Starting phenix.real_space_refine
on Tue Jan 21 22:33:05 2025 by dcliebschner
===============================================================================
Processing files:
-------------------------------------------------------------------------------
Found model, /net/cci-nas-00/data/ceres_data/9avg_43901/01_2025/9avg_43901.cif
Found real_map, /net/cci-nas-00/data/ceres_data/9avg_43901/01_2025/9avg_43901.map
Processing PHIL parameters:
-------------------------------------------------------------------------------
Adding command-line PHIL:
-------------------------
refinement.macro_cycles=10
scattering_table=electron
resolution=3.6
write_initial_geo_file=False
Final processed PHIL parameters:
-------------------------------------------------------------------------------
data_manager {
real_map_files = "/net/cci-nas-00/data/ceres_data/9avg_43901/01_2025/9avg_43901.map"
default_real_map = "/net/cci-nas-00/data/ceres_data/9avg_43901/01_2025/9avg_43901.map"
model {
file = "/net/cci-nas-00/data/ceres_data/9avg_43901/01_2025/9avg_43901.cif"
}
default_model = "/net/cci-nas-00/data/ceres_data/9avg_43901/01_2025/9avg_43901.cif"
}
resolution = 3.6
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= 0.040
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: 7
Type Number sf(0) Gaussians
Ca 6 9.91 5
P 3 5.49 5
S 93 5.16 5
Cl 2 4.86 5
C 11311 2.51 5
N 2883 2.21 5
O 3200 1.98 5
sf(0) = scattering factor at diffraction angle 0.
Process input model
Symmetric amino acids flipped. Time to flip 18 residue(s): 0.05s
Monomer Library directory:
"/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
Total number of atoms: 17498
Number of models: 1
Model: ""
Number of chains: 13
Chain: "Q"
Number of atoms: 6280
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 797, 6280
Classifications: {'peptide': 797}
Incomplete info: {'truncation_to_alanine': 15}
Link IDs: {'CIS': 1, 'PTRANS': 31, 'TRANS': 764}
Chain breaks: 3
Unresolved non-hydrogen bonds: 58
Unresolved non-hydrogen angles: 71
Unresolved non-hydrogen dihedrals: 45
Planarities with less than four sites: {'GLU:plan': 8, 'ARG:plan': 1, 'ASP:plan': 4}
Unresolved non-hydrogen planarities: 49
Chain: "R"
Number of atoms: 6294
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 796, 6294
Classifications: {'peptide': 796}
Incomplete info: {'truncation_to_alanine': 10}
Link IDs: {'CIS': 1, 'PTRANS': 31, 'TRANS': 763}
Chain breaks: 3
Unresolved non-hydrogen bonds: 46
Unresolved non-hydrogen angles: 60
Unresolved non-hydrogen dihedrals: 39
Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 1, 'TRP:plan': 1, 'ASP:plan': 3}
Unresolved non-hydrogen planarities: 43
Chain: "A"
Number of atoms: 1738
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 223, 1738
Classifications: {'peptide': 223}
Modifications used: {'COO': 1}
Incomplete info: {'truncation_to_alanine': 30}
Link IDs: {'PTRANS': 6, 'TRANS': 216}
Chain breaks: 2
Unresolved non-hydrogen bonds: 109
Unresolved non-hydrogen angles: 131
Unresolved non-hydrogen dihedrals: 87
Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 4, 'ASN:plan1': 3, 'ASP:plan': 8}
Unresolved non-hydrogen planarities: 81
Chain: "B"
Number of atoms: 2450
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 337, 2450
Classifications: {'peptide': 337}
Modifications used: {'COO': 1}
Incomplete info: {'truncation_to_alanine': 41}
Link IDs: {'PTRANS': 5, 'TRANS': 331}
Unresolved non-hydrogen bonds: 142
Unresolved non-hydrogen angles: 168
Unresolved non-hydrogen dihedrals: 116
Unresolved non-hydrogen chiralities: 2
Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ARG:plan': 6, 'ASN:plan1': 1, 'ASP:plan': 10}
Unresolved non-hydrogen planarities: 91
Chain: "G"
Number of atoms: 378
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 55, 378
Classifications: {'peptide': 55}
Incomplete info: {'truncation_to_alanine': 13}
Link IDs: {'PTRANS': 4, 'TRANS': 50}
Unresolved non-hydrogen bonds: 46
Unresolved non-hydrogen angles: 52
Unresolved non-hydrogen dihedrals: 40
Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 3}
Unresolved non-hydrogen planarities: 22
Chain: "C"
Number of atoms: 28
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 2, 28
Unusual residues: {'NAG': 2}
Classifications: {'undetermined': 2}
Link IDs: {None: 1}
Unresolved non-hydrogen bonds: 2
Unresolved non-hydrogen angles: 4
Unresolved non-hydrogen dihedrals: 6
Unresolved non-hydrogen chiralities: 2
Chain: "D"
Number of atoms: 28
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 2, 28
Unusual residues: {'NAG': 2}
Classifications: {'undetermined': 2}
Link IDs: {None: 1}
Unresolved non-hydrogen bonds: 2
Unresolved non-hydrogen angles: 4
Unresolved non-hydrogen dihedrals: 6
Unresolved non-hydrogen chiralities: 2
Chain: "E"
Number of atoms: 28
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 2, 28
Unusual residues: {'NAG': 2}
Classifications: {'undetermined': 2}
Link IDs: {None: 1}
Unresolved non-hydrogen bonds: 2
Unresolved non-hydrogen angles: 4
Unresolved non-hydrogen dihedrals: 6
Unresolved non-hydrogen chiralities: 2
Chain: "F"
Number of atoms: 28
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 2, 28
Unusual residues: {'NAG': 2}
Classifications: {'undetermined': 2}
Link IDs: {None: 1}
Unresolved non-hydrogen bonds: 2
Unresolved non-hydrogen angles: 4
Unresolved non-hydrogen dihedrals: 6
Unresolved non-hydrogen chiralities: 2
Chain: "Q"
Number of atoms: 58
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 4, 58
Unusual residues: {'NAG': 3, 'TCR': 1}
Classifications: {'undetermined': 4}
Link IDs: {None: 3}
Unresolved non-hydrogen bonds: 3
Unresolved non-hydrogen angles: 6
Unresolved non-hydrogen dihedrals: 9
Unresolved non-hydrogen chiralities: 3
Chain: "Q"
Number of atoms: 64
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 6, 64
Unusual residues: {' CA': 3, '9IG': 1, 'PO4': 1, 'Y01': 1}
Classifications: {'undetermined': 6}
Link IDs: {None: 5}
Chain: "R"
Number of atoms: 44
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 3, 44
Unusual residues: {'NAG': 2, 'TCR': 1}
Classifications: {'undetermined': 3}
Link IDs: {None: 2}
Unresolved non-hydrogen bonds: 2
Unresolved non-hydrogen angles: 4
Unresolved non-hydrogen dihedrals: 6
Unresolved non-hydrogen chiralities: 2
Chain: "R"
Number of atoms: 80
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 6, 80
Unusual residues: {' CA': 3, '9IG': 1, 'A1AF7': 1, 'PO4': 1}
Classifications: {'undetermined': 6}
Link IDs: {None: 5}
Time building chain proxies: 10.06, per 1000 atoms: 0.57
Number of scatterers: 17498
At special positions: 0
Unit cell: (117.15, 97.35, 237.6, 90, 90, 90)
Space group: P 1 (No. 1)
Number of sites at special positions: 0
Number of scattering types: 7
Type Number sf(0)
Ca 6 19.99
Cl 2 17.00
S 93 16.00
P 3 15.00
O 3200 8.00
N 2883 7.00
C 11311 6.00
sf(0) = scattering factor at diffraction angle 0.
Number of disulfides: simple=16, symmetry=0
Simple disulfide: pdb=" SG CYS Q 60 " - pdb=" SG CYS Q 101 " distance=2.03
Simple disulfide: pdb=" SG CYS Q 236 " - pdb=" SG CYS Q 561 " distance=2.03
Simple disulfide: pdb=" SG CYS Q 358 " - pdb=" SG CYS Q 395 " distance=2.03
Simple disulfide: pdb=" SG CYS Q 437 " - pdb=" SG CYS Q 449 " distance=2.03
Simple disulfide: pdb=" SG CYS Q 542 " - pdb=" SG CYS Q 562 " distance=2.03
Simple disulfide: pdb=" SG CYS Q 546 " - pdb=" SG CYS Q 565 " distance=2.03
Simple disulfide: pdb=" SG CYS Q 677 " - pdb=" SG CYS Q 765 " distance=2.03
Simple disulfide: pdb=" SG CYS R 60 " - pdb=" SG CYS R 101 " distance=2.03
Simple disulfide: pdb=" SG CYS R 236 " - pdb=" SG CYS R 561 " distance=2.03
Simple disulfide: pdb=" SG CYS R 358 " - pdb=" SG CYS R 395 " distance=2.03
Simple disulfide: pdb=" SG CYS R 437 " - pdb=" SG CYS R 449 " distance=2.03
Simple disulfide: pdb=" SG CYS R 542 " - pdb=" SG CYS R 562 " distance=2.03
Simple disulfide: pdb=" SG CYS R 546 " - pdb=" SG CYS R 565 " distance=2.03
Simple disulfide: pdb=" SG CYS R 568 " - pdb=" SG CYS R 582 " distance=2.03
Simple disulfide: pdb=" SG CYS R 585 " - pdb=" SG CYS R 598 " distance=2.03
Simple disulfide: pdb=" SG CYS R 677 " - pdb=" SG CYS R 765 " distance=2.03
Automatic linking
Parameters for automatic linking
Linking & cutoffs
Metal : Auto - 3.00
Amino acid : True - 1.90
Carbohydrate : True - 1.99
Ligands : True - 1.99
Small molecules : False - 1.98
Amino acid - RNA/DNA : False
Number of custom bonds: simple=0, symmetry=0
Links applied
BETA1-4
" NAG C 1 " - " NAG C 2 "
" NAG D 1 " - " NAG D 2 "
" NAG E 1 " - " NAG E 2 "
" NAG F 1 " - " NAG F 2 "
NAG-ASN
" NAG C 1 " - " ASN Q 488 "
" NAG D 1 " - " ASN Q 541 "
" NAG E 1 " - " ASN R 488 "
" NAG F 1 " - " ASN R 541 "
" NAG Q1001 " - " ASN Q 261 "
" NAG Q1002 " - " ASN Q 287 "
" NAG Q1003 " - " ASN Q 468 "
" NAG R1001 " - " ASN R 287 "
" NAG R1002 " - " ASN R 468 "
Time building additional restraints: 4.69
Conformation dependent library (CDL) restraints added in 2.2 seconds
4364 Ramachandran restraints generated.
2182 Oldfield, 0 Emsley, 2182 emsley8k and 0 Phi/Psi/2.
Adding C-beta torsion restraints...
Number of C-beta restraints generated: 4164
Finding SS restraints...
Secondary structure from input PDB file:
75 helices and 24 sheets defined
45.4% alpha, 15.1% beta
0 base pairs and 0 stacking pairs defined.
Time for finding SS restraints: 2.56
Creating SS restraints...
Processing helix chain 'Q' and resid 64 through 83
Processing helix chain 'Q' and resid 103 through 113
Processing helix chain 'Q' and resid 115 through 123
Processing helix chain 'Q' and resid 146 through 158
Processing helix chain 'Q' and resid 171 through 176
removed outlier: 3.609A pdb=" N LEU Q 174 " --> pdb=" O SER Q 171 " (cutoff:3.500A)
Processing helix chain 'Q' and resid 190 through 204
Processing helix chain 'Q' and resid 218 through 233
removed outlier: 3.551A pdb=" N GLY Q 222 " --> pdb=" O TYR Q 218 " (cutoff:3.500A)
Processing helix chain 'Q' and resid 248 through 261
Processing helix chain 'Q' and resid 272 through 287
Proline residue: Q 278 - end of helix
Processing helix chain 'Q' and resid 307 through 309
No H-bonds generated for 'chain 'Q' and resid 307 through 309'
Processing helix chain 'Q' and resid 310 through 315
Processing helix chain 'Q' and resid 329 through 336
Processing helix chain 'Q' and resid 347 through 357
Processing helix chain 'Q' and resid 415 through 436
Processing helix chain 'Q' and resid 438 through 442
removed outlier: 3.866A pdb=" N GLY Q 442 " --> pdb=" O PRO Q 439 " (cutoff:3.500A)
Processing helix chain 'Q' and resid 444 through 448
Processing helix chain 'Q' and resid 456 through 466
Processing helix chain 'Q' and resid 525 through 528
Processing helix chain 'Q' and resid 529 through 533
Processing helix chain 'Q' and resid 610 through 637
Processing helix chain 'Q' and resid 640 through 646
removed outlier: 3.755A pdb=" N THR Q 646 " --> pdb=" O ILE Q 642 " (cutoff:3.500A)
Processing helix chain 'Q' and resid 647 through 665
removed outlier: 3.729A pdb=" N SER Q 665 " --> pdb=" O CYS Q 661 " (cutoff:3.500A)
Processing helix chain 'Q' and resid 666 through 669
Processing helix chain 'Q' and resid 673 through 699
removed outlier: 4.976A pdb=" N GLN Q 681 " --> pdb=" O CYS Q 677 " (cutoff:3.500A)
Proline residue: Q 682 - end of helix
Processing helix chain 'Q' and resid 702 through 708
Processing helix chain 'Q' and resid 723 through 746
removed outlier: 4.092A pdb=" N GLN Q 735 " --> pdb=" O CYS Q 731 " (cutoff:3.500A)
Processing helix chain 'Q' and resid 769 through 793
removed outlier: 3.721A pdb=" N LYS Q 793 " --> pdb=" O PHE Q 789 " (cutoff:3.500A)
Processing helix chain 'Q' and resid 802 through 820
Processing helix chain 'Q' and resid 820 through 827
removed outlier: 3.690A pdb=" N ALA Q 824 " --> pdb=" O SER Q 820 " (cutoff:3.500A)
Processing helix chain 'Q' and resid 831 through 862
removed outlier: 4.093A pdb=" N ALA Q 835 " --> pdb=" O LYS Q 831 " (cutoff:3.500A)
removed outlier: 7.002A pdb=" N ASN Q 855 " --> pdb=" O CYS Q 851 " (cutoff:3.500A)
removed outlier: 5.401A pdb=" N LYS Q 856 " --> pdb=" O ILE Q 852 " (cutoff:3.500A)
Processing helix chain 'Q' and resid 863 through 867
removed outlier: 3.663A pdb=" N ARG Q 866 " --> pdb=" O LYS Q 863 " (cutoff:3.500A)
Processing helix chain 'R' and resid 64 through 84
Processing helix chain 'R' and resid 103 through 115
Processing helix chain 'R' and resid 115 through 122
Processing helix chain 'R' and resid 146 through 158
removed outlier: 3.641A pdb=" N LEU R 156 " --> pdb=" O ALA R 152 " (cutoff:3.500A)
Processing helix chain 'R' and resid 171 through 176
Processing helix chain 'R' and resid 190 through 204
Processing helix chain 'R' and resid 218 through 233
removed outlier: 3.503A pdb=" N GLY R 222 " --> pdb=" O TYR R 218 " (cutoff:3.500A)
Processing helix chain 'R' and resid 248 through 261
Processing helix chain 'R' and resid 272 through 286
Proline residue: R 278 - end of helix
Processing helix chain 'R' and resid 296 through 301
removed outlier: 4.413A pdb=" N SER R 301 " --> pdb=" O GLU R 297 " (cutoff:3.500A)
Processing helix chain 'R' and resid 307 through 309
No H-bonds generated for 'chain 'R' and resid 307 through 309'
Processing helix chain 'R' and resid 310 through 315
Processing helix chain 'R' and resid 329 through 336
Processing helix chain 'R' and resid 347 through 357
Processing helix chain 'R' and resid 400 through 404
Processing helix chain 'R' and resid 415 through 436
Processing helix chain 'R' and resid 444 through 448
Processing helix chain 'R' and resid 451 through 455
removed outlier: 3.843A pdb=" N VAL R 455 " --> pdb=" O ILE R 452 " (cutoff:3.500A)
Processing helix chain 'R' and resid 456 through 465
Processing helix chain 'R' and resid 525 through 528
Processing helix chain 'R' and resid 529 through 533
Processing helix chain 'R' and resid 610 through 637
Processing helix chain 'R' and resid 640 through 645
Processing helix chain 'R' and resid 647 through 665
removed outlier: 3.630A pdb=" N SER R 665 " --> pdb=" O CYS R 661 " (cutoff:3.500A)
Processing helix chain 'R' and resid 666 through 669
Processing helix chain 'R' and resid 673 through 708
removed outlier: 4.752A pdb=" N GLN R 681 " --> pdb=" O CYS R 677 " (cutoff:3.500A)
Proline residue: R 682 - end of helix
Processing helix chain 'R' and resid 719 through 746
Processing helix chain 'R' and resid 770 through 794
removed outlier: 3.632A pdb=" N THR R 780 " --> pdb=" O LEU R 776 " (cutoff:3.500A)
removed outlier: 3.694A pdb=" N ALA R 785 " --> pdb=" O CYS R 781 " (cutoff:3.500A)
Processing helix chain 'R' and resid 798 through 802
Processing helix chain 'R' and resid 803 through 821
Processing helix chain 'R' and resid 821 through 827
removed outlier: 3.771A pdb=" N SER R 827 " --> pdb=" O PRO R 823 " (cutoff:3.500A)
Processing helix chain 'R' and resid 830 through 861
removed outlier: 3.970A pdb=" N SER R 834 " --> pdb=" O GLY R 830 " (cutoff:3.500A)
removed outlier: 5.020A pdb=" N ASN R 855 " --> pdb=" O CYS R 851 " (cutoff:3.500A)
removed outlier: 5.281A pdb=" N LYS R 856 " --> pdb=" O ILE R 852 " (cutoff:3.500A)
Processing helix chain 'A' and resid 7 through 31
removed outlier: 3.739A pdb=" N VAL A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A)
Processing helix chain 'A' and resid 45 through 56
removed outlier: 4.163A pdb=" N ILE A 49 " --> pdb=" O GLY A 45 " (cutoff:3.500A)
removed outlier: 3.541A pdb=" N LEU A 56 " --> pdb=" O GLN A 52 " (cutoff:3.500A)
Processing helix chain 'A' and resid 114 through 130
removed outlier: 3.715A pdb=" N GLN A 119 " --> pdb=" O TYR A 115 " (cutoff:3.500A)
removed outlier: 4.050A pdb=" N GLU A 120 " --> pdb=" O ASN A 116 " (cutoff:3.500A)
Processing helix chain 'A' and resid 145 through 155
removed outlier: 3.504A pdb=" N ALA A 155 " --> pdb=" O GLU A 151 " (cutoff:3.500A)
Processing helix chain 'A' and resid 159 through 164
removed outlier: 4.365A pdb=" N TYR A 163 " --> pdb=" O LYS A 159 " (cutoff:3.500A)
Processing helix chain 'A' and resid 165 through 168
Processing helix chain 'A' and resid 183 through 204
removed outlier: 4.154A pdb=" N ILE A 200 " --> pdb=" O GLU A 196 " (cutoff:3.500A)
removed outlier: 3.813A pdb=" N SER A 201 " --> pdb=" O PHE A 197 " (cutoff:3.500A)
Processing helix chain 'A' and resid 222 through 243
Processing helix chain 'B' and resid 5 through 26
Processing helix chain 'B' and resid 29 through 34
Processing helix chain 'G' and resid 9 through 24
Processing helix chain 'G' and resid 29 through 44
removed outlier: 3.653A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A)
removed outlier: 3.609A pdb=" N HIS G 44 " --> pdb=" O TYR G 40 " (cutoff:3.500A)
Processing sheet with id=AA1, first strand: chain 'Q' and resid 26 through 28
removed outlier: 6.054A pdb=" N ILE Q 32 " --> pdb=" O GLY Q 94 " (cutoff:3.500A)
removed outlier: 7.640A pdb=" N ARG Q 96 " --> pdb=" O ILE Q 32 " (cutoff:3.500A)
removed outlier: 6.548A pdb=" N LEU Q 34 " --> pdb=" O ARG Q 96 " (cutoff:3.500A)
removed outlier: 7.595A pdb=" N PHE Q 98 " --> pdb=" O LEU Q 34 " (cutoff:3.500A)
removed outlier: 6.509A pdb=" N GLY Q 36 " --> pdb=" O PHE Q 98 " (cutoff:3.500A)
removed outlier: 6.777A pdb=" N ILE Q 33 " --> pdb=" O THR Q 138 " (cutoff:3.500A)
removed outlier: 4.206A pdb=" N ALA Q 140 " --> pdb=" O ILE Q 33 " (cutoff:3.500A)
removed outlier: 8.454A pdb=" N VAL Q 165 " --> pdb=" O ILE Q 139 " (cutoff:3.500A)
removed outlier: 6.362A pdb=" N VAL Q 141 " --> pdb=" O VAL Q 165 " (cutoff:3.500A)
removed outlier: 5.969A pdb=" N GLN Q 164 " --> pdb=" O LEU Q 184 " (cutoff:3.500A)
Processing sheet with id=AA2, first strand: chain 'Q' and resid 41 through 44
removed outlier: 6.247A pdb=" N HIS Q 41 " --> pdb=" O TYR Q 63 " (cutoff:3.500A)
removed outlier: 6.483A pdb=" N TYR Q 63 " --> pdb=" O HIS Q 41 " (cutoff:3.500A)
Processing sheet with id=AA3, first strand: chain 'Q' and resid 236 through 243
removed outlier: 7.954A pdb=" N VAL Q 209 " --> pdb=" O ASP Q 238 " (cutoff:3.500A)
removed outlier: 6.839A pdb=" N SER Q 240 " --> pdb=" O VAL Q 209 " (cutoff:3.500A)
removed outlier: 6.821A pdb=" N THR Q 211 " --> pdb=" O SER Q 240 " (cutoff:3.500A)
removed outlier: 5.658A pdb=" N LEU Q 242 " --> pdb=" O THR Q 211 " (cutoff:3.500A)
removed outlier: 6.366A pdb=" N ALA Q 213 " --> pdb=" O LEU Q 242 " (cutoff:3.500A)
removed outlier: 6.960A pdb=" N TRP Q 208 " --> pdb=" O VAL Q 266 " (cutoff:3.500A)
removed outlier: 8.291A pdb=" N VAL Q 268 " --> pdb=" O TRP Q 208 " (cutoff:3.500A)
removed outlier: 6.459A pdb=" N GLY Q 210 " --> pdb=" O VAL Q 268 " (cutoff:3.500A)
removed outlier: 7.829A pdb=" N PHE Q 270 " --> pdb=" O GLY Q 210 " (cutoff:3.500A)
removed outlier: 6.869A pdb=" N ILE Q 212 " --> pdb=" O PHE Q 270 " (cutoff:3.500A)
removed outlier: 6.812A pdb=" N TYR Q 489 " --> pdb=" O TYR Q 510 " (cutoff:3.500A)
removed outlier: 4.814A pdb=" N TYR Q 510 " --> pdb=" O TYR Q 489 " (cutoff:3.500A)
removed outlier: 6.431A pdb=" N ILE Q 491 " --> pdb=" O VAL Q 508 " (cutoff:3.500A)
Processing sheet with id=AA4, first strand: chain 'Q' and resid 468 through 470
Processing sheet with id=AA5, first strand: chain 'Q' and resid 550 through 554
Processing sheet with id=AA6, first strand: chain 'Q' and resid 572 through 573
Processing sheet with id=AA7, first strand: chain 'Q' and resid 589 through 591
Processing sheet with id=AA8, first strand: chain 'Q' and resid 602 through 604
Processing sheet with id=AA9, first strand: chain 'R' and resid 25 through 28
removed outlier: 6.212A pdb=" N ILE R 32 " --> pdb=" O GLY R 94 " (cutoff:3.500A)
removed outlier: 7.565A pdb=" N ARG R 96 " --> pdb=" O ILE R 32 " (cutoff:3.500A)
removed outlier: 6.393A pdb=" N LEU R 34 " --> pdb=" O ARG R 96 " (cutoff:3.500A)
removed outlier: 7.703A pdb=" N PHE R 98 " --> pdb=" O LEU R 34 " (cutoff:3.500A)
removed outlier: 6.472A pdb=" N GLY R 36 " --> pdb=" O PHE R 98 " (cutoff:3.500A)
removed outlier: 6.822A pdb=" N ILE R 33 " --> pdb=" O THR R 138 " (cutoff:3.500A)
removed outlier: 3.986A pdb=" N ALA R 140 " --> pdb=" O ILE R 33 " (cutoff:3.500A)
removed outlier: 8.586A pdb=" N VAL R 165 " --> pdb=" O ILE R 139 " (cutoff:3.500A)
removed outlier: 6.449A pdb=" N VAL R 141 " --> pdb=" O VAL R 165 " (cutoff:3.500A)
removed outlier: 5.988A pdb=" N GLN R 164 " --> pdb=" O LEU R 184 " (cutoff:3.500A)
Processing sheet with id=AB1, first strand: chain 'R' and resid 236 through 243
removed outlier: 6.556A pdb=" N VAL R 209 " --> pdb=" O ILE R 237 " (cutoff:3.500A)
removed outlier: 4.494A pdb=" N PHE R 239 " --> pdb=" O VAL R 209 " (cutoff:3.500A)
removed outlier: 4.606A pdb=" N VAL R 266 " --> pdb=" O TRP R 208 " (cutoff:3.500A)
removed outlier: 6.439A pdb=" N ILE R 267 " --> pdb=" O LEU R 294 " (cutoff:3.500A)
removed outlier: 6.254A pdb=" N TRP R 293 " --> pdb=" O ILE R 318 " (cutoff:3.500A)
removed outlier: 8.033A pdb=" N PHE R 320 " --> pdb=" O TRP R 293 " (cutoff:3.500A)
removed outlier: 7.352A pdb=" N ALA R 295 " --> pdb=" O PHE R 320 " (cutoff:3.500A)
removed outlier: 9.422A pdb=" N LEU R 322 " --> pdb=" O ALA R 295 " (cutoff:3.500A)
removed outlier: 6.785A pdb=" N TYR R 489 " --> pdb=" O TYR R 510 " (cutoff:3.500A)
removed outlier: 4.731A pdb=" N TYR R 510 " --> pdb=" O TYR R 489 " (cutoff:3.500A)
removed outlier: 6.605A pdb=" N ILE R 491 " --> pdb=" O VAL R 508 " (cutoff:3.500A)
Processing sheet with id=AB2, first strand: chain 'R' and resid 469 through 470
removed outlier: 3.525A pdb=" N PHE R 469 " --> pdb=" O VAL R 477 " (cutoff:3.500A)
Processing sheet with id=AB3, first strand: chain 'R' and resid 550 through 554
Processing sheet with id=AB4, first strand: chain 'R' and resid 572 through 573
Processing sheet with id=AB5, first strand: chain 'R' and resid 589 through 591
Processing sheet with id=AB6, first strand: chain 'R' and resid 602 through 604
removed outlier: 5.970A pdb=" N GLU R 602 " --> pdb=" O ILE R 761 " (cutoff:3.500A)
removed outlier: 7.181A pdb=" N ILE R 763 " --> pdb=" O GLU R 602 " (cutoff:3.500A)
removed outlier: 6.813A pdb=" N GLU R 604 " --> pdb=" O ILE R 763 " (cutoff:3.500A)
removed outlier: 8.612A pdb=" N CYS R 765 " --> pdb=" O GLU R 604 " (cutoff:3.500A)
Processing sheet with id=AB7, first strand: chain 'A' and resid 75 through 76
removed outlier: 3.884A pdb=" N ALA A 105 " --> pdb=" O ARG A 35 " (cutoff:3.500A)
removed outlier: 3.513A pdb=" N LEU A 37 " --> pdb=" O ALA A 105 " (cutoff:3.500A)
Processing sheet with id=AB8, first strand: chain 'A' and resid 109 through 111
removed outlier: 5.847A pdb=" N VAL A 110 " --> pdb=" O ASN A 144 " (cutoff:3.500A)
Processing sheet with id=AB9, first strand: chain 'B' and resid 46 through 52
removed outlier: 5.744A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A)
removed outlier: 7.190A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A)
removed outlier: 3.850A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A)
removed outlier: 4.108A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A)
Processing sheet with id=AC1, first strand: chain 'B' and resid 58 through 63
removed outlier: 3.751A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A)
removed outlier: 5.295A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A)
removed outlier: 4.184A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A)
removed outlier: 6.648A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A)
Processing sheet with id=AC2, first strand: chain 'B' and resid 100 through 105
removed outlier: 4.304A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A)
removed outlier: 4.692A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A)
removed outlier: 3.685A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A)
removed outlier: 6.332A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A)
removed outlier: 6.735A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A)
Processing sheet with id=AC3, first strand: chain 'B' and resid 149 through 151
removed outlier: 3.934A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A)
removed outlier: 7.025A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A)
removed outlier: 6.676A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A)
Processing sheet with id=AC4, first strand: chain 'B' and resid 187 through 192
removed outlier: 3.929A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A)
removed outlier: 4.591A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A)
Processing sheet with id=AC5, first strand: chain 'B' and resid 229 through 232
removed outlier: 6.402A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A)
removed outlier: 4.561A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A)
removed outlier: 6.634A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A)
removed outlier: 3.905A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A)
Processing sheet with id=AC6, first strand: chain 'B' and resid 273 through 278
removed outlier: 6.789A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A)
removed outlier: 4.635A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A)
removed outlier: 6.999A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A)
removed outlier: 5.436A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A)
removed outlier: 7.112A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A)
removed outlier: 6.661A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A)
removed outlier: 6.908A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A)
837 hydrogen bonds defined for protein.
2406 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: 7.41
Time building geometry restraints manager: 5.26 seconds
NOTE: a complete listing of the restraints can be obtained by requesting
output of .geo file.
Histogram of bond lengths:
1.21 - 1.33: 4666
1.33 - 1.45: 3780
1.45 - 1.58: 9345
1.58 - 1.70: 2
1.70 - 1.82: 114
Bond restraints: 17907
Sorted by residual:
bond pdb=" CAI Y01 Q1010 "
pdb=" CAK Y01 Q1010 "
ideal model delta sigma weight residual
1.492 1.406 0.086 2.00e-02 2.50e+03 1.86e+01
bond pdb=" CB TCR R1003 "
pdb=" CG TCR R1003 "
ideal model delta sigma weight residual
1.494 1.426 0.068 2.00e-02 2.50e+03 1.14e+01
bond pdb=" O3 PO4 R1004 "
pdb=" P PO4 R1004 "
ideal model delta sigma weight residual
1.569 1.504 0.065 2.00e-02 2.50e+03 1.06e+01
bond pdb=" O2 PO4 R1004 "
pdb=" P PO4 R1004 "
ideal model delta sigma weight residual
1.567 1.503 0.064 2.00e-02 2.50e+03 1.02e+01
bond pdb=" O3 PO4 Q1005 "
pdb=" P PO4 Q1005 "
ideal model delta sigma weight residual
1.569 1.505 0.064 2.00e-02 2.50e+03 1.01e+01
... (remaining 17902 not shown)
Histogram of bond angle deviations from ideal:
0.00 - 2.35: 23964
2.35 - 4.69: 331
4.69 - 7.04: 25
7.04 - 9.39: 5
9.39 - 11.74: 3
Bond angle restraints: 24328
Sorted by residual:
angle pdb=" C ALA A 7 "
pdb=" CA ALA A 7 "
pdb=" CB ALA A 7 "
ideal model delta sigma weight residual
116.63 110.19 6.44 1.16e+00 7.43e-01 3.08e+01
angle pdb=" C LEU R 743 "
pdb=" N TYR R 744 "
pdb=" CA TYR R 744 "
ideal model delta sigma weight residual
122.26 115.93 6.33 1.59e+00 3.96e-01 1.59e+01
angle pdb=" OAG Y01 Q1010 "
pdb=" CAY Y01 Q1010 "
pdb=" OAW Y01 Q1010 "
ideal model delta sigma weight residual
123.38 111.64 11.74 3.00e+00 1.11e-01 1.53e+01
angle pdb=" CAM Y01 Q1010 "
pdb=" CAY Y01 Q1010 "
pdb=" OAW Y01 Q1010 "
ideal model delta sigma weight residual
111.19 122.63 -11.44 3.00e+00 1.11e-01 1.45e+01
angle pdb=" N ILE A 193 "
pdb=" CA ILE A 193 "
pdb=" CB ILE A 193 "
ideal model delta sigma weight residual
110.55 114.66 -4.11 1.17e+00 7.31e-01 1.23e+01
... (remaining 24323 not shown)
Histogram of dihedral angle deviations from ideal:
0.00 - 18.06: 9874
18.06 - 36.12: 742
36.12 - 54.18: 112
54.18 - 72.24: 30
72.24 - 90.29: 8
Dihedral angle restraints: 10766
sinusoidal: 4338
harmonic: 6428
Sorted by residual:
dihedral pdb=" CA PHE A 142 "
pdb=" C PHE A 142 "
pdb=" N LEU A 143 "
pdb=" CA LEU A 143 "
ideal model delta harmonic sigma weight residual
180.00 157.42 22.58 0 5.00e+00 4.00e-02 2.04e+01
dihedral pdb=" CA ILE Q 852 "
pdb=" C ILE Q 852 "
pdb=" N PHE Q 853 "
pdb=" CA PHE Q 853 "
ideal model delta harmonic sigma weight residual
-180.00 -159.07 -20.93 0 5.00e+00 4.00e-02 1.75e+01
dihedral pdb=" CA PHE B 234 "
pdb=" C PHE B 234 "
pdb=" N PHE B 235 "
pdb=" CA PHE B 235 "
ideal model delta harmonic sigma weight residual
180.00 159.70 20.30 0 5.00e+00 4.00e-02 1.65e+01
... (remaining 10763 not shown)
Histogram of chiral volume deviations from ideal:
0.000 - 0.048: 2138
0.048 - 0.097: 525
0.097 - 0.145: 117
0.145 - 0.194: 6
0.194 - 0.242: 4
Chirality restraints: 2790
Sorted by residual:
chirality pdb=" C02 A1AF7 R1009 "
pdb=" C01 A1AF7 R1009 "
pdb=" C03 A1AF7 R1009 "
pdb=" O01 A1AF7 R1009 "
both_signs ideal model delta sigma weight residual
False 2.54 2.78 -0.24 2.00e-01 2.50e+01 1.46e+00
chirality pdb=" C1 NAG Q1002 "
pdb=" ND2 ASN Q 287 "
pdb=" C2 NAG Q1002 "
pdb=" O5 NAG Q1002 "
both_signs ideal model delta sigma weight residual
False -2.40 -2.17 -0.23 2.00e-01 2.50e+01 1.28e+00
chirality pdb=" CB ILE B 81 "
pdb=" CA ILE B 81 "
pdb=" CG1 ILE B 81 "
pdb=" CG2 ILE B 81 "
both_signs ideal model delta sigma weight residual
False 2.64 2.43 0.22 2.00e-01 2.50e+01 1.21e+00
... (remaining 2787 not shown)
Planarity restraints: 3065
Sorted by residual:
delta sigma weight rms_deltas residual
plane pdb=" C ARG R 54 " -0.055 5.00e-02 4.00e+02 8.25e-02 1.09e+01
pdb=" N PRO R 55 " 0.143 5.00e-02 4.00e+02
pdb=" CA PRO R 55 " -0.043 5.00e-02 4.00e+02
pdb=" CD PRO R 55 " -0.045 5.00e-02 4.00e+02
delta sigma weight rms_deltas residual
plane pdb=" C CYS Q 568 " 0.041 5.00e-02 4.00e+02 6.21e-02 6.17e+00
pdb=" N PRO Q 569 " -0.107 5.00e-02 4.00e+02
pdb=" CA PRO Q 569 " 0.033 5.00e-02 4.00e+02
pdb=" CD PRO Q 569 " 0.034 5.00e-02 4.00e+02
delta sigma weight rms_deltas residual
plane pdb=" CA ALA Q 850 " -0.012 2.00e-02 2.50e+03 2.44e-02 5.95e+00
pdb=" C ALA Q 850 " 0.042 2.00e-02 2.50e+03
pdb=" O ALA Q 850 " -0.016 2.00e-02 2.50e+03
pdb=" N CYS Q 851 " -0.014 2.00e-02 2.50e+03
... (remaining 3062 not shown)
Histogram of nonbonded interaction distances:
2.11 - 2.67: 280
2.67 - 3.23: 17178
3.23 - 3.78: 28491
3.78 - 4.34: 39608
4.34 - 4.90: 63001
Nonbonded interactions: 148558
Sorted by model distance:
nonbonded pdb=" O ILE B 58 "
pdb=" OG SER B 316 "
model vdw
2.112 3.040
nonbonded pdb=" O MET A 18 "
pdb=" NE2 GLN A 22 "
model vdw
2.207 3.120
nonbonded pdb=" NE2 HIS B 54 "
pdb=" OG SER B 72 "
model vdw
2.218 3.120
nonbonded pdb=" OD2 ASP R 238 "
pdb=" OG SER R 262 "
model vdw
2.226 3.040
nonbonded pdb=" OG1 THR R 470 "
pdb=" OE1 GLN R 476 "
model vdw
2.226 3.040
... (remaining 148553 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 'C'
selection = chain 'D'
selection = chain 'E'
selection = chain 'F'
}
ncs_group {
reference = (chain 'Q' and (resid 22 through 49 or (resid 50 and (name N or name CA or name \
C or name O or name CB )) or resid 51 through 120 or (resid 121 and (name N or n \
ame CA or name C or name O or name CB )) or resid 122 or resid 135 through 230 o \
r (resid 231 and (name N or name CA or name C or name O or name CB )) or resid 2 \
32 through 360 or (resid 392 and (name N or name CA or name C or name O or name \
CB )) or resid 393 through 404 or (resid 405 and (name N or name CA or name C or \
name O or name CB )) or resid 406 through 518 or (resid 519 and (name N or name \
CA or name C or name O or name CB )) or resid 520 through 864 or resid 1002 thr \
ough 1004 or resid 1005 through 1009))
selection = (chain 'R' and (resid 22 through 46 or (resid 47 through 48 and (name N or name \
CA or name C or name O or name CB )) or resid 49 through 55 or (resid 56 and (na \
me N or name CA or name C or name O or name CB )) or resid 57 through 247 or (re \
sid 248 through 250 and (name N or name CA or name C or name O or name CB )) or \
resid 251 through 453 or (resid 454 and (name N or name CA or name C or name O o \
r name CB )) or resid 455 through 499 or (resid 500 and (name N or name CA or na \
me C or name O or name CB )) or resid 501 through 525 or (resid 526 and (name N \
or name CA or name C or name O or name CB )) or resid 527 through 609 or (resid \
610 and (name N or name CA or name C or name O or name CB )) or resid 611 throug \
h 637 or (resid 638 and (name N or name CA or name C or name O or name CB )) or \
resid 639 through 708 or resid 722 through 864 or resid 1001 through 1003 or res \
id 1004 through 1008))
}
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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
Set random seed: 0.000
Set model cs if undefined: 0.000
Decide on map wrapping: 0.000
Normalize map: mean=0, sd=1: 10.570
Set stop_for_unknowns flag: 0.000
Assert model is a single copy model: 0.000
Assert all atoms have isotropic ADPs: 0.000
Construct map_model_manager: 0.020
Extract box with map and model: 0.770
Check model and map are aligned: 0.120
Set scattering table: 0.160
Process input model: 43.240
Find NCS groups from input model: 0.670
Set up NCS constraints: 0.090
Set refine NCS operators: 0.000
Adjust number of macro_cycles: 0.000
Reset NCS operators: 0.000
Extract rigid body selections: 0.000
Check and reset occupancies: 0.010
Load rotamer database and sin/cos tables:2.790
Set ADP refinement strategy: 0.000
Make a string to write initial .geo file:0.000
Internal consistency checks: 0.000
Total: 58.440
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7219
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 0.086 17907 Z= 0.327
Angle : 0.692 11.736 24328 Z= 0.381
Chirality : 0.044 0.242 2790
Planarity : 0.005 0.082 3056
Dihedral : 12.938 90.294 6554
Min Nonbonded Distance : 2.112
Molprobity Statistics.
All-atom Clashscore : 8.93
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 3.16 %
Favored : 96.84 %
Rotamer:
Outliers : 0.00 %
Allowed : 0.17 %
Favored : 99.83 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.09 %
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: -0.83 (0.17), residues: 2182
helix: 0.25 (0.16), residues: 911
sheet: -1.52 (0.26), residues: 371
loop : -0.80 (0.20), residues: 900
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.023 0.002 TRP R 352
HIS 0.008 0.001 HIS A 209
PHE 0.033 0.002 PHE Q 634
TYR 0.014 0.002 TYR B 289
ARG 0.007 0.001 ARG R 25
*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
4364 Ramachandran restraints generated.
2182 Oldfield, 0 Emsley, 2182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
4364 Ramachandran restraints generated.
2182 Oldfield, 0 Emsley, 2182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
384 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 0
poor density : 384
time to evaluate : 1.907
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: R 92 THR cc_start: 0.6822 (t) cc_final: 0.6593 (t)
REVERT: R 248 ASP cc_start: 0.6710 (m-30) cc_final: 0.6418 (m-30)
REVERT: R 309 GLN cc_start: 0.8048 (pm20) cc_final: 0.7666 (pm20)
REVERT: A 38 LEU cc_start: 0.8231 (tp) cc_final: 0.8013 (tp)
REVERT: A 122 LEU cc_start: 0.7931 (tp) cc_final: 0.7643 (tp)
REVERT: A 235 ILE cc_start: 0.8711 (mm) cc_final: 0.8403 (mp)
REVERT: B 36 ASN cc_start: 0.5165 (m-40) cc_final: 0.4784 (p0)
REVERT: B 81 ILE cc_start: 0.8370 (tp) cc_final: 0.8158 (tp)
REVERT: B 333 ASP cc_start: 0.7677 (p0) cc_final: 0.6411 (t0)
outliers start: 0
outliers final: 0
residues processed: 384
average time/residue: 0.3206
time to fit residues: 182.8946
Evaluate side-chains
348 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 0
poor density : 348
time to evaluate : 2.054
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 218
random chunks:
chunk 184 optimal weight: 0.8980
chunk 165 optimal weight: 0.0870
chunk 91 optimal weight: 0.9990
chunk 56 optimal weight: 0.9990
chunk 111 optimal weight: 0.9990
chunk 88 optimal weight: 0.1980
chunk 170 optimal weight: 1.9990
chunk 66 optimal weight: 0.5980
chunk 103 optimal weight: 0.5980
chunk 127 optimal weight: 0.9990
chunk 197 optimal weight: 0.7980
overall best weight: 0.4558
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.116241 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.098819 restraints weight = 28408.149|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.098835 restraints weight = 24211.283|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.100281 restraints weight = 22633.125|
|-----------------------------------------------------------------------------|
r_work (final): 0.3228
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7205
moved from start: 0.0906
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.004 0.036 17907 Z= 0.257
Angle : 0.555 7.651 24328 Z= 0.297
Chirality : 0.043 0.167 2790
Planarity : 0.005 0.062 3056
Dihedral : 7.589 65.123 2791
Min Nonbonded Distance : 2.456
Molprobity Statistics.
All-atom Clashscore : 7.62
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 3.48 %
Favored : 96.52 %
Rotamer:
Outliers : 0.89 %
Allowed : 6.77 %
Favored : 92.34 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.09 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: -0.51 (0.17), residues: 2182
helix: 0.66 (0.16), residues: 919
sheet: -1.48 (0.26), residues: 373
loop : -0.73 (0.20), residues: 890
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.014 0.002 TRP B 297
HIS 0.008 0.001 HIS A 209
PHE 0.022 0.002 PHE R 788
TYR 0.013 0.002 TYR R 421
ARG 0.005 0.000 ARG Q 62
*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
4364 Ramachandran restraints generated.
2182 Oldfield, 0 Emsley, 2182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
4364 Ramachandran restraints generated.
2182 Oldfield, 0 Emsley, 2182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
388 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 16
poor density : 372
time to evaluate : 1.943
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: Q 860 ILE cc_start: 0.7918 (OUTLIER) cc_final: 0.7717 (mt)
REVERT: R 248 ASP cc_start: 0.6542 (m-30) cc_final: 0.6137 (m-30)
REVERT: R 282 GLU cc_start: 0.6628 (tp30) cc_final: 0.6411 (tp30)
REVERT: R 309 GLN cc_start: 0.8069 (pm20) cc_final: 0.7470 (pm20)
REVERT: A 122 LEU cc_start: 0.7645 (tp) cc_final: 0.7356 (tp)
REVERT: A 234 ILE cc_start: 0.9017 (OUTLIER) cc_final: 0.8762 (mp)
REVERT: A 235 ILE cc_start: 0.8715 (mm) cc_final: 0.8400 (mp)
REVERT: B 71 VAL cc_start: 0.8546 (m) cc_final: 0.8343 (t)
REVERT: B 198 LEU cc_start: 0.8893 (mm) cc_final: 0.8582 (mp)
REVERT: B 263 THR cc_start: 0.6934 (m) cc_final: 0.6497 (p)
outliers start: 16
outliers final: 12
residues processed: 377
average time/residue: 0.3484
time to fit residues: 199.8625
Evaluate side-chains
358 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 14
poor density : 344
time to evaluate : 1.869
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain Q residue 485 LEU
Chi-restraints excluded: chain Q residue 566 VAL
Chi-restraints excluded: chain Q residue 727 LEU
Chi-restraints excluded: chain Q residue 736 ILE
Chi-restraints excluded: chain Q residue 740 VAL
Chi-restraints excluded: chain Q residue 860 ILE
Chi-restraints excluded: chain R residue 336 LYS
Chi-restraints excluded: chain R residue 592 ASN
Chi-restraints excluded: chain R residue 609 THR
Chi-restraints excluded: chain R residue 624 ILE
Chi-restraints excluded: chain A residue 29 VAL
Chi-restraints excluded: chain A residue 234 ILE
Chi-restraints excluded: chain B residue 243 THR
Chi-restraints excluded: chain B residue 327 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 218
random chunks:
chunk 164 optimal weight: 5.9990
chunk 207 optimal weight: 2.9990
chunk 204 optimal weight: 0.9980
chunk 46 optimal weight: 0.9990
chunk 199 optimal weight: 0.6980
chunk 70 optimal weight: 0.9980
chunk 176 optimal weight: 4.9990
chunk 45 optimal weight: 1.9990
chunk 105 optimal weight: 0.6980
chunk 59 optimal weight: 0.9990
chunk 138 optimal weight: 0.8980
overall best weight: 0.8580
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.114334 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.096853 restraints weight = 28358.557|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3182 r_free = 0.3182 target = 0.096811 restraints weight = 24711.799|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.097354 restraints weight = 23448.599|
|-----------------------------------------------------------------------------|
r_work (final): 0.3189
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7260
moved from start: 0.1226
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.006 0.051 17907 Z= 0.392
Angle : 0.590 7.938 24328 Z= 0.313
Chirality : 0.045 0.177 2790
Planarity : 0.005 0.052 3056
Dihedral : 7.454 69.412 2791
Min Nonbonded Distance : 2.439
Molprobity Statistics.
All-atom Clashscore : 7.94
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 3.85 %
Favored : 96.15 %
Rotamer:
Outliers : 1.94 %
Allowed : 9.66 %
Favored : 88.40 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.09 %
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: -0.53 (0.17), residues: 2182
helix: 0.60 (0.16), residues: 919
sheet: -1.46 (0.26), residues: 365
loop : -0.73 (0.20), residues: 898
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.020 0.002 TRP B 82
HIS 0.007 0.001 HIS Q 338
PHE 0.027 0.002 PHE R 788
TYR 0.020 0.002 TYR R 744
ARG 0.008 0.001 ARG Q 185
*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
4364 Ramachandran restraints generated.
2182 Oldfield, 0 Emsley, 2182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
4364 Ramachandran restraints generated.
2182 Oldfield, 0 Emsley, 2182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
397 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 35
poor density : 362
time to evaluate : 1.667
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: Q 702 VAL cc_start: 0.7123 (OUTLIER) cc_final: 0.6769 (t)
REVERT: R 248 ASP cc_start: 0.6549 (m-30) cc_final: 0.6196 (m-30)
REVERT: R 309 GLN cc_start: 0.7984 (pm20) cc_final: 0.7507 (pm20)
REVERT: R 422 LEU cc_start: 0.8228 (OUTLIER) cc_final: 0.7655 (mp)
REVERT: A 106 ILE cc_start: 0.8310 (mm) cc_final: 0.8029 (mm)
REVERT: A 122 LEU cc_start: 0.7708 (tp) cc_final: 0.7393 (tp)
REVERT: A 192 PHE cc_start: 0.6382 (t80) cc_final: 0.6172 (t80)
REVERT: A 234 ILE cc_start: 0.8985 (OUTLIER) cc_final: 0.8775 (mp)
REVERT: B 71 VAL cc_start: 0.8504 (m) cc_final: 0.8037 (t)
REVERT: B 81 ILE cc_start: 0.8568 (tp) cc_final: 0.8246 (tp)
REVERT: B 198 LEU cc_start: 0.8931 (mm) cc_final: 0.8621 (mp)
REVERT: B 263 THR cc_start: 0.6976 (m) cc_final: 0.6509 (p)
outliers start: 35
outliers final: 21
residues processed: 375
average time/residue: 0.3334
time to fit residues: 184.7519
Evaluate side-chains
370 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 24
poor density : 346
time to evaluate : 2.073
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain Q residue 92 THR
Chi-restraints excluded: chain Q residue 409 ILE
Chi-restraints excluded: chain Q residue 422 LEU
Chi-restraints excluded: chain Q residue 436 THR
Chi-restraints excluded: chain Q residue 485 LEU
Chi-restraints excluded: chain Q residue 566 VAL
Chi-restraints excluded: chain Q residue 702 VAL
Chi-restraints excluded: chain Q residue 727 LEU
Chi-restraints excluded: chain Q residue 736 ILE
Chi-restraints excluded: chain Q residue 740 VAL
Chi-restraints excluded: chain R residue 422 LEU
Chi-restraints excluded: chain R residue 592 ASN
Chi-restraints excluded: chain R residue 609 THR
Chi-restraints excluded: chain R residue 624 ILE
Chi-restraints excluded: chain R residue 739 CYS
Chi-restraints excluded: chain A residue 29 VAL
Chi-restraints excluded: chain A residue 37 LEU
Chi-restraints excluded: chain A residue 110 VAL
Chi-restraints excluded: chain A residue 124 ASP
Chi-restraints excluded: chain A residue 234 ILE
Chi-restraints excluded: chain B residue 243 THR
Chi-restraints excluded: chain B residue 245 SER
Chi-restraints excluded: chain B residue 269 ILE
Chi-restraints excluded: chain B residue 327 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 218
random chunks:
chunk 57 optimal weight: 0.7980
chunk 38 optimal weight: 0.9990
chunk 2 optimal weight: 0.6980
chunk 182 optimal weight: 0.0040
chunk 207 optimal weight: 1.9990
chunk 109 optimal weight: 0.7980
chunk 148 optimal weight: 0.8980
chunk 11 optimal weight: 0.5980
chunk 129 optimal weight: 0.9980
chunk 61 optimal weight: 0.9990
chunk 134 optimal weight: 0.8980
overall best weight: 0.5792
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.115063 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.097157 restraints weight = 28385.462|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.097166 restraints weight = 23469.059|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.098062 restraints weight = 22545.588|
|-----------------------------------------------------------------------------|
r_work (final): 0.3201
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7247
moved from start: 0.1376
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.004 0.040 17907 Z= 0.286
Angle : 0.546 7.736 24328 Z= 0.289
Chirality : 0.043 0.147 2790
Planarity : 0.004 0.050 3056
Dihedral : 7.216 71.921 2791
Min Nonbonded Distance : 2.360
Molprobity Statistics.
All-atom Clashscore : 7.77
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 3.25 %
Favored : 96.75 %
Rotamer:
Outliers : 2.44 %
Allowed : 10.99 %
Favored : 86.57 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.09 %
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: -0.45 (0.17), residues: 2182
helix: 0.69 (0.16), residues: 927
sheet: -1.42 (0.26), residues: 366
loop : -0.73 (0.20), residues: 889
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.014 0.002 TRP B 82
HIS 0.005 0.001 HIS A 209
PHE 0.023 0.002 PHE A 100
TYR 0.020 0.002 TYR R 744
ARG 0.005 0.000 ARG Q 185
*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
4364 Ramachandran restraints generated.
2182 Oldfield, 0 Emsley, 2182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
4364 Ramachandran restraints generated.
2182 Oldfield, 0 Emsley, 2182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
402 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 44
poor density : 358
time to evaluate : 1.967
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: Q 702 VAL cc_start: 0.7079 (OUTLIER) cc_final: 0.6724 (t)
REVERT: R 248 ASP cc_start: 0.6527 (m-30) cc_final: 0.6142 (m-30)
REVERT: R 282 GLU cc_start: 0.6679 (tp30) cc_final: 0.6428 (tp30)
REVERT: R 422 LEU cc_start: 0.8202 (OUTLIER) cc_final: 0.7668 (mp)
REVERT: A 106 ILE cc_start: 0.8317 (mm) cc_final: 0.8019 (mm)
REVERT: A 122 LEU cc_start: 0.7730 (tp) cc_final: 0.7427 (tp)
REVERT: A 192 PHE cc_start: 0.6460 (t80) cc_final: 0.6256 (t80)
REVERT: A 234 ILE cc_start: 0.8956 (OUTLIER) cc_final: 0.8689 (mp)
REVERT: A 235 ILE cc_start: 0.8675 (mm) cc_final: 0.8438 (mp)
REVERT: B 36 ASN cc_start: 0.5213 (m-40) cc_final: 0.4881 (p0)
REVERT: B 81 ILE cc_start: 0.8621 (tp) cc_final: 0.8235 (tp)
REVERT: B 198 LEU cc_start: 0.8916 (mm) cc_final: 0.8639 (mp)
REVERT: B 263 THR cc_start: 0.6956 (m) cc_final: 0.6463 (p)
outliers start: 44
outliers final: 31
residues processed: 383
average time/residue: 0.3536
time to fit residues: 205.6525
Evaluate side-chains
374 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 34
poor density : 340
time to evaluate : 1.992
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain Q residue 139 ILE
Chi-restraints excluded: chain Q residue 184 LEU
Chi-restraints excluded: chain Q residue 223 ILE
Chi-restraints excluded: chain Q residue 409 ILE
Chi-restraints excluded: chain Q residue 422 LEU
Chi-restraints excluded: chain Q residue 436 THR
Chi-restraints excluded: chain Q residue 485 LEU
Chi-restraints excluded: chain Q residue 566 VAL
Chi-restraints excluded: chain Q residue 702 VAL
Chi-restraints excluded: chain Q residue 727 LEU
Chi-restraints excluded: chain Q residue 736 ILE
Chi-restraints excluded: chain Q residue 740 VAL
Chi-restraints excluded: chain Q residue 775 PHE
Chi-restraints excluded: chain Q residue 859 ILE
Chi-restraints excluded: chain Q residue 860 ILE
Chi-restraints excluded: chain R residue 422 LEU
Chi-restraints excluded: chain R residue 592 ASN
Chi-restraints excluded: chain R residue 609 THR
Chi-restraints excluded: chain R residue 624 ILE
Chi-restraints excluded: chain R residue 689 VAL
Chi-restraints excluded: chain R residue 739 CYS
Chi-restraints excluded: chain R residue 836 VAL
Chi-restraints excluded: chain A residue 29 VAL
Chi-restraints excluded: chain A residue 37 LEU
Chi-restraints excluded: chain A residue 124 ASP
Chi-restraints excluded: chain A residue 128 ILE
Chi-restraints excluded: chain A residue 234 ILE
Chi-restraints excluded: chain B residue 17 GLN
Chi-restraints excluded: chain B residue 178 THR
Chi-restraints excluded: chain B residue 243 THR
Chi-restraints excluded: chain B residue 245 SER
Chi-restraints excluded: chain B residue 269 ILE
Chi-restraints excluded: chain B residue 274 THR
Chi-restraints excluded: chain B residue 327 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 218
random chunks:
chunk 46 optimal weight: 0.8980
chunk 100 optimal weight: 1.9990
chunk 0 optimal weight: 1.9990
chunk 153 optimal weight: 0.6980
chunk 217 optimal weight: 0.0770
chunk 26 optimal weight: 0.9980
chunk 52 optimal weight: 1.9990
chunk 150 optimal weight: 0.9990
chunk 207 optimal weight: 1.9990
chunk 16 optimal weight: 0.5980
chunk 75 optimal weight: 0.5980
overall best weight: 0.5738
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.115051 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3191 r_free = 0.3191 target = 0.097182 restraints weight = 28573.580|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.097205 restraints weight = 23217.151|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.098201 restraints weight = 23074.408|
|-----------------------------------------------------------------------------|
r_work (final): 0.3202
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7245
moved from start: 0.1501
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.004 0.040 17907 Z= 0.282
Angle : 0.539 8.442 24328 Z= 0.284
Chirality : 0.043 0.196 2790
Planarity : 0.004 0.051 3056
Dihedral : 7.021 72.795 2791
Min Nonbonded Distance : 2.402
Molprobity Statistics.
All-atom Clashscore : 7.62
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 3.21 %
Favored : 96.79 %
Rotamer:
Outliers : 2.72 %
Allowed : 12.82 %
Favored : 84.46 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.09 %
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: -0.36 (0.17), residues: 2182
helix: 0.79 (0.16), residues: 926
sheet: -1.36 (0.26), residues: 365
loop : -0.71 (0.20), residues: 891
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.014 0.002 TRP Q 299
HIS 0.004 0.001 HIS A 209
PHE 0.033 0.002 PHE A 100
TYR 0.021 0.002 TYR R 744
ARG 0.004 0.000 ARG Q 185
*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
4364 Ramachandran restraints generated.
2182 Oldfield, 0 Emsley, 2182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
4364 Ramachandran restraints generated.
2182 Oldfield, 0 Emsley, 2182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
405 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 49
poor density : 356
time to evaluate : 1.809
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: Q 702 VAL cc_start: 0.7072 (OUTLIER) cc_final: 0.6711 (t)
REVERT: R 248 ASP cc_start: 0.6517 (m-30) cc_final: 0.6140 (m-30)
REVERT: R 422 LEU cc_start: 0.8204 (OUTLIER) cc_final: 0.7659 (mp)
REVERT: A 106 ILE cc_start: 0.8352 (mm) cc_final: 0.8017 (mm)
REVERT: A 122 LEU cc_start: 0.7700 (tp) cc_final: 0.7392 (tp)
REVERT: A 153 VAL cc_start: 0.8360 (p) cc_final: 0.8133 (t)
REVERT: A 192 PHE cc_start: 0.6498 (t80) cc_final: 0.6269 (t80)
REVERT: A 234 ILE cc_start: 0.8938 (OUTLIER) cc_final: 0.8701 (mp)
REVERT: B 36 ASN cc_start: 0.5168 (m-40) cc_final: 0.4865 (p0)
REVERT: B 198 LEU cc_start: 0.8912 (mm) cc_final: 0.8646 (mp)
REVERT: B 314 ARG cc_start: 0.8431 (mtm-85) cc_final: 0.8229 (mtp-110)
outliers start: 49
outliers final: 36
residues processed: 382
average time/residue: 0.3169
time to fit residues: 181.5042
Evaluate side-chains
371 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 39
poor density : 332
time to evaluate : 1.976
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain Q residue 92 THR
Chi-restraints excluded: chain Q residue 139 ILE
Chi-restraints excluded: chain Q residue 184 LEU
Chi-restraints excluded: chain Q residue 223 ILE
Chi-restraints excluded: chain Q residue 409 ILE
Chi-restraints excluded: chain Q residue 422 LEU
Chi-restraints excluded: chain Q residue 436 THR
Chi-restraints excluded: chain Q residue 485 LEU
Chi-restraints excluded: chain Q residue 566 VAL
Chi-restraints excluded: chain Q residue 702 VAL
Chi-restraints excluded: chain Q residue 727 LEU
Chi-restraints excluded: chain Q residue 736 ILE
Chi-restraints excluded: chain Q residue 740 VAL
Chi-restraints excluded: chain Q residue 775 PHE
Chi-restraints excluded: chain Q residue 859 ILE
Chi-restraints excluded: chain Q residue 860 ILE
Chi-restraints excluded: chain R residue 223 ILE
Chi-restraints excluded: chain R residue 422 LEU
Chi-restraints excluded: chain R residue 592 ASN
Chi-restraints excluded: chain R residue 609 THR
Chi-restraints excluded: chain R residue 624 ILE
Chi-restraints excluded: chain R residue 689 VAL
Chi-restraints excluded: chain R residue 739 CYS
Chi-restraints excluded: chain R residue 836 VAL
Chi-restraints excluded: chain A residue 29 VAL
Chi-restraints excluded: chain A residue 37 LEU
Chi-restraints excluded: chain A residue 124 ASP
Chi-restraints excluded: chain A residue 128 ILE
Chi-restraints excluded: chain A residue 234 ILE
Chi-restraints excluded: chain B residue 40 VAL
Chi-restraints excluded: chain B residue 61 MET
Chi-restraints excluded: chain B residue 79 LEU
Chi-restraints excluded: chain B residue 87 THR
Chi-restraints excluded: chain B residue 178 THR
Chi-restraints excluded: chain B residue 243 THR
Chi-restraints excluded: chain B residue 245 SER
Chi-restraints excluded: chain B residue 269 ILE
Chi-restraints excluded: chain B residue 274 THR
Chi-restraints excluded: chain B residue 327 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 218
random chunks:
chunk 198 optimal weight: 0.2980
chunk 130 optimal weight: 0.0980
chunk 133 optimal weight: 0.9990
chunk 74 optimal weight: 0.9980
chunk 24 optimal weight: 0.9980
chunk 52 optimal weight: 1.9990
chunk 190 optimal weight: 0.0970
chunk 131 optimal weight: 0.9990
chunk 183 optimal weight: 8.9990
chunk 2 optimal weight: 1.9990
chunk 96 optimal weight: 0.9980
overall best weight: 0.4978
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.115326 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.097801 restraints weight = 28530.196|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.097705 restraints weight = 21236.793|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.098550 restraints weight = 20945.557|
|-----------------------------------------------------------------------------|
r_work (final): 0.3204
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7244
moved from start: 0.1622
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.004 0.037 17907 Z= 0.257
Angle : 0.528 9.900 24328 Z= 0.278
Chirality : 0.043 0.144 2790
Planarity : 0.004 0.054 3056
Dihedral : 6.840 73.146 2791
Min Nonbonded Distance : 2.391
Molprobity Statistics.
All-atom Clashscore : 7.30
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 2.93 %
Favored : 97.07 %
Rotamer:
Outliers : 3.00 %
Allowed : 13.43 %
Favored : 83.57 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.09 %
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 (0.17), residues: 2182
helix: 0.89 (0.16), residues: 927
sheet: -1.29 (0.26), residues: 360
loop : -0.70 (0.20), residues: 895
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.013 0.002 TRP Q 299
HIS 0.004 0.001 HIS A 209
PHE 0.031 0.002 PHE A 100
TYR 0.021 0.002 TYR R 744
ARG 0.005 0.000 ARG R 535
*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
4364 Ramachandran restraints generated.
2182 Oldfield, 0 Emsley, 2182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
4364 Ramachandran restraints generated.
2182 Oldfield, 0 Emsley, 2182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
403 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 54
poor density : 349
time to evaluate : 1.899
Fit side-chains
revert: symmetry clash
REVERT: Q 270 PHE cc_start: 0.7272 (OUTLIER) cc_final: 0.6897 (m-80)
REVERT: R 248 ASP cc_start: 0.6517 (m-30) cc_final: 0.6144 (m-30)
REVERT: R 277 GLU cc_start: 0.7891 (tt0) cc_final: 0.7453 (tt0)
REVERT: R 422 LEU cc_start: 0.8175 (OUTLIER) cc_final: 0.7660 (mp)
REVERT: R 679 LEU cc_start: 0.6782 (tp) cc_final: 0.6442 (mt)
REVERT: A 122 LEU cc_start: 0.7752 (tp) cc_final: 0.7447 (tp)
REVERT: A 135 ARG cc_start: 0.8046 (ttp80) cc_final: 0.7487 (ttp80)
REVERT: A 192 PHE cc_start: 0.6534 (t80) cc_final: 0.6270 (t80)
REVERT: A 234 ILE cc_start: 0.8923 (OUTLIER) cc_final: 0.8671 (mp)
REVERT: A 235 ILE cc_start: 0.8675 (mm) cc_final: 0.8412 (mp)
REVERT: B 198 LEU cc_start: 0.8902 (mm) cc_final: 0.8649 (mp)
outliers start: 54
outliers final: 35
residues processed: 378
average time/residue: 0.3224
time to fit residues: 181.6615
Evaluate side-chains
376 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 38
poor density : 338
time to evaluate : 2.115
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain Q residue 139 ILE
Chi-restraints excluded: chain Q residue 184 LEU
Chi-restraints excluded: chain Q residue 223 ILE
Chi-restraints excluded: chain Q residue 270 PHE
Chi-restraints excluded: chain Q residue 409 ILE
Chi-restraints excluded: chain Q residue 422 LEU
Chi-restraints excluded: chain Q residue 436 THR
Chi-restraints excluded: chain Q residue 485 LEU
Chi-restraints excluded: chain Q residue 727 LEU
Chi-restraints excluded: chain Q residue 736 ILE
Chi-restraints excluded: chain Q residue 740 VAL
Chi-restraints excluded: chain Q residue 757 GLU
Chi-restraints excluded: chain Q residue 775 PHE
Chi-restraints excluded: chain Q residue 859 ILE
Chi-restraints excluded: chain Q residue 860 ILE
Chi-restraints excluded: chain R residue 223 ILE
Chi-restraints excluded: chain R residue 422 LEU
Chi-restraints excluded: chain R residue 592 ASN
Chi-restraints excluded: chain R residue 609 THR
Chi-restraints excluded: chain R residue 624 ILE
Chi-restraints excluded: chain R residue 689 VAL
Chi-restraints excluded: chain R residue 739 CYS
Chi-restraints excluded: chain R residue 836 VAL
Chi-restraints excluded: chain A residue 37 LEU
Chi-restraints excluded: chain A residue 38 LEU
Chi-restraints excluded: chain A residue 124 ASP
Chi-restraints excluded: chain A residue 128 ILE
Chi-restraints excluded: chain A residue 154 LEU
Chi-restraints excluded: chain A residue 234 ILE
Chi-restraints excluded: chain B residue 61 MET
Chi-restraints excluded: chain B residue 87 THR
Chi-restraints excluded: chain B residue 157 ILE
Chi-restraints excluded: chain B residue 178 THR
Chi-restraints excluded: chain B residue 243 THR
Chi-restraints excluded: chain B residue 245 SER
Chi-restraints excluded: chain B residue 269 ILE
Chi-restraints excluded: chain B residue 274 THR
Chi-restraints excluded: chain B residue 327 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 218
random chunks:
chunk 82 optimal weight: 0.0980
chunk 166 optimal weight: 0.6980
chunk 162 optimal weight: 0.2980
chunk 179 optimal weight: 3.9990
chunk 25 optimal weight: 0.9990
chunk 5 optimal weight: 0.9990
chunk 199 optimal weight: 0.5980
chunk 13 optimal weight: 0.8980
chunk 48 optimal weight: 0.0980
chunk 203 optimal weight: 0.6980
chunk 165 optimal weight: 0.6980
overall best weight: 0.3580
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.116251 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.098466 restraints weight = 28426.077|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.098326 restraints weight = 22021.754|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.098959 restraints weight = 19133.721|
|-----------------------------------------------------------------------------|
r_work (final): 0.3211
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7234
moved from start: 0.1728
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.063 17907 Z= 0.216
Angle : 0.526 9.285 24328 Z= 0.275
Chirality : 0.042 0.167 2790
Planarity : 0.004 0.055 3056
Dihedral : 6.685 71.945 2791
Min Nonbonded Distance : 2.388
Molprobity Statistics.
All-atom Clashscore : 7.42
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 3.16 %
Favored : 96.84 %
Rotamer:
Outliers : 2.44 %
Allowed : 14.98 %
Favored : 82.57 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.09 %
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: -0.16 (0.17), residues: 2182
helix: 1.02 (0.16), residues: 928
sheet: -1.33 (0.25), residues: 373
loop : -0.65 (0.20), residues: 881
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.018 0.001 TRP B 169
HIS 0.005 0.001 HIS B 54
PHE 0.029 0.001 PHE A 100
TYR 0.021 0.001 TYR Q 510
ARG 0.006 0.000 ARG A 208
*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
4364 Ramachandran restraints generated.
2182 Oldfield, 0 Emsley, 2182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
4364 Ramachandran restraints generated.
2182 Oldfield, 0 Emsley, 2182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
398 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 44
poor density : 354
time to evaluate : 2.006
Fit side-chains
REVERT: Q 561 CYS cc_start: 0.5011 (m) cc_final: 0.4786 (m)
REVERT: R 248 ASP cc_start: 0.6540 (m-30) cc_final: 0.6155 (m-30)
REVERT: R 277 GLU cc_start: 0.7874 (tt0) cc_final: 0.7427 (tt0)
REVERT: R 282 GLU cc_start: 0.6738 (tp30) cc_final: 0.6337 (tp30)
REVERT: R 422 LEU cc_start: 0.8187 (OUTLIER) cc_final: 0.7662 (mp)
REVERT: R 679 LEU cc_start: 0.6859 (tp) cc_final: 0.6524 (mt)
REVERT: R 795 ARG cc_start: 0.7560 (ptt-90) cc_final: 0.7320 (ptt-90)
REVERT: A 106 ILE cc_start: 0.8307 (mm) cc_final: 0.7953 (mm)
REVERT: A 122 LEU cc_start: 0.7674 (tp) cc_final: 0.7401 (tp)
REVERT: A 135 ARG cc_start: 0.7963 (ttp80) cc_final: 0.7704 (ttp80)
REVERT: A 192 PHE cc_start: 0.6507 (t80) cc_final: 0.6223 (t80)
REVERT: A 234 ILE cc_start: 0.8920 (OUTLIER) cc_final: 0.8705 (mp)
REVERT: A 235 ILE cc_start: 0.8677 (mm) cc_final: 0.8450 (mp)
REVERT: B 36 ASN cc_start: 0.5138 (m-40) cc_final: 0.4865 (p0)
REVERT: B 198 LEU cc_start: 0.8898 (mm) cc_final: 0.8652 (mp)
REVERT: B 261 LEU cc_start: 0.7203 (mm) cc_final: 0.6873 (mp)
REVERT: B 285 LEU cc_start: 0.8915 (tp) cc_final: 0.8502 (tt)
outliers start: 44
outliers final: 31
residues processed: 376
average time/residue: 0.3445
time to fit residues: 195.1507
Evaluate side-chains
365 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 33
poor density : 332
time to evaluate : 1.955
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain Q residue 139 ILE
Chi-restraints excluded: chain Q residue 223 ILE
Chi-restraints excluded: chain Q residue 409 ILE
Chi-restraints excluded: chain Q residue 422 LEU
Chi-restraints excluded: chain Q residue 436 THR
Chi-restraints excluded: chain Q residue 485 LEU
Chi-restraints excluded: chain Q residue 727 LEU
Chi-restraints excluded: chain Q residue 736 ILE
Chi-restraints excluded: chain Q residue 757 GLU
Chi-restraints excluded: chain Q residue 775 PHE
Chi-restraints excluded: chain Q residue 859 ILE
Chi-restraints excluded: chain Q residue 860 ILE
Chi-restraints excluded: chain R residue 223 ILE
Chi-restraints excluded: chain R residue 336 LYS
Chi-restraints excluded: chain R residue 422 LEU
Chi-restraints excluded: chain R residue 592 ASN
Chi-restraints excluded: chain R residue 609 THR
Chi-restraints excluded: chain R residue 624 ILE
Chi-restraints excluded: chain R residue 689 VAL
Chi-restraints excluded: chain R residue 836 VAL
Chi-restraints excluded: chain R residue 848 LEU
Chi-restraints excluded: chain A residue 38 LEU
Chi-restraints excluded: chain A residue 124 ASP
Chi-restraints excluded: chain A residue 234 ILE
Chi-restraints excluded: chain B residue 40 VAL
Chi-restraints excluded: chain B residue 61 MET
Chi-restraints excluded: chain B residue 87 THR
Chi-restraints excluded: chain B residue 178 THR
Chi-restraints excluded: chain B residue 243 THR
Chi-restraints excluded: chain B residue 245 SER
Chi-restraints excluded: chain B residue 269 ILE
Chi-restraints excluded: chain B residue 274 THR
Chi-restraints excluded: chain B residue 327 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 218
random chunks:
chunk 70 optimal weight: 0.9980
chunk 133 optimal weight: 1.9990
chunk 202 optimal weight: 3.9990
chunk 93 optimal weight: 0.8980
chunk 47 optimal weight: 0.8980
chunk 158 optimal weight: 0.0970
chunk 118 optimal weight: 0.9990
chunk 199 optimal weight: 0.0970
chunk 121 optimal weight: 1.9990
chunk 102 optimal weight: 1.9990
chunk 66 optimal weight: 0.5980
overall best weight: 0.5176
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.116110 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.098438 restraints weight = 28246.781|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.098620 restraints weight = 23781.569|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.099509 restraints weight = 23139.109|
|-----------------------------------------------------------------------------|
r_work (final): 0.3216
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7227
moved from start: 0.1841
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.004 0.050 17907 Z= 0.268
Angle : 0.545 9.849 24328 Z= 0.285
Chirality : 0.043 0.146 2790
Planarity : 0.004 0.050 3056
Dihedral : 6.702 71.756 2791
Min Nonbonded Distance : 2.386
Molprobity Statistics.
All-atom Clashscore : 7.39
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 3.30 %
Favored : 96.70 %
Rotamer:
Outliers : 2.28 %
Allowed : 15.70 %
Favored : 82.02 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.09 %
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: -0.20 (0.17), residues: 2182
helix: 0.97 (0.16), residues: 931
sheet: -1.32 (0.26), residues: 368
loop : -0.67 (0.20), residues: 883
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.019 0.002 TRP B 169
HIS 0.006 0.001 HIS B 54
PHE 0.024 0.002 PHE A 100
TYR 0.021 0.002 TYR Q 510
ARG 0.008 0.000 ARG A 135
*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
4364 Ramachandran restraints generated.
2182 Oldfield, 0 Emsley, 2182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
4364 Ramachandran restraints generated.
2182 Oldfield, 0 Emsley, 2182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
385 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 41
poor density : 344
time to evaluate : 2.012
Fit side-chains
revert: symmetry clash
REVERT: Q 270 PHE cc_start: 0.7252 (OUTLIER) cc_final: 0.6913 (m-80)
REVERT: Q 561 CYS cc_start: 0.4991 (m) cc_final: 0.4773 (m)
REVERT: R 248 ASP cc_start: 0.6521 (m-30) cc_final: 0.6164 (m-30)
REVERT: R 277 GLU cc_start: 0.7871 (tt0) cc_final: 0.7408 (tt0)
REVERT: R 422 LEU cc_start: 0.8206 (OUTLIER) cc_final: 0.7678 (mp)
REVERT: R 526 GLU cc_start: 0.6715 (pp20) cc_final: 0.6446 (pp20)
REVERT: R 592 ASN cc_start: 0.7954 (OUTLIER) cc_final: 0.7692 (p0)
REVERT: R 679 LEU cc_start: 0.6822 (tp) cc_final: 0.6528 (mt)
REVERT: A 106 ILE cc_start: 0.8307 (mm) cc_final: 0.7945 (mm)
REVERT: A 122 LEU cc_start: 0.7633 (tp) cc_final: 0.7345 (tp)
REVERT: A 192 PHE cc_start: 0.6445 (t80) cc_final: 0.6195 (t80)
REVERT: A 234 ILE cc_start: 0.8940 (OUTLIER) cc_final: 0.8740 (mp)
REVERT: A 235 ILE cc_start: 0.8649 (mm) cc_final: 0.8403 (mp)
REVERT: B 36 ASN cc_start: 0.5133 (m-40) cc_final: 0.4899 (p0)
REVERT: B 198 LEU cc_start: 0.8890 (mm) cc_final: 0.8617 (mp)
REVERT: B 261 LEU cc_start: 0.7183 (mm) cc_final: 0.6850 (mp)
REVERT: B 285 LEU cc_start: 0.8927 (tp) cc_final: 0.8521 (tt)
outliers start: 41
outliers final: 34
residues processed: 368
average time/residue: 0.3590
time to fit residues: 194.0859
Evaluate side-chains
381 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 38
poor density : 343
time to evaluate : 2.022
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain Q residue 139 ILE
Chi-restraints excluded: chain Q residue 184 LEU
Chi-restraints excluded: chain Q residue 223 ILE
Chi-restraints excluded: chain Q residue 270 PHE
Chi-restraints excluded: chain Q residue 409 ILE
Chi-restraints excluded: chain Q residue 422 LEU
Chi-restraints excluded: chain Q residue 436 THR
Chi-restraints excluded: chain Q residue 485 LEU
Chi-restraints excluded: chain Q residue 566 VAL
Chi-restraints excluded: chain Q residue 727 LEU
Chi-restraints excluded: chain Q residue 736 ILE
Chi-restraints excluded: chain Q residue 740 VAL
Chi-restraints excluded: chain Q residue 757 GLU
Chi-restraints excluded: chain Q residue 775 PHE
Chi-restraints excluded: chain Q residue 859 ILE
Chi-restraints excluded: chain Q residue 860 ILE
Chi-restraints excluded: chain R residue 223 ILE
Chi-restraints excluded: chain R residue 336 LYS
Chi-restraints excluded: chain R residue 422 LEU
Chi-restraints excluded: chain R residue 592 ASN
Chi-restraints excluded: chain R residue 609 THR
Chi-restraints excluded: chain R residue 624 ILE
Chi-restraints excluded: chain R residue 689 VAL
Chi-restraints excluded: chain R residue 739 CYS
Chi-restraints excluded: chain R residue 836 VAL
Chi-restraints excluded: chain A residue 38 LEU
Chi-restraints excluded: chain A residue 124 ASP
Chi-restraints excluded: chain A residue 234 ILE
Chi-restraints excluded: chain B residue 40 VAL
Chi-restraints excluded: chain B residue 61 MET
Chi-restraints excluded: chain B residue 87 THR
Chi-restraints excluded: chain B residue 178 THR
Chi-restraints excluded: chain B residue 243 THR
Chi-restraints excluded: chain B residue 245 SER
Chi-restraints excluded: chain B residue 269 ILE
Chi-restraints excluded: chain B residue 270 ILE
Chi-restraints excluded: chain B residue 274 THR
Chi-restraints excluded: chain B residue 327 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 218
random chunks:
chunk 2 optimal weight: 1.9990
chunk 101 optimal weight: 0.9990
chunk 133 optimal weight: 1.9990
chunk 168 optimal weight: 0.6980
chunk 125 optimal weight: 0.6980
chunk 170 optimal weight: 0.9990
chunk 98 optimal weight: 0.8980
chunk 145 optimal weight: 0.9990
chunk 43 optimal weight: 0.5980
chunk 5 optimal weight: 0.9990
chunk 148 optimal weight: 0.7980
overall best weight: 0.7380
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.115362 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.097551 restraints weight = 28547.514|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.097560 restraints weight = 22230.198|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.098633 restraints weight = 21097.533|
|-----------------------------------------------------------------------------|
r_work (final): 0.3200
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7251
moved from start: 0.1860
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.005 0.051 17907 Z= 0.344
Angle : 0.577 9.087 24328 Z= 0.302
Chirality : 0.044 0.148 2790
Planarity : 0.004 0.051 3056
Dihedral : 6.768 72.965 2791
Min Nonbonded Distance : 2.357
Molprobity Statistics.
All-atom Clashscore : 7.65
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 3.94 %
Favored : 96.06 %
Rotamer:
Outliers : 2.50 %
Allowed : 15.93 %
Favored : 81.58 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.09 %
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 (0.17), residues: 2182
helix: 0.85 (0.16), residues: 931
sheet: -1.32 (0.25), residues: 368
loop : -0.71 (0.20), residues: 883
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.014 0.002 TRP Q 299
HIS 0.005 0.001 HIS Q 466
PHE 0.026 0.002 PHE A 100
TYR 0.020 0.002 TYR R 744
ARG 0.011 0.001 ARG A 135
*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
4364 Ramachandran restraints generated.
2182 Oldfield, 0 Emsley, 2182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
4364 Ramachandran restraints generated.
2182 Oldfield, 0 Emsley, 2182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
390 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 45
poor density : 345
time to evaluate : 2.311
Fit side-chains
REVERT: Q 270 PHE cc_start: 0.7259 (OUTLIER) cc_final: 0.6857 (m-80)
REVERT: Q 335 LYS cc_start: 0.7593 (mmtp) cc_final: 0.7310 (mmtp)
REVERT: Q 561 CYS cc_start: 0.5019 (m) cc_final: 0.4793 (m)
REVERT: Q 564 GLU cc_start: 0.6266 (OUTLIER) cc_final: 0.5981 (pt0)
REVERT: R 248 ASP cc_start: 0.6562 (m-30) cc_final: 0.6192 (m-30)
REVERT: R 422 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7698 (mp)
REVERT: R 526 GLU cc_start: 0.6736 (pp20) cc_final: 0.6466 (pp20)
REVERT: R 679 LEU cc_start: 0.6848 (tp) cc_final: 0.6545 (mt)
REVERT: R 725 PHE cc_start: 0.7650 (m-10) cc_final: 0.7445 (m-10)
REVERT: R 795 ARG cc_start: 0.7620 (ptt-90) cc_final: 0.7334 (ptt-90)
REVERT: A 106 ILE cc_start: 0.8370 (mm) cc_final: 0.8015 (mm)
REVERT: A 122 LEU cc_start: 0.7725 (tp) cc_final: 0.7439 (tp)
REVERT: A 192 PHE cc_start: 0.6500 (t80) cc_final: 0.6211 (t80)
REVERT: A 235 ILE cc_start: 0.8651 (mm) cc_final: 0.8404 (mp)
REVERT: B 36 ASN cc_start: 0.5187 (m-40) cc_final: 0.4926 (p0)
REVERT: B 198 LEU cc_start: 0.8934 (mm) cc_final: 0.8672 (mp)
REVERT: B 285 LEU cc_start: 0.8917 (tp) cc_final: 0.8511 (tt)
REVERT: B 311 HIS cc_start: 0.6532 (m-70) cc_final: 0.6069 (t-90)
outliers start: 45
outliers final: 38
residues processed: 369
average time/residue: 0.3305
time to fit residues: 180.8326
Evaluate side-chains
369 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 41
poor density : 328
time to evaluate : 1.925
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain Q residue 92 THR
Chi-restraints excluded: chain Q residue 139 ILE
Chi-restraints excluded: chain Q residue 184 LEU
Chi-restraints excluded: chain Q residue 223 ILE
Chi-restraints excluded: chain Q residue 270 PHE
Chi-restraints excluded: chain Q residue 409 ILE
Chi-restraints excluded: chain Q residue 422 LEU
Chi-restraints excluded: chain Q residue 436 THR
Chi-restraints excluded: chain Q residue 485 LEU
Chi-restraints excluded: chain Q residue 564 GLU
Chi-restraints excluded: chain Q residue 566 VAL
Chi-restraints excluded: chain Q residue 727 LEU
Chi-restraints excluded: chain Q residue 736 ILE
Chi-restraints excluded: chain Q residue 740 VAL
Chi-restraints excluded: chain Q residue 757 GLU
Chi-restraints excluded: chain Q residue 775 PHE
Chi-restraints excluded: chain Q residue 859 ILE
Chi-restraints excluded: chain Q residue 860 ILE
Chi-restraints excluded: chain R residue 24 GLN
Chi-restraints excluded: chain R residue 223 ILE
Chi-restraints excluded: chain R residue 336 LYS
Chi-restraints excluded: chain R residue 422 LEU
Chi-restraints excluded: chain R residue 609 THR
Chi-restraints excluded: chain R residue 624 ILE
Chi-restraints excluded: chain R residue 689 VAL
Chi-restraints excluded: chain R residue 739 CYS
Chi-restraints excluded: chain R residue 836 VAL
Chi-restraints excluded: chain A residue 124 ASP
Chi-restraints excluded: chain A residue 153 VAL
Chi-restraints excluded: chain A residue 154 LEU
Chi-restraints excluded: chain B residue 40 VAL
Chi-restraints excluded: chain B residue 61 MET
Chi-restraints excluded: chain B residue 87 THR
Chi-restraints excluded: chain B residue 171 ILE
Chi-restraints excluded: chain B residue 178 THR
Chi-restraints excluded: chain B residue 243 THR
Chi-restraints excluded: chain B residue 245 SER
Chi-restraints excluded: chain B residue 269 ILE
Chi-restraints excluded: chain B residue 270 ILE
Chi-restraints excluded: chain B residue 274 THR
Chi-restraints excluded: chain B residue 327 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 218
random chunks:
chunk 82 optimal weight: 0.5980
chunk 185 optimal weight: 1.9990
chunk 211 optimal weight: 0.5980
chunk 104 optimal weight: 0.2980
chunk 124 optimal weight: 0.9990
chunk 135 optimal weight: 0.9990
chunk 150 optimal weight: 0.5980
chunk 139 optimal weight: 0.9980
chunk 123 optimal weight: 0.5980
chunk 91 optimal weight: 0.6980
chunk 144 optimal weight: 0.0070
overall best weight: 0.4198
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.116129 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.098179 restraints weight = 28396.421|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.098224 restraints weight = 22689.920|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.099347 restraints weight = 21097.607|
|-----------------------------------------------------------------------------|
r_work (final): 0.3217
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7229
moved from start: 0.1943
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.004 0.079 17907 Z= 0.238
Angle : 0.544 8.710 24328 Z= 0.286
Chirality : 0.042 0.143 2790
Planarity : 0.004 0.049 3056
Dihedral : 6.607 72.545 2791
Min Nonbonded Distance : 2.344
Molprobity Statistics.
All-atom Clashscore : 7.30
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 3.16 %
Favored : 96.84 %
Rotamer:
Outliers : 2.05 %
Allowed : 16.32 %
Favored : 81.63 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.09 %
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: -0.20 (0.17), residues: 2182
helix: 0.93 (0.16), residues: 932
sheet: -1.19 (0.26), residues: 359
loop : -0.71 (0.20), residues: 891
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.017 0.002 TRP B 169
HIS 0.005 0.001 HIS B 54
PHE 0.024 0.002 PHE A 100
TYR 0.019 0.001 TYR R 744
ARG 0.011 0.000 ARG A 208
********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
4364 Ramachandran restraints generated.
2182 Oldfield, 0 Emsley, 2182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
4364 Ramachandran restraints generated.
2182 Oldfield, 0 Emsley, 2182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
373 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 37
poor density : 336
time to evaluate : 1.987
Fit side-chains
revert: symmetry clash
REVERT: Q 270 PHE cc_start: 0.7222 (OUTLIER) cc_final: 0.6853 (m-80)
REVERT: Q 335 LYS cc_start: 0.7541 (mmtp) cc_final: 0.7265 (mmtp)
REVERT: Q 436 THR cc_start: 0.8147 (OUTLIER) cc_final: 0.7937 (p)
REVERT: Q 561 CYS cc_start: 0.5023 (m) cc_final: 0.4803 (m)
REVERT: Q 564 GLU cc_start: 0.6320 (OUTLIER) cc_final: 0.6050 (pt0)
REVERT: R 248 ASP cc_start: 0.6545 (m-30) cc_final: 0.6170 (m-30)
REVERT: R 277 GLU cc_start: 0.7882 (tt0) cc_final: 0.7437 (tt0)
REVERT: R 282 GLU cc_start: 0.6786 (tp30) cc_final: 0.6362 (tp30)
REVERT: R 422 LEU cc_start: 0.8190 (OUTLIER) cc_final: 0.7686 (mp)
REVERT: R 526 GLU cc_start: 0.6732 (pp20) cc_final: 0.6461 (pp20)
REVERT: R 679 LEU cc_start: 0.6816 (tp) cc_final: 0.6523 (mt)
REVERT: A 106 ILE cc_start: 0.8364 (mm) cc_final: 0.8014 (mm)
REVERT: A 122 LEU cc_start: 0.7712 (tp) cc_final: 0.7434 (tp)
REVERT: A 192 PHE cc_start: 0.6489 (t80) cc_final: 0.6196 (t80)
REVERT: B 198 LEU cc_start: 0.8910 (mm) cc_final: 0.8634 (mp)
REVERT: B 285 LEU cc_start: 0.8903 (tp) cc_final: 0.8495 (tt)
REVERT: B 311 HIS cc_start: 0.6452 (m-70) cc_final: 0.6082 (t-90)
outliers start: 37
outliers final: 30
residues processed: 356
average time/residue: 0.3253
time to fit residues: 172.3101
Evaluate side-chains
369 residues out of total 1911 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 34
poor density : 335
time to evaluate : 1.816
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain Q residue 139 ILE
Chi-restraints excluded: chain Q residue 223 ILE
Chi-restraints excluded: chain Q residue 270 PHE
Chi-restraints excluded: chain Q residue 409 ILE
Chi-restraints excluded: chain Q residue 422 LEU
Chi-restraints excluded: chain Q residue 436 THR
Chi-restraints excluded: chain Q residue 485 LEU
Chi-restraints excluded: chain Q residue 564 GLU
Chi-restraints excluded: chain Q residue 566 VAL
Chi-restraints excluded: chain Q residue 727 LEU
Chi-restraints excluded: chain Q residue 736 ILE
Chi-restraints excluded: chain Q residue 757 GLU
Chi-restraints excluded: chain Q residue 775 PHE
Chi-restraints excluded: chain Q residue 859 ILE
Chi-restraints excluded: chain Q residue 860 ILE
Chi-restraints excluded: chain R residue 223 ILE
Chi-restraints excluded: chain R residue 336 LYS
Chi-restraints excluded: chain R residue 422 LEU
Chi-restraints excluded: chain R residue 609 THR
Chi-restraints excluded: chain R residue 624 ILE
Chi-restraints excluded: chain R residue 689 VAL
Chi-restraints excluded: chain R residue 739 CYS
Chi-restraints excluded: chain R residue 836 VAL
Chi-restraints excluded: chain A residue 124 ASP
Chi-restraints excluded: chain A residue 154 LEU
Chi-restraints excluded: chain B residue 40 VAL
Chi-restraints excluded: chain B residue 61 MET
Chi-restraints excluded: chain B residue 87 THR
Chi-restraints excluded: chain B residue 178 THR
Chi-restraints excluded: chain B residue 243 THR
Chi-restraints excluded: chain B residue 269 ILE
Chi-restraints excluded: chain B residue 270 ILE
Chi-restraints excluded: chain B residue 274 THR
Chi-restraints excluded: chain B residue 327 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 218
random chunks:
chunk 144 optimal weight: 0.5980
chunk 197 optimal weight: 0.5980
chunk 106 optimal weight: 0.0970
chunk 115 optimal weight: 0.9980
chunk 84 optimal weight: 0.1980
chunk 78 optimal weight: 0.5980
chunk 147 optimal weight: 0.7980
chunk 62 optimal weight: 0.5980
chunk 8 optimal weight: 0.5980
chunk 202 optimal weight: 3.9990
chunk 38 optimal weight: 0.9980
overall best weight: 0.4178
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.116304 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.098151 restraints weight = 28298.629|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.098417 restraints weight = 22976.471|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.099252 restraints weight = 21920.192|
|-----------------------------------------------------------------------------|
r_work (final): 0.3216
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7228
moved from start: 0.1998
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.004 0.069 17907 Z= 0.238
Angle : 0.544 8.399 24328 Z= 0.286
Chirality : 0.042 0.145 2790
Planarity : 0.004 0.046 3056
Dihedral : 6.528 71.685 2791
Min Nonbonded Distance : 2.338
Molprobity Statistics.
All-atom Clashscore : 7.07
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 3.39 %
Favored : 96.61 %
Rotamer:
Outliers : 1.94 %
Allowed : 16.48 %
Favored : 81.58 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.09 %
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 (0.17), residues: 2182
helix: 0.96 (0.16), residues: 932
sheet: -1.14 (0.27), residues: 342
loop : -0.74 (0.20), residues: 908
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.016 0.002 TRP B 169
HIS 0.003 0.001 HIS B 54
PHE 0.024 0.002 PHE A 100
TYR 0.019 0.001 TYR R 744
ARG 0.007 0.000 ARG A 135
Origin is already at (0, 0, 0), no shifts will be applied
Model does not fit in PDB format.
===============================================================================
Job complete
usr+sys time: 5493.11 seconds
wall clock time: 99 minutes 48.46 seconds (5988.46 seconds total)