Starting phenix.real_space_refine
on Tue Mar  3 18:28:54 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6lle_0912/03_2026/6lle_0912.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6lle_0912/03_2026/6lle_0912.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6lle_0912/03_2026/6lle_0912.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6lle_0912/03_2026/6lle_0912.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6lle_0912/03_2026/6lle_0912.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6lle_0912/03_2026/6lle_0912.cif"
  }
  resolution = 2.9
  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=   0.020
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 7
    Type Number    sf(0)   Gaussians
     Ca      2      9.91       5
     P       3      5.49       5
     Mg      1      5.21       5
     S      58      5.16       5
     C    5038      2.51       5
     N    1319      2.21       5
     O    1495      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 29 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7916
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 7882
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1020, 7882
          Classifications: {'peptide': 1020}
          Link IDs: {'PTRANS': 46, 'TRANS': 973}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 34
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 34
          Unusual residues: {' CA': 2, ' MG': 1, 'ACP': 1}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
  Time building chain proxies: 1.67, per 1000 atoms: 0.21
  Number of scatterers: 7916
  At special positions: 0
  Unit cell: (93.375, 78.435, 141.93, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     Ca      2     19.99
     S      58     16.00
     P       3     15.00
     Mg      1     11.99
     O    1495      8.00
     N    1319      7.00
     C    5038      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: 0.52
  Conformation dependent library (CDL) restraints added in 273.0 milliseconds
  

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1910

  Finding SS restraints...
    Secondary structure from input PDB file:
      42 helices and 6 sheets defined
      52.6% alpha, 15.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.35
  Creating SS restraints...
    Processing helix  chain 'A' and resid 8 through 17
      removed outlier: 3.874A  pdb=" N   PHE A  16 " --> pdb=" O   VAL A  12 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 25 through 37
    Processing helix  chain 'A' and resid 48 through 55
    Processing helix  chain 'A' and resid 56 through 58
      No H-bonds generated for 'chain 'A' and resid 56 through 58'
    Processing helix  chain 'A' and resid 59 through 76
    Processing helix  chain 'A' and resid 88 through 120
      removed outlier: 3.801A  pdb=" N   PHE A  92 " --> pdb=" O   PHE A  88 " (cutoff:3.500A)
      removed outlier: 3.992A  pdb=" N   ILE A  97 " --> pdb=" O   VAL A  93 " (cutoff:3.500A)
      removed outlier: 3.848A  pdb=" N   LEU A  98 " --> pdb=" O   ILE A  94 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 177 through 182
    Processing helix  chain 'A' and resid 226 through 230
      removed outlier: 3.603A  pdb=" N   THR A 230 " --> pdb=" O   GLY A 227 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 247 through 274
    Processing helix  chain 'A' and resid 276 through 280
      removed outlier: 3.631A  pdb=" N   PHE A 279 " --> pdb=" O   ILE A 276 " (cutoff:3.500A)
      removed outlier: 4.229A  pdb=" N   ASN A 280 " --> pdb=" O   GLY A 277 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 276 through 280'
    Processing helix  chain 'A' and resid 287 through 307
      removed outlier: 3.512A  pdb=" N   TYR A 294 " --> pdb=" O   ARG A 290 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 310 through 328
    Processing helix  chain 'A' and resid 335 through 344
      removed outlier: 3.715A  pdb=" N   GLU A 340 " --> pdb=" O   PRO A 337 " (cutoff:3.500A)
      removed outlier: 3.908A  pdb=" N   THR A 341 " --> pdb=" O   SER A 338 " (cutoff:3.500A)
      removed outlier: 4.720A  pdb=" N   LEU A 342 " --> pdb=" O   VAL A 339 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 408 through 420
      removed outlier: 3.732A  pdb=" N   GLU A 412 " --> pdb=" O   ASP A 408 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 439 through 453
    Processing helix  chain 'A' and resid 469 through 477
    Processing helix  chain 'A' and resid 516 through 523
      removed outlier: 3.602A  pdb=" N   ARG A 523 " --> pdb=" O   GLY A 519 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 537 through 554
      removed outlier: 3.687A  pdb=" N   LYS A 541 " --> pdb=" O   THR A 537 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   MET A 545 " --> pdb=" O   LYS A 541 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 571 through 575
    Processing helix  chain 'A' and resid 579 through 586
      removed outlier: 4.110A  pdb=" N   ILE A 584 " --> pdb=" O   ALA A 581 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 605 through 616
      removed outlier: 3.511A  pdb=" N   LYS A 611 " --> pdb=" O   ALA A 607 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 627 through 639
    Processing helix  chain 'A' and resid 654 through 659
    Processing helix  chain 'A' and resid 661 through 672
      removed outlier: 4.005A  pdb=" N   CYS A 669 " --> pdb=" O   GLN A 665 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   LEU A 670 " --> pdb=" O   ARG A 666 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 679 through 693
      removed outlier: 3.640A  pdb=" N   VAL A 687 " --> pdb=" O   LYS A 683 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 706 through 713
      removed outlier: 3.513A  pdb=" N   LYS A 712 " --> pdb=" O   PRO A 708 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 723 through 729
    Processing helix  chain 'A' and resid 740 through 781
      removed outlier: 3.543A  pdb=" N   ALA A 744 " --> pdb=" O   SER A 740 " (cutoff:3.500A)
      removed outlier: 3.831A  pdb=" N   GLY A 769 " --> pdb=" O   SER A 765 " (cutoff:3.500A)
      removed outlier: 3.827A  pdb=" N   ILE A 774 " --> pdb=" O   GLU A 770 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 787 through 799
    Processing helix  chain 'A' and resid 800 through 805
    Processing helix  chain 'A' and resid 806 through 809
    Processing helix  chain 'A' and resid 829 through 857
      removed outlier: 3.683A  pdb=" N   TRP A 854 " --> pdb=" O   ALA A 850 " (cutoff:3.500A)
      removed outlier: 4.179A  pdb=" N   PHE A 855 " --> pdb=" O   ALA A 851 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 865 through 871
    Processing helix  chain 'A' and resid 872 through 875
    Processing helix  chain 'A' and resid 886 through 890
    Processing helix  chain 'A' and resid 892 through 913
      removed outlier: 4.329A  pdb=" N   MET A 896 " --> pdb=" O   SER A 892 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   LEU A 912 " --> pdb=" O   MET A 908 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   ASN A 913 " --> pdb=" O   CYS A 909 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 925 through 928
    Processing helix  chain 'A' and resid 929 through 949
    Processing helix  chain 'A' and resid 952 through 957
    Processing helix  chain 'A' and resid 962 through 974
      removed outlier: 3.641A  pdb=" N   MET A 968 " --> pdb=" O   THR A 964 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 974 through 990
      removed outlier: 3.915A  pdb=" N   LEU A 978 " --> pdb=" O   LEU A 974 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1015 through 1030
      removed outlier: 3.638A  pdb=" N   LEU A1021 " --> pdb=" O   PRO A1017 " (cutoff:3.500A)
      Proline residue:  A1024  - end of helix
    Processing sheet with id=AA1, first strand: chain 'A' and resid 138 through 141
      removed outlier: 4.556A  pdb=" N   LYS A 128 " --> pdb=" O   GLU A 152 " (cutoff:3.500A)
      removed outlier: 4.194A  pdb=" N   ILE A 150 " --> pdb=" O   TYR A 130 " (cutoff:3.500A)
      removed outlier: 7.064A  pdb=" N   MET A 220 " --> pdb=" O   THR A 166 " (cutoff:3.500A)
      removed outlier: 7.137A  pdb=" N   ASP A 162 " --> pdb=" O   VAL A 224 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 187 through 188
      removed outlier: 6.294A  pdb=" N   ARG A 174 " --> pdb=" O   ALA A 215 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 331 through 333
      removed outlier: 6.331A  pdb=" N   GLY A 716 " --> pdb=" O   MET A 732 " (cutoff:3.500A)
      removed outlier: 7.571A  pdb=" N   LEU A 734 " --> pdb=" O   GLY A 716 " (cutoff:3.500A)
      removed outlier: 6.928A  pdb=" N   ALA A 718 " --> pdb=" O   LEU A 734 " (cutoff:3.500A)
      removed outlier: 6.969A  pdb=" N   THR A 697 " --> pdb=" O   ILE A 715 " (cutoff:3.500A)
      removed outlier: 8.124A  pdb=" N   ILE A 717 " --> pdb=" O   THR A 697 " (cutoff:3.500A)
      removed outlier: 6.613A  pdb=" N   MET A 699 " --> pdb=" O   ILE A 717 " (cutoff:3.500A)
      removed outlier: 8.117A  pdb=" N   MET A 719 " --> pdb=" O   MET A 699 " (cutoff:3.500A)
      removed outlier: 7.920A  pdb=" N   GLY A 701 " --> pdb=" O   MET A 719 " (cutoff:3.500A)
      removed outlier: 6.710A  pdb=" N   VAL A 347 " --> pdb=" O   ALA A 698 " (cutoff:3.500A)
      removed outlier: 7.835A  pdb=" N   THR A 700 " --> pdb=" O   VAL A 347 " (cutoff:3.500A)
      removed outlier: 6.636A  pdb=" N   CYS A 349 " --> pdb=" O   THR A 700 " (cutoff:3.500A)
      removed outlier: 8.239A  pdb=" N   PHE A 675 " --> pdb=" O   VAL A 620 " (cutoff:3.500A)
      removed outlier: 6.045A  pdb=" N   MET A 622 " --> pdb=" O   PHE A 675 " (cutoff:3.500A)
      removed outlier: 6.556A  pdb=" N   PHE A 652 " --> pdb=" O   ALA A 676 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 395 through 396
      removed outlier: 6.927A  pdb=" N   THR A 376 " --> pdb=" O   VAL A 372 " (cutoff:3.500A)
      removed outlier: 4.848A  pdb=" N   VAL A 372 " --> pdb=" O   THR A 376 " (cutoff:3.500A)
      removed outlier: 6.736A  pdb=" N   SER A 378 " --> pdb=" O   ASP A 370 " (cutoff:3.500A)
      removed outlier: 4.881A  pdb=" N   CYS A 364 " --> pdb=" O   ILE A 384 " (cutoff:3.500A)
      removed outlier: 5.607A  pdb=" N   VAL A 363 " --> pdb=" O   LEU A 599 " (cutoff:3.500A)
      removed outlier: 6.213A  pdb=" N   LEU A 599 " --> pdb=" O   VAL A 363 " (cutoff:3.500A)
      removed outlier: 4.238A  pdb=" N   LEU A 369 " --> pdb=" O   VAL A 593 " (cutoff:3.500A)
      removed outlier: 8.524A  pdb=" N   VAL A 593 " --> pdb=" O   LEU A 369 " (cutoff:3.500A)
      removed outlier: 14.085A  pdb=" N   ARG A 371 " --> pdb=" O   THR A 591 " (cutoff:3.500A)
      removed outlier: 15.739A  pdb=" N   THR A 591 " --> pdb=" O   ARG A 371 " (cutoff:3.500A)
      removed outlier: 5.370A  pdb=" N   PHE A 592 " --> pdb=" O   THR A 565 " (cutoff:3.500A)
      removed outlier: 6.075A  pdb=" N   THR A 565 " --> pdb=" O   PHE A 592 " (cutoff:3.500A)
      removed outlier: 6.357A  pdb=" N   SER A 493 " --> pdb=" O   GLU A 486 " (cutoff:3.500A)
      removed outlier: 6.129A  pdb=" N   GLU A 486 " --> pdb=" O   SER A 493 " (cutoff:3.500A)
      removed outlier: 6.586A  pdb=" N   SER A 495 " --> pdb=" O   THR A 484 " (cutoff:3.500A)
      removed outlier: 4.742A  pdb=" N   THR A 484 " --> pdb=" O   SER A 495 " (cutoff:3.500A)
      removed outlier: 6.720A  pdb=" N   TYR A 497 " --> pdb=" O   GLU A 482 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 395 through 396
      removed outlier: 6.927A  pdb=" N   THR A 376 " --> pdb=" O   VAL A 372 " (cutoff:3.500A)
      removed outlier: 4.848A  pdb=" N   VAL A 372 " --> pdb=" O   THR A 376 " (cutoff:3.500A)
      removed outlier: 6.736A  pdb=" N   SER A 378 " --> pdb=" O   ASP A 370 " (cutoff:3.500A)
      removed outlier: 4.881A  pdb=" N   CYS A 364 " --> pdb=" O   ILE A 384 " (cutoff:3.500A)
      removed outlier: 5.607A  pdb=" N   VAL A 363 " --> pdb=" O   LEU A 599 " (cutoff:3.500A)
      removed outlier: 6.213A  pdb=" N   LEU A 599 " --> pdb=" O   VAL A 363 " (cutoff:3.500A)
      removed outlier: 4.238A  pdb=" N   LEU A 369 " --> pdb=" O   VAL A 593 " (cutoff:3.500A)
      removed outlier: 8.524A  pdb=" N   VAL A 593 " --> pdb=" O   LEU A 369 " (cutoff:3.500A)
      removed outlier: 14.085A  pdb=" N   ARG A 371 " --> pdb=" O   THR A 591 " (cutoff:3.500A)
      removed outlier: 15.739A  pdb=" N   THR A 591 " --> pdb=" O   ARG A 371 " (cutoff:3.500A)
      removed outlier: 5.908A  pdb=" N   LEU A 590 " --> pdb=" O   CYS A 524 " (cutoff:3.500A)
      removed outlier: 6.558A  pdb=" N   GLY A 594 " --> pdb=" O   ARG A 528 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 424 through 428

    427 hydrogen bonds defined for protein.
    1209 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: 1.41

  Time building geometry restraints manager: 0.74 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        1.23 -     1.35: 2592
        1.35 -     1.48: 1830
        1.48 -     1.61: 3546
        1.61 -     1.73: 4
        1.73 -     1.86: 92
  Bond restraints: 8064
  Sorted by residual:
  bond pdb=" C1' ACP A2001 "
       pdb=" O4' ACP A2001 "
    ideal  model  delta    sigma   weight residual
    1.390  1.617 -0.227 2.00e-02 2.50e+03 1.29e+02
  bond pdb=" C1' ACP A2001 "
       pdb=" C2' ACP A2001 "
    ideal  model  delta    sigma   weight residual
    1.527  1.306  0.221 2.00e-02 2.50e+03 1.23e+02
  bond pdb=" C4' ACP A2001 "
       pdb=" O4' ACP A2001 "
    ideal  model  delta    sigma   weight residual
    1.428  1.299  0.129 2.00e-02 2.50e+03 4.16e+01
  bond pdb=" C6  ACP A2001 "
       pdb=" N6  ACP A2001 "
    ideal  model  delta    sigma   weight residual
    1.335  1.451 -0.116 2.00e-02 2.50e+03 3.34e+01
  bond pdb=" C2' ACP A2001 "
       pdb=" O2' ACP A2001 "
    ideal  model  delta    sigma   weight residual
    1.401  1.493 -0.092 2.00e-02 2.50e+03 2.13e+01
  ... (remaining 8059 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.05: 10885
        3.05 -     6.10: 56
        6.10 -     9.14: 5
        9.14 -    12.19: 4
       12.19 -    15.24: 1
  Bond angle restraints: 10951
  Sorted by residual:
  angle pdb=" O3A ACP A2001 "
        pdb=" PA  ACP A2001 "
        pdb=" O5' ACP A2001 "
      ideal   model   delta    sigma   weight residual
      93.75  108.99  -15.24 3.00e+00 1.11e-01 2.58e+01
  angle pdb=" C3B ACP A2001 "
        pdb=" PB  ACP A2001 "
        pdb=" O3A ACP A2001 "
      ideal   model   delta    sigma   weight residual
      98.05  110.24  -12.19 3.00e+00 1.11e-01 1.65e+01
  angle pdb=" O1B ACP A2001 "
        pdb=" PB  ACP A2001 "
        pdb=" O2B ACP A2001 "
      ideal   model   delta    sigma   weight residual
     119.60  109.22   10.38 3.00e+00 1.11e-01 1.20e+01
  angle pdb=" N1  ACP A2001 "
        pdb=" C6  ACP A2001 "
        pdb=" N6  ACP A2001 "
      ideal   model   delta    sigma   weight residual
     119.32  109.04   10.28 3.00e+00 1.11e-01 1.17e+01
  angle pdb=" O1A ACP A2001 "
        pdb=" PA  ACP A2001 "
        pdb=" O2A ACP A2001 "
      ideal   model   delta    sigma   weight residual
     118.95  108.80   10.15 3.00e+00 1.11e-01 1.14e+01
  ... (remaining 10946 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    23.50: 4684
       23.50 -    47.00: 182
       47.00 -    70.49: 20
       70.49 -    93.99: 10
       93.99 -   117.49: 1
  Dihedral angle restraints: 4897
    sinusoidal: 1951
      harmonic: 2946
  Sorted by residual:
  dihedral pdb=" CA  ILE A 153 "
           pdb=" C   ILE A 153 "
           pdb=" N   ALA A 154 "
           pdb=" CA  ALA A 154 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.82   27.18     0      5.00e+00 4.00e-02 2.95e+01
  dihedral pdb=" O1A ACP A2001 "
           pdb=" O3A ACP A2001 "
           pdb=" PA  ACP A2001 "
           pdb=" PB  ACP A2001 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -48.75   68.74 -117.49     1      3.00e+01 1.11e-03 1.56e+01
  dihedral pdb=" CA  VAL A 949 "
           pdb=" C   VAL A 949 "
           pdb=" N   GLU A 950 "
           pdb=" CA  GLU A 950 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.47  -17.53     0      5.00e+00 4.00e-02 1.23e+01
  ... (remaining 4894 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.079: 1184
       0.079 -    0.158: 97
       0.158 -    0.237: 1
       0.237 -    0.316: 0
       0.316 -    0.395: 1
  Chirality restraints: 1283
  Sorted by residual:
  chirality pdb=" C2' ACP A2001 "
            pdb=" C1' ACP A2001 "
            pdb=" C3' ACP A2001 "
            pdb=" O2' ACP A2001 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.75   -2.36   -0.40 2.00e-01 2.50e+01 3.90e+00
  chirality pdb=" CB  ILE A 153 "
            pdb=" CA  ILE A 153 "
            pdb=" CG1 ILE A 153 "
            pdb=" CG2 ILE A 153 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.83   -0.18 2.00e-01 2.50e+01 8.37e-01
  chirality pdb=" CA  ILE A 623 "
            pdb=" N   ILE A 623 "
            pdb=" C   ILE A 623 "
            pdb=" CB  ILE A 623 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.01e-01
  ... (remaining 1280 not shown)

  Planarity restraints: 1390
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TRP A1016 "   -0.024 5.00e-02 4.00e+02   3.60e-02 2.08e+00
        pdb=" N   PRO A1017 "    0.062 5.00e-02 4.00e+02
        pdb=" CA  PRO A1017 "   -0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO A1017 "   -0.020 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A 661 "   -0.021 5.00e-02 4.00e+02   3.11e-02 1.55e+00
        pdb=" N   PRO A 662 "    0.054 5.00e-02 4.00e+02
        pdb=" CA  PRO A 662 "   -0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO A 662 "   -0.017 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 974 "   -0.020 5.00e-02 4.00e+02   3.02e-02 1.46e+00
        pdb=" N   PRO A 975 "    0.052 5.00e-02 4.00e+02
        pdb=" CA  PRO A 975 "   -0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO A 975 "   -0.017 5.00e-02 4.00e+02
  ... (remaining 1387 not shown)

  Histogram of nonbonded interaction distances:
        2.05 -     2.62: 91
        2.62 -     3.19: 6955
        3.19 -     3.76: 12323
        3.76 -     4.33: 17608
        4.33 -     4.90: 29040
  Nonbonded interactions: 66017
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP A 351 "
            pdb="MG    MG A2002 "
     model   vdw
     2.050 2.170
  nonbonded pdb=" O   THR A 353 "
            pdb="MG    MG A2002 "
     model   vdw
     2.114 2.170
  nonbonded pdb=" OD1 ASP A 351 "
            pdb="MG    MG A2002 "
     model   vdw
     2.170 2.170
  nonbonded pdb=" O3G ACP A2001 "
            pdb="MG    MG A2002 "
     model   vdw
     2.171 2.170
  nonbonded pdb=" OD1 ASP A 702 "
            pdb="MG    MG A2002 "
     model   vdw
     2.192 2.170
  ... (remaining 66012 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.260
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.090
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     8.200
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  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:6.970
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.620
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7841
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.227   8064  Z= 0.260
  Angle     :  0.632  15.238  10951  Z= 0.315
  Chirality :  0.043   0.395   1283
  Planarity :  0.004   0.036   1390
  Dihedral  : 13.044 117.490   2987
  Min Nonbonded Distance : 2.050

Molprobity Statistics.
  All-atom Clashscore : 6.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.32 %
    Favored  : 96.68 %
  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 are not related in a simple way.
  whole: -1.87 (0.24), residues: 1014
  helix: -0.83 (0.22), residues: 472
  sheet: -1.09 (0.47), residues: 104
  loop : -1.62 (0.27), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 677 
 TYR   0.015   0.001   TYR A 842 
 PHE   0.012   0.001   PHE A 367 
 TRP   0.009   0.001   TRP A 793 
 HIS   0.007   0.001   HIS A 566 

Details of bonding type rmsd
  covalent geometry    : bond        0.00540 ( 8064)
  covalent geometry    : angle       0.63241 (10951)
  hydrogen bonds       : bond        0.14837 (  415)
  hydrogen bonds       : angle       6.66692 ( 1209)

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 183
  time to evaluate  : 0.303 
Fit side-chains
REVERT: A  251 GLN cc_start: 0.7762 (mt0) cc_final: 0.7538 (mt0)
REVERT: A  394 GLU cc_start: 0.7494 (mt-10) cc_final: 0.7073 (mt-10)
REVERT: A  439 GLU cc_start: 0.7554 (tt0) cc_final: 0.7331 (tt0)
REVERT: A  479 MET cc_start: 0.7209 (mtt) cc_final: 0.6970 (mtp)
REVERT: A  531 SER cc_start: 0.9135 (p) cc_final: 0.8890 (p)
REVERT: A  545 MET cc_start: 0.8044 (mmm) cc_final: 0.7714 (mmm)
REVERT: A  572 ARG cc_start: 0.6945 (tpt90) cc_final: 0.6681 (tpt-90)
REVERT: A  575 MET cc_start: 0.9284 (mtt) cc_final: 0.8931 (mtt)
REVERT: A  667 ASP cc_start: 0.7962 (t0) cc_final: 0.7745 (t0)
REVERT: A  816 MET cc_start: 0.8749 (mmm) cc_final: 0.8485 (mmm)
REVERT: A  917 GLU cc_start: 0.7797 (tt0) cc_final: 0.7484 (tt0)
REVERT: A  940 MET cc_start: 0.8639 (mmm) cc_final: 0.8180 (mmm)
REVERT: A 1023 MET cc_start: 0.6803 (tpp) cc_final: 0.6589 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 183
  average time/residue: 0.5622
  time to fit residues: 108.4385
Evaluate side-chains
  126 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 126
  time to evaluate  : 0.245 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 49 optimal weight:    0.9980
   chunk 97 optimal weight:    0.8980
   chunk 53 optimal weight:    4.9990
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    4.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    1.9990
   chunk 100 optimal weight:    8.9990
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:    0.8980
   overall best weight:    1.1582

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

Flipped N/Q/H residues before XYZ refinement:
A  15 HIS
A 190 HIS
A 275 ASN
A 469 ASN
A 817 ASN
A 913 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.140024 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.108488 restraints weight = 8466.785|
|-----------------------------------------------------------------------------|
r_work (start): 0.3102 rms_B_bonded: 1.66
r_work: 0.2939 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.2798 rms_B_bonded: 3.89 restraints_weight: 0.2500
r_work (final): 0.2798
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8127
moved from start:          0.1357

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8064  Z= 0.147
  Angle     :  0.547   6.850  10951  Z= 0.282
  Chirality :  0.043   0.152   1283
  Planarity :  0.004   0.036   1390
  Dihedral  :  8.185 146.480   1110
  Min Nonbonded Distance : 2.084

Molprobity Statistics.
  All-atom Clashscore : 5.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  3.32 %
    Allowed  : 11.91 %
    Favored  : 84.77 %
  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 are not related in a simple way.
  whole: -0.64 (0.26), residues: 1014
  helix:  0.41 (0.24), residues: 485
  sheet: -0.91 (0.44), residues: 117
  loop : -1.20 (0.29), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 365 
 TYR   0.015   0.002   TYR A 842 
 PHE   0.020   0.001   PHE A 367 
 TRP   0.010   0.001   TRP A 793 
 HIS   0.007   0.001   HIS A 566 

Details of bonding type rmsd
  covalent geometry    : bond        0.00350 ( 8064)
  covalent geometry    : angle       0.54658 (10951)
  hydrogen bonds       : bond        0.04054 (  415)
  hydrogen bonds       : angle       4.68024 ( 1209)

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 124
  time to evaluate  : 0.301 
Fit side-chains
REVERT: A   31 LYS cc_start: 0.7743 (mtpt) cc_final: 0.7447 (mtmm)
REVERT: A   40 GLU cc_start: 0.8513 (pt0) cc_final: 0.8311 (pt0)
REVERT: A   51 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.7553 (pt0)
REVERT: A  135 LYS cc_start: 0.8730 (tptp) cc_final: 0.8290 (mtpp)
REVERT: A  251 GLN cc_start: 0.8007 (mt0) cc_final: 0.7729 (mt0)
REVERT: A  280 ASN cc_start: 0.8182 (OUTLIER) cc_final: 0.7823 (p0)
REVERT: A  309 GLU cc_start: 0.8835 (pm20) cc_final: 0.8489 (pm20)
REVERT: A  394 GLU cc_start: 0.8070 (mt-10) cc_final: 0.7597 (mt-10)
REVERT: A  479 MET cc_start: 0.7270 (mtt) cc_final: 0.6969 (mtp)
REVERT: A  531 SER cc_start: 0.9131 (p) cc_final: 0.8910 (p)
REVERT: A  545 MET cc_start: 0.8222 (mmm) cc_final: 0.7864 (mmm)
REVERT: A  572 ARG cc_start: 0.7023 (tpt90) cc_final: 0.6732 (tpt-90)
REVERT: A  575 MET cc_start: 0.9187 (mtt) cc_final: 0.8794 (mtt)
REVERT: A  599 LEU cc_start: 0.8977 (pp) cc_final: 0.8643 (pt)
REVERT: A  816 MET cc_start: 0.8902 (mmm) cc_final: 0.8594 (mmm)
REVERT: A  917 GLU cc_start: 0.8440 (tt0) cc_final: 0.8026 (tt0)
  outliers start: 29
  outliers final: 11
  residues processed: 140
  average time/residue: 0.4845
  time to fit residues: 72.2447
Evaluate side-chains
  127 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 114
  time to evaluate  : 0.209 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 GLU
Chi-restraints excluded: chain A residue  155 VAL
Chi-restraints excluded: chain A residue  265 SER
Chi-restraints excluded: chain A residue  280 ASN
Chi-restraints excluded: chain A residue  463 SER
Chi-restraints excluded: chain A residue  561 LEU
Chi-restraints excluded: chain A residue  608 SER
Chi-restraints excluded: chain A residue  649 SER
Chi-restraints excluded: chain A residue  661 ASN
Chi-restraints excluded: chain A residue  702 ASP
Chi-restraints excluded: chain A residue  916 SER
Chi-restraints excluded: chain A residue  954 LEU
Chi-restraints excluded: chain A residue  967 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 40 optimal weight:    4.9990
   chunk 20 optimal weight:    3.9990
   chunk 3 optimal weight:    5.9990
   chunk 41 optimal weight:    0.7980
   chunk 62 optimal weight:    1.9990
   chunk 97 optimal weight:    4.9990
   chunk 9 optimal weight:    0.9980
   chunk 71 optimal weight:    2.9990
   chunk 100 optimal weight:    4.9990
   chunk 78 optimal weight:    4.9990
   chunk 98 optimal weight:    1.9990
   overall best weight:    1.7586

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

Flipped N/Q/H residues before XYZ refinement:
A 566 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.141289 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.110268 restraints weight = 8483.286|
|-----------------------------------------------------------------------------|
r_work (start): 0.3075 rms_B_bonded: 1.61
r_work: 0.2910 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.2767 rms_B_bonded: 3.83 restraints_weight: 0.2500
r_work (final): 0.2767
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8186
moved from start:          0.1606

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   8064  Z= 0.192
  Angle     :  0.591   7.768  10951  Z= 0.302
  Chirality :  0.045   0.227   1283
  Planarity :  0.004   0.041   1390
  Dihedral  :  8.471 154.952   1110
  Min Nonbonded Distance : 2.071

Molprobity Statistics.
  All-atom Clashscore : 5.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  3.78 %
    Allowed  : 13.52 %
    Favored  : 82.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.25 (0.26), residues: 1014
  helix:  0.76 (0.24), residues: 492
  sheet: -0.73 (0.44), residues: 117
  loop : -1.07 (0.30), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 677 
 TYR   0.017   0.002   TYR A 842 
 PHE   0.020   0.001   PHE A 367 
 TRP   0.010   0.001   TRP A 793 
 HIS   0.007   0.001   HIS A 566 

Details of bonding type rmsd
  covalent geometry    : bond        0.00470 ( 8064)
  covalent geometry    : angle       0.59144 (10951)
  hydrogen bonds       : bond        0.04218 (  415)
  hydrogen bonds       : angle       4.65583 ( 1209)

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 119
  time to evaluate  : 0.197 
Fit side-chains
REVERT: A   10 GLU cc_start: 0.7870 (mm-30) cc_final: 0.7635 (mm-30)
REVERT: A   40 GLU cc_start: 0.8511 (pt0) cc_final: 0.8311 (pt0)
REVERT: A   51 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7609 (pt0)
REVERT: A  135 LYS cc_start: 0.8755 (tptp) cc_final: 0.8337 (mtmt)
REVERT: A  198 ARG cc_start: 0.8182 (OUTLIER) cc_final: 0.7438 (mmp80)
REVERT: A  280 ASN cc_start: 0.8268 (OUTLIER) cc_final: 0.7909 (p0)
REVERT: A  309 GLU cc_start: 0.8894 (pm20) cc_final: 0.8483 (pm20)
REVERT: A  394 GLU cc_start: 0.8078 (mt-10) cc_final: 0.7626 (mt-10)
REVERT: A  479 MET cc_start: 0.7270 (mtt) cc_final: 0.6942 (mtp)
REVERT: A  531 SER cc_start: 0.9146 (p) cc_final: 0.8933 (p)
REVERT: A  545 MET cc_start: 0.8412 (mmm) cc_final: 0.8068 (mmm)
REVERT: A  572 ARG cc_start: 0.7119 (tpt90) cc_final: 0.6889 (tpt-90)
REVERT: A  575 MET cc_start: 0.9151 (mtt) cc_final: 0.8777 (mtt)
REVERT: A  623 ILE cc_start: 0.9178 (OUTLIER) cc_final: 0.8882 (mt)
REVERT: A  816 MET cc_start: 0.8939 (mmm) cc_final: 0.8647 (mmm)
REVERT: A  940 MET cc_start: 0.8785 (mmm) cc_final: 0.8429 (mmm)
REVERT: A 1039 MET cc_start: 0.5366 (mmm) cc_final: 0.5120 (mmm)
  outliers start: 33
  outliers final: 14
  residues processed: 139
  average time/residue: 0.4947
  time to fit residues: 73.1202
Evaluate side-chains
  131 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 113
  time to evaluate  : 0.256 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 GLU
Chi-restraints excluded: chain A residue  117 GLU
Chi-restraints excluded: chain A residue  152 GLU
Chi-restraints excluded: chain A residue  155 VAL
Chi-restraints excluded: chain A residue  178 SER
Chi-restraints excluded: chain A residue  198 ARG
Chi-restraints excluded: chain A residue  255 GLU
Chi-restraints excluded: chain A residue  265 SER
Chi-restraints excluded: chain A residue  276 ILE
Chi-restraints excluded: chain A residue  280 ASN
Chi-restraints excluded: chain A residue  463 SER
Chi-restraints excluded: chain A residue  561 LEU
Chi-restraints excluded: chain A residue  608 SER
Chi-restraints excluded: chain A residue  623 ILE
Chi-restraints excluded: chain A residue  649 SER
Chi-restraints excluded: chain A residue  702 ASP
Chi-restraints excluded: chain A residue  731 GLU
Chi-restraints excluded: chain A residue  967 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 2 optimal weight:    0.6980
   chunk 53 optimal weight:    3.9990
   chunk 50 optimal weight:    0.0870
   chunk 6 optimal weight:    0.5980
   chunk 17 optimal weight:    0.7980
   chunk 93 optimal weight:    0.9990
   chunk 100 optimal weight:    2.9990
   chunk 61 optimal weight:    2.9990
   chunk 79 optimal weight:    0.5980
   chunk 74 optimal weight:    0.6980
   chunk 26 optimal weight:    0.7980
   overall best weight:    0.5358

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

Flipped N/Q/H residues before XYZ refinement:
A 251 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.146191 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.115730 restraints weight = 8621.578|
|-----------------------------------------------------------------------------|
r_work (start): 0.3222 rms_B_bonded: 1.62
r_work: 0.3064 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.2924 rms_B_bonded: 3.90 restraints_weight: 0.2500
r_work (final): 0.2924
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8134
moved from start:          0.1797

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   8064  Z= 0.103
  Angle     :  0.503   7.629  10951  Z= 0.257
  Chirality :  0.041   0.169   1283
  Planarity :  0.003   0.040   1390
  Dihedral  :  8.292 155.495   1110
  Min Nonbonded Distance : 2.084

Molprobity Statistics.
  All-atom Clashscore : 5.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  3.67 %
    Allowed  : 14.66 %
    Favored  : 81.67 %
  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 are not related in a simple way.
  whole:  0.35 (0.27), residues: 1014
  helix:  1.35 (0.24), residues: 486
  sheet: -0.51 (0.46), residues: 117
  loop : -0.85 (0.31), residues: 411

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 666 
 TYR   0.013   0.001   TYR A 842 
 PHE   0.014   0.001   PHE A 367 
 TRP   0.009   0.001   TRP A 793 
 HIS   0.002   0.000   HIS A 682 

Details of bonding type rmsd
  covalent geometry    : bond        0.00233 ( 8064)
  covalent geometry    : angle       0.50314 (10951)
  hydrogen bonds       : bond        0.03212 (  415)
  hydrogen bonds       : angle       4.22792 ( 1209)

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 124
  time to evaluate  : 0.292 
Fit side-chains
REVERT: A   10 GLU cc_start: 0.7858 (mm-30) cc_final: 0.7645 (mm-30)
REVERT: A   51 GLU cc_start: 0.7956 (tt0) cc_final: 0.7559 (pt0)
REVERT: A   77 TRP cc_start: 0.6624 (OUTLIER) cc_final: 0.5889 (m100)
REVERT: A  135 LYS cc_start: 0.8746 (tptp) cc_final: 0.8323 (mtmt)
REVERT: A  280 ASN cc_start: 0.8197 (OUTLIER) cc_final: 0.7854 (p0)
REVERT: A  309 GLU cc_start: 0.8847 (pm20) cc_final: 0.8567 (pm20)
REVERT: A  394 GLU cc_start: 0.8038 (mt-10) cc_final: 0.7537 (mt-10)
REVERT: A  479 MET cc_start: 0.7226 (mtt) cc_final: 0.6882 (mtp)
REVERT: A  531 SER cc_start: 0.9171 (p) cc_final: 0.8964 (p)
REVERT: A  545 MET cc_start: 0.8384 (mmm) cc_final: 0.8053 (mmm)
REVERT: A  575 MET cc_start: 0.9108 (mtt) cc_final: 0.8721 (mtt)
REVERT: A  623 ILE cc_start: 0.9099 (OUTLIER) cc_final: 0.8798 (mt)
REVERT: A  816 MET cc_start: 0.8918 (mmm) cc_final: 0.8589 (mmm)
REVERT: A  940 MET cc_start: 0.8792 (mmm) cc_final: 0.8457 (mmm)
REVERT: A  979 MET cc_start: 0.8632 (ttm) cc_final: 0.8375 (ttm)
REVERT: A 1039 MET cc_start: 0.5537 (mmm) cc_final: 0.5298 (mmm)
  outliers start: 32
  outliers final: 12
  residues processed: 141
  average time/residue: 0.5152
  time to fit residues: 77.2580
Evaluate side-chains
  130 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 115
  time to evaluate  : 0.233 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue   77 TRP
Chi-restraints excluded: chain A residue   96 LEU
Chi-restraints excluded: chain A residue  117 GLU
Chi-restraints excluded: chain A residue  155 VAL
Chi-restraints excluded: chain A residue  178 SER
Chi-restraints excluded: chain A residue  222 VAL
Chi-restraints excluded: chain A residue  265 SER
Chi-restraints excluded: chain A residue  276 ILE
Chi-restraints excluded: chain A residue  280 ASN
Chi-restraints excluded: chain A residue  385 THR
Chi-restraints excluded: chain A residue  608 SER
Chi-restraints excluded: chain A residue  623 ILE
Chi-restraints excluded: chain A residue  702 ASP
Chi-restraints excluded: chain A residue  967 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 32 optimal weight:    1.9990
   chunk 97 optimal weight:    0.9990
   chunk 99 optimal weight:    6.9990
   chunk 78 optimal weight:    0.9980
   chunk 98 optimal weight:    0.6980
   chunk 42 optimal weight:    2.9990
   chunk 92 optimal weight:    0.9990
   chunk 53 optimal weight:    3.9990
   chunk 19 optimal weight:    2.9990
   chunk 93 optimal weight:    0.6980
   chunk 96 optimal weight:    1.9990
   overall best weight:    0.8784

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

Flipped N/Q/H residues before XYZ refinement:
A 251 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.140356 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3163 r_free = 0.3163 target = 0.108675 restraints weight = 8517.696|
|-----------------------------------------------------------------------------|
r_work (start): 0.3074 rms_B_bonded: 1.68
r_work: 0.2909 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.2768 rms_B_bonded: 3.93 restraints_weight: 0.2500
r_work (final): 0.2768
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8108
moved from start:          0.1878

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8064  Z= 0.124
  Angle     :  0.526   7.480  10951  Z= 0.267
  Chirality :  0.042   0.180   1283
  Planarity :  0.003   0.040   1390
  Dihedral  :  8.340 153.940   1110
  Min Nonbonded Distance : 2.142

Molprobity Statistics.
  All-atom Clashscore : 5.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 16.49 %
    Favored  : 80.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.56 (0.27), residues: 1014
  helix:  1.54 (0.24), residues: 485
  sheet: -0.44 (0.46), residues: 117
  loop : -0.76 (0.31), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 572 
 TYR   0.015   0.001   TYR A 842 
 PHE   0.017   0.001   PHE A 367 
 TRP   0.008   0.001   TRP A 793 
 HIS   0.002   0.001   HIS A 566 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 ( 8064)
  covalent geometry    : angle       0.52600 (10951)
  hydrogen bonds       : bond        0.03382 (  415)
  hydrogen bonds       : angle       4.23760 ( 1209)

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 116
  time to evaluate  : 0.239 
Fit side-chains
REVERT: A   10 GLU cc_start: 0.7832 (mm-30) cc_final: 0.7542 (mm-30)
REVERT: A   31 LYS cc_start: 0.7717 (mtpt) cc_final: 0.7433 (mtmt)
REVERT: A   33 LYS cc_start: 0.8003 (tttt) cc_final: 0.7567 (ttmt)
REVERT: A   51 GLU cc_start: 0.7958 (tt0) cc_final: 0.7563 (pt0)
REVERT: A   77 TRP cc_start: 0.6787 (OUTLIER) cc_final: 0.6178 (m100)
REVERT: A  135 LYS cc_start: 0.8729 (tptp) cc_final: 0.8299 (mtmt)
REVERT: A  309 GLU cc_start: 0.8856 (pm20) cc_final: 0.8516 (pm20)
REVERT: A  394 GLU cc_start: 0.8039 (mt-10) cc_final: 0.7521 (mt-10)
REVERT: A  479 MET cc_start: 0.7287 (mtt) cc_final: 0.6942 (mtp)
REVERT: A  531 SER cc_start: 0.9151 (p) cc_final: 0.8939 (p)
REVERT: A  545 MET cc_start: 0.8457 (mmm) cc_final: 0.8109 (mmm)
REVERT: A  575 MET cc_start: 0.9093 (mtt) cc_final: 0.8741 (mtt)
REVERT: A  623 ILE cc_start: 0.9124 (OUTLIER) cc_final: 0.8843 (mt)
REVERT: A  816 MET cc_start: 0.8890 (mmm) cc_final: 0.8605 (mmm)
REVERT: A  940 MET cc_start: 0.8762 (mmm) cc_final: 0.8415 (mmm)
REVERT: A  979 MET cc_start: 0.8641 (ttm) cc_final: 0.8345 (ttm)
REVERT: A 1039 MET cc_start: 0.5546 (mmm) cc_final: 0.5278 (mmm)
  outliers start: 27
  outliers final: 13
  residues processed: 135
  average time/residue: 0.5147
  time to fit residues: 73.9043
Evaluate side-chains
  133 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 118
  time to evaluate  : 0.286 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 ILE
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue   77 TRP
Chi-restraints excluded: chain A residue  117 GLU
Chi-restraints excluded: chain A residue  155 VAL
Chi-restraints excluded: chain A residue  178 SER
Chi-restraints excluded: chain A residue  222 VAL
Chi-restraints excluded: chain A residue  276 ILE
Chi-restraints excluded: chain A residue  385 THR
Chi-restraints excluded: chain A residue  561 LEU
Chi-restraints excluded: chain A residue  608 SER
Chi-restraints excluded: chain A residue  623 ILE
Chi-restraints excluded: chain A residue  649 SER
Chi-restraints excluded: chain A residue  801 LEU
Chi-restraints excluded: chain A residue  967 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 20 optimal weight:    1.9990
   chunk 56 optimal weight:    0.8980
   chunk 101 optimal weight:    5.9990
   chunk 80 optimal weight:    0.5980
   chunk 82 optimal weight:    4.9990
   chunk 30 optimal weight:    0.2980
   chunk 100 optimal weight:    3.9990
   chunk 48 optimal weight:    2.9990
   chunk 22 optimal weight:    4.9990
   chunk 29 optimal weight:    0.9990
   chunk 78 optimal weight:    2.9990
   overall best weight:    0.9584

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

Flipped N/Q/H residues before XYZ refinement:
A 251 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.136404 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3088 r_free = 0.3088 target = 0.103943 restraints weight = 8504.971|
|-----------------------------------------------------------------------------|
r_work (start): 0.3055 rms_B_bonded: 1.70
r_work: 0.2887 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.2743 rms_B_bonded: 3.99 restraints_weight: 0.2500
r_work (final): 0.2743
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8075
moved from start:          0.1946

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8064  Z= 0.127
  Angle     :  0.527   7.850  10951  Z= 0.267
  Chirality :  0.042   0.171   1283
  Planarity :  0.003   0.040   1390
  Dihedral  :  8.329 154.707   1110
  Min Nonbonded Distance : 2.197

Molprobity Statistics.
  All-atom Clashscore : 5.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  3.55 %
    Allowed  : 16.95 %
    Favored  : 79.50 %
  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 are not related in a simple way.
  whole:  0.69 (0.27), residues: 1014
  helix:  1.64 (0.24), residues: 485
  sheet: -0.35 (0.47), residues: 117
  loop : -0.69 (0.31), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 572 
 TYR   0.015   0.001   TYR A 842 
 PHE   0.018   0.001   PHE A 367 
 TRP   0.008   0.001   TRP A 793 
 HIS   0.003   0.001   HIS A 566 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 ( 8064)
  covalent geometry    : angle       0.52728 (10951)
  hydrogen bonds       : bond        0.03427 (  415)
  hydrogen bonds       : angle       4.22952 ( 1209)

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 120
  time to evaluate  : 0.289 
Fit side-chains
REVERT: A   10 GLU cc_start: 0.7827 (mm-30) cc_final: 0.7541 (mm-30)
REVERT: A   31 LYS cc_start: 0.7647 (mtpt) cc_final: 0.7351 (mtmt)
REVERT: A   33 LYS cc_start: 0.7978 (tttt) cc_final: 0.7525 (ttmt)
REVERT: A   51 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.7591 (pt0)
REVERT: A   77 TRP cc_start: 0.6842 (OUTLIER) cc_final: 0.6335 (m100)
REVERT: A  135 LYS cc_start: 0.8631 (tptp) cc_final: 0.8260 (mtmt)
REVERT: A  280 ASN cc_start: 0.8114 (OUTLIER) cc_final: 0.7804 (p0)
REVERT: A  309 GLU cc_start: 0.8849 (pm20) cc_final: 0.8458 (pm20)
REVERT: A  394 GLU cc_start: 0.8050 (mt-10) cc_final: 0.7545 (mt-10)
REVERT: A  479 MET cc_start: 0.7280 (mtt) cc_final: 0.6922 (mtp)
REVERT: A  531 SER cc_start: 0.9151 (p) cc_final: 0.8941 (p)
REVERT: A  545 MET cc_start: 0.8414 (mmm) cc_final: 0.8053 (mmm)
REVERT: A  574 GLU cc_start: 0.7964 (mt-10) cc_final: 0.7732 (mt-10)
REVERT: A  575 MET cc_start: 0.9077 (mtt) cc_final: 0.8739 (mtt)
REVERT: A  623 ILE cc_start: 0.9124 (OUTLIER) cc_final: 0.8842 (mt)
REVERT: A  814 ASP cc_start: 0.7188 (t70) cc_final: 0.6697 (t0)
REVERT: A  816 MET cc_start: 0.8884 (mmm) cc_final: 0.8592 (mmm)
REVERT: A  940 MET cc_start: 0.8727 (mmm) cc_final: 0.8371 (mmm)
REVERT: A 1039 MET cc_start: 0.5691 (mmm) cc_final: 0.5415 (mmm)
  outliers start: 31
  outliers final: 17
  residues processed: 139
  average time/residue: 0.5350
  time to fit residues: 78.9354
Evaluate side-chains
  136 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 115
  time to evaluate  : 0.358 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 GLU
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue   77 TRP
Chi-restraints excluded: chain A residue  117 GLU
Chi-restraints excluded: chain A residue  155 VAL
Chi-restraints excluded: chain A residue  178 SER
Chi-restraints excluded: chain A residue  208 LEU
Chi-restraints excluded: chain A residue  222 VAL
Chi-restraints excluded: chain A residue  276 ILE
Chi-restraints excluded: chain A residue  280 ASN
Chi-restraints excluded: chain A residue  369 LEU
Chi-restraints excluded: chain A residue  385 THR
Chi-restraints excluded: chain A residue  561 LEU
Chi-restraints excluded: chain A residue  608 SER
Chi-restraints excluded: chain A residue  623 ILE
Chi-restraints excluded: chain A residue  630 THR
Chi-restraints excluded: chain A residue  649 SER
Chi-restraints excluded: chain A residue  702 ASP
Chi-restraints excluded: chain A residue  801 LEU
Chi-restraints excluded: chain A residue  954 LEU
Chi-restraints excluded: chain A residue  967 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 74 optimal weight:    1.9990
   chunk 43 optimal weight:    4.9990
   chunk 18 optimal weight:    3.9990
   chunk 75 optimal weight:    0.5980
   chunk 63 optimal weight:    1.9990
   chunk 37 optimal weight:    7.9990
   chunk 77 optimal weight:    0.5980
   chunk 29 optimal weight:    1.9990
   chunk 7 optimal weight:    0.9990
   chunk 45 optimal weight:    0.9990
   chunk 16 optimal weight:    0.7980
   overall best weight:    0.7984

-------------------------------------------------------------------------------
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 = 0.3507 r_free = 0.3507 target = 0.138465 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3128 r_free = 0.3128 target = 0.106378 restraints weight = 8560.355|
|-----------------------------------------------------------------------------|
r_work (start): 0.3077 rms_B_bonded: 1.69
r_work: 0.2911 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.2769 rms_B_bonded: 3.95 restraints_weight: 0.2500
r_work (final): 0.2769
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8080
moved from start:          0.2028

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8064  Z= 0.115
  Angle     :  0.516   8.348  10951  Z= 0.260
  Chirality :  0.042   0.152   1283
  Planarity :  0.003   0.040   1390
  Dihedral  :  8.281 153.936   1110
  Min Nonbonded Distance : 2.194

Molprobity Statistics.
  All-atom Clashscore : 5.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  : 17.41 %
    Favored  : 79.15 %
  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 are not related in a simple way.
  whole:  0.81 (0.27), residues: 1014
  helix:  1.74 (0.24), residues: 486
  sheet: -0.30 (0.47), residues: 117
  loop : -0.65 (0.31), residues: 411

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 572 
 TYR   0.014   0.001   TYR A 842 
 PHE   0.017   0.001   PHE A 367 
 TRP   0.008   0.001   TRP A 793 
 HIS   0.002   0.000   HIS A 566 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 ( 8064)
  covalent geometry    : angle       0.51576 (10951)
  hydrogen bonds       : bond        0.03286 (  415)
  hydrogen bonds       : angle       4.17341 ( 1209)

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 124
  time to evaluate  : 0.309 
Fit side-chains
REVERT: A   10 GLU cc_start: 0.7843 (mm-30) cc_final: 0.7561 (mm-30)
REVERT: A   31 LYS cc_start: 0.7657 (mtpt) cc_final: 0.7372 (mtmt)
REVERT: A   33 LYS cc_start: 0.7946 (tttt) cc_final: 0.7516 (ttmt)
REVERT: A   51 GLU cc_start: 0.8007 (tt0) cc_final: 0.7602 (pt0)
REVERT: A   71 ILE cc_start: 0.8662 (mt) cc_final: 0.8411 (mt)
REVERT: A   77 TRP cc_start: 0.6832 (OUTLIER) cc_final: 0.6424 (m100)
REVERT: A  135 LYS cc_start: 0.8637 (tptp) cc_final: 0.8259 (mtpp)
REVERT: A  280 ASN cc_start: 0.7967 (OUTLIER) cc_final: 0.7655 (p0)
REVERT: A  309 GLU cc_start: 0.8854 (pm20) cc_final: 0.8453 (pm20)
REVERT: A  394 GLU cc_start: 0.8042 (mt-10) cc_final: 0.7585 (mt-10)
REVERT: A  479 MET cc_start: 0.7276 (mtt) cc_final: 0.6893 (mtp)
REVERT: A  531 SER cc_start: 0.9156 (p) cc_final: 0.8950 (p)
REVERT: A  545 MET cc_start: 0.8423 (mmm) cc_final: 0.8061 (mmm)
REVERT: A  575 MET cc_start: 0.9071 (mtt) cc_final: 0.8725 (mtt)
REVERT: A  623 ILE cc_start: 0.9120 (OUTLIER) cc_final: 0.8844 (mt)
REVERT: A  814 ASP cc_start: 0.6892 (t70) cc_final: 0.6533 (t0)
REVERT: A  816 MET cc_start: 0.8872 (mmm) cc_final: 0.8547 (mmm)
REVERT: A  940 MET cc_start: 0.8708 (mmm) cc_final: 0.8338 (mmm)
REVERT: A  979 MET cc_start: 0.8619 (ttm) cc_final: 0.8319 (ttm)
REVERT: A 1023 MET cc_start: 0.6438 (tpt) cc_final: 0.6102 (tpp)
  outliers start: 30
  outliers final: 21
  residues processed: 144
  average time/residue: 0.4799
  time to fit residues: 73.6900
Evaluate side-chains
  143 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 119
  time to evaluate  : 0.295 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue   77 TRP
Chi-restraints excluded: chain A residue  117 GLU
Chi-restraints excluded: chain A residue  155 VAL
Chi-restraints excluded: chain A residue  178 SER
Chi-restraints excluded: chain A residue  207 MET
Chi-restraints excluded: chain A residue  208 LEU
Chi-restraints excluded: chain A residue  222 VAL
Chi-restraints excluded: chain A residue  238 GLU
Chi-restraints excluded: chain A residue  276 ILE
Chi-restraints excluded: chain A residue  280 ASN
Chi-restraints excluded: chain A residue  369 LEU
Chi-restraints excluded: chain A residue  385 THR
Chi-restraints excluded: chain A residue  561 LEU
Chi-restraints excluded: chain A residue  608 SER
Chi-restraints excluded: chain A residue  623 ILE
Chi-restraints excluded: chain A residue  630 THR
Chi-restraints excluded: chain A residue  649 SER
Chi-restraints excluded: chain A residue  681 SER
Chi-restraints excluded: chain A residue  702 ASP
Chi-restraints excluded: chain A residue  801 LEU
Chi-restraints excluded: chain A residue  806 LEU
Chi-restraints excluded: chain A residue  954 LEU
Chi-restraints excluded: chain A residue  967 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 38 optimal weight:    4.9990
   chunk 86 optimal weight:    3.9990
   chunk 65 optimal weight:    0.8980
   chunk 79 optimal weight:    0.7980
   chunk 13 optimal weight:    1.9990
   chunk 19 optimal weight:    0.0470
   chunk 91 optimal weight:    4.9990
   chunk 44 optimal weight:    0.7980
   chunk 26 optimal weight:    0.9990
   chunk 0 optimal weight:    5.9990
   chunk 11 optimal weight:    5.9990
   overall best weight:    0.7080

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

Flipped N/Q/H residues before XYZ refinement:
A 421 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.140273 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.108551 restraints weight = 8536.644|
|-----------------------------------------------------------------------------|
r_work (start): 0.3098 rms_B_bonded: 1.66
r_work: 0.2934 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.2791 rms_B_bonded: 3.94 restraints_weight: 0.2500
r_work (final): 0.2791
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8093
moved from start:          0.2083

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8064  Z= 0.110
  Angle     :  0.516  10.669  10951  Z= 0.259
  Chirality :  0.041   0.145   1283
  Planarity :  0.003   0.040   1390
  Dihedral  :  8.244 153.165   1110
  Min Nonbonded Distance : 2.193

Molprobity Statistics.
  All-atom Clashscore : 5.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  : 17.53 %
    Favored  : 79.04 %
  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 are not related in a simple way.
  whole:  0.89 (0.27), residues: 1014
  helix:  1.79 (0.24), residues: 487
  sheet: -0.25 (0.47), residues: 117
  loop : -0.58 (0.31), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 572 
 TYR   0.014   0.001   TYR A 842 
 PHE   0.017   0.001   PHE A 367 
 TRP   0.008   0.001   TRP A 793 
 HIS   0.002   0.000   HIS A 566 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 ( 8064)
  covalent geometry    : angle       0.51621 (10951)
  hydrogen bonds       : bond        0.03210 (  415)
  hydrogen bonds       : angle       4.12997 ( 1209)

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 124
  time to evaluate  : 0.279 
Fit side-chains
REVERT: A   10 GLU cc_start: 0.7854 (mm-30) cc_final: 0.7610 (mm-30)
REVERT: A   31 LYS cc_start: 0.7675 (mtpt) cc_final: 0.7389 (mtmt)
REVERT: A   33 LYS cc_start: 0.7930 (tttt) cc_final: 0.7514 (ttmt)
REVERT: A   51 GLU cc_start: 0.7999 (tt0) cc_final: 0.7636 (pt0)
REVERT: A   71 ILE cc_start: 0.8676 (mt) cc_final: 0.8426 (mt)
REVERT: A   77 TRP cc_start: 0.6799 (OUTLIER) cc_final: 0.6436 (m100)
REVERT: A  135 LYS cc_start: 0.8743 (tptp) cc_final: 0.8331 (mtpp)
REVERT: A  280 ASN cc_start: 0.7974 (OUTLIER) cc_final: 0.7676 (p0)
REVERT: A  309 GLU cc_start: 0.8856 (pm20) cc_final: 0.8486 (pm20)
REVERT: A  394 GLU cc_start: 0.8039 (mt-10) cc_final: 0.7586 (mt-10)
REVERT: A  479 MET cc_start: 0.7281 (mtt) cc_final: 0.6886 (mtp)
REVERT: A  531 SER cc_start: 0.9157 (p) cc_final: 0.8956 (p)
REVERT: A  545 MET cc_start: 0.8449 (mmm) cc_final: 0.8088 (mmm)
REVERT: A  575 MET cc_start: 0.9070 (mtt) cc_final: 0.8760 (mtt)
REVERT: A  623 ILE cc_start: 0.9104 (OUTLIER) cc_final: 0.8829 (mt)
REVERT: A  814 ASP cc_start: 0.7125 (t70) cc_final: 0.6851 (t0)
REVERT: A  816 MET cc_start: 0.8881 (mmm) cc_final: 0.8552 (mmm)
REVERT: A  940 MET cc_start: 0.8723 (mmm) cc_final: 0.8352 (mmm)
REVERT: A 1023 MET cc_start: 0.6532 (tpt) cc_final: 0.6197 (tpp)
  outliers start: 30
  outliers final: 22
  residues processed: 144
  average time/residue: 0.4989
  time to fit residues: 76.4355
Evaluate side-chains
  144 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 119
  time to evaluate  : 0.321 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue   77 TRP
Chi-restraints excluded: chain A residue  117 GLU
Chi-restraints excluded: chain A residue  155 VAL
Chi-restraints excluded: chain A residue  178 SER
Chi-restraints excluded: chain A residue  207 MET
Chi-restraints excluded: chain A residue  208 LEU
Chi-restraints excluded: chain A residue  222 VAL
Chi-restraints excluded: chain A residue  238 GLU
Chi-restraints excluded: chain A residue  276 ILE
Chi-restraints excluded: chain A residue  280 ASN
Chi-restraints excluded: chain A residue  369 LEU
Chi-restraints excluded: chain A residue  385 THR
Chi-restraints excluded: chain A residue  561 LEU
Chi-restraints excluded: chain A residue  563 LEU
Chi-restraints excluded: chain A residue  608 SER
Chi-restraints excluded: chain A residue  623 ILE
Chi-restraints excluded: chain A residue  630 THR
Chi-restraints excluded: chain A residue  649 SER
Chi-restraints excluded: chain A residue  681 SER
Chi-restraints excluded: chain A residue  702 ASP
Chi-restraints excluded: chain A residue  801 LEU
Chi-restraints excluded: chain A residue  806 LEU
Chi-restraints excluded: chain A residue  954 LEU
Chi-restraints excluded: chain A residue  967 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 51 optimal weight:    0.0970
   chunk 32 optimal weight:    1.9990
   chunk 4 optimal weight:    0.4980
   chunk 42 optimal weight:    4.9990
   chunk 80 optimal weight:    0.0020
   chunk 16 optimal weight:    0.9980
   chunk 45 optimal weight:    2.9990
   chunk 96 optimal weight:    3.9990
   chunk 101 optimal weight:   10.0000
   chunk 85 optimal weight:    2.9990
   chunk 62 optimal weight:    0.0980
   overall best weight:    0.3386

-------------------------------------------------------------------------------
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 = 0.3550 r_free = 0.3550 target = 0.142111 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3182 r_free = 0.3182 target = 0.110488 restraints weight = 8478.277|
|-----------------------------------------------------------------------------|
r_work (start): 0.3149 rms_B_bonded: 1.69
r_work: 0.2990 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.2849 rms_B_bonded: 3.99 restraints_weight: 0.2500
r_work (final): 0.2849
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8048
moved from start:          0.2277

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   8064  Z= 0.091
  Angle     :  0.493  11.387  10951  Z= 0.247
  Chirality :  0.040   0.140   1283
  Planarity :  0.003   0.039   1390
  Dihedral  :  8.101 152.033   1110
  Min Nonbonded Distance : 2.194

Molprobity Statistics.
  All-atom Clashscore : 5.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 19.13 %
    Favored  : 78.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.09 (0.27), residues: 1014
  helix:  2.00 (0.25), residues: 479
  sheet: -0.02 (0.47), residues: 115
  loop : -0.54 (0.31), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 666 
 TYR   0.014   0.001   TYR A 990 
 PHE   0.014   0.001   PHE A 367 
 TRP   0.011   0.001   TRP A 927 
 HIS   0.001   0.000   HIS A 278 

Details of bonding type rmsd
  covalent geometry    : bond        0.00204 ( 8064)
  covalent geometry    : angle       0.49330 (10951)
  hydrogen bonds       : bond        0.02844 (  415)
  hydrogen bonds       : angle       3.98874 ( 1209)

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 130
  time to evaluate  : 0.304 
Fit side-chains
REVERT: A   10 GLU cc_start: 0.7859 (mm-30) cc_final: 0.7600 (mm-30)
REVERT: A   31 LYS cc_start: 0.7655 (mtpt) cc_final: 0.7366 (mtmt)
REVERT: A   51 GLU cc_start: 0.7979 (tt0) cc_final: 0.7627 (pt0)
REVERT: A   71 ILE cc_start: 0.8682 (mt) cc_final: 0.8449 (mt)
REVERT: A   77 TRP cc_start: 0.6705 (OUTLIER) cc_final: 0.6331 (m100)
REVERT: A  117 GLU cc_start: 0.7508 (OUTLIER) cc_final: 0.7307 (pt0)
REVERT: A  135 LYS cc_start: 0.8761 (tptp) cc_final: 0.8369 (mtpp)
REVERT: A  309 GLU cc_start: 0.8865 (pm20) cc_final: 0.8569 (pm20)
REVERT: A  394 GLU cc_start: 0.8025 (mt-10) cc_final: 0.7551 (mt-10)
REVERT: A  479 MET cc_start: 0.7213 (mtt) cc_final: 0.6823 (mtp)
REVERT: A  531 SER cc_start: 0.9149 (p) cc_final: 0.8941 (p)
REVERT: A  545 MET cc_start: 0.8486 (mmm) cc_final: 0.8140 (mmm)
REVERT: A  574 GLU cc_start: 0.8054 (mt-10) cc_final: 0.7847 (mt-10)
REVERT: A  575 MET cc_start: 0.9057 (mtt) cc_final: 0.8742 (mtt)
REVERT: A  682 HIS cc_start: 0.8193 (m-70) cc_final: 0.7775 (m170)
REVERT: A  816 MET cc_start: 0.8863 (mmm) cc_final: 0.8523 (mmm)
REVERT: A  940 MET cc_start: 0.8721 (mmm) cc_final: 0.8497 (mmm)
REVERT: A 1023 MET cc_start: 0.6541 (tpt) cc_final: 0.6158 (tpp)
  outliers start: 22
  outliers final: 15
  residues processed: 145
  average time/residue: 0.5483
  time to fit residues: 84.3816
Evaluate side-chains
  137 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 120
  time to evaluate  : 0.250 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue   77 TRP
Chi-restraints excluded: chain A residue  117 GLU
Chi-restraints excluded: chain A residue  155 VAL
Chi-restraints excluded: chain A residue  178 SER
Chi-restraints excluded: chain A residue  207 MET
Chi-restraints excluded: chain A residue  222 VAL
Chi-restraints excluded: chain A residue  238 GLU
Chi-restraints excluded: chain A residue  276 ILE
Chi-restraints excluded: chain A residue  369 LEU
Chi-restraints excluded: chain A residue  385 THR
Chi-restraints excluded: chain A residue  561 LEU
Chi-restraints excluded: chain A residue  563 LEU
Chi-restraints excluded: chain A residue  608 SER
Chi-restraints excluded: chain A residue  681 SER
Chi-restraints excluded: chain A residue  806 LEU
Chi-restraints excluded: chain A residue  954 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 9 optimal weight:    0.6980
   chunk 2 optimal weight:    0.9980
   chunk 81 optimal weight:    0.3980
   chunk 29 optimal weight:    0.7980
   chunk 88 optimal weight:    6.9990
   chunk 71 optimal weight:    2.9990
   chunk 70 optimal weight:    0.8980
   chunk 36 optimal weight:    3.9990
   chunk 44 optimal weight:    0.5980
   chunk 91 optimal weight:    1.9990
   chunk 90 optimal weight:    0.9990
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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 = 0.3639 r_free = 0.3639 target = 0.149042 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.118809 restraints weight = 8477.360|
|-----------------------------------------------------------------------------|
r_work (start): 0.3217 rms_B_bonded: 1.59
r_work: 0.3058 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.2920 rms_B_bonded: 3.89 restraints_weight: 0.2500
r_work (final): 0.2920
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8151
moved from start:          0.2257

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   8064  Z= 0.110
  Angle     :  0.519  11.906  10951  Z= 0.264
  Chirality :  0.041   0.153   1283
  Planarity :  0.003   0.039   1390
  Dihedral  :  8.164 151.383   1110
  Min Nonbonded Distance : 2.195

Molprobity Statistics.
  All-atom Clashscore : 5.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 19.82 %
    Favored  : 78.24 %
  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 are not related in a simple way.
  whole:  1.07 (0.27), residues: 1014
  helix:  1.91 (0.24), residues: 487
  sheet: -0.18 (0.47), residues: 117
  loop : -0.45 (0.32), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 666 
 TYR   0.018   0.001   TYR A 122 
 PHE   0.018   0.001   PHE A 367 
 TRP   0.008   0.001   TRP A 927 
 HIS   0.002   0.000   HIS A 566 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 ( 8064)
  covalent geometry    : angle       0.51933 (10951)
  hydrogen bonds       : bond        0.03110 (  415)
  hydrogen bonds       : angle       4.06209 ( 1209)

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

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

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2028 Ramachandran restraints generated.
    1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 119
  time to evaluate  : 0.256 
Fit side-chains
REVERT: A   10 GLU cc_start: 0.7903 (mm-30) cc_final: 0.7662 (mm-30)
REVERT: A   31 LYS cc_start: 0.7762 (mtpt) cc_final: 0.7471 (mtmt)
REVERT: A   51 GLU cc_start: 0.8018 (tt0) cc_final: 0.7673 (pt0)
REVERT: A   71 ILE cc_start: 0.8793 (mt) cc_final: 0.8566 (mt)
REVERT: A   77 TRP cc_start: 0.6767 (OUTLIER) cc_final: 0.6455 (m100)
REVERT: A  135 LYS cc_start: 0.8753 (tptp) cc_final: 0.8374 (mtpp)
REVERT: A  309 GLU cc_start: 0.8876 (pm20) cc_final: 0.8434 (pm20)
REVERT: A  394 GLU cc_start: 0.8052 (mt-10) cc_final: 0.7567 (mt-10)
REVERT: A  479 MET cc_start: 0.7275 (mtt) cc_final: 0.6915 (mtp)
REVERT: A  531 SER cc_start: 0.9161 (p) cc_final: 0.8949 (p)
REVERT: A  545 MET cc_start: 0.8571 (mmm) cc_final: 0.8231 (mmm)
REVERT: A  575 MET cc_start: 0.9069 (mtt) cc_final: 0.8712 (mtt)
REVERT: A  682 HIS cc_start: 0.8209 (m-70) cc_final: 0.7786 (m170)
REVERT: A  816 MET cc_start: 0.8863 (mmm) cc_final: 0.8494 (mmm)
REVERT: A  940 MET cc_start: 0.8771 (mmm) cc_final: 0.8522 (mmm)
REVERT: A 1023 MET cc_start: 0.6631 (tpt) cc_final: 0.6246 (tpp)
  outliers start: 17
  outliers final: 14
  residues processed: 132
  average time/residue: 0.5067
  time to fit residues: 71.3782
Evaluate side-chains
  132 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 117
  time to evaluate  : 0.366 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue   77 TRP
Chi-restraints excluded: chain A residue  155 VAL
Chi-restraints excluded: chain A residue  178 SER
Chi-restraints excluded: chain A residue  207 MET
Chi-restraints excluded: chain A residue  222 VAL
Chi-restraints excluded: chain A residue  238 GLU
Chi-restraints excluded: chain A residue  276 ILE
Chi-restraints excluded: chain A residue  385 THR
Chi-restraints excluded: chain A residue  561 LEU
Chi-restraints excluded: chain A residue  563 LEU
Chi-restraints excluded: chain A residue  608 SER
Chi-restraints excluded: chain A residue  630 THR
Chi-restraints excluded: chain A residue  681 SER
Chi-restraints excluded: chain A residue  806 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 60 optimal weight:    0.7980
   chunk 26 optimal weight:    0.5980
   chunk 90 optimal weight:    0.7980
   chunk 77 optimal weight:    0.8980
   chunk 68 optimal weight:    1.9990
   chunk 33 optimal weight:    7.9990
   chunk 89 optimal weight:    0.8980
   chunk 19 optimal weight:    1.9990
   chunk 54 optimal weight:    3.9990
   chunk 80 optimal weight:    0.9990
   chunk 24 optimal weight:    0.7980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A 251 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.142814 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.111576 restraints weight = 8423.747|
|-----------------------------------------------------------------------------|
r_work (start): 0.3128 rms_B_bonded: 1.64
r_work: 0.2966 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.2826 rms_B_bonded: 3.90 restraints_weight: 0.2500
r_work (final): 0.2826
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8096
moved from start:          0.2251

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   8064  Z= 0.117
  Angle     :  0.529  11.952  10951  Z= 0.268
  Chirality :  0.042   0.140   1283
  Planarity :  0.003   0.039   1390
  Dihedral  :  8.193 152.340   1110
  Min Nonbonded Distance : 2.189

Molprobity Statistics.
  All-atom Clashscore : 5.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 19.47 %
    Favored  : 78.47 %
  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 are not related in a simple way.
  whole:  1.03 (0.27), residues: 1014
  helix:  1.86 (0.24), residues: 487
  sheet: -0.20 (0.47), residues: 117
  loop : -0.45 (0.32), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 334 
 TYR   0.014   0.001   TYR A 842 
 PHE   0.018   0.001   PHE A 367 
 TRP   0.007   0.001   TRP A 927 
 HIS   0.002   0.000   HIS A 566 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 8064)
  covalent geometry    : angle       0.52878 (10951)
  hydrogen bonds       : bond        0.03204 (  415)
  hydrogen bonds       : angle       4.09732 ( 1209)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2648.01 seconds
wall clock time: 45 minutes 49.35 seconds (2749.35 seconds total)