Starting phenix.real_space_refine
on Sat Aug 10 13:36:24 2024 by dcliebschner
===============================================================================
Processing files:
-------------------------------------------------------------------------------
Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u66_41946/08_2024/8u66_41946.cif
Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u66_41946/08_2024/8u66_41946.map
Processing PHIL parameters:
-------------------------------------------------------------------------------
Adding command-line PHIL:
-------------------------
refinement.macro_cycles=10
scattering_table=electron
resolution=2.21
write_initial_geo_file=False
Final processed PHIL parameters:
-------------------------------------------------------------------------------
data_manager {
real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u66_41946/08_2024/8u66_41946.map"
default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u66_41946/08_2024/8u66_41946.map"
model {
file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u66_41946/08_2024/8u66_41946.cif"
}
default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u66_41946/08_2024/8u66_41946.cif"
}
resolution = 2.21
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= 0.092
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: 6
Type Number sf(0) Gaussians
P 16 5.49 5
Mg 8 5.21 5
S 128 5.16 5
C 17968 2.51 5
N 5064 2.21 5
O 6181 1.98 5
sf(0) = scattering factor at diffraction angle 0.
Process input model
Symmetric amino acids flipped
Residue "A TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "A PHE 388": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "B TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "B PHE 388": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "C TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "C PHE 388": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "D TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "D PHE 388": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "E TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "E PHE 388": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "F TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "F PHE 388": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "G TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "G PHE 388": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "H TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "H PHE 388": "CD1" <-> "CD2" "CE1" <-> "CE2"
Time to flip residues: 0.08s
Monomer Library directory:
"/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib"
Total number of atoms: 29365
Number of models: 1
Model: ""
Number of chains: 24
Chain: "A"
Number of atoms: 3526
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 448, 3526
Classifications: {'peptide': 448}
Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 423}
Unresolved non-hydrogen bonds: 1
Unresolved non-hydrogen angles: 2
Planarities with less than four sites: {'KCX:plan-1': 1}
Unresolved non-hydrogen planarities: 1
Chain: "B"
Number of atoms: 3526
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 448, 3526
Classifications: {'peptide': 448}
Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 423}
Unresolved non-hydrogen bonds: 1
Unresolved non-hydrogen angles: 2
Planarities with less than four sites: {'KCX:plan-1': 1}
Unresolved non-hydrogen planarities: 1
Chain: "C"
Number of atoms: 3526
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 448, 3526
Classifications: {'peptide': 448}
Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 423}
Unresolved non-hydrogen bonds: 1
Unresolved non-hydrogen angles: 2
Planarities with less than four sites: {'KCX:plan-1': 1}
Unresolved non-hydrogen planarities: 1
Chain: "D"
Number of atoms: 3526
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 448, 3526
Classifications: {'peptide': 448}
Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 423}
Unresolved non-hydrogen bonds: 1
Unresolved non-hydrogen angles: 2
Planarities with less than four sites: {'KCX:plan-1': 1}
Unresolved non-hydrogen planarities: 1
Chain: "E"
Number of atoms: 3526
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 448, 3526
Classifications: {'peptide': 448}
Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 423}
Unresolved non-hydrogen bonds: 1
Unresolved non-hydrogen angles: 2
Planarities with less than four sites: {'KCX:plan-1': 1}
Unresolved non-hydrogen planarities: 1
Chain: "F"
Number of atoms: 3526
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 448, 3526
Classifications: {'peptide': 448}
Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 423}
Unresolved non-hydrogen bonds: 1
Unresolved non-hydrogen angles: 2
Planarities with less than four sites: {'KCX:plan-1': 1}
Unresolved non-hydrogen planarities: 1
Chain: "G"
Number of atoms: 3526
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 448, 3526
Classifications: {'peptide': 448}
Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 423}
Unresolved non-hydrogen bonds: 1
Unresolved non-hydrogen angles: 2
Planarities with less than four sites: {'KCX:plan-1': 1}
Unresolved non-hydrogen planarities: 1
Chain: "H"
Number of atoms: 3526
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 448, 3526
Classifications: {'peptide': 448}
Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 423}
Unresolved non-hydrogen bonds: 1
Unresolved non-hydrogen angles: 2
Planarities with less than four sites: {'KCX:plan-1': 1}
Unresolved non-hydrogen planarities: 1
Chain: "A"
Number of atoms: 22
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 2, 22
Unusual residues: {' MG': 1, 'CAP': 1}
Classifications: {'undetermined': 2}
Link IDs: {None: 1}
Chain: "B"
Number of atoms: 22
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 2, 22
Unusual residues: {' MG': 1, 'CAP': 1}
Classifications: {'undetermined': 2}
Link IDs: {None: 1}
Chain: "C"
Number of atoms: 22
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 2, 22
Unusual residues: {' MG': 1, 'CAP': 1}
Classifications: {'undetermined': 2}
Link IDs: {None: 1}
Chain: "D"
Number of atoms: 22
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 2, 22
Unusual residues: {' MG': 1, 'CAP': 1}
Classifications: {'undetermined': 2}
Link IDs: {None: 1}
Chain: "E"
Number of atoms: 22
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 2, 22
Unusual residues: {' MG': 1, 'CAP': 1}
Classifications: {'undetermined': 2}
Link IDs: {None: 1}
Chain: "F"
Number of atoms: 22
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 2, 22
Unusual residues: {' MG': 1, 'CAP': 1}
Classifications: {'undetermined': 2}
Link IDs: {None: 1}
Chain: "G"
Number of atoms: 22
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 2, 22
Unusual residues: {' MG': 1, 'CAP': 1}
Classifications: {'undetermined': 2}
Link IDs: {None: 1}
Chain: "H"
Number of atoms: 22
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 2, 22
Unusual residues: {' MG': 1, 'CAP': 1}
Classifications: {'undetermined': 2}
Link IDs: {None: 1}
Chain: "A"
Number of atoms: 124
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 124, 124
Classifications: {'water': 124}
Link IDs: {None: 123}
Chain: "B"
Number of atoms: 125
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 125, 125
Classifications: {'water': 125}
Link IDs: {None: 124}
Chain: "C"
Number of atoms: 122
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 122, 122
Classifications: {'water': 122}
Link IDs: {None: 121}
Chain: "D"
Number of atoms: 121
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 121, 121
Classifications: {'water': 121}
Link IDs: {None: 120}
Chain: "E"
Number of atoms: 125
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 125, 125
Classifications: {'water': 125}
Link IDs: {None: 124}
Chain: "F"
Number of atoms: 121
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 121, 121
Classifications: {'water': 121}
Link IDs: {None: 120}
Chain: "G"
Number of atoms: 121
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 121, 121
Classifications: {'water': 121}
Link IDs: {None: 120}
Chain: "H"
Number of atoms: 122
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 122, 122
Classifications: {'water': 122}
Link IDs: {None: 121}
Time building chain proxies: 15.60, per 1000 atoms: 0.53
Number of scatterers: 29365
At special positions: 0
Unit cell: (122.85, 122.85, 108.15, 90, 90, 90)
Space group: P 1 (No. 1)
Number of sites at special positions: 0
Number of scattering types: 6
Type Number sf(0)
S 128 16.00
P 16 15.00
Mg 8 11.99
O 6181 8.00
N 5064 7.00
C 17968 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 - 3.50
Amino acid : False - 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: 12.76
Conformation dependent library (CDL) restraints added in 5.0 seconds
7088 Ramachandran restraints generated.
3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2.
Adding C-beta torsion restraints...
Number of C-beta restraints generated: 6464
Finding SS restraints...
Secondary structure from input PDB file:
184 helices and 24 sheets defined
54.2% alpha, 12.1% beta
0 base pairs and 0 stacking pairs defined.
Time for finding SS restraints: 3.65
Creating SS restraints...
Processing helix chain 'A' and resid 13 through 18
Processing helix chain 'A' and resid 42 through 56
Processing helix chain 'A' and resid 62 through 68
Processing helix chain 'A' and resid 69 through 74
Processing helix chain 'A' and resid 90 through 94
Processing helix chain 'A' and resid 98 through 107
Processing helix chain 'A' and resid 109 through 113
removed outlier: 3.614A pdb=" N PHE A 113 " --> pdb=" O VAL A 110 " (cutoff:3.500A)
Processing helix chain 'A' and resid 127 through 132
Processing helix chain 'A' and resid 140 through 149
Processing helix chain 'A' and resid 167 through 182
Processing helix chain 'A' and resid 199 through 219
Processing helix chain 'A' and resid 232 through 246
Processing helix chain 'A' and resid 255 through 259
Processing helix chain 'A' and resid 259 through 274
Processing helix chain 'A' and resid 284 through 289
removed outlier: 3.553A pdb=" N ARG A 289 " --> pdb=" O ALA A 285 " (cutoff:3.500A)
Processing helix chain 'A' and resid 296 through 308
removed outlier: 3.682A pdb=" N VAL A 300 " --> pdb=" O HIS A 296 " (cutoff:3.500A)
Processing helix chain 'A' and resid 324 through 337
Processing helix chain 'A' and resid 369 through 371
No H-bonds generated for 'chain 'A' and resid 369 through 371'
Processing helix chain 'A' and resid 372 through 381
Processing helix chain 'A' and resid 389 through 394
Processing helix chain 'A' and resid 398 through 419
Processing helix chain 'A' and resid 422 through 436
removed outlier: 5.851A pdb=" N ARG A 428 " --> pdb=" O LEU A 424 " (cutoff:3.500A)
removed outlier: 5.740A pdb=" N GLN A 429 " --> pdb=" O ALA A 425 " (cutoff:3.500A)
Processing helix chain 'A' and resid 438 through 448
Processing helix chain 'B' and resid 13 through 18
Processing helix chain 'B' and resid 42 through 56
Processing helix chain 'B' and resid 62 through 68
Processing helix chain 'B' and resid 69 through 74
Processing helix chain 'B' and resid 90 through 94
Processing helix chain 'B' and resid 98 through 107
Processing helix chain 'B' and resid 109 through 113
removed outlier: 3.614A pdb=" N PHE B 113 " --> pdb=" O VAL B 110 " (cutoff:3.500A)
Processing helix chain 'B' and resid 127 through 132
Processing helix chain 'B' and resid 140 through 149
Processing helix chain 'B' and resid 167 through 182
Processing helix chain 'B' and resid 199 through 219
Processing helix chain 'B' and resid 232 through 246
Processing helix chain 'B' and resid 255 through 259
Processing helix chain 'B' and resid 259 through 274
Processing helix chain 'B' and resid 284 through 289
removed outlier: 3.552A pdb=" N ARG B 289 " --> pdb=" O ALA B 285 " (cutoff:3.500A)
Processing helix chain 'B' and resid 296 through 308
removed outlier: 3.682A pdb=" N VAL B 300 " --> pdb=" O HIS B 296 " (cutoff:3.500A)
Processing helix chain 'B' and resid 324 through 337
Processing helix chain 'B' and resid 369 through 371
No H-bonds generated for 'chain 'B' and resid 369 through 371'
Processing helix chain 'B' and resid 372 through 381
Processing helix chain 'B' and resid 389 through 394
Processing helix chain 'B' and resid 398 through 419
Processing helix chain 'B' and resid 422 through 436
removed outlier: 5.851A pdb=" N ARG B 428 " --> pdb=" O LEU B 424 " (cutoff:3.500A)
removed outlier: 5.740A pdb=" N GLN B 429 " --> pdb=" O ALA B 425 " (cutoff:3.500A)
Processing helix chain 'B' and resid 438 through 448
Processing helix chain 'C' and resid 13 through 18
Processing helix chain 'C' and resid 42 through 56
Processing helix chain 'C' and resid 62 through 68
Processing helix chain 'C' and resid 69 through 74
Processing helix chain 'C' and resid 90 through 94
Processing helix chain 'C' and resid 98 through 107
Processing helix chain 'C' and resid 109 through 113
removed outlier: 3.614A pdb=" N PHE C 113 " --> pdb=" O VAL C 110 " (cutoff:3.500A)
Processing helix chain 'C' and resid 127 through 132
Processing helix chain 'C' and resid 140 through 149
Processing helix chain 'C' and resid 167 through 182
Processing helix chain 'C' and resid 199 through 219
Processing helix chain 'C' and resid 232 through 246
Processing helix chain 'C' and resid 255 through 259
Processing helix chain 'C' and resid 259 through 274
Processing helix chain 'C' and resid 284 through 289
removed outlier: 3.553A pdb=" N ARG C 289 " --> pdb=" O ALA C 285 " (cutoff:3.500A)
Processing helix chain 'C' and resid 296 through 308
removed outlier: 3.682A pdb=" N VAL C 300 " --> pdb=" O HIS C 296 " (cutoff:3.500A)
Processing helix chain 'C' and resid 324 through 337
Processing helix chain 'C' and resid 369 through 371
No H-bonds generated for 'chain 'C' and resid 369 through 371'
Processing helix chain 'C' and resid 372 through 381
Processing helix chain 'C' and resid 389 through 394
Processing helix chain 'C' and resid 398 through 419
Processing helix chain 'C' and resid 422 through 436
removed outlier: 5.850A pdb=" N ARG C 428 " --> pdb=" O LEU C 424 " (cutoff:3.500A)
removed outlier: 5.740A pdb=" N GLN C 429 " --> pdb=" O ALA C 425 " (cutoff:3.500A)
Processing helix chain 'C' and resid 438 through 448
Processing helix chain 'D' and resid 13 through 18
Processing helix chain 'D' and resid 42 through 56
Processing helix chain 'D' and resid 62 through 68
Processing helix chain 'D' and resid 69 through 74
Processing helix chain 'D' and resid 90 through 94
Processing helix chain 'D' and resid 98 through 107
Processing helix chain 'D' and resid 109 through 113
removed outlier: 3.614A pdb=" N PHE D 113 " --> pdb=" O VAL D 110 " (cutoff:3.500A)
Processing helix chain 'D' and resid 127 through 132
Processing helix chain 'D' and resid 140 through 149
Processing helix chain 'D' and resid 167 through 182
Processing helix chain 'D' and resid 199 through 219
Processing helix chain 'D' and resid 232 through 246
Processing helix chain 'D' and resid 255 through 259
Processing helix chain 'D' and resid 259 through 274
Processing helix chain 'D' and resid 284 through 289
removed outlier: 3.553A pdb=" N ARG D 289 " --> pdb=" O ALA D 285 " (cutoff:3.500A)
Processing helix chain 'D' and resid 296 through 308
removed outlier: 3.682A pdb=" N VAL D 300 " --> pdb=" O HIS D 296 " (cutoff:3.500A)
Processing helix chain 'D' and resid 324 through 337
Processing helix chain 'D' and resid 369 through 371
No H-bonds generated for 'chain 'D' and resid 369 through 371'
Processing helix chain 'D' and resid 372 through 381
Processing helix chain 'D' and resid 389 through 394
Processing helix chain 'D' and resid 398 through 419
Processing helix chain 'D' and resid 422 through 436
removed outlier: 5.851A pdb=" N ARG D 428 " --> pdb=" O LEU D 424 " (cutoff:3.500A)
removed outlier: 5.740A pdb=" N GLN D 429 " --> pdb=" O ALA D 425 " (cutoff:3.500A)
Processing helix chain 'D' and resid 438 through 448
Processing helix chain 'E' and resid 13 through 18
Processing helix chain 'E' and resid 42 through 56
Processing helix chain 'E' and resid 62 through 68
Processing helix chain 'E' and resid 69 through 74
Processing helix chain 'E' and resid 90 through 94
Processing helix chain 'E' and resid 98 through 107
Processing helix chain 'E' and resid 109 through 113
removed outlier: 3.613A pdb=" N PHE E 113 " --> pdb=" O VAL E 110 " (cutoff:3.500A)
Processing helix chain 'E' and resid 127 through 132
Processing helix chain 'E' and resid 140 through 149
Processing helix chain 'E' and resid 167 through 182
Processing helix chain 'E' and resid 199 through 219
Processing helix chain 'E' and resid 232 through 246
Processing helix chain 'E' and resid 255 through 259
Processing helix chain 'E' and resid 259 through 274
Processing helix chain 'E' and resid 284 through 289
removed outlier: 3.553A pdb=" N ARG E 289 " --> pdb=" O ALA E 285 " (cutoff:3.500A)
Processing helix chain 'E' and resid 296 through 308
removed outlier: 3.682A pdb=" N VAL E 300 " --> pdb=" O HIS E 296 " (cutoff:3.500A)
Processing helix chain 'E' and resid 324 through 337
Processing helix chain 'E' and resid 369 through 371
No H-bonds generated for 'chain 'E' and resid 369 through 371'
Processing helix chain 'E' and resid 372 through 381
Processing helix chain 'E' and resid 389 through 394
Processing helix chain 'E' and resid 398 through 419
Processing helix chain 'E' and resid 422 through 436
removed outlier: 5.850A pdb=" N ARG E 428 " --> pdb=" O LEU E 424 " (cutoff:3.500A)
removed outlier: 5.740A pdb=" N GLN E 429 " --> pdb=" O ALA E 425 " (cutoff:3.500A)
Processing helix chain 'E' and resid 438 through 448
Processing helix chain 'F' and resid 13 through 18
Processing helix chain 'F' and resid 42 through 56
Processing helix chain 'F' and resid 62 through 68
Processing helix chain 'F' and resid 69 through 74
Processing helix chain 'F' and resid 90 through 94
Processing helix chain 'F' and resid 98 through 107
Processing helix chain 'F' and resid 109 through 113
removed outlier: 3.614A pdb=" N PHE F 113 " --> pdb=" O VAL F 110 " (cutoff:3.500A)
Processing helix chain 'F' and resid 127 through 132
Processing helix chain 'F' and resid 140 through 149
Processing helix chain 'F' and resid 167 through 182
Processing helix chain 'F' and resid 199 through 219
Processing helix chain 'F' and resid 232 through 246
Processing helix chain 'F' and resid 255 through 259
Processing helix chain 'F' and resid 259 through 274
Processing helix chain 'F' and resid 284 through 289
removed outlier: 3.553A pdb=" N ARG F 289 " --> pdb=" O ALA F 285 " (cutoff:3.500A)
Processing helix chain 'F' and resid 296 through 308
removed outlier: 3.682A pdb=" N VAL F 300 " --> pdb=" O HIS F 296 " (cutoff:3.500A)
Processing helix chain 'F' and resid 324 through 337
Processing helix chain 'F' and resid 369 through 371
No H-bonds generated for 'chain 'F' and resid 369 through 371'
Processing helix chain 'F' and resid 372 through 381
Processing helix chain 'F' and resid 389 through 394
Processing helix chain 'F' and resid 398 through 419
Processing helix chain 'F' and resid 422 through 436
removed outlier: 5.850A pdb=" N ARG F 428 " --> pdb=" O LEU F 424 " (cutoff:3.500A)
removed outlier: 5.740A pdb=" N GLN F 429 " --> pdb=" O ALA F 425 " (cutoff:3.500A)
Processing helix chain 'F' and resid 438 through 448
Processing helix chain 'G' and resid 13 through 18
Processing helix chain 'G' and resid 42 through 56
Processing helix chain 'G' and resid 62 through 68
Processing helix chain 'G' and resid 69 through 74
Processing helix chain 'G' and resid 90 through 94
Processing helix chain 'G' and resid 98 through 107
Processing helix chain 'G' and resid 109 through 113
removed outlier: 3.614A pdb=" N PHE G 113 " --> pdb=" O VAL G 110 " (cutoff:3.500A)
Processing helix chain 'G' and resid 127 through 132
Processing helix chain 'G' and resid 140 through 149
Processing helix chain 'G' and resid 167 through 182
Processing helix chain 'G' and resid 199 through 219
Processing helix chain 'G' and resid 232 through 246
Processing helix chain 'G' and resid 255 through 259
Processing helix chain 'G' and resid 259 through 274
Processing helix chain 'G' and resid 284 through 289
removed outlier: 3.553A pdb=" N ARG G 289 " --> pdb=" O ALA G 285 " (cutoff:3.500A)
Processing helix chain 'G' and resid 296 through 308
removed outlier: 3.682A pdb=" N VAL G 300 " --> pdb=" O HIS G 296 " (cutoff:3.500A)
Processing helix chain 'G' and resid 324 through 337
Processing helix chain 'G' and resid 369 through 371
No H-bonds generated for 'chain 'G' and resid 369 through 371'
Processing helix chain 'G' and resid 372 through 381
Processing helix chain 'G' and resid 389 through 394
Processing helix chain 'G' and resid 398 through 419
Processing helix chain 'G' and resid 422 through 436
removed outlier: 5.850A pdb=" N ARG G 428 " --> pdb=" O LEU G 424 " (cutoff:3.500A)
removed outlier: 5.740A pdb=" N GLN G 429 " --> pdb=" O ALA G 425 " (cutoff:3.500A)
Processing helix chain 'G' and resid 438 through 448
Processing helix chain 'H' and resid 13 through 18
Processing helix chain 'H' and resid 42 through 56
Processing helix chain 'H' and resid 62 through 68
Processing helix chain 'H' and resid 69 through 74
Processing helix chain 'H' and resid 90 through 94
Processing helix chain 'H' and resid 98 through 107
Processing helix chain 'H' and resid 109 through 113
removed outlier: 3.614A pdb=" N PHE H 113 " --> pdb=" O VAL H 110 " (cutoff:3.500A)
Processing helix chain 'H' and resid 127 through 132
Processing helix chain 'H' and resid 140 through 149
Processing helix chain 'H' and resid 167 through 182
Processing helix chain 'H' and resid 199 through 219
Processing helix chain 'H' and resid 232 through 246
Processing helix chain 'H' and resid 255 through 259
Processing helix chain 'H' and resid 259 through 274
Processing helix chain 'H' and resid 284 through 289
removed outlier: 3.553A pdb=" N ARG H 289 " --> pdb=" O ALA H 285 " (cutoff:3.500A)
Processing helix chain 'H' and resid 296 through 308
removed outlier: 3.682A pdb=" N VAL H 300 " --> pdb=" O HIS H 296 " (cutoff:3.500A)
Processing helix chain 'H' and resid 324 through 337
Processing helix chain 'H' and resid 369 through 371
No H-bonds generated for 'chain 'H' and resid 369 through 371'
Processing helix chain 'H' and resid 372 through 381
Processing helix chain 'H' and resid 389 through 394
Processing helix chain 'H' and resid 398 through 419
Processing helix chain 'H' and resid 422 through 436
removed outlier: 5.850A pdb=" N ARG H 428 " --> pdb=" O LEU H 424 " (cutoff:3.500A)
removed outlier: 5.740A pdb=" N GLN H 429 " --> pdb=" O ALA H 425 " (cutoff:3.500A)
Processing helix chain 'H' and resid 438 through 448
Processing sheet with id=AA1, first strand: chain 'A' and resid 76 through 81
removed outlier: 6.732A pdb=" N TYR A 86 " --> pdb=" O TYR A 78 " (cutoff:3.500A)
removed outlier: 4.433A pdb=" N ILE A 80 " --> pdb=" O THR A 84 " (cutoff:3.500A)
removed outlier: 6.397A pdb=" N THR A 84 " --> pdb=" O ILE A 80 " (cutoff:3.500A)
removed outlier: 3.798A pdb=" N ASP A 123 " --> pdb=" O ALA A 32 " (cutoff:3.500A)
removed outlier: 6.739A pdb=" N ARG A 34 " --> pdb=" O LEU A 121 " (cutoff:3.500A)
removed outlier: 5.579A pdb=" N LEU A 121 " --> pdb=" O ARG A 34 " (cutoff:3.500A)
removed outlier: 7.325A pdb=" N GLU A 36 " --> pdb=" O LEU A 119 " (cutoff:3.500A)
removed outlier: 5.585A pdb=" N LEU A 119 " --> pdb=" O GLU A 36 " (cutoff:3.500A)
Processing sheet with id=AA2, first strand: chain 'A' and resid 155 through 157
removed outlier: 6.394A pdb=" N LEU A 155 " --> pdb=" O PHE A 386 " (cutoff:3.500A)
removed outlier: 3.517A pdb=" N HIS A 313 " --> pdb=" O CYS A 279 " (cutoff:3.500A)
removed outlier: 6.635A pdb=" N ILE A 251 " --> pdb=" O HIS A 278 " (cutoff:3.500A)
removed outlier: 7.726A pdb=" N HIS A 280 " --> pdb=" O ILE A 251 " (cutoff:3.500A)
removed outlier: 6.376A pdb=" N VAL A 253 " --> pdb=" O HIS A 280 " (cutoff:3.500A)
removed outlier: 5.925A pdb=" N HIS A 224 " --> pdb=" O TYR A 250 " (cutoff:3.500A)
removed outlier: 6.334A pdb=" N MET A 252 " --> pdb=" O HIS A 224 " (cutoff:3.500A)
removed outlier: 6.031A pdb=" N LEU A 226 " --> pdb=" O MET A 252 " (cutoff:3.500A)
removed outlier: 8.160A pdb=" N ASP A 254 " --> pdb=" O LEU A 226 " (cutoff:3.500A)
removed outlier: 7.257A pdb=" N THR A 186 " --> pdb=" O TRP A 225 " (cutoff:3.500A)
removed outlier: 7.854A pdb=" N ASN A 227 " --> pdb=" O THR A 186 " (cutoff:3.500A)
Processing sheet with id=AA3, first strand: chain 'A' and resid 339 through 340
Processing sheet with id=AA4, first strand: chain 'B' and resid 76 through 81
removed outlier: 6.732A pdb=" N TYR B 86 " --> pdb=" O TYR B 78 " (cutoff:3.500A)
removed outlier: 4.433A pdb=" N ILE B 80 " --> pdb=" O THR B 84 " (cutoff:3.500A)
removed outlier: 6.398A pdb=" N THR B 84 " --> pdb=" O ILE B 80 " (cutoff:3.500A)
removed outlier: 3.798A pdb=" N ASP B 123 " --> pdb=" O ALA B 32 " (cutoff:3.500A)
removed outlier: 6.739A pdb=" N ARG B 34 " --> pdb=" O LEU B 121 " (cutoff:3.500A)
removed outlier: 5.578A pdb=" N LEU B 121 " --> pdb=" O ARG B 34 " (cutoff:3.500A)
removed outlier: 7.325A pdb=" N GLU B 36 " --> pdb=" O LEU B 119 " (cutoff:3.500A)
removed outlier: 5.584A pdb=" N LEU B 119 " --> pdb=" O GLU B 36 " (cutoff:3.500A)
Processing sheet with id=AA5, first strand: chain 'B' and resid 155 through 157
removed outlier: 6.394A pdb=" N LEU B 155 " --> pdb=" O PHE B 386 " (cutoff:3.500A)
removed outlier: 3.517A pdb=" N HIS B 313 " --> pdb=" O CYS B 279 " (cutoff:3.500A)
removed outlier: 6.636A pdb=" N ILE B 251 " --> pdb=" O HIS B 278 " (cutoff:3.500A)
removed outlier: 7.725A pdb=" N HIS B 280 " --> pdb=" O ILE B 251 " (cutoff:3.500A)
removed outlier: 6.376A pdb=" N VAL B 253 " --> pdb=" O HIS B 280 " (cutoff:3.500A)
removed outlier: 5.924A pdb=" N HIS B 224 " --> pdb=" O TYR B 250 " (cutoff:3.500A)
removed outlier: 6.332A pdb=" N MET B 252 " --> pdb=" O HIS B 224 " (cutoff:3.500A)
removed outlier: 6.031A pdb=" N LEU B 226 " --> pdb=" O MET B 252 " (cutoff:3.500A)
removed outlier: 8.160A pdb=" N ASP B 254 " --> pdb=" O LEU B 226 " (cutoff:3.500A)
removed outlier: 7.256A pdb=" N THR B 186 " --> pdb=" O TRP B 225 " (cutoff:3.500A)
removed outlier: 7.854A pdb=" N ASN B 227 " --> pdb=" O THR B 186 " (cutoff:3.500A)
Processing sheet with id=AA6, first strand: chain 'B' and resid 339 through 340
Processing sheet with id=AA7, first strand: chain 'C' and resid 76 through 81
removed outlier: 6.732A pdb=" N TYR C 86 " --> pdb=" O TYR C 78 " (cutoff:3.500A)
removed outlier: 4.433A pdb=" N ILE C 80 " --> pdb=" O THR C 84 " (cutoff:3.500A)
removed outlier: 6.397A pdb=" N THR C 84 " --> pdb=" O ILE C 80 " (cutoff:3.500A)
removed outlier: 3.798A pdb=" N ASP C 123 " --> pdb=" O ALA C 32 " (cutoff:3.500A)
removed outlier: 6.739A pdb=" N ARG C 34 " --> pdb=" O LEU C 121 " (cutoff:3.500A)
removed outlier: 5.578A pdb=" N LEU C 121 " --> pdb=" O ARG C 34 " (cutoff:3.500A)
removed outlier: 7.325A pdb=" N GLU C 36 " --> pdb=" O LEU C 119 " (cutoff:3.500A)
removed outlier: 5.584A pdb=" N LEU C 119 " --> pdb=" O GLU C 36 " (cutoff:3.500A)
Processing sheet with id=AA8, first strand: chain 'C' and resid 155 through 157
removed outlier: 6.395A pdb=" N LEU C 155 " --> pdb=" O PHE C 386 " (cutoff:3.500A)
removed outlier: 3.518A pdb=" N HIS C 313 " --> pdb=" O CYS C 279 " (cutoff:3.500A)
removed outlier: 6.635A pdb=" N ILE C 251 " --> pdb=" O HIS C 278 " (cutoff:3.500A)
removed outlier: 7.725A pdb=" N HIS C 280 " --> pdb=" O ILE C 251 " (cutoff:3.500A)
removed outlier: 6.376A pdb=" N VAL C 253 " --> pdb=" O HIS C 280 " (cutoff:3.500A)
removed outlier: 5.924A pdb=" N HIS C 224 " --> pdb=" O TYR C 250 " (cutoff:3.500A)
removed outlier: 6.333A pdb=" N MET C 252 " --> pdb=" O HIS C 224 " (cutoff:3.500A)
removed outlier: 6.031A pdb=" N LEU C 226 " --> pdb=" O MET C 252 " (cutoff:3.500A)
removed outlier: 8.160A pdb=" N ASP C 254 " --> pdb=" O LEU C 226 " (cutoff:3.500A)
removed outlier: 7.256A pdb=" N THR C 186 " --> pdb=" O TRP C 225 " (cutoff:3.500A)
removed outlier: 7.855A pdb=" N ASN C 227 " --> pdb=" O THR C 186 " (cutoff:3.500A)
Processing sheet with id=AA9, first strand: chain 'C' and resid 339 through 340
Processing sheet with id=AB1, first strand: chain 'D' and resid 76 through 81
removed outlier: 6.732A pdb=" N TYR D 86 " --> pdb=" O TYR D 78 " (cutoff:3.500A)
removed outlier: 4.433A pdb=" N ILE D 80 " --> pdb=" O THR D 84 " (cutoff:3.500A)
removed outlier: 6.397A pdb=" N THR D 84 " --> pdb=" O ILE D 80 " (cutoff:3.500A)
removed outlier: 3.799A pdb=" N ASP D 123 " --> pdb=" O ALA D 32 " (cutoff:3.500A)
removed outlier: 6.738A pdb=" N ARG D 34 " --> pdb=" O LEU D 121 " (cutoff:3.500A)
removed outlier: 5.578A pdb=" N LEU D 121 " --> pdb=" O ARG D 34 " (cutoff:3.500A)
removed outlier: 7.324A pdb=" N GLU D 36 " --> pdb=" O LEU D 119 " (cutoff:3.500A)
removed outlier: 5.584A pdb=" N LEU D 119 " --> pdb=" O GLU D 36 " (cutoff:3.500A)
Processing sheet with id=AB2, first strand: chain 'D' and resid 155 through 157
removed outlier: 6.394A pdb=" N LEU D 155 " --> pdb=" O PHE D 386 " (cutoff:3.500A)
removed outlier: 3.517A pdb=" N HIS D 313 " --> pdb=" O CYS D 279 " (cutoff:3.500A)
removed outlier: 6.636A pdb=" N ILE D 251 " --> pdb=" O HIS D 278 " (cutoff:3.500A)
removed outlier: 7.726A pdb=" N HIS D 280 " --> pdb=" O ILE D 251 " (cutoff:3.500A)
removed outlier: 6.376A pdb=" N VAL D 253 " --> pdb=" O HIS D 280 " (cutoff:3.500A)
removed outlier: 5.925A pdb=" N HIS D 224 " --> pdb=" O TYR D 250 " (cutoff:3.500A)
removed outlier: 6.333A pdb=" N MET D 252 " --> pdb=" O HIS D 224 " (cutoff:3.500A)
removed outlier: 6.031A pdb=" N LEU D 226 " --> pdb=" O MET D 252 " (cutoff:3.500A)
removed outlier: 8.159A pdb=" N ASP D 254 " --> pdb=" O LEU D 226 " (cutoff:3.500A)
removed outlier: 7.257A pdb=" N THR D 186 " --> pdb=" O TRP D 225 " (cutoff:3.500A)
removed outlier: 7.854A pdb=" N ASN D 227 " --> pdb=" O THR D 186 " (cutoff:3.500A)
Processing sheet with id=AB3, first strand: chain 'D' and resid 339 through 340
Processing sheet with id=AB4, first strand: chain 'E' and resid 76 through 81
removed outlier: 6.732A pdb=" N TYR E 86 " --> pdb=" O TYR E 78 " (cutoff:3.500A)
removed outlier: 4.433A pdb=" N ILE E 80 " --> pdb=" O THR E 84 " (cutoff:3.500A)
removed outlier: 6.397A pdb=" N THR E 84 " --> pdb=" O ILE E 80 " (cutoff:3.500A)
removed outlier: 3.798A pdb=" N ASP E 123 " --> pdb=" O ALA E 32 " (cutoff:3.500A)
removed outlier: 6.739A pdb=" N ARG E 34 " --> pdb=" O LEU E 121 " (cutoff:3.500A)
removed outlier: 5.579A pdb=" N LEU E 121 " --> pdb=" O ARG E 34 " (cutoff:3.500A)
removed outlier: 7.325A pdb=" N GLU E 36 " --> pdb=" O LEU E 119 " (cutoff:3.500A)
removed outlier: 5.584A pdb=" N LEU E 119 " --> pdb=" O GLU E 36 " (cutoff:3.500A)
Processing sheet with id=AB5, first strand: chain 'E' and resid 155 through 157
removed outlier: 6.394A pdb=" N LEU E 155 " --> pdb=" O PHE E 386 " (cutoff:3.500A)
removed outlier: 3.518A pdb=" N HIS E 313 " --> pdb=" O CYS E 279 " (cutoff:3.500A)
removed outlier: 6.635A pdb=" N ILE E 251 " --> pdb=" O HIS E 278 " (cutoff:3.500A)
removed outlier: 7.725A pdb=" N HIS E 280 " --> pdb=" O ILE E 251 " (cutoff:3.500A)
removed outlier: 6.376A pdb=" N VAL E 253 " --> pdb=" O HIS E 280 " (cutoff:3.500A)
removed outlier: 5.925A pdb=" N HIS E 224 " --> pdb=" O TYR E 250 " (cutoff:3.500A)
removed outlier: 6.333A pdb=" N MET E 252 " --> pdb=" O HIS E 224 " (cutoff:3.500A)
removed outlier: 6.030A pdb=" N LEU E 226 " --> pdb=" O MET E 252 " (cutoff:3.500A)
removed outlier: 8.160A pdb=" N ASP E 254 " --> pdb=" O LEU E 226 " (cutoff:3.500A)
removed outlier: 7.256A pdb=" N THR E 186 " --> pdb=" O TRP E 225 " (cutoff:3.500A)
removed outlier: 7.853A pdb=" N ASN E 227 " --> pdb=" O THR E 186 " (cutoff:3.500A)
Processing sheet with id=AB6, first strand: chain 'E' and resid 339 through 340
Processing sheet with id=AB7, first strand: chain 'F' and resid 76 through 81
removed outlier: 6.732A pdb=" N TYR F 86 " --> pdb=" O TYR F 78 " (cutoff:3.500A)
removed outlier: 4.432A pdb=" N ILE F 80 " --> pdb=" O THR F 84 " (cutoff:3.500A)
removed outlier: 6.397A pdb=" N THR F 84 " --> pdb=" O ILE F 80 " (cutoff:3.500A)
removed outlier: 3.798A pdb=" N ASP F 123 " --> pdb=" O ALA F 32 " (cutoff:3.500A)
removed outlier: 6.738A pdb=" N ARG F 34 " --> pdb=" O LEU F 121 " (cutoff:3.500A)
removed outlier: 5.578A pdb=" N LEU F 121 " --> pdb=" O ARG F 34 " (cutoff:3.500A)
removed outlier: 7.325A pdb=" N GLU F 36 " --> pdb=" O LEU F 119 " (cutoff:3.500A)
removed outlier: 5.584A pdb=" N LEU F 119 " --> pdb=" O GLU F 36 " (cutoff:3.500A)
Processing sheet with id=AB8, first strand: chain 'F' and resid 155 through 157
removed outlier: 6.395A pdb=" N LEU F 155 " --> pdb=" O PHE F 386 " (cutoff:3.500A)
removed outlier: 3.517A pdb=" N HIS F 313 " --> pdb=" O CYS F 279 " (cutoff:3.500A)
removed outlier: 6.636A pdb=" N ILE F 251 " --> pdb=" O HIS F 278 " (cutoff:3.500A)
removed outlier: 7.725A pdb=" N HIS F 280 " --> pdb=" O ILE F 251 " (cutoff:3.500A)
removed outlier: 6.376A pdb=" N VAL F 253 " --> pdb=" O HIS F 280 " (cutoff:3.500A)
removed outlier: 5.924A pdb=" N HIS F 224 " --> pdb=" O TYR F 250 " (cutoff:3.500A)
removed outlier: 6.333A pdb=" N MET F 252 " --> pdb=" O HIS F 224 " (cutoff:3.500A)
removed outlier: 6.030A pdb=" N LEU F 226 " --> pdb=" O MET F 252 " (cutoff:3.500A)
removed outlier: 8.159A pdb=" N ASP F 254 " --> pdb=" O LEU F 226 " (cutoff:3.500A)
removed outlier: 7.256A pdb=" N THR F 186 " --> pdb=" O TRP F 225 " (cutoff:3.500A)
removed outlier: 7.854A pdb=" N ASN F 227 " --> pdb=" O THR F 186 " (cutoff:3.500A)
Processing sheet with id=AB9, first strand: chain 'F' and resid 339 through 340
Processing sheet with id=AC1, first strand: chain 'G' and resid 76 through 81
removed outlier: 6.732A pdb=" N TYR G 86 " --> pdb=" O TYR G 78 " (cutoff:3.500A)
removed outlier: 4.432A pdb=" N ILE G 80 " --> pdb=" O THR G 84 " (cutoff:3.500A)
removed outlier: 6.398A pdb=" N THR G 84 " --> pdb=" O ILE G 80 " (cutoff:3.500A)
removed outlier: 3.798A pdb=" N ASP G 123 " --> pdb=" O ALA G 32 " (cutoff:3.500A)
removed outlier: 6.738A pdb=" N ARG G 34 " --> pdb=" O LEU G 121 " (cutoff:3.500A)
removed outlier: 5.577A pdb=" N LEU G 121 " --> pdb=" O ARG G 34 " (cutoff:3.500A)
removed outlier: 7.325A pdb=" N GLU G 36 " --> pdb=" O LEU G 119 " (cutoff:3.500A)
removed outlier: 5.584A pdb=" N LEU G 119 " --> pdb=" O GLU G 36 " (cutoff:3.500A)
Processing sheet with id=AC2, first strand: chain 'G' and resid 155 through 157
removed outlier: 6.394A pdb=" N LEU G 155 " --> pdb=" O PHE G 386 " (cutoff:3.500A)
removed outlier: 3.518A pdb=" N HIS G 313 " --> pdb=" O CYS G 279 " (cutoff:3.500A)
removed outlier: 6.635A pdb=" N ILE G 251 " --> pdb=" O HIS G 278 " (cutoff:3.500A)
removed outlier: 7.725A pdb=" N HIS G 280 " --> pdb=" O ILE G 251 " (cutoff:3.500A)
removed outlier: 6.376A pdb=" N VAL G 253 " --> pdb=" O HIS G 280 " (cutoff:3.500A)
removed outlier: 5.925A pdb=" N HIS G 224 " --> pdb=" O TYR G 250 " (cutoff:3.500A)
removed outlier: 6.333A pdb=" N MET G 252 " --> pdb=" O HIS G 224 " (cutoff:3.500A)
removed outlier: 6.031A pdb=" N LEU G 226 " --> pdb=" O MET G 252 " (cutoff:3.500A)
removed outlier: 8.159A pdb=" N ASP G 254 " --> pdb=" O LEU G 226 " (cutoff:3.500A)
removed outlier: 7.256A pdb=" N THR G 186 " --> pdb=" O TRP G 225 " (cutoff:3.500A)
removed outlier: 7.854A pdb=" N ASN G 227 " --> pdb=" O THR G 186 " (cutoff:3.500A)
Processing sheet with id=AC3, first strand: chain 'G' and resid 339 through 340
Processing sheet with id=AC4, first strand: chain 'H' and resid 76 through 81
removed outlier: 6.731A pdb=" N TYR H 86 " --> pdb=" O TYR H 78 " (cutoff:3.500A)
removed outlier: 4.433A pdb=" N ILE H 80 " --> pdb=" O THR H 84 " (cutoff:3.500A)
removed outlier: 6.397A pdb=" N THR H 84 " --> pdb=" O ILE H 80 " (cutoff:3.500A)
removed outlier: 3.798A pdb=" N ASP H 123 " --> pdb=" O ALA H 32 " (cutoff:3.500A)
removed outlier: 6.738A pdb=" N ARG H 34 " --> pdb=" O LEU H 121 " (cutoff:3.500A)
removed outlier: 5.578A pdb=" N LEU H 121 " --> pdb=" O ARG H 34 " (cutoff:3.500A)
removed outlier: 7.325A pdb=" N GLU H 36 " --> pdb=" O LEU H 119 " (cutoff:3.500A)
removed outlier: 5.585A pdb=" N LEU H 119 " --> pdb=" O GLU H 36 " (cutoff:3.500A)
Processing sheet with id=AC5, first strand: chain 'H' and resid 155 through 157
removed outlier: 6.394A pdb=" N LEU H 155 " --> pdb=" O PHE H 386 " (cutoff:3.500A)
removed outlier: 3.518A pdb=" N HIS H 313 " --> pdb=" O CYS H 279 " (cutoff:3.500A)
removed outlier: 6.636A pdb=" N ILE H 251 " --> pdb=" O HIS H 278 " (cutoff:3.500A)
removed outlier: 7.725A pdb=" N HIS H 280 " --> pdb=" O ILE H 251 " (cutoff:3.500A)
removed outlier: 6.376A pdb=" N VAL H 253 " --> pdb=" O HIS H 280 " (cutoff:3.500A)
removed outlier: 5.925A pdb=" N HIS H 224 " --> pdb=" O TYR H 250 " (cutoff:3.500A)
removed outlier: 6.332A pdb=" N MET H 252 " --> pdb=" O HIS H 224 " (cutoff:3.500A)
removed outlier: 6.030A pdb=" N LEU H 226 " --> pdb=" O MET H 252 " (cutoff:3.500A)
removed outlier: 8.160A pdb=" N ASP H 254 " --> pdb=" O LEU H 226 " (cutoff:3.500A)
removed outlier: 7.256A pdb=" N THR H 186 " --> pdb=" O TRP H 225 " (cutoff:3.500A)
removed outlier: 7.853A pdb=" N ASN H 227 " --> pdb=" O THR H 186 " (cutoff:3.500A)
Processing sheet with id=AC6, first strand: chain 'H' and resid 339 through 340
1384 hydrogen bonds defined for protein.
3840 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: 11.97
Time building geometry restraints manager: 13.67 seconds
NOTE: a complete listing of the restraints can be obtained by requesting
output of .geo file.
Histogram of bond lengths:
1.20 - 1.32: 4693
1.32 - 1.44: 8100
1.44 - 1.56: 16079
1.56 - 1.68: 16
1.68 - 1.81: 208
Bond restraints: 29096
Sorted by residual:
bond pdb=" NZ KCX E 187 "
pdb=" CX KCX E 187 "
ideal model delta sigma weight residual
1.411 1.329 0.082 2.00e-02 2.50e+03 1.67e+01
bond pdb=" NZ KCX F 187 "
pdb=" CX KCX F 187 "
ideal model delta sigma weight residual
1.411 1.331 0.080 2.00e-02 2.50e+03 1.58e+01
bond pdb=" NZ KCX D 187 "
pdb=" CX KCX D 187 "
ideal model delta sigma weight residual
1.411 1.332 0.079 2.00e-02 2.50e+03 1.58e+01
bond pdb=" NZ KCX H 187 "
pdb=" CX KCX H 187 "
ideal model delta sigma weight residual
1.411 1.334 0.077 2.00e-02 2.50e+03 1.49e+01
bond pdb=" NZ KCX C 187 "
pdb=" CX KCX C 187 "
ideal model delta sigma weight residual
1.411 1.334 0.077 2.00e-02 2.50e+03 1.47e+01
... (remaining 29091 not shown)
Histogram of bond angle deviations from ideal:
100.03 - 106.82: 969
106.82 - 113.62: 15435
113.62 - 120.42: 11103
120.42 - 127.21: 11516
127.21 - 134.01: 449
Bond angle restraints: 39472
Sorted by residual:
angle pdb=" C3 CAP H 502 "
pdb=" C4 CAP H 502 "
pdb=" C5 CAP H 502 "
ideal model delta sigma weight residual
111.00 124.20 -13.20 3.00e+00 1.11e-01 1.94e+01
angle pdb=" C3 CAP E 502 "
pdb=" C4 CAP E 502 "
pdb=" C5 CAP E 502 "
ideal model delta sigma weight residual
111.00 124.18 -13.18 3.00e+00 1.11e-01 1.93e+01
angle pdb=" C3 CAP G 502 "
pdb=" C4 CAP G 502 "
pdb=" C5 CAP G 502 "
ideal model delta sigma weight residual
111.00 124.18 -13.18 3.00e+00 1.11e-01 1.93e+01
angle pdb=" C3 CAP D 502 "
pdb=" C4 CAP D 502 "
pdb=" C5 CAP D 502 "
ideal model delta sigma weight residual
111.00 124.18 -13.18 3.00e+00 1.11e-01 1.93e+01
angle pdb=" C3 CAP B 502 "
pdb=" C4 CAP B 502 "
pdb=" C5 CAP B 502 "
ideal model delta sigma weight residual
111.00 124.16 -13.16 3.00e+00 1.11e-01 1.92e+01
... (remaining 39467 not shown)
Histogram of dihedral angle deviations from ideal:
0.00 - 34.78: 16529
34.78 - 69.56: 507
69.56 - 104.34: 84
104.34 - 139.12: 4
139.12 - 173.90: 4
Dihedral angle restraints: 17128
sinusoidal: 6952
harmonic: 10176
Sorted by residual:
dihedral pdb=" C3 CAP H 502 "
pdb=" C CAP H 502 "
pdb=" C2 CAP H 502 "
pdb=" O6 CAP H 502 "
ideal model delta sinusoidal sigma weight residual
81.86 -92.04 173.90 1 2.00e+01 2.50e-03 4.79e+01
dihedral pdb=" C3 CAP D 502 "
pdb=" C CAP D 502 "
pdb=" C2 CAP D 502 "
pdb=" O6 CAP D 502 "
ideal model delta sinusoidal sigma weight residual
81.86 -92.04 173.90 1 2.00e+01 2.50e-03 4.79e+01
dihedral pdb=" C3 CAP E 502 "
pdb=" C CAP E 502 "
pdb=" C2 CAP E 502 "
pdb=" O6 CAP E 502 "
ideal model delta sinusoidal sigma weight residual
81.86 -92.03 173.89 1 2.00e+01 2.50e-03 4.79e+01
... (remaining 17125 not shown)
Histogram of chiral volume deviations from ideal:
0.000 - 0.350: 4144
0.350 - 0.700: 0
0.700 - 1.050: 0
1.050 - 1.400: 0
1.400 - 1.750: 8
Chirality restraints: 4152
Sorted by residual:
chirality pdb=" C4 CAP B 502 "
pdb=" C3 CAP B 502 "
pdb=" C5 CAP B 502 "
pdb=" O4 CAP B 502 "
both_signs ideal model delta sigma weight residual
False -2.47 -0.72 -1.75 2.00e-01 2.50e+01 7.66e+01
chirality pdb=" C4 CAP H 502 "
pdb=" C3 CAP H 502 "
pdb=" C5 CAP H 502 "
pdb=" O4 CAP H 502 "
both_signs ideal model delta sigma weight residual
False -2.47 -0.72 -1.75 2.00e-01 2.50e+01 7.63e+01
chirality pdb=" C4 CAP G 502 "
pdb=" C3 CAP G 502 "
pdb=" C5 CAP G 502 "
pdb=" O4 CAP G 502 "
both_signs ideal model delta sigma weight residual
False -2.47 -0.72 -1.75 2.00e-01 2.50e+01 7.63e+01
... (remaining 4149 not shown)
Planarity restraints: 5168
Sorted by residual:
delta sigma weight rms_deltas residual
plane pdb=" CA KCX F 187 " -0.009 2.00e-02 2.50e+03 1.93e-02 3.73e+00
pdb=" C KCX F 187 " 0.033 2.00e-02 2.50e+03
pdb=" O KCX F 187 " -0.012 2.00e-02 2.50e+03
pdb=" N ASP F 188 " -0.011 2.00e-02 2.50e+03
delta sigma weight rms_deltas residual
plane pdb=" CA KCX A 187 " -0.009 2.00e-02 2.50e+03 1.92e-02 3.68e+00
pdb=" C KCX A 187 " 0.033 2.00e-02 2.50e+03
pdb=" O KCX A 187 " -0.012 2.00e-02 2.50e+03
pdb=" N ASP A 188 " -0.011 2.00e-02 2.50e+03
delta sigma weight rms_deltas residual
plane pdb=" CA KCX B 187 " 0.009 2.00e-02 2.50e+03 1.88e-02 3.54e+00
pdb=" C KCX B 187 " -0.033 2.00e-02 2.50e+03
pdb=" O KCX B 187 " 0.012 2.00e-02 2.50e+03
pdb=" N ASP B 188 " 0.011 2.00e-02 2.50e+03
... (remaining 5165 not shown)
Histogram of nonbonded interaction distances:
1.87 - 2.48: 188
2.48 - 3.08: 21060
3.08 - 3.69: 51577
3.69 - 4.29: 83912
4.29 - 4.90: 129116
Nonbonded interactions: 285853
Sorted by model distance:
nonbonded pdb=" OD1 ASP E 189 "
pdb="MG MG E 501 "
model vdw
1.869 2.170
nonbonded pdb=" OD1 ASP G 189 "
pdb="MG MG G 501 "
model vdw
1.870 2.170
nonbonded pdb=" OD1 ASP C 189 "
pdb="MG MG C 501 "
model vdw
1.871 2.170
nonbonded pdb=" OD1 ASP H 189 "
pdb="MG MG H 501 "
model vdw
1.871 2.170
nonbonded pdb=" OD1 ASP B 189 "
pdb="MG MG B 501 "
model vdw
1.872 2.170
... (remaining 285848 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 'A'
selection = chain 'B'
selection = chain 'C'
selection = chain 'D'
selection = chain 'E'
selection = chain 'F'
selection = chain 'G'
selection = chain 'H'
}
Set up NCS constraints
No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
Set random seed: 0.000
Set model cs if undefined: 0.000
Decide on map wrapping: 0.000
Normalize map: mean=0, sd=1: 1.180
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: 0.020
Extract box with map and model: 0.950
Check model and map are aligned: 0.220
Set scattering table: 0.300
Process input model: 81.820
Find NCS groups from input model: 1.330
Set up NCS constraints: 0.130
Set refine NCS operators: 0.000
Adjust number of macro_cycles: 0.000
Reset NCS operators: 0.000
Extract rigid body selections: 0.000
Check and reset occupancies: 0.000
Load rotamer database and sin/cos tables:16.120
Set ADP refinement strategy: 0.000
Make a string to write initial .geo file:0.000
Internal consistency checks: 0.000
Total: 102.070
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8133
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 : 0.004 0.082 29096 Z= 0.230
Angle : 0.561 13.198 39472 Z= 0.263
Chirality : 0.085 1.750 4152
Planarity : 0.003 0.022 5168
Dihedral : 16.747 173.903 10664
Min Nonbonded Distance : 1.869
Molprobity Statistics.
All-atom Clashscore : 2.66
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 3.39 %
Favored : 96.61 %
Rotamer:
Outliers : 0.28 %
Allowed : 11.41 %
Favored : 88.31 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 4.17 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 2.01 (0.15), residues: 3544
helix: 1.76 (0.13), residues: 1664
sheet: 0.50 (0.25), residues: 424
loop : 1.32 (0.18), residues: 1456
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.009 0.001 TRP G 354
HIS 0.003 0.001 HIS E 311
PHE 0.012 0.001 PHE E 297
TYR 0.016 0.001 TYR C 263
ARG 0.001 0.000 ARG B 249
*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
7088 Ramachandran restraints generated.
3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
7088 Ramachandran restraints generated.
3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
449 residues out of total 2832 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 8
poor density : 441
time to evaluate : 3.248
Fit side-chains
REVERT: A 149 LYS cc_start: 0.8079 (mmtt) cc_final: 0.7795 (mtmt)
REVERT: A 208 MET cc_start: 0.8963 (mmm) cc_final: 0.8719 (mmm)
REVERT: A 216 GLU cc_start: 0.7191 (tm-30) cc_final: 0.6925 (tm-30)
REVERT: A 429 GLN cc_start: 0.6828 (tp-100) cc_final: 0.6564 (tp-100)
REVERT: B 208 MET cc_start: 0.8936 (mmm) cc_final: 0.8718 (mmm)
REVERT: B 216 GLU cc_start: 0.7212 (tm-30) cc_final: 0.6914 (tm-30)
REVERT: B 429 GLN cc_start: 0.6971 (tp-100) cc_final: 0.6697 (tp-100)
REVERT: C 23 GLU cc_start: 0.7680 (mm-30) cc_final: 0.7186 (mt-10)
REVERT: C 216 GLU cc_start: 0.7174 (tm-30) cc_final: 0.6830 (tm-30)
REVERT: C 429 GLN cc_start: 0.6872 (tp-100) cc_final: 0.6455 (tp-100)
REVERT: D 23 GLU cc_start: 0.7658 (mm-30) cc_final: 0.7183 (mt-10)
REVERT: D 149 LYS cc_start: 0.8067 (mmtt) cc_final: 0.7709 (mtmt)
REVERT: D 216 GLU cc_start: 0.7207 (tm-30) cc_final: 0.6866 (tm-30)
REVERT: D 217 GLU cc_start: 0.7270 (mt-10) cc_final: 0.7054 (mt-10)
REVERT: D 252 MET cc_start: 0.9283 (ptm) cc_final: 0.9025 (ptm)
REVERT: D 429 GLN cc_start: 0.6873 (tp-100) cc_final: 0.6535 (tp-100)
REVERT: E 65 GLN cc_start: 0.6959 (pt0) cc_final: 0.6626 (pt0)
REVERT: E 149 LYS cc_start: 0.8102 (mmtt) cc_final: 0.7789 (mtmt)
REVERT: E 208 MET cc_start: 0.8917 (mmm) cc_final: 0.8678 (mmm)
REVERT: E 216 GLU cc_start: 0.7208 (tm-30) cc_final: 0.6891 (tm-30)
REVERT: E 429 GLN cc_start: 0.6942 (tp-100) cc_final: 0.6679 (tp-100)
REVERT: F 149 LYS cc_start: 0.8107 (mmtt) cc_final: 0.7791 (mtmt)
REVERT: F 208 MET cc_start: 0.8952 (mmm) cc_final: 0.8727 (mmm)
REVERT: F 216 GLU cc_start: 0.7202 (tm-30) cc_final: 0.6851 (tm-30)
REVERT: F 429 GLN cc_start: 0.6821 (tp-100) cc_final: 0.6548 (tp-100)
REVERT: G 65 GLN cc_start: 0.7020 (pt0) cc_final: 0.6710 (pt0)
REVERT: G 149 LYS cc_start: 0.8135 (mmtt) cc_final: 0.7822 (mtmt)
REVERT: G 208 MET cc_start: 0.8935 (mmm) cc_final: 0.8726 (mmm)
REVERT: G 216 GLU cc_start: 0.7265 (tm-30) cc_final: 0.6933 (tm-30)
REVERT: G 429 GLN cc_start: 0.6902 (tp-100) cc_final: 0.6645 (tp-100)
REVERT: H 208 MET cc_start: 0.8932 (mmm) cc_final: 0.8729 (mmm)
REVERT: H 216 GLU cc_start: 0.7235 (tm-30) cc_final: 0.6932 (tm-30)
REVERT: H 429 GLN cc_start: 0.6883 (tp-100) cc_final: 0.6615 (tp-100)
outliers start: 8
outliers final: 8
residues processed: 441
average time/residue: 2.0874
time to fit residues: 1027.9557
Evaluate side-chains
411 residues out of total 2832 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 8
poor density : 403
time to evaluate : 3.150
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 311 HIS
Chi-restraints excluded: chain B residue 311 HIS
Chi-restraints excluded: chain C residue 311 HIS
Chi-restraints excluded: chain D residue 311 HIS
Chi-restraints excluded: chain E residue 311 HIS
Chi-restraints excluded: chain F residue 311 HIS
Chi-restraints excluded: chain G residue 311 HIS
Chi-restraints excluded: chain H residue 311 HIS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 352
random chunks:
chunk 297 optimal weight: 0.9980
chunk 266 optimal weight: 5.9990
chunk 148 optimal weight: 0.9990
chunk 91 optimal weight: 0.0000
chunk 179 optimal weight: 0.0980
chunk 142 optimal weight: 4.9990
chunk 275 optimal weight: 0.8980
chunk 106 optimal weight: 4.9990
chunk 167 optimal weight: 0.0770
chunk 205 optimal weight: 2.9990
chunk 319 optimal weight: 6.9990
overall best weight: 0.4142
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 345 GLN
B 345 GLN
C 345 GLN
D 109 ASN
D 345 GLN
E 345 GLN
F 345 GLN
G 345 GLN
Total number of N/Q/H flips: 8
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8138
moved from start: 0.1104
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.002 0.027 29096 Z= 0.161
Angle : 0.505 5.060 39472 Z= 0.266
Chirality : 0.039 0.134 4152
Planarity : 0.004 0.024 5168
Dihedral : 9.278 179.887 4144
Min Nonbonded Distance : 1.928
Molprobity Statistics.
All-atom Clashscore : 3.02
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 3.13 %
Favored : 96.87 %
Rotamer:
Outliers : 1.69 %
Allowed : 11.72 %
Favored : 86.58 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 4.17 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 1.98 (0.15), residues: 3544
helix: 1.77 (0.13), residues: 1632
sheet: 0.76 (0.24), residues: 464
loop : 1.18 (0.18), residues: 1448
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.009 0.001 TRP D 63
HIS 0.004 0.001 HIS F 393
PHE 0.013 0.002 PHE G 297
TYR 0.020 0.001 TYR D 263
ARG 0.004 0.000 ARG B 442
*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
7088 Ramachandran restraints generated.
3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
7088 Ramachandran restraints generated.
3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
471 residues out of total 2832 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 48
poor density : 423
time to evaluate : 3.798
Fit side-chains
REVERT: A 208 MET cc_start: 0.8984 (mmm) cc_final: 0.8766 (mmm)
REVERT: A 216 GLU cc_start: 0.7266 (tm-30) cc_final: 0.6977 (tm-30)
REVERT: A 276 MET cc_start: 0.9090 (mtm) cc_final: 0.8854 (mtm)
REVERT: A 277 ILE cc_start: 0.8449 (mt) cc_final: 0.7952 (mt)
REVERT: A 429 GLN cc_start: 0.6848 (tp-100) cc_final: 0.6538 (tp-100)
REVERT: B 149 LYS cc_start: 0.8258 (mttt) cc_final: 0.7863 (mtmt)
REVERT: B 208 MET cc_start: 0.9005 (mmm) cc_final: 0.8700 (mmm)
REVERT: B 216 GLU cc_start: 0.7274 (tm-30) cc_final: 0.6948 (tm-30)
REVERT: B 429 GLN cc_start: 0.6971 (tp-100) cc_final: 0.6529 (tp-100)
REVERT: C 149 LYS cc_start: 0.8190 (mttp) cc_final: 0.7809 (mtmt)
REVERT: C 208 MET cc_start: 0.8961 (mmm) cc_final: 0.8517 (mmp)
REVERT: C 216 GLU cc_start: 0.7176 (tm-30) cc_final: 0.6855 (tm-30)
REVERT: C 429 GLN cc_start: 0.6874 (tp-100) cc_final: 0.6564 (tp-100)
REVERT: D 65 GLN cc_start: 0.7002 (pt0) cc_final: 0.6629 (pt0)
REVERT: D 149 LYS cc_start: 0.8015 (mmtt) cc_final: 0.7634 (mtmt)
REVERT: D 208 MET cc_start: 0.8960 (mmm) cc_final: 0.8544 (mmp)
REVERT: D 216 GLU cc_start: 0.7317 (tm-30) cc_final: 0.6975 (tm-30)
REVERT: D 276 MET cc_start: 0.9028 (mtm) cc_final: 0.8797 (mtm)
REVERT: E 208 MET cc_start: 0.8972 (mmm) cc_final: 0.8665 (mmm)
REVERT: E 216 GLU cc_start: 0.7237 (tm-30) cc_final: 0.6918 (tm-30)
REVERT: E 429 GLN cc_start: 0.6937 (tp-100) cc_final: 0.6505 (tp-100)
REVERT: F 208 MET cc_start: 0.9012 (mmm) cc_final: 0.8702 (mmm)
REVERT: F 216 GLU cc_start: 0.7276 (tm-30) cc_final: 0.6917 (tm-30)
REVERT: F 276 MET cc_start: 0.9068 (mtm) cc_final: 0.8812 (mtm)
REVERT: F 429 GLN cc_start: 0.6863 (tp-100) cc_final: 0.6576 (tp-100)
REVERT: G 65 GLN cc_start: 0.6915 (pt0) cc_final: 0.6594 (pt0)
REVERT: G 149 LYS cc_start: 0.8025 (mmtt) cc_final: 0.7705 (mtmt)
REVERT: G 208 MET cc_start: 0.8995 (mmm) cc_final: 0.8692 (mmm)
REVERT: G 216 GLU cc_start: 0.7271 (tm-30) cc_final: 0.6952 (tm-30)
REVERT: G 276 MET cc_start: 0.9063 (mtm) cc_final: 0.8817 (mtm)
REVERT: G 429 GLN cc_start: 0.6886 (tp-100) cc_final: 0.6507 (tp-100)
REVERT: H 149 LYS cc_start: 0.8251 (mttt) cc_final: 0.7831 (mtmt)
REVERT: H 208 MET cc_start: 0.8993 (mmm) cc_final: 0.8698 (mmm)
REVERT: H 216 GLU cc_start: 0.7294 (tm-30) cc_final: 0.6990 (tm-30)
REVERT: H 429 GLN cc_start: 0.6888 (tp-100) cc_final: 0.6502 (tp-100)
outliers start: 48
outliers final: 8
residues processed: 439
average time/residue: 2.0046
time to fit residues: 987.6263
Evaluate side-chains
407 residues out of total 2832 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 8
poor density : 399
time to evaluate : 3.306
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 311 HIS
Chi-restraints excluded: chain B residue 311 HIS
Chi-restraints excluded: chain C residue 311 HIS
Chi-restraints excluded: chain D residue 311 HIS
Chi-restraints excluded: chain E residue 311 HIS
Chi-restraints excluded: chain F residue 311 HIS
Chi-restraints excluded: chain G residue 311 HIS
Chi-restraints excluded: chain H residue 311 HIS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 352
random chunks:
chunk 177 optimal weight: 0.2980
chunk 99 optimal weight: 9.9990
chunk 266 optimal weight: 6.9990
chunk 217 optimal weight: 0.9980
chunk 88 optimal weight: 10.0000
chunk 320 optimal weight: 0.3980
chunk 345 optimal weight: 7.9990
chunk 285 optimal weight: 0.0870
chunk 317 optimal weight: 5.9990
chunk 109 optimal weight: 1.9990
chunk 256 optimal weight: 0.0050
overall best weight: 0.3572
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 345 GLN
C 345 GLN
D 345 GLN
** G 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 345 GLN
Total number of N/Q/H flips: 4
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8126
moved from start: 0.1369
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.002 0.020 29096 Z= 0.139
Angle : 0.481 4.850 39472 Z= 0.252
Chirality : 0.039 0.130 4152
Planarity : 0.003 0.025 5168
Dihedral : 8.847 172.874 4144
Min Nonbonded Distance : 1.936
Molprobity Statistics.
All-atom Clashscore : 3.48
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 2.68 %
Favored : 97.32 %
Rotamer:
Outliers : 1.55 %
Allowed : 12.82 %
Favored : 85.63 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 4.17 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 1.81 (0.14), residues: 3544
helix: 1.70 (0.13), residues: 1632
sheet: 0.97 (0.26), residues: 368
loop : 0.90 (0.17), residues: 1544
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.009 0.001 TRP F 354
HIS 0.003 0.001 HIS E 311
PHE 0.012 0.001 PHE G 297
TYR 0.019 0.001 TYR A 263
ARG 0.005 0.000 ARG G 442
*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
7088 Ramachandran restraints generated.
3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
7088 Ramachandran restraints generated.
3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
455 residues out of total 2832 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 44
poor density : 411
time to evaluate : 3.277
Fit side-chains
REVERT: A 216 GLU cc_start: 0.7302 (tm-30) cc_final: 0.6939 (tm-30)
REVERT: A 217 GLU cc_start: 0.7160 (mt-10) cc_final: 0.6959 (mt-10)
REVERT: A 276 MET cc_start: 0.9104 (mtm) cc_final: 0.8874 (mtm)
REVERT: A 277 ILE cc_start: 0.8327 (mt) cc_final: 0.7751 (mt)
REVERT: A 429 GLN cc_start: 0.6900 (tp-100) cc_final: 0.6567 (tp-100)
REVERT: B 149 LYS cc_start: 0.8257 (mttt) cc_final: 0.7861 (mtmt)
REVERT: B 216 GLU cc_start: 0.7247 (tm-30) cc_final: 0.6880 (tm-30)
REVERT: B 429 GLN cc_start: 0.7003 (tp-100) cc_final: 0.6580 (tp-100)
REVERT: C 208 MET cc_start: 0.8975 (mmm) cc_final: 0.8551 (mmp)
REVERT: C 216 GLU cc_start: 0.7262 (tm-30) cc_final: 0.6909 (tm-30)
REVERT: C 422 ASP cc_start: 0.7876 (t0) cc_final: 0.7539 (t70)
REVERT: C 429 GLN cc_start: 0.6952 (tp-100) cc_final: 0.6595 (tp-100)
REVERT: D 208 MET cc_start: 0.8957 (mmm) cc_final: 0.8508 (mmp)
REVERT: D 216 GLU cc_start: 0.7319 (tm-30) cc_final: 0.6967 (tm-30)
REVERT: D 217 GLU cc_start: 0.7209 (mt-10) cc_final: 0.6990 (mt-10)
REVERT: D 276 MET cc_start: 0.9080 (mtm) cc_final: 0.8830 (mtm)
REVERT: D 422 ASP cc_start: 0.7873 (t0) cc_final: 0.7553 (t70)
REVERT: D 429 GLN cc_start: 0.6901 (tp-100) cc_final: 0.6235 (tp40)
REVERT: E 216 GLU cc_start: 0.7302 (tm-30) cc_final: 0.6960 (tm-30)
REVERT: E 429 GLN cc_start: 0.6986 (tp-100) cc_final: 0.6568 (tp-100)
REVERT: F 216 GLU cc_start: 0.7309 (tm-30) cc_final: 0.6920 (tm-30)
REVERT: F 276 MET cc_start: 0.9113 (mtm) cc_final: 0.8874 (mtm)
REVERT: F 277 ILE cc_start: 0.8343 (mt) cc_final: 0.7776 (mt)
REVERT: F 429 GLN cc_start: 0.6913 (tp-100) cc_final: 0.6605 (tp-100)
REVERT: G 65 GLN cc_start: 0.7005 (pt0) cc_final: 0.6709 (pt0)
REVERT: G 216 GLU cc_start: 0.7292 (tm-30) cc_final: 0.6940 (tm-30)
REVERT: G 276 MET cc_start: 0.9109 (mtm) cc_final: 0.8852 (mtm)
REVERT: G 429 GLN cc_start: 0.6911 (tp-100) cc_final: 0.6507 (tp-100)
REVERT: H 149 LYS cc_start: 0.8252 (mttt) cc_final: 0.7856 (mtmt)
REVERT: H 216 GLU cc_start: 0.7263 (tm-30) cc_final: 0.6899 (tm-30)
REVERT: H 429 GLN cc_start: 0.6954 (tp-100) cc_final: 0.6541 (tp-100)
outliers start: 44
outliers final: 17
residues processed: 427
average time/residue: 2.0780
time to fit residues: 992.7373
Evaluate side-chains
419 residues out of total 2832 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 17
poor density : 402
time to evaluate : 3.310
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 64 SER
Chi-restraints excluded: chain A residue 311 HIS
Chi-restraints excluded: chain B residue 64 SER
Chi-restraints excluded: chain B residue 311 HIS
Chi-restraints excluded: chain C residue 64 SER
Chi-restraints excluded: chain C residue 311 HIS
Chi-restraints excluded: chain D residue 64 SER
Chi-restraints excluded: chain D residue 311 HIS
Chi-restraints excluded: chain E residue 64 SER
Chi-restraints excluded: chain E residue 311 HIS
Chi-restraints excluded: chain F residue 64 SER
Chi-restraints excluded: chain F residue 202 ASP
Chi-restraints excluded: chain F residue 311 HIS
Chi-restraints excluded: chain G residue 64 SER
Chi-restraints excluded: chain G residue 311 HIS
Chi-restraints excluded: chain H residue 64 SER
Chi-restraints excluded: chain H residue 311 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 352
random chunks:
chunk 316 optimal weight: 2.9990
chunk 240 optimal weight: 9.9990
chunk 166 optimal weight: 9.9990
chunk 35 optimal weight: 4.9990
chunk 152 optimal weight: 3.9990
chunk 215 optimal weight: 4.9990
chunk 321 optimal weight: 0.0010
chunk 340 optimal weight: 2.9990
chunk 167 optimal weight: 4.9990
chunk 304 optimal weight: 6.9990
chunk 91 optimal weight: 0.5980
overall best weight: 2.1192
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 193 ASN
** A 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 429 GLN
B 193 ASN
** B 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 429 GLN
C 193 ASN
** C 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 429 GLN
D 193 ASN
** D 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 429 GLN
E 193 ASN
** E 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 429 GLN
F 193 ASN
** F 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 429 GLN
G 193 ASN
** G 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 429 GLN
H 193 ASN
** H 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 429 GLN
Total number of N/Q/H flips: 16
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8259
moved from start: 0.1718
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.005 0.034 29096 Z= 0.301
Angle : 0.630 7.468 39472 Z= 0.331
Chirality : 0.044 0.144 4152
Planarity : 0.005 0.026 5168
Dihedral : 9.313 170.452 4144
Min Nonbonded Distance : 1.834
Molprobity Statistics.
All-atom Clashscore : 4.07
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 3.98 %
Favored : 96.02 %
Rotamer:
Outliers : 1.41 %
Allowed : 12.75 %
Favored : 85.84 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 4.17 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 1.51 (0.14), residues: 3544
helix: 1.42 (0.13), residues: 1576
sheet: 0.78 (0.22), residues: 472
loop : 0.81 (0.17), residues: 1496
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.015 0.002 TRP C 354
HIS 0.004 0.001 HIS B 296
PHE 0.023 0.003 PHE G 297
TYR 0.032 0.002 TYR B 263
ARG 0.003 0.001 ARG F 120
*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
7088 Ramachandran restraints generated.
3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
7088 Ramachandran restraints generated.
3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
460 residues out of total 2832 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 40
poor density : 420
time to evaluate : 3.370
Fit side-chains
REVERT: A 65 GLN cc_start: 0.7059 (pt0) cc_final: 0.6793 (pt0)
REVERT: A 216 GLU cc_start: 0.7311 (tm-30) cc_final: 0.7013 (tm-30)
REVERT: A 429 GLN cc_start: 0.7191 (tp40) cc_final: 0.6861 (tp-100)
REVERT: B 65 GLN cc_start: 0.7058 (pt0) cc_final: 0.6640 (pt0)
REVERT: B 216 GLU cc_start: 0.7187 (tm-30) cc_final: 0.6867 (tm-30)
REVERT: B 429 GLN cc_start: 0.7134 (tp40) cc_final: 0.6803 (tp-100)
REVERT: C 65 GLN cc_start: 0.7079 (pt0) cc_final: 0.6793 (pt0)
REVERT: C 216 GLU cc_start: 0.7172 (tm-30) cc_final: 0.6855 (tm-30)
REVERT: C 422 ASP cc_start: 0.7923 (t0) cc_final: 0.7617 (t70)
REVERT: C 429 GLN cc_start: 0.7128 (tp40) cc_final: 0.6822 (tp-100)
REVERT: D 65 GLN cc_start: 0.7073 (pt0) cc_final: 0.6770 (pt0)
REVERT: D 216 GLU cc_start: 0.7225 (tm-30) cc_final: 0.6932 (tm-30)
REVERT: D 422 ASP cc_start: 0.7933 (t0) cc_final: 0.7644 (t70)
REVERT: D 429 GLN cc_start: 0.7204 (tp40) cc_final: 0.6669 (tp-100)
REVERT: E 65 GLN cc_start: 0.7059 (pt0) cc_final: 0.6640 (pt0)
REVERT: E 216 GLU cc_start: 0.7197 (tm-30) cc_final: 0.6903 (tm-30)
REVERT: E 429 GLN cc_start: 0.7134 (tp40) cc_final: 0.6796 (tp-100)
REVERT: F 65 GLN cc_start: 0.7197 (pt0) cc_final: 0.6728 (pt0)
REVERT: F 216 GLU cc_start: 0.7178 (tm-30) cc_final: 0.6890 (tm-30)
REVERT: F 429 GLN cc_start: 0.7109 (tp40) cc_final: 0.6790 (tp-100)
REVERT: G 65 GLN cc_start: 0.7082 (pt0) cc_final: 0.6781 (pt0)
REVERT: G 216 GLU cc_start: 0.7200 (tm-30) cc_final: 0.6904 (tm-30)
REVERT: G 429 GLN cc_start: 0.7196 (tp40) cc_final: 0.6868 (tp-100)
REVERT: H 65 GLN cc_start: 0.7080 (pt0) cc_final: 0.6797 (pt0)
REVERT: H 216 GLU cc_start: 0.7199 (tm-30) cc_final: 0.6903 (tm-30)
REVERT: H 429 GLN cc_start: 0.7125 (tp40) cc_final: 0.6806 (tp-100)
outliers start: 40
outliers final: 25
residues processed: 449
average time/residue: 2.1828
time to fit residues: 1091.0298
Evaluate side-chains
431 residues out of total 2832 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 25
poor density : 406
time to evaluate : 3.351
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 180 VAL
Chi-restraints excluded: chain A residue 286 VAL
Chi-restraints excluded: chain A residue 311 HIS
Chi-restraints excluded: chain B residue 180 VAL
Chi-restraints excluded: chain B residue 286 VAL
Chi-restraints excluded: chain B residue 311 HIS
Chi-restraints excluded: chain C residue 180 VAL
Chi-restraints excluded: chain C residue 286 VAL
Chi-restraints excluded: chain C residue 311 HIS
Chi-restraints excluded: chain D residue 180 VAL
Chi-restraints excluded: chain D residue 311 HIS
Chi-restraints excluded: chain E residue 26 GLU
Chi-restraints excluded: chain E residue 180 VAL
Chi-restraints excluded: chain E residue 286 VAL
Chi-restraints excluded: chain E residue 311 HIS
Chi-restraints excluded: chain F residue 180 VAL
Chi-restraints excluded: chain F residue 286 VAL
Chi-restraints excluded: chain F residue 311 HIS
Chi-restraints excluded: chain G residue 180 VAL
Chi-restraints excluded: chain G residue 286 VAL
Chi-restraints excluded: chain G residue 311 HIS
Chi-restraints excluded: chain H residue 26 GLU
Chi-restraints excluded: chain H residue 180 VAL
Chi-restraints excluded: chain H residue 286 VAL
Chi-restraints excluded: chain H residue 311 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 352
random chunks:
chunk 283 optimal weight: 1.9990
chunk 193 optimal weight: 2.9990
chunk 4 optimal weight: 0.8980
chunk 253 optimal weight: 4.9990
chunk 140 optimal weight: 2.9990
chunk 290 optimal weight: 10.0000
chunk 235 optimal weight: 0.8980
chunk 0 optimal weight: 5.9990
chunk 173 optimal weight: 3.9990
chunk 305 optimal weight: 3.9990
chunk 85 optimal weight: 3.9990
overall best weight: 1.9586
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** A 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Total number of N/Q/H flips: 0
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8256
moved from start: 0.1809
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.004 0.031 29096 Z= 0.278
Angle : 0.606 7.146 39472 Z= 0.320
Chirality : 0.043 0.138 4152
Planarity : 0.004 0.026 5168
Dihedral : 9.449 169.761 4144
Min Nonbonded Distance : 1.832
Molprobity Statistics.
All-atom Clashscore : 4.46
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 3.58 %
Favored : 96.42 %
Rotamer:
Outliers : 2.08 %
Allowed : 12.18 %
Favored : 85.73 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 4.17 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 1.34 (0.14), residues: 3544
helix: 1.25 (0.12), residues: 1576
sheet: 0.51 (0.22), residues: 488
loop : 0.85 (0.17), residues: 1480
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.017 0.002 TRP G 354
HIS 0.004 0.001 HIS E 311
PHE 0.021 0.002 PHE F 297
TYR 0.030 0.002 TYR A 263
ARG 0.005 0.001 ARG D 442
*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
7088 Ramachandran restraints generated.
3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
7088 Ramachandran restraints generated.
3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
482 residues out of total 2832 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 59
poor density : 423
time to evaluate : 3.634
Fit side-chains
REVERT: A 65 GLN cc_start: 0.7099 (pt0) cc_final: 0.6883 (pt0)
REVERT: A 173 ARG cc_start: 0.8298 (OUTLIER) cc_final: 0.7515 (ttt-90)
REVERT: A 216 GLU cc_start: 0.7195 (tm-30) cc_final: 0.6867 (tm-30)
REVERT: A 252 MET cc_start: 0.9409 (OUTLIER) cc_final: 0.8812 (ptm)
REVERT: A 429 GLN cc_start: 0.7226 (tp40) cc_final: 0.6941 (tp-100)
REVERT: B 65 GLN cc_start: 0.7104 (pt0) cc_final: 0.6893 (pt0)
REVERT: B 117 ARG cc_start: 0.7958 (OUTLIER) cc_final: 0.7569 (ttp-170)
REVERT: B 216 GLU cc_start: 0.7170 (tm-30) cc_final: 0.6815 (tm-30)
REVERT: B 252 MET cc_start: 0.9406 (OUTLIER) cc_final: 0.8823 (ptm)
REVERT: B 429 GLN cc_start: 0.7262 (tp40) cc_final: 0.6959 (tp-100)
REVERT: C 65 GLN cc_start: 0.7104 (pt0) cc_final: 0.6895 (pt0)
REVERT: C 216 GLU cc_start: 0.7170 (tm-30) cc_final: 0.6824 (tm-30)
REVERT: C 252 MET cc_start: 0.9406 (OUTLIER) cc_final: 0.8821 (ptm)
REVERT: C 422 ASP cc_start: 0.7920 (t0) cc_final: 0.7633 (t70)
REVERT: C 429 GLN cc_start: 0.7215 (tp40) cc_final: 0.6894 (tp-100)
REVERT: D 65 GLN cc_start: 0.7099 (pt0) cc_final: 0.6881 (pt0)
REVERT: D 173 ARG cc_start: 0.8284 (OUTLIER) cc_final: 0.7507 (ttt-90)
REVERT: D 216 GLU cc_start: 0.7204 (tm-30) cc_final: 0.6871 (tm-30)
REVERT: D 252 MET cc_start: 0.9405 (OUTLIER) cc_final: 0.8815 (ptm)
REVERT: D 429 GLN cc_start: 0.7283 (tp40) cc_final: 0.6902 (mm-40)
REVERT: E 65 GLN cc_start: 0.7097 (pt0) cc_final: 0.6885 (pt0)
REVERT: E 173 ARG cc_start: 0.8311 (OUTLIER) cc_final: 0.7532 (ttt-90)
REVERT: E 216 GLU cc_start: 0.7166 (tm-30) cc_final: 0.6843 (tm-30)
REVERT: E 252 MET cc_start: 0.9411 (OUTLIER) cc_final: 0.8817 (ptm)
REVERT: E 429 GLN cc_start: 0.7263 (tp40) cc_final: 0.6954 (tp-100)
REVERT: F 65 GLN cc_start: 0.7237 (pt0) cc_final: 0.6998 (pt0)
REVERT: F 173 ARG cc_start: 0.8302 (OUTLIER) cc_final: 0.7513 (ttt-90)
REVERT: F 216 GLU cc_start: 0.7163 (tm-30) cc_final: 0.6839 (tm-30)
REVERT: F 252 MET cc_start: 0.9405 (OUTLIER) cc_final: 0.8824 (ptm)
REVERT: F 429 GLN cc_start: 0.7231 (tp40) cc_final: 0.6942 (tp-100)
REVERT: G 216 GLU cc_start: 0.7162 (tm-30) cc_final: 0.6842 (tm-30)
REVERT: G 252 MET cc_start: 0.9405 (OUTLIER) cc_final: 0.8824 (ptm)
REVERT: G 429 GLN cc_start: 0.7240 (tp40) cc_final: 0.6953 (tp-100)
REVERT: H 65 GLN cc_start: 0.7103 (pt0) cc_final: 0.6721 (pt0)
REVERT: H 216 GLU cc_start: 0.7183 (tm-30) cc_final: 0.6827 (tm-30)
REVERT: H 429 GLN cc_start: 0.7252 (tp40) cc_final: 0.6941 (tp-100)
outliers start: 59
outliers final: 32
residues processed: 461
average time/residue: 2.1473
time to fit residues: 1105.0271
Evaluate side-chains
457 residues out of total 2832 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 44
poor density : 413
time to evaluate : 3.212
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 26 GLU
Chi-restraints excluded: chain A residue 173 ARG
Chi-restraints excluded: chain A residue 180 VAL
Chi-restraints excluded: chain A residue 252 MET
Chi-restraints excluded: chain A residue 286 VAL
Chi-restraints excluded: chain A residue 311 HIS
Chi-restraints excluded: chain B residue 26 GLU
Chi-restraints excluded: chain B residue 117 ARG
Chi-restraints excluded: chain B residue 180 VAL
Chi-restraints excluded: chain B residue 252 MET
Chi-restraints excluded: chain B residue 286 VAL
Chi-restraints excluded: chain B residue 311 HIS
Chi-restraints excluded: chain C residue 26 GLU
Chi-restraints excluded: chain C residue 180 VAL
Chi-restraints excluded: chain C residue 252 MET
Chi-restraints excluded: chain C residue 286 VAL
Chi-restraints excluded: chain C residue 311 HIS
Chi-restraints excluded: chain D residue 26 GLU
Chi-restraints excluded: chain D residue 173 ARG
Chi-restraints excluded: chain D residue 180 VAL
Chi-restraints excluded: chain D residue 252 MET
Chi-restraints excluded: chain D residue 286 VAL
Chi-restraints excluded: chain D residue 311 HIS
Chi-restraints excluded: chain E residue 26 GLU
Chi-restraints excluded: chain E residue 173 ARG
Chi-restraints excluded: chain E residue 180 VAL
Chi-restraints excluded: chain E residue 252 MET
Chi-restraints excluded: chain E residue 286 VAL
Chi-restraints excluded: chain E residue 311 HIS
Chi-restraints excluded: chain F residue 26 GLU
Chi-restraints excluded: chain F residue 173 ARG
Chi-restraints excluded: chain F residue 180 VAL
Chi-restraints excluded: chain F residue 252 MET
Chi-restraints excluded: chain F residue 286 VAL
Chi-restraints excluded: chain F residue 311 HIS
Chi-restraints excluded: chain G residue 26 GLU
Chi-restraints excluded: chain G residue 180 VAL
Chi-restraints excluded: chain G residue 252 MET
Chi-restraints excluded: chain G residue 286 VAL
Chi-restraints excluded: chain G residue 311 HIS
Chi-restraints excluded: chain H residue 26 GLU
Chi-restraints excluded: chain H residue 180 VAL
Chi-restraints excluded: chain H residue 286 VAL
Chi-restraints excluded: chain H residue 311 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 352
random chunks:
chunk 114 optimal weight: 9.9990
chunk 306 optimal weight: 7.9990
chunk 67 optimal weight: 4.9990
chunk 199 optimal weight: 4.9990
chunk 83 optimal weight: 6.9990
chunk 340 optimal weight: 0.8980
chunk 282 optimal weight: 0.6980
chunk 157 optimal weight: 0.8980
chunk 28 optimal weight: 0.9990
chunk 112 optimal weight: 0.7980
chunk 178 optimal weight: 0.6980
overall best weight: 0.7980
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** A 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 65 GLN
** G 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Total number of N/Q/H flips: 1
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8215
moved from start: 0.1786
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.023 29096 Z= 0.178
Angle : 0.536 5.822 39472 Z= 0.282
Chirality : 0.040 0.129 4152
Planarity : 0.004 0.026 5168
Dihedral : 9.160 169.121 4144
Min Nonbonded Distance : 1.894
Molprobity Statistics.
All-atom Clashscore : 4.57
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 3.30 %
Favored : 96.70 %
Rotamer:
Outliers : 1.84 %
Allowed : 12.92 %
Favored : 85.24 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 4.17 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 1.53 (0.14), residues: 3544
helix: 1.28 (0.13), residues: 1632
sheet: 0.66 (0.23), residues: 472
loop : 1.06 (0.18), residues: 1440
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.014 0.001 TRP A 354
HIS 0.003 0.001 HIS C 224
PHE 0.015 0.002 PHE C 297
TYR 0.024 0.001 TYR A 263
ARG 0.006 0.000 ARG E 442
*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
7088 Ramachandran restraints generated.
3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
7088 Ramachandran restraints generated.
3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
471 residues out of total 2832 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 52
poor density : 419
time to evaluate : 3.421
Fit side-chains
REVERT: A 65 GLN cc_start: 0.7207 (pt0) cc_final: 0.6862 (pt0)
REVERT: A 173 ARG cc_start: 0.8267 (OUTLIER) cc_final: 0.7386 (ttt-90)
REVERT: A 216 GLU cc_start: 0.7172 (tm-30) cc_final: 0.6800 (tm-30)
REVERT: A 252 MET cc_start: 0.9383 (OUTLIER) cc_final: 0.8776 (ptm)
REVERT: A 429 GLN cc_start: 0.7100 (tp40) cc_final: 0.6778 (tp-100)
REVERT: B 65 GLN cc_start: 0.7207 (pt0) cc_final: 0.6868 (pt0)
REVERT: B 117 ARG cc_start: 0.7943 (OUTLIER) cc_final: 0.7531 (ttp-170)
REVERT: B 216 GLU cc_start: 0.7123 (tm-30) cc_final: 0.6764 (tm-30)
REVERT: B 252 MET cc_start: 0.9374 (OUTLIER) cc_final: 0.8786 (ptm)
REVERT: B 429 GLN cc_start: 0.7164 (tp40) cc_final: 0.6858 (tp-100)
REVERT: C 65 GLN cc_start: 0.7215 (pt0) cc_final: 0.6963 (pt0)
REVERT: C 216 GLU cc_start: 0.7120 (tm-30) cc_final: 0.6763 (tm-30)
REVERT: C 252 MET cc_start: 0.9372 (OUTLIER) cc_final: 0.8784 (ptm)
REVERT: C 422 ASP cc_start: 0.7895 (t0) cc_final: 0.7598 (t70)
REVERT: C 429 GLN cc_start: 0.7152 (tp40) cc_final: 0.6824 (tp-100)
REVERT: D 65 GLN cc_start: 0.7077 (pt0) cc_final: 0.6764 (pt0)
REVERT: D 173 ARG cc_start: 0.8265 (OUTLIER) cc_final: 0.7392 (ttt-90)
REVERT: D 216 GLU cc_start: 0.7184 (tm-30) cc_final: 0.6845 (tm-30)
REVERT: D 252 MET cc_start: 0.9376 (OUTLIER) cc_final: 0.8771 (ptm)
REVERT: D 429 GLN cc_start: 0.7181 (tp40) cc_final: 0.6581 (tp40)
REVERT: E 65 GLN cc_start: 0.7205 (pt0) cc_final: 0.6865 (pt0)
REVERT: E 173 ARG cc_start: 0.8265 (OUTLIER) cc_final: 0.7386 (ttt-90)
REVERT: E 216 GLU cc_start: 0.7141 (tm-30) cc_final: 0.6783 (tm-30)
REVERT: E 252 MET cc_start: 0.9387 (OUTLIER) cc_final: 0.8716 (ptm)
REVERT: E 429 GLN cc_start: 0.7098 (tp40) cc_final: 0.6793 (tp-100)
REVERT: F 65 GLN cc_start: 0.7210 (pt0) cc_final: 0.6872 (pt0)
REVERT: F 173 ARG cc_start: 0.8274 (OUTLIER) cc_final: 0.7398 (ttt-90)
REVERT: F 216 GLU cc_start: 0.7138 (tm-30) cc_final: 0.6776 (tm-30)
REVERT: F 252 MET cc_start: 0.9372 (OUTLIER) cc_final: 0.8789 (ptm)
REVERT: F 429 GLN cc_start: 0.7093 (tp40) cc_final: 0.6799 (tp-100)
REVERT: G 65 GLN cc_start: 0.6965 (pt0) cc_final: 0.6660 (pt0)
REVERT: G 216 GLU cc_start: 0.7138 (tm-30) cc_final: 0.6781 (tm-30)
REVERT: G 252 MET cc_start: 0.9374 (OUTLIER) cc_final: 0.8787 (ptm)
REVERT: G 429 GLN cc_start: 0.7090 (tp40) cc_final: 0.6791 (tp-100)
REVERT: H 65 GLN cc_start: 0.7210 (pt0) cc_final: 0.6870 (pt0)
REVERT: H 216 GLU cc_start: 0.7138 (tm-30) cc_final: 0.6780 (tm-30)
REVERT: H 252 MET cc_start: 0.9363 (OUTLIER) cc_final: 0.8663 (ptm)
REVERT: H 429 GLN cc_start: 0.7099 (tp40) cc_final: 0.6802 (tp-100)
outliers start: 52
outliers final: 17
residues processed: 449
average time/residue: 2.1687
time to fit residues: 1085.3593
Evaluate side-chains
445 residues out of total 2832 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 30
poor density : 415
time to evaluate : 3.322
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 173 ARG
Chi-restraints excluded: chain A residue 252 MET
Chi-restraints excluded: chain A residue 286 VAL
Chi-restraints excluded: chain A residue 311 HIS
Chi-restraints excluded: chain B residue 117 ARG
Chi-restraints excluded: chain B residue 252 MET
Chi-restraints excluded: chain B residue 286 VAL
Chi-restraints excluded: chain B residue 311 HIS
Chi-restraints excluded: chain C residue 26 GLU
Chi-restraints excluded: chain C residue 252 MET
Chi-restraints excluded: chain C residue 286 VAL
Chi-restraints excluded: chain C residue 311 HIS
Chi-restraints excluded: chain D residue 173 ARG
Chi-restraints excluded: chain D residue 252 MET
Chi-restraints excluded: chain D residue 286 VAL
Chi-restraints excluded: chain D residue 311 HIS
Chi-restraints excluded: chain E residue 173 ARG
Chi-restraints excluded: chain E residue 252 MET
Chi-restraints excluded: chain E residue 286 VAL
Chi-restraints excluded: chain E residue 311 HIS
Chi-restraints excluded: chain F residue 173 ARG
Chi-restraints excluded: chain F residue 252 MET
Chi-restraints excluded: chain F residue 286 VAL
Chi-restraints excluded: chain F residue 311 HIS
Chi-restraints excluded: chain G residue 252 MET
Chi-restraints excluded: chain G residue 286 VAL
Chi-restraints excluded: chain G residue 311 HIS
Chi-restraints excluded: chain H residue 252 MET
Chi-restraints excluded: chain H residue 286 VAL
Chi-restraints excluded: chain H residue 311 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 352
random chunks:
chunk 328 optimal weight: 2.9990
chunk 38 optimal weight: 10.0000
chunk 194 optimal weight: 0.6980
chunk 248 optimal weight: 4.9990
chunk 192 optimal weight: 9.9990
chunk 286 optimal weight: 9.9990
chunk 190 optimal weight: 1.9990
chunk 339 optimal weight: 7.9990
chunk 212 optimal weight: 2.9990
chunk 206 optimal weight: 20.0000
chunk 156 optimal weight: 1.9990
overall best weight: 2.1388
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** A 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Total number of N/Q/H flips: 0
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8262
moved from start: 0.1888
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.005 0.033 29096 Z= 0.300
Angle : 0.627 7.318 39472 Z= 0.329
Chirality : 0.043 0.145 4152
Planarity : 0.004 0.028 5168
Dihedral : 9.558 169.419 4144
Min Nonbonded Distance : 1.850
Molprobity Statistics.
All-atom Clashscore : 4.85
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 4.06 %
Favored : 95.94 %
Rotamer:
Outliers : 1.73 %
Allowed : 13.88 %
Favored : 84.39 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 4.17 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 1.35 (0.14), residues: 3544
helix: 1.26 (0.13), residues: 1576
sheet: 0.37 (0.22), residues: 488
loop : 0.91 (0.18), residues: 1480
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.016 0.002 TRP G 354
HIS 0.004 0.001 HIS B 224
PHE 0.022 0.003 PHE G 297
TYR 0.032 0.002 TYR A 263
ARG 0.007 0.001 ARG A 442
*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
7088 Ramachandran restraints generated.
3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
7088 Ramachandran restraints generated.
3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
467 residues out of total 2832 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 49
poor density : 418
time to evaluate : 3.290
Fit side-chains
REVERT: A 65 GLN cc_start: 0.7094 (pt0) cc_final: 0.6858 (pt0)
REVERT: A 173 ARG cc_start: 0.8287 (OUTLIER) cc_final: 0.7397 (ttt-90)
REVERT: A 216 GLU cc_start: 0.7155 (tm-30) cc_final: 0.6795 (tm-30)
REVERT: A 252 MET cc_start: 0.9423 (OUTLIER) cc_final: 0.8748 (ptm)
REVERT: B 65 GLN cc_start: 0.7231 (pt0) cc_final: 0.6970 (pt0)
REVERT: B 216 GLU cc_start: 0.7039 (tm-30) cc_final: 0.6676 (tm-30)
REVERT: B 252 MET cc_start: 0.9421 (OUTLIER) cc_final: 0.8753 (ptm)
REVERT: C 65 GLN cc_start: 0.7238 (pt0) cc_final: 0.6981 (pt0)
REVERT: C 216 GLU cc_start: 0.7039 (tm-30) cc_final: 0.6679 (tm-30)
REVERT: C 252 MET cc_start: 0.9421 (OUTLIER) cc_final: 0.8752 (ptm)
REVERT: D 65 GLN cc_start: 0.7118 (pt0) cc_final: 0.6767 (pt0)
REVERT: D 173 ARG cc_start: 0.8284 (OUTLIER) cc_final: 0.7382 (ttt-90)
REVERT: D 216 GLU cc_start: 0.7156 (tm-30) cc_final: 0.6838 (tm-30)
REVERT: D 252 MET cc_start: 0.9419 (OUTLIER) cc_final: 0.8743 (ptm)
REVERT: D 429 GLN cc_start: 0.7309 (tp40) cc_final: 0.6832 (tp-100)
REVERT: E 65 GLN cc_start: 0.7092 (pt0) cc_final: 0.6860 (pt0)
REVERT: E 173 ARG cc_start: 0.8285 (OUTLIER) cc_final: 0.7394 (ttt-90)
REVERT: E 216 GLU cc_start: 0.7153 (tm-30) cc_final: 0.6779 (tm-30)
REVERT: E 252 MET cc_start: 0.9403 (OUTLIER) cc_final: 0.8749 (ptm)
REVERT: F 65 GLN cc_start: 0.7229 (pt0) cc_final: 0.6967 (pt0)
REVERT: F 173 ARG cc_start: 0.8288 (OUTLIER) cc_final: 0.7399 (ttt-90)
REVERT: F 216 GLU cc_start: 0.7145 (tm-30) cc_final: 0.6773 (tm-30)
REVERT: F 252 MET cc_start: 0.9420 (OUTLIER) cc_final: 0.8756 (ptm)
REVERT: G 65 GLN cc_start: 0.7030 (pt0) cc_final: 0.6680 (pt0)
REVERT: G 216 GLU cc_start: 0.7148 (tm-30) cc_final: 0.6775 (tm-30)
REVERT: G 252 MET cc_start: 0.9421 (OUTLIER) cc_final: 0.8753 (ptm)
REVERT: H 65 GLN cc_start: 0.7097 (pt0) cc_final: 0.6868 (pt0)
REVERT: H 216 GLU cc_start: 0.7036 (tm-30) cc_final: 0.6673 (tm-30)
REVERT: H 252 MET cc_start: 0.9398 (OUTLIER) cc_final: 0.8698 (ptm)
outliers start: 49
outliers final: 20
residues processed: 453
average time/residue: 2.2297
time to fit residues: 1124.8071
Evaluate side-chains
447 residues out of total 2832 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 32
poor density : 415
time to evaluate : 3.596
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 173 ARG
Chi-restraints excluded: chain A residue 252 MET
Chi-restraints excluded: chain A residue 286 VAL
Chi-restraints excluded: chain A residue 311 HIS
Chi-restraints excluded: chain B residue 252 MET
Chi-restraints excluded: chain B residue 286 VAL
Chi-restraints excluded: chain B residue 311 HIS
Chi-restraints excluded: chain C residue 26 GLU
Chi-restraints excluded: chain C residue 105 SER
Chi-restraints excluded: chain C residue 252 MET
Chi-restraints excluded: chain C residue 286 VAL
Chi-restraints excluded: chain C residue 311 HIS
Chi-restraints excluded: chain D residue 173 ARG
Chi-restraints excluded: chain D residue 252 MET
Chi-restraints excluded: chain D residue 286 VAL
Chi-restraints excluded: chain D residue 311 HIS
Chi-restraints excluded: chain E residue 105 SER
Chi-restraints excluded: chain E residue 173 ARG
Chi-restraints excluded: chain E residue 252 MET
Chi-restraints excluded: chain E residue 286 VAL
Chi-restraints excluded: chain E residue 311 HIS
Chi-restraints excluded: chain F residue 105 SER
Chi-restraints excluded: chain F residue 173 ARG
Chi-restraints excluded: chain F residue 252 MET
Chi-restraints excluded: chain F residue 286 VAL
Chi-restraints excluded: chain F residue 311 HIS
Chi-restraints excluded: chain G residue 252 MET
Chi-restraints excluded: chain G residue 286 VAL
Chi-restraints excluded: chain G residue 311 HIS
Chi-restraints excluded: chain H residue 252 MET
Chi-restraints excluded: chain H residue 286 VAL
Chi-restraints excluded: chain H residue 311 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 352
random chunks:
chunk 209 optimal weight: 0.9980
chunk 135 optimal weight: 5.9990
chunk 202 optimal weight: 0.9980
chunk 102 optimal weight: 0.8980
chunk 66 optimal weight: 1.9990
chunk 65 optimal weight: 1.9990
chunk 215 optimal weight: 3.9990
chunk 231 optimal weight: 3.9990
chunk 167 optimal weight: 0.9990
chunk 31 optimal weight: 5.9990
chunk 266 optimal weight: 5.9990
overall best weight: 1.1784
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** A 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Total number of N/Q/H flips: 0
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8237
moved from start: 0.1852
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.026 29096 Z= 0.214
Angle : 0.572 6.480 39472 Z= 0.301
Chirality : 0.041 0.130 4152
Planarity : 0.004 0.027 5168
Dihedral : 9.376 169.322 4144
Min Nonbonded Distance : 1.885
Molprobity Statistics.
All-atom Clashscore : 4.57
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 3.53 %
Favored : 96.47 %
Rotamer:
Outliers : 1.59 %
Allowed : 14.19 %
Favored : 84.22 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 4.17 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 1.07 (0.14), residues: 3544
helix: 0.98 (0.12), residues: 1672
sheet: 0.55 (0.23), residues: 472
loop : 0.66 (0.18), residues: 1400
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.016 0.001 TRP A 354
HIS 0.004 0.001 HIS B 224
PHE 0.017 0.002 PHE C 297
TYR 0.027 0.002 TYR A 263
ARG 0.008 0.000 ARG B 442
*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
7088 Ramachandran restraints generated.
3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
7088 Ramachandran restraints generated.
3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
460 residues out of total 2832 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 45
poor density : 415
time to evaluate : 3.524
Fit side-chains
REVERT: A 65 GLN cc_start: 0.7206 (pt0) cc_final: 0.6805 (pt0)
REVERT: A 173 ARG cc_start: 0.8250 (OUTLIER) cc_final: 0.7345 (ttt-90)
REVERT: A 216 GLU cc_start: 0.7135 (tm-30) cc_final: 0.6753 (tm-30)
REVERT: A 252 MET cc_start: 0.9402 (OUTLIER) cc_final: 0.8734 (ptm)
REVERT: A 429 GLN cc_start: 0.7155 (tp-100) cc_final: 0.6735 (tp-100)
REVERT: B 65 GLN cc_start: 0.7208 (pt0) cc_final: 0.6852 (pt0)
REVERT: B 117 ARG cc_start: 0.7959 (OUTLIER) cc_final: 0.7551 (ttp-170)
REVERT: B 216 GLU cc_start: 0.7018 (tm-30) cc_final: 0.6640 (tm-30)
REVERT: B 252 MET cc_start: 0.9397 (OUTLIER) cc_final: 0.8746 (ptm)
REVERT: B 429 GLN cc_start: 0.7304 (tp-100) cc_final: 0.6884 (tp-100)
REVERT: C 65 GLN cc_start: 0.7218 (pt0) cc_final: 0.6865 (pt0)
REVERT: C 216 GLU cc_start: 0.7016 (tm-30) cc_final: 0.6636 (tm-30)
REVERT: C 252 MET cc_start: 0.9396 (OUTLIER) cc_final: 0.8742 (ptm)
REVERT: C 429 GLN cc_start: 0.7296 (tp-100) cc_final: 0.6868 (tp-100)
REVERT: D 65 GLN cc_start: 0.7076 (pt0) cc_final: 0.6708 (pt0)
REVERT: D 173 ARG cc_start: 0.8296 (OUTLIER) cc_final: 0.7402 (ttt-90)
REVERT: D 216 GLU cc_start: 0.7151 (tm-30) cc_final: 0.6801 (tm-30)
REVERT: D 252 MET cc_start: 0.9397 (OUTLIER) cc_final: 0.8727 (ptm)
REVERT: D 429 GLN cc_start: 0.7326 (tp40) cc_final: 0.6844 (tp-100)
REVERT: E 65 GLN cc_start: 0.7204 (pt0) cc_final: 0.6809 (pt0)
REVERT: E 173 ARG cc_start: 0.8283 (OUTLIER) cc_final: 0.7371 (ttt-90)
REVERT: E 216 GLU cc_start: 0.7133 (tm-30) cc_final: 0.6700 (tm-30)
REVERT: E 252 MET cc_start: 0.9402 (OUTLIER) cc_final: 0.8734 (ptm)
REVERT: E 429 GLN cc_start: 0.7304 (tp-100) cc_final: 0.6887 (tp-100)
REVERT: F 65 GLN cc_start: 0.7212 (pt0) cc_final: 0.6860 (pt0)
REVERT: F 173 ARG cc_start: 0.8288 (OUTLIER) cc_final: 0.7367 (ttt-90)
REVERT: F 216 GLU cc_start: 0.7018 (tm-30) cc_final: 0.6639 (tm-30)
REVERT: F 252 MET cc_start: 0.9396 (OUTLIER) cc_final: 0.8748 (ptm)
REVERT: F 429 GLN cc_start: 0.7158 (tp-100) cc_final: 0.6737 (tp-100)
REVERT: G 65 GLN cc_start: 0.6984 (pt0) cc_final: 0.6708 (pt0)
REVERT: G 216 GLU cc_start: 0.7020 (tm-30) cc_final: 0.6640 (tm-30)
REVERT: G 252 MET cc_start: 0.9397 (OUTLIER) cc_final: 0.8747 (ptm)
REVERT: G 429 GLN cc_start: 0.7158 (tp-100) cc_final: 0.6736 (tp-100)
REVERT: H 65 GLN cc_start: 0.7211 (pt0) cc_final: 0.6854 (pt0)
REVERT: H 216 GLU cc_start: 0.7019 (tm-30) cc_final: 0.6652 (tm-30)
REVERT: H 252 MET cc_start: 0.9380 (OUTLIER) cc_final: 0.8685 (ptm)
REVERT: H 429 GLN cc_start: 0.7245 (tp-100) cc_final: 0.6829 (tp-100)
outliers start: 45
outliers final: 27
residues processed: 444
average time/residue: 2.1518
time to fit residues: 1064.8292
Evaluate side-chains
451 residues out of total 2832 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 40
poor density : 411
time to evaluate : 3.244
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 105 SER
Chi-restraints excluded: chain A residue 173 ARG
Chi-restraints excluded: chain A residue 252 MET
Chi-restraints excluded: chain A residue 286 VAL
Chi-restraints excluded: chain A residue 311 HIS
Chi-restraints excluded: chain B residue 26 GLU
Chi-restraints excluded: chain B residue 105 SER
Chi-restraints excluded: chain B residue 117 ARG
Chi-restraints excluded: chain B residue 252 MET
Chi-restraints excluded: chain B residue 286 VAL
Chi-restraints excluded: chain B residue 311 HIS
Chi-restraints excluded: chain C residue 26 GLU
Chi-restraints excluded: chain C residue 252 MET
Chi-restraints excluded: chain C residue 286 VAL
Chi-restraints excluded: chain C residue 311 HIS
Chi-restraints excluded: chain D residue 105 SER
Chi-restraints excluded: chain D residue 173 ARG
Chi-restraints excluded: chain D residue 252 MET
Chi-restraints excluded: chain D residue 286 VAL
Chi-restraints excluded: chain D residue 311 HIS
Chi-restraints excluded: chain E residue 26 GLU
Chi-restraints excluded: chain E residue 173 ARG
Chi-restraints excluded: chain E residue 252 MET
Chi-restraints excluded: chain E residue 286 VAL
Chi-restraints excluded: chain E residue 311 HIS
Chi-restraints excluded: chain F residue 26 GLU
Chi-restraints excluded: chain F residue 173 ARG
Chi-restraints excluded: chain F residue 252 MET
Chi-restraints excluded: chain F residue 286 VAL
Chi-restraints excluded: chain F residue 311 HIS
Chi-restraints excluded: chain G residue 26 GLU
Chi-restraints excluded: chain G residue 105 SER
Chi-restraints excluded: chain G residue 252 MET
Chi-restraints excluded: chain G residue 286 VAL
Chi-restraints excluded: chain G residue 311 HIS
Chi-restraints excluded: chain H residue 26 GLU
Chi-restraints excluded: chain H residue 105 SER
Chi-restraints excluded: chain H residue 252 MET
Chi-restraints excluded: chain H residue 286 VAL
Chi-restraints excluded: chain H residue 311 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 352
random chunks:
chunk 308 optimal weight: 4.9990
chunk 325 optimal weight: 2.9990
chunk 296 optimal weight: 3.9990
chunk 316 optimal weight: 2.9990
chunk 324 optimal weight: 2.9990
chunk 190 optimal weight: 1.9990
chunk 137 optimal weight: 2.9990
chunk 248 optimal weight: 1.9990
chunk 97 optimal weight: 0.5980
chunk 285 optimal weight: 0.2980
chunk 299 optimal weight: 4.9990
overall best weight: 1.5786
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** A 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Total number of N/Q/H flips: 0
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8248
moved from start: 0.1883
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.004 0.030 29096 Z= 0.248
Angle : 0.599 6.763 39472 Z= 0.315
Chirality : 0.042 0.135 4152
Planarity : 0.004 0.034 5168
Dihedral : 9.457 169.256 4144
Min Nonbonded Distance : 1.868
Molprobity Statistics.
All-atom Clashscore : 4.69
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 3.64 %
Favored : 96.36 %
Rotamer:
Outliers : 1.94 %
Allowed : 14.02 %
Favored : 84.04 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 4.17 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 1.02 (0.14), residues: 3544
helix: 0.93 (0.12), residues: 1672
sheet: 0.51 (0.23), residues: 472
loop : 0.66 (0.17), residues: 1400
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.016 0.002 TRP D 354
HIS 0.004 0.001 HIS C 224
PHE 0.020 0.002 PHE C 297
TYR 0.029 0.002 TYR A 263
ARG 0.010 0.001 ARG D 442
*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
7088 Ramachandran restraints generated.
3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
7088 Ramachandran restraints generated.
3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
470 residues out of total 2832 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 55
poor density : 415
time to evaluate : 3.297
Fit side-chains
REVERT: A 65 GLN cc_start: 0.7083 (pt0) cc_final: 0.6721 (pt0)
REVERT: A 173 ARG cc_start: 0.8273 (OUTLIER) cc_final: 0.7384 (ttt-90)
REVERT: A 216 GLU cc_start: 0.7021 (tm-30) cc_final: 0.6669 (tm-30)
REVERT: A 252 MET cc_start: 0.9399 (OUTLIER) cc_final: 0.8747 (ptm)
REVERT: A 429 GLN cc_start: 0.7228 (tp-100) cc_final: 0.6807 (tp-100)
REVERT: B 65 GLN cc_start: 0.7219 (pt0) cc_final: 0.6859 (pt0)
REVERT: B 216 GLU cc_start: 0.7021 (tm-30) cc_final: 0.6637 (tm-30)
REVERT: B 252 MET cc_start: 0.9412 (OUTLIER) cc_final: 0.8747 (ptm)
REVERT: B 429 GLN cc_start: 0.7333 (tp-100) cc_final: 0.6912 (tp-100)
REVERT: C 65 GLN cc_start: 0.7222 (pt0) cc_final: 0.6950 (pt0)
REVERT: C 216 GLU cc_start: 0.7012 (tm-30) cc_final: 0.6633 (tm-30)
REVERT: C 252 MET cc_start: 0.9410 (OUTLIER) cc_final: 0.8742 (ptm)
REVERT: C 429 GLN cc_start: 0.7311 (tp-100) cc_final: 0.6887 (tp-100)
REVERT: D 65 GLN cc_start: 0.7083 (pt0) cc_final: 0.6712 (pt0)
REVERT: D 173 ARG cc_start: 0.8270 (OUTLIER) cc_final: 0.7507 (ttt-90)
REVERT: D 216 GLU cc_start: 0.7027 (tm-30) cc_final: 0.6687 (tm-30)
REVERT: D 252 MET cc_start: 0.9410 (OUTLIER) cc_final: 0.8733 (ptm)
REVERT: D 429 GLN cc_start: 0.7334 (tp40) cc_final: 0.6842 (tp-100)
REVERT: E 65 GLN cc_start: 0.7081 (pt0) cc_final: 0.6725 (pt0)
REVERT: E 173 ARG cc_start: 0.8307 (OUTLIER) cc_final: 0.7406 (ttt-90)
REVERT: E 216 GLU cc_start: 0.6966 (tm-30) cc_final: 0.6621 (tm-30)
REVERT: E 252 MET cc_start: 0.9400 (OUTLIER) cc_final: 0.8748 (ptm)
REVERT: E 429 GLN cc_start: 0.7332 (tp-100) cc_final: 0.6910 (tp-100)
REVERT: F 65 GLN cc_start: 0.7218 (pt0) cc_final: 0.6946 (pt0)
REVERT: F 173 ARG cc_start: 0.8276 (OUTLIER) cc_final: 0.7374 (ttt-90)
REVERT: F 216 GLU cc_start: 0.7020 (tm-30) cc_final: 0.6672 (tm-30)
REVERT: F 252 MET cc_start: 0.9396 (OUTLIER) cc_final: 0.8754 (ptm)
REVERT: F 429 GLN cc_start: 0.7231 (tp-100) cc_final: 0.6817 (tp-100)
REVERT: G 65 GLN cc_start: 0.6991 (pt0) cc_final: 0.6708 (pt0)
REVERT: G 216 GLU cc_start: 0.6959 (tm-30) cc_final: 0.6575 (tm-30)
REVERT: G 252 MET cc_start: 0.9397 (OUTLIER) cc_final: 0.8755 (ptm)
REVERT: G 429 GLN cc_start: 0.7231 (tp-100) cc_final: 0.6808 (tp-100)
REVERT: H 65 GLN cc_start: 0.7219 (pt0) cc_final: 0.6947 (pt0)
REVERT: H 216 GLU cc_start: 0.7021 (tm-30) cc_final: 0.6639 (tm-30)
REVERT: H 252 MET cc_start: 0.9400 (OUTLIER) cc_final: 0.8697 (ptm)
REVERT: H 429 GLN cc_start: 0.7299 (tp-100) cc_final: 0.6873 (tp-100)
outliers start: 55
outliers final: 41
residues processed: 455
average time/residue: 2.1416
time to fit residues: 1087.1299
Evaluate side-chains
470 residues out of total 2832 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 53
poor density : 417
time to evaluate : 3.406
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 105 SER
Chi-restraints excluded: chain A residue 173 ARG
Chi-restraints excluded: chain A residue 180 VAL
Chi-restraints excluded: chain A residue 252 MET
Chi-restraints excluded: chain A residue 286 VAL
Chi-restraints excluded: chain A residue 291 LYS
Chi-restraints excluded: chain A residue 311 HIS
Chi-restraints excluded: chain B residue 26 GLU
Chi-restraints excluded: chain B residue 105 SER
Chi-restraints excluded: chain B residue 180 VAL
Chi-restraints excluded: chain B residue 252 MET
Chi-restraints excluded: chain B residue 286 VAL
Chi-restraints excluded: chain B residue 311 HIS
Chi-restraints excluded: chain B residue 378 SER
Chi-restraints excluded: chain C residue 26 GLU
Chi-restraints excluded: chain C residue 180 VAL
Chi-restraints excluded: chain C residue 252 MET
Chi-restraints excluded: chain C residue 286 VAL
Chi-restraints excluded: chain C residue 311 HIS
Chi-restraints excluded: chain C residue 378 SER
Chi-restraints excluded: chain D residue 105 SER
Chi-restraints excluded: chain D residue 173 ARG
Chi-restraints excluded: chain D residue 180 VAL
Chi-restraints excluded: chain D residue 252 MET
Chi-restraints excluded: chain D residue 286 VAL
Chi-restraints excluded: chain D residue 311 HIS
Chi-restraints excluded: chain D residue 378 SER
Chi-restraints excluded: chain E residue 26 GLU
Chi-restraints excluded: chain E residue 173 ARG
Chi-restraints excluded: chain E residue 180 VAL
Chi-restraints excluded: chain E residue 252 MET
Chi-restraints excluded: chain E residue 286 VAL
Chi-restraints excluded: chain E residue 311 HIS
Chi-restraints excluded: chain E residue 378 SER
Chi-restraints excluded: chain F residue 26 GLU
Chi-restraints excluded: chain F residue 173 ARG
Chi-restraints excluded: chain F residue 180 VAL
Chi-restraints excluded: chain F residue 252 MET
Chi-restraints excluded: chain F residue 286 VAL
Chi-restraints excluded: chain F residue 311 HIS
Chi-restraints excluded: chain G residue 26 GLU
Chi-restraints excluded: chain G residue 105 SER
Chi-restraints excluded: chain G residue 180 VAL
Chi-restraints excluded: chain G residue 252 MET
Chi-restraints excluded: chain G residue 286 VAL
Chi-restraints excluded: chain G residue 311 HIS
Chi-restraints excluded: chain H residue 26 GLU
Chi-restraints excluded: chain H residue 105 SER
Chi-restraints excluded: chain H residue 180 VAL
Chi-restraints excluded: chain H residue 252 MET
Chi-restraints excluded: chain H residue 286 VAL
Chi-restraints excluded: chain H residue 311 HIS
Chi-restraints excluded: chain H residue 378 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 352
random chunks:
chunk 315 optimal weight: 4.9990
chunk 207 optimal weight: 6.9990
chunk 334 optimal weight: 5.9990
chunk 204 optimal weight: 0.9980
chunk 158 optimal weight: 1.9990
chunk 232 optimal weight: 0.8980
chunk 350 optimal weight: 5.9990
chunk 322 optimal weight: 1.9990
chunk 279 optimal weight: 0.9980
chunk 28 optimal weight: 0.9980
chunk 215 optimal weight: 0.7980
overall best weight: 0.9380
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** A 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Total number of N/Q/H flips: 0
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8221
moved from start: 0.1852
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.027 29096 Z= 0.193
Angle : 0.561 6.016 39472 Z= 0.295
Chirality : 0.040 0.129 4152
Planarity : 0.004 0.040 5168
Dihedral : 9.265 168.949 4144
Min Nonbonded Distance : 1.904
Molprobity Statistics.
All-atom Clashscore : 4.87
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 3.22 %
Favored : 96.78 %
Rotamer:
Outliers : 1.62 %
Allowed : 14.90 %
Favored : 83.47 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 4.17 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 1.13 (0.14), residues: 3544
helix: 1.05 (0.13), residues: 1672
sheet: 0.79 (0.25), residues: 400
loop : 0.59 (0.17), residues: 1472
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.016 0.001 TRP G 354
HIS 0.004 0.001 HIS H 224
PHE 0.016 0.002 PHE B 297
TYR 0.026 0.002 TYR G 263
ARG 0.010 0.000 ARG F 442
********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
7088 Ramachandran restraints generated.
3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
7088 Ramachandran restraints generated.
3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
450 residues out of total 2832 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 46
poor density : 404
time to evaluate : 3.437
Fit side-chains
REVERT: A 65 GLN cc_start: 0.7068 (pt0) cc_final: 0.6735 (pt0)
REVERT: A 173 ARG cc_start: 0.8269 (OUTLIER) cc_final: 0.7366 (ttt-90)
REVERT: A 216 GLU cc_start: 0.6943 (tm-30) cc_final: 0.6570 (tm-30)
REVERT: A 252 MET cc_start: 0.9395 (OUTLIER) cc_final: 0.8733 (ptm)
REVERT: A 429 GLN cc_start: 0.7262 (tp-100) cc_final: 0.6831 (tp-100)
REVERT: B 65 GLN cc_start: 0.7063 (pt0) cc_final: 0.6732 (pt0)
REVERT: B 216 GLU cc_start: 0.6960 (tm-30) cc_final: 0.6579 (tm-30)
REVERT: B 252 MET cc_start: 0.9388 (OUTLIER) cc_final: 0.8736 (ptm)
REVERT: B 429 GLN cc_start: 0.7210 (tp-100) cc_final: 0.6774 (tp-100)
REVERT: C 65 GLN cc_start: 0.7064 (pt0) cc_final: 0.6704 (pt0)
REVERT: C 216 GLU cc_start: 0.6936 (tm-30) cc_final: 0.6639 (tm-30)
REVERT: C 252 MET cc_start: 0.9386 (OUTLIER) cc_final: 0.8794 (ptm)
REVERT: C 429 GLN cc_start: 0.7204 (tp-100) cc_final: 0.6785 (tp-100)
REVERT: D 65 GLN cc_start: 0.7062 (pt0) cc_final: 0.6789 (pt0)
REVERT: D 173 ARG cc_start: 0.8276 (OUTLIER) cc_final: 0.7376 (ttt-90)
REVERT: D 216 GLU cc_start: 0.6938 (tm-30) cc_final: 0.6639 (tm-30)
REVERT: D 252 MET cc_start: 0.9388 (OUTLIER) cc_final: 0.8714 (ptm)
REVERT: D 429 GLN cc_start: 0.7318 (tp40) cc_final: 0.6756 (tp-100)
REVERT: E 65 GLN cc_start: 0.7060 (pt0) cc_final: 0.6729 (pt0)
REVERT: E 173 ARG cc_start: 0.8267 (OUTLIER) cc_final: 0.7384 (ttt-90)
REVERT: E 216 GLU cc_start: 0.6946 (tm-30) cc_final: 0.6643 (tm-30)
REVERT: E 252 MET cc_start: 0.9396 (OUTLIER) cc_final: 0.8736 (ptm)
REVERT: E 429 GLN cc_start: 0.7305 (tp-100) cc_final: 0.6873 (tp-100)
REVERT: F 65 GLN cc_start: 0.7063 (pt0) cc_final: 0.6731 (pt0)
REVERT: F 173 ARG cc_start: 0.8266 (OUTLIER) cc_final: 0.7381 (ttt-90)
REVERT: F 216 GLU cc_start: 0.6940 (tm-30) cc_final: 0.6633 (tm-30)
REVERT: F 252 MET cc_start: 0.9387 (OUTLIER) cc_final: 0.8738 (ptm)
REVERT: F 429 GLN cc_start: 0.7304 (tp-100) cc_final: 0.6875 (tp-100)
REVERT: G 65 GLN cc_start: 0.6963 (pt0) cc_final: 0.6658 (pt0)
REVERT: G 216 GLU cc_start: 0.6939 (tm-30) cc_final: 0.6638 (tm-30)
REVERT: G 252 MET cc_start: 0.9388 (OUTLIER) cc_final: 0.8738 (ptm)
REVERT: G 429 GLN cc_start: 0.7267 (tp-100) cc_final: 0.6836 (tp-100)
REVERT: H 65 GLN cc_start: 0.7065 (pt0) cc_final: 0.6704 (pt0)
REVERT: H 216 GLU cc_start: 0.6940 (tm-30) cc_final: 0.6643 (tm-30)
REVERT: H 252 MET cc_start: 0.9380 (OUTLIER) cc_final: 0.8684 (ptm)
REVERT: H 429 GLN cc_start: 0.7273 (tp-100) cc_final: 0.6838 (tp-100)
outliers start: 46
outliers final: 32
residues processed: 434
average time/residue: 2.1725
time to fit residues: 1053.6913
Evaluate side-chains
448 residues out of total 2832 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 44
poor density : 404
time to evaluate : 3.243
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 26 GLU
Chi-restraints excluded: chain A residue 105 SER
Chi-restraints excluded: chain A residue 173 ARG
Chi-restraints excluded: chain A residue 252 MET
Chi-restraints excluded: chain A residue 286 VAL
Chi-restraints excluded: chain A residue 311 HIS
Chi-restraints excluded: chain B residue 26 GLU
Chi-restraints excluded: chain B residue 105 SER
Chi-restraints excluded: chain B residue 252 MET
Chi-restraints excluded: chain B residue 286 VAL
Chi-restraints excluded: chain B residue 311 HIS
Chi-restraints excluded: chain C residue 26 GLU
Chi-restraints excluded: chain C residue 252 MET
Chi-restraints excluded: chain C residue 286 VAL
Chi-restraints excluded: chain C residue 311 HIS
Chi-restraints excluded: chain D residue 173 ARG
Chi-restraints excluded: chain D residue 180 VAL
Chi-restraints excluded: chain D residue 252 MET
Chi-restraints excluded: chain D residue 286 VAL
Chi-restraints excluded: chain D residue 311 HIS
Chi-restraints excluded: chain D residue 378 SER
Chi-restraints excluded: chain E residue 26 GLU
Chi-restraints excluded: chain E residue 173 ARG
Chi-restraints excluded: chain E residue 180 VAL
Chi-restraints excluded: chain E residue 252 MET
Chi-restraints excluded: chain E residue 286 VAL
Chi-restraints excluded: chain E residue 311 HIS
Chi-restraints excluded: chain F residue 26 GLU
Chi-restraints excluded: chain F residue 173 ARG
Chi-restraints excluded: chain F residue 252 MET
Chi-restraints excluded: chain F residue 286 VAL
Chi-restraints excluded: chain F residue 311 HIS
Chi-restraints excluded: chain G residue 26 GLU
Chi-restraints excluded: chain G residue 105 SER
Chi-restraints excluded: chain G residue 252 MET
Chi-restraints excluded: chain G residue 286 VAL
Chi-restraints excluded: chain G residue 311 HIS
Chi-restraints excluded: chain G residue 378 SER
Chi-restraints excluded: chain H residue 26 GLU
Chi-restraints excluded: chain H residue 105 SER
Chi-restraints excluded: chain H residue 252 MET
Chi-restraints excluded: chain H residue 286 VAL
Chi-restraints excluded: chain H residue 311 HIS
Chi-restraints excluded: chain H residue 378 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 352
random chunks:
chunk 171 optimal weight: 5.9990
chunk 221 optimal weight: 0.4980
chunk 297 optimal weight: 3.9990
chunk 85 optimal weight: 0.7980
chunk 257 optimal weight: 2.9990
chunk 41 optimal weight: 1.9990
chunk 77 optimal weight: 3.9990
chunk 279 optimal weight: 0.8980
chunk 117 optimal weight: 5.9990
chunk 287 optimal weight: 3.9990
chunk 35 optimal weight: 0.6980
overall best weight: 0.9782
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** A 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Total number of N/Q/H flips: 0
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.131555 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.117932 restraints weight = 26200.244|
|-----------------------------------------------------------------------------|
r_work (start): 0.3324 rms_B_bonded: 0.81
r_work: 0.3242 rms_B_bonded: 1.22 restraints_weight: 0.5000
r_work: 0.3149 rms_B_bonded: 2.12 restraints_weight: 0.2500
r_work (final): 0.3149
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8480
moved from start: 0.1851
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.027 29096 Z= 0.195
Angle : 0.562 6.071 39472 Z= 0.295
Chirality : 0.041 0.130 4152
Planarity : 0.004 0.039 5168
Dihedral : 9.238 168.839 4144
Min Nonbonded Distance : 1.900
Molprobity Statistics.
All-atom Clashscore : 5.10
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 3.39 %
Favored : 96.61 %
Rotamer:
Outliers : 1.91 %
Allowed : 14.76 %
Favored : 83.33 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 4.17 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 1.14 (0.14), residues: 3544
helix: 1.07 (0.13), residues: 1672
sheet: 0.75 (0.25), residues: 400
loop : 0.58 (0.17), residues: 1472
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.015 0.001 TRP G 354
HIS 0.004 0.001 HIS E 224
PHE 0.017 0.002 PHE G 297
TYR 0.026 0.002 TYR A 263
ARG 0.010 0.000 ARG E 442
Origin is already at (0, 0, 0), no shifts will be applied
===============================================================================
Job complete
usr+sys time: 14125.61 seconds
wall clock time: 246 minutes 57.96 seconds (14817.96 seconds total)