Starting phenix.real_space_refine
on Tue Jan 21 04:38:49 2025 by dcliebschner
===============================================================================
Processing files:
-------------------------------------------------------------------------------
Found model, /net/cci-nas-00/data/ceres_data/9b3t_44155/01_2025/9b3t_44155.cif
Found real_map, /net/cci-nas-00/data/ceres_data/9b3t_44155/01_2025/9b3t_44155.map
Processing PHIL parameters:
-------------------------------------------------------------------------------
Adding command-line PHIL:
-------------------------
refinement.macro_cycles=10
scattering_table=electron
resolution=3.53
write_initial_geo_file=False
Final processed PHIL parameters:
-------------------------------------------------------------------------------
data_manager {
real_map_files = "/net/cci-nas-00/data/ceres_data/9b3t_44155/01_2025/9b3t_44155.map"
default_real_map = "/net/cci-nas-00/data/ceres_data/9b3t_44155/01_2025/9b3t_44155.map"
model {
file = "/net/cci-nas-00/data/ceres_data/9b3t_44155/01_2025/9b3t_44155.cif"
}
default_model = "/net/cci-nas-00/data/ceres_data/9b3t_44155/01_2025/9b3t_44155.cif"
}
resolution = 3.53
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= -0.000 sd= 0.005
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 100 5.16 5
C 10404 2.51 5
N 2840 2.21 5
O 3045 1.98 5
sf(0) = scattering factor at diffraction angle 0.
Process input model
Symmetric amino acids flipped. Time to flip 8 residue(s): 0.06s
Monomer Library directory:
"/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
Total number of atoms: 16389
Number of models: 1
Model: ""
Number of chains: 8
Chain: "A"
Number of atoms: 2055
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 257, 2055
Classifications: {'peptide': 257}
Link IDs: {'PTRANS': 8, 'TRANS': 248}
Chain breaks: 5
Chain: "B"
Number of atoms: 2052
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 257, 2052
Classifications: {'peptide': 257}
Incomplete info: {'truncation_to_alanine': 1}
Link IDs: {'PTRANS': 8, 'TRANS': 248}
Chain breaks: 4
Unresolved non-hydrogen bonds: 6
Unresolved non-hydrogen angles: 7
Unresolved non-hydrogen dihedrals: 5
Planarities with less than four sites: {'ARG:plan': 1}
Unresolved non-hydrogen planarities: 5
Chain: "C"
Number of atoms: 2066
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 257, 2066
Classifications: {'peptide': 257}
Link IDs: {'PTRANS': 8, 'TRANS': 248}
Chain breaks: 5
Chain: "D"
Number of atoms: 2004
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 251, 2004
Classifications: {'peptide': 251}
Link IDs: {'PTRANS': 8, 'TRANS': 242}
Chain breaks: 6
Chain: "E"
Number of atoms: 2023
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 253, 2023
Classifications: {'peptide': 253}
Link IDs: {'PTRANS': 8, 'TRANS': 244}
Chain breaks: 6
Chain: "F"
Number of atoms: 2084
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 260, 2084
Classifications: {'peptide': 260}
Link IDs: {'PTRANS': 8, 'TRANS': 251}
Chain breaks: 4
Chain: "G"
Number of atoms: 2104
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 263, 2104
Classifications: {'peptide': 263}
Link IDs: {'PTRANS': 8, 'TRANS': 254}
Chain breaks: 5
Chain: "H"
Number of atoms: 2001
Number of conformers: 1
Conformer: ""
Number of residues, atoms: 251, 2001
Classifications: {'peptide': 251}
Link IDs: {'PTRANS': 8, 'TRANS': 242}
Chain breaks: 5
Time building chain proxies: 10.51, per 1000 atoms: 0.64
Number of scatterers: 16389
At special positions: 0
Unit cell: (130.68, 132.84, 88.56, 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 100 16.00
O 3045 8.00
N 2840 7.00
C 10404 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: 4.14
Conformation dependent library (CDL) restraints added in 2.0 seconds
3906 Ramachandran restraints generated.
1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2.
Adding C-beta torsion restraints...
Number of C-beta restraints generated: 3894
Finding SS restraints...
Secondary structure from input PDB file:
106 helices and 0 sheets defined
82.8% alpha, 0.0% 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 377 through 386
removed outlier: 3.682A pdb=" N ILE A 383 " --> pdb=" O PRO A 379 " (cutoff:3.500A)
removed outlier: 3.525A pdb=" N SER A 385 " --> pdb=" O ASP A 381 " (cutoff:3.500A)
Processing helix chain 'A' and resid 391 through 404
removed outlier: 3.730A pdb=" N PHE A 395 " --> pdb=" O VAL A 391 " (cutoff:3.500A)
removed outlier: 4.249A pdb=" N TRP A 402 " --> pdb=" O ALA A 398 " (cutoff:3.500A)
Processing helix chain 'A' and resid 411 through 432
removed outlier: 3.683A pdb=" N ALA A 416 " --> pdb=" O LYS A 412 " (cutoff:3.500A)
removed outlier: 3.729A pdb=" N PHE A 430 " --> pdb=" O LEU A 426 " (cutoff:3.500A)
Processing helix chain 'A' and resid 442 through 447
removed outlier: 3.561A pdb=" N ILE A 446 " --> pdb=" O SER A 442 " (cutoff:3.500A)
Processing helix chain 'A' and resid 448 through 470
removed outlier: 3.616A pdb=" N ILE A 461 " --> pdb=" O THR A 457 " (cutoff:3.500A)
removed outlier: 4.053A pdb=" N PHE A 470 " --> pdb=" O GLN A 466 " (cutoff:3.500A)
Processing helix chain 'A' and resid 476 through 500
removed outlier: 3.751A pdb=" N SER A 482 " --> pdb=" O GLU A 478 " (cutoff:3.500A)
Processing helix chain 'A' and resid 504 through 516
Processing helix chain 'A' and resid 516 through 530
removed outlier: 4.236A pdb=" N PHE A 520 " --> pdb=" O THR A 516 " (cutoff:3.500A)
Processing helix chain 'A' and resid 545 through 562
removed outlier: 3.769A pdb=" N GLN A 556 " --> pdb=" O GLY A 552 " (cutoff:3.500A)
Processing helix chain 'A' and resid 585 through 592
Processing helix chain 'A' and resid 598 through 610
removed outlier: 3.872A pdb=" N LYS A 610 " --> pdb=" O SER A 606 " (cutoff:3.500A)
Processing helix chain 'A' and resid 616 through 630
removed outlier: 3.572A pdb=" N LEU A 623 " --> pdb=" O LYS A 619 " (cutoff:3.500A)
Processing helix chain 'A' and resid 630 through 653
removed outlier: 3.910A pdb=" N TYR A 634 " --> pdb=" O LYS A 630 " (cutoff:3.500A)
removed outlier: 3.578A pdb=" N ILE A 653 " --> pdb=" O GLU A 649 " (cutoff:3.500A)
Processing helix chain 'B' and resid 372 through 385
removed outlier: 3.820A pdb=" N LEU B 376 " --> pdb=" O GLU B 372 " (cutoff:3.500A)
Proline residue: B 379 - end of helix
Processing helix chain 'B' and resid 390 through 404
removed outlier: 3.625A pdb=" N ASP B 401 " --> pdb=" O ASP B 397 " (cutoff:3.500A)
removed outlier: 3.976A pdb=" N TRP B 402 " --> pdb=" O ALA B 398 " (cutoff:3.500A)
Processing helix chain 'B' and resid 406 through 432
removed outlier: 3.585A pdb=" N PHE B 430 " --> pdb=" O LEU B 426 " (cutoff:3.500A)
Processing helix chain 'B' and resid 448 through 470
removed outlier: 3.561A pdb=" N VAL B 453 " --> pdb=" O SER B 449 " (cutoff:3.500A)
removed outlier: 3.646A pdb=" N PHE B 470 " --> pdb=" O GLN B 466 " (cutoff:3.500A)
Processing helix chain 'B' and resid 475 through 500
removed outlier: 4.140A pdb=" N VAL B 479 " --> pdb=" O SER B 475 " (cutoff:3.500A)
removed outlier: 3.549A pdb=" N GLN B 490 " --> pdb=" O LEU B 486 " (cutoff:3.500A)
Processing helix chain 'B' and resid 506 through 530
removed outlier: 4.139A pdb=" N ARG B 510 " --> pdb=" O GLU B 506 " (cutoff:3.500A)
removed outlier: 4.067A pdb=" N GLN B 518 " --> pdb=" O GLN B 514 " (cutoff:3.500A)
removed outlier: 5.504A pdb=" N LEU B 519 " --> pdb=" O LYS B 515 " (cutoff:3.500A)
removed outlier: 3.815A pdb=" N PHE B 520 " --> pdb=" O THR B 516 " (cutoff:3.500A)
Processing helix chain 'B' and resid 545 through 563
removed outlier: 3.693A pdb=" N ASP B 559 " --> pdb=" O PHE B 555 " (cutoff:3.500A)
removed outlier: 3.871A pdb=" N ASP B 560 " --> pdb=" O GLN B 556 " (cutoff:3.500A)
removed outlier: 3.639A pdb=" N TYR B 561 " --> pdb=" O ILE B 557 " (cutoff:3.500A)
Processing helix chain 'B' and resid 587 through 591
removed outlier: 4.271A pdb=" N MET B 591 " --> pdb=" O ALA B 587 " (cutoff:3.500A)
No H-bonds generated for 'chain 'B' and resid 587 through 591'
Processing helix chain 'B' and resid 598 through 606
removed outlier: 3.547A pdb=" N SER B 606 " --> pdb=" O LEU B 602 " (cutoff:3.500A)
Processing helix chain 'B' and resid 616 through 630
removed outlier: 3.534A pdb=" N GLU B 627 " --> pdb=" O LEU B 623 " (cutoff:3.500A)
Processing helix chain 'B' and resid 630 through 657
removed outlier: 3.711A pdb=" N MET B 639 " --> pdb=" O THR B 635 " (cutoff:3.500A)
removed outlier: 3.855A pdb=" N MET B 640 " --> pdb=" O ARG B 636 " (cutoff:3.500A)
removed outlier: 3.794A pdb=" N GLU B 649 " --> pdb=" O GLN B 645 " (cutoff:3.500A)
Processing helix chain 'B' and resid 662 through 669
removed outlier: 3.604A pdb=" N GLU B 669 " --> pdb=" O ARG B 665 " (cutoff:3.500A)
Processing helix chain 'C' and resid 377 through 385
removed outlier: 3.641A pdb=" N ILE C 383 " --> pdb=" O PRO C 379 " (cutoff:3.500A)
Processing helix chain 'C' and resid 390 through 404
removed outlier: 3.844A pdb=" N GLN C 394 " --> pdb=" O GLY C 390 " (cutoff:3.500A)
removed outlier: 3.573A pdb=" N ILE C 396 " --> pdb=" O ARG C 392 " (cutoff:3.500A)
removed outlier: 3.587A pdb=" N ASP C 397 " --> pdb=" O ASP C 393 " (cutoff:3.500A)
removed outlier: 4.765A pdb=" N TRP C 402 " --> pdb=" O ALA C 398 " (cutoff:3.500A)
removed outlier: 3.657A pdb=" N LEU C 403 " --> pdb=" O LEU C 399 " (cutoff:3.500A)
Processing helix chain 'C' and resid 410 through 432
removed outlier: 3.519A pdb=" N PHE C 430 " --> pdb=" O LEU C 426 " (cutoff:3.500A)
Processing helix chain 'C' and resid 442 through 446
Processing helix chain 'C' and resid 448 through 471
removed outlier: 3.596A pdb=" N ILE C 467 " --> pdb=" O ALA C 463 " (cutoff:3.500A)
removed outlier: 3.720A pdb=" N GLU C 469 " --> pdb=" O GLY C 465 " (cutoff:3.500A)
Processing helix chain 'C' and resid 475 through 500
removed outlier: 3.540A pdb=" N SER C 482 " --> pdb=" O GLU C 478 " (cutoff:3.500A)
removed outlier: 3.628A pdb=" N LEU C 486 " --> pdb=" O SER C 482 " (cutoff:3.500A)
removed outlier: 3.704A pdb=" N PHE C 487 " --> pdb=" O ILE C 483 " (cutoff:3.500A)
removed outlier: 3.528A pdb=" N GLN C 488 " --> pdb=" O MET C 484 " (cutoff:3.500A)
removed outlier: 3.539A pdb=" N GLN C 490 " --> pdb=" O LEU C 486 " (cutoff:3.500A)
Processing helix chain 'C' and resid 507 through 516
Processing helix chain 'C' and resid 516 through 530
removed outlier: 4.220A pdb=" N PHE C 520 " --> pdb=" O THR C 516 " (cutoff:3.500A)
removed outlier: 3.623A pdb=" N SER C 521 " --> pdb=" O GLY C 517 " (cutoff:3.500A)
Processing helix chain 'C' and resid 546 through 563
removed outlier: 3.727A pdb=" N ASN C 563 " --> pdb=" O ASP C 559 " (cutoff:3.500A)
Processing helix chain 'C' and resid 585 through 593
Processing helix chain 'C' and resid 597 through 609
removed outlier: 3.509A pdb=" N LEU C 601 " --> pdb=" O SER C 597 " (cutoff:3.500A)
removed outlier: 3.565A pdb=" N ARG C 609 " --> pdb=" O LEU C 605 " (cutoff:3.500A)
Processing helix chain 'C' and resid 618 through 629
removed outlier: 3.894A pdb=" N GLU C 627 " --> pdb=" O LEU C 623 " (cutoff:3.500A)
removed outlier: 3.554A pdb=" N GLU C 628 " --> pdb=" O ASP C 624 " (cutoff:3.500A)
Processing helix chain 'C' and resid 630 through 654
removed outlier: 3.736A pdb=" N ALA C 648 " --> pdb=" O VAL C 644 " (cutoff:3.500A)
removed outlier: 3.573A pdb=" N GLY C 651 " --> pdb=" O ARG C 647 " (cutoff:3.500A)
removed outlier: 3.808A pdb=" N ILE C 653 " --> pdb=" O GLU C 649 " (cutoff:3.500A)
removed outlier: 3.653A pdb=" N GLU C 654 " --> pdb=" O ILE C 650 " (cutoff:3.500A)
Processing helix chain 'C' and resid 663 through 672
removed outlier: 3.941A pdb=" N ARG C 672 " --> pdb=" O LEU C 668 " (cutoff:3.500A)
Processing helix chain 'D' and resid 377 through 385
Processing helix chain 'D' and resid 390 through 401
removed outlier: 3.607A pdb=" N GLN D 394 " --> pdb=" O GLY D 390 " (cutoff:3.500A)
removed outlier: 3.522A pdb=" N ASP D 401 " --> pdb=" O ASP D 397 " (cutoff:3.500A)
Processing helix chain 'D' and resid 410 through 432
removed outlier: 3.655A pdb=" N PHE D 430 " --> pdb=" O LEU D 426 " (cutoff:3.500A)
Processing helix chain 'D' and resid 442 through 447
Processing helix chain 'D' and resid 447 through 470
removed outlier: 4.300A pdb=" N GLN D 451 " --> pdb=" O PHE D 447 " (cutoff:3.500A)
removed outlier: 3.687A pdb=" N PHE D 470 " --> pdb=" O GLN D 466 " (cutoff:3.500A)
Processing helix chain 'D' and resid 475 through 500
removed outlier: 3.750A pdb=" N ILE D 483 " --> pdb=" O VAL D 479 " (cutoff:3.500A)
removed outlier: 3.621A pdb=" N GLN D 490 " --> pdb=" O LEU D 486 " (cutoff:3.500A)
Processing helix chain 'D' and resid 504 through 530
removed outlier: 4.537A pdb=" N GLN D 518 " --> pdb=" O GLN D 514 " (cutoff:3.500A)
removed outlier: 4.762A pdb=" N LEU D 519 " --> pdb=" O LYS D 515 " (cutoff:3.500A)
removed outlier: 4.404A pdb=" N PHE D 520 " --> pdb=" O THR D 516 " (cutoff:3.500A)
removed outlier: 3.586A pdb=" N ALA D 530 " --> pdb=" O LEU D 526 " (cutoff:3.500A)
Processing helix chain 'D' and resid 544 through 562
removed outlier: 3.666A pdb=" N GLN D 556 " --> pdb=" O GLY D 552 " (cutoff:3.500A)
removed outlier: 3.605A pdb=" N ILE D 557 " --> pdb=" O ARG D 553 " (cutoff:3.500A)
Processing helix chain 'D' and resid 587 through 592
Processing helix chain 'D' and resid 598 through 606
removed outlier: 3.802A pdb=" N SER D 606 " --> pdb=" O LEU D 602 " (cutoff:3.500A)
Processing helix chain 'D' and resid 616 through 630
removed outlier: 3.707A pdb=" N VAL D 622 " --> pdb=" O GLN D 618 " (cutoff:3.500A)
removed outlier: 4.012A pdb=" N LEU D 623 " --> pdb=" O LYS D 619 " (cutoff:3.500A)
Processing helix chain 'D' and resid 630 through 654
Processing helix chain 'D' and resid 663 through 669
removed outlier: 3.613A pdb=" N LEU D 667 " --> pdb=" O ALA D 663 " (cutoff:3.500A)
removed outlier: 3.546A pdb=" N GLU D 669 " --> pdb=" O ARG D 665 " (cutoff:3.500A)
Processing helix chain 'E' and resid 377 through 385
removed outlier: 3.589A pdb=" N ILE E 383 " --> pdb=" O PRO E 379 " (cutoff:3.500A)
Processing helix chain 'E' and resid 391 through 403
removed outlier: 3.536A pdb=" N TRP E 402 " --> pdb=" O ALA E 398 " (cutoff:3.500A)
Processing helix chain 'E' and resid 412 through 432
removed outlier: 4.098A pdb=" N ALA E 416 " --> pdb=" O LYS E 412 " (cutoff:3.500A)
removed outlier: 3.545A pdb=" N LEU E 420 " --> pdb=" O ALA E 416 " (cutoff:3.500A)
removed outlier: 3.885A pdb=" N PHE E 430 " --> pdb=" O LEU E 426 " (cutoff:3.500A)
Processing helix chain 'E' and resid 442 through 447
removed outlier: 4.020A pdb=" N ILE E 446 " --> pdb=" O SER E 442 " (cutoff:3.500A)
Processing helix chain 'E' and resid 448 through 471
removed outlier: 3.635A pdb=" N ILE E 460 " --> pdb=" O ALA E 456 " (cutoff:3.500A)
removed outlier: 3.632A pdb=" N ILE E 461 " --> pdb=" O THR E 457 " (cutoff:3.500A)
Processing helix chain 'E' and resid 479 through 500
Processing helix chain 'E' and resid 504 through 516
Processing helix chain 'E' and resid 516 through 531
removed outlier: 4.287A pdb=" N PHE E 520 " --> pdb=" O THR E 516 " (cutoff:3.500A)
Processing helix chain 'E' and resid 545 through 563
removed outlier: 3.536A pdb=" N GLN E 556 " --> pdb=" O GLY E 552 " (cutoff:3.500A)
Processing helix chain 'E' and resid 585 through 592
removed outlier: 3.506A pdb=" N MET E 591 " --> pdb=" O ALA E 587 " (cutoff:3.500A)
removed outlier: 3.503A pdb=" N ILE E 592 " --> pdb=" O LEU E 588 " (cutoff:3.500A)
Processing helix chain 'E' and resid 598 through 610
removed outlier: 3.620A pdb=" N ASN E 603 " --> pdb=" O MET E 599 " (cutoff:3.500A)
Processing helix chain 'E' and resid 616 through 624
removed outlier: 4.780A pdb=" N GLN E 620 " --> pdb=" O LEU E 616 " (cutoff:3.500A)
removed outlier: 3.972A pdb=" N PHE E 621 " --> pdb=" O GLU E 617 " (cutoff:3.500A)
removed outlier: 3.658A pdb=" N LEU E 623 " --> pdb=" O LYS E 619 " (cutoff:3.500A)
removed outlier: 3.716A pdb=" N ASP E 624 " --> pdb=" O GLN E 620 " (cutoff:3.500A)
Processing helix chain 'E' and resid 632 through 652
removed outlier: 3.970A pdb=" N ARG E 636 " --> pdb=" O LEU E 632 " (cutoff:3.500A)
removed outlier: 3.947A pdb=" N GLY E 651 " --> pdb=" O ARG E 647 " (cutoff:3.500A)
removed outlier: 3.862A pdb=" N ARG E 652 " --> pdb=" O ALA E 648 " (cutoff:3.500A)
Processing helix chain 'E' and resid 662 through 672
Processing helix chain 'F' and resid 372 through 385
removed outlier: 3.832A pdb=" N LEU F 376 " --> pdb=" O GLU F 372 " (cutoff:3.500A)
Proline residue: F 379 - end of helix
Processing helix chain 'F' and resid 391 through 403
removed outlier: 3.601A pdb=" N ASP F 401 " --> pdb=" O ASP F 397 " (cutoff:3.500A)
removed outlier: 4.224A pdb=" N TRP F 402 " --> pdb=" O ALA F 398 " (cutoff:3.500A)
Processing helix chain 'F' and resid 406 through 433
removed outlier: 3.917A pdb=" N LYS F 412 " --> pdb=" O VAL F 408 " (cutoff:3.500A)
removed outlier: 3.504A pdb=" N LEU F 420 " --> pdb=" O ALA F 416 " (cutoff:3.500A)
Processing helix chain 'F' and resid 442 through 447
Processing helix chain 'F' and resid 447 through 470
removed outlier: 4.297A pdb=" N GLN F 451 " --> pdb=" O PHE F 447 " (cutoff:3.500A)
removed outlier: 3.501A pdb=" N THR F 452 " --> pdb=" O GLY F 448 " (cutoff:3.500A)
removed outlier: 3.673A pdb=" N VAL F 453 " --> pdb=" O SER F 449 " (cutoff:3.500A)
removed outlier: 3.727A pdb=" N PHE F 470 " --> pdb=" O GLN F 466 " (cutoff:3.500A)
Processing helix chain 'F' and resid 476 through 500
removed outlier: 3.511A pdb=" N LEU F 486 " --> pdb=" O SER F 482 " (cutoff:3.500A)
removed outlier: 3.784A pdb=" N PHE F 487 " --> pdb=" O ILE F 483 " (cutoff:3.500A)
removed outlier: 3.636A pdb=" N GLN F 488 " --> pdb=" O MET F 484 " (cutoff:3.500A)
Processing helix chain 'F' and resid 508 through 516
Processing helix chain 'F' and resid 516 through 530
removed outlier: 4.020A pdb=" N PHE F 520 " --> pdb=" O THR F 516 " (cutoff:3.500A)
Processing helix chain 'F' and resid 544 through 563
removed outlier: 3.630A pdb=" N GLY F 552 " --> pdb=" O THR F 548 " (cutoff:3.500A)
removed outlier: 3.778A pdb=" N ILE F 557 " --> pdb=" O ARG F 553 " (cutoff:3.500A)
Processing helix chain 'F' and resid 585 through 591
removed outlier: 4.246A pdb=" N MET F 591 " --> pdb=" O ALA F 587 " (cutoff:3.500A)
Processing helix chain 'F' and resid 598 through 608
removed outlier: 3.801A pdb=" N GLY F 608 " --> pdb=" O VAL F 604 " (cutoff:3.500A)
Processing helix chain 'F' and resid 616 through 630
removed outlier: 3.696A pdb=" N ILE F 626 " --> pdb=" O VAL F 622 " (cutoff:3.500A)
Processing helix chain 'F' and resid 630 through 657
removed outlier: 3.694A pdb=" N TYR F 634 " --> pdb=" O LYS F 630 " (cutoff:3.500A)
removed outlier: 3.683A pdb=" N LEU F 656 " --> pdb=" O ARG F 652 " (cutoff:3.500A)
Processing helix chain 'F' and resid 661 through 669
removed outlier: 3.913A pdb=" N ARG F 665 " --> pdb=" O ASN F 661 " (cutoff:3.500A)
Processing helix chain 'G' and resid 377 through 385
Processing helix chain 'G' and resid 391 through 404
removed outlier: 3.711A pdb=" N ILE G 396 " --> pdb=" O ARG G 392 " (cutoff:3.500A)
removed outlier: 3.816A pdb=" N ASP G 397 " --> pdb=" O ASP G 393 " (cutoff:3.500A)
removed outlier: 4.235A pdb=" N TRP G 402 " --> pdb=" O ALA G 398 " (cutoff:3.500A)
Processing helix chain 'G' and resid 410 through 433
removed outlier: 3.510A pdb=" N ASP G 415 " --> pdb=" O GLY G 411 " (cutoff:3.500A)
Processing helix chain 'G' and resid 448 through 469
removed outlier: 3.585A pdb=" N GLU G 469 " --> pdb=" O GLY G 465 " (cutoff:3.500A)
Processing helix chain 'G' and resid 475 through 499
removed outlier: 3.836A pdb=" N VAL G 479 " --> pdb=" O SER G 475 " (cutoff:3.500A)
removed outlier: 3.547A pdb=" N PHE G 487 " --> pdb=" O ILE G 483 " (cutoff:3.500A)
removed outlier: 3.734A pdb=" N GLN G 488 " --> pdb=" O MET G 484 " (cutoff:3.500A)
Processing helix chain 'G' and resid 504 through 516
Processing helix chain 'G' and resid 516 through 530
removed outlier: 4.164A pdb=" N PHE G 520 " --> pdb=" O THR G 516 " (cutoff:3.500A)
removed outlier: 3.518A pdb=" N LEU G 527 " --> pdb=" O ALA G 523 " (cutoff:3.500A)
Processing helix chain 'G' and resid 545 through 565
removed outlier: 3.765A pdb=" N VAL G 565 " --> pdb=" O TYR G 561 " (cutoff:3.500A)
Processing helix chain 'G' and resid 585 through 594
removed outlier: 3.711A pdb=" N LYS G 594 " --> pdb=" O HIS G 590 " (cutoff:3.500A)
Processing helix chain 'G' and resid 597 through 609
Processing helix chain 'G' and resid 615 through 629
removed outlier: 3.552A pdb=" N ILE G 626 " --> pdb=" O VAL G 622 " (cutoff:3.500A)
removed outlier: 3.953A pdb=" N GLU G 627 " --> pdb=" O LEU G 623 " (cutoff:3.500A)
removed outlier: 3.583A pdb=" N GLU G 628 " --> pdb=" O ASP G 624 " (cutoff:3.500A)
Processing helix chain 'G' and resid 630 through 654
removed outlier: 4.042A pdb=" N ARG G 636 " --> pdb=" O LEU G 632 " (cutoff:3.500A)
removed outlier: 3.546A pdb=" N ASP G 641 " --> pdb=" O SER G 637 " (cutoff:3.500A)
removed outlier: 3.636A pdb=" N GLY G 651 " --> pdb=" O ARG G 647 " (cutoff:3.500A)
removed outlier: 3.541A pdb=" N GLU G 654 " --> pdb=" O ILE G 650 " (cutoff:3.500A)
Processing helix chain 'G' and resid 661 through 672
removed outlier: 4.400A pdb=" N ARG G 665 " --> pdb=" O ASN G 661 " (cutoff:3.500A)
Processing helix chain 'H' and resid 377 through 386
removed outlier: 3.968A pdb=" N MET H 386 " --> pdb=" O TYR H 382 " (cutoff:3.500A)
Processing helix chain 'H' and resid 391 through 403
removed outlier: 4.270A pdb=" N TRP H 402 " --> pdb=" O ALA H 398 " (cutoff:3.500A)
Processing helix chain 'H' and resid 410 through 432
removed outlier: 3.520A pdb=" N PHE H 430 " --> pdb=" O LEU H 426 " (cutoff:3.500A)
Processing helix chain 'H' and resid 442 through 446
Processing helix chain 'H' and resid 447 through 471
removed outlier: 4.209A pdb=" N GLN H 451 " --> pdb=" O PHE H 447 " (cutoff:3.500A)
removed outlier: 3.626A pdb=" N THR H 452 " --> pdb=" O GLY H 448 " (cutoff:3.500A)
removed outlier: 3.546A pdb=" N ILE H 461 " --> pdb=" O THR H 457 " (cutoff:3.500A)
removed outlier: 3.814A pdb=" N PHE H 470 " --> pdb=" O GLN H 466 " (cutoff:3.500A)
Processing helix chain 'H' and resid 474 through 499
removed outlier: 3.579A pdb=" N GLN H 488 " --> pdb=" O MET H 484 " (cutoff:3.500A)
removed outlier: 3.540A pdb=" N GLN H 490 " --> pdb=" O LEU H 486 " (cutoff:3.500A)
Processing helix chain 'H' and resid 504 through 530
removed outlier: 4.460A pdb=" N GLN H 518 " --> pdb=" O GLN H 514 " (cutoff:3.500A)
removed outlier: 4.445A pdb=" N LEU H 519 " --> pdb=" O LYS H 515 " (cutoff:3.500A)
removed outlier: 4.155A pdb=" N PHE H 520 " --> pdb=" O THR H 516 " (cutoff:3.500A)
Processing helix chain 'H' and resid 544 through 562
removed outlier: 3.523A pdb=" N GLN H 556 " --> pdb=" O GLY H 552 " (cutoff:3.500A)
removed outlier: 3.552A pdb=" N GLN H 562 " --> pdb=" O ARG H 558 " (cutoff:3.500A)
Processing helix chain 'H' and resid 587 through 591
removed outlier: 3.981A pdb=" N MET H 591 " --> pdb=" O ALA H 587 " (cutoff:3.500A)
No H-bonds generated for 'chain 'H' and resid 587 through 591'
Processing helix chain 'H' and resid 598 through 606
removed outlier: 3.549A pdb=" N VAL H 604 " --> pdb=" O ALA H 600 " (cutoff:3.500A)
Processing helix chain 'H' and resid 616 through 628
Processing helix chain 'H' and resid 630 through 657
removed outlier: 3.602A pdb=" N GLY H 651 " --> pdb=" O ARG H 647 " (cutoff:3.500A)
removed outlier: 3.539A pdb=" N LEU H 657 " --> pdb=" O ILE H 653 " (cutoff:3.500A)
Processing helix chain 'H' and resid 667 through 671
removed outlier: 3.626A pdb=" N LEU H 670 " --> pdb=" O LEU H 667 " (cutoff:3.500A)
1108 hydrogen bonds defined for protein.
3309 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: 4.50
Time building geometry restraints manager: 4.80 seconds
NOTE: a complete listing of the restraints can be obtained by requesting
output of .geo file.
Histogram of bond lengths:
1.21 - 1.33: 4565
1.33 - 1.46: 2575
1.46 - 1.58: 9314
1.58 - 1.70: 0
1.70 - 1.82: 189
Bond restraints: 16643
Sorted by residual:
bond pdb=" N ASP D 432 "
pdb=" CA ASP D 432 "
ideal model delta sigma weight residual
1.456 1.492 -0.037 1.26e-02 6.30e+03 8.45e+00
bond pdb=" N VAL B 638 "
pdb=" CA VAL B 638 "
ideal model delta sigma weight residual
1.463 1.496 -0.033 1.14e-02 7.69e+03 8.41e+00
bond pdb=" N ILE B 655 "
pdb=" CA ILE B 655 "
ideal model delta sigma weight residual
1.459 1.494 -0.035 1.23e-02 6.61e+03 8.15e+00
bond pdb=" N ASN B 661 "
pdb=" CA ASN B 661 "
ideal model delta sigma weight residual
1.453 1.490 -0.037 1.30e-02 5.92e+03 8.01e+00
bond pdb=" N VAL F 604 "
pdb=" CA VAL F 604 "
ideal model delta sigma weight residual
1.461 1.494 -0.034 1.19e-02 7.06e+03 7.94e+00
... (remaining 16638 not shown)
Histogram of bond angle deviations from ideal:
0.00 - 1.86: 21903
1.86 - 3.72: 451
3.72 - 5.58: 55
5.58 - 7.43: 17
7.43 - 9.29: 4
Bond angle restraints: 22430
Sorted by residual:
angle pdb=" CA GLY H 473 "
pdb=" C GLY H 473 "
pdb=" O GLY H 473 "
ideal model delta sigma weight residual
122.82 117.77 5.05 1.29e+00 6.01e-01 1.53e+01
angle pdb=" N TYR B 634 "
pdb=" CA TYR B 634 "
pdb=" C TYR B 634 "
ideal model delta sigma weight residual
111.28 107.06 4.22 1.09e+00 8.42e-01 1.50e+01
angle pdb=" N PRO B 662 "
pdb=" CA PRO B 662 "
pdb=" CB PRO B 662 "
ideal model delta sigma weight residual
103.25 99.65 3.60 1.05e+00 9.07e-01 1.17e+01
angle pdb=" N ASP F 393 "
pdb=" CA ASP F 393 "
pdb=" C ASP F 393 "
ideal model delta sigma weight residual
111.07 107.43 3.64 1.07e+00 8.73e-01 1.15e+01
angle pdb=" CA GLU E 474 "
pdb=" CB GLU E 474 "
pdb=" CG GLU E 474 "
ideal model delta sigma weight residual
114.10 120.62 -6.52 2.00e+00 2.50e-01 1.06e+01
... (remaining 22425 not shown)
Histogram of dihedral angle deviations from ideal:
0.00 - 17.96: 8420
17.96 - 35.93: 1273
35.93 - 53.89: 354
53.89 - 71.86: 58
71.86 - 89.82: 29
Dihedral angle restraints: 10134
sinusoidal: 4175
harmonic: 5959
Sorted by residual:
dihedral pdb=" CG ARG E 558 "
pdb=" CD ARG E 558 "
pdb=" NE ARG E 558 "
pdb=" CZ ARG E 558 "
ideal model delta sinusoidal sigma weight residual
90.00 44.54 45.46 2 1.50e+01 4.44e-03 1.08e+01
dihedral pdb=" CB GLU A 377 "
pdb=" CG GLU A 377 "
pdb=" CD GLU A 377 "
pdb=" OE1 GLU A 377 "
ideal model delta sinusoidal sigma weight residual
0.00 -89.82 89.82 1 3.00e+01 1.11e-03 1.06e+01
dihedral pdb=" CA ASP F 407 "
pdb=" CB ASP F 407 "
pdb=" CG ASP F 407 "
pdb=" OD1 ASP F 407 "
ideal model delta sinusoidal sigma weight residual
-30.00 -85.61 55.61 1 2.00e+01 2.50e-03 1.04e+01
... (remaining 10131 not shown)
Histogram of chiral volume deviations from ideal:
0.000 - 0.040: 1971
0.040 - 0.079: 505
0.079 - 0.119: 78
0.119 - 0.158: 14
0.158 - 0.198: 8
Chirality restraints: 2576
Sorted by residual:
chirality pdb=" CA ILE B 655 "
pdb=" N ILE B 655 "
pdb=" C ILE B 655 "
pdb=" CB ILE B 655 "
both_signs ideal model delta sigma weight residual
False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.78e-01
chirality pdb=" CA ILE B 650 "
pdb=" N ILE B 650 "
pdb=" C ILE B 650 "
pdb=" CB ILE B 650 "
both_signs ideal model delta sigma weight residual
False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.57e-01
chirality pdb=" CA LEU B 657 "
pdb=" N LEU B 657 "
pdb=" C LEU B 657 "
pdb=" CB LEU B 657 "
both_signs ideal model delta sigma weight residual
False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.53e-01
... (remaining 2573 not shown)
Planarity restraints: 2851
Sorted by residual:
delta sigma weight rms_deltas residual
plane pdb=" CA ASN A 661 " -0.012 2.00e-02 2.50e+03 2.37e-02 5.61e+00
pdb=" C ASN A 661 " 0.041 2.00e-02 2.50e+03
pdb=" O ASN A 661 " -0.015 2.00e-02 2.50e+03
pdb=" N PRO A 662 " -0.014 2.00e-02 2.50e+03
delta sigma weight rms_deltas residual
plane pdb=" CA GLU H 469 " -0.010 2.00e-02 2.50e+03 1.98e-02 3.92e+00
pdb=" C GLU H 469 " 0.034 2.00e-02 2.50e+03
pdb=" O GLU H 469 " -0.013 2.00e-02 2.50e+03
pdb=" N PHE H 470 " -0.011 2.00e-02 2.50e+03
delta sigma weight rms_deltas residual
plane pdb=" C VAL A 502 " -0.030 5.00e-02 4.00e+02 4.48e-02 3.22e+00
pdb=" N PRO A 503 " 0.078 5.00e-02 4.00e+02
pdb=" CA PRO A 503 " -0.023 5.00e-02 4.00e+02
pdb=" CD PRO A 503 " -0.025 5.00e-02 4.00e+02
... (remaining 2848 not shown)
Histogram of nonbonded interaction distances:
2.21 - 2.75: 2602
2.75 - 3.29: 16539
3.29 - 3.83: 26548
3.83 - 4.36: 30510
4.36 - 4.90: 50687
Nonbonded interactions: 126886
Sorted by model distance:
nonbonded pdb=" O TYR H 634 "
pdb=" OG SER H 637 "
model vdw
2.215 3.040
nonbonded pdb=" OE2 GLU G 654 "
pdb=" NH2 ARG G 665 "
model vdw
2.217 3.120
nonbonded pdb=" O SER E 597 "
pdb=" OG SER E 597 "
model vdw
2.219 3.040
nonbonded pdb=" O TYR D 634 "
pdb=" OG SER D 637 "
model vdw
2.236 3.040
nonbonded pdb=" N GLU F 617 "
pdb=" OE1 GLU F 617 "
model vdw
2.242 3.120
... (remaining 126881 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' and (resid 374 through 406 or resid 411 through 530 or resid 544 thro \
ugh 563 or resid 587 through 591 or resid 597 through 608 or resid 616 through 6 \
52 or resid 658 through 664 or (resid 665 and (name N or name CA or name C or na \
me O or name CB )) or resid 666 through 669))
selection = (chain 'B' and (resid 374 through 406 or resid 411 through 563 or resid 587 thro \
ugh 591 or resid 597 through 608 or resid 616 through 652 or resid 658 through 6 \
69))
selection = (chain 'C' and (resid 374 through 406 or resid 411 through 563 or resid 587 thro \
ugh 591 or resid 597 through 608 or resid 616 through 652 or resid 658 through 6 \
64 or (resid 665 and (name N or name CA or name C or name O or name CB )) or res \
id 666 through 669))
selection = (chain 'D' and (resid 374 through 406 or resid 411 through 530 or resid 544 thro \
ugh 563 or resid 587 through 591 or resid 597 through 608 or resid 616 through 6 \
52 or resid 658 through 664 or (resid 665 and (name N or name CA or name C or na \
me O or name CB )) or resid 666 through 669))
selection = (chain 'E' and (resid 374 through 530 or resid 544 through 563 or resid 587 thro \
ugh 591 or resid 597 through 608 or resid 616 through 664 or (resid 665 and (nam \
e N or name CA or name C or name O or name CB )) or resid 666 through 669))
selection = (chain 'F' and (resid 374 through 406 or resid 411 through 530 or resid 544 thro \
ugh 563 or resid 587 through 591 or resid 597 through 608 or resid 616 through 6 \
52 or resid 658 through 664 or (resid 665 and (name N or name CA or name C or na \
me O or name CB )) or resid 666 through 669))
selection = (chain 'G' and (resid 374 through 406 or resid 411 through 563 or resid 587 thro \
ugh 591 or resid 597 through 608 or resid 616 through 652 or resid 658 through 6 \
64 or (resid 665 and (name N or name CA or name C or name O or name CB )) or res \
id 666 through 669))
selection = (chain 'H' and (resid 374 through 406 or resid 411 through 530 or resid 544 thro \
ugh 563 or resid 587 through 608 or resid 616 through 652 or resid 658 through 6 \
64 or (resid 665 and (name N or name CA or name C or name O or name CB )) or res \
id 666 through 669))
}
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: 2.820
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: 0.660
Check model and map are aligned: 0.120
Set scattering table: 0.150
Process input model: 36.740
Find NCS groups from input model: 0.960
Set up NCS constraints: 0.070
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:2.930
Set ADP refinement strategy: 0.000
Make a string to write initial .geo file:0.000
Internal consistency checks: 0.000
Total: 44.460
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7662
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 0.037 16643 Z= 0.220
Angle : 0.615 9.292 22430 Z= 0.359
Chirality : 0.037 0.198 2576
Planarity : 0.003 0.045 2851
Dihedral : 18.610 89.820 6240
Min Nonbonded Distance : 2.215
Molprobity Statistics.
All-atom Clashscore : 11.95
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 3.33 %
Favored : 96.67 %
Rotamer:
Outliers : 2.81 %
Allowed : 35.63 %
Favored : 61.56 %
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 (0.18), residues: 1953
helix: 0.66 (0.13), residues: 1543
sheet: None (None), residues: 0
loop : -1.30 (0.30), residues: 410
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.012 0.001 TRP B 496
HIS 0.004 0.001 HIS B 444
PHE 0.016 0.001 PHE G 470
TYR 0.008 0.001 TYR F 508
ARG 0.009 0.001 ARG E 558
*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
3906 Ramachandran restraints generated.
1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
3906 Ramachandran restraints generated.
1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
553 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 51
poor density : 502
time to evaluate : 2.093
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: 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: symmetry clash
revert: symmetry clash
REVERT: B 492 MET cc_start: 0.8261 (OUTLIER) cc_final: 0.7997 (tpp)
REVERT: B 507 GLU cc_start: 0.5969 (pt0) cc_final: 0.5589 (pt0)
REVERT: D 643 HIS cc_start: 0.8088 (OUTLIER) cc_final: 0.7769 (m-70)
REVERT: E 447 PHE cc_start: 0.7958 (m-80) cc_final: 0.7729 (m-10)
REVERT: E 589 ILE cc_start: 0.8668 (mm) cc_final: 0.8421 (tt)
REVERT: E 618 GLN cc_start: 0.8240 (OUTLIER) cc_final: 0.7525 (tt0)
REVERT: F 386 MET cc_start: 0.7058 (mmm) cc_final: 0.5730 (mtp)
REVERT: F 639 MET cc_start: 0.7798 (mmm) cc_final: 0.7050 (tpt)
REVERT: G 555 PHE cc_start: 0.7893 (t80) cc_final: 0.7674 (t80)
REVERT: G 599 MET cc_start: 0.7679 (mmm) cc_final: 0.7426 (mmm)
REVERT: H 381 ASP cc_start: 0.7584 (t0) cc_final: 0.7380 (t0)
REVERT: H 599 MET cc_start: 0.8415 (mmm) cc_final: 0.8104 (mmm)
REVERT: H 603 ASN cc_start: 0.8466 (m110) cc_final: 0.8248 (m110)
outliers start: 51
outliers final: 19
residues processed: 538
average time/residue: 0.3629
time to fit residues: 270.9428
Evaluate side-chains
310 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 22
poor density : 288
time to evaluate : 2.007
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 633 ASP
Chi-restraints excluded: chain B residue 492 MET
Chi-restraints excluded: chain B residue 547 LEU
Chi-restraints excluded: chain B residue 642 LEU
Chi-restraints excluded: chain B residue 657 LEU
Chi-restraints excluded: chain B residue 661 ASN
Chi-restraints excluded: chain C residue 592 ILE
Chi-restraints excluded: chain D residue 391 VAL
Chi-restraints excluded: chain D residue 399 LEU
Chi-restraints excluded: chain D residue 443 THR
Chi-restraints excluded: chain D residue 502 VAL
Chi-restraints excluded: chain D residue 624 ASP
Chi-restraints excluded: chain D residue 643 HIS
Chi-restraints excluded: chain E residue 432 ASP
Chi-restraints excluded: chain E residue 618 GLN
Chi-restraints excluded: chain E residue 658 ASP
Chi-restraints excluded: chain F residue 405 VAL
Chi-restraints excluded: chain F residue 443 THR
Chi-restraints excluded: chain F residue 619 LYS
Chi-restraints excluded: chain G residue 650 ILE
Chi-restraints excluded: chain H residue 383 ILE
Chi-restraints excluded: chain H residue 633 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 202
random chunks:
chunk 170 optimal weight: 1.9990
chunk 153 optimal weight: 0.9980
chunk 84 optimal weight: 0.9990
chunk 52 optimal weight: 3.9990
chunk 103 optimal weight: 0.9980
chunk 81 optimal weight: 4.9990
chunk 158 optimal weight: 1.9990
chunk 61 optimal weight: 0.6980
chunk 96 optimal weight: 0.9990
chunk 117 optimal weight: 0.6980
chunk 183 optimal weight: 0.0870
overall best weight: 0.6958
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 445 ASN
** A 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 529 ASN
A 661 ASN
B 545 HIS
B 590 HIS
** C 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 529 ASN
C 598 HIS
D 477 GLN
D 514 GLN
D 529 ASN
** D 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 603 ASN
F 444 HIS
F 556 GLN
** G 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 444 HIS
** H 590 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Total number of N/Q/H flips: 14
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.089824 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.068190 restraints weight = 51912.935|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.071173 restraints weight = 28847.017|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.073144 restraints weight = 20233.448|
|-----------------------------------------------------------------------------|
r_work (final): 0.3376
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8199
moved from start: 0.3670
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.004 0.041 16643 Z= 0.248
Angle : 0.691 9.388 22430 Z= 0.359
Chirality : 0.040 0.152 2576
Planarity : 0.005 0.052 2851
Dihedral : 4.964 53.194 2232
Min Nonbonded Distance : 2.390
Molprobity Statistics.
All-atom Clashscore : 11.65
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 3.12 %
Favored : 96.88 %
Rotamer:
Outliers : 5.12 %
Allowed : 30.01 %
Favored : 64.87 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 1.41 (0.19), residues: 1953
helix: 1.50 (0.13), residues: 1584
sheet: None (None), residues: 0
loop : -1.47 (0.31), residues: 369
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.013 0.001 TRP D 402
HIS 0.009 0.001 HIS H 590
PHE 0.016 0.002 PHE H 470
TYR 0.021 0.002 TYR D 508
ARG 0.010 0.001 ARG D 418
*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
3906 Ramachandran restraints generated.
1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
3906 Ramachandran restraints generated.
1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
414 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 93
poor density : 321
time to evaluate : 1.917
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: A 386 MET cc_start: 0.8015 (tmm) cc_final: 0.7648 (tmm)
REVERT: A 549 ARG cc_start: 0.8557 (tpp-160) cc_final: 0.8270 (tpm170)
REVERT: A 639 MET cc_start: 0.8591 (tpp) cc_final: 0.8352 (tpt)
REVERT: B 386 MET cc_start: 0.8896 (mmp) cc_final: 0.8547 (mmp)
REVERT: B 446 ILE cc_start: 0.9381 (OUTLIER) cc_final: 0.9171 (mt)
REVERT: B 469 GLU cc_start: 0.8897 (OUTLIER) cc_final: 0.8664 (pt0)
REVERT: B 484 MET cc_start: 0.8525 (mtm) cc_final: 0.8245 (mtm)
REVERT: B 488 GLN cc_start: 0.8875 (tm-30) cc_final: 0.8553 (tm-30)
REVERT: B 492 MET cc_start: 0.9001 (OUTLIER) cc_final: 0.8675 (tpp)
REVERT: B 510 ARG cc_start: 0.8496 (tmm160) cc_final: 0.8211 (tmm-80)
REVERT: B 556 GLN cc_start: 0.9272 (OUTLIER) cc_final: 0.8759 (tm-30)
REVERT: B 634 TYR cc_start: 0.8338 (m-10) cc_final: 0.8094 (m-80)
REVERT: B 639 MET cc_start: 0.7709 (mmm) cc_final: 0.6889 (mmm)
REVERT: B 650 ILE cc_start: 0.7841 (mm) cc_final: 0.7538 (mm)
REVERT: B 657 LEU cc_start: 0.7912 (OUTLIER) cc_final: 0.7460 (tt)
REVERT: C 451 GLN cc_start: 0.8676 (OUTLIER) cc_final: 0.8192 (mt0)
REVERT: C 509 TYR cc_start: 0.8421 (m-10) cc_final: 0.8015 (m-10)
REVERT: C 513 ASP cc_start: 0.9030 (m-30) cc_final: 0.8680 (m-30)
REVERT: C 514 GLN cc_start: 0.8259 (mt0) cc_final: 0.8045 (mm-40)
REVERT: D 414 LYS cc_start: 0.9036 (mtpp) cc_final: 0.8570 (mtmm)
REVERT: D 445 ASN cc_start: 0.9411 (OUTLIER) cc_final: 0.8689 (m-40)
REVERT: E 447 PHE cc_start: 0.8646 (m-80) cc_final: 0.8338 (m-10)
REVERT: E 480 MET cc_start: 0.7843 (tpp) cc_final: 0.7598 (mpp)
REVERT: E 584 TRP cc_start: 0.7797 (m100) cc_final: 0.7445 (m100)
REVERT: E 669 GLU cc_start: 0.8810 (mm-30) cc_final: 0.8590 (mm-30)
REVERT: F 484 MET cc_start: 0.8704 (mtm) cc_final: 0.8465 (mtm)
REVERT: F 492 MET cc_start: 0.8544 (mmt) cc_final: 0.8290 (mmt)
REVERT: F 549 ARG cc_start: 0.8915 (ttp80) cc_final: 0.8555 (ttp80)
REVERT: F 556 GLN cc_start: 0.8800 (tp40) cc_final: 0.8446 (tp-100)
REVERT: F 558 ARG cc_start: 0.9190 (OUTLIER) cc_final: 0.8832 (ttt180)
REVERT: G 414 LYS cc_start: 0.8770 (mtmm) cc_final: 0.8340 (mtmm)
REVERT: G 507 GLU cc_start: 0.7441 (mt-10) cc_final: 0.6985 (mt-10)
REVERT: G 549 ARG cc_start: 0.8703 (ttp80) cc_final: 0.8418 (ttp80)
REVERT: G 645 GLN cc_start: 0.8991 (OUTLIER) cc_final: 0.8700 (pp30)
REVERT: H 377 GLU cc_start: 0.7766 (tm-30) cc_final: 0.7338 (tm-30)
REVERT: H 381 ASP cc_start: 0.9117 (t0) cc_final: 0.8876 (t0)
REVERT: H 546 ARG cc_start: 0.8569 (mmp80) cc_final: 0.8346 (mmp80)
outliers start: 93
outliers final: 35
residues processed: 395
average time/residue: 0.3474
time to fit residues: 194.8190
Evaluate side-chains
305 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 44
poor density : 261
time to evaluate : 1.888
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 447 PHE
Chi-restraints excluded: chain A residue 650 ILE
Chi-restraints excluded: chain B residue 391 VAL
Chi-restraints excluded: chain B residue 446 ILE
Chi-restraints excluded: chain B residue 469 GLU
Chi-restraints excluded: chain B residue 492 MET
Chi-restraints excluded: chain B residue 556 GLN
Chi-restraints excluded: chain B residue 559 ASP
Chi-restraints excluded: chain B residue 657 LEU
Chi-restraints excluded: chain B residue 661 ASN
Chi-restraints excluded: chain C residue 383 ILE
Chi-restraints excluded: chain C residue 451 GLN
Chi-restraints excluded: chain C residue 497 THR
Chi-restraints excluded: chain C residue 555 PHE
Chi-restraints excluded: chain C residue 592 ILE
Chi-restraints excluded: chain C residue 597 SER
Chi-restraints excluded: chain C residue 602 LEU
Chi-restraints excluded: chain C residue 635 THR
Chi-restraints excluded: chain D residue 376 LEU
Chi-restraints excluded: chain D residue 443 THR
Chi-restraints excluded: chain D residue 445 ASN
Chi-restraints excluded: chain D residue 482 SER
Chi-restraints excluded: chain D residue 497 THR
Chi-restraints excluded: chain D residue 502 VAL
Chi-restraints excluded: chain D residue 620 GLN
Chi-restraints excluded: chain E residue 446 ILE
Chi-restraints excluded: chain E residue 451 GLN
Chi-restraints excluded: chain E residue 512 ILE
Chi-restraints excluded: chain E residue 522 ILE
Chi-restraints excluded: chain E residue 589 ILE
Chi-restraints excluded: chain F residue 389 LYS
Chi-restraints excluded: chain F residue 408 VAL
Chi-restraints excluded: chain F residue 522 ILE
Chi-restraints excluded: chain F residue 544 LEU
Chi-restraints excluded: chain F residue 558 ARG
Chi-restraints excluded: chain G residue 494 LEU
Chi-restraints excluded: chain G residue 522 ILE
Chi-restraints excluded: chain G residue 592 ILE
Chi-restraints excluded: chain G residue 615 THR
Chi-restraints excluded: chain G residue 645 GLN
Chi-restraints excluded: chain G residue 650 ILE
Chi-restraints excluded: chain G residue 671 LEU
Chi-restraints excluded: chain H residue 446 ILE
Chi-restraints excluded: chain H residue 512 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 202
random chunks:
chunk 185 optimal weight: 0.7980
chunk 25 optimal weight: 0.3980
chunk 82 optimal weight: 1.9990
chunk 1 optimal weight: 4.9990
chunk 167 optimal weight: 0.6980
chunk 11 optimal weight: 0.9990
chunk 4 optimal weight: 0.8980
chunk 35 optimal weight: 1.9990
chunk 55 optimal weight: 0.8980
chunk 117 optimal weight: 1.9990
chunk 109 optimal weight: 3.9990
overall best weight: 0.7380
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 488 GLN
A 529 ASN
A 661 ASN
B 590 HIS
** C 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 556 GLN
D 645 GLN
E 598 HIS
F 444 HIS
G 477 GLN
G 514 GLN
** G 593 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 400 ASN
H 514 GLN
** H 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Total number of N/Q/H flips: 12
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.089703 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.068705 restraints weight = 52219.678|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.071673 restraints weight = 28563.328|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.073612 restraints weight = 19931.399|
|-----------------------------------------------------------------------------|
r_work (final): 0.3433
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8210
moved from start: 0.4340
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.035 16643 Z= 0.222
Angle : 0.631 13.399 22430 Z= 0.322
Chirality : 0.039 0.144 2576
Planarity : 0.004 0.060 2851
Dihedral : 4.287 58.775 2202
Min Nonbonded Distance : 2.382
Molprobity Statistics.
All-atom Clashscore : 11.10
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 3.12 %
Favored : 96.88 %
Rotamer:
Outliers : 4.57 %
Allowed : 29.30 %
Favored : 66.13 %
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 (0.19), residues: 1953
helix: 1.76 (0.13), residues: 1577
sheet: None (None), residues: 0
loop : -1.43 (0.31), residues: 376
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.020 0.001 TRP C 584
HIS 0.011 0.001 HIS F 444
PHE 0.010 0.001 PHE A 470
TYR 0.015 0.001 TYR H 634
ARG 0.008 0.001 ARG G 553
*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
3906 Ramachandran restraints generated.
1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
3906 Ramachandran restraints generated.
1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
357 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 83
poor density : 274
time to evaluate : 1.942
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: A 377 GLU cc_start: 0.8699 (mt-10) cc_final: 0.8429 (mm-30)
REVERT: A 549 ARG cc_start: 0.8514 (tpp-160) cc_final: 0.8167 (tpm170)
REVERT: B 440 LYS cc_start: 0.8992 (mtmm) cc_final: 0.8679 (mtmm)
REVERT: B 446 ILE cc_start: 0.9407 (OUTLIER) cc_final: 0.9200 (mt)
REVERT: B 492 MET cc_start: 0.9049 (OUTLIER) cc_final: 0.8679 (tpp)
REVERT: B 556 GLN cc_start: 0.9257 (OUTLIER) cc_final: 0.8671 (tm-30)
REVERT: B 639 MET cc_start: 0.7960 (mmm) cc_final: 0.7759 (mmm)
REVERT: B 650 ILE cc_start: 0.8094 (mm) cc_final: 0.7815 (mm)
REVERT: C 468 MET cc_start: 0.8343 (mtm) cc_final: 0.7627 (mtm)
REVERT: C 482 SER cc_start: 0.9491 (OUTLIER) cc_final: 0.9184 (t)
REVERT: C 510 ARG cc_start: 0.8430 (tpt170) cc_final: 0.7706 (tpp-160)
REVERT: C 511 MET cc_start: 0.8027 (tmm) cc_final: 0.7773 (tmm)
REVERT: C 514 GLN cc_start: 0.8355 (mt0) cc_final: 0.8099 (mm-40)
REVERT: D 397 ASP cc_start: 0.9280 (t0) cc_final: 0.8387 (p0)
REVERT: D 414 LYS cc_start: 0.9094 (mtpp) cc_final: 0.8566 (mtmm)
REVERT: D 445 ASN cc_start: 0.9410 (OUTLIER) cc_final: 0.8718 (m-40)
REVERT: D 498 TYR cc_start: 0.8957 (t80) cc_final: 0.8640 (t80)
REVERT: D 511 MET cc_start: 0.8361 (tmm) cc_final: 0.8112 (tmm)
REVERT: D 546 ARG cc_start: 0.8556 (ptt90) cc_final: 0.8213 (ptt-90)
REVERT: D 599 MET cc_start: 0.9235 (mmm) cc_final: 0.8691 (mmm)
REVERT: E 447 PHE cc_start: 0.8652 (m-80) cc_final: 0.8308 (m-10)
REVERT: E 561 TYR cc_start: 0.8974 (t80) cc_final: 0.8690 (t80)
REVERT: F 371 PHE cc_start: 0.6972 (p90) cc_final: 0.6424 (p90)
REVERT: F 386 MET cc_start: 0.8569 (mmm) cc_final: 0.8100 (mmm)
REVERT: F 484 MET cc_start: 0.8708 (mtm) cc_final: 0.8451 (mtm)
REVERT: F 492 MET cc_start: 0.8581 (mmt) cc_final: 0.8369 (mmt)
REVERT: F 549 ARG cc_start: 0.8847 (ttp80) cc_final: 0.8552 (ttp80)
REVERT: G 415 ASP cc_start: 0.8926 (t0) cc_final: 0.8632 (p0)
REVERT: G 488 GLN cc_start: 0.8581 (tp40) cc_final: 0.7963 (tm-30)
REVERT: G 492 MET cc_start: 0.9003 (mmm) cc_final: 0.8657 (mmp)
REVERT: G 549 ARG cc_start: 0.8726 (ttp80) cc_final: 0.8481 (ttp80)
REVERT: G 599 MET cc_start: 0.8169 (mmm) cc_final: 0.7903 (mmm)
REVERT: G 642 LEU cc_start: 0.9159 (OUTLIER) cc_final: 0.8944 (tt)
REVERT: G 645 GLN cc_start: 0.9021 (OUTLIER) cc_final: 0.8726 (pp30)
REVERT: H 377 GLU cc_start: 0.7830 (tm-30) cc_final: 0.7576 (tm-30)
REVERT: H 381 ASP cc_start: 0.9069 (t0) cc_final: 0.8832 (t0)
REVERT: H 511 MET cc_start: 0.8480 (tmm) cc_final: 0.7989 (tmm)
REVERT: H 528 LEU cc_start: 0.9332 (OUTLIER) cc_final: 0.9117 (mp)
outliers start: 83
outliers final: 32
residues processed: 338
average time/residue: 0.3207
time to fit residues: 156.0615
Evaluate side-chains
294 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 40
poor density : 254
time to evaluate : 2.104
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 522 ILE
Chi-restraints excluded: chain A residue 591 MET
Chi-restraints excluded: chain B residue 383 ILE
Chi-restraints excluded: chain B residue 420 LEU
Chi-restraints excluded: chain B residue 446 ILE
Chi-restraints excluded: chain B residue 492 MET
Chi-restraints excluded: chain B residue 522 ILE
Chi-restraints excluded: chain B residue 547 LEU
Chi-restraints excluded: chain B residue 556 GLN
Chi-restraints excluded: chain B residue 637 SER
Chi-restraints excluded: chain C residue 383 ILE
Chi-restraints excluded: chain C residue 482 SER
Chi-restraints excluded: chain C residue 548 THR
Chi-restraints excluded: chain C residue 591 MET
Chi-restraints excluded: chain C residue 592 ILE
Chi-restraints excluded: chain C residue 602 LEU
Chi-restraints excluded: chain C residue 631 SER
Chi-restraints excluded: chain C residue 635 THR
Chi-restraints excluded: chain D residue 445 ASN
Chi-restraints excluded: chain D residue 502 VAL
Chi-restraints excluded: chain D residue 620 GLN
Chi-restraints excluded: chain E residue 446 ILE
Chi-restraints excluded: chain E residue 451 GLN
Chi-restraints excluded: chain E residue 512 ILE
Chi-restraints excluded: chain E residue 522 ILE
Chi-restraints excluded: chain E residue 589 ILE
Chi-restraints excluded: chain F residue 392 ARG
Chi-restraints excluded: chain F residue 405 VAL
Chi-restraints excluded: chain F residue 408 VAL
Chi-restraints excluded: chain F residue 443 THR
Chi-restraints excluded: chain F residue 507 GLU
Chi-restraints excluded: chain F residue 544 LEU
Chi-restraints excluded: chain G residue 494 LEU
Chi-restraints excluded: chain G residue 615 THR
Chi-restraints excluded: chain G residue 642 LEU
Chi-restraints excluded: chain G residue 645 GLN
Chi-restraints excluded: chain G residue 650 ILE
Chi-restraints excluded: chain H residue 512 ILE
Chi-restraints excluded: chain H residue 528 LEU
Chi-restraints excluded: chain H residue 590 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 202
random chunks:
chunk 82 optimal weight: 0.8980
chunk 46 optimal weight: 3.9990
chunk 111 optimal weight: 0.5980
chunk 182 optimal weight: 1.9990
chunk 123 optimal weight: 4.9990
chunk 44 optimal weight: 0.4980
chunk 152 optimal weight: 0.0010
chunk 196 optimal weight: 6.9990
chunk 97 optimal weight: 0.8980
chunk 93 optimal weight: 0.9990
chunk 87 optimal weight: 0.0170
overall best weight: 0.4024
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 529 ASN
A 661 ASN
B 590 HIS
** C 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 618 GLN
D 645 GLN
E 598 HIS
F 400 ASN
F 444 HIS
** G 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Total number of N/Q/H flips: 8
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.090395 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.069335 restraints weight = 52236.720|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.072308 restraints weight = 28752.810|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.074241 restraints weight = 20095.484|
|-----------------------------------------------------------------------------|
r_work (final): 0.3398
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8195
moved from start: 0.4729
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.040 16643 Z= 0.188
Angle : 0.609 10.530 22430 Z= 0.306
Chirality : 0.038 0.204 2576
Planarity : 0.003 0.049 2851
Dihedral : 4.021 49.830 2197
Min Nonbonded Distance : 2.359
Molprobity Statistics.
All-atom Clashscore : 10.58
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 3.17 %
Favored : 96.83 %
Rotamer:
Outliers : 4.41 %
Allowed : 28.96 %
Favored : 66.63 %
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: 1.93 (0.19), residues: 1953
helix: 1.86 (0.13), residues: 1586
sheet: None (None), residues: 0
loop : -1.28 (0.33), residues: 367
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.019 0.001 TRP A 584
HIS 0.011 0.001 HIS H 590
PHE 0.014 0.001 PHE E 621
TYR 0.016 0.001 TYR A 458
ARG 0.007 0.000 ARG B 510
*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
3906 Ramachandran restraints generated.
1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
3906 Ramachandran restraints generated.
1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
357 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 80
poor density : 277
time to evaluate : 2.119
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 656 LEU cc_start: 0.8089 (tt) cc_final: 0.7559 (mp)
REVERT: B 440 LYS cc_start: 0.8917 (mtmm) cc_final: 0.8609 (mtmm)
REVERT: B 484 MET cc_start: 0.8474 (mtm) cc_final: 0.8265 (mtm)
REVERT: B 492 MET cc_start: 0.9006 (tpp) cc_final: 0.8552 (mmt)
REVERT: B 549 ARG cc_start: 0.8909 (ttp80) cc_final: 0.8516 (ttp80)
REVERT: B 639 MET cc_start: 0.8034 (mmm) cc_final: 0.7775 (mmm)
REVERT: C 482 SER cc_start: 0.9438 (OUTLIER) cc_final: 0.9127 (t)
REVERT: C 510 ARG cc_start: 0.8350 (tpt170) cc_final: 0.7797 (tpt170)
REVERT: C 511 MET cc_start: 0.8050 (tmm) cc_final: 0.7793 (tmm)
REVERT: C 514 GLN cc_start: 0.8339 (mt0) cc_final: 0.7203 (mt0)
REVERT: D 445 ASN cc_start: 0.9370 (OUTLIER) cc_final: 0.8705 (m-40)
REVERT: D 498 TYR cc_start: 0.8894 (t80) cc_final: 0.8605 (t80)
REVERT: D 508 TYR cc_start: 0.8177 (t80) cc_final: 0.7942 (t80)
REVERT: D 511 MET cc_start: 0.8371 (tmm) cc_final: 0.8060 (tmm)
REVERT: D 546 ARG cc_start: 0.8551 (ptt90) cc_final: 0.8203 (ptt-90)
REVERT: D 599 MET cc_start: 0.9249 (mmm) cc_final: 0.8688 (mmm)
REVERT: D 639 MET cc_start: 0.9246 (tpp) cc_final: 0.8933 (mmt)
REVERT: E 447 PHE cc_start: 0.8556 (m-80) cc_final: 0.8232 (m-10)
REVERT: E 508 TYR cc_start: 0.8381 (t80) cc_final: 0.8060 (t80)
REVERT: E 549 ARG cc_start: 0.8622 (tpp80) cc_final: 0.8187 (tpp80)
REVERT: E 561 TYR cc_start: 0.8876 (t80) cc_final: 0.8660 (t80)
REVERT: E 640 MET cc_start: 0.8716 (mmm) cc_final: 0.8390 (mmt)
REVERT: F 371 PHE cc_start: 0.7053 (p90) cc_final: 0.6805 (p90)
REVERT: F 484 MET cc_start: 0.8669 (mtm) cc_final: 0.8444 (mtm)
REVERT: F 492 MET cc_start: 0.8556 (mmt) cc_final: 0.8330 (mmt)
REVERT: F 549 ARG cc_start: 0.8893 (ttp80) cc_final: 0.8578 (ttp80)
REVERT: F 558 ARG cc_start: 0.9138 (OUTLIER) cc_final: 0.8917 (ttt180)
REVERT: F 640 MET cc_start: 0.7216 (mpp) cc_final: 0.6798 (mpp)
REVERT: G 488 GLN cc_start: 0.8636 (tp40) cc_final: 0.7863 (tm-30)
REVERT: G 492 MET cc_start: 0.8958 (mmm) cc_final: 0.8432 (mmt)
REVERT: G 549 ARG cc_start: 0.8761 (ttp80) cc_final: 0.8509 (ttp80)
REVERT: G 599 MET cc_start: 0.8215 (mmm) cc_final: 0.7255 (mmm)
REVERT: G 642 LEU cc_start: 0.9181 (OUTLIER) cc_final: 0.8948 (tt)
REVERT: G 645 GLN cc_start: 0.9032 (OUTLIER) cc_final: 0.8743 (pp30)
REVERT: H 377 GLU cc_start: 0.7685 (tm-30) cc_final: 0.7353 (tm-30)
REVERT: H 381 ASP cc_start: 0.9018 (t0) cc_final: 0.8780 (t0)
REVERT: H 510 ARG cc_start: 0.7636 (ttp80) cc_final: 0.7427 (ttp80)
REVERT: H 511 MET cc_start: 0.8470 (tmm) cc_final: 0.8067 (tmm)
REVERT: H 591 MET cc_start: 0.7109 (pmm) cc_final: 0.6894 (pmm)
REVERT: H 640 MET cc_start: 0.9443 (mmm) cc_final: 0.9213 (mmm)
REVERT: H 642 LEU cc_start: 0.9529 (OUTLIER) cc_final: 0.9065 (tt)
outliers start: 80
outliers final: 36
residues processed: 341
average time/residue: 0.3303
time to fit residues: 160.9845
Evaluate side-chains
295 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 42
poor density : 253
time to evaluate : 1.887
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 375 VAL
Chi-restraints excluded: chain A residue 598 HIS
Chi-restraints excluded: chain A residue 667 LEU
Chi-restraints excluded: chain B residue 420 LEU
Chi-restraints excluded: chain B residue 522 ILE
Chi-restraints excluded: chain B residue 637 SER
Chi-restraints excluded: chain C residue 383 ILE
Chi-restraints excluded: chain C residue 396 ILE
Chi-restraints excluded: chain C residue 482 SER
Chi-restraints excluded: chain C residue 548 THR
Chi-restraints excluded: chain C residue 602 LEU
Chi-restraints excluded: chain C residue 605 LEU
Chi-restraints excluded: chain C residue 631 SER
Chi-restraints excluded: chain D residue 445 ASN
Chi-restraints excluded: chain D residue 502 VAL
Chi-restraints excluded: chain D residue 618 GLN
Chi-restraints excluded: chain E residue 446 ILE
Chi-restraints excluded: chain E residue 451 GLN
Chi-restraints excluded: chain E residue 512 ILE
Chi-restraints excluded: chain E residue 589 ILE
Chi-restraints excluded: chain E residue 592 ILE
Chi-restraints excluded: chain E residue 598 HIS
Chi-restraints excluded: chain F residue 392 ARG
Chi-restraints excluded: chain F residue 405 VAL
Chi-restraints excluded: chain F residue 408 VAL
Chi-restraints excluded: chain F residue 443 THR
Chi-restraints excluded: chain F residue 507 GLU
Chi-restraints excluded: chain F residue 522 ILE
Chi-restraints excluded: chain F residue 544 LEU
Chi-restraints excluded: chain F residue 558 ARG
Chi-restraints excluded: chain G residue 425 LEU
Chi-restraints excluded: chain G residue 494 LEU
Chi-restraints excluded: chain G residue 548 THR
Chi-restraints excluded: chain G residue 615 THR
Chi-restraints excluded: chain G residue 631 SER
Chi-restraints excluded: chain G residue 642 LEU
Chi-restraints excluded: chain G residue 645 GLN
Chi-restraints excluded: chain G residue 650 ILE
Chi-restraints excluded: chain H residue 504 SER
Chi-restraints excluded: chain H residue 512 ILE
Chi-restraints excluded: chain H residue 590 HIS
Chi-restraints excluded: chain H residue 642 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 202
random chunks:
chunk 31 optimal weight: 0.0870
chunk 179 optimal weight: 2.9990
chunk 92 optimal weight: 2.9990
chunk 183 optimal weight: 0.6980
chunk 193 optimal weight: 2.9990
chunk 43 optimal weight: 6.9990
chunk 129 optimal weight: 0.7980
chunk 94 optimal weight: 0.9980
chunk 56 optimal weight: 8.9990
chunk 26 optimal weight: 0.9980
chunk 91 optimal weight: 0.9980
overall best weight: 0.7158
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 529 ASN
B 590 HIS
** C 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 477 GLN
** D 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 645 GLN
E 598 HIS
F 444 HIS
G 481 ASN
** G 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 603 ASN
** H 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 645 GLN
Total number of N/Q/H flips: 9
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.091004 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.068993 restraints weight = 52209.186|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.072040 restraints weight = 28244.319|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.074003 restraints weight = 19615.375|
|-----------------------------------------------------------------------------|
r_work (final): 0.3370
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8203
moved from start: 0.4940
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.045 16643 Z= 0.206
Angle : 0.611 10.902 22430 Z= 0.306
Chirality : 0.037 0.137 2576
Planarity : 0.003 0.037 2851
Dihedral : 3.709 20.602 2192
Min Nonbonded Distance : 2.436
Molprobity Statistics.
All-atom Clashscore : 10.71
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 2.92 %
Favored : 97.08 %
Rotamer:
Outliers : 4.74 %
Allowed : 28.74 %
Favored : 66.52 %
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: 2.14 (0.19), residues: 1953
helix: 2.01 (0.13), residues: 1575
sheet: None (None), residues: 0
loop : -1.13 (0.33), residues: 378
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.030 0.001 TRP C 584
HIS 0.013 0.001 HIS E 598
PHE 0.011 0.001 PHE E 621
TYR 0.016 0.001 TYR B 634
ARG 0.005 0.000 ARG F 510
*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
3906 Ramachandran restraints generated.
1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
3906 Ramachandran restraints generated.
1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
351 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 86
poor density : 265
time to evaluate : 1.910
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 386 MET cc_start: 0.8113 (tmm) cc_final: 0.7909 (tmm)
REVERT: A 549 ARG cc_start: 0.8499 (tpp-160) cc_final: 0.7984 (tpp80)
REVERT: A 656 LEU cc_start: 0.8183 (tt) cc_final: 0.7800 (mp)
REVERT: B 440 LYS cc_start: 0.8929 (mtmm) cc_final: 0.8536 (mtmm)
REVERT: B 484 MET cc_start: 0.8566 (mtm) cc_final: 0.8133 (mtm)
REVERT: B 492 MET cc_start: 0.9018 (tpp) cc_final: 0.8577 (tpp)
REVERT: B 507 GLU cc_start: 0.7435 (pt0) cc_final: 0.6891 (pt0)
REVERT: B 549 ARG cc_start: 0.8915 (ttp80) cc_final: 0.8534 (ttp80)
REVERT: B 639 MET cc_start: 0.7948 (mmm) cc_final: 0.7700 (mmm)
REVERT: C 468 MET cc_start: 0.8569 (mtm) cc_final: 0.8028 (mtm)
REVERT: C 510 ARG cc_start: 0.8430 (tpt170) cc_final: 0.7720 (tpp-160)
REVERT: C 511 MET cc_start: 0.7962 (tmm) cc_final: 0.7706 (tmm)
REVERT: C 514 GLN cc_start: 0.8325 (mt0) cc_final: 0.7463 (mt0)
REVERT: C 549 ARG cc_start: 0.8329 (mmm160) cc_final: 0.8128 (mmm160)
REVERT: D 414 LYS cc_start: 0.9039 (mtpp) cc_final: 0.8620 (mtmm)
REVERT: D 445 ASN cc_start: 0.9412 (OUTLIER) cc_final: 0.8751 (m110)
REVERT: D 498 TYR cc_start: 0.8922 (t80) cc_final: 0.8592 (t80)
REVERT: D 508 TYR cc_start: 0.8186 (t80) cc_final: 0.7923 (t80)
REVERT: D 511 MET cc_start: 0.8419 (tmm) cc_final: 0.8113 (tmm)
REVERT: D 546 ARG cc_start: 0.8595 (ptt90) cc_final: 0.8244 (ptt-90)
REVERT: D 599 MET cc_start: 0.9312 (mmm) cc_final: 0.8753 (mmm)
REVERT: E 447 PHE cc_start: 0.8629 (m-80) cc_final: 0.8274 (m-10)
REVERT: E 599 MET cc_start: 0.8926 (tpp) cc_final: 0.8335 (mmm)
REVERT: E 669 GLU cc_start: 0.8931 (mm-30) cc_final: 0.8677 (mm-30)
REVERT: F 371 PHE cc_start: 0.7038 (p90) cc_final: 0.6751 (p90)
REVERT: F 402 TRP cc_start: 0.8792 (m-10) cc_final: 0.8572 (m-10)
REVERT: F 484 MET cc_start: 0.8724 (mtm) cc_final: 0.8403 (mtm)
REVERT: F 549 ARG cc_start: 0.8946 (ttp80) cc_final: 0.8604 (ttp80)
REVERT: F 558 ARG cc_start: 0.9136 (OUTLIER) cc_final: 0.8914 (ttt180)
REVERT: G 488 GLN cc_start: 0.8701 (tp40) cc_final: 0.7913 (tm-30)
REVERT: G 492 MET cc_start: 0.8935 (mmm) cc_final: 0.8384 (mmt)
REVERT: G 593 HIS cc_start: 0.8629 (OUTLIER) cc_final: 0.8395 (m90)
REVERT: G 599 MET cc_start: 0.8257 (mmm) cc_final: 0.7311 (mmm)
REVERT: G 642 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8923 (tt)
REVERT: G 645 GLN cc_start: 0.9078 (OUTLIER) cc_final: 0.8799 (pp30)
REVERT: H 377 GLU cc_start: 0.7776 (tm-30) cc_final: 0.7323 (tm-30)
REVERT: H 381 ASP cc_start: 0.9103 (t0) cc_final: 0.8765 (t0)
REVERT: H 508 TYR cc_start: 0.8131 (t80) cc_final: 0.7750 (t80)
REVERT: H 510 ARG cc_start: 0.7669 (ttp80) cc_final: 0.7463 (ttp80)
REVERT: H 511 MET cc_start: 0.8489 (tmm) cc_final: 0.8009 (tmm)
REVERT: H 546 ARG cc_start: 0.8558 (mmp80) cc_final: 0.8226 (mmp80)
REVERT: H 640 MET cc_start: 0.9507 (mmm) cc_final: 0.9263 (mmm)
REVERT: H 642 LEU cc_start: 0.9422 (OUTLIER) cc_final: 0.9210 (tt)
outliers start: 86
outliers final: 49
residues processed: 335
average time/residue: 0.3312
time to fit residues: 158.6027
Evaluate side-chains
305 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 55
poor density : 250
time to evaluate : 2.056
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 375 VAL
Chi-restraints excluded: chain A residue 598 HIS
Chi-restraints excluded: chain A residue 667 LEU
Chi-restraints excluded: chain B residue 375 VAL
Chi-restraints excluded: chain B residue 391 VAL
Chi-restraints excluded: chain B residue 420 LEU
Chi-restraints excluded: chain B residue 522 ILE
Chi-restraints excluded: chain B residue 547 LEU
Chi-restraints excluded: chain B residue 637 SER
Chi-restraints excluded: chain B residue 657 LEU
Chi-restraints excluded: chain C residue 383 ILE
Chi-restraints excluded: chain C residue 396 ILE
Chi-restraints excluded: chain C residue 548 THR
Chi-restraints excluded: chain C residue 602 LEU
Chi-restraints excluded: chain C residue 631 SER
Chi-restraints excluded: chain D residue 397 ASP
Chi-restraints excluded: chain D residue 399 LEU
Chi-restraints excluded: chain D residue 443 THR
Chi-restraints excluded: chain D residue 445 ASN
Chi-restraints excluded: chain D residue 467 ILE
Chi-restraints excluded: chain D residue 502 VAL
Chi-restraints excluded: chain D residue 645 GLN
Chi-restraints excluded: chain E residue 446 ILE
Chi-restraints excluded: chain E residue 451 GLN
Chi-restraints excluded: chain E residue 512 ILE
Chi-restraints excluded: chain E residue 522 ILE
Chi-restraints excluded: chain E residue 589 ILE
Chi-restraints excluded: chain E residue 592 ILE
Chi-restraints excluded: chain E residue 598 HIS
Chi-restraints excluded: chain F residue 389 LYS
Chi-restraints excluded: chain F residue 392 ARG
Chi-restraints excluded: chain F residue 405 VAL
Chi-restraints excluded: chain F residue 408 VAL
Chi-restraints excluded: chain F residue 443 THR
Chi-restraints excluded: chain F residue 494 LEU
Chi-restraints excluded: chain F residue 507 GLU
Chi-restraints excluded: chain F residue 522 ILE
Chi-restraints excluded: chain F residue 544 LEU
Chi-restraints excluded: chain F residue 558 ARG
Chi-restraints excluded: chain G residue 425 LEU
Chi-restraints excluded: chain G residue 494 LEU
Chi-restraints excluded: chain G residue 548 THR
Chi-restraints excluded: chain G residue 563 ASN
Chi-restraints excluded: chain G residue 593 HIS
Chi-restraints excluded: chain G residue 605 LEU
Chi-restraints excluded: chain G residue 615 THR
Chi-restraints excluded: chain G residue 631 SER
Chi-restraints excluded: chain G residue 642 LEU
Chi-restraints excluded: chain G residue 645 GLN
Chi-restraints excluded: chain G residue 650 ILE
Chi-restraints excluded: chain G residue 670 LEU
Chi-restraints excluded: chain H residue 504 SER
Chi-restraints excluded: chain H residue 550 LEU
Chi-restraints excluded: chain H residue 590 HIS
Chi-restraints excluded: chain H residue 642 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 202
random chunks:
chunk 137 optimal weight: 0.8980
chunk 168 optimal weight: 6.9990
chunk 151 optimal weight: 0.6980
chunk 143 optimal weight: 0.1980
chunk 2 optimal weight: 1.9990
chunk 167 optimal weight: 0.9990
chunk 160 optimal weight: 2.9990
chunk 170 optimal weight: 0.0000
chunk 14 optimal weight: 0.9980
chunk 138 optimal weight: 0.2980
chunk 173 optimal weight: 3.9990
overall best weight: 0.4184
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 477 GLN
A 529 ASN
B 590 HIS
** C 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 556 GLN
D 618 GLN
D 645 GLN
E 598 HIS
F 444 HIS
G 481 ASN
** G 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 499 ASN
** H 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 645 GLN
Total number of N/Q/H flips: 11
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.092299 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.069826 restraints weight = 51691.354|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.072908 restraints weight = 28151.366|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.074901 restraints weight = 19664.991|
|-----------------------------------------------------------------------------|
r_work (final): 0.3446
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8180
moved from start: 0.5124
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.040 16643 Z= 0.176
Angle : 0.609 10.366 22430 Z= 0.302
Chirality : 0.037 0.234 2576
Planarity : 0.003 0.037 2851
Dihedral : 3.713 21.114 2192
Min Nonbonded Distance : 2.497
Molprobity Statistics.
All-atom Clashscore : 9.88
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 3.12 %
Favored : 96.88 %
Rotamer:
Outliers : 4.19 %
Allowed : 29.46 %
Favored : 66.35 %
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: 2.20 (0.19), residues: 1953
helix: 2.05 (0.13), residues: 1579
sheet: None (None), residues: 0
loop : -1.13 (0.33), residues: 374
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.024 0.001 TRP C 584
HIS 0.011 0.001 HIS H 590
PHE 0.022 0.001 PHE C 470
TYR 0.019 0.001 TYR H 634
ARG 0.007 0.000 ARG G 549
*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
3906 Ramachandran restraints generated.
1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
3906 Ramachandran restraints generated.
1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
347 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 76
poor density : 271
time to evaluate : 2.031
Fit side-chains
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
revert: symmetry clash
REVERT: A 446 ILE cc_start: 0.9682 (OUTLIER) cc_final: 0.9440 (tt)
REVERT: A 549 ARG cc_start: 0.8456 (tpp-160) cc_final: 0.7962 (tpp80)
REVERT: B 386 MET cc_start: 0.8796 (mmp) cc_final: 0.8354 (mmp)
REVERT: B 484 MET cc_start: 0.8584 (mtm) cc_final: 0.8142 (mtm)
REVERT: B 492 MET cc_start: 0.9003 (tpp) cc_final: 0.8624 (tpp)
REVERT: B 549 ARG cc_start: 0.8874 (ttp80) cc_final: 0.8533 (ttp80)
REVERT: C 511 MET cc_start: 0.7945 (tmm) cc_final: 0.7722 (tmm)
REVERT: D 414 LYS cc_start: 0.9028 (mtpp) cc_final: 0.8590 (mtmm)
REVERT: D 445 ASN cc_start: 0.9421 (OUTLIER) cc_final: 0.8744 (m110)
REVERT: D 498 TYR cc_start: 0.8909 (t80) cc_final: 0.8583 (t80)
REVERT: D 511 MET cc_start: 0.8393 (tmm) cc_final: 0.8149 (tmm)
REVERT: D 515 LYS cc_start: 0.8401 (OUTLIER) cc_final: 0.8111 (ttmt)
REVERT: D 546 ARG cc_start: 0.8585 (ptt90) cc_final: 0.8225 (ptt-90)
REVERT: D 599 MET cc_start: 0.9288 (mmm) cc_final: 0.8681 (mmm)
REVERT: E 447 PHE cc_start: 0.8603 (m-80) cc_final: 0.8204 (m-10)
REVERT: E 508 TYR cc_start: 0.8399 (t80) cc_final: 0.8129 (t80)
REVERT: E 549 ARG cc_start: 0.8542 (tpp80) cc_final: 0.8059 (tpp80)
REVERT: E 599 MET cc_start: 0.8915 (tpp) cc_final: 0.8534 (mmm)
REVERT: E 639 MET cc_start: 0.8473 (tpt) cc_final: 0.8231 (mmt)
REVERT: E 640 MET cc_start: 0.8718 (mmm) cc_final: 0.8384 (mmt)
REVERT: E 669 GLU cc_start: 0.8898 (mm-30) cc_final: 0.8615 (mm-30)
REVERT: F 371 PHE cc_start: 0.7100 (p90) cc_final: 0.6785 (p90)
REVERT: F 386 MET cc_start: 0.8595 (mmm) cc_final: 0.8276 (mmm)
REVERT: F 484 MET cc_start: 0.8684 (mtm) cc_final: 0.8414 (mtm)
REVERT: F 558 ARG cc_start: 0.9116 (OUTLIER) cc_final: 0.8900 (ttt180)
REVERT: G 488 GLN cc_start: 0.8720 (tp40) cc_final: 0.7872 (tm-30)
REVERT: G 492 MET cc_start: 0.8942 (mmm) cc_final: 0.8466 (tpp)
REVERT: G 549 ARG cc_start: 0.8765 (ttp80) cc_final: 0.8481 (ttp80)
REVERT: G 584 TRP cc_start: 0.8113 (m100) cc_final: 0.7819 (m100)
REVERT: G 593 HIS cc_start: 0.8546 (OUTLIER) cc_final: 0.8286 (m90)
REVERT: G 599 MET cc_start: 0.8213 (mmm) cc_final: 0.7270 (mmm)
REVERT: G 642 LEU cc_start: 0.9134 (OUTLIER) cc_final: 0.8907 (tt)
REVERT: G 645 GLN cc_start: 0.9093 (OUTLIER) cc_final: 0.8818 (pp30)
REVERT: H 377 GLU cc_start: 0.7816 (tm-30) cc_final: 0.7307 (tm-30)
REVERT: H 381 ASP cc_start: 0.9119 (t0) cc_final: 0.8763 (t0)
REVERT: H 510 ARG cc_start: 0.7651 (ttp80) cc_final: 0.7431 (ttp80)
REVERT: H 640 MET cc_start: 0.9513 (mmm) cc_final: 0.9275 (mmm)
outliers start: 76
outliers final: 49
residues processed: 333
average time/residue: 0.3273
time to fit residues: 156.5576
Evaluate side-chains
308 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 56
poor density : 252
time to evaluate : 2.050
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 375 VAL
Chi-restraints excluded: chain A residue 446 ILE
Chi-restraints excluded: chain A residue 494 LEU
Chi-restraints excluded: chain A residue 598 HIS
Chi-restraints excluded: chain A residue 667 LEU
Chi-restraints excluded: chain B residue 375 VAL
Chi-restraints excluded: chain B residue 383 ILE
Chi-restraints excluded: chain B residue 391 VAL
Chi-restraints excluded: chain B residue 420 LEU
Chi-restraints excluded: chain B residue 522 ILE
Chi-restraints excluded: chain B residue 637 SER
Chi-restraints excluded: chain B residue 657 LEU
Chi-restraints excluded: chain C residue 383 ILE
Chi-restraints excluded: chain C residue 396 ILE
Chi-restraints excluded: chain C residue 548 THR
Chi-restraints excluded: chain C residue 602 LEU
Chi-restraints excluded: chain C residue 605 LEU
Chi-restraints excluded: chain C residue 631 SER
Chi-restraints excluded: chain D residue 397 ASP
Chi-restraints excluded: chain D residue 443 THR
Chi-restraints excluded: chain D residue 445 ASN
Chi-restraints excluded: chain D residue 502 VAL
Chi-restraints excluded: chain D residue 515 LYS
Chi-restraints excluded: chain D residue 645 GLN
Chi-restraints excluded: chain E residue 375 VAL
Chi-restraints excluded: chain E residue 446 ILE
Chi-restraints excluded: chain E residue 494 LEU
Chi-restraints excluded: chain E residue 512 ILE
Chi-restraints excluded: chain E residue 522 ILE
Chi-restraints excluded: chain E residue 547 LEU
Chi-restraints excluded: chain E residue 589 ILE
Chi-restraints excluded: chain E residue 592 ILE
Chi-restraints excluded: chain F residue 389 LYS
Chi-restraints excluded: chain F residue 392 ARG
Chi-restraints excluded: chain F residue 405 VAL
Chi-restraints excluded: chain F residue 408 VAL
Chi-restraints excluded: chain F residue 443 THR
Chi-restraints excluded: chain F residue 494 LEU
Chi-restraints excluded: chain F residue 507 GLU
Chi-restraints excluded: chain F residue 522 ILE
Chi-restraints excluded: chain F residue 544 LEU
Chi-restraints excluded: chain F residue 558 ARG
Chi-restraints excluded: chain G residue 425 LEU
Chi-restraints excluded: chain G residue 494 LEU
Chi-restraints excluded: chain G residue 548 THR
Chi-restraints excluded: chain G residue 593 HIS
Chi-restraints excluded: chain G residue 605 LEU
Chi-restraints excluded: chain G residue 615 THR
Chi-restraints excluded: chain G residue 631 SER
Chi-restraints excluded: chain G residue 642 LEU
Chi-restraints excluded: chain G residue 645 GLN
Chi-restraints excluded: chain G residue 650 ILE
Chi-restraints excluded: chain G residue 670 LEU
Chi-restraints excluded: chain H residue 469 GLU
Chi-restraints excluded: chain H residue 504 SER
Chi-restraints excluded: chain H residue 590 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 202
random chunks:
chunk 0 optimal weight: 2.9990
chunk 2 optimal weight: 0.9980
chunk 170 optimal weight: 0.8980
chunk 159 optimal weight: 0.6980
chunk 40 optimal weight: 0.6980
chunk 73 optimal weight: 0.0030
chunk 199 optimal weight: 0.9980
chunk 19 optimal weight: 3.9990
chunk 148 optimal weight: 0.7980
chunk 150 optimal weight: 2.9990
chunk 124 optimal weight: 3.9990
overall best weight: 0.6190
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 529 ASN
** C 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 643 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 618 GLN
D 645 GLN
F 444 HIS
G 481 ASN
** G 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Total number of N/Q/H flips: 5
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.093227 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.072041 restraints weight = 50115.644|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.074948 restraints weight = 27038.515|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.076865 restraints weight = 18675.119|
|-----------------------------------------------------------------------------|
r_work (final): 0.3465
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8214
moved from start: 0.5237
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.060 16643 Z= 0.198
Angle : 0.618 9.446 22430 Z= 0.307
Chirality : 0.038 0.257 2576
Planarity : 0.003 0.037 2851
Dihedral : 3.672 21.298 2192
Min Nonbonded Distance : 2.470
Molprobity Statistics.
All-atom Clashscore : 10.40
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 3.07 %
Favored : 96.93 %
Rotamer:
Outliers : 4.19 %
Allowed : 28.69 %
Favored : 67.13 %
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: 2.30 (0.20), residues: 1953
helix: 2.10 (0.13), residues: 1579
sheet: None (None), residues: 0
loop : -1.01 (0.33), residues: 374
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.023 0.001 TRP C 584
HIS 0.010 0.001 HIS H 590
PHE 0.011 0.001 PHE F 555
TYR 0.021 0.001 TYR H 634
ARG 0.006 0.000 ARG F 510
*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
3906 Ramachandran restraints generated.
1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
3906 Ramachandran restraints generated.
1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
336 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 76
poor density : 260
time to evaluate : 2.388
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 402 TRP cc_start: 0.6842 (p90) cc_final: 0.6450 (p90)
REVERT: A 446 ILE cc_start: 0.9691 (OUTLIER) cc_final: 0.9432 (tt)
REVERT: A 549 ARG cc_start: 0.8336 (tpp-160) cc_final: 0.7810 (tpp80)
REVERT: B 386 MET cc_start: 0.8796 (mmp) cc_final: 0.8411 (mmp)
REVERT: B 440 LYS cc_start: 0.9036 (mptt) cc_final: 0.8741 (mptt)
REVERT: B 480 MET cc_start: 0.9038 (tpp) cc_final: 0.8806 (tpp)
REVERT: B 484 MET cc_start: 0.8385 (mtm) cc_final: 0.8010 (mtm)
REVERT: B 492 MET cc_start: 0.9008 (tpp) cc_final: 0.8570 (tpp)
REVERT: B 507 GLU cc_start: 0.7529 (pt0) cc_final: 0.7064 (pt0)
REVERT: C 511 MET cc_start: 0.8097 (tmm) cc_final: 0.7878 (tmm)
REVERT: C 514 GLN cc_start: 0.8309 (mt0) cc_final: 0.8064 (mp10)
REVERT: C 549 ARG cc_start: 0.8172 (mmm160) cc_final: 0.7971 (mmm160)
REVERT: D 414 LYS cc_start: 0.9059 (mtpp) cc_final: 0.8589 (mtmm)
REVERT: D 445 ASN cc_start: 0.9359 (OUTLIER) cc_final: 0.8682 (m110)
REVERT: D 498 TYR cc_start: 0.8870 (t80) cc_final: 0.8558 (t80)
REVERT: D 511 MET cc_start: 0.8482 (tmm) cc_final: 0.8226 (tmm)
REVERT: D 515 LYS cc_start: 0.8524 (OUTLIER) cc_final: 0.8253 (ttmt)
REVERT: D 546 ARG cc_start: 0.8406 (ptt90) cc_final: 0.8090 (ptt-90)
REVERT: D 599 MET cc_start: 0.9227 (mmm) cc_final: 0.8619 (mmm)
REVERT: D 640 MET cc_start: 0.9393 (mmm) cc_final: 0.9133 (mmm)
REVERT: E 447 PHE cc_start: 0.8632 (m-80) cc_final: 0.8246 (m-10)
REVERT: E 508 TYR cc_start: 0.8495 (t80) cc_final: 0.8215 (t80)
REVERT: E 599 MET cc_start: 0.8815 (tpp) cc_final: 0.8359 (mmm)
REVERT: E 639 MET cc_start: 0.8553 (tpt) cc_final: 0.8280 (mmt)
REVERT: E 640 MET cc_start: 0.8688 (mmm) cc_final: 0.8301 (mmt)
REVERT: E 669 GLU cc_start: 0.8760 (mm-30) cc_final: 0.8513 (mm-30)
REVERT: F 371 PHE cc_start: 0.7228 (p90) cc_final: 0.6947 (p90)
REVERT: F 484 MET cc_start: 0.8513 (mtm) cc_final: 0.8210 (mtm)
REVERT: F 558 ARG cc_start: 0.9129 (OUTLIER) cc_final: 0.8884 (ttt180)
REVERT: G 380 TYR cc_start: 0.8991 (t80) cc_final: 0.8781 (t80)
REVERT: G 488 GLN cc_start: 0.8703 (tp40) cc_final: 0.7674 (tm-30)
REVERT: G 492 MET cc_start: 0.8919 (mmm) cc_final: 0.8388 (tpp)
REVERT: G 549 ARG cc_start: 0.8700 (ttp80) cc_final: 0.8441 (ttp80)
REVERT: G 593 HIS cc_start: 0.8359 (OUTLIER) cc_final: 0.8112 (m90)
REVERT: G 599 MET cc_start: 0.8319 (mmm) cc_final: 0.7395 (mmm)
REVERT: G 642 LEU cc_start: 0.9220 (OUTLIER) cc_final: 0.9003 (tt)
REVERT: G 645 GLN cc_start: 0.9020 (OUTLIER) cc_final: 0.8746 (pp30)
REVERT: H 377 GLU cc_start: 0.7681 (tm-30) cc_final: 0.7227 (tm-30)
REVERT: H 381 ASP cc_start: 0.8963 (t0) cc_final: 0.8586 (t0)
REVERT: H 511 MET cc_start: 0.8498 (tmm) cc_final: 0.8161 (tmm)
outliers start: 76
outliers final: 50
residues processed: 324
average time/residue: 0.3317
time to fit residues: 155.4016
Evaluate side-chains
306 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 57
poor density : 249
time to evaluate : 2.010
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 375 VAL
Chi-restraints excluded: chain A residue 446 ILE
Chi-restraints excluded: chain A residue 494 LEU
Chi-restraints excluded: chain A residue 522 ILE
Chi-restraints excluded: chain A residue 528 LEU
Chi-restraints excluded: chain A residue 598 HIS
Chi-restraints excluded: chain A residue 667 LEU
Chi-restraints excluded: chain B residue 375 VAL
Chi-restraints excluded: chain B residue 391 VAL
Chi-restraints excluded: chain B residue 420 LEU
Chi-restraints excluded: chain B residue 446 ILE
Chi-restraints excluded: chain B residue 522 ILE
Chi-restraints excluded: chain B residue 637 SER
Chi-restraints excluded: chain B residue 657 LEU
Chi-restraints excluded: chain C residue 383 ILE
Chi-restraints excluded: chain C residue 592 ILE
Chi-restraints excluded: chain C residue 602 LEU
Chi-restraints excluded: chain C residue 605 LEU
Chi-restraints excluded: chain C residue 631 SER
Chi-restraints excluded: chain D residue 397 ASP
Chi-restraints excluded: chain D residue 443 THR
Chi-restraints excluded: chain D residue 445 ASN
Chi-restraints excluded: chain D residue 502 VAL
Chi-restraints excluded: chain D residue 515 LYS
Chi-restraints excluded: chain D residue 645 GLN
Chi-restraints excluded: chain E residue 375 VAL
Chi-restraints excluded: chain E residue 446 ILE
Chi-restraints excluded: chain E residue 512 ILE
Chi-restraints excluded: chain E residue 522 ILE
Chi-restraints excluded: chain E residue 547 LEU
Chi-restraints excluded: chain E residue 589 ILE
Chi-restraints excluded: chain E residue 592 ILE
Chi-restraints excluded: chain F residue 389 LYS
Chi-restraints excluded: chain F residue 392 ARG
Chi-restraints excluded: chain F residue 405 VAL
Chi-restraints excluded: chain F residue 408 VAL
Chi-restraints excluded: chain F residue 443 THR
Chi-restraints excluded: chain F residue 494 LEU
Chi-restraints excluded: chain F residue 522 ILE
Chi-restraints excluded: chain F residue 544 LEU
Chi-restraints excluded: chain F residue 558 ARG
Chi-restraints excluded: chain F residue 602 LEU
Chi-restraints excluded: chain G residue 425 LEU
Chi-restraints excluded: chain G residue 494 LEU
Chi-restraints excluded: chain G residue 548 THR
Chi-restraints excluded: chain G residue 591 MET
Chi-restraints excluded: chain G residue 593 HIS
Chi-restraints excluded: chain G residue 605 LEU
Chi-restraints excluded: chain G residue 615 THR
Chi-restraints excluded: chain G residue 631 SER
Chi-restraints excluded: chain G residue 642 LEU
Chi-restraints excluded: chain G residue 645 GLN
Chi-restraints excluded: chain G residue 650 ILE
Chi-restraints excluded: chain G residue 670 LEU
Chi-restraints excluded: chain H residue 469 GLU
Chi-restraints excluded: chain H residue 504 SER
Chi-restraints excluded: chain H residue 590 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 202
random chunks:
chunk 92 optimal weight: 4.9990
chunk 168 optimal weight: 0.0070
chunk 48 optimal weight: 0.8980
chunk 34 optimal weight: 0.7980
chunk 5 optimal weight: 0.7980
chunk 115 optimal weight: 0.9990
chunk 139 optimal weight: 1.9990
chunk 6 optimal weight: 0.8980
chunk 105 optimal weight: 0.0370
chunk 33 optimal weight: 0.5980
chunk 123 optimal weight: 4.9990
overall best weight: 0.4476
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 529 ASN
** C 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 643 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 618 GLN
D 645 GLN
F 444 HIS
G 645 GLN
** H 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Total number of N/Q/H flips: 5
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.089940 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.066384 restraints weight = 55230.954|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.069393 restraints weight = 30232.824|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.071302 restraints weight = 21167.576|
|-----------------------------------------------------------------------------|
r_work (final): 0.3362
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8128
moved from start: 0.5395
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.046 16643 Z= 0.185
Angle : 0.639 13.033 22430 Z= 0.313
Chirality : 0.037 0.270 2576
Planarity : 0.003 0.049 2851
Dihedral : 3.682 21.998 2192
Min Nonbonded Distance : 2.472
Molprobity Statistics.
All-atom Clashscore : 10.34
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 3.23 %
Favored : 96.77 %
Rotamer:
Outliers : 4.07 %
Allowed : 29.41 %
Favored : 66.52 %
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: 2.28 (0.20), residues: 1953
helix: 2.09 (0.13), residues: 1580
sheet: None (None), residues: 0
loop : -1.04 (0.33), residues: 373
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.033 0.001 TRP G 584
HIS 0.009 0.001 HIS E 598
PHE 0.057 0.001 PHE D 470
TYR 0.026 0.001 TYR H 634
ARG 0.008 0.000 ARG E 510
*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
3906 Ramachandran restraints generated.
1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
3906 Ramachandran restraints generated.
1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
329 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 74
poor density : 255
time to evaluate : 2.051
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 402 TRP cc_start: 0.6762 (p90) cc_final: 0.6431 (p90)
REVERT: A 446 ILE cc_start: 0.9658 (OUTLIER) cc_final: 0.9426 (tt)
REVERT: A 480 MET cc_start: 0.9011 (tpp) cc_final: 0.8627 (mmm)
REVERT: A 510 ARG cc_start: 0.7986 (ttp-110) cc_final: 0.7558 (ttp-170)
REVERT: A 524 THR cc_start: 0.9199 (OUTLIER) cc_final: 0.8992 (p)
REVERT: A 549 ARG cc_start: 0.8363 (tpp-160) cc_final: 0.7756 (tpp80)
REVERT: B 386 MET cc_start: 0.8813 (mmp) cc_final: 0.8557 (mmp)
REVERT: B 440 LYS cc_start: 0.9069 (mptt) cc_final: 0.8725 (mptt)
REVERT: B 484 MET cc_start: 0.8719 (mtm) cc_final: 0.8202 (mtm)
REVERT: B 492 MET cc_start: 0.8946 (tpp) cc_final: 0.8556 (tpp)
REVERT: B 549 ARG cc_start: 0.8808 (ttp80) cc_final: 0.8530 (ttp80)
REVERT: C 482 SER cc_start: 0.9277 (OUTLIER) cc_final: 0.9033 (t)
REVERT: C 514 GLN cc_start: 0.8270 (mt0) cc_final: 0.7828 (mp10)
REVERT: C 549 ARG cc_start: 0.8466 (mmm160) cc_final: 0.8222 (mmm160)
REVERT: D 445 ASN cc_start: 0.9449 (OUTLIER) cc_final: 0.8710 (m110)
REVERT: D 498 TYR cc_start: 0.8895 (t80) cc_final: 0.8557 (t80)
REVERT: D 511 MET cc_start: 0.8350 (tmm) cc_final: 0.8071 (tmm)
REVERT: D 515 LYS cc_start: 0.8189 (OUTLIER) cc_final: 0.7888 (ttmt)
REVERT: D 546 ARG cc_start: 0.8706 (ptt90) cc_final: 0.8291 (ptt-90)
REVERT: D 640 MET cc_start: 0.9550 (mmm) cc_final: 0.9323 (mmm)
REVERT: D 664 MET cc_start: 0.8947 (mmm) cc_final: 0.8717 (mmt)
REVERT: E 447 PHE cc_start: 0.8585 (m-80) cc_final: 0.8179 (m-10)
REVERT: E 508 TYR cc_start: 0.8283 (t80) cc_final: 0.8035 (t80)
REVERT: E 599 MET cc_start: 0.8933 (tpp) cc_final: 0.8599 (mmm)
REVERT: E 639 MET cc_start: 0.8326 (tpt) cc_final: 0.8035 (mmt)
REVERT: E 640 MET cc_start: 0.8842 (mmm) cc_final: 0.8469 (mmt)
REVERT: E 669 GLU cc_start: 0.8981 (mm-30) cc_final: 0.8674 (mm-30)
REVERT: F 371 PHE cc_start: 0.6949 (p90) cc_final: 0.6541 (p90)
REVERT: F 443 THR cc_start: 0.8653 (OUTLIER) cc_final: 0.8424 (m)
REVERT: F 484 MET cc_start: 0.8818 (mtm) cc_final: 0.8482 (mtm)
REVERT: F 639 MET cc_start: 0.6484 (mmm) cc_final: 0.6273 (tpt)
REVERT: F 640 MET cc_start: 0.7233 (mpp) cc_final: 0.6966 (mpp)
REVERT: F 664 MET cc_start: 0.9309 (mmt) cc_final: 0.8721 (mmm)
REVERT: G 380 TYR cc_start: 0.8878 (t80) cc_final: 0.8647 (t80)
REVERT: G 386 MET cc_start: 0.8889 (OUTLIER) cc_final: 0.8624 (ttt)
REVERT: G 488 GLN cc_start: 0.8839 (tp40) cc_final: 0.7846 (tm-30)
REVERT: G 492 MET cc_start: 0.8972 (mmm) cc_final: 0.8401 (tpp)
REVERT: G 593 HIS cc_start: 0.8541 (OUTLIER) cc_final: 0.8332 (m90)
REVERT: G 599 MET cc_start: 0.8238 (mmm) cc_final: 0.7330 (mmm)
REVERT: G 645 GLN cc_start: 0.9060 (OUTLIER) cc_final: 0.8820 (pp30)
REVERT: H 377 GLU cc_start: 0.7821 (tm-30) cc_final: 0.7346 (tm-30)
REVERT: H 381 ASP cc_start: 0.9186 (t0) cc_final: 0.8791 (t0)
REVERT: H 511 MET cc_start: 0.8238 (tmm) cc_final: 0.7886 (tmm)
REVERT: H 640 MET cc_start: 0.9610 (mmp) cc_final: 0.9394 (mmm)
outliers start: 74
outliers final: 51
residues processed: 313
average time/residue: 0.3176
time to fit residues: 143.1984
Evaluate side-chains
303 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 60
poor density : 243
time to evaluate : 1.883
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 375 VAL
Chi-restraints excluded: chain A residue 446 ILE
Chi-restraints excluded: chain A residue 494 LEU
Chi-restraints excluded: chain A residue 522 ILE
Chi-restraints excluded: chain A residue 524 THR
Chi-restraints excluded: chain A residue 667 LEU
Chi-restraints excluded: chain B residue 375 VAL
Chi-restraints excluded: chain B residue 383 ILE
Chi-restraints excluded: chain B residue 391 VAL
Chi-restraints excluded: chain B residue 420 LEU
Chi-restraints excluded: chain B residue 446 ILE
Chi-restraints excluded: chain B residue 522 ILE
Chi-restraints excluded: chain B residue 544 LEU
Chi-restraints excluded: chain B residue 637 SER
Chi-restraints excluded: chain B residue 657 LEU
Chi-restraints excluded: chain C residue 383 ILE
Chi-restraints excluded: chain C residue 482 SER
Chi-restraints excluded: chain C residue 548 THR
Chi-restraints excluded: chain C residue 602 LEU
Chi-restraints excluded: chain C residue 605 LEU
Chi-restraints excluded: chain C residue 631 SER
Chi-restraints excluded: chain D residue 397 ASP
Chi-restraints excluded: chain D residue 443 THR
Chi-restraints excluded: chain D residue 445 ASN
Chi-restraints excluded: chain D residue 502 VAL
Chi-restraints excluded: chain D residue 515 LYS
Chi-restraints excluded: chain D residue 646 LEU
Chi-restraints excluded: chain E residue 375 VAL
Chi-restraints excluded: chain E residue 446 ILE
Chi-restraints excluded: chain E residue 494 LEU
Chi-restraints excluded: chain E residue 512 ILE
Chi-restraints excluded: chain E residue 522 ILE
Chi-restraints excluded: chain E residue 547 LEU
Chi-restraints excluded: chain E residue 589 ILE
Chi-restraints excluded: chain E residue 592 ILE
Chi-restraints excluded: chain F residue 389 LYS
Chi-restraints excluded: chain F residue 392 ARG
Chi-restraints excluded: chain F residue 396 ILE
Chi-restraints excluded: chain F residue 405 VAL
Chi-restraints excluded: chain F residue 408 VAL
Chi-restraints excluded: chain F residue 443 THR
Chi-restraints excluded: chain F residue 494 LEU
Chi-restraints excluded: chain F residue 522 ILE
Chi-restraints excluded: chain F residue 544 LEU
Chi-restraints excluded: chain G residue 386 MET
Chi-restraints excluded: chain G residue 425 LEU
Chi-restraints excluded: chain G residue 494 LEU
Chi-restraints excluded: chain G residue 548 THR
Chi-restraints excluded: chain G residue 591 MET
Chi-restraints excluded: chain G residue 593 HIS
Chi-restraints excluded: chain G residue 605 LEU
Chi-restraints excluded: chain G residue 615 THR
Chi-restraints excluded: chain G residue 631 SER
Chi-restraints excluded: chain G residue 645 GLN
Chi-restraints excluded: chain G residue 650 ILE
Chi-restraints excluded: chain G residue 670 LEU
Chi-restraints excluded: chain H residue 469 GLU
Chi-restraints excluded: chain H residue 504 SER
Chi-restraints excluded: chain H residue 512 ILE
Chi-restraints excluded: chain H residue 590 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 202
random chunks:
chunk 43 optimal weight: 4.9990
chunk 49 optimal weight: 0.0570
chunk 7 optimal weight: 0.9990
chunk 29 optimal weight: 0.8980
chunk 91 optimal weight: 0.8980
chunk 1 optimal weight: 4.9990
chunk 152 optimal weight: 0.7980
chunk 3 optimal weight: 2.9990
chunk 99 optimal weight: 0.0050
chunk 162 optimal weight: 0.6980
chunk 36 optimal weight: 1.9990
overall best weight: 0.4912
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 529 ASN
** C 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 643 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F 444 HIS
G 466 GLN
G 481 ASN
G 645 GLN
** H 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Total number of N/Q/H flips: 5
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.090233 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.066045 restraints weight = 55478.295|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.069072 restraints weight = 30836.156|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.070997 restraints weight = 21778.859|
|-----------------------------------------------------------------------------|
r_work (final): 0.3355
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8132
moved from start: 0.5505
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.038 16643 Z= 0.190
Angle : 0.647 12.764 22430 Z= 0.317
Chirality : 0.038 0.288 2576
Planarity : 0.003 0.042 2851
Dihedral : 3.704 28.966 2192
Min Nonbonded Distance : 2.430
Molprobity Statistics.
All-atom Clashscore : 10.31
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 3.38 %
Favored : 96.62 %
Rotamer:
Outliers : 3.52 %
Allowed : 30.01 %
Favored : 66.46 %
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: 2.30 (0.20), residues: 1953
helix: 2.09 (0.13), residues: 1579
sheet: None (None), residues: 0
loop : -0.97 (0.33), residues: 374
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.046 0.002 TRP G 584
HIS 0.010 0.001 HIS E 598
PHE 0.043 0.001 PHE D 470
TYR 0.030 0.001 TYR A 634
ARG 0.012 0.000 ARG G 549
*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
3906 Ramachandran restraints generated.
1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
3906 Ramachandran restraints generated.
1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
318 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 64
poor density : 254
time to evaluate : 2.162
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 402 TRP cc_start: 0.6755 (p90) cc_final: 0.6416 (p90)
REVERT: A 446 ILE cc_start: 0.9658 (OUTLIER) cc_final: 0.9423 (tt)
REVERT: A 480 MET cc_start: 0.8974 (tpp) cc_final: 0.8661 (mmm)
REVERT: A 510 ARG cc_start: 0.8003 (ttp-110) cc_final: 0.7572 (ttp-170)
REVERT: A 549 ARG cc_start: 0.8387 (tpp-160) cc_final: 0.7777 (tpp80)
REVERT: A 555 PHE cc_start: 0.8708 (t80) cc_final: 0.8489 (m-80)
REVERT: B 386 MET cc_start: 0.8821 (mmp) cc_final: 0.8555 (mmp)
REVERT: B 440 LYS cc_start: 0.9065 (mptt) cc_final: 0.8705 (mptt)
REVERT: B 484 MET cc_start: 0.8746 (mtm) cc_final: 0.8221 (mtm)
REVERT: B 492 MET cc_start: 0.8955 (tpp) cc_final: 0.8470 (tpp)
REVERT: B 507 GLU cc_start: 0.7849 (pt0) cc_final: 0.7328 (pt0)
REVERT: B 549 ARG cc_start: 0.8802 (ttp80) cc_final: 0.8540 (ttp80)
REVERT: C 482 SER cc_start: 0.9265 (OUTLIER) cc_final: 0.9031 (t)
REVERT: C 514 GLN cc_start: 0.8242 (mt0) cc_final: 0.7851 (mp10)
REVERT: C 549 ARG cc_start: 0.8481 (mmm160) cc_final: 0.8216 (mmm160)
REVERT: D 445 ASN cc_start: 0.9445 (OUTLIER) cc_final: 0.8689 (m110)
REVERT: D 498 TYR cc_start: 0.8893 (t80) cc_final: 0.8552 (t80)
REVERT: D 511 MET cc_start: 0.8364 (tmm) cc_final: 0.8106 (tmm)
REVERT: D 515 LYS cc_start: 0.8150 (OUTLIER) cc_final: 0.7850 (ttmt)
REVERT: D 546 ARG cc_start: 0.8718 (ptt90) cc_final: 0.8301 (ptt-90)
REVERT: D 640 MET cc_start: 0.9571 (mmm) cc_final: 0.9321 (mmm)
REVERT: E 447 PHE cc_start: 0.8595 (m-80) cc_final: 0.8333 (m-10)
REVERT: E 508 TYR cc_start: 0.8337 (t80) cc_final: 0.8047 (t80)
REVERT: E 549 ARG cc_start: 0.8509 (tpp80) cc_final: 0.8063 (tpp80)
REVERT: E 599 MET cc_start: 0.8919 (tpp) cc_final: 0.8532 (mmm)
REVERT: E 640 MET cc_start: 0.8864 (mmm) cc_final: 0.8472 (mmt)
REVERT: E 669 GLU cc_start: 0.9011 (mm-30) cc_final: 0.8686 (mm-30)
REVERT: F 371 PHE cc_start: 0.7162 (p90) cc_final: 0.6766 (p90)
REVERT: F 443 THR cc_start: 0.8645 (OUTLIER) cc_final: 0.8358 (m)
REVERT: F 484 MET cc_start: 0.8809 (mtm) cc_final: 0.8457 (mtm)
REVERT: F 639 MET cc_start: 0.6549 (mmm) cc_final: 0.6300 (tpt)
REVERT: F 640 MET cc_start: 0.7272 (mpp) cc_final: 0.7023 (mpp)
REVERT: F 664 MET cc_start: 0.9317 (mmt) cc_final: 0.8708 (mmm)
REVERT: G 380 TYR cc_start: 0.8871 (t80) cc_final: 0.8642 (t80)
REVERT: G 386 MET cc_start: 0.8887 (OUTLIER) cc_final: 0.8606 (ttt)
REVERT: G 468 MET cc_start: 0.8566 (tmm) cc_final: 0.8129 (tmm)
REVERT: G 488 GLN cc_start: 0.8855 (tp40) cc_final: 0.7861 (tm-30)
REVERT: G 492 MET cc_start: 0.8964 (mmm) cc_final: 0.8401 (tpp)
REVERT: G 549 ARG cc_start: 0.8861 (ttp80) cc_final: 0.8606 (ttp80)
REVERT: G 645 GLN cc_start: 0.9187 (OUTLIER) cc_final: 0.8743 (pp30)
REVERT: H 377 GLU cc_start: 0.7839 (tm-30) cc_final: 0.7352 (tm-30)
REVERT: H 381 ASP cc_start: 0.9199 (t0) cc_final: 0.8800 (t0)
REVERT: H 511 MET cc_start: 0.8235 (tmm) cc_final: 0.8010 (tmm)
REVERT: H 640 MET cc_start: 0.9625 (mmp) cc_final: 0.9386 (mmm)
outliers start: 64
outliers final: 48
residues processed: 308
average time/residue: 0.3191
time to fit residues: 142.7032
Evaluate side-chains
300 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 55
poor density : 245
time to evaluate : 1.978
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 375 VAL
Chi-restraints excluded: chain A residue 446 ILE
Chi-restraints excluded: chain A residue 494 LEU
Chi-restraints excluded: chain A residue 522 ILE
Chi-restraints excluded: chain B residue 375 VAL
Chi-restraints excluded: chain B residue 383 ILE
Chi-restraints excluded: chain B residue 391 VAL
Chi-restraints excluded: chain B residue 420 LEU
Chi-restraints excluded: chain B residue 446 ILE
Chi-restraints excluded: chain B residue 544 LEU
Chi-restraints excluded: chain B residue 637 SER
Chi-restraints excluded: chain B residue 657 LEU
Chi-restraints excluded: chain C residue 383 ILE
Chi-restraints excluded: chain C residue 482 SER
Chi-restraints excluded: chain C residue 592 ILE
Chi-restraints excluded: chain C residue 602 LEU
Chi-restraints excluded: chain C residue 605 LEU
Chi-restraints excluded: chain C residue 631 SER
Chi-restraints excluded: chain D residue 397 ASP
Chi-restraints excluded: chain D residue 443 THR
Chi-restraints excluded: chain D residue 445 ASN
Chi-restraints excluded: chain D residue 502 VAL
Chi-restraints excluded: chain D residue 515 LYS
Chi-restraints excluded: chain E residue 375 VAL
Chi-restraints excluded: chain E residue 446 ILE
Chi-restraints excluded: chain E residue 494 LEU
Chi-restraints excluded: chain E residue 512 ILE
Chi-restraints excluded: chain E residue 522 ILE
Chi-restraints excluded: chain E residue 547 LEU
Chi-restraints excluded: chain E residue 592 ILE
Chi-restraints excluded: chain F residue 389 LYS
Chi-restraints excluded: chain F residue 391 VAL
Chi-restraints excluded: chain F residue 392 ARG
Chi-restraints excluded: chain F residue 396 ILE
Chi-restraints excluded: chain F residue 405 VAL
Chi-restraints excluded: chain F residue 408 VAL
Chi-restraints excluded: chain F residue 443 THR
Chi-restraints excluded: chain F residue 494 LEU
Chi-restraints excluded: chain F residue 507 GLU
Chi-restraints excluded: chain F residue 522 ILE
Chi-restraints excluded: chain F residue 544 LEU
Chi-restraints excluded: chain G residue 386 MET
Chi-restraints excluded: chain G residue 425 LEU
Chi-restraints excluded: chain G residue 494 LEU
Chi-restraints excluded: chain G residue 548 THR
Chi-restraints excluded: chain G residue 605 LEU
Chi-restraints excluded: chain G residue 615 THR
Chi-restraints excluded: chain G residue 631 SER
Chi-restraints excluded: chain G residue 645 GLN
Chi-restraints excluded: chain G residue 650 ILE
Chi-restraints excluded: chain G residue 670 LEU
Chi-restraints excluded: chain H residue 469 GLU
Chi-restraints excluded: chain H residue 494 LEU
Chi-restraints excluded: chain H residue 504 SER
Chi-restraints excluded: chain H residue 590 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 202
random chunks:
chunk 142 optimal weight: 2.9990
chunk 58 optimal weight: 0.6980
chunk 68 optimal weight: 0.2980
chunk 55 optimal weight: 0.0870
chunk 20 optimal weight: 0.0870
chunk 80 optimal weight: 0.9980
chunk 195 optimal weight: 2.9990
chunk 135 optimal weight: 5.9990
chunk 36 optimal weight: 1.9990
chunk 2 optimal weight: 2.9990
chunk 94 optimal weight: 4.9990
overall best weight: 0.4336
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 529 ASN
** C 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 643 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F 444 HIS
G 645 GLN
Total number of N/Q/H flips: 3
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.090643 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.066514 restraints weight = 55432.453|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.069568 restraints weight = 30825.570|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.071500 restraints weight = 21739.998|
|-----------------------------------------------------------------------------|
r_work (final): 0.3395
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8193
moved from start: 0.5594
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.050 16643 Z= 0.193
Angle : 0.676 14.038 22430 Z= 0.328
Chirality : 0.038 0.315 2576
Planarity : 0.003 0.042 2851
Dihedral : 3.743 33.943 2192
Min Nonbonded Distance : 2.491
Molprobity Statistics.
All-atom Clashscore : 10.19
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 3.07 %
Favored : 96.93 %
Rotamer:
Outliers : 3.19 %
Allowed : 30.62 %
Favored : 66.19 %
Cbeta Deviations : 0.00 %
Peptide Plane:
Cis-proline : 0.00 %
Cis-general : 0.00 %
Twisted Proline : 0.00 %
Twisted General : 0.00 %
Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
whole: 2.27 (0.20), residues: 1953
helix: 2.06 (0.13), residues: 1580
sheet: None (None), residues: 0
loop : -0.94 (0.33), residues: 373
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.042 0.002 TRP F 402
HIS 0.013 0.001 HIS D 590
PHE 0.044 0.001 PHE D 470
TYR 0.043 0.001 TYR A 634
ARG 0.010 0.000 ARG G 549
********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************
-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************
3906 Ramachandran restraints generated.
1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
favored: oldfield
allowed: oldfield
outlier: oldfield
3906 Ramachandran restraints generated.
1953 Oldfield, 0 Emsley, 1953 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
314 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 58
poor density : 256
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: symmetry clash
REVERT: A 402 TRP cc_start: 0.6872 (p90) cc_final: 0.6461 (p90)
REVERT: A 446 ILE cc_start: 0.9678 (OUTLIER) cc_final: 0.9423 (tt)
REVERT: A 510 ARG cc_start: 0.7988 (ttp-110) cc_final: 0.7594 (ttp-170)
REVERT: A 549 ARG cc_start: 0.8331 (tpp-160) cc_final: 0.7739 (tpp80)
REVERT: A 555 PHE cc_start: 0.8582 (t80) cc_final: 0.8378 (m-80)
REVERT: A 645 GLN cc_start: 0.8928 (mt0) cc_final: 0.8568 (mt0)
REVERT: B 386 MET cc_start: 0.8814 (mmp) cc_final: 0.8511 (mmp)
REVERT: B 440 LYS cc_start: 0.9081 (mptt) cc_final: 0.8678 (mptt)
REVERT: B 492 MET cc_start: 0.8959 (tpp) cc_final: 0.8521 (tpp)
REVERT: B 549 ARG cc_start: 0.8783 (ttp80) cc_final: 0.8503 (ttp80)
REVERT: C 482 SER cc_start: 0.9313 (OUTLIER) cc_final: 0.9090 (t)
REVERT: C 514 GLN cc_start: 0.8232 (mt0) cc_final: 0.7899 (mp10)
REVERT: C 549 ARG cc_start: 0.8421 (mmm160) cc_final: 0.8155 (mmm160)
REVERT: D 414 LYS cc_start: 0.9130 (mtmm) cc_final: 0.8812 (mtmm)
REVERT: D 445 ASN cc_start: 0.9405 (OUTLIER) cc_final: 0.8668 (m110)
REVERT: D 498 TYR cc_start: 0.8874 (t80) cc_final: 0.8540 (t80)
REVERT: D 511 MET cc_start: 0.8487 (tmm) cc_final: 0.8227 (tmm)
REVERT: D 515 LYS cc_start: 0.8299 (OUTLIER) cc_final: 0.8020 (ttmt)
REVERT: D 546 ARG cc_start: 0.8607 (ptt90) cc_final: 0.8235 (ptt-90)
REVERT: D 640 MET cc_start: 0.9536 (mmm) cc_final: 0.9303 (mmm)
REVERT: E 447 PHE cc_start: 0.8580 (m-80) cc_final: 0.8349 (m-10)
REVERT: E 508 TYR cc_start: 0.8459 (t80) cc_final: 0.8173 (t80)
REVERT: E 549 ARG cc_start: 0.8462 (tpp80) cc_final: 0.8004 (tpp80)
REVERT: E 599 MET cc_start: 0.8873 (tpp) cc_final: 0.8526 (mmm)
REVERT: E 639 MET cc_start: 0.8495 (tpt) cc_final: 0.8029 (mmt)
REVERT: E 640 MET cc_start: 0.8841 (mmm) cc_final: 0.8422 (mmt)
REVERT: F 371 PHE cc_start: 0.7284 (p90) cc_final: 0.6914 (p90)
REVERT: F 443 THR cc_start: 0.8795 (OUTLIER) cc_final: 0.8518 (m)
REVERT: F 484 MET cc_start: 0.8689 (mtm) cc_final: 0.8406 (mtm)
REVERT: F 639 MET cc_start: 0.6687 (mmm) cc_final: 0.6484 (tpt)
REVERT: F 640 MET cc_start: 0.7308 (mpp) cc_final: 0.7038 (mpp)
REVERT: F 664 MET cc_start: 0.9298 (mmt) cc_final: 0.8675 (mmm)
REVERT: G 380 TYR cc_start: 0.8955 (t80) cc_final: 0.8748 (t80)
REVERT: G 386 MET cc_start: 0.8758 (OUTLIER) cc_final: 0.8525 (ttt)
REVERT: G 468 MET cc_start: 0.8479 (tmm) cc_final: 0.8074 (tmm)
REVERT: G 488 GLN cc_start: 0.8824 (tp40) cc_final: 0.7829 (tm-30)
REVERT: G 492 MET cc_start: 0.8916 (mmm) cc_final: 0.8386 (tpp)
REVERT: G 549 ARG cc_start: 0.8811 (ttp80) cc_final: 0.8572 (ttp80)
REVERT: G 645 GLN cc_start: 0.9161 (OUTLIER) cc_final: 0.8672 (pp30)
REVERT: H 377 GLU cc_start: 0.7720 (tm-30) cc_final: 0.7240 (tm-30)
REVERT: H 381 ASP cc_start: 0.9069 (t0) cc_final: 0.8665 (t0)
REVERT: H 498 TYR cc_start: 0.8990 (t80) cc_final: 0.8752 (t80)
REVERT: H 511 MET cc_start: 0.8333 (tmm) cc_final: 0.8103 (tmm)
REVERT: H 546 ARG cc_start: 0.8623 (mmp80) cc_final: 0.8275 (mmp80)
REVERT: H 640 MET cc_start: 0.9593 (mmp) cc_final: 0.9345 (mmm)
outliers start: 58
outliers final: 46
residues processed: 307
average time/residue: 0.3137
time to fit residues: 139.7423
Evaluate side-chains
305 residues out of total 1817 (non-[ALA,GLY,PRO]) need to be fit.
rotamer outliers: 53
poor density : 252
time to evaluate : 1.991
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 375 VAL
Chi-restraints excluded: chain A residue 446 ILE
Chi-restraints excluded: chain A residue 494 LEU
Chi-restraints excluded: chain A residue 667 LEU
Chi-restraints excluded: chain B residue 375 VAL
Chi-restraints excluded: chain B residue 383 ILE
Chi-restraints excluded: chain B residue 391 VAL
Chi-restraints excluded: chain B residue 446 ILE
Chi-restraints excluded: chain B residue 637 SER
Chi-restraints excluded: chain B residue 657 LEU
Chi-restraints excluded: chain C residue 383 ILE
Chi-restraints excluded: chain C residue 482 SER
Chi-restraints excluded: chain C residue 592 ILE
Chi-restraints excluded: chain C residue 602 LEU
Chi-restraints excluded: chain C residue 605 LEU
Chi-restraints excluded: chain C residue 631 SER
Chi-restraints excluded: chain D residue 397 ASP
Chi-restraints excluded: chain D residue 443 THR
Chi-restraints excluded: chain D residue 445 ASN
Chi-restraints excluded: chain D residue 502 VAL
Chi-restraints excluded: chain D residue 515 LYS
Chi-restraints excluded: chain E residue 375 VAL
Chi-restraints excluded: chain E residue 446 ILE
Chi-restraints excluded: chain E residue 494 LEU
Chi-restraints excluded: chain E residue 512 ILE
Chi-restraints excluded: chain E residue 522 ILE
Chi-restraints excluded: chain E residue 547 LEU
Chi-restraints excluded: chain E residue 592 ILE
Chi-restraints excluded: chain F residue 389 LYS
Chi-restraints excluded: chain F residue 391 VAL
Chi-restraints excluded: chain F residue 392 ARG
Chi-restraints excluded: chain F residue 396 ILE
Chi-restraints excluded: chain F residue 405 VAL
Chi-restraints excluded: chain F residue 408 VAL
Chi-restraints excluded: chain F residue 443 THR
Chi-restraints excluded: chain F residue 494 LEU
Chi-restraints excluded: chain F residue 507 GLU
Chi-restraints excluded: chain F residue 522 ILE
Chi-restraints excluded: chain F residue 544 LEU
Chi-restraints excluded: chain G residue 386 MET
Chi-restraints excluded: chain G residue 425 LEU
Chi-restraints excluded: chain G residue 494 LEU
Chi-restraints excluded: chain G residue 548 THR
Chi-restraints excluded: chain G residue 605 LEU
Chi-restraints excluded: chain G residue 615 THR
Chi-restraints excluded: chain G residue 631 SER
Chi-restraints excluded: chain G residue 645 GLN
Chi-restraints excluded: chain G residue 650 ILE
Chi-restraints excluded: chain G residue 670 LEU
Chi-restraints excluded: chain H residue 469 GLU
Chi-restraints excluded: chain H residue 494 LEU
Chi-restraints excluded: chain H residue 504 SER
Chi-restraints excluded: chain H residue 590 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
number of chunks: 202
random chunks:
chunk 128 optimal weight: 3.9990
chunk 95 optimal weight: 0.4980
chunk 127 optimal weight: 0.8980
chunk 79 optimal weight: 0.7980
chunk 84 optimal weight: 0.8980
chunk 174 optimal weight: 0.9980
chunk 177 optimal weight: 1.9990
chunk 52 optimal weight: 0.8980
chunk 50 optimal weight: 0.9990
chunk 67 optimal weight: 9.9990
chunk 106 optimal weight: 0.4980
overall best weight: 0.7180
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
Flipped N/Q/H residues before XYZ refinement:
A 529 ASN
** C 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 514 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 643 HIS
** D 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 563 ASN
F 444 HIS
G 477 GLN
G 645 GLN
** H 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Total number of N/Q/H flips: 6
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.092190 restraints weight = None |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.067497 restraints weight = 56303.205|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.070376 restraints weight = 31123.405|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.072258 restraints weight = 21882.440|
|-----------------------------------------------------------------------------|
r_work (final): 0.3352
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8142
moved from start: 0.5664
Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
Bond : 0.003 0.045 16643 Z= 0.216
Angle : 0.688 13.299 22430 Z= 0.337
Chirality : 0.038 0.274 2576
Planarity : 0.003 0.044 2851
Dihedral : 3.758 40.214 2192
Min Nonbonded Distance : 2.285
Molprobity Statistics.
All-atom Clashscore : 10.34
Ramachandran Plot:
Outliers : 0.00 %
Allowed : 3.12 %
Favored : 96.88 %
Rotamer:
Outliers : 3.52 %
Allowed : 30.45 %
Favored : 66.02 %
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: 2.26 (0.20), residues: 1953
helix: 2.04 (0.13), residues: 1577
sheet: None (None), residues: 0
loop : -0.84 (0.33), residues: 376
Max deviation from planes:
Type MaxDev MeanDev LineInFile
TRP 0.042 0.002 TRP F 402
HIS 0.011 0.001 HIS E 598
PHE 0.040 0.001 PHE D 470
TYR 0.059 0.002 TYR A 634
ARG 0.010 0.000 ARG G 549
Origin is already at (0, 0, 0), no shifts will be applied
===============================================================================
Job complete
usr+sys time: 5465.46 seconds
wall clock time: 98 minutes 53.76 seconds (5933.76 seconds total)