Starting phenix.real_space_refine
on Wed Aug 7 10:45:56 2024 by dcliebschner
===============================================================================
Processing files:
-------------------------------------------------------------------------------
Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u4l_41886/08_2024/8u4l_41886_trim.cif
Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u4l_41886/08_2024/8u4l_41886.map
Processing PHIL parameters:
-------------------------------------------------------------------------------
Adding command-line PHIL:
-------------------------
refinement.macro_cycles=10
scattering_table=electron
resolution=3.31
write_initial_geo_file=False
Final processed PHIL parameters:
-------------------------------------------------------------------------------
data_manager {
real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u4l_41886/08_2024/8u4l_41886.map"
default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u4l_41886/08_2024/8u4l_41886.map"
model {
file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u4l_41886/08_2024/8u4l_41886_trim.cif"
}
default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u4l_41886/08_2024/8u4l_41886_trim.cif"
}
resolution = 3.31
write_initial_geo_file = False
refinement {
macro_cycles = 10
}
qi {
qm_restraints {
package {
program = *test
}
}
}
Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.
Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
Set to: 0
Set model cs if undefined
Decide on map wrapping
Map wrapping is set to: False
Normalize map: mean=0, sd=1
Input map: mean= -0.000 sd= 0.028
Set stop_for_unknowns flag
Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
Set to: electron
Number of scattering types: 5
Type Number sf(0) Gaussians
S 118 5.16 5
C 6179 2.51 5
N 1708 2.21 5
O 1984 1.98 5
H 9080 0.53 5
sf(0) = scattering factor at diffraction angle 0.
Process input model
Symmetric amino acids flipped
Residue "A ARG 47": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
Residue "A ARG 50": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
Residue "A ARG 72": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
Residue "A ARG 78": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
Residue "A ARG 81": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
Residue "A ARG 95": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
Residue "A ARG 103": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
Residue "A ARG 106": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
Residue "A ARG 114": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
Residue "A ARG 124": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
Residue "A ARG 168": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
Residue "A ARG 188": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
Residue "A ARG 196": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
Residue "A ARG 210": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
Residue "A ARG 220": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
Residue "A ARG 232": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
Residue "A PHE 279": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
Residue "A ARG 306": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
Residue "A ARG 393": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
Residue "A ARG 396": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
Residue "A ARG 426": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
Residue "A ARG 484": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
Residue "A ARG 488": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
Residue "A ARG 491": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
Residue "A ARG 524": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
Residue "A ARG 525": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
Residue "A ARG 528": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
Residue "A ARG 530": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
Residue "A ARG 544": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
Residue "A ARG 612": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
Residue "B ARG 34": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
Residue "B ARG 47": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
Residue "B ARG 92": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
Residue "B ARG 98": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
Residue "B ARG 100": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
Residue "B ARG 103": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
Residue "B ARG 138": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
Residue "B ARG 143": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
Residue "B ARG 157": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
Residue "B ARG 188": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
Residue "B ARG 190": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
Residue "B ARG 203": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
Residue "B ARG 217": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
Residue "B ARG 226": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
Residue "B ARG 288": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
Residue "B ARG 330": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
Residue "B ARG 340": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
Residue "B ARG 351": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
Residue "B ARG 354": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
Residue "B ARG 432": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
Residue "B ARG 434": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
Residue "B ARG 456": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
Residue "B ARG 459": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
Residue "B ARG 487": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
Residue "B ARG 499": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
Residue "B ARG 517": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
Residue "B ARG 536": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
Residue "B ARG 545": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
Residue "B ARG 552": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
Residue "B ARG 558": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
Residue "B ARG 599": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
Residue "C ARG 207": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
Residue "C ARG 220": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22"
Time to flip residues: 0.03s
Monomer Library directory:
"/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib"
Total number of atoms: 19069
Number of models: 1
Model: ""
Number of chains: 15
Chain: "A"
Number of atoms: 9061
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 598, 9061
Classifications: {'peptide': 598}
Modifications used: {'NH3': 1}
Link IDs: {'PTRANS': 27, 'TRANS': 570}
Chain breaks: 3
Chain: "B"
Number of atoms: 8787
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 582, 8787
Classifications: {'peptide': 582}
Modifications used: {'NH3': 1}
Link IDs: {'PTRANS': 38, 'TRANS': 543}
Chain breaks: 2
Chain: "C"
Number of atoms: 767
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 50, 767
Classifications: {'peptide': 50}
Modifications used: {'NH3': 1}
Link IDs: {'PTRANS': 2, 'TRANS': 47}
Chain breaks: 1
Chain: "D"
Number of atoms: 50
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 4, 50
Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2}
Classifications: {'undetermined': 4}
Link IDs: {None: 3}
Unresolved non-hydrogen bonds: 4
Unresolved non-hydrogen angles: 8
Unresolved non-hydrogen dihedrals: 12
Unresolved non-hydrogen chiralities: 4
Chain: "E"
Number of atoms: 61
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 5, 61
Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2}
Classifications: {'undetermined': 5}
Link IDs: {None: 4}
Unresolved non-hydrogen bonds: 5
Unresolved non-hydrogen angles: 10
Unresolved non-hydrogen dihedrals: 15
Unresolved non-hydrogen chiralities: 5
Chain: "F"
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: 9
Unresolved non-hydrogen chiralities: 3
Chain: "G"
Number of atoms: 50
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 4, 50
Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2}
Classifications: {'undetermined': 4}
Link IDs: {None: 3}
Unresolved non-hydrogen bonds: 4
Unresolved non-hydrogen angles: 8
Unresolved non-hydrogen dihedrals: 12
Unresolved non-hydrogen chiralities: 4
Chain: "H"
Number of atoms: 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: 9
Unresolved non-hydrogen chiralities: 3
Chain: "I"
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: 9
Unresolved non-hydrogen chiralities: 3
Chain: "J"
Number of atoms: 28
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 2, 28
Unusual residues: {'NAG': 2}
Classifications: {'undetermined': 2}
Link IDs: {None: 1}
Unresolved non-hydrogen bonds: 2
Unresolved non-hydrogen angles: 4
Unresolved non-hydrogen dihedrals: 6
Unresolved non-hydrogen chiralities: 2
Chain: "K"
Number of atoms: 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: 9
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: 9
Unresolved non-hydrogen chiralities: 3
Chain: "M"
Number of atoms: 28
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 2, 28
Unusual residues: {'NAG': 2}
Classifications: {'undetermined': 2}
Link IDs: {None: 1}
Unresolved non-hydrogen bonds: 2
Unresolved non-hydrogen angles: 4
Unresolved non-hydrogen dihedrals: 6
Unresolved non-hydrogen chiralities: 2
Chain: "A"
Number of atoms: 28
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 2, 28
Unusual residues: {'NAG': 2}
Classifications: {'undetermined': 2}
Link IDs: {None: 1}
Unresolved non-hydrogen bonds: 2
Unresolved non-hydrogen angles: 4
Unresolved non-hydrogen dihedrals: 6
Unresolved non-hydrogen chiralities: 2
Chain: "B"
Number of atoms: 14
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 1, 14
Unusual residues: {'NAG': 1}
Classifications: {'undetermined': 1}
Unresolved non-hydrogen bonds: 1
Unresolved non-hydrogen angles: 2
Unresolved non-hydrogen dihedrals: 3
Unresolved non-hydrogen chiralities: 1
Time building chain proxies: 9.08, per 1000 atoms: 0.48
Number of scatterers: 19069
At special positions: 0
Unit cell: (80.995, 146.96, 136.94, 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 118 16.00
O 1984 8.00
N 1708 7.00
C 6179 6.00
H 9080 1.00
sf(0) = scattering factor at diffraction angle 0.
Number of disulfides: simple=51, symmetry=0
Simple disulfide: pdb=" SG CYS A 29 " - pdb=" SG CYS A 56 " distance=2.08
Simple disulfide: pdb=" SG CYS A 156 " - pdb=" SG CYS A 186 " distance=2.03
Simple disulfide: pdb=" SG CYS A 189 " - pdb=" SG CYS A 197 " distance=2.08
Simple disulfide: pdb=" SG CYS A 193 " - pdb=" SG CYS A 205 " distance=2.08
Simple disulfide: pdb=" SG CYS A 213 " - pdb=" SG CYS A 221 " distance=2.03
Simple disulfide: pdb=" SG CYS A 217 " - pdb=" SG CYS A 229 " distance=2.02
Simple disulfide: pdb=" SG CYS A 230 " - pdb=" SG CYS A 238 " distance=1.84
Simple disulfide: pdb=" SG CYS A 234 " - pdb=" SG CYS A 246 " distance=1.99
Simple disulfide: pdb=" SG CYS A 249 " - pdb=" SG CYS A 258 " distance=2.04
Simple disulfide: pdb=" SG CYS A 262 " - pdb=" SG CYS A 289 " distance=2.02
Simple disulfide: pdb=" SG CYS A 293 " - pdb=" SG CYS A 304 " distance=2.02
Simple disulfide: pdb=" SG CYS A 308 " - pdb=" SG CYS A 323 " distance=2.02
Simple disulfide: pdb=" SG CYS A 326 " - pdb=" SG CYS A 330 " distance=2.03
Simple disulfide: pdb=" SG CYS A 334 " - pdb=" SG CYS A 359 " distance=2.06
Simple disulfide: pdb=" SG CYS A 467 " - pdb=" SG CYS A 496 " distance=2.03
Simple disulfide: pdb=" SG CYS A 503 " - pdb=" SG CYS A 512 " distance=2.08
Simple disulfide: pdb=" SG CYS A 507 " - pdb=" SG CYS A 520 " distance=2.04
Simple disulfide: pdb=" SG CYS A 523 " - pdb=" SG CYS A 532 " distance=2.02
Simple disulfide: pdb=" SG CYS A 536 " - pdb=" SG CYS A 552 " distance=2.02
Simple disulfide: pdb=" SG CYS A 555 " - pdb=" SG CYS A 569 " distance=2.03
Simple disulfide: pdb=" SG CYS A 559 " - pdb=" SG CYS A 577 " distance=2.03
Simple disulfide: pdb=" SG CYS A 580 " - pdb=" SG CYS A 589 " distance=2.07
Simple disulfide: pdb=" SG CYS A 593 " - pdb=" SG CYS A 614 " distance=2.12
Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 625 " distance=2.01
Simple disulfide: pdb=" SG CYS A 621 " - pdb=" SG CYS A 633 " distance=2.13
Simple disulfide: pdb=" SG CYS B 26 " - pdb=" SG CYS B 53 " distance=2.07
Simple disulfide: pdb=" SG CYS B 162 " - pdb=" SG CYS B 192 " distance=2.06
Simple disulfide: pdb=" SG CYS B 195 " - pdb=" SG CYS B 204 " distance=2.01
Simple disulfide: pdb=" SG CYS B 199 " - pdb=" SG CYS B 212 " distance=2.08
Simple disulfide: pdb=" SG CYS B 220 " - pdb=" SG CYS B 227 " distance=2.02
Simple disulfide: pdb=" SG CYS B 224 " - pdb=" SG CYS B 235 " distance=2.02
Simple disulfide: pdb=" SG CYS B 236 " - pdb=" SG CYS B 244 " distance=2.02
Simple disulfide: pdb=" SG CYS B 240 " - pdb=" SG CYS B 252 " distance=2.04
Simple disulfide: pdb=" SG CYS B 255 " - pdb=" SG CYS B 264 " distance=2.15
Simple disulfide: pdb=" SG CYS B 268 " - pdb=" SG CYS B 295 " distance=2.15
Simple disulfide: pdb=" SG CYS B 299 " - pdb=" SG CYS B 311 " distance=1.98
Simple disulfide: pdb=" SG CYS B 315 " - pdb=" SG CYS B 331 " distance=2.11
Simple disulfide: pdb=" SG CYS B 334 " - pdb=" SG CYS B 338 " distance=2.14
Simple disulfide: pdb=" SG CYS B 342 " - pdb=" SG CYS B 367 " distance=2.02
Simple disulfide: pdb=" SG CYS B 475 " - pdb=" SG CYS B 504 " distance=2.03
Simple disulfide: pdb=" SG CYS B 511 " - pdb=" SG CYS B 520 " distance=2.03
Simple disulfide: pdb=" SG CYS B 515 " - pdb=" SG CYS B 528 " distance=2.03
Simple disulfide: pdb=" SG CYS B 531 " - pdb=" SG CYS B 540 " distance=2.03
Simple disulfide: pdb=" SG CYS B 544 " - pdb=" SG CYS B 560 " distance=2.02
Simple disulfide: pdb=" SG CYS B 563 " - pdb=" SG CYS B 576 " distance=2.35
Simple disulfide: pdb=" SG CYS B 567 " - pdb=" SG CYS B 584 " distance=2.11
Simple disulfide: pdb=" SG CYS B 587 " - pdb=" SG CYS B 596 " distance=2.03
Simple disulfide: pdb=" SG CYS B 600 " - pdb=" SG CYS B 623 " distance=2.03
Simple disulfide: pdb=" SG CYS C 182 " - pdb=" SG CYS C 196 " distance=2.05
Simple disulfide: pdb=" SG CYS C 190 " - pdb=" SG CYS C 210 " distance=2.02
Simple disulfide: pdb=" SG CYS C 212 " - pdb=" SG CYS C 221 " distance=2.04
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
ALPHA1-3
" BMA D 3 " - " MAN D 4 "
" BMA E 3 " - " MAN E 4 "
ALPHA1-6
" BMA E 3 " - " MAN E 5 "
" BMA G 3 " - " MAN G 4 "
BETA1-4
" 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 F 2 " - " BMA F 3 "
" NAG G 1 " - " NAG G 2 "
" NAG G 2 " - " BMA G 3 "
" NAG H 1 " - " NAG H 2 "
" NAG H 2 " - " BMA H 3 "
" NAG I 1 " - " NAG I 2 "
" NAG I 2 " - " BMA I 3 "
" NAG J 1 " - " NAG J 2 "
" 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-ASN
" NAG A 701 " - " ASN A 410 "
" NAG A 702 " - " ASN A 495 "
" NAG B 701 " - " ASN B 68 "
" NAG D 1 " - " ASN A 138 "
" NAG E 1 " - " ASN A 358 "
" NAG F 1 " - " ASN A 473 "
" NAG G 1 " - " ASN A 576 "
" NAG H 1 " - " ASN A 548 "
" NAG I 1 " - " ASN A 253 "
" NAG J 1 " - " ASN B 187 "
" NAG K 1 " - " ASN B 259 "
" NAG L 1 " - " ASN B 530 "
" NAG M 1 " - " ASN B 571 "
Time building additional restraints: 10.03
Conformation dependent library (CDL) restraints added in 1.2 seconds
2424 Ramachandran restraints generated.
1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
Adding C-beta torsion restraints...
Number of C-beta restraints generated: 2270
Finding SS restraints...
Secondary structure from input PDB file:
35 helices and 30 sheets defined
16.7% alpha, 15.3% beta
0 base pairs and 0 stacking pairs defined.
Time for finding SS restraints: 1.15
Creating SS restraints...
Processing helix chain 'A' and resid 41 through 54
Processing helix chain 'A' and resid 74 through 80
removed outlier: 3.931A pdb=" N SER A 79 " --> pdb=" O PHE A 76 " (cutoff:3.500A)
Processing helix chain 'A' and resid 110 through 113
Processing helix chain 'A' and resid 162 through 167
removed outlier: 4.070A pdb=" N ILE A 166 " --> pdb=" O HIS A 162 " (cutoff:3.500A)
Processing helix chain 'A' and resid 201 through 205
removed outlier: 3.811A pdb=" N CYS A 205 " --> pdb=" O GLU A 202 " (cutoff:3.500A)
Processing helix chain 'A' and resid 225 through 229
removed outlier: 3.928A pdb=" N CYS A 229 " --> pdb=" O VAL A 226 " (cutoff:3.500A)
Processing helix chain 'A' and resid 339 through 343
Processing helix chain 'A' and resid 352 through 357
Processing helix chain 'A' and resid 369 through 374
Processing helix chain 'A' and resid 385 through 395
removed outlier: 3.781A pdb=" N THR A 394 " --> pdb=" O VAL A 391 " (cutoff:3.500A)
Processing helix chain 'A' and resid 468 through 472
Processing helix chain 'A' and resid 473 through 477
Processing helix chain 'A' and resid 492 through 500
Processing helix chain 'A' and resid 573 through 577
removed outlier: 3.853A pdb=" N CYS A 577 " --> pdb=" O PRO A 574 " (cutoff:3.500A)
Processing helix chain 'A' and resid 629 through 633
removed outlier: 4.317A pdb=" N CYS A 633 " --> pdb=" O SER A 630 " (cutoff:3.500A)
Processing helix chain 'B' and resid 38 through 40
No H-bonds generated for 'chain 'B' and resid 38 through 40'
Processing helix chain 'B' and resid 41 through 51
Processing helix chain 'B' and resid 71 through 77
removed outlier: 4.345A pdb=" N ASP B 76 " --> pdb=" O PHE B 73 " (cutoff:3.500A)
Processing helix chain 'B' and resid 107 through 110
Processing helix chain 'B' and resid 168 through 172
Processing helix chain 'B' and resid 208 through 212
removed outlier: 4.138A pdb=" N CYS B 212 " --> pdb=" O SER B 209 " (cutoff:3.500A)
Processing helix chain 'B' and resid 231 through 235
Processing helix chain 'B' and resid 347 through 351
Processing helix chain 'B' and resid 360 through 365
Processing helix chain 'B' and resid 384 through 388
removed outlier: 3.590A pdb=" N ASN B 388 " --> pdb=" O PRO B 385 " (cutoff:3.500A)
Processing helix chain 'B' and resid 393 through 398
removed outlier: 3.811A pdb=" N GLN B 398 " --> pdb=" O PRO B 394 " (cutoff:3.500A)
Processing helix chain 'B' and resid 399 through 401
No H-bonds generated for 'chain 'B' and resid 399 through 401'
Processing helix chain 'B' and resid 422 through 426
Processing helix chain 'B' and resid 436 through 439
Processing helix chain 'B' and resid 475 through 479
removed outlier: 3.712A pdb=" N HIS B 478 " --> pdb=" O CYS B 475 " (cutoff:3.500A)
Processing helix chain 'B' and resid 481 through 486
removed outlier: 3.873A pdb=" N LEU B 485 " --> pdb=" O PRO B 481 " (cutoff:3.500A)
Processing helix chain 'B' and resid 500 through 507
removed outlier: 3.666A pdb=" N GLU B 507 " --> pdb=" O GLU B 503 " (cutoff:3.500A)
Processing helix chain 'B' and resid 515 through 519
removed outlier: 3.785A pdb=" N GLY B 518 " --> pdb=" O CYS B 515 " (cutoff:3.500A)
Processing helix chain 'B' and resid 580 through 584
Processing helix chain 'C' and resid 186 through 190
removed outlier: 3.925A pdb=" N CYS C 190 " --> pdb=" O LYS C 187 " (cutoff:3.500A)
Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30
removed outlier: 6.553A pdb=" N CYS A 29 " --> pdb=" O MET A 60 " (cutoff:3.500A)
Processing sheet with id=AA2, first strand: chain 'A' and resid 38 through 39
removed outlier: 7.077A pdb=" N SER A 38 " --> pdb=" O CYS C 212 " (cutoff:3.500A)
Processing sheet with id=AA3, first strand: chain 'A' and resid 63 through 66
removed outlier: 5.666A pdb=" N GLY A 146 " --> pdb=" O TYR A 115 " (cutoff:3.500A)
Processing sheet with id=AA4, first strand: chain 'A' and resid 234 through 238
removed outlier: 5.623A pdb=" N ALA A 235 " --> pdb=" O CYS A 249 " (cutoff:3.500A)
removed outlier: 4.776A pdb=" N CYS A 249 " --> pdb=" O ALA A 235 " (cutoff:3.500A)
removed outlier: 7.177A pdb=" N GLY A 237 " --> pdb=" O PHE A 247 " (cutoff:3.500A)
Processing sheet with id=AA5, first strand: chain 'A' and resid 252 through 254
Processing sheet with id=AA6, first strand: chain 'A' and resid 266 through 268
Processing sheet with id=AA7, first strand: chain 'A' and resid 283 through 285
Processing sheet with id=AA8, first strand: chain 'A' and resid 298 through 299
Processing sheet with id=AA9, first strand: chain 'A' and resid 312 through 317
Processing sheet with id=AB1, first strand: chain 'A' and resid 334 through 335
removed outlier: 6.425A pdb=" N CYS A 334 " --> pdb=" O ASN A 363 " (cutoff:3.500A)
Processing sheet with id=AB2, first strand: chain 'A' and resid 366 through 368
removed outlier: 7.632A pdb=" N TYR A 459 " --> pdb=" O SER A 433 " (cutoff:3.500A)
removed outlier: 4.446A pdb=" N LEU A 435 " --> pdb=" O TYR A 459 " (cutoff:3.500A)
removed outlier: 7.833A pdb=" N THR A 461 " --> pdb=" O LEU A 435 " (cutoff:3.500A)
removed outlier: 4.585A pdb=" N LEU A 437 " --> pdb=" O THR A 461 " (cutoff:3.500A)
removed outlier: 6.578A pdb=" N ILE A 458 " --> pdb=" O VAL A 486 " (cutoff:3.500A)
removed outlier: 8.290A pdb=" N ARG A 488 " --> pdb=" O ILE A 458 " (cutoff:3.500A)
removed outlier: 6.655A pdb=" N ILE A 460 " --> pdb=" O ARG A 488 " (cutoff:3.500A)
Processing sheet with id=AB3, first strand: chain 'A' and resid 526 through 528
Processing sheet with id=AB4, first strand: chain 'A' and resid 545 through 546
Processing sheet with id=AB5, first strand: chain 'A' and resid 583 through 585
removed outlier: 3.690A pdb=" N PHE A 583 " --> pdb=" O VAL A 590 " (cutoff:3.500A)
Processing sheet with id=AB6, first strand: chain 'A' and resid 606 through 607
Processing sheet with id=AB7, first strand: chain 'B' and resid 25 through 27
removed outlier: 6.669A pdb=" N CYS B 26 " --> pdb=" O GLN B 57 " (cutoff:3.500A)
Processing sheet with id=AB8, first strand: chain 'B' and resid 60 through 63
removed outlier: 5.348A pdb=" N GLY B 152 " --> pdb=" O TYR B 112 " (cutoff:3.500A)
Processing sheet with id=AB9, first strand: chain 'B' and resid 240 through 244
removed outlier: 7.514A pdb=" N GLY B 243 " --> pdb=" O CYS B 252 " (cutoff:3.500A)
removed outlier: 5.196A pdb=" N CYS B 252 " --> pdb=" O GLY B 243 " (cutoff:3.500A)
Processing sheet with id=AC1, first strand: chain 'B' and resid 258 through 260
Processing sheet with id=AC2, first strand: chain 'B' and resid 272 through 275
removed outlier: 3.752A pdb=" N GLU B 280 " --> pdb=" O ASN B 275 " (cutoff:3.500A)
Processing sheet with id=AC3, first strand: chain 'B' and resid 289 through 291
Processing sheet with id=AC4, first strand: chain 'B' and resid 304 through 306
removed outlier: 3.623A pdb=" N SER B 310 " --> pdb=" O THR B 306 " (cutoff:3.500A)
Processing sheet with id=AC5, first strand: chain 'B' and resid 319 through 322
Processing sheet with id=AC6, first strand: chain 'B' and resid 369 through 370
Processing sheet with id=AC7, first strand: chain 'B' and resid 374 through 376
removed outlier: 4.597A pdb=" N TYR B 441 " --> pdb=" O LEU B 465 " (cutoff:3.500A)
removed outlier: 7.393A pdb=" N LEU B 467 " --> pdb=" O TYR B 441 " (cutoff:3.500A)
removed outlier: 6.632A pdb=" N LEU B 443 " --> pdb=" O LEU B 467 " (cutoff:3.500A)
removed outlier: 8.044A pdb=" N HIS B 469 " --> pdb=" O LEU B 443 " (cutoff:3.500A)
removed outlier: 6.571A pdb=" N LEU B 445 " --> pdb=" O HIS B 469 " (cutoff:3.500A)
removed outlier: 6.390A pdb=" N ALA B 466 " --> pdb=" O LEU B 494 " (cutoff:3.500A)
removed outlier: 8.352A pdb=" N THR B 496 " --> pdb=" O ALA B 466 " (cutoff:3.500A)
removed outlier: 6.781A pdb=" N ILE B 468 " --> pdb=" O THR B 496 " (cutoff:3.500A)
Processing sheet with id=AC8, first strand: chain 'B' and resid 534 through 536
Processing sheet with id=AC9, first strand: chain 'B' and resid 553 through 555
Processing sheet with id=AD1, first strand: chain 'B' and resid 591 through 592
Processing sheet with id=AD2, first strand: chain 'B' and resid 615 through 617
Processing sheet with id=AD3, first strand: chain 'C' and resid 216 through 217
194 hydrogen bonds defined for protein.
363 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: 4.88
Time building geometry restraints manager: 10.70 seconds
NOTE: a complete listing of the restraints can be obtained by requesting
output of .geo file.
Histogram of bond lengths:
0.96 - 1.13: 9079
1.13 - 1.30: 1704
1.30 - 1.48: 3989
1.48 - 1.65: 4373
1.65 - 1.82: 133
Bond restraints: 19278
Sorted by residual:
bond pdb=" N MET B 282 "
pdb=" H MET B 282 "
ideal model delta sigma weight residual
0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01
bond pdb=" NE2 GLN A 206 "
pdb="HE21 GLN A 206 "
ideal model delta sigma weight residual
0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01
bond pdb=" ND2 ASN A 352 "
pdb="HD22 ASN A 352 "
ideal model delta sigma weight residual
0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01
bond pdb=" N ASN A 358 "
pdb=" H ASN A 358 "
ideal model delta sigma weight residual
0.860 1.011 -0.151 2.00e-02 2.50e+03 5.67e+01
bond pdb=" N CYS A 625 "
pdb=" H CYS A 625 "
ideal model delta sigma weight residual
0.860 1.011 -0.151 2.00e-02 2.50e+03 5.67e+01
... (remaining 19273 not shown)
Histogram of bond angle deviations from ideal:
99.57 - 106.61: 499
106.61 - 113.66: 21575
113.66 - 120.70: 8612
120.70 - 127.74: 3791
127.74 - 134.79: 77
Bond angle restraints: 34554
Sorted by residual:
angle pdb=" N GLU A 141 "
pdb=" CA GLU A 141 "
pdb=" C GLU A 141 "
ideal model delta sigma weight residual
108.99 118.71 -9.72 1.57e+00 4.06e-01 3.83e+01
angle pdb=" C GLU B 348 "
pdb=" CA GLU B 348 "
pdb=" CB GLU B 348 "
ideal model delta sigma weight residual
116.54 109.47 7.07 1.15e+00 7.56e-01 3.78e+01
angle pdb=" C ASP A 328 "
pdb=" CA ASP A 328 "
pdb=" CB ASP A 328 "
ideal model delta sigma weight residual
116.54 109.93 6.61 1.15e+00 7.56e-01 3.31e+01
angle pdb=" C LYS A 35 "
pdb=" CA LYS A 35 "
pdb=" CB LYS A 35 "
ideal model delta sigma weight residual
116.63 110.14 6.49 1.16e+00 7.43e-01 3.13e+01
angle pdb=" C LYS B 32 "
pdb=" CA LYS B 32 "
pdb=" CB LYS B 32 "
ideal model delta sigma weight residual
116.54 110.22 6.32 1.15e+00 7.56e-01 3.02e+01
... (remaining 34549 not shown)
Histogram of dihedral angle deviations from ideal:
0.00 - 21.25: 9033
21.25 - 42.49: 420
42.49 - 63.74: 234
63.74 - 84.98: 68
84.98 - 106.23: 36
Dihedral angle restraints: 9791
sinusoidal: 5677
harmonic: 4114
Sorted by residual:
dihedral pdb=" CB CYS A 217 "
pdb=" SG CYS A 217 "
pdb=" SG CYS A 229 "
pdb=" CB CYS A 229 "
ideal model delta sinusoidal sigma weight residual
-86.00 -176.48 90.48 1 1.00e+01 1.00e-02 9.68e+01
dihedral pdb=" CB CYS A 293 "
pdb=" SG CYS A 293 "
pdb=" SG CYS A 304 "
pdb=" CB CYS A 304 "
ideal model delta sinusoidal sigma weight residual
93.00 177.18 -84.18 1 1.00e+01 1.00e-02 8.63e+01
dihedral pdb=" CB CYS B 315 "
pdb=" SG CYS B 315 "
pdb=" SG CYS B 331 "
pdb=" CB CYS B 331 "
ideal model delta sinusoidal sigma weight residual
93.00 176.91 -83.91 1 1.00e+01 1.00e-02 8.58e+01
... (remaining 9788 not shown)
Histogram of chiral volume deviations from ideal:
0.000 - 0.095: 1310
0.095 - 0.189: 252
0.189 - 0.284: 40
0.284 - 0.379: 15
0.379 - 0.474: 3
Chirality restraints: 1620
Sorted by residual:
chirality pdb=" C1 NAG E 2 "
pdb=" O4 NAG E 1 "
pdb=" C2 NAG E 2 "
pdb=" O5 NAG E 2 "
both_signs ideal model delta sigma weight residual
False -2.40 -2.01 -0.39 2.00e-02 2.50e+03 3.75e+02
chirality pdb=" C1 NAG G 2 "
pdb=" O4 NAG G 1 "
pdb=" C2 NAG G 2 "
pdb=" O5 NAG G 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 MAN D 4 "
pdb=" O3 BMA D 3 "
pdb=" C2 MAN D 4 "
pdb=" O5 MAN D 4 "
both_signs ideal model delta sigma weight residual
False 2.40 2.10 0.30 2.00e-02 2.50e+03 2.22e+02
... (remaining 1617 not shown)
Planarity restraints: 2940
Sorted by residual:
delta sigma weight rms_deltas residual
plane pdb=" C2 NAG E 1 " -0.319 2.00e-02 2.50e+03 2.70e-01 9.13e+02
pdb=" C7 NAG E 1 " 0.085 2.00e-02 2.50e+03
pdb=" C8 NAG E 1 " -0.184 2.00e-02 2.50e+03
pdb=" N2 NAG E 1 " 0.469 2.00e-02 2.50e+03
pdb=" O7 NAG E 1 " -0.051 2.00e-02 2.50e+03
delta sigma weight rms_deltas residual
plane pdb=" CB ASN A 410 " 0.250 2.00e-02 2.50e+03 1.99e-01 5.97e+02
pdb=" CG ASN A 410 " -0.021 2.00e-02 2.50e+03
pdb=" OD1 ASN A 410 " -0.198 2.00e-02 2.50e+03
pdb=" ND2 ASN A 410 " -0.034 2.00e-02 2.50e+03
pdb="HD21 ASN A 410 " -0.258 2.00e-02 2.50e+03
pdb=" C1 NAG A 701 " 0.262 2.00e-02 2.50e+03
delta sigma weight rms_deltas residual
plane pdb=" C2 NAG E 2 " -0.189 2.00e-02 2.50e+03 1.58e-01 3.13e+02
pdb=" C7 NAG E 2 " 0.042 2.00e-02 2.50e+03
pdb=" C8 NAG E 2 " -0.132 2.00e-02 2.50e+03
pdb=" N2 NAG E 2 " 0.265 2.00e-02 2.50e+03
pdb=" O7 NAG E 2 " 0.015 2.00e-02 2.50e+03
... (remaining 2937 not shown)
Histogram of nonbonded interaction distances:
1.45 - 2.08: 746
2.08 - 2.71: 25626
2.71 - 3.34: 52693
3.34 - 3.97: 68678
3.97 - 4.60: 99884
Nonbonded interactions: 247627
Sorted by model distance:
nonbonded pdb=" OE2 GLU A 317 "
pdb=" HZ1 LYS A 324 "
model vdw
1.452 2.450
nonbonded pdb=" HB3 LYS B 32 "
pdb=" H LEU B 33 "
model vdw
1.504 2.270
nonbonded pdb=" HG SER B 358 "
pdb=" O ALA B 390 "
model vdw
1.531 2.450
nonbonded pdb=" OE1 GLU A 202 "
pdb=" H GLU A 202 "
model vdw
1.601 2.450
nonbonded pdb=" OG1 THR A 209 "
pdb="HH11 ARG A 220 "
model vdw
1.610 2.450
... (remaining 247622 not shown)
NOTE: a complete listing of the restraints can be obtained by requesting
output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
reference = chain 'D'
selection = chain 'G'
}
ncs_group {
reference = chain 'F'
selection = chain 'H'
selection = chain 'I'
selection = chain 'K'
selection = chain 'L'
}
ncs_group {
reference = chain 'J'
selection = chain 'M'
}
Set up NCS constraints
No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
Set random seed: 0.000
Set model cs if undefined: 0.000
Decide on map wrapping: 0.000
Normalize map: mean=0, sd=1: 16.980
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: 0.280
Extract box with map and model: 0.700
Check model and map are aligned: 0.120
Set scattering table: 0.170
Process input model: 45.160
Find NCS groups from input model: 0.280
Set up NCS constraints: 0.070
Set refine NCS operators: 0.000
Adjust number of macro_cycles: 0.000
Reset NCS operators: 0.000
Extract rigid body selections: 0.000
Check and reset occupancies: 0.010
Load rotamer database and sin/cos tables:2.670
Set ADP refinement strategy: 0.000
Make a string to write initial .geo file:0.000
Internal consistency checks: 0.000
Total: 66.440
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8164
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 : 0.013 0.085 10198 Z= 0.825
Angle : 1.524 9.721 13829 Z= 1.019
Chirality : 0.085 0.474 1620
Planarity : 0.013 0.270 1772
Dihedral : 15.706 106.231 4294
Min Nonbonded Distance : 2.364
Molprobity Statistics.
All-atom Clashscore : 1.08
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 1.98 %
Favored : 98.02 %
Rotamer:
Outliers : 0.09 %
Allowed : 0.93 %
Favored : 98.98 %
Cbeta Deviations : 0.18 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: -0.38 (0.22), residues: 1212
helix: -2.96 (0.45), residues: 80
sheet: -0.96 (0.39), residues: 139
loop : 0.16 (0.19), residues: 993
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.101 0.007 TRP B 205
HIS 0.007 0.001 HIS B 519
PHE 0.050 0.003 PHE A 252
TYR 0.083 0.007 TYR B 303
ARG 0.006 0.001 ARG A 106
*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
2424 Ramachandran restraints generated.
1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
2424 Ramachandran restraints generated.
1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
157 residues out of total 1076 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 1
poor density : 156
time to evaluate : 1.566
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: A 165 ASP cc_start: 0.7880 (t70) cc_final: 0.7579 (t0)
REVERT: C 188 THR cc_start: 0.8279 (p) cc_final: 0.8069 (t)
outliers start: 1
outliers final: 1
residues processed: 157
average time/residue: 0.5894
time to fit residues: 121.1372
Evaluate side-chains
74 residues out of total 1076 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 1
poor density : 73
time to evaluate : 1.409
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 280 ASN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 122
random chunks:
chunk 103 optimal weight: 0.9990
chunk 92 optimal weight: 0.8980
chunk 51 optimal weight: 5.9990
chunk 31 optimal weight: 0.7980
chunk 62 optimal weight: 0.7980
chunk 49 optimal weight: 5.9990
chunk 95 optimal weight: 0.9990
chunk 37 optimal weight: 0.6980
chunk 58 optimal weight: 7.9990
chunk 71 optimal weight: 0.9990
chunk 110 optimal weight: 7.9990
overall best weight: 0.8382
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** A 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 346 GLN
B 239 GLN
B 302 ASN
B 329 GLN
B 470 HIS
C 222 GLN
Total number of N/Q/H flips: 6
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8272
moved from start: 0.2704
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.004 0.076 10198 Z= 0.264
Angle : 0.719 10.357 13829 Z= 0.377
Chirality : 0.051 0.474 1620
Planarity : 0.005 0.043 1772
Dihedral : 13.789 77.282 2035
Min Nonbonded Distance : 2.260
Molprobity Statistics.
All-atom Clashscore : 2.83
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 1.90 %
Favored : 98.10 %
Rotamer:
Outliers : 0.93 %
Allowed : 5.20 %
Favored : 93.87 %
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: -0.66 (0.23), residues: 1212
helix: -2.57 (0.47), residues: 92
sheet: -0.83 (0.36), residues: 161
loop : -0.10 (0.19), residues: 959
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.018 0.002 TRP B 205
HIS 0.007 0.001 HIS A 505
PHE 0.012 0.001 PHE A 447
TYR 0.011 0.001 TYR B 303
ARG 0.003 0.001 ARG A 81
*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
2424 Ramachandran restraints generated.
1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
2424 Ramachandran restraints generated.
1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
90 residues out of total 1076 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 10
poor density : 80
time to evaluate : 1.329
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: A 462 ASP cc_start: 0.7902 (t0) cc_final: 0.7697 (t0)
outliers start: 10
outliers final: 8
residues processed: 90
average time/residue: 0.5192
time to fit residues: 64.1124
Evaluate side-chains
72 residues out of total 1076 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 8
poor density : 64
time to evaluate : 1.629
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 384 ILE
Chi-restraints excluded: chain A residue 570 HIS
Chi-restraints excluded: chain B residue 59 ASN
Chi-restraints excluded: chain B residue 158 ASN
Chi-restraints excluded: chain B residue 166 THR
Chi-restraints excluded: chain B residue 255 CYS
Chi-restraints excluded: chain B residue 302 ASN
Chi-restraints excluded: chain B residue 373 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 122
random chunks:
chunk 61 optimal weight: 1.9990
chunk 34 optimal weight: 1.9990
chunk 92 optimal weight: 1.9990
chunk 75 optimal weight: 1.9990
chunk 30 optimal weight: 0.0970
chunk 110 optimal weight: 0.0370
chunk 119 optimal weight: 0.5980
chunk 98 optimal weight: 1.9990
chunk 37 optimal weight: 0.7980
chunk 89 optimal weight: 0.7980
chunk 109 optimal weight: 4.9990
overall best weight: 0.4656
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 204 HIS
A 346 GLN
Total number of N/Q/H flips: 2
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8263
moved from start: 0.3173
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.085 10198 Z= 0.183
Angle : 0.637 8.910 13829 Z= 0.327
Chirality : 0.050 0.383 1620
Planarity : 0.004 0.037 1772
Dihedral : 10.145 62.482 2033
Min Nonbonded Distance : 2.382
Molprobity Statistics.
All-atom Clashscore : 2.21
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 2.31 %
Favored : 97.69 %
Rotamer:
Outliers : 0.56 %
Allowed : 6.41 %
Favored : 93.03 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: -0.75 (0.23), residues: 1212
helix: -2.30 (0.51), residues: 89
sheet: -0.87 (0.36), residues: 173
loop : -0.20 (0.20), residues: 950
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.012 0.001 TRP B 205
HIS 0.007 0.001 HIS A 70
PHE 0.015 0.001 PHE A 583
TYR 0.011 0.001 TYR B 303
ARG 0.002 0.000 ARG B 487
*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
2424 Ramachandran restraints generated.
1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
2424 Ramachandran restraints generated.
1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
75 residues out of total 1076 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 6
poor density : 69
time to evaluate : 1.585
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: B 184 ILE cc_start: 0.8138 (mm) cc_final: 0.7689 (pt)
REVERT: B 193 HIS cc_start: 0.8063 (t70) cc_final: 0.7781 (t70)
outliers start: 6
outliers final: 4
residues processed: 75
average time/residue: 0.5201
time to fit residues: 54.0092
Evaluate side-chains
68 residues out of total 1076 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 4
poor density : 64
time to evaluate : 1.459
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 384 ILE
Chi-restraints excluded: chain A residue 570 HIS
Chi-restraints excluded: chain B residue 158 ASN
Chi-restraints excluded: chain B residue 373 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 122
random chunks:
chunk 83 optimal weight: 1.9990
chunk 57 optimal weight: 7.9990
chunk 12 optimal weight: 1.9990
chunk 52 optimal weight: 1.9990
chunk 74 optimal weight: 7.9990
chunk 111 optimal weight: 10.0000
chunk 117 optimal weight: 2.9990
chunk 58 optimal weight: 6.9990
chunk 105 optimal weight: 2.9990
chunk 31 optimal weight: 1.9990
chunk 98 optimal weight: 0.9980
overall best weight: 1.7988
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 162 HIS
A 346 GLN
A 439 GLN
B 249 HIS
B 329 GLN
B 538 GLN
Total number of N/Q/H flips: 6
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8408
moved from start: 0.3745
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.006 0.162 10198 Z= 0.415
Angle : 0.674 8.058 13829 Z= 0.351
Chirality : 0.050 0.335 1620
Planarity : 0.005 0.038 1772
Dihedral : 7.617 49.910 2033
Min Nonbonded Distance : 2.313
Molprobity Statistics.
All-atom Clashscore : 3.14
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 3.80 %
Favored : 96.20 %
Rotamer:
Outliers : 1.30 %
Allowed : 6.04 %
Favored : 92.66 %
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: -1.08 (0.23), residues: 1212
helix: -2.08 (0.52), residues: 89
sheet: -0.86 (0.37), residues: 174
loop : -0.56 (0.19), residues: 949
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.013 0.002 TRP B 614
HIS 0.007 0.001 HIS B 174
PHE 0.021 0.002 PHE A 447
TYR 0.022 0.002 TYR B 303
ARG 0.004 0.001 ARG A 396
*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
2424 Ramachandran restraints generated.
1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
2424 Ramachandran restraints generated.
1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
78 residues out of total 1076 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 14
poor density : 64
time to evaluate : 1.506
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: A 583 PHE cc_start: 0.5989 (p90) cc_final: 0.5739 (p90)
REVERT: B 193 HIS cc_start: 0.8121 (t70) cc_final: 0.7830 (t70)
outliers start: 14
outliers final: 11
residues processed: 77
average time/residue: 0.5147
time to fit residues: 54.9298
Evaluate side-chains
68 residues out of total 1076 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 11
poor density : 57
time to evaluate : 1.487
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 258 CYS
Chi-restraints excluded: chain A residue 384 ILE
Chi-restraints excluded: chain A residue 440 GLN
Chi-restraints excluded: chain A residue 570 HIS
Chi-restraints excluded: chain B residue 59 ASN
Chi-restraints excluded: chain B residue 166 THR
Chi-restraints excluded: chain B residue 185 ASP
Chi-restraints excluded: chain B residue 255 CYS
Chi-restraints excluded: chain B residue 373 SER
Chi-restraints excluded: chain B residue 377 LEU
Chi-restraints excluded: chain B residue 379 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 122
random chunks:
chunk 66 optimal weight: 0.5980
chunk 1 optimal weight: 1.9990
chunk 87 optimal weight: 4.9990
chunk 48 optimal weight: 1.9990
chunk 100 optimal weight: 0.9990
chunk 81 optimal weight: 0.9980
chunk 0 optimal weight: 1.9990
chunk 60 optimal weight: 2.9990
chunk 105 optimal weight: 0.6980
chunk 29 optimal weight: 7.9990
chunk 39 optimal weight: 0.8980
overall best weight: 0.8382
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 320 GLN
Total number of N/Q/H flips: 1
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8373
moved from start: 0.3934
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.047 10198 Z= 0.203
Angle : 0.572 7.578 13829 Z= 0.295
Chirality : 0.046 0.314 1620
Planarity : 0.004 0.042 1772
Dihedral : 6.590 52.649 2033
Min Nonbonded Distance : 2.406
Molprobity Statistics.
All-atom Clashscore : 2.67
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 3.14 %
Favored : 96.86 %
Rotamer:
Outliers : 0.65 %
Allowed : 7.16 %
Favored : 92.19 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: -0.92 (0.23), residues: 1212
helix: -2.03 (0.52), residues: 89
sheet: -0.78 (0.38), residues: 174
loop : -0.43 (0.20), residues: 949
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.008 0.001 TRP B 205
HIS 0.004 0.001 HIS B 564
PHE 0.013 0.001 PHE A 447
TYR 0.009 0.001 TYR B 303
ARG 0.008 0.000 ARG B 138
*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
2424 Ramachandran restraints generated.
1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
2424 Ramachandran restraints generated.
1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
68 residues out of total 1076 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 7
poor density : 61
time to evaluate : 1.417
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: A 583 PHE cc_start: 0.6009 (p90) cc_final: 0.5775 (p90)
REVERT: B 44 ASP cc_start: 0.7962 (m-30) cc_final: 0.7487 (m-30)
outliers start: 7
outliers final: 7
residues processed: 67
average time/residue: 0.5189
time to fit residues: 48.3627
Evaluate side-chains
64 residues out of total 1076 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 7
poor density : 57
time to evaluate : 1.437
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 238 CYS
Chi-restraints excluded: chain A residue 258 CYS
Chi-restraints excluded: chain A residue 384 ILE
Chi-restraints excluded: chain A residue 570 HIS
Chi-restraints excluded: chain B residue 185 ASP
Chi-restraints excluded: chain B residue 377 LEU
Chi-restraints excluded: chain B residue 379 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 122
random chunks:
chunk 106 optimal weight: 4.9990
chunk 23 optimal weight: 0.9980
chunk 69 optimal weight: 0.9990
chunk 29 optimal weight: 4.9990
chunk 118 optimal weight: 3.9990
chunk 97 optimal weight: 1.9990
chunk 54 optimal weight: 3.9990
chunk 9 optimal weight: 0.7980
chunk 39 optimal weight: 0.7980
chunk 61 optimal weight: 1.9990
chunk 113 optimal weight: 10.0000
overall best weight: 1.1184
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
Total number of N/Q/H flips: 0
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8405
moved from start: 0.4206
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.004 0.049 10198 Z= 0.267
Angle : 0.574 7.449 13829 Z= 0.298
Chirality : 0.047 0.299 1620
Planarity : 0.004 0.041 1772
Dihedral : 6.153 55.417 2033
Min Nonbonded Distance : 2.415
Molprobity Statistics.
All-atom Clashscore : 2.72
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 3.96 %
Favored : 96.04 %
Rotamer:
Outliers : 1.02 %
Allowed : 7.34 %
Favored : 91.64 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: -0.90 (0.24), residues: 1212
helix: -2.05 (0.52), residues: 89
sheet: -0.70 (0.39), residues: 172
loop : -0.42 (0.20), residues: 951
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.008 0.001 TRP B 205
HIS 0.005 0.001 HIS B 174
PHE 0.014 0.001 PHE A 447
TYR 0.011 0.001 TYR B 303
ARG 0.005 0.000 ARG B 138
*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
2424 Ramachandran restraints generated.
1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
2424 Ramachandran restraints generated.
1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
68 residues out of total 1076 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 11
poor density : 57
time to evaluate : 1.501
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: A 583 PHE cc_start: 0.6048 (p90) cc_final: 0.5816 (p90)
REVERT: B 193 HIS cc_start: 0.8096 (t70) cc_final: 0.7786 (t70)
outliers start: 11
outliers final: 11
residues processed: 67
average time/residue: 0.5567
time to fit residues: 51.0018
Evaluate side-chains
64 residues out of total 1076 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 11
poor density : 53
time to evaluate : 1.432
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 238 CYS
Chi-restraints excluded: chain A residue 258 CYS
Chi-restraints excluded: chain A residue 384 ILE
Chi-restraints excluded: chain A residue 423 ILE
Chi-restraints excluded: chain A residue 570 HIS
Chi-restraints excluded: chain B residue 59 ASN
Chi-restraints excluded: chain B residue 185 ASP
Chi-restraints excluded: chain B residue 249 HIS
Chi-restraints excluded: chain B residue 373 SER
Chi-restraints excluded: chain B residue 377 LEU
Chi-restraints excluded: chain B residue 379 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 122
random chunks:
chunk 13 optimal weight: 0.9990
chunk 67 optimal weight: 1.9990
chunk 86 optimal weight: 0.6980
chunk 66 optimal weight: 0.6980
chunk 99 optimal weight: 0.9990
chunk 65 optimal weight: 0.9980
chunk 117 optimal weight: 0.9980
chunk 73 optimal weight: 1.9990
chunk 71 optimal weight: 2.9990
chunk 54 optimal weight: 10.0000
chunk 72 optimal weight: 0.5980
overall best weight: 0.7980
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
Total number of N/Q/H flips: 0
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8388
moved from start: 0.4340
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.036 10198 Z= 0.188
Angle : 0.541 7.325 13829 Z= 0.280
Chirality : 0.045 0.286 1620
Planarity : 0.004 0.039 1772
Dihedral : 5.892 57.765 2033
Min Nonbonded Distance : 2.422
Molprobity Statistics.
All-atom Clashscore : 3.14
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 3.55 %
Favored : 96.45 %
Rotamer:
Outliers : 1.02 %
Allowed : 7.34 %
Favored : 91.64 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: -0.79 (0.24), residues: 1212
helix: -2.11 (0.50), residues: 89
sheet: -0.54 (0.41), residues: 162
loop : -0.35 (0.20), residues: 961
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.006 0.001 TRP B 205
HIS 0.003 0.001 HIS B 267
PHE 0.012 0.001 PHE A 546
TYR 0.011 0.001 TYR A 469
ARG 0.004 0.000 ARG B 138
*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
2424 Ramachandran restraints generated.
1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
2424 Ramachandran restraints generated.
1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
66 residues out of total 1076 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 11
poor density : 55
time to evaluate : 1.510
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: A 583 PHE cc_start: 0.6071 (p90) cc_final: 0.5850 (p90)
REVERT: B 44 ASP cc_start: 0.7999 (OUTLIER) cc_final: 0.7486 (m-30)
REVERT: B 193 HIS cc_start: 0.8057 (t70) cc_final: 0.7761 (t70)
outliers start: 11
outliers final: 10
residues processed: 63
average time/residue: 0.5579
time to fit residues: 48.6597
Evaluate side-chains
64 residues out of total 1076 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 11
poor density : 53
time to evaluate : 1.586
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 238 CYS
Chi-restraints excluded: chain A residue 258 CYS
Chi-restraints excluded: chain A residue 384 ILE
Chi-restraints excluded: chain A residue 423 ILE
Chi-restraints excluded: chain A residue 570 HIS
Chi-restraints excluded: chain B residue 44 ASP
Chi-restraints excluded: chain B residue 185 ASP
Chi-restraints excluded: chain B residue 249 HIS
Chi-restraints excluded: chain B residue 373 SER
Chi-restraints excluded: chain B residue 377 LEU
Chi-restraints excluded: chain B residue 379 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 122
random chunks:
chunk 46 optimal weight: 2.9990
chunk 70 optimal weight: 0.8980
chunk 35 optimal weight: 0.5980
chunk 23 optimal weight: 0.9980
chunk 22 optimal weight: 0.6980
chunk 74 optimal weight: 1.9990
chunk 80 optimal weight: 0.9980
chunk 58 optimal weight: 10.0000
chunk 10 optimal weight: 2.9990
chunk 92 optimal weight: 1.9990
chunk 106 optimal weight: 4.9990
overall best weight: 0.8380
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
Total number of N/Q/H flips: 0
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8396
moved from start: 0.4506
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.040 10198 Z= 0.203
Angle : 0.537 7.193 13829 Z= 0.278
Chirality : 0.045 0.277 1620
Planarity : 0.004 0.038 1772
Dihedral : 5.733 59.984 2033
Min Nonbonded Distance : 2.433
Molprobity Statistics.
All-atom Clashscore : 3.19
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 4.46 %
Favored : 95.54 %
Rotamer:
Outliers : 1.12 %
Allowed : 7.62 %
Favored : 91.26 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: -0.77 (0.24), residues: 1212
helix: -2.14 (0.50), residues: 89
sheet: -0.51 (0.41), residues: 174
loop : -0.32 (0.21), residues: 949
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.006 0.001 TRP B 205
HIS 0.004 0.001 HIS B 478
PHE 0.012 0.001 PHE A 546
TYR 0.009 0.001 TYR B 303
ARG 0.007 0.000 ARG A 95
*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
2424 Ramachandran restraints generated.
1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
2424 Ramachandran restraints generated.
1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
63 residues out of total 1076 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 12
poor density : 51
time to evaluate : 1.463
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: A 583 PHE cc_start: 0.6054 (p90) cc_final: 0.5845 (p90)
REVERT: B 44 ASP cc_start: 0.8040 (OUTLIER) cc_final: 0.7521 (m-30)
REVERT: B 193 HIS cc_start: 0.8061 (t70) cc_final: 0.7746 (t70)
outliers start: 12
outliers final: 11
residues processed: 60
average time/residue: 0.4438
time to fit residues: 39.0773
Evaluate side-chains
63 residues out of total 1076 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 12
poor density : 51
time to evaluate : 1.490
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 238 CYS
Chi-restraints excluded: chain A residue 258 CYS
Chi-restraints excluded: chain A residue 384 ILE
Chi-restraints excluded: chain A residue 423 ILE
Chi-restraints excluded: chain A residue 570 HIS
Chi-restraints excluded: chain B residue 44 ASP
Chi-restraints excluded: chain B residue 59 ASN
Chi-restraints excluded: chain B residue 185 ASP
Chi-restraints excluded: chain B residue 249 HIS
Chi-restraints excluded: chain B residue 373 SER
Chi-restraints excluded: chain B residue 377 LEU
Chi-restraints excluded: chain B residue 379 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 122
random chunks:
chunk 112 optimal weight: 0.0060
chunk 102 optimal weight: 1.9990
chunk 109 optimal weight: 1.9990
chunk 65 optimal weight: 0.8980
chunk 47 optimal weight: 1.9990
chunk 86 optimal weight: 0.6980
chunk 33 optimal weight: 1.9990
chunk 99 optimal weight: 0.9980
chunk 103 optimal weight: 0.0870
chunk 71 optimal weight: 2.9990
chunk 115 optimal weight: 7.9990
overall best weight: 0.5374
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
B 302 ASN
Total number of N/Q/H flips: 1
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8372
moved from start: 0.4592
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.002 0.032 10198 Z= 0.146
Angle : 0.514 6.998 13829 Z= 0.265
Chirality : 0.044 0.267 1620
Planarity : 0.004 0.037 1772
Dihedral : 5.525 59.898 2033
Min Nonbonded Distance : 2.434
Molprobity Statistics.
All-atom Clashscore : 3.29
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 3.96 %
Favored : 96.04 %
Rotamer:
Outliers : 1.02 %
Allowed : 7.81 %
Favored : 91.17 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: -0.70 (0.24), residues: 1212
helix: -2.12 (0.50), residues: 89
sheet: -0.56 (0.41), residues: 166
loop : -0.25 (0.21), residues: 957
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.005 0.001 TRP B 205
HIS 0.002 0.000 HIS B 478
PHE 0.015 0.001 PHE A 543
TYR 0.006 0.001 TYR B 411
ARG 0.004 0.000 ARG B 138
*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
2424 Ramachandran restraints generated.
1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
2424 Ramachandran restraints generated.
1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
64 residues out of total 1076 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 11
poor density : 53
time to evaluate : 1.693
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: B 44 ASP cc_start: 0.7927 (OUTLIER) cc_final: 0.7451 (m-30)
REVERT: B 193 HIS cc_start: 0.8061 (t70) cc_final: 0.7793 (t70)
outliers start: 11
outliers final: 9
residues processed: 62
average time/residue: 0.4590
time to fit residues: 42.3001
Evaluate side-chains
60 residues out of total 1076 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 10
poor density : 50
time to evaluate : 1.467
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 238 CYS
Chi-restraints excluded: chain A residue 258 CYS
Chi-restraints excluded: chain A residue 384 ILE
Chi-restraints excluded: chain A residue 423 ILE
Chi-restraints excluded: chain A residue 570 HIS
Chi-restraints excluded: chain B residue 44 ASP
Chi-restraints excluded: chain B residue 249 HIS
Chi-restraints excluded: chain B residue 373 SER
Chi-restraints excluded: chain B residue 377 LEU
Chi-restraints excluded: chain B residue 379 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 122
random chunks:
chunk 70 optimal weight: 0.9990
chunk 54 optimal weight: 10.0000
chunk 80 optimal weight: 0.9980
chunk 121 optimal weight: 2.9990
chunk 111 optimal weight: 0.9990
chunk 96 optimal weight: 1.9990
chunk 10 optimal weight: 2.9990
chunk 74 optimal weight: 0.9980
chunk 59 optimal weight: 2.9990
chunk 76 optimal weight: 2.9990
chunk 103 optimal weight: 0.5980
overall best weight: 0.9184
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
Total number of N/Q/H flips: 0
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8400
moved from start: 0.4704
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.052 10198 Z= 0.212
Angle : 0.529 6.970 13829 Z= 0.274
Chirality : 0.045 0.267 1620
Planarity : 0.004 0.038 1772
Dihedral : 5.517 58.353 2033
Min Nonbonded Distance : 2.427
Molprobity Statistics.
All-atom Clashscore : 3.29
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 4.87 %
Favored : 95.13 %
Rotamer:
Outliers : 0.93 %
Allowed : 7.90 %
Favored : 91.17 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: -0.71 (0.24), residues: 1212
helix: -2.12 (0.51), residues: 89
sheet: -0.57 (0.40), residues: 176
loop : -0.26 (0.21), residues: 947
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.007 0.001 TRP B 205
HIS 0.003 0.001 HIS B 490
PHE 0.014 0.001 PHE A 583
TYR 0.009 0.001 TYR B 303
ARG 0.002 0.000 ARG A 95
********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
2424 Ramachandran restraints generated.
1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
2424 Ramachandran restraints generated.
1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
63 residues out of total 1076 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 10
poor density : 53
time to evaluate : 1.665
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: B 193 HIS cc_start: 0.8078 (t70) cc_final: 0.7754 (t70)
outliers start: 10
outliers final: 9
residues processed: 61
average time/residue: 0.4374
time to fit residues: 39.4687
Evaluate side-chains
59 residues out of total 1076 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 9
poor density : 50
time to evaluate : 1.464
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 238 CYS
Chi-restraints excluded: chain A residue 258 CYS
Chi-restraints excluded: chain A residue 384 ILE
Chi-restraints excluded: chain A residue 423 ILE
Chi-restraints excluded: chain A residue 570 HIS
Chi-restraints excluded: chain B residue 249 HIS
Chi-restraints excluded: chain B residue 373 SER
Chi-restraints excluded: chain B residue 377 LEU
Chi-restraints excluded: chain B residue 379 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 122
random chunks:
chunk 29 optimal weight: 0.6980
chunk 89 optimal weight: 0.9980
chunk 14 optimal weight: 0.0470
chunk 26 optimal weight: 0.7980
chunk 96 optimal weight: 1.9990
chunk 40 optimal weight: 0.9980
chunk 99 optimal weight: 0.5980
chunk 12 optimal weight: 0.3980
chunk 17 optimal weight: 0.9980
chunk 85 optimal weight: 0.7980
chunk 5 optimal weight: 0.9980
overall best weight: 0.5078
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
Total number of N/Q/H flips: 0
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4083 r_free = 0.4083 target = 0.136102 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.087036 restraints weight = 49857.813|
|-----------------------------------------------------------------------------|
r_work (start): 0.3329 rms_B_bonded: 3.64
r_work: 0.3169 rms_B_bonded: 3.48 restraints_weight: 0.5000
r_work (final): 0.3169
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8147
moved from start: 0.4776
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.002 0.033 10198 Z= 0.147
Angle : 0.507 6.829 13829 Z= 0.262
Chirality : 0.044 0.259 1620
Planarity : 0.004 0.036 1772
Dihedral : 5.369 57.093 2033
Min Nonbonded Distance : 2.431
Molprobity Statistics.
All-atom Clashscore : 3.39
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 4.21 %
Favored : 95.79 %
Rotamer:
Outliers : 0.84 %
Allowed : 7.81 %
Favored : 91.36 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: -0.65 (0.24), residues: 1212
helix: -2.09 (0.51), residues: 89
sheet: -0.54 (0.40), residues: 176
loop : -0.21 (0.21), residues: 947
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.005 0.001 TRP B 205
HIS 0.003 0.001 HIS B 48
PHE 0.014 0.001 PHE A 546
TYR 0.007 0.001 TYR B 554
ARG 0.004 0.000 ARG B 138
Origin is already at (0, 0, 0), no shifts will be applied
===============================================================================
Job complete
usr+sys time: 4230.07 seconds
wall clock time: 81 minutes 42.07 seconds (4902.07 seconds total)