Starting phenix.real_space_refine
on Sat Jan 25 15:48:34 2025 by dcliebschner
===============================================================================
Processing files:
-------------------------------------------------------------------------------
Found model, /net/cci-nas-00/data/ceres_data/8ydb_39167/01_2025/8ydb_39167.cif
Found real_map, /net/cci-nas-00/data/ceres_data/8ydb_39167/01_2025/8ydb_39167.map
Processing PHIL parameters:
-------------------------------------------------------------------------------
Adding command-line PHIL:
-------------------------
refinement.macro_cycles=10
scattering_table=electron
resolution=3.4
write_initial_geo_file=False
Final processed PHIL parameters:
-------------------------------------------------------------------------------
data_manager {
real_map_files = "/net/cci-nas-00/data/ceres_data/8ydb_39167/01_2025/8ydb_39167.map"
default_real_map = "/net/cci-nas-00/data/ceres_data/8ydb_39167/01_2025/8ydb_39167.map"
model {
file = "/net/cci-nas-00/data/ceres_data/8ydb_39167/01_2025/8ydb_39167.cif"
}
default_model = "/net/cci-nas-00/data/ceres_data/8ydb_39167/01_2025/8ydb_39167.cif"
}
resolution = 3.4
write_initial_geo_file = False
refinement {
macro_cycles = 10
}
qi {
qm_restraints {
package {
program = *test
}
}
}
Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.
Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
Set to: 0
Set model cs if undefined
Decide on map wrapping
Map wrapping is set to: False
Normalize map: mean=0, sd=1
Input map: mean= 0.000 sd= 0.001
Set stop_for_unknowns flag
Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
Set to: electron
Number of scattering types: 5
Type Number sf(0) Gaussians
P 102 5.49 5
S 119 5.16 5
C 14874 2.51 5
N 4010 2.21 5
O 4775 1.98 5
sf(0) = scattering factor at diffraction angle 0.
Process input model
Symmetric amino acids flipped. Time to flip 38 residue(s): 0.08s
Monomer Library directory:
"/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
Total number of atoms: 23880
Number of models: 1
Model: ""
Number of chains: 12
Chain: "A"
Number of atoms: 2002
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 254, 2002
Classifications: {'peptide': 254}
Link IDs: {'PTRANS': 8, 'TRANS': 245}
Chain: "B"
Number of atoms: 1415
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 175, 1415
Classifications: {'peptide': 175}
Link IDs: {'PTRANS': 6, 'TRANS': 168}
Chain: "C"
Number of atoms: 1287
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 60, 1287
Classifications: {'RNA': 60}
Modifications used: {'5*END': 1, 'rna2p_pur': 16, 'rna2p_pyr': 11, 'rna3p_pur': 21, 'rna3p_pyr': 11}
Link IDs: {'rna2p': 26, 'rna3p': 33}
Unresolved non-hydrogen bonds: 1
Unresolved non-hydrogen angles: 1
Unresolved non-hydrogen dihedrals: 1
Chain: "I"
Number of atoms: 2639
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 324, 2639
Classifications: {'peptide': 324}
Link IDs: {'PTRANS': 15, 'TRANS': 308}
Chain: "H"
Number of atoms: 2621
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 322, 2621
Classifications: {'peptide': 322}
Link IDs: {'PTRANS': 15, 'TRANS': 306}
Chain: "G"
Number of atoms: 2646
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 325, 2646
Classifications: {'peptide': 325}
Link IDs: {'PTRANS': 15, 'TRANS': 309}
Chain: "F"
Number of atoms: 2628
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 323, 2628
Classifications: {'peptide': 323}
Link IDs: {'PTRANS': 15, 'TRANS': 307}
Chain: "E"
Number of atoms: 2635
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 324, 2635
Classifications: {'peptide': 324}
Link IDs: {'PTRANS': 15, 'TRANS': 308}
Chain: "D"
Number of atoms: 2409
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 295, 2409
Classifications: {'peptide': 295}
Link IDs: {'PTRANS': 11, 'TRANS': 283}
Chain breaks: 1
Chain: "J"
Number of atoms: 2718
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 340, 2718
Classifications: {'peptide': 340}
Incomplete info: {'truncation_to_alanine': 1}
Link IDs: {'PTRANS': 17, 'TRANS': 322}
Unresolved non-hydrogen bonds: 6
Unresolved non-hydrogen angles: 8
Unresolved non-hydrogen dihedrals: 6
Planarities with less than four sites: {'HIS:plan': 1}
Unresolved non-hydrogen planarities: 5
Chain: "T"
Number of atoms: 650
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 32, 650
Classifications: {'DNA': 32}
Link IDs: {'rna3p': 31}
Chain: "N"
Number of atoms: 230
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 11, 230
Classifications: {'DNA': 11}
Link IDs: {'rna3p': 10}
Time building chain proxies: 14.63, per 1000 atoms: 0.61
Number of scatterers: 23880
At special positions: 0
Unit cell: (138.55, 142.8, 161.5, 90, 90, 90)
Space group: P 1 (No. 1)
Number of sites at special positions: 0
Number of scattering types: 5
Type Number sf(0)
S 119 16.00
P 102 15.00
O 4775 8.00
N 4010 7.00
C 14874 6.00
sf(0) = scattering factor at diffraction angle 0.
Number of disulfides: simple=0, symmetry=0
Automatic linking
Parameters for automatic linking
Linking & cutoffs
Metal : Auto - 3.00
Amino acid : True - 1.90
Carbohydrate : True - 1.99
Ligands : True - 1.99
Small molecules : False - 1.98
Amino acid - RNA/DNA : False
Number of custom bonds: simple=0, symmetry=0
Time building additional restraints: 5.78
Conformation dependent library (CDL) restraints added in 2.8 seconds
5324 Ramachandran restraints generated.
2662 Oldfield, 0 Emsley, 2662 emsley8k and 0 Phi/Psi/2.
Adding C-beta torsion restraints...
Number of C-beta restraints generated: 5110
Finding SS restraints...
Secondary structure from input PDB file:
88 helices and 43 sheets defined
35.1% alpha, 20.1% beta
32 base pairs and 48 stacking pairs defined.
Time for finding SS restraints: 9.07
Creating SS restraints...
Processing helix chain 'A' and resid 28 through 46
removed outlier: 3.844A pdb=" N PHE A 32 " --> pdb=" O ALA A 28 " (cutoff:3.500A)
Processing helix chain 'A' and resid 118 through 129
Processing helix chain 'A' and resid 150 through 154
Processing helix chain 'A' and resid 163 through 169
removed outlier: 3.700A pdb=" N LEU A 167 " --> pdb=" O ARG A 163 " (cutoff:3.500A)
Processing helix chain 'A' and resid 174 through 186
Processing helix chain 'A' and resid 236 through 240
removed outlier: 3.702A pdb=" N LEU A 240 " --> pdb=" O ASN A 237 " (cutoff:3.500A)
Processing helix chain 'B' and resid 15 through 24
removed outlier: 3.664A pdb=" N ILE B 19 " --> pdb=" O SER B 15 " (cutoff:3.500A)
removed outlier: 3.592A pdb=" N ILE B 24 " --> pdb=" O ILE B 20 " (cutoff:3.500A)
Processing helix chain 'B' and resid 24 through 35
Processing helix chain 'B' and resid 65 through 72
removed outlier: 3.735A pdb=" N CYS B 72 " --> pdb=" O LEU B 68 " (cutoff:3.500A)
Processing helix chain 'B' and resid 72 through 77
removed outlier: 3.703A pdb=" N HIS B 76 " --> pdb=" O CYS B 72 " (cutoff:3.500A)
Processing helix chain 'B' and resid 107 through 118
Processing helix chain 'B' and resid 123 through 139
removed outlier: 4.505A pdb=" N GLU B 128 " --> pdb=" O GLY B 124 " (cutoff:3.500A)
removed outlier: 5.005A pdb=" N MET B 129 " --> pdb=" O ARG B 125 " (cutoff:3.500A)
removed outlier: 4.151A pdb=" N LYS B 134 " --> pdb=" O HIS B 130 " (cutoff:3.500A)
removed outlier: 3.626A pdb=" N GLN B 137 " --> pdb=" O LYS B 133 " (cutoff:3.500A)
Processing helix chain 'I' and resid 36 through 40
Processing helix chain 'I' and resid 102 through 106
removed outlier: 3.990A pdb=" N MET I 106 " --> pdb=" O LYS I 103 " (cutoff:3.500A)
Processing helix chain 'I' and resid 112 through 129
Processing helix chain 'I' and resid 131 through 144
removed outlier: 3.614A pdb=" N ALA I 135 " --> pdb=" O PHE I 131 " (cutoff:3.500A)
Processing helix chain 'I' and resid 173 through 177
removed outlier: 3.580A pdb=" N PHE I 177 " --> pdb=" O SER I 174 " (cutoff:3.500A)
Processing helix chain 'I' and resid 186 through 202
Processing helix chain 'I' and resid 250 through 259
Processing helix chain 'I' and resid 267 through 271
Processing helix chain 'I' and resid 296 through 305
Processing helix chain 'I' and resid 312 through 326
Processing helix chain 'H' and resid 63 through 68
removed outlier: 4.240A pdb=" N GLU H 68 " --> pdb=" O PRO H 64 " (cutoff:3.500A)
Processing helix chain 'H' and resid 102 through 104
No H-bonds generated for 'chain 'H' and resid 102 through 104'
Processing helix chain 'H' and resid 112 through 129
Processing helix chain 'H' and resid 131 through 144
removed outlier: 3.675A pdb=" N ALA H 135 " --> pdb=" O PHE H 131 " (cutoff:3.500A)
Processing helix chain 'H' and resid 145 through 153
removed outlier: 3.555A pdb=" N TRP H 149 " --> pdb=" O ARG H 146 " (cutoff:3.500A)
removed outlier: 6.325A pdb=" N ARG H 150 " --> pdb=" O PHE H 147 " (cutoff:3.500A)
removed outlier: 3.583A pdb=" N LYS H 153 " --> pdb=" O ARG H 150 " (cutoff:3.500A)
Processing helix chain 'H' and resid 186 through 202
removed outlier: 3.674A pdb=" N GLN H 195 " --> pdb=" O GLU H 191 " (cutoff:3.500A)
Processing helix chain 'H' and resid 250 through 259
removed outlier: 3.682A pdb=" N ASN H 256 " --> pdb=" O GLN H 252 " (cutoff:3.500A)
removed outlier: 3.641A pdb=" N ALA H 257 " --> pdb=" O LYS H 253 " (cutoff:3.500A)
Processing helix chain 'H' and resid 267 through 272
removed outlier: 3.937A pdb=" N TYR H 271 " --> pdb=" O ASP H 267 " (cutoff:3.500A)
Processing helix chain 'H' and resid 296 through 306
removed outlier: 3.650A pdb=" N ASP H 302 " --> pdb=" O TYR H 298 " (cutoff:3.500A)
removed outlier: 3.551A pdb=" N ARG H 303 " --> pdb=" O LYS H 299 " (cutoff:3.500A)
Processing helix chain 'H' and resid 312 through 326
Processing helix chain 'G' and resid 63 through 71
removed outlier: 3.756A pdb=" N ILE G 71 " --> pdb=" O LEU G 67 " (cutoff:3.500A)
Processing helix chain 'G' and resid 102 through 104
No H-bonds generated for 'chain 'G' and resid 102 through 104'
Processing helix chain 'G' and resid 111 through 129
Processing helix chain 'G' and resid 131 through 144
removed outlier: 3.559A pdb=" N ALA G 135 " --> pdb=" O PHE G 131 " (cutoff:3.500A)
Processing helix chain 'G' and resid 145 through 153
removed outlier: 3.530A pdb=" N TRP G 149 " --> pdb=" O ARG G 146 " (cutoff:3.500A)
removed outlier: 6.305A pdb=" N ARG G 150 " --> pdb=" O PHE G 147 " (cutoff:3.500A)
removed outlier: 3.601A pdb=" N LYS G 153 " --> pdb=" O ARG G 150 " (cutoff:3.500A)
Processing helix chain 'G' and resid 186 through 201
Processing helix chain 'G' and resid 250 through 259
removed outlier: 3.533A pdb=" N ASN G 256 " --> pdb=" O GLN G 252 " (cutoff:3.500A)
removed outlier: 3.598A pdb=" N ALA G 257 " --> pdb=" O LYS G 253 " (cutoff:3.500A)
Processing helix chain 'G' and resid 267 through 272
removed outlier: 3.866A pdb=" N TYR G 271 " --> pdb=" O ASP G 267 " (cutoff:3.500A)
Processing helix chain 'G' and resid 296 through 307
removed outlier: 3.585A pdb=" N LYS G 307 " --> pdb=" O ARG G 303 " (cutoff:3.500A)
Processing helix chain 'G' and resid 312 through 326
Processing helix chain 'F' and resid 63 through 71
removed outlier: 3.888A pdb=" N LYS F 69 " --> pdb=" O ASP F 65 " (cutoff:3.500A)
Processing helix chain 'F' and resid 102 through 104
No H-bonds generated for 'chain 'F' and resid 102 through 104'
Processing helix chain 'F' and resid 112 through 129
Processing helix chain 'F' and resid 131 through 144
removed outlier: 3.695A pdb=" N ALA F 135 " --> pdb=" O PHE F 131 " (cutoff:3.500A)
Processing helix chain 'F' and resid 145 through 153
removed outlier: 3.503A pdb=" N TRP F 149 " --> pdb=" O ARG F 146 " (cutoff:3.500A)
removed outlier: 6.287A pdb=" N ARG F 150 " --> pdb=" O PHE F 147 " (cutoff:3.500A)
Processing helix chain 'F' and resid 186 through 202
Processing helix chain 'F' and resid 250 through 260
removed outlier: 3.648A pdb=" N ALA F 257 " --> pdb=" O LYS F 253 " (cutoff:3.500A)
removed outlier: 3.551A pdb=" N THR F 260 " --> pdb=" O ASN F 256 " (cutoff:3.500A)
Processing helix chain 'F' and resid 267 through 272
removed outlier: 3.962A pdb=" N TYR F 271 " --> pdb=" O ASP F 267 " (cutoff:3.500A)
Processing helix chain 'F' and resid 296 through 306
Processing helix chain 'F' and resid 312 through 326
Processing helix chain 'E' and resid 36 through 40
removed outlier: 3.623A pdb=" N ARG E 40 " --> pdb=" O PHE E 37 " (cutoff:3.500A)
Processing helix chain 'E' and resid 66 through 73
removed outlier: 4.496A pdb=" N GLU E 70 " --> pdb=" O LYS E 66 " (cutoff:3.500A)
removed outlier: 3.696A pdb=" N MET E 72 " --> pdb=" O GLU E 68 " (cutoff:3.500A)
Processing helix chain 'E' and resid 102 through 104
No H-bonds generated for 'chain 'E' and resid 102 through 104'
Processing helix chain 'E' and resid 111 through 129
Processing helix chain 'E' and resid 131 through 144
removed outlier: 3.688A pdb=" N ALA E 135 " --> pdb=" O PHE E 131 " (cutoff:3.500A)
Processing helix chain 'E' and resid 145 through 153
removed outlier: 3.677A pdb=" N LEU E 148 " --> pdb=" O ALA E 145 " (cutoff:3.500A)
removed outlier: 3.741A pdb=" N TRP E 149 " --> pdb=" O ARG E 146 " (cutoff:3.500A)
removed outlier: 6.294A pdb=" N ARG E 150 " --> pdb=" O PHE E 147 " (cutoff:3.500A)
Processing helix chain 'E' and resid 186 through 202
Processing helix chain 'E' and resid 250 through 259
removed outlier: 3.733A pdb=" N ALA E 257 " --> pdb=" O LYS E 253 " (cutoff:3.500A)
Processing helix chain 'E' and resid 267 through 272
removed outlier: 4.167A pdb=" N TYR E 271 " --> pdb=" O ASP E 267 " (cutoff:3.500A)
Processing helix chain 'E' and resid 296 through 307
Processing helix chain 'E' and resid 312 through 326
Processing helix chain 'D' and resid 102 through 104
No H-bonds generated for 'chain 'D' and resid 102 through 104'
Processing helix chain 'D' and resid 111 through 129
Processing helix chain 'D' and resid 131 through 144
removed outlier: 3.648A pdb=" N ALA D 135 " --> pdb=" O PHE D 131 " (cutoff:3.500A)
Processing helix chain 'D' and resid 145 through 153
removed outlier: 3.542A pdb=" N LEU D 148 " --> pdb=" O ALA D 145 " (cutoff:3.500A)
removed outlier: 6.241A pdb=" N ARG D 150 " --> pdb=" O PHE D 147 " (cutoff:3.500A)
Processing helix chain 'D' and resid 175 through 177
No H-bonds generated for 'chain 'D' and resid 175 through 177'
Processing helix chain 'D' and resid 186 through 201
Processing helix chain 'D' and resid 250 through 260
removed outlier: 3.670A pdb=" N ILE D 254 " --> pdb=" O HIS D 250 " (cutoff:3.500A)
removed outlier: 3.559A pdb=" N THR D 260 " --> pdb=" O ASN D 256 " (cutoff:3.500A)
Processing helix chain 'D' and resid 267 through 272
removed outlier: 3.529A pdb=" N TYR D 271 " --> pdb=" O ASP D 267 " (cutoff:3.500A)
Processing helix chain 'D' and resid 296 through 306
Processing helix chain 'D' and resid 312 through 326
Processing helix chain 'J' and resid 2 through 10
Processing helix chain 'J' and resid 15 through 31
removed outlier: 4.098A pdb=" N GLY J 26 " --> pdb=" O LYS J 22 " (cutoff:3.500A)
removed outlier: 3.853A pdb=" N LEU J 27 " --> pdb=" O TYR J 23 " (cutoff:3.500A)
removed outlier: 3.921A pdb=" N PHE J 28 " --> pdb=" O ILE J 24 " (cutoff:3.500A)
removed outlier: 4.346A pdb=" N GLN J 29 " --> pdb=" O GLU J 25 " (cutoff:3.500A)
Processing helix chain 'J' and resid 87 through 94
removed outlier: 3.835A pdb=" N GLY J 91 " --> pdb=" O LYS J 87 " (cutoff:3.500A)
Processing helix chain 'J' and resid 102 through 110
Processing helix chain 'J' and resid 111 through 122
Processing helix chain 'J' and resid 124 through 134
removed outlier: 4.224A pdb=" N ASN J 134 " --> pdb=" O ASP J 130 " (cutoff:3.500A)
Processing helix chain 'J' and resid 166 through 179
Processing helix chain 'J' and resid 191 through 199
removed outlier: 4.038A pdb=" N GLY J 199 " --> pdb=" O ALA J 195 " (cutoff:3.500A)
Processing helix chain 'J' and resid 200 through 206
Processing helix chain 'J' and resid 217 through 221
Processing helix chain 'J' and resid 223 through 230
removed outlier: 3.658A pdb=" N LYS J 230 " --> pdb=" O LYS J 226 " (cutoff:3.500A)
Processing helix chain 'J' and resid 255 through 265
Processing helix chain 'J' and resid 281 through 292
removed outlier: 4.247A pdb=" N VAL J 285 " --> pdb=" O LYS J 281 " (cutoff:3.500A)
removed outlier: 3.594A pdb=" N GLN J 286 " --> pdb=" O GLU J 282 " (cutoff:3.500A)
Processing helix chain 'J' and resid 308 through 312
removed outlier: 3.580A pdb=" N GLY J 312 " --> pdb=" O LEU J 309 " (cutoff:3.500A)
Processing helix chain 'J' and resid 325 through 339
Processing sheet with id=AA1, first strand: chain 'A' and resid 133 through 134
removed outlier: 3.537A pdb=" N ILE A 134 " --> pdb=" O GLY A 137 " (cutoff:3.500A)
removed outlier: 3.641A pdb=" N TYR A 5 " --> pdb=" O ILE A 148 " (cutoff:3.500A)
removed outlier: 3.695A pdb=" N LYS A 144 " --> pdb=" O GLU A 9 " (cutoff:3.500A)
Processing sheet with id=AA2, first strand: chain 'A' and resid 133 through 134
removed outlier: 3.537A pdb=" N ILE A 134 " --> pdb=" O GLY A 137 " (cutoff:3.500A)
removed outlier: 3.896A pdb=" N LYS A 10 " --> pdb=" O MET A 106 " (cutoff:3.500A)
removed outlier: 5.760A pdb=" N MET A 106 " --> pdb=" O LYS A 10 " (cutoff:3.500A)
removed outlier: 4.694A pdb=" N ASN A 12 " --> pdb=" O LEU A 104 " (cutoff:3.500A)
removed outlier: 6.864A pdb=" N LEU A 104 " --> pdb=" O ASN A 12 " (cutoff:3.500A)
removed outlier: 5.062A pdb=" N GLU A 14 " --> pdb=" O ILE A 102 " (cutoff:3.500A)
removed outlier: 6.750A pdb=" N ILE A 102 " --> pdb=" O GLU A 14 " (cutoff:3.500A)
removed outlier: 6.251A pdb=" N SER A 107 " --> pdb=" O PHE A 59 " (cutoff:3.500A)
removed outlier: 5.324A pdb=" N PHE A 59 " --> pdb=" O SER A 107 " (cutoff:3.500A)
removed outlier: 7.018A pdb=" N LEU A 109 " --> pdb=" O LEU A 57 " (cutoff:3.500A)
removed outlier: 5.674A pdb=" N LEU A 57 " --> pdb=" O LEU A 109 " (cutoff:3.500A)
removed outlier: 7.326A pdb=" N GLU A 111 " --> pdb=" O VAL A 55 " (cutoff:3.500A)
removed outlier: 6.679A pdb=" N VAL A 55 " --> pdb=" O GLU A 111 " (cutoff:3.500A)
removed outlier: 6.734A pdb=" N GLU A 113 " --> pdb=" O ASN A 53 " (cutoff:3.500A)
removed outlier: 7.115A pdb=" N ASN A 53 " --> pdb=" O GLU A 113 " (cutoff:3.500A)
removed outlier: 14.246A pdb=" N VAL A 55 " --> pdb=" O LEU A 162 " (cutoff:3.500A)
removed outlier: 9.771A pdb=" N LEU A 162 " --> pdb=" O VAL A 55 " (cutoff:3.500A)
removed outlier: 5.446A pdb=" N LEU A 57 " --> pdb=" O LEU A 160 " (cutoff:3.500A)
removed outlier: 3.532A pdb=" N LEU A 160 " --> pdb=" O LEU A 57 " (cutoff:3.500A)
removed outlier: 3.503A pdb=" N GLY A 226 " --> pdb=" O THR A 161 " (cutoff:3.500A)
removed outlier: 3.676A pdb=" N GLY A 195 " --> pdb=" O ILE A 221 " (cutoff:3.500A)
removed outlier: 6.356A pdb=" N SER A 223 " --> pdb=" O ALA A 193 " (cutoff:3.500A)
removed outlier: 5.220A pdb=" N ALA A 193 " --> pdb=" O SER A 223 " (cutoff:3.500A)
removed outlier: 6.372A pdb=" N GLY A 225 " --> pdb=" O PRO A 191 " (cutoff:3.500A)
Processing sheet with id=AA3, first strand: chain 'A' and resid 23 through 25
removed outlier: 5.972A pdb=" N VAL A 24 " --> pdb=" O ALA J 214 " (cutoff:3.500A)
Processing sheet with id=AA4, first strand: chain 'A' and resid 66 through 68
Processing sheet with id=AA5, first strand: chain 'A' and resid 214 through 216
removed outlier: 5.763A pdb=" N ASP A 214 " --> pdb=" O LEU J 160 " (cutoff:3.500A)
Processing sheet with id=AA6, first strand: chain 'A' and resid 242 through 244
Processing sheet with id=AA7, first strand: chain 'B' and resid 39 through 42
Processing sheet with id=AA8, first strand: chain 'B' and resid 39 through 42
removed outlier: 3.804A pdb=" N THR B 91 " --> pdb=" O SER B 3 " (cutoff:3.500A)
Processing sheet with id=AA9, first strand: chain 'B' and resid 98 through 102
removed outlier: 4.181A pdb=" N LEU B 98 " --> pdb=" O THR B 162 " (cutoff:3.500A)
removed outlier: 3.618A pdb=" N ILE B 102 " --> pdb=" O PHE B 158 " (cutoff:3.500A)
removed outlier: 4.438A pdb=" N PHE B 158 " --> pdb=" O ILE B 102 " (cutoff:3.500A)
removed outlier: 4.026A pdb=" N ALA B 142 " --> pdb=" O LEU B 159 " (cutoff:3.500A)
Processing sheet with id=AB1, first strand: chain 'I' and resid 19 through 20
removed outlier: 3.831A pdb=" N SER I 108 " --> pdb=" O SER I 20 " (cutoff:3.500A)
Processing sheet with id=AB2, first strand: chain 'I' and resid 25 through 27
WARNING: can't find start of bonding for strands!
previous: chain 'I' and resid 30 through 35
current: chain 'I' and resid 158 through 163
Processing sheet with id=AB3, first strand: chain 'I' and resid 45 through 46
WARNING: can't find start of bonding for strands!
previous: chain 'I' and resid 90 through 99
current: chain 'I' and resid 242 through 243
Processing sheet with id=AB4, first strand: chain 'I' and resid 50 through 57
removed outlier: 4.569A pdb=" N CYS I 82 " --> pdb=" O VAL I 223 " (cutoff:3.500A)
removed outlier: 3.508A pdb=" N VAL I 223 " --> pdb=" O CYS I 82 " (cutoff:3.500A)
Processing sheet with id=AB5, first strand: chain 'H' and resid 106 through 109
removed outlier: 3.605A pdb=" N SER H 108 " --> pdb=" O SER H 20 " (cutoff:3.500A)
Processing sheet with id=AB6, first strand: chain 'H' and resid 25 through 27
removed outlier: 3.826A pdb=" N ILE H 157 " --> pdb=" O LYS H 216 " (cutoff:3.500A)
Processing sheet with id=AB7, first strand: chain 'H' and resid 45 through 46
removed outlier: 3.826A pdb=" N ILE H 157 " --> pdb=" O LYS H 216 " (cutoff:3.500A)
removed outlier: 3.650A pdb=" N THR H 160 " --> pdb=" O PHE H 172 " (cutoff:3.500A)
Processing sheet with id=AB8, first strand: chain 'H' and resid 50 through 56
Processing sheet with id=AB9, first strand: chain 'H' and resid 242 through 243
Processing sheet with id=AC1, first strand: chain 'H' and resid 260 through 262
Processing sheet with id=AC2, first strand: chain 'G' and resid 20 through 21
Processing sheet with id=AC3, first strand: chain 'G' and resid 25 through 27
WARNING: can't find start of bonding for strands!
previous: chain 'G' and resid 30 through 35
current: chain 'G' and resid 157 through 163
removed outlier: 3.521A pdb=" N THR G 160 " --> pdb=" O PHE G 172 " (cutoff:3.500A)
Processing sheet with id=AC4, first strand: chain 'G' and resid 45 through 46
Processing sheet with id=AC5, first strand: chain 'G' and resid 50 through 56
removed outlier: 4.471A pdb=" N CYS G 82 " --> pdb=" O VAL G 223 " (cutoff:3.500A)
Processing sheet with id=AC6, first strand: chain 'G' and resid 227 through 228
removed outlier: 4.529A pdb=" N LYS G 239 " --> pdb=" O GLU G 228 " (cutoff:3.500A)
Processing sheet with id=AC7, first strand: chain 'G' and resid 260 through 262
Processing sheet with id=AC8, first strand: chain 'G' and resid 282 through 283
removed outlier: 3.634A pdb=" N ALA G 283 " --> pdb=" O ILE G 288 " (cutoff:3.500A)
removed outlier: 3.723A pdb=" N ILE G 288 " --> pdb=" O ALA G 283 " (cutoff:3.500A)
No H-bonds generated for sheet with id=AC8
Processing sheet with id=AC9, first strand: chain 'F' and resid 20 through 21
Processing sheet with id=AD1, first strand: chain 'F' and resid 25 through 27
Processing sheet with id=AD2, first strand: chain 'F' and resid 45 through 46
Processing sheet with id=AD3, first strand: chain 'F' and resid 50 through 56
removed outlier: 4.527A pdb=" N CYS F 82 " --> pdb=" O VAL F 223 " (cutoff:3.500A)
Processing sheet with id=AD4, first strand: chain 'F' and resid 227 through 228
removed outlier: 4.224A pdb=" N LYS F 239 " --> pdb=" O GLU F 228 " (cutoff:3.500A)
Processing sheet with id=AD5, first strand: chain 'F' and resid 242 through 243
Processing sheet with id=AD6, first strand: chain 'E' and resid 19 through 21
removed outlier: 3.754A pdb=" N SER E 108 " --> pdb=" O SER E 20 " (cutoff:3.500A)
Processing sheet with id=AD7, first strand: chain 'E' and resid 25 through 27
WARNING: can't find start of bonding for strands!
previous: chain 'E' and resid 30 through 35
current: chain 'E' and resid 157 through 163
Processing sheet with id=AD8, first strand: chain 'E' and resid 45 through 46
Processing sheet with id=AD9, first strand: chain 'E' and resid 50 through 55
Processing sheet with id=AE1, first strand: chain 'E' and resid 260 through 262
Processing sheet with id=AE2, first strand: chain 'D' and resid 19 through 21
removed outlier: 3.752A pdb=" N SER D 108 " --> pdb=" O SER D 20 " (cutoff:3.500A)
Processing sheet with id=AE3, first strand: chain 'D' and resid 25 through 27
Processing sheet with id=AE4, first strand: chain 'D' and resid 25 through 27
removed outlier: 3.587A pdb=" N ILE D 93 " --> pdb=" O CYS D 213 " (cutoff:3.500A)
Processing sheet with id=AE5, first strand: chain 'D' and resid 242 through 243
Processing sheet with id=AE6, first strand: chain 'J' and resid 35 through 37
Processing sheet with id=AE7, first strand: chain 'J' and resid 301 through 304
853 hydrogen bonds defined for protein.
2286 hydrogen bond angles defined for protein.
Restraints generated for nucleic acids:
80 hydrogen bonds
160 hydrogen bond angles
0 basepair planarities
32 basepair parallelities
48 stacking parallelities
Total time for adding SS restraints: 9.50
Time building geometry restraints manager: 6.69 seconds
NOTE: a complete listing of the restraints can be obtained by requesting
output of .geo file.
Histogram of bond lengths:
1.21 - 1.34: 6953
1.34 - 1.46: 5322
1.46 - 1.58: 11941
1.58 - 1.70: 202
1.70 - 1.82: 191
Bond restraints: 24609
Sorted by residual:
bond pdb=" CA ARG I 146 "
pdb=" C ARG I 146 "
ideal model delta sigma weight residual
1.522 1.497 0.025 1.40e-02 5.10e+03 3.31e+00
bond pdb=" O5' C C 58 "
pdb=" C5' C C 58 "
ideal model delta sigma weight residual
1.420 1.442 -0.022 1.50e-02 4.44e+03 2.06e+00
bond pdb=" CB GLU E 29 "
pdb=" CG GLU E 29 "
ideal model delta sigma weight residual
1.520 1.560 -0.040 3.00e-02 1.11e+03 1.82e+00
bond pdb=" CG1 ILE J 251 "
pdb=" CD1 ILE J 251 "
ideal model delta sigma weight residual
1.513 1.462 0.051 3.90e-02 6.57e+02 1.70e+00
bond pdb=" CA ILE I 288 "
pdb=" CB ILE I 288 "
ideal model delta sigma weight residual
1.537 1.553 -0.016 1.29e-02 6.01e+03 1.53e+00
... (remaining 24604 not shown)
Histogram of bond angle deviations from ideal:
0.00 - 2.11: 33231
2.11 - 4.21: 417
4.21 - 6.32: 42
6.32 - 8.42: 3
8.42 - 10.53: 7
Bond angle restraints: 33700
Sorted by residual:
angle pdb=" CB GLU E 29 "
pdb=" CG GLU E 29 "
pdb=" CD GLU E 29 "
ideal model delta sigma weight residual
112.60 118.74 -6.14 1.70e+00 3.46e-01 1.30e+01
angle pdb=" C ILE D 164 "
pdb=" N GLU D 165 "
pdb=" CA GLU D 165 "
ideal model delta sigma weight residual
120.82 126.17 -5.35 1.50e+00 4.44e-01 1.27e+01
angle pdb=" CB MET D 221 "
pdb=" CG MET D 221 "
pdb=" SD MET D 221 "
ideal model delta sigma weight residual
112.70 123.23 -10.53 3.00e+00 1.11e-01 1.23e+01
angle pdb=" N ARG I 146 "
pdb=" CA ARG I 146 "
pdb=" C ARG I 146 "
ideal model delta sigma weight residual
112.54 108.46 4.08 1.22e+00 6.72e-01 1.12e+01
angle pdb=" CA GLY D 218 "
pdb=" C GLY D 218 "
pdb=" N CYS D 219 "
ideal model delta sigma weight residual
114.23 117.13 -2.90 8.80e-01 1.29e+00 1.09e+01
... (remaining 33695 not shown)
Histogram of dihedral angle deviations from ideal:
0.00 - 33.17: 13910
33.17 - 66.35: 907
66.35 - 99.52: 76
99.52 - 132.70: 0
132.70 - 165.87: 1
Dihedral angle restraints: 14894
sinusoidal: 6984
harmonic: 7910
Sorted by residual:
dihedral pdb=" O4' U C 42 "
pdb=" C1' U C 42 "
pdb=" N1 U C 42 "
pdb=" C2 U C 42 "
ideal model delta sinusoidal sigma weight residual
232.00 66.13 165.87 1 1.70e+01 3.46e-03 6.54e+01
dihedral pdb=" O4' C C 16 "
pdb=" C1' C C 16 "
pdb=" N1 C C 16 "
pdb=" C2 C C 16 "
ideal model delta sinusoidal sigma weight residual
-128.00 -50.55 -77.45 1 1.70e+01 3.46e-03 2.60e+01
dihedral pdb=" CA ASP B 36 "
pdb=" C ASP B 36 "
pdb=" N LYS B 37 "
pdb=" CA LYS B 37 "
ideal model delta harmonic sigma weight residual
180.00 156.37 23.63 0 5.00e+00 4.00e-02 2.23e+01
... (remaining 14891 not shown)
Histogram of chiral volume deviations from ideal:
0.000 - 0.039: 2677
0.039 - 0.077: 811
0.077 - 0.116: 176
0.116 - 0.154: 69
0.154 - 0.193: 6
Chirality restraints: 3739
Sorted by residual:
chirality pdb=" C2' U C 1 "
pdb=" C3' U C 1 "
pdb=" O2' U C 1 "
pdb=" C1' U C 1 "
both_signs ideal model delta sigma weight residual
False -2.79 -2.60 -0.19 2.00e-01 2.50e+01 9.30e-01
chirality pdb=" C3' G C 41 "
pdb=" C4' G C 41 "
pdb=" O3' G C 41 "
pdb=" C2' G C 41 "
both_signs ideal model delta sigma weight residual
False -2.48 -2.66 0.19 2.00e-01 2.50e+01 8.73e-01
chirality pdb=" C1' A C 22 "
pdb=" O4' A C 22 "
pdb=" C2' A C 22 "
pdb=" N9 A C 22 "
both_signs ideal model delta sigma weight residual
False 2.46 2.27 0.18 2.00e-01 2.50e+01 8.39e-01
... (remaining 3736 not shown)
Planarity restraints: 3950
Sorted by residual:
delta sigma weight rms_deltas residual
plane pdb=" C ASN H 75 " 0.044 5.00e-02 4.00e+02 6.68e-02 7.13e+00
pdb=" N PRO H 76 " -0.115 5.00e-02 4.00e+02
pdb=" CA PRO H 76 " 0.035 5.00e-02 4.00e+02
pdb=" CD PRO H 76 " 0.036 5.00e-02 4.00e+02
delta sigma weight rms_deltas residual
plane pdb=" CB PHE F 273 " 0.012 2.00e-02 2.50e+03 1.80e-02 5.69e+00
pdb=" CG PHE F 273 " -0.041 2.00e-02 2.50e+03
pdb=" CD1 PHE F 273 " 0.015 2.00e-02 2.50e+03
pdb=" CD2 PHE F 273 " 0.014 2.00e-02 2.50e+03
pdb=" CE1 PHE F 273 " -0.001 2.00e-02 2.50e+03
pdb=" CE2 PHE F 273 " 0.000 2.00e-02 2.50e+03
pdb=" CZ PHE F 273 " -0.000 2.00e-02 2.50e+03
delta sigma weight rms_deltas residual
plane pdb=" C ILE I 288 " 0.033 5.00e-02 4.00e+02 5.03e-02 4.04e+00
pdb=" N PRO I 289 " -0.087 5.00e-02 4.00e+02
pdb=" CA PRO I 289 " 0.026 5.00e-02 4.00e+02
pdb=" CD PRO I 289 " 0.028 5.00e-02 4.00e+02
... (remaining 3947 not shown)
Histogram of nonbonded interaction distances:
2.22 - 2.76: 3923
2.76 - 3.29: 21305
3.29 - 3.83: 39441
3.83 - 4.36: 46178
4.36 - 4.90: 81021
Nonbonded interactions: 191868
Sorted by model distance:
nonbonded pdb=" O2' G C 5 "
pdb=" O PHE I 21 "
model vdw
2.225 3.040
nonbonded pdb=" OH TYR B 108 "
pdb=" O GLY B 124 "
model vdw
2.226 3.040
nonbonded pdb=" O ALA D 143 "
pdb=" OG SER D 174 "
model vdw
2.226 3.040
nonbonded pdb=" O2' C C 29 "
pdb=" O PHE E 21 "
model vdw
2.237 3.040
nonbonded pdb=" O SER D 105 "
pdb=" OG SER D 105 "
model vdw
2.261 3.040
... (remaining 191863 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 'D' and resid 12 through 332)
selection = (chain 'E' and (resid 12 through 51 or resid 79 through 332))
selection = (chain 'F' and (resid 12 through 51 or resid 79 through 332))
selection = (chain 'G' and (resid 12 through 51 or resid 79 through 332))
selection = (chain 'H' and (resid 12 through 51 or resid 79 through 332))
selection = (chain 'I' and (resid 12 through 51 or resid 79 through 332))
}
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: 2.750
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: 0.030
Extract box with map and model: 0.980
Check model and map are aligned: 0.170
Set scattering table: 0.210
Process input model: 60.150
Find NCS groups from input model: 0.840
Set up NCS constraints: 0.110
Set refine NCS operators: 0.000
Adjust number of macro_cycles: 0.000
Reset NCS operators: 0.000
Extract rigid body selections: 0.000
Check and reset occupancies: 0.010
Load rotamer database and sin/cos tables:2.720
Set ADP refinement strategy: 0.000
Make a string to write initial .geo file:0.000
Internal consistency checks: 0.000
Total: 67.970
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7657
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 0.051 24609 Z= 0.213
Angle : 0.585 10.526 33700 Z= 0.317
Chirality : 0.041 0.193 3739
Planarity : 0.004 0.067 3950
Dihedral : 19.622 165.872 9784
Min Nonbonded Distance : 2.225
Molprobity Statistics.
All-atom Clashscore : 5.90
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 6.20 %
Favored : 93.80 %
Rotamer:
Outliers : 0.42 %
Allowed : 29.07 %
Favored : 70.51 %
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: -0.84 (0.16), residues: 2662
helix: 0.47 (0.18), residues: 770
sheet: 1.02 (0.27), residues: 430
loop : -1.70 (0.15), residues: 1462
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.008 0.001 TRP J 74
HIS 0.015 0.001 HIS A 181
PHE 0.041 0.001 PHE F 273
TYR 0.016 0.001 TYR A 142
ARG 0.006 0.000 ARG A 51
*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
5324 Ramachandran restraints generated.
2662 Oldfield, 0 Emsley, 2662 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
5324 Ramachandran restraints generated.
2662 Oldfield, 0 Emsley, 2662 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
217 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 10
poor density : 207
time to evaluate : 2.564
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: H 229 MET cc_start: 0.8355 (tpp) cc_final: 0.7945 (tpp)
outliers start: 10
outliers final: 2
residues processed: 214
average time/residue: 0.3548
time to fit residues: 119.6601
Evaluate side-chains
140 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 2
poor density : 138
time to evaluate : 2.722
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue 171 SER
Chi-restraints excluded: chain G residue 42 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 275
random chunks:
chunk 232 optimal weight: 2.9990
chunk 208 optimal weight: 0.9990
chunk 115 optimal weight: 10.0000
chunk 71 optimal weight: 9.9990
chunk 140 optimal weight: 9.9990
chunk 111 optimal weight: 10.0000
chunk 215 optimal weight: 1.9990
chunk 83 optimal weight: 4.9990
chunk 131 optimal weight: 10.0000
chunk 160 optimal weight: 7.9990
chunk 249 optimal weight: 10.0000
overall best weight: 3.7990
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 21 ASN
A 53 ASN
** H 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
J 106 HIS
Total number of N/Q/H flips: 3
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3085 r_free = 0.3085 target = 0.047597 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.2585 r_free = 0.2585 target = 0.032197 restraints weight = 117350.768|
|-----------------------------------------------------------------------------|
r_work (start): 0.2573 rms_B_bonded: 4.32
r_work (final): 0.2573
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8865
moved from start: 0.1274
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.004 0.071 24609 Z= 0.275
Angle : 0.568 8.625 33700 Z= 0.303
Chirality : 0.039 0.221 3739
Planarity : 0.004 0.061 3950
Dihedral : 16.112 159.589 4301
Min Nonbonded Distance : 2.432
Molprobity Statistics.
All-atom Clashscore : 6.89
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 6.61 %
Favored : 93.39 %
Rotamer:
Outliers : 2.51 %
Allowed : 26.64 %
Favored : 70.85 %
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 (0.17), residues: 2662
helix: 1.16 (0.19), residues: 799
sheet: 0.88 (0.27), residues: 435
loop : -1.48 (0.16), residues: 1428
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.010 0.001 TRP G 33
HIS 0.007 0.001 HIS J 116
PHE 0.012 0.001 PHE H 95
TYR 0.013 0.001 TYR B 155
ARG 0.009 0.000 ARG A 146
*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
5324 Ramachandran restraints generated.
2662 Oldfield, 0 Emsley, 2662 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
5324 Ramachandran restraints generated.
2662 Oldfield, 0 Emsley, 2662 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
197 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 60
poor density : 137
time to evaluate : 2.648
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: A 71 ARG cc_start: 0.9311 (mpp80) cc_final: 0.8939 (mpp80)
REVERT: A 163 ARG cc_start: 0.8699 (mmm-85) cc_final: 0.8475 (mmm-85)
REVERT: A 249 LEU cc_start: 0.9561 (OUTLIER) cc_final: 0.9334 (mm)
REVERT: B 71 LEU cc_start: 0.9393 (mt) cc_final: 0.9129 (mt)
REVERT: B 83 TYR cc_start: 0.9116 (m-80) cc_final: 0.8806 (m-80)
REVERT: B 115 MET cc_start: 0.9283 (tpt) cc_final: 0.8670 (tpt)
REVERT: H 91 LEU cc_start: 0.9221 (OUTLIER) cc_final: 0.8804 (tp)
REVERT: H 229 MET cc_start: 0.9134 (tpp) cc_final: 0.7649 (tpp)
REVERT: G 120 GLN cc_start: 0.8601 (tm-30) cc_final: 0.8326 (tm-30)
REVERT: G 249 MET cc_start: 0.9071 (mtp) cc_final: 0.8786 (ttm)
REVERT: F 62 MET cc_start: 0.7375 (pmm) cc_final: 0.6654 (pmm)
REVERT: F 120 GLN cc_start: 0.8868 (tm-30) cc_final: 0.8574 (tm-30)
REVERT: E 313 ILE cc_start: 0.8966 (OUTLIER) cc_final: 0.8759 (tp)
REVERT: D 221 MET cc_start: 0.7703 (mmm) cc_final: 0.7387 (mmm)
REVERT: J 62 MET cc_start: 0.8057 (mpt) cc_final: 0.7837 (mmt)
REVERT: J 138 MET cc_start: 0.8230 (ppp) cc_final: 0.7530 (ppp)
outliers start: 60
outliers final: 27
residues processed: 188
average time/residue: 0.3921
time to fit residues: 116.8651
Evaluate side-chains
151 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 30
poor density : 121
time to evaluate : 2.707
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 8 LEU
Chi-restraints excluded: chain A residue 104 LEU
Chi-restraints excluded: chain A residue 121 THR
Chi-restraints excluded: chain A residue 150 THR
Chi-restraints excluded: chain A residue 192 ILE
Chi-restraints excluded: chain A residue 249 LEU
Chi-restraints excluded: chain B residue 42 THR
Chi-restraints excluded: chain B residue 123 LEU
Chi-restraints excluded: chain I residue 102 VAL
Chi-restraints excluded: chain I residue 223 VAL
Chi-restraints excluded: chain I residue 270 THR
Chi-restraints excluded: chain I residue 277 VAL
Chi-restraints excluded: chain H residue 91 LEU
Chi-restraints excluded: chain H residue 116 THR
Chi-restraints excluded: chain G residue 27 THR
Chi-restraints excluded: chain G residue 329 PHE
Chi-restraints excluded: chain F residue 267 ASP
Chi-restraints excluded: chain E residue 83 THR
Chi-restraints excluded: chain E residue 296 SER
Chi-restraints excluded: chain E residue 313 ILE
Chi-restraints excluded: chain D residue 88 CYS
Chi-restraints excluded: chain D residue 99 VAL
Chi-restraints excluded: chain D residue 142 ILE
Chi-restraints excluded: chain D residue 212 THR
Chi-restraints excluded: chain D residue 223 VAL
Chi-restraints excluded: chain D residue 233 ASP
Chi-restraints excluded: chain D residue 324 ILE
Chi-restraints excluded: chain J residue 167 THR
Chi-restraints excluded: chain J residue 272 ARG
Chi-restraints excluded: chain J residue 320 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 275
random chunks:
chunk 248 optimal weight: 20.0000
chunk 5 optimal weight: 20.0000
chunk 206 optimal weight: 10.0000
chunk 189 optimal weight: 6.9990
chunk 53 optimal weight: 5.9990
chunk 141 optimal weight: 9.9990
chunk 211 optimal weight: 4.9990
chunk 54 optimal weight: 20.0000
chunk 34 optimal weight: 6.9990
chunk 187 optimal weight: 5.9990
chunk 57 optimal weight: 9.9990
overall best weight: 6.1990
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
B 29 HIS
** H 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 140 ASN
J 106 HIS
Total number of N/Q/H flips: 3
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3050 r_free = 0.3050 target = 0.045704 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2563 r_free = 0.2563 target = 0.031035 restraints weight = 120098.242|
|-----------------------------------------------------------------------------|
r_work (start): 0.2519 rms_B_bonded: 4.11
r_work: 0.2364 rms_B_bonded: 4.89 restraints_weight: 0.5000
r_work (final): 0.2364
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9022
moved from start: 0.1891
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.006 0.110 24609 Z= 0.416
Angle : 0.621 6.929 33700 Z= 0.329
Chirality : 0.041 0.246 3739
Planarity : 0.004 0.061 3950
Dihedral : 16.268 162.411 4299
Min Nonbonded Distance : 2.438
Molprobity Statistics.
All-atom Clashscore : 8.97
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 6.91 %
Favored : 93.09 %
Rotamer:
Outliers : 4.31 %
Allowed : 25.22 %
Favored : 70.47 %
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: -0.46 (0.17), residues: 2662
helix: 1.22 (0.19), residues: 798
sheet: 0.39 (0.27), residues: 432
loop : -1.48 (0.16), residues: 1432
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.010 0.001 TRP G 33
HIS 0.007 0.001 HIS J 116
PHE 0.024 0.002 PHE J 92
TYR 0.021 0.002 TYR J 301
ARG 0.004 0.001 ARG J 88
*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
5324 Ramachandran restraints generated.
2662 Oldfield, 0 Emsley, 2662 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
5324 Ramachandran restraints generated.
2662 Oldfield, 0 Emsley, 2662 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
222 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 103
poor density : 119
time to evaluate : 2.639
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: A 163 ARG cc_start: 0.8993 (mmm-85) cc_final: 0.8595 (mmm-85)
REVERT: A 249 LEU cc_start: 0.9573 (OUTLIER) cc_final: 0.9344 (mm)
REVERT: B 71 LEU cc_start: 0.9447 (mt) cc_final: 0.9175 (mt)
REVERT: B 83 TYR cc_start: 0.9167 (m-80) cc_final: 0.8854 (m-80)
REVERT: B 115 MET cc_start: 0.9099 (tpt) cc_final: 0.8552 (tpt)
REVERT: I 106 MET cc_start: 0.9302 (ttp) cc_final: 0.8770 (tmm)
REVERT: H 91 LEU cc_start: 0.9417 (OUTLIER) cc_final: 0.8956 (tp)
REVERT: H 204 ARG cc_start: 0.9178 (OUTLIER) cc_final: 0.8892 (ttm110)
REVERT: H 229 MET cc_start: 0.9423 (tpp) cc_final: 0.7998 (tpp)
REVERT: G 120 GLN cc_start: 0.9008 (tm-30) cc_final: 0.8667 (tm-30)
REVERT: G 236 LYS cc_start: 0.9448 (OUTLIER) cc_final: 0.9062 (mmtt)
REVERT: G 304 MET cc_start: 0.9492 (ttt) cc_final: 0.9239 (tmm)
REVERT: F 120 GLN cc_start: 0.9195 (tm-30) cc_final: 0.8935 (tm-30)
REVERT: E 221 MET cc_start: 0.9097 (mmt) cc_final: 0.8876 (mmt)
REVERT: D 221 MET cc_start: 0.8223 (mmm) cc_final: 0.7948 (mmm)
REVERT: D 259 ARG cc_start: 0.8816 (OUTLIER) cc_final: 0.7505 (ttp80)
REVERT: J 46 THR cc_start: 0.9749 (OUTLIER) cc_final: 0.9402 (t)
REVERT: J 62 MET cc_start: 0.8252 (mpt) cc_final: 0.7964 (mmt)
REVERT: J 104 MET cc_start: 0.8675 (OUTLIER) cc_final: 0.8350 (mtm)
REVERT: J 135 MET cc_start: 0.8606 (OUTLIER) cc_final: 0.8331 (tmm)
REVERT: J 138 MET cc_start: 0.8609 (ppp) cc_final: 0.8292 (ppp)
outliers start: 103
outliers final: 55
residues processed: 211
average time/residue: 0.3702
time to fit residues: 124.4355
Evaluate side-chains
172 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 63
poor density : 109
time to evaluate : 2.952
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 8 LEU
Chi-restraints excluded: chain A residue 40 GLU
Chi-restraints excluded: chain A residue 76 THR
Chi-restraints excluded: chain A residue 104 LEU
Chi-restraints excluded: chain A residue 121 THR
Chi-restraints excluded: chain A residue 150 THR
Chi-restraints excluded: chain A residue 192 ILE
Chi-restraints excluded: chain A residue 205 VAL
Chi-restraints excluded: chain A residue 249 LEU
Chi-restraints excluded: chain B residue 19 ILE
Chi-restraints excluded: chain B residue 27 VAL
Chi-restraints excluded: chain B residue 42 THR
Chi-restraints excluded: chain B residue 60 VAL
Chi-restraints excluded: chain B residue 64 ASP
Chi-restraints excluded: chain B residue 123 LEU
Chi-restraints excluded: chain B residue 146 VAL
Chi-restraints excluded: chain I residue 102 VAL
Chi-restraints excluded: chain I residue 113 ASN
Chi-restraints excluded: chain I residue 181 THR
Chi-restraints excluded: chain I residue 223 VAL
Chi-restraints excluded: chain I residue 270 THR
Chi-restraints excluded: chain I residue 277 VAL
Chi-restraints excluded: chain H residue 83 THR
Chi-restraints excluded: chain H residue 91 LEU
Chi-restraints excluded: chain H residue 99 VAL
Chi-restraints excluded: chain H residue 108 SER
Chi-restraints excluded: chain H residue 116 THR
Chi-restraints excluded: chain H residue 185 ASP
Chi-restraints excluded: chain H residue 204 ARG
Chi-restraints excluded: chain H residue 267 ASP
Chi-restraints excluded: chain G residue 27 THR
Chi-restraints excluded: chain G residue 73 ASP
Chi-restraints excluded: chain G residue 236 LYS
Chi-restraints excluded: chain G residue 329 PHE
Chi-restraints excluded: chain F residue 27 THR
Chi-restraints excluded: chain F residue 140 ASN
Chi-restraints excluded: chain F residue 253 LYS
Chi-restraints excluded: chain F residue 267 ASP
Chi-restraints excluded: chain E residue 27 THR
Chi-restraints excluded: chain E residue 83 THR
Chi-restraints excluded: chain E residue 91 LEU
Chi-restraints excluded: chain E residue 132 LEU
Chi-restraints excluded: chain E residue 296 SER
Chi-restraints excluded: chain D residue 50 THR
Chi-restraints excluded: chain D residue 88 CYS
Chi-restraints excluded: chain D residue 99 VAL
Chi-restraints excluded: chain D residue 212 THR
Chi-restraints excluded: chain D residue 223 VAL
Chi-restraints excluded: chain D residue 233 ASP
Chi-restraints excluded: chain D residue 259 ARG
Chi-restraints excluded: chain D residue 275 ILE
Chi-restraints excluded: chain D residue 324 ILE
Chi-restraints excluded: chain D residue 329 PHE
Chi-restraints excluded: chain J residue 46 THR
Chi-restraints excluded: chain J residue 75 LYS
Chi-restraints excluded: chain J residue 104 MET
Chi-restraints excluded: chain J residue 111 SER
Chi-restraints excluded: chain J residue 116 HIS
Chi-restraints excluded: chain J residue 135 MET
Chi-restraints excluded: chain J residue 167 THR
Chi-restraints excluded: chain J residue 250 LEU
Chi-restraints excluded: chain J residue 272 ARG
Chi-restraints excluded: chain J residue 285 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 275
random chunks:
chunk 88 optimal weight: 7.9990
chunk 118 optimal weight: 20.0000
chunk 25 optimal weight: 10.0000
chunk 20 optimal weight: 9.9990
chunk 137 optimal weight: 0.7980
chunk 130 optimal weight: 5.9990
chunk 0 optimal weight: 10.0000
chunk 196 optimal weight: 4.9990
chunk 271 optimal weight: 20.0000
chunk 214 optimal weight: 5.9990
chunk 93 optimal weight: 0.8980
overall best weight: 3.7386
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
H 120 GLN
H 178 ASN
Total number of N/Q/H flips: 2
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3044 r_free = 0.3044 target = 0.045914 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2550 r_free = 0.2550 target = 0.031016 restraints weight = 119071.995|
|-----------------------------------------------------------------------------|
r_work (start): 0.2537 rms_B_bonded: 4.19
r_work: 0.2382 rms_B_bonded: 4.95 restraints_weight: 0.5000
r_work (final): 0.2382
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9002
moved from start: 0.2025
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.004 0.064 24609 Z= 0.261
Angle : 0.549 8.222 33700 Z= 0.291
Chirality : 0.039 0.242 3739
Planarity : 0.004 0.054 3950
Dihedral : 16.257 161.051 4299
Min Nonbonded Distance : 2.458
Molprobity Statistics.
All-atom Clashscore : 7.60
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 6.09 %
Favored : 93.91 %
Rotamer:
Outliers : 3.55 %
Allowed : 25.68 %
Favored : 70.77 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: -0.32 (0.17), residues: 2662
helix: 1.41 (0.19), residues: 798
sheet: 0.52 (0.27), residues: 425
loop : -1.45 (0.16), residues: 1439
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.006 0.001 TRP G 33
HIS 0.007 0.001 HIS J 116
PHE 0.020 0.001 PHE J 92
TYR 0.027 0.001 TYR G 169
ARG 0.010 0.000 ARG A 146
*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
5324 Ramachandran restraints generated.
2662 Oldfield, 0 Emsley, 2662 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
5324 Ramachandran restraints generated.
2662 Oldfield, 0 Emsley, 2662 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
202 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 85
poor density : 117
time to evaluate : 2.652
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: A 73 GLN cc_start: 0.9103 (pm20) cc_final: 0.8676 (pm20)
REVERT: A 163 ARG cc_start: 0.8925 (mmm-85) cc_final: 0.8569 (mmm-85)
REVERT: A 249 LEU cc_start: 0.9573 (OUTLIER) cc_final: 0.9340 (mm)
REVERT: B 49 ASP cc_start: 0.9426 (p0) cc_final: 0.9198 (p0)
REVERT: B 71 LEU cc_start: 0.9443 (mt) cc_final: 0.9175 (mt)
REVERT: B 115 MET cc_start: 0.9087 (tpt) cc_final: 0.8617 (tpt)
REVERT: I 70 GLU cc_start: 0.9168 (OUTLIER) cc_final: 0.8857 (mp0)
REVERT: I 106 MET cc_start: 0.9278 (ttp) cc_final: 0.8788 (tmm)
REVERT: H 229 MET cc_start: 0.9352 (tpp) cc_final: 0.7891 (tpp)
REVERT: H 304 MET cc_start: 0.9462 (ttt) cc_final: 0.9189 (tmm)
REVERT: G 120 GLN cc_start: 0.8970 (tm-30) cc_final: 0.8596 (tm-30)
REVERT: G 236 LYS cc_start: 0.9451 (OUTLIER) cc_final: 0.9099 (mmtt)
REVERT: G 304 MET cc_start: 0.9464 (ttt) cc_final: 0.9237 (tmm)
REVERT: G 328 MET cc_start: 0.9113 (ppp) cc_final: 0.8901 (ppp)
REVERT: F 62 MET cc_start: 0.7351 (pmm) cc_final: 0.6698 (pmm)
REVERT: F 120 GLN cc_start: 0.9217 (tm-30) cc_final: 0.8942 (tm-30)
REVERT: E 106 MET cc_start: 0.8856 (ttp) cc_final: 0.8534 (tmm)
REVERT: E 221 MET cc_start: 0.9140 (mmt) cc_final: 0.8928 (mmt)
REVERT: D 221 MET cc_start: 0.8225 (mmm) cc_final: 0.7928 (mmm)
REVERT: D 301 ILE cc_start: 0.9527 (OUTLIER) cc_final: 0.9271 (tp)
REVERT: J 62 MET cc_start: 0.8308 (mpt) cc_final: 0.8053 (mmt)
REVERT: J 104 MET cc_start: 0.8665 (OUTLIER) cc_final: 0.8348 (mtm)
REVERT: J 135 MET cc_start: 0.8437 (OUTLIER) cc_final: 0.8195 (tmm)
REVERT: J 322 MET cc_start: 0.7966 (tpp) cc_final: 0.7745 (tpp)
outliers start: 85
outliers final: 53
residues processed: 189
average time/residue: 0.3600
time to fit residues: 110.3062
Evaluate side-chains
170 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 59
poor density : 111
time to evaluate : 2.994
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 8 LEU
Chi-restraints excluded: chain A residue 33 LEU
Chi-restraints excluded: chain A residue 76 THR
Chi-restraints excluded: chain A residue 104 LEU
Chi-restraints excluded: chain A residue 106 MET
Chi-restraints excluded: chain A residue 121 THR
Chi-restraints excluded: chain A residue 150 THR
Chi-restraints excluded: chain A residue 192 ILE
Chi-restraints excluded: chain A residue 205 VAL
Chi-restraints excluded: chain A residue 249 LEU
Chi-restraints excluded: chain A residue 250 TYR
Chi-restraints excluded: chain B residue 19 ILE
Chi-restraints excluded: chain B residue 42 THR
Chi-restraints excluded: chain B residue 60 VAL
Chi-restraints excluded: chain B residue 123 LEU
Chi-restraints excluded: chain B residue 146 VAL
Chi-restraints excluded: chain I residue 70 GLU
Chi-restraints excluded: chain I residue 93 ILE
Chi-restraints excluded: chain I residue 102 VAL
Chi-restraints excluded: chain I residue 113 ASN
Chi-restraints excluded: chain I residue 223 VAL
Chi-restraints excluded: chain I residue 270 THR
Chi-restraints excluded: chain I residue 277 VAL
Chi-restraints excluded: chain H residue 83 THR
Chi-restraints excluded: chain H residue 108 SER
Chi-restraints excluded: chain H residue 116 THR
Chi-restraints excluded: chain H residue 142 ILE
Chi-restraints excluded: chain H residue 185 ASP
Chi-restraints excluded: chain G residue 27 THR
Chi-restraints excluded: chain G residue 73 ASP
Chi-restraints excluded: chain G residue 236 LYS
Chi-restraints excluded: chain G residue 267 ASP
Chi-restraints excluded: chain G residue 329 PHE
Chi-restraints excluded: chain F residue 27 THR
Chi-restraints excluded: chain F residue 267 ASP
Chi-restraints excluded: chain E residue 83 THR
Chi-restraints excluded: chain E residue 91 LEU
Chi-restraints excluded: chain E residue 296 SER
Chi-restraints excluded: chain D residue 27 THR
Chi-restraints excluded: chain D residue 50 THR
Chi-restraints excluded: chain D residue 88 CYS
Chi-restraints excluded: chain D residue 99 VAL
Chi-restraints excluded: chain D residue 113 ASN
Chi-restraints excluded: chain D residue 142 ILE
Chi-restraints excluded: chain D residue 212 THR
Chi-restraints excluded: chain D residue 223 VAL
Chi-restraints excluded: chain D residue 230 THR
Chi-restraints excluded: chain D residue 233 ASP
Chi-restraints excluded: chain D residue 301 ILE
Chi-restraints excluded: chain D residue 329 PHE
Chi-restraints excluded: chain J residue 75 LYS
Chi-restraints excluded: chain J residue 104 MET
Chi-restraints excluded: chain J residue 111 SER
Chi-restraints excluded: chain J residue 135 MET
Chi-restraints excluded: chain J residue 167 THR
Chi-restraints excluded: chain J residue 250 LEU
Chi-restraints excluded: chain J residue 272 ARG
Chi-restraints excluded: chain J residue 285 VAL
Chi-restraints excluded: chain J residue 320 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 275
random chunks:
chunk 133 optimal weight: 8.9990
chunk 83 optimal weight: 1.9990
chunk 167 optimal weight: 10.0000
chunk 74 optimal weight: 1.9990
chunk 84 optimal weight: 2.9990
chunk 20 optimal weight: 0.0070
chunk 169 optimal weight: 9.9990
chunk 8 optimal weight: 0.8980
chunk 166 optimal weight: 0.3980
chunk 13 optimal weight: 0.6980
chunk 99 optimal weight: 6.9990
overall best weight: 0.8000
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
F 140 ASN
** J 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 149 GLN ** 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 = 0.3089 r_free = 0.3089 target = 0.047459 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2610 r_free = 0.2610 target = 0.032536 restraints weight = 116358.388|
|-----------------------------------------------------------------------------|
r_work (start): 0.2597 rms_B_bonded: 4.23
r_work: 0.2441 rms_B_bonded: 4.99 restraints_weight: 0.5000
r_work (final): 0.2441
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8949
moved from start: 0.2086
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.002 0.036 24609 Z= 0.125
Angle : 0.501 8.090 33700 Z= 0.264
Chirality : 0.039 0.234 3739
Planarity : 0.004 0.047 3950
Dihedral : 16.210 158.663 4299
Min Nonbonded Distance : 2.452
Molprobity Statistics.
All-atom Clashscore : 5.90
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 5.94 %
Favored : 94.06 %
Rotamer:
Outliers : 2.43 %
Allowed : 26.73 %
Favored : 70.85 %
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: -0.11 (0.17), residues: 2662
helix: 1.60 (0.19), residues: 796
sheet: 0.77 (0.27), residues: 443
loop : -1.41 (0.16), residues: 1423
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.007 0.001 TRP J 74
HIS 0.006 0.001 HIS J 116
PHE 0.027 0.001 PHE J 92
TYR 0.014 0.001 TYR G 169
ARG 0.007 0.000 ARG A 146
*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
5324 Ramachandran restraints generated.
2662 Oldfield, 0 Emsley, 2662 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
5324 Ramachandran restraints generated.
2662 Oldfield, 0 Emsley, 2662 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
190 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 58
poor density : 132
time to evaluate : 2.843
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: A 73 GLN cc_start: 0.9157 (pm20) cc_final: 0.8801 (pm20)
REVERT: A 249 LEU cc_start: 0.9565 (OUTLIER) cc_final: 0.9322 (mm)
REVERT: B 71 LEU cc_start: 0.9427 (mt) cc_final: 0.9144 (mt)
REVERT: B 83 TYR cc_start: 0.9086 (m-80) cc_final: 0.8794 (m-80)
REVERT: B 115 MET cc_start: 0.9067 (tpt) cc_final: 0.8594 (tpt)
REVERT: B 134 LYS cc_start: 0.9386 (OUTLIER) cc_final: 0.9085 (mttt)
REVERT: I 70 GLU cc_start: 0.9154 (OUTLIER) cc_final: 0.8824 (mp0)
REVERT: I 244 GLU cc_start: 0.8811 (mt-10) cc_final: 0.8602 (mt-10)
REVERT: I 304 MET cc_start: 0.9667 (ttm) cc_final: 0.9222 (tmm)
REVERT: H 91 LEU cc_start: 0.9351 (OUTLIER) cc_final: 0.8887 (tp)
REVERT: H 229 MET cc_start: 0.9328 (tpp) cc_final: 0.7742 (tpp)
REVERT: G 120 GLN cc_start: 0.8917 (tm-30) cc_final: 0.8534 (tm-30)
REVERT: G 304 MET cc_start: 0.9455 (ttt) cc_final: 0.9242 (tmm)
REVERT: G 328 MET cc_start: 0.9071 (ppp) cc_final: 0.8852 (ppp)
REVERT: F 62 MET cc_start: 0.7319 (pmm) cc_final: 0.6659 (pmm)
REVERT: F 120 GLN cc_start: 0.9207 (tm-30) cc_final: 0.8919 (tm-30)
REVERT: E 106 MET cc_start: 0.8884 (ttp) cc_final: 0.8557 (tmm)
REVERT: E 221 MET cc_start: 0.9101 (mmt) cc_final: 0.8837 (mmt)
REVERT: D 221 MET cc_start: 0.8172 (mmm) cc_final: 0.7857 (mmm)
REVERT: D 229 MET cc_start: 0.7377 (ttt) cc_final: 0.7072 (ttp)
REVERT: D 259 ARG cc_start: 0.8706 (OUTLIER) cc_final: 0.7531 (ttp80)
REVERT: J 46 THR cc_start: 0.9757 (OUTLIER) cc_final: 0.9448 (t)
REVERT: J 104 MET cc_start: 0.8652 (mtt) cc_final: 0.8312 (mtm)
REVERT: J 135 MET cc_start: 0.8419 (OUTLIER) cc_final: 0.8142 (tmm)
REVERT: J 322 MET cc_start: 0.8143 (tpp) cc_final: 0.7935 (tpp)
outliers start: 58
outliers final: 29
residues processed: 182
average time/residue: 0.3577
time to fit residues: 104.2720
Evaluate side-chains
159 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 36
poor density : 123
time to evaluate : 2.816
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 8 LEU
Chi-restraints excluded: chain A residue 106 MET
Chi-restraints excluded: chain A residue 121 THR
Chi-restraints excluded: chain A residue 249 LEU
Chi-restraints excluded: chain A residue 250 TYR
Chi-restraints excluded: chain B residue 60 VAL
Chi-restraints excluded: chain B residue 123 LEU
Chi-restraints excluded: chain B residue 134 LYS
Chi-restraints excluded: chain B residue 146 VAL
Chi-restraints excluded: chain I residue 70 GLU
Chi-restraints excluded: chain I residue 270 THR
Chi-restraints excluded: chain H residue 91 LEU
Chi-restraints excluded: chain G residue 73 ASP
Chi-restraints excluded: chain G residue 329 PHE
Chi-restraints excluded: chain F residue 140 ASN
Chi-restraints excluded: chain F residue 223 VAL
Chi-restraints excluded: chain E residue 55 LEU
Chi-restraints excluded: chain E residue 91 LEU
Chi-restraints excluded: chain E residue 229 MET
Chi-restraints excluded: chain D residue 88 CYS
Chi-restraints excluded: chain D residue 102 VAL
Chi-restraints excluded: chain D residue 142 ILE
Chi-restraints excluded: chain D residue 212 THR
Chi-restraints excluded: chain D residue 259 ARG
Chi-restraints excluded: chain D residue 329 PHE
Chi-restraints excluded: chain J residue 46 THR
Chi-restraints excluded: chain J residue 106 HIS
Chi-restraints excluded: chain J residue 121 LEU
Chi-restraints excluded: chain J residue 135 MET
Chi-restraints excluded: chain J residue 167 THR
Chi-restraints excluded: chain J residue 250 LEU
Chi-restraints excluded: chain J residue 272 ARG
Chi-restraints excluded: chain J residue 285 VAL
Chi-restraints excluded: chain J residue 292 TYR
Chi-restraints excluded: chain J residue 303 VAL
Chi-restraints excluded: chain J residue 320 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 275
random chunks:
chunk 183 optimal weight: 10.0000
chunk 257 optimal weight: 9.9990
chunk 155 optimal weight: 1.9990
chunk 232 optimal weight: 10.0000
chunk 221 optimal weight: 0.9990
chunk 84 optimal weight: 20.0000
chunk 32 optimal weight: 9.9990
chunk 131 optimal weight: 9.9990
chunk 249 optimal weight: 9.9990
chunk 78 optimal weight: 9.9990
chunk 264 optimal weight: 1.9990
overall best weight: 4.9990
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
H 120 GLN
F 140 ASN
** J 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Total number of N/Q/H flips: 2
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3060 r_free = 0.3060 target = 0.045848 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2580 r_free = 0.2580 target = 0.031286 restraints weight = 119805.728|
|-----------------------------------------------------------------------------|
r_work (start): 0.2538 rms_B_bonded: 4.10
r_work: 0.2384 rms_B_bonded: 4.88 restraints_weight: 0.5000
r_work (final): 0.2384
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9011
moved from start: 0.2282
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.005 0.081 24609 Z= 0.344
Angle : 0.583 11.447 33700 Z= 0.303
Chirality : 0.040 0.240 3739
Planarity : 0.004 0.048 3950
Dihedral : 16.233 163.072 4299
Min Nonbonded Distance : 2.487
Molprobity Statistics.
All-atom Clashscore : 8.03
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 6.39 %
Favored : 93.61 %
Rotamer:
Outliers : 3.39 %
Allowed : 25.68 %
Favored : 70.93 %
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: -0.21 (0.17), residues: 2662
helix: 1.55 (0.19), residues: 797
sheet: 0.50 (0.27), residues: 438
loop : -1.41 (0.16), residues: 1427
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.008 0.001 TRP G 33
HIS 0.005 0.001 HIS B 120
PHE 0.020 0.002 PHE J 92
TYR 0.013 0.001 TYR G 169
ARG 0.004 0.000 ARG A 146
*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
5324 Ramachandran restraints generated.
2662 Oldfield, 0 Emsley, 2662 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
5324 Ramachandran restraints generated.
2662 Oldfield, 0 Emsley, 2662 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
198 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 81
poor density : 117
time to evaluate : 2.697
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: A 73 GLN cc_start: 0.9121 (pm20) cc_final: 0.8777 (pm20)
REVERT: A 249 LEU cc_start: 0.9588 (OUTLIER) cc_final: 0.9342 (mm)
REVERT: B 1 MET cc_start: 0.8632 (mmm) cc_final: 0.8147 (tpp)
REVERT: B 71 LEU cc_start: 0.9427 (mt) cc_final: 0.9150 (mt)
REVERT: B 83 TYR cc_start: 0.9160 (m-80) cc_final: 0.8829 (m-80)
REVERT: B 115 MET cc_start: 0.9086 (tpt) cc_final: 0.8613 (tpt)
REVERT: I 70 GLU cc_start: 0.9172 (OUTLIER) cc_final: 0.8898 (mp0)
REVERT: I 236 LYS cc_start: 0.9634 (mtmt) cc_final: 0.9319 (mppt)
REVERT: I 304 MET cc_start: 0.9670 (ttm) cc_final: 0.9228 (tmm)
REVERT: H 91 LEU cc_start: 0.9388 (OUTLIER) cc_final: 0.8937 (tp)
REVERT: H 229 MET cc_start: 0.9420 (tpp) cc_final: 0.7977 (tpp)
REVERT: H 304 MET cc_start: 0.9436 (ttt) cc_final: 0.9167 (tmm)
REVERT: G 36 ASP cc_start: 0.8971 (OUTLIER) cc_final: 0.8169 (p0)
REVERT: G 120 GLN cc_start: 0.8998 (tm-30) cc_final: 0.8577 (tm-30)
REVERT: G 236 LYS cc_start: 0.9461 (OUTLIER) cc_final: 0.9124 (mmtt)
REVERT: G 328 MET cc_start: 0.9103 (ppp) cc_final: 0.8854 (ppp)
REVERT: F 62 MET cc_start: 0.7462 (pmm) cc_final: 0.6912 (pmm)
REVERT: F 120 GLN cc_start: 0.9234 (tm-30) cc_final: 0.8939 (tm-30)
REVERT: F 253 LYS cc_start: 0.9479 (OUTLIER) cc_final: 0.9037 (tptp)
REVERT: E 106 MET cc_start: 0.8903 (ttp) cc_final: 0.8553 (tmm)
REVERT: E 229 MET cc_start: 0.9136 (OUTLIER) cc_final: 0.8853 (mmp)
REVERT: D 106 MET cc_start: 0.8592 (tmm) cc_final: 0.7960 (tmm)
REVERT: D 221 MET cc_start: 0.8275 (mmm) cc_final: 0.7960 (mmm)
REVERT: D 259 ARG cc_start: 0.8772 (OUTLIER) cc_final: 0.7445 (ttp80)
REVERT: D 301 ILE cc_start: 0.9536 (OUTLIER) cc_final: 0.9278 (tp)
REVERT: J 62 MET cc_start: 0.8272 (mpt) cc_final: 0.8011 (mmt)
REVERT: J 104 MET cc_start: 0.8682 (OUTLIER) cc_final: 0.8346 (mtm)
REVERT: J 135 MET cc_start: 0.8445 (OUTLIER) cc_final: 0.8193 (tmm)
REVERT: J 138 MET cc_start: 0.8297 (ppp) cc_final: 0.7674 (ppp)
REVERT: J 233 LEU cc_start: 0.9603 (OUTLIER) cc_final: 0.9298 (pp)
outliers start: 81
outliers final: 51
residues processed: 188
average time/residue: 0.3568
time to fit residues: 107.2309
Evaluate side-chains
178 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 63
poor density : 115
time to evaluate : 2.743
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 8 LEU
Chi-restraints excluded: chain A residue 104 LEU
Chi-restraints excluded: chain A residue 106 MET
Chi-restraints excluded: chain A residue 121 THR
Chi-restraints excluded: chain A residue 249 LEU
Chi-restraints excluded: chain A residue 250 TYR
Chi-restraints excluded: chain B residue 19 ILE
Chi-restraints excluded: chain B residue 27 VAL
Chi-restraints excluded: chain B residue 42 THR
Chi-restraints excluded: chain B residue 60 VAL
Chi-restraints excluded: chain B residue 64 ASP
Chi-restraints excluded: chain B residue 81 THR
Chi-restraints excluded: chain B residue 98 LEU
Chi-restraints excluded: chain B residue 123 LEU
Chi-restraints excluded: chain B residue 146 VAL
Chi-restraints excluded: chain I residue 70 GLU
Chi-restraints excluded: chain I residue 78 LYS
Chi-restraints excluded: chain I residue 93 ILE
Chi-restraints excluded: chain I residue 102 VAL
Chi-restraints excluded: chain I residue 113 ASN
Chi-restraints excluded: chain I residue 223 VAL
Chi-restraints excluded: chain I residue 270 THR
Chi-restraints excluded: chain H residue 91 LEU
Chi-restraints excluded: chain H residue 99 VAL
Chi-restraints excluded: chain H residue 116 THR
Chi-restraints excluded: chain H residue 185 ASP
Chi-restraints excluded: chain G residue 27 THR
Chi-restraints excluded: chain G residue 36 ASP
Chi-restraints excluded: chain G residue 73 ASP
Chi-restraints excluded: chain G residue 236 LYS
Chi-restraints excluded: chain G residue 329 PHE
Chi-restraints excluded: chain F residue 27 THR
Chi-restraints excluded: chain F residue 35 THR
Chi-restraints excluded: chain F residue 38 LEU
Chi-restraints excluded: chain F residue 223 VAL
Chi-restraints excluded: chain F residue 253 LYS
Chi-restraints excluded: chain E residue 27 THR
Chi-restraints excluded: chain E residue 55 LEU
Chi-restraints excluded: chain E residue 81 SER
Chi-restraints excluded: chain E residue 91 LEU
Chi-restraints excluded: chain E residue 229 MET
Chi-restraints excluded: chain D residue 27 THR
Chi-restraints excluded: chain D residue 88 CYS
Chi-restraints excluded: chain D residue 102 VAL
Chi-restraints excluded: chain D residue 132 LEU
Chi-restraints excluded: chain D residue 212 THR
Chi-restraints excluded: chain D residue 223 VAL
Chi-restraints excluded: chain D residue 233 ASP
Chi-restraints excluded: chain D residue 259 ARG
Chi-restraints excluded: chain D residue 275 ILE
Chi-restraints excluded: chain D residue 301 ILE
Chi-restraints excluded: chain D residue 329 PHE
Chi-restraints excluded: chain J residue 104 MET
Chi-restraints excluded: chain J residue 106 HIS
Chi-restraints excluded: chain J residue 121 LEU
Chi-restraints excluded: chain J residue 135 MET
Chi-restraints excluded: chain J residue 167 THR
Chi-restraints excluded: chain J residue 233 LEU
Chi-restraints excluded: chain J residue 272 ARG
Chi-restraints excluded: chain J residue 285 VAL
Chi-restraints excluded: chain J residue 292 TYR
Chi-restraints excluded: chain J residue 303 VAL
Chi-restraints excluded: chain J residue 320 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 275
random chunks:
chunk 201 optimal weight: 2.9990
chunk 64 optimal weight: 10.0000
chunk 168 optimal weight: 3.9990
chunk 174 optimal weight: 10.0000
chunk 189 optimal weight: 2.9990
chunk 251 optimal weight: 8.9990
chunk 78 optimal weight: 10.0000
chunk 136 optimal weight: 4.9990
chunk 113 optimal weight: 6.9990
chunk 89 optimal weight: 7.9990
chunk 213 optimal weight: 8.9990
overall best weight: 4.3990
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** I 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 120 GLN
F 140 ASN
** J 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Total number of N/Q/H flips: 2
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3059 r_free = 0.3059 target = 0.045811 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2580 r_free = 0.2580 target = 0.031250 restraints weight = 120371.612|
|-----------------------------------------------------------------------------|
r_work (start): 0.2538 rms_B_bonded: 4.12
r_work: 0.2382 rms_B_bonded: 4.88 restraints_weight: 0.5000
r_work (final): 0.2382
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9014
moved from start: 0.2426
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.005 0.069 24609 Z= 0.297
Angle : 0.568 11.830 33700 Z= 0.296
Chirality : 0.040 0.243 3739
Planarity : 0.004 0.045 3950
Dihedral : 16.286 162.376 4299
Min Nonbonded Distance : 2.464
Molprobity Statistics.
All-atom Clashscore : 7.68
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 6.42 %
Favored : 93.58 %
Rotamer:
Outliers : 3.39 %
Allowed : 25.85 %
Favored : 70.77 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: -0.27 (0.17), residues: 2662
helix: 1.48 (0.19), residues: 799
sheet: 0.39 (0.27), residues: 438
loop : -1.40 (0.16), residues: 1425
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.008 0.001 TRP G 33
HIS 0.003 0.001 HIS B 120
PHE 0.023 0.001 PHE J 92
TYR 0.023 0.001 TYR A 62
ARG 0.004 0.000 ARG A 146
*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
5324 Ramachandran restraints generated.
2662 Oldfield, 0 Emsley, 2662 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
5324 Ramachandran restraints generated.
2662 Oldfield, 0 Emsley, 2662 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
198 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 81
poor density : 117
time to evaluate : 2.972
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: A 73 GLN cc_start: 0.9144 (pm20) cc_final: 0.8819 (pm20)
REVERT: A 163 ARG cc_start: 0.8851 (mmm-85) cc_final: 0.8533 (mmt90)
REVERT: A 249 LEU cc_start: 0.9580 (OUTLIER) cc_final: 0.9338 (mm)
REVERT: B 1 MET cc_start: 0.8580 (mmm) cc_final: 0.8113 (tpp)
REVERT: B 71 LEU cc_start: 0.9441 (mt) cc_final: 0.9162 (mt)
REVERT: B 115 MET cc_start: 0.9084 (tpt) cc_final: 0.8598 (tpt)
REVERT: B 134 LYS cc_start: 0.9372 (OUTLIER) cc_final: 0.8967 (mttt)
REVERT: I 70 GLU cc_start: 0.9174 (OUTLIER) cc_final: 0.8908 (mp0)
REVERT: I 236 LYS cc_start: 0.9628 (mtmt) cc_final: 0.9317 (mppt)
REVERT: I 304 MET cc_start: 0.9668 (ttm) cc_final: 0.9225 (tmm)
REVERT: H 91 LEU cc_start: 0.9389 (OUTLIER) cc_final: 0.8935 (tp)
REVERT: H 229 MET cc_start: 0.9386 (tpp) cc_final: 0.7936 (tpp)
REVERT: G 36 ASP cc_start: 0.8982 (OUTLIER) cc_final: 0.8158 (p0)
REVERT: G 120 GLN cc_start: 0.9003 (tm-30) cc_final: 0.8568 (tm-30)
REVERT: G 236 LYS cc_start: 0.9466 (OUTLIER) cc_final: 0.9129 (mmtt)
REVERT: G 328 MET cc_start: 0.9123 (ppp) cc_final: 0.8849 (ppp)
REVERT: F 62 MET cc_start: 0.7386 (pmm) cc_final: 0.6978 (pmm)
REVERT: F 120 GLN cc_start: 0.9212 (tm-30) cc_final: 0.8917 (tm-30)
REVERT: E 106 MET cc_start: 0.8922 (ttp) cc_final: 0.8568 (tmm)
REVERT: D 221 MET cc_start: 0.8278 (mmm) cc_final: 0.7883 (mmm)
REVERT: D 259 ARG cc_start: 0.8755 (OUTLIER) cc_final: 0.7515 (ttp80)
REVERT: D 301 ILE cc_start: 0.9535 (OUTLIER) cc_final: 0.9274 (tp)
REVERT: J 104 MET cc_start: 0.8675 (OUTLIER) cc_final: 0.8327 (mtm)
REVERT: J 135 MET cc_start: 0.8367 (OUTLIER) cc_final: 0.8127 (tmm)
outliers start: 81
outliers final: 54
residues processed: 188
average time/residue: 0.3626
time to fit residues: 108.8894
Evaluate side-chains
178 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 64
poor density : 114
time to evaluate : 2.891
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 8 LEU
Chi-restraints excluded: chain A residue 104 LEU
Chi-restraints excluded: chain A residue 106 MET
Chi-restraints excluded: chain A residue 121 THR
Chi-restraints excluded: chain A residue 192 ILE
Chi-restraints excluded: chain A residue 249 LEU
Chi-restraints excluded: chain B residue 27 VAL
Chi-restraints excluded: chain B residue 60 VAL
Chi-restraints excluded: chain B residue 81 THR
Chi-restraints excluded: chain B residue 98 LEU
Chi-restraints excluded: chain B residue 134 LYS
Chi-restraints excluded: chain B residue 146 VAL
Chi-restraints excluded: chain I residue 70 GLU
Chi-restraints excluded: chain I residue 78 LYS
Chi-restraints excluded: chain I residue 93 ILE
Chi-restraints excluded: chain I residue 102 VAL
Chi-restraints excluded: chain I residue 113 ASN
Chi-restraints excluded: chain I residue 223 VAL
Chi-restraints excluded: chain I residue 270 THR
Chi-restraints excluded: chain I residue 277 VAL
Chi-restraints excluded: chain H residue 83 THR
Chi-restraints excluded: chain H residue 91 LEU
Chi-restraints excluded: chain H residue 108 SER
Chi-restraints excluded: chain H residue 116 THR
Chi-restraints excluded: chain H residue 267 ASP
Chi-restraints excluded: chain G residue 27 THR
Chi-restraints excluded: chain G residue 36 ASP
Chi-restraints excluded: chain G residue 73 ASP
Chi-restraints excluded: chain G residue 236 LYS
Chi-restraints excluded: chain G residue 267 ASP
Chi-restraints excluded: chain G residue 329 PHE
Chi-restraints excluded: chain F residue 27 THR
Chi-restraints excluded: chain F residue 38 LEU
Chi-restraints excluded: chain F residue 113 ASN
Chi-restraints excluded: chain F residue 223 VAL
Chi-restraints excluded: chain F residue 267 ASP
Chi-restraints excluded: chain F residue 296 SER
Chi-restraints excluded: chain E residue 27 THR
Chi-restraints excluded: chain E residue 55 LEU
Chi-restraints excluded: chain E residue 81 SER
Chi-restraints excluded: chain E residue 229 MET
Chi-restraints excluded: chain E residue 296 SER
Chi-restraints excluded: chain D residue 27 THR
Chi-restraints excluded: chain D residue 88 CYS
Chi-restraints excluded: chain D residue 102 VAL
Chi-restraints excluded: chain D residue 142 ILE
Chi-restraints excluded: chain D residue 212 THR
Chi-restraints excluded: chain D residue 223 VAL
Chi-restraints excluded: chain D residue 233 ASP
Chi-restraints excluded: chain D residue 259 ARG
Chi-restraints excluded: chain D residue 275 ILE
Chi-restraints excluded: chain D residue 301 ILE
Chi-restraints excluded: chain D residue 329 PHE
Chi-restraints excluded: chain J residue 75 LYS
Chi-restraints excluded: chain J residue 86 TYR
Chi-restraints excluded: chain J residue 104 MET
Chi-restraints excluded: chain J residue 111 SER
Chi-restraints excluded: chain J residue 121 LEU
Chi-restraints excluded: chain J residue 135 MET
Chi-restraints excluded: chain J residue 167 THR
Chi-restraints excluded: chain J residue 250 LEU
Chi-restraints excluded: chain J residue 272 ARG
Chi-restraints excluded: chain J residue 285 VAL
Chi-restraints excluded: chain J residue 292 TYR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 275
random chunks:
chunk 216 optimal weight: 4.9990
chunk 66 optimal weight: 3.9990
chunk 224 optimal weight: 8.9990
chunk 181 optimal weight: 9.9990
chunk 98 optimal weight: 7.9990
chunk 31 optimal weight: 4.9990
chunk 67 optimal weight: 5.9990
chunk 161 optimal weight: 3.9990
chunk 243 optimal weight: 4.9990
chunk 229 optimal weight: 1.9990
chunk 184 optimal weight: 7.9990
overall best weight: 3.9990
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** I 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 140 ASN
J 106 HIS
** J 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Total number of N/Q/H flips: 2
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3039 r_free = 0.3039 target = 0.045520 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2547 r_free = 0.2547 target = 0.030725 restraints weight = 119346.130|
|-----------------------------------------------------------------------------|
r_work (start): 0.2536 rms_B_bonded: 4.15
r_work: 0.2382 rms_B_bonded: 4.90 restraints_weight: 0.5000
r_work (final): 0.2382
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9020
moved from start: 0.2544
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.004 0.064 24609 Z= 0.279
Angle : 0.571 12.100 33700 Z= 0.296
Chirality : 0.040 0.238 3739
Planarity : 0.004 0.044 3950
Dihedral : 16.342 162.419 4299
Min Nonbonded Distance : 2.473
Molprobity Statistics.
All-atom Clashscore : 7.68
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 6.61 %
Favored : 93.39 %
Rotamer:
Outliers : 3.68 %
Allowed : 25.47 %
Favored : 70.85 %
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: -0.28 (0.17), residues: 2662
helix: 1.46 (0.19), residues: 800
sheet: 0.42 (0.27), residues: 424
loop : -1.40 (0.16), residues: 1438
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.007 0.001 TRP G 33
HIS 0.004 0.001 HIS J 106
PHE 0.023 0.001 PHE J 92
TYR 0.016 0.001 TYR A 62
ARG 0.003 0.000 ARG J 142
*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
5324 Ramachandran restraints generated.
2662 Oldfield, 0 Emsley, 2662 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
5324 Ramachandran restraints generated.
2662 Oldfield, 0 Emsley, 2662 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
205 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 88
poor density : 117
time to evaluate : 2.670
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: A 51 ARG cc_start: 0.8536 (mmm-85) cc_final: 0.8021 (mmm160)
REVERT: A 163 ARG cc_start: 0.8943 (mmm-85) cc_final: 0.8601 (mmt90)
REVERT: A 249 LEU cc_start: 0.9589 (OUTLIER) cc_final: 0.9344 (mm)
REVERT: B 1 MET cc_start: 0.8629 (mmm) cc_final: 0.8185 (tpp)
REVERT: B 71 LEU cc_start: 0.9440 (mt) cc_final: 0.9161 (mt)
REVERT: B 72 CYS cc_start: 0.9250 (OUTLIER) cc_final: 0.8941 (t)
REVERT: B 115 MET cc_start: 0.9069 (tpt) cc_final: 0.8572 (tpt)
REVERT: B 134 LYS cc_start: 0.9370 (OUTLIER) cc_final: 0.8971 (mttt)
REVERT: I 70 GLU cc_start: 0.9173 (OUTLIER) cc_final: 0.8908 (mp0)
REVERT: I 236 LYS cc_start: 0.9627 (mtmt) cc_final: 0.9334 (mppt)
REVERT: I 304 MET cc_start: 0.9670 (ttm) cc_final: 0.9219 (tmm)
REVERT: H 91 LEU cc_start: 0.9397 (OUTLIER) cc_final: 0.8964 (tp)
REVERT: H 229 MET cc_start: 0.9394 (tpp) cc_final: 0.7940 (tpp)
REVERT: G 36 ASP cc_start: 0.8957 (OUTLIER) cc_final: 0.8109 (p0)
REVERT: G 120 GLN cc_start: 0.8987 (tm-30) cc_final: 0.8539 (tm-30)
REVERT: G 236 LYS cc_start: 0.9478 (OUTLIER) cc_final: 0.9145 (mmtt)
REVERT: G 328 MET cc_start: 0.9115 (ppp) cc_final: 0.8842 (ppp)
REVERT: F 62 MET cc_start: 0.7490 (pmm) cc_final: 0.7068 (pmm)
REVERT: F 120 GLN cc_start: 0.9213 (tm-30) cc_final: 0.8924 (tm-30)
REVERT: F 328 MET cc_start: 0.8929 (tpp) cc_final: 0.8648 (mpp)
REVERT: E 106 MET cc_start: 0.8914 (ttp) cc_final: 0.8589 (tmm)
REVERT: E 229 MET cc_start: 0.9092 (OUTLIER) cc_final: 0.8778 (mmp)
REVERT: D 221 MET cc_start: 0.8320 (mmm) cc_final: 0.7983 (mmm)
REVERT: D 229 MET cc_start: 0.7469 (ttt) cc_final: 0.7124 (ttp)
REVERT: D 259 ARG cc_start: 0.8745 (OUTLIER) cc_final: 0.7497 (ttp80)
REVERT: D 301 ILE cc_start: 0.9526 (OUTLIER) cc_final: 0.9268 (tp)
REVERT: J 135 MET cc_start: 0.8321 (OUTLIER) cc_final: 0.8078 (tmm)
REVERT: J 138 MET cc_start: 0.8421 (ppp) cc_final: 0.7982 (ppp)
REVERT: J 322 MET cc_start: 0.8514 (tpp) cc_final: 0.8099 (tpp)
outliers start: 88
outliers final: 68
residues processed: 194
average time/residue: 0.3606
time to fit residues: 112.5214
Evaluate side-chains
193 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 79
poor density : 114
time to evaluate : 2.815
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 8 LEU
Chi-restraints excluded: chain A residue 76 THR
Chi-restraints excluded: chain A residue 104 LEU
Chi-restraints excluded: chain A residue 106 MET
Chi-restraints excluded: chain A residue 112 VAL
Chi-restraints excluded: chain A residue 121 THR
Chi-restraints excluded: chain A residue 192 ILE
Chi-restraints excluded: chain A residue 205 VAL
Chi-restraints excluded: chain A residue 249 LEU
Chi-restraints excluded: chain B residue 19 ILE
Chi-restraints excluded: chain B residue 27 VAL
Chi-restraints excluded: chain B residue 42 THR
Chi-restraints excluded: chain B residue 60 VAL
Chi-restraints excluded: chain B residue 64 ASP
Chi-restraints excluded: chain B residue 72 CYS
Chi-restraints excluded: chain B residue 81 THR
Chi-restraints excluded: chain B residue 98 LEU
Chi-restraints excluded: chain B residue 134 LYS
Chi-restraints excluded: chain B residue 146 VAL
Chi-restraints excluded: chain I residue 70 GLU
Chi-restraints excluded: chain I residue 78 LYS
Chi-restraints excluded: chain I residue 93 ILE
Chi-restraints excluded: chain I residue 102 VAL
Chi-restraints excluded: chain I residue 113 ASN
Chi-restraints excluded: chain I residue 223 VAL
Chi-restraints excluded: chain I residue 270 THR
Chi-restraints excluded: chain I residue 277 VAL
Chi-restraints excluded: chain H residue 83 THR
Chi-restraints excluded: chain H residue 91 LEU
Chi-restraints excluded: chain H residue 108 SER
Chi-restraints excluded: chain H residue 142 ILE
Chi-restraints excluded: chain H residue 185 ASP
Chi-restraints excluded: chain H residue 267 ASP
Chi-restraints excluded: chain G residue 27 THR
Chi-restraints excluded: chain G residue 36 ASP
Chi-restraints excluded: chain G residue 73 ASP
Chi-restraints excluded: chain G residue 236 LYS
Chi-restraints excluded: chain G residue 267 ASP
Chi-restraints excluded: chain G residue 329 PHE
Chi-restraints excluded: chain F residue 27 THR
Chi-restraints excluded: chain F residue 35 THR
Chi-restraints excluded: chain F residue 38 LEU
Chi-restraints excluded: chain F residue 113 ASN
Chi-restraints excluded: chain F residue 140 ASN
Chi-restraints excluded: chain F residue 223 VAL
Chi-restraints excluded: chain F residue 236 LYS
Chi-restraints excluded: chain F residue 267 ASP
Chi-restraints excluded: chain F residue 296 SER
Chi-restraints excluded: chain E residue 27 THR
Chi-restraints excluded: chain E residue 55 LEU
Chi-restraints excluded: chain E residue 81 SER
Chi-restraints excluded: chain E residue 83 THR
Chi-restraints excluded: chain E residue 229 MET
Chi-restraints excluded: chain E residue 296 SER
Chi-restraints excluded: chain D residue 27 THR
Chi-restraints excluded: chain D residue 50 THR
Chi-restraints excluded: chain D residue 88 CYS
Chi-restraints excluded: chain D residue 99 VAL
Chi-restraints excluded: chain D residue 102 VAL
Chi-restraints excluded: chain D residue 132 LEU
Chi-restraints excluded: chain D residue 142 ILE
Chi-restraints excluded: chain D residue 212 THR
Chi-restraints excluded: chain D residue 223 VAL
Chi-restraints excluded: chain D residue 233 ASP
Chi-restraints excluded: chain D residue 259 ARG
Chi-restraints excluded: chain D residue 275 ILE
Chi-restraints excluded: chain D residue 301 ILE
Chi-restraints excluded: chain D residue 329 PHE
Chi-restraints excluded: chain J residue 75 LYS
Chi-restraints excluded: chain J residue 86 TYR
Chi-restraints excluded: chain J residue 111 SER
Chi-restraints excluded: chain J residue 121 LEU
Chi-restraints excluded: chain J residue 135 MET
Chi-restraints excluded: chain J residue 167 THR
Chi-restraints excluded: chain J residue 250 LEU
Chi-restraints excluded: chain J residue 272 ARG
Chi-restraints excluded: chain J residue 285 VAL
Chi-restraints excluded: chain J residue 292 TYR
Chi-restraints excluded: chain J residue 320 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 275
random chunks:
chunk 182 optimal weight: 6.9990
chunk 15 optimal weight: 8.9990
chunk 40 optimal weight: 9.9990
chunk 254 optimal weight: 10.0000
chunk 221 optimal weight: 1.9990
chunk 117 optimal weight: 0.9990
chunk 219 optimal weight: 6.9990
chunk 177 optimal weight: 8.9990
chunk 166 optimal weight: 9.9990
chunk 77 optimal weight: 0.9990
chunk 242 optimal weight: 9.9990
overall best weight: 3.5990
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** I 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 120 GLN
F 140 ASN
J 106 HIS
** J 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Total number of N/Q/H flips: 3
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3063 r_free = 0.3063 target = 0.045863 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2582 r_free = 0.2582 target = 0.031271 restraints weight = 120527.458|
|-----------------------------------------------------------------------------|
r_work (start): 0.2540 rms_B_bonded: 4.14
r_work: 0.2386 rms_B_bonded: 4.92 restraints_weight: 0.5000
r_work (final): 0.2386
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9013
moved from start: 0.2596
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.004 0.056 24609 Z= 0.255
Angle : 0.569 12.192 33700 Z= 0.293
Chirality : 0.039 0.245 3739
Planarity : 0.004 0.046 3950
Dihedral : 16.365 162.229 4299
Min Nonbonded Distance : 2.477
Molprobity Statistics.
All-atom Clashscore : 7.55
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 6.46 %
Favored : 93.54 %
Rotamer:
Outliers : 3.47 %
Allowed : 25.72 %
Favored : 70.81 %
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: -0.27 (0.17), residues: 2662
helix: 1.45 (0.19), residues: 800
sheet: 0.40 (0.27), residues: 433
loop : -1.37 (0.16), residues: 1429
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.007 0.001 TRP H 264
HIS 0.003 0.001 HIS B 35
PHE 0.021 0.001 PHE J 92
TYR 0.014 0.001 TYR A 62
ARG 0.003 0.000 ARG J 142
*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
5324 Ramachandran restraints generated.
2662 Oldfield, 0 Emsley, 2662 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
5324 Ramachandran restraints generated.
2662 Oldfield, 0 Emsley, 2662 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
203 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 83
poor density : 120
time to evaluate : 2.683
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: A 51 ARG cc_start: 0.8525 (mmm-85) cc_final: 0.7999 (mmm160)
REVERT: A 73 GLN cc_start: 0.9325 (pm20) cc_final: 0.9010 (pm20)
REVERT: A 163 ARG cc_start: 0.8952 (mmm-85) cc_final: 0.8614 (mmt90)
REVERT: A 249 LEU cc_start: 0.9597 (OUTLIER) cc_final: 0.9351 (mm)
REVERT: B 1 MET cc_start: 0.8598 (mmm) cc_final: 0.8161 (tpp)
REVERT: B 71 LEU cc_start: 0.9443 (mt) cc_final: 0.9167 (mt)
REVERT: B 72 CYS cc_start: 0.9266 (OUTLIER) cc_final: 0.8952 (t)
REVERT: B 115 MET cc_start: 0.9053 (tpt) cc_final: 0.8546 (tpt)
REVERT: B 134 LYS cc_start: 0.9359 (OUTLIER) cc_final: 0.8953 (mttt)
REVERT: I 70 GLU cc_start: 0.9172 (OUTLIER) cc_final: 0.8909 (mp0)
REVERT: I 236 LYS cc_start: 0.9628 (mtmt) cc_final: 0.9333 (mppt)
REVERT: I 304 MET cc_start: 0.9680 (ttm) cc_final: 0.9223 (tmm)
REVERT: H 91 LEU cc_start: 0.9386 (OUTLIER) cc_final: 0.8953 (tp)
REVERT: H 229 MET cc_start: 0.9382 (tpp) cc_final: 0.7930 (tpp)
REVERT: H 328 MET cc_start: 0.8417 (ttt) cc_final: 0.8134 (ttm)
REVERT: G 120 GLN cc_start: 0.9019 (tm-30) cc_final: 0.8572 (tm-30)
REVERT: G 236 LYS cc_start: 0.9480 (OUTLIER) cc_final: 0.9147 (mmtt)
REVERT: G 328 MET cc_start: 0.9120 (ppp) cc_final: 0.8843 (ppp)
REVERT: F 62 MET cc_start: 0.7469 (pmm) cc_final: 0.7197 (pmm)
REVERT: F 120 GLN cc_start: 0.9219 (tm-30) cc_final: 0.8929 (tm-30)
REVERT: F 253 LYS cc_start: 0.9441 (OUTLIER) cc_final: 0.9094 (tptp)
REVERT: F 328 MET cc_start: 0.8896 (tpp) cc_final: 0.8632 (mpp)
REVERT: E 106 MET cc_start: 0.8916 (ttp) cc_final: 0.8589 (tmm)
REVERT: E 229 MET cc_start: 0.9064 (OUTLIER) cc_final: 0.8750 (mmp)
REVERT: D 221 MET cc_start: 0.8299 (mmm) cc_final: 0.7891 (mmm)
REVERT: D 229 MET cc_start: 0.7557 (ttt) cc_final: 0.7210 (ttp)
REVERT: D 259 ARG cc_start: 0.8746 (OUTLIER) cc_final: 0.7482 (ttp80)
REVERT: J 104 MET cc_start: 0.8962 (mtm) cc_final: 0.8707 (mpp)
REVERT: J 121 LEU cc_start: 0.9350 (OUTLIER) cc_final: 0.9010 (mm)
REVERT: J 135 MET cc_start: 0.8282 (OUTLIER) cc_final: 0.8055 (tmm)
REVERT: J 138 MET cc_start: 0.8412 (ppp) cc_final: 0.8011 (ppp)
REVERT: J 322 MET cc_start: 0.8578 (tpp) cc_final: 0.8108 (tpp)
outliers start: 83
outliers final: 66
residues processed: 194
average time/residue: 0.3606
time to fit residues: 112.1796
Evaluate side-chains
195 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 77
poor density : 118
time to evaluate : 2.830
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 8 LEU
Chi-restraints excluded: chain A residue 76 THR
Chi-restraints excluded: chain A residue 104 LEU
Chi-restraints excluded: chain A residue 106 MET
Chi-restraints excluded: chain A residue 112 VAL
Chi-restraints excluded: chain A residue 121 THR
Chi-restraints excluded: chain A residue 192 ILE
Chi-restraints excluded: chain A residue 205 VAL
Chi-restraints excluded: chain A residue 249 LEU
Chi-restraints excluded: chain B residue 19 ILE
Chi-restraints excluded: chain B residue 27 VAL
Chi-restraints excluded: chain B residue 42 THR
Chi-restraints excluded: chain B residue 60 VAL
Chi-restraints excluded: chain B residue 72 CYS
Chi-restraints excluded: chain B residue 81 THR
Chi-restraints excluded: chain B residue 98 LEU
Chi-restraints excluded: chain B residue 134 LYS
Chi-restraints excluded: chain B residue 146 VAL
Chi-restraints excluded: chain I residue 70 GLU
Chi-restraints excluded: chain I residue 78 LYS
Chi-restraints excluded: chain I residue 93 ILE
Chi-restraints excluded: chain I residue 102 VAL
Chi-restraints excluded: chain I residue 113 ASN
Chi-restraints excluded: chain I residue 223 VAL
Chi-restraints excluded: chain I residue 270 THR
Chi-restraints excluded: chain I residue 277 VAL
Chi-restraints excluded: chain H residue 83 THR
Chi-restraints excluded: chain H residue 91 LEU
Chi-restraints excluded: chain H residue 99 VAL
Chi-restraints excluded: chain H residue 108 SER
Chi-restraints excluded: chain H residue 116 THR
Chi-restraints excluded: chain H residue 142 ILE
Chi-restraints excluded: chain H residue 185 ASP
Chi-restraints excluded: chain H residue 267 ASP
Chi-restraints excluded: chain G residue 27 THR
Chi-restraints excluded: chain G residue 73 ASP
Chi-restraints excluded: chain G residue 236 LYS
Chi-restraints excluded: chain G residue 267 ASP
Chi-restraints excluded: chain G residue 329 PHE
Chi-restraints excluded: chain F residue 27 THR
Chi-restraints excluded: chain F residue 35 THR
Chi-restraints excluded: chain F residue 38 LEU
Chi-restraints excluded: chain F residue 113 ASN
Chi-restraints excluded: chain F residue 140 ASN
Chi-restraints excluded: chain F residue 223 VAL
Chi-restraints excluded: chain F residue 236 LYS
Chi-restraints excluded: chain F residue 253 LYS
Chi-restraints excluded: chain F residue 267 ASP
Chi-restraints excluded: chain F residue 296 SER
Chi-restraints excluded: chain E residue 27 THR
Chi-restraints excluded: chain E residue 55 LEU
Chi-restraints excluded: chain E residue 81 SER
Chi-restraints excluded: chain E residue 132 LEU
Chi-restraints excluded: chain E residue 229 MET
Chi-restraints excluded: chain E residue 296 SER
Chi-restraints excluded: chain D residue 50 THR
Chi-restraints excluded: chain D residue 88 CYS
Chi-restraints excluded: chain D residue 99 VAL
Chi-restraints excluded: chain D residue 102 VAL
Chi-restraints excluded: chain D residue 142 ILE
Chi-restraints excluded: chain D residue 212 THR
Chi-restraints excluded: chain D residue 223 VAL
Chi-restraints excluded: chain D residue 233 ASP
Chi-restraints excluded: chain D residue 259 ARG
Chi-restraints excluded: chain D residue 275 ILE
Chi-restraints excluded: chain D residue 329 PHE
Chi-restraints excluded: chain J residue 75 LYS
Chi-restraints excluded: chain J residue 86 TYR
Chi-restraints excluded: chain J residue 111 SER
Chi-restraints excluded: chain J residue 121 LEU
Chi-restraints excluded: chain J residue 135 MET
Chi-restraints excluded: chain J residue 167 THR
Chi-restraints excluded: chain J residue 250 LEU
Chi-restraints excluded: chain J residue 272 ARG
Chi-restraints excluded: chain J residue 285 VAL
Chi-restraints excluded: chain J residue 292 TYR
Chi-restraints excluded: chain J residue 320 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 275
random chunks:
chunk 23 optimal weight: 0.2980
chunk 162 optimal weight: 0.9990
chunk 60 optimal weight: 2.9990
chunk 247 optimal weight: 7.9990
chunk 80 optimal weight: 9.9990
chunk 15 optimal weight: 8.9990
chunk 184 optimal weight: 3.9990
chunk 35 optimal weight: 20.0000
chunk 37 optimal weight: 5.9990
chunk 148 optimal weight: 10.0000
chunk 31 optimal weight: 3.9990
overall best weight: 2.4588
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** I 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 120 GLN
F 140 ASN
** J 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Total number of N/Q/H flips: 2
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3075 r_free = 0.3075 target = 0.046273 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2598 r_free = 0.2598 target = 0.031665 restraints weight = 119575.096|
|-----------------------------------------------------------------------------|
r_work (start): 0.2556 rms_B_bonded: 4.14
r_work: 0.2401 rms_B_bonded: 4.92 restraints_weight: 0.5000
r_work (final): 0.2401
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9000
moved from start: 0.2619
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.036 24609 Z= 0.195
Angle : 0.554 12.271 33700 Z= 0.285
Chirality : 0.039 0.306 3739
Planarity : 0.004 0.050 3950
Dihedral : 16.367 161.450 4299
Min Nonbonded Distance : 2.467
Molprobity Statistics.
All-atom Clashscore : 6.95
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 6.31 %
Favored : 93.69 %
Rotamer:
Outliers : 3.14 %
Allowed : 26.14 %
Favored : 70.72 %
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: -0.18 (0.17), residues: 2662
helix: 1.55 (0.19), residues: 797
sheet: 0.47 (0.27), residues: 428
loop : -1.34 (0.16), residues: 1437
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.011 0.001 TRP J 74
HIS 0.003 0.001 HIS B 35
PHE 0.022 0.001 PHE J 92
TYR 0.012 0.001 TYR G 169
ARG 0.003 0.000 ARG E 150
********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
5324 Ramachandran restraints generated.
2662 Oldfield, 0 Emsley, 2662 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
5324 Ramachandran restraints generated.
2662 Oldfield, 0 Emsley, 2662 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
198 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 75
poor density : 123
time to evaluate : 2.860
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: A 51 ARG cc_start: 0.8523 (mmm-85) cc_final: 0.7959 (mmm-85)
REVERT: A 73 GLN cc_start: 0.9334 (pm20) cc_final: 0.9086 (pm20)
REVERT: A 163 ARG cc_start: 0.8958 (mmm-85) cc_final: 0.8616 (mmt90)
REVERT: A 249 LEU cc_start: 0.9595 (OUTLIER) cc_final: 0.9338 (mm)
REVERT: B 1 MET cc_start: 0.8585 (mmm) cc_final: 0.8169 (tpp)
REVERT: B 71 LEU cc_start: 0.9444 (mt) cc_final: 0.9171 (mt)
REVERT: B 72 CYS cc_start: 0.9266 (OUTLIER) cc_final: 0.8952 (t)
REVERT: B 83 TYR cc_start: 0.9135 (m-80) cc_final: 0.8800 (m-80)
REVERT: B 115 MET cc_start: 0.9054 (tpt) cc_final: 0.8531 (tpt)
REVERT: B 134 LYS cc_start: 0.9361 (OUTLIER) cc_final: 0.8979 (mttt)
REVERT: I 70 GLU cc_start: 0.9174 (OUTLIER) cc_final: 0.8858 (mp0)
REVERT: I 236 LYS cc_start: 0.9620 (mtmt) cc_final: 0.9327 (mppt)
REVERT: I 304 MET cc_start: 0.9680 (ttm) cc_final: 0.9219 (tmm)
REVERT: H 72 MET cc_start: 0.8712 (mmt) cc_final: 0.8056 (mmt)
REVERT: H 91 LEU cc_start: 0.9374 (OUTLIER) cc_final: 0.8935 (tp)
REVERT: H 229 MET cc_start: 0.9370 (tpp) cc_final: 0.7865 (tpp)
REVERT: H 328 MET cc_start: 0.8382 (ttt) cc_final: 0.8122 (ttm)
REVERT: G 120 GLN cc_start: 0.9001 (tm-30) cc_final: 0.8560 (tm-30)
REVERT: G 236 LYS cc_start: 0.9470 (OUTLIER) cc_final: 0.9147 (mmtt)
REVERT: G 328 MET cc_start: 0.9106 (ppp) cc_final: 0.8825 (ppp)
REVERT: F 62 MET cc_start: 0.7497 (pmm) cc_final: 0.7093 (pmm)
REVERT: F 120 GLN cc_start: 0.9201 (tm-30) cc_final: 0.8912 (tm-30)
REVERT: F 328 MET cc_start: 0.8899 (tpp) cc_final: 0.8624 (mpp)
REVERT: E 106 MET cc_start: 0.8918 (ttp) cc_final: 0.8586 (tmm)
REVERT: E 229 MET cc_start: 0.9015 (OUTLIER) cc_final: 0.8708 (mmp)
REVERT: D 221 MET cc_start: 0.8285 (mmm) cc_final: 0.7944 (mmm)
REVERT: D 229 MET cc_start: 0.7508 (ttt) cc_final: 0.7174 (ttp)
REVERT: D 259 ARG cc_start: 0.8731 (OUTLIER) cc_final: 0.7547 (ttp80)
REVERT: D 301 ILE cc_start: 0.9524 (OUTLIER) cc_final: 0.9266 (tp)
REVERT: J 104 MET cc_start: 0.8926 (mtm) cc_final: 0.8679 (mpp)
REVERT: J 121 LEU cc_start: 0.9352 (OUTLIER) cc_final: 0.9028 (mm)
REVERT: J 135 MET cc_start: 0.8234 (OUTLIER) cc_final: 0.8005 (tmm)
REVERT: J 138 MET cc_start: 0.8363 (ppp) cc_final: 0.7956 (ppp)
REVERT: J 322 MET cc_start: 0.8583 (tpp) cc_final: 0.8188 (tpp)
outliers start: 75
outliers final: 62
residues processed: 189
average time/residue: 0.3648
time to fit residues: 110.9101
Evaluate side-chains
191 residues out of total 2392 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 73
poor density : 118
time to evaluate : 2.665
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 8 LEU
Chi-restraints excluded: chain A residue 76 THR
Chi-restraints excluded: chain A residue 104 LEU
Chi-restraints excluded: chain A residue 106 MET
Chi-restraints excluded: chain A residue 112 VAL
Chi-restraints excluded: chain A residue 121 THR
Chi-restraints excluded: chain A residue 192 ILE
Chi-restraints excluded: chain A residue 205 VAL
Chi-restraints excluded: chain A residue 249 LEU
Chi-restraints excluded: chain B residue 19 ILE
Chi-restraints excluded: chain B residue 27 VAL
Chi-restraints excluded: chain B residue 42 THR
Chi-restraints excluded: chain B residue 60 VAL
Chi-restraints excluded: chain B residue 64 ASP
Chi-restraints excluded: chain B residue 72 CYS
Chi-restraints excluded: chain B residue 81 THR
Chi-restraints excluded: chain B residue 98 LEU
Chi-restraints excluded: chain B residue 134 LYS
Chi-restraints excluded: chain B residue 146 VAL
Chi-restraints excluded: chain I residue 70 GLU
Chi-restraints excluded: chain I residue 78 LYS
Chi-restraints excluded: chain I residue 93 ILE
Chi-restraints excluded: chain I residue 102 VAL
Chi-restraints excluded: chain I residue 113 ASN
Chi-restraints excluded: chain I residue 223 VAL
Chi-restraints excluded: chain I residue 270 THR
Chi-restraints excluded: chain I residue 277 VAL
Chi-restraints excluded: chain H residue 83 THR
Chi-restraints excluded: chain H residue 91 LEU
Chi-restraints excluded: chain H residue 108 SER
Chi-restraints excluded: chain H residue 120 GLN
Chi-restraints excluded: chain H residue 142 ILE
Chi-restraints excluded: chain H residue 185 ASP
Chi-restraints excluded: chain G residue 73 ASP
Chi-restraints excluded: chain G residue 236 LYS
Chi-restraints excluded: chain G residue 267 ASP
Chi-restraints excluded: chain G residue 329 PHE
Chi-restraints excluded: chain F residue 27 THR
Chi-restraints excluded: chain F residue 35 THR
Chi-restraints excluded: chain F residue 140 ASN
Chi-restraints excluded: chain F residue 223 VAL
Chi-restraints excluded: chain F residue 236 LYS
Chi-restraints excluded: chain E residue 27 THR
Chi-restraints excluded: chain E residue 55 LEU
Chi-restraints excluded: chain E residue 81 SER
Chi-restraints excluded: chain E residue 83 THR
Chi-restraints excluded: chain E residue 132 LEU
Chi-restraints excluded: chain E residue 229 MET
Chi-restraints excluded: chain E residue 296 SER
Chi-restraints excluded: chain D residue 27 THR
Chi-restraints excluded: chain D residue 50 THR
Chi-restraints excluded: chain D residue 88 CYS
Chi-restraints excluded: chain D residue 102 VAL
Chi-restraints excluded: chain D residue 132 LEU
Chi-restraints excluded: chain D residue 142 ILE
Chi-restraints excluded: chain D residue 212 THR
Chi-restraints excluded: chain D residue 233 ASP
Chi-restraints excluded: chain D residue 259 ARG
Chi-restraints excluded: chain D residue 301 ILE
Chi-restraints excluded: chain D residue 329 PHE
Chi-restraints excluded: chain J residue 75 LYS
Chi-restraints excluded: chain J residue 86 TYR
Chi-restraints excluded: chain J residue 106 HIS
Chi-restraints excluded: chain J residue 111 SER
Chi-restraints excluded: chain J residue 116 HIS
Chi-restraints excluded: chain J residue 121 LEU
Chi-restraints excluded: chain J residue 135 MET
Chi-restraints excluded: chain J residue 167 THR
Chi-restraints excluded: chain J residue 250 LEU
Chi-restraints excluded: chain J residue 272 ARG
Chi-restraints excluded: chain J residue 285 VAL
Chi-restraints excluded: chain J residue 292 TYR
Chi-restraints excluded: chain J residue 320 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 275
random chunks:
chunk 160 optimal weight: 3.9990
chunk 257 optimal weight: 10.0000
chunk 138 optimal weight: 9.9990
chunk 224 optimal weight: 0.7980
chunk 140 optimal weight: 8.9990
chunk 128 optimal weight: 0.5980
chunk 83 optimal weight: 2.9990
chunk 185 optimal weight: 6.9990
chunk 154 optimal weight: 9.9990
chunk 72 optimal weight: 6.9990
chunk 1 optimal weight: 9.9990
overall best weight: 3.0786
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** I 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 120 GLN
F 140 ASN
** J 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Total number of N/Q/H flips: 2
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3070 r_free = 0.3070 target = 0.046114 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2593 r_free = 0.2593 target = 0.031546 restraints weight = 119071.329|
|-----------------------------------------------------------------------------|
r_work (start): 0.2551 rms_B_bonded: 4.11
r_work: 0.2397 rms_B_bonded: 4.90 restraints_weight: 0.5000
r_work (final): 0.2397
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9004
moved from start: 0.2645
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.004 0.045 24609 Z= 0.226
Angle : 0.555 11.824 33700 Z= 0.286
Chirality : 0.039 0.269 3739
Planarity : 0.004 0.050 3950
Dihedral : 16.370 161.843 4299
Min Nonbonded Distance : 2.471
Molprobity Statistics.
All-atom Clashscore : 7.17
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 6.50 %
Favored : 93.50 %
Rotamer:
Outliers : 3.51 %
Allowed : 25.72 %
Favored : 70.77 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: -0.19 (0.17), residues: 2662
helix: 1.53 (0.19), residues: 800
sheet: 0.44 (0.27), residues: 433
loop : -1.33 (0.16), residues: 1429
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.008 0.001 TRP J 74
HIS 0.006 0.001 HIS A 181
PHE 0.021 0.001 PHE J 92
TYR 0.012 0.001 TYR G 169
ARG 0.003 0.000 ARG J 142
Origin is already at (0, 0, 0), no shifts will be applied
===============================================================================
Job complete
usr+sys time: 11302.87 seconds
wall clock time: 203 minutes 31.97 seconds (12211.97 seconds total)