains
187 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 30
poor density : 157
time to evaluate : 0.917
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 32 VAL
Chi-restraints excluded: chain A residue 111 VAL
Chi-restraints excluded: chain A residue 173 SER
Chi-restraints excluded: chain A residue 185 MET
Chi-restraints excluded: chain A residue 206 CYS
Chi-restraints excluded: chain A residue 213 SER
Chi-restraints excluded: chain A residue 228 CYS
Chi-restraints excluded: chain A residue 266 LEU
Chi-restraints excluded: chain A residue 271 LEU
Chi-restraints excluded: chain B residue 46 MET
Chi-restraints excluded: chain B residue 60 MET
Chi-restraints excluded: chain B residue 65 ILE
Chi-restraints excluded: chain B residue 121 LEU
Chi-restraints excluded: chain B residue 225 HIS
Chi-restraints excluded: chain B residue 252 ILE
Chi-restraints excluded: chain B residue 293 VAL
Chi-restraints excluded: chain D residue 83 GLU
Chi-restraints excluded: chain D residue 93 CYS
Chi-restraints excluded: chain D residue 110 THR
Chi-restraints excluded: chain E residue 48 THR
Chi-restraints excluded: chain E residue 98 CYS
Chi-restraints excluded: chain E residue 112 LEU
Chi-restraints excluded: chain E residue 119 CYS
Chi-restraints excluded: chain E residue 122 CYS
Chi-restraints excluded: chain E residue 145 LEU
Chi-restraints excluded: chain E residue 146 LEU
Chi-restraints excluded: chain G residue 33 VAL
Chi-restraints excluded: chain G residue 129 LEU
Chi-restraints excluded: chain X residue 23 SER
Chi-restraints excluded: chain X residue 31 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 101
random chunks:
chunk 90 optimal weight: 0.9980
chunk 89 optimal weight: 4.9990
chunk 22 optimal weight: 0.6980
chunk 19 optimal weight: 0.7980
chunk 34 optimal weight: 6.9990
chunk 57 optimal weight: 4.9990
chunk 41 optimal weight: 0.8980
chunk 88 optimal weight: 0.7980
chunk 27 optimal weight: 0.6980
chunk 42 optimal weight: 0.0030
chunk 69 optimal weight: 1.9990
overall best weight: 0.5990
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 53 GLN
** G 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
Total number of N/Q/H flips: 1
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.060954 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3086 r_free = 0.3086 target = 0.048781 restraints weight = 39877.861|
|-----------------------------------------------------------------------------|
r_work (start): 0.3052 rms_B_bonded: 5.16
r_work (final): 0.3052
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8349
moved from start: 0.2705
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.074 8621 Z= 0.211
Angle : 0.865 15.645 11734 Z= 0.410
Chirality : 0.050 0.417 1393
Planarity : 0.003 0.030 1464
Dihedral : 8.246 56.951 1631
Min Nonbonded Distance : 2.457
Molprobity Statistics.
All-atom Clashscore : 10.43
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 3.96 %
Favored : 96.04 %
Rotamer:
Outliers : 2.92 %
Allowed : 24.41 %
Favored : 72.67 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 11.63 %
Cis-general : 0.20 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 0.23 (0.26), residues: 1036
helix: 0.52 (0.33), residues: 235
sheet: 1.59 (0.32), residues: 269
loop : -0.78 (0.27), residues: 532
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.009 0.001 TRP D 43
HIS 0.002 0.000 HIS B 66
PHE 0.043 0.002 PHE Y 50
TYR 0.012 0.001 TYR D 79
ARG 0.005 0.000 ARG E 115
********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
2072 Ramachandran restraints generated.
1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
2072 Ramachandran restraints generated.
1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
193 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 26
poor density : 167
time to evaluate : 0.942
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: A 134 TYR cc_start: 0.8808 (t80) cc_final: 0.8355 (t80)
REVERT: A 213 SER cc_start: 0.8596 (OUTLIER) cc_final: 0.8191 (m)
REVERT: A 254 ARG cc_start: 0.9032 (mtp180) cc_final: 0.8757 (mtp180)
REVERT: A 263 PHE cc_start: 0.8767 (t80) cc_final: 0.8399 (t80)
REVERT: A 267 MET cc_start: 0.8325 (mmp) cc_final: 0.7911 (mmp)
REVERT: B 301 MET cc_start: 0.8981 (ppp) cc_final: 0.8757 (ppp)
REVERT: D 28 GLU cc_start: 0.8165 (mt-10) cc_final: 0.7947 (mt-10)
REVERT: E 86 GLU cc_start: 0.8694 (mp0) cc_final: 0.8284 (pm20)
REVERT: F 147 LEU cc_start: 0.8534 (tp) cc_final: 0.8164 (mm)
REVERT: X 30 LYS cc_start: 0.9547 (mtmt) cc_final: 0.9086 (mmmt)
outliers start: 26
outliers final: 24
residues processed: 183
average time/residue: 0.2053
time to fit residues: 51.3110
Evaluate side-chains
188 residues out of total 925 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 25
poor density : 163
time to evaluate : 0.926
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 32 VAL
Chi-restraints excluded: chain A residue 53 GLN
Chi-restraints excluded: chain A residue 111 VAL
Chi-restraints excluded: chain A residue 173 SER
Chi-restraints excluded: chain A residue 185 MET
Chi-restraints excluded: chain A residue 206 CYS
Chi-restraints excluded: chain A residue 213 SER
Chi-restraints excluded: chain A residue 271 LEU
Chi-restraints excluded: chain B residue 46 MET
Chi-restraints excluded: chain B residue 60 MET
Chi-restraints excluded: chain B residue 65 ILE
Chi-restraints excluded: chain B residue 121 LEU
Chi-restraints excluded: chain B residue 252 ILE
Chi-restraints excluded: chain B residue 293 VAL
Chi-restraints excluded: chain D residue 83 GLU
Chi-restraints excluded: chain D residue 93 CYS
Chi-restraints excluded: chain D residue 110 THR
Chi-restraints excluded: chain E residue 98 CYS
Chi-restraints excluded: chain E residue 112 LEU
Chi-restraints excluded: chain E residue 119 CYS
Chi-restraints excluded: chain E residue 122 CYS
Chi-restraints excluded: chain E residue 146 LEU
Chi-restraints excluded: chain G residue 33 VAL
Chi-restraints excluded: chain G residue 129 LEU
Chi-restraints excluded: chain X residue 23 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 101
random chunks:
chunk 100 optimal weight: 8.9990
chunk 55 optimal weight: 4.9990
chunk 99 optimal weight: 0.9990
chunk 75 optimal weight: 0.8980
chunk 58 optimal weight: 5.9990
chunk 25 optimal weight: 3.9990
chunk 68 optimal weight: 7.9990
chunk 73 optimal weight: 1.9990
chunk 34 optimal weight: 9.9990
chunk 70 optimal weight: 2.9990
chunk 93 optimal weight: 0.9990
overall best weight: 1.5788
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** A 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
Total number of N/Q/H flips: 0
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.060046 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3057 r_free = 0.3057 target = 0.047783 restraints weight = 41203.968|
|-----------------------------------------------------------------------------|
r_work (start): 0.3020 rms_B_bonded: 5.21
r_work (final): 0.3020
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8381
moved from start: 0.2703
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.004 0.070 8621 Z= 0.276
Angle : 0.845 13.195 11734 Z= 0.404
Chirality : 0.050 0.435 1393
Planarity : 0.003 0.032 1464
Dihedral : 8.389 59.025 1631
Min Nonbonded Distance : 2.450
Molprobity Statistics.
All-atom Clashscore : 11.40
Ramachandran Plot:
Outliers : 0.10 %
Allowed : 4.63 %
Favored : 95.27 %
Rotamer:
Outliers : 3.26 %
Allowed : 24.18 %
Favored : 72.55 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 11.63 %
Cis-general : 0.20 %
Twisted Proline : 0.00 %
Twisted General : 0.10 %
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: 0.25 (0.26), residues: 1036
helix: 0.62 (0.32), residues: 235
sheet: 1.54 (0.32), residues: 269
loop : -0.78 (0.27), residues: 532
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.010 0.001 TRP A 198
HIS 0.002 0.001 HIS B 225
PHE 0.019 0.001 PHE Y 50
TYR 0.013 0.001 TYR D 79
ARG 0.005 0.000 ARG E 115
Origin is already at (0, 0, 0), no shifts will be applied
===============================================================================
Job complete
usr+sys time: 3286.70 seconds
wall clock time: 59 minutes 47.18 seconds (3587.18 seconds total)