Starting phenix.real_space_refine
on Mon Jan 20 17:02:07 2025 by dcliebschner
===============================================================================
Processing files:
-------------------------------------------------------------------------------
Found model, /net/cci-nas-00/data/ceres_data/8yaj_39100/01_2025/8yaj_39100.cif
Found real_map, /net/cci-nas-00/data/ceres_data/8yaj_39100/01_2025/8yaj_39100.map
Processing PHIL parameters:
-------------------------------------------------------------------------------
Adding command-line PHIL:
-------------------------
refinement.macro_cycles=10
scattering_table=electron
resolution=3.2
write_initial_geo_file=False
Final processed PHIL parameters:
-------------------------------------------------------------------------------
data_manager {
real_map_files = "/net/cci-nas-00/data/ceres_data/8yaj_39100/01_2025/8yaj_39100.map"
default_real_map = "/net/cci-nas-00/data/ceres_data/8yaj_39100/01_2025/8yaj_39100.map"
model {
file = "/net/cci-nas-00/data/ceres_data/8yaj_39100/01_2025/8yaj_39100.cif"
}
default_model = "/net/cci-nas-00/data/ceres_data/8yaj_39100/01_2025/8yaj_39100.cif"
}
resolution = 3.2
write_initial_geo_file = False
refinement {
macro_cycles = 10
}
qi {
qm_restraints {
package {
program = *test
}
}
}
Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.
Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
Set to: 0
Set model cs if undefined
Decide on map wrapping
Map wrapping is set to: False
Normalize map: mean=0, sd=1
Input map: mean= -0.001 sd= 0.039
Set stop_for_unknowns flag
Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
Set to: electron
Number of scattering types: 5
Type Number sf(0) Gaussians
P 12 5.49 5
S 107 5.16 5
C 9738 2.51 5
N 2646 2.21 5
O 2980 1.98 5
sf(0) = scattering factor at diffraction angle 0.
Process input model
Symmetric amino acids flipped. Time to flip 26 residue(s): 0.07s
Monomer Library directory:
"/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
Total number of atoms: 15483
Number of models: 1
Model: ""
Number of chains: 11
Chain: "B"
Number of atoms: 3429
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 439, 3429
Classifications: {'peptide': 439}
Incomplete info: {'truncation_to_alanine': 1}
Link IDs: {'PTRANS': 21, 'TRANS': 417}
Unresolved non-hydrogen bonds: 4
Unresolved non-hydrogen angles: 4
Unresolved non-hydrogen dihedrals: 4
Chain: "C"
Number of atoms: 1476
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 189, 1476
Classifications: {'peptide': 189}
Incomplete info: {'truncation_to_alanine': 20}
Link IDs: {'PTRANS': 5, 'TRANS': 183}
Unresolved non-hydrogen bonds: 81
Unresolved non-hydrogen angles: 98
Unresolved non-hydrogen dihedrals: 64
Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 7, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 4}
Unresolved non-hydrogen planarities: 66
Chain: "D"
Number of atoms: 3360
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 427, 3360
Classifications: {'peptide': 427}
Link IDs: {'PTRANS': 20, 'TRANS': 406}
Chain: "E"
Number of atoms: 3345
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 431, 3345
Classifications: {'peptide': 431}
Incomplete info: {'truncation_to_alanine': 8}
Link IDs: {'PTRANS': 21, 'TRANS': 409}
Chain breaks: 1
Unresolved non-hydrogen bonds: 37
Unresolved non-hydrogen angles: 43
Unresolved non-hydrogen dihedrals: 31
Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 3, 'ASP:plan': 1}
Unresolved non-hydrogen planarities: 26
Chain: "F"
Number of atoms: 3356
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 427, 3356
Classifications: {'peptide': 427}
Incomplete info: {'truncation_to_alanine': 1}
Link IDs: {'PTRANS': 20, 'TRANS': 406}
Unresolved non-hydrogen bonds: 4
Unresolved non-hydrogen angles: 5
Unresolved non-hydrogen dihedrals: 3
Planarities with less than four sites: {'GLU:plan': 1}
Unresolved non-hydrogen planarities: 4
Chain: "I"
Number of atoms: 371
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 50, 371
Classifications: {'peptide': 50}
Modifications used: {'COO': 1}
Incomplete info: {'truncation_to_alanine': 7}
Link IDs: {'PTRANS': 4, 'TRANS': 45}
Unresolved non-hydrogen bonds: 27
Unresolved non-hydrogen angles: 33
Unresolved non-hydrogen dihedrals: 21
Unresolved non-hydrogen chiralities: 2
Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1}
Unresolved non-hydrogen planarities: 17
Chain: "B"
Number of atoms: 32
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 1, 32
Unusual residues: {'GTP': 1}
Classifications: {'undetermined': 1}
Chain: "C"
Number of atoms: 18
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 1, 18
Unusual residues: {'PIN': 1}
Classifications: {'undetermined': 1}
Chain: "D"
Number of atoms: 32
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 1, 32
Unusual residues: {'G2P': 1}
Classifications: {'undetermined': 1}
Chain: "E"
Number of atoms: 32
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 1, 32
Unusual residues: {'GTP': 1}
Classifications: {'undetermined': 1}
Chain: "F"
Number of atoms: 32
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 1, 32
Unusual residues: {'G2P': 1}
Classifications: {'undetermined': 1}
Time building chain proxies: 10.03, per 1000 atoms: 0.65
Number of scatterers: 15483
At special positions: 0
Unit cell: (113.42, 110.24, 121.9, 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 107 16.00
P 12 15.00
O 2980 8.00
N 2646 7.00
C 9738 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: 4.37
Conformation dependent library (CDL) restraints added in 2.0 seconds
3898 Ramachandran restraints generated.
1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2.
Adding C-beta torsion restraints...
Number of C-beta restraints generated: 3644
Finding SS restraints...
Secondary structure from input PDB file:
97 helices and 17 sheets defined
53.3% alpha, 17.4% beta
0 base pairs and 0 stacking pairs defined.
Time for finding SS restraints: 1.98
Creating SS restraints...
Processing helix chain 'B' and resid 10 through 28
removed outlier: 3.549A pdb=" N ALA B 19 " --> pdb=" O GLN B 15 " (cutoff:3.500A)
Processing helix chain 'B' and resid 43 through 51
removed outlier: 3.685A pdb=" N ASP B 47 " --> pdb=" O GLY B 44 " (cutoff:3.500A)
removed outlier: 3.932A pdb=" N SER B 48 " --> pdb=" O SER B 45 " (cutoff:3.500A)
removed outlier: 4.236A pdb=" N PHE B 49 " --> pdb=" O ASP B 46 " (cutoff:3.500A)
Processing helix chain 'B' and resid 72 through 80
Processing helix chain 'B' and resid 81 through 85
removed outlier: 4.528A pdb=" N SER B 85 " --> pdb=" O THR B 82 " (cutoff:3.500A)
Processing helix chain 'B' and resid 102 through 108
Processing helix chain 'B' and resid 110 through 129
removed outlier: 4.052A pdb=" N ILE B 114 " --> pdb=" O ILE B 110 " (cutoff:3.500A)
removed outlier: 4.949A pdb=" N ASP B 116 " --> pdb=" O LYS B 112 " (cutoff:3.500A)
removed outlier: 5.462A pdb=" N LEU B 117 " --> pdb=" O GLU B 113 " (cutoff:3.500A)
Processing helix chain 'B' and resid 144 through 161
removed outlier: 4.353A pdb=" N THR B 150 " --> pdb=" O GLY B 146 " (cutoff:3.500A)
Processing helix chain 'B' and resid 182 through 198
removed outlier: 3.607A pdb=" N ASN B 186 " --> pdb=" O VAL B 182 " (cutoff:3.500A)
removed outlier: 3.720A pdb=" N HIS B 192 " --> pdb=" O ILE B 188 " (cutoff:3.500A)
removed outlier: 4.230A pdb=" N THR B 193 " --> pdb=" O LEU B 189 " (cutoff:3.500A)
removed outlier: 3.554A pdb=" N SER B 198 " --> pdb=" O THR B 194 " (cutoff:3.500A)
Processing helix chain 'B' and resid 206 through 217
Processing helix chain 'B' and resid 223 through 240
removed outlier: 3.780A pdb=" N LEU B 227 " --> pdb=" O SER B 223 " (cutoff:3.500A)
Processing helix chain 'B' and resid 241 through 243
No H-bonds generated for 'chain 'B' and resid 241 through 243'
Processing helix chain 'B' and resid 251 through 260
Processing helix chain 'B' and resid 279 through 284
removed outlier: 4.051A pdb=" N HIS B 283 " --> pdb=" O GLU B 279 " (cutoff:3.500A)
Processing helix chain 'B' and resid 287 through 297
removed outlier: 3.550A pdb=" N CYS B 295 " --> pdb=" O ILE B 291 " (cutoff:3.500A)
removed outlier: 4.053A pdb=" N PHE B 296 " --> pdb=" O THR B 292 " (cutoff:3.500A)
removed outlier: 3.768A pdb=" N GLU B 297 " --> pdb=" O ASN B 293 " (cutoff:3.500A)
Processing helix chain 'B' and resid 298 through 301
removed outlier: 3.618A pdb=" N GLN B 301 " --> pdb=" O PRO B 298 " (cutoff:3.500A)
No H-bonds generated for 'chain 'B' and resid 298 through 301'
Processing helix chain 'B' and resid 306 through 310
removed outlier: 3.541A pdb=" N HIS B 309 " --> pdb=" O ASP B 306 " (cutoff:3.500A)
Processing helix chain 'B' and resid 324 through 337
removed outlier: 3.508A pdb=" N VAL B 328 " --> pdb=" O VAL B 324 " (cutoff:3.500A)
Processing helix chain 'B' and resid 384 through 400
Processing helix chain 'B' and resid 404 through 410
removed outlier: 3.837A pdb=" N TYR B 408 " --> pdb=" O PHE B 404 " (cutoff:3.500A)
Processing helix chain 'B' and resid 415 through 437
removed outlier: 4.083A pdb=" N SER B 419 " --> pdb=" O GLU B 415 " (cutoff:3.500A)
Processing helix chain 'C' and resid 6 through 10
Processing helix chain 'C' and resid 19 through 26
Processing helix chain 'C' and resid 31 through 50
removed outlier: 3.952A pdb=" N ALA C 35 " --> pdb=" O TYR C 31 " (cutoff:3.500A)
Processing helix chain 'C' and resid 57 through 63
Processing helix chain 'C' and resid 99 through 103
removed outlier: 3.606A pdb=" N GLN C 102 " --> pdb=" O ASP C 99 " (cutoff:3.500A)
Processing helix chain 'C' and resid 118 through 123
removed outlier: 4.473A pdb=" N ARG C 123 " --> pdb=" O PRO C 119 " (cutoff:3.500A)
Processing helix chain 'C' and resid 126 through 139
Processing helix chain 'C' and resid 141 through 143
No H-bonds generated for 'chain 'C' and resid 141 through 143'
Processing helix chain 'C' and resid 151 through 162
Processing helix chain 'D' and resid 10 through 29
Processing helix chain 'D' and resid 40 through 45
removed outlier: 3.832A pdb=" N LEU D 44 " --> pdb=" O SER D 40 " (cutoff:3.500A)
Processing helix chain 'D' and resid 46 through 49
removed outlier: 3.930A pdb=" N VAL D 49 " --> pdb=" O ARG D 46 " (cutoff:3.500A)
No H-bonds generated for 'chain 'D' and resid 46 through 49'
Processing helix chain 'D' and resid 69 through 79
removed outlier: 3.914A pdb=" N MET D 73 " --> pdb=" O GLU D 69 " (cutoff:3.500A)
Processing helix chain 'D' and resid 81 through 85
removed outlier: 3.685A pdb=" N PHE D 85 " --> pdb=" O GLY D 82 " (cutoff:3.500A)
Processing helix chain 'D' and resid 86 through 88
No H-bonds generated for 'chain 'D' and resid 86 through 88'
Processing helix chain 'D' and resid 100 through 106
Processing helix chain 'D' and resid 107 through 127
removed outlier: 4.109A pdb=" N ASP D 114 " --> pdb=" O ALA D 110 " (cutoff:3.500A)
removed outlier: 4.657A pdb=" N ASN D 115 " --> pdb=" O GLU D 111 " (cutoff:3.500A)
removed outlier: 3.570A pdb=" N SER D 126 " --> pdb=" O LYS D 122 " (cutoff:3.500A)
removed outlier: 3.599A pdb=" N THR D 127 " --> pdb=" O GLU D 123 " (cutoff:3.500A)
Processing helix chain 'D' and resid 142 through 159
Processing helix chain 'D' and resid 172 through 176
Processing helix chain 'D' and resid 180 through 195
removed outlier: 3.568A pdb=" N ASN D 184 " --> pdb=" O VAL D 180 " (cutoff:3.500A)
removed outlier: 4.105A pdb=" N HIS D 190 " --> pdb=" O THR D 186 " (cutoff:3.500A)
removed outlier: 4.328A pdb=" N GLN D 191 " --> pdb=" O LEU D 187 " (cutoff:3.500A)
Processing helix chain 'D' and resid 204 through 214
Processing helix chain 'D' and resid 221 through 237
removed outlier: 3.719A pdb=" N LEU D 225 " --> pdb=" O THR D 221 " (cutoff:3.500A)
removed outlier: 3.786A pdb=" N THR D 237 " --> pdb=" O MET D 233 " (cutoff:3.500A)
Processing helix chain 'D' and resid 237 through 242
removed outlier: 4.048A pdb=" N ARG D 241 " --> pdb=" O THR D 237 " (cutoff:3.500A)
Processing helix chain 'D' and resid 249 through 258
Processing helix chain 'D' and resid 285 through 294
Processing helix chain 'D' and resid 304 through 308
Processing helix chain 'D' and resid 322 through 336
Processing helix chain 'D' and resid 337 through 341
Processing helix chain 'D' and resid 373 through 391
removed outlier: 3.868A pdb=" N LEU D 377 " --> pdb=" O ALA D 373 " (cutoff:3.500A)
removed outlier: 3.824A pdb=" N ILE D 381 " --> pdb=" O LEU D 377 " (cutoff:3.500A)
removed outlier: 4.134A pdb=" N ARG D 391 " --> pdb=" O ALA D 387 " (cutoff:3.500A)
Processing helix chain 'D' and resid 394 through 400
removed outlier: 4.092A pdb=" N TYR D 398 " --> pdb=" O PHE D 394 " (cutoff:3.500A)
Processing helix chain 'D' and resid 404 through 425
removed outlier: 3.760A pdb=" N TYR D 425 " --> pdb=" O GLU D 421 " (cutoff:3.500A)
Processing helix chain 'E' and resid 10 through 29
Processing helix chain 'E' and resid 47 through 51
removed outlier: 3.885A pdb=" N THR E 51 " --> pdb=" O SER E 48 " (cutoff:3.500A)
Processing helix chain 'E' and resid 72 through 80
Processing helix chain 'E' and resid 81 through 86
removed outlier: 4.401A pdb=" N SER E 85 " --> pdb=" O THR E 82 " (cutoff:3.500A)
Processing helix chain 'E' and resid 88 through 90
No H-bonds generated for 'chain 'E' and resid 88 through 90'
Processing helix chain 'E' and resid 102 through 108
Processing helix chain 'E' and resid 110 through 128
removed outlier: 4.022A pdb=" N ILE E 114 " --> pdb=" O ILE E 110 " (cutoff:3.500A)
removed outlier: 4.797A pdb=" N ASP E 116 " --> pdb=" O LYS E 112 " (cutoff:3.500A)
removed outlier: 5.552A pdb=" N LEU E 117 " --> pdb=" O GLU E 113 " (cutoff:3.500A)
Processing helix chain 'E' and resid 144 through 161
removed outlier: 4.524A pdb=" N THR E 150 " --> pdb=" O GLY E 146 " (cutoff:3.500A)
removed outlier: 3.644A pdb=" N VAL E 159 " --> pdb=" O GLU E 155 " (cutoff:3.500A)
Processing helix chain 'E' and resid 182 through 198
removed outlier: 3.816A pdb=" N HIS E 192 " --> pdb=" O ILE E 188 " (cutoff:3.500A)
removed outlier: 4.064A pdb=" N THR E 193 " --> pdb=" O LEU E 189 " (cutoff:3.500A)
removed outlier: 3.734A pdb=" N LEU E 195 " --> pdb=" O THR E 191 " (cutoff:3.500A)
removed outlier: 3.547A pdb=" N GLU E 196 " --> pdb=" O HIS E 192 " (cutoff:3.500A)
Processing helix chain 'E' and resid 206 through 216
Processing helix chain 'E' and resid 226 through 240
Processing helix chain 'E' and resid 241 through 243
No H-bonds generated for 'chain 'E' and resid 241 through 243'
Processing helix chain 'E' and resid 251 through 260
Processing helix chain 'E' and resid 277 through 282
removed outlier: 3.795A pdb=" N TYR E 282 " --> pdb=" O ALA E 278 " (cutoff:3.500A)
Processing helix chain 'E' and resid 287 through 296
removed outlier: 3.934A pdb=" N PHE E 296 " --> pdb=" O THR E 292 " (cutoff:3.500A)
Processing helix chain 'E' and resid 297 through 301
removed outlier: 3.707A pdb=" N GLN E 301 " --> pdb=" O PRO E 298 " (cutoff:3.500A)
Processing helix chain 'E' and resid 306 through 310
Processing helix chain 'E' and resid 324 through 338
Processing helix chain 'E' and resid 384 through 401
removed outlier: 3.755A pdb=" N TRP E 388 " --> pdb=" O ILE E 384 " (cutoff:3.500A)
removed outlier: 4.359A pdb=" N LYS E 401 " --> pdb=" O LEU E 397 " (cutoff:3.500A)
Processing helix chain 'E' and resid 404 through 410
removed outlier: 3.929A pdb=" N TYR E 408 " --> pdb=" O PHE E 404 " (cutoff:3.500A)
Processing helix chain 'E' and resid 415 through 437
removed outlier: 4.198A pdb=" N SER E 419 " --> pdb=" O GLU E 415 " (cutoff:3.500A)
Processing helix chain 'F' and resid 10 through 29
Processing helix chain 'F' and resid 40 through 44
Processing helix chain 'F' and resid 46 through 49
Processing helix chain 'F' and resid 69 through 78
removed outlier: 4.508A pdb=" N MET F 73 " --> pdb=" O GLU F 69 " (cutoff:3.500A)
Processing helix chain 'F' and resid 86 through 88
No H-bonds generated for 'chain 'F' and resid 86 through 88'
Processing helix chain 'F' and resid 100 through 106
Processing helix chain 'F' and resid 107 through 126
removed outlier: 3.748A pdb=" N LEU F 112 " --> pdb=" O GLU F 108 " (cutoff:3.500A)
removed outlier: 4.183A pdb=" N ASP F 114 " --> pdb=" O ALA F 110 " (cutoff:3.500A)
removed outlier: 4.921A pdb=" N ASN F 115 " --> pdb=" O GLU F 111 " (cutoff:3.500A)
removed outlier: 3.645A pdb=" N SER F 126 " --> pdb=" O LYS F 122 " (cutoff:3.500A)
Processing helix chain 'F' and resid 142 through 159
removed outlier: 4.048A pdb=" N THR F 149 " --> pdb=" O SER F 145 " (cutoff:3.500A)
Processing helix chain 'F' and resid 172 through 176
Processing helix chain 'F' and resid 180 through 196
removed outlier: 3.675A pdb=" N ASN F 184 " --> pdb=" O VAL F 180 " (cutoff:3.500A)
removed outlier: 4.227A pdb=" N GLN F 191 " --> pdb=" O LEU F 187 " (cutoff:3.500A)
removed outlier: 3.877A pdb=" N GLU F 194 " --> pdb=" O HIS F 190 " (cutoff:3.500A)
Processing helix chain 'F' and resid 204 through 214
Processing helix chain 'F' and resid 221 through 237
removed outlier: 3.555A pdb=" N LEU F 225 " --> pdb=" O THR F 221 " (cutoff:3.500A)
removed outlier: 3.527A pdb=" N THR F 237 " --> pdb=" O MET F 233 " (cutoff:3.500A)
Processing helix chain 'F' and resid 238 through 241
removed outlier: 3.513A pdb=" N ARG F 241 " --> pdb=" O THR F 238 " (cutoff:3.500A)
No H-bonds generated for 'chain 'F' and resid 238 through 241'
Processing helix chain 'F' and resid 249 through 258
Processing helix chain 'F' and resid 285 through 295
Processing helix chain 'F' and resid 296 through 299
Processing helix chain 'F' and resid 304 through 308
Processing helix chain 'F' and resid 322 through 337
Processing helix chain 'F' and resid 338 through 341
removed outlier: 3.713A pdb=" N PHE F 341 " --> pdb=" O SER F 338 " (cutoff:3.500A)
No H-bonds generated for 'chain 'F' and resid 338 through 341'
Processing helix chain 'F' and resid 374 through 390
removed outlier: 3.939A pdb=" N PHE F 378 " --> pdb=" O ILE F 374 " (cutoff:3.500A)
Processing helix chain 'F' and resid 394 through 400
removed outlier: 4.097A pdb=" N TYR F 398 " --> pdb=" O PHE F 394 " (cutoff:3.500A)
Processing helix chain 'F' and resid 404 through 425
removed outlier: 3.583A pdb=" N PHE F 408 " --> pdb=" O ASP F 404 " (cutoff:3.500A)
removed outlier: 3.584A pdb=" N TYR F 425 " --> pdb=" O GLU F 421 " (cutoff:3.500A)
Processing helix chain 'I' and resid 220 through 224
Processing helix chain 'I' and resid 226 through 231
Processing helix chain 'I' and resid 247 through 256
Processing sheet with id=AA1, first strand: chain 'B' and resid 93 through 94
removed outlier: 8.710A pdb=" N VAL B 66 " --> pdb=" O VAL B 4 " (cutoff:3.500A)
removed outlier: 7.231A pdb=" N SER B 6 " --> pdb=" O VAL B 66 " (cutoff:3.500A)
removed outlier: 7.678A pdb=" N VAL B 68 " --> pdb=" O SER B 6 " (cutoff:3.500A)
removed outlier: 6.135A pdb=" N HIS B 8 " --> pdb=" O VAL B 68 " (cutoff:3.500A)
removed outlier: 7.521A pdb=" N GLU B 3 " --> pdb=" O GLN B 133 " (cutoff:3.500A)
removed outlier: 6.730A pdb=" N PHE B 135 " --> pdb=" O GLU B 3 " (cutoff:3.500A)
removed outlier: 6.289A pdb=" N ILE B 5 " --> pdb=" O PHE B 135 " (cutoff:3.500A)
removed outlier: 5.348A pdb=" N VAL B 137 " --> pdb=" O ILE B 5 " (cutoff:3.500A)
removed outlier: 6.631A pdb=" N ILE B 7 " --> pdb=" O VAL B 137 " (cutoff:3.500A)
removed outlier: 5.665A pdb=" N HIS B 139 " --> pdb=" O ILE B 7 " (cutoff:3.500A)
removed outlier: 7.231A pdb=" N ILE B 9 " --> pdb=" O HIS B 139 " (cutoff:3.500A)
removed outlier: 7.176A pdb=" N GLN B 133 " --> pdb=" O ALA B 165 " (cutoff:3.500A)
removed outlier: 8.115A pdb=" N LEU B 167 " --> pdb=" O GLN B 133 " (cutoff:3.500A)
removed outlier: 6.241A pdb=" N PHE B 135 " --> pdb=" O LEU B 167 " (cutoff:3.500A)
removed outlier: 7.589A pdb=" N PHE B 169 " --> pdb=" O PHE B 135 " (cutoff:3.500A)
removed outlier: 6.762A pdb=" N VAL B 137 " --> pdb=" O PHE B 169 " (cutoff:3.500A)
removed outlier: 7.839A pdb=" N ILE B 171 " --> pdb=" O VAL B 137 " (cutoff:3.500A)
removed outlier: 8.059A pdb=" N HIS B 139 " --> pdb=" O ILE B 171 " (cutoff:3.500A)
removed outlier: 3.634A pdb=" N CYS B 200 " --> pdb=" O LYS B 166 " (cutoff:3.500A)
Processing sheet with id=AA2, first strand: chain 'B' and resid 93 through 94
removed outlier: 8.710A pdb=" N VAL B 66 " --> pdb=" O VAL B 4 " (cutoff:3.500A)
removed outlier: 7.231A pdb=" N SER B 6 " --> pdb=" O VAL B 66 " (cutoff:3.500A)
removed outlier: 7.678A pdb=" N VAL B 68 " --> pdb=" O SER B 6 " (cutoff:3.500A)
removed outlier: 6.135A pdb=" N HIS B 8 " --> pdb=" O VAL B 68 " (cutoff:3.500A)
removed outlier: 7.521A pdb=" N GLU B 3 " --> pdb=" O GLN B 133 " (cutoff:3.500A)
removed outlier: 6.730A pdb=" N PHE B 135 " --> pdb=" O GLU B 3 " (cutoff:3.500A)
removed outlier: 6.289A pdb=" N ILE B 5 " --> pdb=" O PHE B 135 " (cutoff:3.500A)
removed outlier: 5.348A pdb=" N VAL B 137 " --> pdb=" O ILE B 5 " (cutoff:3.500A)
removed outlier: 6.631A pdb=" N ILE B 7 " --> pdb=" O VAL B 137 " (cutoff:3.500A)
removed outlier: 5.665A pdb=" N HIS B 139 " --> pdb=" O ILE B 7 " (cutoff:3.500A)
removed outlier: 7.231A pdb=" N ILE B 9 " --> pdb=" O HIS B 139 " (cutoff:3.500A)
removed outlier: 7.176A pdb=" N GLN B 133 " --> pdb=" O ALA B 165 " (cutoff:3.500A)
removed outlier: 8.115A pdb=" N LEU B 167 " --> pdb=" O GLN B 133 " (cutoff:3.500A)
removed outlier: 6.241A pdb=" N PHE B 135 " --> pdb=" O LEU B 167 " (cutoff:3.500A)
removed outlier: 7.589A pdb=" N PHE B 169 " --> pdb=" O PHE B 135 " (cutoff:3.500A)
removed outlier: 6.762A pdb=" N VAL B 137 " --> pdb=" O PHE B 169 " (cutoff:3.500A)
removed outlier: 7.839A pdb=" N ILE B 171 " --> pdb=" O VAL B 137 " (cutoff:3.500A)
removed outlier: 8.059A pdb=" N HIS B 139 " --> pdb=" O ILE B 171 " (cutoff:3.500A)
Processing sheet with id=AA3, first strand: chain 'B' and resid 53 through 55
Processing sheet with id=AA4, first strand: chain 'B' and resid 351 through 354
removed outlier: 6.562A pdb=" N VAL B 315 " --> pdb=" O LYS B 352 " (cutoff:3.500A)
removed outlier: 7.650A pdb=" N GLY B 354 " --> pdb=" O VAL B 315 " (cutoff:3.500A)
removed outlier: 6.194A pdb=" N LEU B 317 " --> pdb=" O GLY B 354 " (cutoff:3.500A)
removed outlier: 3.652A pdb=" N ALA B 374 " --> pdb=" O ARG B 320 " (cutoff:3.500A)
Processing sheet with id=AA5, first strand: chain 'C' and resid 2 through 3
removed outlier: 5.788A pdb=" N LEU C 84 " --> pdb=" O GLU C 75 " (cutoff:3.500A)
removed outlier: 6.913A pdb=" N GLU C 75 " --> pdb=" O LEU C 84 " (cutoff:3.500A)
removed outlier: 3.821A pdb=" N GLY C 86 " --> pdb=" O MET C 73 " (cutoff:3.500A)
removed outlier: 3.948A pdb=" N MET C 73 " --> pdb=" O GLY C 86 " (cutoff:3.500A)
removed outlier: 3.756A pdb=" N ILE C 72 " --> pdb=" O GLN C 16 " (cutoff:3.500A)
Processing sheet with id=AA6, first strand: chain 'C' and resid 2 through 3
removed outlier: 7.355A pdb=" N GLY C 91 " --> pdb=" O ILE C 112 " (cutoff:3.500A)
removed outlier: 5.390A pdb=" N ILE C 112 " --> pdb=" O GLY C 91 " (cutoff:3.500A)
removed outlier: 6.305A pdb=" N LYS C 93 " --> pdb=" O MET C 110 " (cutoff:3.500A)
removed outlier: 5.692A pdb=" N MET C 110 " --> pdb=" O LYS C 93 " (cutoff:3.500A)
removed outlier: 7.070A pdb=" N LEU C 95 " --> pdb=" O LYS C 108 " (cutoff:3.500A)
removed outlier: 5.653A pdb=" N LYS C 108 " --> pdb=" O LEU C 95 " (cutoff:3.500A)
removed outlier: 8.298A pdb=" N ALA C 146 " --> pdb=" O LYS C 108 " (cutoff:3.500A)
removed outlier: 6.167A pdb=" N MET C 110 " --> pdb=" O ALA C 146 " (cutoff:3.500A)
Processing sheet with id=AA7, first strand: chain 'C' and resid 168 through 169
Processing sheet with id=AA8, first strand: chain 'D' and resid 90 through 92
removed outlier: 8.299A pdb=" N VAL D 91 " --> pdb=" O ALA D 63 " (cutoff:3.500A)
removed outlier: 6.364A pdb=" N LEU D 65 " --> pdb=" O VAL D 91 " (cutoff:3.500A)
removed outlier: 8.167A pdb=" N VAL D 64 " --> pdb=" O ILE D 4 " (cutoff:3.500A)
removed outlier: 6.726A pdb=" N HIS D 6 " --> pdb=" O VAL D 64 " (cutoff:3.500A)
removed outlier: 7.479A pdb=" N VAL D 66 " --> pdb=" O HIS D 6 " (cutoff:3.500A)
removed outlier: 5.643A pdb=" N GLN D 8 " --> pdb=" O VAL D 66 " (cutoff:3.500A)
removed outlier: 6.797A pdb=" N GLU D 3 " --> pdb=" O GLY D 132 " (cutoff:3.500A)
removed outlier: 7.897A pdb=" N GLN D 134 " --> pdb=" O GLU D 3 " (cutoff:3.500A)
removed outlier: 6.013A pdb=" N VAL D 5 " --> pdb=" O GLN D 134 " (cutoff:3.500A)
removed outlier: 7.775A pdb=" N THR D 136 " --> pdb=" O VAL D 5 " (cutoff:3.500A)
removed outlier: 6.561A pdb=" N ILE D 7 " --> pdb=" O THR D 136 " (cutoff:3.500A)
removed outlier: 8.770A pdb=" N SER D 138 " --> pdb=" O ILE D 7 " (cutoff:3.500A)
removed outlier: 8.476A pdb=" N ALA D 9 " --> pdb=" O SER D 138 " (cutoff:3.500A)
removed outlier: 3.826A pdb=" N HIS D 137 " --> pdb=" O PHE D 167 " (cutoff:3.500A)
Processing sheet with id=AA9, first strand: chain 'D' and resid 90 through 92
removed outlier: 8.299A pdb=" N VAL D 91 " --> pdb=" O ALA D 63 " (cutoff:3.500A)
removed outlier: 6.364A pdb=" N LEU D 65 " --> pdb=" O VAL D 91 " (cutoff:3.500A)
removed outlier: 8.167A pdb=" N VAL D 64 " --> pdb=" O ILE D 4 " (cutoff:3.500A)
removed outlier: 6.726A pdb=" N HIS D 6 " --> pdb=" O VAL D 64 " (cutoff:3.500A)
removed outlier: 7.479A pdb=" N VAL D 66 " --> pdb=" O HIS D 6 " (cutoff:3.500A)
removed outlier: 5.643A pdb=" N GLN D 8 " --> pdb=" O VAL D 66 " (cutoff:3.500A)
removed outlier: 6.797A pdb=" N GLU D 3 " --> pdb=" O GLY D 132 " (cutoff:3.500A)
removed outlier: 7.897A pdb=" N GLN D 134 " --> pdb=" O GLU D 3 " (cutoff:3.500A)
removed outlier: 6.013A pdb=" N VAL D 5 " --> pdb=" O GLN D 134 " (cutoff:3.500A)
removed outlier: 7.775A pdb=" N THR D 136 " --> pdb=" O VAL D 5 " (cutoff:3.500A)
removed outlier: 6.561A pdb=" N ILE D 7 " --> pdb=" O THR D 136 " (cutoff:3.500A)
removed outlier: 8.770A pdb=" N SER D 138 " --> pdb=" O ILE D 7 " (cutoff:3.500A)
removed outlier: 8.476A pdb=" N ALA D 9 " --> pdb=" O SER D 138 " (cutoff:3.500A)
removed outlier: 3.826A pdb=" N HIS D 137 " --> pdb=" O PHE D 167 " (cutoff:3.500A)
removed outlier: 6.204A pdb=" N MET D 164 " --> pdb=" O SER D 198 " (cutoff:3.500A)
removed outlier: 7.603A pdb=" N PHE D 200 " --> pdb=" O MET D 164 " (cutoff:3.500A)
removed outlier: 6.765A pdb=" N THR D 166 " --> pdb=" O PHE D 200 " (cutoff:3.500A)
removed outlier: 7.109A pdb=" N THR D 199 " --> pdb=" O PHE D 266 " (cutoff:3.500A)
Processing sheet with id=AB1, first strand: chain 'D' and resid 51 through 53
Processing sheet with id=AB2, first strand: chain 'D' and resid 349 through 354
removed outlier: 4.049A pdb=" N THR D 312 " --> pdb=" O ASN D 370 " (cutoff:3.500A)
Processing sheet with id=AB3, first strand: chain 'E' and resid 92 through 94
removed outlier: 3.503A pdb=" N ASP E 69 " --> pdb=" O ILE E 93 " (cutoff:3.500A)
removed outlier: 4.485A pdb=" N SER E 140 " --> pdb=" O ILE E 9 " (cutoff:3.500A)
removed outlier: 5.485A pdb=" N PHE E 135 " --> pdb=" O LEU E 167 " (cutoff:3.500A)
removed outlier: 6.875A pdb=" N PHE E 169 " --> pdb=" O PHE E 135 " (cutoff:3.500A)
removed outlier: 6.110A pdb=" N VAL E 137 " --> pdb=" O PHE E 169 " (cutoff:3.500A)
removed outlier: 7.377A pdb=" N ILE E 171 " --> pdb=" O VAL E 137 " (cutoff:3.500A)
removed outlier: 7.158A pdb=" N HIS E 139 " --> pdb=" O ILE E 171 " (cutoff:3.500A)
removed outlier: 3.517A pdb=" N CYS E 200 " --> pdb=" O LYS E 166 " (cutoff:3.500A)
Processing sheet with id=AB4, first strand: chain 'E' and resid 92 through 94
removed outlier: 3.503A pdb=" N ASP E 69 " --> pdb=" O ILE E 93 " (cutoff:3.500A)
removed outlier: 4.485A pdb=" N SER E 140 " --> pdb=" O ILE E 9 " (cutoff:3.500A)
removed outlier: 5.485A pdb=" N PHE E 135 " --> pdb=" O LEU E 167 " (cutoff:3.500A)
removed outlier: 6.875A pdb=" N PHE E 169 " --> pdb=" O PHE E 135 " (cutoff:3.500A)
removed outlier: 6.110A pdb=" N VAL E 137 " --> pdb=" O PHE E 169 " (cutoff:3.500A)
removed outlier: 7.377A pdb=" N ILE E 171 " --> pdb=" O VAL E 137 " (cutoff:3.500A)
removed outlier: 7.158A pdb=" N HIS E 139 " --> pdb=" O ILE E 171 " (cutoff:3.500A)
Processing sheet with id=AB5, first strand: chain 'E' and resid 53 through 55
Processing sheet with id=AB6, first strand: chain 'E' and resid 246 through 247
Processing sheet with id=AB7, first strand: chain 'F' and resid 90 through 92
removed outlier: 8.135A pdb=" N VAL F 91 " --> pdb=" O ALA F 63 " (cutoff:3.500A)
removed outlier: 6.090A pdb=" N LEU F 65 " --> pdb=" O VAL F 91 " (cutoff:3.500A)
removed outlier: 8.277A pdb=" N VAL F 64 " --> pdb=" O ILE F 4 " (cutoff:3.500A)
removed outlier: 6.681A pdb=" N HIS F 6 " --> pdb=" O VAL F 64 " (cutoff:3.500A)
removed outlier: 7.670A pdb=" N VAL F 66 " --> pdb=" O HIS F 6 " (cutoff:3.500A)
removed outlier: 5.730A pdb=" N GLN F 8 " --> pdb=" O VAL F 66 " (cutoff:3.500A)
removed outlier: 6.932A pdb=" N GLU F 3 " --> pdb=" O GLN F 131 " (cutoff:3.500A)
removed outlier: 6.104A pdb=" N PHE F 133 " --> pdb=" O GLU F 3 " (cutoff:3.500A)
removed outlier: 6.276A pdb=" N VAL F 5 " --> pdb=" O PHE F 133 " (cutoff:3.500A)
removed outlier: 5.219A pdb=" N LEU F 135 " --> pdb=" O VAL F 5 " (cutoff:3.500A)
removed outlier: 6.486A pdb=" N ILE F 7 " --> pdb=" O LEU F 135 " (cutoff:3.500A)
removed outlier: 5.828A pdb=" N HIS F 137 " --> pdb=" O ILE F 7 " (cutoff:3.500A)
removed outlier: 7.404A pdb=" N ALA F 9 " --> pdb=" O HIS F 137 " (cutoff:3.500A)
removed outlier: 7.085A pdb=" N GLN F 131 " --> pdb=" O ILE F 163 " (cutoff:3.500A)
removed outlier: 8.110A pdb=" N ASN F 165 " --> pdb=" O GLN F 131 " (cutoff:3.500A)
removed outlier: 5.954A pdb=" N PHE F 133 " --> pdb=" O ASN F 165 " (cutoff:3.500A)
removed outlier: 7.494A pdb=" N PHE F 167 " --> pdb=" O PHE F 133 " (cutoff:3.500A)
removed outlier: 6.920A pdb=" N LEU F 135 " --> pdb=" O PHE F 167 " (cutoff:3.500A)
removed outlier: 7.743A pdb=" N VAL F 169 " --> pdb=" O LEU F 135 " (cutoff:3.500A)
removed outlier: 7.440A pdb=" N HIS F 137 " --> pdb=" O VAL F 169 " (cutoff:3.500A)
removed outlier: 6.499A pdb=" N MET F 164 " --> pdb=" O SER F 198 " (cutoff:3.500A)
removed outlier: 7.705A pdb=" N PHE F 200 " --> pdb=" O MET F 164 " (cutoff:3.500A)
removed outlier: 6.831A pdb=" N THR F 166 " --> pdb=" O PHE F 200 " (cutoff:3.500A)
removed outlier: 7.505A pdb=" N ILE F 202 " --> pdb=" O THR F 166 " (cutoff:3.500A)
removed outlier: 6.567A pdb=" N SER F 168 " --> pdb=" O ILE F 202 " (cutoff:3.500A)
removed outlier: 6.860A pdb=" N THR F 199 " --> pdb=" O PHE F 266 " (cutoff:3.500A)
removed outlier: 7.998A pdb=" N CYS F 201 " --> pdb=" O PRO F 268 " (cutoff:3.500A)
removed outlier: 7.270A pdb=" N PHE F 265 " --> pdb=" O SER F 371 " (cutoff:3.500A)
removed outlier: 4.844A pdb=" N SER F 371 " --> pdb=" O PHE F 265 " (cutoff:3.500A)
removed outlier: 8.225A pdb=" N LYS F 350 " --> pdb=" O LEU F 311 " (cutoff:3.500A)
removed outlier: 6.435A pdb=" N ALA F 313 " --> pdb=" O LYS F 350 " (cutoff:3.500A)
removed outlier: 8.149A pdb=" N ALA F 352 " --> pdb=" O ALA F 313 " (cutoff:3.500A)
removed outlier: 6.353A pdb=" N ALA F 315 " --> pdb=" O ALA F 352 " (cutoff:3.500A)
removed outlier: 7.696A pdb=" N CYS F 354 " --> pdb=" O ALA F 315 " (cutoff:3.500A)
removed outlier: 6.801A pdb=" N PHE F 317 " --> pdb=" O CYS F 354 " (cutoff:3.500A)
Processing sheet with id=AB8, first strand: chain 'F' and resid 51 through 53
718 hydrogen bonds defined for protein.
2019 hydrogen bond angles defined for protein.
Restraints generated for nucleic acids:
0 hydrogen bonds
0 hydrogen bond angles
0 basepair planarities
0 basepair parallelities
0 stacking parallelities
Total time for adding SS restraints: 5.52
Time building geometry restraints manager: 4.81 seconds
NOTE: a complete listing of the restraints can be obtained by requesting
output of .geo file.
Histogram of bond lengths:
1.19 - 1.34: 5097
1.34 - 1.48: 3982
1.48 - 1.62: 6575
1.62 - 1.77: 10
1.77 - 1.91: 176
Bond restraints: 15840
Sorted by residual:
bond pdb=" O5' GTP E 501 "
pdb=" PA GTP E 501 "
ideal model delta sigma weight residual
1.610 1.833 -0.223 2.00e-02 2.50e+03 1.25e+02
bond pdb=" O5' GTP B 501 "
pdb=" PA GTP B 501 "
ideal model delta sigma weight residual
1.610 1.829 -0.219 2.00e-02 2.50e+03 1.20e+02
bond pdb=" C3A G2P D 501 "
pdb=" PA G2P D 501 "
ideal model delta sigma weight residual
1.818 1.656 0.162 2.00e-02 2.50e+03 6.52e+01
bond pdb=" C3A G2P F 501 "
pdb=" PA G2P F 501 "
ideal model delta sigma weight residual
1.818 1.658 0.160 2.00e-02 2.50e+03 6.38e+01
bond pdb=" O3A GTP B 501 "
pdb=" PB GTP B 501 "
ideal model delta sigma weight residual
1.610 1.747 -0.137 2.00e-02 2.50e+03 4.69e+01
... (remaining 15835 not shown)
Histogram of bond angle deviations from ideal:
0.00 - 2.72: 21290
2.72 - 5.45: 170
5.45 - 8.17: 41
8.17 - 10.90: 14
10.90 - 13.62: 8
Bond angle restraints: 21523
Sorted by residual:
angle pdb=" O1A GTP E 501 "
pdb=" PA GTP E 501 "
pdb=" O5' GTP E 501 "
ideal model delta sigma weight residual
108.20 94.58 13.62 3.00e+00 1.11e-01 2.06e+01
angle pdb=" O1A GTP B 501 "
pdb=" PA GTP B 501 "
pdb=" O5' GTP B 501 "
ideal model delta sigma weight residual
108.20 94.88 13.32 3.00e+00 1.11e-01 1.97e+01
angle pdb=" O2A GTP E 501 "
pdb=" PA GTP E 501 "
pdb=" O5' GTP E 501 "
ideal model delta sigma weight residual
109.50 96.83 12.67 3.00e+00 1.11e-01 1.78e+01
angle pdb=" O2A GTP B 501 "
pdb=" PA GTP B 501 "
pdb=" O5' GTP B 501 "
ideal model delta sigma weight residual
109.50 96.84 12.66 3.00e+00 1.11e-01 1.78e+01
angle pdb=" O1A GTP B 501 "
pdb=" PA GTP B 501 "
pdb=" O3A GTP B 501 "
ideal model delta sigma weight residual
108.20 120.49 -12.29 3.00e+00 1.11e-01 1.68e+01
... (remaining 21518 not shown)
Histogram of dihedral angle deviations from ideal:
0.00 - 35.92: 9260
35.92 - 71.83: 169
71.83 - 107.75: 17
107.75 - 143.66: 5
143.66 - 179.58: 5
Dihedral angle restraints: 9456
sinusoidal: 3782
harmonic: 5674
Sorted by residual:
dihedral pdb=" C5' GTP E 501 "
pdb=" O5' GTP E 501 "
pdb=" PA GTP E 501 "
pdb=" O3A GTP E 501 "
ideal model delta sinusoidal sigma weight residual
69.27 -111.15 -179.58 1 2.00e+01 2.50e-03 4.80e+01
dihedral pdb=" C5' GTP B 501 "
pdb=" O5' GTP B 501 "
pdb=" PA GTP B 501 "
pdb=" O3A GTP B 501 "
ideal model delta sinusoidal sigma weight residual
69.27 -95.66 164.93 1 2.00e+01 2.50e-03 4.72e+01
dihedral pdb=" C8 GTP B 501 "
pdb=" C1' GTP B 501 "
pdb=" N9 GTP B 501 "
pdb=" O4' GTP B 501 "
ideal model delta sinusoidal sigma weight residual
104.59 -58.45 163.04 1 2.00e+01 2.50e-03 4.70e+01
... (remaining 9453 not shown)
Histogram of chiral volume deviations from ideal:
0.000 - 0.057: 1944
0.057 - 0.113: 364
0.113 - 0.170: 33
0.170 - 0.226: 9
0.226 - 0.283: 6
Chirality restraints: 2356
Sorted by residual:
chirality pdb=" C3' GTP E 501 "
pdb=" C2' GTP E 501 "
pdb=" C4' GTP E 501 "
pdb=" O3' GTP E 501 "
both_signs ideal model delta sigma weight residual
False -2.47 -2.76 0.28 2.00e-01 2.50e+01 2.00e+00
chirality pdb=" C3' GTP B 501 "
pdb=" C2' GTP B 501 "
pdb=" C4' GTP B 501 "
pdb=" O3' GTP B 501 "
both_signs ideal model delta sigma weight residual
False -2.47 -2.73 0.26 2.00e-01 2.50e+01 1.67e+00
chirality pdb=" C2' GTP E 501 "
pdb=" C1' GTP E 501 "
pdb=" C3' GTP E 501 "
pdb=" O2' GTP E 501 "
both_signs ideal model delta sigma weight residual
False -2.47 -2.73 0.26 2.00e-01 2.50e+01 1.64e+00
... (remaining 2353 not shown)
Planarity restraints: 2794
Sorted by residual:
delta sigma weight rms_deltas residual
plane pdb=" CA TYR E 108 " 0.011 2.00e-02 2.50e+03 2.13e-02 4.53e+00
pdb=" C TYR E 108 " -0.037 2.00e-02 2.50e+03
pdb=" O TYR E 108 " 0.014 2.00e-02 2.50e+03
pdb=" N THR E 109 " 0.012 2.00e-02 2.50e+03
delta sigma weight rms_deltas residual
plane pdb=" CB TRP B 388 " 0.014 2.00e-02 2.50e+03 1.27e-02 4.01e+00
pdb=" CG TRP B 388 " -0.035 2.00e-02 2.50e+03
pdb=" CD1 TRP B 388 " 0.013 2.00e-02 2.50e+03
pdb=" CD2 TRP B 388 " 0.001 2.00e-02 2.50e+03
pdb=" NE1 TRP B 388 " 0.000 2.00e-02 2.50e+03
pdb=" CE2 TRP B 388 " 0.000 2.00e-02 2.50e+03
pdb=" CE3 TRP B 388 " 0.006 2.00e-02 2.50e+03
pdb=" CZ2 TRP B 388 " 0.003 2.00e-02 2.50e+03
pdb=" CZ3 TRP B 388 " -0.001 2.00e-02 2.50e+03
pdb=" CH2 TRP B 388 " -0.001 2.00e-02 2.50e+03
delta sigma weight rms_deltas residual
plane pdb=" C ILE F 356 " 0.032 5.00e-02 4.00e+02 4.83e-02 3.73e+00
pdb=" N PRO F 357 " -0.083 5.00e-02 4.00e+02
pdb=" CA PRO F 357 " 0.025 5.00e-02 4.00e+02
pdb=" CD PRO F 357 " 0.026 5.00e-02 4.00e+02
... (remaining 2791 not shown)
Histogram of nonbonded interaction distances:
2.21 - 2.75: 1766
2.75 - 3.29: 15577
3.29 - 3.82: 26608
3.82 - 4.36: 31782
4.36 - 4.90: 55742
Nonbonded interactions: 131475
Sorted by model distance:
nonbonded pdb=" OD1 ASN B 186 "
pdb=" OH TYR B 408 "
model vdw
2.209 3.040
nonbonded pdb=" NE2 GLN F 279 "
pdb=" O ARG I 232 "
model vdw
2.242 3.120
nonbonded pdb=" OE2 GLU F 27 "
pdb=" OG SER F 234 "
model vdw
2.279 3.040
nonbonded pdb=" OD1 ASN F 52 "
pdb=" NH1 ARG F 62 "
model vdw
2.279 3.120
nonbonded pdb=" O LEU D 192 "
pdb=" OG1 THR D 196 "
model vdw
2.289 3.040
... (remaining 131470 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 'B' and (resid 1 through 37 or resid 46 through 59 or (resid 60 and (name \
N or name CA or name C or name O or name CB )) or resid 61 through 112 or (resi \
d 113 and (name N or name CA or name C or name O or name CB )) or resid 114 thro \
ugh 219 or (resid 220 and (name N or name CA or name C or name O or name CB )) o \
r resid 221 through 338 or (resid 339 and (name N or name CA or name C or name O \
or name CB )) or resid 340 through 366 or (resid 367 and (name N or name CA or \
name C or name O or name CB )) or resid 368 through 400 or (resid 401 through 40 \
3 and (name N or name CA or name C or name O or name CB )) or resid 404 through \
439 or resid 501))
selection = chain 'E'
}
ncs_group {
reference = (chain 'D' and (resid 1 through 156 or (resid 157 and (name N or name CA or name \
C or name O or name CB )) or resid 158 through 427 or resid 501))
selection = chain 'F'
}
Set up NCS constraints
No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
ADPs will be refined as 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: 5.820
Set stop_for_unknowns flag: 0.000
Assert model is a single copy model: 0.000
Assert all atoms have isotropic ADPs: 0.000
Construct map_model_manager: 0.010
Extract box with map and model: 0.510
Check model and map are aligned: 0.110
Set scattering table: 0.130
Process input model: 37.070
Find NCS groups from input model: 0.620
Set up NCS constraints: 0.060
Set refine NCS operators: 0.000
Adjust number of macro_cycles: 0.000
Reset NCS operators: 0.000
Extract rigid body selections: 0.000
Check and reset occupancies: 0.010
Load rotamer database and sin/cos tables:2.580
Set ADP refinement strategy: 0.000
Make a string to write initial .geo file:0.000
Internal consistency checks: 0.000
Total: 46.920
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8268
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 : 0.006 0.223 15840 Z= 0.367
Angle : 0.701 13.624 21523 Z= 0.310
Chirality : 0.046 0.283 2356
Planarity : 0.004 0.048 2794
Dihedral : 15.603 179.578 5812
Min Nonbonded Distance : 2.209
Molprobity Statistics.
All-atom Clashscore : 7.97
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 3.64 %
Favored : 96.36 %
Rotamer:
Outliers : 0.00 %
Allowed : 0.36 %
Favored : 99.64 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 0.53 (0.19), residues: 1949
helix: 1.65 (0.18), residues: 848
sheet: -0.42 (0.34), residues: 266
loop : -0.71 (0.21), residues: 835
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.035 0.001 TRP B 388
HIS 0.006 0.001 HIS E 8
PHE 0.013 0.001 PHE D 260
TYR 0.031 0.001 TYR D 425
ARG 0.007 0.000 ARG I 219
*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
3898 Ramachandran restraints generated.
1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
3898 Ramachandran restraints generated.
1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
153 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 0
poor density : 153
time to evaluate : 1.917
Fit side-chains
revert: symmetry clash
REVERT: C 124 SER cc_start: 0.9244 (m) cc_final: 0.8874 (p)
REVERT: C 130 MET cc_start: 0.9527 (ttm) cc_final: 0.9322 (ttm)
REVERT: C 138 GLU cc_start: 0.9072 (mm-30) cc_final: 0.8841 (mm-30)
REVERT: C 155 GLN cc_start: 0.9218 (mm110) cc_final: 0.8968 (mp10)
REVERT: D 257 MET cc_start: 0.8166 (mmm) cc_final: 0.7852 (mmt)
outliers start: 0
outliers final: 0
residues processed: 153
average time/residue: 0.2536
time to fit residues: 60.4354
Evaluate side-chains
123 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 0
poor density : 123
time to evaluate : 2.003
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 193
random chunks:
chunk 162 optimal weight: 0.4980
chunk 146 optimal weight: 5.9990
chunk 81 optimal weight: 0.8980
chunk 49 optimal weight: 3.9990
chunk 98 optimal weight: 5.9990
chunk 78 optimal weight: 3.9990
chunk 151 optimal weight: 1.9990
chunk 58 optimal weight: 3.9990
chunk 91 optimal weight: 2.9990
chunk 112 optimal weight: 0.8980
chunk 175 optimal weight: 0.6980
overall best weight: 0.9982
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
B 301 GLN
** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 185 HIS
I 224 HIS
Total number of N/Q/H flips: 3
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.046408 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2966 r_free = 0.2966 target = 0.037478 restraints weight = 77076.941|
|-----------------------------------------------------------------------------|
r_work (start): 0.2958 rms_B_bonded: 4.30
r_work: 0.2806 rms_B_bonded: 4.86 restraints_weight: 0.5000
r_work (final): 0.2806
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8575
moved from start: 0.0941
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.070 15840 Z= 0.190
Angle : 0.535 8.191 21523 Z= 0.271
Chirality : 0.043 0.222 2356
Planarity : 0.004 0.038 2794
Dihedral : 12.345 178.011 2235
Min Nonbonded Distance : 2.303
Molprobity Statistics.
All-atom Clashscore : 7.38
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 3.13 %
Favored : 96.87 %
Rotamer:
Outliers : 0.54 %
Allowed : 4.71 %
Favored : 94.75 %
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: 0.68 (0.19), residues: 1949
helix: 1.73 (0.18), residues: 857
sheet: -0.39 (0.34), residues: 254
loop : -0.58 (0.21), residues: 838
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.034 0.001 TRP B 388
HIS 0.007 0.001 HIS E 8
PHE 0.013 0.001 PHE E 255
TYR 0.015 0.001 TYR D 425
ARG 0.003 0.000 ARG I 260
*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
3898 Ramachandran restraints generated.
1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
3898 Ramachandran restraints generated.
1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
142 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 9
poor density : 133
time to evaluate : 1.814
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: B 388 TRP cc_start: 0.8426 (m-90) cc_final: 0.7932 (m-90)
REVERT: C 20 ARG cc_start: 0.8057 (ttp80) cc_final: 0.7524 (ttm-80)
REVERT: C 44 MET cc_start: 0.9035 (mtm) cc_final: 0.8716 (mtm)
REVERT: C 61 ILE cc_start: 0.9105 (mt) cc_final: 0.8770 (mp)
REVERT: C 89 ARG cc_start: 0.8828 (ttp80) cc_final: 0.8626 (ttp80)
REVERT: C 106 MET cc_start: 0.9114 (ttt) cc_final: 0.8815 (tpp)
REVERT: C 124 SER cc_start: 0.9065 (m) cc_final: 0.8768 (p)
REVERT: C 155 GLN cc_start: 0.9266 (mm110) cc_final: 0.8986 (mt0)
REVERT: D 257 MET cc_start: 0.9092 (mmm) cc_final: 0.7896 (mmm)
REVERT: D 403 MET cc_start: 0.9013 (tpp) cc_final: 0.8478 (mmm)
REVERT: F 321 MET cc_start: 0.9120 (ptp) cc_final: 0.8872 (ptp)
outliers start: 9
outliers final: 5
residues processed: 137
average time/residue: 0.2635
time to fit residues: 56.7669
Evaluate side-chains
128 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 5
poor density : 123
time to evaluate : 1.853
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue 192 LEU
Chi-restraints excluded: chain D residue 351 THR
Chi-restraints excluded: chain F residue 111 GLU
Chi-restraints excluded: chain I residue 230 LEU
Chi-restraints excluded: chain I residue 239 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 193
random chunks:
chunk 143 optimal weight: 6.9990
chunk 134 optimal weight: 5.9990
chunk 70 optimal weight: 5.9990
chunk 116 optimal weight: 4.9990
chunk 32 optimal weight: 0.9990
chunk 38 optimal weight: 4.9990
chunk 170 optimal weight: 7.9990
chunk 49 optimal weight: 0.0970
chunk 142 optimal weight: 0.0070
chunk 132 optimal weight: 3.9990
chunk 139 optimal weight: 4.9990
overall best weight: 2.0202
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** B 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 61 HIS
C 36 GLN
D 414 ASN
** E 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F 396 HIS
** I 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
Total number of N/Q/H flips: 4
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.045086 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2929 r_free = 0.2929 target = 0.036223 restraints weight = 77323.513|
|-----------------------------------------------------------------------------|
r_work (start): 0.2920 rms_B_bonded: 4.24
r_work: 0.2766 rms_B_bonded: 4.80 restraints_weight: 0.5000
r_work (final): 0.2766
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8620
moved from start: 0.1289
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.004 0.089 15840 Z= 0.268
Angle : 0.528 7.818 21523 Z= 0.267
Chirality : 0.042 0.176 2356
Planarity : 0.004 0.038 2794
Dihedral : 11.653 176.249 2235
Min Nonbonded Distance : 2.379
Molprobity Statistics.
All-atom Clashscore : 7.45
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 3.18 %
Favored : 96.82 %
Rotamer:
Outliers : 0.66 %
Allowed : 7.91 %
Favored : 91.43 %
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: 0.80 (0.20), residues: 1949
helix: 1.83 (0.18), residues: 861
sheet: -0.61 (0.32), residues: 284
loop : -0.41 (0.22), residues: 804
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.016 0.001 TRP B 388
HIS 0.006 0.001 HIS E 8
PHE 0.014 0.001 PHE E 255
TYR 0.018 0.001 TYR B 432
ARG 0.005 0.000 ARG I 260
*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
3898 Ramachandran restraints generated.
1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
3898 Ramachandran restraints generated.
1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
133 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 11
poor density : 122
time to evaluate : 1.775
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: B 388 TRP cc_start: 0.8588 (m-90) cc_final: 0.7920 (m-90)
REVERT: C 36 GLN cc_start: 0.9380 (tt0) cc_final: 0.9122 (tm-30)
REVERT: C 44 MET cc_start: 0.9051 (mtm) cc_final: 0.8742 (mtm)
REVERT: C 73 MET cc_start: 0.9096 (ttp) cc_final: 0.8889 (ttm)
REVERT: C 106 MET cc_start: 0.9091 (ttt) cc_final: 0.8825 (tpp)
REVERT: C 114 ASP cc_start: 0.9019 (t0) cc_final: 0.8795 (t0)
REVERT: C 124 SER cc_start: 0.9007 (m) cc_final: 0.8725 (p)
REVERT: C 138 GLU cc_start: 0.9570 (mm-30) cc_final: 0.9084 (mm-30)
REVERT: C 155 GLN cc_start: 0.9320 (mm110) cc_final: 0.8924 (mt0)
REVERT: C 159 GLU cc_start: 0.9446 (pp20) cc_final: 0.9211 (pp20)
REVERT: C 185 HIS cc_start: 0.8471 (m170) cc_final: 0.8205 (m90)
REVERT: D 257 MET cc_start: 0.9087 (mmm) cc_final: 0.7951 (mmm)
REVERT: D 403 MET cc_start: 0.8882 (OUTLIER) cc_final: 0.8525 (mmm)
REVERT: E 377 MET cc_start: 0.9058 (tmm) cc_final: 0.8764 (tmm)
REVERT: E 413 MET cc_start: 0.9252 (tmm) cc_final: 0.8934 (tmm)
REVERT: F 6 HIS cc_start: 0.9037 (t70) cc_final: 0.8777 (t70)
REVERT: I 219 ARG cc_start: 0.7947 (mmt90) cc_final: 0.7691 (mtt90)
outliers start: 11
outliers final: 5
residues processed: 128
average time/residue: 0.2901
time to fit residues: 56.9037
Evaluate side-chains
124 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 6
poor density : 118
time to evaluate : 1.760
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue 234 ILE
Chi-restraints excluded: chain B residue 398 MET
Chi-restraints excluded: chain D residue 192 LEU
Chi-restraints excluded: chain D residue 403 MET
Chi-restraints excluded: chain I residue 230 LEU
Chi-restraints excluded: chain I residue 239 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 193
random chunks:
chunk 128 optimal weight: 1.9990
chunk 101 optimal weight: 0.0020
chunk 151 optimal weight: 1.9990
chunk 171 optimal weight: 4.9990
chunk 67 optimal weight: 0.9990
chunk 109 optimal weight: 0.9990
chunk 26 optimal weight: 5.9990
chunk 64 optimal weight: 7.9990
chunk 136 optimal weight: 0.0980
chunk 42 optimal weight: 0.8980
chunk 161 optimal weight: 0.9990
overall best weight: 0.5992
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** E 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
I 224 HIS
Total number of N/Q/H flips: 1
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.046201 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2972 r_free = 0.2972 target = 0.037377 restraints weight = 75805.492|
|-----------------------------------------------------------------------------|
r_work (start): 0.2960 rms_B_bonded: 4.24
r_work: 0.2808 rms_B_bonded: 4.80 restraints_weight: 0.5000
r_work (final): 0.2808
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8585
moved from start: 0.1420
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.002 0.044 15840 Z= 0.143
Angle : 0.483 7.111 21523 Z= 0.242
Chirality : 0.041 0.168 2356
Planarity : 0.003 0.038 2794
Dihedral : 10.897 179.204 2235
Min Nonbonded Distance : 2.464
Molprobity Statistics.
All-atom Clashscore : 6.95
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 2.98 %
Favored : 97.02 %
Rotamer:
Outliers : 0.60 %
Allowed : 9.06 %
Favored : 90.34 %
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: 0.80 (0.20), residues: 1949
helix: 1.88 (0.18), residues: 861
sheet: -0.70 (0.31), residues: 275
loop : -0.43 (0.22), residues: 813
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.011 0.001 TRP B 388
HIS 0.003 0.001 HIS B 61
PHE 0.012 0.001 PHE B 255
TYR 0.012 0.001 TYR B 432
ARG 0.005 0.000 ARG I 260
*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
3898 Ramachandran restraints generated.
1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
3898 Ramachandran restraints generated.
1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
133 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 10
poor density : 123
time to evaluate : 1.848
Fit side-chains
REVERT: B 388 TRP cc_start: 0.8604 (m-90) cc_final: 0.7811 (m-90)
REVERT: C 20 ARG cc_start: 0.8259 (ttp80) cc_final: 0.7678 (ttm-80)
REVERT: C 36 GLN cc_start: 0.9356 (tt0) cc_final: 0.9133 (tm-30)
REVERT: C 44 MET cc_start: 0.9085 (mtm) cc_final: 0.8825 (mtm)
REVERT: C 106 MET cc_start: 0.9074 (ttt) cc_final: 0.8821 (tpp)
REVERT: C 124 SER cc_start: 0.9030 (m) cc_final: 0.8746 (p)
REVERT: C 138 GLU cc_start: 0.9577 (mm-30) cc_final: 0.9058 (mm-30)
REVERT: C 155 GLN cc_start: 0.9324 (mm110) cc_final: 0.8973 (mt0)
REVERT: C 159 GLU cc_start: 0.9434 (pp20) cc_final: 0.9218 (pp20)
REVERT: C 185 HIS cc_start: 0.8417 (m170) cc_final: 0.8123 (m90)
REVERT: D 257 MET cc_start: 0.9054 (mmm) cc_final: 0.8005 (mmm)
REVERT: D 403 MET cc_start: 0.8835 (tpp) cc_final: 0.8398 (mmm)
REVERT: E 377 MET cc_start: 0.9057 (tmm) cc_final: 0.8648 (tmm)
REVERT: F 6 HIS cc_start: 0.8980 (t70) cc_final: 0.8744 (t70)
REVERT: F 164 MET cc_start: 0.8636 (mmm) cc_final: 0.8427 (mmm)
REVERT: F 321 MET cc_start: 0.9186 (ptp) cc_final: 0.8895 (ptp)
REVERT: F 323 MET cc_start: 0.8876 (mmm) cc_final: 0.8541 (mtm)
outliers start: 10
outliers final: 7
residues processed: 131
average time/residue: 0.2645
time to fit residues: 54.1867
Evaluate side-chains
127 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 7
poor density : 120
time to evaluate : 1.806
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue 234 ILE
Chi-restraints excluded: chain C residue 176 LEU
Chi-restraints excluded: chain D residue 135 LEU
Chi-restraints excluded: chain D residue 192 LEU
Chi-restraints excluded: chain E residue 295 CYS
Chi-restraints excluded: chain I residue 230 LEU
Chi-restraints excluded: chain I residue 239 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 193
random chunks:
chunk 162 optimal weight: 3.9990
chunk 49 optimal weight: 7.9990
chunk 169 optimal weight: 5.9990
chunk 11 optimal weight: 3.9990
chunk 103 optimal weight: 8.9990
chunk 44 optimal weight: 5.9990
chunk 100 optimal weight: 3.9990
chunk 39 optimal weight: 4.9990
chunk 91 optimal weight: 8.9990
chunk 110 optimal weight: 0.9980
chunk 78 optimal weight: 7.9990
overall best weight: 3.5988
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
C 144 GLN
D 195 ASN
** E 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
I 224 HIS
Total number of N/Q/H flips: 3
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.043689 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2882 r_free = 0.2882 target = 0.034943 restraints weight = 79377.196|
|-----------------------------------------------------------------------------|
r_work (start): 0.2870 rms_B_bonded: 4.20
r_work: 0.2719 rms_B_bonded: 4.71 restraints_weight: 0.5000
r_work (final): 0.2719
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8678
moved from start: 0.1707
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.007 0.134 15840 Z= 0.447
Angle : 0.619 7.956 21523 Z= 0.311
Chirality : 0.044 0.138 2356
Planarity : 0.004 0.038 2794
Dihedral : 10.683 173.359 2235
Min Nonbonded Distance : 2.411
Molprobity Statistics.
All-atom Clashscore : 8.30
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 3.80 %
Favored : 96.20 %
Rotamer:
Outliers : 1.09 %
Allowed : 9.84 %
Favored : 89.07 %
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: 0.73 (0.20), residues: 1949
helix: 1.81 (0.18), residues: 861
sheet: -0.97 (0.31), residues: 281
loop : -0.35 (0.23), residues: 807
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.010 0.001 TRP E 21
HIS 0.007 0.001 HIS F 227
PHE 0.014 0.001 PHE F 85
TYR 0.027 0.001 TYR B 432
ARG 0.006 0.000 ARG I 260
*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
3898 Ramachandran restraints generated.
1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
3898 Ramachandran restraints generated.
1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
136 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 18
poor density : 118
time to evaluate : 1.951
Fit side-chains
revert: symmetry clash
REVERT: B 388 TRP cc_start: 0.8888 (m-90) cc_final: 0.8011 (m-90)
REVERT: C 20 ARG cc_start: 0.8262 (ttp80) cc_final: 0.7717 (ttm-80)
REVERT: C 36 GLN cc_start: 0.9350 (tt0) cc_final: 0.9147 (tm-30)
REVERT: C 44 MET cc_start: 0.9080 (mtm) cc_final: 0.8600 (mtt)
REVERT: C 106 MET cc_start: 0.9077 (ttt) cc_final: 0.8806 (tpp)
REVERT: C 124 SER cc_start: 0.8934 (m) cc_final: 0.8678 (p)
REVERT: C 138 GLU cc_start: 0.9582 (mm-30) cc_final: 0.9067 (mm-30)
REVERT: C 155 GLN cc_start: 0.9303 (mm110) cc_final: 0.9020 (mt0)
REVERT: C 185 HIS cc_start: 0.8465 (m170) cc_final: 0.8082 (m-70)
REVERT: D 257 MET cc_start: 0.9102 (mmm) cc_final: 0.8034 (mmt)
REVERT: D 403 MET cc_start: 0.8898 (OUTLIER) cc_final: 0.8359 (mmm)
REVERT: E 377 MET cc_start: 0.9048 (tmm) cc_final: 0.8546 (tmm)
REVERT: F 6 HIS cc_start: 0.9089 (t70) cc_final: 0.8808 (t70)
REVERT: F 321 MET cc_start: 0.9276 (ptp) cc_final: 0.9001 (ptp)
outliers start: 18
outliers final: 9
residues processed: 132
average time/residue: 0.2666
time to fit residues: 55.3353
Evaluate side-chains
125 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 10
poor density : 115
time to evaluate : 1.907
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue 234 ILE
Chi-restraints excluded: chain B residue 398 MET
Chi-restraints excluded: chain C residue 176 LEU
Chi-restraints excluded: chain D residue 192 LEU
Chi-restraints excluded: chain D residue 232 THR
Chi-restraints excluded: chain D residue 403 MET
Chi-restraints excluded: chain E residue 295 CYS
Chi-restraints excluded: chain F residue 113 VAL
Chi-restraints excluded: chain I residue 230 LEU
Chi-restraints excluded: chain I residue 239 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 193
random chunks:
chunk 43 optimal weight: 3.9990
chunk 81 optimal weight: 0.6980
chunk 24 optimal weight: 2.9990
chunk 189 optimal weight: 7.9990
chunk 21 optimal weight: 3.9990
chunk 74 optimal weight: 1.9990
chunk 122 optimal weight: 1.9990
chunk 183 optimal weight: 3.9990
chunk 83 optimal weight: 0.6980
chunk 67 optimal weight: 0.9990
chunk 68 optimal weight: 0.9980
overall best weight: 1.0784
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
C 144 GLN
** E 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 224 HIS ** 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 = 0.3208 r_free = 0.3208 target = 0.045095 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2938 r_free = 0.2938 target = 0.036335 restraints weight = 77901.238|
|-----------------------------------------------------------------------------|
r_work (start): 0.2927 rms_B_bonded: 4.23
r_work: 0.2774 rms_B_bonded: 4.78 restraints_weight: 0.5000
r_work (final): 0.2774
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8623
moved from start: 0.1715
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.057 15840 Z= 0.178
Angle : 0.498 8.004 21523 Z= 0.250
Chirality : 0.042 0.149 2356
Planarity : 0.003 0.039 2794
Dihedral : 10.486 177.754 2235
Min Nonbonded Distance : 2.464
Molprobity Statistics.
All-atom Clashscore : 7.41
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 2.98 %
Favored : 97.02 %
Rotamer:
Outliers : 0.91 %
Allowed : 10.87 %
Favored : 88.22 %
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: 0.81 (0.20), residues: 1949
helix: 1.88 (0.18), residues: 863
sheet: -0.88 (0.31), residues: 286
loop : -0.34 (0.23), residues: 800
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.012 0.001 TRP B 21
HIS 0.004 0.001 HIS F 105
PHE 0.013 0.001 PHE B 255
TYR 0.017 0.001 TYR B 432
ARG 0.005 0.000 ARG I 260
*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
3898 Ramachandran restraints generated.
1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
3898 Ramachandran restraints generated.
1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
140 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 15
poor density : 125
time to evaluate : 1.753
Fit side-chains
revert: symmetry clash
REVERT: B 388 TRP cc_start: 0.8814 (m-90) cc_final: 0.7935 (m-90)
REVERT: C 20 ARG cc_start: 0.8351 (ttp80) cc_final: 0.7806 (ttm-80)
REVERT: C 36 GLN cc_start: 0.9355 (tt0) cc_final: 0.9155 (tm-30)
REVERT: C 44 MET cc_start: 0.9108 (mtm) cc_final: 0.8617 (mtt)
REVERT: C 71 TYR cc_start: 0.8668 (m-80) cc_final: 0.7878 (m-80)
REVERT: C 106 MET cc_start: 0.9075 (ttt) cc_final: 0.8858 (tpp)
REVERT: C 124 SER cc_start: 0.8958 (m) cc_final: 0.8692 (p)
REVERT: C 138 GLU cc_start: 0.9538 (mm-30) cc_final: 0.9057 (mm-30)
REVERT: C 155 GLN cc_start: 0.9262 (mm110) cc_final: 0.9057 (mt0)
REVERT: C 185 HIS cc_start: 0.8459 (m170) cc_final: 0.8132 (m90)
REVERT: D 257 MET cc_start: 0.9054 (mmm) cc_final: 0.7995 (mmt)
REVERT: D 403 MET cc_start: 0.8913 (OUTLIER) cc_final: 0.8363 (mmm)
REVERT: E 377 MET cc_start: 0.9068 (tmm) cc_final: 0.8634 (tmm)
REVERT: F 6 HIS cc_start: 0.9043 (t70) cc_final: 0.8790 (t70)
REVERT: F 233 MET cc_start: 0.9092 (mmm) cc_final: 0.8819 (mmm)
REVERT: F 323 MET cc_start: 0.8916 (mmm) cc_final: 0.8578 (mtm)
REVERT: F 363 MET cc_start: 0.8920 (ttp) cc_final: 0.8546 (ttp)
outliers start: 15
outliers final: 9
residues processed: 134
average time/residue: 0.2526
time to fit residues: 53.1613
Evaluate side-chains
131 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 10
poor density : 121
time to evaluate : 1.906
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue 188 ILE
Chi-restraints excluded: chain B residue 234 ILE
Chi-restraints excluded: chain B residue 398 MET
Chi-restraints excluded: chain B residue 413 MET
Chi-restraints excluded: chain C residue 176 LEU
Chi-restraints excluded: chain D residue 192 LEU
Chi-restraints excluded: chain D residue 403 MET
Chi-restraints excluded: chain E residue 295 CYS
Chi-restraints excluded: chain I residue 230 LEU
Chi-restraints excluded: chain I residue 239 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 193
random chunks:
chunk 138 optimal weight: 0.0870
chunk 119 optimal weight: 10.0000
chunk 157 optimal weight: 0.9990
chunk 177 optimal weight: 3.9990
chunk 43 optimal weight: 3.9990
chunk 147 optimal weight: 4.9990
chunk 129 optimal weight: 1.9990
chunk 176 optimal weight: 0.6980
chunk 141 optimal weight: 0.8980
chunk 85 optimal weight: 1.9990
chunk 93 optimal weight: 0.9980
overall best weight: 0.7360
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
C 144 GLN
** E 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 107 HIS
I 224 HIS
Total number of N/Q/H flips: 3
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.045488 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2950 r_free = 0.2950 target = 0.036629 restraints weight = 79090.749|
|-----------------------------------------------------------------------------|
r_work (start): 0.2941 rms_B_bonded: 4.34
r_work: 0.2790 rms_B_bonded: 4.87 restraints_weight: 0.5000
r_work (final): 0.2790
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8615
moved from start: 0.1816
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.002 0.049 15840 Z= 0.156
Angle : 0.497 7.900 21523 Z= 0.248
Chirality : 0.042 0.136 2356
Planarity : 0.003 0.039 2794
Dihedral : 10.196 179.316 2235
Min Nonbonded Distance : 2.474
Molprobity Statistics.
All-atom Clashscore : 7.18
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 2.87 %
Favored : 97.13 %
Rotamer:
Outliers : 1.15 %
Allowed : 11.41 %
Favored : 87.44 %
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: 0.83 (0.20), residues: 1949
helix: 1.91 (0.18), residues: 861
sheet: -0.94 (0.31), residues: 287
loop : -0.30 (0.23), residues: 801
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.010 0.001 TRP B 21
HIS 0.007 0.001 HIS B 107
PHE 0.009 0.001 PHE E 255
TYR 0.014 0.001 TYR B 432
ARG 0.004 0.000 ARG I 260
*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
3898 Ramachandran restraints generated.
1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
3898 Ramachandran restraints generated.
1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
146 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 19
poor density : 127
time to evaluate : 1.913
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: B 388 TRP cc_start: 0.8868 (m-90) cc_final: 0.7969 (m-90)
REVERT: C 20 ARG cc_start: 0.8366 (ttp80) cc_final: 0.7839 (ttm-80)
REVERT: C 36 GLN cc_start: 0.9345 (tt0) cc_final: 0.9134 (tm-30)
REVERT: C 44 MET cc_start: 0.9100 (mtm) cc_final: 0.8747 (mtm)
REVERT: C 71 TYR cc_start: 0.8713 (m-80) cc_final: 0.7951 (m-80)
REVERT: C 92 TYR cc_start: 0.9135 (m-80) cc_final: 0.8781 (m-80)
REVERT: C 110 MET cc_start: 0.9087 (tpp) cc_final: 0.8039 (tpp)
REVERT: C 124 SER cc_start: 0.8962 (m) cc_final: 0.8595 (p)
REVERT: C 138 GLU cc_start: 0.9493 (mm-30) cc_final: 0.8966 (mm-30)
REVERT: C 155 GLN cc_start: 0.9290 (mm110) cc_final: 0.8994 (mt0)
REVERT: C 185 HIS cc_start: 0.8429 (m170) cc_final: 0.8092 (m90)
REVERT: D 257 MET cc_start: 0.8997 (mmm) cc_final: 0.7943 (mmt)
REVERT: D 267 MET cc_start: 0.8781 (ttm) cc_final: 0.8505 (ttm)
REVERT: D 403 MET cc_start: 0.8904 (OUTLIER) cc_final: 0.8345 (mmm)
REVERT: E 302 MET cc_start: 0.9413 (mtt) cc_final: 0.9172 (mmt)
REVERT: E 377 MET cc_start: 0.9110 (tmm) cc_final: 0.8647 (tmm)
REVERT: E 432 TYR cc_start: 0.8607 (OUTLIER) cc_final: 0.8266 (t80)
REVERT: F 300 MET cc_start: 0.8657 (mtt) cc_final: 0.8398 (mtt)
REVERT: F 323 MET cc_start: 0.8955 (mmm) cc_final: 0.8563 (mtm)
outliers start: 19
outliers final: 12
residues processed: 141
average time/residue: 0.2583
time to fit residues: 57.6129
Evaluate side-chains
134 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 14
poor density : 120
time to evaluate : 1.845
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue 188 ILE
Chi-restraints excluded: chain B residue 234 ILE
Chi-restraints excluded: chain B residue 398 MET
Chi-restraints excluded: chain C residue 168 VAL
Chi-restraints excluded: chain C residue 176 LEU
Chi-restraints excluded: chain D residue 135 LEU
Chi-restraints excluded: chain D residue 192 LEU
Chi-restraints excluded: chain D residue 199 THR
Chi-restraints excluded: chain D residue 403 MET
Chi-restraints excluded: chain E residue 119 LEU
Chi-restraints excluded: chain E residue 295 CYS
Chi-restraints excluded: chain E residue 432 TYR
Chi-restraints excluded: chain I residue 230 LEU
Chi-restraints excluded: chain I residue 239 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 193
random chunks:
chunk 143 optimal weight: 0.2980
chunk 128 optimal weight: 0.8980
chunk 40 optimal weight: 7.9990
chunk 140 optimal weight: 0.3980
chunk 1 optimal weight: 5.9990
chunk 68 optimal weight: 3.9990
chunk 154 optimal weight: 0.9980
chunk 135 optimal weight: 4.9990
chunk 150 optimal weight: 1.9990
chunk 115 optimal weight: 0.9990
chunk 9 optimal weight: 0.7980
overall best weight: 0.6780
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** E 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F 137 HIS
** I 224 HIS ** 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 = 0.3238 r_free = 0.3238 target = 0.045675 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2972 r_free = 0.2972 target = 0.036978 restraints weight = 78750.172|
|-----------------------------------------------------------------------------|
r_work (start): 0.2956 rms_B_bonded: 4.25
r_work: 0.2807 rms_B_bonded: 4.80 restraints_weight: 0.5000
r_work (final): 0.2807
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8615
moved from start: 0.1897
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.002 0.048 15840 Z= 0.153
Angle : 0.516 11.404 21523 Z= 0.253
Chirality : 0.041 0.135 2356
Planarity : 0.003 0.039 2794
Dihedral : 9.979 176.412 2235
Min Nonbonded Distance : 2.475
Molprobity Statistics.
All-atom Clashscore : 7.41
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 2.57 %
Favored : 97.43 %
Rotamer:
Outliers : 1.03 %
Allowed : 11.96 %
Favored : 87.02 %
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: 0.86 (0.20), residues: 1949
helix: 1.92 (0.18), residues: 861
sheet: -0.90 (0.31), residues: 277
loop : -0.30 (0.22), residues: 811
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.010 0.001 TRP F 21
HIS 0.003 0.001 HIS B 61
PHE 0.015 0.001 PHE B 255
TYR 0.018 0.001 TYR B 108
ARG 0.006 0.000 ARG I 260
*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
3898 Ramachandran restraints generated.
1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
3898 Ramachandran restraints generated.
1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
141 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 17
poor density : 124
time to evaluate : 1.754
Fit side-chains
REVERT: B 388 TRP cc_start: 0.8879 (m-90) cc_final: 0.7990 (m-90)
REVERT: C 20 ARG cc_start: 0.8469 (ttp80) cc_final: 0.7572 (ttt-90)
REVERT: C 44 MET cc_start: 0.9110 (mtm) cc_final: 0.8737 (mtm)
REVERT: C 71 TYR cc_start: 0.8829 (m-80) cc_final: 0.8245 (m-80)
REVERT: C 92 TYR cc_start: 0.9254 (m-80) cc_final: 0.8958 (m-80)
REVERT: C 110 MET cc_start: 0.9164 (tpp) cc_final: 0.8675 (tpp)
REVERT: C 124 SER cc_start: 0.8939 (m) cc_final: 0.8651 (p)
REVERT: C 138 GLU cc_start: 0.9498 (mm-30) cc_final: 0.9093 (mm-30)
REVERT: C 155 GLN cc_start: 0.9285 (mm110) cc_final: 0.8970 (mp10)
REVERT: C 185 HIS cc_start: 0.8361 (m170) cc_final: 0.8073 (m90)
REVERT: D 257 MET cc_start: 0.8972 (mmm) cc_final: 0.7945 (mmt)
REVERT: D 267 MET cc_start: 0.8789 (ttm) cc_final: 0.8537 (ttm)
REVERT: D 403 MET cc_start: 0.8925 (OUTLIER) cc_final: 0.8362 (mmm)
REVERT: E 302 MET cc_start: 0.9379 (mtt) cc_final: 0.9171 (mmt)
REVERT: E 377 MET cc_start: 0.9165 (tmm) cc_final: 0.8676 (tmm)
REVERT: E 432 TYR cc_start: 0.8616 (OUTLIER) cc_final: 0.8283 (t80)
REVERT: F 233 MET cc_start: 0.9107 (mmm) cc_final: 0.8889 (mmt)
REVERT: F 300 MET cc_start: 0.8554 (mtt) cc_final: 0.8315 (mtt)
REVERT: F 323 MET cc_start: 0.8941 (mmm) cc_final: 0.8523 (mtm)
REVERT: I 219 ARG cc_start: 0.7758 (mmt90) cc_final: 0.7346 (mtt90)
outliers start: 17
outliers final: 11
residues processed: 137
average time/residue: 0.2576
time to fit residues: 55.5213
Evaluate side-chains
134 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 13
poor density : 121
time to evaluate : 1.801
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue 188 ILE
Chi-restraints excluded: chain B residue 234 ILE
Chi-restraints excluded: chain B residue 398 MET
Chi-restraints excluded: chain C residue 168 VAL
Chi-restraints excluded: chain C residue 176 LEU
Chi-restraints excluded: chain D residue 192 LEU
Chi-restraints excluded: chain D residue 199 THR
Chi-restraints excluded: chain D residue 403 MET
Chi-restraints excluded: chain E residue 119 LEU
Chi-restraints excluded: chain E residue 295 CYS
Chi-restraints excluded: chain E residue 432 TYR
Chi-restraints excluded: chain I residue 230 LEU
Chi-restraints excluded: chain I residue 239 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 193
random chunks:
chunk 157 optimal weight: 0.7980
chunk 53 optimal weight: 6.9990
chunk 145 optimal weight: 2.9990
chunk 121 optimal weight: 1.9990
chunk 27 optimal weight: 0.9990
chunk 19 optimal weight: 0.8980
chunk 58 optimal weight: 7.9990
chunk 138 optimal weight: 4.9990
chunk 186 optimal weight: 0.5980
chunk 67 optimal weight: 0.9990
chunk 165 optimal weight: 0.0670
overall best weight: 0.6720
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
C 144 GLN
** E 8 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
I 224 HIS
Total number of N/Q/H flips: 2
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.045828 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2983 r_free = 0.2983 target = 0.037226 restraints weight = 78774.392|
|-----------------------------------------------------------------------------|
r_work (start): 0.2969 rms_B_bonded: 4.27
r_work: 0.2821 rms_B_bonded: 4.81 restraints_weight: 0.5000
r_work (final): 0.2821
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8611
moved from start: 0.1998
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.002 0.046 15840 Z= 0.152
Angle : 0.515 11.897 21523 Z= 0.253
Chirality : 0.041 0.135 2356
Planarity : 0.003 0.039 2794
Dihedral : 9.711 171.821 2235
Min Nonbonded Distance : 2.476
Molprobity Statistics.
All-atom Clashscore : 7.08
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 2.67 %
Favored : 97.33 %
Rotamer:
Outliers : 1.03 %
Allowed : 12.20 %
Favored : 86.78 %
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: 0.90 (0.20), residues: 1949
helix: 1.93 (0.18), residues: 865
sheet: -0.87 (0.31), residues: 277
loop : -0.27 (0.23), residues: 807
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.009 0.001 TRP F 21
HIS 0.003 0.000 HIS B 61
PHE 0.013 0.001 PHE D 133
TYR 0.015 0.001 TYR B 108
ARG 0.003 0.000 ARG I 260
*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
3898 Ramachandran restraints generated.
1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
3898 Ramachandran restraints generated.
1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
143 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 17
poor density : 126
time to evaluate : 2.204
Fit side-chains
revert: symmetry clash
REVERT: B 388 TRP cc_start: 0.8947 (m-90) cc_final: 0.8000 (m-90)
REVERT: C 20 ARG cc_start: 0.8484 (ttp80) cc_final: 0.7909 (ttm-80)
REVERT: C 44 MET cc_start: 0.9097 (mtm) cc_final: 0.8587 (mtm)
REVERT: C 66 GLU cc_start: 0.8690 (pm20) cc_final: 0.8459 (pm20)
REVERT: C 71 TYR cc_start: 0.8862 (m-80) cc_final: 0.8172 (m-80)
REVERT: C 92 TYR cc_start: 0.9270 (m-80) cc_final: 0.8920 (m-80)
REVERT: C 110 MET cc_start: 0.9127 (tpp) cc_final: 0.8604 (tpp)
REVERT: C 124 SER cc_start: 0.8963 (m) cc_final: 0.8671 (p)
REVERT: C 138 GLU cc_start: 0.9469 (mm-30) cc_final: 0.9031 (mm-30)
REVERT: C 155 GLN cc_start: 0.9287 (mm110) cc_final: 0.9053 (mt0)
REVERT: C 185 HIS cc_start: 0.8347 (m170) cc_final: 0.8074 (m90)
REVERT: D 257 MET cc_start: 0.8910 (mmm) cc_final: 0.7903 (mmt)
REVERT: D 267 MET cc_start: 0.8795 (ttm) cc_final: 0.8551 (ttm)
REVERT: D 403 MET cc_start: 0.8947 (OUTLIER) cc_final: 0.8358 (mmm)
REVERT: E 302 MET cc_start: 0.9396 (mtt) cc_final: 0.9191 (mmt)
REVERT: E 377 MET cc_start: 0.9186 (tmm) cc_final: 0.8687 (tmm)
REVERT: E 432 TYR cc_start: 0.8596 (OUTLIER) cc_final: 0.8299 (t80)
REVERT: F 323 MET cc_start: 0.9034 (mmm) cc_final: 0.8519 (mtm)
REVERT: I 219 ARG cc_start: 0.7809 (mmt90) cc_final: 0.7399 (mtt90)
outliers start: 17
outliers final: 12
residues processed: 138
average time/residue: 0.2607
time to fit residues: 55.6098
Evaluate side-chains
137 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 14
poor density : 123
time to evaluate : 1.712
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue 188 ILE
Chi-restraints excluded: chain B residue 234 ILE
Chi-restraints excluded: chain B residue 398 MET
Chi-restraints excluded: chain C residue 168 VAL
Chi-restraints excluded: chain C residue 176 LEU
Chi-restraints excluded: chain D residue 192 LEU
Chi-restraints excluded: chain D residue 199 THR
Chi-restraints excluded: chain D residue 232 THR
Chi-restraints excluded: chain D residue 403 MET
Chi-restraints excluded: chain E residue 119 LEU
Chi-restraints excluded: chain E residue 295 CYS
Chi-restraints excluded: chain E residue 432 TYR
Chi-restraints excluded: chain I residue 230 LEU
Chi-restraints excluded: chain I residue 239 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 193
random chunks:
chunk 140 optimal weight: 0.6980
chunk 158 optimal weight: 4.9990
chunk 169 optimal weight: 6.9990
chunk 61 optimal weight: 6.9990
chunk 190 optimal weight: 20.0000
chunk 84 optimal weight: 9.9990
chunk 124 optimal weight: 0.0020
chunk 8 optimal weight: 0.0000
chunk 131 optimal weight: 0.7980
chunk 101 optimal weight: 0.0000
chunk 102 optimal weight: 0.9990
overall best weight: 0.2996
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** I 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
Total number of N/Q/H flips: 0
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.046498 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3007 r_free = 0.3007 target = 0.037957 restraints weight = 78652.932|
|-----------------------------------------------------------------------------|
r_work (start): 0.2993 rms_B_bonded: 4.24
r_work: 0.2848 rms_B_bonded: 4.77 restraints_weight: 0.5000
r_work (final): 0.2848
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8597
moved from start: 0.2124
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.002 0.039 15840 Z= 0.137
Angle : 0.521 12.130 21523 Z= 0.254
Chirality : 0.041 0.146 2356
Planarity : 0.003 0.039 2794
Dihedral : 9.455 166.094 2235
Min Nonbonded Distance : 2.481
Molprobity Statistics.
All-atom Clashscore : 6.82
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 2.36 %
Favored : 97.64 %
Rotamer:
Outliers : 0.91 %
Allowed : 12.44 %
Favored : 86.65 %
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: 0.91 (0.20), residues: 1949
helix: 1.94 (0.18), residues: 865
sheet: -0.93 (0.31), residues: 291
loop : -0.20 (0.23), residues: 793
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.010 0.001 TRP F 21
HIS 0.010 0.001 HIS F 6
PHE 0.017 0.001 PHE B 255
TYR 0.015 0.001 TYR B 108
ARG 0.005 0.000 ARG I 260
********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
3898 Ramachandran restraints generated.
1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
3898 Ramachandran restraints generated.
1949 Oldfield, 0 Emsley, 1949 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
143 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 15
poor density : 128
time to evaluate : 1.750
Fit side-chains
revert: symmetry clash
REVERT: B 388 TRP cc_start: 0.8970 (m-90) cc_final: 0.8076 (m-90)
REVERT: C 20 ARG cc_start: 0.8533 (ttp80) cc_final: 0.8275 (ttm-80)
REVERT: C 36 GLN cc_start: 0.9346 (tt0) cc_final: 0.9059 (tm-30)
REVERT: C 44 MET cc_start: 0.9081 (mtm) cc_final: 0.8555 (mtm)
REVERT: C 71 TYR cc_start: 0.8866 (m-80) cc_final: 0.8183 (m-80)
REVERT: C 92 TYR cc_start: 0.9290 (m-80) cc_final: 0.8893 (m-80)
REVERT: C 110 MET cc_start: 0.9130 (tpp) cc_final: 0.8637 (tpp)
REVERT: C 124 SER cc_start: 0.8962 (m) cc_final: 0.8657 (p)
REVERT: C 138 GLU cc_start: 0.9443 (mm-30) cc_final: 0.9017 (mm-30)
REVERT: C 155 GLN cc_start: 0.9296 (mm110) cc_final: 0.9088 (mt0)
REVERT: C 185 HIS cc_start: 0.8308 (m170) cc_final: 0.8049 (m90)
REVERT: D 257 MET cc_start: 0.8848 (mmm) cc_final: 0.7910 (mmm)
REVERT: D 267 MET cc_start: 0.8811 (ttm) cc_final: 0.8475 (ttm)
REVERT: D 403 MET cc_start: 0.8945 (OUTLIER) cc_final: 0.8374 (mmm)
REVERT: E 377 MET cc_start: 0.9208 (tmm) cc_final: 0.8704 (tmm)
REVERT: E 432 TYR cc_start: 0.8564 (OUTLIER) cc_final: 0.8293 (t80)
REVERT: F 323 MET cc_start: 0.8962 (mmm) cc_final: 0.8362 (mtm)
REVERT: I 219 ARG cc_start: 0.7803 (mmt90) cc_final: 0.7398 (mtt90)
outliers start: 15
outliers final: 11
residues processed: 138
average time/residue: 0.2630
time to fit residues: 57.5281
Evaluate side-chains
137 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 13
poor density : 124
time to evaluate : 2.027
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue 188 ILE
Chi-restraints excluded: chain B residue 234 ILE
Chi-restraints excluded: chain B residue 398 MET
Chi-restraints excluded: chain C residue 168 VAL
Chi-restraints excluded: chain C residue 176 LEU
Chi-restraints excluded: chain D residue 192 LEU
Chi-restraints excluded: chain D residue 232 THR
Chi-restraints excluded: chain D residue 403 MET
Chi-restraints excluded: chain E residue 119 LEU
Chi-restraints excluded: chain E residue 295 CYS
Chi-restraints excluded: chain E residue 432 TYR
Chi-restraints excluded: chain I residue 230 LEU
Chi-restraints excluded: chain I residue 239 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 193
random chunks:
chunk 137 optimal weight: 0.9990
chunk 179 optimal weight: 6.9990
chunk 159 optimal weight: 6.9990
chunk 28 optimal weight: 8.9990
chunk 75 optimal weight: 0.8980
chunk 124 optimal weight: 0.0170
chunk 46 optimal weight: 0.9980
chunk 32 optimal weight: 0.7980
chunk 50 optimal weight: 2.9990
chunk 55 optimal weight: 4.9990
chunk 139 optimal weight: 3.9990
overall best weight: 0.7420
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** I 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
Total number of N/Q/H flips: 0
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.046149 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3002 r_free = 0.3002 target = 0.037742 restraints weight = 79134.546|
|-----------------------------------------------------------------------------|
r_work (start): 0.2987 rms_B_bonded: 4.22
r_work: 0.2840 rms_B_bonded: 4.75 restraints_weight: 0.5000
r_work (final): 0.2840
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8614
moved from start: 0.2152
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.002 0.047 15840 Z= 0.157
Angle : 0.524 12.467 21523 Z= 0.254
Chirality : 0.041 0.141 2356
Planarity : 0.003 0.039 2794
Dihedral : 9.334 162.869 2235
Min Nonbonded Distance : 2.476
Molprobity Statistics.
All-atom Clashscore : 7.02
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 2.62 %
Favored : 97.38 %
Rotamer:
Outliers : 0.85 %
Allowed : 12.38 %
Favored : 86.78 %
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: 0.95 (0.20), residues: 1949
helix: 1.97 (0.18), residues: 865
sheet: -0.90 (0.31), residues: 291
loop : -0.18 (0.23), residues: 793
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.010 0.001 TRP F 21
HIS 0.014 0.001 HIS F 6
PHE 0.009 0.001 PHE E 255
TYR 0.015 0.001 TYR D 36
ARG 0.005 0.000 ARG I 260
Origin is already at (0, 0, 0), no shifts will be applied
===============================================================================
Job complete
usr+sys time: 7091.81 seconds
wall clock time: 129 minutes 25.96 seconds (7765.96 seconds total)