Starting phenix.real_space_refine
on Fri Aug 9 10:41:01 2024 by dcliebschner
===============================================================================
Processing files:
-------------------------------------------------------------------------------
Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u29_41842/08_2024/8u29_41842.cif
Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u29_41842/08_2024/8u29_41842.map
Processing PHIL parameters:
-------------------------------------------------------------------------------
Adding command-line PHIL:
-------------------------
refinement.macro_cycles=10
scattering_table=electron
resolution=2.8
write_initial_geo_file=False
Final processed PHIL parameters:
-------------------------------------------------------------------------------
data_manager {
real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u29_41842/08_2024/8u29_41842.map"
default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u29_41842/08_2024/8u29_41842.map"
model {
file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u29_41842/08_2024/8u29_41842.cif"
}
default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u29_41842/08_2024/8u29_41842.cif"
}
resolution = 2.8
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= 0.002 sd= 0.096
Set stop_for_unknowns flag
Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
Set to: electron
Number of scattering types: 4
Type Number sf(0) Gaussians
S 123 5.16 5
C 16434 2.51 5
N 4206 2.21 5
O 4963 1.98 5
sf(0) = scattering factor at diffraction angle 0.
Process input model
Symmetric amino acids flipped
Residue "A TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "A PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "A PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "A PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "A PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "A PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "A PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "A PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "A PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "A PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "A PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "A ASP 251": "OD1" <-> "OD2"
Residue "A PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "A PHE 328": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "A PHE 332": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "A TYR 355": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "A PHE 365": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "A PHE 368": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "A TYR 371": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "A PHE 383": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "A TYR 387": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "A TYR 390": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "A PHE 440": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "A TYR 442": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "A PHE 445": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "A TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "A TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "A PHE 486": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "A TYR 494": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "A PHE 504": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "A PHE 551": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "A PHE 554": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "A ASP 563": "OD1" <-> "OD2"
Residue "A ASP 567": "OD1" <-> "OD2"
Residue "A GLU 572": "OE1" <-> "OE2"
Residue "A TYR 601": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "A TYR 625": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "A TYR 651": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "A PHE 701": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "A PHE 765": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "A TYR 772": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "A PHE 780": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "A ASP 831": "OD1" <-> "OD2"
Residue "A TYR 856": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "A TYR 900": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "A PHE 953": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "A TYR 1030": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "A PHE 1035": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "A PHE 1045": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "A TYR 1050": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "A PHE 1078": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "A PHE 1086": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "A PHE 1104": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "B TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "B PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "B PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "B PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "B PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "B PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "B PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "B PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "B PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "B PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "B PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "B ASP 251": "OD1" <-> "OD2"
Residue "B PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "B PHE 328": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "B PHE 332": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "B TYR 355": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "B PHE 365": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "B PHE 368": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "B TYR 371": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "B PHE 383": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "B TYR 387": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "B TYR 390": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "B PHE 440": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "B TYR 442": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "B PHE 445": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "B TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "B TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "B PHE 486": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "B TYR 494": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "B PHE 504": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "B PHE 551": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "B PHE 554": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "B ASP 563": "OD1" <-> "OD2"
Residue "B ASP 567": "OD1" <-> "OD2"
Residue "B GLU 572": "OE1" <-> "OE2"
Residue "B TYR 601": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "B TYR 625": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "B TYR 651": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "B PHE 701": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "B PHE 765": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "B TYR 772": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "B PHE 780": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "B ASP 831": "OD1" <-> "OD2"
Residue "B TYR 856": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "B TYR 900": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "B PHE 953": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "B TYR 1030": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "B PHE 1035": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "B PHE 1045": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "B TYR 1050": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "B PHE 1078": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "B PHE 1086": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "B PHE 1104": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "C TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "C PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "C PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "C PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "C PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "C PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "C PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "C PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "C PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "C PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "C PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "C ASP 251": "OD1" <-> "OD2"
Residue "C PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "C PHE 328": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "C PHE 332": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "C TYR 355": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "C PHE 365": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "C PHE 368": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "C TYR 371": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "C PHE 383": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "C TYR 387": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "C TYR 390": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "C PHE 440": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "C TYR 442": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "C PHE 445": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "C TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "C TYR 484": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "C PHE 486": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "C TYR 494": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "C PHE 504": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "C PHE 551": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "C PHE 554": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "C ASP 563": "OD1" <-> "OD2"
Residue "C ASP 567": "OD1" <-> "OD2"
Residue "C GLU 572": "OE1" <-> "OE2"
Residue "C TYR 601": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "C TYR 625": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "C TYR 651": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "C PHE 701": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "C PHE 765": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "C TYR 772": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "C PHE 780": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "C ASP 831": "OD1" <-> "OD2"
Residue "C TYR 856": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "C TYR 900": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "C PHE 953": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "C TYR 1030": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "C PHE 1035": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "C PHE 1045": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "C TYR 1050": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "C PHE 1078": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "C PHE 1086": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "C PHE 1104": "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: 25726
Number of models: 1
Model: ""
Number of chains: 36
Chain: "A"
Number of atoms: 8073
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 1082, 8073
Classifications: {'peptide': 1082}
Incomplete info: {'truncation_to_alanine': 144}
Link IDs: {'PTRANS': 52, 'TRANS': 1029}
Chain breaks: 2
Unresolved non-hydrogen bonds: 337
Unresolved non-hydrogen angles: 429
Unresolved non-hydrogen dihedrals: 251
Unresolved non-hydrogen chiralities: 45
Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 2, 'ASN:plan1': 7, 'ASP:plan': 16, 'GLU:plan': 11, 'ARG:plan': 3}
Unresolved non-hydrogen planarities: 158
Chain: "B"
Number of atoms: 8075
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 1082, 8075
Classifications: {'peptide': 1082}
Incomplete info: {'truncation_to_alanine': 143}
Link IDs: {'PTRANS': 52, 'TRANS': 1029}
Chain breaks: 2
Unresolved non-hydrogen bonds: 335
Unresolved non-hydrogen angles: 426
Unresolved non-hydrogen dihedrals: 250
Unresolved non-hydrogen chiralities: 44
Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 2, 'ASN:plan1': 7, 'ASP:plan': 16, 'GLU:plan': 11, 'ARG:plan': 3}
Unresolved non-hydrogen planarities: 158
Chain: "C"
Number of atoms: 8078
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 1082, 8078
Classifications: {'peptide': 1082}
Incomplete info: {'truncation_to_alanine': 142}
Link IDs: {'PTRANS': 52, 'TRANS': 1029}
Chain breaks: 2
Unresolved non-hydrogen bonds: 332
Unresolved non-hydrogen angles: 422
Unresolved non-hydrogen dihedrals: 248
Unresolved non-hydrogen chiralities: 44
Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 2, 'ASN:plan1': 7, 'ASP:plan': 15, 'GLU:plan': 11, 'ARG:plan': 3}
Unresolved non-hydrogen planarities: 155
Chain: "D"
Number of atoms: 28
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 2, 28
Unusual residues: {'NAG': 2}
Classifications: {'undetermined': 2}
Link IDs: {None: 1}
Unresolved non-hydrogen bonds: 2
Unresolved non-hydrogen angles: 4
Unresolved non-hydrogen dihedrals: 6
Unresolved non-hydrogen chiralities: 2
Chain: "E"
Number of atoms: 28
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 2, 28
Unusual residues: {'NAG': 2}
Classifications: {'undetermined': 2}
Link IDs: {None: 1}
Unresolved non-hydrogen bonds: 2
Unresolved non-hydrogen angles: 4
Unresolved non-hydrogen dihedrals: 6
Unresolved non-hydrogen chiralities: 2
Chain: "F"
Number of atoms: 28
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 2, 28
Unusual residues: {'NAG': 2}
Classifications: {'undetermined': 2}
Link IDs: {None: 1}
Unresolved non-hydrogen bonds: 2
Unresolved non-hydrogen angles: 4
Unresolved non-hydrogen dihedrals: 6
Unresolved non-hydrogen chiralities: 2
Chain: "G"
Number of atoms: 50
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 4, 50
Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2}
Classifications: {'undetermined': 4}
Link IDs: {None: 3}
Unresolved non-hydrogen bonds: 4
Unresolved non-hydrogen angles: 8
Unresolved non-hydrogen dihedrals: 12
Unresolved non-hydrogen chiralities: 4
Chain: "H"
Number of atoms: 72
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 6, 72
Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2}
Classifications: {'undetermined': 6}
Link IDs: {None: 5}
Unresolved non-hydrogen bonds: 6
Unresolved non-hydrogen angles: 12
Unresolved non-hydrogen dihedrals: 18
Unresolved non-hydrogen chiralities: 6
Chain: "I"
Number of atoms: 28
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 2, 28
Unusual residues: {'NAG': 2}
Classifications: {'undetermined': 2}
Link IDs: {None: 1}
Unresolved non-hydrogen bonds: 2
Unresolved non-hydrogen angles: 4
Unresolved non-hydrogen dihedrals: 6
Unresolved non-hydrogen chiralities: 2
Chain: "J"
Number of atoms: 28
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 2, 28
Unusual residues: {'NAG': 2}
Classifications: {'undetermined': 2}
Link IDs: {None: 1}
Unresolved non-hydrogen bonds: 2
Unresolved non-hydrogen angles: 4
Unresolved non-hydrogen dihedrals: 6
Unresolved non-hydrogen chiralities: 2
Chain: "K"
Number of atoms: 28
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 2, 28
Unusual residues: {'NAG': 2}
Classifications: {'undetermined': 2}
Link IDs: {None: 1}
Unresolved non-hydrogen bonds: 2
Unresolved non-hydrogen angles: 4
Unresolved non-hydrogen dihedrals: 6
Unresolved non-hydrogen chiralities: 2
Chain: "L"
Number of atoms: 28
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 2, 28
Unusual residues: {'NAG': 2}
Classifications: {'undetermined': 2}
Link IDs: {None: 1}
Unresolved non-hydrogen bonds: 2
Unresolved non-hydrogen angles: 4
Unresolved non-hydrogen dihedrals: 6
Unresolved non-hydrogen chiralities: 2
Chain: "M"
Number of atoms: 28
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 2, 28
Unusual residues: {'NAG': 2}
Classifications: {'undetermined': 2}
Link IDs: {None: 1}
Unresolved non-hydrogen bonds: 2
Unresolved non-hydrogen angles: 4
Unresolved non-hydrogen dihedrals: 6
Unresolved non-hydrogen chiralities: 2
Chain: "N"
Number of atoms: 28
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 2, 28
Unusual residues: {'NAG': 2}
Classifications: {'undetermined': 2}
Link IDs: {None: 1}
Unresolved non-hydrogen bonds: 2
Unresolved non-hydrogen angles: 4
Unresolved non-hydrogen dihedrals: 6
Unresolved non-hydrogen chiralities: 2
Chain: "O"
Number of atoms: 28
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 2, 28
Unusual residues: {'NAG': 2}
Classifications: {'undetermined': 2}
Link IDs: {None: 1}
Unresolved non-hydrogen bonds: 2
Unresolved non-hydrogen angles: 4
Unresolved non-hydrogen dihedrals: 6
Unresolved non-hydrogen chiralities: 2
Chain: "P"
Number of atoms: 28
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 2, 28
Unusual residues: {'NAG': 2}
Classifications: {'undetermined': 2}
Link IDs: {None: 1}
Unresolved non-hydrogen bonds: 2
Unresolved non-hydrogen angles: 4
Unresolved non-hydrogen dihedrals: 6
Unresolved non-hydrogen chiralities: 2
Chain: "Q"
Number of atoms: 50
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 4, 50
Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2}
Classifications: {'undetermined': 4}
Link IDs: {None: 3}
Unresolved non-hydrogen bonds: 4
Unresolved non-hydrogen angles: 8
Unresolved non-hydrogen dihedrals: 12
Unresolved non-hydrogen chiralities: 4
Chain: "R"
Number of atoms: 72
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 6, 72
Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2}
Classifications: {'undetermined': 6}
Link IDs: {None: 5}
Unresolved non-hydrogen bonds: 6
Unresolved non-hydrogen angles: 12
Unresolved non-hydrogen dihedrals: 18
Unresolved non-hydrogen chiralities: 6
Chain: "S"
Number of atoms: 28
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 2, 28
Unusual residues: {'NAG': 2}
Classifications: {'undetermined': 2}
Link IDs: {None: 1}
Unresolved non-hydrogen bonds: 2
Unresolved non-hydrogen angles: 4
Unresolved non-hydrogen dihedrals: 6
Unresolved non-hydrogen chiralities: 2
Chain: "T"
Number of atoms: 28
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 2, 28
Unusual residues: {'NAG': 2}
Classifications: {'undetermined': 2}
Link IDs: {None: 1}
Unresolved non-hydrogen bonds: 2
Unresolved non-hydrogen angles: 4
Unresolved non-hydrogen dihedrals: 6
Unresolved non-hydrogen chiralities: 2
Chain: "U"
Number of atoms: 28
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 2, 28
Unusual residues: {'NAG': 2}
Classifications: {'undetermined': 2}
Link IDs: {None: 1}
Unresolved non-hydrogen bonds: 2
Unresolved non-hydrogen angles: 4
Unresolved non-hydrogen dihedrals: 6
Unresolved non-hydrogen chiralities: 2
Chain: "V"
Number of atoms: 28
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 2, 28
Unusual residues: {'NAG': 2}
Classifications: {'undetermined': 2}
Link IDs: {None: 1}
Unresolved non-hydrogen bonds: 2
Unresolved non-hydrogen angles: 4
Unresolved non-hydrogen dihedrals: 6
Unresolved non-hydrogen chiralities: 2
Chain: "W"
Number of atoms: 28
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 2, 28
Unusual residues: {'NAG': 2}
Classifications: {'undetermined': 2}
Link IDs: {None: 1}
Unresolved non-hydrogen bonds: 2
Unresolved non-hydrogen angles: 4
Unresolved non-hydrogen dihedrals: 6
Unresolved non-hydrogen chiralities: 2
Chain: "X"
Number of atoms: 28
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 2, 28
Unusual residues: {'NAG': 2}
Classifications: {'undetermined': 2}
Link IDs: {None: 1}
Unresolved non-hydrogen bonds: 2
Unresolved non-hydrogen angles: 4
Unresolved non-hydrogen dihedrals: 6
Unresolved non-hydrogen chiralities: 2
Chain: "Y"
Number of atoms: 28
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 2, 28
Unusual residues: {'NAG': 2}
Classifications: {'undetermined': 2}
Link IDs: {None: 1}
Unresolved non-hydrogen bonds: 2
Unresolved non-hydrogen angles: 4
Unresolved non-hydrogen dihedrals: 6
Unresolved non-hydrogen chiralities: 2
Chain: "Z"
Number of atoms: 28
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 2, 28
Unusual residues: {'NAG': 2}
Classifications: {'undetermined': 2}
Link IDs: {None: 1}
Unresolved non-hydrogen bonds: 2
Unresolved non-hydrogen angles: 4
Unresolved non-hydrogen dihedrals: 6
Unresolved non-hydrogen chiralities: 2
Chain: "a"
Number of atoms: 50
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 4, 50
Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2}
Classifications: {'undetermined': 4}
Link IDs: {None: 3}
Unresolved non-hydrogen bonds: 4
Unresolved non-hydrogen angles: 8
Unresolved non-hydrogen dihedrals: 12
Unresolved non-hydrogen chiralities: 4
Chain: "b"
Number of atoms: 72
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 6, 72
Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2}
Classifications: {'undetermined': 6}
Link IDs: {None: 5}
Unresolved non-hydrogen bonds: 6
Unresolved non-hydrogen angles: 12
Unresolved non-hydrogen dihedrals: 18
Unresolved non-hydrogen chiralities: 6
Chain: "c"
Number of atoms: 28
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 2, 28
Unusual residues: {'NAG': 2}
Classifications: {'undetermined': 2}
Link IDs: {None: 1}
Unresolved non-hydrogen bonds: 2
Unresolved non-hydrogen angles: 4
Unresolved non-hydrogen dihedrals: 6
Unresolved non-hydrogen chiralities: 2
Chain: "d"
Number of atoms: 28
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 2, 28
Unusual residues: {'NAG': 2}
Classifications: {'undetermined': 2}
Link IDs: {None: 1}
Unresolved non-hydrogen bonds: 2
Unresolved non-hydrogen angles: 4
Unresolved non-hydrogen dihedrals: 6
Unresolved non-hydrogen chiralities: 2
Chain: "e"
Number of atoms: 28
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 2, 28
Unusual residues: {'NAG': 2}
Classifications: {'undetermined': 2}
Link IDs: {None: 1}
Unresolved non-hydrogen bonds: 2
Unresolved non-hydrogen angles: 4
Unresolved non-hydrogen dihedrals: 6
Unresolved non-hydrogen chiralities: 2
Chain: "f"
Number of atoms: 28
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 2, 28
Unusual residues: {'NAG': 2}
Classifications: {'undetermined': 2}
Link IDs: {None: 1}
Unresolved non-hydrogen bonds: 2
Unresolved non-hydrogen angles: 4
Unresolved non-hydrogen dihedrals: 6
Unresolved non-hydrogen chiralities: 2
Chain: "g"
Number of atoms: 28
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 2, 28
Unusual residues: {'NAG': 2}
Classifications: {'undetermined': 2}
Link IDs: {None: 1}
Unresolved non-hydrogen bonds: 2
Unresolved non-hydrogen angles: 4
Unresolved non-hydrogen dihedrals: 6
Unresolved non-hydrogen chiralities: 2
Chain: "A"
Number of atoms: 154
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 11, 154
Unusual residues: {'NAG': 11}
Classifications: {'undetermined': 11}
Link IDs: {None: 10}
Unresolved non-hydrogen bonds: 11
Unresolved non-hydrogen angles: 22
Unresolved non-hydrogen dihedrals: 33
Unresolved non-hydrogen chiralities: 11
Chain: "B"
Number of atoms: 154
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 11, 154
Unusual residues: {'NAG': 11}
Classifications: {'undetermined': 11}
Link IDs: {None: 10}
Unresolved non-hydrogen bonds: 11
Unresolved non-hydrogen angles: 22
Unresolved non-hydrogen dihedrals: 33
Unresolved non-hydrogen chiralities: 11
Chain: "C"
Number of atoms: 154
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 11, 154
Unusual residues: {'NAG': 11}
Classifications: {'undetermined': 11}
Link IDs: {None: 10}
Unresolved non-hydrogen bonds: 11
Unresolved non-hydrogen angles: 22
Unresolved non-hydrogen dihedrals: 33
Unresolved non-hydrogen chiralities: 11
Time building chain proxies: 16.74, per 1000 atoms: 0.65
Number of scatterers: 25726
At special positions: 0
Unit cell: (156, 142, 170, 90, 90, 90)
Space group: P 1 (No. 1)
Number of sites at special positions: 0
Number of scattering types: 4
Type Number sf(0)
S 123 16.00
O 4963 8.00
N 4206 7.00
C 16434 6.00
sf(0) = scattering factor at diffraction angle 0.
Number of disulfides: simple=42, symmetry=0
Simple disulfide: pdb=" SG CYS A 19 " - pdb=" SG CYS A 139 " distance=2.04
Simple disulfide: pdb=" SG CYS A 134 " - pdb=" SG CYS A 163 " distance=2.03
Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 291 " distance=2.02
Simple disulfide: pdb=" SG CYS A 326 " - pdb=" SG CYS A 351 " distance=2.10
Simple disulfide: pdb=" SG CYS A 370 " - pdb=" SG CYS A 423 " distance=2.05
Simple disulfide: pdb=" SG CYS A 382 " - pdb=" SG CYS A 514 " distance=2.08
Simple disulfide: pdb=" SG CYS A 469 " - pdb=" SG CYS A 477 " distance=2.02
Simple disulfide: pdb=" SG CYS A 527 " - pdb=" SG CYS A 579 " distance=2.03
Simple disulfide: pdb=" SG CYS A 606 " - pdb=" SG CYS A 640 " distance=2.03
Simple disulfide: pdb=" SG CYS A 653 " - pdb=" SG CYS A 662 " distance=2.04
Simple disulfide: pdb=" SG CYS A 721 " - pdb=" SG CYS A 743 " distance=2.04
Simple disulfide: pdb=" SG CYS A 726 " - pdb=" SG CYS A 732 " distance=2.12
Simple disulfide: pdb=" SG CYS A1015 " - pdb=" SG CYS A1026 " distance=2.02
Simple disulfide: pdb=" SG CYS A1065 " - pdb=" SG CYS A1109 " distance=2.22
Simple disulfide: pdb=" SG CYS B 19 " - pdb=" SG CYS B 139 " distance=2.04
Simple disulfide: pdb=" SG CYS B 134 " - pdb=" SG CYS B 163 " distance=2.03
Simple disulfide: pdb=" SG CYS B 281 " - pdb=" SG CYS B 291 " distance=2.02
Simple disulfide: pdb=" SG CYS B 326 " - pdb=" SG CYS B 351 " distance=2.10
Simple disulfide: pdb=" SG CYS B 370 " - pdb=" SG CYS B 423 " distance=2.05
Simple disulfide: pdb=" SG CYS B 382 " - pdb=" SG CYS B 514 " distance=2.08
Simple disulfide: pdb=" SG CYS B 469 " - pdb=" SG CYS B 477 " distance=2.02
Simple disulfide: pdb=" SG CYS B 527 " - pdb=" SG CYS B 579 " distance=2.03
Simple disulfide: pdb=" SG CYS B 606 " - pdb=" SG CYS B 640 " distance=2.03
Simple disulfide: pdb=" SG CYS B 653 " - pdb=" SG CYS B 662 " distance=2.04
Simple disulfide: pdb=" SG CYS B 721 " - pdb=" SG CYS B 743 " distance=2.04
Simple disulfide: pdb=" SG CYS B 726 " - pdb=" SG CYS B 732 " distance=2.12
Simple disulfide: pdb=" SG CYS B1015 " - pdb=" SG CYS B1026 " distance=2.02
Simple disulfide: pdb=" SG CYS B1065 " - pdb=" SG CYS B1109 " distance=2.22
Simple disulfide: pdb=" SG CYS C 19 " - pdb=" SG CYS C 139 " distance=2.04
Simple disulfide: pdb=" SG CYS C 134 " - pdb=" SG CYS C 163 " distance=2.03
Simple disulfide: pdb=" SG CYS C 281 " - pdb=" SG CYS C 291 " distance=2.02
Simple disulfide: pdb=" SG CYS C 326 " - pdb=" SG CYS C 351 " distance=2.10
Simple disulfide: pdb=" SG CYS C 370 " - pdb=" SG CYS C 423 " distance=2.05
Simple disulfide: pdb=" SG CYS C 382 " - pdb=" SG CYS C 514 " distance=2.08
Simple disulfide: pdb=" SG CYS C 469 " - pdb=" SG CYS C 477 " distance=2.02
Simple disulfide: pdb=" SG CYS C 527 " - pdb=" SG CYS C 579 " distance=2.03
Simple disulfide: pdb=" SG CYS C 606 " - pdb=" SG CYS C 640 " distance=2.03
Simple disulfide: pdb=" SG CYS C 653 " - pdb=" SG CYS C 662 " distance=2.04
Simple disulfide: pdb=" SG CYS C 721 " - pdb=" SG CYS C 743 " distance=2.04
Simple disulfide: pdb=" SG CYS C 726 " - pdb=" SG CYS C 732 " distance=2.12
Simple disulfide: pdb=" SG CYS C1015 " - pdb=" SG CYS C1026 " distance=2.02
Simple disulfide: pdb=" SG CYS C1065 " - pdb=" SG CYS C1109 " distance=2.22
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
Links applied
ALPHA1-2
" MAN H 4 " - " MAN H 5 "
" MAN R 4 " - " MAN R 5 "
" MAN b 4 " - " MAN b 5 "
ALPHA1-3
" BMA G 3 " - " MAN G 4 "
" BMA H 3 " - " MAN H 4 "
" BMA Q 3 " - " MAN Q 4 "
" BMA R 3 " - " MAN R 4 "
" BMA a 3 " - " MAN a 4 "
" BMA b 3 " - " MAN b 4 "
ALPHA1-6
" BMA H 3 " - " MAN H 6 "
" BMA R 3 " - " MAN R 6 "
" BMA b 3 " - " MAN b 6 "
BETA1-4
" NAG D 1 " - " NAG D 2 "
" NAG E 1 " - " NAG E 2 "
" NAG F 1 " - " NAG F 2 "
" NAG G 1 " - " NAG G 2 "
" NAG G 2 " - " BMA G 3 "
" NAG H 1 " - " NAG H 2 "
" NAG H 2 " - " BMA H 3 "
" NAG I 1 " - " NAG I 2 "
" NAG J 1 " - " NAG J 2 "
" NAG K 1 " - " NAG K 2 "
" NAG L 1 " - " NAG L 2 "
" NAG M 1 " - " NAG M 2 "
" NAG N 1 " - " NAG N 2 "
" NAG O 1 " - " NAG O 2 "
" NAG P 1 " - " NAG P 2 "
" NAG Q 1 " - " NAG Q 2 "
" NAG Q 2 " - " BMA Q 3 "
" NAG R 1 " - " NAG R 2 "
" NAG R 2 " - " BMA R 3 "
" NAG S 1 " - " NAG S 2 "
" NAG T 1 " - " NAG T 2 "
" NAG U 1 " - " NAG U 2 "
" NAG V 1 " - " NAG V 2 "
" NAG W 1 " - " NAG W 2 "
" NAG X 1 " - " NAG X 2 "
" NAG Y 1 " - " NAG Y 2 "
" NAG Z 1 " - " NAG Z 2 "
" NAG a 1 " - " NAG a 2 "
" NAG a 2 " - " BMA a 3 "
" NAG b 1 " - " NAG b 2 "
" NAG b 2 " - " BMA b 3 "
" NAG c 1 " - " NAG c 2 "
" NAG d 1 " - " NAG d 2 "
" NAG e 1 " - " NAG e 2 "
" NAG f 1 " - " NAG f 2 "
" NAG g 1 " - " NAG g 2 "
NAG-ASN
" NAG A1301 " - " ASN A 24 "
" NAG A1302 " - " ASN A 159 "
" NAG A1303 " - " ASN A 272 "
" NAG A1304 " - " ASN A 333 "
" NAG A1305 " - " ASN A 360 "
" NAG A1306 " - " ASN A 592 "
" NAG A1307 " - " ASN A 605 "
" NAG A1308 " - " ASN A 648 "
" NAG A1309 " - " ASN A1117 "
" NAG A1310 " - " ASN A 148 "
" NAG A1311 " - " ASN A1057 "
" NAG B1301 " - " ASN B 24 "
" NAG B1302 " - " ASN B 159 "
" NAG B1303 " - " ASN B 272 "
" NAG B1304 " - " ASN B 333 "
" NAG B1305 " - " ASN B 360 "
" NAG B1306 " - " ASN B 592 "
" NAG B1307 " - " ASN B 605 "
" NAG B1308 " - " ASN B 648 "
" NAG B1309 " - " ASN B1117 "
" NAG B1310 " - " ASN B 148 "
" NAG B1311 " - " ASN B1057 "
" NAG C1301 " - " ASN C 24 "
" NAG C1302 " - " ASN C 159 "
" NAG C1303 " - " ASN C 272 "
" NAG C1304 " - " ASN C 333 "
" NAG C1305 " - " ASN C 360 "
" NAG C1306 " - " ASN C 592 "
" NAG C1307 " - " ASN C 605 "
" NAG C1308 " - " ASN C 648 "
" NAG C1309 " - " ASN C1117 "
" NAG C1310 " - " ASN C 148 "
" NAG C1311 " - " ASN C1057 "
" NAG D 1 " - " ASN A 65 "
" NAG E 1 " - " ASN A 115 "
" NAG F 1 " - " ASN A 125 "
" NAG G 1 " - " ASN A 162 "
" NAG H 1 " - " ASN A 230 "
" NAG I 1 " - " ASN A 321 "
" NAG J 1 " - " ASN A 692 "
" NAG K 1 " - " ASN A 700 "
" NAG L 1 " - " ASN A 784 "
" NAG M 1 " - " ASN A1081 "
" NAG N 1 " - " ASN B 65 "
" NAG O 1 " - " ASN B 115 "
" NAG P 1 " - " ASN B 125 "
" NAG Q 1 " - " ASN B 162 "
" NAG R 1 " - " ASN B 230 "
" NAG S 1 " - " ASN B 321 "
" NAG T 1 " - " ASN B 692 "
" NAG U 1 " - " ASN B 700 "
" NAG V 1 " - " ASN B 784 "
" NAG W 1 " - " ASN B1081 "
" NAG X 1 " - " ASN C 65 "
" NAG Y 1 " - " ASN C 115 "
" NAG Z 1 " - " ASN C 125 "
" NAG a 1 " - " ASN C 162 "
" NAG b 1 " - " ASN C 230 "
" NAG c 1 " - " ASN C 321 "
" NAG d 1 " - " ASN C 692 "
" NAG e 1 " - " ASN C 700 "
" NAG f 1 " - " ASN C 784 "
" NAG g 1 " - " ASN C1081 "
Time building additional restraints: 11.34
Conformation dependent library (CDL) restraints added in 4.3 seconds
6444 Ramachandran restraints generated.
3222 Oldfield, 0 Emsley, 3222 emsley8k and 0 Phi/Psi/2.
Adding C-beta torsion restraints...
Number of C-beta restraints generated: 6072
Finding SS restraints...
Secondary structure from input PDB file:
81 helices and 54 sheets defined
24.9% alpha, 32.3% beta
0 base pairs and 0 stacking pairs defined.
Time for finding SS restraints: 3.86
Creating SS restraints...
Processing helix chain 'A' and resid 243 through 246
removed outlier: 4.375A pdb=" N SER A 246 " --> pdb=" O PRO A 243 " (cutoff:3.500A)
No H-bonds generated for 'chain 'A' and resid 243 through 246'
Processing helix chain 'A' and resid 284 through 285
No H-bonds generated for 'chain 'A' and resid 284 through 285'
Processing helix chain 'A' and resid 287 through 293
Processing helix chain 'A' and resid 328 through 333
Processing helix chain 'A' and resid 339 through 343
removed outlier: 3.871A pdb=" N TRP A 343 " --> pdb=" O VAL A 340 " (cutoff:3.500A)
Processing helix chain 'A' and resid 356 through 360
Processing helix chain 'A' and resid 377 through 380
Processing helix chain 'A' and resid 396 through 401
removed outlier: 4.280A pdb=" N ARG A 399 " --> pdb=" O ASP A 396 " (cutoff:3.500A)
Processing helix chain 'A' and resid 407 through 413
Processing helix chain 'A' and resid 429 through 434
removed outlier: 3.723A pdb=" N SER A 434 " --> pdb=" O ASN A 430 " (cutoff:3.500A)
Processing helix chain 'A' and resid 608 through 613
Processing helix chain 'A' and resid 622 through 627
Processing helix chain 'A' and resid 720 through 726
removed outlier: 3.595A pdb=" N ILE A 725 " --> pdb=" O CYS A 721 " (cutoff:3.500A)
Processing helix chain 'A' and resid 729 through 737
Processing helix chain 'A' and resid 738 through 740
No H-bonds generated for 'chain 'A' and resid 738 through 740'
Processing helix chain 'A' and resid 741 through 766
removed outlier: 3.803A pdb=" N ASP A 758 " --> pdb=" O ALA A 754 " (cutoff:3.500A)
removed outlier: 3.573A pdb=" N VAL A 764 " --> pdb=" O ASN A 760 " (cutoff:3.500A)
Processing helix chain 'A' and resid 799 through 807
Processing helix chain 'A' and resid 832 through 839
Processing helix chain 'A' and resid 849 through 866
removed outlier: 3.552A pdb=" N THR A 866 " --> pdb=" O SER A 862 " (cutoff:3.500A)
Processing helix chain 'A' and resid 880 through 891
Processing helix chain 'A' and resid 896 through 902
Processing helix chain 'A' and resid 902 through 923
removed outlier: 3.681A pdb=" N ILE A 917 " --> pdb=" O ALA A 913 " (cutoff:3.500A)
removed outlier: 4.049A pdb=" N GLN A 918 " --> pdb=" O ILE A 914 " (cutoff:3.500A)
removed outlier: 3.723A pdb=" N ASP A 919 " --> pdb=" O SER A 915 " (cutoff:3.500A)
Processing helix chain 'A' and resid 924 through 927
Processing helix chain 'A' and resid 928 through 947
removed outlier: 3.536A pdb=" N VAL A 934 " --> pdb=" O LYS A 930 " (cutoff:3.500A)
Processing helix chain 'A' and resid 948 through 950
No H-bonds generated for 'chain 'A' and resid 948 through 950'
Processing helix chain 'A' and resid 959 through 967
Processing helix chain 'A' and resid 968 through 1015
removed outlier: 5.209A pdb=" N VAL A 974 " --> pdb=" O PRO A 970 " (cutoff:3.500A)
Processing helix chain 'B' and resid 243 through 246
removed outlier: 4.375A pdb=" N SER B 246 " --> pdb=" O PRO B 243 " (cutoff:3.500A)
No H-bonds generated for 'chain 'B' and resid 243 through 246'
Processing helix chain 'B' and resid 284 through 285
No H-bonds generated for 'chain 'B' and resid 284 through 285'
Processing helix chain 'B' and resid 287 through 293
Processing helix chain 'B' and resid 328 through 333
Processing helix chain 'B' and resid 339 through 343
removed outlier: 3.871A pdb=" N TRP B 343 " --> pdb=" O VAL B 340 " (cutoff:3.500A)
Processing helix chain 'B' and resid 356 through 360
Processing helix chain 'B' and resid 377 through 380
Processing helix chain 'B' and resid 396 through 401
removed outlier: 4.280A pdb=" N ARG B 399 " --> pdb=" O ASP B 396 " (cutoff:3.500A)
Processing helix chain 'B' and resid 407 through 413
Processing helix chain 'B' and resid 429 through 434
removed outlier: 3.723A pdb=" N SER B 434 " --> pdb=" O ASN B 430 " (cutoff:3.500A)
Processing helix chain 'B' and resid 608 through 613
Processing helix chain 'B' and resid 622 through 627
Processing helix chain 'B' and resid 720 through 726
removed outlier: 3.594A pdb=" N ILE B 725 " --> pdb=" O CYS B 721 " (cutoff:3.500A)
Processing helix chain 'B' and resid 729 through 737
Processing helix chain 'B' and resid 738 through 740
No H-bonds generated for 'chain 'B' and resid 738 through 740'
Processing helix chain 'B' and resid 741 through 766
removed outlier: 3.803A pdb=" N ASP B 758 " --> pdb=" O ALA B 754 " (cutoff:3.500A)
removed outlier: 3.573A pdb=" N VAL B 764 " --> pdb=" O ASN B 760 " (cutoff:3.500A)
Processing helix chain 'B' and resid 799 through 807
Processing helix chain 'B' and resid 832 through 839
Processing helix chain 'B' and resid 849 through 866
removed outlier: 3.552A pdb=" N THR B 866 " --> pdb=" O SER B 862 " (cutoff:3.500A)
Processing helix chain 'B' and resid 880 through 891
Processing helix chain 'B' and resid 896 through 902
Processing helix chain 'B' and resid 902 through 923
removed outlier: 3.680A pdb=" N ILE B 917 " --> pdb=" O ALA B 913 " (cutoff:3.500A)
removed outlier: 4.049A pdb=" N GLN B 918 " --> pdb=" O ILE B 914 " (cutoff:3.500A)
removed outlier: 3.723A pdb=" N ASP B 919 " --> pdb=" O SER B 915 " (cutoff:3.500A)
Processing helix chain 'B' and resid 924 through 927
Processing helix chain 'B' and resid 928 through 947
removed outlier: 3.536A pdb=" N VAL B 934 " --> pdb=" O LYS B 930 " (cutoff:3.500A)
Processing helix chain 'B' and resid 948 through 950
No H-bonds generated for 'chain 'B' and resid 948 through 950'
Processing helix chain 'B' and resid 959 through 967
Processing helix chain 'B' and resid 968 through 1015
removed outlier: 5.209A pdb=" N VAL B 974 " --> pdb=" O PRO B 970 " (cutoff:3.500A)
Processing helix chain 'C' and resid 243 through 246
removed outlier: 4.375A pdb=" N SER C 246 " --> pdb=" O PRO C 243 " (cutoff:3.500A)
No H-bonds generated for 'chain 'C' and resid 243 through 246'
Processing helix chain 'C' and resid 284 through 285
No H-bonds generated for 'chain 'C' and resid 284 through 285'
Processing helix chain 'C' and resid 287 through 293
Processing helix chain 'C' and resid 328 through 333
Processing helix chain 'C' and resid 339 through 343
removed outlier: 3.872A pdb=" N TRP C 343 " --> pdb=" O VAL C 340 " (cutoff:3.500A)
Processing helix chain 'C' and resid 356 through 360
Processing helix chain 'C' and resid 377 through 380
Processing helix chain 'C' and resid 396 through 401
removed outlier: 4.280A pdb=" N ARG C 399 " --> pdb=" O ASP C 396 " (cutoff:3.500A)
Processing helix chain 'C' and resid 407 through 413
Processing helix chain 'C' and resid 429 through 434
removed outlier: 3.723A pdb=" N SER C 434 " --> pdb=" O ASN C 430 " (cutoff:3.500A)
Processing helix chain 'C' and resid 608 through 613
Processing helix chain 'C' and resid 622 through 627
Processing helix chain 'C' and resid 720 through 726
removed outlier: 3.594A pdb=" N ILE C 725 " --> pdb=" O CYS C 721 " (cutoff:3.500A)
Processing helix chain 'C' and resid 729 through 737
Processing helix chain 'C' and resid 738 through 740
No H-bonds generated for 'chain 'C' and resid 738 through 740'
Processing helix chain 'C' and resid 741 through 766
removed outlier: 3.803A pdb=" N ASP C 758 " --> pdb=" O ALA C 754 " (cutoff:3.500A)
removed outlier: 3.573A pdb=" N VAL C 764 " --> pdb=" O ASN C 760 " (cutoff:3.500A)
Processing helix chain 'C' and resid 799 through 807
Processing helix chain 'C' and resid 832 through 839
Processing helix chain 'C' and resid 849 through 866
removed outlier: 3.552A pdb=" N THR C 866 " --> pdb=" O SER C 862 " (cutoff:3.500A)
Processing helix chain 'C' and resid 880 through 891
Processing helix chain 'C' and resid 896 through 902
Processing helix chain 'C' and resid 902 through 923
removed outlier: 3.681A pdb=" N ILE C 917 " --> pdb=" O ALA C 913 " (cutoff:3.500A)
removed outlier: 4.049A pdb=" N GLN C 918 " --> pdb=" O ILE C 914 " (cutoff:3.500A)
removed outlier: 3.723A pdb=" N ASP C 919 " --> pdb=" O SER C 915 " (cutoff:3.500A)
Processing helix chain 'C' and resid 924 through 927
Processing helix chain 'C' and resid 928 through 947
removed outlier: 3.536A pdb=" N VAL C 934 " --> pdb=" O LYS C 930 " (cutoff:3.500A)
Processing helix chain 'C' and resid 948 through 950
No H-bonds generated for 'chain 'C' and resid 948 through 950'
Processing helix chain 'C' and resid 959 through 967
Processing helix chain 'C' and resid 968 through 1015
removed outlier: 5.209A pdb=" N VAL C 974 " --> pdb=" O PRO C 970 " (cutoff:3.500A)
Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 34
removed outlier: 7.772A pdb=" N ASN A 65 " --> pdb=" O HIS A 259 " (cutoff:3.500A)
removed outlier: 5.617A pdb=" N HIS A 259 " --> pdb=" O ASN A 65 " (cutoff:3.500A)
removed outlier: 4.075A pdb=" N HIS A 184 " --> pdb=" O GLU A 99 " (cutoff:3.500A)
removed outlier: 3.946A pdb=" N ILE A 183 " --> pdb=" O ALA A 206 " (cutoff:3.500A)
removed outlier: 5.880A pdb=" N LEU A 197 " --> pdb=" O LYS A 224 " (cutoff:3.500A)
removed outlier: 4.064A pdb=" N LYS A 224 " --> pdb=" O LEU A 197 " (cutoff:3.500A)
removed outlier: 6.765A pdb=" N VAL A 199 " --> pdb=" O ILE A 222 " (cutoff:3.500A)
removed outlier: 6.920A pdb=" N TYR A 203 " --> pdb=" O VAL A 218 " (cutoff:3.500A)
removed outlier: 9.286A pdb=" N VAL A 218 " --> pdb=" O TYR A 203 " (cutoff:3.500A)
removed outlier: 10.772A pdb=" N ARG A 205 " --> pdb=" O PHE A 216 " (cutoff:3.500A)
removed outlier: 10.666A pdb=" N PHE A 216 " --> pdb=" O ARG A 205 " (cutoff:3.500A)
removed outlier: 5.632A pdb=" N ARG A 38 " --> pdb=" O SER A 217 " (cutoff:3.500A)
removed outlier: 8.707A pdb=" N LEU A 219 " --> pdb=" O ARG A 38 " (cutoff:3.500A)
removed outlier: 7.167A pdb=" N PHE A 40 " --> pdb=" O LEU A 219 " (cutoff:3.500A)
Processing sheet with id=AA2, first strand: chain 'A' and resid 32 through 34
Processing sheet with id=AA3, first strand: chain 'A' and resid 51 through 59
removed outlier: 4.069A pdb=" N ASP A 277 " --> pdb=" O GLU A 268 " (cutoff:3.500A)
Processing sheet with id=AA4, first strand: chain 'A' and resid 87 through 88
removed outlier: 13.853A pdb=" N PHE A 234 " --> pdb=" O PHE A 136 " (cutoff:3.500A)
removed outlier: 13.711A pdb=" N PHE A 138 " --> pdb=" O PHE A 234 " (cutoff:3.500A)
removed outlier: 12.969A pdb=" N VAL A 236 " --> pdb=" O PHE A 138 " (cutoff:3.500A)
removed outlier: 10.461A pdb=" N GLN A 140 " --> pdb=" O VAL A 236 " (cutoff:3.500A)
removed outlier: 10.203A pdb=" N MET A 238 " --> pdb=" O GLN A 140 " (cutoff:3.500A)
removed outlier: 7.763A pdb=" N LEU A 240 " --> pdb=" O PRO A 142 " (cutoff:3.500A)
removed outlier: 6.408A pdb=" N LEU A 144 " --> pdb=" O LEU A 240 " (cutoff:3.500A)
removed outlier: 6.538A pdb=" N TYR A 137 " --> pdb=" O LEU A 158 " (cutoff:3.500A)
removed outlier: 7.373A pdb=" N VAL A 156 " --> pdb=" O CYS A 139 " (cutoff:3.500A)
removed outlier: 11.247A pdb=" N ASP A 141 " --> pdb=" O SER A 154 " (cutoff:3.500A)
removed outlier: 10.455A pdb=" N SER A 154 " --> pdb=" O ASP A 141 " (cutoff:3.500A)
removed outlier: 12.264A pdb=" N MET A 143 " --> pdb=" O TYR A 152 " (cutoff:3.500A)
removed outlier: 9.565A pdb=" N TYR A 152 " --> pdb=" O MET A 143 " (cutoff:3.500A)
removed outlier: 7.768A pdb=" N THR A 145 " --> pdb=" O SER A 150 " (cutoff:3.500A)
removed outlier: 7.602A pdb=" N SER A 150 " --> pdb=" O THR A 145 " (cutoff:3.500A)
Processing sheet with id=AA5, first strand: chain 'A' and resid 87 through 88
removed outlier: 6.452A pdb=" N THR A 239 " --> pdb=" O ILE A 104 " (cutoff:3.500A)
removed outlier: 6.181A pdb=" N ILE A 104 " --> pdb=" O THR A 239 " (cutoff:3.500A)
removed outlier: 5.857A pdb=" N ARG A 105 " --> pdb=" O ASN A 124 " (cutoff:3.500A)
removed outlier: 3.586A pdb=" N TYR A 165 " --> pdb=" O VAL A 133 " (cutoff:3.500A)
Processing sheet with id=AA6, first strand: chain 'A' and resid 301 through 304
Processing sheet with id=AA7, first strand: chain 'A' and resid 315 through 318
removed outlier: 5.098A pdb=" N ASP A 563 " --> pdb=" O ILE A 576 " (cutoff:3.500A)
removed outlier: 3.513A pdb=" N SER A 564 " --> pdb=" O GLY A 555 " (cutoff:3.500A)
Processing sheet with id=AA8, first strand: chain 'A' and resid 344 through 348
removed outlier: 4.014A pdb=" N VAL A 386 " --> pdb=" O ILE A 348 " (cutoff:3.500A)
removed outlier: 3.911A pdb=" N SER A 385 " --> pdb=" O GLU A 505 " (cutoff:3.500A)
Processing sheet with id=AA9, first strand: chain 'A' and resid 351 through 352
removed outlier: 6.462A pdb=" N CYS A 351 " --> pdb=" O CYS A 514 " (cutoff:3.500A)
Processing sheet with id=AB1, first strand: chain 'A' and resid 441 through 443
Processing sheet with id=AB2, first strand: chain 'A' and resid 462 through 463
Processing sheet with id=AB3, first strand: chain 'A' and resid 645 through 651
removed outlier: 6.250A pdb=" N THR A 645 " --> pdb=" O ALA A 677 " (cutoff:3.500A)
removed outlier: 8.464A pdb=" N THR A 679 " --> pdb=" O THR A 645 " (cutoff:3.500A)
removed outlier: 8.590A pdb=" N GLU A 647 " --> pdb=" O THR A 679 " (cutoff:3.500A)
Processing sheet with id=AB4, first strand: chain 'A' and resid 685 through 686
Processing sheet with id=AB5, first strand: chain 'A' and resid 694 through 711
removed outlier: 6.288A pdb=" N THR A 694 " --> pdb=" O THR A1059 " (cutoff:3.500A)
removed outlier: 6.720A pdb=" N THR A1059 " --> pdb=" O THR A 694 " (cutoff:3.500A)
removed outlier: 6.757A pdb=" N ALA A 696 " --> pdb=" O ASN A1057 " (cutoff:3.500A)
removed outlier: 6.731A pdb=" N ASN A1057 " --> pdb=" O ALA A 696 " (cutoff:3.500A)
removed outlier: 6.242A pdb=" N GLN A1055 " --> pdb=" O PRO A 698 " (cutoff:3.500A)
removed outlier: 6.036A pdb=" N TYR A1050 " --> pdb=" O HIS A1031 " (cutoff:3.500A)
removed outlier: 5.755A pdb=" N HIS A1031 " --> pdb=" O TYR A1050 " (cutoff:3.500A)
Processing sheet with id=AB6, first strand: chain 'A' and resid 694 through 711
removed outlier: 6.288A pdb=" N THR A 694 " --> pdb=" O THR A1059 " (cutoff:3.500A)
removed outlier: 6.720A pdb=" N THR A1059 " --> pdb=" O THR A 694 " (cutoff:3.500A)
removed outlier: 6.757A pdb=" N ALA A 696 " --> pdb=" O ASN A1057 " (cutoff:3.500A)
removed outlier: 6.731A pdb=" N ASN A1057 " --> pdb=" O ALA A 696 " (cutoff:3.500A)
removed outlier: 6.242A pdb=" N GLN A1055 " --> pdb=" O PRO A 698 " (cutoff:3.500A)
removed outlier: 3.771A pdb=" N THR A1059 " --> pdb=" O MET A1080 " (cutoff:3.500A)
removed outlier: 3.774A pdb=" N ALA A1061 " --> pdb=" O PHE A1078 " (cutoff:3.500A)
removed outlier: 4.539A pdb=" N PHE A1078 " --> pdb=" O ALA A1061 " (cutoff:3.500A)
Processing sheet with id=AB7, first strand: chain 'A' and resid 716 through 719
removed outlier: 4.252A pdb=" N LYS A 716 " --> pdb=" O LEU A 844 " (cutoff:3.500A)
Processing sheet with id=AB8, first strand: chain 'A' and resid 771 through 772
removed outlier: 5.749A pdb=" N ILE A 771 " --> pdb=" O GLN C 686 " (cutoff:3.500A)
No H-bonds generated for sheet with id=AB8
Processing sheet with id=AB9, first strand: chain 'A' and resid 867 through 868
Processing sheet with id=AC1, first strand: chain 'A' and resid 1103 through 1105
Processing sheet with id=AC2, first strand: chain 'B' and resid 32 through 34
removed outlier: 7.772A pdb=" N ASN B 65 " --> pdb=" O HIS B 259 " (cutoff:3.500A)
removed outlier: 5.617A pdb=" N HIS B 259 " --> pdb=" O ASN B 65 " (cutoff:3.500A)
removed outlier: 4.075A pdb=" N HIS B 184 " --> pdb=" O GLU B 99 " (cutoff:3.500A)
removed outlier: 3.946A pdb=" N ILE B 183 " --> pdb=" O ALA B 206 " (cutoff:3.500A)
removed outlier: 5.880A pdb=" N LEU B 197 " --> pdb=" O LYS B 224 " (cutoff:3.500A)
removed outlier: 4.063A pdb=" N LYS B 224 " --> pdb=" O LEU B 197 " (cutoff:3.500A)
removed outlier: 6.765A pdb=" N VAL B 199 " --> pdb=" O ILE B 222 " (cutoff:3.500A)
removed outlier: 6.920A pdb=" N TYR B 203 " --> pdb=" O VAL B 218 " (cutoff:3.500A)
removed outlier: 9.286A pdb=" N VAL B 218 " --> pdb=" O TYR B 203 " (cutoff:3.500A)
removed outlier: 10.771A pdb=" N ARG B 205 " --> pdb=" O PHE B 216 " (cutoff:3.500A)
removed outlier: 10.666A pdb=" N PHE B 216 " --> pdb=" O ARG B 205 " (cutoff:3.500A)
removed outlier: 5.633A pdb=" N ARG B 38 " --> pdb=" O SER B 217 " (cutoff:3.500A)
removed outlier: 8.707A pdb=" N LEU B 219 " --> pdb=" O ARG B 38 " (cutoff:3.500A)
removed outlier: 7.167A pdb=" N PHE B 40 " --> pdb=" O LEU B 219 " (cutoff:3.500A)
Processing sheet with id=AC3, first strand: chain 'B' and resid 32 through 34
Processing sheet with id=AC4, first strand: chain 'B' and resid 51 through 59
removed outlier: 4.069A pdb=" N ASP B 277 " --> pdb=" O GLU B 268 " (cutoff:3.500A)
Processing sheet with id=AC5, first strand: chain 'B' and resid 87 through 88
removed outlier: 13.853A pdb=" N PHE B 234 " --> pdb=" O PHE B 136 " (cutoff:3.500A)
removed outlier: 13.711A pdb=" N PHE B 138 " --> pdb=" O PHE B 234 " (cutoff:3.500A)
removed outlier: 12.969A pdb=" N VAL B 236 " --> pdb=" O PHE B 138 " (cutoff:3.500A)
removed outlier: 10.461A pdb=" N GLN B 140 " --> pdb=" O VAL B 236 " (cutoff:3.500A)
removed outlier: 10.204A pdb=" N MET B 238 " --> pdb=" O GLN B 140 " (cutoff:3.500A)
removed outlier: 7.764A pdb=" N LEU B 240 " --> pdb=" O PRO B 142 " (cutoff:3.500A)
removed outlier: 6.408A pdb=" N LEU B 144 " --> pdb=" O LEU B 240 " (cutoff:3.500A)
removed outlier: 6.538A pdb=" N TYR B 137 " --> pdb=" O LEU B 158 " (cutoff:3.500A)
removed outlier: 7.374A pdb=" N VAL B 156 " --> pdb=" O CYS B 139 " (cutoff:3.500A)
removed outlier: 11.248A pdb=" N ASP B 141 " --> pdb=" O SER B 154 " (cutoff:3.500A)
removed outlier: 10.455A pdb=" N SER B 154 " --> pdb=" O ASP B 141 " (cutoff:3.500A)
removed outlier: 12.264A pdb=" N MET B 143 " --> pdb=" O TYR B 152 " (cutoff:3.500A)
removed outlier: 9.565A pdb=" N TYR B 152 " --> pdb=" O MET B 143 " (cutoff:3.500A)
removed outlier: 7.768A pdb=" N THR B 145 " --> pdb=" O SER B 150 " (cutoff:3.500A)
removed outlier: 7.602A pdb=" N SER B 150 " --> pdb=" O THR B 145 " (cutoff:3.500A)
Processing sheet with id=AC6, first strand: chain 'B' and resid 87 through 88
removed outlier: 6.453A pdb=" N THR B 239 " --> pdb=" O ILE B 104 " (cutoff:3.500A)
removed outlier: 6.181A pdb=" N ILE B 104 " --> pdb=" O THR B 239 " (cutoff:3.500A)
removed outlier: 5.857A pdb=" N ARG B 105 " --> pdb=" O ASN B 124 " (cutoff:3.500A)
removed outlier: 3.585A pdb=" N TYR B 165 " --> pdb=" O VAL B 133 " (cutoff:3.500A)
Processing sheet with id=AC7, first strand: chain 'B' and resid 301 through 304
Processing sheet with id=AC8, first strand: chain 'B' and resid 315 through 318
removed outlier: 5.098A pdb=" N ASP B 563 " --> pdb=" O ILE B 576 " (cutoff:3.500A)
removed outlier: 3.512A pdb=" N SER B 564 " --> pdb=" O GLY B 555 " (cutoff:3.500A)
Processing sheet with id=AC9, first strand: chain 'B' and resid 344 through 348
removed outlier: 4.013A pdb=" N VAL B 386 " --> pdb=" O ILE B 348 " (cutoff:3.500A)
removed outlier: 3.910A pdb=" N SER B 385 " --> pdb=" O GLU B 505 " (cutoff:3.500A)
Processing sheet with id=AD1, first strand: chain 'B' and resid 351 through 352
removed outlier: 6.462A pdb=" N CYS B 351 " --> pdb=" O CYS B 514 " (cutoff:3.500A)
Processing sheet with id=AD2, first strand: chain 'B' and resid 441 through 443
Processing sheet with id=AD3, first strand: chain 'B' and resid 462 through 463
Processing sheet with id=AD4, first strand: chain 'B' and resid 645 through 651
removed outlier: 6.250A pdb=" N THR B 645 " --> pdb=" O ALA B 677 " (cutoff:3.500A)
removed outlier: 8.464A pdb=" N THR B 679 " --> pdb=" O THR B 645 " (cutoff:3.500A)
removed outlier: 8.590A pdb=" N GLU B 647 " --> pdb=" O THR B 679 " (cutoff:3.500A)
Processing sheet with id=AD5, first strand: chain 'B' and resid 685 through 686
Processing sheet with id=AD6, first strand: chain 'B' and resid 694 through 711
removed outlier: 6.288A pdb=" N THR B 694 " --> pdb=" O THR B1059 " (cutoff:3.500A)
removed outlier: 6.720A pdb=" N THR B1059 " --> pdb=" O THR B 694 " (cutoff:3.500A)
removed outlier: 6.757A pdb=" N ALA B 696 " --> pdb=" O ASN B1057 " (cutoff:3.500A)
removed outlier: 6.730A pdb=" N ASN B1057 " --> pdb=" O ALA B 696 " (cutoff:3.500A)
removed outlier: 6.242A pdb=" N GLN B1055 " --> pdb=" O PRO B 698 " (cutoff:3.500A)
removed outlier: 6.037A pdb=" N TYR B1050 " --> pdb=" O HIS B1031 " (cutoff:3.500A)
removed outlier: 5.755A pdb=" N HIS B1031 " --> pdb=" O TYR B1050 " (cutoff:3.500A)
Processing sheet with id=AD7, first strand: chain 'B' and resid 694 through 711
removed outlier: 6.288A pdb=" N THR B 694 " --> pdb=" O THR B1059 " (cutoff:3.500A)
removed outlier: 6.720A pdb=" N THR B1059 " --> pdb=" O THR B 694 " (cutoff:3.500A)
removed outlier: 6.757A pdb=" N ALA B 696 " --> pdb=" O ASN B1057 " (cutoff:3.500A)
removed outlier: 6.730A pdb=" N ASN B1057 " --> pdb=" O ALA B 696 " (cutoff:3.500A)
removed outlier: 6.242A pdb=" N GLN B1055 " --> pdb=" O PRO B 698 " (cutoff:3.500A)
removed outlier: 3.771A pdb=" N THR B1059 " --> pdb=" O MET B1080 " (cutoff:3.500A)
removed outlier: 3.773A pdb=" N ALA B1061 " --> pdb=" O PHE B1078 " (cutoff:3.500A)
removed outlier: 4.539A pdb=" N PHE B1078 " --> pdb=" O ALA B1061 " (cutoff:3.500A)
Processing sheet with id=AD8, first strand: chain 'B' and resid 716 through 719
removed outlier: 4.252A pdb=" N LYS B 716 " --> pdb=" O LEU B 844 " (cutoff:3.500A)
Processing sheet with id=AD9, first strand: chain 'B' and resid 867 through 868
Processing sheet with id=AE1, first strand: chain 'B' and resid 1103 through 1105
Processing sheet with id=AE2, first strand: chain 'C' and resid 32 through 34
removed outlier: 7.772A pdb=" N ASN C 65 " --> pdb=" O HIS C 259 " (cutoff:3.500A)
removed outlier: 5.617A pdb=" N HIS C 259 " --> pdb=" O ASN C 65 " (cutoff:3.500A)
removed outlier: 4.075A pdb=" N HIS C 184 " --> pdb=" O GLU C 99 " (cutoff:3.500A)
removed outlier: 3.946A pdb=" N ILE C 183 " --> pdb=" O ALA C 206 " (cutoff:3.500A)
removed outlier: 5.880A pdb=" N LEU C 197 " --> pdb=" O LYS C 224 " (cutoff:3.500A)
removed outlier: 4.063A pdb=" N LYS C 224 " --> pdb=" O LEU C 197 " (cutoff:3.500A)
removed outlier: 6.765A pdb=" N VAL C 199 " --> pdb=" O ILE C 222 " (cutoff:3.500A)
removed outlier: 6.920A pdb=" N TYR C 203 " --> pdb=" O VAL C 218 " (cutoff:3.500A)
removed outlier: 9.287A pdb=" N VAL C 218 " --> pdb=" O TYR C 203 " (cutoff:3.500A)
removed outlier: 10.772A pdb=" N ARG C 205 " --> pdb=" O PHE C 216 " (cutoff:3.500A)
removed outlier: 10.666A pdb=" N PHE C 216 " --> pdb=" O ARG C 205 " (cutoff:3.500A)
removed outlier: 5.633A pdb=" N ARG C 38 " --> pdb=" O SER C 217 " (cutoff:3.500A)
removed outlier: 8.707A pdb=" N LEU C 219 " --> pdb=" O ARG C 38 " (cutoff:3.500A)
removed outlier: 7.167A pdb=" N PHE C 40 " --> pdb=" O LEU C 219 " (cutoff:3.500A)
Processing sheet with id=AE3, first strand: chain 'C' and resid 32 through 34
Processing sheet with id=AE4, first strand: chain 'C' and resid 51 through 59
removed outlier: 4.068A pdb=" N ASP C 277 " --> pdb=" O GLU C 268 " (cutoff:3.500A)
Processing sheet with id=AE5, first strand: chain 'C' and resid 87 through 88
removed outlier: 13.853A pdb=" N PHE C 234 " --> pdb=" O PHE C 136 " (cutoff:3.500A)
removed outlier: 13.711A pdb=" N PHE C 138 " --> pdb=" O PHE C 234 " (cutoff:3.500A)
removed outlier: 12.969A pdb=" N VAL C 236 " --> pdb=" O PHE C 138 " (cutoff:3.500A)
removed outlier: 10.461A pdb=" N GLN C 140 " --> pdb=" O VAL C 236 " (cutoff:3.500A)
removed outlier: 10.203A pdb=" N MET C 238 " --> pdb=" O GLN C 140 " (cutoff:3.500A)
removed outlier: 7.763A pdb=" N LEU C 240 " --> pdb=" O PRO C 142 " (cutoff:3.500A)
removed outlier: 6.407A pdb=" N LEU C 144 " --> pdb=" O LEU C 240 " (cutoff:3.500A)
removed outlier: 6.538A pdb=" N TYR C 137 " --> pdb=" O LEU C 158 " (cutoff:3.500A)
removed outlier: 7.373A pdb=" N VAL C 156 " --> pdb=" O CYS C 139 " (cutoff:3.500A)
removed outlier: 11.248A pdb=" N ASP C 141 " --> pdb=" O SER C 154 " (cutoff:3.500A)
removed outlier: 10.455A pdb=" N SER C 154 " --> pdb=" O ASP C 141 " (cutoff:3.500A)
removed outlier: 12.264A pdb=" N MET C 143 " --> pdb=" O TYR C 152 " (cutoff:3.500A)
removed outlier: 9.565A pdb=" N TYR C 152 " --> pdb=" O MET C 143 " (cutoff:3.500A)
removed outlier: 7.768A pdb=" N THR C 145 " --> pdb=" O SER C 150 " (cutoff:3.500A)
removed outlier: 7.602A pdb=" N SER C 150 " --> pdb=" O THR C 145 " (cutoff:3.500A)
Processing sheet with id=AE6, first strand: chain 'C' and resid 87 through 88
removed outlier: 6.453A pdb=" N THR C 239 " --> pdb=" O ILE C 104 " (cutoff:3.500A)
removed outlier: 6.180A pdb=" N ILE C 104 " --> pdb=" O THR C 239 " (cutoff:3.500A)
removed outlier: 5.857A pdb=" N ARG C 105 " --> pdb=" O ASN C 124 " (cutoff:3.500A)
removed outlier: 3.585A pdb=" N TYR C 165 " --> pdb=" O VAL C 133 " (cutoff:3.500A)
Processing sheet with id=AE7, first strand: chain 'C' and resid 301 through 304
Processing sheet with id=AE8, first strand: chain 'C' and resid 315 through 318
removed outlier: 5.098A pdb=" N ASP C 563 " --> pdb=" O ILE C 576 " (cutoff:3.500A)
removed outlier: 3.513A pdb=" N SER C 564 " --> pdb=" O GLY C 555 " (cutoff:3.500A)
Processing sheet with id=AE9, first strand: chain 'C' and resid 344 through 348
removed outlier: 4.014A pdb=" N VAL C 386 " --> pdb=" O ILE C 348 " (cutoff:3.500A)
removed outlier: 3.910A pdb=" N SER C 385 " --> pdb=" O GLU C 505 " (cutoff:3.500A)
Processing sheet with id=AF1, first strand: chain 'C' and resid 351 through 352
removed outlier: 6.463A pdb=" N CYS C 351 " --> pdb=" O CYS C 514 " (cutoff:3.500A)
Processing sheet with id=AF2, first strand: chain 'C' and resid 441 through 443
Processing sheet with id=AF3, first strand: chain 'C' and resid 462 through 463
Processing sheet with id=AF4, first strand: chain 'C' and resid 645 through 651
removed outlier: 6.250A pdb=" N THR C 645 " --> pdb=" O ALA C 677 " (cutoff:3.500A)
removed outlier: 8.464A pdb=" N THR C 679 " --> pdb=" O THR C 645 " (cutoff:3.500A)
removed outlier: 8.590A pdb=" N GLU C 647 " --> pdb=" O THR C 679 " (cutoff:3.500A)
Processing sheet with id=AF5, first strand: chain 'C' and resid 694 through 711
removed outlier: 6.288A pdb=" N THR C 694 " --> pdb=" O THR C1059 " (cutoff:3.500A)
removed outlier: 6.720A pdb=" N THR C1059 " --> pdb=" O THR C 694 " (cutoff:3.500A)
removed outlier: 6.757A pdb=" N ALA C 696 " --> pdb=" O ASN C1057 " (cutoff:3.500A)
removed outlier: 6.730A pdb=" N ASN C1057 " --> pdb=" O ALA C 696 " (cutoff:3.500A)
removed outlier: 6.242A pdb=" N GLN C1055 " --> pdb=" O PRO C 698 " (cutoff:3.500A)
removed outlier: 6.037A pdb=" N TYR C1050 " --> pdb=" O HIS C1031 " (cutoff:3.500A)
removed outlier: 5.755A pdb=" N HIS C1031 " --> pdb=" O TYR C1050 " (cutoff:3.500A)
Processing sheet with id=AF6, first strand: chain 'C' and resid 694 through 711
removed outlier: 6.288A pdb=" N THR C 694 " --> pdb=" O THR C1059 " (cutoff:3.500A)
removed outlier: 6.720A pdb=" N THR C1059 " --> pdb=" O THR C 694 " (cutoff:3.500A)
removed outlier: 6.757A pdb=" N ALA C 696 " --> pdb=" O ASN C1057 " (cutoff:3.500A)
removed outlier: 6.730A pdb=" N ASN C1057 " --> pdb=" O ALA C 696 " (cutoff:3.500A)
removed outlier: 6.242A pdb=" N GLN C1055 " --> pdb=" O PRO C 698 " (cutoff:3.500A)
removed outlier: 3.771A pdb=" N THR C1059 " --> pdb=" O MET C1080 " (cutoff:3.500A)
removed outlier: 3.773A pdb=" N ALA C1061 " --> pdb=" O PHE C1078 " (cutoff:3.500A)
removed outlier: 4.539A pdb=" N PHE C1078 " --> pdb=" O ALA C1061 " (cutoff:3.500A)
Processing sheet with id=AF7, first strand: chain 'C' and resid 716 through 719
removed outlier: 4.252A pdb=" N LYS C 716 " --> pdb=" O LEU C 844 " (cutoff:3.500A)
Processing sheet with id=AF8, first strand: chain 'C' and resid 867 through 868
Processing sheet with id=AF9, first strand: chain 'C' and resid 1103 through 1105
1058 hydrogen bonds defined for protein.
2904 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: 13.57
Time building geometry restraints manager: 12.36 seconds
NOTE: a complete listing of the restraints can be obtained by requesting
output of .geo file.
Histogram of bond lengths:
1.16 - 1.50: 15841
1.50 - 1.84: 10464
1.84 - 2.18: 0
2.18 - 2.52: 0
2.52 - 2.87: 3
Bond restraints: 26308
Sorted by residual:
bond pdb=" C PRO A 285 "
pdb=" N LEU A 286 "
ideal model delta sigma weight residual
1.335 2.866 -1.531 1.38e-02 5.25e+03 1.23e+04
bond pdb=" C PRO B 285 "
pdb=" N LEU B 286 "
ideal model delta sigma weight residual
1.335 2.865 -1.530 1.38e-02 5.25e+03 1.23e+04
bond pdb=" C PRO C 285 "
pdb=" N LEU C 286 "
ideal model delta sigma weight residual
1.335 2.865 -1.530 1.38e-02 5.25e+03 1.23e+04
bond pdb=" C ASN A 148 "
pdb=" O ASN A 148 "
ideal model delta sigma weight residual
1.233 1.159 0.074 1.29e-02 6.01e+03 3.29e+01
bond pdb=" C ASN C 148 "
pdb=" O ASN C 148 "
ideal model delta sigma weight residual
1.233 1.159 0.074 1.29e-02 6.01e+03 3.27e+01
... (remaining 26303 not shown)
Histogram of bond angle deviations from ideal:
87.79 - 97.33: 3
97.33 - 106.87: 785
106.87 - 116.41: 17699
116.41 - 125.95: 17181
125.95 - 135.49: 243
Bond angle restraints: 35911
Sorted by residual:
angle pdb=" C PRO B 285 "
pdb=" N LEU B 286 "
pdb=" CA LEU B 286 "
ideal model delta sigma weight residual
120.72 87.79 32.93 1.67e+00 3.59e-01 3.89e+02
angle pdb=" C PRO A 285 "
pdb=" N LEU A 286 "
pdb=" CA LEU A 286 "
ideal model delta sigma weight residual
120.72 87.80 32.92 1.67e+00 3.59e-01 3.89e+02
angle pdb=" C PRO C 285 "
pdb=" N LEU C 286 "
pdb=" CA LEU C 286 "
ideal model delta sigma weight residual
120.72 87.82 32.90 1.67e+00 3.59e-01 3.88e+02
angle pdb=" N HIS C 614 "
pdb=" CA HIS C 614 "
pdb=" CB HIS C 614 "
ideal model delta sigma weight residual
110.49 135.49 -25.00 1.69e+00 3.50e-01 2.19e+02
angle pdb=" N HIS B 614 "
pdb=" CA HIS B 614 "
pdb=" CB HIS B 614 "
ideal model delta sigma weight residual
110.49 135.49 -25.00 1.69e+00 3.50e-01 2.19e+02
... (remaining 35906 not shown)
Histogram of dihedral angle deviations from ideal:
0.00 - 21.62: 16286
21.62 - 43.25: 488
43.25 - 64.87: 105
64.87 - 86.49: 54
86.49 - 108.12: 30
Dihedral angle restraints: 16963
sinusoidal: 7501
harmonic: 9462
Sorted by residual:
dihedral pdb=" C LEU A 613 "
pdb=" N LEU A 613 "
pdb=" CA LEU A 613 "
pdb=" CB LEU A 613 "
ideal model delta harmonic sigma weight residual
-122.60 -161.96 39.36 0 2.50e+00 1.60e-01 2.48e+02
dihedral pdb=" C LEU C 613 "
pdb=" N LEU C 613 "
pdb=" CA LEU C 613 "
pdb=" CB LEU C 613 "
ideal model delta harmonic sigma weight residual
-122.60 -161.96 39.36 0 2.50e+00 1.60e-01 2.48e+02
dihedral pdb=" C LEU B 613 "
pdb=" N LEU B 613 "
pdb=" CA LEU B 613 "
pdb=" CB LEU B 613 "
ideal model delta harmonic sigma weight residual
-122.60 -161.92 39.32 0 2.50e+00 1.60e-01 2.47e+02
... (remaining 16960 not shown)
Histogram of chiral volume deviations from ideal:
0.000 - 0.340: 4391
0.340 - 0.680: 18
0.680 - 1.020: 0
1.020 - 1.360: 0
1.360 - 1.700: 9
Chirality restraints: 4418
Sorted by residual:
chirality pdb=" C1 NAG C1310 "
pdb=" ND2 ASN C 148 "
pdb=" C2 NAG C1310 "
pdb=" O5 NAG C1310 "
both_signs ideal model delta sigma weight residual
False -2.40 -0.70 -1.70 2.00e-01 2.50e+01 7.22e+01
chirality pdb=" C1 NAG A1310 "
pdb=" ND2 ASN A 148 "
pdb=" C2 NAG A1310 "
pdb=" O5 NAG A1310 "
both_signs ideal model delta sigma weight residual
False -2.40 -0.70 -1.70 2.00e-01 2.50e+01 7.22e+01
chirality pdb=" C1 NAG B1310 "
pdb=" ND2 ASN B 148 "
pdb=" C2 NAG B1310 "
pdb=" O5 NAG B1310 "
both_signs ideal model delta sigma weight residual
False -2.40 -0.70 -1.70 2.00e-01 2.50e+01 7.22e+01
... (remaining 4415 not shown)
Planarity restraints: 4588
Sorted by residual:
delta sigma weight rms_deltas residual
plane pdb=" CA PRO B 285 " -0.056 2.00e-02 2.50e+03 1.03e-01 1.06e+02
pdb=" C PRO B 285 " 0.175 2.00e-02 2.50e+03
pdb=" O PRO B 285 " -0.088 2.00e-02 2.50e+03
pdb=" N LEU B 286 " -0.032 2.00e-02 2.50e+03
delta sigma weight rms_deltas residual
plane pdb=" CA PRO A 285 " -0.056 2.00e-02 2.50e+03 1.03e-01 1.06e+02
pdb=" C PRO A 285 " 0.175 2.00e-02 2.50e+03
pdb=" O PRO A 285 " -0.088 2.00e-02 2.50e+03
pdb=" N LEU A 286 " -0.031 2.00e-02 2.50e+03
delta sigma weight rms_deltas residual
plane pdb=" CA PRO C 285 " -0.056 2.00e-02 2.50e+03 1.03e-01 1.06e+02
pdb=" C PRO C 285 " 0.175 2.00e-02 2.50e+03
pdb=" O PRO C 285 " -0.088 2.00e-02 2.50e+03
pdb=" N LEU C 286 " -0.032 2.00e-02 2.50e+03
... (remaining 4585 not shown)
Histogram of nonbonded interaction distances:
2.49 - 2.97: 12786
2.97 - 3.46: 22373
3.46 - 3.94: 42075
3.94 - 4.42: 47191
4.42 - 4.90: 77853
Nonbonded interactions: 202278
Sorted by model distance:
nonbonded pdb=" O GLY B 891 "
pdb=" NZ LYS B1021 "
model vdw
2.492 3.120
nonbonded pdb=" O GLY C 891 "
pdb=" NZ LYS C1021 "
model vdw
2.492 3.120
nonbonded pdb=" O GLY A 891 "
pdb=" NZ LYS A1021 "
model vdw
2.492 3.120
nonbonded pdb=" OD1 ASP C 44 "
pdb=" N ASP C 45 "
model vdw
2.528 3.120
nonbonded pdb=" OD1 ASP A 44 "
pdb=" N ASP A 45 "
model vdw
2.528 3.120
... (remaining 202273 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' and (resid 18 through 97 or (resid 98 through 99 and (name N or name \
CA or name C or name O or name CB )) or resid 100 through 1125 or resid 1301 thr \
ough 1311))
selection = (chain 'C' and (resid 18 through 97 or (resid 98 through 99 and (name N or name \
CA or name C or name O or name CB )) or resid 100 through 559 or (resid 560 and \
(name N or name CA or name C or name O or name CB )) or resid 561 through 1125 o \
r resid 1301 through 1311))
}
ncs_group {
reference = chain 'D'
selection = chain 'E'
selection = chain 'F'
selection = chain 'I'
selection = chain 'J'
selection = chain 'K'
selection = chain 'L'
selection = chain 'M'
selection = chain 'N'
selection = chain 'O'
selection = chain 'P'
selection = chain 'S'
selection = chain 'T'
selection = chain 'U'
selection = chain 'V'
selection = chain 'W'
selection = chain 'X'
selection = chain 'Y'
selection = chain 'Z'
selection = chain 'c'
selection = chain 'd'
selection = chain 'e'
selection = chain 'f'
selection = chain 'g'
}
ncs_group {
reference = chain 'G'
selection = chain 'Q'
selection = chain 'a'
}
ncs_group {
reference = chain 'H'
selection = chain 'R'
selection = chain 'b'
}
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: 10.960
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: 1.200
Check model and map are aligned: 0.210
Set scattering table: 0.270
Process input model: 76.880
Find NCS groups from input model: 1.520
Set up NCS constraints: 0.200
Set refine NCS operators: 0.000
Adjust number of macro_cycles: 0.000
Reset NCS operators: 0.000
Extract rigid body selections: 0.000
Check and reset occupancies: 0.010
Load rotamer database and sin/cos tables:13.490
Set ADP refinement strategy: 0.000
Make a string to write initial .geo file:0.000
Internal consistency checks: 0.000
Total: 104.760
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7628
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 : 0.020 1.531 26308 Z= 1.632
Angle : 1.411 32.925 35911 Z= 0.921
Chirality : 0.117 1.700 4418
Planarity : 0.006 0.103 4525
Dihedral : 12.485 108.116 10765
Min Nonbonded Distance : 2.492
Molprobity Statistics.
All-atom Clashscore : 1.63
Ramachandran Plot:
Outliers : 0.19 %
Allowed : 4.38 %
Favored : 95.44 %
Rotamer:
Outliers : 1.13 %
Allowed : 1.38 %
Favored : 97.50 %
Cbeta Deviations : 0.20 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 0.02 (0.14), residues: 3222
helix: -0.11 (0.18), residues: 729
sheet: 1.20 (0.18), residues: 702
loop : -0.36 (0.13), residues: 1791
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.026 0.005 TRP B1085
HIS 0.005 0.001 HIS B 128
PHE 0.021 0.003 PHE A 234
TYR 0.035 0.004 TYR B 203
ARG 0.005 0.000 ARG C 347
*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
6444 Ramachandran restraints generated.
3222 Oldfield, 0 Emsley, 3222 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
6444 Ramachandran restraints generated.
3222 Oldfield, 0 Emsley, 3222 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
412 residues out of total 2826 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 27
poor density : 385
time to evaluate : 2.895
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: A 1084 HIS cc_start: 0.7971 (m90) cc_final: 0.7724 (m90)
REVERT: A 1102 ASN cc_start: 0.6093 (m-40) cc_final: 0.5721 (m-40)
REVERT: B 166 ASN cc_start: 0.7638 (t0) cc_final: 0.7336 (t0)
REVERT: B 952 ASN cc_start: 0.7475 (m-40) cc_final: 0.7226 (m-40)
REVERT: B 976 ILE cc_start: 0.8452 (mt) cc_final: 0.8236 (mp)
outliers start: 27
outliers final: 6
residues processed: 405
average time/residue: 1.4275
time to fit residues: 664.8169
Evaluate side-chains
198 residues out of total 2826 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 6
poor density : 192
time to evaluate : 2.835
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 125 ASN
Chi-restraints excluded: chain A residue 1117 ASN
Chi-restraints excluded: chain B residue 125 ASN
Chi-restraints excluded: chain B residue 905 GLN
Chi-restraints excluded: chain B residue 1117 ASN
Chi-restraints excluded: chain C residue 1117 ASN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 324
random chunks:
chunk 273 optimal weight: 0.8980
chunk 245 optimal weight: 0.6980
chunk 136 optimal weight: 0.0980
chunk 83 optimal weight: 0.7980
chunk 165 optimal weight: 0.9980
chunk 131 optimal weight: 0.5980
chunk 253 optimal weight: 0.6980
chunk 98 optimal weight: 0.5980
chunk 154 optimal weight: 0.4980
chunk 189 optimal weight: 0.7980
chunk 294 optimal weight: 1.9990
overall best weight: 0.4980
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 184 HIS
A 304 GLN
A 474 GLN
A 602 GLN
A 738 GLN
A 878 GLN
A 988 GLN
B 436 GLN
B 602 GLN
B 787 GLN
B 918 GLN
C 602 GLN
C 787 GLN
C 878 GLN
C 918 GLN
C 988 GLN
Total number of N/Q/H flips: 16
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7716
moved from start: 0.1709
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.045 26308 Z= 0.206
Angle : 0.620 7.956 35911 Z= 0.328
Chirality : 0.051 0.968 4418
Planarity : 0.004 0.035 4525
Dihedral : 9.929 93.867 5800
Min Nonbonded Distance : 2.422
Molprobity Statistics.
All-atom Clashscore : 2.42
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 1.33 %
Favored : 98.67 %
Rotamer:
Outliers : 1.88 %
Allowed : 8.39 %
Favored : 89.74 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 0.64 (0.14), residues: 3228
helix: 1.42 (0.20), residues: 735
sheet: 1.43 (0.20), residues: 633
loop : -0.33 (0.13), residues: 1860
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.013 0.001 TRP C 622
HIS 0.010 0.001 HIS A 184
PHE 0.016 0.001 PHE C 123
TYR 0.020 0.001 TYR B1050
ARG 0.006 0.001 ARG A 205
*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
6456 Ramachandran restraints generated.
3228 Oldfield, 0 Emsley, 3228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
6456 Ramachandran restraints generated.
3228 Oldfield, 0 Emsley, 3228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
284 residues out of total 2826 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 45
poor density : 239
time to evaluate : 3.013
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: A 762 ARG cc_start: 0.7935 (ttm110) cc_final: 0.7667 (ttp-110)
REVERT: A 1084 HIS cc_start: 0.7951 (m90) cc_final: 0.7696 (m90)
REVERT: B 184 HIS cc_start: 0.6703 (m-70) cc_final: 0.6457 (p90)
REVERT: B 344 GLU cc_start: 0.7988 (mt-10) cc_final: 0.7762 (mt-10)
REVERT: B 1033 MET cc_start: 0.8372 (ptm) cc_final: 0.8082 (ptp)
REVERT: C 723 MET cc_start: 0.8843 (ttt) cc_final: 0.8623 (ttm)
REVERT: C 916 LYS cc_start: 0.7793 (OUTLIER) cc_final: 0.7196 (mppt)
outliers start: 45
outliers final: 11
residues processed: 259
average time/residue: 1.2067
time to fit residues: 368.6143
Evaluate side-chains
195 residues out of total 2826 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 12
poor density : 183
time to evaluate : 2.711
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 325 LEU
Chi-restraints excluded: chain A residue 517 LYS
Chi-restraints excluded: chain A residue 947 LYS
Chi-restraints excluded: chain A residue 1117 ASN
Chi-restraints excluded: chain B residue 325 LEU
Chi-restraints excluded: chain B residue 505 GLU
Chi-restraints excluded: chain B residue 624 VAL
Chi-restraints excluded: chain B residue 688 ILE
Chi-restraints excluded: chain B residue 947 LYS
Chi-restraints excluded: chain C residue 688 ILE
Chi-restraints excluded: chain C residue 916 LYS
Chi-restraints excluded: chain C residue 947 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 324
random chunks:
chunk 163 optimal weight: 0.9990
chunk 91 optimal weight: 3.9990
chunk 244 optimal weight: 0.0970
chunk 200 optimal weight: 1.9990
chunk 81 optimal weight: 3.9990
chunk 294 optimal weight: 4.9990
chunk 318 optimal weight: 0.9990
chunk 262 optimal weight: 0.0030
chunk 292 optimal weight: 0.7980
chunk 100 optimal weight: 0.9990
chunk 236 optimal weight: 0.6980
overall best weight: 0.5190
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 201 HIS
A 233 GLN
A 304 GLN
A 324 ASN
A 878 GLN
B 201 HIS
B 324 ASN
B 436 GLN
B 988 GLN
C 118 GLN
C 201 HIS
C 324 ASN
Total number of N/Q/H flips: 12
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7748
moved from start: 0.2222
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.038 26308 Z= 0.182
Angle : 0.581 11.417 35911 Z= 0.299
Chirality : 0.053 1.269 4418
Planarity : 0.004 0.034 4525
Dihedral : 8.442 88.318 5789
Min Nonbonded Distance : 2.482
Molprobity Statistics.
All-atom Clashscore : 2.16
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 1.95 %
Favored : 98.05 %
Rotamer:
Outliers : 1.79 %
Allowed : 9.01 %
Favored : 89.19 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 0.51 (0.14), residues: 3228
helix: 1.46 (0.20), residues: 756
sheet: 1.25 (0.20), residues: 657
loop : -0.48 (0.13), residues: 1815
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.010 0.001 TRP A 622
HIS 0.005 0.001 HIS C 151
PHE 0.018 0.001 PHE B1104
TYR 0.020 0.001 TYR B1050
ARG 0.006 0.000 ARG A 205
*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
6456 Ramachandran restraints generated.
3228 Oldfield, 0 Emsley, 3228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
6456 Ramachandran restraints generated.
3228 Oldfield, 0 Emsley, 3228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
261 residues out of total 2826 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 43
poor density : 218
time to evaluate : 2.880
Fit side-chains
revert: symmetry clash
revert: symmetry clash
REVERT: A 517 LYS cc_start: 0.7767 (OUTLIER) cc_final: 0.6843 (mmtm)
REVERT: A 714 MET cc_start: 0.8422 (OUTLIER) cc_final: 0.8119 (mtp)
REVERT: A 1084 HIS cc_start: 0.7929 (m90) cc_final: 0.7707 (m90)
REVERT: B 123 PHE cc_start: 0.8361 (p90) cc_final: 0.8134 (p90)
REVERT: B 344 GLU cc_start: 0.7951 (mt-10) cc_final: 0.7744 (mt-10)
REVERT: B 937 GLN cc_start: 0.8212 (mt0) cc_final: 0.7930 (pt0)
REVERT: C 723 MET cc_start: 0.8916 (ttt) cc_final: 0.8636 (ttm)
outliers start: 43
outliers final: 8
residues processed: 236
average time/residue: 1.2284
time to fit residues: 340.8064
Evaluate side-chains
195 residues out of total 2826 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 10
poor density : 185
time to evaluate : 2.639
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 44 ASP
Chi-restraints excluded: chain A residue 325 LEU
Chi-restraints excluded: chain A residue 517 LYS
Chi-restraints excluded: chain A residue 714 MET
Chi-restraints excluded: chain B residue 325 LEU
Chi-restraints excluded: chain B residue 535 LEU
Chi-restraints excluded: chain B residue 624 VAL
Chi-restraints excluded: chain B residue 688 ILE
Chi-restraints excluded: chain C residue 184 HIS
Chi-restraints excluded: chain C residue 688 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 324
random chunks:
chunk 291 optimal weight: 0.6980
chunk 221 optimal weight: 0.8980
chunk 152 optimal weight: 0.0980
chunk 32 optimal weight: 0.0870
chunk 140 optimal weight: 0.6980
chunk 197 optimal weight: 4.9990
chunk 295 optimal weight: 1.9990
chunk 313 optimal weight: 2.9990
chunk 154 optimal weight: 1.9990
chunk 280 optimal weight: 3.9990
chunk 84 optimal weight: 1.9990
overall best weight: 0.4958
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 151 HIS
A 304 GLN
A 324 ASN
B 151 HIS
B 324 ASN
C 324 ASN
Total number of N/Q/H flips: 6
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7760
moved from start: 0.2505
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.051 26308 Z= 0.166
Angle : 0.549 10.997 35911 Z= 0.282
Chirality : 0.052 1.031 4418
Planarity : 0.004 0.036 4525
Dihedral : 7.641 83.625 5787
Min Nonbonded Distance : 2.510
Molprobity Statistics.
All-atom Clashscore : 2.26
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 1.36 %
Favored : 98.64 %
Rotamer:
Outliers : 1.54 %
Allowed : 9.85 %
Favored : 88.61 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 0.58 (0.14), residues: 3228
helix: 1.76 (0.20), residues: 732
sheet: 1.13 (0.19), residues: 708
loop : -0.51 (0.13), residues: 1788
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.011 0.001 TRP A 622
HIS 0.005 0.001 HIS A 184
PHE 0.015 0.001 PHE C 123
TYR 0.019 0.001 TYR B1050
ARG 0.008 0.000 ARG A 205
*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
6456 Ramachandran restraints generated.
3228 Oldfield, 0 Emsley, 3228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
6456 Ramachandran restraints generated.
3228 Oldfield, 0 Emsley, 3228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
258 residues out of total 2826 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 37
poor density : 221
time to evaluate : 2.527
Fit side-chains
revert: symmetry clash
revert: symmetry clash
REVERT: A 505 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.7527 (mm-30)
REVERT: A 517 LYS cc_start: 0.7879 (OUTLIER) cc_final: 0.6820 (mmtm)
REVERT: A 1084 HIS cc_start: 0.7908 (m90) cc_final: 0.7687 (m90)
REVERT: B 123 PHE cc_start: 0.8348 (p90) cc_final: 0.8135 (p90)
REVERT: B 937 GLN cc_start: 0.8201 (mt0) cc_final: 0.7943 (pt0)
REVERT: C 233 GLN cc_start: 0.7758 (OUTLIER) cc_final: 0.7430 (mp10)
REVERT: C 723 MET cc_start: 0.8904 (ttt) cc_final: 0.8669 (ttm)
outliers start: 37
outliers final: 15
residues processed: 234
average time/residue: 1.2139
time to fit residues: 336.3718
Evaluate side-chains
211 residues out of total 2826 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 18
poor density : 193
time to evaluate : 2.808
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 325 LEU
Chi-restraints excluded: chain A residue 408 VAL
Chi-restraints excluded: chain A residue 505 GLU
Chi-restraints excluded: chain A residue 517 LYS
Chi-restraints excluded: chain A residue 864 THR
Chi-restraints excluded: chain B residue 184 HIS
Chi-restraints excluded: chain B residue 325 LEU
Chi-restraints excluded: chain B residue 408 VAL
Chi-restraints excluded: chain B residue 517 LYS
Chi-restraints excluded: chain B residue 535 LEU
Chi-restraints excluded: chain B residue 624 VAL
Chi-restraints excluded: chain B residue 688 ILE
Chi-restraints excluded: chain C residue 184 HIS
Chi-restraints excluded: chain C residue 233 GLN
Chi-restraints excluded: chain C residue 315 GLU
Chi-restraints excluded: chain C residue 325 LEU
Chi-restraints excluded: chain C residue 408 VAL
Chi-restraints excluded: chain C residue 844 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 324
random chunks:
chunk 260 optimal weight: 0.5980
chunk 177 optimal weight: 0.0570
chunk 4 optimal weight: 1.9990
chunk 233 optimal weight: 1.9990
chunk 129 optimal weight: 0.9980
chunk 267 optimal weight: 0.8980
chunk 216 optimal weight: 10.0000
chunk 0 optimal weight: 10.0000
chunk 159 optimal weight: 3.9990
chunk 281 optimal weight: 2.9990
chunk 79 optimal weight: 0.8980
overall best weight: 0.6898
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 324 ASN
B 324 ASN
C 324 ASN
Total number of N/Q/H flips: 3
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7790
moved from start: 0.2754
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.034 26308 Z= 0.194
Angle : 0.556 7.937 35911 Z= 0.286
Chirality : 0.052 0.629 4418
Planarity : 0.004 0.038 4525
Dihedral : 7.347 81.636 5787
Min Nonbonded Distance : 2.443
Molprobity Statistics.
All-atom Clashscore : 2.32
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 1.92 %
Favored : 98.08 %
Rotamer:
Outliers : 1.84 %
Allowed : 9.80 %
Favored : 88.36 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 0.50 (0.14), residues: 3228
helix: 1.78 (0.20), residues: 732
sheet: 1.08 (0.19), residues: 708
loop : -0.61 (0.13), residues: 1788
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.010 0.001 TRP C 622
HIS 0.005 0.001 HIS C 201
PHE 0.016 0.001 PHE B 665
TYR 0.018 0.001 TYR B1050
ARG 0.007 0.001 ARG A 205
*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
6456 Ramachandran restraints generated.
3228 Oldfield, 0 Emsley, 3228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
6456 Ramachandran restraints generated.
3228 Oldfield, 0 Emsley, 3228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
257 residues out of total 2826 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 44
poor density : 213
time to evaluate : 3.372
Fit side-chains
revert: symmetry clash
REVERT: A 505 GLU cc_start: 0.7766 (mt-10) cc_final: 0.7519 (mm-30)
REVERT: A 517 LYS cc_start: 0.7975 (OUTLIER) cc_final: 0.6854 (mmtm)
REVERT: A 1084 HIS cc_start: 0.7891 (m90) cc_final: 0.7650 (m90)
REVERT: B 595 LYS cc_start: 0.7823 (OUTLIER) cc_final: 0.7529 (mmtt)
REVERT: B 937 GLN cc_start: 0.8256 (mt0) cc_final: 0.7979 (pt0)
REVERT: C 233 GLN cc_start: 0.7792 (OUTLIER) cc_final: 0.7527 (mp10)
REVERT: C 723 MET cc_start: 0.8948 (ttt) cc_final: 0.8629 (ttm)
REVERT: C 1102 ASN cc_start: 0.6963 (m-40) cc_final: 0.6361 (m110)
outliers start: 44
outliers final: 20
residues processed: 236
average time/residue: 1.1755
time to fit residues: 330.0917
Evaluate side-chains
214 residues out of total 2826 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 23
poor density : 191
time to evaluate : 2.828
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 325 LEU
Chi-restraints excluded: chain A residue 408 VAL
Chi-restraints excluded: chain A residue 490 VAL
Chi-restraints excluded: chain A residue 517 LYS
Chi-restraints excluded: chain A residue 595 LYS
Chi-restraints excluded: chain A residue 864 THR
Chi-restraints excluded: chain B residue 184 HIS
Chi-restraints excluded: chain B residue 220 LYS
Chi-restraints excluded: chain B residue 325 LEU
Chi-restraints excluded: chain B residue 408 VAL
Chi-restraints excluded: chain B residue 490 VAL
Chi-restraints excluded: chain B residue 535 LEU
Chi-restraints excluded: chain B residue 595 LYS
Chi-restraints excluded: chain B residue 624 VAL
Chi-restraints excluded: chain B residue 688 ILE
Chi-restraints excluded: chain C residue 184 HIS
Chi-restraints excluded: chain C residue 233 GLN
Chi-restraints excluded: chain C residue 315 GLU
Chi-restraints excluded: chain C residue 325 LEU
Chi-restraints excluded: chain C residue 408 VAL
Chi-restraints excluded: chain C residue 490 VAL
Chi-restraints excluded: chain C residue 688 ILE
Chi-restraints excluded: chain C residue 844 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 324
random chunks:
chunk 105 optimal weight: 0.0670
chunk 282 optimal weight: 0.4980
chunk 61 optimal weight: 4.9990
chunk 183 optimal weight: 0.9990
chunk 77 optimal weight: 1.9990
chunk 313 optimal weight: 2.9990
chunk 260 optimal weight: 0.7980
chunk 145 optimal weight: 0.5980
chunk 26 optimal weight: 2.9990
chunk 103 optimal weight: 2.9990
chunk 164 optimal weight: 0.9980
overall best weight: 0.5918
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 324 ASN
B 135 ASN
B 324 ASN
C 324 ASN
Total number of N/Q/H flips: 4
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7790
moved from start: 0.2910
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.037 26308 Z= 0.175
Angle : 0.545 8.547 35911 Z= 0.280
Chirality : 0.050 0.572 4418
Planarity : 0.004 0.040 4525
Dihedral : 7.263 79.425 5787
Min Nonbonded Distance : 2.448
Molprobity Statistics.
All-atom Clashscore : 2.74
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 1.46 %
Favored : 98.54 %
Rotamer:
Outliers : 1.67 %
Allowed : 10.35 %
Favored : 87.98 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 0.48 (0.14), residues: 3228
helix: 1.86 (0.20), residues: 732
sheet: 1.07 (0.20), residues: 705
loop : -0.66 (0.13), residues: 1791
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.010 0.001 TRP A 622
HIS 0.004 0.001 HIS A 201
PHE 0.015 0.001 PHE B1104
TYR 0.019 0.001 TYR B1050
ARG 0.008 0.000 ARG A 205
*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
6456 Ramachandran restraints generated.
3228 Oldfield, 0 Emsley, 3228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
6456 Ramachandran restraints generated.
3228 Oldfield, 0 Emsley, 3228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
245 residues out of total 2826 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 40
poor density : 205
time to evaluate : 2.822
Fit side-chains
revert: symmetry clash
revert: symmetry clash
REVERT: A 505 GLU cc_start: 0.7738 (OUTLIER) cc_final: 0.7493 (mm-30)
REVERT: A 1084 HIS cc_start: 0.7866 (m90) cc_final: 0.7633 (m90)
REVERT: B 165 TYR cc_start: 0.7252 (t80) cc_final: 0.6957 (t80)
REVERT: B 937 GLN cc_start: 0.8239 (mt0) cc_final: 0.7992 (pt0)
REVERT: C 233 GLN cc_start: 0.7750 (OUTLIER) cc_final: 0.7490 (mp10)
REVERT: C 723 MET cc_start: 0.8948 (ttt) cc_final: 0.8630 (ttm)
REVERT: C 1002 ARG cc_start: 0.8601 (OUTLIER) cc_final: 0.8211 (tpm170)
REVERT: C 1102 ASN cc_start: 0.7021 (m-40) cc_final: 0.6654 (m110)
outliers start: 40
outliers final: 19
residues processed: 227
average time/residue: 1.2219
time to fit residues: 328.9985
Evaluate side-chains
209 residues out of total 2826 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 22
poor density : 187
time to evaluate : 2.918
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 408 VAL
Chi-restraints excluded: chain A residue 490 VAL
Chi-restraints excluded: chain A residue 505 GLU
Chi-restraints excluded: chain A residue 595 LYS
Chi-restraints excluded: chain A residue 864 THR
Chi-restraints excluded: chain B residue 184 HIS
Chi-restraints excluded: chain B residue 325 LEU
Chi-restraints excluded: chain B residue 408 VAL
Chi-restraints excluded: chain B residue 490 VAL
Chi-restraints excluded: chain B residue 535 LEU
Chi-restraints excluded: chain B residue 624 VAL
Chi-restraints excluded: chain B residue 688 ILE
Chi-restraints excluded: chain C residue 45 ASP
Chi-restraints excluded: chain C residue 184 HIS
Chi-restraints excluded: chain C residue 233 GLN
Chi-restraints excluded: chain C residue 315 GLU
Chi-restraints excluded: chain C residue 325 LEU
Chi-restraints excluded: chain C residue 408 VAL
Chi-restraints excluded: chain C residue 490 VAL
Chi-restraints excluded: chain C residue 688 ILE
Chi-restraints excluded: chain C residue 1002 ARG
Chi-restraints excluded: chain C residue 1064 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 324
random chunks:
chunk 302 optimal weight: 0.9980
chunk 35 optimal weight: 0.7980
chunk 178 optimal weight: 0.9980
chunk 228 optimal weight: 0.8980
chunk 177 optimal weight: 0.9980
chunk 263 optimal weight: 5.9990
chunk 175 optimal weight: 0.5980
chunk 312 optimal weight: 2.9990
chunk 195 optimal weight: 0.6980
chunk 190 optimal weight: 7.9990
chunk 144 optimal weight: 1.9990
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 324 ASN
A 738 GLN
B 324 ASN
C 324 ASN
Total number of N/Q/H flips: 4
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7813
moved from start: 0.3017
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.040 26308 Z= 0.209
Angle : 0.556 9.199 35911 Z= 0.286
Chirality : 0.050 0.511 4418
Planarity : 0.004 0.038 4525
Dihedral : 7.262 78.616 5787
Min Nonbonded Distance : 2.293
Molprobity Statistics.
All-atom Clashscore : 2.74
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 2.14 %
Favored : 97.86 %
Rotamer:
Outliers : 1.59 %
Allowed : 10.35 %
Favored : 88.07 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 0.41 (0.14), residues: 3228
helix: 1.82 (0.20), residues: 735
sheet: 1.03 (0.19), residues: 738
loop : -0.77 (0.13), residues: 1755
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.010 0.001 TRP B 427
HIS 0.005 0.001 HIS A 201
PHE 0.023 0.002 PHE B 665
TYR 0.018 0.001 TYR B1050
ARG 0.007 0.001 ARG A 205
*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
6456 Ramachandran restraints generated.
3228 Oldfield, 0 Emsley, 3228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
6456 Ramachandran restraints generated.
3228 Oldfield, 0 Emsley, 3228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
240 residues out of total 2826 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 38
poor density : 202
time to evaluate : 2.688
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: A 505 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.7522 (mm-30)
REVERT: A 1084 HIS cc_start: 0.7872 (m90) cc_final: 0.7632 (m90)
REVERT: B 165 TYR cc_start: 0.7246 (t80) cc_final: 0.6933 (t80)
REVERT: B 937 GLN cc_start: 0.8234 (mt0) cc_final: 0.7997 (pt0)
REVERT: C 233 GLN cc_start: 0.7791 (OUTLIER) cc_final: 0.7528 (mp10)
REVERT: C 723 MET cc_start: 0.8971 (ttt) cc_final: 0.8683 (ttt)
REVERT: C 1002 ARG cc_start: 0.8611 (OUTLIER) cc_final: 0.8177 (tpm170)
REVERT: C 1102 ASN cc_start: 0.7216 (m-40) cc_final: 0.6916 (m110)
outliers start: 38
outliers final: 21
residues processed: 224
average time/residue: 1.2136
time to fit residues: 321.0080
Evaluate side-chains
213 residues out of total 2826 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 24
poor density : 189
time to evaluate : 2.612
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 408 VAL
Chi-restraints excluded: chain A residue 490 VAL
Chi-restraints excluded: chain A residue 505 GLU
Chi-restraints excluded: chain A residue 595 LYS
Chi-restraints excluded: chain A residue 864 THR
Chi-restraints excluded: chain B residue 184 HIS
Chi-restraints excluded: chain B residue 325 LEU
Chi-restraints excluded: chain B residue 408 VAL
Chi-restraints excluded: chain B residue 490 VAL
Chi-restraints excluded: chain B residue 535 LEU
Chi-restraints excluded: chain B residue 624 VAL
Chi-restraints excluded: chain B residue 688 ILE
Chi-restraints excluded: chain C residue 45 ASP
Chi-restraints excluded: chain C residue 129 ILE
Chi-restraints excluded: chain C residue 184 HIS
Chi-restraints excluded: chain C residue 233 GLN
Chi-restraints excluded: chain C residue 315 GLU
Chi-restraints excluded: chain C residue 325 LEU
Chi-restraints excluded: chain C residue 408 VAL
Chi-restraints excluded: chain C residue 490 VAL
Chi-restraints excluded: chain C residue 688 ILE
Chi-restraints excluded: chain C residue 844 LEU
Chi-restraints excluded: chain C residue 1002 ARG
Chi-restraints excluded: chain C residue 1064 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 324
random chunks:
chunk 193 optimal weight: 2.9990
chunk 124 optimal weight: 8.9990
chunk 186 optimal weight: 3.9990
chunk 94 optimal weight: 1.9990
chunk 61 optimal weight: 5.9990
chunk 60 optimal weight: 3.9990
chunk 198 optimal weight: 0.8980
chunk 212 optimal weight: 0.9980
chunk 154 optimal weight: 1.9990
chunk 29 optimal weight: 1.9990
chunk 245 optimal weight: 0.9990
overall best weight: 1.3786
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 324 ASN
B 324 ASN
C 324 ASN
Total number of N/Q/H flips: 3
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7871
moved from start: 0.3187
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.005 0.054 26308 Z= 0.325
Angle : 0.630 8.785 35911 Z= 0.325
Chirality : 0.052 0.476 4418
Planarity : 0.005 0.041 4525
Dihedral : 7.676 80.365 5787
Min Nonbonded Distance : 2.431
Molprobity Statistics.
All-atom Clashscore : 2.66
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 2.57 %
Favored : 97.43 %
Rotamer:
Outliers : 1.79 %
Allowed : 10.26 %
Favored : 87.94 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 0.11 (0.14), residues: 3228
helix: 1.53 (0.19), residues: 735
sheet: 0.98 (0.19), residues: 723
loop : -0.99 (0.13), residues: 1770
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.012 0.002 TRP B 427
HIS 0.008 0.002 HIS A 201
PHE 0.023 0.002 PHE A 665
TYR 0.024 0.002 TYR C 484
ARG 0.006 0.001 ARG A 347
*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
6456 Ramachandran restraints generated.
3228 Oldfield, 0 Emsley, 3228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
6456 Ramachandran restraints generated.
3228 Oldfield, 0 Emsley, 3228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
245 residues out of total 2826 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 43
poor density : 202
time to evaluate : 3.240
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: A 947 LYS cc_start: 0.8112 (OUTLIER) cc_final: 0.7895 (tppt)
REVERT: A 1084 HIS cc_start: 0.7900 (m90) cc_final: 0.7657 (m90)
REVERT: B 165 TYR cc_start: 0.7338 (t80) cc_final: 0.7091 (t80)
REVERT: B 937 GLN cc_start: 0.8286 (mt0) cc_final: 0.8033 (pt0)
REVERT: C 347 ARG cc_start: 0.8054 (OUTLIER) cc_final: 0.7637 (ttt-90)
REVERT: C 1002 ARG cc_start: 0.8615 (OUTLIER) cc_final: 0.7797 (tpm170)
outliers start: 43
outliers final: 26
residues processed: 228
average time/residue: 1.2152
time to fit residues: 329.7139
Evaluate side-chains
217 residues out of total 2826 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 29
poor density : 188
time to evaluate : 2.829
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 159 ASN
Chi-restraints excluded: chain A residue 325 LEU
Chi-restraints excluded: chain A residue 408 VAL
Chi-restraints excluded: chain A residue 490 VAL
Chi-restraints excluded: chain A residue 595 LYS
Chi-restraints excluded: chain A residue 899 LEU
Chi-restraints excluded: chain A residue 905 GLN
Chi-restraints excluded: chain A residue 947 LYS
Chi-restraints excluded: chain B residue 184 HIS
Chi-restraints excluded: chain B residue 325 LEU
Chi-restraints excluded: chain B residue 408 VAL
Chi-restraints excluded: chain B residue 490 VAL
Chi-restraints excluded: chain B residue 535 LEU
Chi-restraints excluded: chain B residue 624 VAL
Chi-restraints excluded: chain B residue 688 ILE
Chi-restraints excluded: chain B residue 899 LEU
Chi-restraints excluded: chain B residue 1064 ILE
Chi-restraints excluded: chain C residue 45 ASP
Chi-restraints excluded: chain C residue 129 ILE
Chi-restraints excluded: chain C residue 184 HIS
Chi-restraints excluded: chain C residue 315 GLU
Chi-restraints excluded: chain C residue 325 LEU
Chi-restraints excluded: chain C residue 347 ARG
Chi-restraints excluded: chain C residue 408 VAL
Chi-restraints excluded: chain C residue 490 VAL
Chi-restraints excluded: chain C residue 688 ILE
Chi-restraints excluded: chain C residue 844 LEU
Chi-restraints excluded: chain C residue 1002 ARG
Chi-restraints excluded: chain C residue 1064 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 324
random chunks:
chunk 284 optimal weight: 0.5980
chunk 299 optimal weight: 0.9980
chunk 272 optimal weight: 0.4980
chunk 291 optimal weight: 0.2980
chunk 175 optimal weight: 0.9990
chunk 126 optimal weight: 1.9990
chunk 228 optimal weight: 4.9990
chunk 89 optimal weight: 0.9990
chunk 262 optimal weight: 0.0050
chunk 275 optimal weight: 2.9990
chunk 289 optimal weight: 0.6980
overall best weight: 0.4194
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 324 ASN
A1054 GLN
B 324 ASN
B 734 ASN
B1102 ASN
C 324 ASN
Total number of N/Q/H flips: 6
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7817
moved from start: 0.3263
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.002 0.034 26308 Z= 0.155
Angle : 0.549 11.429 35911 Z= 0.283
Chirality : 0.049 0.465 4418
Planarity : 0.004 0.053 4525
Dihedral : 7.515 77.424 5787
Min Nonbonded Distance : 2.449
Molprobity Statistics.
All-atom Clashscore : 3.13
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 2.08 %
Favored : 97.92 %
Rotamer:
Outliers : 1.42 %
Allowed : 10.76 %
Favored : 87.82 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 0.28 (0.14), residues: 3228
helix: 1.84 (0.20), residues: 738
sheet: 0.97 (0.19), residues: 735
loop : -0.93 (0.13), residues: 1755
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.012 0.001 TRP A 622
HIS 0.003 0.001 HIS A 201
PHE 0.019 0.001 PHE A 665
TYR 0.019 0.001 TYR B1050
ARG 0.007 0.000 ARG A 347
*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
6456 Ramachandran restraints generated.
3228 Oldfield, 0 Emsley, 3228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
6456 Ramachandran restraints generated.
3228 Oldfield, 0 Emsley, 3228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
235 residues out of total 2826 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 34
poor density : 201
time to evaluate : 2.635
Fit side-chains
revert: symmetry clash
revert: symmetry clash
REVERT: A 1084 HIS cc_start: 0.7841 (m90) cc_final: 0.7593 (m90)
REVERT: B 165 TYR cc_start: 0.7254 (t80) cc_final: 0.6986 (t80)
REVERT: B 937 GLN cc_start: 0.8218 (mt0) cc_final: 0.7992 (pt0)
REVERT: C 1002 ARG cc_start: 0.8592 (OUTLIER) cc_final: 0.8346 (tpt170)
outliers start: 34
outliers final: 21
residues processed: 223
average time/residue: 1.2032
time to fit residues: 318.7291
Evaluate side-chains
209 residues out of total 2826 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 22
poor density : 187
time to evaluate : 2.780
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 159 ASN
Chi-restraints excluded: chain A residue 325 LEU
Chi-restraints excluded: chain A residue 408 VAL
Chi-restraints excluded: chain A residue 490 VAL
Chi-restraints excluded: chain A residue 899 LEU
Chi-restraints excluded: chain B residue 184 HIS
Chi-restraints excluded: chain B residue 325 LEU
Chi-restraints excluded: chain B residue 408 VAL
Chi-restraints excluded: chain B residue 490 VAL
Chi-restraints excluded: chain B residue 604 VAL
Chi-restraints excluded: chain B residue 624 VAL
Chi-restraints excluded: chain B residue 899 LEU
Chi-restraints excluded: chain B residue 1064 ILE
Chi-restraints excluded: chain C residue 45 ASP
Chi-restraints excluded: chain C residue 129 ILE
Chi-restraints excluded: chain C residue 184 HIS
Chi-restraints excluded: chain C residue 325 LEU
Chi-restraints excluded: chain C residue 408 VAL
Chi-restraints excluded: chain C residue 490 VAL
Chi-restraints excluded: chain C residue 844 LEU
Chi-restraints excluded: chain C residue 1002 ARG
Chi-restraints excluded: chain C residue 1064 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 324
random chunks:
chunk 191 optimal weight: 1.9990
chunk 307 optimal weight: 3.9990
chunk 187 optimal weight: 3.9990
chunk 145 optimal weight: 0.4980
chunk 213 optimal weight: 0.5980
chunk 322 optimal weight: 0.7980
chunk 297 optimal weight: 1.9990
chunk 257 optimal weight: 0.0000
chunk 26 optimal weight: 2.9990
chunk 198 optimal weight: 2.9990
chunk 157 optimal weight: 2.9990
overall best weight: 0.7786
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 324 ASN
A 602 GLN
A1102 ASN
B 324 ASN
C 324 ASN
Total number of N/Q/H flips: 5
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7831
moved from start: 0.3300
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.040 26308 Z= 0.208
Angle : 0.569 11.529 35911 Z= 0.293
Chirality : 0.051 0.771 4418
Planarity : 0.004 0.050 4525
Dihedral : 7.501 80.593 5787
Min Nonbonded Distance : 2.401
Molprobity Statistics.
All-atom Clashscore : 3.01
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 2.39 %
Favored : 97.61 %
Rotamer:
Outliers : 1.17 %
Allowed : 11.39 %
Favored : 87.44 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.03 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 0.24 (0.14), residues: 3228
helix: 1.83 (0.20), residues: 738
sheet: 0.94 (0.19), residues: 735
loop : -0.96 (0.13), residues: 1755
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.012 0.001 TRP A 622
HIS 0.005 0.001 HIS A 201
PHE 0.019 0.001 PHE B 665
TYR 0.020 0.001 TYR C 33
ARG 0.006 0.001 ARG A 347
********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
6456 Ramachandran restraints generated.
3228 Oldfield, 0 Emsley, 3228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
6456 Ramachandran restraints generated.
3228 Oldfield, 0 Emsley, 3228 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
224 residues out of total 2826 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 28
poor density : 196
time to evaluate : 2.572
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: A 947 LYS cc_start: 0.8054 (OUTLIER) cc_final: 0.7790 (tppt)
REVERT: A 1084 HIS cc_start: 0.7857 (m90) cc_final: 0.7629 (m90)
REVERT: B 165 TYR cc_start: 0.7326 (t80) cc_final: 0.7055 (t80)
REVERT: B 937 GLN cc_start: 0.8229 (mt0) cc_final: 0.8001 (pt0)
REVERT: C 1002 ARG cc_start: 0.8604 (OUTLIER) cc_final: 0.7990 (tpm170)
outliers start: 28
outliers final: 22
residues processed: 212
average time/residue: 1.1614
time to fit residues: 292.9103
Evaluate side-chains
215 residues out of total 2826 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 24
poor density : 191
time to evaluate : 2.768
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 159 ASN
Chi-restraints excluded: chain A residue 408 VAL
Chi-restraints excluded: chain A residue 490 VAL
Chi-restraints excluded: chain A residue 899 LEU
Chi-restraints excluded: chain A residue 947 LYS
Chi-restraints excluded: chain A residue 1102 ASN
Chi-restraints excluded: chain B residue 184 HIS
Chi-restraints excluded: chain B residue 325 LEU
Chi-restraints excluded: chain B residue 408 VAL
Chi-restraints excluded: chain B residue 490 VAL
Chi-restraints excluded: chain B residue 604 VAL
Chi-restraints excluded: chain B residue 624 VAL
Chi-restraints excluded: chain B residue 688 ILE
Chi-restraints excluded: chain B residue 899 LEU
Chi-restraints excluded: chain B residue 1064 ILE
Chi-restraints excluded: chain C residue 45 ASP
Chi-restraints excluded: chain C residue 129 ILE
Chi-restraints excluded: chain C residue 184 HIS
Chi-restraints excluded: chain C residue 325 LEU
Chi-restraints excluded: chain C residue 408 VAL
Chi-restraints excluded: chain C residue 490 VAL
Chi-restraints excluded: chain C residue 844 LEU
Chi-restraints excluded: chain C residue 1002 ARG
Chi-restraints excluded: chain C residue 1064 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 324
random chunks:
chunk 204 optimal weight: 1.9990
chunk 273 optimal weight: 2.9990
chunk 78 optimal weight: 2.9990
chunk 237 optimal weight: 0.4980
chunk 37 optimal weight: 1.9990
chunk 71 optimal weight: 1.9990
chunk 257 optimal weight: 0.0370
chunk 107 optimal weight: 2.9990
chunk 264 optimal weight: 1.9990
chunk 32 optimal weight: 0.2980
chunk 47 optimal weight: 0.0040
overall best weight: 0.5672
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 324 ASN
A1102 ASN
B 324 ASN
C 324 ASN
Total number of N/Q/H flips: 4
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.153454 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.122481 restraints weight = 29255.334|
|-----------------------------------------------------------------------------|
r_work (start): 0.3368 rms_B_bonded: 2.20
r_work: 0.3201 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.3079 rms_B_bonded: 3.90 restraints_weight: 0.2500
r_work (final): 0.3079
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8230
moved from start: 0.3351
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.036 26308 Z= 0.173
Angle : 0.552 10.455 35911 Z= 0.285
Chirality : 0.050 0.801 4418
Planarity : 0.004 0.049 4525
Dihedral : 7.373 80.363 5787
Min Nonbonded Distance : 2.428
Molprobity Statistics.
All-atom Clashscore : 2.99
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 2.17 %
Favored : 97.83 %
Rotamer:
Outliers : 1.13 %
Allowed : 11.56 %
Favored : 87.32 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.03 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 0.29 (0.14), residues: 3228
helix: 1.92 (0.20), residues: 738
sheet: 0.93 (0.19), residues: 735
loop : -0.93 (0.13), residues: 1755
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.013 0.001 TRP A 622
HIS 0.004 0.001 HIS A 201
PHE 0.016 0.001 PHE A 665
TYR 0.019 0.001 TYR B1050
ARG 0.007 0.000 ARG A 347
Origin is already at (0, 0, 0), no shifts will be applied
===============================================================================
Job complete
usr+sys time: 7736.16 seconds
wall clock time: 138 minutes 43.06 seconds (8323.06 seconds total)