Starting phenix.real_space_refine
on Sat Aug 23 13:50:26 2025 by dcliebschner
===============================================================================

Processing files:
-------------------------------------------------------------------------------

  Found model, /net/cci-nas-00/data/ceres_data/7yuh_34107/08_2025/7yuh_34107.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7yuh_34107/08_2025/7yuh_34107.map

Processing PHIL parameters:
-------------------------------------------------------------------------------

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7yuh_34107/08_2025/7yuh_34107.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7yuh_34107/08_2025/7yuh_34107.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7yuh_34107/08_2025/7yuh_34107.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7yuh_34107/08_2025/7yuh_34107.map"
  }
  resolution = 3.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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=   0.056
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      45      5.16       5
     C    7860      2.51       5
     N    2178      2.21       5
     O    2349      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 58 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 12432
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 4144
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 532, 4144
          Classifications: {'peptide': 532}
          Link IDs: {'PTRANS': 32, 'TRANS': 499}
    Chain: "B"
      Number of atoms: 4144
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 532, 4144
          Classifications: {'peptide': 532}
          Link IDs: {'PTRANS': 32, 'TRANS': 499}
    Chain: "C"
      Number of atoms: 4144
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 532, 4144
          Classifications: {'peptide': 532}
          Link IDs: {'PTRANS': 32, 'TRANS': 499}
  Time building chain proxies: 3.10, per 1000 atoms: 0.25
  Number of scatterers: 12432
  At special positions: 0
  Unit cell: (97.58, 109.88, 138.58, 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      45     16.00
     O    2349      8.00
     N    2178      7.00
     C    7860      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: 1.01
  Conformation dependent library (CDL) restraints added in 621.8 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  3180 Ramachandran restraints generated.
    1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2928

  Finding SS restraints...
    Secondary structure from input PDB file:
      71 helices and 14 sheets defined
      46.7% alpha, 10.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.51
  Creating SS restraints...
    Processing helix  chain 'A' and resid 243 through 256
      removed outlier: 3.899A  pdb=" N   ILE A 253 " --> pdb=" O   LEU A 249 " (cutoff:3.500A)
      removed outlier: 4.130A  pdb=" N   GLU A 254 " --> pdb=" O   ARG A 250 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   VAL A 256 " --> pdb=" O   LYS A 252 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 259 through 273
    Processing helix  chain 'A' and resid 280 through 294
      removed outlier: 4.009A  pdb=" N   THR A 284 " --> pdb=" O   SER A 280 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   ALA A 286 " --> pdb=" O   GLU A 282 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 308 through 316
    Processing helix  chain 'A' and resid 324 through 336
      removed outlier: 3.736A  pdb=" N   ARG A 328 " --> pdb=" O   ASP A 324 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 360 through 372
    Processing helix  chain 'A' and resid 403 through 412
    Processing helix  chain 'A' and resid 424 through 427
      removed outlier: 3.774A  pdb=" N   MET A 427 " --> pdb=" O   ILE A 424 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 424 through 427'
    Processing helix  chain 'A' and resid 434 through 443
      removed outlier: 4.164A  pdb=" N   ALA A 438 " --> pdb=" O   ASP A 434 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 447 through 451
    Processing helix  chain 'A' and resid 479 through 483
      removed outlier: 3.569A  pdb=" N   ASP A 483 " --> pdb=" O   PRO A 480 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 494 through 505
    Processing helix  chain 'A' and resid 505 through 513
      removed outlier: 3.999A  pdb=" N   LYS A 509 " --> pdb=" O   TYR A 505 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 523 through 535
      removed outlier: 3.549A  pdb=" N   ILE A 527 " --> pdb=" O   THR A 523 " (cutoff:3.500A)
      removed outlier: 4.053A  pdb=" N   THR A 535 " --> pdb=" O   ILE A 531 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 540 through 560
      removed outlier: 3.701A  pdb=" N   GLU A 544 " --> pdb=" O   VAL A 540 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 573 through 578
      removed outlier: 4.089A  pdb=" N   TYR A 577 " --> pdb=" O   ASP A 573 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 587 through 591
      removed outlier: 4.309A  pdb=" N   GLU A 591 " --> pdb=" O   ALA A 588 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 630 through 645
    Processing helix  chain 'A' and resid 679 through 693
    Processing helix  chain 'A' and resid 717 through 728
      removed outlier: 3.901A  pdb=" N   LYS A 721 " --> pdb=" O   GLY A 717 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 738 through 740
      No H-bonds generated for 'chain 'A' and resid 738 through 740'
    Processing helix  chain 'A' and resid 741 through 746
      removed outlier: 3.727A  pdb=" N   LEU A 746 " --> pdb=" O   LEU A 743 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 747 through 752
      removed outlier: 3.595A  pdb=" N   LEU A 751 " --> pdb=" O   PRO A 747 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 761 through 770
      removed outlier: 3.603A  pdb=" N   VAL A 765 " --> pdb=" O   ASP A 761 " (cutoff:3.500A)
      removed outlier: 3.831A  pdb=" N   LEU A 770 " --> pdb=" O   LEU A 766 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 244 through 254
    Processing helix  chain 'B' and resid 259 through 273
    Processing helix  chain 'B' and resid 281 through 296
      removed outlier: 3.759A  pdb=" N   ALA B 286 " --> pdb=" O   GLU B 282 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 308 through 315
    Processing helix  chain 'B' and resid 324 through 339
      removed outlier: 3.774A  pdb=" N   THR B 339 " --> pdb=" O   VAL B 335 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 361 through 373
    Processing helix  chain 'B' and resid 386 through 391
      removed outlier: 3.857A  pdb=" N   ILE B 390 " --> pdb=" O   ASP B 386 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 403 through 411
      removed outlier: 3.808A  pdb=" N   HIS B 407 " --> pdb=" O   GLY B 403 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 436 through 444
    Processing helix  chain 'B' and resid 447 through 451
      removed outlier: 3.673A  pdb=" N   PHE B 451 " --> pdb=" O   ASN B 448 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 478 through 483
      removed outlier: 3.677A  pdb=" N   ASP B 483 " --> pdb=" O   ARG B 479 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 494 through 505
    Processing helix  chain 'B' and resid 506 through 514
    Processing helix  chain 'B' and resid 523 through 535
      removed outlier: 3.664A  pdb=" N   TYR B 534 " --> pdb=" O   VAL B 530 " (cutoff:3.500A)
      removed outlier: 3.905A  pdb=" N   THR B 535 " --> pdb=" O   ILE B 531 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 540 through 560
      removed outlier: 3.500A  pdb=" N   GLU B 544 " --> pdb=" O   VAL B 540 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 573 through 579
      removed outlier: 3.998A  pdb=" N   TYR B 577 " --> pdb=" O   ASP B 573 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 586 through 590
      removed outlier: 3.997A  pdb=" N   GLU B 589 " --> pdb=" O   ASP B 586 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 630 through 647
      removed outlier: 3.861A  pdb=" N   LYS B 634 " --> pdb=" O   GLY B 630 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 648 through 652
      removed outlier: 3.780A  pdb=" N   TYR B 651 " --> pdb=" O   THR B 648 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   GLY B 652 " --> pdb=" O   GLN B 649 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 648 through 652'
    Processing helix  chain 'B' and resid 679 through 693
    Processing helix  chain 'B' and resid 717 through 728
      removed outlier: 3.750A  pdb=" N   LYS B 721 " --> pdb=" O   GLY B 717 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 736 through 738
      No H-bonds generated for 'chain 'B' and resid 736 through 738'
    Processing helix  chain 'B' and resid 739 through 744
      removed outlier: 3.764A  pdb=" N   GLU B 744 " --> pdb=" O   GLU B 740 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 761 through 769
      removed outlier: 3.759A  pdb=" N   VAL B 765 " --> pdb=" O   ASP B 761 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 244 through 256
    Processing helix  chain 'C' and resid 259 through 271
    Processing helix  chain 'C' and resid 282 through 294
    Processing helix  chain 'C' and resid 307 through 316
      removed outlier: 3.631A  pdb=" N   THR C 311 " --> pdb=" O   ASP C 307 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   ARG C 312 " --> pdb=" O   ILE C 308 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 324 through 339
    Processing helix  chain 'C' and resid 360 through 372
    Processing helix  chain 'C' and resid 386 through 391
      removed outlier: 3.647A  pdb=" N   ILE C 390 " --> pdb=" O   ASP C 386 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 403 through 411
    Processing helix  chain 'C' and resid 434 through 444
      removed outlier: 4.158A  pdb=" N   ALA C 438 " --> pdb=" O   ASP C 434 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   MET C 439 " --> pdb=" O   PRO C 435 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 446 through 451
      removed outlier: 3.500A  pdb=" N   THR C 450 " --> pdb=" O   GLN C 447 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 478 through 483
      removed outlier: 3.784A  pdb=" N   ASP C 483 " --> pdb=" O   ARG C 479 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 494 through 505
    Processing helix  chain 'C' and resid 505 through 513
      removed outlier: 3.651A  pdb=" N   LYS C 509 " --> pdb=" O   TYR C 505 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 523 through 533
      removed outlier: 3.798A  pdb=" N   ILE C 527 " --> pdb=" O   THR C 523 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 540 through 560
      removed outlier: 3.795A  pdb=" N   GLU C 560 " --> pdb=" O   LYS C 556 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 574 through 579
    Processing helix  chain 'C' and resid 630 through 647
      removed outlier: 4.096A  pdb=" N   LYS C 634 " --> pdb=" O   GLY C 630 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   HIS C 647 " --> pdb=" O   TYR C 643 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 648 through 652
      removed outlier: 4.199A  pdb=" N   TYR C 651 " --> pdb=" O   THR C 648 " (cutoff:3.500A)
      removed outlier: 4.182A  pdb=" N   GLY C 652 " --> pdb=" O   GLN C 649 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 648 through 652'
    Processing helix  chain 'C' and resid 679 through 693
    Processing helix  chain 'C' and resid 717 through 728
      removed outlier: 3.642A  pdb=" N   LYS C 721 " --> pdb=" O   GLY C 717 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 738 through 745
      removed outlier: 4.349A  pdb=" N   ALA C 741 " --> pdb=" O   ASP C 738 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 747 through 754
      removed outlier: 4.275A  pdb=" N   LEU C 751 " --> pdb=" O   PRO C 747 " (cutoff:3.500A)
      removed outlier: 3.893A  pdb=" N   GLU C 752 " --> pdb=" O   LYS C 748 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   GLY C 753 " --> pdb=" O   GLU C 749 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 762 through 769
    Processing sheet with id=AA1, first strand: chain 'A' and resid 375 through 380
      removed outlier: 6.824A  pdb=" N   LYS A 375 " --> pdb=" O   VAL A 418 " (cutoff:3.500A)
      removed outlier: 7.848A  pdb=" N   LEU A 420 " --> pdb=" O   LYS A 375 " (cutoff:3.500A)
      removed outlier: 6.891A  pdb=" N   HIS A 377 " --> pdb=" O   LEU A 420 " (cutoff:3.500A)
      removed outlier: 7.447A  pdb=" N   ASP A 422 " --> pdb=" O   HIS A 377 " (cutoff:3.500A)
      removed outlier: 6.622A  pdb=" N   ILE A 379 " --> pdb=" O   ASP A 422 " (cutoff:3.500A)
      removed outlier: 6.875A  pdb=" N   ILE A 468 " --> pdb=" O   PRO A 417 " (cutoff:3.500A)
      removed outlier: 5.584A  pdb=" N   ILE A 419 " --> pdb=" O   ILE A 468 " (cutoff:3.500A)
      removed outlier: 7.131A  pdb=" N   THR A 470 " --> pdb=" O   ILE A 419 " (cutoff:3.500A)
      removed outlier: 6.103A  pdb=" N   LEU A 421 " --> pdb=" O   THR A 470 " (cutoff:3.500A)
      removed outlier: 5.548A  pdb=" N   LEU A 353 " --> pdb=" O   ALA A 471 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   ILE A 488 " --> pdb=" O   VAL A 352 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 520 through 522
      removed outlier: 7.208A  pdb=" N   GLU A 521 " --> pdb=" O   ILE A 569 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 597 through 603
      removed outlier: 6.668A  pdb=" N   SER A 624 " --> pdb=" O   VAL A 665 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 701 through 702
      removed outlier: 7.008A  pdb=" N   ILE A 733 " --> pdb=" O   LYS A 757 " (cutoff:3.500A)
      removed outlier: 7.138A  pdb=" N   VAL A 759 " --> pdb=" O   ILE A 733 " (cutoff:3.500A)
      removed outlier: 5.614A  pdb=" N   LEU A 735 " --> pdb=" O   VAL A 759 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 352 through 354
      removed outlier: 6.132A  pdb=" N   VAL B 352 " --> pdb=" O   ILE B 488 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'B' and resid 376 through 380
    Processing sheet with id=AA7, first strand: chain 'B' and resid 596 through 603
      removed outlier: 3.541A  pdb=" N   THR B 603 " --> pdb=" O   GLY B 606 " (cutoff:3.500A)
      removed outlier: 6.718A  pdb=" N   SER B 624 " --> pdb=" O   VAL B 665 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 700 through 702
    Processing sheet with id=AA9, first strand: chain 'B' and resid 705 through 707
      removed outlier: 4.121A  pdb=" N   GLU B 705 " --> pdb=" O   MET B 713 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   LYS B 711 " --> pdb=" O   SER B 707 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 376 through 380
      removed outlier: 3.804A  pdb=" N   LEU C 420 " --> pdb=" O   HIS C 377 " (cutoff:3.500A)
      removed outlier: 6.346A  pdb=" N   LEU C 353 " --> pdb=" O   ALA C 471 " (cutoff:3.500A)
      removed outlier: 6.365A  pdb=" N   VAL C 352 " --> pdb=" O   ILE C 488 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 520 through 522
      removed outlier: 5.967A  pdb=" N   GLU C 521 " --> pdb=" O   ILE C 569 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB2
    Processing sheet with id=AB3, first strand: chain 'C' and resid 596 through 603
      removed outlier: 5.988A  pdb=" N   SER C 624 " --> pdb=" O   VAL C 665 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'C' and resid 701 through 702
      removed outlier: 6.758A  pdb=" N   ALA C 701 " --> pdb=" O   VAL C 734 " (cutoff:3.500A)
      removed outlier: 6.309A  pdb=" N   ILE C 733 " --> pdb=" O   LYS C 757 " (cutoff:3.500A)
      removed outlier: 7.069A  pdb=" N   VAL C 759 " --> pdb=" O   ILE C 733 " (cutoff:3.500A)
      removed outlier: 6.179A  pdb=" N   LEU C 735 " --> pdb=" O   VAL C 759 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB4
    Processing sheet with id=AB5, first strand: chain 'C' and resid 705 through 707
      removed outlier: 4.050A  pdb=" N   GLU C 705 " --> pdb=" O   MET C 713 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   LYS C 711 " --> pdb=" O   SER C 707 " (cutoff:3.500A)

    481 hydrogen bonds defined for protein.
    1380 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: 2.13

  Time building geometry restraints manager: 1.36 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: 3592
        1.33 -     1.45: 1928
        1.45 -     1.57: 7053
        1.57 -     1.69: 0
        1.69 -     1.81: 90
  Bond restraints: 12663
  Sorted by residual:
  bond pdb=" C   ARG C 479 "
       pdb=" N   PRO C 480 "
    ideal  model  delta    sigma   weight residual
    1.336  1.379 -0.043 1.20e-02 6.94e+03 1.27e+01
  bond pdb=" C   LEU C 771 "
       pdb=" N   PRO C 772 "
    ideal  model  delta    sigma   weight residual
    1.333  1.370 -0.037 1.20e-02 6.94e+03 9.42e+00
  bond pdb=" C   LEU C 381 "
       pdb=" N   GLY C 382 "
    ideal  model  delta    sigma   weight residual
    1.331  1.312  0.019 6.60e-03 2.30e+04 8.38e+00
  bond pdb=" C   LEU B 351 "
       pdb=" N   VAL B 352 "
    ideal  model  delta    sigma   weight residual
    1.334  1.303  0.031 1.24e-02 6.50e+03 6.06e+00
  bond pdb=" C   GLY C 321 "
       pdb=" N   LEU C 322 "
    ideal  model  delta    sigma   weight residual
    1.333  1.300  0.032 1.38e-02 5.25e+03 5.54e+00
  ... (remaining 12658 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.50: 16370
        2.50 -     5.00: 677
        5.00 -     7.50: 86
        7.50 -    10.00: 26
       10.00 -    12.50: 4
  Bond angle restraints: 17163
  Sorted by residual:
  angle pdb=" N   GLY B 341 "
        pdb=" CA  GLY B 341 "
        pdb=" C   GLY B 341 "
      ideal   model   delta    sigma   weight residual
     115.00  107.27    7.73 1.44e+00 4.82e-01 2.88e+01
  angle pdb=" C   GLY B 321 "
        pdb=" N   LEU B 322 "
        pdb=" CA  LEU B 322 "
      ideal   model   delta    sigma   weight residual
     121.54  131.18   -9.64 1.91e+00 2.74e-01 2.55e+01
  angle pdb=" N   PRO A 592 "
        pdb=" CA  PRO A 592 "
        pdb=" C   PRO A 592 "
      ideal   model   delta    sigma   weight residual
     112.47  122.78  -10.31 2.06e+00 2.36e-01 2.50e+01
  angle pdb=" N   PRO B 281 "
        pdb=" CA  PRO B 281 "
        pdb=" C   PRO B 281 "
      ideal   model   delta    sigma   weight residual
     112.47  121.60   -9.13 2.06e+00 2.36e-01 1.97e+01
  angle pdb=" C   GLU A 591 "
        pdb=" N   PRO A 592 "
        pdb=" CA  PRO A 592 "
      ideal   model   delta    sigma   weight residual
     119.84  125.07   -5.23 1.25e+00 6.40e-01 1.75e+01
  ... (remaining 17158 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.45: 7280
       15.45 -    30.90: 407
       30.90 -    46.36: 83
       46.36 -    61.81: 7
       61.81 -    77.26: 14
  Dihedral angle restraints: 7791
    sinusoidal: 3225
      harmonic: 4566
  Sorted by residual:
  dihedral pdb=" CA  SER B 280 "
           pdb=" C   SER B 280 "
           pdb=" N   PRO B 281 "
           pdb=" CA  PRO B 281 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -140.53  -39.47     0      5.00e+00 4.00e-02 6.23e+01
  dihedral pdb=" CA  LEU C 306 "
           pdb=" C   LEU C 306 "
           pdb=" N   ASP C 307 "
           pdb=" CA  ASP C 307 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -140.66  -39.34     0      5.00e+00 4.00e-02 6.19e+01
  dihedral pdb=" CA  GLY B 279 "
           pdb=" C   GLY B 279 "
           pdb=" N   SER B 280 "
           pdb=" CA  SER B 280 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  145.73   34.27     0      5.00e+00 4.00e-02 4.70e+01
  ... (remaining 7788 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.062: 1306
       0.062 -    0.124: 547
       0.124 -    0.185: 81
       0.185 -    0.247: 12
       0.247 -    0.309: 7
  Chirality restraints: 1953
  Sorted by residual:
  chirality pdb=" CB  ILE B 468 "
            pdb=" CA  ILE B 468 "
            pdb=" CG1 ILE B 468 "
            pdb=" CG2 ILE B 468 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.34    0.31 2.00e-01 2.50e+01 2.39e+00
  chirality pdb=" CB  ILE C 468 "
            pdb=" CA  ILE C 468 "
            pdb=" CG1 ILE C 468 "
            pdb=" CG2 ILE C 468 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.35    0.30 2.00e-01 2.50e+01 2.23e+00
  chirality pdb=" CB  ILE B 398 "
            pdb=" CA  ILE B 398 "
            pdb=" CG1 ILE B 398 "
            pdb=" CG2 ILE B 398 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.37    0.27 2.00e-01 2.50e+01 1.86e+00
  ... (remaining 1950 not shown)

  Planarity restraints: 2229
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU C 771 "    0.054 5.00e-02 4.00e+02   8.13e-02 1.06e+01
        pdb=" N   PRO C 772 "   -0.141 5.00e-02 4.00e+02
        pdb=" CA  PRO C 772 "    0.040 5.00e-02 4.00e+02
        pdb=" CD  PRO C 772 "    0.047 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TRP B 507 "   -0.046 5.00e-02 4.00e+02   6.91e-02 7.63e+00
        pdb=" N   PRO B 508 "    0.119 5.00e-02 4.00e+02
        pdb=" CA  PRO B 508 "   -0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO B 508 "   -0.039 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TRP A 507 "   -0.045 5.00e-02 4.00e+02   6.66e-02 7.10e+00
        pdb=" N   PRO A 508 "    0.115 5.00e-02 4.00e+02
        pdb=" CA  PRO A 508 "   -0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO A 508 "   -0.038 5.00e-02 4.00e+02
  ... (remaining 2226 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 2707
        2.78 -     3.31: 11149
        3.31 -     3.84: 19725
        3.84 -     4.37: 22730
        4.37 -     4.90: 38493
  Nonbonded interactions: 94804
  Sorted by model distance:
  nonbonded pdb=" O   PRO A 297 "
            pdb=" OH  TYR A 460 "
     model   vdw
     2.253 3.040
  nonbonded pdb=" OG1 THR A 672 "
            pdb=" O   LYS A 674 "
     model   vdw
     2.282 3.040
  nonbonded pdb=" OD1 ASP A 422 "
            pdb=" OG1 THR A 470 "
     model   vdw
     2.284 3.040
  nonbonded pdb=" OG1 THR B 603 "
            pdb=" O   GLY B 606 "
     model   vdw
     2.286 3.040
  nonbonded pdb=" O   PRO B 297 "
            pdb=" OH  TYR B 460 "
     model   vdw
     2.286 3.040
  ... (remaining 94799 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
}

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=0.00 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:             2.570
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.190
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     12.940
  Find NCS groups from input model:        0.220
  Set up NCS constraints:                  0.020
  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:1.390
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.410
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7594
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      :  0.010   0.089  12663  Z= 0.401
  Angle     :  1.176  12.505  17163  Z= 0.628
  Chirality :  0.065   0.309   1953
  Planarity :  0.009   0.081   2229
  Dihedral  : 10.784  77.262   4863
  Min Nonbonded Distance : 2.253

Molprobity Statistics.
  All-atom Clashscore : 6.57
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  : 10.94 %
    Favored  : 88.93 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  3.84 %
    Favored  : 96.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.08 %
    Twisted General : 0.20 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.68 (0.16), residues: 1590
  helix: -2.80 (0.15), residues: 638
  sheet: -2.89 (0.31), residues: 195
  loop : -3.43 (0.18), residues: 757

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.019   0.002   ARG B 336 
 TYR   0.032   0.003   TYR A 289 
 PHE   0.029   0.004   PHE C 466 
 TRP   0.023   0.004   TRP B 558 
 HIS   0.020   0.003   HIS C 319 

Details of bonding type rmsd
  covalent geometry    : bond        0.00957 (12663)
  covalent geometry    : angle       1.17571 (17163)
  hydrogen bonds       : bond        0.16583 (  481)
  hydrogen bonds       : angle       7.34267 ( 1380)

*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3180 Ramachandran restraints generated.
    1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3180 Ramachandran restraints generated.
    1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  323 residues out of total 1329 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 321
  time to evaluate  : 0.521 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  276 MET cc_start: 0.6217 (mtt) cc_final: 0.5102 (tpp)
REVERT: A  439 MET cc_start: 0.8421 (mmm) cc_final: 0.8210 (mmm)
REVERT: A  453 ASP cc_start: 0.6704 (m-30) cc_final: 0.6323 (m-30)
REVERT: A  454 HIS cc_start: 0.7609 (m90) cc_final: 0.7402 (m-70)
REVERT: A  469 THR cc_start: 0.9165 (m) cc_final: 0.8837 (p)
REVERT: A  516 MET cc_start: 0.8151 (mmm) cc_final: 0.7566 (mtm)
REVERT: A  520 ILE cc_start: 0.8595 (mt) cc_final: 0.8350 (mm)
REVERT: A  553 LYS cc_start: 0.8785 (mmmm) cc_final: 0.8465 (mmmt)
REVERT: A  608 THR cc_start: 0.8551 (t) cc_final: 0.8132 (p)
REVERT: A  641 LEU cc_start: 0.8396 (mt) cc_final: 0.8132 (mm)
REVERT: B  292 TRP cc_start: 0.7638 (m100) cc_final: 0.7363 (m100)
REVERT: B  385 ARG cc_start: 0.7692 (pmt170) cc_final: 0.7188 (mtm-85)
REVERT: B  439 MET cc_start: 0.7732 (mmp) cc_final: 0.7484 (mmp)
REVERT: C  244 SER cc_start: 0.8386 (p) cc_final: 0.8083 (t)
REVERT: C  290 LEU cc_start: 0.8822 (mt) cc_final: 0.8498 (pp)
REVERT: C  721 LYS cc_start: 0.8397 (mttm) cc_final: 0.8156 (mtpp)
  outliers start: 2
  outliers final: 1
  residues processed: 323
  average time/residue: 0.1551
  time to fit residues: 66.2339
Evaluate side-chains
  165 residues out of total 1329 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 164
  time to evaluate  : 0.490 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  590 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 98 optimal weight:    0.9990
   chunk 107 optimal weight:    0.3980
   chunk 10 optimal weight:    0.8980
   chunk 66 optimal weight:    0.8980
   chunk 130 optimal weight:    6.9990
   chunk 124 optimal weight:    3.9990
   chunk 103 optimal weight:    0.8980
   chunk 77 optimal weight:    3.9990
   chunk 122 optimal weight:    2.9990
   chunk 91 optimal weight:    2.9990
   chunk 149 optimal weight:    4.9990
   overall best weight:    0.8182

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 277 GLN
A 310 HIS
A 319 HIS
A 411 GLN
A 739 ASN
B 346 ASN
B 447 GLN
B 449 ASN
B 664 HIS
C 277 GLN
C 346 ASN
C 393 HIS
C 449 ASN
C 454 HIS
C 472 ASN
C 598 GLN
C 647 HIS

Total number of N/Q/H flips: 17

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4107 r_free = 0.4107 target = 0.138805 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.114176 restraints weight = 28905.333|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.113091 restraints weight = 19074.666|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.114444 restraints weight = 16268.724|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.115100 restraints weight = 13211.290|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.115055 restraints weight = 12704.793|
|-----------------------------------------------------------------------------|
r_work (final): 0.3759
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7498
moved from start:          0.2944

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.064  12663  Z= 0.144
  Angle     :  0.730   8.689  17163  Z= 0.371
  Chirality :  0.046   0.207   1953
  Planarity :  0.007   0.066   2229
  Dihedral  :  6.550  35.145   1744
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 9.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.42 %
    Favored  : 92.58 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 11.59 %
    Favored  : 86.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.21 (0.19), residues: 1590
  helix: -1.14 (0.19), residues: 672
  sheet: -2.41 (0.34), residues: 197
  loop : -3.03 (0.20), residues: 721

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 552 
 TYR   0.022   0.002   TYR A 289 
 PHE   0.009   0.001   PHE A 451 
 TRP   0.025   0.002   TRP C 558 
 HIS   0.009   0.001   HIS A 310 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 (12663)
  covalent geometry    : angle       0.73009 (17163)
  hydrogen bonds       : bond        0.04266 (  481)
  hydrogen bonds       : angle       5.39034 ( 1380)

*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3180 Ramachandran restraints generated.
    1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3180 Ramachandran restraints generated.
    1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  246 residues out of total 1329 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 218
  time to evaluate  : 0.504 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  276 MET cc_start: 0.6300 (mtt) cc_final: 0.5237 (tpp)
REVERT: A  469 THR cc_start: 0.8951 (m) cc_final: 0.8570 (p)
REVERT: A  516 MET cc_start: 0.7950 (mmm) cc_final: 0.7525 (mtm)
REVERT: A  520 ILE cc_start: 0.8540 (mt) cc_final: 0.8148 (mm)
REVERT: A  553 LYS cc_start: 0.8623 (mmmm) cc_final: 0.8342 (mmmt)
REVERT: A  608 THR cc_start: 0.8440 (t) cc_final: 0.7904 (p)
REVERT: A  620 SER cc_start: 0.9017 (p) cc_final: 0.8766 (t)
REVERT: A  631 GLU cc_start: 0.7652 (tp30) cc_final: 0.6533 (tp30)
REVERT: A  674 LYS cc_start: 0.3858 (pttp) cc_final: 0.3067 (ttmt)
REVERT: A  698 MET cc_start: 0.7840 (mmm) cc_final: 0.7628 (mmm)
REVERT: B  385 ARG cc_start: 0.7657 (pmt170) cc_final: 0.7273 (mtm-85)
REVERT: B  552 ARG cc_start: 0.7922 (mtt-85) cc_final: 0.7543 (mtt-85)
  outliers start: 28
  outliers final: 9
  residues processed: 234
  average time/residue: 0.1351
  time to fit residues: 43.3868
Evaluate side-chains
  172 residues out of total 1329 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 163
  time to evaluate  : 0.509 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  338 LEU
Chi-restraints excluded: chain A residue  726 HIS
Chi-restraints excluded: chain B residue  456 LEU
Chi-restraints excluded: chain B residue  617 VAL
Chi-restraints excluded: chain B residue  681 ILE
Chi-restraints excluded: chain C residue  305 VAL
Chi-restraints excluded: chain C residue  475 GLN
Chi-restraints excluded: chain C residue  703 THR
Chi-restraints excluded: chain C residue  723 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 119 optimal weight:    2.9990
   chunk 98 optimal weight:    2.9990
   chunk 49 optimal weight:    7.9990
   chunk 97 optimal weight:    0.9990
   chunk 63 optimal weight:    0.0970
   chunk 26 optimal weight:    0.6980
   chunk 104 optimal weight:    4.9990
   chunk 13 optimal weight:    4.9990
   chunk 16 optimal weight:    9.9990
   chunk 81 optimal weight:    0.8980
   chunk 85 optimal weight:    0.9980
   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 310 HIS
B 454 HIS
C 407 HIS
C 666 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4119 r_free = 0.4119 target = 0.139444 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.112611 restraints weight = 29555.335|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.114076 restraints weight = 19714.273|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.115300 restraints weight = 14427.133|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.115802 restraints weight = 12425.372|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.115997 restraints weight = 11643.728|
|-----------------------------------------------------------------------------|
r_work (final): 0.3774
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7483
moved from start:          0.3611

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  12663  Z= 0.124
  Angle     :  0.672   9.545  17163  Z= 0.334
  Chirality :  0.045   0.189   1953
  Planarity :  0.006   0.064   2229
  Dihedral  :  5.767  30.352   1743
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 9.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.30 %
    Favored  : 92.70 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 12.94 %
    Favored  : 84.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.47 (0.20), residues: 1590
  helix: -0.38 (0.20), residues: 670
  sheet: -1.96 (0.36), residues: 198
  loop : -2.81 (0.21), residues: 722

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 541 
 TYR   0.018   0.002   TYR A 289 
 PHE   0.008   0.001   PHE A 467 
 TRP   0.013   0.001   TRP A 292 
 HIS   0.007   0.001   HIS A 310 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 (12663)
  covalent geometry    : angle       0.67162 (17163)
  hydrogen bonds       : bond        0.03645 (  481)
  hydrogen bonds       : angle       4.89135 ( 1380)

*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3180 Ramachandran restraints generated.
    1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3180 Ramachandran restraints generated.
    1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  227 residues out of total 1329 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 192
  time to evaluate  : 0.438 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  276 MET cc_start: 0.6367 (mtt) cc_final: 0.5172 (tpp)
REVERT: A  401 MET cc_start: 0.5340 (tmm) cc_final: 0.5085 (tmm)
REVERT: A  423 GLU cc_start: 0.7937 (mt-10) cc_final: 0.7569 (tt0)
REVERT: A  469 THR cc_start: 0.9032 (m) cc_final: 0.8680 (p)
REVERT: A  516 MET cc_start: 0.7923 (mmm) cc_final: 0.7511 (mtm)
REVERT: A  520 ILE cc_start: 0.8501 (mt) cc_final: 0.8103 (mm)
REVERT: A  553 LYS cc_start: 0.8553 (mmmm) cc_final: 0.8310 (mmmt)
REVERT: A  608 THR cc_start: 0.8332 (t) cc_final: 0.7862 (p)
REVERT: A  620 SER cc_start: 0.8956 (p) cc_final: 0.8725 (t)
REVERT: A  638 GLN cc_start: 0.8535 (mm-40) cc_final: 0.8306 (mm-40)
REVERT: A  758 LEU cc_start: 0.7556 (mt) cc_final: 0.7323 (mt)
REVERT: B  276 MET cc_start: 0.1608 (pmm) cc_final: 0.1027 (pmm)
REVERT: B  385 ARG cc_start: 0.7690 (pmt170) cc_final: 0.7183 (mtm-85)
REVERT: B  546 GLU cc_start: 0.8034 (OUTLIER) cc_final: 0.7463 (mp0)
  outliers start: 35
  outliers final: 16
  residues processed: 216
  average time/residue: 0.1363
  time to fit residues: 40.7108
Evaluate side-chains
  172 residues out of total 1329 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 155
  time to evaluate  : 0.509 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  338 LEU
Chi-restraints excluded: chain A residue  411 GLN
Chi-restraints excluded: chain A residue  487 VAL
Chi-restraints excluded: chain A residue  629 LEU
Chi-restraints excluded: chain A residue  641 LEU
Chi-restraints excluded: chain A residue  726 HIS
Chi-restraints excluded: chain B residue  342 LEU
Chi-restraints excluded: chain B residue  350 ILE
Chi-restraints excluded: chain B residue  546 GLU
Chi-restraints excluded: chain B residue  617 VAL
Chi-restraints excluded: chain B residue  635 GLU
Chi-restraints excluded: chain B residue  681 ILE
Chi-restraints excluded: chain B residue  726 HIS
Chi-restraints excluded: chain C residue  305 VAL
Chi-restraints excluded: chain C residue  475 GLN
Chi-restraints excluded: chain C residue  723 LEU
Chi-restraints excluded: chain C residue  746 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 59 optimal weight:    0.2980
   chunk 6 optimal weight:    0.8980
   chunk 143 optimal weight:    6.9990
   chunk 149 optimal weight:    0.0980
   chunk 31 optimal weight:    2.9990
   chunk 25 optimal weight:    0.8980
   chunk 13 optimal weight:    3.9990
   chunk 61 optimal weight:    0.3980
   chunk 10 optimal weight:    4.9990
   chunk 92 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9990
   overall best weight:    0.5180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 310 HIS
A 407 HIS
A 664 HIS
C 472 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4121 r_free = 0.4121 target = 0.139782 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.113225 restraints weight = 29163.211|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.113662 restraints weight = 19450.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.114825 restraints weight = 14843.791|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.115266 restraints weight = 13215.537|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.115370 restraints weight = 12418.325|
|-----------------------------------------------------------------------------|
r_work (final): 0.3765
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7485
moved from start:          0.4082

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  12663  Z= 0.115
  Angle     :  0.640   8.398  17163  Z= 0.316
  Chirality :  0.044   0.165   1953
  Planarity :  0.006   0.064   2229
  Dihedral  :  5.310  26.195   1743
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 9.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.86 %
    Favored  : 93.14 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 13.32 %
    Favored  : 83.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.94 (0.21), residues: 1590
  helix:  0.15 (0.21), residues: 670
  sheet: -1.71 (0.36), residues: 196
  loop : -2.62 (0.22), residues: 724

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 312 
 TYR   0.023   0.001   TYR A 289 
 PHE   0.019   0.001   PHE B 657 
 TRP   0.039   0.002   TRP A 292 
 HIS   0.015   0.001   HIS A 407 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 (12663)
  covalent geometry    : angle       0.63952 (17163)
  hydrogen bonds       : bond        0.03335 (  481)
  hydrogen bonds       : angle       4.59882 ( 1380)

*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3180 Ramachandran restraints generated.
    1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3180 Ramachandran restraints generated.
    1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  221 residues out of total 1329 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 179
  time to evaluate  : 0.504 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  276 MET cc_start: 0.6447 (mtt) cc_final: 0.5267 (tpp)
REVERT: A  423 GLU cc_start: 0.7999 (mt-10) cc_final: 0.7521 (tt0)
REVERT: A  469 THR cc_start: 0.9055 (m) cc_final: 0.8730 (p)
REVERT: A  482 LEU cc_start: 0.8346 (OUTLIER) cc_final: 0.8033 (mp)
REVERT: A  516 MET cc_start: 0.7920 (mmm) cc_final: 0.7463 (mtm)
REVERT: A  520 ILE cc_start: 0.8485 (mt) cc_final: 0.8090 (mm)
REVERT: A  608 THR cc_start: 0.8325 (t) cc_final: 0.7860 (p)
REVERT: A  620 SER cc_start: 0.8942 (p) cc_final: 0.8708 (t)
REVERT: A  631 GLU cc_start: 0.7461 (tp30) cc_final: 0.7148 (tp30)
REVERT: A  698 MET cc_start: 0.7482 (mmm) cc_final: 0.6937 (mmm)
REVERT: B  385 ARG cc_start: 0.7677 (pmt170) cc_final: 0.7188 (mtm-85)
REVERT: B  681 ILE cc_start: 0.8357 (OUTLIER) cc_final: 0.7935 (mm)
REVERT: C  516 MET cc_start: 0.5298 (OUTLIER) cc_final: 0.4249 (mmm)
REVERT: C  524 ASP cc_start: 0.8229 (p0) cc_final: 0.7989 (t0)
  outliers start: 42
  outliers final: 22
  residues processed: 202
  average time/residue: 0.1258
  time to fit residues: 35.7563
Evaluate side-chains
  174 residues out of total 1329 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 149
  time to evaluate  : 0.457 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  309 ASN
Chi-restraints excluded: chain A residue  338 LEU
Chi-restraints excluded: chain A residue  344 VAL
Chi-restraints excluded: chain A residue  411 GLN
Chi-restraints excluded: chain A residue  420 LEU
Chi-restraints excluded: chain A residue  476 THR
Chi-restraints excluded: chain A residue  482 LEU
Chi-restraints excluded: chain A residue  629 LEU
Chi-restraints excluded: chain A residue  641 LEU
Chi-restraints excluded: chain A residue  726 HIS
Chi-restraints excluded: chain B residue  258 MET
Chi-restraints excluded: chain B residue  342 LEU
Chi-restraints excluded: chain B residue  350 ILE
Chi-restraints excluded: chain B residue  514 SER
Chi-restraints excluded: chain B residue  617 VAL
Chi-restraints excluded: chain B residue  635 GLU
Chi-restraints excluded: chain B residue  681 ILE
Chi-restraints excluded: chain B residue  726 HIS
Chi-restraints excluded: chain C residue  305 VAL
Chi-restraints excluded: chain C residue  475 GLN
Chi-restraints excluded: chain C residue  516 MET
Chi-restraints excluded: chain C residue  623 LEU
Chi-restraints excluded: chain C residue  682 THR
Chi-restraints excluded: chain C residue  746 LEU
Chi-restraints excluded: chain C residue  768 TYR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 24 optimal weight:    0.9990
   chunk 98 optimal weight:    0.8980
   chunk 116 optimal weight:    2.9990
   chunk 66 optimal weight:    1.9990
   chunk 64 optimal weight:    0.6980
   chunk 155 optimal weight:    3.9990
   chunk 111 optimal weight:    4.9990
   chunk 39 optimal weight:    0.8980
   chunk 50 optimal weight:    9.9990
   chunk 61 optimal weight:    1.9990
   chunk 16 optimal weight:   20.0000
   overall best weight:    1.0984

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 310 HIS
A 346 ASN
** A 407 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 277 GLN
C 598 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4099 r_free = 0.4099 target = 0.138382 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.112621 restraints weight = 29340.289|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.112157 restraints weight = 19802.638|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.113125 restraints weight = 15715.442|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.113669 restraints weight = 13984.196|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.113989 restraints weight = 12946.713|
|-----------------------------------------------------------------------------|
r_work (final): 0.3740
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7530
moved from start:          0.4280

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  12663  Z= 0.130
  Angle     :  0.644   9.169  17163  Z= 0.318
  Chirality :  0.044   0.161   1953
  Planarity :  0.005   0.062   2229
  Dihedral  :  5.108  24.677   1743
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 9.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.42 %
    Favored  : 92.58 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 14.00 %
    Favored  : 82.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.76 (0.21), residues: 1590
  helix:  0.34 (0.21), residues: 680
  sheet: -1.55 (0.35), residues: 208
  loop : -2.63 (0.22), residues: 702

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 479 
 TYR   0.013   0.001   TYR A 289 
 PHE   0.016   0.001   PHE B 657 
 TRP   0.040   0.002   TRP A 292 
 HIS   0.006   0.001   HIS C 319 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 (12663)
  covalent geometry    : angle       0.64354 (17163)
  hydrogen bonds       : bond        0.03430 (  481)
  hydrogen bonds       : angle       4.53258 ( 1380)

*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3180 Ramachandran restraints generated.
    1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3180 Ramachandran restraints generated.
    1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 1329 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 153
  time to evaluate  : 0.343 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  276 MET cc_start: 0.6403 (mtt) cc_final: 0.5182 (tpp)
REVERT: A  407 HIS cc_start: 0.6886 (OUTLIER) cc_final: 0.6607 (t-90)
REVERT: A  423 GLU cc_start: 0.8055 (mt-10) cc_final: 0.7596 (tt0)
REVERT: A  469 THR cc_start: 0.9064 (m) cc_final: 0.8787 (p)
REVERT: A  482 LEU cc_start: 0.8408 (OUTLIER) cc_final: 0.8107 (mp)
REVERT: A  516 MET cc_start: 0.7897 (mmm) cc_final: 0.7419 (mtm)
REVERT: A  520 ILE cc_start: 0.8529 (mt) cc_final: 0.8148 (mm)
REVERT: A  608 THR cc_start: 0.8349 (t) cc_final: 0.7876 (p)
REVERT: A  620 SER cc_start: 0.8911 (p) cc_final: 0.8673 (t)
REVERT: A  631 GLU cc_start: 0.7503 (tp30) cc_final: 0.6998 (tp30)
REVERT: A  635 GLU cc_start: 0.8327 (mm-30) cc_final: 0.7701 (mm-30)
REVERT: B  546 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7650 (mp0)
REVERT: B  681 ILE cc_start: 0.8348 (OUTLIER) cc_final: 0.8046 (mm)
REVERT: C  479 ARG cc_start: 0.7998 (tpm170) cc_final: 0.7726 (tpm170)
REVERT: C  715 ILE cc_start: 0.7846 (pp) cc_final: 0.7503 (mt)
  outliers start: 43
  outliers final: 24
  residues processed: 181
  average time/residue: 0.1100
  time to fit residues: 28.2750
Evaluate side-chains
  174 residues out of total 1329 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 146
  time to evaluate  : 0.344 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  338 LEU
Chi-restraints excluded: chain A residue  407 HIS
Chi-restraints excluded: chain A residue  411 GLN
Chi-restraints excluded: chain A residue  420 LEU
Chi-restraints excluded: chain A residue  476 THR
Chi-restraints excluded: chain A residue  482 LEU
Chi-restraints excluded: chain A residue  629 LEU
Chi-restraints excluded: chain A residue  641 LEU
Chi-restraints excluded: chain A residue  726 HIS
Chi-restraints excluded: chain A residue  735 LEU
Chi-restraints excluded: chain B residue  258 MET
Chi-restraints excluded: chain B residue  319 HIS
Chi-restraints excluded: chain B residue  342 LEU
Chi-restraints excluded: chain B residue  350 ILE
Chi-restraints excluded: chain B residue  546 GLU
Chi-restraints excluded: chain B residue  617 VAL
Chi-restraints excluded: chain B residue  681 ILE
Chi-restraints excluded: chain B residue  726 HIS
Chi-restraints excluded: chain B residue  743 LEU
Chi-restraints excluded: chain B residue  746 LEU
Chi-restraints excluded: chain C residue  352 VAL
Chi-restraints excluded: chain C residue  475 GLN
Chi-restraints excluded: chain C residue  611 THR
Chi-restraints excluded: chain C residue  623 LEU
Chi-restraints excluded: chain C residue  682 THR
Chi-restraints excluded: chain C residue  708 LEU
Chi-restraints excluded: chain C residue  746 LEU
Chi-restraints excluded: chain C residue  768 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 1 optimal weight:    5.9990
   chunk 121 optimal weight:    0.0270
   chunk 144 optimal weight:    6.9990
   chunk 28 optimal weight:    1.9990
   chunk 49 optimal weight:    7.9990
   chunk 108 optimal weight:   10.0000
   chunk 25 optimal weight:    0.6980
   chunk 138 optimal weight:    0.9980
   chunk 38 optimal weight:    8.9990
   chunk 84 optimal weight:    0.9990
   chunk 22 optimal weight:    1.9990
   overall best weight:    0.9442

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 310 HIS
A 407 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4104 r_free = 0.4104 target = 0.138707 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.112297 restraints weight = 29112.232|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.112810 restraints weight = 19985.894|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.113424 restraints weight = 15257.253|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.113872 restraints weight = 14519.027|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.114096 restraints weight = 13478.539|
|-----------------------------------------------------------------------------|
r_work (final): 0.3744
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7524
moved from start:          0.4461

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  12663  Z= 0.120
  Angle     :  0.629   7.715  17163  Z= 0.308
  Chirality :  0.044   0.158   1953
  Planarity :  0.005   0.061   2229
  Dihedral  :  4.940  23.433   1743
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 9.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.04 %
    Favored  : 92.96 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 14.52 %
    Favored  : 82.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.55 (0.21), residues: 1590
  helix:  0.50 (0.21), residues: 677
  sheet: -1.42 (0.37), residues: 191
  loop : -2.48 (0.22), residues: 722

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 541 
 TYR   0.018   0.001   TYR C 643 
 PHE   0.015   0.001   PHE B 657 
 TRP   0.027   0.002   TRP A 292 
 HIS   0.004   0.001   HIS C 319 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 (12663)
  covalent geometry    : angle       0.62858 (17163)
  hydrogen bonds       : bond        0.03245 (  481)
  hydrogen bonds       : angle       4.37255 ( 1380)

*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3180 Ramachandran restraints generated.
    1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3180 Ramachandran restraints generated.
    1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 1329 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 157
  time to evaluate  : 0.507 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  276 MET cc_start: 0.6451 (mtt) cc_final: 0.5177 (tpp)
REVERT: A  423 GLU cc_start: 0.8072 (mt-10) cc_final: 0.7608 (tt0)
REVERT: A  482 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.8116 (mp)
REVERT: A  516 MET cc_start: 0.7873 (mmm) cc_final: 0.7382 (mtm)
REVERT: A  520 ILE cc_start: 0.8543 (mt) cc_final: 0.8141 (mm)
REVERT: A  608 THR cc_start: 0.8286 (t) cc_final: 0.7833 (p)
REVERT: A  620 SER cc_start: 0.8938 (p) cc_final: 0.8679 (t)
REVERT: A  635 GLU cc_start: 0.8341 (mm-30) cc_final: 0.8043 (mm-30)
REVERT: B  546 GLU cc_start: 0.8116 (OUTLIER) cc_final: 0.7642 (mp0)
REVERT: B  681 ILE cc_start: 0.8224 (OUTLIER) cc_final: 0.8022 (mm)
REVERT: B  698 MET cc_start: 0.7626 (mmt) cc_final: 0.7371 (mmt)
REVERT: C  401 MET cc_start: 0.7533 (ppp) cc_final: 0.7327 (ppp)
REVERT: C  409 MET cc_start: 0.8146 (mmm) cc_final: 0.7817 (mmm)
REVERT: C  516 MET cc_start: 0.5219 (OUTLIER) cc_final: 0.4068 (mmm)
  outliers start: 44
  outliers final: 30
  residues processed: 186
  average time/residue: 0.1168
  time to fit residues: 30.3840
Evaluate side-chains
  181 residues out of total 1329 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 147
  time to evaluate  : 0.472 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  338 LEU
Chi-restraints excluded: chain A residue  407 HIS
Chi-restraints excluded: chain A residue  411 GLN
Chi-restraints excluded: chain A residue  420 LEU
Chi-restraints excluded: chain A residue  476 THR
Chi-restraints excluded: chain A residue  482 LEU
Chi-restraints excluded: chain A residue  487 VAL
Chi-restraints excluded: chain A residue  629 LEU
Chi-restraints excluded: chain A residue  641 LEU
Chi-restraints excluded: chain A residue  726 HIS
Chi-restraints excluded: chain A residue  735 LEU
Chi-restraints excluded: chain B residue  258 MET
Chi-restraints excluded: chain B residue  319 HIS
Chi-restraints excluded: chain B residue  342 LEU
Chi-restraints excluded: chain B residue  350 ILE
Chi-restraints excluded: chain B residue  458 VAL
Chi-restraints excluded: chain B residue  501 ILE
Chi-restraints excluded: chain B residue  514 SER
Chi-restraints excluded: chain B residue  546 GLU
Chi-restraints excluded: chain B residue  617 VAL
Chi-restraints excluded: chain B residue  681 ILE
Chi-restraints excluded: chain B residue  726 HIS
Chi-restraints excluded: chain B residue  743 LEU
Chi-restraints excluded: chain B residue  746 LEU
Chi-restraints excluded: chain C residue  305 VAL
Chi-restraints excluded: chain C residue  352 VAL
Chi-restraints excluded: chain C residue  443 LEU
Chi-restraints excluded: chain C residue  475 GLN
Chi-restraints excluded: chain C residue  516 MET
Chi-restraints excluded: chain C residue  611 THR
Chi-restraints excluded: chain C residue  623 LEU
Chi-restraints excluded: chain C residue  682 THR
Chi-restraints excluded: chain C residue  708 LEU
Chi-restraints excluded: chain C residue  768 TYR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 35 optimal weight:    0.3980
   chunk 144 optimal weight:    5.9990
   chunk 11 optimal weight:    2.9990
   chunk 7 optimal weight:    2.9990
   chunk 59 optimal weight:    0.3980
   chunk 134 optimal weight:    3.9990
   chunk 148 optimal weight:    1.9990
   chunk 155 optimal weight:    0.9980
   chunk 51 optimal weight:    3.9990
   chunk 120 optimal weight:    9.9990
   chunk 147 optimal weight:    5.9990
   overall best weight:    1.3584

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4094 r_free = 0.4094 target = 0.137885 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.110407 restraints weight = 29159.773|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.111876 restraints weight = 19257.028|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.113071 restraints weight = 14572.286|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.113690 restraints weight = 12366.421|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.113931 restraints weight = 11228.000|
|-----------------------------------------------------------------------------|
r_work (final): 0.3738
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7541
moved from start:          0.4533

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050  12663  Z= 0.139
  Angle     :  0.644   8.156  17163  Z= 0.317
  Chirality :  0.044   0.232   1953
  Planarity :  0.005   0.062   2229
  Dihedral  :  4.941  22.975   1743
  Min Nonbonded Distance : 2.382

Molprobity Statistics.
  All-atom Clashscore : 10.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.42 %
    Favored  : 92.58 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 15.43 %
    Favored  : 82.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.46 (0.22), residues: 1590
  helix:  0.56 (0.21), residues: 676
  sheet: -1.38 (0.37), residues: 191
  loop : -2.40 (0.23), residues: 723

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 479 
 TYR   0.017   0.001   TYR C 643 
 PHE   0.014   0.001   PHE B 657 
 TRP   0.036   0.002   TRP B 431 
 HIS   0.013   0.001   HIS A 407 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 (12663)
  covalent geometry    : angle       0.64414 (17163)
  hydrogen bonds       : bond        0.03440 (  481)
  hydrogen bonds       : angle       4.42505 ( 1380)

*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3180 Ramachandran restraints generated.
    1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3180 Ramachandran restraints generated.
    1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  192 residues out of total 1329 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 158
  time to evaluate  : 0.519 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  276 MET cc_start: 0.6446 (mtt) cc_final: 0.5141 (tpp)
REVERT: A  423 GLU cc_start: 0.8111 (mt-10) cc_final: 0.7616 (tt0)
REVERT: A  482 LEU cc_start: 0.8389 (OUTLIER) cc_final: 0.8110 (mp)
REVERT: A  516 MET cc_start: 0.7864 (mmm) cc_final: 0.7640 (mmp)
REVERT: A  608 THR cc_start: 0.8291 (t) cc_final: 0.7833 (p)
REVERT: A  620 SER cc_start: 0.8930 (p) cc_final: 0.8679 (t)
REVERT: B  546 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.7592 (mp0)
REVERT: C  516 MET cc_start: 0.5246 (OUTLIER) cc_final: 0.4072 (mmm)
  outliers start: 34
  outliers final: 29
  residues processed: 180
  average time/residue: 0.1248
  time to fit residues: 31.6374
Evaluate side-chains
  175 residues out of total 1329 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 143
  time to evaluate  : 0.472 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  338 LEU
Chi-restraints excluded: chain A residue  411 GLN
Chi-restraints excluded: chain A residue  476 THR
Chi-restraints excluded: chain A residue  482 LEU
Chi-restraints excluded: chain A residue  487 VAL
Chi-restraints excluded: chain A residue  629 LEU
Chi-restraints excluded: chain A residue  641 LEU
Chi-restraints excluded: chain A residue  726 HIS
Chi-restraints excluded: chain B residue  258 MET
Chi-restraints excluded: chain B residue  319 HIS
Chi-restraints excluded: chain B residue  342 LEU
Chi-restraints excluded: chain B residue  350 ILE
Chi-restraints excluded: chain B residue  458 VAL
Chi-restraints excluded: chain B residue  501 ILE
Chi-restraints excluded: chain B residue  514 SER
Chi-restraints excluded: chain B residue  546 GLU
Chi-restraints excluded: chain B residue  617 VAL
Chi-restraints excluded: chain B residue  632 VAL
Chi-restraints excluded: chain B residue  726 HIS
Chi-restraints excluded: chain B residue  743 LEU
Chi-restraints excluded: chain B residue  746 LEU
Chi-restraints excluded: chain C residue  305 VAL
Chi-restraints excluded: chain C residue  352 VAL
Chi-restraints excluded: chain C residue  401 MET
Chi-restraints excluded: chain C residue  443 LEU
Chi-restraints excluded: chain C residue  475 GLN
Chi-restraints excluded: chain C residue  516 MET
Chi-restraints excluded: chain C residue  611 THR
Chi-restraints excluded: chain C residue  623 LEU
Chi-restraints excluded: chain C residue  682 THR
Chi-restraints excluded: chain C residue  708 LEU
Chi-restraints excluded: chain C residue  768 TYR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 88 optimal weight:    0.7980
   chunk 59 optimal weight:    1.9990
   chunk 70 optimal weight:    0.0870
   chunk 72 optimal weight:    0.8980
   chunk 65 optimal weight:    1.9990
   chunk 38 optimal weight:    8.9990
   chunk 125 optimal weight:    1.9990
   chunk 19 optimal weight:   10.0000
   chunk 127 optimal weight:    6.9990
   chunk 153 optimal weight:    5.9990
   chunk 103 optimal weight:    0.5980
   overall best weight:    0.8760

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4103 r_free = 0.4103 target = 0.138566 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.111047 restraints weight = 28959.910|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.112399 restraints weight = 19223.030|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.113454 restraints weight = 14209.127|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.114630 restraints weight = 12188.017|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.114465 restraints weight = 11015.285|
|-----------------------------------------------------------------------------|
r_work (final): 0.3752
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7523
moved from start:          0.4706

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  12663  Z= 0.118
  Angle     :  0.651  12.668  17163  Z= 0.316
  Chirality :  0.044   0.168   1953
  Planarity :  0.005   0.062   2229
  Dihedral  :  4.849  22.275   1743
  Min Nonbonded Distance : 2.367

Molprobity Statistics.
  All-atom Clashscore : 10.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.86 %
    Favored  : 93.14 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 15.65 %
    Favored  : 81.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.30 (0.22), residues: 1590
  helix:  0.68 (0.21), residues: 677
  sheet: -1.10 (0.38), residues: 188
  loop : -2.38 (0.22), residues: 725

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 479 
 TYR   0.014   0.001   TYR C 643 
 PHE   0.012   0.001   PHE B 657 
 TRP   0.049   0.002   TRP A 292 
 HIS   0.009   0.001   HIS A 310 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 (12663)
  covalent geometry    : angle       0.65051 (17163)
  hydrogen bonds       : bond        0.03197 (  481)
  hydrogen bonds       : angle       4.33035 ( 1380)

*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3180 Ramachandran restraints generated.
    1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3180 Ramachandran restraints generated.
    1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 1329 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 156
  time to evaluate  : 0.472 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  276 MET cc_start: 0.6384 (mtt) cc_final: 0.4995 (tpp)
REVERT: A  423 GLU cc_start: 0.8136 (mt-10) cc_final: 0.7606 (tt0)
REVERT: A  479 ARG cc_start: 0.8721 (tpt90) cc_final: 0.8501 (mmm160)
REVERT: A  482 LEU cc_start: 0.8327 (OUTLIER) cc_final: 0.7639 (mp)
REVERT: A  608 THR cc_start: 0.8250 (t) cc_final: 0.7770 (p)
REVERT: A  620 SER cc_start: 0.8915 (p) cc_final: 0.8688 (t)
REVERT: A  631 GLU cc_start: 0.7183 (tp30) cc_final: 0.6592 (tp30)
REVERT: B  546 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7580 (mp0)
REVERT: C  483 ASP cc_start: 0.7384 (t0) cc_final: 0.7086 (p0)
REVERT: C  516 MET cc_start: 0.5261 (OUTLIER) cc_final: 0.4070 (mmm)
REVERT: C  558 TRP cc_start: 0.8577 (t60) cc_final: 0.8314 (t-100)
  outliers start: 35
  outliers final: 27
  residues processed: 179
  average time/residue: 0.1089
  time to fit residues: 27.8303
Evaluate side-chains
  177 residues out of total 1329 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 147
  time to evaluate  : 0.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  338 LEU
Chi-restraints excluded: chain A residue  407 HIS
Chi-restraints excluded: chain A residue  411 GLN
Chi-restraints excluded: chain A residue  476 THR
Chi-restraints excluded: chain A residue  482 LEU
Chi-restraints excluded: chain A residue  487 VAL
Chi-restraints excluded: chain A residue  629 LEU
Chi-restraints excluded: chain A residue  632 VAL
Chi-restraints excluded: chain A residue  641 LEU
Chi-restraints excluded: chain A residue  726 HIS
Chi-restraints excluded: chain B residue  258 MET
Chi-restraints excluded: chain B residue  319 HIS
Chi-restraints excluded: chain B residue  342 LEU
Chi-restraints excluded: chain B residue  350 ILE
Chi-restraints excluded: chain B residue  458 VAL
Chi-restraints excluded: chain B residue  546 GLU
Chi-restraints excluded: chain B residue  617 VAL
Chi-restraints excluded: chain B residue  726 HIS
Chi-restraints excluded: chain B residue  743 LEU
Chi-restraints excluded: chain C residue  305 VAL
Chi-restraints excluded: chain C residue  352 VAL
Chi-restraints excluded: chain C residue  401 MET
Chi-restraints excluded: chain C residue  443 LEU
Chi-restraints excluded: chain C residue  475 GLN
Chi-restraints excluded: chain C residue  516 MET
Chi-restraints excluded: chain C residue  611 THR
Chi-restraints excluded: chain C residue  623 LEU
Chi-restraints excluded: chain C residue  682 THR
Chi-restraints excluded: chain C residue  708 LEU
Chi-restraints excluded: chain C residue  768 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 53 optimal weight:    9.9990
   chunk 51 optimal weight:    5.9990
   chunk 94 optimal weight:    5.9990
   chunk 147 optimal weight:    8.9990
   chunk 116 optimal weight:    3.9990
   chunk 156 optimal weight:    0.0270
   chunk 46 optimal weight:    2.9990
   chunk 5 optimal weight:    9.9990
   chunk 57 optimal weight:    0.9980
   chunk 9 optimal weight:    0.7980
   chunk 41 optimal weight:    5.9990
   overall best weight:    1.7642

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4074 r_free = 0.4074 target = 0.136467 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.108930 restraints weight = 29192.039|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.110467 restraints weight = 19044.732|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.111818 restraints weight = 13772.732|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.112031 restraints weight = 12235.388|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.112093 restraints weight = 11386.251|
|-----------------------------------------------------------------------------|
r_work (final): 0.3709
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7597
moved from start:          0.4694

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054  12663  Z= 0.167
  Angle     :  0.704  11.561  17163  Z= 0.342
  Chirality :  0.045   0.156   1953
  Planarity :  0.005   0.061   2229
  Dihedral  :  5.004  21.997   1743
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 11.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.92 %
    Favored  : 92.08 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 16.63 %
    Favored  : 81.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.37 (0.22), residues: 1590
  helix:  0.59 (0.21), residues: 678
  sheet: -1.11 (0.38), residues: 192
  loop : -2.40 (0.23), residues: 720

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B 479 
 TYR   0.015   0.002   TYR C 643 
 PHE   0.013   0.002   PHE C 466 
 TRP   0.037   0.002   TRP B 431 
 HIS   0.009   0.001   HIS A 310 

Details of bonding type rmsd
  covalent geometry    : bond        0.00399 (12663)
  covalent geometry    : angle       0.70386 (17163)
  hydrogen bonds       : bond        0.03661 (  481)
  hydrogen bonds       : angle       4.54440 ( 1380)

*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3180 Ramachandran restraints generated.
    1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3180 Ramachandran restraints generated.
    1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 1329 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 150
  time to evaluate  : 0.516 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  276 MET cc_start: 0.6367 (mtt) cc_final: 0.4916 (tpp)
REVERT: A  423 GLU cc_start: 0.8185 (mt-10) cc_final: 0.7683 (tt0)
REVERT: A  608 THR cc_start: 0.8346 (t) cc_final: 0.7834 (p)
REVERT: A  620 SER cc_start: 0.8917 (p) cc_final: 0.8670 (t)
REVERT: A  631 GLU cc_start: 0.7467 (tp30) cc_final: 0.7210 (tp30)
REVERT: B  345 ARG cc_start: 0.7440 (mpt180) cc_final: 0.7208 (mmt180)
REVERT: B  546 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7596 (mp0)
REVERT: C  516 MET cc_start: 0.5397 (OUTLIER) cc_final: 0.4245 (mmm)
  outliers start: 29
  outliers final: 26
  residues processed: 170
  average time/residue: 0.1159
  time to fit residues: 28.0964
Evaluate side-chains
  173 residues out of total 1329 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 145
  time to evaluate  : 0.491 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  338 LEU
Chi-restraints excluded: chain A residue  407 HIS
Chi-restraints excluded: chain A residue  411 GLN
Chi-restraints excluded: chain A residue  476 THR
Chi-restraints excluded: chain A residue  487 VAL
Chi-restraints excluded: chain A residue  629 LEU
Chi-restraints excluded: chain A residue  641 LEU
Chi-restraints excluded: chain A residue  726 HIS
Chi-restraints excluded: chain B residue  258 MET
Chi-restraints excluded: chain B residue  319 HIS
Chi-restraints excluded: chain B residue  342 LEU
Chi-restraints excluded: chain B residue  350 ILE
Chi-restraints excluded: chain B residue  458 VAL
Chi-restraints excluded: chain B residue  501 ILE
Chi-restraints excluded: chain B residue  546 GLU
Chi-restraints excluded: chain B residue  617 VAL
Chi-restraints excluded: chain B residue  632 VAL
Chi-restraints excluded: chain B residue  726 HIS
Chi-restraints excluded: chain B residue  743 LEU
Chi-restraints excluded: chain C residue  352 VAL
Chi-restraints excluded: chain C residue  401 MET
Chi-restraints excluded: chain C residue  475 GLN
Chi-restraints excluded: chain C residue  516 MET
Chi-restraints excluded: chain C residue  623 LEU
Chi-restraints excluded: chain C residue  663 LEU
Chi-restraints excluded: chain C residue  682 THR
Chi-restraints excluded: chain C residue  708 LEU
Chi-restraints excluded: chain C residue  768 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 21 optimal weight:    0.1980
   chunk 43 optimal weight:    0.0770
   chunk 142 optimal weight:    0.0970
   chunk 152 optimal weight:    1.9990
   chunk 156 optimal weight:    0.7980
   chunk 153 optimal weight:    0.7980
   chunk 150 optimal weight:    0.9990
   chunk 11 optimal weight:    0.8980
   chunk 54 optimal weight:    0.0870
   chunk 100 optimal weight:    0.0470
   chunk 69 optimal weight:    1.9990
   overall best weight:    0.1012

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4124 r_free = 0.4124 target = 0.140041 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.112920 restraints weight = 28907.536|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.114438 restraints weight = 19165.248|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.115481 restraints weight = 13798.702|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.116306 restraints weight = 12002.348|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.116400 restraints weight = 11022.751|
|-----------------------------------------------------------------------------|
r_work (final): 0.3783
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7461
moved from start:          0.5015

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037  12663  Z= 0.108
  Angle     :  0.653  11.736  17163  Z= 0.314
  Chirality :  0.043   0.195   1953
  Planarity :  0.005   0.061   2229
  Dihedral  :  4.679  21.969   1743
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 9.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.04 %
    Favored  : 93.96 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 17.01 %
    Favored  : 81.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.96 (0.22), residues: 1590
  helix:  0.98 (0.21), residues: 672
  sheet: -0.88 (0.39), residues: 190
  loop : -2.20 (0.23), residues: 728

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 545 
 TYR   0.018   0.001   TYR C 643 
 PHE   0.009   0.001   PHE B 657 
 TRP   0.046   0.002   TRP B 431 
 HIS   0.010   0.001   HIS A 310 

Details of bonding type rmsd
  covalent geometry    : bond        0.00238 (12663)
  covalent geometry    : angle       0.65305 (17163)
  hydrogen bonds       : bond        0.02916 (  481)
  hydrogen bonds       : angle       4.25488 ( 1380)

********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3180 Ramachandran restraints generated.
    1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3180 Ramachandran restraints generated.
    1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 1329 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 174
  time to evaluate  : 0.418 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  276 MET cc_start: 0.6370 (mtt) cc_final: 0.4894 (tpp)
REVERT: A  423 GLU cc_start: 0.8046 (mt-10) cc_final: 0.7573 (tt0)
REVERT: A  608 THR cc_start: 0.8207 (t) cc_final: 0.7730 (p)
REVERT: A  620 SER cc_start: 0.8871 (p) cc_final: 0.8636 (t)
REVERT: B  345 ARG cc_start: 0.7384 (mpt180) cc_final: 0.7154 (mmt180)
REVERT: B  439 MET cc_start: 0.7461 (mmp) cc_final: 0.7246 (tpp)
REVERT: B  546 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7639 (mp0)
REVERT: C  516 MET cc_start: 0.5168 (OUTLIER) cc_final: 0.4033 (mmm)
  outliers start: 24
  outliers final: 19
  residues processed: 186
  average time/residue: 0.1044
  time to fit residues: 28.2209
Evaluate side-chains
  171 residues out of total 1329 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 150
  time to evaluate  : 0.485 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  338 LEU
Chi-restraints excluded: chain A residue  407 HIS
Chi-restraints excluded: chain A residue  411 GLN
Chi-restraints excluded: chain A residue  476 THR
Chi-restraints excluded: chain A residue  629 LEU
Chi-restraints excluded: chain A residue  641 LEU
Chi-restraints excluded: chain A residue  726 HIS
Chi-restraints excluded: chain B residue  319 HIS
Chi-restraints excluded: chain B residue  342 LEU
Chi-restraints excluded: chain B residue  458 VAL
Chi-restraints excluded: chain B residue  516 MET
Chi-restraints excluded: chain B residue  546 GLU
Chi-restraints excluded: chain B residue  632 VAL
Chi-restraints excluded: chain B residue  726 HIS
Chi-restraints excluded: chain B residue  743 LEU
Chi-restraints excluded: chain C residue  352 VAL
Chi-restraints excluded: chain C residue  401 MET
Chi-restraints excluded: chain C residue  516 MET
Chi-restraints excluded: chain C residue  682 THR
Chi-restraints excluded: chain C residue  708 LEU
Chi-restraints excluded: chain C residue  768 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 149 optimal weight:    0.7980
   chunk 62 optimal weight:    2.9990
   chunk 35 optimal weight:    0.9990
   chunk 119 optimal weight:    4.9990
   chunk 70 optimal weight:    3.9990
   chunk 116 optimal weight:    0.0570
   chunk 69 optimal weight:    0.9990
   chunk 64 optimal weight:    0.4980
   chunk 30 optimal weight:    0.8980
   chunk 68 optimal weight:   10.0000
   chunk 130 optimal weight:    2.9990
   overall best weight:    0.6500

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4116 r_free = 0.4116 target = 0.139419 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.112163 restraints weight = 29196.733|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.113619 restraints weight = 18888.020|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.115060 restraints weight = 13834.602|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.115525 restraints weight = 12014.677|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.115888 restraints weight = 11145.720|
|-----------------------------------------------------------------------------|
r_work (final): 0.3773
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7485
moved from start:          0.5148

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  12663  Z= 0.111
  Angle     :  0.649  11.190  17163  Z= 0.312
  Chirality :  0.043   0.188   1953
  Planarity :  0.005   0.062   2229
  Dihedral  :  4.635  21.064   1743
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 9.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.04 %
    Favored  : 92.96 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 17.98 %
    Favored  : 80.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.92 (0.22), residues: 1590
  helix:  1.02 (0.21), residues: 680
  sheet: -0.73 (0.38), residues: 188
  loop : -2.26 (0.23), residues: 722

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 545 
 TYR   0.014   0.001   TYR C 643 
 PHE   0.010   0.001   PHE B 657 
 TRP   0.042   0.002   TRP B 431 
 HIS   0.009   0.001   HIS A 310 

Details of bonding type rmsd
  covalent geometry    : bond        0.00256 (12663)
  covalent geometry    : angle       0.64916 (17163)
  hydrogen bonds       : bond        0.02951 (  481)
  hydrogen bonds       : angle       4.22277 ( 1380)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2047.48 seconds
wall clock time: 36 minutes 7.37 seconds (2167.37 seconds total)