Starting phenix.real_space_refine (version: dev)
on Thu Jul 7 11:42:24 2022 by dcliebschner
===============================================================================
Processing files:
-------------------------------------------------------------------------------
Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7llk_23424/07_2022/7llk_23424_trim.pdb
Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7llk_23424/07_2022/7llk_23424.map
Processing PHIL parameters:
-------------------------------------------------------------------------------
Adding command-line PHIL:
-------------------------
refinement.macro_cycles=10
scattering_table=electron
resolution=4.8
write_initial_geo_file=False
Final processed PHIL parameters:
-------------------------------------------------------------------------------
data_manager {
real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7llk_23424/07_2022/7llk_23424.map"
default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7llk_23424/07_2022/7llk_23424.map"
model {
file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7llk_23424/07_2022/7llk_23424_trim.pdb"
}
default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7llk_23424/07_2022/7llk_23424_trim.pdb"
}
resolution = 4.8
write_initial_geo_file = False
refinement {
macro_cycles = 10
}
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
-------------------------------------------------------------------------------
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= 0.004 sd= 0.111
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
Convert atoms to be neutral
Process input model
Symmetric amino acids flipped
Residue "A TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "A TYR 435": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "D GLU 85": "OE1" <-> "OE2"
Time to flip residues: 0.06s
Monomer Library directory:
"/net/cci-filer2/raid1/xp/phenix/phenix-dev-4648/modules/chem_data/mon_lib"
Total number of atoms: 38982
Number of models: 1
Model: ""
Number of chains: 47
Chain: "E"
Number of atoms: 6894
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 440, 6894
Classifications: {'peptide': 440}
Link IDs: {'PTRANS': 22, 'TRANS': 417}
Chain breaks: 3
Chain: "F"
Number of atoms: 2005
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 126, 2005
Classifications: {'peptide': 126}
Modifications used: {'COO': 1}
Link IDs: {'PTRANS': 1, 'TRANS': 124}
Chain breaks: 1
Chain: "G"
Number of atoms: 2100
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 131, 2100
Classifications: {'peptide': 131}
Modifications used: {'NH3': 1}
Link IDs: {'PTRANS': 3, 'TRANS': 127}
Chain: "H"
Number of atoms: 1525
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 102, 1525
Classifications: {'peptide': 102}
Link IDs: {'PTRANS': 5, 'TRANS': 96}
Chain breaks: 1
Chain: "A"
Number of atoms: 6894
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 440, 6894
Classifications: {'peptide': 440}
Link IDs: {'PTRANS': 22, 'TRANS': 417}
Chain breaks: 3
Chain: "B"
Number of atoms: 2005
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 126, 2005
Classifications: {'peptide': 126}
Modifications used: {'COO': 1}
Link IDs: {'PTRANS': 1, 'TRANS': 124}
Chain breaks: 1
Chain: "C"
Number of atoms: 2100
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 131, 2100
Classifications: {'peptide': 131}
Modifications used: {'NH3': 1}
Link IDs: {'PTRANS': 3, 'TRANS': 127}
Chain: "D"
Number of atoms: 1525
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 102, 1525
Classifications: {'peptide': 102}
Link IDs: {'PTRANS': 5, 'TRANS': 96}
Chain breaks: 1
Chain: "I"
Number of atoms: 6894
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 440, 6894
Classifications: {'peptide': 440}
Link IDs: {'PTRANS': 22, 'TRANS': 417}
Chain breaks: 3
Chain: "J"
Number of atoms: 2005
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 126, 2005
Classifications: {'peptide': 126}
Modifications used: {'COO': 1}
Link IDs: {'PTRANS': 1, 'TRANS': 124}
Chain breaks: 1
Chain: "K"
Number of atoms: 2100
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 131, 2100
Classifications: {'peptide': 131}
Modifications used: {'NH3': 1}
Link IDs: {'PTRANS': 3, 'TRANS': 127}
Chain: "L"
Number of atoms: 1525
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 102, 1525
Classifications: {'peptide': 102}
Link IDs: {'PTRANS': 5, 'TRANS': 96}
Chain breaks: 1
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 chiralities: 2
Chain: "N"
Number of atoms: 39
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 3, 39
Unusual residues: {'BMA': 1, 'NAG': 2}
Classifications: {'undetermined': 3}
Link IDs: {None: 2}
Unresolved non-hydrogen bonds: 3
Unresolved non-hydrogen angles: 6
Unresolved non-hydrogen dihedrals: 1
Unresolved non-hydrogen chiralities: 3
Chain: "O"
Number of atoms: 39
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 3, 39
Unusual residues: {'BMA': 1, 'NAG': 2}
Classifications: {'undetermined': 3}
Link IDs: {None: 2}
Unresolved non-hydrogen bonds: 3
Unresolved non-hydrogen angles: 6
Unresolved non-hydrogen dihedrals: 1
Unresolved non-hydrogen chiralities: 3
Chain: "P"
Number of atoms: 39
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 3, 39
Unusual residues: {'BMA': 1, 'NAG': 2}
Classifications: {'undetermined': 3}
Link IDs: {None: 2}
Unresolved non-hydrogen bonds: 3
Unresolved non-hydrogen angles: 6
Unresolved non-hydrogen dihedrals: 1
Unresolved non-hydrogen chiralities: 3
Chain: "Q"
Number of atoms: 39
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 3, 39
Unusual residues: {'BMA': 1, 'NAG': 2}
Classifications: {'undetermined': 3}
Link IDs: {None: 2}
Unresolved non-hydrogen bonds: 3
Unresolved non-hydrogen angles: 6
Unresolved non-hydrogen dihedrals: 1
Unresolved non-hydrogen chiralities: 3
Chain: "R"
Number of atoms: 39
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 3, 39
Unusual residues: {'BMA': 1, 'NAG': 2}
Classifications: {'undetermined': 3}
Link IDs: {None: 2}
Unresolved non-hydrogen bonds: 3
Unresolved non-hydrogen angles: 6
Unresolved non-hydrogen dihedrals: 1
Unresolved non-hydrogen chiralities: 3
Chain: "S"
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: 2
Unresolved non-hydrogen chiralities: 4
Chain: "T"
Number of atoms: 39
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 3, 39
Unusual residues: {'BMA': 1, 'NAG': 2}
Classifications: {'undetermined': 3}
Link IDs: {None: 2}
Unresolved non-hydrogen bonds: 3
Unresolved non-hydrogen angles: 6
Unresolved non-hydrogen dihedrals: 1
Unresolved non-hydrogen chiralities: 3
Chain: "U"
Number of atoms: 39
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 3, 39
Unusual residues: {'BMA': 1, 'NAG': 2}
Classifications: {'undetermined': 3}
Link IDs: {None: 2}
Unresolved non-hydrogen bonds: 3
Unresolved non-hydrogen angles: 6
Unresolved non-hydrogen dihedrals: 1
Unresolved non-hydrogen chiralities: 3
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 chiralities: 2
Chain: "W"
Number of atoms: 39
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 3, 39
Unusual residues: {'BMA': 1, 'NAG': 2}
Classifications: {'undetermined': 3}
Link IDs: {None: 2}
Unresolved non-hydrogen bonds: 3
Unresolved non-hydrogen angles: 6
Unresolved non-hydrogen dihedrals: 1
Unresolved non-hydrogen chiralities: 3
Chain: "X"
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: 2
Unresolved non-hydrogen chiralities: 4
Chain: "Y"
Number of atoms: 39
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 3, 39
Unusual residues: {'BMA': 1, 'NAG': 2}
Classifications: {'undetermined': 3}
Link IDs: {None: 2}
Unresolved non-hydrogen bonds: 3
Unresolved non-hydrogen angles: 6
Unresolved non-hydrogen dihedrals: 1
Unresolved non-hydrogen chiralities: 3
Chain: "Z"
Number of atoms: 39
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 3, 39
Unusual residues: {'BMA': 1, 'NAG': 2}
Classifications: {'undetermined': 3}
Link IDs: {None: 2}
Unresolved non-hydrogen bonds: 3
Unresolved non-hydrogen angles: 6
Unresolved non-hydrogen dihedrals: 1
Unresolved non-hydrogen chiralities: 3
Chain: "a"
Number of atoms: 39
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 3, 39
Unusual residues: {'BMA': 1, 'NAG': 2}
Classifications: {'undetermined': 3}
Link IDs: {None: 2}
Unresolved non-hydrogen bonds: 3
Unresolved non-hydrogen angles: 6
Unresolved non-hydrogen dihedrals: 1
Unresolved non-hydrogen chiralities: 3
Chain: "b"
Number of atoms: 39
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 3, 39
Unusual residues: {'BMA': 1, 'NAG': 2}
Classifications: {'undetermined': 3}
Link IDs: {None: 2}
Unresolved non-hydrogen bonds: 3
Unresolved non-hydrogen angles: 6
Unresolved non-hydrogen dihedrals: 1
Unresolved non-hydrogen chiralities: 3
Chain: "c"
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: 2
Unresolved non-hydrogen chiralities: 4
Chain: "d"
Number of atoms: 39
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 3, 39
Unusual residues: {'BMA': 1, 'NAG': 2}
Classifications: {'undetermined': 3}
Link IDs: {None: 2}
Unresolved non-hydrogen bonds: 3
Unresolved non-hydrogen angles: 6
Unresolved non-hydrogen dihedrals: 1
Unresolved non-hydrogen chiralities: 3
Chain: "e"
Number of atoms: 39
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 3, 39
Unusual residues: {'BMA': 1, 'NAG': 2}
Classifications: {'undetermined': 3}
Link IDs: {None: 2}
Unresolved non-hydrogen bonds: 3
Unresolved non-hydrogen angles: 6
Unresolved non-hydrogen dihedrals: 1
Unresolved non-hydrogen chiralities: 3
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 chiralities: 2
Chain: "g"
Number of atoms: 39
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 3, 39
Unusual residues: {'BMA': 1, 'NAG': 2}
Classifications: {'undetermined': 3}
Link IDs: {None: 2}
Unresolved non-hydrogen bonds: 3
Unresolved non-hydrogen angles: 6
Unresolved non-hydrogen dihedrals: 1
Unresolved non-hydrogen chiralities: 3
Chain: "h"
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: 2
Unresolved non-hydrogen chiralities: 4
Chain: "j"
Number of atoms: 39
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 3, 39
Unusual residues: {'BMA': 1, 'NAG': 2}
Classifications: {'undetermined': 3}
Link IDs: {None: 2}
Unresolved non-hydrogen bonds: 3
Unresolved non-hydrogen angles: 6
Unresolved non-hydrogen dihedrals: 1
Unresolved non-hydrogen chiralities: 3
Chain: "k"
Number of atoms: 39
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 3, 39
Unusual residues: {'BMA': 1, 'NAG': 2}
Classifications: {'undetermined': 3}
Link IDs: {None: 2}
Unresolved non-hydrogen bonds: 3
Unresolved non-hydrogen angles: 6
Unresolved non-hydrogen dihedrals: 1
Unresolved non-hydrogen chiralities: 3
Chain: "l"
Number of atoms: 39
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 3, 39
Unusual residues: {'BMA': 1, 'NAG': 2}
Classifications: {'undetermined': 3}
Link IDs: {None: 2}
Unresolved non-hydrogen bonds: 3
Unresolved non-hydrogen angles: 6
Unresolved non-hydrogen dihedrals: 1
Unresolved non-hydrogen chiralities: 3
Chain: "m"
Number of atoms: 39
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 3, 39
Unusual residues: {'BMA': 1, 'NAG': 2}
Classifications: {'undetermined': 3}
Link IDs: {None: 2}
Unresolved non-hydrogen bonds: 3
Unresolved non-hydrogen angles: 6
Unresolved non-hydrogen dihedrals: 1
Unresolved non-hydrogen chiralities: 3
Chain: "n"
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: 2
Unresolved non-hydrogen chiralities: 4
Chain: "o"
Number of atoms: 39
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 3, 39
Unusual residues: {'BMA': 1, 'NAG': 2}
Classifications: {'undetermined': 3}
Link IDs: {None: 2}
Unresolved non-hydrogen bonds: 3
Unresolved non-hydrogen angles: 6
Unresolved non-hydrogen dihedrals: 1
Unresolved non-hydrogen chiralities: 3
Chain: "p"
Number of atoms: 39
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 3, 39
Unusual residues: {'BMA': 1, 'NAG': 2}
Classifications: {'undetermined': 3}
Link IDs: {None: 2}
Unresolved non-hydrogen bonds: 3
Unresolved non-hydrogen angles: 6
Unresolved non-hydrogen dihedrals: 1
Unresolved non-hydrogen chiralities: 3
Chain: "q"
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 chiralities: 2
Chain: "r"
Number of atoms: 39
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 3, 39
Unusual residues: {'BMA': 1, 'NAG': 2}
Classifications: {'undetermined': 3}
Link IDs: {None: 2}
Unresolved non-hydrogen bonds: 3
Unresolved non-hydrogen angles: 6
Unresolved non-hydrogen dihedrals: 1
Unresolved non-hydrogen chiralities: 3
Chain: "s"
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: 2
Unresolved non-hydrogen chiralities: 4
Chain: "E"
Number of atoms: 42
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 3, 42
Unusual residues: {'NAG': 3}
Classifications: {'undetermined': 3}
Link IDs: {None: 2}
Unresolved non-hydrogen bonds: 3
Unresolved non-hydrogen angles: 6
Unresolved non-hydrogen chiralities: 3
Chain: "A"
Number of atoms: 56
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 4, 56
Unusual residues: {'NAG': 4}
Classifications: {'undetermined': 4}
Link IDs: {None: 3}
Unresolved non-hydrogen bonds: 4
Unresolved non-hydrogen angles: 8
Unresolved non-hydrogen chiralities: 4
Chain: "I"
Number of atoms: 42
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 3, 42
Unusual residues: {'NAG': 3}
Classifications: {'undetermined': 3}
Link IDs: {None: 2}
Unresolved non-hydrogen bonds: 3
Unresolved non-hydrogen angles: 6
Unresolved non-hydrogen chiralities: 3
Time building chain proxies: 18.70, per 1000 atoms: 0.48
Number of scatterers: 38982
At special positions: 0
Unit cell: (159.104, 166.108, 121.079, 90, 90, 90)
Space group: P 1 (No. 1)
Number of sites at special positions: 0
Number of scattering types: 5
Type Number sf(0)
S 123 16.00
O 4089 8.00
N 3404 7.00
C 12739 6.00
H 18627 1.00
sf(0) = scattering factor at diffraction angle 0.
Number of disulfides: simple=39, symmetry=0
Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.03
Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.11
Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.04
Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.02
Simple disulfide: pdb=" SG CYS E 201 " - pdb=" SG CYS E 433 " distance=2.03
Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.02
Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.04
Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03
Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.02
Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.04
Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS F 605 " distance=2.04
Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03
Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.05
Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03
Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.08
Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03
Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03
Simple disulfide: pdb=" SG CYS A 201 " - pdb=" SG CYS A 433 " distance=2.02
Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.01
Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.04
Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.02
Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.01
Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.04
Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.02
Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.04
Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.05
Simple disulfide: pdb=" SG CYS I 54 " - pdb=" SG CYS I 74 " distance=2.03
Simple disulfide: pdb=" SG CYS I 119 " - pdb=" SG CYS I 205 " distance=2.08
Simple disulfide: pdb=" SG CYS I 126 " - pdb=" SG CYS I 196 " distance=2.02
Simple disulfide: pdb=" SG CYS I 131 " - pdb=" SG CYS I 157 " distance=2.03
Simple disulfide: pdb=" SG CYS I 201 " - pdb=" SG CYS I 433 " distance=2.03
Simple disulfide: pdb=" SG CYS I 218 " - pdb=" SG CYS I 247 " distance=2.02
Simple disulfide: pdb=" SG CYS I 228 " - pdb=" SG CYS I 239 " distance=2.04
Simple disulfide: pdb=" SG CYS I 296 " - pdb=" SG CYS I 331 " distance=2.02
Simple disulfide: pdb=" SG CYS I 378 " - pdb=" SG CYS I 445 " distance=2.03
Simple disulfide: pdb=" SG CYS I 385 " - pdb=" SG CYS I 418 " distance=2.05
Simple disulfide: pdb=" SG CYS I 501 " - pdb=" SG CYS J 605 " distance=2.03
Simple disulfide: pdb=" SG CYS J 598 " - pdb=" SG CYS J 604 " distance=2.03
Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.07
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
ALPHA1-6
" BMA S 3 " - " MAN S 4 "
" BMA X 3 " - " MAN X 4 "
" BMA c 3 " - " MAN c 4 "
" BMA h 3 " - " MAN h 4 "
" BMA n 3 " - " MAN n 4 "
" BMA s 3 " - " MAN s 4 "
BETA1-4
" NAG M 1 " - " NAG M 2 "
" NAG N 1 " - " NAG N 2 "
" NAG N 2 " - " BMA N 3 "
" NAG O 1 " - " NAG O 2 "
" NAG O 2 " - " BMA O 3 "
" NAG P 1 " - " NAG P 2 "
" NAG P 2 " - " BMA P 3 "
" 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 S 2 " - " BMA S 3 "
" NAG T 1 " - " NAG T 2 "
" NAG T 2 " - " BMA T 3 "
" NAG U 1 " - " NAG U 2 "
" NAG U 2 " - " BMA U 3 "
" NAG V 1 " - " NAG V 2 "
" NAG W 1 " - " NAG W 2 "
" NAG W 2 " - " BMA W 3 "
" NAG X 1 " - " NAG X 2 "
" NAG X 2 " - " BMA X 3 "
" NAG Y 1 " - " NAG Y 2 "
" NAG Y 2 " - " BMA Y 3 "
" NAG Z 1 " - " NAG Z 2 "
" NAG Z 2 " - " BMA Z 3 "
" 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 c 2 " - " BMA c 3 "
" NAG d 1 " - " NAG d 2 "
" NAG d 2 " - " BMA d 3 "
" NAG e 1 " - " NAG e 2 "
" NAG e 2 " - " BMA e 3 "
" 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 j 1 " - " NAG j 2 "
" NAG j 2 " - " BMA j 3 "
" NAG k 1 " - " NAG k 2 "
" NAG k 2 " - " BMA k 3 "
" NAG l 1 " - " NAG l 2 "
" NAG l 2 " - " BMA l 3 "
" NAG m 1 " - " NAG m 2 "
" NAG m 2 " - " BMA m 3 "
" NAG n 1 " - " NAG n 2 "
" NAG n 2 " - " BMA n 3 "
" NAG o 1 " - " NAG o 2 "
" NAG o 2 " - " BMA o 3 "
" NAG p 1 " - " NAG p 2 "
" NAG p 2 " - " BMA p 3 "
" NAG q 1 " - " NAG q 2 "
" NAG r 1 " - " NAG r 2 "
" NAG r 2 " - " BMA r 3 "
" NAG s 1 " - " NAG s 2 "
" NAG s 2 " - " BMA s 3 "
NAG-ASN
" NAG A 601 " - " ASN A 133 "
" NAG A 602 " - " ASN A 363 "
" NAG A 603 " - " ASN A 448 "
" NAG A 604 " - " ASN A 88 "
" NAG E 601 " - " ASN E 133 "
" NAG E 602 " - " ASN E 363 "
" NAG E 603 " - " ASN E 448 "
" NAG I 601 " - " ASN I 133 "
" NAG I 602 " - " ASN I 363 "
" NAG I 603 " - " ASN I 448 "
" NAG M 1 " - " ASN E 88 "
" NAG N 1 " - " ASN I 88 "
" NAG O 1 " - " ASN E 160 "
" NAG Q 1 " - " ASN E 234 "
" NAG R 1 " - " ASN E 392 "
" NAG S 1 " - " ASN E 262 "
" NAG T 1 " - " ASN E 301 "
" NAG U 1 " - " ASN E 156 "
" NAG V 1 " - " ASN E 197 "
" NAG W 1 " - " ASN E 465 "
" NAG Y 1 " - " ASN A 160 "
" NAG a 1 " - " ASN A 234 "
" NAG b 1 " - " ASN A 392 "
" NAG c 1 " - " ASN A 262 "
" NAG d 1 " - " ASN A 301 "
" NAG e 1 " - " ASN A 156 "
" NAG f 1 " - " ASN A 197 "
" NAG g 1 " - " ASN A 465 "
" NAG j 1 " - " ASN I 160 "
" NAG l 1 " - " ASN I 234 "
" NAG m 1 " - " ASN I 392 "
" NAG n 1 " - " ASN I 262 "
" NAG o 1 " - " ASN I 301 "
" NAG p 1 " - " ASN I 156 "
" NAG q 1 " - " ASN I 197 "
" NAG r 1 " - " ASN I 465 "
Time building additional restraints: 35.75
Conformation dependent library (CDL) restraints added in 3.2 seconds
4686 Ramachandran restraints generated.
2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2.
Adding C-beta torsion restraints...
Number of C-beta restraints generated: 4458
Finding SS restraints...
Secondary structure from input PDB file:
49 helices and 49 sheets defined
21.3% alpha, 23.0% beta
0 base pairs and 0 stacking pairs defined.
Time for finding SS restraints: 1.24
Creating SS restraints...
Processing helix chain 'E' and resid 99 through 117
Processing helix chain 'E' and resid 334 through 354
removed outlier: 4.135A pdb=" N TRP E 338 " --> pdb=" O SER E 334 " (cutoff:3.500A)
removed outlier: 3.633A pdb=" N THR E 351 " --> pdb=" O GLU E 347 " (cutoff:3.500A)
removed outlier: 4.376A pdb=" N TYR E 352 " --> pdb=" O LYS E 348 " (cutoff:3.500A)
removed outlier: 3.802A pdb=" N PHE E 353 " --> pdb=" O LEU E 349 " (cutoff:3.500A)
Processing helix chain 'E' and resid 368 through 373
Processing helix chain 'E' and resid 387 through 391
Processing helix chain 'E' and resid 425 through 429
removed outlier: 3.854A pdb=" N ARG E 429 " --> pdb=" O MET E 426 " (cutoff:3.500A)
Processing helix chain 'E' and resid 474 through 484
removed outlier: 5.355A pdb=" N GLU E 482 " --> pdb=" O ASN E 478 " (cutoff:3.500A)
Processing helix chain 'F' and resid 529 through 534
Processing helix chain 'F' and resid 537 through 544
Processing helix chain 'F' and resid 569 through 596
removed outlier: 3.651A pdb=" N ILE F 573 " --> pdb=" O THR F 569 " (cutoff:3.500A)
Processing helix chain 'F' and resid 618 through 625
Processing helix chain 'F' and resid 627 through 646
removed outlier: 6.298A pdb=" N ASN F 637 " --> pdb=" O LYS F 633 " (cutoff:3.500A)
removed outlier: 5.385A pdb=" N TYR F 638 " --> pdb=" O GLU F 634 " (cutoff:3.500A)
removed outlier: 4.351A pdb=" N GLN F 640 " --> pdb=" O ASN F 636 " (cutoff:3.500A)
removed outlier: 6.079A pdb=" N LEU F 641 " --> pdb=" O ASN F 637 " (cutoff:3.500A)
removed outlier: 3.642A pdb=" N ARG F 644 " --> pdb=" O GLN F 640 " (cutoff:3.500A)
Processing helix chain 'F' and resid 648 through 653
Processing helix chain 'F' and resid 654 through 663
removed outlier: 4.840A pdb=" N LEU F 660 " --> pdb=" O ASN F 656 " (cutoff:3.500A)
removed outlier: 3.674A pdb=" N LEU F 661 " --> pdb=" O GLU F 657 " (cutoff:3.500A)
Processing helix chain 'G' and resid 62 through 67
removed outlier: 3.854A pdb=" N GLY G 65 " --> pdb=" O SER G 62 " (cutoff:3.500A)
removed outlier: 4.560A pdb=" N ARG G 66 " --> pdb=" O VAL G 63 " (cutoff:3.500A)
Processing helix chain 'G' and resid 74 through 77
Processing helix chain 'G' and resid 83 through 87
Processing helix chain 'A' and resid 99 through 117
removed outlier: 3.567A pdb=" N ILE A 109 " --> pdb=" O HIS A 105 " (cutoff:3.500A)
Processing helix chain 'A' and resid 205 through 209
removed outlier: 4.007A pdb=" N SER A 209 " --> pdb=" O PRO A 206 " (cutoff:3.500A)
Processing helix chain 'A' and resid 334 through 354
removed outlier: 4.094A pdb=" N TRP A 338 " --> pdb=" O SER A 334 " (cutoff:3.500A)
removed outlier: 3.662A pdb=" N TYR A 352 " --> pdb=" O LYS A 348 " (cutoff:3.500A)
Processing helix chain 'A' and resid 368 through 373
Processing helix chain 'A' and resid 387 through 391
Processing helix chain 'A' and resid 425 through 429
removed outlier: 3.797A pdb=" N ARG A 429 " --> pdb=" O MET A 426 " (cutoff:3.500A)
Processing helix chain 'A' and resid 474 through 484
removed outlier: 5.214A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A)
Processing helix chain 'B' and resid 529 through 534
Processing helix chain 'B' and resid 537 through 546
removed outlier: 3.786A pdb=" N LEU B 545 " --> pdb=" O ALA B 541 " (cutoff:3.500A)
Processing helix chain 'B' and resid 569 through 596
Processing helix chain 'B' and resid 618 through 625
Processing helix chain 'B' and resid 627 through 646
removed outlier: 5.938A pdb=" N ASN B 637 " --> pdb=" O LYS B 633 " (cutoff:3.500A)
removed outlier: 5.509A pdb=" N TYR B 638 " --> pdb=" O GLU B 634 " (cutoff:3.500A)
removed outlier: 4.169A pdb=" N GLN B 640 " --> pdb=" O ASN B 636 " (cutoff:3.500A)
removed outlier: 6.062A pdb=" N LEU B 641 " --> pdb=" O ASN B 637 " (cutoff:3.500A)
removed outlier: 3.598A pdb=" N ILE B 642 " --> pdb=" O TYR B 638 " (cutoff:3.500A)
removed outlier: 4.126A pdb=" N ARG B 644 " --> pdb=" O GLN B 640 " (cutoff:3.500A)
Processing helix chain 'B' and resid 654 through 663
removed outlier: 4.910A pdb=" N LEU B 660 " --> pdb=" O ASN B 656 " (cutoff:3.500A)
removed outlier: 3.588A pdb=" N LEU B 661 " --> pdb=" O GLU B 657 " (cutoff:3.500A)
Processing helix chain 'C' and resid 62 through 67
removed outlier: 4.481A pdb=" N ARG C 66 " --> pdb=" O VAL C 63 " (cutoff:3.500A)
Processing helix chain 'C' and resid 74 through 77
Processing helix chain 'C' and resid 83 through 87
Processing helix chain 'I' and resid 99 through 117
Processing helix chain 'I' and resid 205 through 209
removed outlier: 3.517A pdb=" N SER I 209 " --> pdb=" O PRO I 206 " (cutoff:3.500A)
Processing helix chain 'I' and resid 334 through 354
removed outlier: 4.155A pdb=" N TRP I 338 " --> pdb=" O SER I 334 " (cutoff:3.500A)
removed outlier: 3.647A pdb=" N TYR I 352 " --> pdb=" O LYS I 348 " (cutoff:3.500A)
Processing helix chain 'I' and resid 368 through 373
Processing helix chain 'I' and resid 387 through 391
Processing helix chain 'I' and resid 425 through 429
removed outlier: 3.821A pdb=" N ARG I 429 " --> pdb=" O MET I 426 " (cutoff:3.500A)
Processing helix chain 'I' and resid 474 through 484
removed outlier: 5.295A pdb=" N GLU I 482 " --> pdb=" O ASN I 478 " (cutoff:3.500A)
Processing helix chain 'J' and resid 529 through 534
Processing helix chain 'J' and resid 537 through 546
removed outlier: 3.788A pdb=" N LEU J 545 " --> pdb=" O ALA J 541 " (cutoff:3.500A)
Processing helix chain 'J' and resid 569 through 596
Processing helix chain 'J' and resid 618 through 625
Processing helix chain 'J' and resid 627 through 646
removed outlier: 3.509A pdb=" N GLU J 634 " --> pdb=" O GLN J 630 " (cutoff:3.500A)
removed outlier: 6.239A pdb=" N ASN J 637 " --> pdb=" O LYS J 633 " (cutoff:3.500A)
removed outlier: 5.621A pdb=" N TYR J 638 " --> pdb=" O GLU J 634 " (cutoff:3.500A)
removed outlier: 4.091A pdb=" N GLN J 640 " --> pdb=" O ASN J 636 " (cutoff:3.500A)
removed outlier: 5.782A pdb=" N LEU J 641 " --> pdb=" O ASN J 637 " (cutoff:3.500A)
removed outlier: 3.524A pdb=" N ILE J 642 " --> pdb=" O TYR J 638 " (cutoff:3.500A)
Processing helix chain 'J' and resid 648 through 653
Processing helix chain 'J' and resid 654 through 663
removed outlier: 4.764A pdb=" N LEU J 660 " --> pdb=" O ASN J 656 " (cutoff:3.500A)
removed outlier: 3.527A pdb=" N LEU J 661 " --> pdb=" O GLU J 657 " (cutoff:3.500A)
Processing helix chain 'K' and resid 62 through 65
removed outlier: 3.803A pdb=" N GLY K 65 " --> pdb=" O SER K 62 " (cutoff:3.500A)
No H-bonds generated for 'chain 'K' and resid 62 through 65'
Processing helix chain 'K' and resid 74 through 77
Processing helix chain 'K' and resid 83 through 87
Processing sheet with id=AA1, first strand: chain 'E' and resid 494 through 499
removed outlier: 3.736A pdb=" N VAL E 38 " --> pdb=" O CYS F 604 " (cutoff:3.500A)
Processing sheet with id=AA2, first strand: chain 'E' and resid 45 through 47
Processing sheet with id=AA3, first strand: chain 'E' and resid 53 through 55
Processing sheet with id=AA4, first strand: chain 'E' and resid 91 through 94
removed outlier: 4.209A pdb=" N GLU E 91 " --> pdb=" O CYS E 239 " (cutoff:3.500A)
removed outlier: 3.578A pdb=" N CYS E 239 " --> pdb=" O GLU E 91 " (cutoff:3.500A)
removed outlier: 3.529A pdb=" N GLY E 237 " --> pdb=" O PHE E 93 " (cutoff:3.500A)
Processing sheet with id=AA5, first strand: chain 'E' and resid 120 through 121
Processing sheet with id=AA6, first strand: chain 'E' and resid 129 through 132
Processing sheet with id=AA7, first strand: chain 'E' and resid 181 through 183
Processing sheet with id=AA8, first strand: chain 'E' and resid 259 through 261
removed outlier: 6.576A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A)
removed outlier: 6.544A pdb=" N GLY E 451 " --> pdb=" O GLN E 290 " (cutoff:3.500A)
removed outlier: 10.797A pdb=" N GLN E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A)
removed outlier: 12.231A pdb=" N LEU E 453 " --> pdb=" O LEU E 288 " (cutoff:3.500A)
removed outlier: 12.122A pdb=" N LEU E 288 " --> pdb=" O LEU E 453 " (cutoff:3.500A)
removed outlier: 10.381A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A)
removed outlier: 10.542A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A)
Processing sheet with id=AA9, first strand: chain 'E' and resid 259 through 261
removed outlier: 6.576A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A)
removed outlier: 6.280A pdb=" N ILE E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A)
Processing sheet with id=AB1, first strand: chain 'E' and resid 303 through 308
Processing sheet with id=AB2, first strand: chain 'E' and resid 329 through 330
removed outlier: 3.929A pdb=" N PHE E 382 " --> pdb=" O LYS E 421 " (cutoff:3.500A)
removed outlier: 3.549A pdb=" N PHE E 376 " --> pdb=" O PHE E 383 " (cutoff:3.500A)
Processing sheet with id=AB3, first strand: chain 'G' and resid 18 through 21
Processing sheet with id=AB4, first strand: chain 'G' and resid 88 through 95
removed outlier: 3.998A pdb=" N THR G 107 " --> pdb=" O TYR G 90 " (cutoff:3.500A)
removed outlier: 4.558A pdb=" N CYS G 92 " --> pdb=" O ARG G 105 " (cutoff:3.500A)
removed outlier: 5.355A pdb=" N ARG G 105 " --> pdb=" O CYS G 92 " (cutoff:3.500A)
removed outlier: 7.159A pdb=" N ARG G 94 " --> pdb=" O TRP G 103 " (cutoff:3.500A)
removed outlier: 6.188A pdb=" N TRP G 103 " --> pdb=" O ARG G 94 " (cutoff:3.500A)
Processing sheet with id=AB5, first strand: chain 'H' and resid 19 through 23
removed outlier: 3.931A pdb=" N ALA H 19 " --> pdb=" O ILE H 75 " (cutoff:3.500A)
Processing sheet with id=AB6, first strand: chain 'H' and resid 53 through 54
removed outlier: 6.916A pdb=" N TRP H 35 " --> pdb=" O VAL H 47 " (cutoff:3.500A)
removed outlier: 3.569A pdb=" N SER H 34 " --> pdb=" O GLN H 89 " (cutoff:3.500A)
removed outlier: 3.618A pdb=" N GLU H 85 " --> pdb=" O GLN H 38 " (cutoff:3.500A)
removed outlier: 6.550A pdb=" N TYR H 86 " --> pdb=" O GLY H 101 " (cutoff:3.500A)
removed outlier: 4.159A pdb=" N GLY H 101 " --> pdb=" O TYR H 86 " (cutoff:3.500A)
removed outlier: 4.094A pdb=" N ASP H 92 " --> pdb=" O TYR H 95A" (cutoff:3.500A)
removed outlier: 6.039A pdb=" N TYR H 95A" --> pdb=" O ASP H 92 " (cutoff:3.500A)
Processing sheet with id=AB7, first strand: chain 'A' and resid 494 through 499
removed outlier: 4.697A pdb=" N VAL A 36 " --> pdb=" O THR B 606 " (cutoff:3.500A)
removed outlier: 3.876A pdb=" N THR B 606 " --> pdb=" O VAL A 36 " (cutoff:3.500A)
removed outlier: 3.506A pdb=" N VAL A 38 " --> pdb=" O CYS B 604 " (cutoff:3.500A)
Processing sheet with id=AB8, first strand: chain 'A' and resid 45 through 47
Processing sheet with id=AB9, first strand: chain 'A' and resid 53 through 55
Processing sheet with id=AC1, first strand: chain 'A' and resid 91 through 94
removed outlier: 3.700A pdb=" N GLU A 91 " --> pdb=" O CYS A 239 " (cutoff:3.500A)
removed outlier: 3.736A pdb=" N GLY A 237 " --> pdb=" O PHE A 93 " (cutoff:3.500A)
Processing sheet with id=AC2, first strand: chain 'A' and resid 130 through 132
Processing sheet with id=AC3, first strand: chain 'A' and resid 181 through 183
Processing sheet with id=AC4, first strand: chain 'A' and resid 201 through 202
Processing sheet with id=AC5, first strand: chain 'A' and resid 259 through 261
removed outlier: 6.267A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A)
removed outlier: 6.386A pdb=" N GLY A 451 " --> pdb=" O GLN A 290 " (cutoff:3.500A)
removed outlier: 10.732A pdb=" N GLN A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A)
removed outlier: 12.153A pdb=" N LEU A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A)
removed outlier: 12.209A pdb=" N LEU A 288 " --> pdb=" O LEU A 453 " (cutoff:3.500A)
removed outlier: 10.455A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A)
removed outlier: 10.519A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A)
Processing sheet with id=AC6, first strand: chain 'A' and resid 259 through 261
removed outlier: 6.267A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A)
Processing sheet with id=AC7, first strand: chain 'A' and resid 303 through 308
Processing sheet with id=AC8, first strand: chain 'A' and resid 329 through 330
removed outlier: 3.810A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A)
removed outlier: 3.543A pdb=" N PHE A 376 " --> pdb=" O PHE A 383 " (cutoff:3.500A)
Processing sheet with id=AC9, first strand: chain 'A' and resid 359 through 361
Processing sheet with id=AD1, first strand: chain 'C' and resid 18 through 21
Processing sheet with id=AD2, first strand: chain 'C' and resid 88 through 89
Processing sheet with id=AD3, first strand: chain 'C' and resid 92 through 95
removed outlier: 4.524A pdb=" N LEU C 102 " --> pdb=" O ARG C 94 " (cutoff:3.500A)
Processing sheet with id=AD4, first strand: chain 'D' and resid 21 through 23
Processing sheet with id=AD5, first strand: chain 'D' and resid 53 through 54
removed outlier: 3.514A pdb=" N VAL D 47 " --> pdb=" O TRP D 35 " (cutoff:3.500A)
removed outlier: 7.196A pdb=" N TRP D 35 " --> pdb=" O VAL D 47 " (cutoff:3.500A)
removed outlier: 3.630A pdb=" N SER D 34 " --> pdb=" O GLN D 89 " (cutoff:3.500A)
removed outlier: 3.543A pdb=" N GLN D 89 " --> pdb=" O SER D 34 " (cutoff:3.500A)
removed outlier: 3.723A pdb=" N GLU D 85 " --> pdb=" O GLN D 38 " (cutoff:3.500A)
removed outlier: 6.490A pdb=" N TYR D 86 " --> pdb=" O GLY D 101 " (cutoff:3.500A)
removed outlier: 4.182A pdb=" N GLY D 101 " --> pdb=" O TYR D 86 " (cutoff:3.500A)
removed outlier: 4.066A pdb=" N ASP D 92 " --> pdb=" O TYR D 95A" (cutoff:3.500A)
removed outlier: 6.168A pdb=" N TYR D 95A" --> pdb=" O ASP D 92 " (cutoff:3.500A)
Processing sheet with id=AD6, first strand: chain 'I' and resid 494 through 499
removed outlier: 4.610A pdb=" N VAL I 36 " --> pdb=" O THR J 606 " (cutoff:3.500A)
removed outlier: 3.822A pdb=" N THR J 606 " --> pdb=" O VAL I 36 " (cutoff:3.500A)
Processing sheet with id=AD7, first strand: chain 'I' and resid 45 through 47
Processing sheet with id=AD8, first strand: chain 'I' and resid 53 through 55
Processing sheet with id=AD9, first strand: chain 'I' and resid 91 through 94
removed outlier: 3.966A pdb=" N GLU I 91 " --> pdb=" O CYS I 239 " (cutoff:3.500A)
Processing sheet with id=AE1, first strand: chain 'I' and resid 120 through 121
Processing sheet with id=AE2, first strand: chain 'I' and resid 129 through 132
Processing sheet with id=AE3, first strand: chain 'I' and resid 181 through 183
Processing sheet with id=AE4, first strand: chain 'I' and resid 259 through 261
removed outlier: 6.492A pdb=" N LEU I 260 " --> pdb=" O THR I 450 " (cutoff:3.500A)
removed outlier: 10.033A pdb=" N ASN I 448 " --> pdb=" O GLN I 290 " (cutoff:3.500A)
removed outlier: 11.622A pdb=" N GLN I 290 " --> pdb=" O ASN I 448 " (cutoff:3.500A)
removed outlier: 7.375A pdb=" N THR I 450 " --> pdb=" O LEU I 288 " (cutoff:3.500A)
Processing sheet with id=AE5, first strand: chain 'I' and resid 259 through 261
removed outlier: 6.492A pdb=" N LEU I 260 " --> pdb=" O THR I 450 " (cutoff:3.500A)
Processing sheet with id=AE6, first strand: chain 'I' and resid 303 through 308
Processing sheet with id=AE7, first strand: chain 'I' and resid 329 through 330
removed outlier: 3.664A pdb=" N ALA I 329 " --> pdb=" O CYS I 418 " (cutoff:3.500A)
removed outlier: 3.963A pdb=" N PHE I 382 " --> pdb=" O LYS I 421 " (cutoff:3.500A)
Processing sheet with id=AE8, first strand: chain 'I' and resid 359 through 361
Processing sheet with id=AE9, first strand: chain 'K' and resid 18 through 21
Processing sheet with id=AF1, first strand: chain 'K' and resid 88 through 89
Processing sheet with id=AF2, first strand: chain 'K' and resid 92 through 95
removed outlier: 4.763A pdb=" N LEU K 102 " --> pdb=" O ARG K 94 " (cutoff:3.500A)
Processing sheet with id=AF3, first strand: chain 'L' and resid 19 through 23
removed outlier: 3.938A pdb=" N ALA L 19 " --> pdb=" O ILE L 75 " (cutoff:3.500A)
Processing sheet with id=AF4, first strand: chain 'L' and resid 53 through 54
removed outlier: 7.095A pdb=" N TRP L 35 " --> pdb=" O VAL L 47 " (cutoff:3.500A)
removed outlier: 3.546A pdb=" N SER L 34 " --> pdb=" O GLN L 89 " (cutoff:3.500A)
removed outlier: 3.817A pdb=" N GLU L 85 " --> pdb=" O GLN L 38 " (cutoff:3.500A)
removed outlier: 6.545A pdb=" N TYR L 86 " --> pdb=" O GLY L 101 " (cutoff:3.500A)
removed outlier: 4.196A pdb=" N GLY L 101 " --> pdb=" O TYR L 86 " (cutoff:3.500A)
removed outlier: 4.026A pdb=" N ASP L 92 " --> pdb=" O TYR L 95A" (cutoff:3.500A)
removed outlier: 5.960A pdb=" N TYR L 95A" --> pdb=" O ASP L 92 " (cutoff:3.500A)
603 hydrogen bonds defined for protein.
1563 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: 14.62
Time building geometry restraints manager: 36.77 seconds
NOTE: a complete listing of the restraints can be obtained by requesting
output of .geo file.
Histogram of bond lengths:
0.83 - 1.03: 5281
1.03 - 1.23: 15611
1.23 - 1.43: 6339
1.43 - 1.63: 11985
1.63 - 1.83: 162
Bond restraints: 39378
Sorted by residual:
bond pdb=" C4 NAG U 2 "
pdb=" O4 NAG U 2 "
ideal model delta sigma weight residual
1.423 1.499 -0.076 1.00e-02 1.00e+04 5.85e+01
bond pdb=" C ARG L 37 "
pdb=" O ARG L 37 "
ideal model delta sigma weight residual
1.233 1.136 0.097 1.28e-02 6.10e+03 5.72e+01
bond pdb=" CD1 TRP C 100C"
pdb=" HD1 TRP C 100C"
ideal model delta sigma weight residual
0.930 1.080 -0.150 2.00e-02 2.50e+03 5.59e+01
bond pdb=" CD2 PHE C 67 "
pdb=" HD2 PHE C 67 "
ideal model delta sigma weight residual
0.930 1.079 -0.149 2.00e-02 2.50e+03 5.58e+01
bond pdb=" CD2 PHE I 353 "
pdb=" HD2 PHE I 353 "
ideal model delta sigma weight residual
0.930 1.079 -0.149 2.00e-02 2.50e+03 5.58e+01
... (remaining 39373 not shown)
Histogram of bond angle deviations from ideal:
90.29 - 99.48: 31
99.48 - 108.67: 17786
108.67 - 117.87: 34213
117.87 - 127.06: 17834
127.06 - 136.25: 482
Bond angle restraints: 70346
Sorted by residual:
angle pdb=" C1 NAG M 1 "
pdb=" C2 NAG M 1 "
pdb=" N2 NAG M 1 "
ideal model delta sigma weight residual
111.03 94.64 16.39 1.25e+00 6.40e-01 1.72e+02
angle pdb=" C1 NAG M 1 "
pdb=" C2 NAG M 1 "
pdb=" C3 NAG M 1 "
ideal model delta sigma weight residual
110.19 99.37 10.82 9.25e-01 1.17e+00 1.37e+02
angle pdb=" C5 NAG M 1 "
pdb=" C6 NAG M 1 "
pdb=" O6 NAG M 1 "
ideal model delta sigma weight residual
111.45 90.29 21.16 1.89e+00 2.79e-01 1.25e+02
angle pdb=" C2 NAG A 604 "
pdb=" C1 NAG A 604 "
pdb=" O5 NAG A 604 "
ideal model delta sigma weight residual
109.64 115.63 -5.99 5.38e-01 3.45e+00 1.24e+02
angle pdb=" N PRO E 253 "
pdb=" CA PRO E 253 "
pdb=" C PRO E 253 "
ideal model delta sigma weight residual
113.65 99.64 14.01 1.35e+00 5.49e-01 1.08e+02
... (remaining 70341 not shown)
Histogram of dihedral angle deviations from ideal:
0.00 - 18.40: 14218
18.40 - 36.80: 1283
36.80 - 55.20: 295
55.20 - 73.60: 242
73.60 - 92.00: 40
Dihedral angle restraints: 16078
sinusoidal: 7954
harmonic: 8124
Sorted by residual:
dihedral pdb=" C VAL L 26 "
pdb=" N VAL L 26 "
pdb=" CA VAL L 26 "
pdb=" CB VAL L 26 "
ideal model delta harmonic sigma weight residual
-122.00 -136.71 14.71 0 2.50e+00 1.60e-01 3.46e+01
dihedral pdb=" CA ASN E 302 "
pdb=" C ASN E 302 "
pdb=" N THR E 303 "
pdb=" CA THR E 303 "
ideal model delta harmonic sigma weight residual
180.00 -150.71 -29.29 0 5.00e+00 4.00e-02 3.43e+01
dihedral pdb=" CA SER G 49 "
pdb=" C SER G 49 "
pdb=" N SER G 50 "
pdb=" CA SER G 50 "
ideal model delta harmonic sigma weight residual
180.00 150.86 29.14 0 5.00e+00 4.00e-02 3.40e+01
... (remaining 16075 not shown)
Histogram of chiral volume deviations from ideal:
0.000 - 0.311: 3418
0.311 - 0.622: 40
0.622 - 0.933: 3
0.933 - 1.244: 0
1.244 - 1.554: 1
Chirality restraints: 3462
Sorted by residual:
chirality pdb=" C1 NAG M 2 "
pdb=" O4 NAG M 1 "
pdb=" C2 NAG M 2 "
pdb=" O5 NAG M 2 "
both_signs ideal model delta sigma weight residual
False -2.40 -2.09 -0.31 2.00e-02 2.50e+03 2.39e+02
chirality pdb=" C1 BMA a 3 "
pdb=" O4 NAG a 2 "
pdb=" C2 BMA a 3 "
pdb=" O5 BMA a 3 "
both_signs ideal model delta sigma weight residual
False -2.40 -2.63 0.23 2.00e-02 2.50e+03 1.37e+02
chirality pdb=" C1 NAG m 2 "
pdb=" O4 NAG m 1 "
pdb=" C2 NAG m 2 "
pdb=" O5 NAG m 2 "
both_signs ideal model delta sigma weight residual
False -2.40 -2.63 0.23 2.00e-02 2.50e+03 1.27e+02
... (remaining 3459 not shown)
Planarity restraints: 5735
Sorted by residual:
delta sigma weight rms_deltas residual
plane pdb=" CG GLN I 203 " -0.241 2.00e-02 2.50e+03 3.80e-01 2.17e+03
pdb=" CD GLN I 203 " 0.012 2.00e-02 2.50e+03
pdb=" OE1 GLN I 203 " 0.235 2.00e-02 2.50e+03
pdb=" NE2 GLN I 203 " -0.003 2.00e-02 2.50e+03
pdb="HE21 GLN I 203 " 0.612 2.00e-02 2.50e+03
pdb="HE22 GLN I 203 " -0.615 2.00e-02 2.50e+03
delta sigma weight rms_deltas residual
plane pdb=" CG GLN E 203 " -0.242 2.00e-02 2.50e+03 3.75e-01 2.10e+03
pdb=" CD GLN E 203 " 0.010 2.00e-02 2.50e+03
pdb=" OE1 GLN E 203 " 0.239 2.00e-02 2.50e+03
pdb=" NE2 GLN E 203 " -0.004 2.00e-02 2.50e+03
pdb="HE21 GLN E 203 " 0.601 2.00e-02 2.50e+03
pdb="HE22 GLN E 203 " -0.603 2.00e-02 2.50e+03
delta sigma weight rms_deltas residual
plane pdb=" CG GLN I 246 " -0.253 2.00e-02 2.50e+03 3.35e-01 1.68e+03
pdb=" CD GLN I 246 " 0.020 2.00e-02 2.50e+03
pdb=" OE1 GLN I 246 " 0.245 2.00e-02 2.50e+03
pdb=" NE2 GLN I 246 " -0.004 2.00e-02 2.50e+03
pdb="HE21 GLN I 246 " 0.519 2.00e-02 2.50e+03
pdb="HE22 GLN I 246 " -0.527 2.00e-02 2.50e+03
... (remaining 5732 not shown)
Histogram of nonbonded interaction distances:
1.37 - 2.01: 1137
2.01 - 2.66: 46837
2.66 - 3.31: 116842
3.31 - 3.95: 148719
3.95 - 4.60: 221386
Nonbonded interactions: 534921
Sorted by model distance:
nonbonded pdb=" HG3 PRO I 212 "
pdb="HG21 VAL I 254 "
model vdw
1.366 2.440
nonbonded pdb=" HG SER H 67 "
pdb=" OD1 ASP H 69 "
model vdw
1.522 1.850
nonbonded pdb=" HG SER L 67 "
pdb=" OD1 ASP L 69 "
model vdw
1.562 1.850
nonbonded pdb=" HG1 THR I 138 "
pdb=" OD1 ASP I 325 "
model vdw
1.573 1.850
nonbonded pdb=" HG SER D 67 "
pdb=" OD1 ASP D 69 "
model vdw
1.588 1.850
... (remaining 534916 not shown)
NOTE: a complete listing of the restraints can be obtained by requesting
output of .geo file.
Find NCS groups from input model
Found NCS groups:
ncs_group {
reference = (chain 'A' and (resid 32 through 504 or resid 601 through 603))
selection = chain 'E'
selection = chain 'I'
}
ncs_group {
reference = chain 'B'
selection = chain 'F'
selection = chain 'J'
}
ncs_group {
reference = chain 'C'
selection = chain 'G'
selection = chain 'K'
}
ncs_group {
reference = chain 'D'
selection = chain 'H'
selection = chain 'L'
}
ncs_group {
reference = chain 'M'
selection = chain 'V'
selection = chain 'f'
selection = chain 'q'
}
ncs_group {
reference = chain 'N'
selection = chain 'O'
selection = chain 'P'
selection = chain 'Q'
selection = chain 'R'
selection = chain 'T'
selection = chain 'U'
selection = chain 'W'
selection = chain 'Y'
selection = chain 'Z'
selection = chain 'a'
selection = chain 'b'
selection = chain 'd'
selection = chain 'e'
selection = chain 'g'
selection = chain 'j'
selection = chain 'k'
selection = chain 'l'
selection = chain 'm'
selection = chain 'o'
selection = chain 'p'
selection = chain 'r'
}
ncs_group {
reference = chain 'S'
selection = chain 'X'
selection = chain 'c'
selection = chain 'h'
selection = chain 'n'
selection = chain 's'
}
Set up NCS constraints
No NCS constraints will be used in refinement.
Set refine NCS operators
Set scattering table
Set to: electron
Number of scattering types: 5
Type Number sf(0) Gaussians
S 123 5.16 5
C 12739 2.51 5
N 3404 2.21 5
O 4089 1.98 5
H 18627 0.53 5
sf(0) = scattering factor at diffraction angle 0.
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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
Set random seed: 0.000
Set model cs if undefined: 0.000
Decide on map wrapping: 0.000
Normalize map: mean=0, sd=1: 1.680
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: 0.630
Extract box with map and model: 10.690
Check model and map are aligned: 0.660
Convert atoms to be neutral: 0.350
Process input model: 119.990
Find NCS groups from input model: 1.990
Set up NCS constraints: 0.620
Set refine NCS operators: 0.000
Set scattering table: 0.010
Adjust number of macro_cycles: 0.000
Reset NCS operators: 0.000
Extract rigid body selections: 0.000
Check and reset occupancies: 0.010
Load rotamer database and sin/cos tables:2.740
Set ADP refinement strategy: 0.000
Make a string to write initial .geo file:0.000
Internal consistency checks: 0.000
Total: 139.370
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7275
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 : 0.014 0.097 20751 Z= 0.933
Angle : 2.124 21.164 28151 Z= 1.409
Chirality : 0.117 1.554 3462
Planarity : 0.020 0.290 3422
Dihedral : 15.774 92.001 7837
Min Nonbonded Distance : 2.051
Molprobity Statistics.
All-atom Clashscore : 2.46
Ramachandran Plot:
Outliers : 2.60 %
Allowed : 12.59 %
Favored : 84.81 %
Rotamer Outliers : 4.52 %
Cbeta Deviations : 0.63 %
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: -3.42 (0.14), residues: 2343
helix: -2.28 (0.21), residues: 372
sheet: -1.51 (0.29), residues: 279
loop : -2.60 (0.13), residues: 1692
*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
4686 Ramachandran restraints generated.
2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
4686 Ramachandran restraints generated.
2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
311 residues out of total 2100 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 95
poor density : 216
time to evaluate : 3.657
Fit side-chains
revert: symmetry clash
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revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
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revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
outliers start: 95
outliers final: 56
residues processed: 302
average time/residue: 0.8301
time to fit residues: 372.0435
Evaluate side-chains
226 residues out of total 2100 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 56
poor density : 170
time to evaluate : 3.367
Switching outliers to nearest non-outliers
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
outliers start: 56
outliers final: 13
residues processed: 56
average time/residue: 0.6028
time to fit residues: 58.5576
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 237
random chunks:
chunk 200 optimal weight: 5.9990
chunk 179 optimal weight: 6.9990
chunk 99 optimal weight: 7.9990
chunk 61 optimal weight: 5.9990
chunk 121 optimal weight: 5.9990
chunk 95 optimal weight: 6.9990
chunk 185 optimal weight: 5.9990
chunk 71 optimal weight: 6.9990
chunk 112 optimal weight: 6.9990
chunk 138 optimal weight: 8.9990
chunk 215 optimal weight: 20.0000
overall best weight: 6.1990
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** E 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 302 ASN
E 478 ASN
H 95 ASN
** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 302 ASN
A 398 ASN
B 652 GLN
** I 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
I 241 ASN
I 302 ASN
I 332 ASN
Total number of N/Q/H flips: 9
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7394
moved from start: 0.3046
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
Bond : 0.006 0.087 20751 Z= 0.420
Angle : 0.957 11.830 28151 Z= 0.535
Chirality : 0.065 1.082 3462
Planarity : 0.007 0.133 3422
Dihedral : 9.673 58.109 3367
Min Nonbonded Distance : 1.844
Molprobity Statistics.
All-atom Clashscore : 17.14
Ramachandran Plot:
Outliers : 0.68 %
Allowed : 12.51 %
Favored : 86.81 %
Rotamer Outliers : 0.43 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.26 %
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: -3.60 (0.15), residues: 2343
helix: -2.11 (0.22), residues: 378
sheet: -1.99 (0.25), residues: 360
loop : -2.73 (0.13), residues: 1605
*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
4686 Ramachandran restraints generated.
2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
4686 Ramachandran restraints generated.
2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
191 residues out of total 2100 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 9
poor density : 182
time to evaluate : 3.520
Fit side-chains
revert: symmetry clash
revert: symmetry clash
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revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
outliers start: 9
outliers final: 9
residues processed: 191
average time/residue: 0.8372
time to fit residues: 232.2184
Evaluate side-chains
159 residues out of total 2100 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 9
poor density : 150
time to evaluate : 3.373
Switching outliers to nearest non-outliers
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
outliers start: 9
outliers final: 5
residues processed: 9
average time/residue: 0.3993
time to fit residues: 10.7032
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 237
random chunks:
chunk 119 optimal weight: 9.9990
chunk 66 optimal weight: 9.9990
chunk 179 optimal weight: 20.0000
chunk 146 optimal weight: 8.9990
chunk 59 optimal weight: 8.9990
chunk 215 optimal weight: 0.9980
chunk 232 optimal weight: 0.0030
chunk 192 optimal weight: 8.9990
chunk 213 optimal weight: 5.9990
chunk 73 optimal weight: 10.0000
chunk 172 optimal weight: 10.0000
overall best weight: 4.9996
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** E 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 95 ASN
** I 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Total number of N/Q/H flips: 1
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7411
moved from start: 0.3604
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
Bond : 0.005 0.077 20751 Z= 0.326
Angle : 0.833 9.941 28151 Z= 0.465
Chirality : 0.059 0.977 3462
Planarity : 0.006 0.102 3422
Dihedral : 9.014 52.066 3367
Min Nonbonded Distance : 1.902
Molprobity Statistics.
All-atom Clashscore : 18.53
Ramachandran Plot:
Outliers : 0.64 %
Allowed : 14.00 %
Favored : 85.36 %
Rotamer Outliers : 0.38 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.18 %
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: -3.42 (0.15), residues: 2343
helix: -1.82 (0.23), residues: 378
sheet: -1.85 (0.25), residues: 408
loop : -2.67 (0.14), residues: 1557
*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
4686 Ramachandran restraints generated.
2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
4686 Ramachandran restraints generated.
2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
180 residues out of total 2100 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 8
poor density : 172
time to evaluate : 3.505
Fit side-chains
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revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
outliers start: 8
outliers final: 8
residues processed: 180
average time/residue: 0.8208
time to fit residues: 216.4283
Evaluate side-chains
155 residues out of total 2100 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 8
poor density : 147
time to evaluate : 3.468
Switching outliers to nearest non-outliers
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
outliers start: 8
outliers final: 5
residues processed: 8
average time/residue: 0.4550
time to fit residues: 10.3288
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 237
random chunks:
chunk 213 optimal weight: 9.9990
chunk 162 optimal weight: 0.3980
chunk 111 optimal weight: 9.9990
chunk 23 optimal weight: 10.0000
chunk 102 optimal weight: 1.9990
chunk 144 optimal weight: 20.0000
chunk 216 optimal weight: 7.9990
chunk 229 optimal weight: 4.9990
chunk 113 optimal weight: 7.9990
chunk 205 optimal weight: 10.0000
chunk 61 optimal weight: 3.9990
overall best weight: 3.8788
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** E 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
K 96 HIS
** L 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Total number of N/Q/H flips: 1
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7408
moved from start: 0.4038
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
Bond : 0.004 0.061 20751 Z= 0.274
Angle : 0.757 8.950 28151 Z= 0.421
Chirality : 0.057 0.905 3462
Planarity : 0.006 0.121 3422
Dihedral : 8.536 49.459 3367
Min Nonbonded Distance : 1.920
Molprobity Statistics.
All-atom Clashscore : 18.33
Ramachandran Plot:
Outliers : 0.60 %
Allowed : 13.96 %
Favored : 85.45 %
Rotamer Outliers : 0.38 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.13 %
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: -3.33 (0.16), residues: 2343
helix: -1.58 (0.24), residues: 381
sheet: -1.85 (0.26), residues: 390
loop : -2.64 (0.14), residues: 1572
*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
4686 Ramachandran restraints generated.
2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
4686 Ramachandran restraints generated.
2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
177 residues out of total 2100 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 8
poor density : 169
time to evaluate : 3.381
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
outliers start: 8
outliers final: 8
residues processed: 177
average time/residue: 0.8274
time to fit residues: 216.0296
Evaluate side-chains
151 residues out of total 2100 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 8
poor density : 143
time to evaluate : 3.391
Switching outliers to nearest non-outliers
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
outliers start: 8
outliers final: 5
residues processed: 8
average time/residue: 0.4181
time to fit residues: 10.3335
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 237
random chunks:
chunk 190 optimal weight: 9.9990
chunk 130 optimal weight: 3.9990
chunk 3 optimal weight: 10.0000
chunk 170 optimal weight: 10.0000
chunk 94 optimal weight: 5.9990
chunk 195 optimal weight: 10.0000
chunk 158 optimal weight: 4.9990
chunk 0 optimal weight: 10.0000
chunk 116 optimal weight: 4.9990
chunk 205 optimal weight: 10.0000
chunk 57 optimal weight: 7.9990
overall best weight: 5.5990
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** E 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
I 216 HIS
I 302 ASN
J 636 ASN
L 95 ASN
Total number of N/Q/H flips: 4
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7501
moved from start: 0.4596
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
Bond : 0.005 0.085 20751 Z= 0.348
Angle : 0.786 8.620 28151 Z= 0.436
Chirality : 0.056 0.911 3462
Planarity : 0.005 0.084 3422
Dihedral : 8.320 52.357 3367
Min Nonbonded Distance : 1.856
Molprobity Statistics.
All-atom Clashscore : 23.96
Ramachandran Plot:
Outliers : 0.51 %
Allowed : 15.02 %
Favored : 84.46 %
Rotamer Outliers : 0.19 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 1.08 %
Twisted General : 0.13 %
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: -3.53 (0.16), residues: 2343
helix: -1.82 (0.24), residues: 381
sheet: -2.10 (0.26), residues: 390
loop : -2.72 (0.14), residues: 1572
*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
4686 Ramachandran restraints generated.
2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
4686 Ramachandran restraints generated.
2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
166 residues out of total 2100 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 4
poor density : 162
time to evaluate : 3.419
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
outliers start: 4
outliers final: 4
residues processed: 166
average time/residue: 0.8463
time to fit residues: 209.5986
Evaluate side-chains
145 residues out of total 2100 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 4
poor density : 141
time to evaluate : 3.429
Switching outliers to nearest non-outliers
revert: symmetry clash
revert: symmetry clash
outliers start: 4
outliers final: 4
residues processed: 4
average time/residue: 0.4396
time to fit residues: 7.3176
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 237
random chunks:
chunk 77 optimal weight: 3.9990
chunk 206 optimal weight: 3.9990
chunk 45 optimal weight: 10.0000
chunk 134 optimal weight: 1.9990
chunk 56 optimal weight: 10.0000
chunk 229 optimal weight: 7.9990
chunk 190 optimal weight: 8.9990
chunk 106 optimal weight: 10.0000
chunk 19 optimal weight: 0.9980
chunk 75 optimal weight: 0.9980
chunk 120 optimal weight: 8.9990
overall best weight: 2.3986
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** E 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
J 652 GLN
Total number of N/Q/H flips: 1
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7421
moved from start: 0.4769
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
Bond : 0.004 0.057 20751 Z= 0.236
Angle : 0.706 7.203 28151 Z= 0.390
Chirality : 0.055 0.843 3462
Planarity : 0.005 0.081 3422
Dihedral : 7.948 54.988 3367
Min Nonbonded Distance : 1.900
Molprobity Statistics.
All-atom Clashscore : 20.22
Ramachandran Plot:
Outliers : 0.47 %
Allowed : 13.53 %
Favored : 86.00 %
Rotamer Outliers : 0.14 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 1.08 %
Twisted General : 0.09 %
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: -3.50 (0.16), residues: 2343
helix: -1.79 (0.23), residues: 399
sheet: -2.30 (0.24), residues: 417
loop : -2.62 (0.14), residues: 1527
*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
4686 Ramachandran restraints generated.
2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
4686 Ramachandran restraints generated.
2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
170 residues out of total 2100 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 3
poor density : 167
time to evaluate : 3.485
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
outliers start: 3
outliers final: 3
residues processed: 170
average time/residue: 0.8284
time to fit residues: 207.7931
Evaluate side-chains
147 residues out of total 2100 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 3
poor density : 144
time to evaluate : 3.346
Switching outliers to nearest non-outliers
revert: symmetry clash
revert: symmetry clash
outliers start: 3
outliers final: 3
residues processed: 3
average time/residue: 0.4101
time to fit residues: 6.3997
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 237
random chunks:
chunk 221 optimal weight: 5.9990
chunk 25 optimal weight: 3.9990
chunk 130 optimal weight: 6.9990
chunk 167 optimal weight: 10.0000
chunk 129 optimal weight: 0.9990
chunk 193 optimal weight: 3.9990
chunk 128 optimal weight: 0.8980
chunk 228 optimal weight: 20.0000
chunk 142 optimal weight: 2.9990
chunk 139 optimal weight: 10.0000
chunk 105 optimal weight: 6.9990
overall best weight: 2.5788
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** E 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
Total number of N/Q/H flips: 0
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7418
moved from start: 0.4961
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
Bond : 0.004 0.080 20751 Z= 0.235
Angle : 0.673 6.365 28151 Z= 0.373
Chirality : 0.054 0.832 3462
Planarity : 0.005 0.089 3422
Dihedral : 7.643 57.615 3367
Min Nonbonded Distance : 1.895
Molprobity Statistics.
All-atom Clashscore : 19.43
Ramachandran Plot:
Outliers : 0.47 %
Allowed : 13.96 %
Favored : 85.57 %
Rotamer Outliers : 0.14 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 1.08 %
Twisted General : 0.13 %
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: -3.35 (0.16), residues: 2343
helix: -1.57 (0.24), residues: 399
sheet: -2.16 (0.25), residues: 420
loop : -2.56 (0.15), residues: 1524
*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
4686 Ramachandran restraints generated.
2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
4686 Ramachandran restraints generated.
2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
166 residues out of total 2100 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 3
poor density : 163
time to evaluate : 3.420
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
outliers start: 3
outliers final: 3
residues processed: 166
average time/residue: 0.8512
time to fit residues: 207.3214
Evaluate side-chains
147 residues out of total 2100 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 3
poor density : 144
time to evaluate : 3.414
Switching outliers to nearest non-outliers
revert: symmetry clash
revert: symmetry clash
outliers start: 3
outliers final: 3
residues processed: 3
average time/residue: 0.4064
time to fit residues: 6.3270
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 237
random chunks:
chunk 141 optimal weight: 9.9990
chunk 91 optimal weight: 10.0000
chunk 136 optimal weight: 8.9990
chunk 68 optimal weight: 20.0000
chunk 44 optimal weight: 20.0000
chunk 145 optimal weight: 9.9990
chunk 155 optimal weight: 9.9990
chunk 112 optimal weight: 9.9990
chunk 21 optimal weight: 10.0000
chunk 179 optimal weight: 10.0000
chunk 207 optimal weight: 7.9990
overall best weight: 9.3990
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** E 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 535 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
Total number of N/Q/H flips: 0
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7675
moved from start: 0.5679
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
Bond : 0.008 0.083 20751 Z= 0.538
Angle : 0.923 10.462 28151 Z= 0.514
Chirality : 0.056 0.883 3462
Planarity : 0.007 0.201 3422
Dihedral : 8.298 46.310 3367
Min Nonbonded Distance : 1.745
Molprobity Statistics.
All-atom Clashscore : 46.94
Ramachandran Plot:
Outliers : 0.47 %
Allowed : 17.16 %
Favored : 82.37 %
Rotamer Outliers : 0.19 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 1.08 %
Twisted General : 0.22 %
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: -4.05 (0.15), residues: 2343
helix: -2.28 (0.22), residues: 381
sheet: -2.70 (0.24), residues: 399
loop : -2.97 (0.14), residues: 1563
*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
4686 Ramachandran restraints generated.
2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
4686 Ramachandran restraints generated.
2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
155 residues out of total 2100 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 4
poor density : 151
time to evaluate : 3.817
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
outliers start: 4
outliers final: 4
residues processed: 155
average time/residue: 0.8316
time to fit residues: 190.6591
Evaluate side-chains
130 residues out of total 2100 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 4
poor density : 126
time to evaluate : 3.081
Switching outliers to nearest non-outliers
revert: symmetry clash
revert: symmetry clash
outliers start: 4
outliers final: 4
residues processed: 4
average time/residue: 0.3866
time to fit residues: 6.6110
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 237
random chunks:
chunk 218 optimal weight: 9.9990
chunk 199 optimal weight: 5.9990
chunk 212 optimal weight: 2.9990
chunk 128 optimal weight: 0.9980
chunk 92 optimal weight: 6.9990
chunk 167 optimal weight: 9.9990
chunk 65 optimal weight: 7.9990
chunk 192 optimal weight: 3.9990
chunk 201 optimal weight: 0.9980
chunk 139 optimal weight: 8.9990
chunk 225 optimal weight: 3.9990
overall best weight: 2.5986
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** E 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
J 535 ASN
Total number of N/Q/H flips: 1
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7509
moved from start: 0.5575
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
Bond : 0.004 0.066 20751 Z= 0.252
Angle : 0.702 7.171 28151 Z= 0.390
Chirality : 0.054 0.839 3462
Planarity : 0.005 0.077 3422
Dihedral : 7.762 45.698 3367
Min Nonbonded Distance : 1.824
Molprobity Statistics.
All-atom Clashscore : 24.93
Ramachandran Plot:
Outliers : 0.51 %
Allowed : 13.96 %
Favored : 85.53 %
Rotamer Outliers : 0.10 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 1.08 %
Twisted General : 0.18 %
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: -3.69 (0.16), residues: 2343
helix: -1.87 (0.23), residues: 399
sheet: -2.52 (0.24), residues: 390
loop : -2.75 (0.14), residues: 1554
*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
4686 Ramachandran restraints generated.
2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
4686 Ramachandran restraints generated.
2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
157 residues out of total 2100 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 2
poor density : 155
time to evaluate : 3.161
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
outliers start: 2
outliers final: 2
residues processed: 157
average time/residue: 0.8600
time to fit residues: 196.4017
Evaluate side-chains
137 residues out of total 2100 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 2
poor density : 135
time to evaluate : 3.391
Switching outliers to nearest non-outliers
revert: symmetry clash
revert: symmetry clash
outliers start: 2
outliers final: 2
residues processed: 2
average time/residue: 0.4175
time to fit residues: 5.6279
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 237
random chunks:
chunk 137 optimal weight: 10.0000
chunk 106 optimal weight: 10.0000
chunk 156 optimal weight: 7.9990
chunk 236 optimal weight: 5.9990
chunk 217 optimal weight: 10.0000
chunk 188 optimal weight: 0.0370
chunk 19 optimal weight: 0.8980
chunk 145 optimal weight: 2.9990
chunk 115 optimal weight: 4.9990
chunk 149 optimal weight: 4.9990
chunk 200 optimal weight: 6.9990
overall best weight: 2.7864
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** E 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
Total number of N/Q/H flips: 0
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7498
moved from start: 0.5667
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
Bond : 0.004 0.065 20751 Z= 0.243
Angle : 0.670 6.879 28151 Z= 0.373
Chirality : 0.053 0.812 3462
Planarity : 0.005 0.071 3422
Dihedral : 7.453 45.006 3367
Min Nonbonded Distance : 1.756
Molprobity Statistics.
All-atom Clashscore : 23.46
Ramachandran Plot:
Outliers : 0.47 %
Allowed : 14.64 %
Favored : 84.89 %
Rotamer Outliers : 0.10 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.09 %
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: -3.59 (0.16), residues: 2343
helix: -1.71 (0.24), residues: 399
sheet: -2.62 (0.23), residues: 420
loop : -2.64 (0.15), residues: 1524
********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
4686 Ramachandran restraints generated.
2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
4686 Ramachandran restraints generated.
2343 Oldfield, 0 Emsley, 2343 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
153 residues out of total 2100 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 2
poor density : 151
time to evaluate : 3.552
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
outliers start: 2
outliers final: 2
residues processed: 153
average time/residue: 0.8917
time to fit residues: 201.5078
Evaluate side-chains
136 residues out of total 2100 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 2
poor density : 134
time to evaluate : 3.524
Switching outliers to nearest non-outliers
revert: symmetry clash
revert: symmetry clash
outliers start: 2
outliers final: 2
residues processed: 2
average time/residue: 0.4351
time to fit residues: 5.7859
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 237
random chunks:
chunk 57 optimal weight: 5.9990
chunk 173 optimal weight: 7.9990
chunk 27 optimal weight: 9.9990
chunk 52 optimal weight: 8.9990
chunk 188 optimal weight: 9.9990
chunk 78 optimal weight: 10.0000
chunk 193 optimal weight: 10.0000
chunk 23 optimal weight: 10.0000
chunk 34 optimal weight: 9.9990
chunk 165 optimal weight: 6.9990
chunk 10 optimal weight: 9.9990
overall best weight: 7.9990
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** E 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 302 ASN
** A 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
Total number of N/Q/H flips: 1
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.039025 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.033516 restraints weight = 955638.237|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.034880 restraints weight = 436089.229|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.035715 restraints weight = 241326.745|
|-----------------------------------------------------------------------------|
r_work (final): 0.3014
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7921
moved from start: 0.6073
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
Bond : 0.006 0.072 20751 Z= 0.424
Angle : 0.799 9.385 28151 Z= 0.448
Chirality : 0.054 0.842 3462
Planarity : 0.006 0.080 3422
Dihedral : 7.843 56.354 3367
Min Nonbonded Distance : 1.729
Molprobity Statistics.
All-atom Clashscore : 39.65
Ramachandran Plot:
Outliers : 0.47 %
Allowed : 17.88 %
Favored : 81.65 %
Rotamer Outliers : 0.14 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 1.08 %
Twisted General : 0.22 %
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: -3.92 (0.15), residues: 2343
helix: -1.91 (0.23), residues: 381
sheet: -2.92 (0.25), residues: 357
loop : -2.89 (0.14), residues: 1605
===============================================================================
Job complete
usr+sys time: 6470.22 seconds
wall clock time: 117 minutes 33.49 seconds (7053.49 seconds total)