Starting phenix.real_space_refine
on Thu Jan 16 19:21:17 2025 by dcliebschner
===============================================================================
Processing files:
-------------------------------------------------------------------------------
Found model, /net/cci-nas-00/data/ceres_data/9c0c_45079/01_2025/9c0c_45079.cif
Found real_map, /net/cci-nas-00/data/ceres_data/9c0c_45079/01_2025/9c0c_45079.map
Processing PHIL parameters:
-------------------------------------------------------------------------------
Adding command-line PHIL:
-------------------------
refinement.macro_cycles=10
scattering_table=electron
resolution=3.41
write_initial_geo_file=False
Final processed PHIL parameters:
-------------------------------------------------------------------------------
data_manager {
real_map_files = "/net/cci-nas-00/data/ceres_data/9c0c_45079/01_2025/9c0c_45079.map"
default_real_map = "/net/cci-nas-00/data/ceres_data/9c0c_45079/01_2025/9c0c_45079.map"
model {
file = "/net/cci-nas-00/data/ceres_data/9c0c_45079/01_2025/9c0c_45079.cif"
}
default_model = "/net/cci-nas-00/data/ceres_data/9c0c_45079/01_2025/9c0c_45079.cif"
}
resolution = 3.41
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= 0.003 sd= 0.071
Set stop_for_unknowns flag
Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
Set to: electron
Number of scattering types: 4
Type Number sf(0) Gaussians
S 280 5.16 5
C 33558 2.51 5
N 9310 2.21 5
O 10822 1.98 5
sf(0) = scattering factor at diffraction angle 0.
Process input model
Symmetric amino acids flipped. Time to flip 39 residue(s): 0.14s
Monomer Library directory:
"/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
Total number of atoms: 53970
Number of models: 1
Model: ""
Number of chains: 14
Chain: "A"
Number of atoms: 3855
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 524, 3855
Classifications: {'peptide': 524}
Link IDs: {'PTRANS': 14, 'TRANS': 509}
Chain: "N"
Number of atoms: 3855
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 524, 3855
Classifications: {'peptide': 524}
Link IDs: {'PTRANS': 14, 'TRANS': 509}
Chain: "B"
Number of atoms: 3855
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 524, 3855
Classifications: {'peptide': 524}
Link IDs: {'PTRANS': 14, 'TRANS': 509}
Chain: "H"
Number of atoms: 3855
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 524, 3855
Classifications: {'peptide': 524}
Link IDs: {'PTRANS': 14, 'TRANS': 509}
Chain: "C"
Number of atoms: 3855
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 524, 3855
Classifications: {'peptide': 524}
Link IDs: {'PTRANS': 14, 'TRANS': 509}
Chain: "I"
Number of atoms: 3855
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 524, 3855
Classifications: {'peptide': 524}
Link IDs: {'PTRANS': 14, 'TRANS': 509}
Chain: "D"
Number of atoms: 3855
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 524, 3855
Classifications: {'peptide': 524}
Link IDs: {'PTRANS': 14, 'TRANS': 509}
Chain: "J"
Number of atoms: 3855
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 524, 3855
Classifications: {'peptide': 524}
Link IDs: {'PTRANS': 14, 'TRANS': 509}
Chain: "E"
Number of atoms: 3855
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 524, 3855
Classifications: {'peptide': 524}
Link IDs: {'PTRANS': 14, 'TRANS': 509}
Chain: "K"
Number of atoms: 3855
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 524, 3855
Classifications: {'peptide': 524}
Link IDs: {'PTRANS': 14, 'TRANS': 509}
Chain: "F"
Number of atoms: 3855
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 524, 3855
Classifications: {'peptide': 524}
Link IDs: {'PTRANS': 14, 'TRANS': 509}
Chain: "L"
Number of atoms: 3855
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 524, 3855
Classifications: {'peptide': 524}
Link IDs: {'PTRANS': 14, 'TRANS': 509}
Chain: "G"
Number of atoms: 3855
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 524, 3855
Classifications: {'peptide': 524}
Link IDs: {'PTRANS': 14, 'TRANS': 509}
Chain: "M"
Number of atoms: 3855
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 524, 3855
Classifications: {'peptide': 524}
Link IDs: {'PTRANS': 14, 'TRANS': 509}
Time building chain proxies: 23.85, per 1000 atoms: 0.44
Number of scatterers: 53970
At special positions: 0
Unit cell: (159.85, 161, 158.7, 90, 90, 90)
Space group: P 1 (No. 1)
Number of sites at special positions: 0
Number of scattering types: 4
Type Number sf(0)
S 280 16.00
O 10822 8.00
N 9310 7.00
C 33558 6.00
sf(0) = scattering factor at diffraction angle 0.
Number of disulfides: simple=0, symmetry=0
Automatic linking
Parameters for automatic linking
Linking & cutoffs
Metal : Auto - 3.00
Amino acid : True - 1.90
Carbohydrate : True - 1.99
Ligands : True - 1.99
Small molecules : False - 1.98
Amino acid - RNA/DNA : False
Number of custom bonds: simple=0, symmetry=0
Time building additional restraints: 11.20
Conformation dependent library (CDL) restraints added in 5.8 seconds
14616 Ramachandran restraints generated.
7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2.
Adding C-beta torsion restraints...
Number of C-beta restraints generated: 13272
Finding SS restraints...
Secondary structure from input PDB file:
290 helices and 96 sheets defined
58.8% alpha, 14.3% beta
0 base pairs and 0 stacking pairs defined.
Time for finding SS restraints: 6.35
Creating SS restraints...
Processing helix chain 'A' and resid 9 through 29
removed outlier: 4.110A pdb=" N VAL A 29 " --> pdb=" O ASP A 25 " (cutoff:3.500A)
Processing helix chain 'A' and resid 52 through 60
removed outlier: 3.644A pdb=" N VAL A 56 " --> pdb=" O ASP A 52 " (cutoff:3.500A)
Processing helix chain 'A' and resid 64 through 86
removed outlier: 3.790A pdb=" N LYS A 80 " --> pdb=" O GLU A 76 " (cutoff:3.500A)
removed outlier: 4.130A pdb=" N ALA A 81 " --> pdb=" O VAL A 77 " (cutoff:3.500A)
removed outlier: 3.755A pdb=" N ASN A 82 " --> pdb=" O ALA A 78 " (cutoff:3.500A)
Processing helix chain 'A' and resid 88 through 108
Processing helix chain 'A' and resid 112 through 135
Processing helix chain 'A' and resid 140 through 152
Processing helix chain 'A' and resid 155 through 170
Processing helix chain 'A' and resid 201 through 205
Processing helix chain 'A' and resid 233 through 244
Processing helix chain 'A' and resid 258 through 266
Processing helix chain 'A' and resid 282 through 297
removed outlier: 3.533A pdb=" N LYS A 286 " --> pdb=" O GLY A 282 " (cutoff:3.500A)
Processing helix chain 'A' and resid 308 through 312
Processing helix chain 'A' and resid 338 through 355
Processing helix chain 'A' and resid 358 through 375
removed outlier: 4.287A pdb=" N GLY A 375 " --> pdb=" O LYS A 371 " (cutoff:3.500A)
Processing helix chain 'A' and resid 385 through 410
Processing helix chain 'A' and resid 416 through 426
removed outlier: 3.925A pdb=" N ILE A 420 " --> pdb=" O GLY A 416 " (cutoff:3.500A)
Processing helix chain 'A' and resid 433 through 447
Processing helix chain 'A' and resid 448 through 458
Processing helix chain 'A' and resid 461 through 472
removed outlier: 3.697A pdb=" N VAL A 465 " --> pdb=" O GLU A 461 " (cutoff:3.500A)
Processing helix chain 'A' and resid 488 through 492
Processing helix chain 'A' and resid 497 through 516
Processing helix chain 'N' and resid 9 through 29
removed outlier: 4.202A pdb=" N VAL N 29 " --> pdb=" O ASP N 25 " (cutoff:3.500A)
Processing helix chain 'N' and resid 52 through 60
removed outlier: 3.584A pdb=" N VAL N 56 " --> pdb=" O ASP N 52 " (cutoff:3.500A)
Processing helix chain 'N' and resid 64 through 86
removed outlier: 3.822A pdb=" N LYS N 80 " --> pdb=" O GLU N 76 " (cutoff:3.500A)
removed outlier: 3.852A pdb=" N ALA N 81 " --> pdb=" O VAL N 77 " (cutoff:3.500A)
removed outlier: 3.650A pdb=" N ASN N 82 " --> pdb=" O ALA N 78 " (cutoff:3.500A)
Processing helix chain 'N' and resid 88 through 108
Processing helix chain 'N' and resid 112 through 135
Processing helix chain 'N' and resid 140 through 152
Processing helix chain 'N' and resid 155 through 170
removed outlier: 3.541A pdb=" N GLY N 159 " --> pdb=" O ASP N 155 " (cutoff:3.500A)
Processing helix chain 'N' and resid 201 through 205
Processing helix chain 'N' and resid 233 through 244
Processing helix chain 'N' and resid 258 through 266
removed outlier: 3.567A pdb=" N LEU N 262 " --> pdb=" O ALA N 258 " (cutoff:3.500A)
Processing helix chain 'N' and resid 282 through 297
removed outlier: 3.558A pdb=" N LYS N 286 " --> pdb=" O GLY N 282 " (cutoff:3.500A)
Processing helix chain 'N' and resid 308 through 312
Processing helix chain 'N' and resid 338 through 355
Processing helix chain 'N' and resid 358 through 375
removed outlier: 4.351A pdb=" N GLY N 375 " --> pdb=" O LYS N 371 " (cutoff:3.500A)
Processing helix chain 'N' and resid 385 through 410
Processing helix chain 'N' and resid 416 through 426
removed outlier: 3.878A pdb=" N ILE N 420 " --> pdb=" O GLY N 416 " (cutoff:3.500A)
Processing helix chain 'N' and resid 433 through 447
removed outlier: 3.575A pdb=" N ASN N 437 " --> pdb=" O ASN N 433 " (cutoff:3.500A)
Processing helix chain 'N' and resid 448 through 458
Processing helix chain 'N' and resid 461 through 472
removed outlier: 3.596A pdb=" N VAL N 465 " --> pdb=" O GLU N 461 " (cutoff:3.500A)
Processing helix chain 'N' and resid 497 through 516
Processing helix chain 'B' and resid 9 through 29
removed outlier: 4.154A pdb=" N VAL B 29 " --> pdb=" O ASP B 25 " (cutoff:3.500A)
Processing helix chain 'B' and resid 52 through 60
removed outlier: 3.626A pdb=" N VAL B 56 " --> pdb=" O ASP B 52 " (cutoff:3.500A)
Processing helix chain 'B' and resid 64 through 86
removed outlier: 3.835A pdb=" N LYS B 80 " --> pdb=" O GLU B 76 " (cutoff:3.500A)
removed outlier: 4.134A pdb=" N ALA B 81 " --> pdb=" O VAL B 77 " (cutoff:3.500A)
removed outlier: 3.780A pdb=" N ASN B 82 " --> pdb=" O ALA B 78 " (cutoff:3.500A)
Processing helix chain 'B' and resid 88 through 108
Processing helix chain 'B' and resid 112 through 135
Processing helix chain 'B' and resid 140 through 152
Processing helix chain 'B' and resid 155 through 170
Processing helix chain 'B' and resid 201 through 205
Processing helix chain 'B' and resid 233 through 244
Processing helix chain 'B' and resid 258 through 266
Processing helix chain 'B' and resid 282 through 297
removed outlier: 3.530A pdb=" N LYS B 286 " --> pdb=" O GLY B 282 " (cutoff:3.500A)
Processing helix chain 'B' and resid 308 through 312
Processing helix chain 'B' and resid 338 through 355
Processing helix chain 'B' and resid 358 through 375
removed outlier: 4.275A pdb=" N GLY B 375 " --> pdb=" O LYS B 371 " (cutoff:3.500A)
Processing helix chain 'B' and resid 385 through 410
Processing helix chain 'B' and resid 416 through 426
removed outlier: 3.878A pdb=" N ILE B 420 " --> pdb=" O GLY B 416 " (cutoff:3.500A)
Processing helix chain 'B' and resid 433 through 447
Processing helix chain 'B' and resid 448 through 458
Processing helix chain 'B' and resid 461 through 472
removed outlier: 3.699A pdb=" N VAL B 465 " --> pdb=" O GLU B 461 " (cutoff:3.500A)
Processing helix chain 'B' and resid 488 through 492
Processing helix chain 'B' and resid 497 through 516
Processing helix chain 'H' and resid 9 through 29
removed outlier: 4.102A pdb=" N VAL H 29 " --> pdb=" O ASP H 25 " (cutoff:3.500A)
Processing helix chain 'H' and resid 52 through 60
removed outlier: 3.612A pdb=" N VAL H 56 " --> pdb=" O ASP H 52 " (cutoff:3.500A)
Processing helix chain 'H' and resid 64 through 86
removed outlier: 3.878A pdb=" N LYS H 80 " --> pdb=" O GLU H 76 " (cutoff:3.500A)
removed outlier: 3.882A pdb=" N ALA H 81 " --> pdb=" O VAL H 77 " (cutoff:3.500A)
removed outlier: 3.646A pdb=" N ASN H 82 " --> pdb=" O ALA H 78 " (cutoff:3.500A)
Processing helix chain 'H' and resid 88 through 108
Processing helix chain 'H' and resid 112 through 135
Processing helix chain 'H' and resid 140 through 152
Processing helix chain 'H' and resid 155 through 170
removed outlier: 3.535A pdb=" N GLY H 159 " --> pdb=" O ASP H 155 " (cutoff:3.500A)
Processing helix chain 'H' and resid 201 through 205
Processing helix chain 'H' and resid 233 through 244
Processing helix chain 'H' and resid 258 through 266
Processing helix chain 'H' and resid 282 through 297
removed outlier: 3.557A pdb=" N LYS H 286 " --> pdb=" O GLY H 282 " (cutoff:3.500A)
Processing helix chain 'H' and resid 308 through 312
Processing helix chain 'H' and resid 338 through 355
Processing helix chain 'H' and resid 358 through 375
removed outlier: 4.356A pdb=" N GLY H 375 " --> pdb=" O LYS H 371 " (cutoff:3.500A)
Processing helix chain 'H' and resid 385 through 410
Processing helix chain 'H' and resid 416 through 426
removed outlier: 3.846A pdb=" N ILE H 420 " --> pdb=" O GLY H 416 " (cutoff:3.500A)
Processing helix chain 'H' and resid 433 through 447
removed outlier: 3.623A pdb=" N ASN H 437 " --> pdb=" O ASN H 433 " (cutoff:3.500A)
Processing helix chain 'H' and resid 448 through 458
Processing helix chain 'H' and resid 461 through 472
removed outlier: 3.610A pdb=" N VAL H 465 " --> pdb=" O GLU H 461 " (cutoff:3.500A)
Processing helix chain 'H' and resid 488 through 492
Processing helix chain 'H' and resid 497 through 516
Processing helix chain 'C' and resid 9 through 29
removed outlier: 4.097A pdb=" N VAL C 29 " --> pdb=" O ASP C 25 " (cutoff:3.500A)
Processing helix chain 'C' and resid 52 through 60
removed outlier: 3.644A pdb=" N VAL C 56 " --> pdb=" O ASP C 52 " (cutoff:3.500A)
Processing helix chain 'C' and resid 64 through 86
removed outlier: 3.821A pdb=" N LYS C 80 " --> pdb=" O GLU C 76 " (cutoff:3.500A)
removed outlier: 4.155A pdb=" N ALA C 81 " --> pdb=" O VAL C 77 " (cutoff:3.500A)
removed outlier: 3.795A pdb=" N ASN C 82 " --> pdb=" O ALA C 78 " (cutoff:3.500A)
Processing helix chain 'C' and resid 88 through 108
Processing helix chain 'C' and resid 112 through 135
Processing helix chain 'C' and resid 140 through 152
Processing helix chain 'C' and resid 155 through 170
Processing helix chain 'C' and resid 201 through 205
Processing helix chain 'C' and resid 233 through 244
Processing helix chain 'C' and resid 258 through 266
removed outlier: 3.573A pdb=" N LEU C 262 " --> pdb=" O ALA C 258 " (cutoff:3.500A)
Processing helix chain 'C' and resid 282 through 297
removed outlier: 3.519A pdb=" N LYS C 286 " --> pdb=" O GLY C 282 " (cutoff:3.500A)
Processing helix chain 'C' and resid 308 through 312
Processing helix chain 'C' and resid 338 through 355
Processing helix chain 'C' and resid 358 through 375
removed outlier: 4.258A pdb=" N GLY C 375 " --> pdb=" O LYS C 371 " (cutoff:3.500A)
Processing helix chain 'C' and resid 385 through 410
Processing helix chain 'C' and resid 416 through 426
removed outlier: 3.823A pdb=" N ILE C 420 " --> pdb=" O GLY C 416 " (cutoff:3.500A)
Processing helix chain 'C' and resid 433 through 447
Processing helix chain 'C' and resid 448 through 458
Processing helix chain 'C' and resid 461 through 472
removed outlier: 3.697A pdb=" N VAL C 465 " --> pdb=" O GLU C 461 " (cutoff:3.500A)
Processing helix chain 'C' and resid 497 through 516
Processing helix chain 'I' and resid 9 through 29
removed outlier: 4.177A pdb=" N VAL I 29 " --> pdb=" O ASP I 25 " (cutoff:3.500A)
Processing helix chain 'I' and resid 52 through 60
removed outlier: 3.616A pdb=" N VAL I 56 " --> pdb=" O ASP I 52 " (cutoff:3.500A)
Processing helix chain 'I' and resid 64 through 86
removed outlier: 3.900A pdb=" N LYS I 80 " --> pdb=" O GLU I 76 " (cutoff:3.500A)
removed outlier: 3.898A pdb=" N ALA I 81 " --> pdb=" O VAL I 77 " (cutoff:3.500A)
removed outlier: 3.648A pdb=" N ASN I 82 " --> pdb=" O ALA I 78 " (cutoff:3.500A)
Processing helix chain 'I' and resid 88 through 108
Processing helix chain 'I' and resid 112 through 135
Processing helix chain 'I' and resid 140 through 152
Processing helix chain 'I' and resid 155 through 170
removed outlier: 3.535A pdb=" N GLY I 159 " --> pdb=" O ASP I 155 " (cutoff:3.500A)
Processing helix chain 'I' and resid 201 through 205
Processing helix chain 'I' and resid 229 through 232
removed outlier: 3.658A pdb=" N GLU I 232 " --> pdb=" O ASN I 229 " (cutoff:3.500A)
No H-bonds generated for 'chain 'I' and resid 229 through 232'
Processing helix chain 'I' and resid 233 through 244
Processing helix chain 'I' and resid 258 through 265
removed outlier: 3.549A pdb=" N LEU I 262 " --> pdb=" O ALA I 258 " (cutoff:3.500A)
Processing helix chain 'I' and resid 282 through 297
removed outlier: 3.564A pdb=" N LYS I 286 " --> pdb=" O GLY I 282 " (cutoff:3.500A)
Processing helix chain 'I' and resid 308 through 312
Processing helix chain 'I' and resid 338 through 355
Processing helix chain 'I' and resid 358 through 375
removed outlier: 4.378A pdb=" N GLY I 375 " --> pdb=" O LYS I 371 " (cutoff:3.500A)
Processing helix chain 'I' and resid 385 through 410
Processing helix chain 'I' and resid 416 through 426
removed outlier: 3.837A pdb=" N ILE I 420 " --> pdb=" O GLY I 416 " (cutoff:3.500A)
Processing helix chain 'I' and resid 433 through 447
removed outlier: 3.614A pdb=" N ASN I 437 " --> pdb=" O ASN I 433 " (cutoff:3.500A)
Processing helix chain 'I' and resid 448 through 458
Processing helix chain 'I' and resid 461 through 472
removed outlier: 3.628A pdb=" N VAL I 465 " --> pdb=" O GLU I 461 " (cutoff:3.500A)
Processing helix chain 'I' and resid 488 through 492
Processing helix chain 'I' and resid 497 through 516
Processing helix chain 'D' and resid 9 through 29
removed outlier: 4.081A pdb=" N VAL D 29 " --> pdb=" O ASP D 25 " (cutoff:3.500A)
Processing helix chain 'D' and resid 52 through 60
removed outlier: 3.620A pdb=" N VAL D 56 " --> pdb=" O ASP D 52 " (cutoff:3.500A)
Processing helix chain 'D' and resid 64 through 86
removed outlier: 3.876A pdb=" N LYS D 80 " --> pdb=" O GLU D 76 " (cutoff:3.500A)
removed outlier: 4.064A pdb=" N ALA D 81 " --> pdb=" O VAL D 77 " (cutoff:3.500A)
removed outlier: 3.781A pdb=" N ASN D 82 " --> pdb=" O ALA D 78 " (cutoff:3.500A)
Processing helix chain 'D' and resid 88 through 108
Processing helix chain 'D' and resid 112 through 135
Processing helix chain 'D' and resid 140 through 152
Processing helix chain 'D' and resid 155 through 170
Processing helix chain 'D' and resid 201 through 205
Processing helix chain 'D' and resid 233 through 244
Processing helix chain 'D' and resid 258 through 266
removed outlier: 3.530A pdb=" N LEU D 262 " --> pdb=" O ALA D 258 " (cutoff:3.500A)
Processing helix chain 'D' and resid 282 through 297
Processing helix chain 'D' and resid 308 through 312
Processing helix chain 'D' and resid 338 through 355
Processing helix chain 'D' and resid 358 through 375
removed outlier: 4.204A pdb=" N GLY D 375 " --> pdb=" O LYS D 371 " (cutoff:3.500A)
Processing helix chain 'D' and resid 385 through 410
Processing helix chain 'D' and resid 416 through 426
removed outlier: 3.965A pdb=" N ILE D 420 " --> pdb=" O GLY D 416 " (cutoff:3.500A)
Processing helix chain 'D' and resid 433 through 447
Processing helix chain 'D' and resid 448 through 458
Processing helix chain 'D' and resid 461 through 472
removed outlier: 3.714A pdb=" N VAL D 465 " --> pdb=" O GLU D 461 " (cutoff:3.500A)
Processing helix chain 'D' and resid 488 through 492
Processing helix chain 'D' and resid 497 through 516
Processing helix chain 'J' and resid 9 through 29
removed outlier: 4.129A pdb=" N VAL J 29 " --> pdb=" O ASP J 25 " (cutoff:3.500A)
Processing helix chain 'J' and resid 52 through 60
removed outlier: 3.619A pdb=" N VAL J 56 " --> pdb=" O ASP J 52 " (cutoff:3.500A)
Processing helix chain 'J' and resid 64 through 86
removed outlier: 3.842A pdb=" N LYS J 80 " --> pdb=" O GLU J 76 " (cutoff:3.500A)
removed outlier: 3.878A pdb=" N ALA J 81 " --> pdb=" O VAL J 77 " (cutoff:3.500A)
removed outlier: 3.644A pdb=" N ASN J 82 " --> pdb=" O ALA J 78 " (cutoff:3.500A)
Processing helix chain 'J' and resid 88 through 108
Processing helix chain 'J' and resid 112 through 135
Processing helix chain 'J' and resid 140 through 152
Processing helix chain 'J' and resid 155 through 170
removed outlier: 3.541A pdb=" N GLY J 159 " --> pdb=" O ASP J 155 " (cutoff:3.500A)
Processing helix chain 'J' and resid 201 through 205
Processing helix chain 'J' and resid 233 through 244
Processing helix chain 'J' and resid 258 through 266
removed outlier: 3.537A pdb=" N LEU J 262 " --> pdb=" O ALA J 258 " (cutoff:3.500A)
Processing helix chain 'J' and resid 282 through 297
removed outlier: 3.567A pdb=" N LYS J 286 " --> pdb=" O GLY J 282 " (cutoff:3.500A)
Processing helix chain 'J' and resid 308 through 312
Processing helix chain 'J' and resid 338 through 355
Processing helix chain 'J' and resid 358 through 375
removed outlier: 4.277A pdb=" N GLY J 375 " --> pdb=" O LYS J 371 " (cutoff:3.500A)
Processing helix chain 'J' and resid 385 through 410
Processing helix chain 'J' and resid 416 through 426
removed outlier: 3.831A pdb=" N ILE J 420 " --> pdb=" O GLY J 416 " (cutoff:3.500A)
Processing helix chain 'J' and resid 433 through 447
removed outlier: 3.608A pdb=" N ASN J 437 " --> pdb=" O ASN J 433 " (cutoff:3.500A)
Processing helix chain 'J' and resid 448 through 458
Processing helix chain 'J' and resid 461 through 472
removed outlier: 3.613A pdb=" N VAL J 465 " --> pdb=" O GLU J 461 " (cutoff:3.500A)
Processing helix chain 'J' and resid 497 through 516
Processing helix chain 'E' and resid 9 through 29
removed outlier: 4.125A pdb=" N VAL E 29 " --> pdb=" O ASP E 25 " (cutoff:3.500A)
Processing helix chain 'E' and resid 52 through 60
removed outlier: 3.590A pdb=" N VAL E 56 " --> pdb=" O ASP E 52 " (cutoff:3.500A)
Processing helix chain 'E' and resid 64 through 86
removed outlier: 3.866A pdb=" N LYS E 80 " --> pdb=" O GLU E 76 " (cutoff:3.500A)
removed outlier: 4.053A pdb=" N ALA E 81 " --> pdb=" O VAL E 77 " (cutoff:3.500A)
removed outlier: 3.772A pdb=" N ASN E 82 " --> pdb=" O ALA E 78 " (cutoff:3.500A)
Processing helix chain 'E' and resid 88 through 108
Processing helix chain 'E' and resid 112 through 135
Processing helix chain 'E' and resid 140 through 152
Processing helix chain 'E' and resid 155 through 170
Processing helix chain 'E' and resid 201 through 205
Processing helix chain 'E' and resid 233 through 244
Processing helix chain 'E' and resid 258 through 265
removed outlier: 3.620A pdb=" N LEU E 262 " --> pdb=" O ALA E 258 " (cutoff:3.500A)
Processing helix chain 'E' and resid 282 through 297
removed outlier: 3.533A pdb=" N LYS E 286 " --> pdb=" O GLY E 282 " (cutoff:3.500A)
Processing helix chain 'E' and resid 308 through 312
Processing helix chain 'E' and resid 338 through 355
Processing helix chain 'E' and resid 358 through 375
removed outlier: 4.263A pdb=" N GLY E 375 " --> pdb=" O LYS E 371 " (cutoff:3.500A)
Processing helix chain 'E' and resid 385 through 410
Processing helix chain 'E' and resid 416 through 426
removed outlier: 3.916A pdb=" N ILE E 420 " --> pdb=" O GLY E 416 " (cutoff:3.500A)
Processing helix chain 'E' and resid 433 through 447
Processing helix chain 'E' and resid 448 through 458
Processing helix chain 'E' and resid 461 through 472
removed outlier: 3.700A pdb=" N VAL E 465 " --> pdb=" O GLU E 461 " (cutoff:3.500A)
Processing helix chain 'E' and resid 488 through 492
Processing helix chain 'E' and resid 497 through 516
Processing helix chain 'K' and resid 9 through 29
removed outlier: 4.165A pdb=" N VAL K 29 " --> pdb=" O ASP K 25 " (cutoff:3.500A)
Processing helix chain 'K' and resid 52 through 60
removed outlier: 3.631A pdb=" N VAL K 56 " --> pdb=" O ASP K 52 " (cutoff:3.500A)
Processing helix chain 'K' and resid 64 through 86
removed outlier: 3.816A pdb=" N LYS K 80 " --> pdb=" O GLU K 76 " (cutoff:3.500A)
removed outlier: 3.867A pdb=" N ALA K 81 " --> pdb=" O VAL K 77 " (cutoff:3.500A)
removed outlier: 3.634A pdb=" N ASN K 82 " --> pdb=" O ALA K 78 " (cutoff:3.500A)
Processing helix chain 'K' and resid 88 through 108
Processing helix chain 'K' and resid 112 through 135
Processing helix chain 'K' and resid 140 through 152
Processing helix chain 'K' and resid 155 through 170
removed outlier: 3.540A pdb=" N GLY K 159 " --> pdb=" O ASP K 155 " (cutoff:3.500A)
Processing helix chain 'K' and resid 201 through 205
Processing helix chain 'K' and resid 233 through 244
Processing helix chain 'K' and resid 258 through 265
removed outlier: 3.502A pdb=" N LEU K 262 " --> pdb=" O ALA K 258 " (cutoff:3.500A)
Processing helix chain 'K' and resid 282 through 297
removed outlier: 3.546A pdb=" N LYS K 286 " --> pdb=" O GLY K 282 " (cutoff:3.500A)
Processing helix chain 'K' and resid 308 through 312
Processing helix chain 'K' and resid 338 through 355
Processing helix chain 'K' and resid 358 through 375
removed outlier: 4.366A pdb=" N GLY K 375 " --> pdb=" O LYS K 371 " (cutoff:3.500A)
Processing helix chain 'K' and resid 385 through 410
Processing helix chain 'K' and resid 416 through 426
removed outlier: 3.854A pdb=" N ILE K 420 " --> pdb=" O GLY K 416 " (cutoff:3.500A)
Processing helix chain 'K' and resid 433 through 447
removed outlier: 3.552A pdb=" N ASN K 437 " --> pdb=" O ASN K 433 " (cutoff:3.500A)
Processing helix chain 'K' and resid 448 through 458
Processing helix chain 'K' and resid 461 through 472
removed outlier: 3.605A pdb=" N VAL K 465 " --> pdb=" O GLU K 461 " (cutoff:3.500A)
Processing helix chain 'K' and resid 497 through 516
Processing helix chain 'F' and resid 9 through 29
removed outlier: 4.100A pdb=" N VAL F 29 " --> pdb=" O ASP F 25 " (cutoff:3.500A)
Processing helix chain 'F' and resid 52 through 60
removed outlier: 3.638A pdb=" N VAL F 56 " --> pdb=" O ASP F 52 " (cutoff:3.500A)
Processing helix chain 'F' and resid 64 through 86
removed outlier: 3.742A pdb=" N LYS F 80 " --> pdb=" O GLU F 76 " (cutoff:3.500A)
removed outlier: 4.168A pdb=" N ALA F 81 " --> pdb=" O VAL F 77 " (cutoff:3.500A)
removed outlier: 3.749A pdb=" N ASN F 82 " --> pdb=" O ALA F 78 " (cutoff:3.500A)
Processing helix chain 'F' and resid 88 through 108
Processing helix chain 'F' and resid 112 through 135
Processing helix chain 'F' and resid 140 through 152
Processing helix chain 'F' and resid 155 through 170
Processing helix chain 'F' and resid 201 through 205
Processing helix chain 'F' and resid 233 through 244
Processing helix chain 'F' and resid 258 through 266
removed outlier: 3.519A pdb=" N LEU F 262 " --> pdb=" O ALA F 258 " (cutoff:3.500A)
Processing helix chain 'F' and resid 282 through 297
removed outlier: 3.504A pdb=" N LYS F 286 " --> pdb=" O GLY F 282 " (cutoff:3.500A)
Processing helix chain 'F' and resid 308 through 312
Processing helix chain 'F' and resid 338 through 355
removed outlier: 3.503A pdb=" N ILE F 342 " --> pdb=" O GLU F 338 " (cutoff:3.500A)
Processing helix chain 'F' and resid 358 through 375
removed outlier: 4.230A pdb=" N GLY F 375 " --> pdb=" O LYS F 371 " (cutoff:3.500A)
Processing helix chain 'F' and resid 385 through 410
Processing helix chain 'F' and resid 416 through 426
removed outlier: 3.862A pdb=" N ILE F 420 " --> pdb=" O GLY F 416 " (cutoff:3.500A)
Processing helix chain 'F' and resid 433 through 447
Processing helix chain 'F' and resid 448 through 458
Processing helix chain 'F' and resid 461 through 472
removed outlier: 3.698A pdb=" N VAL F 465 " --> pdb=" O GLU F 461 " (cutoff:3.500A)
Processing helix chain 'F' and resid 488 through 492
Processing helix chain 'F' and resid 497 through 516
Processing helix chain 'L' and resid 9 through 29
removed outlier: 4.164A pdb=" N VAL L 29 " --> pdb=" O ASP L 25 " (cutoff:3.500A)
Processing helix chain 'L' and resid 52 through 60
removed outlier: 3.615A pdb=" N VAL L 56 " --> pdb=" O ASP L 52 " (cutoff:3.500A)
Processing helix chain 'L' and resid 64 through 86
removed outlier: 3.805A pdb=" N LYS L 80 " --> pdb=" O GLU L 76 " (cutoff:3.500A)
removed outlier: 3.889A pdb=" N ALA L 81 " --> pdb=" O VAL L 77 " (cutoff:3.500A)
removed outlier: 3.643A pdb=" N ASN L 82 " --> pdb=" O ALA L 78 " (cutoff:3.500A)
Processing helix chain 'L' and resid 88 through 108
Processing helix chain 'L' and resid 112 through 135
Processing helix chain 'L' and resid 140 through 152
Processing helix chain 'L' and resid 155 through 170
removed outlier: 3.541A pdb=" N GLY L 159 " --> pdb=" O ASP L 155 " (cutoff:3.500A)
Processing helix chain 'L' and resid 201 through 205
Processing helix chain 'L' and resid 233 through 244
Processing helix chain 'L' and resid 258 through 265
removed outlier: 3.523A pdb=" N LEU L 262 " --> pdb=" O ALA L 258 " (cutoff:3.500A)
Processing helix chain 'L' and resid 282 through 297
removed outlier: 3.531A pdb=" N LYS L 286 " --> pdb=" O GLY L 282 " (cutoff:3.500A)
Processing helix chain 'L' and resid 308 through 312
Processing helix chain 'L' and resid 338 through 355
Processing helix chain 'L' and resid 358 through 375
removed outlier: 4.261A pdb=" N GLY L 375 " --> pdb=" O LYS L 371 " (cutoff:3.500A)
Processing helix chain 'L' and resid 385 through 410
Processing helix chain 'L' and resid 416 through 426
removed outlier: 3.857A pdb=" N ILE L 420 " --> pdb=" O GLY L 416 " (cutoff:3.500A)
Processing helix chain 'L' and resid 433 through 447
removed outlier: 3.572A pdb=" N ASN L 437 " --> pdb=" O ASN L 433 " (cutoff:3.500A)
Processing helix chain 'L' and resid 448 through 458
Processing helix chain 'L' and resid 461 through 472
removed outlier: 3.609A pdb=" N VAL L 465 " --> pdb=" O GLU L 461 " (cutoff:3.500A)
Processing helix chain 'L' and resid 488 through 492
Processing helix chain 'L' and resid 497 through 516
Processing helix chain 'G' and resid 9 through 29
removed outlier: 4.123A pdb=" N VAL G 29 " --> pdb=" O ASP G 25 " (cutoff:3.500A)
Processing helix chain 'G' and resid 52 through 60
removed outlier: 3.609A pdb=" N VAL G 56 " --> pdb=" O ASP G 52 " (cutoff:3.500A)
Processing helix chain 'G' and resid 64 through 86
removed outlier: 3.791A pdb=" N LYS G 80 " --> pdb=" O GLU G 76 " (cutoff:3.500A)
removed outlier: 4.126A pdb=" N ALA G 81 " --> pdb=" O VAL G 77 " (cutoff:3.500A)
removed outlier: 3.757A pdb=" N ASN G 82 " --> pdb=" O ALA G 78 " (cutoff:3.500A)
Processing helix chain 'G' and resid 88 through 108
Processing helix chain 'G' and resid 112 through 135
Processing helix chain 'G' and resid 140 through 152
Processing helix chain 'G' and resid 155 through 170
Processing helix chain 'G' and resid 201 through 205
Processing helix chain 'G' and resid 233 through 244
Processing helix chain 'G' and resid 258 through 266
Processing helix chain 'G' and resid 282 through 297
removed outlier: 3.540A pdb=" N LYS G 286 " --> pdb=" O GLY G 282 " (cutoff:3.500A)
Processing helix chain 'G' and resid 308 through 312
Processing helix chain 'G' and resid 338 through 355
removed outlier: 3.502A pdb=" N ILE G 342 " --> pdb=" O GLU G 338 " (cutoff:3.500A)
Processing helix chain 'G' and resid 358 through 375
removed outlier: 4.250A pdb=" N GLY G 375 " --> pdb=" O LYS G 371 " (cutoff:3.500A)
Processing helix chain 'G' and resid 385 through 410
Processing helix chain 'G' and resid 416 through 426
removed outlier: 3.885A pdb=" N ILE G 420 " --> pdb=" O GLY G 416 " (cutoff:3.500A)
Processing helix chain 'G' and resid 433 through 447
Processing helix chain 'G' and resid 448 through 458
Processing helix chain 'G' and resid 461 through 472
removed outlier: 3.692A pdb=" N VAL G 465 " --> pdb=" O GLU G 461 " (cutoff:3.500A)
Processing helix chain 'G' and resid 488 through 492
Processing helix chain 'G' and resid 497 through 516
Processing helix chain 'M' and resid 9 through 29
removed outlier: 4.141A pdb=" N VAL M 29 " --> pdb=" O ASP M 25 " (cutoff:3.500A)
Processing helix chain 'M' and resid 52 through 60
removed outlier: 3.642A pdb=" N VAL M 56 " --> pdb=" O ASP M 52 " (cutoff:3.500A)
Processing helix chain 'M' and resid 64 through 86
removed outlier: 3.842A pdb=" N LYS M 80 " --> pdb=" O GLU M 76 " (cutoff:3.500A)
removed outlier: 3.881A pdb=" N ALA M 81 " --> pdb=" O VAL M 77 " (cutoff:3.500A)
removed outlier: 3.662A pdb=" N ASN M 82 " --> pdb=" O ALA M 78 " (cutoff:3.500A)
Processing helix chain 'M' and resid 88 through 108
Processing helix chain 'M' and resid 112 through 135
Processing helix chain 'M' and resid 140 through 152
Processing helix chain 'M' and resid 155 through 170
removed outlier: 3.539A pdb=" N GLY M 159 " --> pdb=" O ASP M 155 " (cutoff:3.500A)
Processing helix chain 'M' and resid 201 through 205
Processing helix chain 'M' and resid 233 through 244
Processing helix chain 'M' and resid 258 through 266
removed outlier: 3.570A pdb=" N LEU M 262 " --> pdb=" O ALA M 258 " (cutoff:3.500A)
Processing helix chain 'M' and resid 282 through 297
removed outlier: 3.540A pdb=" N LYS M 286 " --> pdb=" O GLY M 282 " (cutoff:3.500A)
Processing helix chain 'M' and resid 308 through 312
Processing helix chain 'M' and resid 338 through 355
Processing helix chain 'M' and resid 358 through 375
removed outlier: 4.338A pdb=" N GLY M 375 " --> pdb=" O LYS M 371 " (cutoff:3.500A)
Processing helix chain 'M' and resid 385 through 410
Processing helix chain 'M' and resid 416 through 426
removed outlier: 3.840A pdb=" N ILE M 420 " --> pdb=" O GLY M 416 " (cutoff:3.500A)
Processing helix chain 'M' and resid 433 through 447
removed outlier: 3.506A pdb=" N ASN M 437 " --> pdb=" O ASN M 433 " (cutoff:3.500A)
Processing helix chain 'M' and resid 448 through 458
Processing helix chain 'M' and resid 461 through 472
removed outlier: 3.602A pdb=" N VAL M 465 " --> pdb=" O GLU M 461 " (cutoff:3.500A)
Processing helix chain 'M' and resid 497 through 516
Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 8
removed outlier: 6.097A pdb=" N ASN G 37 " --> pdb=" O THR A 517 " (cutoff:3.500A)
removed outlier: 3.824A pdb=" N CYS A 519 " --> pdb=" O ASN G 37 " (cutoff:3.500A)
Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 50
removed outlier: 6.955A pdb=" N ASN A 37 " --> pdb=" O CYS B 519 " (cutoff:3.500A)
removed outlier: 8.294A pdb=" N VAL B 521 " --> pdb=" O ASN A 37 " (cutoff:3.500A)
removed outlier: 6.415A pdb=" N VAL A 39 " --> pdb=" O VAL B 521 " (cutoff:3.500A)
removed outlier: 8.466A pdb=" N ASP B 523 " --> pdb=" O VAL A 39 " (cutoff:3.500A)
Processing sheet with id=AA3, first strand: chain 'A' and resid 174 through 179
Processing sheet with id=AA4, first strand: chain 'A' and resid 193 through 195
Processing sheet with id=AA5, first strand: chain 'A' and resid 273 through 277
removed outlier: 6.165A pdb=" N PHE A 219 " --> pdb=" O LEU A 248 " (cutoff:3.500A)
removed outlier: 7.289A pdb=" N ILE A 250 " --> pdb=" O PHE A 219 " (cutoff:3.500A)
removed outlier: 6.294A pdb=" N LEU A 221 " --> pdb=" O ILE A 250 " (cutoff:3.500A)
removed outlier: 8.720A pdb=" N ILE A 301 " --> pdb=" O ILE A 220 " (cutoff:3.500A)
removed outlier: 7.049A pdb=" N LEU A 222 " --> pdb=" O ILE A 301 " (cutoff:3.500A)
Processing sheet with id=AA6, first strand: chain 'A' and resid 273 through 277
removed outlier: 6.165A pdb=" N PHE A 219 " --> pdb=" O LEU A 248 " (cutoff:3.500A)
removed outlier: 7.289A pdb=" N ILE A 250 " --> pdb=" O PHE A 219 " (cutoff:3.500A)
removed outlier: 6.294A pdb=" N LEU A 221 " --> pdb=" O ILE A 250 " (cutoff:3.500A)
Processing sheet with id=AA7, first strand: chain 'A' and resid 411 through 413
Processing sheet with id=AA8, first strand: chain 'A' and resid 476 through 479
Processing sheet with id=AA9, first strand: chain 'N' and resid 4 through 8
removed outlier: 3.505A pdb=" N LYS N 7 " --> pdb=" O MET N 520 " (cutoff:3.500A)
removed outlier: 7.578A pdb=" N VAL H 39 " --> pdb=" O GLU N 518 " (cutoff:3.500A)
removed outlier: 4.591A pdb=" N MET N 520 " --> pdb=" O VAL H 39 " (cutoff:3.500A)
Processing sheet with id=AB1, first strand: chain 'N' and resid 48 through 50
removed outlier: 6.725A pdb=" N ASN N 37 " --> pdb=" O CYS M 519 " (cutoff:3.500A)
removed outlier: 8.317A pdb=" N VAL M 521 " --> pdb=" O ASN N 37 " (cutoff:3.500A)
removed outlier: 6.426A pdb=" N VAL N 39 " --> pdb=" O VAL M 521 " (cutoff:3.500A)
removed outlier: 8.454A pdb=" N ASP M 523 " --> pdb=" O VAL N 39 " (cutoff:3.500A)
Processing sheet with id=AB2, first strand: chain 'N' and resid 174 through 179
removed outlier: 3.558A pdb=" N VAL N 381 " --> pdb=" O GLU N 178 " (cutoff:3.500A)
Processing sheet with id=AB3, first strand: chain 'N' and resid 193 through 195
Processing sheet with id=AB4, first strand: chain 'N' and resid 273 through 277
removed outlier: 6.029A pdb=" N PHE N 219 " --> pdb=" O LEU N 248 " (cutoff:3.500A)
removed outlier: 7.217A pdb=" N ILE N 250 " --> pdb=" O PHE N 219 " (cutoff:3.500A)
removed outlier: 6.338A pdb=" N LEU N 221 " --> pdb=" O ILE N 250 " (cutoff:3.500A)
removed outlier: 8.737A pdb=" N ILE N 301 " --> pdb=" O ILE N 220 " (cutoff:3.500A)
removed outlier: 7.120A pdb=" N LEU N 222 " --> pdb=" O ILE N 301 " (cutoff:3.500A)
Processing sheet with id=AB5, first strand: chain 'N' and resid 273 through 277
removed outlier: 6.029A pdb=" N PHE N 219 " --> pdb=" O LEU N 248 " (cutoff:3.500A)
removed outlier: 7.217A pdb=" N ILE N 250 " --> pdb=" O PHE N 219 " (cutoff:3.500A)
removed outlier: 6.338A pdb=" N LEU N 221 " --> pdb=" O ILE N 250 " (cutoff:3.500A)
Processing sheet with id=AB6, first strand: chain 'N' and resid 411 through 413
Processing sheet with id=AB7, first strand: chain 'N' and resid 476 through 479
Processing sheet with id=AB8, first strand: chain 'B' and resid 48 through 50
removed outlier: 6.843A pdb=" N ASN B 37 " --> pdb=" O CYS C 519 " (cutoff:3.500A)
removed outlier: 8.300A pdb=" N VAL C 521 " --> pdb=" O ASN B 37 " (cutoff:3.500A)
removed outlier: 6.425A pdb=" N VAL B 39 " --> pdb=" O VAL C 521 " (cutoff:3.500A)
removed outlier: 8.455A pdb=" N ASP C 523 " --> pdb=" O VAL B 39 " (cutoff:3.500A)
Processing sheet with id=AB9, first strand: chain 'B' and resid 174 through 179
Processing sheet with id=AC1, first strand: chain 'B' and resid 193 through 195
Processing sheet with id=AC2, first strand: chain 'B' and resid 273 through 277
removed outlier: 6.155A pdb=" N PHE B 219 " --> pdb=" O LEU B 248 " (cutoff:3.500A)
removed outlier: 7.264A pdb=" N ILE B 250 " --> pdb=" O PHE B 219 " (cutoff:3.500A)
removed outlier: 6.265A pdb=" N LEU B 221 " --> pdb=" O ILE B 250 " (cutoff:3.500A)
removed outlier: 8.575A pdb=" N ILE B 301 " --> pdb=" O ILE B 220 " (cutoff:3.500A)
removed outlier: 7.005A pdb=" N LEU B 222 " --> pdb=" O ILE B 301 " (cutoff:3.500A)
Processing sheet with id=AC3, first strand: chain 'B' and resid 273 through 277
removed outlier: 6.155A pdb=" N PHE B 219 " --> pdb=" O LEU B 248 " (cutoff:3.500A)
removed outlier: 7.264A pdb=" N ILE B 250 " --> pdb=" O PHE B 219 " (cutoff:3.500A)
removed outlier: 6.265A pdb=" N LEU B 221 " --> pdb=" O ILE B 250 " (cutoff:3.500A)
Processing sheet with id=AC4, first strand: chain 'B' and resid 411 through 413
Processing sheet with id=AC5, first strand: chain 'B' and resid 476 through 479
Processing sheet with id=AC6, first strand: chain 'H' and resid 4 through 8
removed outlier: 5.985A pdb=" N ASN I 37 " --> pdb=" O THR H 517 " (cutoff:3.500A)
removed outlier: 3.758A pdb=" N CYS H 519 " --> pdb=" O ASN I 37 " (cutoff:3.500A)
Processing sheet with id=AC7, first strand: chain 'H' and resid 174 through 179
Processing sheet with id=AC8, first strand: chain 'H' and resid 193 through 195
Processing sheet with id=AC9, first strand: chain 'H' and resid 273 through 277
removed outlier: 6.037A pdb=" N PHE H 219 " --> pdb=" O LEU H 248 " (cutoff:3.500A)
removed outlier: 7.219A pdb=" N ILE H 250 " --> pdb=" O PHE H 219 " (cutoff:3.500A)
removed outlier: 6.341A pdb=" N LEU H 221 " --> pdb=" O ILE H 250 " (cutoff:3.500A)
removed outlier: 8.696A pdb=" N ILE H 301 " --> pdb=" O ILE H 220 " (cutoff:3.500A)
removed outlier: 7.134A pdb=" N LEU H 222 " --> pdb=" O ILE H 301 " (cutoff:3.500A)
Processing sheet with id=AD1, first strand: chain 'H' and resid 273 through 277
removed outlier: 6.037A pdb=" N PHE H 219 " --> pdb=" O LEU H 248 " (cutoff:3.500A)
removed outlier: 7.219A pdb=" N ILE H 250 " --> pdb=" O PHE H 219 " (cutoff:3.500A)
removed outlier: 6.341A pdb=" N LEU H 221 " --> pdb=" O ILE H 250 " (cutoff:3.500A)
Processing sheet with id=AD2, first strand: chain 'H' and resid 411 through 413
Processing sheet with id=AD3, first strand: chain 'H' and resid 476 through 479
Processing sheet with id=AD4, first strand: chain 'C' and resid 48 through 50
removed outlier: 7.088A pdb=" N ASN C 37 " --> pdb=" O CYS E 519 " (cutoff:3.500A)
removed outlier: 8.420A pdb=" N VAL E 521 " --> pdb=" O ASN C 37 " (cutoff:3.500A)
removed outlier: 6.469A pdb=" N VAL C 39 " --> pdb=" O VAL E 521 " (cutoff:3.500A)
removed outlier: 8.453A pdb=" N ASP E 523 " --> pdb=" O VAL C 39 " (cutoff:3.500A)
Processing sheet with id=AD5, first strand: chain 'C' and resid 174 through 179
Processing sheet with id=AD6, first strand: chain 'C' and resid 193 through 195
Processing sheet with id=AD7, first strand: chain 'C' and resid 273 through 277
removed outlier: 6.060A pdb=" N PHE C 219 " --> pdb=" O LEU C 248 " (cutoff:3.500A)
removed outlier: 7.234A pdb=" N ILE C 250 " --> pdb=" O PHE C 219 " (cutoff:3.500A)
removed outlier: 6.291A pdb=" N LEU C 221 " --> pdb=" O ILE C 250 " (cutoff:3.500A)
Processing sheet with id=AD8, first strand: chain 'C' and resid 411 through 413
Processing sheet with id=AD9, first strand: chain 'C' and resid 476 through 479
Processing sheet with id=AE1, first strand: chain 'I' and resid 4 through 8
removed outlier: 5.933A pdb=" N ASN K 37 " --> pdb=" O THR I 517 " (cutoff:3.500A)
removed outlier: 3.708A pdb=" N CYS I 519 " --> pdb=" O ASN K 37 " (cutoff:3.500A)
Processing sheet with id=AE2, first strand: chain 'I' and resid 174 through 179
Processing sheet with id=AE3, first strand: chain 'I' and resid 193 through 195
Processing sheet with id=AE4, first strand: chain 'I' and resid 273 through 277
removed outlier: 3.513A pdb=" N ALA I 251 " --> pdb=" O VAL I 276 " (cutoff:3.500A)
removed outlier: 5.966A pdb=" N PHE I 219 " --> pdb=" O LEU I 248 " (cutoff:3.500A)
removed outlier: 7.127A pdb=" N ILE I 250 " --> pdb=" O PHE I 219 " (cutoff:3.500A)
removed outlier: 6.018A pdb=" N LEU I 221 " --> pdb=" O ILE I 250 " (cutoff:3.500A)
removed outlier: 8.733A pdb=" N ILE I 301 " --> pdb=" O ILE I 220 " (cutoff:3.500A)
removed outlier: 7.145A pdb=" N LEU I 222 " --> pdb=" O ILE I 301 " (cutoff:3.500A)
Processing sheet with id=AE5, first strand: chain 'I' and resid 273 through 277
removed outlier: 3.513A pdb=" N ALA I 251 " --> pdb=" O VAL I 276 " (cutoff:3.500A)
removed outlier: 5.966A pdb=" N PHE I 219 " --> pdb=" O LEU I 248 " (cutoff:3.500A)
removed outlier: 7.127A pdb=" N ILE I 250 " --> pdb=" O PHE I 219 " (cutoff:3.500A)
removed outlier: 6.018A pdb=" N LEU I 221 " --> pdb=" O ILE I 250 " (cutoff:3.500A)
Processing sheet with id=AE6, first strand: chain 'I' and resid 411 through 413
Processing sheet with id=AE7, first strand: chain 'I' and resid 476 through 479
Processing sheet with id=AE8, first strand: chain 'D' and resid 4 through 8
removed outlier: 6.108A pdb=" N ASN E 37 " --> pdb=" O THR D 517 " (cutoff:3.500A)
removed outlier: 3.850A pdb=" N CYS D 519 " --> pdb=" O ASN E 37 " (cutoff:3.500A)
Processing sheet with id=AE9, first strand: chain 'D' and resid 48 through 50
removed outlier: 6.940A pdb=" N ASN D 37 " --> pdb=" O CYS F 519 " (cutoff:3.500A)
removed outlier: 8.390A pdb=" N VAL F 521 " --> pdb=" O ASN D 37 " (cutoff:3.500A)
removed outlier: 6.518A pdb=" N VAL D 39 " --> pdb=" O VAL F 521 " (cutoff:3.500A)
removed outlier: 8.548A pdb=" N ASP F 523 " --> pdb=" O VAL D 39 " (cutoff:3.500A)
Processing sheet with id=AF1, first strand: chain 'D' and resid 174 through 179
Processing sheet with id=AF2, first strand: chain 'D' and resid 193 through 195
Processing sheet with id=AF3, first strand: chain 'D' and resid 273 through 277
removed outlier: 6.068A pdb=" N PHE D 219 " --> pdb=" O LEU D 248 " (cutoff:3.500A)
removed outlier: 7.252A pdb=" N ILE D 250 " --> pdb=" O PHE D 219 " (cutoff:3.500A)
removed outlier: 6.275A pdb=" N LEU D 221 " --> pdb=" O ILE D 250 " (cutoff:3.500A)
removed outlier: 8.618A pdb=" N ILE D 301 " --> pdb=" O ILE D 220 " (cutoff:3.500A)
removed outlier: 7.089A pdb=" N LEU D 222 " --> pdb=" O ILE D 301 " (cutoff:3.500A)
Processing sheet with id=AF4, first strand: chain 'D' and resid 273 through 277
removed outlier: 6.068A pdb=" N PHE D 219 " --> pdb=" O LEU D 248 " (cutoff:3.500A)
removed outlier: 7.252A pdb=" N ILE D 250 " --> pdb=" O PHE D 219 " (cutoff:3.500A)
removed outlier: 6.275A pdb=" N LEU D 221 " --> pdb=" O ILE D 250 " (cutoff:3.500A)
Processing sheet with id=AF5, first strand: chain 'D' and resid 411 through 413
Processing sheet with id=AF6, first strand: chain 'D' and resid 476 through 479
Processing sheet with id=AF7, first strand: chain 'J' and resid 4 through 8
removed outlier: 6.017A pdb=" N ASN L 37 " --> pdb=" O THR J 517 " (cutoff:3.500A)
removed outlier: 3.787A pdb=" N CYS J 519 " --> pdb=" O ASN L 37 " (cutoff:3.500A)
Processing sheet with id=AF8, first strand: chain 'J' and resid 48 through 50
removed outlier: 6.804A pdb=" N ASN J 37 " --> pdb=" O CYS K 519 " (cutoff:3.500A)
removed outlier: 8.359A pdb=" N VAL K 521 " --> pdb=" O ASN J 37 " (cutoff:3.500A)
removed outlier: 6.429A pdb=" N VAL J 39 " --> pdb=" O VAL K 521 " (cutoff:3.500A)
removed outlier: 8.459A pdb=" N ASP K 523 " --> pdb=" O VAL J 39 " (cutoff:3.500A)
Processing sheet with id=AF9, first strand: chain 'J' and resid 174 through 179
removed outlier: 3.563A pdb=" N VAL J 381 " --> pdb=" O GLU J 178 " (cutoff:3.500A)
Processing sheet with id=AG1, first strand: chain 'J' and resid 193 through 195
Processing sheet with id=AG2, first strand: chain 'J' and resid 273 through 277
removed outlier: 6.023A pdb=" N PHE J 219 " --> pdb=" O LEU J 248 " (cutoff:3.500A)
removed outlier: 7.206A pdb=" N ILE J 250 " --> pdb=" O PHE J 219 " (cutoff:3.500A)
removed outlier: 6.326A pdb=" N LEU J 221 " --> pdb=" O ILE J 250 " (cutoff:3.500A)
removed outlier: 8.733A pdb=" N ILE J 301 " --> pdb=" O ILE J 220 " (cutoff:3.500A)
removed outlier: 7.110A pdb=" N LEU J 222 " --> pdb=" O ILE J 301 " (cutoff:3.500A)
Processing sheet with id=AG3, first strand: chain 'J' and resid 273 through 277
removed outlier: 6.023A pdb=" N PHE J 219 " --> pdb=" O LEU J 248 " (cutoff:3.500A)
removed outlier: 7.206A pdb=" N ILE J 250 " --> pdb=" O PHE J 219 " (cutoff:3.500A)
removed outlier: 6.326A pdb=" N LEU J 221 " --> pdb=" O ILE J 250 " (cutoff:3.500A)
Processing sheet with id=AG4, first strand: chain 'J' and resid 411 through 413
Processing sheet with id=AG5, first strand: chain 'J' and resid 476 through 479
Processing sheet with id=AG6, first strand: chain 'E' and resid 174 through 179
Processing sheet with id=AG7, first strand: chain 'E' and resid 193 through 195
Processing sheet with id=AG8, first strand: chain 'E' and resid 273 through 277
removed outlier: 6.180A pdb=" N PHE E 219 " --> pdb=" O LEU E 248 " (cutoff:3.500A)
removed outlier: 7.295A pdb=" N ILE E 250 " --> pdb=" O PHE E 219 " (cutoff:3.500A)
removed outlier: 6.281A pdb=" N LEU E 221 " --> pdb=" O ILE E 250 " (cutoff:3.500A)
removed outlier: 8.590A pdb=" N ILE E 301 " --> pdb=" O ILE E 220 " (cutoff:3.500A)
removed outlier: 7.007A pdb=" N LEU E 222 " --> pdb=" O ILE E 301 " (cutoff:3.500A)
Processing sheet with id=AG9, first strand: chain 'E' and resid 273 through 277
removed outlier: 6.180A pdb=" N PHE E 219 " --> pdb=" O LEU E 248 " (cutoff:3.500A)
removed outlier: 7.295A pdb=" N ILE E 250 " --> pdb=" O PHE E 219 " (cutoff:3.500A)
removed outlier: 6.281A pdb=" N LEU E 221 " --> pdb=" O ILE E 250 " (cutoff:3.500A)
Processing sheet with id=AH1, first strand: chain 'E' and resid 411 through 413
Processing sheet with id=AH2, first strand: chain 'E' and resid 476 through 479
Processing sheet with id=AH3, first strand: chain 'K' and resid 174 through 179
Processing sheet with id=AH4, first strand: chain 'K' and resid 193 through 195
Processing sheet with id=AH5, first strand: chain 'K' and resid 273 through 277
removed outlier: 6.034A pdb=" N PHE K 219 " --> pdb=" O LEU K 248 " (cutoff:3.500A)
removed outlier: 7.221A pdb=" N ILE K 250 " --> pdb=" O PHE K 219 " (cutoff:3.500A)
removed outlier: 6.333A pdb=" N LEU K 221 " --> pdb=" O ILE K 250 " (cutoff:3.500A)
removed outlier: 8.846A pdb=" N ILE K 301 " --> pdb=" O ILE K 220 " (cutoff:3.500A)
removed outlier: 7.192A pdb=" N LEU K 222 " --> pdb=" O ILE K 301 " (cutoff:3.500A)
Processing sheet with id=AH6, first strand: chain 'K' and resid 273 through 277
removed outlier: 6.034A pdb=" N PHE K 219 " --> pdb=" O LEU K 248 " (cutoff:3.500A)
removed outlier: 7.221A pdb=" N ILE K 250 " --> pdb=" O PHE K 219 " (cutoff:3.500A)
removed outlier: 6.333A pdb=" N LEU K 221 " --> pdb=" O ILE K 250 " (cutoff:3.500A)
Processing sheet with id=AH7, first strand: chain 'K' and resid 411 through 413
Processing sheet with id=AH8, first strand: chain 'K' and resid 476 through 479
Processing sheet with id=AH9, first strand: chain 'F' and resid 48 through 50
removed outlier: 6.992A pdb=" N ASN F 37 " --> pdb=" O CYS G 519 " (cutoff:3.500A)
removed outlier: 8.426A pdb=" N VAL G 521 " --> pdb=" O ASN F 37 " (cutoff:3.500A)
removed outlier: 6.585A pdb=" N VAL F 39 " --> pdb=" O VAL G 521 " (cutoff:3.500A)
removed outlier: 8.611A pdb=" N ASP G 523 " --> pdb=" O VAL F 39 " (cutoff:3.500A)
Processing sheet with id=AI1, first strand: chain 'F' and resid 174 through 179
Processing sheet with id=AI2, first strand: chain 'F' and resid 193 through 195
Processing sheet with id=AI3, first strand: chain 'F' and resid 273 through 277
removed outlier: 6.064A pdb=" N PHE F 219 " --> pdb=" O LEU F 248 " (cutoff:3.500A)
removed outlier: 7.237A pdb=" N ILE F 250 " --> pdb=" O PHE F 219 " (cutoff:3.500A)
removed outlier: 6.274A pdb=" N LEU F 221 " --> pdb=" O ILE F 250 " (cutoff:3.500A)
Processing sheet with id=AI4, first strand: chain 'F' and resid 411 through 413
Processing sheet with id=AI5, first strand: chain 'F' and resid 476 through 479
Processing sheet with id=AI6, first strand: chain 'L' and resid 4 through 8
removed outlier: 6.008A pdb=" N ASN M 37 " --> pdb=" O THR L 517 " (cutoff:3.500A)
removed outlier: 3.783A pdb=" N CYS L 519 " --> pdb=" O ASN M 37 " (cutoff:3.500A)
Processing sheet with id=AI7, first strand: chain 'L' and resid 174 through 179
Processing sheet with id=AI8, first strand: chain 'L' and resid 193 through 195
Processing sheet with id=AI9, first strand: chain 'L' and resid 273 through 277
removed outlier: 6.028A pdb=" N PHE L 219 " --> pdb=" O LEU L 248 " (cutoff:3.500A)
removed outlier: 7.219A pdb=" N ILE L 250 " --> pdb=" O PHE L 219 " (cutoff:3.500A)
removed outlier: 6.355A pdb=" N LEU L 221 " --> pdb=" O ILE L 250 " (cutoff:3.500A)
removed outlier: 8.739A pdb=" N ILE L 301 " --> pdb=" O ILE L 220 " (cutoff:3.500A)
removed outlier: 7.124A pdb=" N LEU L 222 " --> pdb=" O ILE L 301 " (cutoff:3.500A)
Processing sheet with id=AJ1, first strand: chain 'L' and resid 273 through 277
removed outlier: 6.028A pdb=" N PHE L 219 " --> pdb=" O LEU L 248 " (cutoff:3.500A)
removed outlier: 7.219A pdb=" N ILE L 250 " --> pdb=" O PHE L 219 " (cutoff:3.500A)
removed outlier: 6.355A pdb=" N LEU L 221 " --> pdb=" O ILE L 250 " (cutoff:3.500A)
Processing sheet with id=AJ2, first strand: chain 'L' and resid 411 through 413
Processing sheet with id=AJ3, first strand: chain 'L' and resid 476 through 479
Processing sheet with id=AJ4, first strand: chain 'G' and resid 174 through 179
Processing sheet with id=AJ5, first strand: chain 'G' and resid 193 through 195
Processing sheet with id=AJ6, first strand: chain 'G' and resid 273 through 277
removed outlier: 3.516A pdb=" N ALA G 251 " --> pdb=" O VAL G 276 " (cutoff:3.500A)
removed outlier: 6.147A pdb=" N PHE G 219 " --> pdb=" O LEU G 248 " (cutoff:3.500A)
removed outlier: 7.263A pdb=" N ILE G 250 " --> pdb=" O PHE G 219 " (cutoff:3.500A)
removed outlier: 6.265A pdb=" N LEU G 221 " --> pdb=" O ILE G 250 " (cutoff:3.500A)
removed outlier: 8.555A pdb=" N ILE G 301 " --> pdb=" O ILE G 220 " (cutoff:3.500A)
removed outlier: 7.020A pdb=" N LEU G 222 " --> pdb=" O ILE G 301 " (cutoff:3.500A)
Processing sheet with id=AJ7, first strand: chain 'G' and resid 273 through 277
removed outlier: 3.516A pdb=" N ALA G 251 " --> pdb=" O VAL G 276 " (cutoff:3.500A)
removed outlier: 6.147A pdb=" N PHE G 219 " --> pdb=" O LEU G 248 " (cutoff:3.500A)
removed outlier: 7.263A pdb=" N ILE G 250 " --> pdb=" O PHE G 219 " (cutoff:3.500A)
removed outlier: 6.265A pdb=" N LEU G 221 " --> pdb=" O ILE G 250 " (cutoff:3.500A)
Processing sheet with id=AJ8, first strand: chain 'G' and resid 411 through 413
Processing sheet with id=AJ9, first strand: chain 'G' and resid 476 through 479
Processing sheet with id=AK1, first strand: chain 'M' and resid 174 through 179
Processing sheet with id=AK2, first strand: chain 'M' and resid 193 through 195
Processing sheet with id=AK3, first strand: chain 'M' and resid 273 through 277
removed outlier: 6.025A pdb=" N PHE M 219 " --> pdb=" O LEU M 248 " (cutoff:3.500A)
removed outlier: 7.204A pdb=" N ILE M 250 " --> pdb=" O PHE M 219 " (cutoff:3.500A)
removed outlier: 6.311A pdb=" N LEU M 221 " --> pdb=" O ILE M 250 " (cutoff:3.500A)
removed outlier: 8.747A pdb=" N ILE M 301 " --> pdb=" O ILE M 220 " (cutoff:3.500A)
removed outlier: 7.121A pdb=" N LEU M 222 " --> pdb=" O ILE M 301 " (cutoff:3.500A)
Processing sheet with id=AK4, first strand: chain 'M' and resid 273 through 277
removed outlier: 6.025A pdb=" N PHE M 219 " --> pdb=" O LEU M 248 " (cutoff:3.500A)
removed outlier: 7.204A pdb=" N ILE M 250 " --> pdb=" O PHE M 219 " (cutoff:3.500A)
removed outlier: 6.311A pdb=" N LEU M 221 " --> pdb=" O ILE M 250 " (cutoff:3.500A)
Processing sheet with id=AK5, first strand: chain 'M' and resid 411 through 413
Processing sheet with id=AK6, first strand: chain 'M' and resid 476 through 479
3660 hydrogen bonds defined for protein.
10518 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: 28.07
Time building geometry restraints manager: 13.11 seconds
NOTE: a complete listing of the restraints can be obtained by requesting
output of .geo file.
Histogram of bond lengths:
1.23 - 1.34: 18774
1.34 - 1.46: 9400
1.46 - 1.58: 25670
1.58 - 1.70: 0
1.70 - 1.82: 518
Bond restraints: 54362
Sorted by residual:
bond pdb=" CB VAL J 510 "
pdb=" CG2 VAL J 510 "
ideal model delta sigma weight residual
1.521 1.479 0.042 3.30e-02 9.18e+02 1.58e+00
bond pdb=" CB VAL M 510 "
pdb=" CG2 VAL M 510 "
ideal model delta sigma weight residual
1.521 1.480 0.041 3.30e-02 9.18e+02 1.58e+00
bond pdb=" CB GLU A 76 "
pdb=" CG GLU A 76 "
ideal model delta sigma weight residual
1.520 1.556 -0.036 3.00e-02 1.11e+03 1.48e+00
bond pdb=" CB VAL K 510 "
pdb=" CG2 VAL K 510 "
ideal model delta sigma weight residual
1.521 1.481 0.040 3.30e-02 9.18e+02 1.46e+00
bond pdb=" CB VAL L 510 "
pdb=" CG2 VAL L 510 "
ideal model delta sigma weight residual
1.521 1.481 0.040 3.30e-02 9.18e+02 1.44e+00
... (remaining 54357 not shown)
Histogram of bond angle deviations from ideal:
0.00 - 2.85: 72907
2.85 - 5.70: 441
5.70 - 8.56: 30
8.56 - 11.41: 10
11.41 - 14.26: 14
Bond angle restraints: 73402
Sorted by residual:
angle pdb=" CB MET B 267 "
pdb=" CG MET B 267 "
pdb=" SD MET B 267 "
ideal model delta sigma weight residual
112.70 126.96 -14.26 3.00e+00 1.11e-01 2.26e+01
angle pdb=" CB MET K 267 "
pdb=" CG MET K 267 "
pdb=" SD MET K 267 "
ideal model delta sigma weight residual
112.70 126.39 -13.69 3.00e+00 1.11e-01 2.08e+01
angle pdb=" CB MET H 267 "
pdb=" CG MET H 267 "
pdb=" SD MET H 267 "
ideal model delta sigma weight residual
112.70 125.99 -13.29 3.00e+00 1.11e-01 1.96e+01
angle pdb=" CB MET I 267 "
pdb=" CG MET I 267 "
pdb=" SD MET I 267 "
ideal model delta sigma weight residual
112.70 125.95 -13.25 3.00e+00 1.11e-01 1.95e+01
angle pdb=" CB MET C 267 "
pdb=" CG MET C 267 "
pdb=" SD MET C 267 "
ideal model delta sigma weight residual
112.70 125.93 -13.23 3.00e+00 1.11e-01 1.94e+01
... (remaining 73397 not shown)
Histogram of dihedral angle deviations from ideal:
0.00 - 18.00: 30481
18.00 - 35.99: 2512
35.99 - 53.99: 588
53.99 - 71.98: 122
71.98 - 89.98: 65
Dihedral angle restraints: 33768
sinusoidal: 13076
harmonic: 20692
Sorted by residual:
dihedral pdb=" CA ARG M 231 "
pdb=" C ARG M 231 "
pdb=" N GLU M 232 "
pdb=" CA GLU M 232 "
ideal model delta harmonic sigma weight residual
-180.00 -163.56 -16.44 0 5.00e+00 4.00e-02 1.08e+01
dihedral pdb=" CG ARG H 58 "
pdb=" CD ARG H 58 "
pdb=" NE ARG H 58 "
pdb=" CZ ARG H 58 "
ideal model delta sinusoidal sigma weight residual
180.00 135.06 44.94 2 1.50e+01 4.44e-03 1.06e+01
dihedral pdb=" CG ARG L 58 "
pdb=" CD ARG L 58 "
pdb=" NE ARG L 58 "
pdb=" CZ ARG L 58 "
ideal model delta sinusoidal sigma weight residual
90.00 134.91 -44.91 2 1.50e+01 4.44e-03 1.06e+01
... (remaining 33765 not shown)
Histogram of chiral volume deviations from ideal:
0.000 - 0.029: 5611
0.029 - 0.058: 2069
0.058 - 0.087: 745
0.087 - 0.116: 445
0.116 - 0.145: 62
Chirality restraints: 8932
Sorted by residual:
chirality pdb=" CA GLU A 232 "
pdb=" N GLU A 232 "
pdb=" C GLU A 232 "
pdb=" CB GLU A 232 "
both_signs ideal model delta sigma weight residual
False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.29e-01
chirality pdb=" CA GLU D 232 "
pdb=" N GLU D 232 "
pdb=" C GLU D 232 "
pdb=" CB GLU D 232 "
both_signs ideal model delta sigma weight residual
False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.94e-01
chirality pdb=" CA VAL F 271 "
pdb=" N VAL F 271 "
pdb=" C VAL F 271 "
pdb=" CB VAL F 271 "
both_signs ideal model delta sigma weight residual
False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.70e-01
... (remaining 8929 not shown)
Planarity restraints: 9618
Sorted by residual:
delta sigma weight rms_deltas residual
plane pdb=" CA MET B 267 " -0.010 2.00e-02 2.50e+03 2.01e-02 4.04e+00
pdb=" C MET B 267 " 0.035 2.00e-02 2.50e+03
pdb=" O MET B 267 " -0.013 2.00e-02 2.50e+03
pdb=" N ARG B 268 " -0.012 2.00e-02 2.50e+03
delta sigma weight rms_deltas residual
plane pdb=" CA MET C 267 " -0.010 2.00e-02 2.50e+03 2.01e-02 4.04e+00
pdb=" C MET C 267 " 0.035 2.00e-02 2.50e+03
pdb=" O MET C 267 " -0.013 2.00e-02 2.50e+03
pdb=" N ARG C 268 " -0.012 2.00e-02 2.50e+03
delta sigma weight rms_deltas residual
plane pdb=" CG GLU F 76 " 0.010 2.00e-02 2.50e+03 2.01e-02 4.03e+00
pdb=" CD GLU F 76 " -0.035 2.00e-02 2.50e+03
pdb=" OE1 GLU F 76 " 0.013 2.00e-02 2.50e+03
pdb=" OE2 GLU F 76 " 0.012 2.00e-02 2.50e+03
... (remaining 9615 not shown)
Histogram of nonbonded interaction distances:
2.21 - 2.74: 6317
2.74 - 3.28: 54878
3.28 - 3.82: 91620
3.82 - 4.36: 98267
4.36 - 4.90: 180686
Nonbonded interactions: 431768
Sorted by model distance:
nonbonded pdb=" NH2 ARG J 421 "
pdb=" O VAL J 469 "
model vdw
2.206 3.120
nonbonded pdb=" NH2 ARG M 421 "
pdb=" O VAL M 469 "
model vdw
2.209 3.120
nonbonded pdb=" NH2 ARG H 421 "
pdb=" O VAL H 469 "
model vdw
2.209 3.120
nonbonded pdb=" O ILE A 270 "
pdb=" ND2 ASN B 229 "
model vdw
2.210 3.120
nonbonded pdb=" ND2 ASN A 229 "
pdb=" O ILE G 270 "
model vdw
2.210 3.120
... (remaining 431763 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: 0.03
Found NCS groups:
ncs_group {
reference = chain 'A'
selection = chain 'B'
selection = chain 'C'
selection = chain 'D'
selection = chain 'E'
selection = chain 'F'
selection = chain 'G'
selection = chain 'H'
selection = chain 'I'
selection = chain 'J'
selection = chain 'K'
selection = chain 'L'
selection = chain 'M'
selection = chain 'N'
}
Set up NCS constraints
No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
Set random seed: 0.000
Set model cs if undefined: 0.000
Decide on map wrapping: 0.000
Normalize map: mean=0, sd=1: 0.720
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: 0.080
Extract box with map and model: 1.710
Check model and map are aligned: 0.340
Set scattering table: 0.390
Process input model: 105.630
Find NCS groups from input model: 1.620
Set up NCS constraints: 0.320
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:2.430
Set ADP refinement strategy: 0.000
Make a string to write initial .geo file:0.000
Internal consistency checks: 0.000
Total: 113.250
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6952
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 : 0.003 0.042 54362 Z= 0.219
Angle : 0.581 14.260 73402 Z= 0.294
Chirality : 0.040 0.145 8932
Planarity : 0.003 0.027 9618
Dihedral : 14.856 89.981 20496
Min Nonbonded Distance : 2.206
Molprobity Statistics.
All-atom Clashscore : 8.91
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 2.07 %
Favored : 97.93 %
Rotamer:
Outliers : 0.58 %
Allowed : 9.64 %
Favored : 89.78 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 1.80 (0.10), residues: 7308
helix: 2.39 (0.08), residues: 4032
sheet: -0.01 (0.14), residues: 1232
loop : -0.43 (0.13), residues: 2044
Max deviation from planes:
Type MaxDev MeanDev LineInFile
HIS 0.001 0.000 HIS L 401
PHE 0.024 0.001 PHE B 44
TYR 0.011 0.001 TYR J 478
ARG 0.005 0.000 ARG J 13
*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
14616 Ramachandran restraints generated.
7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
14616 Ramachandran restraints generated.
7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
770 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 33
poor density : 737
time to evaluate : 4.800
Fit side-chains
revert: symmetry clash
REVERT: A 321 LYS cc_start: 0.8099 (ttpt) cc_final: 0.7677 (mmtp)
REVERT: A 322 ARG cc_start: 0.7508 (ttp80) cc_final: 0.7201 (ttm110)
REVERT: A 461 GLU cc_start: 0.7671 (pm20) cc_final: 0.7379 (pm20)
REVERT: A 514 MET cc_start: 0.8393 (mtp) cc_final: 0.7936 (mtp)
REVERT: N 69 MET cc_start: 0.5509 (mtm) cc_final: 0.5233 (mtp)
REVERT: N 121 ASP cc_start: 0.7417 (m-30) cc_final: 0.7204 (m-30)
REVERT: N 267 MET cc_start: 0.6336 (tmm) cc_final: 0.5363 (mmp)
REVERT: N 321 LYS cc_start: 0.7892 (ttpt) cc_final: 0.7490 (mmtp)
REVERT: N 447 MET cc_start: 0.8065 (mtm) cc_final: 0.7828 (mtp)
REVERT: B 160 LYS cc_start: 0.7755 (mtpp) cc_final: 0.7545 (ttmm)
REVERT: B 193 MET cc_start: 0.6529 (tpt) cc_final: 0.6091 (tpt)
REVERT: B 233 MET cc_start: 0.5060 (pmm) cc_final: 0.4814 (ptt)
REVERT: B 321 LYS cc_start: 0.7978 (ttpt) cc_final: 0.7529 (mmtp)
REVERT: B 523 ASP cc_start: 0.8055 (OUTLIER) cc_final: 0.7778 (m-30)
REVERT: H 121 ASP cc_start: 0.7221 (m-30) cc_final: 0.6887 (m-30)
REVERT: H 321 LYS cc_start: 0.7961 (ttpt) cc_final: 0.7640 (mmtp)
REVERT: H 514 MET cc_start: 0.8246 (mtp) cc_final: 0.7936 (mtp)
REVERT: C 61 GLU cc_start: 0.7535 (pp20) cc_final: 0.7059 (pt0)
REVERT: C 252 GLU cc_start: 0.7057 (tt0) cc_final: 0.6624 (tt0)
REVERT: C 277 LYS cc_start: 0.7956 (mttt) cc_final: 0.7670 (mmmm)
REVERT: C 288 MET cc_start: 0.5971 (ptp) cc_final: 0.5621 (mtp)
REVERT: C 321 LYS cc_start: 0.8396 (ttpt) cc_final: 0.7892 (mmtp)
REVERT: C 322 ARG cc_start: 0.7538 (ttp80) cc_final: 0.7299 (ttm110)
REVERT: C 493 ILE cc_start: 0.8121 (mt) cc_final: 0.7879 (tt)
REVERT: C 514 MET cc_start: 0.8550 (mtp) cc_final: 0.8179 (mtp)
REVERT: C 523 ASP cc_start: 0.7597 (OUTLIER) cc_final: 0.7357 (m-30)
REVERT: I 121 ASP cc_start: 0.7011 (m-30) cc_final: 0.6754 (m-30)
REVERT: I 193 MET cc_start: 0.6747 (tpt) cc_final: 0.6541 (tpt)
REVERT: I 204 PHE cc_start: 0.7807 (m-80) cc_final: 0.7508 (m-80)
REVERT: I 267 MET cc_start: 0.6556 (tmm) cc_final: 0.5466 (mmp)
REVERT: I 321 LYS cc_start: 0.7674 (ttpt) cc_final: 0.7375 (mmtp)
REVERT: I 336 VAL cc_start: 0.8094 (p) cc_final: 0.7718 (m)
REVERT: I 351 GLN cc_start: 0.8382 (tp40) cc_final: 0.8177 (tp-100)
REVERT: I 514 MET cc_start: 0.8317 (mtm) cc_final: 0.8059 (mtp)
REVERT: D 321 LYS cc_start: 0.8092 (ttpt) cc_final: 0.7499 (mmmt)
REVERT: D 495 ASP cc_start: 0.7499 (m-30) cc_final: 0.7271 (m-30)
REVERT: J 204 PHE cc_start: 0.7669 (m-80) cc_final: 0.7259 (m-80)
REVERT: J 336 VAL cc_start: 0.7996 (p) cc_final: 0.7591 (m)
REVERT: J 351 GLN cc_start: 0.8374 (tp40) cc_final: 0.8124 (tp40)
REVERT: E 72 GLN cc_start: 0.7634 (mm110) cc_final: 0.7344 (mm110)
REVERT: E 102 GLU cc_start: 0.7185 (mt-10) cc_final: 0.6807 (mp0)
REVERT: E 166 MET cc_start: 0.7059 (mtt) cc_final: 0.6806 (mtt)
REVERT: E 233 MET cc_start: 0.5877 (ppp) cc_final: 0.5528 (ptt)
REVERT: E 252 GLU cc_start: 0.7005 (tt0) cc_final: 0.6741 (tt0)
REVERT: E 321 LYS cc_start: 0.8274 (ttpt) cc_final: 0.7695 (mmpt)
REVERT: E 520 MET cc_start: 0.8259 (mtt) cc_final: 0.7838 (mtt)
REVERT: K 267 MET cc_start: 0.6289 (tmm) cc_final: 0.4982 (mmm)
REVERT: K 351 GLN cc_start: 0.8539 (tp40) cc_final: 0.8307 (tp40)
REVERT: K 514 MET cc_start: 0.8302 (mtm) cc_final: 0.7931 (mtp)
REVERT: F 61 GLU cc_start: 0.7272 (pt0) cc_final: 0.6642 (pt0)
REVERT: F 160 LYS cc_start: 0.7821 (mtpp) cc_final: 0.7563 (ttmm)
REVERT: F 233 MET cc_start: 0.5417 (pmm) cc_final: 0.5137 (ptt)
REVERT: F 321 LYS cc_start: 0.8109 (ttpt) cc_final: 0.7603 (mmtp)
REVERT: F 389 MET cc_start: 0.6298 (tmt) cc_final: 0.5841 (tmm)
REVERT: L 61 GLU cc_start: 0.7359 (tm-30) cc_final: 0.7112 (pt0)
REVERT: L 69 MET cc_start: 0.6809 (mtm) cc_final: 0.6537 (mtp)
REVERT: L 121 ASP cc_start: 0.7332 (m-30) cc_final: 0.7110 (m-30)
REVERT: L 255 GLU cc_start: 0.7116 (pm20) cc_final: 0.6908 (pm20)
REVERT: L 267 MET cc_start: 0.5973 (tmm) cc_final: 0.4831 (mmm)
REVERT: L 321 LYS cc_start: 0.7875 (ttpt) cc_final: 0.7644 (mmtp)
REVERT: L 351 GLN cc_start: 0.8375 (tp40) cc_final: 0.8119 (tp40)
REVERT: L 433 ASN cc_start: 0.6264 (p0) cc_final: 0.5910 (p0)
REVERT: G 61 GLU cc_start: 0.7409 (pp20) cc_final: 0.7063 (pt0)
REVERT: G 277 LYS cc_start: 0.8069 (mttt) cc_final: 0.7691 (mmmm)
REVERT: G 321 LYS cc_start: 0.7987 (ttpt) cc_final: 0.7578 (mmmt)
REVERT: G 322 ARG cc_start: 0.7604 (ttp80) cc_final: 0.7323 (mtp-110)
REVERT: G 461 GLU cc_start: 0.7787 (pm20) cc_final: 0.7513 (pm20)
REVERT: M 321 LYS cc_start: 0.7806 (ttpt) cc_final: 0.7543 (mmtp)
REVERT: M 351 GLN cc_start: 0.8396 (tp40) cc_final: 0.8151 (tp40)
REVERT: M 397 GLU cc_start: 0.7699 (tp30) cc_final: 0.7368 (tt0)
REVERT: M 433 ASN cc_start: 0.6184 (p0) cc_final: 0.5716 (p0)
REVERT: M 491 MET cc_start: 0.7226 (ptm) cc_final: 0.7009 (ptm)
outliers start: 33
outliers final: 21
residues processed: 763
average time/residue: 0.5011
time to fit residues: 649.6205
Evaluate side-chains
515 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 23
poor density : 492
time to evaluate : 4.791
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 240 VAL
Chi-restraints excluded: chain A residue 517 THR
Chi-restraints excluded: chain A residue 523 ASP
Chi-restraints excluded: chain N residue 11 ASP
Chi-restraints excluded: chain N residue 240 VAL
Chi-restraints excluded: chain B residue 523 ASP
Chi-restraints excluded: chain H residue 11 ASP
Chi-restraints excluded: chain H residue 240 VAL
Chi-restraints excluded: chain H residue 442 VAL
Chi-restraints excluded: chain C residue 517 THR
Chi-restraints excluded: chain C residue 523 ASP
Chi-restraints excluded: chain I residue 11 ASP
Chi-restraints excluded: chain I residue 240 VAL
Chi-restraints excluded: chain D residue 240 VAL
Chi-restraints excluded: chain D residue 261 THR
Chi-restraints excluded: chain D residue 523 ASP
Chi-restraints excluded: chain E residue 240 VAL
Chi-restraints excluded: chain K residue 240 VAL
Chi-restraints excluded: chain F residue 261 THR
Chi-restraints excluded: chain F residue 517 THR
Chi-restraints excluded: chain F residue 523 ASP
Chi-restraints excluded: chain G residue 447 MET
Chi-restraints excluded: chain G residue 523 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 728
random chunks:
chunk 614 optimal weight: 0.3980
chunk 551 optimal weight: 20.0000
chunk 306 optimal weight: 1.9990
chunk 188 optimal weight: 2.9990
chunk 372 optimal weight: 9.9990
chunk 294 optimal weight: 9.9990
chunk 570 optimal weight: 1.9990
chunk 220 optimal weight: 3.9990
chunk 346 optimal weight: 5.9990
chunk 424 optimal weight: 1.9990
chunk 661 optimal weight: 9.9990
overall best weight: 1.8788
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 112 ASN
A 348 GLN
C 112 ASN
C 146 GLN
D 112 ASN
D 184 GLN
E 112 ASN
E 184 GLN
F 112 ASN
F 348 GLN
G 112 ASN
G 348 GLN
Total number of N/Q/H flips: 12
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.153095 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.114207 restraints weight = 68602.183|
|-----------------------------------------------------------------------------|
r_work (start): 0.3361 rms_B_bonded: 1.74
r_work: 0.3211 rms_B_bonded: 2.14 restraints_weight: 0.5000
r_work: 0.3065 rms_B_bonded: 3.69 restraints_weight: 0.2500
r_work (final): 0.3065
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8393
moved from start: 0.1240
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.051 54362 Z= 0.213
Angle : 0.527 11.519 73402 Z= 0.280
Chirality : 0.042 0.201 8932
Planarity : 0.003 0.054 9618
Dihedral : 3.998 28.800 7762
Min Nonbonded Distance : 2.590
Molprobity Statistics.
All-atom Clashscore : 7.38
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 1.68 %
Favored : 98.32 %
Rotamer:
Outliers : 1.98 %
Allowed : 11.26 %
Favored : 86.76 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 1.75 (0.10), residues: 7308
helix: 2.28 (0.08), residues: 4088
sheet: 0.29 (0.16), residues: 980
loop : -0.52 (0.12), residues: 2240
Max deviation from planes:
Type MaxDev MeanDev LineInFile
HIS 0.000 0.000 HIS H 401
PHE 0.009 0.001 PHE H 44
TYR 0.009 0.001 TYR B 478
ARG 0.008 0.000 ARG N 345
*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
14616 Ramachandran restraints generated.
7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
14616 Ramachandran restraints generated.
7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
647 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 112
poor density : 535
time to evaluate : 4.918
Fit side-chains
REVERT: A 267 MET cc_start: 0.5923 (mmm) cc_final: 0.4969 (mmm)
REVERT: A 307 MET cc_start: 0.8607 (mtm) cc_final: 0.8059 (ptp)
REVERT: N 69 MET cc_start: 0.7608 (mtm) cc_final: 0.7355 (mtp)
REVERT: N 111 MET cc_start: 0.8795 (OUTLIER) cc_final: 0.8421 (mtt)
REVERT: N 267 MET cc_start: 0.6565 (tmm) cc_final: 0.5757 (mmp)
REVERT: N 442 VAL cc_start: 0.9047 (OUTLIER) cc_final: 0.8798 (t)
REVERT: N 447 MET cc_start: 0.9081 (mtm) cc_final: 0.8844 (mtp)
REVERT: B 160 LYS cc_start: 0.8511 (mtpp) cc_final: 0.8291 (ttmm)
REVERT: B 193 MET cc_start: 0.8213 (tpt) cc_final: 0.8010 (tpt)
REVERT: B 233 MET cc_start: 0.5975 (pmm) cc_final: 0.5506 (ptt)
REVERT: B 267 MET cc_start: 0.6371 (tmm) cc_final: 0.4962 (mmm)
REVERT: B 367 GLU cc_start: 0.8453 (pp20) cc_final: 0.8160 (pp20)
REVERT: H 262 LEU cc_start: 0.7184 (OUTLIER) cc_final: 0.6631 (tt)
REVERT: H 267 MET cc_start: 0.6273 (tmm) cc_final: 0.5284 (mmp)
REVERT: C 61 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.7930 (pt0)
REVERT: C 267 MET cc_start: 0.6475 (tmm) cc_final: 0.5628 (mmp)
REVERT: C 288 MET cc_start: 0.7170 (ptp) cc_final: 0.6548 (mtp)
REVERT: C 321 LYS cc_start: 0.8757 (ttpt) cc_final: 0.8477 (mmtp)
REVERT: I 204 PHE cc_start: 0.8414 (m-80) cc_final: 0.8000 (m-80)
REVERT: I 233 MET cc_start: 0.5877 (pmm) cc_final: 0.5416 (ptt)
REVERT: I 267 MET cc_start: 0.7008 (tmm) cc_final: 0.5971 (mmp)
REVERT: D 193 MET cc_start: 0.8315 (OUTLIER) cc_final: 0.8096 (tpt)
REVERT: D 242 LYS cc_start: 0.8095 (mmtt) cc_final: 0.7894 (mmtt)
REVERT: D 321 LYS cc_start: 0.8704 (ttpt) cc_final: 0.8447 (mmmt)
REVERT: J 204 PHE cc_start: 0.8325 (m-80) cc_final: 0.7762 (m-80)
REVERT: J 267 MET cc_start: 0.6267 (tmm) cc_final: 0.5007 (mmm)
REVERT: J 389 MET cc_start: 0.7990 (tmt) cc_final: 0.7673 (tmm)
REVERT: J 442 VAL cc_start: 0.9035 (OUTLIER) cc_final: 0.8787 (t)
REVERT: E 204 PHE cc_start: 0.8407 (m-80) cc_final: 0.8205 (m-80)
REVERT: E 233 MET cc_start: 0.6513 (ppp) cc_final: 0.6094 (ptt)
REVERT: E 252 GLU cc_start: 0.7412 (tt0) cc_final: 0.7193 (tt0)
REVERT: E 321 LYS cc_start: 0.8627 (ttpt) cc_final: 0.8417 (mmpt)
REVERT: K 267 MET cc_start: 0.6893 (tmm) cc_final: 0.5409 (mmp)
REVERT: F 160 LYS cc_start: 0.8603 (mtpp) cc_final: 0.8275 (ttmm)
REVERT: F 233 MET cc_start: 0.6258 (pmm) cc_final: 0.5959 (ptt)
REVERT: F 267 MET cc_start: 0.5952 (mmm) cc_final: 0.5145 (tmm)
REVERT: F 389 MET cc_start: 0.7738 (tmt) cc_final: 0.7348 (tmm)
REVERT: L 61 GLU cc_start: 0.8516 (tm-30) cc_final: 0.8216 (tt0)
REVERT: L 69 MET cc_start: 0.8347 (OUTLIER) cc_final: 0.7966 (mtp)
REVERT: L 262 LEU cc_start: 0.7270 (OUTLIER) cc_final: 0.6879 (tp)
REVERT: L 267 MET cc_start: 0.6596 (tmm) cc_final: 0.5206 (mmm)
REVERT: L 351 GLN cc_start: 0.8095 (tp40) cc_final: 0.7878 (tp40)
REVERT: G 61 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.7773 (pt0)
REVERT: G 160 LYS cc_start: 0.8754 (OUTLIER) cc_final: 0.8482 (ptmm)
REVERT: G 267 MET cc_start: 0.6093 (tmm) cc_final: 0.5177 (mmm)
REVERT: M 13 ARG cc_start: 0.8280 (OUTLIER) cc_final: 0.7731 (mpt-90)
REVERT: M 267 MET cc_start: 0.6764 (tmm) cc_final: 0.5513 (mmm)
REVERT: M 351 GLN cc_start: 0.8118 (tp40) cc_final: 0.7915 (tp40)
outliers start: 112
outliers final: 57
residues processed: 611
average time/residue: 0.4939
time to fit residues: 521.6042
Evaluate side-chains
518 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 68
poor density : 450
time to evaluate : 4.785
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 213 VAL
Chi-restraints excluded: chain A residue 240 VAL
Chi-restraints excluded: chain A residue 348 GLN
Chi-restraints excluded: chain A residue 351 GLN
Chi-restraints excluded: chain A residue 447 MET
Chi-restraints excluded: chain A residue 463 SER
Chi-restraints excluded: chain N residue 50 THR
Chi-restraints excluded: chain N residue 111 MET
Chi-restraints excluded: chain N residue 114 MET
Chi-restraints excluded: chain N residue 240 VAL
Chi-restraints excluded: chain N residue 442 VAL
Chi-restraints excluded: chain B residue 48 THR
Chi-restraints excluded: chain B residue 50 THR
Chi-restraints excluded: chain B residue 213 VAL
Chi-restraints excluded: chain B residue 261 THR
Chi-restraints excluded: chain H residue 61 GLU
Chi-restraints excluded: chain H residue 234 LEU
Chi-restraints excluded: chain H residue 240 VAL
Chi-restraints excluded: chain H residue 262 LEU
Chi-restraints excluded: chain H residue 442 VAL
Chi-restraints excluded: chain C residue 61 GLU
Chi-restraints excluded: chain C residue 213 VAL
Chi-restraints excluded: chain C residue 234 LEU
Chi-restraints excluded: chain C residue 300 VAL
Chi-restraints excluded: chain C residue 307 MET
Chi-restraints excluded: chain C residue 351 GLN
Chi-restraints excluded: chain I residue 61 GLU
Chi-restraints excluded: chain I residue 146 GLN
Chi-restraints excluded: chain I residue 228 SER
Chi-restraints excluded: chain I residue 234 LEU
Chi-restraints excluded: chain I residue 240 VAL
Chi-restraints excluded: chain I residue 514 MET
Chi-restraints excluded: chain D residue 48 THR
Chi-restraints excluded: chain D residue 50 THR
Chi-restraints excluded: chain D residue 193 MET
Chi-restraints excluded: chain D residue 213 VAL
Chi-restraints excluded: chain D residue 261 THR
Chi-restraints excluded: chain J residue 442 VAL
Chi-restraints excluded: chain E residue 48 THR
Chi-restraints excluded: chain E residue 213 VAL
Chi-restraints excluded: chain E residue 240 VAL
Chi-restraints excluded: chain K residue 62 LEU
Chi-restraints excluded: chain K residue 240 VAL
Chi-restraints excluded: chain K residue 273 VAL
Chi-restraints excluded: chain K residue 288 MET
Chi-restraints excluded: chain K residue 463 SER
Chi-restraints excluded: chain F residue 48 THR
Chi-restraints excluded: chain F residue 50 THR
Chi-restraints excluded: chain F residue 193 MET
Chi-restraints excluded: chain F residue 213 VAL
Chi-restraints excluded: chain F residue 261 THR
Chi-restraints excluded: chain F residue 348 GLN
Chi-restraints excluded: chain F residue 447 MET
Chi-restraints excluded: chain F residue 463 SER
Chi-restraints excluded: chain F residue 524 LEU
Chi-restraints excluded: chain L residue 50 THR
Chi-restraints excluded: chain L residue 69 MET
Chi-restraints excluded: chain L residue 146 GLN
Chi-restraints excluded: chain L residue 262 LEU
Chi-restraints excluded: chain G residue 48 THR
Chi-restraints excluded: chain G residue 61 GLU
Chi-restraints excluded: chain G residue 160 LYS
Chi-restraints excluded: chain G residue 234 LEU
Chi-restraints excluded: chain G residue 300 VAL
Chi-restraints excluded: chain G residue 348 GLN
Chi-restraints excluded: chain M residue 13 ARG
Chi-restraints excluded: chain M residue 61 GLU
Chi-restraints excluded: chain M residue 259 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 728
random chunks:
chunk 558 optimal weight: 4.9990
chunk 258 optimal weight: 0.8980
chunk 337 optimal weight: 20.0000
chunk 97 optimal weight: 2.9990
chunk 46 optimal weight: 1.9990
chunk 622 optimal weight: 4.9990
chunk 153 optimal weight: 7.9990
chunk 703 optimal weight: 0.8980
chunk 33 optimal weight: 20.0000
chunk 446 optimal weight: 2.9990
chunk 453 optimal weight: 10.0000
overall best weight: 1.9586
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
B 351 GLN
H 37 ASN
C 467 ASN
G 351 GLN
Total number of N/Q/H flips: 4
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.152356 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.114403 restraints weight = 68963.847|
|-----------------------------------------------------------------------------|
r_work (start): 0.3366 rms_B_bonded: 1.76
r_work: 0.3204 rms_B_bonded: 2.09 restraints_weight: 0.5000
r_work: 0.3061 rms_B_bonded: 3.59 restraints_weight: 0.2500
r_work (final): 0.3061
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8405
moved from start: 0.1606
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.050 54362 Z= 0.206
Angle : 0.491 9.036 73402 Z= 0.262
Chirality : 0.042 0.152 8932
Planarity : 0.003 0.034 9618
Dihedral : 3.901 27.209 7737
Min Nonbonded Distance : 2.594
Molprobity Statistics.
All-atom Clashscore : 6.85
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 1.56 %
Favored : 98.44 %
Rotamer:
Outliers : 2.30 %
Allowed : 12.61 %
Favored : 85.10 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 1.77 (0.10), residues: 7308
helix: 2.26 (0.08), residues: 4088
sheet: 0.38 (0.16), residues: 980
loop : -0.50 (0.12), residues: 2240
Max deviation from planes:
Type MaxDev MeanDev LineInFile
HIS 0.001 0.000 HIS H 401
PHE 0.009 0.001 PHE M 219
TYR 0.009 0.001 TYR K 476
ARG 0.005 0.000 ARG L 345
*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
14616 Ramachandran restraints generated.
7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
14616 Ramachandran restraints generated.
7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
637 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 130
poor density : 507
time to evaluate : 4.898
Fit side-chains
revert: symmetry clash
REVERT: A 267 MET cc_start: 0.5948 (mmm) cc_final: 0.5032 (mmm)
REVERT: A 307 MET cc_start: 0.8645 (mtm) cc_final: 0.8150 (ptp)
REVERT: A 367 GLU cc_start: 0.8548 (pp20) cc_final: 0.8239 (pp20)
REVERT: A 514 MET cc_start: 0.9098 (mtm) cc_final: 0.8708 (mtp)
REVERT: N 16 MET cc_start: 0.8542 (mmm) cc_final: 0.8156 (mtt)
REVERT: N 111 MET cc_start: 0.8816 (OUTLIER) cc_final: 0.8422 (mtt)
REVERT: N 267 MET cc_start: 0.6480 (tmm) cc_final: 0.5794 (mmp)
REVERT: N 442 VAL cc_start: 0.8986 (OUTLIER) cc_final: 0.8759 (t)
REVERT: B 160 LYS cc_start: 0.8512 (mtpp) cc_final: 0.8257 (ttmm)
REVERT: B 193 MET cc_start: 0.8196 (tpt) cc_final: 0.7945 (ttm)
REVERT: B 233 MET cc_start: 0.6227 (pmm) cc_final: 0.6005 (ptt)
REVERT: B 267 MET cc_start: 0.6194 (tmm) cc_final: 0.5567 (mmp)
REVERT: B 319 GLN cc_start: 0.7975 (mt0) cc_final: 0.7722 (mt0)
REVERT: B 367 GLU cc_start: 0.8472 (pp20) cc_final: 0.8162 (pp20)
REVERT: B 494 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8701 (pp)
REVERT: H 262 LEU cc_start: 0.7173 (OUTLIER) cc_final: 0.6621 (tt)
REVERT: H 267 MET cc_start: 0.6718 (tmm) cc_final: 0.5146 (mmm)
REVERT: C 61 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.7995 (pt0)
REVERT: C 267 MET cc_start: 0.6577 (tmm) cc_final: 0.5682 (mmp)
REVERT: C 288 MET cc_start: 0.7112 (ptp) cc_final: 0.6508 (mtp)
REVERT: C 367 GLU cc_start: 0.8568 (pp20) cc_final: 0.8230 (pp20)
REVERT: C 494 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8772 (pp)
REVERT: I 193 MET cc_start: 0.8504 (OUTLIER) cc_final: 0.8203 (ttm)
REVERT: I 204 PHE cc_start: 0.8437 (m-80) cc_final: 0.8038 (m-80)
REVERT: I 267 MET cc_start: 0.6685 (tmm) cc_final: 0.5870 (mmp)
REVERT: I 351 GLN cc_start: 0.8513 (OUTLIER) cc_final: 0.8121 (pp30)
REVERT: D 242 LYS cc_start: 0.8096 (mmtt) cc_final: 0.7827 (mmmt)
REVERT: D 267 MET cc_start: 0.5543 (tmm) cc_final: 0.5206 (mmp)
REVERT: D 321 LYS cc_start: 0.8786 (ttpt) cc_final: 0.8528 (mmmt)
REVERT: D 367 GLU cc_start: 0.8580 (pp20) cc_final: 0.8327 (pp20)
REVERT: J 204 PHE cc_start: 0.8366 (m-80) cc_final: 0.7922 (m-80)
REVERT: J 267 MET cc_start: 0.6044 (tmm) cc_final: 0.4935 (mmm)
REVERT: J 442 VAL cc_start: 0.8995 (OUTLIER) cc_final: 0.8753 (t)
REVERT: E 111 MET cc_start: 0.8723 (OUTLIER) cc_final: 0.8147 (mtt)
REVERT: E 233 MET cc_start: 0.6358 (ppp) cc_final: 0.6016 (ptt)
REVERT: E 252 GLU cc_start: 0.7387 (tt0) cc_final: 0.7108 (tt0)
REVERT: E 267 MET cc_start: 0.6061 (tmm) cc_final: 0.5397 (mmp)
REVERT: E 447 MET cc_start: 0.9171 (OUTLIER) cc_final: 0.8889 (mtp)
REVERT: E 494 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8838 (pp)
REVERT: K 267 MET cc_start: 0.6809 (tmm) cc_final: 0.5469 (mmp)
REVERT: F 102 GLU cc_start: 0.7683 (mt-10) cc_final: 0.7320 (mp0)
REVERT: F 160 LYS cc_start: 0.8609 (mtpp) cc_final: 0.8362 (ptmm)
REVERT: F 204 PHE cc_start: 0.8418 (m-80) cc_final: 0.8101 (m-80)
REVERT: F 367 GLU cc_start: 0.8436 (pp20) cc_final: 0.8144 (pp20)
REVERT: L 61 GLU cc_start: 0.8586 (tm-30) cc_final: 0.8297 (tt0)
REVERT: L 69 MET cc_start: 0.8435 (mtm) cc_final: 0.8050 (mtp)
REVERT: L 267 MET cc_start: 0.6435 (tmm) cc_final: 0.5242 (mmm)
REVERT: L 288 MET cc_start: 0.7745 (OUTLIER) cc_final: 0.6757 (mpp)
REVERT: L 351 GLN cc_start: 0.8125 (tp40) cc_final: 0.7908 (tp40)
REVERT: L 389 MET cc_start: 0.7818 (OUTLIER) cc_final: 0.7493 (tmm)
REVERT: G 61 GLU cc_start: 0.8473 (OUTLIER) cc_final: 0.7926 (pt0)
REVERT: G 160 LYS cc_start: 0.8718 (OUTLIER) cc_final: 0.8450 (ptmm)
REVERT: G 267 MET cc_start: 0.6205 (tmm) cc_final: 0.5349 (mmm)
REVERT: G 322 ARG cc_start: 0.8732 (mtp-110) cc_final: 0.8405 (ttm110)
REVERT: G 367 GLU cc_start: 0.8529 (pp20) cc_final: 0.8238 (pp20)
REVERT: G 491 MET cc_start: 0.9036 (mtt) cc_final: 0.8800 (mtt)
REVERT: G 494 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8833 (pp)
REVERT: M 267 MET cc_start: 0.6691 (tmm) cc_final: 0.5542 (mmm)
REVERT: M 351 GLN cc_start: 0.8161 (tp40) cc_final: 0.7925 (tp40)
outliers start: 130
outliers final: 72
residues processed: 601
average time/residue: 0.4758
time to fit residues: 500.5399
Evaluate side-chains
552 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 89
poor density : 463
time to evaluate : 6.032
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 169 VAL
Chi-restraints excluded: chain A residue 213 VAL
Chi-restraints excluded: chain A residue 240 VAL
Chi-restraints excluded: chain A residue 300 VAL
Chi-restraints excluded: chain A residue 463 SER
Chi-restraints excluded: chain A residue 517 THR
Chi-restraints excluded: chain N residue 50 THR
Chi-restraints excluded: chain N residue 111 MET
Chi-restraints excluded: chain N residue 234 LEU
Chi-restraints excluded: chain N residue 240 VAL
Chi-restraints excluded: chain N residue 442 VAL
Chi-restraints excluded: chain B residue 48 THR
Chi-restraints excluded: chain B residue 50 THR
Chi-restraints excluded: chain B residue 124 VAL
Chi-restraints excluded: chain B residue 213 VAL
Chi-restraints excluded: chain B residue 234 LEU
Chi-restraints excluded: chain B residue 300 VAL
Chi-restraints excluded: chain B residue 463 SER
Chi-restraints excluded: chain B residue 494 LEU
Chi-restraints excluded: chain H residue 61 GLU
Chi-restraints excluded: chain H residue 240 VAL
Chi-restraints excluded: chain H residue 262 LEU
Chi-restraints excluded: chain H residue 442 VAL
Chi-restraints excluded: chain C residue 61 GLU
Chi-restraints excluded: chain C residue 169 VAL
Chi-restraints excluded: chain C residue 213 VAL
Chi-restraints excluded: chain C residue 261 THR
Chi-restraints excluded: chain C residue 271 VAL
Chi-restraints excluded: chain C residue 494 LEU
Chi-restraints excluded: chain C residue 517 THR
Chi-restraints excluded: chain I residue 61 GLU
Chi-restraints excluded: chain I residue 124 VAL
Chi-restraints excluded: chain I residue 193 MET
Chi-restraints excluded: chain I residue 201 SER
Chi-restraints excluded: chain I residue 234 LEU
Chi-restraints excluded: chain I residue 351 GLN
Chi-restraints excluded: chain I residue 442 VAL
Chi-restraints excluded: chain D residue 43 SER
Chi-restraints excluded: chain D residue 48 THR
Chi-restraints excluded: chain D residue 169 VAL
Chi-restraints excluded: chain D residue 213 VAL
Chi-restraints excluded: chain D residue 240 VAL
Chi-restraints excluded: chain D residue 259 LEU
Chi-restraints excluded: chain D residue 261 THR
Chi-restraints excluded: chain D residue 351 GLN
Chi-restraints excluded: chain D residue 447 MET
Chi-restraints excluded: chain J residue 232 GLU
Chi-restraints excluded: chain J residue 273 VAL
Chi-restraints excluded: chain J residue 388 GLU
Chi-restraints excluded: chain J residue 442 VAL
Chi-restraints excluded: chain E residue 48 THR
Chi-restraints excluded: chain E residue 50 THR
Chi-restraints excluded: chain E residue 111 MET
Chi-restraints excluded: chain E residue 213 VAL
Chi-restraints excluded: chain E residue 240 VAL
Chi-restraints excluded: chain E residue 288 MET
Chi-restraints excluded: chain E residue 300 VAL
Chi-restraints excluded: chain E residue 447 MET
Chi-restraints excluded: chain E residue 494 LEU
Chi-restraints excluded: chain K residue 43 SER
Chi-restraints excluded: chain K residue 62 LEU
Chi-restraints excluded: chain K residue 240 VAL
Chi-restraints excluded: chain K residue 273 VAL
Chi-restraints excluded: chain K residue 288 MET
Chi-restraints excluded: chain K residue 442 VAL
Chi-restraints excluded: chain K residue 463 SER
Chi-restraints excluded: chain F residue 48 THR
Chi-restraints excluded: chain F residue 50 THR
Chi-restraints excluded: chain F residue 193 MET
Chi-restraints excluded: chain F residue 213 VAL
Chi-restraints excluded: chain F residue 261 THR
Chi-restraints excluded: chain F residue 351 GLN
Chi-restraints excluded: chain F residue 463 SER
Chi-restraints excluded: chain F residue 517 THR
Chi-restraints excluded: chain F residue 524 LEU
Chi-restraints excluded: chain L residue 288 MET
Chi-restraints excluded: chain L residue 389 MET
Chi-restraints excluded: chain L residue 442 VAL
Chi-restraints excluded: chain G residue 48 THR
Chi-restraints excluded: chain G residue 61 GLU
Chi-restraints excluded: chain G residue 160 LYS
Chi-restraints excluded: chain G residue 169 VAL
Chi-restraints excluded: chain G residue 234 LEU
Chi-restraints excluded: chain G residue 300 VAL
Chi-restraints excluded: chain G residue 307 MET
Chi-restraints excluded: chain G residue 494 LEU
Chi-restraints excluded: chain M residue 61 GLU
Chi-restraints excluded: chain M residue 259 LEU
Chi-restraints excluded: chain M residue 463 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 728
random chunks:
chunk 315 optimal weight: 2.9990
chunk 389 optimal weight: 9.9990
chunk 510 optimal weight: 0.9980
chunk 398 optimal weight: 10.0000
chunk 657 optimal weight: 0.7980
chunk 331 optimal weight: 20.0000
chunk 514 optimal weight: 0.9980
chunk 34 optimal weight: 6.9990
chunk 69 optimal weight: 10.0000
chunk 554 optimal weight: 9.9990
chunk 156 optimal weight: 8.9990
overall best weight: 2.5584
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 112 ASN
C 112 ASN
C 467 ASN
I 319 GLN
D 112 ASN
E 112 ASN
K 37 ASN
F 112 ASN
M 37 ASN
Total number of N/Q/H flips: 9
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.150754 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.112011 restraints weight = 68645.911|
|-----------------------------------------------------------------------------|
r_work (start): 0.3334 rms_B_bonded: 1.76
r_work: 0.3161 rms_B_bonded: 2.16 restraints_weight: 0.5000
r_work: 0.3013 rms_B_bonded: 3.71 restraints_weight: 0.2500
r_work (final): 0.3013
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8440
moved from start: 0.1894
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.004 0.065 54362 Z= 0.250
Angle : 0.505 7.912 73402 Z= 0.268
Chirality : 0.042 0.167 8932
Planarity : 0.003 0.031 9618
Dihedral : 3.937 27.072 7736
Min Nonbonded Distance : 2.550
Molprobity Statistics.
All-atom Clashscore : 6.62
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 1.53 %
Favored : 98.47 %
Rotamer:
Outliers : 3.20 %
Allowed : 12.89 %
Favored : 83.91 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 1.78 (0.10), residues: 7308
helix: 2.21 (0.08), residues: 4088
sheet: 0.63 (0.17), residues: 938
loop : -0.46 (0.12), residues: 2282
Max deviation from planes:
Type MaxDev MeanDev LineInFile
HIS 0.001 0.000 HIS C 401
PHE 0.011 0.001 PHE J 66
TYR 0.010 0.001 TYR I 478
ARG 0.006 0.000 ARG C 322
*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
14616 Ramachandran restraints generated.
7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
14616 Ramachandran restraints generated.
7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
692 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 181
poor density : 511
time to evaluate : 4.878
Fit side-chains
revert: symmetry clash
REVERT: A 267 MET cc_start: 0.6065 (mmm) cc_final: 0.5086 (mmm)
REVERT: A 367 GLU cc_start: 0.8525 (pp20) cc_final: 0.8231 (pp20)
REVERT: N 16 MET cc_start: 0.8605 (mmm) cc_final: 0.8329 (mtt)
REVERT: N 111 MET cc_start: 0.8870 (OUTLIER) cc_final: 0.8453 (mtt)
REVERT: N 201 SER cc_start: 0.8378 (t) cc_final: 0.8081 (m)
REVERT: N 267 MET cc_start: 0.6415 (tmm) cc_final: 0.5849 (mmp)
REVERT: N 442 VAL cc_start: 0.9005 (OUTLIER) cc_final: 0.8784 (t)
REVERT: N 494 LEU cc_start: 0.9158 (OUTLIER) cc_final: 0.8868 (pp)
REVERT: B 160 LYS cc_start: 0.8527 (mtpp) cc_final: 0.8195 (ptmm)
REVERT: B 233 MET cc_start: 0.6457 (pmm) cc_final: 0.6215 (ptt)
REVERT: B 267 MET cc_start: 0.6143 (tmm) cc_final: 0.5560 (mmp)
REVERT: B 319 GLN cc_start: 0.8005 (mt0) cc_final: 0.7744 (mt0)
REVERT: B 367 GLU cc_start: 0.8484 (pp20) cc_final: 0.8151 (pp20)
REVERT: B 389 MET cc_start: 0.8311 (tmm) cc_final: 0.8055 (ttp)
REVERT: B 494 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8703 (pp)
REVERT: H 267 MET cc_start: 0.6670 (tmm) cc_final: 0.5377 (mmm)
REVERT: H 514 MET cc_start: 0.9065 (mtp) cc_final: 0.8789 (mtm)
REVERT: C 61 GLU cc_start: 0.8595 (OUTLIER) cc_final: 0.8118 (pt0)
REVERT: C 69 MET cc_start: 0.8489 (mtp) cc_final: 0.8195 (ttm)
REVERT: C 102 GLU cc_start: 0.7785 (mt-10) cc_final: 0.7408 (mp0)
REVERT: C 267 MET cc_start: 0.6556 (tmm) cc_final: 0.5788 (mmp)
REVERT: C 288 MET cc_start: 0.7050 (ptp) cc_final: 0.6631 (mtp)
REVERT: C 367 GLU cc_start: 0.8512 (pp20) cc_final: 0.8163 (pp20)
REVERT: C 514 MET cc_start: 0.9070 (mtp) cc_final: 0.8780 (mtm)
REVERT: I 193 MET cc_start: 0.8455 (OUTLIER) cc_final: 0.8201 (ttm)
REVERT: I 204 PHE cc_start: 0.8433 (m-80) cc_final: 0.8059 (m-80)
REVERT: I 267 MET cc_start: 0.6634 (tmm) cc_final: 0.5947 (mmp)
REVERT: I 351 GLN cc_start: 0.8558 (OUTLIER) cc_final: 0.8152 (pp30)
REVERT: I 494 LEU cc_start: 0.9120 (OUTLIER) cc_final: 0.8864 (pp)
REVERT: D 242 LYS cc_start: 0.8081 (mmtt) cc_final: 0.7814 (mmmt)
REVERT: D 267 MET cc_start: 0.6347 (tmm) cc_final: 0.5553 (mmm)
REVERT: D 321 LYS cc_start: 0.8807 (ttpt) cc_final: 0.8519 (mmmt)
REVERT: D 367 GLU cc_start: 0.8670 (pp20) cc_final: 0.8389 (pp20)
REVERT: J 16 MET cc_start: 0.8691 (mtp) cc_final: 0.8396 (mtm)
REVERT: J 204 PHE cc_start: 0.8334 (m-80) cc_final: 0.7972 (m-80)
REVERT: J 267 MET cc_start: 0.6017 (tmm) cc_final: 0.5028 (mmm)
REVERT: J 442 VAL cc_start: 0.8986 (OUTLIER) cc_final: 0.8762 (t)
REVERT: J 494 LEU cc_start: 0.9028 (OUTLIER) cc_final: 0.8819 (pp)
REVERT: E 111 MET cc_start: 0.8775 (OUTLIER) cc_final: 0.8210 (mtt)
REVERT: E 267 MET cc_start: 0.6482 (tmm) cc_final: 0.5757 (mmp)
REVERT: E 367 GLU cc_start: 0.8613 (pp20) cc_final: 0.8329 (pp20)
REVERT: E 447 MET cc_start: 0.9179 (OUTLIER) cc_final: 0.8885 (mtp)
REVERT: E 494 LEU cc_start: 0.9174 (OUTLIER) cc_final: 0.8847 (pp)
REVERT: E 514 MET cc_start: 0.9207 (ttm) cc_final: 0.8813 (mtp)
REVERT: K 267 MET cc_start: 0.6682 (tmm) cc_final: 0.5391 (mmp)
REVERT: F 160 LYS cc_start: 0.8651 (mtpp) cc_final: 0.8364 (ptmm)
REVERT: F 367 GLU cc_start: 0.8418 (pp20) cc_final: 0.8098 (pp20)
REVERT: L 61 GLU cc_start: 0.8644 (tm-30) cc_final: 0.8232 (tm-30)
REVERT: L 69 MET cc_start: 0.8538 (OUTLIER) cc_final: 0.8117 (mtp)
REVERT: L 262 LEU cc_start: 0.7365 (OUTLIER) cc_final: 0.6953 (tp)
REVERT: L 267 MET cc_start: 0.6339 (tmm) cc_final: 0.5332 (mmm)
REVERT: L 288 MET cc_start: 0.7761 (OUTLIER) cc_final: 0.6783 (mpp)
REVERT: L 351 GLN cc_start: 0.8182 (tp40) cc_final: 0.7951 (tp40)
REVERT: G 61 GLU cc_start: 0.8612 (OUTLIER) cc_final: 0.8020 (pt0)
REVERT: G 160 LYS cc_start: 0.8767 (OUTLIER) cc_final: 0.8499 (ptmm)
REVERT: G 166 MET cc_start: 0.8800 (OUTLIER) cc_final: 0.8007 (mtt)
REVERT: G 267 MET cc_start: 0.6203 (tmm) cc_final: 0.5319 (mmp)
REVERT: G 367 GLU cc_start: 0.8608 (pp20) cc_final: 0.8274 (pp20)
REVERT: G 494 LEU cc_start: 0.9102 (OUTLIER) cc_final: 0.8866 (pp)
REVERT: M 13 ARG cc_start: 0.8320 (OUTLIER) cc_final: 0.7949 (mpt-90)
REVERT: M 267 MET cc_start: 0.6677 (tmm) cc_final: 0.5780 (mmt)
outliers start: 181
outliers final: 109
residues processed: 647
average time/residue: 0.4766
time to fit residues: 542.2480
Evaluate side-chains
591 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 130
poor density : 461
time to evaluate : 5.440
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 61 GLU
Chi-restraints excluded: chain A residue 169 VAL
Chi-restraints excluded: chain A residue 205 ILE
Chi-restraints excluded: chain A residue 213 VAL
Chi-restraints excluded: chain A residue 300 VAL
Chi-restraints excluded: chain A residue 331 THR
Chi-restraints excluded: chain A residue 463 SER
Chi-restraints excluded: chain A residue 517 THR
Chi-restraints excluded: chain N residue 50 THR
Chi-restraints excluded: chain N residue 111 MET
Chi-restraints excluded: chain N residue 114 MET
Chi-restraints excluded: chain N residue 200 LEU
Chi-restraints excluded: chain N residue 213 VAL
Chi-restraints excluded: chain N residue 234 LEU
Chi-restraints excluded: chain N residue 240 VAL
Chi-restraints excluded: chain N residue 442 VAL
Chi-restraints excluded: chain N residue 494 LEU
Chi-restraints excluded: chain N residue 517 THR
Chi-restraints excluded: chain B residue 48 THR
Chi-restraints excluded: chain B residue 50 THR
Chi-restraints excluded: chain B residue 124 VAL
Chi-restraints excluded: chain B residue 205 ILE
Chi-restraints excluded: chain B residue 213 VAL
Chi-restraints excluded: chain B residue 234 LEU
Chi-restraints excluded: chain B residue 271 VAL
Chi-restraints excluded: chain B residue 300 VAL
Chi-restraints excluded: chain B residue 307 MET
Chi-restraints excluded: chain B residue 463 SER
Chi-restraints excluded: chain B residue 494 LEU
Chi-restraints excluded: chain B residue 517 THR
Chi-restraints excluded: chain H residue 61 GLU
Chi-restraints excluded: chain H residue 146 GLN
Chi-restraints excluded: chain H residue 187 LEU
Chi-restraints excluded: chain H residue 213 VAL
Chi-restraints excluded: chain H residue 228 SER
Chi-restraints excluded: chain H residue 240 VAL
Chi-restraints excluded: chain H residue 273 VAL
Chi-restraints excluded: chain H residue 442 VAL
Chi-restraints excluded: chain H residue 517 THR
Chi-restraints excluded: chain C residue 61 GLU
Chi-restraints excluded: chain C residue 169 VAL
Chi-restraints excluded: chain C residue 187 LEU
Chi-restraints excluded: chain C residue 205 ILE
Chi-restraints excluded: chain C residue 213 VAL
Chi-restraints excluded: chain C residue 228 SER
Chi-restraints excluded: chain C residue 234 LEU
Chi-restraints excluded: chain C residue 261 THR
Chi-restraints excluded: chain C residue 300 VAL
Chi-restraints excluded: chain C residue 314 LEU
Chi-restraints excluded: chain C residue 517 THR
Chi-restraints excluded: chain I residue 61 GLU
Chi-restraints excluded: chain I residue 124 VAL
Chi-restraints excluded: chain I residue 193 MET
Chi-restraints excluded: chain I residue 201 SER
Chi-restraints excluded: chain I residue 213 VAL
Chi-restraints excluded: chain I residue 234 LEU
Chi-restraints excluded: chain I residue 240 VAL
Chi-restraints excluded: chain I residue 351 GLN
Chi-restraints excluded: chain I residue 442 VAL
Chi-restraints excluded: chain I residue 494 LEU
Chi-restraints excluded: chain D residue 48 THR
Chi-restraints excluded: chain D residue 169 VAL
Chi-restraints excluded: chain D residue 205 ILE
Chi-restraints excluded: chain D residue 213 VAL
Chi-restraints excluded: chain D residue 240 VAL
Chi-restraints excluded: chain D residue 259 LEU
Chi-restraints excluded: chain D residue 261 THR
Chi-restraints excluded: chain D residue 351 GLN
Chi-restraints excluded: chain D residue 517 THR
Chi-restraints excluded: chain J residue 146 GLN
Chi-restraints excluded: chain J residue 232 GLU
Chi-restraints excluded: chain J residue 273 VAL
Chi-restraints excluded: chain J residue 388 GLU
Chi-restraints excluded: chain J residue 433 ASN
Chi-restraints excluded: chain J residue 442 VAL
Chi-restraints excluded: chain J residue 494 LEU
Chi-restraints excluded: chain E residue 11 ASP
Chi-restraints excluded: chain E residue 48 THR
Chi-restraints excluded: chain E residue 50 THR
Chi-restraints excluded: chain E residue 111 MET
Chi-restraints excluded: chain E residue 177 VAL
Chi-restraints excluded: chain E residue 205 ILE
Chi-restraints excluded: chain E residue 213 VAL
Chi-restraints excluded: chain E residue 288 MET
Chi-restraints excluded: chain E residue 300 VAL
Chi-restraints excluded: chain E residue 447 MET
Chi-restraints excluded: chain E residue 494 LEU
Chi-restraints excluded: chain K residue 43 SER
Chi-restraints excluded: chain K residue 62 LEU
Chi-restraints excluded: chain K residue 146 GLN
Chi-restraints excluded: chain K residue 213 VAL
Chi-restraints excluded: chain K residue 240 VAL
Chi-restraints excluded: chain K residue 273 VAL
Chi-restraints excluded: chain K residue 288 MET
Chi-restraints excluded: chain K residue 307 MET
Chi-restraints excluded: chain K residue 463 SER
Chi-restraints excluded: chain K residue 517 THR
Chi-restraints excluded: chain F residue 48 THR
Chi-restraints excluded: chain F residue 50 THR
Chi-restraints excluded: chain F residue 124 VAL
Chi-restraints excluded: chain F residue 169 VAL
Chi-restraints excluded: chain F residue 193 MET
Chi-restraints excluded: chain F residue 205 ILE
Chi-restraints excluded: chain F residue 213 VAL
Chi-restraints excluded: chain F residue 255 GLU
Chi-restraints excluded: chain F residue 351 GLN
Chi-restraints excluded: chain F residue 463 SER
Chi-restraints excluded: chain F residue 517 THR
Chi-restraints excluded: chain F residue 524 LEU
Chi-restraints excluded: chain L residue 50 THR
Chi-restraints excluded: chain L residue 69 MET
Chi-restraints excluded: chain L residue 124 VAL
Chi-restraints excluded: chain L residue 213 VAL
Chi-restraints excluded: chain L residue 262 LEU
Chi-restraints excluded: chain L residue 288 MET
Chi-restraints excluded: chain L residue 517 THR
Chi-restraints excluded: chain G residue 11 ASP
Chi-restraints excluded: chain G residue 61 GLU
Chi-restraints excluded: chain G residue 160 LYS
Chi-restraints excluded: chain G residue 166 MET
Chi-restraints excluded: chain G residue 234 LEU
Chi-restraints excluded: chain G residue 300 VAL
Chi-restraints excluded: chain G residue 307 MET
Chi-restraints excluded: chain G residue 494 LEU
Chi-restraints excluded: chain M residue 13 ARG
Chi-restraints excluded: chain M residue 61 GLU
Chi-restraints excluded: chain M residue 442 VAL
Chi-restraints excluded: chain M residue 463 SER
Chi-restraints excluded: chain M residue 489 ILE
Chi-restraints excluded: chain M residue 517 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 728
random chunks:
chunk 164 optimal weight: 10.0000
chunk 62 optimal weight: 1.9990
chunk 470 optimal weight: 0.7980
chunk 455 optimal weight: 2.9990
chunk 353 optimal weight: 4.9990
chunk 334 optimal weight: 9.9990
chunk 578 optimal weight: 6.9990
chunk 673 optimal weight: 5.9990
chunk 565 optimal weight: 1.9990
chunk 558 optimal weight: 8.9990
chunk 644 optimal weight: 1.9990
overall best weight: 1.9588
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
C 319 GLN
E 348 GLN
L 319 GLN
Total number of N/Q/H flips: 3
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.150147 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.108103 restraints weight = 68456.092|
|-----------------------------------------------------------------------------|
r_work (start): 0.3275 rms_B_bonded: 1.74
r_work: 0.3142 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.2989 rms_B_bonded: 3.93 restraints_weight: 0.2500
r_work (final): 0.2989
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8429
moved from start: 0.2028
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.051 54362 Z= 0.202
Angle : 0.485 12.007 73402 Z= 0.256
Chirality : 0.041 0.165 8932
Planarity : 0.003 0.030 9618
Dihedral : 3.865 26.099 7733
Min Nonbonded Distance : 2.512
Molprobity Statistics.
All-atom Clashscore : 6.60
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 1.42 %
Favored : 98.58 %
Rotamer:
Outliers : 2.69 %
Allowed : 14.14 %
Favored : 83.17 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 1.83 (0.10), residues: 7308
helix: 2.25 (0.08), residues: 4088
sheet: 0.63 (0.17), residues: 938
loop : -0.43 (0.12), residues: 2282
Max deviation from planes:
Type MaxDev MeanDev LineInFile
HIS 0.000 0.000 HIS N 401
PHE 0.011 0.001 PHE G 204
TYR 0.010 0.001 TYR K 476
ARG 0.004 0.000 ARG L 345
*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
14616 Ramachandran restraints generated.
7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
14616 Ramachandran restraints generated.
7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
655 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 152
poor density : 503
time to evaluate : 4.912
Fit side-chains
revert: symmetry clash
REVERT: A 267 MET cc_start: 0.6120 (mmm) cc_final: 0.5147 (mmm)
REVERT: A 367 GLU cc_start: 0.8419 (pp20) cc_final: 0.8122 (pp20)
REVERT: A 514 MET cc_start: 0.9247 (mtm) cc_final: 0.8909 (mtp)
REVERT: N 16 MET cc_start: 0.8627 (mmm) cc_final: 0.8334 (mtt)
REVERT: N 69 MET cc_start: 0.7984 (mtm) cc_final: 0.7608 (mtp)
REVERT: N 111 MET cc_start: 0.8974 (OUTLIER) cc_final: 0.8461 (mtt)
REVERT: N 201 SER cc_start: 0.8365 (t) cc_final: 0.8070 (m)
REVERT: N 267 MET cc_start: 0.6330 (tmm) cc_final: 0.5930 (mmp)
REVERT: N 442 VAL cc_start: 0.8986 (OUTLIER) cc_final: 0.8784 (t)
REVERT: N 494 LEU cc_start: 0.9145 (OUTLIER) cc_final: 0.8855 (pp)
REVERT: B 160 LYS cc_start: 0.8558 (mtpp) cc_final: 0.8229 (ptmm)
REVERT: B 204 PHE cc_start: 0.8472 (m-80) cc_final: 0.8148 (m-80)
REVERT: B 267 MET cc_start: 0.6083 (tmm) cc_final: 0.5540 (mmp)
REVERT: B 367 GLU cc_start: 0.8465 (pp20) cc_final: 0.8124 (pp20)
REVERT: B 389 MET cc_start: 0.8255 (tmm) cc_final: 0.8042 (ttp)
REVERT: B 494 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8668 (pp)
REVERT: H 267 MET cc_start: 0.6340 (tmm) cc_final: 0.5311 (mmm)
REVERT: H 514 MET cc_start: 0.9087 (mtp) cc_final: 0.8836 (mtp)
REVERT: C 61 GLU cc_start: 0.8610 (OUTLIER) cc_final: 0.8131 (pt0)
REVERT: C 267 MET cc_start: 0.6492 (tmm) cc_final: 0.5791 (mmp)
REVERT: C 288 MET cc_start: 0.7001 (ptp) cc_final: 0.6661 (mtp)
REVERT: C 322 ARG cc_start: 0.8926 (mtp-110) cc_final: 0.8690 (ttm110)
REVERT: C 367 GLU cc_start: 0.8487 (pp20) cc_final: 0.8109 (pp20)
REVERT: C 488 MET cc_start: 0.9039 (tpt) cc_final: 0.8651 (mmt)
REVERT: C 514 MET cc_start: 0.9104 (mtp) cc_final: 0.8881 (mtm)
REVERT: I 193 MET cc_start: 0.8463 (tpt) cc_final: 0.8230 (ttm)
REVERT: I 204 PHE cc_start: 0.8451 (m-80) cc_final: 0.8150 (m-80)
REVERT: I 267 MET cc_start: 0.6678 (tmm) cc_final: 0.5812 (mmp)
REVERT: I 351 GLN cc_start: 0.8560 (OUTLIER) cc_final: 0.8146 (pp30)
REVERT: I 494 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8830 (pp)
REVERT: D 242 LYS cc_start: 0.8039 (mmtt) cc_final: 0.7777 (mmmt)
REVERT: D 267 MET cc_start: 0.6286 (tmm) cc_final: 0.5507 (mmm)
REVERT: D 321 LYS cc_start: 0.8821 (ttpt) cc_final: 0.8516 (mmmt)
REVERT: D 367 GLU cc_start: 0.8674 (pp20) cc_final: 0.8369 (pp20)
REVERT: J 16 MET cc_start: 0.8800 (mtp) cc_final: 0.8536 (mtm)
REVERT: J 204 PHE cc_start: 0.8325 (m-80) cc_final: 0.7978 (m-80)
REVERT: J 267 MET cc_start: 0.5962 (tmm) cc_final: 0.5042 (mmm)
REVERT: J 442 VAL cc_start: 0.8943 (OUTLIER) cc_final: 0.8725 (t)
REVERT: J 494 LEU cc_start: 0.9028 (OUTLIER) cc_final: 0.8817 (pp)
REVERT: E 102 GLU cc_start: 0.7747 (mt-10) cc_final: 0.7401 (mp0)
REVERT: E 111 MET cc_start: 0.8878 (OUTLIER) cc_final: 0.8310 (mtt)
REVERT: E 267 MET cc_start: 0.6500 (tmm) cc_final: 0.5822 (mmp)
REVERT: E 367 GLU cc_start: 0.8540 (pp20) cc_final: 0.8241 (pp20)
REVERT: E 447 MET cc_start: 0.9201 (OUTLIER) cc_final: 0.8912 (mtp)
REVERT: E 494 LEU cc_start: 0.9142 (OUTLIER) cc_final: 0.8821 (pp)
REVERT: E 514 MET cc_start: 0.9132 (ttm) cc_final: 0.8919 (mtp)
REVERT: K 267 MET cc_start: 0.6683 (tmm) cc_final: 0.5483 (mmp)
REVERT: K 514 MET cc_start: 0.9241 (ttm) cc_final: 0.8859 (mtp)
REVERT: F 102 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.7354 (mp0)
REVERT: F 160 LYS cc_start: 0.8655 (mtpp) cc_final: 0.8387 (ptmm)
REVERT: F 321 LYS cc_start: 0.8803 (mmtt) cc_final: 0.8402 (mmtp)
REVERT: F 367 GLU cc_start: 0.8382 (pp20) cc_final: 0.8097 (pp20)
REVERT: L 61 GLU cc_start: 0.8720 (tm-30) cc_final: 0.8256 (tm-30)
REVERT: L 69 MET cc_start: 0.8483 (mtm) cc_final: 0.8057 (mtp)
REVERT: L 262 LEU cc_start: 0.7420 (OUTLIER) cc_final: 0.7018 (tp)
REVERT: L 267 MET cc_start: 0.6174 (tmm) cc_final: 0.5243 (mmm)
REVERT: L 288 MET cc_start: 0.7780 (OUTLIER) cc_final: 0.6810 (mpp)
REVERT: L 351 GLN cc_start: 0.8179 (tp40) cc_final: 0.7942 (tp40)
REVERT: L 461 GLU cc_start: 0.7906 (pm20) cc_final: 0.7528 (pm20)
REVERT: G 61 GLU cc_start: 0.8669 (OUTLIER) cc_final: 0.8053 (pt0)
REVERT: G 160 LYS cc_start: 0.8735 (OUTLIER) cc_final: 0.8464 (ptmm)
REVERT: G 204 PHE cc_start: 0.8487 (m-80) cc_final: 0.8218 (m-80)
REVERT: G 267 MET cc_start: 0.6258 (tmm) cc_final: 0.5412 (mmp)
REVERT: G 367 GLU cc_start: 0.8508 (pp20) cc_final: 0.8148 (pp20)
REVERT: G 494 LEU cc_start: 0.9102 (OUTLIER) cc_final: 0.8889 (pp)
REVERT: M 13 ARG cc_start: 0.8336 (OUTLIER) cc_final: 0.7979 (mpt-90)
REVERT: M 267 MET cc_start: 0.6541 (tmm) cc_final: 0.5749 (mmm)
outliers start: 152
outliers final: 108
residues processed: 622
average time/residue: 0.5013
time to fit residues: 551.3913
Evaluate side-chains
590 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 127
poor density : 463
time to evaluate : 4.813
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 48 THR
Chi-restraints excluded: chain A residue 61 GLU
Chi-restraints excluded: chain A residue 169 VAL
Chi-restraints excluded: chain A residue 213 VAL
Chi-restraints excluded: chain A residue 240 VAL
Chi-restraints excluded: chain A residue 300 VAL
Chi-restraints excluded: chain A residue 463 SER
Chi-restraints excluded: chain A residue 517 THR
Chi-restraints excluded: chain N residue 11 ASP
Chi-restraints excluded: chain N residue 50 THR
Chi-restraints excluded: chain N residue 111 MET
Chi-restraints excluded: chain N residue 442 VAL
Chi-restraints excluded: chain N residue 494 LEU
Chi-restraints excluded: chain B residue 48 THR
Chi-restraints excluded: chain B residue 50 THR
Chi-restraints excluded: chain B residue 124 VAL
Chi-restraints excluded: chain B residue 213 VAL
Chi-restraints excluded: chain B residue 234 LEU
Chi-restraints excluded: chain B residue 237 LEU
Chi-restraints excluded: chain B residue 300 VAL
Chi-restraints excluded: chain B residue 307 MET
Chi-restraints excluded: chain B residue 331 THR
Chi-restraints excluded: chain B residue 463 SER
Chi-restraints excluded: chain B residue 494 LEU
Chi-restraints excluded: chain B residue 517 THR
Chi-restraints excluded: chain H residue 61 GLU
Chi-restraints excluded: chain H residue 146 GLN
Chi-restraints excluded: chain H residue 213 VAL
Chi-restraints excluded: chain H residue 228 SER
Chi-restraints excluded: chain H residue 273 VAL
Chi-restraints excluded: chain H residue 442 VAL
Chi-restraints excluded: chain C residue 61 GLU
Chi-restraints excluded: chain C residue 169 VAL
Chi-restraints excluded: chain C residue 213 VAL
Chi-restraints excluded: chain C residue 228 SER
Chi-restraints excluded: chain C residue 234 LEU
Chi-restraints excluded: chain C residue 261 THR
Chi-restraints excluded: chain C residue 271 VAL
Chi-restraints excluded: chain C residue 300 VAL
Chi-restraints excluded: chain C residue 314 LEU
Chi-restraints excluded: chain C residue 331 THR
Chi-restraints excluded: chain C residue 517 THR
Chi-restraints excluded: chain I residue 61 GLU
Chi-restraints excluded: chain I residue 124 VAL
Chi-restraints excluded: chain I residue 201 SER
Chi-restraints excluded: chain I residue 213 VAL
Chi-restraints excluded: chain I residue 234 LEU
Chi-restraints excluded: chain I residue 240 VAL
Chi-restraints excluded: chain I residue 351 GLN
Chi-restraints excluded: chain I residue 442 VAL
Chi-restraints excluded: chain I residue 494 LEU
Chi-restraints excluded: chain D residue 43 SER
Chi-restraints excluded: chain D residue 48 THR
Chi-restraints excluded: chain D residue 124 VAL
Chi-restraints excluded: chain D residue 169 VAL
Chi-restraints excluded: chain D residue 213 VAL
Chi-restraints excluded: chain D residue 240 VAL
Chi-restraints excluded: chain D residue 259 LEU
Chi-restraints excluded: chain D residue 261 THR
Chi-restraints excluded: chain D residue 331 THR
Chi-restraints excluded: chain D residue 351 GLN
Chi-restraints excluded: chain D residue 517 THR
Chi-restraints excluded: chain J residue 213 VAL
Chi-restraints excluded: chain J residue 232 GLU
Chi-restraints excluded: chain J residue 273 VAL
Chi-restraints excluded: chain J residue 388 GLU
Chi-restraints excluded: chain J residue 433 ASN
Chi-restraints excluded: chain J residue 442 VAL
Chi-restraints excluded: chain J residue 494 LEU
Chi-restraints excluded: chain J residue 517 THR
Chi-restraints excluded: chain E residue 48 THR
Chi-restraints excluded: chain E residue 50 THR
Chi-restraints excluded: chain E residue 111 MET
Chi-restraints excluded: chain E residue 213 VAL
Chi-restraints excluded: chain E residue 240 VAL
Chi-restraints excluded: chain E residue 288 MET
Chi-restraints excluded: chain E residue 300 VAL
Chi-restraints excluded: chain E residue 331 THR
Chi-restraints excluded: chain E residue 348 GLN
Chi-restraints excluded: chain E residue 447 MET
Chi-restraints excluded: chain E residue 494 LEU
Chi-restraints excluded: chain E residue 517 THR
Chi-restraints excluded: chain K residue 43 SER
Chi-restraints excluded: chain K residue 62 LEU
Chi-restraints excluded: chain K residue 213 VAL
Chi-restraints excluded: chain K residue 273 VAL
Chi-restraints excluded: chain K residue 288 MET
Chi-restraints excluded: chain K residue 307 MET
Chi-restraints excluded: chain K residue 463 SER
Chi-restraints excluded: chain F residue 48 THR
Chi-restraints excluded: chain F residue 50 THR
Chi-restraints excluded: chain F residue 102 GLU
Chi-restraints excluded: chain F residue 169 VAL
Chi-restraints excluded: chain F residue 193 MET
Chi-restraints excluded: chain F residue 213 VAL
Chi-restraints excluded: chain F residue 255 GLU
Chi-restraints excluded: chain F residue 331 THR
Chi-restraints excluded: chain F residue 351 GLN
Chi-restraints excluded: chain F residue 369 VAL
Chi-restraints excluded: chain F residue 463 SER
Chi-restraints excluded: chain F residue 517 THR
Chi-restraints excluded: chain F residue 524 LEU
Chi-restraints excluded: chain L residue 50 THR
Chi-restraints excluded: chain L residue 146 GLN
Chi-restraints excluded: chain L residue 213 VAL
Chi-restraints excluded: chain L residue 262 LEU
Chi-restraints excluded: chain L residue 288 MET
Chi-restraints excluded: chain L residue 517 THR
Chi-restraints excluded: chain G residue 11 ASP
Chi-restraints excluded: chain G residue 48 THR
Chi-restraints excluded: chain G residue 50 THR
Chi-restraints excluded: chain G residue 61 GLU
Chi-restraints excluded: chain G residue 160 LYS
Chi-restraints excluded: chain G residue 169 VAL
Chi-restraints excluded: chain G residue 300 VAL
Chi-restraints excluded: chain G residue 307 MET
Chi-restraints excluded: chain G residue 494 LEU
Chi-restraints excluded: chain G residue 517 THR
Chi-restraints excluded: chain M residue 13 ARG
Chi-restraints excluded: chain M residue 61 GLU
Chi-restraints excluded: chain M residue 124 VAL
Chi-restraints excluded: chain M residue 146 GLN
Chi-restraints excluded: chain M residue 187 LEU
Chi-restraints excluded: chain M residue 259 LEU
Chi-restraints excluded: chain M residue 262 LEU
Chi-restraints excluded: chain M residue 442 VAL
Chi-restraints excluded: chain M residue 463 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 728
random chunks:
chunk 505 optimal weight: 0.8980
chunk 379 optimal weight: 4.9990
chunk 549 optimal weight: 7.9990
chunk 23 optimal weight: 10.0000
chunk 140 optimal weight: 5.9990
chunk 690 optimal weight: 5.9990
chunk 199 optimal weight: 0.7980
chunk 679 optimal weight: 4.9990
chunk 691 optimal weight: 5.9990
chunk 421 optimal weight: 6.9990
chunk 20 optimal weight: 1.9990
overall best weight: 2.7386
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
B 348 GLN
J 351 GLN
M 351 GLN
Total number of N/Q/H flips: 3
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.148829 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.106590 restraints weight = 68515.929|
|-----------------------------------------------------------------------------|
r_work (start): 0.3253 rms_B_bonded: 1.74
r_work: 0.3112 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.2958 rms_B_bonded: 3.96 restraints_weight: 0.2500
r_work (final): 0.2958
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8451
moved from start: 0.2169
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.004 0.061 54362 Z= 0.259
Angle : 0.506 10.738 73402 Z= 0.267
Chirality : 0.042 0.176 8932
Planarity : 0.003 0.035 9618
Dihedral : 3.882 19.159 7730
Min Nonbonded Distance : 2.508
Molprobity Statistics.
All-atom Clashscore : 6.74
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 1.74 %
Favored : 98.26 %
Rotamer:
Outliers : 3.18 %
Allowed : 14.48 %
Favored : 82.34 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 1.76 (0.10), residues: 7308
helix: 2.19 (0.08), residues: 4088
sheet: 0.60 (0.17), residues: 938
loop : -0.45 (0.12), residues: 2282
Max deviation from planes:
Type MaxDev MeanDev LineInFile
HIS 0.001 0.000 HIS C 401
PHE 0.008 0.001 PHE L 8
TYR 0.010 0.001 TYR I 478
ARG 0.005 0.000 ARG E 345
*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
14616 Ramachandran restraints generated.
7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
14616 Ramachandran restraints generated.
7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
664 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 180
poor density : 484
time to evaluate : 4.834
Fit side-chains
revert: symmetry clash
revert: symmetry clash
REVERT: A 267 MET cc_start: 0.6167 (mmm) cc_final: 0.5188 (mmm)
REVERT: A 367 GLU cc_start: 0.8407 (pp20) cc_final: 0.8110 (pp20)
REVERT: N 111 MET cc_start: 0.9003 (OUTLIER) cc_final: 0.8482 (mtt)
REVERT: N 201 SER cc_start: 0.8378 (t) cc_final: 0.8081 (m)
REVERT: N 267 MET cc_start: 0.6330 (tmm) cc_final: 0.5948 (mmp)
REVERT: N 442 VAL cc_start: 0.9048 (OUTLIER) cc_final: 0.8813 (t)
REVERT: N 494 LEU cc_start: 0.9154 (OUTLIER) cc_final: 0.8850 (pp)
REVERT: N 514 MET cc_start: 0.9174 (ttm) cc_final: 0.8743 (mtp)
REVERT: N 520 MET cc_start: 0.8859 (OUTLIER) cc_final: 0.8523 (mmt)
REVERT: B 160 LYS cc_start: 0.8559 (mtpp) cc_final: 0.8216 (ptmm)
REVERT: B 204 PHE cc_start: 0.8493 (m-80) cc_final: 0.8173 (m-80)
REVERT: B 267 MET cc_start: 0.6544 (tmm) cc_final: 0.5404 (mmp)
REVERT: B 367 GLU cc_start: 0.8461 (pp20) cc_final: 0.8149 (pp20)
REVERT: B 389 MET cc_start: 0.8253 (tmm) cc_final: 0.8049 (ttp)
REVERT: B 494 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8661 (pp)
REVERT: H 267 MET cc_start: 0.6409 (tmm) cc_final: 0.5349 (mmp)
REVERT: H 514 MET cc_start: 0.9120 (mtp) cc_final: 0.8850 (mtm)
REVERT: C 61 GLU cc_start: 0.8618 (OUTLIER) cc_final: 0.8102 (pt0)
REVERT: C 69 MET cc_start: 0.8486 (mtp) cc_final: 0.8071 (ttm)
REVERT: C 267 MET cc_start: 0.6425 (tmm) cc_final: 0.5775 (mmp)
REVERT: C 288 MET cc_start: 0.7011 (ptp) cc_final: 0.6776 (mtp)
REVERT: C 322 ARG cc_start: 0.8929 (mtp-110) cc_final: 0.8724 (ttm110)
REVERT: C 367 GLU cc_start: 0.8471 (pp20) cc_final: 0.8080 (pp20)
REVERT: C 494 LEU cc_start: 0.9013 (OUTLIER) cc_final: 0.8747 (pp)
REVERT: C 514 MET cc_start: 0.9097 (mtp) cc_final: 0.8832 (mtm)
REVERT: I 193 MET cc_start: 0.8491 (OUTLIER) cc_final: 0.8273 (ttm)
REVERT: I 204 PHE cc_start: 0.8457 (m-80) cc_final: 0.8136 (m-80)
REVERT: I 267 MET cc_start: 0.6650 (tmm) cc_final: 0.5870 (mmp)
REVERT: I 351 GLN cc_start: 0.8560 (OUTLIER) cc_final: 0.8152 (pp30)
REVERT: I 494 LEU cc_start: 0.9054 (OUTLIER) cc_final: 0.8809 (pp)
REVERT: I 514 MET cc_start: 0.9197 (ttm) cc_final: 0.8827 (mtp)
REVERT: D 242 LYS cc_start: 0.8040 (mmtt) cc_final: 0.7780 (mmmt)
REVERT: D 267 MET cc_start: 0.6631 (tmm) cc_final: 0.5863 (mmm)
REVERT: D 321 LYS cc_start: 0.8823 (ttpt) cc_final: 0.8499 (mmmt)
REVERT: D 367 GLU cc_start: 0.8619 (pp20) cc_final: 0.8287 (pp20)
REVERT: J 16 MET cc_start: 0.8850 (mtp) cc_final: 0.8598 (mtm)
REVERT: J 204 PHE cc_start: 0.8350 (m-80) cc_final: 0.8014 (m-80)
REVERT: J 267 MET cc_start: 0.6001 (tmm) cc_final: 0.5109 (mmm)
REVERT: J 442 VAL cc_start: 0.8978 (OUTLIER) cc_final: 0.8759 (t)
REVERT: J 494 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8852 (pp)
REVERT: E 102 GLU cc_start: 0.7819 (mt-10) cc_final: 0.7461 (mp0)
REVERT: E 111 MET cc_start: 0.8920 (OUTLIER) cc_final: 0.8354 (mtt)
REVERT: E 267 MET cc_start: 0.6799 (tmm) cc_final: 0.5817 (mmp)
REVERT: E 367 GLU cc_start: 0.8546 (pp20) cc_final: 0.8231 (pp20)
REVERT: E 389 MET cc_start: 0.7922 (tmm) cc_final: 0.7653 (tmt)
REVERT: E 447 MET cc_start: 0.9208 (OUTLIER) cc_final: 0.8920 (mtp)
REVERT: E 494 LEU cc_start: 0.9157 (OUTLIER) cc_final: 0.8839 (pp)
REVERT: E 514 MET cc_start: 0.9178 (ttm) cc_final: 0.8949 (mtp)
REVERT: K 142 LYS cc_start: 0.8604 (tppt) cc_final: 0.8338 (ttpp)
REVERT: K 267 MET cc_start: 0.6660 (tmm) cc_final: 0.5508 (mmp)
REVERT: K 514 MET cc_start: 0.9237 (ttm) cc_final: 0.8946 (mtp)
REVERT: F 102 GLU cc_start: 0.7837 (mt-10) cc_final: 0.7390 (mp0)
REVERT: F 111 MET cc_start: 0.8995 (mtp) cc_final: 0.8667 (mtt)
REVERT: F 160 LYS cc_start: 0.8674 (mtpp) cc_final: 0.8390 (ptmm)
REVERT: F 321 LYS cc_start: 0.8814 (mmtt) cc_final: 0.8408 (mmtp)
REVERT: F 367 GLU cc_start: 0.8382 (pp20) cc_final: 0.8062 (pp20)
REVERT: L 69 MET cc_start: 0.8565 (OUTLIER) cc_final: 0.8118 (mtp)
REVERT: L 262 LEU cc_start: 0.7425 (OUTLIER) cc_final: 0.6947 (tp)
REVERT: L 267 MET cc_start: 0.6194 (tmm) cc_final: 0.5319 (mmm)
REVERT: L 288 MET cc_start: 0.7682 (OUTLIER) cc_final: 0.6720 (mpp)
REVERT: L 351 GLN cc_start: 0.8221 (tp40) cc_final: 0.7978 (tp40)
REVERT: G 61 GLU cc_start: 0.8718 (OUTLIER) cc_final: 0.8091 (pt0)
REVERT: G 160 LYS cc_start: 0.8754 (OUTLIER) cc_final: 0.8496 (ptmm)
REVERT: G 166 MET cc_start: 0.8781 (OUTLIER) cc_final: 0.7990 (mtt)
REVERT: G 204 PHE cc_start: 0.8545 (m-80) cc_final: 0.8242 (m-80)
REVERT: G 267 MET cc_start: 0.6266 (tmm) cc_final: 0.5479 (mmp)
REVERT: G 367 GLU cc_start: 0.8491 (pp20) cc_final: 0.8119 (pp20)
REVERT: G 494 LEU cc_start: 0.9092 (OUTLIER) cc_final: 0.8891 (pp)
REVERT: M 13 ARG cc_start: 0.8333 (OUTLIER) cc_final: 0.7959 (mpt-90)
REVERT: M 267 MET cc_start: 0.6483 (tmm) cc_final: 0.5678 (mmm)
outliers start: 180
outliers final: 134
residues processed: 631
average time/residue: 0.4580
time to fit residues: 509.8252
Evaluate side-chains
613 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 157
poor density : 456
time to evaluate : 4.721
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 48 THR
Chi-restraints excluded: chain A residue 61 GLU
Chi-restraints excluded: chain A residue 169 VAL
Chi-restraints excluded: chain A residue 205 ILE
Chi-restraints excluded: chain A residue 232 GLU
Chi-restraints excluded: chain A residue 240 VAL
Chi-restraints excluded: chain A residue 300 VAL
Chi-restraints excluded: chain A residue 331 THR
Chi-restraints excluded: chain A residue 463 SER
Chi-restraints excluded: chain A residue 517 THR
Chi-restraints excluded: chain N residue 11 ASP
Chi-restraints excluded: chain N residue 50 THR
Chi-restraints excluded: chain N residue 111 MET
Chi-restraints excluded: chain N residue 213 VAL
Chi-restraints excluded: chain N residue 230 ILE
Chi-restraints excluded: chain N residue 234 LEU
Chi-restraints excluded: chain N residue 442 VAL
Chi-restraints excluded: chain N residue 494 LEU
Chi-restraints excluded: chain N residue 517 THR
Chi-restraints excluded: chain N residue 520 MET
Chi-restraints excluded: chain B residue 48 THR
Chi-restraints excluded: chain B residue 50 THR
Chi-restraints excluded: chain B residue 61 GLU
Chi-restraints excluded: chain B residue 124 VAL
Chi-restraints excluded: chain B residue 213 VAL
Chi-restraints excluded: chain B residue 234 LEU
Chi-restraints excluded: chain B residue 261 THR
Chi-restraints excluded: chain B residue 300 VAL
Chi-restraints excluded: chain B residue 307 MET
Chi-restraints excluded: chain B residue 331 THR
Chi-restraints excluded: chain B residue 348 GLN
Chi-restraints excluded: chain B residue 463 SER
Chi-restraints excluded: chain B residue 494 LEU
Chi-restraints excluded: chain B residue 517 THR
Chi-restraints excluded: chain H residue 61 GLU
Chi-restraints excluded: chain H residue 146 GLN
Chi-restraints excluded: chain H residue 213 VAL
Chi-restraints excluded: chain H residue 240 VAL
Chi-restraints excluded: chain H residue 273 VAL
Chi-restraints excluded: chain H residue 300 VAL
Chi-restraints excluded: chain H residue 442 VAL
Chi-restraints excluded: chain H residue 517 THR
Chi-restraints excluded: chain C residue 61 GLU
Chi-restraints excluded: chain C residue 169 VAL
Chi-restraints excluded: chain C residue 205 ILE
Chi-restraints excluded: chain C residue 213 VAL
Chi-restraints excluded: chain C residue 228 SER
Chi-restraints excluded: chain C residue 234 LEU
Chi-restraints excluded: chain C residue 261 THR
Chi-restraints excluded: chain C residue 271 VAL
Chi-restraints excluded: chain C residue 300 VAL
Chi-restraints excluded: chain C residue 314 LEU
Chi-restraints excluded: chain C residue 331 THR
Chi-restraints excluded: chain C residue 494 LEU
Chi-restraints excluded: chain C residue 517 THR
Chi-restraints excluded: chain I residue 61 GLU
Chi-restraints excluded: chain I residue 124 VAL
Chi-restraints excluded: chain I residue 146 GLN
Chi-restraints excluded: chain I residue 193 MET
Chi-restraints excluded: chain I residue 213 VAL
Chi-restraints excluded: chain I residue 234 LEU
Chi-restraints excluded: chain I residue 240 VAL
Chi-restraints excluded: chain I residue 351 GLN
Chi-restraints excluded: chain I residue 442 VAL
Chi-restraints excluded: chain I residue 494 LEU
Chi-restraints excluded: chain I residue 517 THR
Chi-restraints excluded: chain D residue 43 SER
Chi-restraints excluded: chain D residue 48 THR
Chi-restraints excluded: chain D residue 61 GLU
Chi-restraints excluded: chain D residue 124 VAL
Chi-restraints excluded: chain D residue 169 VAL
Chi-restraints excluded: chain D residue 205 ILE
Chi-restraints excluded: chain D residue 213 VAL
Chi-restraints excluded: chain D residue 240 VAL
Chi-restraints excluded: chain D residue 259 LEU
Chi-restraints excluded: chain D residue 331 THR
Chi-restraints excluded: chain D residue 351 GLN
Chi-restraints excluded: chain D residue 517 THR
Chi-restraints excluded: chain J residue 146 GLN
Chi-restraints excluded: chain J residue 213 VAL
Chi-restraints excluded: chain J residue 232 GLU
Chi-restraints excluded: chain J residue 273 VAL
Chi-restraints excluded: chain J residue 314 LEU
Chi-restraints excluded: chain J residue 388 GLU
Chi-restraints excluded: chain J residue 433 ASN
Chi-restraints excluded: chain J residue 442 VAL
Chi-restraints excluded: chain J residue 494 LEU
Chi-restraints excluded: chain J residue 517 THR
Chi-restraints excluded: chain E residue 48 THR
Chi-restraints excluded: chain E residue 50 THR
Chi-restraints excluded: chain E residue 111 MET
Chi-restraints excluded: chain E residue 177 VAL
Chi-restraints excluded: chain E residue 205 ILE
Chi-restraints excluded: chain E residue 213 VAL
Chi-restraints excluded: chain E residue 240 VAL
Chi-restraints excluded: chain E residue 271 VAL
Chi-restraints excluded: chain E residue 288 MET
Chi-restraints excluded: chain E residue 300 VAL
Chi-restraints excluded: chain E residue 331 THR
Chi-restraints excluded: chain E residue 447 MET
Chi-restraints excluded: chain E residue 494 LEU
Chi-restraints excluded: chain E residue 517 THR
Chi-restraints excluded: chain K residue 43 SER
Chi-restraints excluded: chain K residue 62 LEU
Chi-restraints excluded: chain K residue 146 GLN
Chi-restraints excluded: chain K residue 213 VAL
Chi-restraints excluded: chain K residue 273 VAL
Chi-restraints excluded: chain K residue 288 MET
Chi-restraints excluded: chain K residue 307 MET
Chi-restraints excluded: chain K residue 463 SER
Chi-restraints excluded: chain K residue 517 THR
Chi-restraints excluded: chain F residue 48 THR
Chi-restraints excluded: chain F residue 50 THR
Chi-restraints excluded: chain F residue 124 VAL
Chi-restraints excluded: chain F residue 169 VAL
Chi-restraints excluded: chain F residue 193 MET
Chi-restraints excluded: chain F residue 213 VAL
Chi-restraints excluded: chain F residue 255 GLU
Chi-restraints excluded: chain F residue 331 THR
Chi-restraints excluded: chain F residue 351 GLN
Chi-restraints excluded: chain F residue 369 VAL
Chi-restraints excluded: chain F residue 463 SER
Chi-restraints excluded: chain F residue 517 THR
Chi-restraints excluded: chain F residue 524 LEU
Chi-restraints excluded: chain L residue 50 THR
Chi-restraints excluded: chain L residue 69 MET
Chi-restraints excluded: chain L residue 124 VAL
Chi-restraints excluded: chain L residue 146 GLN
Chi-restraints excluded: chain L residue 213 VAL
Chi-restraints excluded: chain L residue 262 LEU
Chi-restraints excluded: chain L residue 288 MET
Chi-restraints excluded: chain L residue 517 THR
Chi-restraints excluded: chain G residue 11 ASP
Chi-restraints excluded: chain G residue 48 THR
Chi-restraints excluded: chain G residue 50 THR
Chi-restraints excluded: chain G residue 61 GLU
Chi-restraints excluded: chain G residue 160 LYS
Chi-restraints excluded: chain G residue 166 MET
Chi-restraints excluded: chain G residue 169 VAL
Chi-restraints excluded: chain G residue 205 ILE
Chi-restraints excluded: chain G residue 300 VAL
Chi-restraints excluded: chain G residue 307 MET
Chi-restraints excluded: chain G residue 494 LEU
Chi-restraints excluded: chain G residue 517 THR
Chi-restraints excluded: chain M residue 11 ASP
Chi-restraints excluded: chain M residue 13 ARG
Chi-restraints excluded: chain M residue 61 GLU
Chi-restraints excluded: chain M residue 124 VAL
Chi-restraints excluded: chain M residue 146 GLN
Chi-restraints excluded: chain M residue 187 LEU
Chi-restraints excluded: chain M residue 205 ILE
Chi-restraints excluded: chain M residue 259 LEU
Chi-restraints excluded: chain M residue 262 LEU
Chi-restraints excluded: chain M residue 442 VAL
Chi-restraints excluded: chain M residue 463 SER
Chi-restraints excluded: chain M residue 489 ILE
Chi-restraints excluded: chain M residue 517 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 728
random chunks:
chunk 683 optimal weight: 0.7980
chunk 420 optimal weight: 0.7980
chunk 280 optimal weight: 0.4980
chunk 214 optimal weight: 4.9990
chunk 536 optimal weight: 4.9990
chunk 223 optimal weight: 4.9990
chunk 498 optimal weight: 7.9990
chunk 51 optimal weight: 2.9990
chunk 265 optimal weight: 4.9990
chunk 241 optimal weight: 10.0000
chunk 351 optimal weight: 1.9990
overall best weight: 1.4184
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
B 351 GLN
C 467 ASN
Total number of N/Q/H flips: 2
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.150581 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.109638 restraints weight = 68254.565|
|-----------------------------------------------------------------------------|
r_work (start): 0.3292 rms_B_bonded: 1.79
r_work: 0.3145 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.2991 rms_B_bonded: 3.94 restraints_weight: 0.2500
r_work (final): 0.2991
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8413
moved from start: 0.2207
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.048 54362 Z= 0.172
Angle : 0.482 10.095 73402 Z= 0.254
Chirality : 0.041 0.172 8932
Planarity : 0.003 0.033 9618
Dihedral : 3.815 18.675 7729
Min Nonbonded Distance : 2.474
Molprobity Statistics.
All-atom Clashscore : 6.54
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 1.45 %
Favored : 98.55 %
Rotamer:
Outliers : 2.72 %
Allowed : 15.33 %
Favored : 81.95 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 1.86 (0.10), residues: 7308
helix: 2.27 (0.08), residues: 4088
sheet: 0.63 (0.17), residues: 938
loop : -0.41 (0.12), residues: 2282
Max deviation from planes:
Type MaxDev MeanDev LineInFile
HIS 0.000 0.000 HIS N 401
PHE 0.008 0.001 PHE L 204
TYR 0.010 0.001 TYR J 476
ARG 0.006 0.000 ARG B 345
*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
14616 Ramachandran restraints generated.
7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
14616 Ramachandran restraints generated.
7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
651 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 154
poor density : 497
time to evaluate : 4.820
Fit side-chains
revert: symmetry clash
REVERT: A 267 MET cc_start: 0.6163 (mmm) cc_final: 0.5192 (mmm)
REVERT: A 367 GLU cc_start: 0.8417 (pp20) cc_final: 0.8121 (pp20)
REVERT: N 69 MET cc_start: 0.7911 (mtm) cc_final: 0.7549 (mtp)
REVERT: N 111 MET cc_start: 0.8954 (OUTLIER) cc_final: 0.8423 (mtt)
REVERT: N 201 SER cc_start: 0.8331 (t) cc_final: 0.8011 (m)
REVERT: N 267 MET cc_start: 0.6218 (tmm) cc_final: 0.5971 (mmp)
REVERT: N 442 VAL cc_start: 0.8980 (OUTLIER) cc_final: 0.8767 (t)
REVERT: N 494 LEU cc_start: 0.9155 (OUTLIER) cc_final: 0.8861 (pp)
REVERT: N 520 MET cc_start: 0.8774 (mmt) cc_final: 0.8546 (mmt)
REVERT: B 160 LYS cc_start: 0.8614 (mtpp) cc_final: 0.8257 (ptmm)
REVERT: B 204 PHE cc_start: 0.8456 (m-80) cc_final: 0.8092 (m-80)
REVERT: B 267 MET cc_start: 0.6527 (tmm) cc_final: 0.5406 (mmp)
REVERT: B 367 GLU cc_start: 0.8409 (pp20) cc_final: 0.8101 (pp20)
REVERT: B 494 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8659 (pp)
REVERT: H 267 MET cc_start: 0.6298 (tmm) cc_final: 0.5341 (mmp)
REVERT: C 61 GLU cc_start: 0.8572 (OUTLIER) cc_final: 0.8076 (pt0)
REVERT: C 69 MET cc_start: 0.8358 (mtp) cc_final: 0.8015 (ttm)
REVERT: C 267 MET cc_start: 0.6422 (tmm) cc_final: 0.5745 (mmp)
REVERT: C 322 ARG cc_start: 0.8961 (mtp-110) cc_final: 0.8688 (ttm110)
REVERT: C 367 GLU cc_start: 0.8429 (pp20) cc_final: 0.8026 (pp20)
REVERT: C 514 MET cc_start: 0.9092 (mtp) cc_final: 0.8865 (mtm)
REVERT: I 193 MET cc_start: 0.8450 (OUTLIER) cc_final: 0.8231 (ttm)
REVERT: I 204 PHE cc_start: 0.8421 (m-80) cc_final: 0.8144 (m-80)
REVERT: I 267 MET cc_start: 0.6536 (tmm) cc_final: 0.5793 (mmp)
REVERT: I 351 GLN cc_start: 0.8577 (OUTLIER) cc_final: 0.8157 (pp30)
REVERT: I 494 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8797 (pp)
REVERT: I 514 MET cc_start: 0.9201 (ttm) cc_final: 0.8907 (mtp)
REVERT: D 242 LYS cc_start: 0.8043 (mmtt) cc_final: 0.7778 (mmmt)
REVERT: D 267 MET cc_start: 0.6600 (tmm) cc_final: 0.5816 (mmm)
REVERT: D 321 LYS cc_start: 0.8820 (ttpt) cc_final: 0.8480 (mmmt)
REVERT: D 367 GLU cc_start: 0.8616 (pp20) cc_final: 0.8271 (pp20)
REVERT: J 16 MET cc_start: 0.8813 (mtp) cc_final: 0.8592 (mtm)
REVERT: J 204 PHE cc_start: 0.8305 (m-80) cc_final: 0.7980 (m-80)
REVERT: J 267 MET cc_start: 0.5697 (tmm) cc_final: 0.4914 (mmm)
REVERT: J 442 VAL cc_start: 0.8913 (OUTLIER) cc_final: 0.8706 (t)
REVERT: E 267 MET cc_start: 0.6737 (tmm) cc_final: 0.5859 (mmp)
REVERT: E 351 GLN cc_start: 0.8309 (OUTLIER) cc_final: 0.7939 (tp-100)
REVERT: E 367 GLU cc_start: 0.8548 (pp20) cc_final: 0.8204 (pp20)
REVERT: E 389 MET cc_start: 0.7908 (tmm) cc_final: 0.7598 (tmt)
REVERT: E 447 MET cc_start: 0.9208 (OUTLIER) cc_final: 0.8919 (mtp)
REVERT: E 494 LEU cc_start: 0.9131 (OUTLIER) cc_final: 0.8801 (pp)
REVERT: E 514 MET cc_start: 0.9145 (ttm) cc_final: 0.8732 (mtp)
REVERT: K 238 GLU cc_start: 0.7100 (mm-30) cc_final: 0.6898 (mm-30)
REVERT: K 267 MET cc_start: 0.6531 (tmm) cc_final: 0.5425 (mmp)
REVERT: K 514 MET cc_start: 0.9165 (ttm) cc_final: 0.8913 (mtp)
REVERT: F 102 GLU cc_start: 0.7765 (mt-10) cc_final: 0.7292 (mp0)
REVERT: F 111 MET cc_start: 0.8973 (mtp) cc_final: 0.8635 (mtt)
REVERT: F 160 LYS cc_start: 0.8662 (mtpp) cc_final: 0.8383 (ptmm)
REVERT: F 321 LYS cc_start: 0.8784 (mmtt) cc_final: 0.8377 (mmtp)
REVERT: F 367 GLU cc_start: 0.8360 (pp20) cc_final: 0.8054 (pp20)
REVERT: L 61 GLU cc_start: 0.8721 (tm-30) cc_final: 0.8408 (tm-30)
REVERT: L 69 MET cc_start: 0.8469 (mtm) cc_final: 0.8035 (mtp)
REVERT: L 262 LEU cc_start: 0.7399 (OUTLIER) cc_final: 0.7033 (tp)
REVERT: L 267 MET cc_start: 0.6129 (tmm) cc_final: 0.5373 (mmm)
REVERT: L 288 MET cc_start: 0.7689 (OUTLIER) cc_final: 0.6727 (mpp)
REVERT: L 351 GLN cc_start: 0.8219 (tp40) cc_final: 0.7969 (tp40)
REVERT: G 61 GLU cc_start: 0.8678 (OUTLIER) cc_final: 0.8071 (pt0)
REVERT: G 166 MET cc_start: 0.8715 (OUTLIER) cc_final: 0.7914 (mtt)
REVERT: G 204 PHE cc_start: 0.8541 (m-80) cc_final: 0.8212 (m-80)
REVERT: G 267 MET cc_start: 0.6185 (tmm) cc_final: 0.5487 (mmp)
REVERT: G 367 GLU cc_start: 0.8470 (pp20) cc_final: 0.8095 (pp20)
REVERT: G 494 LEU cc_start: 0.9076 (OUTLIER) cc_final: 0.8842 (pp)
REVERT: M 267 MET cc_start: 0.6367 (tmm) cc_final: 0.5690 (mmm)
outliers start: 154
outliers final: 118
residues processed: 624
average time/residue: 0.4663
time to fit residues: 513.3552
Evaluate side-chains
593 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 135
poor density : 458
time to evaluate : 4.801
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 48 THR
Chi-restraints excluded: chain A residue 61 GLU
Chi-restraints excluded: chain A residue 213 VAL
Chi-restraints excluded: chain A residue 240 VAL
Chi-restraints excluded: chain A residue 300 VAL
Chi-restraints excluded: chain A residue 463 SER
Chi-restraints excluded: chain A residue 517 THR
Chi-restraints excluded: chain N residue 11 ASP
Chi-restraints excluded: chain N residue 50 THR
Chi-restraints excluded: chain N residue 111 MET
Chi-restraints excluded: chain N residue 213 VAL
Chi-restraints excluded: chain N residue 234 LEU
Chi-restraints excluded: chain N residue 240 VAL
Chi-restraints excluded: chain N residue 442 VAL
Chi-restraints excluded: chain N residue 494 LEU
Chi-restraints excluded: chain N residue 499 VAL
Chi-restraints excluded: chain N residue 517 THR
Chi-restraints excluded: chain B residue 48 THR
Chi-restraints excluded: chain B residue 50 THR
Chi-restraints excluded: chain B residue 213 VAL
Chi-restraints excluded: chain B residue 237 LEU
Chi-restraints excluded: chain B residue 300 VAL
Chi-restraints excluded: chain B residue 307 MET
Chi-restraints excluded: chain B residue 331 THR
Chi-restraints excluded: chain B residue 494 LEU
Chi-restraints excluded: chain B residue 517 THR
Chi-restraints excluded: chain H residue 61 GLU
Chi-restraints excluded: chain H residue 146 GLN
Chi-restraints excluded: chain H residue 213 VAL
Chi-restraints excluded: chain H residue 240 VAL
Chi-restraints excluded: chain H residue 300 VAL
Chi-restraints excluded: chain H residue 442 VAL
Chi-restraints excluded: chain C residue 61 GLU
Chi-restraints excluded: chain C residue 174 VAL
Chi-restraints excluded: chain C residue 205 ILE
Chi-restraints excluded: chain C residue 213 VAL
Chi-restraints excluded: chain C residue 228 SER
Chi-restraints excluded: chain C residue 261 THR
Chi-restraints excluded: chain C residue 271 VAL
Chi-restraints excluded: chain C residue 300 VAL
Chi-restraints excluded: chain C residue 314 LEU
Chi-restraints excluded: chain C residue 331 THR
Chi-restraints excluded: chain C residue 517 THR
Chi-restraints excluded: chain I residue 61 GLU
Chi-restraints excluded: chain I residue 124 VAL
Chi-restraints excluded: chain I residue 146 GLN
Chi-restraints excluded: chain I residue 193 MET
Chi-restraints excluded: chain I residue 213 VAL
Chi-restraints excluded: chain I residue 234 LEU
Chi-restraints excluded: chain I residue 240 VAL
Chi-restraints excluded: chain I residue 351 GLN
Chi-restraints excluded: chain I residue 442 VAL
Chi-restraints excluded: chain I residue 494 LEU
Chi-restraints excluded: chain I residue 499 VAL
Chi-restraints excluded: chain D residue 43 SER
Chi-restraints excluded: chain D residue 48 THR
Chi-restraints excluded: chain D residue 61 GLU
Chi-restraints excluded: chain D residue 124 VAL
Chi-restraints excluded: chain D residue 169 VAL
Chi-restraints excluded: chain D residue 213 VAL
Chi-restraints excluded: chain D residue 240 VAL
Chi-restraints excluded: chain D residue 259 LEU
Chi-restraints excluded: chain D residue 331 THR
Chi-restraints excluded: chain D residue 351 GLN
Chi-restraints excluded: chain D residue 447 MET
Chi-restraints excluded: chain D residue 517 THR
Chi-restraints excluded: chain J residue 11 ASP
Chi-restraints excluded: chain J residue 146 GLN
Chi-restraints excluded: chain J residue 213 VAL
Chi-restraints excluded: chain J residue 232 GLU
Chi-restraints excluded: chain J residue 388 GLU
Chi-restraints excluded: chain J residue 433 ASN
Chi-restraints excluded: chain J residue 442 VAL
Chi-restraints excluded: chain J residue 517 THR
Chi-restraints excluded: chain E residue 48 THR
Chi-restraints excluded: chain E residue 50 THR
Chi-restraints excluded: chain E residue 177 VAL
Chi-restraints excluded: chain E residue 205 ILE
Chi-restraints excluded: chain E residue 213 VAL
Chi-restraints excluded: chain E residue 240 VAL
Chi-restraints excluded: chain E residue 271 VAL
Chi-restraints excluded: chain E residue 288 MET
Chi-restraints excluded: chain E residue 300 VAL
Chi-restraints excluded: chain E residue 331 THR
Chi-restraints excluded: chain E residue 351 GLN
Chi-restraints excluded: chain E residue 447 MET
Chi-restraints excluded: chain E residue 494 LEU
Chi-restraints excluded: chain K residue 62 LEU
Chi-restraints excluded: chain K residue 146 GLN
Chi-restraints excluded: chain K residue 213 VAL
Chi-restraints excluded: chain K residue 240 VAL
Chi-restraints excluded: chain K residue 273 VAL
Chi-restraints excluded: chain K residue 288 MET
Chi-restraints excluded: chain K residue 307 MET
Chi-restraints excluded: chain K residue 463 SER
Chi-restraints excluded: chain F residue 48 THR
Chi-restraints excluded: chain F residue 50 THR
Chi-restraints excluded: chain F residue 169 VAL
Chi-restraints excluded: chain F residue 193 MET
Chi-restraints excluded: chain F residue 205 ILE
Chi-restraints excluded: chain F residue 213 VAL
Chi-restraints excluded: chain F residue 255 GLU
Chi-restraints excluded: chain F residue 270 ILE
Chi-restraints excluded: chain F residue 331 THR
Chi-restraints excluded: chain F residue 351 GLN
Chi-restraints excluded: chain F residue 369 VAL
Chi-restraints excluded: chain F residue 463 SER
Chi-restraints excluded: chain F residue 491 MET
Chi-restraints excluded: chain F residue 517 THR
Chi-restraints excluded: chain F residue 524 LEU
Chi-restraints excluded: chain L residue 50 THR
Chi-restraints excluded: chain L residue 146 GLN
Chi-restraints excluded: chain L residue 213 VAL
Chi-restraints excluded: chain L residue 262 LEU
Chi-restraints excluded: chain L residue 288 MET
Chi-restraints excluded: chain G residue 11 ASP
Chi-restraints excluded: chain G residue 48 THR
Chi-restraints excluded: chain G residue 50 THR
Chi-restraints excluded: chain G residue 61 GLU
Chi-restraints excluded: chain G residue 160 LYS
Chi-restraints excluded: chain G residue 166 MET
Chi-restraints excluded: chain G residue 169 VAL
Chi-restraints excluded: chain G residue 205 ILE
Chi-restraints excluded: chain G residue 300 VAL
Chi-restraints excluded: chain G residue 307 MET
Chi-restraints excluded: chain G residue 331 THR
Chi-restraints excluded: chain G residue 494 LEU
Chi-restraints excluded: chain M residue 11 ASP
Chi-restraints excluded: chain M residue 61 GLU
Chi-restraints excluded: chain M residue 124 VAL
Chi-restraints excluded: chain M residue 146 GLN
Chi-restraints excluded: chain M residue 259 LEU
Chi-restraints excluded: chain M residue 262 LEU
Chi-restraints excluded: chain M residue 442 VAL
Chi-restraints excluded: chain M residue 463 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 728
random chunks:
chunk 86 optimal weight: 2.9990
chunk 554 optimal weight: 9.9990
chunk 274 optimal weight: 6.9990
chunk 172 optimal weight: 0.9990
chunk 465 optimal weight: 4.9990
chunk 412 optimal weight: 6.9990
chunk 483 optimal weight: 0.0010
chunk 594 optimal weight: 20.0000
chunk 604 optimal weight: 10.0000
chunk 579 optimal weight: 3.9990
chunk 59 optimal weight: 0.8980
overall best weight: 1.7792
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
J 351 GLN
K 351 GLN
G 351 GLN
Total number of N/Q/H flips: 3
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.150346 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.108384 restraints weight = 68509.381|
|-----------------------------------------------------------------------------|
r_work (start): 0.3274 rms_B_bonded: 1.79
r_work: 0.3132 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.2976 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.2976
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8425
moved from start: 0.2287
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.050 54362 Z= 0.193
Angle : 0.488 9.616 73402 Z= 0.256
Chirality : 0.041 0.172 8932
Planarity : 0.003 0.035 9618
Dihedral : 3.811 18.585 7729
Min Nonbonded Distance : 2.459
Molprobity Statistics.
All-atom Clashscore : 6.68
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 1.57 %
Favored : 98.43 %
Rotamer:
Outliers : 2.90 %
Allowed : 15.22 %
Favored : 81.88 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 1.85 (0.10), residues: 7308
helix: 2.26 (0.08), residues: 4088
sheet: 0.62 (0.17), residues: 938
loop : -0.41 (0.12), residues: 2282
Max deviation from planes:
Type MaxDev MeanDev LineInFile
HIS 0.000 0.000 HIS N 401
PHE 0.007 0.001 PHE L 8
TYR 0.010 0.001 TYR J 476
ARG 0.004 0.000 ARG I 345
*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
14616 Ramachandran restraints generated.
7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
14616 Ramachandran restraints generated.
7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
648 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 164
poor density : 484
time to evaluate : 5.633
Fit side-chains
REVERT: A 267 MET cc_start: 0.6053 (mmm) cc_final: 0.5121 (mmm)
REVERT: A 367 GLU cc_start: 0.8398 (pp20) cc_final: 0.8083 (pp20)
REVERT: N 69 MET cc_start: 0.7954 (mtm) cc_final: 0.7588 (mtp)
REVERT: N 111 MET cc_start: 0.8973 (OUTLIER) cc_final: 0.8443 (mtt)
REVERT: N 201 SER cc_start: 0.8324 (t) cc_final: 0.8013 (m)
REVERT: N 267 MET cc_start: 0.6682 (tmm) cc_final: 0.5882 (mmp)
REVERT: N 442 VAL cc_start: 0.9005 (OUTLIER) cc_final: 0.8801 (t)
REVERT: N 494 LEU cc_start: 0.9168 (OUTLIER) cc_final: 0.8870 (pp)
REVERT: B 160 LYS cc_start: 0.8623 (mtpp) cc_final: 0.8268 (ptmm)
REVERT: B 204 PHE cc_start: 0.8466 (m-80) cc_final: 0.8099 (m-80)
REVERT: B 267 MET cc_start: 0.6605 (tmm) cc_final: 0.5535 (mmp)
REVERT: B 367 GLU cc_start: 0.8417 (pp20) cc_final: 0.8105 (pp20)
REVERT: B 494 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8607 (pp)
REVERT: H 69 MET cc_start: 0.8705 (mtp) cc_final: 0.8502 (mtt)
REVERT: H 267 MET cc_start: 0.6226 (tmm) cc_final: 0.5202 (mmp)
REVERT: C 61 GLU cc_start: 0.8602 (OUTLIER) cc_final: 0.8055 (pt0)
REVERT: C 69 MET cc_start: 0.8362 (mtp) cc_final: 0.8020 (ttm)
REVERT: C 267 MET cc_start: 0.6679 (tmm) cc_final: 0.6023 (mmp)
REVERT: C 322 ARG cc_start: 0.8973 (mtp-110) cc_final: 0.8599 (ttm110)
REVERT: C 367 GLU cc_start: 0.8424 (pp20) cc_final: 0.8011 (pp20)
REVERT: C 514 MET cc_start: 0.9076 (mtp) cc_final: 0.8842 (mtm)
REVERT: I 193 MET cc_start: 0.8490 (OUTLIER) cc_final: 0.8272 (ttm)
REVERT: I 204 PHE cc_start: 0.8412 (m-80) cc_final: 0.8156 (m-80)
REVERT: I 267 MET cc_start: 0.6535 (tmm) cc_final: 0.5847 (mmp)
REVERT: I 351 GLN cc_start: 0.8627 (OUTLIER) cc_final: 0.8185 (pp30)
REVERT: I 494 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8803 (pp)
REVERT: I 514 MET cc_start: 0.9208 (ttm) cc_final: 0.8918 (mtp)
REVERT: D 242 LYS cc_start: 0.8043 (mmtt) cc_final: 0.7781 (mmmt)
REVERT: D 267 MET cc_start: 0.6576 (tmm) cc_final: 0.5764 (mmm)
REVERT: D 321 LYS cc_start: 0.8811 (ttpt) cc_final: 0.8462 (mmmt)
REVERT: D 367 GLU cc_start: 0.8591 (pp20) cc_final: 0.8239 (pp20)
REVERT: J 16 MET cc_start: 0.8826 (mtp) cc_final: 0.8615 (mtm)
REVERT: J 204 PHE cc_start: 0.8305 (m-80) cc_final: 0.7989 (m-80)
REVERT: J 267 MET cc_start: 0.5661 (tmm) cc_final: 0.4908 (mmm)
REVERT: J 389 MET cc_start: 0.8229 (tmm) cc_final: 0.7983 (tmm)
REVERT: E 267 MET cc_start: 0.6582 (tmm) cc_final: 0.5812 (mmp)
REVERT: E 351 GLN cc_start: 0.8345 (OUTLIER) cc_final: 0.8110 (mm110)
REVERT: E 367 GLU cc_start: 0.8537 (pp20) cc_final: 0.8266 (pp20)
REVERT: E 389 MET cc_start: 0.7907 (tmm) cc_final: 0.7704 (tmm)
REVERT: E 447 MET cc_start: 0.9204 (mtm) cc_final: 0.8936 (mtp)
REVERT: E 494 LEU cc_start: 0.9146 (OUTLIER) cc_final: 0.8851 (pp)
REVERT: E 514 MET cc_start: 0.9154 (ttm) cc_final: 0.8717 (mtp)
REVERT: K 142 LYS cc_start: 0.8621 (tppt) cc_final: 0.8356 (ttpp)
REVERT: K 267 MET cc_start: 0.6539 (tmm) cc_final: 0.5476 (mmp)
REVERT: F 102 GLU cc_start: 0.7767 (mt-10) cc_final: 0.7265 (mp0)
REVERT: F 111 MET cc_start: 0.8996 (mtp) cc_final: 0.8651 (mtt)
REVERT: F 160 LYS cc_start: 0.8667 (mtpp) cc_final: 0.8383 (ptmm)
REVERT: F 234 LEU cc_start: 0.7871 (tp) cc_final: 0.7641 (tp)
REVERT: F 321 LYS cc_start: 0.8795 (mmtt) cc_final: 0.8390 (mmtp)
REVERT: F 367 GLU cc_start: 0.8362 (pp20) cc_final: 0.8057 (pp20)
REVERT: L 61 GLU cc_start: 0.8685 (tm-30) cc_final: 0.8376 (tm-30)
REVERT: L 69 MET cc_start: 0.8511 (mtm) cc_final: 0.8068 (mtp)
REVERT: L 267 MET cc_start: 0.6114 (tmm) cc_final: 0.5370 (mmm)
REVERT: L 288 MET cc_start: 0.7693 (OUTLIER) cc_final: 0.6654 (mpp)
REVERT: L 351 GLN cc_start: 0.8222 (tp40) cc_final: 0.7974 (tp40)
REVERT: G 61 GLU cc_start: 0.8698 (OUTLIER) cc_final: 0.8085 (pt0)
REVERT: G 166 MET cc_start: 0.8730 (OUTLIER) cc_final: 0.7900 (mtt)
REVERT: G 204 PHE cc_start: 0.8500 (m-80) cc_final: 0.8172 (m-80)
REVERT: G 267 MET cc_start: 0.6346 (tmm) cc_final: 0.5823 (mmp)
REVERT: G 367 GLU cc_start: 0.8486 (pp20) cc_final: 0.8113 (pp20)
REVERT: G 494 LEU cc_start: 0.9101 (OUTLIER) cc_final: 0.8861 (pp)
REVERT: M 13 ARG cc_start: 0.8258 (OUTLIER) cc_final: 0.7858 (mpt-90)
REVERT: M 267 MET cc_start: 0.6355 (tmm) cc_final: 0.5714 (mmm)
outliers start: 164
outliers final: 136
residues processed: 620
average time/residue: 0.4745
time to fit residues: 521.3993
Evaluate side-chains
620 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 151
poor density : 469
time to evaluate : 5.617
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 48 THR
Chi-restraints excluded: chain A residue 61 GLU
Chi-restraints excluded: chain A residue 169 VAL
Chi-restraints excluded: chain A residue 205 ILE
Chi-restraints excluded: chain A residue 213 VAL
Chi-restraints excluded: chain A residue 240 VAL
Chi-restraints excluded: chain A residue 300 VAL
Chi-restraints excluded: chain A residue 331 THR
Chi-restraints excluded: chain A residue 463 SER
Chi-restraints excluded: chain A residue 517 THR
Chi-restraints excluded: chain N residue 11 ASP
Chi-restraints excluded: chain N residue 50 THR
Chi-restraints excluded: chain N residue 111 MET
Chi-restraints excluded: chain N residue 213 VAL
Chi-restraints excluded: chain N residue 230 ILE
Chi-restraints excluded: chain N residue 234 LEU
Chi-restraints excluded: chain N residue 240 VAL
Chi-restraints excluded: chain N residue 442 VAL
Chi-restraints excluded: chain N residue 494 LEU
Chi-restraints excluded: chain N residue 499 VAL
Chi-restraints excluded: chain N residue 517 THR
Chi-restraints excluded: chain B residue 48 THR
Chi-restraints excluded: chain B residue 50 THR
Chi-restraints excluded: chain B residue 124 VAL
Chi-restraints excluded: chain B residue 213 VAL
Chi-restraints excluded: chain B residue 237 LEU
Chi-restraints excluded: chain B residue 261 THR
Chi-restraints excluded: chain B residue 300 VAL
Chi-restraints excluded: chain B residue 307 MET
Chi-restraints excluded: chain B residue 331 THR
Chi-restraints excluded: chain B residue 494 LEU
Chi-restraints excluded: chain B residue 517 THR
Chi-restraints excluded: chain H residue 61 GLU
Chi-restraints excluded: chain H residue 146 GLN
Chi-restraints excluded: chain H residue 213 VAL
Chi-restraints excluded: chain H residue 240 VAL
Chi-restraints excluded: chain H residue 300 VAL
Chi-restraints excluded: chain H residue 442 VAL
Chi-restraints excluded: chain H residue 517 THR
Chi-restraints excluded: chain C residue 61 GLU
Chi-restraints excluded: chain C residue 169 VAL
Chi-restraints excluded: chain C residue 174 VAL
Chi-restraints excluded: chain C residue 205 ILE
Chi-restraints excluded: chain C residue 213 VAL
Chi-restraints excluded: chain C residue 228 SER
Chi-restraints excluded: chain C residue 234 LEU
Chi-restraints excluded: chain C residue 261 THR
Chi-restraints excluded: chain C residue 271 VAL
Chi-restraints excluded: chain C residue 300 VAL
Chi-restraints excluded: chain C residue 314 LEU
Chi-restraints excluded: chain C residue 331 THR
Chi-restraints excluded: chain C residue 517 THR
Chi-restraints excluded: chain I residue 61 GLU
Chi-restraints excluded: chain I residue 124 VAL
Chi-restraints excluded: chain I residue 146 GLN
Chi-restraints excluded: chain I residue 193 MET
Chi-restraints excluded: chain I residue 213 VAL
Chi-restraints excluded: chain I residue 234 LEU
Chi-restraints excluded: chain I residue 240 VAL
Chi-restraints excluded: chain I residue 351 GLN
Chi-restraints excluded: chain I residue 442 VAL
Chi-restraints excluded: chain I residue 494 LEU
Chi-restraints excluded: chain I residue 499 VAL
Chi-restraints excluded: chain D residue 43 SER
Chi-restraints excluded: chain D residue 48 THR
Chi-restraints excluded: chain D residue 61 GLU
Chi-restraints excluded: chain D residue 124 VAL
Chi-restraints excluded: chain D residue 169 VAL
Chi-restraints excluded: chain D residue 213 VAL
Chi-restraints excluded: chain D residue 240 VAL
Chi-restraints excluded: chain D residue 259 LEU
Chi-restraints excluded: chain D residue 331 THR
Chi-restraints excluded: chain D residue 351 GLN
Chi-restraints excluded: chain D residue 447 MET
Chi-restraints excluded: chain D residue 517 THR
Chi-restraints excluded: chain J residue 11 ASP
Chi-restraints excluded: chain J residue 146 GLN
Chi-restraints excluded: chain J residue 213 VAL
Chi-restraints excluded: chain J residue 273 VAL
Chi-restraints excluded: chain J residue 388 GLU
Chi-restraints excluded: chain J residue 433 ASN
Chi-restraints excluded: chain J residue 517 THR
Chi-restraints excluded: chain E residue 48 THR
Chi-restraints excluded: chain E residue 50 THR
Chi-restraints excluded: chain E residue 177 VAL
Chi-restraints excluded: chain E residue 205 ILE
Chi-restraints excluded: chain E residue 213 VAL
Chi-restraints excluded: chain E residue 240 VAL
Chi-restraints excluded: chain E residue 271 VAL
Chi-restraints excluded: chain E residue 288 MET
Chi-restraints excluded: chain E residue 300 VAL
Chi-restraints excluded: chain E residue 331 THR
Chi-restraints excluded: chain E residue 351 GLN
Chi-restraints excluded: chain E residue 494 LEU
Chi-restraints excluded: chain E residue 517 THR
Chi-restraints excluded: chain K residue 43 SER
Chi-restraints excluded: chain K residue 62 LEU
Chi-restraints excluded: chain K residue 146 GLN
Chi-restraints excluded: chain K residue 213 VAL
Chi-restraints excluded: chain K residue 240 VAL
Chi-restraints excluded: chain K residue 273 VAL
Chi-restraints excluded: chain K residue 288 MET
Chi-restraints excluded: chain K residue 307 MET
Chi-restraints excluded: chain K residue 463 SER
Chi-restraints excluded: chain F residue 11 ASP
Chi-restraints excluded: chain F residue 48 THR
Chi-restraints excluded: chain F residue 124 VAL
Chi-restraints excluded: chain F residue 169 VAL
Chi-restraints excluded: chain F residue 193 MET
Chi-restraints excluded: chain F residue 205 ILE
Chi-restraints excluded: chain F residue 213 VAL
Chi-restraints excluded: chain F residue 255 GLU
Chi-restraints excluded: chain F residue 270 ILE
Chi-restraints excluded: chain F residue 300 VAL
Chi-restraints excluded: chain F residue 331 THR
Chi-restraints excluded: chain F residue 351 GLN
Chi-restraints excluded: chain F residue 369 VAL
Chi-restraints excluded: chain F residue 463 SER
Chi-restraints excluded: chain F residue 491 MET
Chi-restraints excluded: chain F residue 494 LEU
Chi-restraints excluded: chain F residue 517 THR
Chi-restraints excluded: chain F residue 524 LEU
Chi-restraints excluded: chain L residue 50 THR
Chi-restraints excluded: chain L residue 124 VAL
Chi-restraints excluded: chain L residue 146 GLN
Chi-restraints excluded: chain L residue 213 VAL
Chi-restraints excluded: chain L residue 288 MET
Chi-restraints excluded: chain L residue 494 LEU
Chi-restraints excluded: chain L residue 517 THR
Chi-restraints excluded: chain G residue 11 ASP
Chi-restraints excluded: chain G residue 48 THR
Chi-restraints excluded: chain G residue 50 THR
Chi-restraints excluded: chain G residue 61 GLU
Chi-restraints excluded: chain G residue 160 LYS
Chi-restraints excluded: chain G residue 166 MET
Chi-restraints excluded: chain G residue 169 VAL
Chi-restraints excluded: chain G residue 300 VAL
Chi-restraints excluded: chain G residue 307 MET
Chi-restraints excluded: chain G residue 331 THR
Chi-restraints excluded: chain G residue 494 LEU
Chi-restraints excluded: chain M residue 11 ASP
Chi-restraints excluded: chain M residue 13 ARG
Chi-restraints excluded: chain M residue 61 GLU
Chi-restraints excluded: chain M residue 124 VAL
Chi-restraints excluded: chain M residue 146 GLN
Chi-restraints excluded: chain M residue 205 ILE
Chi-restraints excluded: chain M residue 259 LEU
Chi-restraints excluded: chain M residue 262 LEU
Chi-restraints excluded: chain M residue 442 VAL
Chi-restraints excluded: chain M residue 463 SER
Chi-restraints excluded: chain M residue 517 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 728
random chunks:
chunk 581 optimal weight: 1.9990
chunk 646 optimal weight: 6.9990
chunk 253 optimal weight: 0.9980
chunk 543 optimal weight: 0.0970
chunk 334 optimal weight: 20.0000
chunk 255 optimal weight: 4.9990
chunk 600 optimal weight: 1.9990
chunk 371 optimal weight: 0.8980
chunk 381 optimal weight: 6.9990
chunk 92 optimal weight: 2.9990
chunk 27 optimal weight: 10.0000
overall best weight: 1.1982
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
E 467 ASN
Total number of N/Q/H flips: 1
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.151666 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.109829 restraints weight = 68309.399|
|-----------------------------------------------------------------------------|
r_work (start): 0.3296 rms_B_bonded: 1.74
r_work: 0.3161 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.3009 rms_B_bonded: 3.93 restraints_weight: 0.2500
r_work (final): 0.3009
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8400
moved from start: 0.2323
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.002 0.048 54362 Z= 0.161
Angle : 0.488 13.079 73402 Z= 0.255
Chirality : 0.040 0.170 8932
Planarity : 0.003 0.037 9618
Dihedral : 3.771 18.721 7729
Min Nonbonded Distance : 2.499
Molprobity Statistics.
All-atom Clashscore : 6.60
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 1.42 %
Favored : 98.58 %
Rotamer:
Outliers : 2.63 %
Allowed : 15.51 %
Favored : 81.86 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 1.91 (0.10), residues: 7308
helix: 2.31 (0.08), residues: 4088
sheet: 0.65 (0.17), residues: 938
loop : -0.41 (0.12), residues: 2282
Max deviation from planes:
Type MaxDev MeanDev LineInFile
HIS 0.000 0.000 HIS N 401
PHE 0.007 0.001 PHE N 195
TYR 0.010 0.001 TYR J 476
ARG 0.004 0.000 ARG I 345
*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
14616 Ramachandran restraints generated.
7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
14616 Ramachandran restraints generated.
7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
650 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 149
poor density : 501
time to evaluate : 4.852
Fit side-chains
REVERT: A 238 GLU cc_start: 0.7071 (mm-30) cc_final: 0.6870 (mm-30)
REVERT: A 267 MET cc_start: 0.6010 (mmm) cc_final: 0.5058 (mmm)
REVERT: A 367 GLU cc_start: 0.8366 (pp20) cc_final: 0.8056 (pp20)
REVERT: N 69 MET cc_start: 0.7900 (mtm) cc_final: 0.7472 (mtp)
REVERT: N 111 MET cc_start: 0.8930 (OUTLIER) cc_final: 0.8372 (mtt)
REVERT: N 201 SER cc_start: 0.8109 (t) cc_final: 0.7807 (m)
REVERT: N 267 MET cc_start: 0.6702 (tmm) cc_final: 0.5921 (mmp)
REVERT: N 494 LEU cc_start: 0.9170 (OUTLIER) cc_final: 0.8878 (pp)
REVERT: N 514 MET cc_start: 0.9126 (ttm) cc_final: 0.8742 (mtp)
REVERT: N 520 MET cc_start: 0.8805 (mmm) cc_final: 0.8429 (mtt)
REVERT: B 160 LYS cc_start: 0.8614 (mtpp) cc_final: 0.8269 (ptmm)
REVERT: B 204 PHE cc_start: 0.8461 (m-80) cc_final: 0.8080 (m-80)
REVERT: B 267 MET cc_start: 0.6479 (tmm) cc_final: 0.5467 (mmp)
REVERT: B 367 GLU cc_start: 0.8429 (pp20) cc_final: 0.8196 (pp20)
REVERT: B 494 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8629 (pp)
REVERT: H 238 GLU cc_start: 0.6978 (mm-30) cc_final: 0.6736 (mm-30)
REVERT: H 267 MET cc_start: 0.6264 (tmm) cc_final: 0.5335 (mmp)
REVERT: H 514 MET cc_start: 0.9052 (mtp) cc_final: 0.8803 (mtm)
REVERT: C 61 GLU cc_start: 0.8595 (OUTLIER) cc_final: 0.8120 (pt0)
REVERT: C 69 MET cc_start: 0.8271 (mtp) cc_final: 0.7987 (ttm)
REVERT: C 267 MET cc_start: 0.6577 (tmm) cc_final: 0.5931 (mmp)
REVERT: C 322 ARG cc_start: 0.8957 (mtp-110) cc_final: 0.8701 (ttm110)
REVERT: C 367 GLU cc_start: 0.8435 (pp20) cc_final: 0.8024 (pp20)
REVERT: I 193 MET cc_start: 0.8469 (OUTLIER) cc_final: 0.8246 (ttm)
REVERT: I 204 PHE cc_start: 0.8412 (m-80) cc_final: 0.8133 (m-80)
REVERT: I 267 MET cc_start: 0.6457 (tmm) cc_final: 0.5900 (mmp)
REVERT: I 288 MET cc_start: 0.7784 (mmp) cc_final: 0.7581 (mmp)
REVERT: I 351 GLN cc_start: 0.8539 (OUTLIER) cc_final: 0.8108 (pp30)
REVERT: I 494 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8771 (pp)
REVERT: I 514 MET cc_start: 0.9172 (ttm) cc_final: 0.8904 (mtp)
REVERT: D 267 MET cc_start: 0.6526 (tmm) cc_final: 0.5726 (mmm)
REVERT: D 321 LYS cc_start: 0.8799 (ttpt) cc_final: 0.8495 (mmmt)
REVERT: D 367 GLU cc_start: 0.8600 (pp20) cc_final: 0.8251 (pp20)
REVERT: J 204 PHE cc_start: 0.8296 (m-80) cc_final: 0.7971 (m-80)
REVERT: J 267 MET cc_start: 0.5577 (tmm) cc_final: 0.4896 (mmm)
REVERT: J 389 MET cc_start: 0.8179 (tmm) cc_final: 0.7928 (tmm)
REVERT: E 267 MET cc_start: 0.6471 (tmm) cc_final: 0.5853 (mmp)
REVERT: E 367 GLU cc_start: 0.8487 (pp20) cc_final: 0.8194 (pp20)
REVERT: E 389 MET cc_start: 0.7886 (tmm) cc_final: 0.7671 (tmm)
REVERT: E 447 MET cc_start: 0.9163 (OUTLIER) cc_final: 0.8894 (mtp)
REVERT: E 494 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8839 (pp)
REVERT: E 514 MET cc_start: 0.9086 (ttm) cc_final: 0.8719 (mtp)
REVERT: K 204 PHE cc_start: 0.8283 (m-80) cc_final: 0.7892 (m-80)
REVERT: K 267 MET cc_start: 0.6451 (tmm) cc_final: 0.5518 (mmp)
REVERT: F 102 GLU cc_start: 0.7680 (mt-10) cc_final: 0.7174 (mp0)
REVERT: F 111 MET cc_start: 0.8945 (mtp) cc_final: 0.8640 (mtt)
REVERT: F 160 LYS cc_start: 0.8645 (mtpp) cc_final: 0.8372 (ptmm)
REVERT: F 234 LEU cc_start: 0.7904 (tp) cc_final: 0.7671 (tp)
REVERT: F 321 LYS cc_start: 0.8779 (mmtt) cc_final: 0.8425 (mmtp)
REVERT: F 367 GLU cc_start: 0.8359 (pp20) cc_final: 0.8157 (pp20)
REVERT: L 61 GLU cc_start: 0.8697 (tm-30) cc_final: 0.8436 (tm-30)
REVERT: L 69 MET cc_start: 0.8379 (mtm) cc_final: 0.7940 (mtp)
REVERT: L 76 GLU cc_start: 0.8809 (tm-30) cc_final: 0.8558 (tm-30)
REVERT: L 267 MET cc_start: 0.6067 (tmm) cc_final: 0.5379 (mmm)
REVERT: L 288 MET cc_start: 0.7694 (OUTLIER) cc_final: 0.6650 (mpp)
REVERT: L 351 GLN cc_start: 0.8188 (tp40) cc_final: 0.7951 (tp40)
REVERT: G 61 GLU cc_start: 0.8664 (OUTLIER) cc_final: 0.8062 (pt0)
REVERT: G 166 MET cc_start: 0.8725 (OUTLIER) cc_final: 0.7910 (mtt)
REVERT: G 204 PHE cc_start: 0.8488 (m-80) cc_final: 0.8213 (m-80)
REVERT: G 267 MET cc_start: 0.6191 (tmm) cc_final: 0.5856 (mmp)
REVERT: G 367 GLU cc_start: 0.8487 (pp20) cc_final: 0.8194 (pp20)
REVERT: G 494 LEU cc_start: 0.9081 (OUTLIER) cc_final: 0.8861 (pp)
REVERT: M 267 MET cc_start: 0.6288 (tmm) cc_final: 0.5727 (mmm)
outliers start: 149
outliers final: 121
residues processed: 624
average time/residue: 0.4669
time to fit residues: 516.4114
Evaluate side-chains
606 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 134
poor density : 472
time to evaluate : 5.226
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 48 THR
Chi-restraints excluded: chain A residue 61 GLU
Chi-restraints excluded: chain A residue 169 VAL
Chi-restraints excluded: chain A residue 205 ILE
Chi-restraints excluded: chain A residue 213 VAL
Chi-restraints excluded: chain A residue 240 VAL
Chi-restraints excluded: chain A residue 300 VAL
Chi-restraints excluded: chain A residue 331 THR
Chi-restraints excluded: chain A residue 517 THR
Chi-restraints excluded: chain N residue 11 ASP
Chi-restraints excluded: chain N residue 50 THR
Chi-restraints excluded: chain N residue 111 MET
Chi-restraints excluded: chain N residue 213 VAL
Chi-restraints excluded: chain N residue 230 ILE
Chi-restraints excluded: chain N residue 234 LEU
Chi-restraints excluded: chain N residue 240 VAL
Chi-restraints excluded: chain N residue 494 LEU
Chi-restraints excluded: chain N residue 499 VAL
Chi-restraints excluded: chain N residue 517 THR
Chi-restraints excluded: chain B residue 48 THR
Chi-restraints excluded: chain B residue 213 VAL
Chi-restraints excluded: chain B residue 237 LEU
Chi-restraints excluded: chain B residue 261 THR
Chi-restraints excluded: chain B residue 300 VAL
Chi-restraints excluded: chain B residue 307 MET
Chi-restraints excluded: chain B residue 331 THR
Chi-restraints excluded: chain B residue 494 LEU
Chi-restraints excluded: chain B residue 517 THR
Chi-restraints excluded: chain H residue 61 GLU
Chi-restraints excluded: chain H residue 213 VAL
Chi-restraints excluded: chain H residue 240 VAL
Chi-restraints excluded: chain H residue 300 VAL
Chi-restraints excluded: chain H residue 442 VAL
Chi-restraints excluded: chain H residue 517 THR
Chi-restraints excluded: chain C residue 61 GLU
Chi-restraints excluded: chain C residue 169 VAL
Chi-restraints excluded: chain C residue 174 VAL
Chi-restraints excluded: chain C residue 205 ILE
Chi-restraints excluded: chain C residue 213 VAL
Chi-restraints excluded: chain C residue 228 SER
Chi-restraints excluded: chain C residue 271 VAL
Chi-restraints excluded: chain C residue 300 VAL
Chi-restraints excluded: chain C residue 314 LEU
Chi-restraints excluded: chain C residue 331 THR
Chi-restraints excluded: chain C residue 517 THR
Chi-restraints excluded: chain I residue 61 GLU
Chi-restraints excluded: chain I residue 124 VAL
Chi-restraints excluded: chain I residue 146 GLN
Chi-restraints excluded: chain I residue 193 MET
Chi-restraints excluded: chain I residue 213 VAL
Chi-restraints excluded: chain I residue 240 VAL
Chi-restraints excluded: chain I residue 351 GLN
Chi-restraints excluded: chain I residue 442 VAL
Chi-restraints excluded: chain I residue 494 LEU
Chi-restraints excluded: chain I residue 499 VAL
Chi-restraints excluded: chain D residue 43 SER
Chi-restraints excluded: chain D residue 48 THR
Chi-restraints excluded: chain D residue 61 GLU
Chi-restraints excluded: chain D residue 124 VAL
Chi-restraints excluded: chain D residue 169 VAL
Chi-restraints excluded: chain D residue 205 ILE
Chi-restraints excluded: chain D residue 213 VAL
Chi-restraints excluded: chain D residue 240 VAL
Chi-restraints excluded: chain D residue 259 LEU
Chi-restraints excluded: chain D residue 331 THR
Chi-restraints excluded: chain D residue 351 GLN
Chi-restraints excluded: chain D residue 447 MET
Chi-restraints excluded: chain D residue 517 THR
Chi-restraints excluded: chain J residue 11 ASP
Chi-restraints excluded: chain J residue 146 GLN
Chi-restraints excluded: chain J residue 213 VAL
Chi-restraints excluded: chain J residue 273 VAL
Chi-restraints excluded: chain J residue 388 GLU
Chi-restraints excluded: chain J residue 433 ASN
Chi-restraints excluded: chain J residue 517 THR
Chi-restraints excluded: chain E residue 48 THR
Chi-restraints excluded: chain E residue 50 THR
Chi-restraints excluded: chain E residue 205 ILE
Chi-restraints excluded: chain E residue 213 VAL
Chi-restraints excluded: chain E residue 240 VAL
Chi-restraints excluded: chain E residue 288 MET
Chi-restraints excluded: chain E residue 300 VAL
Chi-restraints excluded: chain E residue 331 THR
Chi-restraints excluded: chain E residue 447 MET
Chi-restraints excluded: chain E residue 491 MET
Chi-restraints excluded: chain E residue 494 LEU
Chi-restraints excluded: chain E residue 517 THR
Chi-restraints excluded: chain K residue 43 SER
Chi-restraints excluded: chain K residue 62 LEU
Chi-restraints excluded: chain K residue 213 VAL
Chi-restraints excluded: chain K residue 240 VAL
Chi-restraints excluded: chain K residue 273 VAL
Chi-restraints excluded: chain K residue 288 MET
Chi-restraints excluded: chain K residue 307 MET
Chi-restraints excluded: chain K residue 463 SER
Chi-restraints excluded: chain K residue 517 THR
Chi-restraints excluded: chain F residue 48 THR
Chi-restraints excluded: chain F residue 50 THR
Chi-restraints excluded: chain F residue 169 VAL
Chi-restraints excluded: chain F residue 193 MET
Chi-restraints excluded: chain F residue 213 VAL
Chi-restraints excluded: chain F residue 255 GLU
Chi-restraints excluded: chain F residue 270 ILE
Chi-restraints excluded: chain F residue 300 VAL
Chi-restraints excluded: chain F residue 331 THR
Chi-restraints excluded: chain F residue 351 GLN
Chi-restraints excluded: chain F residue 369 VAL
Chi-restraints excluded: chain F residue 463 SER
Chi-restraints excluded: chain F residue 494 LEU
Chi-restraints excluded: chain F residue 517 THR
Chi-restraints excluded: chain F residue 524 LEU
Chi-restraints excluded: chain L residue 50 THR
Chi-restraints excluded: chain L residue 124 VAL
Chi-restraints excluded: chain L residue 146 GLN
Chi-restraints excluded: chain L residue 213 VAL
Chi-restraints excluded: chain L residue 288 MET
Chi-restraints excluded: chain L residue 494 LEU
Chi-restraints excluded: chain G residue 11 ASP
Chi-restraints excluded: chain G residue 48 THR
Chi-restraints excluded: chain G residue 61 GLU
Chi-restraints excluded: chain G residue 160 LYS
Chi-restraints excluded: chain G residue 166 MET
Chi-restraints excluded: chain G residue 169 VAL
Chi-restraints excluded: chain G residue 300 VAL
Chi-restraints excluded: chain G residue 307 MET
Chi-restraints excluded: chain G residue 331 THR
Chi-restraints excluded: chain G residue 494 LEU
Chi-restraints excluded: chain M residue 61 GLU
Chi-restraints excluded: chain M residue 124 VAL
Chi-restraints excluded: chain M residue 146 GLN
Chi-restraints excluded: chain M residue 205 ILE
Chi-restraints excluded: chain M residue 442 VAL
Chi-restraints excluded: chain M residue 463 SER
Chi-restraints excluded: chain M residue 517 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 728
random chunks:
chunk 50 optimal weight: 5.9990
chunk 387 optimal weight: 0.9980
chunk 478 optimal weight: 5.9990
chunk 119 optimal weight: 7.9990
chunk 583 optimal weight: 1.9990
chunk 147 optimal weight: 3.9990
chunk 317 optimal weight: 3.9990
chunk 543 optimal weight: 4.9990
chunk 157 optimal weight: 1.9990
chunk 327 optimal weight: 10.0000
chunk 29 optimal weight: 8.9990
overall best weight: 2.5988
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
B 351 GLN
J 351 GLN
E 351 GLN
G 351 GLN
Total number of N/Q/H flips: 4
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.149426 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.107173 restraints weight = 68619.065|
|-----------------------------------------------------------------------------|
r_work (start): 0.3262 rms_B_bonded: 1.74
r_work: 0.3122 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.2969 rms_B_bonded: 3.94 restraints_weight: 0.2500
r_work (final): 0.2969
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8444
moved from start: 0.2408
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.004 0.065 54362 Z= 0.254
Angle : 0.524 11.678 73402 Z= 0.273
Chirality : 0.042 0.155 8932
Planarity : 0.003 0.041 9618
Dihedral : 3.847 19.209 7729
Min Nonbonded Distance : 2.403
Molprobity Statistics.
All-atom Clashscore : 6.85
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 1.92 %
Favored : 98.08 %
Rotamer:
Outliers : 2.62 %
Allowed : 15.61 %
Favored : 81.77 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 1.83 (0.10), residues: 7308
helix: 2.27 (0.08), residues: 4060
sheet: 0.62 (0.17), residues: 938
loop : -0.44 (0.12), residues: 2310
Max deviation from planes:
Type MaxDev MeanDev LineInFile
HIS 0.001 0.000 HIS C 401
PHE 0.009 0.001 PHE H 8
TYR 0.010 0.001 TYR J 476
ARG 0.004 0.000 ARG I 345
********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
14616 Ramachandran restraints generated.
7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
14616 Ramachandran restraints generated.
7308 Oldfield, 0 Emsley, 7308 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
626 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 148
poor density : 478
time to evaluate : 4.848
Fit side-chains
REVERT: A 267 MET cc_start: 0.5966 (mmm) cc_final: 0.5054 (mmm)
REVERT: A 367 GLU cc_start: 0.8398 (pp20) cc_final: 0.8088 (pp20)
REVERT: N 111 MET cc_start: 0.8989 (OUTLIER) cc_final: 0.8443 (mtt)
REVERT: N 201 SER cc_start: 0.8213 (t) cc_final: 0.7899 (m)
REVERT: N 267 MET cc_start: 0.6759 (tmm) cc_final: 0.5953 (mmp)
REVERT: N 494 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8881 (pp)
REVERT: B 160 LYS cc_start: 0.8629 (mtpp) cc_final: 0.8276 (ptmm)
REVERT: B 204 PHE cc_start: 0.8456 (m-80) cc_final: 0.8083 (m-80)
REVERT: B 267 MET cc_start: 0.6605 (tmm) cc_final: 0.5588 (mmp)
REVERT: B 367 GLU cc_start: 0.8449 (pp20) cc_final: 0.8177 (pp20)
REVERT: B 494 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8679 (pp)
REVERT: H 69 MET cc_start: 0.8611 (mtp) cc_final: 0.8373 (mtt)
REVERT: H 267 MET cc_start: 0.6315 (tmm) cc_final: 0.5342 (mmp)
REVERT: H 514 MET cc_start: 0.9160 (mtp) cc_final: 0.8884 (mtm)
REVERT: C 61 GLU cc_start: 0.8605 (OUTLIER) cc_final: 0.8054 (pt0)
REVERT: C 69 MET cc_start: 0.8401 (mtp) cc_final: 0.8009 (ttm)
REVERT: C 267 MET cc_start: 0.6650 (tmm) cc_final: 0.6007 (mmp)
REVERT: C 322 ARG cc_start: 0.8918 (mtp-110) cc_final: 0.8708 (ttm110)
REVERT: C 367 GLU cc_start: 0.8416 (pp20) cc_final: 0.7997 (pp20)
REVERT: I 193 MET cc_start: 0.8501 (OUTLIER) cc_final: 0.8268 (ttm)
REVERT: I 204 PHE cc_start: 0.8439 (m-80) cc_final: 0.8233 (m-80)
REVERT: I 267 MET cc_start: 0.6433 (tmm) cc_final: 0.5882 (mmp)
REVERT: I 288 MET cc_start: 0.7822 (mmp) cc_final: 0.7605 (mmp)
REVERT: I 351 GLN cc_start: 0.8624 (OUTLIER) cc_final: 0.8118 (pp30)
REVERT: I 494 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8816 (pp)
REVERT: I 514 MET cc_start: 0.9157 (ttm) cc_final: 0.8894 (mtp)
REVERT: D 267 MET cc_start: 0.6564 (tmm) cc_final: 0.5769 (mmp)
REVERT: D 321 LYS cc_start: 0.8778 (ttpt) cc_final: 0.8503 (mmmt)
REVERT: D 367 GLU cc_start: 0.8589 (pp20) cc_final: 0.8235 (pp20)
REVERT: J 204 PHE cc_start: 0.8326 (m-80) cc_final: 0.8015 (m-80)
REVERT: J 267 MET cc_start: 0.5615 (tmm) cc_final: 0.4921 (mmm)
REVERT: J 389 MET cc_start: 0.8303 (tmm) cc_final: 0.8072 (tmm)
REVERT: E 267 MET cc_start: 0.6439 (tmm) cc_final: 0.5840 (mmp)
REVERT: E 367 GLU cc_start: 0.8482 (pp20) cc_final: 0.8193 (pp20)
REVERT: E 389 MET cc_start: 0.7918 (tmm) cc_final: 0.7688 (tmm)
REVERT: E 447 MET cc_start: 0.9186 (OUTLIER) cc_final: 0.8918 (mtp)
REVERT: E 514 MET cc_start: 0.9108 (ttm) cc_final: 0.8741 (mtp)
REVERT: K 142 LYS cc_start: 0.8632 (tppt) cc_final: 0.8377 (ttpp)
REVERT: K 204 PHE cc_start: 0.8320 (m-80) cc_final: 0.7921 (m-80)
REVERT: K 267 MET cc_start: 0.6462 (tmm) cc_final: 0.5487 (mmp)
REVERT: F 102 GLU cc_start: 0.7729 (mt-10) cc_final: 0.7241 (mp0)
REVERT: F 111 MET cc_start: 0.8974 (mtp) cc_final: 0.8656 (mtt)
REVERT: F 160 LYS cc_start: 0.8705 (mtpp) cc_final: 0.8394 (ptmm)
REVERT: F 234 LEU cc_start: 0.7909 (tp) cc_final: 0.7681 (tp)
REVERT: F 321 LYS cc_start: 0.8786 (mmtt) cc_final: 0.8381 (mmtp)
REVERT: F 367 GLU cc_start: 0.8366 (pp20) cc_final: 0.8160 (pp20)
REVERT: L 61 GLU cc_start: 0.8702 (tm-30) cc_final: 0.8377 (tm-30)
REVERT: L 69 MET cc_start: 0.8547 (OUTLIER) cc_final: 0.8095 (mtp)
REVERT: L 76 GLU cc_start: 0.8850 (tm-30) cc_final: 0.8599 (tm-30)
REVERT: L 267 MET cc_start: 0.6114 (tmm) cc_final: 0.5393 (mmm)
REVERT: L 288 MET cc_start: 0.7639 (OUTLIER) cc_final: 0.6640 (mpp)
REVERT: L 351 GLN cc_start: 0.8215 (tp40) cc_final: 0.7966 (tp40)
REVERT: G 61 GLU cc_start: 0.8674 (OUTLIER) cc_final: 0.7905 (pt0)
REVERT: G 166 MET cc_start: 0.8737 (OUTLIER) cc_final: 0.7968 (mtt)
REVERT: G 204 PHE cc_start: 0.8506 (m-80) cc_final: 0.8199 (m-80)
REVERT: G 267 MET cc_start: 0.6180 (tmm) cc_final: 0.5813 (mmp)
REVERT: G 367 GLU cc_start: 0.8477 (pp20) cc_final: 0.8178 (pp20)
REVERT: G 494 LEU cc_start: 0.9110 (OUTLIER) cc_final: 0.8873 (pp)
REVERT: M 13 ARG cc_start: 0.8289 (OUTLIER) cc_final: 0.7889 (mpt-90)
REVERT: M 76 GLU cc_start: 0.8928 (tm-30) cc_final: 0.8727 (tm-30)
REVERT: M 267 MET cc_start: 0.6369 (tmm) cc_final: 0.5863 (mmm)
outliers start: 148
outliers final: 124
residues processed: 603
average time/residue: 0.5119
time to fit residues: 548.2854
Evaluate side-chains
601 residues out of total 5656 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 138
poor density : 463
time to evaluate : 4.771
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 48 THR
Chi-restraints excluded: chain A residue 61 GLU
Chi-restraints excluded: chain A residue 169 VAL
Chi-restraints excluded: chain A residue 205 ILE
Chi-restraints excluded: chain A residue 240 VAL
Chi-restraints excluded: chain A residue 300 VAL
Chi-restraints excluded: chain A residue 331 THR
Chi-restraints excluded: chain A residue 517 THR
Chi-restraints excluded: chain N residue 11 ASP
Chi-restraints excluded: chain N residue 50 THR
Chi-restraints excluded: chain N residue 111 MET
Chi-restraints excluded: chain N residue 213 VAL
Chi-restraints excluded: chain N residue 234 LEU
Chi-restraints excluded: chain N residue 240 VAL
Chi-restraints excluded: chain N residue 494 LEU
Chi-restraints excluded: chain N residue 499 VAL
Chi-restraints excluded: chain N residue 517 THR
Chi-restraints excluded: chain B residue 48 THR
Chi-restraints excluded: chain B residue 61 GLU
Chi-restraints excluded: chain B residue 124 VAL
Chi-restraints excluded: chain B residue 213 VAL
Chi-restraints excluded: chain B residue 237 LEU
Chi-restraints excluded: chain B residue 261 THR
Chi-restraints excluded: chain B residue 271 VAL
Chi-restraints excluded: chain B residue 300 VAL
Chi-restraints excluded: chain B residue 307 MET
Chi-restraints excluded: chain B residue 331 THR
Chi-restraints excluded: chain B residue 494 LEU
Chi-restraints excluded: chain B residue 517 THR
Chi-restraints excluded: chain H residue 61 GLU
Chi-restraints excluded: chain H residue 213 VAL
Chi-restraints excluded: chain H residue 240 VAL
Chi-restraints excluded: chain H residue 300 VAL
Chi-restraints excluded: chain H residue 517 THR
Chi-restraints excluded: chain C residue 61 GLU
Chi-restraints excluded: chain C residue 169 VAL
Chi-restraints excluded: chain C residue 174 VAL
Chi-restraints excluded: chain C residue 205 ILE
Chi-restraints excluded: chain C residue 213 VAL
Chi-restraints excluded: chain C residue 228 SER
Chi-restraints excluded: chain C residue 271 VAL
Chi-restraints excluded: chain C residue 300 VAL
Chi-restraints excluded: chain C residue 314 LEU
Chi-restraints excluded: chain C residue 331 THR
Chi-restraints excluded: chain C residue 517 THR
Chi-restraints excluded: chain I residue 61 GLU
Chi-restraints excluded: chain I residue 124 VAL
Chi-restraints excluded: chain I residue 146 GLN
Chi-restraints excluded: chain I residue 193 MET
Chi-restraints excluded: chain I residue 213 VAL
Chi-restraints excluded: chain I residue 240 VAL
Chi-restraints excluded: chain I residue 351 GLN
Chi-restraints excluded: chain I residue 442 VAL
Chi-restraints excluded: chain I residue 494 LEU
Chi-restraints excluded: chain I residue 499 VAL
Chi-restraints excluded: chain D residue 43 SER
Chi-restraints excluded: chain D residue 48 THR
Chi-restraints excluded: chain D residue 61 GLU
Chi-restraints excluded: chain D residue 124 VAL
Chi-restraints excluded: chain D residue 169 VAL
Chi-restraints excluded: chain D residue 205 ILE
Chi-restraints excluded: chain D residue 213 VAL
Chi-restraints excluded: chain D residue 240 VAL
Chi-restraints excluded: chain D residue 259 LEU
Chi-restraints excluded: chain D residue 331 THR
Chi-restraints excluded: chain D residue 351 GLN
Chi-restraints excluded: chain D residue 517 THR
Chi-restraints excluded: chain J residue 11 ASP
Chi-restraints excluded: chain J residue 146 GLN
Chi-restraints excluded: chain J residue 213 VAL
Chi-restraints excluded: chain J residue 273 VAL
Chi-restraints excluded: chain J residue 388 GLU
Chi-restraints excluded: chain J residue 433 ASN
Chi-restraints excluded: chain E residue 11 ASP
Chi-restraints excluded: chain E residue 48 THR
Chi-restraints excluded: chain E residue 50 THR
Chi-restraints excluded: chain E residue 177 VAL
Chi-restraints excluded: chain E residue 205 ILE
Chi-restraints excluded: chain E residue 213 VAL
Chi-restraints excluded: chain E residue 240 VAL
Chi-restraints excluded: chain E residue 288 MET
Chi-restraints excluded: chain E residue 300 VAL
Chi-restraints excluded: chain E residue 331 THR
Chi-restraints excluded: chain E residue 447 MET
Chi-restraints excluded: chain E residue 517 THR
Chi-restraints excluded: chain K residue 43 SER
Chi-restraints excluded: chain K residue 62 LEU
Chi-restraints excluded: chain K residue 146 GLN
Chi-restraints excluded: chain K residue 213 VAL
Chi-restraints excluded: chain K residue 240 VAL
Chi-restraints excluded: chain K residue 273 VAL
Chi-restraints excluded: chain K residue 288 MET
Chi-restraints excluded: chain K residue 307 MET
Chi-restraints excluded: chain K residue 463 SER
Chi-restraints excluded: chain K residue 517 THR
Chi-restraints excluded: chain F residue 11 ASP
Chi-restraints excluded: chain F residue 48 THR
Chi-restraints excluded: chain F residue 50 THR
Chi-restraints excluded: chain F residue 124 VAL
Chi-restraints excluded: chain F residue 169 VAL
Chi-restraints excluded: chain F residue 193 MET
Chi-restraints excluded: chain F residue 213 VAL
Chi-restraints excluded: chain F residue 255 GLU
Chi-restraints excluded: chain F residue 270 ILE
Chi-restraints excluded: chain F residue 300 VAL
Chi-restraints excluded: chain F residue 331 THR
Chi-restraints excluded: chain F residue 351 GLN
Chi-restraints excluded: chain F residue 369 VAL
Chi-restraints excluded: chain F residue 463 SER
Chi-restraints excluded: chain F residue 494 LEU
Chi-restraints excluded: chain F residue 517 THR
Chi-restraints excluded: chain F residue 524 LEU
Chi-restraints excluded: chain L residue 50 THR
Chi-restraints excluded: chain L residue 69 MET
Chi-restraints excluded: chain L residue 124 VAL
Chi-restraints excluded: chain L residue 146 GLN
Chi-restraints excluded: chain L residue 213 VAL
Chi-restraints excluded: chain L residue 288 MET
Chi-restraints excluded: chain L residue 494 LEU
Chi-restraints excluded: chain L residue 517 THR
Chi-restraints excluded: chain G residue 11 ASP
Chi-restraints excluded: chain G residue 48 THR
Chi-restraints excluded: chain G residue 50 THR
Chi-restraints excluded: chain G residue 61 GLU
Chi-restraints excluded: chain G residue 160 LYS
Chi-restraints excluded: chain G residue 166 MET
Chi-restraints excluded: chain G residue 169 VAL
Chi-restraints excluded: chain G residue 300 VAL
Chi-restraints excluded: chain G residue 307 MET
Chi-restraints excluded: chain G residue 494 LEU
Chi-restraints excluded: chain M residue 13 ARG
Chi-restraints excluded: chain M residue 61 GLU
Chi-restraints excluded: chain M residue 124 VAL
Chi-restraints excluded: chain M residue 146 GLN
Chi-restraints excluded: chain M residue 205 ILE
Chi-restraints excluded: chain M residue 442 VAL
Chi-restraints excluded: chain M residue 463 SER
Chi-restraints excluded: chain M residue 517 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 728
random chunks:
chunk 250 optimal weight: 1.9990
chunk 138 optimal weight: 5.9990
chunk 546 optimal weight: 30.0000
chunk 389 optimal weight: 20.0000
chunk 473 optimal weight: 0.9980
chunk 477 optimal weight: 0.7980
chunk 248 optimal weight: 5.9990
chunk 725 optimal weight: 0.0770
chunk 207 optimal weight: 7.9990
chunk 34 optimal weight: 9.9990
chunk 430 optimal weight: 0.9990
overall best weight: 0.9742
-------------------------------------------------------------------------------
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 = 0.3843 r_free = 0.3843 target = 0.151799 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.111953 restraints weight = 68658.860|
|-----------------------------------------------------------------------------|
r_work (start): 0.3325 rms_B_bonded: 1.77
r_work: 0.3187 rms_B_bonded: 2.15 restraints_weight: 0.5000
r_work: 0.3042 rms_B_bonded: 3.67 restraints_weight: 0.2500
r_work (final): 0.3042
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8387
moved from start: 0.2426
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.002 0.046 54362 Z= 0.155
Angle : 0.489 11.779 73402 Z= 0.254
Chirality : 0.040 0.182 8932
Planarity : 0.003 0.042 9618
Dihedral : 3.771 17.999 7728
Min Nonbonded Distance : 2.515
Molprobity Statistics.
All-atom Clashscore : 6.65
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 1.44 %
Favored : 98.56 %
Rotamer:
Outliers : 2.35 %
Allowed : 16.00 %
Favored : 81.65 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 1.92 (0.10), residues: 7308
helix: 2.33 (0.08), residues: 4088
sheet: 0.65 (0.17), residues: 938
loop : -0.41 (0.12), residues: 2282
Max deviation from planes:
Type MaxDev MeanDev LineInFile
HIS 0.000 0.000 HIS N 401
PHE 0.007 0.001 PHE N 195
TYR 0.010 0.001 TYR C 476
ARG 0.004 0.000 ARG I 345
Origin is already at (0, 0, 0), no shifts will be applied
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Job complete
usr+sys time: 23076.01 seconds
wall clock time: 397 minutes 40.00 seconds (23860.00 seconds total)