Starting phenix.real_space_refine
on Mon Dec 30 20:31:38 2024 by dcliebschner
===============================================================================
Processing files:
-------------------------------------------------------------------------------
Found model, /net/cci-nas-00/data/ceres_data/8ztr_60470/12_2024/8ztr_60470.cif
Found real_map, /net/cci-nas-00/data/ceres_data/8ztr_60470/12_2024/8ztr_60470.map
Processing PHIL parameters:
-------------------------------------------------------------------------------
Adding command-line PHIL:
-------------------------
refinement.macro_cycles=10
scattering_table=electron
resolution=3.26
write_initial_geo_file=False
Final processed PHIL parameters:
-------------------------------------------------------------------------------
data_manager {
real_map_files = "/net/cci-nas-00/data/ceres_data/8ztr_60470/12_2024/8ztr_60470.map"
default_real_map = "/net/cci-nas-00/data/ceres_data/8ztr_60470/12_2024/8ztr_60470.map"
model {
file = "/net/cci-nas-00/data/ceres_data/8ztr_60470/12_2024/8ztr_60470.cif"
}
default_model = "/net/cci-nas-00/data/ceres_data/8ztr_60470/12_2024/8ztr_60470.cif"
}
resolution = 3.26
write_initial_geo_file = False
refinement {
macro_cycles = 10
}
qi {
qm_restraints {
package {
program = *test
}
}
}
Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.
Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
Set to: 0
Set model cs if undefined
Decide on map wrapping
Map wrapping is set to: False
Normalize map: mean=0, sd=1
Input map: mean= 0.002 sd= 0.030
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 54 5.16 5
C 9088 2.51 5
N 2254 2.21 5
O 2676 1.98 5
sf(0) = scattering factor at diffraction angle 0.
Process input model
Symmetric amino acids flipped. Time to flip 13 residue(s): 0.04s
Monomer Library directory:
"/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib"
Total number of atoms: 14072
Number of models: 1
Model: ""
Number of chains: 4
Chain: "A"
Number of atoms: 5887
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 702, 5887
Classifications: {'peptide': 702}
Modifications used: {'COO': 1}
Link IDs: {'PTRANS': 9, 'TRANS': 692}
Chain: "B"
Number of atoms: 5887
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 702, 5887
Classifications: {'peptide': 702}
Modifications used: {'COO': 1}
Link IDs: {'PTRANS': 9, 'TRANS': 692}
Chain: "E"
Number of atoms: 1149
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 145, 1149
Classifications: {'peptide': 145}
Link IDs: {'PTRANS': 5, 'TRANS': 139}
Chain breaks: 1
Chain: "F"
Number of atoms: 1149
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 145, 1149
Classifications: {'peptide': 145}
Link IDs: {'PTRANS': 5, 'TRANS': 139}
Chain breaks: 1
Time building chain proxies: 7.96, per 1000 atoms: 0.57
Number of scatterers: 14072
At special positions: 0
Unit cell: (130.48, 100.656, 108.112, 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 54 16.00
O 2676 8.00
N 2254 7.00
C 9088 6.00
sf(0) = scattering factor at diffraction angle 0.
Number of disulfides: simple=0, symmetry=0
Automatic linking
Parameters for automatic linking
Linking & cutoffs
Metal : Auto - 3.00
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=0, symmetry=0
Time building additional restraints: 3.51
Conformation dependent library (CDL) restraints added in 1.8 seconds
3364 Ramachandran restraints generated.
1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2.
Adding C-beta torsion restraints...
Number of C-beta restraints generated: 3232
Finding SS restraints...
Secondary structure from input PDB file:
84 helices and 6 sheets defined
63.8% alpha, 8.9% beta
0 base pairs and 0 stacking pairs defined.
Time for finding SS restraints: 1.57
Creating SS restraints...
Processing helix chain 'A' and resid 304 through 317
removed outlier: 3.543A pdb=" N VAL A 308 " --> pdb=" O LYS A 304 " (cutoff:3.500A)
Processing helix chain 'A' and resid 318 through 321
removed outlier: 3.752A pdb=" N ALA A 321 " --> pdb=" O PRO A 318 " (cutoff:3.500A)
No H-bonds generated for 'chain 'A' and resid 318 through 321'
Processing helix chain 'A' and resid 327 through 334
removed outlier: 3.529A pdb=" N HIS A 332 " --> pdb=" O ASP A 329 " (cutoff:3.500A)
Processing helix chain 'A' and resid 357 through 366
Processing helix chain 'A' and resid 366 through 373
removed outlier: 3.622A pdb=" N LEU A 373 " --> pdb=" O GLU A 369 " (cutoff:3.500A)
Processing helix chain 'A' and resid 374 through 392
Processing helix chain 'A' and resid 417 through 427
Processing helix chain 'A' and resid 431 through 445
Processing helix chain 'A' and resid 447 through 466
Processing helix chain 'A' and resid 467 through 501
removed outlier: 5.424A pdb=" N LEU A 497 " --> pdb=" O ASN A 493 " (cutoff:3.500A)
removed outlier: 5.088A pdb=" N LEU A 498 " --> pdb=" O GLY A 494 " (cutoff:3.500A)
Processing helix chain 'A' and resid 508 through 519
removed outlier: 3.742A pdb=" N MET A 519 " --> pdb=" O ILE A 515 " (cutoff:3.500A)
Processing helix chain 'A' and resid 523 through 527
removed outlier: 3.558A pdb=" N ASP A 526 " --> pdb=" O ASN A 523 " (cutoff:3.500A)
Processing helix chain 'A' and resid 532 through 539
Processing helix chain 'A' and resid 540 through 546
removed outlier: 4.232A pdb=" N PHE A 544 " --> pdb=" O ILE A 541 " (cutoff:3.500A)
Processing helix chain 'A' and resid 551 through 572
removed outlier: 3.772A pdb=" N VAL A 556 " --> pdb=" O TYR A 552 " (cutoff:3.500A)
Processing helix chain 'A' and resid 579 through 598
removed outlier: 3.598A pdb=" N VAL A 583 " --> pdb=" O SER A 579 " (cutoff:3.500A)
removed outlier: 3.549A pdb=" N ASN A 598 " --> pdb=" O PHE A 594 " (cutoff:3.500A)
Processing helix chain 'A' and resid 600 through 604
removed outlier: 3.799A pdb=" N VAL A 603 " --> pdb=" O LEU A 600 " (cutoff:3.500A)
Processing helix chain 'A' and resid 605 through 629
Processing helix chain 'A' and resid 632 through 639
Processing helix chain 'A' and resid 648 through 659
Processing helix chain 'A' and resid 660 through 671
Processing helix chain 'A' and resid 680 through 701
removed outlier: 3.733A pdb=" N ALA A 701 " --> pdb=" O LYS A 697 " (cutoff:3.500A)
Processing helix chain 'A' and resid 705 through 723
removed outlier: 4.237A pdb=" N SER A 714 " --> pdb=" O THR A 710 " (cutoff:3.500A)
removed outlier: 4.821A pdb=" N GLU A 715 " --> pdb=" O GLN A 711 " (cutoff:3.500A)
Processing helix chain 'A' and resid 729 through 743
Processing helix chain 'A' and resid 750 through 764
removed outlier: 4.267A pdb=" N CYS A 764 " --> pdb=" O ARG A 760 " (cutoff:3.500A)
Processing helix chain 'A' and resid 768 through 786
removed outlier: 3.582A pdb=" N ILE A 772 " --> pdb=" O PRO A 768 " (cutoff:3.500A)
Processing helix chain 'A' and resid 800 through 812
removed outlier: 3.622A pdb=" N TYR A 804 " --> pdb=" O TYR A 800 " (cutoff:3.500A)
Processing helix chain 'A' and resid 817 through 827
removed outlier: 3.857A pdb=" N LEU A 825 " --> pdb=" O SER A 821 " (cutoff:3.500A)
removed outlier: 4.068A pdb=" N CYS A 826 " --> pdb=" O GLU A 822 " (cutoff:3.500A)
removed outlier: 3.890A pdb=" N LEU A 827 " --> pdb=" O ILE A 823 " (cutoff:3.500A)
Processing helix chain 'A' and resid 831 through 841
removed outlier: 3.523A pdb=" N ILE A 835 " --> pdb=" O LYS A 831 " (cutoff:3.500A)
Processing helix chain 'A' and resid 846 through 857
Processing helix chain 'A' and resid 861 through 871
Processing helix chain 'A' and resid 878 through 900
Processing helix chain 'A' and resid 908 through 922
removed outlier: 3.638A pdb=" N TYR A 912 " --> pdb=" O SER A 908 " (cutoff:3.500A)
Processing helix chain 'A' and resid 927 through 933
removed outlier: 3.641A pdb=" N MET A 930 " --> pdb=" O ASN A 927 " (cutoff:3.500A)
removed outlier: 3.817A pdb=" N GLU A 931 " --> pdb=" O SER A 928 " (cutoff:3.500A)
removed outlier: 3.698A pdb=" N PHE A 933 " --> pdb=" O MET A 930 " (cutoff:3.500A)
Processing helix chain 'A' and resid 937 through 945
Processing helix chain 'A' and resid 955 through 961
Processing helix chain 'A' and resid 963 through 973
Processing helix chain 'A' and resid 973 through 991
removed outlier: 4.399A pdb=" N HIS A 979 " --> pdb=" O HIS A 975 " (cutoff:3.500A)
Processing helix chain 'A' and resid 993 through 1003
Processing helix chain 'B' and resid 305 through 317
Processing helix chain 'B' and resid 318 through 321
removed outlier: 3.608A pdb=" N ALA B 321 " --> pdb=" O PRO B 318 " (cutoff:3.500A)
No H-bonds generated for 'chain 'B' and resid 318 through 321'
Processing helix chain 'B' and resid 327 through 333
Processing helix chain 'B' and resid 355 through 366
Processing helix chain 'B' and resid 366 through 372
removed outlier: 3.525A pdb=" N ARG B 370 " --> pdb=" O SER B 366 " (cutoff:3.500A)
removed outlier: 3.717A pdb=" N LYS B 372 " --> pdb=" O ASP B 368 " (cutoff:3.500A)
Processing helix chain 'B' and resid 374 through 392
Processing helix chain 'B' and resid 411 through 416
Processing helix chain 'B' and resid 417 through 427
Processing helix chain 'B' and resid 431 through 445
Processing helix chain 'B' and resid 447 through 466
removed outlier: 4.389A pdb=" N ASP B 464 " --> pdb=" O LEU B 460 " (cutoff:3.500A)
Processing helix chain 'B' and resid 467 through 500
removed outlier: 4.962A pdb=" N LEU B 497 " --> pdb=" O ASN B 493 " (cutoff:3.500A)
removed outlier: 4.828A pdb=" N LEU B 498 " --> pdb=" O GLY B 494 " (cutoff:3.500A)
Processing helix chain 'B' and resid 508 through 519
removed outlier: 4.176A pdb=" N MET B 519 " --> pdb=" O ILE B 515 " (cutoff:3.500A)
Processing helix chain 'B' and resid 523 through 527
removed outlier: 3.568A pdb=" N ASP B 526 " --> pdb=" O ASN B 523 " (cutoff:3.500A)
Processing helix chain 'B' and resid 532 through 539
Processing helix chain 'B' and resid 542 through 547
removed outlier: 3.889A pdb=" N SER B 546 " --> pdb=" O LEU B 542 " (cutoff:3.500A)
removed outlier: 4.249A pdb=" N ASP B 547 " --> pdb=" O GLU B 543 " (cutoff:3.500A)
No H-bonds generated for 'chain 'B' and resid 542 through 547'
Processing helix chain 'B' and resid 552 through 572
Processing helix chain 'B' and resid 579 through 598
Processing helix chain 'B' and resid 600 through 604
removed outlier: 3.529A pdb=" N VAL B 603 " --> pdb=" O LEU B 600 " (cutoff:3.500A)
Processing helix chain 'B' and resid 605 through 628
removed outlier: 3.800A pdb=" N THR B 628 " --> pdb=" O GLU B 624 " (cutoff:3.500A)
Processing helix chain 'B' and resid 634 through 639
removed outlier: 4.023A pdb=" N PHE B 639 " --> pdb=" O GLY B 635 " (cutoff:3.500A)
Processing helix chain 'B' and resid 648 through 659
Processing helix chain 'B' and resid 660 through 671
Processing helix chain 'B' and resid 672 through 676
Processing helix chain 'B' and resid 680 through 701
removed outlier: 3.658A pdb=" N ALA B 701 " --> pdb=" O LYS B 697 " (cutoff:3.500A)
Processing helix chain 'B' and resid 705 through 723
removed outlier: 4.426A pdb=" N SER B 714 " --> pdb=" O THR B 710 " (cutoff:3.500A)
removed outlier: 4.877A pdb=" N GLU B 715 " --> pdb=" O GLN B 711 " (cutoff:3.500A)
Processing helix chain 'B' and resid 724 through 726
No H-bonds generated for 'chain 'B' and resid 724 through 726'
Processing helix chain 'B' and resid 729 through 743
Processing helix chain 'B' and resid 750 through 762
Processing helix chain 'B' and resid 768 through 786
removed outlier: 3.561A pdb=" N ILE B 772 " --> pdb=" O PRO B 768 " (cutoff:3.500A)
Processing helix chain 'B' and resid 800 through 812
removed outlier: 3.627A pdb=" N TYR B 804 " --> pdb=" O TYR B 800 " (cutoff:3.500A)
Processing helix chain 'B' and resid 817 through 826
removed outlier: 3.605A pdb=" N CYS B 826 " --> pdb=" O GLU B 822 " (cutoff:3.500A)
Processing helix chain 'B' and resid 831 through 841
removed outlier: 4.072A pdb=" N LYS B 840 " --> pdb=" O ASP B 836 " (cutoff:3.500A)
removed outlier: 4.154A pdb=" N LEU B 841 " --> pdb=" O PHE B 837 " (cutoff:3.500A)
Processing helix chain 'B' and resid 846 through 857
Processing helix chain 'B' and resid 861 through 871
Processing helix chain 'B' and resid 878 through 903
removed outlier: 4.699A pdb=" N GLU B 901 " --> pdb=" O ILE B 897 " (cutoff:3.500A)
removed outlier: 4.236A pdb=" N LYS B 902 " --> pdb=" O VAL B 898 " (cutoff:3.500A)
Processing helix chain 'B' and resid 909 through 922
Processing helix chain 'B' and resid 927 through 934
removed outlier: 3.519A pdb=" N GLU B 931 " --> pdb=" O SER B 928 " (cutoff:3.500A)
Processing helix chain 'B' and resid 939 through 945
removed outlier: 4.035A pdb=" N PHE B 943 " --> pdb=" O GLN B 939 " (cutoff:3.500A)
Processing helix chain 'B' and resid 950 through 954
Processing helix chain 'B' and resid 955 through 960
Processing helix chain 'B' and resid 963 through 972
Processing helix chain 'B' and resid 976 through 991
removed outlier: 3.598A pdb=" N VAL B 980 " --> pdb=" O MET B 976 " (cutoff:3.500A)
Processing helix chain 'B' and resid 993 through 1003
removed outlier: 3.697A pdb=" N LEU B 997 " --> pdb=" O ASP B 993 " (cutoff:3.500A)
Processing helix chain 'E' and resid 69 through 76
removed outlier: 3.723A pdb=" N THR E 76 " --> pdb=" O TRP E 72 " (cutoff:3.500A)
Processing helix chain 'F' and resid 69 through 76
removed outlier: 3.737A pdb=" N THR F 76 " --> pdb=" O TRP F 72 " (cutoff:3.500A)
Processing sheet with id=AA1, first strand: chain 'A' and resid 338 through 340
Processing sheet with id=AA2, first strand: chain 'A' and resid 574 through 575
removed outlier: 6.766A pdb=" N PHE F 13 " --> pdb=" O VAL F 22 " (cutoff:3.500A)
removed outlier: 4.548A pdb=" N THR F 24 " --> pdb=" O VAL F 11 " (cutoff:3.500A)
removed outlier: 6.746A pdb=" N VAL F 11 " --> pdb=" O THR F 24 " (cutoff:3.500A)
removed outlier: 6.823A pdb=" N TYR F 171 " --> pdb=" O ASN F 197 " (cutoff:3.500A)
removed outlier: 3.859A pdb=" N ASN F 197 " --> pdb=" O TYR F 171 " (cutoff:3.500A)
removed outlier: 3.767A pdb=" N ILE F 193 " --> pdb=" O TYR F 175 " (cutoff:3.500A)
Processing sheet with id=AA3, first strand: chain 'A' and resid 574 through 575
removed outlier: 8.409A pdb=" N VAL F 22 " --> pdb=" O PHE F 68 " (cutoff:3.500A)
removed outlier: 5.035A pdb=" N PHE F 68 " --> pdb=" O VAL F 22 " (cutoff:3.500A)
removed outlier: 6.880A pdb=" N THR F 24 " --> pdb=" O ALA F 66 " (cutoff:3.500A)
removed outlier: 4.528A pdb=" N ALA F 66 " --> pdb=" O THR F 24 " (cutoff:3.500A)
removed outlier: 7.171A pdb=" N THR F 62 " --> pdb=" O GLN F 28 " (cutoff:3.500A)
removed outlier: 4.927A pdb=" N ALA F 30 " --> pdb=" O ASN F 60 " (cutoff:3.500A)
removed outlier: 6.969A pdb=" N ASN F 60 " --> pdb=" O ALA F 30 " (cutoff:3.500A)
removed outlier: 5.300A pdb=" N PHE F 32 " --> pdb=" O GLU F 58 " (cutoff:3.500A)
removed outlier: 7.310A pdb=" N GLU F 58 " --> pdb=" O PHE F 32 " (cutoff:3.500A)
removed outlier: 5.542A pdb=" N GLN F 34 " --> pdb=" O GLU F 56 " (cutoff:3.500A)
removed outlier: 7.990A pdb=" N GLU F 56 " --> pdb=" O GLN F 34 " (cutoff:3.500A)
removed outlier: 4.687A pdb=" N ILE F 59 " --> pdb=" O ALA F 222 " (cutoff:3.500A)
removed outlier: 3.766A pdb=" N LEU F 61 " --> pdb=" O PHE F 220 " (cutoff:3.500A)
Processing sheet with id=AA4, first strand: chain 'B' and resid 339 through 340
Processing sheet with id=AA5, first strand: chain 'B' and resid 574 through 575
removed outlier: 4.470A pdb=" N GLU E 26 " --> pdb=" O ASN E 65 " (cutoff:3.500A)
removed outlier: 5.381A pdb=" N ASN E 65 " --> pdb=" O GLU E 26 " (cutoff:3.500A)
removed outlier: 5.536A pdb=" N GLN E 28 " --> pdb=" O VAL E 63 " (cutoff:3.500A)
removed outlier: 7.094A pdb=" N VAL E 63 " --> pdb=" O GLN E 28 " (cutoff:3.500A)
removed outlier: 6.437A pdb=" N ALA E 30 " --> pdb=" O LEU E 61 " (cutoff:3.500A)
removed outlier: 6.513A pdb=" N LEU E 61 " --> pdb=" O ALA E 30 " (cutoff:3.500A)
removed outlier: 6.916A pdb=" N PHE E 32 " --> pdb=" O ILE E 59 " (cutoff:3.500A)
removed outlier: 7.172A pdb=" N ILE E 59 " --> pdb=" O PHE E 32 " (cutoff:3.500A)
removed outlier: 7.315A pdb=" N GLN E 34 " --> pdb=" O LYS E 57 " (cutoff:3.500A)
removed outlier: 7.564A pdb=" N LYS E 57 " --> pdb=" O GLN E 34 " (cutoff:3.500A)
removed outlier: 3.758A pdb=" N LEU E 61 " --> pdb=" O PHE E 220 " (cutoff:3.500A)
Processing sheet with id=AA6, first strand: chain 'B' and resid 574 through 575
removed outlier: 6.698A pdb=" N PHE E 13 " --> pdb=" O VAL E 22 " (cutoff:3.500A)
removed outlier: 4.420A pdb=" N THR E 24 " --> pdb=" O VAL E 11 " (cutoff:3.500A)
removed outlier: 6.525A pdb=" N VAL E 11 " --> pdb=" O THR E 24 " (cutoff:3.500A)
removed outlier: 7.096A pdb=" N TYR E 171 " --> pdb=" O ASN E 197 " (cutoff:3.500A)
removed outlier: 3.966A pdb=" N ASN E 197 " --> pdb=" O TYR E 171 " (cutoff:3.500A)
removed outlier: 3.526A pdb=" N GLN E 194 " --> pdb=" O VAL E 233 " (cutoff:3.500A)
763 hydrogen bonds defined for protein.
2172 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: 5.09
Time building geometry restraints manager: 4.05 seconds
NOTE: a complete listing of the restraints can be obtained by requesting
output of .geo file.
Histogram of bond lengths:
1.18 - 1.31: 2391
1.31 - 1.44: 3992
1.44 - 1.56: 7907
1.56 - 1.69: 0
1.69 - 1.81: 92
Bond restraints: 14382
Sorted by residual:
bond pdb=" C ASN A 598 "
pdb=" O ASN A 598 "
ideal model delta sigma weight residual
1.236 1.184 0.052 1.32e-02 5.74e+03 1.53e+01
bond pdb=" C ASN A 910 "
pdb=" O ASN A 910 "
ideal model delta sigma weight residual
1.236 1.189 0.047 1.26e-02 6.30e+03 1.41e+01
bond pdb=" C ASP A 911 "
pdb=" O ASP A 911 "
ideal model delta sigma weight residual
1.236 1.198 0.038 1.15e-02 7.56e+03 1.11e+01
bond pdb=" C ARG A 447 "
pdb=" O ARG A 447 "
ideal model delta sigma weight residual
1.235 1.196 0.039 1.26e-02 6.30e+03 9.69e+00
bond pdb=" CA ASP A 788 "
pdb=" C ASP A 788 "
ideal model delta sigma weight residual
1.523 1.486 0.037 1.32e-02 5.74e+03 8.07e+00
... (remaining 14377 not shown)
Histogram of bond angle deviations from ideal:
0.00 - 2.51: 18994
2.51 - 5.02: 313
5.02 - 7.53: 32
7.53 - 10.04: 8
10.04 - 12.55: 3
Bond angle restraints: 19350
Sorted by residual:
angle pdb=" N LYS B 660 "
pdb=" CA LYS B 660 "
pdb=" C LYS B 660 "
ideal model delta sigma weight residual
110.46 97.91 12.55 1.48e+00 4.57e-01 7.19e+01
angle pdb=" N PHE B 744 "
pdb=" CA PHE B 744 "
pdb=" C PHE B 744 "
ideal model delta sigma weight residual
109.83 100.76 9.07 1.27e+00 6.20e-01 5.10e+01
angle pdb=" N ARG A 447 "
pdb=" CA ARG A 447 "
pdb=" C ARG A 447 "
ideal model delta sigma weight residual
110.80 99.05 11.75 2.13e+00 2.20e-01 3.04e+01
angle pdb=" C ASN F 210 "
pdb=" CA ASN F 210 "
pdb=" CB ASN F 210 "
ideal model delta sigma weight residual
110.08 101.63 8.45 1.57e+00 4.06e-01 2.90e+01
angle pdb=" N ASN A 702 "
pdb=" CA ASN A 702 "
pdb=" C ASN A 702 "
ideal model delta sigma weight residual
111.28 105.89 5.39 1.09e+00 8.42e-01 2.45e+01
... (remaining 19345 not shown)
Histogram of dihedral angle deviations from ideal:
0.00 - 17.98: 7329
17.98 - 35.96: 947
35.96 - 53.95: 253
53.95 - 71.93: 46
71.93 - 89.91: 21
Dihedral angle restraints: 8596
sinusoidal: 3574
harmonic: 5022
Sorted by residual:
dihedral pdb=" C ASN F 210 "
pdb=" N ASN F 210 "
pdb=" CA ASN F 210 "
pdb=" CB ASN F 210 "
ideal model delta harmonic sigma weight residual
-122.60 -112.10 -10.50 0 2.50e+00 1.60e-01 1.76e+01
dihedral pdb=" CA GLU F 230 "
pdb=" C GLU F 230 "
pdb=" N MET F 231 "
pdb=" CA MET F 231 "
ideal model delta harmonic sigma weight residual
-180.00 -161.79 -18.21 0 5.00e+00 4.00e-02 1.33e+01
dihedral pdb=" CA THR E 8 "
pdb=" C THR E 8 "
pdb=" N ALA E 9 "
pdb=" CA ALA E 9 "
ideal model delta harmonic sigma weight residual
180.00 -162.09 -17.91 0 5.00e+00 4.00e-02 1.28e+01
... (remaining 8593 not shown)
Histogram of chiral volume deviations from ideal:
0.000 - 0.046: 1618
0.046 - 0.093: 333
0.093 - 0.139: 84
0.139 - 0.186: 13
0.186 - 0.232: 4
Chirality restraints: 2052
Sorted by residual:
chirality pdb=" CA TYR B1003 "
pdb=" N TYR B1003 "
pdb=" C TYR B1003 "
pdb=" CB TYR B1003 "
both_signs ideal model delta sigma weight residual
False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.35e+00
chirality pdb=" CA PHE A 907 "
pdb=" N PHE A 907 "
pdb=" C PHE A 907 "
pdb=" CB PHE A 907 "
both_signs ideal model delta sigma weight residual
False 2.51 2.72 -0.20 2.00e-01 2.50e+01 1.05e+00
chirality pdb=" CA ASN A 963 "
pdb=" N ASN A 963 "
pdb=" C ASN A 963 "
pdb=" CB ASN A 963 "
both_signs ideal model delta sigma weight residual
False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.62e-01
... (remaining 2049 not shown)
Planarity restraints: 2480
Sorted by residual:
delta sigma weight rms_deltas residual
plane pdb=" CA TYR B1003 " -0.018 2.00e-02 2.50e+03 3.56e-02 1.27e+01
pdb=" C TYR B1003 " 0.062 2.00e-02 2.50e+03
pdb=" O TYR B1003 " -0.023 2.00e-02 2.50e+03
pdb=" N PHE B1004 " -0.021 2.00e-02 2.50e+03
delta sigma weight rms_deltas residual
plane pdb=" C PHE E 195 " -0.056 5.00e-02 4.00e+02 8.50e-02 1.16e+01
pdb=" N PRO E 196 " 0.147 5.00e-02 4.00e+02
pdb=" CA PRO E 196 " -0.044 5.00e-02 4.00e+02
pdb=" CD PRO E 196 " -0.047 5.00e-02 4.00e+02
delta sigma weight rms_deltas residual
plane pdb=" CA ILE B 409 " -0.013 2.00e-02 2.50e+03 2.61e-02 6.83e+00
pdb=" C ILE B 409 " 0.045 2.00e-02 2.50e+03
pdb=" O ILE B 409 " -0.017 2.00e-02 2.50e+03
pdb=" N ASN B 410 " -0.015 2.00e-02 2.50e+03
... (remaining 2477 not shown)
Histogram of nonbonded interaction distances:
2.20 - 2.74: 1099
2.74 - 3.28: 15609
3.28 - 3.82: 24104
3.82 - 4.36: 28760
4.36 - 4.90: 48426
Nonbonded interactions: 117998
Sorted by model distance:
nonbonded pdb=" O LEU A 551 "
pdb=" OG1 THR A 555 "
model vdw
2.195 3.040
nonbonded pdb=" O LYS B 785 "
pdb=" NZ LYS B 785 "
model vdw
2.207 3.120
nonbonded pdb=" OE2 GLU E 174 "
pdb=" NH2 ARG E 176 "
model vdw
2.230 3.120
nonbonded pdb=" O PHE A 559 "
pdb=" OG1 THR A 562 "
model vdw
2.236 3.040
nonbonded pdb=" O SER A 573 "
pdb=" NH2 ARG A 629 "
model vdw
2.237 3.120
... (remaining 117993 not shown)
NOTE: a complete listing of the restraints can be obtained by requesting
output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
reference = chain 'A'
selection = chain 'B'
}
ncs_group {
reference = chain 'E'
selection = chain 'F'
}
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: 0.880
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: 0.560
Check model and map are aligned: 0.140
Set scattering table: 0.130
Process input model: 33.420
Find NCS groups from input model: 0.380
Set up NCS constraints: 0.050
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:2.810
Set ADP refinement strategy: 0.000
Make a string to write initial .geo file:0.000
Internal consistency checks: 0.000
Total: 38.380
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5810
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 0.055 14382 Z= 0.289
Angle : 0.806 12.553 19350 Z= 0.476
Chirality : 0.043 0.232 2052
Planarity : 0.005 0.085 2480
Dihedral : 17.600 89.912 5364
Min Nonbonded Distance : 2.195
Molprobity Statistics.
All-atom Clashscore : 7.58
Ramachandran Plot:
Outliers : 0.06 %
Allowed : 4.76 %
Favored : 95.18 %
Rotamer:
Outliers : 0.45 %
Allowed : 19.66 %
Favored : 79.88 %
Cbeta Deviations : 0.06 %
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 (0.20), residues: 1682
helix: 0.48 (0.16), residues: 963
sheet: -1.83 (0.44), residues: 112
loop : -1.76 (0.24), residues: 607
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.008 0.001 TRP B 958
HIS 0.004 0.001 HIS A 786
PHE 0.041 0.002 PHE F 32
TYR 0.038 0.002 TYR B1003
ARG 0.005 0.001 ARG A 447
*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
3364 Ramachandran restraints generated.
1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
3364 Ramachandran restraints generated.
1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
225 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 7
poor density : 218
time to evaluate : 1.648
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: A 616 MET cc_start: 0.8397 (mmm) cc_final: 0.7900 (mmt)
REVERT: A 950 ASP cc_start: 0.6581 (p0) cc_final: 0.6357 (p0)
REVERT: B 406 SER cc_start: 0.6640 (t) cc_final: 0.6268 (m)
REVERT: B 607 GLU cc_start: 0.6734 (mp0) cc_final: 0.6529 (mp0)
REVERT: B 693 GLU cc_start: 0.6235 (mp0) cc_final: 0.5352 (mm-30)
REVERT: F 219 LYS cc_start: 0.8026 (mtpp) cc_final: 0.7631 (mtpp)
outliers start: 7
outliers final: 2
residues processed: 224
average time/residue: 0.2731
time to fit residues: 89.8050
Evaluate side-chains
189 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 2
poor density : 187
time to evaluate : 1.703
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue 231 MET
Chi-restraints excluded: chain E residue 233 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 168
random chunks:
chunk 141 optimal weight: 8.9990
chunk 127 optimal weight: 8.9990
chunk 70 optimal weight: 8.9990
chunk 43 optimal weight: 0.6980
chunk 85 optimal weight: 0.9980
chunk 68 optimal weight: 2.9990
chunk 131 optimal weight: 1.9990
chunk 50 optimal weight: 0.6980
chunk 80 optimal weight: 0.8980
chunk 98 optimal weight: 0.7980
chunk 152 optimal weight: 0.8980
overall best weight: 0.7980
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** A 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 382 ASN
A 503 HIS
A 614 ASN
A 797 ASN
B 591 ASN
B 609 HIS
** B 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 852 HIS
B 895 ASN
B 961 ASN
Total number of N/Q/H flips: 9
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5845
moved from start: 0.1636
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.035 14382 Z= 0.208
Angle : 0.587 11.503 19350 Z= 0.312
Chirality : 0.041 0.287 2052
Planarity : 0.004 0.076 2480
Dihedral : 4.650 33.251 1862
Min Nonbonded Distance : 2.542
Molprobity Statistics.
All-atom Clashscore : 8.63
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 4.16 %
Favored : 95.84 %
Rotamer:
Outliers : 2.98 %
Allowed : 20.38 %
Favored : 76.65 %
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: -0.30 (0.20), residues: 1682
helix: 0.84 (0.17), residues: 963
sheet: -1.70 (0.46), residues: 102
loop : -1.56 (0.24), residues: 617
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.018 0.002 TRP A 958
HIS 0.007 0.001 HIS B 852
PHE 0.016 0.002 PHE A 708
TYR 0.016 0.002 TYR B 951
ARG 0.006 0.001 ARG A 870
*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
3364 Ramachandran restraints generated.
1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
3364 Ramachandran restraints generated.
1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
266 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 46
poor density : 220
time to evaluate : 1.697
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 306 ASP cc_start: 0.5276 (OUTLIER) cc_final: 0.4923 (t0)
REVERT: A 381 PHE cc_start: 0.7940 (t80) cc_final: 0.7639 (t80)
REVERT: A 616 MET cc_start: 0.8458 (mmm) cc_final: 0.8173 (mmm)
REVERT: A 626 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7833 (mm-30)
REVERT: A 663 ASP cc_start: 0.6006 (m-30) cc_final: 0.5661 (m-30)
REVERT: B 331 LYS cc_start: 0.7543 (ptpt) cc_final: 0.7275 (pttp)
REVERT: B 406 SER cc_start: 0.6674 (t) cc_final: 0.6423 (m)
REVERT: B 544 PHE cc_start: 0.6679 (t80) cc_final: 0.6379 (t80)
REVERT: B 552 TYR cc_start: 0.5904 (OUTLIER) cc_final: 0.5356 (t80)
REVERT: B 578 MET cc_start: 0.8074 (OUTLIER) cc_final: 0.7777 (ttp)
REVERT: B 857 LYS cc_start: 0.5191 (tttt) cc_final: 0.4350 (ttmt)
outliers start: 46
outliers final: 21
residues processed: 248
average time/residue: 0.2812
time to fit residues: 101.4453
Evaluate side-chains
218 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 25
poor density : 193
time to evaluate : 1.687
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 306 ASP
Chi-restraints excluded: chain A residue 503 HIS
Chi-restraints excluded: chain A residue 544 PHE
Chi-restraints excluded: chain A residue 626 GLU
Chi-restraints excluded: chain A residue 668 GLU
Chi-restraints excluded: chain A residue 807 LEU
Chi-restraints excluded: chain A residue 845 LEU
Chi-restraints excluded: chain B residue 367 CYS
Chi-restraints excluded: chain B residue 470 VAL
Chi-restraints excluded: chain B residue 543 GLU
Chi-restraints excluded: chain B residue 552 TYR
Chi-restraints excluded: chain B residue 578 MET
Chi-restraints excluded: chain B residue 603 VAL
Chi-restraints excluded: chain B residue 656 SER
Chi-restraints excluded: chain B residue 660 LYS
Chi-restraints excluded: chain B residue 707 VAL
Chi-restraints excluded: chain B residue 749 LEU
Chi-restraints excluded: chain B residue 891 THR
Chi-restraints excluded: chain E residue 63 VAL
Chi-restraints excluded: chain E residue 193 ILE
Chi-restraints excluded: chain F residue 67 PHE
Chi-restraints excluded: chain F residue 198 VAL
Chi-restraints excluded: chain F residue 208 LEU
Chi-restraints excluded: chain F residue 221 GLU
Chi-restraints excluded: chain F residue 235 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 168
random chunks:
chunk 84 optimal weight: 0.6980
chunk 47 optimal weight: 0.7980
chunk 126 optimal weight: 4.9990
chunk 103 optimal weight: 6.9990
chunk 42 optimal weight: 0.9980
chunk 152 optimal weight: 0.7980
chunk 165 optimal weight: 7.9990
chunk 136 optimal weight: 0.0980
chunk 151 optimal weight: 3.9990
chunk 52 optimal weight: 7.9990
chunk 122 optimal weight: 0.8980
overall best weight: 0.6580
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 332 HIS
A 503 HIS
** B 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 698 GLN
B 852 HIS
B 961 ASN
E 210 ASN
Total number of N/Q/H flips: 6
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5851
moved from start: 0.2160
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.048 14382 Z= 0.186
Angle : 0.554 10.704 19350 Z= 0.295
Chirality : 0.040 0.229 2052
Planarity : 0.004 0.074 2480
Dihedral : 4.358 29.548 1858
Min Nonbonded Distance : 2.515
Molprobity Statistics.
All-atom Clashscore : 8.88
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 4.22 %
Favored : 95.78 %
Rotamer:
Outliers : 3.10 %
Allowed : 20.96 %
Favored : 75.94 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: -0.31 (0.20), residues: 1682
helix: 0.83 (0.16), residues: 972
sheet: -1.50 (0.46), residues: 102
loop : -1.64 (0.24), residues: 608
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.014 0.001 TRP A 958
HIS 0.007 0.001 HIS B 852
PHE 0.024 0.001 PHE A 387
TYR 0.020 0.001 TYR A 625
ARG 0.004 0.000 ARG A 566
*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
3364 Ramachandran restraints generated.
1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
3364 Ramachandran restraints generated.
1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
262 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 48
poor density : 214
time to evaluate : 1.596
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 306 ASP cc_start: 0.5343 (OUTLIER) cc_final: 0.4974 (t0)
REVERT: A 364 LYS cc_start: 0.7562 (tttt) cc_final: 0.6596 (ttmt)
REVERT: A 503 HIS cc_start: 0.7515 (OUTLIER) cc_final: 0.7164 (p-80)
REVERT: A 616 MET cc_start: 0.8405 (mmm) cc_final: 0.8159 (mmm)
REVERT: A 626 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.7745 (mm-30)
REVERT: A 802 ARG cc_start: 0.6161 (ptt180) cc_final: 0.5153 (ptp90)
REVERT: A 1001 MET cc_start: 0.5614 (mmm) cc_final: 0.5269 (mmm)
REVERT: B 331 LYS cc_start: 0.7529 (ptpt) cc_final: 0.7289 (pttp)
REVERT: B 396 MET cc_start: 0.6203 (mmm) cc_final: 0.5979 (tpp)
REVERT: B 544 PHE cc_start: 0.6029 (t80) cc_final: 0.5562 (t80)
REVERT: B 552 TYR cc_start: 0.5714 (OUTLIER) cc_final: 0.4717 (t80)
REVERT: B 578 MET cc_start: 0.8137 (OUTLIER) cc_final: 0.7932 (ttp)
REVERT: B 763 LYS cc_start: 0.6482 (mptt) cc_final: 0.6216 (mptt)
REVERT: B 765 ASN cc_start: 0.4732 (OUTLIER) cc_final: 0.1419 (t0)
REVERT: E 206 MET cc_start: 0.5441 (mmm) cc_final: 0.4893 (mtp)
REVERT: F 176 ARG cc_start: 0.4813 (tmm160) cc_final: 0.4584 (ttp80)
outliers start: 48
outliers final: 26
residues processed: 244
average time/residue: 0.2785
time to fit residues: 100.2641
Evaluate side-chains
231 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 32
poor density : 199
time to evaluate : 1.651
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 306 ASP
Chi-restraints excluded: chain A residue 346 VAL
Chi-restraints excluded: chain A residue 503 HIS
Chi-restraints excluded: chain A residue 544 PHE
Chi-restraints excluded: chain A residue 626 GLU
Chi-restraints excluded: chain A residue 668 GLU
Chi-restraints excluded: chain A residue 845 LEU
Chi-restraints excluded: chain B residue 346 VAL
Chi-restraints excluded: chain B residue 407 ILE
Chi-restraints excluded: chain B residue 470 VAL
Chi-restraints excluded: chain B residue 497 LEU
Chi-restraints excluded: chain B residue 531 MET
Chi-restraints excluded: chain B residue 543 GLU
Chi-restraints excluded: chain B residue 552 TYR
Chi-restraints excluded: chain B residue 578 MET
Chi-restraints excluded: chain B residue 656 SER
Chi-restraints excluded: chain B residue 707 VAL
Chi-restraints excluded: chain B residue 765 ASN
Chi-restraints excluded: chain B residue 825 LEU
Chi-restraints excluded: chain B residue 891 THR
Chi-restraints excluded: chain E residue 173 VAL
Chi-restraints excluded: chain E residue 193 ILE
Chi-restraints excluded: chain E residue 194 GLN
Chi-restraints excluded: chain E residue 228 THR
Chi-restraints excluded: chain F residue 67 PHE
Chi-restraints excluded: chain F residue 76 THR
Chi-restraints excluded: chain F residue 173 VAL
Chi-restraints excluded: chain F residue 198 VAL
Chi-restraints excluded: chain F residue 208 LEU
Chi-restraints excluded: chain F residue 221 GLU
Chi-restraints excluded: chain F residue 226 THR
Chi-restraints excluded: chain F residue 235 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 168
random chunks:
chunk 151 optimal weight: 9.9990
chunk 114 optimal weight: 3.9990
chunk 79 optimal weight: 6.9990
chunk 16 optimal weight: 0.8980
chunk 72 optimal weight: 0.9980
chunk 102 optimal weight: 2.9990
chunk 153 optimal weight: 8.9990
chunk 162 optimal weight: 5.9990
chunk 80 optimal weight: 0.9990
chunk 145 optimal weight: 3.9990
chunk 43 optimal weight: 0.8980
overall best weight: 1.3584
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 491 GLN
A 503 HIS
B 483 GLN
B 852 HIS
** F 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Total number of N/Q/H flips: 4
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5970
moved from start: 0.2597
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.004 0.042 14382 Z= 0.259
Angle : 0.608 13.454 19350 Z= 0.323
Chirality : 0.042 0.267 2052
Planarity : 0.004 0.081 2480
Dihedral : 4.524 27.330 1858
Min Nonbonded Distance : 2.493
Molprobity Statistics.
All-atom Clashscore : 11.07
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 4.10 %
Favored : 95.90 %
Rotamer:
Outliers : 4.66 %
Allowed : 20.76 %
Favored : 74.58 %
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: -0.35 (0.20), residues: 1682
helix: 0.71 (0.16), residues: 958
sheet: -1.51 (0.46), residues: 102
loop : -1.45 (0.24), residues: 622
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.010 0.002 TRP E 72
HIS 0.009 0.001 HIS B 852
PHE 0.027 0.002 PHE A 646
TYR 0.040 0.002 TYR A 625
ARG 0.005 0.000 ARG A 480
*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
3364 Ramachandran restraints generated.
1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
3364 Ramachandran restraints generated.
1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
292 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 72
poor density : 220
time to evaluate : 1.574
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: A 306 ASP cc_start: 0.5198 (OUTLIER) cc_final: 0.4895 (t0)
REVERT: A 364 LYS cc_start: 0.7608 (tttt) cc_final: 0.6562 (ttmt)
REVERT: A 368 ASP cc_start: 0.7978 (p0) cc_final: 0.7775 (p0)
REVERT: A 389 GLU cc_start: 0.7043 (pp20) cc_final: 0.6795 (pp20)
REVERT: A 442 LEU cc_start: 0.6956 (mt) cc_final: 0.6737 (mt)
REVERT: A 480 ARG cc_start: 0.7156 (mpt180) cc_final: 0.6857 (mmt90)
REVERT: A 503 HIS cc_start: 0.7761 (OUTLIER) cc_final: 0.6822 (p-80)
REVERT: A 616 MET cc_start: 0.8409 (mmm) cc_final: 0.8154 (mmm)
REVERT: A 626 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7834 (mm-30)
REVERT: A 647 MET cc_start: 0.7045 (tpt) cc_final: 0.5355 (tpt)
REVERT: A 687 TYR cc_start: 0.7154 (OUTLIER) cc_final: 0.5692 (t80)
REVERT: A 958 TRP cc_start: 0.6887 (OUTLIER) cc_final: 0.6093 (m-10)
REVERT: A 1001 MET cc_start: 0.5708 (mmm) cc_final: 0.5437 (mmm)
REVERT: B 331 LYS cc_start: 0.7569 (ptpt) cc_final: 0.7353 (pttp)
REVERT: B 396 MET cc_start: 0.6489 (mmm) cc_final: 0.6272 (tpp)
REVERT: B 552 TYR cc_start: 0.5971 (OUTLIER) cc_final: 0.4948 (t80)
REVERT: B 578 MET cc_start: 0.8230 (OUTLIER) cc_final: 0.7938 (ttp)
REVERT: B 765 ASN cc_start: 0.4890 (OUTLIER) cc_final: 0.1529 (t0)
REVERT: B 976 MET cc_start: 0.5798 (tmm) cc_final: 0.4563 (tmm)
outliers start: 72
outliers final: 43
residues processed: 267
average time/residue: 0.2631
time to fit residues: 104.7297
Evaluate side-chains
256 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 51
poor density : 205
time to evaluate : 1.730
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 306 ASP
Chi-restraints excluded: chain A residue 322 LEU
Chi-restraints excluded: chain A residue 503 HIS
Chi-restraints excluded: chain A residue 544 PHE
Chi-restraints excluded: chain A residue 583 VAL
Chi-restraints excluded: chain A residue 585 LEU
Chi-restraints excluded: chain A residue 592 LEU
Chi-restraints excluded: chain A residue 597 GLU
Chi-restraints excluded: chain A residue 626 GLU
Chi-restraints excluded: chain A residue 668 GLU
Chi-restraints excluded: chain A residue 671 CYS
Chi-restraints excluded: chain A residue 687 TYR
Chi-restraints excluded: chain A residue 712 PHE
Chi-restraints excluded: chain A residue 748 ASP
Chi-restraints excluded: chain A residue 845 LEU
Chi-restraints excluded: chain A residue 853 LEU
Chi-restraints excluded: chain A residue 874 ILE
Chi-restraints excluded: chain A residue 957 SER
Chi-restraints excluded: chain A residue 958 TRP
Chi-restraints excluded: chain B residue 407 ILE
Chi-restraints excluded: chain B residue 451 SER
Chi-restraints excluded: chain B residue 470 VAL
Chi-restraints excluded: chain B residue 497 LEU
Chi-restraints excluded: chain B residue 531 MET
Chi-restraints excluded: chain B residue 552 TYR
Chi-restraints excluded: chain B residue 578 MET
Chi-restraints excluded: chain B residue 603 VAL
Chi-restraints excluded: chain B residue 656 SER
Chi-restraints excluded: chain B residue 660 LYS
Chi-restraints excluded: chain B residue 689 VAL
Chi-restraints excluded: chain B residue 704 MET
Chi-restraints excluded: chain B residue 707 VAL
Chi-restraints excluded: chain B residue 749 LEU
Chi-restraints excluded: chain B residue 765 ASN
Chi-restraints excluded: chain B residue 825 LEU
Chi-restraints excluded: chain B residue 853 LEU
Chi-restraints excluded: chain B residue 891 THR
Chi-restraints excluded: chain E residue 11 VAL
Chi-restraints excluded: chain E residue 29 THR
Chi-restraints excluded: chain E residue 63 VAL
Chi-restraints excluded: chain E residue 173 VAL
Chi-restraints excluded: chain E residue 193 ILE
Chi-restraints excluded: chain E residue 194 GLN
Chi-restraints excluded: chain F residue 67 PHE
Chi-restraints excluded: chain F residue 76 THR
Chi-restraints excluded: chain F residue 173 VAL
Chi-restraints excluded: chain F residue 198 VAL
Chi-restraints excluded: chain F residue 208 LEU
Chi-restraints excluded: chain F residue 221 GLU
Chi-restraints excluded: chain F residue 226 THR
Chi-restraints excluded: chain F residue 235 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 168
random chunks:
chunk 135 optimal weight: 0.9980
chunk 92 optimal weight: 3.9990
chunk 2 optimal weight: 0.6980
chunk 120 optimal weight: 4.9990
chunk 67 optimal weight: 6.9990
chunk 138 optimal weight: 10.0000
chunk 112 optimal weight: 0.4980
chunk 0 optimal weight: 10.0000
chunk 82 optimal weight: 0.5980
chunk 145 optimal weight: 0.4980
chunk 40 optimal weight: 0.9990
overall best weight: 0.6580
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 386 ASN
A 895 ASN
B 428 GLN
B 563 ASN
B 852 HIS
B 979 HIS
Total number of N/Q/H flips: 6
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5908
moved from start: 0.2861
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.052 14382 Z= 0.188
Angle : 0.561 10.492 19350 Z= 0.298
Chirality : 0.040 0.201 2052
Planarity : 0.004 0.076 2480
Dihedral : 4.428 27.281 1858
Min Nonbonded Distance : 2.322
Molprobity Statistics.
All-atom Clashscore : 10.24
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 4.04 %
Favored : 95.96 %
Rotamer:
Outliers : 4.14 %
Allowed : 21.67 %
Favored : 74.19 %
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: -0.18 (0.20), residues: 1682
helix: 0.87 (0.17), residues: 946
sheet: -1.33 (0.47), residues: 102
loop : -1.39 (0.24), residues: 634
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.009 0.001 TRP F 72
HIS 0.009 0.001 HIS B 852
PHE 0.030 0.001 PHE B 712
TYR 0.045 0.002 TYR A 625
ARG 0.003 0.000 ARG A 629
*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
3364 Ramachandran restraints generated.
1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
3364 Ramachandran restraints generated.
1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
278 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 64
poor density : 214
time to evaluate : 1.597
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 306 ASP cc_start: 0.5264 (OUTLIER) cc_final: 0.4955 (t0)
REVERT: A 364 LYS cc_start: 0.7545 (tttt) cc_final: 0.6688 (ttmt)
REVERT: A 381 PHE cc_start: 0.7784 (t80) cc_final: 0.7500 (t80)
REVERT: A 389 GLU cc_start: 0.7042 (pp20) cc_final: 0.6765 (pp20)
REVERT: A 503 HIS cc_start: 0.7521 (OUTLIER) cc_final: 0.6955 (p90)
REVERT: A 616 MET cc_start: 0.8428 (mmm) cc_final: 0.8188 (mmm)
REVERT: A 626 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7798 (mm-30)
REVERT: A 647 MET cc_start: 0.7032 (tpt) cc_final: 0.5408 (tpt)
REVERT: A 687 TYR cc_start: 0.7081 (OUTLIER) cc_final: 0.5638 (t80)
REVERT: A 941 ASP cc_start: 0.4837 (m-30) cc_final: 0.4532 (m-30)
REVERT: A 1001 MET cc_start: 0.5705 (mmm) cc_final: 0.5440 (mmm)
REVERT: B 331 LYS cc_start: 0.7565 (ptpt) cc_final: 0.7351 (pttp)
REVERT: B 552 TYR cc_start: 0.6072 (OUTLIER) cc_final: 0.5105 (t80)
REVERT: B 578 MET cc_start: 0.8268 (OUTLIER) cc_final: 0.7928 (ttp)
REVERT: B 624 GLU cc_start: 0.5748 (tp30) cc_final: 0.5535 (tp30)
REVERT: B 711 GLN cc_start: 0.6657 (tm-30) cc_final: 0.6103 (tt0)
REVERT: B 763 LYS cc_start: 0.6698 (mptt) cc_final: 0.6362 (mptt)
REVERT: B 765 ASN cc_start: 0.4841 (OUTLIER) cc_final: 0.1617 (t0)
REVERT: B 976 MET cc_start: 0.5681 (tmm) cc_final: 0.4714 (tmm)
REVERT: B 986 GLU cc_start: 0.7119 (pp20) cc_final: 0.6805 (pp20)
outliers start: 64
outliers final: 39
residues processed: 258
average time/residue: 0.2687
time to fit residues: 103.4041
Evaluate side-chains
250 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 46
poor density : 204
time to evaluate : 1.623
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 306 ASP
Chi-restraints excluded: chain A residue 322 LEU
Chi-restraints excluded: chain A residue 503 HIS
Chi-restraints excluded: chain A residue 544 PHE
Chi-restraints excluded: chain A residue 583 VAL
Chi-restraints excluded: chain A residue 585 LEU
Chi-restraints excluded: chain A residue 592 LEU
Chi-restraints excluded: chain A residue 597 GLU
Chi-restraints excluded: chain A residue 626 GLU
Chi-restraints excluded: chain A residue 668 GLU
Chi-restraints excluded: chain A residue 671 CYS
Chi-restraints excluded: chain A residue 687 TYR
Chi-restraints excluded: chain A residue 712 PHE
Chi-restraints excluded: chain A residue 748 ASP
Chi-restraints excluded: chain A residue 845 LEU
Chi-restraints excluded: chain B residue 451 SER
Chi-restraints excluded: chain B residue 470 VAL
Chi-restraints excluded: chain B residue 497 LEU
Chi-restraints excluded: chain B residue 531 MET
Chi-restraints excluded: chain B residue 552 TYR
Chi-restraints excluded: chain B residue 578 MET
Chi-restraints excluded: chain B residue 602 SER
Chi-restraints excluded: chain B residue 656 SER
Chi-restraints excluded: chain B residue 660 LYS
Chi-restraints excluded: chain B residue 676 ILE
Chi-restraints excluded: chain B residue 689 VAL
Chi-restraints excluded: chain B residue 707 VAL
Chi-restraints excluded: chain B residue 749 LEU
Chi-restraints excluded: chain B residue 765 ASN
Chi-restraints excluded: chain B residue 786 HIS
Chi-restraints excluded: chain B residue 825 LEU
Chi-restraints excluded: chain B residue 891 THR
Chi-restraints excluded: chain E residue 52 ILE
Chi-restraints excluded: chain E residue 173 VAL
Chi-restraints excluded: chain E residue 193 ILE
Chi-restraints excluded: chain E residue 194 GLN
Chi-restraints excluded: chain E residue 228 THR
Chi-restraints excluded: chain F residue 67 PHE
Chi-restraints excluded: chain F residue 76 THR
Chi-restraints excluded: chain F residue 173 VAL
Chi-restraints excluded: chain F residue 191 ILE
Chi-restraints excluded: chain F residue 198 VAL
Chi-restraints excluded: chain F residue 208 LEU
Chi-restraints excluded: chain F residue 221 GLU
Chi-restraints excluded: chain F residue 226 THR
Chi-restraints excluded: chain F residue 235 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 168
random chunks:
chunk 54 optimal weight: 0.2980
chunk 146 optimal weight: 7.9990
chunk 32 optimal weight: 0.6980
chunk 95 optimal weight: 0.7980
chunk 40 optimal weight: 0.8980
chunk 162 optimal weight: 8.9990
chunk 134 optimal weight: 0.6980
chunk 75 optimal weight: 6.9990
chunk 13 optimal weight: 1.9990
chunk 53 optimal weight: 0.8980
chunk 85 optimal weight: 1.9990
overall best weight: 0.6780
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 503 HIS
B 979 HIS
** F 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Total number of N/Q/H flips: 2
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5901
moved from start: 0.3130
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.039 14382 Z= 0.186
Angle : 0.555 9.423 19350 Z= 0.297
Chirality : 0.040 0.217 2052
Planarity : 0.004 0.074 2480
Dihedral : 4.415 26.988 1858
Min Nonbonded Distance : 2.454
Molprobity Statistics.
All-atom Clashscore : 10.06
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 4.04 %
Favored : 95.96 %
Rotamer:
Outliers : 4.08 %
Allowed : 22.06 %
Favored : 73.87 %
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: -0.24 (0.20), residues: 1682
helix: 0.82 (0.17), residues: 963
sheet: -1.25 (0.47), residues: 102
loop : -1.49 (0.24), residues: 617
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.010 0.001 TRP F 72
HIS 0.011 0.001 HIS B 852
PHE 0.037 0.002 PHE B 712
TYR 0.044 0.002 TYR A 625
ARG 0.002 0.000 ARG A 480
*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
3364 Ramachandran restraints generated.
1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
3364 Ramachandran restraints generated.
1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
292 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 63
poor density : 229
time to evaluate : 1.874
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 306 ASP cc_start: 0.5270 (OUTLIER) cc_final: 0.4894 (t0)
REVERT: A 364 LYS cc_start: 0.7555 (tttt) cc_final: 0.6697 (ttmt)
REVERT: A 381 PHE cc_start: 0.7780 (t80) cc_final: 0.7457 (t80)
REVERT: A 389 GLU cc_start: 0.7011 (pp20) cc_final: 0.6763 (pp20)
REVERT: A 616 MET cc_start: 0.8439 (mmm) cc_final: 0.8190 (mmm)
REVERT: A 647 MET cc_start: 0.7088 (tpt) cc_final: 0.5472 (tpt)
REVERT: A 687 TYR cc_start: 0.7119 (OUTLIER) cc_final: 0.5604 (t80)
REVERT: A 941 ASP cc_start: 0.4768 (m-30) cc_final: 0.4452 (m-30)
REVERT: A 1001 MET cc_start: 0.5695 (mmm) cc_final: 0.5459 (mmm)
REVERT: B 331 LYS cc_start: 0.7701 (ptpt) cc_final: 0.7471 (pttp)
REVERT: B 552 TYR cc_start: 0.5830 (OUTLIER) cc_final: 0.5024 (t80)
REVERT: B 578 MET cc_start: 0.8242 (OUTLIER) cc_final: 0.7848 (ttp)
REVERT: B 711 GLN cc_start: 0.6721 (tm-30) cc_final: 0.6169 (tt0)
REVERT: B 763 LYS cc_start: 0.6645 (mptt) cc_final: 0.6241 (mptt)
REVERT: B 765 ASN cc_start: 0.4868 (OUTLIER) cc_final: 0.1853 (t0)
REVERT: B 976 MET cc_start: 0.5660 (tmm) cc_final: 0.4988 (tmm)
REVERT: B 986 GLU cc_start: 0.7167 (pp20) cc_final: 0.6809 (pp20)
outliers start: 63
outliers final: 44
residues processed: 271
average time/residue: 0.2629
time to fit residues: 106.8085
Evaluate side-chains
264 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 49
poor density : 215
time to evaluate : 1.655
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 306 ASP
Chi-restraints excluded: chain A residue 322 LEU
Chi-restraints excluded: chain A residue 503 HIS
Chi-restraints excluded: chain A residue 544 PHE
Chi-restraints excluded: chain A residue 583 VAL
Chi-restraints excluded: chain A residue 592 LEU
Chi-restraints excluded: chain A residue 597 GLU
Chi-restraints excluded: chain A residue 668 GLU
Chi-restraints excluded: chain A residue 671 CYS
Chi-restraints excluded: chain A residue 687 TYR
Chi-restraints excluded: chain A residue 748 ASP
Chi-restraints excluded: chain A residue 845 LEU
Chi-restraints excluded: chain A residue 957 SER
Chi-restraints excluded: chain A residue 958 TRP
Chi-restraints excluded: chain B residue 328 ILE
Chi-restraints excluded: chain B residue 367 CYS
Chi-restraints excluded: chain B residue 407 ILE
Chi-restraints excluded: chain B residue 451 SER
Chi-restraints excluded: chain B residue 470 VAL
Chi-restraints excluded: chain B residue 497 LEU
Chi-restraints excluded: chain B residue 552 TYR
Chi-restraints excluded: chain B residue 578 MET
Chi-restraints excluded: chain B residue 602 SER
Chi-restraints excluded: chain B residue 656 SER
Chi-restraints excluded: chain B residue 660 LYS
Chi-restraints excluded: chain B residue 676 ILE
Chi-restraints excluded: chain B residue 689 VAL
Chi-restraints excluded: chain B residue 707 VAL
Chi-restraints excluded: chain B residue 740 LEU
Chi-restraints excluded: chain B residue 749 LEU
Chi-restraints excluded: chain B residue 765 ASN
Chi-restraints excluded: chain B residue 786 HIS
Chi-restraints excluded: chain B residue 825 LEU
Chi-restraints excluded: chain B residue 891 THR
Chi-restraints excluded: chain E residue 29 THR
Chi-restraints excluded: chain E residue 31 SER
Chi-restraints excluded: chain E residue 173 VAL
Chi-restraints excluded: chain E residue 193 ILE
Chi-restraints excluded: chain E residue 194 GLN
Chi-restraints excluded: chain E residue 223 LEU
Chi-restraints excluded: chain F residue 67 PHE
Chi-restraints excluded: chain F residue 69 ASP
Chi-restraints excluded: chain F residue 173 VAL
Chi-restraints excluded: chain F residue 191 ILE
Chi-restraints excluded: chain F residue 198 VAL
Chi-restraints excluded: chain F residue 208 LEU
Chi-restraints excluded: chain F residue 221 GLU
Chi-restraints excluded: chain F residue 226 THR
Chi-restraints excluded: chain F residue 235 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 168
random chunks:
chunk 156 optimal weight: 3.9990
chunk 18 optimal weight: 0.9990
chunk 92 optimal weight: 5.9990
chunk 118 optimal weight: 0.8980
chunk 91 optimal weight: 0.8980
chunk 136 optimal weight: 0.5980
chunk 90 optimal weight: 0.9980
chunk 161 optimal weight: 6.9990
chunk 101 optimal weight: 2.9990
chunk 98 optimal weight: 0.6980
chunk 74 optimal weight: 0.8980
overall best weight: 0.7980
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 895 ASN
B 852 HIS
B 979 HIS
** F 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Total number of N/Q/H flips: 3
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5917
moved from start: 0.3366
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.039 14382 Z= 0.199
Angle : 0.571 9.153 19350 Z= 0.306
Chirality : 0.041 0.234 2052
Planarity : 0.004 0.074 2480
Dihedral : 4.402 26.963 1858
Min Nonbonded Distance : 2.442
Molprobity Statistics.
All-atom Clashscore : 10.78
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 4.34 %
Favored : 95.66 %
Rotamer:
Outliers : 4.66 %
Allowed : 22.12 %
Favored : 73.22 %
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: -0.25 (0.20), residues: 1682
helix: 0.82 (0.17), residues: 957
sheet: -1.60 (0.45), residues: 112
loop : -1.41 (0.24), residues: 613
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.011 0.001 TRP F 72
HIS 0.010 0.001 HIS B 852
PHE 0.049 0.002 PHE B 708
TYR 0.043 0.002 TYR A 625
ARG 0.004 0.000 ARG A 502
*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
3364 Ramachandran restraints generated.
1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
3364 Ramachandran restraints generated.
1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
290 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 72
poor density : 218
time to evaluate : 1.761
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 306 ASP cc_start: 0.5234 (OUTLIER) cc_final: 0.4961 (t0)
REVERT: A 364 LYS cc_start: 0.7590 (tttt) cc_final: 0.6734 (ttmt)
REVERT: A 381 PHE cc_start: 0.7841 (t80) cc_final: 0.7511 (t80)
REVERT: A 384 LEU cc_start: 0.7569 (tp) cc_final: 0.7307 (mm)
REVERT: A 389 GLU cc_start: 0.7063 (pp20) cc_final: 0.6817 (pp20)
REVERT: A 569 MET cc_start: 0.6343 (OUTLIER) cc_final: 0.4228 (mtt)
REVERT: A 616 MET cc_start: 0.8398 (mmm) cc_final: 0.8136 (mmm)
REVERT: A 647 MET cc_start: 0.7146 (tpt) cc_final: 0.5499 (tpt)
REVERT: A 687 TYR cc_start: 0.7117 (OUTLIER) cc_final: 0.5442 (t80)
REVERT: A 722 PHE cc_start: 0.6545 (t80) cc_final: 0.6288 (t80)
REVERT: A 1001 MET cc_start: 0.5667 (mmm) cc_final: 0.5453 (mmm)
REVERT: B 384 LEU cc_start: 0.7247 (OUTLIER) cc_final: 0.6976 (mm)
REVERT: B 578 MET cc_start: 0.8255 (OUTLIER) cc_final: 0.7837 (ttp)
REVERT: B 585 LEU cc_start: 0.7382 (OUTLIER) cc_final: 0.7152 (tp)
REVERT: B 711 GLN cc_start: 0.6753 (tm-30) cc_final: 0.6272 (tt0)
REVERT: B 713 ILE cc_start: 0.7062 (tp) cc_final: 0.6169 (tp)
REVERT: B 763 LYS cc_start: 0.6631 (mptt) cc_final: 0.6179 (mptt)
REVERT: B 765 ASN cc_start: 0.4839 (OUTLIER) cc_final: 0.1866 (t0)
REVERT: B 976 MET cc_start: 0.5795 (tmm) cc_final: 0.5098 (tmm)
REVERT: B 986 GLU cc_start: 0.7333 (pp20) cc_final: 0.7012 (pp20)
REVERT: E 236 GLU cc_start: 0.4373 (OUTLIER) cc_final: 0.3973 (mp0)
REVERT: F 176 ARG cc_start: 0.4580 (tmm160) cc_final: 0.4275 (tmm160)
REVERT: F 231 MET cc_start: 0.2239 (pmm) cc_final: 0.1743 (pmm)
outliers start: 72
outliers final: 51
residues processed: 267
average time/residue: 0.2611
time to fit residues: 104.5750
Evaluate side-chains
266 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 59
poor density : 207
time to evaluate : 1.510
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 306 ASP
Chi-restraints excluded: chain A residue 322 LEU
Chi-restraints excluded: chain A residue 346 VAL
Chi-restraints excluded: chain A residue 367 CYS
Chi-restraints excluded: chain A residue 544 PHE
Chi-restraints excluded: chain A residue 569 MET
Chi-restraints excluded: chain A residue 583 VAL
Chi-restraints excluded: chain A residue 585 LEU
Chi-restraints excluded: chain A residue 592 LEU
Chi-restraints excluded: chain A residue 597 GLU
Chi-restraints excluded: chain A residue 668 GLU
Chi-restraints excluded: chain A residue 671 CYS
Chi-restraints excluded: chain A residue 687 TYR
Chi-restraints excluded: chain A residue 712 PHE
Chi-restraints excluded: chain A residue 748 ASP
Chi-restraints excluded: chain A residue 845 LEU
Chi-restraints excluded: chain A residue 957 SER
Chi-restraints excluded: chain A residue 958 TRP
Chi-restraints excluded: chain B residue 328 ILE
Chi-restraints excluded: chain B residue 367 CYS
Chi-restraints excluded: chain B residue 384 LEU
Chi-restraints excluded: chain B residue 407 ILE
Chi-restraints excluded: chain B residue 451 SER
Chi-restraints excluded: chain B residue 470 VAL
Chi-restraints excluded: chain B residue 497 LEU
Chi-restraints excluded: chain B residue 575 SER
Chi-restraints excluded: chain B residue 578 MET
Chi-restraints excluded: chain B residue 585 LEU
Chi-restraints excluded: chain B residue 602 SER
Chi-restraints excluded: chain B residue 656 SER
Chi-restraints excluded: chain B residue 660 LYS
Chi-restraints excluded: chain B residue 676 ILE
Chi-restraints excluded: chain B residue 707 VAL
Chi-restraints excluded: chain B residue 710 THR
Chi-restraints excluded: chain B residue 740 LEU
Chi-restraints excluded: chain B residue 749 LEU
Chi-restraints excluded: chain B residue 765 ASN
Chi-restraints excluded: chain B residue 786 HIS
Chi-restraints excluded: chain B residue 825 LEU
Chi-restraints excluded: chain B residue 891 THR
Chi-restraints excluded: chain E residue 29 THR
Chi-restraints excluded: chain E residue 31 SER
Chi-restraints excluded: chain E residue 173 VAL
Chi-restraints excluded: chain E residue 193 ILE
Chi-restraints excluded: chain E residue 194 GLN
Chi-restraints excluded: chain E residue 223 LEU
Chi-restraints excluded: chain E residue 228 THR
Chi-restraints excluded: chain E residue 236 GLU
Chi-restraints excluded: chain F residue 67 PHE
Chi-restraints excluded: chain F residue 69 ASP
Chi-restraints excluded: chain F residue 76 THR
Chi-restraints excluded: chain F residue 173 VAL
Chi-restraints excluded: chain F residue 191 ILE
Chi-restraints excluded: chain F residue 193 ILE
Chi-restraints excluded: chain F residue 198 VAL
Chi-restraints excluded: chain F residue 208 LEU
Chi-restraints excluded: chain F residue 221 GLU
Chi-restraints excluded: chain F residue 226 THR
Chi-restraints excluded: chain F residue 235 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 168
random chunks:
chunk 100 optimal weight: 1.9990
chunk 64 optimal weight: 0.4980
chunk 96 optimal weight: 0.9990
chunk 48 optimal weight: 0.6980
chunk 31 optimal weight: 0.9980
chunk 102 optimal weight: 0.7980
chunk 110 optimal weight: 1.9990
chunk 80 optimal weight: 0.8980
chunk 15 optimal weight: 2.9990
chunk 127 optimal weight: 3.9990
chunk 147 optimal weight: 10.0000
overall best weight: 0.7780
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
B 852 HIS
B 979 HIS
** F 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Total number of N/Q/H flips: 2
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5917
moved from start: 0.3589
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.039 14382 Z= 0.198
Angle : 0.598 14.804 19350 Z= 0.316
Chirality : 0.042 0.382 2052
Planarity : 0.004 0.073 2480
Dihedral : 4.426 26.792 1858
Min Nonbonded Distance : 2.392
Molprobity Statistics.
All-atom Clashscore : 11.18
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 4.34 %
Favored : 95.66 %
Rotamer:
Outliers : 4.53 %
Allowed : 22.38 %
Favored : 73.09 %
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: -0.27 (0.20), residues: 1682
helix: 0.80 (0.17), residues: 954
sheet: -1.68 (0.46), residues: 108
loop : -1.39 (0.24), residues: 620
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.011 0.001 TRP F 72
HIS 0.011 0.001 HIS B 852
PHE 0.039 0.002 PHE B 708
TYR 0.047 0.002 TYR A 625
ARG 0.003 0.000 ARG B 627
*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
3364 Ramachandran restraints generated.
1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
3364 Ramachandran restraints generated.
1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
290 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 70
poor density : 220
time to evaluate : 1.631
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: A 306 ASP cc_start: 0.5077 (OUTLIER) cc_final: 0.4854 (t0)
REVERT: A 364 LYS cc_start: 0.7632 (tttt) cc_final: 0.6788 (ttmt)
REVERT: A 381 PHE cc_start: 0.7774 (t80) cc_final: 0.7486 (t80)
REVERT: A 384 LEU cc_start: 0.7619 (tp) cc_final: 0.7359 (mm)
REVERT: A 389 GLU cc_start: 0.7124 (pp20) cc_final: 0.6905 (pp20)
REVERT: A 569 MET cc_start: 0.6432 (OUTLIER) cc_final: 0.5107 (mmt)
REVERT: A 616 MET cc_start: 0.8390 (mmm) cc_final: 0.8124 (mmm)
REVERT: A 647 MET cc_start: 0.7167 (tpt) cc_final: 0.5535 (tpt)
REVERT: A 687 TYR cc_start: 0.7111 (OUTLIER) cc_final: 0.5581 (t80)
REVERT: A 722 PHE cc_start: 0.6545 (t80) cc_final: 0.6272 (t80)
REVERT: B 578 MET cc_start: 0.8271 (OUTLIER) cc_final: 0.7850 (ttp)
REVERT: B 585 LEU cc_start: 0.7401 (OUTLIER) cc_final: 0.7153 (tp)
REVERT: B 711 GLN cc_start: 0.6693 (tm-30) cc_final: 0.6187 (tt0)
REVERT: B 763 LYS cc_start: 0.6518 (mptt) cc_final: 0.6081 (mptt)
REVERT: B 765 ASN cc_start: 0.4836 (OUTLIER) cc_final: 0.1919 (t0)
REVERT: B 976 MET cc_start: 0.5625 (tmm) cc_final: 0.4816 (tmm)
REVERT: B 986 GLU cc_start: 0.7364 (pp20) cc_final: 0.7017 (pp20)
REVERT: F 176 ARG cc_start: 0.4513 (tmm160) cc_final: 0.4268 (tmm160)
REVERT: F 231 MET cc_start: 0.2235 (pmm) cc_final: 0.1730 (pmm)
outliers start: 70
outliers final: 48
residues processed: 266
average time/residue: 0.3004
time to fit residues: 119.7495
Evaluate side-chains
264 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 54
poor density : 210
time to evaluate : 1.752
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 306 ASP
Chi-restraints excluded: chain A residue 316 ILE
Chi-restraints excluded: chain A residue 322 LEU
Chi-restraints excluded: chain A residue 367 CYS
Chi-restraints excluded: chain A residue 544 PHE
Chi-restraints excluded: chain A residue 552 TYR
Chi-restraints excluded: chain A residue 569 MET
Chi-restraints excluded: chain A residue 583 VAL
Chi-restraints excluded: chain A residue 585 LEU
Chi-restraints excluded: chain A residue 592 LEU
Chi-restraints excluded: chain A residue 597 GLU
Chi-restraints excluded: chain A residue 668 GLU
Chi-restraints excluded: chain A residue 671 CYS
Chi-restraints excluded: chain A residue 687 TYR
Chi-restraints excluded: chain A residue 712 PHE
Chi-restraints excluded: chain A residue 748 ASP
Chi-restraints excluded: chain A residue 845 LEU
Chi-restraints excluded: chain A residue 958 TRP
Chi-restraints excluded: chain B residue 328 ILE
Chi-restraints excluded: chain B residue 367 CYS
Chi-restraints excluded: chain B residue 407 ILE
Chi-restraints excluded: chain B residue 451 SER
Chi-restraints excluded: chain B residue 470 VAL
Chi-restraints excluded: chain B residue 497 LEU
Chi-restraints excluded: chain B residue 575 SER
Chi-restraints excluded: chain B residue 578 MET
Chi-restraints excluded: chain B residue 585 LEU
Chi-restraints excluded: chain B residue 602 SER
Chi-restraints excluded: chain B residue 656 SER
Chi-restraints excluded: chain B residue 660 LYS
Chi-restraints excluded: chain B residue 707 VAL
Chi-restraints excluded: chain B residue 740 LEU
Chi-restraints excluded: chain B residue 765 ASN
Chi-restraints excluded: chain B residue 786 HIS
Chi-restraints excluded: chain B residue 825 LEU
Chi-restraints excluded: chain B residue 891 THR
Chi-restraints excluded: chain E residue 29 THR
Chi-restraints excluded: chain E residue 63 VAL
Chi-restraints excluded: chain E residue 173 VAL
Chi-restraints excluded: chain E residue 193 ILE
Chi-restraints excluded: chain E residue 194 GLN
Chi-restraints excluded: chain E residue 223 LEU
Chi-restraints excluded: chain E residue 228 THR
Chi-restraints excluded: chain F residue 67 PHE
Chi-restraints excluded: chain F residue 69 ASP
Chi-restraints excluded: chain F residue 76 THR
Chi-restraints excluded: chain F residue 173 VAL
Chi-restraints excluded: chain F residue 191 ILE
Chi-restraints excluded: chain F residue 193 ILE
Chi-restraints excluded: chain F residue 198 VAL
Chi-restraints excluded: chain F residue 208 LEU
Chi-restraints excluded: chain F residue 221 GLU
Chi-restraints excluded: chain F residue 226 THR
Chi-restraints excluded: chain F residue 235 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 168
random chunks:
chunk 155 optimal weight: 0.6980
chunk 141 optimal weight: 0.0980
chunk 150 optimal weight: 1.9990
chunk 90 optimal weight: 2.9990
chunk 65 optimal weight: 1.9990
chunk 118 optimal weight: 5.9990
chunk 46 optimal weight: 0.5980
chunk 136 optimal weight: 0.7980
chunk 142 optimal weight: 1.9990
chunk 99 optimal weight: 0.5980
chunk 159 optimal weight: 0.0670
overall best weight: 0.4118
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** B 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 852 HIS
B 979 HIS
F 34 GLN
Total number of N/Q/H flips: 3
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5855
moved from start: 0.3759
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.038 14382 Z= 0.171
Angle : 0.594 12.899 19350 Z= 0.313
Chirality : 0.041 0.274 2052
Planarity : 0.004 0.072 2480
Dihedral : 4.377 27.272 1858
Min Nonbonded Distance : 2.439
Molprobity Statistics.
All-atom Clashscore : 10.68
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 4.10 %
Favored : 95.90 %
Rotamer:
Outliers : 3.30 %
Allowed : 23.87 %
Favored : 72.83 %
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: -0.17 (0.20), residues: 1682
helix: 0.88 (0.17), residues: 946
sheet: -1.45 (0.45), residues: 118
loop : -1.35 (0.24), residues: 618
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.011 0.001 TRP B 601
HIS 0.012 0.001 HIS B 852
PHE 0.035 0.001 PHE A 646
TYR 0.040 0.002 TYR B 552
ARG 0.004 0.000 ARG A 359
*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
3364 Ramachandran restraints generated.
1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
3364 Ramachandran restraints generated.
1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
274 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 51
poor density : 223
time to evaluate : 1.728
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 364 LYS cc_start: 0.7548 (tttt) cc_final: 0.6639 (ttmt)
REVERT: A 381 PHE cc_start: 0.7767 (t80) cc_final: 0.7443 (t80)
REVERT: A 384 LEU cc_start: 0.7595 (tp) cc_final: 0.7327 (mm)
REVERT: A 569 MET cc_start: 0.6017 (mpp) cc_final: 0.5022 (mpp)
REVERT: A 616 MET cc_start: 0.8422 (mmm) cc_final: 0.8186 (mmm)
REVERT: A 647 MET cc_start: 0.7075 (tpt) cc_final: 0.5261 (tpt)
REVERT: A 687 TYR cc_start: 0.7141 (OUTLIER) cc_final: 0.5665 (t80)
REVERT: B 390 LYS cc_start: 0.6249 (ttpt) cc_final: 0.5861 (pttt)
REVERT: B 763 LYS cc_start: 0.6491 (mptt) cc_final: 0.6134 (mptt)
REVERT: B 976 MET cc_start: 0.5756 (tmm) cc_final: 0.4982 (tmm)
REVERT: B 986 GLU cc_start: 0.7339 (pp20) cc_final: 0.6992 (pp20)
outliers start: 51
outliers final: 40
residues processed: 257
average time/residue: 0.2712
time to fit residues: 103.1176
Evaluate side-chains
245 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 41
poor density : 204
time to evaluate : 1.773
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 316 ILE
Chi-restraints excluded: chain A residue 322 LEU
Chi-restraints excluded: chain A residue 346 VAL
Chi-restraints excluded: chain A residue 367 CYS
Chi-restraints excluded: chain A residue 583 VAL
Chi-restraints excluded: chain A residue 585 LEU
Chi-restraints excluded: chain A residue 592 LEU
Chi-restraints excluded: chain A residue 597 GLU
Chi-restraints excluded: chain A residue 668 GLU
Chi-restraints excluded: chain A residue 671 CYS
Chi-restraints excluded: chain A residue 673 ILE
Chi-restraints excluded: chain A residue 687 TYR
Chi-restraints excluded: chain A residue 748 ASP
Chi-restraints excluded: chain A residue 845 LEU
Chi-restraints excluded: chain A residue 957 SER
Chi-restraints excluded: chain B residue 328 ILE
Chi-restraints excluded: chain B residue 407 ILE
Chi-restraints excluded: chain B residue 451 SER
Chi-restraints excluded: chain B residue 470 VAL
Chi-restraints excluded: chain B residue 497 LEU
Chi-restraints excluded: chain B residue 656 SER
Chi-restraints excluded: chain B residue 707 VAL
Chi-restraints excluded: chain B residue 713 ILE
Chi-restraints excluded: chain B residue 765 ASN
Chi-restraints excluded: chain B residue 786 HIS
Chi-restraints excluded: chain B residue 825 LEU
Chi-restraints excluded: chain B residue 891 THR
Chi-restraints excluded: chain E residue 173 VAL
Chi-restraints excluded: chain E residue 193 ILE
Chi-restraints excluded: chain E residue 194 GLN
Chi-restraints excluded: chain E residue 223 LEU
Chi-restraints excluded: chain F residue 67 PHE
Chi-restraints excluded: chain F residue 76 THR
Chi-restraints excluded: chain F residue 173 VAL
Chi-restraints excluded: chain F residue 191 ILE
Chi-restraints excluded: chain F residue 193 ILE
Chi-restraints excluded: chain F residue 198 VAL
Chi-restraints excluded: chain F residue 208 LEU
Chi-restraints excluded: chain F residue 221 GLU
Chi-restraints excluded: chain F residue 226 THR
Chi-restraints excluded: chain F residue 235 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 168
random chunks:
chunk 97 optimal weight: 4.9990
chunk 75 optimal weight: 0.7980
chunk 110 optimal weight: 0.6980
chunk 167 optimal weight: 5.9990
chunk 154 optimal weight: 7.9990
chunk 133 optimal weight: 3.9990
chunk 13 optimal weight: 3.9990
chunk 102 optimal weight: 0.0870
chunk 81 optimal weight: 0.5980
chunk 105 optimal weight: 1.9990
chunk 141 optimal weight: 2.9990
overall best weight: 0.8360
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** A 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 895 ASN
B 852 HIS
B 979 HIS
Total number of N/Q/H flips: 3
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5913
moved from start: 0.3899
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.045 14382 Z= 0.211
Angle : 0.631 13.531 19350 Z= 0.331
Chirality : 0.042 0.344 2052
Planarity : 0.004 0.073 2480
Dihedral : 4.427 27.075 1858
Min Nonbonded Distance : 2.452
Molprobity Statistics.
All-atom Clashscore : 10.93
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 4.34 %
Favored : 95.66 %
Rotamer:
Outliers : 3.49 %
Allowed : 24.39 %
Favored : 72.12 %
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: -0.26 (0.20), residues: 1682
helix: 0.80 (0.17), residues: 952
sheet: -1.42 (0.45), residues: 118
loop : -1.41 (0.24), residues: 612
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.012 0.002 TRP F 72
HIS 0.012 0.001 HIS B 852
PHE 0.035 0.002 PHE B 708
TYR 0.048 0.002 TYR A 611
ARG 0.009 0.001 ARG F 176
********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
3364 Ramachandran restraints generated.
1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
3364 Ramachandran restraints generated.
1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
260 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 54
poor density : 206
time to evaluate : 1.468
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 364 LYS cc_start: 0.7547 (tttt) cc_final: 0.6636 (ttmt)
REVERT: A 381 PHE cc_start: 0.7782 (t80) cc_final: 0.7454 (t80)
REVERT: A 384 LEU cc_start: 0.7578 (tp) cc_final: 0.7341 (mm)
REVERT: A 569 MET cc_start: 0.6004 (OUTLIER) cc_final: 0.4969 (mpp)
REVERT: A 616 MET cc_start: 0.8395 (mmm) cc_final: 0.8189 (mmm)
REVERT: A 647 MET cc_start: 0.7144 (tpt) cc_final: 0.5276 (tpt)
REVERT: A 687 TYR cc_start: 0.7132 (OUTLIER) cc_final: 0.5567 (t80)
REVERT: B 763 LYS cc_start: 0.6518 (mptt) cc_final: 0.6084 (mptt)
REVERT: B 765 ASN cc_start: 0.4799 (OUTLIER) cc_final: 0.1937 (t0)
REVERT: B 976 MET cc_start: 0.5858 (tmm) cc_final: 0.5168 (tmm)
REVERT: B 986 GLU cc_start: 0.7348 (pp20) cc_final: 0.7007 (pp20)
REVERT: E 75 MET cc_start: 0.3447 (ppp) cc_final: 0.2982 (ppp)
outliers start: 54
outliers final: 41
residues processed: 242
average time/residue: 0.2663
time to fit residues: 96.9481
Evaluate side-chains
244 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 44
poor density : 200
time to evaluate : 1.638
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 316 ILE
Chi-restraints excluded: chain A residue 322 LEU
Chi-restraints excluded: chain A residue 346 VAL
Chi-restraints excluded: chain A residue 367 CYS
Chi-restraints excluded: chain A residue 569 MET
Chi-restraints excluded: chain A residue 583 VAL
Chi-restraints excluded: chain A residue 585 LEU
Chi-restraints excluded: chain A residue 597 GLU
Chi-restraints excluded: chain A residue 668 GLU
Chi-restraints excluded: chain A residue 671 CYS
Chi-restraints excluded: chain A residue 687 TYR
Chi-restraints excluded: chain A residue 748 ASP
Chi-restraints excluded: chain A residue 845 LEU
Chi-restraints excluded: chain A residue 874 ILE
Chi-restraints excluded: chain A residue 930 MET
Chi-restraints excluded: chain A residue 957 SER
Chi-restraints excluded: chain B residue 328 ILE
Chi-restraints excluded: chain B residue 367 CYS
Chi-restraints excluded: chain B residue 407 ILE
Chi-restraints excluded: chain B residue 451 SER
Chi-restraints excluded: chain B residue 470 VAL
Chi-restraints excluded: chain B residue 497 LEU
Chi-restraints excluded: chain B residue 543 GLU
Chi-restraints excluded: chain B residue 656 SER
Chi-restraints excluded: chain B residue 707 VAL
Chi-restraints excluded: chain B residue 740 LEU
Chi-restraints excluded: chain B residue 765 ASN
Chi-restraints excluded: chain B residue 786 HIS
Chi-restraints excluded: chain B residue 825 LEU
Chi-restraints excluded: chain B residue 891 THR
Chi-restraints excluded: chain E residue 173 VAL
Chi-restraints excluded: chain E residue 193 ILE
Chi-restraints excluded: chain E residue 194 GLN
Chi-restraints excluded: chain E residue 223 LEU
Chi-restraints excluded: chain F residue 67 PHE
Chi-restraints excluded: chain F residue 76 THR
Chi-restraints excluded: chain F residue 173 VAL
Chi-restraints excluded: chain F residue 191 ILE
Chi-restraints excluded: chain F residue 193 ILE
Chi-restraints excluded: chain F residue 198 VAL
Chi-restraints excluded: chain F residue 208 LEU
Chi-restraints excluded: chain F residue 221 GLU
Chi-restraints excluded: chain F residue 226 THR
Chi-restraints excluded: chain F residue 235 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 168
random chunks:
chunk 40 optimal weight: 0.7980
chunk 122 optimal weight: 0.0060
chunk 19 optimal weight: 1.9990
chunk 37 optimal weight: 2.9990
chunk 133 optimal weight: 0.9980
chunk 55 optimal weight: 6.9990
chunk 137 optimal weight: 2.9990
chunk 16 optimal weight: 8.9990
chunk 24 optimal weight: 0.8980
chunk 117 optimal weight: 1.9990
chunk 7 optimal weight: 0.9980
overall best weight: 0.7396
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 654 ASN
A 895 ASN
A 973 ASN
B 852 HIS
B 979 HIS
F 34 GLN
Total number of N/Q/H flips: 6
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4772 r_free = 0.4772 target = 0.247742 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.4461 r_free = 0.4461 target = 0.214545 restraints weight = 17197.254|
|-----------------------------------------------------------------------------|
r_work (start): 0.4475 rms_B_bonded: 2.18
r_work: 0.4338 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.4338
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5968
moved from start: 0.4011
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.041 14382 Z= 0.200
Angle : 0.622 13.187 19350 Z= 0.327
Chirality : 0.042 0.322 2052
Planarity : 0.004 0.073 2480
Dihedral : 4.431 26.955 1858
Min Nonbonded Distance : 2.468
Molprobity Statistics.
All-atom Clashscore : 11.00
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 4.52 %
Favored : 95.48 %
Rotamer:
Outliers : 3.49 %
Allowed : 24.51 %
Favored : 71.99 %
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: -0.35 (0.20), residues: 1682
helix: 0.75 (0.17), residues: 960
sheet: -1.42 (0.44), residues: 112
loop : -1.53 (0.24), residues: 610
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.013 0.001 TRP B 601
HIS 0.012 0.001 HIS B 852
PHE 0.034 0.002 PHE B 708
TYR 0.055 0.002 TYR A 552
ARG 0.005 0.000 ARG A 480
Origin is already at (0, 0, 0), no shifts will be applied
===============================================================================
Job complete
usr+sys time: 3075.67 seconds
wall clock time: 58 minutes 17.12 seconds (3497.12 seconds total)