Starting phenix.real_space_refine
on Mon Aug 5 05:50:15 2024 by dcliebschner
===============================================================================
Processing files:
-------------------------------------------------------------------------------
Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u1l_41816/08_2024/8u1l_41816.cif
Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u1l_41816/08_2024/8u1l_41816.map
Processing PHIL parameters:
-------------------------------------------------------------------------------
Adding command-line PHIL:
-------------------------
refinement.macro_cycles=10
scattering_table=electron
resolution=3.7
write_initial_geo_file=False
Final processed PHIL parameters:
-------------------------------------------------------------------------------
data_manager {
real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u1l_41816/08_2024/8u1l_41816.map"
default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u1l_41816/08_2024/8u1l_41816.map"
model {
file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u1l_41816/08_2024/8u1l_41816.cif"
}
default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u1l_41816/08_2024/8u1l_41816.cif"
}
resolution = 3.7
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= 0.016
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: 6
Type Number sf(0) Gaussians
P 7 5.49 5
Mg 2 5.21 5
S 61 5.16 5
C 7959 2.51 5
N 2133 2.21 5
O 2433 1.98 5
sf(0) = scattering factor at diffraction angle 0.
Process input model
Symmetric amino acids flipped
Residue "A GLU 70": "OE1" <-> "OE2"
Residue "A GLU 81": "OE1" <-> "OE2"
Residue "A GLU 222": "OE1" <-> "OE2"
Residue "A GLU 298": "OE1" <-> "OE2"
Residue "A GLU 323": "OE1" <-> "OE2"
Residue "A GLU 327": "OE1" <-> "OE2"
Residue "A PHE 328": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "A PHE 333": "CD1" <-> "CD2" "CE1" <-> "CE2"
Residue "A GLU 416": "OE1" <-> "OE2"
Residue "A GLU 423": "OE1" <-> "OE2"
Residue "A GLU 526": "OE1" <-> "OE2"
Residue "A GLU 547": "OE1" <-> "OE2"
Residue "A GLU 575": "OE1" <-> "OE2"
Residue "B GLU 11": "OE1" <-> "OE2"
Residue "B GLU 57": "OE1" <-> "OE2"
Residue "B GLU 81": "OE1" <-> "OE2"
Residue "B GLU 191": "OE1" <-> "OE2"
Residue "B GLU 200": "OE1" <-> "OE2"
Residue "B GLU 279": "OE1" <-> "OE2"
Residue "B GLU 298": "OE1" <-> "OE2"
Residue "B GLU 420": "OE1" <-> "OE2"
Residue "B GLU 488": "OE1" <-> "OE2"
Residue "B GLU 602": "OE1" <-> "OE2"
Residue "C GLU 425": "OE1" <-> "OE2"
Residue "C GLU 545": "OE1" <-> "OE2"
Residue "C GLU 607": "OE1" <-> "OE2"
Time to flip residues: 0.04s
Monomer Library directory:
"/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib"
Total number of atoms: 12595
Number of models: 1
Model: ""
Number of chains: 6
Chain: "A"
Number of atoms: 5171
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 638, 5171
Classifications: {'peptide': 638}
Link IDs: {'PTRANS': 14, 'TRANS': 623}
Chain breaks: 1
Chain: "B"
Number of atoms: 5171
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 638, 5171
Classifications: {'peptide': 638}
Link IDs: {'PTRANS': 14, 'TRANS': 623}
Chain breaks: 1
Chain: "C"
Number of atoms: 1483
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 184, 1483
Classifications: {'peptide': 184}
Link IDs: {'PTRANS': 9, 'TRANS': 174}
Chain breaks: 1
Chain: "D"
Number of atoms: 706
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 83, 706
Classifications: {'peptide': 83}
Link IDs: {'PTRANS': 3, 'TRANS': 79}
Chain breaks: 1
Chain: "A"
Number of atoms: 32
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 2, 32
Unusual residues: {' MG': 1, 'ATP': 1}
Classifications: {'undetermined': 2}
Link IDs: {None: 1}
Chain: "B"
Number of atoms: 32
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 2, 32
Unusual residues: {' MG': 1, 'ATP': 1}
Classifications: {'undetermined': 2}
Link IDs: {None: 1}
Time building chain proxies: 7.31, per 1000 atoms: 0.58
Number of scatterers: 12595
At special positions: 0
Unit cell: (134.706, 117.546, 100.386, 90, 90, 90)
Space group: P 1 (No. 1)
Number of sites at special positions: 0
Number of scattering types: 6
Type Number sf(0)
S 61 16.00
P 7 15.00
Mg 2 11.99
O 2433 8.00
N 2133 7.00
C 7959 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 - 3.50
Amino acid : False - 1.90
Carbohydrate : True - 1.99
Ligands : True - 1.99
Small molecules : False - 1.98
Amino acid - RNA/DNA : False
Number of custom bonds: simple=0, symmetry=0
Time building additional restraints: 4.89
Conformation dependent library (CDL) restraints added in 2.1 seconds
3048 Ramachandran restraints generated.
1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2.
Adding C-beta torsion restraints...
Number of C-beta restraints generated: 2936
Finding SS restraints...
Secondary structure from input PDB file:
62 helices and 14 sheets defined
47.7% alpha, 15.5% beta
0 base pairs and 0 stacking pairs defined.
Time for finding SS restraints: 1.42
Creating SS restraints...
Processing helix chain 'A' and resid 20 through 32
removed outlier: 3.952A pdb=" N PHE A 32 " --> pdb=" O ILE A 28 " (cutoff:3.500A)
Processing helix chain 'A' and resid 37 through 61
removed outlier: 4.081A pdb=" N ARG A 41 " --> pdb=" O GLU A 37 " (cutoff:3.500A)
removed outlier: 3.640A pdb=" N THR A 60 " --> pdb=" O TYR A 56 " (cutoff:3.500A)
Processing helix chain 'A' and resid 62 through 68
removed outlier: 3.630A pdb=" N LEU A 65 " --> pdb=" O PRO A 62 " (cutoff:3.500A)
removed outlier: 4.308A pdb=" N SER A 67 " --> pdb=" O LYS A 64 " (cutoff:3.500A)
Processing helix chain 'A' and resid 94 through 103
Processing helix chain 'A' and resid 108 through 117
Processing helix chain 'A' and resid 131 through 138
Processing helix chain 'A' and resid 187 through 193
removed outlier: 4.186A pdb=" N ALA A 190 " --> pdb=" O GLU A 187 " (cutoff:3.500A)
removed outlier: 5.301A pdb=" N GLU A 191 " --> pdb=" O ASP A 188 " (cutoff:3.500A)
removed outlier: 3.586A pdb=" N TYR A 192 " --> pdb=" O LEU A 189 " (cutoff:3.500A)
Processing helix chain 'A' and resid 194 through 206
Processing helix chain 'A' and resid 286 through 290
Processing helix chain 'A' and resid 291 through 295
Processing helix chain 'A' and resid 296 through 309
Processing helix chain 'A' and resid 370 through 374
Processing helix chain 'A' and resid 397 through 420
removed outlier: 3.815A pdb=" N LYS A 401 " --> pdb=" O ASN A 397 " (cutoff:3.500A)
removed outlier: 3.839A pdb=" N VAL A 402 " --> pdb=" O LYS A 398 " (cutoff:3.500A)
removed outlier: 4.010A pdb=" N GLU A 420 " --> pdb=" O GLU A 416 " (cutoff:3.500A)
Processing helix chain 'A' and resid 421 through 443
removed outlier: 6.394A pdb=" N LYS A 434 " --> pdb=" O GLU A 430 " (cutoff:3.500A)
removed outlier: 6.685A pdb=" N ASN A 435 " --> pdb=" O GLN A 431 " (cutoff:3.500A)
removed outlier: 3.725A pdb=" N LEU A 436 " --> pdb=" O PHE A 432 " (cutoff:3.500A)
Processing helix chain 'A' and resid 446 through 453
removed outlier: 3.810A pdb=" N ASP A 452 " --> pdb=" O THR A 448 " (cutoff:3.500A)
removed outlier: 3.706A pdb=" N LEU A 453 " --> pdb=" O LYS A 449 " (cutoff:3.500A)
Processing helix chain 'A' and resid 468 through 473
Processing helix chain 'A' and resid 489 through 495
removed outlier: 3.513A pdb=" N ASN A 495 " --> pdb=" O ASP A 491 " (cutoff:3.500A)
Processing helix chain 'A' and resid 498 through 505
removed outlier: 4.474A pdb=" N VAL A 502 " --> pdb=" O PHE A 498 " (cutoff:3.500A)
Processing helix chain 'A' and resid 516 through 524
Processing helix chain 'A' and resid 545 through 571
removed outlier: 5.142A pdb=" N GLY A 561 " --> pdb=" O VAL A 557 " (cutoff:3.500A)
removed outlier: 5.282A pdb=" N LEU A 562 " --> pdb=" O LYS A 558 " (cutoff:3.500A)
Processing helix chain 'A' and resid 572 through 574
No H-bonds generated for 'chain 'A' and resid 572 through 574'
Processing helix chain 'A' and resid 598 through 608
Processing helix chain 'A' and resid 612 through 617
removed outlier: 3.630A pdb=" N MET A 616 " --> pdb=" O ASP A 612 " (cutoff:3.500A)
Processing helix chain 'A' and resid 618 through 620
No H-bonds generated for 'chain 'A' and resid 618 through 620'
Processing helix chain 'A' and resid 631 through 644
Processing helix chain 'A' and resid 647 through 665
Processing helix chain 'A' and resid 671 through 688
removed outlier: 3.694A pdb=" N HIS A 675 " --> pdb=" O GLU A 671 " (cutoff:3.500A)
removed outlier: 3.567A pdb=" N LEU A 685 " --> pdb=" O ARG A 681 " (cutoff:3.500A)
Processing helix chain 'B' and resid 20 through 31
Processing helix chain 'B' and resid 35 through 37
No H-bonds generated for 'chain 'B' and resid 35 through 37'
Processing helix chain 'B' and resid 38 through 59
removed outlier: 3.514A pdb=" N GLU B 42 " --> pdb=" O ILE B 38 " (cutoff:3.500A)
Processing helix chain 'B' and resid 60 through 68
removed outlier: 6.653A pdb=" N SER B 63 " --> pdb=" O THR B 60 " (cutoff:3.500A)
removed outlier: 3.872A pdb=" N SER B 67 " --> pdb=" O LYS B 64 " (cutoff:3.500A)
Processing helix chain 'B' and resid 94 through 103
Processing helix chain 'B' and resid 108 through 117
Processing helix chain 'B' and resid 132 through 138
Processing helix chain 'B' and resid 187 through 193
removed outlier: 3.629A pdb=" N ALA B 190 " --> pdb=" O GLU B 187 " (cutoff:3.500A)
removed outlier: 4.943A pdb=" N GLU B 191 " --> pdb=" O ASP B 188 " (cutoff:3.500A)
Processing helix chain 'B' and resid 194 through 206
removed outlier: 3.598A pdb=" N ILE B 198 " --> pdb=" O GLU B 194 " (cutoff:3.500A)
Processing helix chain 'B' and resid 291 through 295
Processing helix chain 'B' and resid 296 through 309
Processing helix chain 'B' and resid 370 through 374
removed outlier: 3.605A pdb=" N LEU B 373 " --> pdb=" O PRO B 370 " (cutoff:3.500A)
Processing helix chain 'B' and resid 397 through 419
removed outlier: 3.991A pdb=" N LYS B 401 " --> pdb=" O ASN B 397 " (cutoff:3.500A)
removed outlier: 3.588A pdb=" N LYS B 405 " --> pdb=" O LYS B 401 " (cutoff:3.500A)
removed outlier: 3.713A pdb=" N ASN B 406 " --> pdb=" O VAL B 402 " (cutoff:3.500A)
removed outlier: 3.559A pdb=" N LYS B 409 " --> pdb=" O LYS B 405 " (cutoff:3.500A)
removed outlier: 3.665A pdb=" N ALA B 419 " --> pdb=" O PHE B 415 " (cutoff:3.500A)
Processing helix chain 'B' and resid 421 through 443
removed outlier: 6.462A pdb=" N LYS B 434 " --> pdb=" O GLU B 430 " (cutoff:3.500A)
removed outlier: 6.438A pdb=" N ASN B 435 " --> pdb=" O GLN B 431 " (cutoff:3.500A)
removed outlier: 3.684A pdb=" N LEU B 436 " --> pdb=" O PHE B 432 " (cutoff:3.500A)
removed outlier: 3.758A pdb=" N HIS B 441 " --> pdb=" O LYS B 437 " (cutoff:3.500A)
removed outlier: 3.628A pdb=" N GLU B 442 " --> pdb=" O LEU B 438 " (cutoff:3.500A)
Processing helix chain 'B' and resid 446 through 452
removed outlier: 3.990A pdb=" N ASP B 452 " --> pdb=" O THR B 448 " (cutoff:3.500A)
Processing helix chain 'B' and resid 468 through 474
Processing helix chain 'B' and resid 489 through 495
Processing helix chain 'B' and resid 498 through 505
removed outlier: 4.345A pdb=" N VAL B 502 " --> pdb=" O PHE B 498 " (cutoff:3.500A)
Processing helix chain 'B' and resid 516 through 524
removed outlier: 3.922A pdb=" N GLN B 523 " --> pdb=" O TYR B 519 " (cutoff:3.500A)
Processing helix chain 'B' and resid 545 through 571
removed outlier: 5.565A pdb=" N GLY B 561 " --> pdb=" O VAL B 557 " (cutoff:3.500A)
removed outlier: 5.471A pdb=" N LEU B 562 " --> pdb=" O LYS B 558 " (cutoff:3.500A)
Processing helix chain 'B' and resid 598 through 608
removed outlier: 3.694A pdb=" N ARG B 603 " --> pdb=" O ALA B 599 " (cutoff:3.500A)
Processing helix chain 'B' and resid 631 through 644
Processing helix chain 'B' and resid 647 through 665
Processing helix chain 'B' and resid 671 through 688
removed outlier: 3.783A pdb=" N HIS B 675 " --> pdb=" O GLU B 671 " (cutoff:3.500A)
Processing helix chain 'C' and resid 429 through 435
Processing helix chain 'C' and resid 441 through 462
Processing helix chain 'C' and resid 513 through 518
Processing helix chain 'C' and resid 526 through 544
Processing helix chain 'C' and resid 553 through 564
Processing helix chain 'C' and resid 569 through 573
Processing helix chain 'C' and resid 578 through 589
Processing helix chain 'C' and resid 598 through 612
removed outlier: 3.542A pdb=" N SER C 612 " --> pdb=" O LEU C 608 " (cutoff:3.500A)
Processing helix chain 'D' and resid 24 through 48
Processing helix chain 'D' and resid 103 through 112
removed outlier: 3.642A pdb=" N LYS D 107 " --> pdb=" O GLU D 103 " (cutoff:3.500A)
removed outlier: 3.756A pdb=" N LYS D 108 " --> pdb=" O GLU D 104 " (cutoff:3.500A)
removed outlier: 3.902A pdb=" N GLU D 109 " --> pdb=" O MET D 105 " (cutoff:3.500A)
removed outlier: 3.965A pdb=" N LYS D 110 " --> pdb=" O ARG D 106 " (cutoff:3.500A)
Processing helix chain 'D' and resid 115 through 119
Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 16
removed outlier: 3.858A pdb=" N SER B 147 " --> pdb=" O TYR B 155 " (cutoff:3.500A)
removed outlier: 4.133A pdb=" N ARG B 142 " --> pdb=" O HIS B 184 " (cutoff:3.500A)
removed outlier: 3.658A pdb=" N GLY B 178 " --> pdb=" O LYS B 148 " (cutoff:3.500A)
removed outlier: 3.678A pdb=" N THR B 85 " --> pdb=" O ILE B 76 " (cutoff:3.500A)
removed outlier: 6.445A pdb=" N ILE B 73 " --> pdb=" O LYS B 214 " (cutoff:3.500A)
removed outlier: 7.662A pdb=" N THR B 216 " --> pdb=" O ILE B 73 " (cutoff:3.500A)
removed outlier: 6.786A pdb=" N ILE B 75 " --> pdb=" O THR B 216 " (cutoff:3.500A)
removed outlier: 8.448A pdb=" N GLU B 218 " --> pdb=" O ILE B 75 " (cutoff:3.500A)
removed outlier: 3.646A pdb=" N VAL B 217 " --> pdb=" O THR B 276 " (cutoff:3.500A)
Processing sheet with id=AA2, first strand: chain 'A' and resid 18 through 19
removed outlier: 6.652A pdb=" N GLN A 18 " --> pdb=" O ILE B 105 " (cutoff:3.500A)
No H-bonds generated for sheet with id=AA2
Processing sheet with id=AA3, first strand: chain 'A' and resid 276 through 278
removed outlier: 3.584A pdb=" N VAL A 217 " --> pdb=" O THR A 276 " (cutoff:3.500A)
removed outlier: 3.763A pdb=" N ASP A 278 " --> pdb=" O LEU A 215 " (cutoff:3.500A)
removed outlier: 3.537A pdb=" N GLY A 178 " --> pdb=" O LYS A 148 " (cutoff:3.500A)
removed outlier: 3.671A pdb=" N LYS A 148 " --> pdb=" O GLY A 178 " (cutoff:3.500A)
removed outlier: 4.045A pdb=" N ARG A 142 " --> pdb=" O HIS A 184 " (cutoff:3.500A)
Processing sheet with id=AA4, first strand: chain 'A' and resid 104 through 105
Processing sheet with id=AA5, first strand: chain 'A' and resid 314 through 322
removed outlier: 6.803A pdb=" N VAL A 334 " --> pdb=" O LEU A 315 " (cutoff:3.500A)
removed outlier: 4.496A pdb=" N VAL A 317 " --> pdb=" O LEU A 332 " (cutoff:3.500A)
removed outlier: 6.686A pdb=" N LEU A 332 " --> pdb=" O VAL A 317 " (cutoff:3.500A)
removed outlier: 4.589A pdb=" N HIS A 319 " --> pdb=" O ALA A 330 " (cutoff:3.500A)
removed outlier: 7.038A pdb=" N ALA A 330 " --> pdb=" O HIS A 319 " (cutoff:3.500A)
removed outlier: 4.626A pdb=" N SER A 321 " --> pdb=" O PHE A 328 " (cutoff:3.500A)
removed outlier: 6.714A pdb=" N PHE A 328 " --> pdb=" O SER A 321 " (cutoff:3.500A)
removed outlier: 3.880A pdb=" N MET A 362 " --> pdb=" O LEU A 354 " (cutoff:3.500A)
removed outlier: 6.170A pdb=" N VAL A 356 " --> pdb=" O PHE A 360 " (cutoff:3.500A)
removed outlier: 5.578A pdb=" N PHE A 360 " --> pdb=" O VAL A 356 " (cutoff:3.500A)
Processing sheet with id=AA6, first strand: chain 'A' and resid 455 through 456
Processing sheet with id=AA7, first strand: chain 'A' and resid 510 through 512
Processing sheet with id=AA8, first strand: chain 'A' and resid 576 through 579
removed outlier: 6.903A pdb=" N LYS A 576 " --> pdb=" O LEU A 625 " (cutoff:3.500A)
removed outlier: 7.991A pdb=" N ILE A 627 " --> pdb=" O LYS A 576 " (cutoff:3.500A)
removed outlier: 6.828A pdb=" N VAL A 578 " --> pdb=" O ILE A 627 " (cutoff:3.500A)
Processing sheet with id=AA9, first strand: chain 'B' and resid 359 through 362
removed outlier: 5.226A pdb=" N PHE B 360 " --> pdb=" O VAL B 356 " (cutoff:3.500A)
removed outlier: 6.221A pdb=" N VAL B 356 " --> pdb=" O PHE B 360 " (cutoff:3.500A)
removed outlier: 3.856A pdb=" N MET B 362 " --> pdb=" O LEU B 354 " (cutoff:3.500A)
removed outlier: 6.877A pdb=" N ASN B 351 " --> pdb=" O GLY B 378 " (cutoff:3.500A)
removed outlier: 7.907A pdb=" N VAL B 380 " --> pdb=" O ASN B 351 " (cutoff:3.500A)
removed outlier: 6.351A pdb=" N LYS B 353 " --> pdb=" O VAL B 380 " (cutoff:3.500A)
removed outlier: 8.025A pdb=" N SER B 382 " --> pdb=" O LYS B 353 " (cutoff:3.500A)
removed outlier: 6.773A pdb=" N TYR B 355 " --> pdb=" O SER B 382 " (cutoff:3.500A)
removed outlier: 3.884A pdb=" N ALA B 316 " --> pdb=" O VAL B 334 " (cutoff:3.500A)
Processing sheet with id=AB1, first strand: chain 'B' and resid 359 through 362
removed outlier: 5.226A pdb=" N PHE B 360 " --> pdb=" O VAL B 356 " (cutoff:3.500A)
removed outlier: 6.221A pdb=" N VAL B 356 " --> pdb=" O PHE B 360 " (cutoff:3.500A)
removed outlier: 3.856A pdb=" N MET B 362 " --> pdb=" O LEU B 354 " (cutoff:3.500A)
removed outlier: 6.877A pdb=" N ASN B 351 " --> pdb=" O GLY B 378 " (cutoff:3.500A)
removed outlier: 7.907A pdb=" N VAL B 380 " --> pdb=" O ASN B 351 " (cutoff:3.500A)
removed outlier: 6.351A pdb=" N LYS B 353 " --> pdb=" O VAL B 380 " (cutoff:3.500A)
removed outlier: 8.025A pdb=" N SER B 382 " --> pdb=" O LYS B 353 " (cutoff:3.500A)
removed outlier: 6.773A pdb=" N TYR B 355 " --> pdb=" O SER B 382 " (cutoff:3.500A)
removed outlier: 3.884A pdb=" N ALA B 316 " --> pdb=" O VAL B 334 " (cutoff:3.500A)
Processing sheet with id=AB2, first strand: chain 'B' and resid 455 through 456
Processing sheet with id=AB3, first strand: chain 'B' and resid 510 through 512
removed outlier: 8.737A pdb=" N VAL B 510 " --> pdb=" O HIS B 481 " (cutoff:3.500A)
removed outlier: 7.233A pdb=" N TYR B 483 " --> pdb=" O VAL B 510 " (cutoff:3.500A)
removed outlier: 7.996A pdb=" N MET B 512 " --> pdb=" O TYR B 483 " (cutoff:3.500A)
removed outlier: 6.390A pdb=" N ILE B 485 " --> pdb=" O MET B 512 " (cutoff:3.500A)
Processing sheet with id=AB4, first strand: chain 'B' and resid 576 through 579
removed outlier: 6.697A pdb=" N LYS B 576 " --> pdb=" O LEU B 625 " (cutoff:3.500A)
removed outlier: 7.807A pdb=" N ILE B 627 " --> pdb=" O LYS B 576 " (cutoff:3.500A)
removed outlier: 6.724A pdb=" N VAL B 578 " --> pdb=" O ILE B 627 " (cutoff:3.500A)
Processing sheet with id=AB5, first strand: chain 'C' and resid 426 through 428
removed outlier: 3.649A pdb=" N PHE C 475 " --> pdb=" O LYS C 483 " (cutoff:3.500A)
595 hydrogen bonds defined for protein.
1647 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: 3.90
Time building geometry restraints manager: 5.36 seconds
NOTE: a complete listing of the restraints can be obtained by requesting
output of .geo file.
Histogram of bond lengths:
1.22 - 1.34: 4108
1.34 - 1.46: 2486
1.46 - 1.58: 6104
1.58 - 1.70: 10
1.70 - 1.82: 105
Bond restraints: 12813
Sorted by residual:
bond pdb=" C5' ATP B 801 "
pdb=" O5' ATP B 801 "
ideal model delta sigma weight residual
1.443 1.219 0.224 1.00e-02 1.00e+04 5.02e+02
bond pdb=" C5' ATP A 801 "
pdb=" O5' ATP A 801 "
ideal model delta sigma weight residual
1.443 1.224 0.219 1.00e-02 1.00e+04 4.80e+02
bond pdb=" C4' ATP A 801 "
pdb=" O4' ATP A 801 "
ideal model delta sigma weight residual
1.444 1.397 0.047 1.10e-02 8.26e+03 1.86e+01
bond pdb=" C3' ATP B 801 "
pdb=" O3' ATP B 801 "
ideal model delta sigma weight residual
1.423 1.378 0.045 1.10e-02 8.26e+03 1.66e+01
bond pdb=" C3' ATP A 801 "
pdb=" O3' ATP A 801 "
ideal model delta sigma weight residual
1.423 1.378 0.045 1.10e-02 8.26e+03 1.64e+01
... (remaining 12808 not shown)
Histogram of bond angle deviations from ideal:
80.41 - 95.57: 7
95.57 - 110.74: 3977
110.74 - 125.91: 13107
125.91 - 141.07: 146
141.07 - 156.24: 2
Bond angle restraints: 17239
Sorted by residual:
angle pdb=" C5' ATP B 801 "
pdb=" O5' ATP B 801 "
pdb=" PA ATP B 801 "
ideal model delta sigma weight residual
121.27 156.24 -34.97 1.00e+00 1.00e+00 1.22e+03
angle pdb=" C5' ATP A 801 "
pdb=" O5' ATP A 801 "
pdb=" PA ATP A 801 "
ideal model delta sigma weight residual
121.27 155.38 -34.11 1.00e+00 1.00e+00 1.16e+03
angle pdb=" C3' ATP B 801 "
pdb=" C4' ATP B 801 "
pdb=" C5' ATP B 801 "
ideal model delta sigma weight residual
115.19 83.09 32.10 1.76e+00 3.23e-01 3.33e+02
angle pdb=" C3' ATP A 801 "
pdb=" C4' ATP A 801 "
pdb=" C5' ATP A 801 "
ideal model delta sigma weight residual
115.19 85.19 30.00 1.76e+00 3.23e-01 2.91e+02
angle pdb=" C4' ATP A 801 "
pdb=" C5' ATP A 801 "
pdb=" O5' ATP A 801 "
ideal model delta sigma weight residual
108.83 140.57 -31.74 2.33e+00 1.85e-01 1.86e+02
... (remaining 17234 not shown)
Histogram of dihedral angle deviations from ideal:
0.00 - 18.23: 7120
18.23 - 36.47: 633
36.47 - 54.70: 120
54.70 - 72.93: 30
72.93 - 91.17: 13
Dihedral angle restraints: 7916
sinusoidal: 3380
harmonic: 4536
Sorted by residual:
dihedral pdb=" CA MET A 475 "
pdb=" C MET A 475 "
pdb=" N LYS A 476 "
pdb=" CA LYS A 476 "
ideal model delta harmonic sigma weight residual
180.00 152.73 27.27 0 5.00e+00 4.00e-02 2.97e+01
dihedral pdb=" CA MET B 93 "
pdb=" C MET B 93 "
pdb=" N THR B 94 "
pdb=" CA THR B 94 "
ideal model delta harmonic sigma weight residual
180.00 157.61 22.39 0 5.00e+00 4.00e-02 2.01e+01
dihedral pdb=" CA LEU C 598 "
pdb=" C LEU C 598 "
pdb=" N PHE C 599 "
pdb=" CA PHE C 599 "
ideal model delta harmonic sigma weight residual
180.00 -157.70 -22.30 0 5.00e+00 4.00e-02 1.99e+01
... (remaining 7913 not shown)
Histogram of chiral volume deviations from ideal:
0.000 - 0.099: 1816
0.099 - 0.198: 71
0.198 - 0.297: 4
0.297 - 0.396: 1
0.396 - 0.495: 2
Chirality restraints: 1894
Sorted by residual:
chirality pdb=" C4' ATP A 801 "
pdb=" C3' ATP A 801 "
pdb=" C5' ATP A 801 "
pdb=" O4' ATP A 801 "
both_signs ideal model delta sigma weight residual
False -2.49 -2.99 0.50 2.00e-01 2.50e+01 6.13e+00
chirality pdb=" C4' ATP B 801 "
pdb=" C3' ATP B 801 "
pdb=" C5' ATP B 801 "
pdb=" O4' ATP B 801 "
both_signs ideal model delta sigma weight residual
False -2.49 -2.97 0.47 2.00e-01 2.50e+01 5.63e+00
chirality pdb=" CG LEU C 538 "
pdb=" CB LEU C 538 "
pdb=" CD1 LEU C 538 "
pdb=" CD2 LEU C 538 "
both_signs ideal model delta sigma weight residual
False -2.59 -2.24 -0.35 2.00e-01 2.50e+01 3.11e+00
... (remaining 1891 not shown)
Planarity restraints: 2194
Sorted by residual:
delta sigma weight rms_deltas residual
plane pdb=" C LEU A 542 " 0.089 5.00e-02 4.00e+02 1.28e-01 2.62e+01
pdb=" N PRO A 543 " -0.221 5.00e-02 4.00e+02
pdb=" CA PRO A 543 " 0.065 5.00e-02 4.00e+02
pdb=" CD PRO A 543 " 0.067 5.00e-02 4.00e+02
delta sigma weight rms_deltas residual
plane pdb=" C MET D 112 " 0.072 5.00e-02 4.00e+02 1.06e-01 1.80e+01
pdb=" N PRO D 113 " -0.183 5.00e-02 4.00e+02
pdb=" CA PRO D 113 " 0.055 5.00e-02 4.00e+02
pdb=" CD PRO D 113 " 0.057 5.00e-02 4.00e+02
delta sigma weight rms_deltas residual
plane pdb=" C LEU B 542 " -0.038 5.00e-02 4.00e+02 5.75e-02 5.29e+00
pdb=" N PRO B 543 " 0.099 5.00e-02 4.00e+02
pdb=" CA PRO B 543 " -0.029 5.00e-02 4.00e+02
pdb=" CD PRO B 543 " -0.032 5.00e-02 4.00e+02
... (remaining 2191 not shown)
Histogram of nonbonded interaction distances:
1.95 - 2.54: 169
2.54 - 3.13: 9989
3.13 - 3.72: 20723
3.72 - 4.31: 28318
4.31 - 4.90: 45173
Nonbonded interactions: 104372
Sorted by model distance:
nonbonded pdb=" O3G ATP B 801 "
pdb="MG MG B 802 "
model vdw
1.947 2.170
nonbonded pdb=" O3A ATP A 801 "
pdb="MG MG A 802 "
model vdw
2.030 2.170
nonbonded pdb=" O1G ATP A 801 "
pdb="MG MG A 802 "
model vdw
2.099 2.170
nonbonded pdb=" OH TYR A 425 "
pdb=" O LEU A 453 "
model vdw
2.176 3.040
nonbonded pdb=" OH TYR A 372 "
pdb=" OD2 ASP A 443 "
model vdw
2.206 3.040
... (remaining 104367 not shown)
NOTE: a complete listing of the restraints can be obtained by requesting
output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
reference = chain 'A'
selection = chain 'B'
}
Set up NCS constraints
No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
Set random seed: 0.000
Set model cs if undefined: 0.000
Decide on map wrapping: 0.000
Normalize map: mean=0, sd=1: 1.270
Set stop_for_unknowns flag: 0.000
Assert model is a single copy model: 0.000
Assert all atoms have isotropic ADPs: 0.000
Construct map_model_manager: 0.010
Extract box with map and model: 0.490
Check model and map are aligned: 0.090
Set scattering table: 0.110
Process input model: 35.180
Find NCS groups from input model: 0.290
Set up NCS constraints: 0.050
Set refine NCS operators: 0.000
Adjust number of macro_cycles: 0.000
Reset NCS operators: 0.000
Extract rigid body selections: 0.000
Check and reset occupancies: 0.000
Load rotamer database and sin/cos tables:2.650
Set ADP refinement strategy: 0.000
Make a string to write initial .geo file:0.000
Internal consistency checks: 0.000
Total: 40.140
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7059
moved from start: 0.0000
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.005 0.224 12813 Z= 0.322
Angle : 1.066 34.971 17239 Z= 0.636
Chirality : 0.046 0.495 1894
Planarity : 0.005 0.128 2194
Dihedral : 14.738 91.169 4980
Min Nonbonded Distance : 1.947
Molprobity Statistics.
All-atom Clashscore : 14.42
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 2.17 %
Favored : 97.83 %
Rotamer:
Outliers : 0.00 %
Allowed : 13.62 %
Favored : 86.38 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 0.39 (0.22), residues: 1524
helix: 0.86 (0.21), residues: 643
sheet: 0.85 (0.37), residues: 201
loop : -0.42 (0.24), residues: 680
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.017 0.002 TRP D 31
HIS 0.006 0.001 HIS B 314
PHE 0.013 0.001 PHE A 303
TYR 0.009 0.001 TYR B 483
ARG 0.016 0.001 ARG C 518
*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
3048 Ramachandran restraints generated.
1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
3048 Ramachandran restraints generated.
1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
108 residues out of total 1388 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 108
time to evaluate : 1.495
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: A 512 MET cc_start: 0.8046 (mmm) cc_final: 0.7781 (mmm)
REVERT: B 475 MET cc_start: 0.4892 (mmt) cc_final: 0.4605 (mmt)
REVERT: C 457 ASP cc_start: 0.9102 (t70) cc_final: 0.8640 (t0)
REVERT: D 105 MET cc_start: 0.3884 (tpp) cc_final: 0.1675 (ptm)
outliers start: 0
outliers final: 0
residues processed: 108
average time/residue: 0.2871
time to fit residues: 44.1057
Evaluate side-chains
94 residues out of total 1388 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 0
poor density : 94
time to evaluate : 1.526
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 152
random chunks:
chunk 128 optimal weight: 9.9990
chunk 115 optimal weight: 7.9990
chunk 63 optimal weight: 8.9990
chunk 39 optimal weight: 0.0970
chunk 77 optimal weight: 10.0000
chunk 61 optimal weight: 9.9990
chunk 119 optimal weight: 40.0000
chunk 46 optimal weight: 6.9990
chunk 72 optimal weight: 5.9990
chunk 88 optimal weight: 20.0000
chunk 138 optimal weight: 9.9990
overall best weight: 6.0186
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 30 ASN
A 345 ASN
** B 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 445 GLN
C 436 GLN
C 556 GLN
D 9 HIS
** D 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 33 HIS
D 44 GLN
Total number of N/Q/H flips: 8
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7193
moved from start: 0.1605
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.005 0.068 12813 Z= 0.295
Angle : 0.666 10.026 17239 Z= 0.351
Chirality : 0.043 0.254 1894
Planarity : 0.005 0.070 2194
Dihedral : 8.747 81.083 1741
Min Nonbonded Distance : 2.007
Molprobity Statistics.
All-atom Clashscore : 15.96
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 2.76 %
Favored : 97.24 %
Rotamer:
Outliers : 2.09 %
Allowed : 12.82 %
Favored : 85.09 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 0.43 (0.22), residues: 1524
helix: 0.96 (0.20), residues: 641
sheet: 0.80 (0.39), residues: 197
loop : -0.45 (0.24), residues: 686
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.015 0.002 TRP C 423
HIS 0.009 0.002 HIS A 314
PHE 0.014 0.002 PHE A 303
TYR 0.027 0.002 TYR A 595
ARG 0.006 0.001 ARG A 638
*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
3048 Ramachandran restraints generated.
1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
3048 Ramachandran restraints generated.
1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
115 residues out of total 1388 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 29
poor density : 86
time to evaluate : 1.585
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: A 31 THR cc_start: 0.8228 (OUTLIER) cc_final: 0.7846 (p)
REVERT: C 429 LEU cc_start: 0.9391 (mm) cc_final: 0.9188 (mm)
REVERT: C 542 MET cc_start: 0.6083 (mmp) cc_final: 0.5530 (mmp)
REVERT: C 572 LYS cc_start: 0.8889 (tptp) cc_final: 0.8662 (tptp)
outliers start: 29
outliers final: 15
residues processed: 107
average time/residue: 0.2571
time to fit residues: 40.7179
Evaluate side-chains
97 residues out of total 1388 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 16
poor density : 81
time to evaluate : 1.440
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 31 THR
Chi-restraints excluded: chain A residue 502 VAL
Chi-restraints excluded: chain A residue 505 ARG
Chi-restraints excluded: chain A residue 578 VAL
Chi-restraints excluded: chain A residue 624 HIS
Chi-restraints excluded: chain A residue 685 LEU
Chi-restraints excluded: chain B residue 88 ASP
Chi-restraints excluded: chain B residue 545 ASP
Chi-restraints excluded: chain C residue 464 ILE
Chi-restraints excluded: chain C residue 477 HIS
Chi-restraints excluded: chain C residue 516 VAL
Chi-restraints excluded: chain C residue 613 LEU
Chi-restraints excluded: chain D residue 9 HIS
Chi-restraints excluded: chain D residue 12 VAL
Chi-restraints excluded: chain D residue 22 ASN
Chi-restraints excluded: chain D residue 131 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 152
random chunks:
chunk 76 optimal weight: 20.0000
chunk 42 optimal weight: 20.0000
chunk 114 optimal weight: 7.9990
chunk 93 optimal weight: 5.9990
chunk 38 optimal weight: 6.9990
chunk 138 optimal weight: 0.9990
chunk 149 optimal weight: 20.0000
chunk 123 optimal weight: 8.9990
chunk 137 optimal weight: 8.9990
chunk 47 optimal weight: 9.9990
chunk 110 optimal weight: 20.0000
overall best weight: 6.1990
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** A 624 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 608 GLN
Total number of N/Q/H flips: 1
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7236
moved from start: 0.2151
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.005 0.082 12813 Z= 0.295
Angle : 0.634 7.638 17239 Z= 0.338
Chirality : 0.043 0.288 1894
Planarity : 0.004 0.073 2194
Dihedral : 8.721 80.437 1741
Min Nonbonded Distance : 1.902
Molprobity Statistics.
All-atom Clashscore : 16.20
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 2.76 %
Favored : 97.24 %
Rotamer:
Outliers : 3.75 %
Allowed : 12.25 %
Favored : 84.01 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 0.27 (0.22), residues: 1524
helix: 0.96 (0.20), residues: 637
sheet: 0.43 (0.40), residues: 191
loop : -0.57 (0.24), residues: 696
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.020 0.002 TRP C 423
HIS 0.028 0.002 HIS D 9
PHE 0.015 0.002 PHE B 133
TYR 0.020 0.002 TYR B 155
ARG 0.006 0.001 ARG A 638
*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
3048 Ramachandran restraints generated.
1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
3048 Ramachandran restraints generated.
1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
136 residues out of total 1388 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 52
poor density : 84
time to evaluate : 1.463
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: A 31 THR cc_start: 0.8204 (OUTLIER) cc_final: 0.7798 (p)
REVERT: A 123 ILE cc_start: 0.7712 (OUTLIER) cc_final: 0.7484 (mm)
REVERT: B 193 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.7926 (mm)
REVERT: C 542 MET cc_start: 0.6432 (mmp) cc_final: 0.5941 (mmp)
REVERT: C 572 LYS cc_start: 0.8963 (tptp) cc_final: 0.8736 (tptp)
outliers start: 52
outliers final: 25
residues processed: 126
average time/residue: 0.2594
time to fit residues: 47.7718
Evaluate side-chains
112 residues out of total 1388 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 28
poor density : 84
time to evaluate : 1.470
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 31 THR
Chi-restraints excluded: chain A residue 123 ILE
Chi-restraints excluded: chain A residue 156 MET
Chi-restraints excluded: chain A residue 502 VAL
Chi-restraints excluded: chain A residue 505 ARG
Chi-restraints excluded: chain A residue 563 CYS
Chi-restraints excluded: chain A residue 578 VAL
Chi-restraints excluded: chain A residue 685 LEU
Chi-restraints excluded: chain B residue 88 ASP
Chi-restraints excluded: chain B residue 122 ASP
Chi-restraints excluded: chain B residue 193 LEU
Chi-restraints excluded: chain B residue 213 ILE
Chi-restraints excluded: chain B residue 332 LEU
Chi-restraints excluded: chain B residue 458 THR
Chi-restraints excluded: chain B residue 545 ASP
Chi-restraints excluded: chain B residue 574 VAL
Chi-restraints excluded: chain C residue 464 ILE
Chi-restraints excluded: chain C residue 477 HIS
Chi-restraints excluded: chain C residue 509 VAL
Chi-restraints excluded: chain C residue 516 VAL
Chi-restraints excluded: chain C residue 559 PHE
Chi-restraints excluded: chain C residue 613 LEU
Chi-restraints excluded: chain D residue 12 VAL
Chi-restraints excluded: chain D residue 22 ASN
Chi-restraints excluded: chain D residue 28 LEU
Chi-restraints excluded: chain D residue 108 LYS
Chi-restraints excluded: chain D residue 109 GLU
Chi-restraints excluded: chain D residue 131 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 152
random chunks:
chunk 136 optimal weight: 6.9990
chunk 103 optimal weight: 10.0000
chunk 71 optimal weight: 20.0000
chunk 15 optimal weight: 40.0000
chunk 65 optimal weight: 2.9990
chunk 92 optimal weight: 10.0000
chunk 138 optimal weight: 7.9990
chunk 146 optimal weight: 5.9990
chunk 72 optimal weight: 9.9990
chunk 131 optimal weight: 5.9990
chunk 39 optimal weight: 0.0370
overall best weight: 4.4066
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** A 624 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 9 HIS
D 20 HIS
Total number of N/Q/H flips: 2
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7217
moved from start: 0.2424
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.004 0.057 12813 Z= 0.228
Angle : 0.593 8.556 17239 Z= 0.313
Chirality : 0.042 0.308 1894
Planarity : 0.004 0.075 2194
Dihedral : 8.623 79.929 1741
Min Nonbonded Distance : 1.941
Molprobity Statistics.
All-atom Clashscore : 15.57
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 2.89 %
Favored : 97.11 %
Rotamer:
Outliers : 3.03 %
Allowed : 13.54 %
Favored : 83.43 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 0.33 (0.22), residues: 1524
helix: 1.08 (0.21), residues: 634
sheet: 0.27 (0.38), residues: 199
loop : -0.54 (0.24), residues: 691
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.014 0.002 TRP D 7
HIS 0.006 0.001 HIS A 314
PHE 0.014 0.001 PHE D 124
TYR 0.015 0.001 TYR A 372
ARG 0.006 0.001 ARG D 39
*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
3048 Ramachandran restraints generated.
1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
3048 Ramachandran restraints generated.
1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
126 residues out of total 1388 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 42
poor density : 84
time to evaluate : 1.525
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: A 31 THR cc_start: 0.8134 (OUTLIER) cc_final: 0.7744 (p)
REVERT: A 123 ILE cc_start: 0.7716 (OUTLIER) cc_final: 0.7453 (mm)
REVERT: A 475 MET cc_start: 0.5507 (OUTLIER) cc_final: 0.4888 (mpp)
REVERT: B 125 MET cc_start: 0.8620 (mmm) cc_final: 0.7130 (mmm)
REVERT: B 193 LEU cc_start: 0.8308 (OUTLIER) cc_final: 0.7912 (mm)
REVERT: B 332 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.8012 (mm)
REVERT: B 622 LYS cc_start: 0.7357 (tptt) cc_final: 0.6841 (tptt)
REVERT: C 542 MET cc_start: 0.6399 (mmp) cc_final: 0.5870 (mmp)
REVERT: C 572 LYS cc_start: 0.8951 (tptp) cc_final: 0.8733 (tptp)
outliers start: 42
outliers final: 25
residues processed: 116
average time/residue: 0.2591
time to fit residues: 43.6848
Evaluate side-chains
112 residues out of total 1388 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 30
poor density : 82
time to evaluate : 1.564
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 31 THR
Chi-restraints excluded: chain A residue 123 ILE
Chi-restraints excluded: chain A residue 156 MET
Chi-restraints excluded: chain A residue 309 ASN
Chi-restraints excluded: chain A residue 426 LYS
Chi-restraints excluded: chain A residue 475 MET
Chi-restraints excluded: chain A residue 502 VAL
Chi-restraints excluded: chain A residue 505 ARG
Chi-restraints excluded: chain A residue 542 LEU
Chi-restraints excluded: chain A residue 563 CYS
Chi-restraints excluded: chain A residue 578 VAL
Chi-restraints excluded: chain A residue 685 LEU
Chi-restraints excluded: chain B residue 88 ASP
Chi-restraints excluded: chain B residue 122 ASP
Chi-restraints excluded: chain B residue 193 LEU
Chi-restraints excluded: chain B residue 213 ILE
Chi-restraints excluded: chain B residue 332 LEU
Chi-restraints excluded: chain B residue 456 TYR
Chi-restraints excluded: chain B residue 458 THR
Chi-restraints excluded: chain B residue 545 ASP
Chi-restraints excluded: chain B residue 634 VAL
Chi-restraints excluded: chain C residue 464 ILE
Chi-restraints excluded: chain C residue 477 HIS
Chi-restraints excluded: chain C residue 516 VAL
Chi-restraints excluded: chain C residue 613 LEU
Chi-restraints excluded: chain D residue 9 HIS
Chi-restraints excluded: chain D residue 20 HIS
Chi-restraints excluded: chain D residue 22 ASN
Chi-restraints excluded: chain D residue 28 LEU
Chi-restraints excluded: chain D residue 131 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 152
random chunks:
chunk 122 optimal weight: 7.9990
chunk 83 optimal weight: 4.9990
chunk 2 optimal weight: 6.9990
chunk 109 optimal weight: 8.9990
chunk 60 optimal weight: 0.9980
chunk 125 optimal weight: 3.9990
chunk 101 optimal weight: 10.0000
chunk 0 optimal weight: 20.0000
chunk 75 optimal weight: 0.9990
chunk 131 optimal weight: 9.9990
chunk 37 optimal weight: 3.9990
overall best weight: 2.9988
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** A 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 624 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 9 HIS
Total number of N/Q/H flips: 1
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7198
moved from start: 0.2562
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.044 12813 Z= 0.182
Angle : 0.588 9.514 17239 Z= 0.304
Chirality : 0.042 0.315 1894
Planarity : 0.004 0.078 2194
Dihedral : 8.502 82.091 1741
Min Nonbonded Distance : 1.969
Molprobity Statistics.
All-atom Clashscore : 13.74
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 2.49 %
Favored : 97.51 %
Rotamer:
Outliers : 2.59 %
Allowed : 14.48 %
Favored : 82.93 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 0.41 (0.22), residues: 1524
helix: 1.19 (0.21), residues: 634
sheet: 0.30 (0.38), residues: 204
loop : -0.55 (0.24), residues: 686
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.013 0.001 TRP B 157
HIS 0.009 0.001 HIS D 20
PHE 0.010 0.001 PHE C 559
TYR 0.013 0.001 TYR A 372
ARG 0.008 0.000 ARG D 39
*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
3048 Ramachandran restraints generated.
1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
3048 Ramachandran restraints generated.
1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
122 residues out of total 1388 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 36
poor density : 86
time to evaluate : 1.457
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: A 31 THR cc_start: 0.8089 (OUTLIER) cc_final: 0.7719 (p)
REVERT: A 125 MET cc_start: 0.8161 (mmm) cc_final: 0.7512 (mmp)
REVERT: B 193 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.8019 (mm)
REVERT: B 332 LEU cc_start: 0.8357 (OUTLIER) cc_final: 0.8088 (mm)
REVERT: B 622 LYS cc_start: 0.7563 (tptt) cc_final: 0.7069 (tptt)
REVERT: C 542 MET cc_start: 0.6385 (mmp) cc_final: 0.5845 (mmp)
REVERT: D 14 ASP cc_start: 0.7415 (p0) cc_final: 0.6963 (p0)
outliers start: 36
outliers final: 27
residues processed: 111
average time/residue: 0.2632
time to fit residues: 42.2135
Evaluate side-chains
113 residues out of total 1388 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 30
poor density : 83
time to evaluate : 1.410
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 31 THR
Chi-restraints excluded: chain A residue 156 MET
Chi-restraints excluded: chain A residue 309 ASN
Chi-restraints excluded: chain A residue 426 LYS
Chi-restraints excluded: chain A residue 458 THR
Chi-restraints excluded: chain A residue 475 MET
Chi-restraints excluded: chain A residue 502 VAL
Chi-restraints excluded: chain A residue 505 ARG
Chi-restraints excluded: chain A residue 563 CYS
Chi-restraints excluded: chain A residue 624 HIS
Chi-restraints excluded: chain B residue 193 LEU
Chi-restraints excluded: chain B residue 213 ILE
Chi-restraints excluded: chain B residue 275 TYR
Chi-restraints excluded: chain B residue 332 LEU
Chi-restraints excluded: chain B residue 368 LEU
Chi-restraints excluded: chain B residue 456 TYR
Chi-restraints excluded: chain B residue 545 ASP
Chi-restraints excluded: chain B residue 574 VAL
Chi-restraints excluded: chain B residue 634 VAL
Chi-restraints excluded: chain C residue 464 ILE
Chi-restraints excluded: chain C residue 477 HIS
Chi-restraints excluded: chain C residue 481 THR
Chi-restraints excluded: chain C residue 516 VAL
Chi-restraints excluded: chain C residue 613 LEU
Chi-restraints excluded: chain D residue 9 HIS
Chi-restraints excluded: chain D residue 12 VAL
Chi-restraints excluded: chain D residue 20 HIS
Chi-restraints excluded: chain D residue 28 LEU
Chi-restraints excluded: chain D residue 108 LYS
Chi-restraints excluded: chain D residue 131 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 152
random chunks:
chunk 49 optimal weight: 0.6980
chunk 132 optimal weight: 20.0000
chunk 29 optimal weight: 0.0170
chunk 86 optimal weight: 0.9990
chunk 36 optimal weight: 6.9990
chunk 147 optimal weight: 8.9990
chunk 122 optimal weight: 7.9990
chunk 68 optimal weight: 20.0000
chunk 12 optimal weight: 6.9990
chunk 48 optimal weight: 20.0000
chunk 77 optimal weight: 5.9990
overall best weight: 2.9424
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** A 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 624 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 9 HIS
Total number of N/Q/H flips: 1
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7195
moved from start: 0.2731
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.041 12813 Z= 0.177
Angle : 0.585 10.203 17239 Z= 0.301
Chirality : 0.041 0.273 1894
Planarity : 0.004 0.078 2194
Dihedral : 8.414 83.677 1741
Min Nonbonded Distance : 1.966
Molprobity Statistics.
All-atom Clashscore : 13.11
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 2.62 %
Favored : 97.38 %
Rotamer:
Outliers : 3.10 %
Allowed : 14.12 %
Favored : 82.78 %
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: 0.41 (0.22), residues: 1524
helix: 1.17 (0.21), residues: 640
sheet: 0.34 (0.37), residues: 205
loop : -0.57 (0.24), residues: 679
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.012 0.001 TRP B 157
HIS 0.014 0.001 HIS D 9
PHE 0.014 0.001 PHE D 124
TYR 0.013 0.001 TYR A 372
ARG 0.007 0.000 ARG D 39
*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
3048 Ramachandran restraints generated.
1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
3048 Ramachandran restraints generated.
1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
133 residues out of total 1388 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 43
poor density : 90
time to evaluate : 1.454
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: A 31 THR cc_start: 0.8078 (OUTLIER) cc_final: 0.7708 (p)
REVERT: A 123 ILE cc_start: 0.7768 (OUTLIER) cc_final: 0.7285 (mm)
REVERT: A 125 MET cc_start: 0.8170 (mmm) cc_final: 0.7334 (mmp)
REVERT: A 601 MET cc_start: 0.6190 (tpp) cc_final: 0.5805 (tpp)
REVERT: B 125 MET cc_start: 0.8750 (mmm) cc_final: 0.7213 (mmm)
REVERT: B 193 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.8050 (mm)
REVERT: B 332 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.8024 (mm)
REVERT: B 622 LYS cc_start: 0.7653 (tptt) cc_final: 0.7232 (tptt)
REVERT: C 542 MET cc_start: 0.6568 (mmp) cc_final: 0.6331 (mmp)
REVERT: D 8 ASP cc_start: 0.4384 (OUTLIER) cc_final: 0.4146 (t0)
REVERT: D 14 ASP cc_start: 0.7254 (p0) cc_final: 0.6820 (p0)
outliers start: 43
outliers final: 28
residues processed: 121
average time/residue: 0.2554
time to fit residues: 44.7778
Evaluate side-chains
117 residues out of total 1388 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 33
poor density : 84
time to evaluate : 1.342
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 31 THR
Chi-restraints excluded: chain A residue 123 ILE
Chi-restraints excluded: chain A residue 156 MET
Chi-restraints excluded: chain A residue 309 ASN
Chi-restraints excluded: chain A residue 426 LYS
Chi-restraints excluded: chain A residue 458 THR
Chi-restraints excluded: chain A residue 472 VAL
Chi-restraints excluded: chain A residue 475 MET
Chi-restraints excluded: chain A residue 502 VAL
Chi-restraints excluded: chain A residue 505 ARG
Chi-restraints excluded: chain A residue 542 LEU
Chi-restraints excluded: chain A residue 563 CYS
Chi-restraints excluded: chain A residue 578 VAL
Chi-restraints excluded: chain A residue 685 LEU
Chi-restraints excluded: chain B residue 122 ASP
Chi-restraints excluded: chain B residue 193 LEU
Chi-restraints excluded: chain B residue 213 ILE
Chi-restraints excluded: chain B residue 275 TYR
Chi-restraints excluded: chain B residue 332 LEU
Chi-restraints excluded: chain B residue 368 LEU
Chi-restraints excluded: chain B residue 456 TYR
Chi-restraints excluded: chain B residue 545 ASP
Chi-restraints excluded: chain B residue 574 VAL
Chi-restraints excluded: chain B residue 634 VAL
Chi-restraints excluded: chain C residue 477 HIS
Chi-restraints excluded: chain C residue 481 THR
Chi-restraints excluded: chain C residue 516 VAL
Chi-restraints excluded: chain C residue 613 LEU
Chi-restraints excluded: chain D residue 8 ASP
Chi-restraints excluded: chain D residue 12 VAL
Chi-restraints excluded: chain D residue 20 HIS
Chi-restraints excluded: chain D residue 28 LEU
Chi-restraints excluded: chain D residue 131 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 152
random chunks:
chunk 141 optimal weight: 10.0000
chunk 16 optimal weight: 20.0000
chunk 83 optimal weight: 0.0270
chunk 107 optimal weight: 8.9990
chunk 123 optimal weight: 4.9990
chunk 82 optimal weight: 5.9990
chunk 146 optimal weight: 8.9990
chunk 91 optimal weight: 5.9990
chunk 89 optimal weight: 7.9990
chunk 67 optimal weight: 6.9990
chunk 90 optimal weight: 7.9990
overall best weight: 4.8046
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** A 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 624 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 325 GLN
** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Total number of N/Q/H flips: 1
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7235
moved from start: 0.3003
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.004 0.063 12813 Z= 0.238
Angle : 0.623 10.870 17239 Z= 0.323
Chirality : 0.042 0.336 1894
Planarity : 0.004 0.083 2194
Dihedral : 8.490 84.223 1741
Min Nonbonded Distance : 1.926
Molprobity Statistics.
All-atom Clashscore : 15.53
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 2.89 %
Favored : 97.11 %
Rotamer:
Outliers : 3.24 %
Allowed : 14.55 %
Favored : 82.20 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 0.30 (0.22), residues: 1524
helix: 1.10 (0.21), residues: 638
sheet: 0.20 (0.38), residues: 201
loop : -0.61 (0.24), residues: 685
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.030 0.002 TRP D 7
HIS 0.006 0.001 HIS A 314
PHE 0.012 0.001 PHE B 133
TYR 0.017 0.002 TYR A 372
ARG 0.008 0.001 ARG D 39
*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
3048 Ramachandran restraints generated.
1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
3048 Ramachandran restraints generated.
1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
133 residues out of total 1388 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 45
poor density : 88
time to evaluate : 1.531
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: A 31 THR cc_start: 0.8102 (OUTLIER) cc_final: 0.7720 (p)
REVERT: A 123 ILE cc_start: 0.7698 (OUTLIER) cc_final: 0.7147 (mm)
REVERT: A 125 MET cc_start: 0.8144 (mmm) cc_final: 0.7172 (mmp)
REVERT: B 193 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.8067 (mm)
REVERT: B 622 LYS cc_start: 0.7639 (tptt) cc_final: 0.7146 (tptt)
REVERT: C 542 MET cc_start: 0.6856 (mmp) cc_final: 0.6566 (mmp)
REVERT: D 14 ASP cc_start: 0.7129 (p0) cc_final: 0.6610 (p0)
REVERT: D 105 MET cc_start: 0.4303 (tpp) cc_final: 0.3048 (mtp)
outliers start: 45
outliers final: 33
residues processed: 121
average time/residue: 0.2540
time to fit residues: 44.9343
Evaluate side-chains
119 residues out of total 1388 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 36
poor density : 83
time to evaluate : 1.577
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 31 THR
Chi-restraints excluded: chain A residue 123 ILE
Chi-restraints excluded: chain A residue 156 MET
Chi-restraints excluded: chain A residue 309 ASN
Chi-restraints excluded: chain A residue 317 VAL
Chi-restraints excluded: chain A residue 426 LYS
Chi-restraints excluded: chain A residue 458 THR
Chi-restraints excluded: chain A residue 475 MET
Chi-restraints excluded: chain A residue 502 VAL
Chi-restraints excluded: chain A residue 505 ARG
Chi-restraints excluded: chain A residue 531 THR
Chi-restraints excluded: chain A residue 563 CYS
Chi-restraints excluded: chain A residue 578 VAL
Chi-restraints excluded: chain A residue 685 LEU
Chi-restraints excluded: chain B residue 88 ASP
Chi-restraints excluded: chain B residue 122 ASP
Chi-restraints excluded: chain B residue 156 MET
Chi-restraints excluded: chain B residue 193 LEU
Chi-restraints excluded: chain B residue 213 ILE
Chi-restraints excluded: chain B residue 275 TYR
Chi-restraints excluded: chain B residue 332 LEU
Chi-restraints excluded: chain B residue 368 LEU
Chi-restraints excluded: chain B residue 456 TYR
Chi-restraints excluded: chain B residue 458 THR
Chi-restraints excluded: chain B residue 545 ASP
Chi-restraints excluded: chain B residue 574 VAL
Chi-restraints excluded: chain B residue 634 VAL
Chi-restraints excluded: chain C residue 464 ILE
Chi-restraints excluded: chain C residue 481 THR
Chi-restraints excluded: chain C residue 516 VAL
Chi-restraints excluded: chain C residue 592 VAL
Chi-restraints excluded: chain C residue 613 LEU
Chi-restraints excluded: chain D residue 12 VAL
Chi-restraints excluded: chain D residue 20 HIS
Chi-restraints excluded: chain D residue 28 LEU
Chi-restraints excluded: chain D residue 131 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 152
random chunks:
chunk 58 optimal weight: 4.9990
chunk 87 optimal weight: 3.9990
chunk 44 optimal weight: 10.0000
chunk 28 optimal weight: 8.9990
chunk 93 optimal weight: 9.9990
chunk 99 optimal weight: 7.9990
chunk 72 optimal weight: 9.9990
chunk 13 optimal weight: 6.9990
chunk 115 optimal weight: 2.9990
chunk 133 optimal weight: 20.0000
chunk 140 optimal weight: 10.0000
overall best weight: 5.3990
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** A 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 523 GLN
** A 624 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 395 GLN
** B 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 477 HIS
C 556 GLN
Total number of N/Q/H flips: 4
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7259
moved from start: 0.3292
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.004 0.068 12813 Z= 0.261
Angle : 0.650 11.489 17239 Z= 0.337
Chirality : 0.043 0.335 1894
Planarity : 0.004 0.084 2194
Dihedral : 8.526 84.502 1741
Min Nonbonded Distance : 1.926
Molprobity Statistics.
All-atom Clashscore : 16.20
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 3.15 %
Favored : 96.85 %
Rotamer:
Outliers : 3.17 %
Allowed : 15.20 %
Favored : 81.63 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 0.19 (0.22), residues: 1524
helix: 1.02 (0.21), residues: 638
sheet: 0.08 (0.38), residues: 201
loop : -0.65 (0.24), residues: 685
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.049 0.003 TRP D 7
HIS 0.006 0.001 HIS A 314
PHE 0.013 0.002 PHE B 133
TYR 0.019 0.002 TYR A 372
ARG 0.010 0.001 ARG D 39
*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
3048 Ramachandran restraints generated.
1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
3048 Ramachandran restraints generated.
1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
127 residues out of total 1388 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 44
poor density : 83
time to evaluate : 1.462
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: A 31 THR cc_start: 0.8101 (OUTLIER) cc_final: 0.7762 (p)
REVERT: A 123 ILE cc_start: 0.7721 (OUTLIER) cc_final: 0.7122 (mm)
REVERT: A 125 MET cc_start: 0.8095 (mmm) cc_final: 0.7135 (mmp)
REVERT: A 601 MET cc_start: 0.6355 (tpp) cc_final: 0.6099 (tpp)
REVERT: B 123 ILE cc_start: 0.7901 (OUTLIER) cc_final: 0.7582 (mm)
REVERT: B 193 LEU cc_start: 0.8478 (OUTLIER) cc_final: 0.8141 (mm)
REVERT: B 332 LEU cc_start: 0.8185 (OUTLIER) cc_final: 0.7922 (mt)
REVERT: C 512 MET cc_start: 0.3246 (mmt) cc_final: 0.2784 (mmt)
REVERT: C 542 MET cc_start: 0.7049 (mmp) cc_final: 0.6785 (mmp)
REVERT: D 14 ASP cc_start: 0.6958 (p0) cc_final: 0.6632 (p0)
REVERT: D 105 MET cc_start: 0.4902 (tpp) cc_final: 0.3610 (mtp)
outliers start: 44
outliers final: 31
residues processed: 117
average time/residue: 0.2572
time to fit residues: 44.3210
Evaluate side-chains
116 residues out of total 1388 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 36
poor density : 80
time to evaluate : 1.546
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 31 THR
Chi-restraints excluded: chain A residue 123 ILE
Chi-restraints excluded: chain A residue 309 ASN
Chi-restraints excluded: chain A residue 317 VAL
Chi-restraints excluded: chain A residue 426 LYS
Chi-restraints excluded: chain A residue 458 THR
Chi-restraints excluded: chain A residue 475 MET
Chi-restraints excluded: chain A residue 505 ARG
Chi-restraints excluded: chain A residue 531 THR
Chi-restraints excluded: chain A residue 563 CYS
Chi-restraints excluded: chain A residue 651 LYS
Chi-restraints excluded: chain A residue 685 LEU
Chi-restraints excluded: chain B residue 88 ASP
Chi-restraints excluded: chain B residue 122 ASP
Chi-restraints excluded: chain B residue 123 ILE
Chi-restraints excluded: chain B residue 156 MET
Chi-restraints excluded: chain B residue 193 LEU
Chi-restraints excluded: chain B residue 213 ILE
Chi-restraints excluded: chain B residue 275 TYR
Chi-restraints excluded: chain B residue 332 LEU
Chi-restraints excluded: chain B residue 368 LEU
Chi-restraints excluded: chain B residue 456 TYR
Chi-restraints excluded: chain B residue 458 THR
Chi-restraints excluded: chain B residue 545 ASP
Chi-restraints excluded: chain B residue 574 VAL
Chi-restraints excluded: chain B residue 634 VAL
Chi-restraints excluded: chain C residue 464 ILE
Chi-restraints excluded: chain C residue 481 THR
Chi-restraints excluded: chain C residue 516 VAL
Chi-restraints excluded: chain C residue 592 VAL
Chi-restraints excluded: chain C residue 613 LEU
Chi-restraints excluded: chain D residue 12 VAL
Chi-restraints excluded: chain D residue 20 HIS
Chi-restraints excluded: chain D residue 22 ASN
Chi-restraints excluded: chain D residue 28 LEU
Chi-restraints excluded: chain D residue 131 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 152
random chunks:
chunk 128 optimal weight: 7.9990
chunk 136 optimal weight: 20.0000
chunk 140 optimal weight: 8.9990
chunk 82 optimal weight: 10.0000
chunk 59 optimal weight: 7.9990
chunk 107 optimal weight: 7.9990
chunk 41 optimal weight: 0.7980
chunk 123 optimal weight: 5.9990
chunk 129 optimal weight: 5.9990
chunk 89 optimal weight: 6.9990
chunk 144 optimal weight: 20.0000
overall best weight: 5.5588
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** A 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 624 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
Total number of N/Q/H flips: 0
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7275
moved from start: 0.3514
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.004 0.071 12813 Z= 0.267
Angle : 0.663 12.158 17239 Z= 0.345
Chirality : 0.043 0.322 1894
Planarity : 0.004 0.084 2194
Dihedral : 8.521 85.230 1741
Min Nonbonded Distance : 1.924
Molprobity Statistics.
All-atom Clashscore : 16.84
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 3.48 %
Favored : 96.52 %
Rotamer:
Outliers : 2.74 %
Allowed : 15.85 %
Favored : 81.41 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 0.11 (0.22), residues: 1524
helix: 0.93 (0.21), residues: 638
sheet: -0.00 (0.37), residues: 201
loop : -0.65 (0.24), residues: 685
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.040 0.002 TRP D 7
HIS 0.007 0.001 HIS A 314
PHE 0.018 0.002 PHE B 113
TYR 0.019 0.002 TYR A 372
ARG 0.008 0.001 ARG D 39
*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
3048 Ramachandran restraints generated.
1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
3048 Ramachandran restraints generated.
1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
124 residues out of total 1388 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 38
poor density : 86
time to evaluate : 1.586
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: A 31 THR cc_start: 0.8087 (OUTLIER) cc_final: 0.7732 (p)
REVERT: A 123 ILE cc_start: 0.7710 (OUTLIER) cc_final: 0.7129 (mm)
REVERT: A 125 MET cc_start: 0.8028 (mmm) cc_final: 0.7157 (mmp)
REVERT: B 193 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.8136 (mm)
REVERT: C 457 ASP cc_start: 0.8978 (t70) cc_final: 0.8617 (t70)
REVERT: C 512 MET cc_start: 0.3421 (mmt) cc_final: 0.3114 (mmt)
REVERT: D 14 ASP cc_start: 0.7505 (p0) cc_final: 0.7147 (p0)
REVERT: D 20 HIS cc_start: 0.6623 (OUTLIER) cc_final: 0.6390 (t-170)
REVERT: D 39 ARG cc_start: 0.8816 (ttp80) cc_final: 0.8269 (tmm-80)
REVERT: D 105 MET cc_start: 0.4953 (tpp) cc_final: 0.4354 (mtp)
outliers start: 38
outliers final: 30
residues processed: 116
average time/residue: 0.2611
time to fit residues: 43.8460
Evaluate side-chains
116 residues out of total 1388 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 34
poor density : 82
time to evaluate : 1.467
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 31 THR
Chi-restraints excluded: chain A residue 123 ILE
Chi-restraints excluded: chain A residue 309 ASN
Chi-restraints excluded: chain A residue 317 VAL
Chi-restraints excluded: chain A residue 426 LYS
Chi-restraints excluded: chain A residue 458 THR
Chi-restraints excluded: chain A residue 475 MET
Chi-restraints excluded: chain A residue 505 ARG
Chi-restraints excluded: chain A residue 531 THR
Chi-restraints excluded: chain A residue 563 CYS
Chi-restraints excluded: chain A residue 651 LYS
Chi-restraints excluded: chain A residue 685 LEU
Chi-restraints excluded: chain B residue 88 ASP
Chi-restraints excluded: chain B residue 122 ASP
Chi-restraints excluded: chain B residue 156 MET
Chi-restraints excluded: chain B residue 193 LEU
Chi-restraints excluded: chain B residue 213 ILE
Chi-restraints excluded: chain B residue 275 TYR
Chi-restraints excluded: chain B residue 368 LEU
Chi-restraints excluded: chain B residue 456 TYR
Chi-restraints excluded: chain B residue 458 THR
Chi-restraints excluded: chain B residue 545 ASP
Chi-restraints excluded: chain B residue 574 VAL
Chi-restraints excluded: chain B residue 634 VAL
Chi-restraints excluded: chain C residue 464 ILE
Chi-restraints excluded: chain C residue 481 THR
Chi-restraints excluded: chain C residue 516 VAL
Chi-restraints excluded: chain C residue 592 VAL
Chi-restraints excluded: chain C residue 613 LEU
Chi-restraints excluded: chain D residue 12 VAL
Chi-restraints excluded: chain D residue 20 HIS
Chi-restraints excluded: chain D residue 22 ASN
Chi-restraints excluded: chain D residue 28 LEU
Chi-restraints excluded: chain D residue 131 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 152
random chunks:
chunk 88 optimal weight: 6.9990
chunk 68 optimal weight: 20.0000
chunk 100 optimal weight: 6.9990
chunk 151 optimal weight: 7.9990
chunk 139 optimal weight: 0.9990
chunk 120 optimal weight: 7.9990
chunk 12 optimal weight: 0.9990
chunk 93 optimal weight: 6.9990
chunk 73 optimal weight: 4.9990
chunk 95 optimal weight: 1.9990
chunk 128 optimal weight: 9.9990
overall best weight: 3.1990
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** A 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 624 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 463 ASN
Total number of N/Q/H flips: 1
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7236
moved from start: 0.3572
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.050 12813 Z= 0.199
Angle : 0.647 12.228 17239 Z= 0.332
Chirality : 0.042 0.312 1894
Planarity : 0.004 0.083 2194
Dihedral : 8.401 85.500 1741
Min Nonbonded Distance : 1.976
Molprobity Statistics.
All-atom Clashscore : 15.21
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 2.76 %
Favored : 97.24 %
Rotamer:
Outliers : 2.38 %
Allowed : 15.92 %
Favored : 81.70 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 0.25 (0.22), residues: 1524
helix: 1.02 (0.21), residues: 638
sheet: 0.14 (0.38), residues: 196
loop : -0.57 (0.24), residues: 690
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.061 0.003 TRP D 7
HIS 0.005 0.001 HIS A 314
PHE 0.018 0.001 PHE B 113
TYR 0.021 0.001 TYR B 428
ARG 0.008 0.000 ARG D 39
********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
3048 Ramachandran restraints generated.
1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
3048 Ramachandran restraints generated.
1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
117 residues out of total 1388 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 33
poor density : 84
time to evaluate : 1.529
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: A 31 THR cc_start: 0.8141 (OUTLIER) cc_final: 0.7806 (p)
REVERT: A 123 ILE cc_start: 0.7714 (OUTLIER) cc_final: 0.7513 (mm)
REVERT: A 125 MET cc_start: 0.8069 (mmm) cc_final: 0.7749 (mmp)
REVERT: A 619 MET cc_start: 0.5739 (tpt) cc_final: 0.5039 (tmm)
REVERT: B 193 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.8184 (mm)
REVERT: C 457 ASP cc_start: 0.8990 (t70) cc_final: 0.8614 (t70)
REVERT: D 14 ASP cc_start: 0.7410 (p0) cc_final: 0.6984 (p0)
REVERT: D 20 HIS cc_start: 0.6532 (OUTLIER) cc_final: 0.6198 (t-170)
REVERT: D 39 ARG cc_start: 0.8785 (ttp80) cc_final: 0.8386 (ttp80)
REVERT: D 105 MET cc_start: 0.5054 (tpp) cc_final: 0.3828 (mtp)
outliers start: 33
outliers final: 27
residues processed: 110
average time/residue: 0.2543
time to fit residues: 40.9638
Evaluate side-chains
113 residues out of total 1388 non-(ALA, GLY, PRO) need fitting.
rotamer outliers: 31
poor density : 82
time to evaluate : 1.485
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 31 THR
Chi-restraints excluded: chain A residue 123 ILE
Chi-restraints excluded: chain A residue 309 ASN
Chi-restraints excluded: chain A residue 317 VAL
Chi-restraints excluded: chain A residue 426 LYS
Chi-restraints excluded: chain A residue 458 THR
Chi-restraints excluded: chain A residue 472 VAL
Chi-restraints excluded: chain A residue 475 MET
Chi-restraints excluded: chain A residue 505 ARG
Chi-restraints excluded: chain A residue 531 THR
Chi-restraints excluded: chain A residue 563 CYS
Chi-restraints excluded: chain A residue 651 LYS
Chi-restraints excluded: chain A residue 685 LEU
Chi-restraints excluded: chain B residue 88 ASP
Chi-restraints excluded: chain B residue 122 ASP
Chi-restraints excluded: chain B residue 156 MET
Chi-restraints excluded: chain B residue 193 LEU
Chi-restraints excluded: chain B residue 213 ILE
Chi-restraints excluded: chain B residue 275 TYR
Chi-restraints excluded: chain B residue 368 LEU
Chi-restraints excluded: chain B residue 456 TYR
Chi-restraints excluded: chain B residue 458 THR
Chi-restraints excluded: chain B residue 545 ASP
Chi-restraints excluded: chain B residue 574 VAL
Chi-restraints excluded: chain B residue 634 VAL
Chi-restraints excluded: chain C residue 481 THR
Chi-restraints excluded: chain C residue 592 VAL
Chi-restraints excluded: chain C residue 613 LEU
Chi-restraints excluded: chain D residue 12 VAL
Chi-restraints excluded: chain D residue 20 HIS
Chi-restraints excluded: chain D residue 131 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 152
random chunks:
chunk 36 optimal weight: 6.9990
chunk 111 optimal weight: 0.7980
chunk 17 optimal weight: 10.0000
chunk 33 optimal weight: 10.0000
chunk 120 optimal weight: 8.9990
chunk 50 optimal weight: 20.0000
chunk 124 optimal weight: 20.0000
chunk 15 optimal weight: 30.0000
chunk 22 optimal weight: 10.0000
chunk 106 optimal weight: 10.0000
chunk 6 optimal weight: 5.9990
overall best weight: 6.5590
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
** A 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 624 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 673 GLN
** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
Total number of N/Q/H flips: 1
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.051776 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.038503 restraints weight = 125572.791|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.039102 restraints weight = 96431.428|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.039382 restraints weight = 81479.272|
|-----------------------------------------------------------------------------|
r_work (final): 0.3308
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8105
moved from start: 0.3854
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.005 0.083 12813 Z= 0.307
Angle : 0.704 12.575 17239 Z= 0.365
Chirality : 0.043 0.307 1894
Planarity : 0.004 0.085 2194
Dihedral : 8.591 84.719 1741
Min Nonbonded Distance : 1.910
Molprobity Statistics.
All-atom Clashscore : 19.02
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 3.74 %
Favored : 96.26 %
Rotamer:
Outliers : 2.45 %
Allowed : 16.07 %
Favored : 81.48 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: -0.06 (0.22), residues: 1524
helix: 0.73 (0.20), residues: 644
sheet: -0.11 (0.38), residues: 201
loop : -0.69 (0.24), residues: 679
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.035 0.002 TRP D 7
HIS 0.007 0.001 HIS A 314
PHE 0.015 0.002 PHE B 113
TYR 0.025 0.002 TYR B 428
ARG 0.008 0.001 ARG D 39
Origin is already at (0, 0, 0), no shifts will be applied
===============================================================================
Job complete
usr+sys time: 2277.97 seconds
wall clock time: 42 minutes 6.03 seconds (2526.03 seconds total)