Starting phenix.real_space_refine
on Tue Jan 14 17:19:23 2025 by dcliebschner
===============================================================================
Processing files:
-------------------------------------------------------------------------------
Found model, /net/cci-nas-00/data/ceres_data/8rk0_19254/01_2025/8rk0_19254.cif
Found real_map, /net/cci-nas-00/data/ceres_data/8rk0_19254/01_2025/8rk0_19254.map
Processing PHIL parameters:
-------------------------------------------------------------------------------
Adding command-line PHIL:
-------------------------
refinement.macro_cycles=10
scattering_table=electron
resolution=3.38
write_initial_geo_file=False
Final processed PHIL parameters:
-------------------------------------------------------------------------------
data_manager {
real_map_files = "/net/cci-nas-00/data/ceres_data/8rk0_19254/01_2025/8rk0_19254.map"
default_real_map = "/net/cci-nas-00/data/ceres_data/8rk0_19254/01_2025/8rk0_19254.map"
model {
file = "/net/cci-nas-00/data/ceres_data/8rk0_19254/01_2025/8rk0_19254.cif"
}
default_model = "/net/cci-nas-00/data/ceres_data/8rk0_19254/01_2025/8rk0_19254.cif"
}
resolution = 3.38
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= 0.004 sd= 0.031
Set stop_for_unknowns flag
Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
Set to: electron
Number of scattering types: 4
Type Number sf(0) Gaussians
S 58 5.16 5
C 4344 2.51 5
N 1136 2.21 5
O 1402 1.98 5
sf(0) = scattering factor at diffraction angle 0.
Process input model
Symmetric amino acids flipped. Time to flip 7 residue(s): 0.02s
Monomer Library directory:
"/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
Total number of atoms: 6940
Number of models: 1
Model: ""
Number of chains: 24
Chain: "C"
Number of atoms: 637
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 84, 637
Classifications: {'peptide': 84}
Incomplete info: {'truncation_to_alanine': 1}
Link IDs: {'PTRANS': 6, 'TRANS': 77}
Chain breaks: 1
Unresolved non-hydrogen bonds: 6
Unresolved non-hydrogen angles: 7
Unresolved non-hydrogen dihedrals: 5
Planarities with less than four sites: {'ARG:plan': 1}
Unresolved non-hydrogen planarities: 5
Chain: "D"
Number of atoms: 2523
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 322, 2523
Classifications: {'peptide': 322}
Link IDs: {'PTRANS': 26, 'TRANS': 295}
Chain breaks: 1
Chain: "A"
Number of atoms: 637
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 84, 637
Classifications: {'peptide': 84}
Incomplete info: {'truncation_to_alanine': 1}
Link IDs: {'PTRANS': 6, 'TRANS': 77}
Chain breaks: 1
Unresolved non-hydrogen bonds: 6
Unresolved non-hydrogen angles: 7
Unresolved non-hydrogen dihedrals: 5
Planarities with less than four sites: {'ARG:plan': 1}
Unresolved non-hydrogen planarities: 5
Chain: "B"
Number of atoms: 2523
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 322, 2523
Classifications: {'peptide': 322}
Link IDs: {'PTRANS': 26, 'TRANS': 295}
Chain breaks: 1
Chain: "L"
Number of atoms: 28
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 2, 28
Unusual residues: {'NAG': 2}
Classifications: {'undetermined': 2}
Link IDs: {None: 1}
Unresolved non-hydrogen bonds: 2
Unresolved non-hydrogen angles: 4
Unresolved non-hydrogen dihedrals: 6
Unresolved non-hydrogen chiralities: 2
Chain: "E"
Number of atoms: 28
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 2, 28
Unusual residues: {'NAG': 2}
Classifications: {'undetermined': 2}
Link IDs: {None: 1}
Unresolved non-hydrogen bonds: 2
Unresolved non-hydrogen angles: 4
Unresolved non-hydrogen dihedrals: 6
Unresolved non-hydrogen chiralities: 2
Chain: "F"
Number of atoms: 28
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 2, 28
Unusual residues: {'NAG': 2}
Classifications: {'undetermined': 2}
Link IDs: {None: 1}
Unresolved non-hydrogen bonds: 2
Unresolved non-hydrogen angles: 4
Unresolved non-hydrogen dihedrals: 6
Unresolved non-hydrogen chiralities: 2
Chain: "G"
Number of atoms: 28
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 2, 28
Unusual residues: {'NAG': 2}
Classifications: {'undetermined': 2}
Link IDs: {None: 1}
Unresolved non-hydrogen bonds: 2
Unresolved non-hydrogen angles: 4
Unresolved non-hydrogen dihedrals: 6
Unresolved non-hydrogen chiralities: 2
Chain: "H"
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: "I"
Number of atoms: 28
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 2, 28
Unusual residues: {'NAG': 2}
Classifications: {'undetermined': 2}
Link IDs: {None: 1}
Unresolved non-hydrogen bonds: 2
Unresolved non-hydrogen angles: 4
Unresolved non-hydrogen dihedrals: 6
Unresolved non-hydrogen chiralities: 2
Chain: "J"
Number of atoms: 28
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 2, 28
Unusual residues: {'NAG': 2}
Classifications: {'undetermined': 2}
Link IDs: {None: 1}
Unresolved non-hydrogen bonds: 2
Unresolved non-hydrogen angles: 4
Unresolved non-hydrogen dihedrals: 6
Unresolved non-hydrogen chiralities: 2
Chain: "K"
Number of atoms: 28
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 2, 28
Unusual residues: {'NAG': 2}
Classifications: {'undetermined': 2}
Link IDs: {None: 1}
Unresolved non-hydrogen bonds: 2
Unresolved non-hydrogen angles: 4
Unresolved non-hydrogen dihedrals: 6
Unresolved non-hydrogen chiralities: 2
Chain: "M"
Number of atoms: 28
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 2, 28
Unusual residues: {'NAG': 2}
Classifications: {'undetermined': 2}
Link IDs: {None: 1}
Unresolved non-hydrogen bonds: 2
Unresolved non-hydrogen angles: 4
Unresolved non-hydrogen dihedrals: 6
Unresolved non-hydrogen chiralities: 2
Chain: "N"
Number of atoms: 28
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 2, 28
Unusual residues: {'NAG': 2}
Classifications: {'undetermined': 2}
Link IDs: {None: 1}
Unresolved non-hydrogen bonds: 2
Unresolved non-hydrogen angles: 4
Unresolved non-hydrogen dihedrals: 6
Unresolved non-hydrogen chiralities: 2
Chain: "O"
Number of atoms: 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: "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: 9
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: 9
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: 9
Unresolved non-hydrogen chiralities: 3
Chain: "S"
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: "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: 9
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: 9
Unresolved non-hydrogen chiralities: 3
Chain: "V"
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: "D"
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
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: 5.84, per 1000 atoms: 0.84
Number of scatterers: 6940
At special positions: 0
Unit cell: (102.176, 88.168, 77.456, 90, 90, 90)
Space group: P 1 (No. 1)
Number of sites at special positions: 0
Number of scattering types: 4
Type Number sf(0)
S 58 16.00
O 1402 8.00
N 1136 7.00
C 4344 6.00
sf(0) = scattering factor at diffraction angle 0.
Number of disulfides: simple=22, symmetry=0
Simple disulfide: pdb=" SG CYS C 207 " - pdb=" SG CYS C 226 " distance=2.03
Simple disulfide: pdb=" SG CYS C 229 " - pdb=" SG CYS C 304 " distance=2.03
Simple disulfide: pdb=" SG CYS C 238 " - pdb=" SG CYS C 306 " distance=2.02
Simple disulfide: pdb=" SG CYS D 429 " - pdb=" SG CYS D 504 " distance=2.03
Simple disulfide: pdb=" SG CYS D 452 " - pdb=" SG CYS D 626 " distance=2.03
Simple disulfide: pdb=" SG CYS D 459 " - pdb=" SG CYS D 487 " distance=2.03
Simple disulfide: pdb=" SG CYS D 495 " - pdb=" SG CYS D 565 " distance=2.03
Simple disulfide: pdb=" SG CYS D 509 " - pdb=" SG CYS D 553 " distance=2.03
Simple disulfide: pdb=" SG CYS D 570 " - pdb=" SG CYS D 603 " distance=2.03
Simple disulfide: pdb=" SG CYS D 587 " - pdb=" SG CYS D 591 " distance=2.03
Simple disulfide: pdb=" SG CYS D 613 " - pdb=" SG CYS D 650 " distance=2.03
Simple disulfide: pdb=" SG CYS A 207 " - pdb=" SG CYS A 226 " distance=2.03
Simple disulfide: pdb=" SG CYS A 229 " - pdb=" SG CYS A 304 " distance=2.03
Simple disulfide: pdb=" SG CYS A 238 " - pdb=" SG CYS A 306 " distance=2.03
Simple disulfide: pdb=" SG CYS B 429 " - pdb=" SG CYS B 504 " distance=2.03
Simple disulfide: pdb=" SG CYS B 452 " - pdb=" SG CYS B 626 " distance=2.03
Simple disulfide: pdb=" SG CYS B 459 " - pdb=" SG CYS B 487 " distance=2.03
Simple disulfide: pdb=" SG CYS B 495 " - pdb=" SG CYS B 565 " distance=2.03
Simple disulfide: pdb=" SG CYS B 509 " - pdb=" SG CYS B 553 " distance=2.03
Simple disulfide: pdb=" SG CYS B 570 " - pdb=" SG CYS B 603 " distance=2.03
Simple disulfide: pdb=" SG CYS B 587 " - pdb=" SG CYS B 591 " distance=2.03
Simple disulfide: pdb=" SG CYS B 613 " - pdb=" SG CYS B 650 " distance=2.03
Automatic linking
Parameters for automatic linking
Linking & cutoffs
Metal : Auto - 3.00
Amino acid : True - 1.90
Carbohydrate : True - 1.99
Ligands : True - 1.99
Small molecules : False - 1.98
Amino acid - RNA/DNA : False
Number of custom bonds: simple=2, symmetry=0
Links applied
BETA1-4
" NAG E 1 " - " NAG E 2 "
" NAG F 1 " - " NAG F 2 "
" NAG G 1 " - " NAG G 2 "
" NAG H 1 " - " NAG H 2 "
" NAG I 1 " - " NAG I 2 "
" NAG J 1 " - " NAG J 2 "
" NAG K 1 " - " NAG K 2 "
" NAG L 1 " - " NAG L 2 "
" NAG M 1 " - " NAG M 2 "
" NAG N 1 " - " NAG N 2 "
" NAG O 1 " - " NAG O 2 "
" NAG 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 V 2 " - " BMA V 3 "
NAG-ASN
" NAG F 1 " - " ASN C 305 "
" NAG I 1 " - " ASN B 448 "
" NAG K 1 " - " ASN A 305 "
" NAG L 1 " - " ASN D 448 "
" NAG N 1 " - " ASN B 423 "
" NAG O 1 " - " ASN D 557 "
" NAG P 1 " - " ASN D 629 "
" NAG Q 1 " - " ASN D 651 "
" NAG S 1 " - " ASN B 557 "
" NAG T 1 " - " ASN B 629 "
" NAG U 1 " - " ASN B 651 "
Number of additional bonds: simple=2, symmetry=0
Coordination:
Other bonds:
Time building additional restraints: 2.14
Conformation dependent library (CDL) restraints added in 897.9 milliseconds
1592 Ramachandran restraints generated.
796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2.
Adding C-beta torsion restraints...
Number of C-beta restraints generated: 1492
Finding SS restraints...
Secondary structure from input PDB file:
15 helices and 18 sheets defined
11.8% alpha, 14.9% beta
0 base pairs and 0 stacking pairs defined.
Time for finding SS restraints: 0.74
Creating SS restraints...
Processing helix chain 'D' and resid 405 through 409
Processing helix chain 'D' and resid 432 through 442
removed outlier: 3.661A pdb=" N PHE D 442 " --> pdb=" O ILE D 438 " (cutoff:3.500A)
Processing helix chain 'D' and resid 451 through 457
Processing helix chain 'D' and resid 461 through 465
removed outlier: 3.621A pdb=" N PHE D 465 " --> pdb=" O ILE D 462 " (cutoff:3.500A)
Processing helix chain 'D' and resid 499 through 503
removed outlier: 3.709A pdb=" N SER D 502 " --> pdb=" O PRO D 499 " (cutoff:3.500A)
Processing helix chain 'D' and resid 599 through 604
Processing helix chain 'D' and resid 619 through 624
Processing helix chain 'B' and resid 405 through 409
Processing helix chain 'B' and resid 432 through 442
removed outlier: 3.645A pdb=" N PHE B 442 " --> pdb=" O ILE B 438 " (cutoff:3.500A)
Processing helix chain 'B' and resid 451 through 457
Processing helix chain 'B' and resid 461 through 465
removed outlier: 3.609A pdb=" N PHE B 465 " --> pdb=" O ILE B 462 " (cutoff:3.500A)
Processing helix chain 'B' and resid 499 through 503
removed outlier: 3.729A pdb=" N SER B 502 " --> pdb=" O PRO B 499 " (cutoff:3.500A)
removed outlier: 3.525A pdb=" N VAL B 503 " --> pdb=" O ALA B 500 " (cutoff:3.500A)
No H-bonds generated for 'chain 'B' and resid 499 through 503'
Processing helix chain 'B' and resid 599 through 604
Processing helix chain 'B' and resid 619 through 624
Processing helix chain 'B' and resid 625 through 630
removed outlier: 4.524A pdb=" N ASN B 629 " --> pdb=" O CYS B 626 " (cutoff:3.500A)
Processing sheet with id=AA1, first strand: chain 'C' and resid 194 through 196
Processing sheet with id=AA2, first strand: chain 'C' and resid 212 through 215
removed outlier: 4.141A pdb=" N VAL C 246 " --> pdb=" O VAL C 242 " (cutoff:3.500A)
Processing sheet with id=AA3, first strand: chain 'C' and resid 229 through 231
Processing sheet with id=AA4, first strand: chain 'D' and resid 413 through 416
Processing sheet with id=AA5, first strand: chain 'D' and resid 473 through 474
Processing sheet with id=AA6, first strand: chain 'D' and resid 514 through 516
removed outlier: 5.460A pdb=" N MET D 556 " --> pdb=" O PRO D 506 " (cutoff:3.500A)
removed outlier: 4.230A pdb=" N GLY D 552 " --> pdb=" O PHE D 510 " (cutoff:3.500A)
Processing sheet with id=AA7, first strand: chain 'D' and resid 613 through 615
Processing sheet with id=AA8, first strand: chain 'D' and resid 664 through 665
removed outlier: 6.114A pdb=" N ASP D 664 " --> pdb=" O PHE D 685 " (cutoff:3.500A)
No H-bonds generated for sheet with id=AA8
Processing sheet with id=AA9, first strand: chain 'D' and resid 677 through 679
removed outlier: 4.643A pdb=" N HIS D 697 " --> pdb=" O TYR D 707 " (cutoff:3.500A)
Processing sheet with id=AB1, first strand: chain 'A' and resid 194 through 196
Processing sheet with id=AB2, first strand: chain 'A' and resid 212 through 215
Processing sheet with id=AB3, first strand: chain 'A' and resid 229 through 231
Processing sheet with id=AB4, first strand: chain 'B' and resid 413 through 416
Processing sheet with id=AB5, first strand: chain 'B' and resid 473 through 474
Processing sheet with id=AB6, first strand: chain 'B' and resid 514 through 517
removed outlier: 4.765A pdb=" N VAL B 507 " --> pdb=" O VAL B 517 " (cutoff:3.500A)
removed outlier: 5.452A pdb=" N MET B 556 " --> pdb=" O PRO B 506 " (cutoff:3.500A)
removed outlier: 4.228A pdb=" N GLY B 552 " --> pdb=" O PHE B 510 " (cutoff:3.500A)
Processing sheet with id=AB7, first strand: chain 'B' and resid 613 through 615
Processing sheet with id=AB8, first strand: chain 'B' and resid 664 through 665
removed outlier: 6.261A pdb=" N ASP B 664 " --> pdb=" O PHE B 685 " (cutoff:3.500A)
No H-bonds generated for sheet with id=AB8
Processing sheet with id=AB9, first strand: chain 'B' and resid 677 through 679
108 hydrogen bonds defined for protein.
273 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: 1.78
Time building geometry restraints manager: 2.44 seconds
NOTE: a complete listing of the restraints can be obtained by requesting
output of .geo file.
Histogram of bond lengths:
1.22 - 1.34: 2119
1.34 - 1.46: 1904
1.46 - 1.58: 3047
1.58 - 1.70: 0
1.70 - 1.82: 68
Bond restraints: 7138
Sorted by residual:
bond pdb=" C1 BMA S 3 "
pdb=" C2 BMA S 3 "
ideal model delta sigma weight residual
1.519 1.568 -0.049 2.00e-02 2.50e+03 5.95e+00
bond pdb=" C1 BMA O 3 "
pdb=" C2 BMA O 3 "
ideal model delta sigma weight residual
1.519 1.567 -0.048 2.00e-02 2.50e+03 5.76e+00
bond pdb=" C1 NAG V 1 "
pdb=" O5 NAG V 1 "
ideal model delta sigma weight residual
1.406 1.449 -0.043 2.00e-02 2.50e+03 4.65e+00
bond pdb=" C1 NAG R 1 "
pdb=" O5 NAG R 1 "
ideal model delta sigma weight residual
1.406 1.446 -0.040 2.00e-02 2.50e+03 3.99e+00
bond pdb=" C1 BMA S 3 "
pdb=" O5 BMA S 3 "
ideal model delta sigma weight residual
1.410 1.449 -0.039 2.00e-02 2.50e+03 3.86e+00
... (remaining 7133 not shown)
Histogram of bond angle deviations from ideal:
0.00 - 2.32: 9413
2.32 - 4.64: 279
4.64 - 6.96: 58
6.96 - 9.28: 5
9.28 - 11.59: 1
Bond angle restraints: 9756
Sorted by residual:
angle pdb=" C CYS C 306 "
pdb=" N SER C 307 "
pdb=" CA SER C 307 "
ideal model delta sigma weight residual
121.54 129.71 -8.17 1.91e+00 2.74e-01 1.83e+01
angle pdb=" N THR B 511 "
pdb=" CA THR B 511 "
pdb=" C THR B 511 "
ideal model delta sigma weight residual
108.47 101.44 7.03 1.79e+00 3.12e-01 1.54e+01
angle pdb=" N THR D 511 "
pdb=" CA THR D 511 "
pdb=" C THR D 511 "
ideal model delta sigma weight residual
108.47 101.74 6.73 1.79e+00 3.12e-01 1.41e+01
angle pdb=" CA LEU A 308 "
pdb=" CB LEU A 308 "
pdb=" CG LEU A 308 "
ideal model delta sigma weight residual
116.30 127.89 -11.59 3.50e+00 8.16e-02 1.10e+01
angle pdb=" C ASP C 233 "
pdb=" CA ASP C 233 "
pdb=" CB ASP C 233 "
ideal model delta sigma weight residual
110.34 114.94 -4.60 1.40e+00 5.10e-01 1.08e+01
... (remaining 9751 not shown)
Histogram of dihedral angle deviations from ideal:
0.00 - 25.77: 4349
25.77 - 51.55: 291
51.55 - 77.32: 73
77.32 - 103.09: 54
103.09 - 128.86: 33
Dihedral angle restraints: 4800
sinusoidal: 2468
harmonic: 2332
Sorted by residual:
dihedral pdb=" CA THR D 511 "
pdb=" C THR D 511 "
pdb=" N PRO D 512 "
pdb=" CA PRO D 512 "
ideal model delta harmonic sigma weight residual
-180.00 -115.21 -64.79 0 5.00e+00 4.00e-02 1.68e+02
dihedral pdb=" CA THR B 511 "
pdb=" C THR B 511 "
pdb=" N PRO B 512 "
pdb=" CA PRO B 512 "
ideal model delta harmonic sigma weight residual
-180.00 -115.46 -64.54 0 5.00e+00 4.00e-02 1.67e+02
dihedral pdb=" CB CYS A 229 "
pdb=" SG CYS A 229 "
pdb=" SG CYS A 304 "
pdb=" CB CYS A 304 "
ideal model delta sinusoidal sigma weight residual
93.00 21.29 71.71 1 1.00e+01 1.00e-02 6.59e+01
... (remaining 4797 not shown)
Histogram of chiral volume deviations from ideal:
0.000 - 0.062: 929
0.062 - 0.125: 219
0.125 - 0.187: 24
0.187 - 0.250: 1
0.250 - 0.312: 12
Chirality restraints: 1185
Sorted by residual:
chirality pdb=" C1 NAG K 1 "
pdb=" ND2 ASN A 305 "
pdb=" C2 NAG K 1 "
pdb=" O5 NAG K 1 "
both_signs ideal model delta sigma weight residual
False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.44e+00
chirality pdb=" C1 NAG N 1 "
pdb=" ND2 ASN B 423 "
pdb=" C2 NAG N 1 "
pdb=" O5 NAG N 1 "
both_signs ideal model delta sigma weight residual
False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.30e+00
chirality pdb=" C5 BMA U 3 "
pdb=" C4 BMA U 3 "
pdb=" C6 BMA U 3 "
pdb=" O5 BMA U 3 "
both_signs ideal model delta sigma weight residual
False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.88e+00
... (remaining 1182 not shown)
Planarity restraints: 1203
Sorted by residual:
delta sigma weight rms_deltas residual
plane pdb=" CA THR D 511 " 0.016 2.00e-02 2.50e+03 3.21e-02 1.03e+01
pdb=" C THR D 511 " -0.055 2.00e-02 2.50e+03
pdb=" O THR D 511 " 0.020 2.00e-02 2.50e+03
pdb=" N PRO D 512 " 0.019 2.00e-02 2.50e+03
delta sigma weight rms_deltas residual
plane pdb=" CA ASP C 233 " 0.016 2.00e-02 2.50e+03 3.19e-02 1.02e+01
pdb=" C ASP C 233 " -0.055 2.00e-02 2.50e+03
pdb=" O ASP C 233 " 0.021 2.00e-02 2.50e+03
pdb=" N ASN C 234 " 0.019 2.00e-02 2.50e+03
delta sigma weight rms_deltas residual
plane pdb=" CA THR B 511 " -0.016 2.00e-02 2.50e+03 3.15e-02 9.92e+00
pdb=" C THR B 511 " 0.055 2.00e-02 2.50e+03
pdb=" O THR B 511 " -0.020 2.00e-02 2.50e+03
pdb=" N PRO B 512 " -0.019 2.00e-02 2.50e+03
... (remaining 1200 not shown)
Histogram of nonbonded interaction distances:
2.11 - 2.67: 283
2.67 - 3.23: 7271
3.23 - 3.78: 11473
3.78 - 4.34: 14495
4.34 - 4.90: 22187
Nonbonded interactions: 55709
Sorted by model distance:
nonbonded pdb=" OH TYR A 309 "
pdb=" O ASN B 659 "
model vdw
2.111 3.040
nonbonded pdb=" OD1 ASP A 232 "
pdb=" OG1 THR A 235 "
model vdw
2.165 3.040
nonbonded pdb=" OD1 ASP C 232 "
pdb=" OG1 THR C 235 "
model vdw
2.187 3.040
nonbonded pdb=" O ASP B 521 "
pdb=" NZ LYS B 525 "
model vdw
2.188 3.120
nonbonded pdb=" OH TYR C 309 "
pdb=" O ASN D 659 "
model vdw
2.202 3.040
... (remaining 55704 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: 0.02
Found NCS groups:
ncs_group {
reference = chain 'A'
selection = chain 'C'
}
ncs_group {
reference = chain 'B'
selection = chain 'D'
}
ncs_group {
reference = chain 'E'
selection = chain 'F'
selection = chain 'G'
selection = chain 'H'
selection = chain 'I'
selection = chain 'J'
selection = chain 'K'
selection = chain 'L'
selection = chain 'M'
selection = chain 'N'
}
ncs_group {
reference = chain 'O'
selection = chain 'P'
selection = chain 'Q'
selection = chain 'R'
selection = chain 'S'
selection = chain 'T'
selection = chain 'U'
selection = chain 'V'
}
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: 2.110
Set stop_for_unknowns flag: 0.000
Assert model is a single copy model: 0.000
Assert all atoms have isotropic ADPs: 0.000
Construct map_model_manager: 0.010
Extract box with map and model: 0.280
Check model and map are aligned: 0.050
Set scattering table: 0.070
Process input model: 20.910
Find NCS groups from input model: 0.290
Set up NCS constraints: 0.040
Set refine NCS operators: 0.000
Adjust number of macro_cycles: 0.000
Reset NCS operators: 0.000
Extract rigid body selections: 0.000
Check and reset occupancies: 0.000
Load rotamer database and sin/cos tables:2.730
Set ADP refinement strategy: 0.000
Make a string to write initial .geo file:0.000
Internal consistency checks: 0.000
Total: 26.490
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8130
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 : 0.005 0.049 7138 Z= 0.285
Angle : 0.916 11.595 9756 Z= 0.428
Chirality : 0.058 0.312 1185
Planarity : 0.006 0.052 1192
Dihedral : 23.310 128.865 3242
Min Nonbonded Distance : 2.111
Molprobity Statistics.
All-atom Clashscore : 16.47
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 12.94 %
Favored : 87.06 %
Rotamer:
Outliers : 0.14 %
Allowed : 30.03 %
Favored : 69.83 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 3.12 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: -2.41 (0.30), residues: 796
helix: -0.68 (0.66), residues: 68
sheet: -0.43 (0.57), residues: 90
loop : -2.08 (0.25), residues: 638
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.019 0.001 TRP B 622
HIS 0.003 0.001 HIS B 673
PHE 0.009 0.001 PHE D 538
TYR 0.021 0.002 TYR D 709
ARG 0.002 0.000 ARG C 297
*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
1592 Ramachandran restraints generated.
796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
1592 Ramachandran restraints generated.
796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
71 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 1
poor density : 70
time to evaluate : 0.748
Fit side-chains
outliers start: 1
outliers final: 1
residues processed: 70
average time/residue: 0.1732
time to fit residues: 17.0939
Evaluate side-chains
66 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 1
poor density : 65
time to evaluate : 0.870
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue 556 MET
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 80
random chunks:
chunk 67 optimal weight: 7.9990
chunk 60 optimal weight: 3.9990
chunk 33 optimal weight: 3.9990
chunk 20 optimal weight: 0.9990
chunk 40 optimal weight: 5.9990
chunk 32 optimal weight: 3.9990
chunk 62 optimal weight: 10.0000
chunk 24 optimal weight: 4.9990
chunk 38 optimal weight: 0.0470
chunk 46 optimal weight: 3.9990
chunk 72 optimal weight: 0.8980
overall best weight: 1.9884
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
C 222 HIS
C 299 GLN
** D 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 423 ASN
B 409 GLN
Total number of N/Q/H flips: 4
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.081514 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.060121 restraints weight = 24837.228|
|-----------------------------------------------------------------------------|
r_work (start): 0.3137 rms_B_bonded: 6.40
r_work (final): 0.3137
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8184
moved from start: 0.1052
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.004 0.038 7138 Z= 0.261
Angle : 0.821 8.029 9756 Z= 0.390
Chirality : 0.052 0.239 1185
Planarity : 0.006 0.053 1192
Dihedral : 18.963 115.262 1835
Min Nonbonded Distance : 2.383
Molprobity Statistics.
All-atom Clashscore : 11.62
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 12.81 %
Favored : 87.19 %
Rotamer:
Outliers : 4.53 %
Allowed : 24.79 %
Favored : 70.68 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 3.12 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: -2.44 (0.29), residues: 796
helix: -0.97 (0.70), residues: 58
sheet: -0.57 (0.57), residues: 90
loop : -2.03 (0.24), residues: 648
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.012 0.001 TRP B 622
HIS 0.003 0.001 HIS A 222
PHE 0.011 0.001 PHE D 538
TYR 0.021 0.001 TYR D 709
ARG 0.005 0.001 ARG B 636
*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
1592 Ramachandran restraints generated.
796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
1592 Ramachandran restraints generated.
796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
99 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 32
poor density : 67
time to evaluate : 0.778
Fit side-chains
REVERT: D 415 ASN cc_start: 0.9282 (t0) cc_final: 0.9040 (t0)
REVERT: D 536 ASP cc_start: 0.7282 (t0) cc_final: 0.6967 (t0)
REVERT: D 673 HIS cc_start: 0.7634 (t-90) cc_final: 0.7251 (t-90)
REVERT: D 706 GLN cc_start: 0.9253 (OUTLIER) cc_final: 0.8758 (tp40)
outliers start: 32
outliers final: 13
residues processed: 92
average time/residue: 0.1553
time to fit residues: 20.5728
Evaluate side-chains
76 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 14
poor density : 62
time to evaluate : 0.815
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue 203 LEU
Chi-restraints excluded: chain C residue 213 VAL
Chi-restraints excluded: chain C residue 221 LEU
Chi-restraints excluded: chain D residue 446 LYS
Chi-restraints excluded: chain D residue 520 THR
Chi-restraints excluded: chain D residue 591 CYS
Chi-restraints excluded: chain D residue 706 GLN
Chi-restraints excluded: chain A residue 203 LEU
Chi-restraints excluded: chain A residue 221 LEU
Chi-restraints excluded: chain A residue 304 CYS
Chi-restraints excluded: chain B residue 405 MET
Chi-restraints excluded: chain B residue 507 VAL
Chi-restraints excluded: chain B residue 591 CYS
Chi-restraints excluded: chain B residue 678 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 80
random chunks:
chunk 32 optimal weight: 3.9990
chunk 27 optimal weight: 7.9990
chunk 50 optimal weight: 0.3980
chunk 61 optimal weight: 2.9990
chunk 35 optimal weight: 5.9990
chunk 43 optimal weight: 1.9990
chunk 10 optimal weight: 3.9990
chunk 71 optimal weight: 0.0570
chunk 48 optimal weight: 9.9990
chunk 28 optimal weight: 6.9990
chunk 64 optimal weight: 4.9990
overall best weight: 1.8904
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** D 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Total number of N/Q/H flips: 0
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.081724 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.060195 restraints weight = 24612.319|
|-----------------------------------------------------------------------------|
r_work (start): 0.3135 rms_B_bonded: 6.38
r_work (final): 0.3135
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8173
moved from start: 0.1337
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.004 0.036 7138 Z= 0.239
Angle : 0.796 8.540 9756 Z= 0.376
Chirality : 0.051 0.248 1185
Planarity : 0.006 0.052 1192
Dihedral : 15.903 115.515 1832
Min Nonbonded Distance : 2.392
Molprobity Statistics.
All-atom Clashscore : 12.00
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 13.19 %
Favored : 86.81 %
Rotamer:
Outliers : 5.10 %
Allowed : 22.66 %
Favored : 72.24 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 4.69 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: -2.41 (0.29), residues: 796
helix: -0.97 (0.70), residues: 58
sheet: -0.70 (0.55), residues: 90
loop : -1.98 (0.24), residues: 648
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.010 0.001 TRP B 622
HIS 0.004 0.001 HIS C 222
PHE 0.012 0.001 PHE B 442
TYR 0.030 0.002 TYR C 250
ARG 0.003 0.000 ARG A 294
*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
1592 Ramachandran restraints generated.
796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
1592 Ramachandran restraints generated.
796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
108 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 36
poor density : 72
time to evaluate : 0.833
Fit side-chains
REVERT: D 536 ASP cc_start: 0.7274 (OUTLIER) cc_final: 0.6975 (t0)
REVERT: D 673 HIS cc_start: 0.7674 (t-90) cc_final: 0.7090 (t-90)
outliers start: 36
outliers final: 18
residues processed: 96
average time/residue: 0.1485
time to fit residues: 20.5630
Evaluate side-chains
82 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 19
poor density : 63
time to evaluate : 0.721
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue 203 LEU
Chi-restraints excluded: chain C residue 213 VAL
Chi-restraints excluded: chain C residue 246 VAL
Chi-restraints excluded: chain D residue 446 LYS
Chi-restraints excluded: chain D residue 497 VAL
Chi-restraints excluded: chain D residue 536 ASP
Chi-restraints excluded: chain D residue 591 CYS
Chi-restraints excluded: chain D residue 678 LEU
Chi-restraints excluded: chain D residue 691 LEU
Chi-restraints excluded: chain D residue 705 VAL
Chi-restraints excluded: chain A residue 203 LEU
Chi-restraints excluded: chain A residue 213 VAL
Chi-restraints excluded: chain A residue 221 LEU
Chi-restraints excluded: chain A residue 246 VAL
Chi-restraints excluded: chain A residue 304 CYS
Chi-restraints excluded: chain B residue 507 VAL
Chi-restraints excluded: chain B residue 520 THR
Chi-restraints excluded: chain B residue 556 MET
Chi-restraints excluded: chain B residue 591 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 80
random chunks:
chunk 41 optimal weight: 2.9990
chunk 43 optimal weight: 6.9990
chunk 65 optimal weight: 0.9990
chunk 12 optimal weight: 7.9990
chunk 19 optimal weight: 2.9990
chunk 7 optimal weight: 1.9990
chunk 54 optimal weight: 0.9980
chunk 15 optimal weight: 0.2980
chunk 59 optimal weight: 0.1980
chunk 30 optimal weight: 0.6980
chunk 2 optimal weight: 6.9990
overall best weight: 0.6382
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** D 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 299 GLN
Total number of N/Q/H flips: 1
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.083613 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.061770 restraints weight = 24307.137|
|-----------------------------------------------------------------------------|
r_work (start): 0.3171 rms_B_bonded: 6.46
r_work (final): 0.3171
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8131
moved from start: 0.1618
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.026 7138 Z= 0.176
Angle : 0.768 10.030 9756 Z= 0.366
Chirality : 0.050 0.265 1185
Planarity : 0.005 0.047 1192
Dihedral : 13.391 113.847 1832
Min Nonbonded Distance : 2.401
Molprobity Statistics.
All-atom Clashscore : 10.51
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 12.94 %
Favored : 87.06 %
Rotamer:
Outliers : 3.68 %
Allowed : 23.94 %
Favored : 72.38 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 4.69 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: -2.33 (0.29), residues: 796
helix: -0.98 (0.71), residues: 58
sheet: -0.44 (0.59), residues: 80
loop : -1.93 (0.24), residues: 658
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.008 0.001 TRP D 622
HIS 0.003 0.001 HIS D 595
PHE 0.010 0.001 PHE B 538
TYR 0.018 0.001 TYR D 709
ARG 0.002 0.000 ARG C 195
*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
1592 Ramachandran restraints generated.
796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
1592 Ramachandran restraints generated.
796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
106 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 26
poor density : 80
time to evaluate : 0.725
Fit side-chains
REVERT: D 415 ASN cc_start: 0.9254 (t0) cc_final: 0.9017 (t0)
REVERT: D 536 ASP cc_start: 0.7164 (OUTLIER) cc_final: 0.6851 (t0)
REVERT: D 673 HIS cc_start: 0.7734 (t-90) cc_final: 0.7298 (t-90)
REVERT: D 706 GLN cc_start: 0.9216 (OUTLIER) cc_final: 0.8791 (tp40)
REVERT: A 294 ARG cc_start: 0.1895 (OUTLIER) cc_final: -0.0390 (mpt180)
REVERT: B 523 LYS cc_start: 0.8435 (mtmm) cc_final: 0.7948 (mmtt)
outliers start: 26
outliers final: 13
residues processed: 93
average time/residue: 0.1686
time to fit residues: 22.2500
Evaluate side-chains
85 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 16
poor density : 69
time to evaluate : 0.794
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue 213 VAL
Chi-restraints excluded: chain C residue 246 VAL
Chi-restraints excluded: chain C residue 304 CYS
Chi-restraints excluded: chain D residue 446 LYS
Chi-restraints excluded: chain D residue 520 THR
Chi-restraints excluded: chain D residue 536 ASP
Chi-restraints excluded: chain D residue 591 CYS
Chi-restraints excluded: chain D residue 691 LEU
Chi-restraints excluded: chain D residue 706 GLN
Chi-restraints excluded: chain A residue 221 LEU
Chi-restraints excluded: chain A residue 246 VAL
Chi-restraints excluded: chain A residue 294 ARG
Chi-restraints excluded: chain A residue 307 SER
Chi-restraints excluded: chain B residue 556 MET
Chi-restraints excluded: chain B residue 591 CYS
Chi-restraints excluded: chain B residue 678 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 80
random chunks:
chunk 5 optimal weight: 0.9980
chunk 0 optimal weight: 6.9990
chunk 45 optimal weight: 1.9990
chunk 27 optimal weight: 7.9990
chunk 30 optimal weight: 2.9990
chunk 35 optimal weight: 7.9990
chunk 46 optimal weight: 10.0000
chunk 28 optimal weight: 0.8980
chunk 38 optimal weight: 5.9990
chunk 20 optimal weight: 0.7980
chunk 65 optimal weight: 7.9990
overall best weight: 1.5384
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** D 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Total number of N/Q/H flips: 0
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.083136 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.061210 restraints weight = 24458.210|
|-----------------------------------------------------------------------------|
r_work (start): 0.3148 rms_B_bonded: 6.50
r_work (final): 0.3148
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8171
moved from start: 0.1820
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.029 7138 Z= 0.221
Angle : 0.761 9.037 9756 Z= 0.364
Chirality : 0.050 0.276 1185
Planarity : 0.005 0.044 1192
Dihedral : 11.951 110.727 1832
Min Nonbonded Distance : 2.416
Molprobity Statistics.
All-atom Clashscore : 11.85
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 12.81 %
Favored : 87.19 %
Rotamer:
Outliers : 5.24 %
Allowed : 23.51 %
Favored : 71.25 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 4.69 %
Twisted General : 0.27 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: -2.30 (0.29), residues: 796
helix: -1.09 (0.70), residues: 58
sheet: -0.44 (0.59), residues: 80
loop : -1.89 (0.24), residues: 658
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.007 0.001 TRP B 622
HIS 0.005 0.001 HIS D 595
PHE 0.017 0.001 PHE D 447
TYR 0.025 0.001 TYR D 617
ARG 0.004 0.000 ARG D 620
*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
1592 Ramachandran restraints generated.
796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
1592 Ramachandran restraints generated.
796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
103 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 37
poor density : 66
time to evaluate : 0.764
Fit side-chains
revert: symmetry clash
REVERT: C 294 ARG cc_start: 0.2027 (OUTLIER) cc_final: -0.0404 (mpt180)
REVERT: D 536 ASP cc_start: 0.7255 (OUTLIER) cc_final: 0.6967 (t0)
REVERT: D 673 HIS cc_start: 0.7772 (t-90) cc_final: 0.7120 (t-90)
REVERT: A 294 ARG cc_start: 0.2143 (OUTLIER) cc_final: -0.0203 (mpt180)
REVERT: B 523 LYS cc_start: 0.8366 (mtmm) cc_final: 0.7988 (mmtt)
REVERT: B 536 ASP cc_start: 0.7778 (m-30) cc_final: 0.7318 (t0)
outliers start: 37
outliers final: 25
residues processed: 89
average time/residue: 0.1957
time to fit residues: 23.9692
Evaluate side-chains
88 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 28
poor density : 60
time to evaluate : 0.818
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue 203 LEU
Chi-restraints excluded: chain C residue 213 VAL
Chi-restraints excluded: chain C residue 246 VAL
Chi-restraints excluded: chain C residue 294 ARG
Chi-restraints excluded: chain D residue 392 VAL
Chi-restraints excluded: chain D residue 446 LYS
Chi-restraints excluded: chain D residue 472 LEU
Chi-restraints excluded: chain D residue 497 VAL
Chi-restraints excluded: chain D residue 520 THR
Chi-restraints excluded: chain D residue 532 GLU
Chi-restraints excluded: chain D residue 536 ASP
Chi-restraints excluded: chain D residue 556 MET
Chi-restraints excluded: chain D residue 591 CYS
Chi-restraints excluded: chain D residue 678 LEU
Chi-restraints excluded: chain D residue 691 LEU
Chi-restraints excluded: chain A residue 203 LEU
Chi-restraints excluded: chain A residue 213 VAL
Chi-restraints excluded: chain A residue 221 LEU
Chi-restraints excluded: chain A residue 246 VAL
Chi-restraints excluded: chain A residue 294 ARG
Chi-restraints excluded: chain A residue 304 CYS
Chi-restraints excluded: chain A residue 307 SER
Chi-restraints excluded: chain B residue 392 VAL
Chi-restraints excluded: chain B residue 446 LYS
Chi-restraints excluded: chain B residue 556 MET
Chi-restraints excluded: chain B residue 591 CYS
Chi-restraints excluded: chain B residue 628 VAL
Chi-restraints excluded: chain B residue 678 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 80
random chunks:
chunk 22 optimal weight: 5.9990
chunk 19 optimal weight: 1.9990
chunk 35 optimal weight: 7.9990
chunk 67 optimal weight: 3.9990
chunk 50 optimal weight: 6.9990
chunk 25 optimal weight: 1.9990
chunk 68 optimal weight: 0.9980
chunk 41 optimal weight: 1.9990
chunk 9 optimal weight: 30.0000
chunk 4 optimal weight: 0.7980
chunk 49 optimal weight: 30.0000
overall best weight: 1.5586
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** D 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Total number of N/Q/H flips: 0
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.083060 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.060969 restraints weight = 24664.773|
|-----------------------------------------------------------------------------|
r_work (start): 0.3143 rms_B_bonded: 6.53
r_work (final): 0.3143
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8166
moved from start: 0.1987
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.029 7138 Z= 0.210
Angle : 0.744 9.442 9756 Z= 0.358
Chirality : 0.049 0.270 1185
Planarity : 0.005 0.045 1192
Dihedral : 11.171 107.161 1832
Min Nonbonded Distance : 2.416
Molprobity Statistics.
All-atom Clashscore : 10.80
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 12.44 %
Favored : 87.56 %
Rotamer:
Outliers : 5.10 %
Allowed : 24.93 %
Favored : 69.97 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 3.12 %
Twisted General : 0.27 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: -2.26 (0.29), residues: 796
helix: -1.08 (0.70), residues: 58
sheet: -0.47 (0.59), residues: 80
loop : -1.85 (0.24), residues: 658
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.009 0.001 TRP B 622
HIS 0.003 0.001 HIS C 222
PHE 0.011 0.001 PHE B 538
TYR 0.025 0.001 TYR C 250
ARG 0.003 0.000 ARG C 294
*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
1592 Ramachandran restraints generated.
796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
1592 Ramachandran restraints generated.
796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
104 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 36
poor density : 68
time to evaluate : 0.756
Fit side-chains
revert: symmetry clash
revert: symmetry clash
REVERT: C 294 ARG cc_start: 0.2054 (OUTLIER) cc_final: -0.0282 (mpt180)
REVERT: D 536 ASP cc_start: 0.7308 (OUTLIER) cc_final: 0.7029 (t0)
REVERT: D 668 GLN cc_start: 0.8915 (mm110) cc_final: 0.8672 (mm110)
REVERT: D 673 HIS cc_start: 0.7751 (t-90) cc_final: 0.7083 (t-90)
REVERT: D 688 MET cc_start: 0.8413 (mtp) cc_final: 0.8197 (mtp)
REVERT: D 706 GLN cc_start: 0.9228 (OUTLIER) cc_final: 0.8799 (tp40)
REVERT: A 294 ARG cc_start: 0.2166 (OUTLIER) cc_final: -0.0344 (mpt180)
REVERT: B 523 LYS cc_start: 0.8333 (mtmm) cc_final: 0.7815 (mmtt)
REVERT: B 536 ASP cc_start: 0.7805 (m-30) cc_final: 0.7370 (t0)
outliers start: 36
outliers final: 27
residues processed: 92
average time/residue: 0.2019
time to fit residues: 25.7582
Evaluate side-chains
95 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 31
poor density : 64
time to evaluate : 0.727
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue 213 VAL
Chi-restraints excluded: chain C residue 246 VAL
Chi-restraints excluded: chain C residue 294 ARG
Chi-restraints excluded: chain D residue 403 PHE
Chi-restraints excluded: chain D residue 446 LYS
Chi-restraints excluded: chain D residue 472 LEU
Chi-restraints excluded: chain D residue 497 VAL
Chi-restraints excluded: chain D residue 520 THR
Chi-restraints excluded: chain D residue 532 GLU
Chi-restraints excluded: chain D residue 536 ASP
Chi-restraints excluded: chain D residue 556 MET
Chi-restraints excluded: chain D residue 591 CYS
Chi-restraints excluded: chain D residue 678 LEU
Chi-restraints excluded: chain D residue 691 LEU
Chi-restraints excluded: chain D residue 706 GLN
Chi-restraints excluded: chain A residue 203 LEU
Chi-restraints excluded: chain A residue 213 VAL
Chi-restraints excluded: chain A residue 221 LEU
Chi-restraints excluded: chain A residue 246 VAL
Chi-restraints excluded: chain A residue 294 ARG
Chi-restraints excluded: chain A residue 304 CYS
Chi-restraints excluded: chain A residue 307 SER
Chi-restraints excluded: chain B residue 392 VAL
Chi-restraints excluded: chain B residue 446 LYS
Chi-restraints excluded: chain B residue 472 LEU
Chi-restraints excluded: chain B residue 520 THR
Chi-restraints excluded: chain B residue 532 GLU
Chi-restraints excluded: chain B residue 556 MET
Chi-restraints excluded: chain B residue 591 CYS
Chi-restraints excluded: chain B residue 628 VAL
Chi-restraints excluded: chain B residue 678 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 80
random chunks:
chunk 10 optimal weight: 2.9990
chunk 19 optimal weight: 2.9990
chunk 8 optimal weight: 0.8980
chunk 9 optimal weight: 20.0000
chunk 52 optimal weight: 7.9990
chunk 6 optimal weight: 10.0000
chunk 17 optimal weight: 6.9990
chunk 11 optimal weight: 4.9990
chunk 54 optimal weight: 6.9990
chunk 43 optimal weight: 1.9990
chunk 36 optimal weight: 2.9990
overall best weight: 2.3788
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** D 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Total number of N/Q/H flips: 0
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.081792 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.059823 restraints weight = 24423.155|
|-----------------------------------------------------------------------------|
r_work (start): 0.3116 rms_B_bonded: 6.44
r_work (final): 0.3116
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8179
moved from start: 0.2157
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.004 0.033 7138 Z= 0.277
Angle : 0.761 8.486 9756 Z= 0.368
Chirality : 0.049 0.282 1185
Planarity : 0.005 0.042 1192
Dihedral : 10.656 101.377 1832
Min Nonbonded Distance : 2.367
Molprobity Statistics.
All-atom Clashscore : 12.22
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 12.44 %
Favored : 87.56 %
Rotamer:
Outliers : 6.37 %
Allowed : 23.94 %
Favored : 69.69 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 3.12 %
Twisted General : 0.27 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: -2.31 (0.30), residues: 796
helix: -1.15 (0.68), residues: 58
sheet: -0.41 (0.54), residues: 100
loop : -1.93 (0.25), residues: 638
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.010 0.002 TRP D 420
HIS 0.006 0.001 HIS C 222
PHE 0.011 0.001 PHE B 538
TYR 0.017 0.001 TYR D 617
ARG 0.004 0.000 ARG C 294
*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
1592 Ramachandran restraints generated.
796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
1592 Ramachandran restraints generated.
796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
107 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 45
poor density : 62
time to evaluate : 0.807
Fit side-chains
revert: symmetry clash
revert: symmetry clash
REVERT: C 294 ARG cc_start: 0.2002 (OUTLIER) cc_final: -0.0373 (mpt180)
REVERT: D 536 ASP cc_start: 0.7439 (OUTLIER) cc_final: 0.7173 (t0)
REVERT: D 673 HIS cc_start: 0.7821 (t-90) cc_final: 0.7133 (t-90)
REVERT: D 688 MET cc_start: 0.8446 (mtp) cc_final: 0.8091 (mtp)
REVERT: A 294 ARG cc_start: 0.1972 (OUTLIER) cc_final: -0.0311 (mpt180)
REVERT: B 536 ASP cc_start: 0.7911 (m-30) cc_final: 0.7428 (t0)
outliers start: 45
outliers final: 32
residues processed: 95
average time/residue: 0.1996
time to fit residues: 25.7914
Evaluate side-chains
93 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 35
poor density : 58
time to evaluate : 0.788
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue 203 LEU
Chi-restraints excluded: chain C residue 213 VAL
Chi-restraints excluded: chain C residue 246 VAL
Chi-restraints excluded: chain C residue 294 ARG
Chi-restraints excluded: chain D residue 392 VAL
Chi-restraints excluded: chain D residue 403 PHE
Chi-restraints excluded: chain D residue 446 LYS
Chi-restraints excluded: chain D residue 472 LEU
Chi-restraints excluded: chain D residue 497 VAL
Chi-restraints excluded: chain D residue 520 THR
Chi-restraints excluded: chain D residue 532 GLU
Chi-restraints excluded: chain D residue 536 ASP
Chi-restraints excluded: chain D residue 556 MET
Chi-restraints excluded: chain D residue 591 CYS
Chi-restraints excluded: chain D residue 678 LEU
Chi-restraints excluded: chain D residue 691 LEU
Chi-restraints excluded: chain D residue 705 VAL
Chi-restraints excluded: chain A residue 203 LEU
Chi-restraints excluded: chain A residue 213 VAL
Chi-restraints excluded: chain A residue 221 LEU
Chi-restraints excluded: chain A residue 246 VAL
Chi-restraints excluded: chain A residue 294 ARG
Chi-restraints excluded: chain A residue 307 SER
Chi-restraints excluded: chain B residue 392 VAL
Chi-restraints excluded: chain B residue 403 PHE
Chi-restraints excluded: chain B residue 446 LYS
Chi-restraints excluded: chain B residue 472 LEU
Chi-restraints excluded: chain B residue 507 VAL
Chi-restraints excluded: chain B residue 520 THR
Chi-restraints excluded: chain B residue 532 GLU
Chi-restraints excluded: chain B residue 556 MET
Chi-restraints excluded: chain B residue 559 THR
Chi-restraints excluded: chain B residue 591 CYS
Chi-restraints excluded: chain B residue 628 VAL
Chi-restraints excluded: chain B residue 678 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 80
random chunks:
chunk 65 optimal weight: 0.7980
chunk 40 optimal weight: 5.9990
chunk 73 optimal weight: 4.9990
chunk 57 optimal weight: 9.9990
chunk 30 optimal weight: 1.9990
chunk 25 optimal weight: 5.9990
chunk 13 optimal weight: 40.0000
chunk 37 optimal weight: 0.9990
chunk 76 optimal weight: 0.0970
chunk 33 optimal weight: 6.9990
chunk 17 optimal weight: 5.9990
overall best weight: 1.7784
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** D 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Total number of N/Q/H flips: 0
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.082223 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.060222 restraints weight = 24692.193|
|-----------------------------------------------------------------------------|
r_work (start): 0.3130 rms_B_bonded: 6.47
r_work (final): 0.3130
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8164
moved from start: 0.2263
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.004 0.033 7138 Z= 0.232
Angle : 0.759 9.243 9756 Z= 0.366
Chirality : 0.049 0.259 1185
Planarity : 0.005 0.043 1192
Dihedral : 10.222 96.701 1832
Min Nonbonded Distance : 2.374
Molprobity Statistics.
All-atom Clashscore : 11.40
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 12.44 %
Favored : 87.56 %
Rotamer:
Outliers : 5.67 %
Allowed : 24.22 %
Favored : 70.11 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 3.12 %
Twisted General : 0.27 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: -2.29 (0.30), residues: 796
helix: -1.15 (0.69), residues: 58
sheet: -0.39 (0.54), residues: 100
loop : -1.92 (0.25), residues: 638
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.011 0.001 TRP B 622
HIS 0.004 0.001 HIS C 222
PHE 0.010 0.001 PHE B 538
TYR 0.017 0.001 TYR D 617
ARG 0.003 0.000 ARG C 294
*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
1592 Ramachandran restraints generated.
796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
1592 Ramachandran restraints generated.
796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
108 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 40
poor density : 68
time to evaluate : 0.793
Fit side-chains
revert: symmetry clash
REVERT: C 294 ARG cc_start: 0.2006 (OUTLIER) cc_final: -0.0618 (mtt90)
REVERT: D 536 ASP cc_start: 0.7398 (OUTLIER) cc_final: 0.7114 (t0)
REVERT: D 673 HIS cc_start: 0.7790 (t-90) cc_final: 0.7074 (t-90)
REVERT: D 688 MET cc_start: 0.8425 (mtp) cc_final: 0.8191 (mtp)
REVERT: D 706 GLN cc_start: 0.9199 (OUTLIER) cc_final: 0.8716 (tp40)
REVERT: A 294 ARG cc_start: 0.2110 (OUTLIER) cc_final: -0.0546 (mtt90)
REVERT: B 536 ASP cc_start: 0.7804 (m-30) cc_final: 0.7328 (t0)
outliers start: 40
outliers final: 31
residues processed: 94
average time/residue: 0.1891
time to fit residues: 24.4265
Evaluate side-chains
95 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 35
poor density : 60
time to evaluate : 0.892
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue 203 LEU
Chi-restraints excluded: chain C residue 212 ILE
Chi-restraints excluded: chain C residue 213 VAL
Chi-restraints excluded: chain C residue 246 VAL
Chi-restraints excluded: chain C residue 294 ARG
Chi-restraints excluded: chain D residue 392 VAL
Chi-restraints excluded: chain D residue 403 PHE
Chi-restraints excluded: chain D residue 427 LEU
Chi-restraints excluded: chain D residue 446 LYS
Chi-restraints excluded: chain D residue 472 LEU
Chi-restraints excluded: chain D residue 497 VAL
Chi-restraints excluded: chain D residue 520 THR
Chi-restraints excluded: chain D residue 532 GLU
Chi-restraints excluded: chain D residue 536 ASP
Chi-restraints excluded: chain D residue 556 MET
Chi-restraints excluded: chain D residue 591 CYS
Chi-restraints excluded: chain D residue 678 LEU
Chi-restraints excluded: chain D residue 691 LEU
Chi-restraints excluded: chain D residue 705 VAL
Chi-restraints excluded: chain D residue 706 GLN
Chi-restraints excluded: chain A residue 203 LEU
Chi-restraints excluded: chain A residue 212 ILE
Chi-restraints excluded: chain A residue 213 VAL
Chi-restraints excluded: chain A residue 221 LEU
Chi-restraints excluded: chain A residue 246 VAL
Chi-restraints excluded: chain A residue 294 ARG
Chi-restraints excluded: chain A residue 307 SER
Chi-restraints excluded: chain B residue 392 VAL
Chi-restraints excluded: chain B residue 446 LYS
Chi-restraints excluded: chain B residue 472 LEU
Chi-restraints excluded: chain B residue 520 THR
Chi-restraints excluded: chain B residue 556 MET
Chi-restraints excluded: chain B residue 559 THR
Chi-restraints excluded: chain B residue 591 CYS
Chi-restraints excluded: chain B residue 628 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 80
random chunks:
chunk 69 optimal weight: 7.9990
chunk 6 optimal weight: 9.9990
chunk 61 optimal weight: 4.9990
chunk 13 optimal weight: 40.0000
chunk 29 optimal weight: 6.9990
chunk 33 optimal weight: 6.9990
chunk 20 optimal weight: 0.6980
chunk 49 optimal weight: 30.0000
chunk 41 optimal weight: 1.9990
chunk 74 optimal weight: 5.9990
chunk 60 optimal weight: 0.0870
overall best weight: 2.7564
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** D 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Total number of N/Q/H flips: 0
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.080756 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3148 r_free = 0.3148 target = 0.058872 restraints weight = 25139.109|
|-----------------------------------------------------------------------------|
r_work (start): 0.3107 rms_B_bonded: 6.45
r_work (final): 0.3107
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8197
moved from start: 0.2453
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.005 0.038 7138 Z= 0.312
Angle : 0.795 8.499 9756 Z= 0.385
Chirality : 0.049 0.262 1185
Planarity : 0.005 0.041 1192
Dihedral : 9.811 89.379 1832
Min Nonbonded Distance : 2.350
Molprobity Statistics.
All-atom Clashscore : 13.41
Ramachandran Plot:
Outliers : 0.13 %
Allowed : 12.69 %
Favored : 87.19 %
Rotamer:
Outliers : 5.24 %
Allowed : 25.78 %
Favored : 68.98 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 3.12 %
Twisted General : 0.27 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: -2.35 (0.29), residues: 796
helix: -1.19 (0.67), residues: 58
sheet: -0.42 (0.54), residues: 100
loop : -1.97 (0.25), residues: 638
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.012 0.002 TRP D 420
HIS 0.006 0.001 HIS C 222
PHE 0.018 0.001 PHE D 447
TYR 0.017 0.002 TYR D 709
ARG 0.005 0.000 ARG C 294
*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
1592 Ramachandran restraints generated.
796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
1592 Ramachandran restraints generated.
796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
93 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 37
poor density : 56
time to evaluate : 0.751
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: C 294 ARG cc_start: 0.2009 (OUTLIER) cc_final: -0.0483 (mtt90)
REVERT: D 536 ASP cc_start: 0.7533 (OUTLIER) cc_final: 0.7289 (t0)
REVERT: D 673 HIS cc_start: 0.7901 (t-90) cc_final: 0.7149 (t-90)
REVERT: D 688 MET cc_start: 0.8444 (mtp) cc_final: 0.8210 (mtp)
REVERT: D 706 GLN cc_start: 0.9173 (OUTLIER) cc_final: 0.8682 (tp40)
REVERT: A 294 ARG cc_start: 0.2042 (OUTLIER) cc_final: -0.0523 (mtt90)
REVERT: B 536 ASP cc_start: 0.7872 (m-30) cc_final: 0.7437 (t0)
outliers start: 37
outliers final: 31
residues processed: 83
average time/residue: 0.1892
time to fit residues: 21.5892
Evaluate side-chains
89 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 35
poor density : 54
time to evaluate : 0.801
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue 203 LEU
Chi-restraints excluded: chain C residue 213 VAL
Chi-restraints excluded: chain C residue 246 VAL
Chi-restraints excluded: chain C residue 294 ARG
Chi-restraints excluded: chain D residue 392 VAL
Chi-restraints excluded: chain D residue 403 PHE
Chi-restraints excluded: chain D residue 427 LEU
Chi-restraints excluded: chain D residue 446 LYS
Chi-restraints excluded: chain D residue 472 LEU
Chi-restraints excluded: chain D residue 497 VAL
Chi-restraints excluded: chain D residue 520 THR
Chi-restraints excluded: chain D residue 532 GLU
Chi-restraints excluded: chain D residue 536 ASP
Chi-restraints excluded: chain D residue 556 MET
Chi-restraints excluded: chain D residue 591 CYS
Chi-restraints excluded: chain D residue 678 LEU
Chi-restraints excluded: chain D residue 691 LEU
Chi-restraints excluded: chain D residue 705 VAL
Chi-restraints excluded: chain D residue 706 GLN
Chi-restraints excluded: chain A residue 203 LEU
Chi-restraints excluded: chain A residue 213 VAL
Chi-restraints excluded: chain A residue 221 LEU
Chi-restraints excluded: chain A residue 246 VAL
Chi-restraints excluded: chain A residue 294 ARG
Chi-restraints excluded: chain A residue 307 SER
Chi-restraints excluded: chain B residue 392 VAL
Chi-restraints excluded: chain B residue 446 LYS
Chi-restraints excluded: chain B residue 472 LEU
Chi-restraints excluded: chain B residue 507 VAL
Chi-restraints excluded: chain B residue 520 THR
Chi-restraints excluded: chain B residue 532 GLU
Chi-restraints excluded: chain B residue 556 MET
Chi-restraints excluded: chain B residue 559 THR
Chi-restraints excluded: chain B residue 591 CYS
Chi-restraints excluded: chain B residue 628 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 80
random chunks:
chunk 4 optimal weight: 5.9990
chunk 24 optimal weight: 0.0470
chunk 6 optimal weight: 9.9990
chunk 74 optimal weight: 6.9990
chunk 52 optimal weight: 5.9990
chunk 17 optimal weight: 9.9990
chunk 41 optimal weight: 0.7980
chunk 22 optimal weight: 40.0000
chunk 45 optimal weight: 0.9990
chunk 27 optimal weight: 5.9990
chunk 73 optimal weight: 5.9990
overall best weight: 2.7684
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** D 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Total number of N/Q/H flips: 0
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.080554 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3138 r_free = 0.3138 target = 0.058585 restraints weight = 25070.304|
|-----------------------------------------------------------------------------|
r_work (start): 0.3094 rms_B_bonded: 6.45
r_work: 0.2925 rms_B_bonded: 6.39 restraints_weight: 2.0000
r_work (final): 0.2925
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8359
moved from start: 0.2664
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.005 0.039 7138 Z= 0.309
Angle : 0.804 9.418 9756 Z= 0.389
Chirality : 0.050 0.235 1185
Planarity : 0.006 0.041 1192
Dihedral : 9.237 78.390 1832
Min Nonbonded Distance : 2.291
Molprobity Statistics.
All-atom Clashscore : 13.34
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 13.19 %
Favored : 86.81 %
Rotamer:
Outliers : 5.38 %
Allowed : 26.20 %
Favored : 68.41 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 3.12 %
Twisted General : 0.27 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: -2.39 (0.29), residues: 796
helix: -1.17 (0.68), residues: 58
sheet: -0.50 (0.62), residues: 80
loop : -1.95 (0.24), residues: 658
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.014 0.002 TRP B 622
HIS 0.005 0.001 HIS B 673
PHE 0.015 0.001 PHE D 447
TYR 0.019 0.002 TYR B 709
ARG 0.005 0.000 ARG C 294
********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
1592 Ramachandran restraints generated.
796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
1592 Ramachandran restraints generated.
796 Oldfield, 0 Emsley, 796 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
101 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 38
poor density : 63
time to evaluate : 0.781
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: C 294 ARG cc_start: 0.4947 (OUTLIER) cc_final: 0.1493 (mpt180)
REVERT: D 536 ASP cc_start: 0.7564 (OUTLIER) cc_final: 0.7296 (t0)
REVERT: D 673 HIS cc_start: 0.8060 (t-90) cc_final: 0.7418 (t-90)
REVERT: D 706 GLN cc_start: 0.9159 (OUTLIER) cc_final: 0.8608 (tp40)
REVERT: A 294 ARG cc_start: 0.5016 (OUTLIER) cc_final: 0.1465 (mpt180)
REVERT: B 536 ASP cc_start: 0.8021 (m-30) cc_final: 0.7477 (t0)
outliers start: 38
outliers final: 33
residues processed: 91
average time/residue: 0.1866
time to fit residues: 23.2890
Evaluate side-chains
94 residues out of total 708 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 37
poor density : 57
time to evaluate : 0.874
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue 203 LEU
Chi-restraints excluded: chain C residue 213 VAL
Chi-restraints excluded: chain C residue 246 VAL
Chi-restraints excluded: chain C residue 294 ARG
Chi-restraints excluded: chain D residue 392 VAL
Chi-restraints excluded: chain D residue 403 PHE
Chi-restraints excluded: chain D residue 427 LEU
Chi-restraints excluded: chain D residue 446 LYS
Chi-restraints excluded: chain D residue 472 LEU
Chi-restraints excluded: chain D residue 497 VAL
Chi-restraints excluded: chain D residue 519 THR
Chi-restraints excluded: chain D residue 520 THR
Chi-restraints excluded: chain D residue 532 GLU
Chi-restraints excluded: chain D residue 536 ASP
Chi-restraints excluded: chain D residue 556 MET
Chi-restraints excluded: chain D residue 591 CYS
Chi-restraints excluded: chain D residue 678 LEU
Chi-restraints excluded: chain D residue 691 LEU
Chi-restraints excluded: chain D residue 705 VAL
Chi-restraints excluded: chain D residue 706 GLN
Chi-restraints excluded: chain A residue 203 LEU
Chi-restraints excluded: chain A residue 213 VAL
Chi-restraints excluded: chain A residue 221 LEU
Chi-restraints excluded: chain A residue 246 VAL
Chi-restraints excluded: chain A residue 294 ARG
Chi-restraints excluded: chain A residue 307 SER
Chi-restraints excluded: chain B residue 392 VAL
Chi-restraints excluded: chain B residue 403 PHE
Chi-restraints excluded: chain B residue 446 LYS
Chi-restraints excluded: chain B residue 472 LEU
Chi-restraints excluded: chain B residue 507 VAL
Chi-restraints excluded: chain B residue 520 THR
Chi-restraints excluded: chain B residue 532 GLU
Chi-restraints excluded: chain B residue 556 MET
Chi-restraints excluded: chain B residue 559 THR
Chi-restraints excluded: chain B residue 591 CYS
Chi-restraints excluded: chain B residue 628 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 80
random chunks:
chunk 70 optimal weight: 2.9990
chunk 29 optimal weight: 5.9990
chunk 34 optimal weight: 4.9990
chunk 32 optimal weight: 0.9980
chunk 28 optimal weight: 3.9990
chunk 56 optimal weight: 3.9990
chunk 19 optimal weight: 1.9990
chunk 21 optimal weight: 4.9990
chunk 75 optimal weight: 1.9990
chunk 57 optimal weight: 8.9990
chunk 12 optimal weight: 8.9990
overall best weight: 2.3988
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** D 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 673 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
Total number of N/Q/H flips: 0
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.081009 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3149 r_free = 0.3149 target = 0.058960 restraints weight = 24584.091|
|-----------------------------------------------------------------------------|
r_work (start): 0.3103 rms_B_bonded: 6.43
r_work (final): 0.3103
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8200
moved from start: 0.2771
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.004 0.038 7138 Z= 0.284
Angle : 0.802 8.698 9756 Z= 0.389
Chirality : 0.049 0.241 1185
Planarity : 0.006 0.041 1192
Dihedral : 8.597 67.549 1832
Min Nonbonded Distance : 2.253
Molprobity Statistics.
All-atom Clashscore : 13.34
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 13.07 %
Favored : 86.93 %
Rotamer:
Outliers : 5.38 %
Allowed : 26.20 %
Favored : 68.41 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 3.12 %
Twisted General : 0.27 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: -2.32 (0.29), residues: 796
helix: -1.22 (0.67), residues: 58
sheet: -0.24 (0.63), residues: 76
loop : -1.92 (0.24), residues: 662
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.013 0.002 TRP B 622
HIS 0.005 0.001 HIS C 222
PHE 0.017 0.001 PHE D 447
TYR 0.018 0.001 TYR D 709
ARG 0.005 0.000 ARG C 294
Origin is already at (0, 0, 0), no shifts will be applied
===============================================================================
Job complete
usr+sys time: 3123.66 seconds
wall clock time: 58 minutes 0.29 seconds (3480.29 seconds total)