Starting phenix.real_space_refine
on Thu Jul  2 04:50:08 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9yhn_72967/07_2026/9yhn_72967.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9yhn_72967/07_2026/9yhn_72967.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.38
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9yhn_72967/07_2026/9yhn_72967.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9yhn_72967/07_2026/9yhn_72967.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9yhn_72967/07_2026/9yhn_72967.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9yhn_72967/07_2026/9yhn_72967.cif"
  }
  resolution = 3.38
  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=   1.000
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: 5
    Type Number    sf(0)   Gaussians
     Ca      3      9.91       5
     S      26      5.16       5
     C    4111      2.51       5
     N    1134      2.21       5
     O    1219      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 6493
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 6490
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 821, 6490
          Classifications: {'peptide': 821}
          Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 789}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 0
          Ad-hoc single atom residues: {' CA': 3}
          Chain breaks: 3
  Time building chain proxies: 1.61, per 1000 atoms: 0.25
  Number of scatterers: 6493
  At special positions: 0
  Unit cell: (67.68, 86.48, 103.4, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Ca      3     19.99
     S      26     16.00
     O    1219      8.00
     N    1134      7.00
     C    4111      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: 0.50
  Conformation dependent library (CDL) restraints added in 377.9 milliseconds
  

  1634 Ramachandran restraints generated.
    817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1548

  Finding SS restraints...
    Secondary structure from input PDB file:
      45 helices and 5 sheets defined
      58.2% alpha, 10.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.23
  Creating SS restraints...
    Processing helix  chain 'A' and resid 18 through 26
      removed outlier: 3.952A  pdb=" N   GLU A  24 " --> pdb=" O   VAL A  20 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   THR A  25 " --> pdb=" O   ALA A  21 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   LEU A  26 " --> pdb=" O   LEU A  22 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 36 through 51
    Processing helix  chain 'A' and resid 71 through 86
      removed outlier: 3.652A  pdb=" N   ASP A  86 " --> pdb=" O   SER A  82 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 97 through 112
    Processing helix  chain 'A' and resid 123 through 128
    Processing helix  chain 'A' and resid 137 through 141
    Processing helix  chain 'A' and resid 149 through 153
      removed outlier: 3.651A  pdb=" N   SER A 153 " --> pdb=" O   HIS A 150 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 163 through 175
      removed outlier: 3.529A  pdb=" N   CYS A 175 " --> pdb=" O   ILE A 171 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 183 through 199
      removed outlier: 3.954A  pdb=" N   HIS A 187 " --> pdb=" O   GLU A 183 " (cutoff:3.500A)
      removed outlier: 5.536A  pdb=" N   THR A 195 " --> pdb=" O   LYS A 191 " (cutoff:3.500A)
      removed outlier: 5.757A  pdb=" N   GLU A 196 " --> pdb=" O   LEU A 192 " (cutoff:3.500A)
      removed outlier: 3.834A  pdb=" N   LEU A 199 " --> pdb=" O   THR A 195 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 202 through 211
    Processing helix  chain 'A' and resid 220 through 227
      removed outlier: 3.533A  pdb=" N   ALA A 226 " --> pdb=" O   TRP A 222 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 227 through 238
    Processing helix  chain 'A' and resid 241 through 246
      removed outlier: 4.205A  pdb=" N   PHE A 246 " --> pdb=" O   LYS A 242 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 247 through 252
      removed outlier: 3.592A  pdb=" N   LEU A 251 " --> pdb=" O   THR A 247 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 254 through 256
      No H-bonds generated for 'chain 'A' and resid 254 through 256'
    Processing helix  chain 'A' and resid 279 through 284
    Processing helix  chain 'A' and resid 297 through 299
      No H-bonds generated for 'chain 'A' and resid 297 through 299'
    Processing helix  chain 'A' and resid 300 through 305
    Processing helix  chain 'A' and resid 308 through 314
      removed outlier: 3.786A  pdb=" N   ILE A 312 " --> pdb=" O   SER A 308 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 331 through 335
    Processing helix  chain 'A' and resid 340 through 349
      removed outlier: 3.708A  pdb=" N   ILE A 344 " --> pdb=" O   ASP A 340 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 368 through 374
      removed outlier: 3.668A  pdb=" N   TRP A 372 " --> pdb=" O   ARG A 368 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 384 through 394
    Processing helix  chain 'A' and resid 413 through 417
      removed outlier: 3.593A  pdb=" N   CYS A 417 " --> pdb=" O   ASP A 414 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 430 through 440
    Processing helix  chain 'A' and resid 443 through 459
      removed outlier: 3.560A  pdb=" N   LEU A 447 " --> pdb=" O   SER A 443 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 475 through 484
    Processing helix  chain 'A' and resid 484 through 489
      removed outlier: 3.868A  pdb=" N   ARG A 489 " --> pdb=" O   VAL A 485 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 492 through 515
    Processing helix  chain 'A' and resid 518 through 532
    Processing helix  chain 'A' and resid 534 through 545
    Processing helix  chain 'A' and resid 546 through 548
      No H-bonds generated for 'chain 'A' and resid 546 through 548'
    Processing helix  chain 'A' and resid 554 through 573
    Processing helix  chain 'A' and resid 575 through 589
      removed outlier: 3.611A  pdb=" N   ALA A 579 " --> pdb=" O   ASP A 575 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 593 through 595
      No H-bonds generated for 'chain 'A' and resid 593 through 595'
    Processing helix  chain 'A' and resid 596 through 608
      removed outlier: 4.035A  pdb=" N   TYR A 600 " --> pdb=" O   ASP A 596 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 612 through 627
    Processing helix  chain 'A' and resid 648 through 659
    Processing helix  chain 'A' and resid 662 through 676
      removed outlier: 3.538A  pdb=" N   ARG A 676 " --> pdb=" O   ASP A 672 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 682 through 697
    Processing helix  chain 'A' and resid 740 through 758
    Processing helix  chain 'A' and resid 788 through 805
      removed outlier: 3.525A  pdb=" N   SER A 805 " --> pdb=" O   ALA A 801 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 810 through 814
      removed outlier: 3.578A  pdb=" N   ASP A 813 " --> pdb=" O   ASN A 810 " (cutoff:3.500A)
      removed outlier: 3.961A  pdb=" N   LEU A 814 " --> pdb=" O   LEU A 811 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 810 through 814'
    Processing helix  chain 'A' and resid 815 through 826
    Processing helix  chain 'A' and resid 829 through 836
    Processing sheet with id=AA1, first strand: chain 'A' and resid 61 through 65
      removed outlier: 6.426A  pdb=" N   ILE A 159 " --> pdb=" O   ILE A 289 " (cutoff:3.500A)
      removed outlier: 8.020A  pdb=" N   MET A 291 " --> pdb=" O   ILE A 159 " (cutoff:3.500A)
      removed outlier: 6.609A  pdb=" N   MET A 161 " --> pdb=" O   MET A 291 " (cutoff:3.500A)
      removed outlier: 6.481A  pdb=" N   VAL A  92 " --> pdb=" O   LEU A 160 " (cutoff:3.500A)
      removed outlier: 6.093A  pdb=" N   SER A 116 " --> pdb=" O   VAL A 134 " (cutoff:3.500A)
      removed outlier: 8.465A  pdb=" N   SER A 136 " --> pdb=" O   SER A 116 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 177 through 180
      removed outlier: 4.732A  pdb=" N   CYS A 260 " --> pdb=" O   VAL A 219 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 326 through 330
      removed outlier: 6.620A  pdb=" N   GLU A 326 " --> pdb=" O   SER A 469 " (cutoff:3.500A)
      removed outlier: 7.199A  pdb=" N   VAL A 471 " --> pdb=" O   GLU A 326 " (cutoff:3.500A)
      removed outlier: 6.107A  pdb=" N   MET A 328 " --> pdb=" O   VAL A 471 " (cutoff:3.500A)
      removed outlier: 6.874A  pdb=" N   ALA A 473 " --> pdb=" O   MET A 328 " (cutoff:3.500A)
      removed outlier: 6.357A  pdb=" N   LEU A 330 " --> pdb=" O   ALA A 473 " (cutoff:3.500A)
      removed outlier: 6.726A  pdb=" N   LEU A 420 " --> pdb=" O   VAL A 472 " (cutoff:3.500A)
      removed outlier: 7.712A  pdb=" N   ILE A 474 " --> pdb=" O   LEU A 420 " (cutoff:3.500A)
      removed outlier: 6.081A  pdb=" N   PHE A 422 " --> pdb=" O   ILE A 474 " (cutoff:3.500A)
      removed outlier: 6.514A  pdb=" N   ILE A 359 " --> pdb=" O   LEU A 401 " (cutoff:3.500A)
      removed outlier: 7.740A  pdb=" N   LEU A 403 " --> pdb=" O   ILE A 359 " (cutoff:3.500A)
      removed outlier: 6.215A  pdb=" N   ALA A 361 " --> pdb=" O   LEU A 403 " (cutoff:3.500A)
      removed outlier: 6.746A  pdb=" N   LYS A 378 " --> pdb=" O   VAL A 402 " (cutoff:3.500A)
      removed outlier: 8.297A  pdb=" N   ALA A 404 " --> pdb=" O   LYS A 378 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 700 through 702
      removed outlier: 3.814A  pdb=" N   ALA A 700 " --> pdb=" O   ALA A 717 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   ASN A 714 " --> pdb=" O   PHE A 726 " (cutoff:3.500A)
      removed outlier: 7.101A  pdb=" N   TYR A 723 " --> pdb=" O   LYS A 764 " (cutoff:3.500A)
      removed outlier: 7.684A  pdb=" N   LEU A 766 " --> pdb=" O   TYR A 723 " (cutoff:3.500A)
      removed outlier: 6.037A  pdb=" N   LEU A 725 " --> pdb=" O   LEU A 766 " (cutoff:3.500A)
      removed outlier: 7.023A  pdb=" N   VAL A 768 " --> pdb=" O   LEU A 725 " (cutoff:3.500A)
      removed outlier: 6.768A  pdb=" N   GLU A 727 " --> pdb=" O   VAL A 768 " (cutoff:3.500A)
      removed outlier: 8.651A  pdb=" N   ASP A 785 " --> pdb=" O   VAL A 763 " (cutoff:3.500A)
      removed outlier: 6.319A  pdb=" N   ARG A 765 " --> pdb=" O   ASP A 785 " (cutoff:3.500A)
      removed outlier: 7.367A  pdb=" N   MET A 787 " --> pdb=" O   ARG A 765 " (cutoff:3.500A)
      removed outlier: 6.753A  pdb=" N   ILE A 767 " --> pdb=" O   MET A 787 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 738 through 739

    314 hydrogen bonds defined for protein.
    924 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: 1.12

  Time building geometry restraints manager: 0.69 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2169
        1.34 -     1.46: 1372
        1.46 -     1.58: 3036
        1.58 -     1.70: 0
        1.70 -     1.82: 40
  Bond restraints: 6617
  Sorted by residual:
  bond pdb=" N   MET A 545 "
       pdb=" CA  MET A 545 "
    ideal  model  delta    sigma   weight residual
    1.458  1.490 -0.032 1.33e-02 5.65e+03 5.91e+00
  bond pdb=" C   ALA A 349 "
       pdb=" N   PRO A 350 "
    ideal  model  delta    sigma   weight residual
    1.331  1.349 -0.019 1.31e-02 5.83e+03 2.06e+00
  bond pdb=" CB  LYS A 114 "
       pdb=" CG  LYS A 114 "
    ideal  model  delta    sigma   weight residual
    1.520  1.562 -0.042 3.00e-02 1.11e+03 1.94e+00
  bond pdb=" CG  ARG A 625 "
       pdb=" CD  ARG A 625 "
    ideal  model  delta    sigma   weight residual
    1.520  1.561 -0.041 3.00e-02 1.11e+03 1.90e+00
  bond pdb=" CA  ASP A 713 "
       pdb=" CB  ASP A 713 "
    ideal  model  delta    sigma   weight residual
    1.528  1.506  0.023 1.66e-02 3.63e+03 1.87e+00
  ... (remaining 6612 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.92: 8766
        1.92 -     3.84: 152
        3.84 -     5.75: 17
        5.75 -     7.67: 10
        7.67 -     9.59: 3
  Bond angle restraints: 8948
  Sorted by residual:
  angle pdb=" CA  LYS A 466 "
        pdb=" CB  LYS A 466 "
        pdb=" CG  LYS A 466 "
      ideal   model   delta    sigma   weight residual
     114.10  122.58   -8.48 2.00e+00 2.50e-01 1.80e+01
  angle pdb=" CB  LYS A 114 "
        pdb=" CG  LYS A 114 "
        pdb=" CD  LYS A 114 "
      ideal   model   delta    sigma   weight residual
     111.30  120.89   -9.59 2.30e+00 1.89e-01 1.74e+01
  angle pdb=" CG  ARG A 625 "
        pdb=" CD  ARG A 625 "
        pdb=" NE  ARG A 625 "
      ideal   model   delta    sigma   weight residual
     112.00  118.56   -6.56 2.20e+00 2.07e-01 8.89e+00
  angle pdb=" CA  GLU A 727 "
        pdb=" CB  GLU A 727 "
        pdb=" CG  GLU A 727 "
      ideal   model   delta    sigma   weight residual
     114.10  119.64   -5.54 2.00e+00 2.50e-01 7.66e+00
  angle pdb=" CB  ARG A 625 "
        pdb=" CG  ARG A 625 "
        pdb=" CD  ARG A 625 "
      ideal   model   delta    sigma   weight residual
     111.30  117.56   -6.26 2.30e+00 1.89e-01 7.40e+00
  ... (remaining 8943 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.16: 3648
       16.16 -    32.31: 274
       32.31 -    48.46: 83
       48.46 -    64.62: 14
       64.62 -    80.77: 4
  Dihedral angle restraints: 4023
    sinusoidal: 1633
      harmonic: 2390
  Sorted by residual:
  dihedral pdb=" CG  ARG A  28 "
           pdb=" CD  ARG A  28 "
           pdb=" NE  ARG A  28 "
           pdb=" CZ  ARG A  28 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -90.00 -135.00   45.00     2      1.50e+01 4.44e-03 1.07e+01
  dihedral pdb=" CG  ARG A 256 "
           pdb=" CD  ARG A 256 "
           pdb=" NE  ARG A 256 "
           pdb=" CZ  ARG A 256 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  135.21   44.79     2      1.50e+01 4.44e-03 1.06e+01
  dihedral pdb=" CG  ARG A 254 "
           pdb=" CD  ARG A 254 "
           pdb=" NE  ARG A 254 "
           pdb=" CZ  ARG A 254 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -136.84  -43.16     2      1.50e+01 4.44e-03 9.98e+00
  ... (remaining 4020 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.050: 773
       0.050 -    0.101: 174
       0.101 -    0.151: 44
       0.151 -    0.202: 3
       0.202 -    0.252: 2
  Chirality restraints: 996
  Sorted by residual:
  chirality pdb=" CB  ILE A 159 "
            pdb=" CA  ILE A 159 "
            pdb=" CG1 ILE A 159 "
            pdb=" CG2 ILE A 159 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.39    0.25 2.00e-01 2.50e+01 1.59e+00
  chirality pdb=" CB  THR A 135 "
            pdb=" CA  THR A 135 "
            pdb=" OG1 THR A 135 "
            pdb=" CG2 THR A 135 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.34    0.21 2.00e-01 2.50e+01 1.12e+00
  chirality pdb=" CB  ILE A 767 "
            pdb=" CA  ILE A 767 "
            pdb=" CG1 ILE A 767 "
            pdb=" CG2 ILE A 767 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.45    0.20 2.00e-01 2.50e+01 9.52e-01
  ... (remaining 993 not shown)

  Planarity restraints: 1159
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASP A 705 "   -0.013 2.00e-02 2.50e+03   2.53e-02 6.39e+00
        pdb=" CG  ASP A 705 "    0.044 2.00e-02 2.50e+03
        pdb=" OD1 ASP A 705 "   -0.015 2.00e-02 2.50e+03
        pdb=" OD2 ASP A 705 "   -0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP A 705 "   -0.008 2.00e-02 2.50e+03   1.57e-02 2.47e+00
        pdb=" C   ASP A 705 "    0.027 2.00e-02 2.50e+03
        pdb=" O   ASP A 705 "   -0.010 2.00e-02 2.50e+03
        pdb=" N   ALA A 706 "   -0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU A 518 "    0.026 5.00e-02 4.00e+02   3.93e-02 2.47e+00
        pdb=" N   PRO A 519 "   -0.068 5.00e-02 4.00e+02
        pdb=" CA  PRO A 519 "    0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO A 519 "    0.022 5.00e-02 4.00e+02
  ... (remaining 1156 not shown)

  Histogram of nonbonded interaction distances:
        2.11 -     2.67: 64
        2.67 -     3.23: 5737
        3.23 -     3.78: 9804
        3.78 -     4.34: 13714
        4.34 -     4.90: 22487
  Nonbonded interactions: 51806
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU A 687 "
            pdb="CA    CA A 902 "
     model   vdw
     2.111 3.250
  nonbonded pdb=" OE1 GLU A 687 "
            pdb="CA    CA A 902 "
     model   vdw
     2.312 3.250
  nonbonded pdb=" OD1 ASP A 713 "
            pdb="CA    CA A 901 "
     model   vdw
     2.320 3.250
  nonbonded pdb=" OE1 GLU A 568 "
            pdb=" OH  TYR A 607 "
     model   vdw
     2.339 3.040
  nonbonded pdb=" OD1 ASP A 411 "
            pdb=" NH2 ARG A 463 "
     model   vdw
     2.346 3.120
  ... (remaining 51801 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:             2.890
  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:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.760
  Find NCS groups from input model:        0.020
  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:0.920
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.770
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7110
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   6617  Z= 0.163
  Angle     :  0.663   9.588   8948  Z= 0.346
  Chirality :  0.046   0.252    996
  Planarity :  0.005   0.040   1159
  Dihedral  : 13.073  80.774   2475
  Min Nonbonded Distance : 2.111

Molprobity Statistics.
  All-atom Clashscore : 2.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  0.43 %
    Allowed  :  5.76 %
    Favored  : 93.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    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:  0.26 (0.27), residues: 817
  helix:  0.23 (0.23), residues: 408
  sheet:  1.26 (0.55), residues: 96
  loop : -0.04 (0.32), residues: 313

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 625 
 TYR   0.015   0.001   TYR A 318 
 PHE   0.016   0.002   PHE A 803 
 TRP   0.013   0.002   TRP A 753 
 HIS   0.002   0.001   HIS A 287 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00345 /  0.16 ( 6617)
  covalent geometry    : angle       0.66341 /  0.35 ( 8948)
  hydrogen bonds       : bond        0.12689 /  8.15 (  314)
  hydrogen bonds       : angle       6.09327 /  4.47 (  924)

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

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

  1634 Ramachandran restraints generated.
    817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1634 Ramachandran restraints generated.
    817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 39
  time to evaluate  : 0.225 
Fit side-chains
   revert: symmetry clash
REVERT: A  114 LYS cc_start: 0.7598 (mmmt) cc_final: 0.7106 (tptp)
REVERT: A  448 MET cc_start: 0.7570 (mtp) cc_final: 0.7342 (mtm)
REVERT: A  626 ASN cc_start: 0.8032 (t0) cc_final: 0.7599 (m-40)
REVERT: A  747 MET cc_start: 0.7426 (tpp) cc_final: 0.7203 (tpp)
REVERT: A  764 LYS cc_start: 0.7476 (tptt) cc_final: 0.6843 (tptt)
  outliers start: 3
  outliers final: 0
  residues processed: 39
  average time/residue: 0.1004
  time to fit residues: 5.1159
Evaluate side-chains
  37 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 37
  time to evaluate  : 0.201 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 49 optimal weight:    0.7980
   chunk 53 optimal weight:    0.7980
   chunk 5 optimal weight:    0.5980
   chunk 33 optimal weight:    0.9980
   chunk 65 optimal weight:    0.6980
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    0.5980
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    0.9980
   chunk 45 optimal weight:    0.1980
   chunk 74 optimal weight:    0.9990
   overall best weight:    0.5780

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4454 r_free = 0.4454 target = 0.234134 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4233 r_free = 0.4233 target = 0.208155 restraints weight = 6234.517|
|-----------------------------------------------------------------------------|
r_work (start): 0.4017 rms_B_bonded: 1.92
r_work: 0.3825 rms_B_bonded: 3.64 restraints_weight: 0.5000
r_work (final): 0.3825
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7254
moved from start:          0.1091

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025   6617  Z= 0.167
  Angle     :  0.507   5.169   8948  Z= 0.261
  Chirality :  0.041   0.141    996
  Planarity :  0.004   0.028   1159
  Dihedral  :  4.034  14.005    890
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 3.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.71 %
    Favored  : 98.29 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  :  6.05 %
    Favored  : 92.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    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:  1.19 (0.28), residues: 817
  helix:  1.27 (0.25), residues: 407
  sheet:  0.95 (0.54), residues: 96
  loop :  0.25 (0.33), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 625 
 TYR   0.010   0.001   TYR A 758 
 PHE   0.011   0.001   PHE A 726 
 TRP   0.013   0.001   TRP A 222 
 HIS   0.003   0.001   HIS A 438 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00381 /  0.17 ( 6617)
  covalent geometry    : angle       0.50743 /  0.26 ( 8948)
  hydrogen bonds       : bond        0.03723 /  2.38 (  314)
  hydrogen bonds       : angle       4.57257 /  3.34 (  924)

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

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

  1634 Ramachandran restraints generated.
    817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1634 Ramachandran restraints generated.
    817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 38
  time to evaluate  : 0.251 
Fit side-chains
REVERT: A   66 LEU cc_start: 0.7492 (OUTLIER) cc_final: 0.7213 (pp)
REVERT: A  114 LYS cc_start: 0.7701 (mmmt) cc_final: 0.7266 (tptp)
REVERT: A  448 MET cc_start: 0.7779 (mtp) cc_final: 0.7504 (mtp)
REVERT: A  545 MET cc_start: 0.8575 (tpp) cc_final: 0.8103 (tpp)
REVERT: A  551 LYS cc_start: 0.7254 (ttpp) cc_final: 0.6818 (ptmm)
REVERT: A  764 LYS cc_start: 0.7495 (tptt) cc_final: 0.6788 (tptt)
  outliers start: 9
  outliers final: 6
  residues processed: 45
  average time/residue: 0.1021
  time to fit residues: 5.8973
Evaluate side-chains
  43 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 36
  time to evaluate  : 0.228 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 LEU
Chi-restraints excluded: chain A residue   92 VAL
Chi-restraints excluded: chain A residue  259 GLN
Chi-restraints excluded: chain A residue  267 LEU
Chi-restraints excluded: chain A residue  299 SER
Chi-restraints excluded: chain A residue  311 THR
Chi-restraints excluded: chain A residue  548 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 65 optimal weight:    0.5980
   chunk 29 optimal weight:    0.9990
   chunk 33 optimal weight:    0.7980
   chunk 48 optimal weight:    0.7980
   chunk 7 optimal weight:    0.9980
   chunk 55 optimal weight:    2.9990
   chunk 57 optimal weight:    0.9980
   chunk 62 optimal weight:    0.7980
   chunk 21 optimal weight:    3.9990
   chunk 27 optimal weight:    0.2980
   chunk 80 optimal weight:    1.9990
   overall best weight:    0.6580

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4169 r_free = 0.4169 target = 0.200736 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3994 r_free = 0.3994 target = 0.180267 restraints weight = 5919.402|
|-----------------------------------------------------------------------------|
r_work (start): 0.3977 rms_B_bonded: 1.37
r_work: 0.3845 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.3692 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.3692
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7369
moved from start:          0.1860

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   6617  Z= 0.179
  Angle     :  0.517   4.995   8948  Z= 0.263
  Chirality :  0.042   0.141    996
  Planarity :  0.004   0.033   1159
  Dihedral  :  4.060  13.779    890
  Min Nonbonded Distance : 2.612

Molprobity Statistics.
  All-atom Clashscore : 3.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.69 %
    Favored  : 97.31 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  :  7.35 %
    Favored  : 91.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    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:  1.33 (0.29), residues: 817
  helix:  1.45 (0.26), residues: 406
  sheet:  0.86 (0.56), residues: 96
  loop :  0.27 (0.34), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 288 
 TYR   0.011   0.001   TYR A  93 
 PHE   0.011   0.001   PHE A 726 
 TRP   0.012   0.001   TRP A 222 
 HIS   0.004   0.001   HIS A 438 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00423 /  0.18 ( 6617)
  covalent geometry    : angle       0.51672 /  0.26 ( 8948)
  hydrogen bonds       : bond        0.03946 /  2.53 (  314)
  hydrogen bonds       : angle       4.35051 /  3.15 (  924)

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

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

  1634 Ramachandran restraints generated.
    817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1634 Ramachandran restraints generated.
    817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 40
  time to evaluate  : 0.321 
Fit side-chains
REVERT: A   66 LEU cc_start: 0.7659 (OUTLIER) cc_final: 0.7356 (pp)
REVERT: A  114 LYS cc_start: 0.7792 (mmmt) cc_final: 0.7496 (mmmt)
REVERT: A  242 LYS cc_start: 0.7139 (mmtt) cc_final: 0.6899 (mtpp)
REVERT: A  378 LYS cc_start: 0.8023 (tttt) cc_final: 0.7391 (mtmt)
REVERT: A  448 MET cc_start: 0.7882 (mtp) cc_final: 0.7634 (mtp)
REVERT: A  466 LYS cc_start: 0.8048 (tptp) cc_final: 0.7659 (tptp)
REVERT: A  551 LYS cc_start: 0.7228 (ttpp) cc_final: 0.6833 (ptmm)
REVERT: A  685 LYS cc_start: 0.7807 (mttt) cc_final: 0.7553 (mtpp)
REVERT: A  761 MET cc_start: 0.6257 (mmm) cc_final: 0.6031 (mmt)
REVERT: A  764 LYS cc_start: 0.7610 (tptt) cc_final: 0.6783 (tptt)
  outliers start: 8
  outliers final: 4
  residues processed: 46
  average time/residue: 0.1111
  time to fit residues: 6.6008
Evaluate side-chains
  44 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 39
  time to evaluate  : 0.202 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 LEU
Chi-restraints excluded: chain A residue   92 VAL
Chi-restraints excluded: chain A residue  380 VAL
Chi-restraints excluded: chain A residue  548 VAL
Chi-restraints excluded: chain A residue  787 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 55 optimal weight:    2.9990
   chunk 62 optimal weight:    0.8980
   chunk 10 optimal weight:    2.9990
   chunk 17 optimal weight:    0.1980
   chunk 36 optimal weight:    1.9990
   chunk 8 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9990
   chunk 57 optimal weight:    0.7980
   chunk 56 optimal weight:    0.6980
   chunk 58 optimal weight:    0.8980
   overall best weight:    0.6980

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4143 r_free = 0.4143 target = 0.197919 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3951 r_free = 0.3951 target = 0.175623 restraints weight = 6017.287|
|-----------------------------------------------------------------------------|
r_work (start): 0.3921 rms_B_bonded: 1.53
r_work: 0.3800 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.3641 rms_B_bonded: 4.69 restraints_weight: 0.2500
r_work (final): 0.3641
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7418
moved from start:          0.2541

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   6617  Z= 0.185
  Angle     :  0.513   5.260   8948  Z= 0.264
  Chirality :  0.042   0.146    996
  Planarity :  0.004   0.037   1159
  Dihedral  :  4.067  14.040    890
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 4.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  :  8.07 %
    Favored  : 90.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    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:  1.27 (0.29), residues: 817
  helix:  1.43 (0.26), residues: 408
  sheet:  1.23 (0.60), residues: 80
  loop :  0.12 (0.34), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 625 
 TYR   0.011   0.001   TYR A 758 
 PHE   0.013   0.001   PHE A 726 
 TRP   0.010   0.001   TRP A 222 
 HIS   0.005   0.001   HIS A 438 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00436 /  0.19 ( 6617)
  covalent geometry    : angle       0.51347 /  0.26 ( 8948)
  hydrogen bonds       : bond        0.03778 /  2.43 (  314)
  hydrogen bonds       : angle       4.24190 /  3.05 (  924)

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

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

  1634 Ramachandran restraints generated.
    817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1634 Ramachandran restraints generated.
    817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 51
  time to evaluate  : 0.198 
Fit side-chains
   revert: symmetry clash
REVERT: A   66 LEU cc_start: 0.7653 (OUTLIER) cc_final: 0.7369 (pp)
REVERT: A  242 LYS cc_start: 0.7050 (mmtt) cc_final: 0.6511 (mmtm)
REVERT: A  334 MET cc_start: 0.7965 (mmt) cc_final: 0.6914 (mtt)
REVERT: A  338 ASP cc_start: 0.7272 (m-30) cc_final: 0.6999 (m-30)
REVERT: A  378 LYS cc_start: 0.8077 (tttt) cc_final: 0.7411 (mtmt)
REVERT: A  448 MET cc_start: 0.7914 (mtp) cc_final: 0.7711 (mtp)
REVERT: A  466 LYS cc_start: 0.8135 (tptp) cc_final: 0.7638 (tptp)
REVERT: A  545 MET cc_start: 0.8591 (tpp) cc_final: 0.8384 (tpp)
REVERT: A  551 LYS cc_start: 0.7170 (ttpp) cc_final: 0.6827 (ptmm)
REVERT: A  685 LYS cc_start: 0.7832 (mttt) cc_final: 0.7534 (mtpp)
REVERT: A  761 MET cc_start: 0.6618 (mmm) cc_final: 0.6348 (mmt)
REVERT: A  764 LYS cc_start: 0.7626 (tptt) cc_final: 0.6740 (tptt)
  outliers start: 9
  outliers final: 5
  residues processed: 58
  average time/residue: 0.1270
  time to fit residues: 9.2289
Evaluate side-chains
  54 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 48
  time to evaluate  : 0.231 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 LEU
Chi-restraints excluded: chain A residue   78 LEU
Chi-restraints excluded: chain A residue   92 VAL
Chi-restraints excluded: chain A residue  311 THR
Chi-restraints excluded: chain A residue  548 VAL
Chi-restraints excluded: chain A residue  787 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 46 optimal weight:    1.9990
   chunk 71 optimal weight:    5.9990
   chunk 23 optimal weight:    0.5980
   chunk 11 optimal weight:    0.9990
   chunk 41 optimal weight:    0.5980
   chunk 70 optimal weight:    0.9990
   chunk 68 optimal weight:    0.2980
   chunk 43 optimal weight:    0.6980
   chunk 49 optimal weight:    0.6980
   chunk 53 optimal weight:    0.9990
   chunk 75 optimal weight:    0.7980
   overall best weight:    0.5780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 494 GLN
A 746 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4146 r_free = 0.4146 target = 0.198394 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3955 r_free = 0.3955 target = 0.176313 restraints weight = 6070.882|
|-----------------------------------------------------------------------------|
r_work (start): 0.3927 rms_B_bonded: 1.52
r_work: 0.3805 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.3645 rms_B_bonded: 4.67 restraints_weight: 0.2500
r_work (final): 0.3645
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7413
moved from start:          0.2798

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   6617  Z= 0.157
  Angle     :  0.486   6.435   8948  Z= 0.248
  Chirality :  0.041   0.141    996
  Planarity :  0.004   0.038   1159
  Dihedral  :  3.919  13.761    890
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 4.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  :  8.65 %
    Favored  : 89.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    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:  1.48 (0.30), residues: 817
  helix:  1.65 (0.26), residues: 407
  sheet:  1.24 (0.61), residues: 80
  loop :  0.18 (0.34), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 625 
 TYR   0.010   0.001   TYR A  93 
 PHE   0.008   0.001   PHE A 726 
 TRP   0.009   0.001   TRP A 222 
 HIS   0.003   0.001   HIS A 438 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00370 /  0.16 ( 6617)
  covalent geometry    : angle       0.48585 /  0.25 ( 8948)
  hydrogen bonds       : bond        0.03502 /  2.24 (  314)
  hydrogen bonds       : angle       4.08484 /  2.93 (  924)

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

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

  1634 Ramachandran restraints generated.
    817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1634 Ramachandran restraints generated.
    817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 46
  time to evaluate  : 0.247 
Fit side-chains
   revert: symmetry clash
REVERT: A   66 LEU cc_start: 0.7632 (OUTLIER) cc_final: 0.7361 (pp)
REVERT: A  114 LYS cc_start: 0.7745 (mmmt) cc_final: 0.7261 (tptp)
REVERT: A  173 ASP cc_start: 0.7407 (OUTLIER) cc_final: 0.6614 (t0)
REVERT: A  242 LYS cc_start: 0.7004 (mmtt) cc_final: 0.6755 (mtpp)
REVERT: A  334 MET cc_start: 0.7999 (mmt) cc_final: 0.6986 (mtt)
REVERT: A  378 LYS cc_start: 0.8120 (tttt) cc_final: 0.7431 (mtmt)
REVERT: A  466 LYS cc_start: 0.8154 (tptp) cc_final: 0.7623 (tptp)
REVERT: A  546 LYS cc_start: 0.8196 (mttm) cc_final: 0.7902 (mttt)
REVERT: A  551 LYS cc_start: 0.7160 (ttpp) cc_final: 0.6846 (ptmm)
REVERT: A  685 LYS cc_start: 0.7837 (mttt) cc_final: 0.7576 (mtpp)
REVERT: A  764 LYS cc_start: 0.7639 (tptt) cc_final: 0.6717 (tptt)
  outliers start: 12
  outliers final: 6
  residues processed: 56
  average time/residue: 0.1135
  time to fit residues: 8.0479
Evaluate side-chains
  51 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 43
  time to evaluate  : 0.169 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 LEU
Chi-restraints excluded: chain A residue   92 VAL
Chi-restraints excluded: chain A residue  173 ASP
Chi-restraints excluded: chain A residue  299 SER
Chi-restraints excluded: chain A residue  311 THR
Chi-restraints excluded: chain A residue  399 THR
Chi-restraints excluded: chain A residue  548 VAL
Chi-restraints excluded: chain A residue  787 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 47 optimal weight:    0.6980
   chunk 62 optimal weight:    0.0770
   chunk 80 optimal weight:    1.9990
   chunk 78 optimal weight:    0.1980
   chunk 35 optimal weight:    1.9990
   chunk 74 optimal weight:    0.8980
   chunk 36 optimal weight:    2.9990
   chunk 81 optimal weight:    1.9990
   chunk 37 optimal weight:    1.9990
   chunk 69 optimal weight:    0.0370
   chunk 67 optimal weight:    0.4980
   overall best weight:    0.3016

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 165 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4190 r_free = 0.4190 target = 0.203377 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3991 r_free = 0.3991 target = 0.179640 restraints weight = 6021.860|
|-----------------------------------------------------------------------------|
r_work (start): 0.3950 rms_B_bonded: 1.68
r_work: 0.3819 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.3652 rms_B_bonded: 4.97 restraints_weight: 0.2500
r_work (final): 0.3652
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7351
moved from start:          0.2903

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   6617  Z= 0.100
  Angle     :  0.430   5.812   8948  Z= 0.219
  Chirality :  0.039   0.141    996
  Planarity :  0.003   0.037   1159
  Dihedral  :  3.629  13.813    890
  Min Nonbonded Distance : 2.613

Molprobity Statistics.
  All-atom Clashscore : 4.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.59 %
    Favored  : 98.41 %
  Rotamer:
    Outliers :  0.86 %
    Allowed  :  9.80 %
    Favored  : 89.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    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:  1.76 (0.30), residues: 817
  helix:  1.91 (0.26), residues: 407
  sheet:  0.71 (0.56), residues: 96
  loop :  0.45 (0.35), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 625 
 TYR   0.008   0.001   TYR A  93 
 PHE   0.008   0.001   PHE A 754 
 TRP   0.008   0.001   TRP A 222 
 HIS   0.002   0.001   HIS A 165 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00226 /  0.10 ( 6617)
  covalent geometry    : angle       0.43013 /  0.22 ( 8948)
  hydrogen bonds       : bond        0.02965 /  1.90 (  314)
  hydrogen bonds       : angle       3.92343 /  2.82 (  924)

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

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

  1634 Ramachandran restraints generated.
    817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1634 Ramachandran restraints generated.
    817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  46 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 40
  time to evaluate  : 0.226 
Fit side-chains
   revert: symmetry clash
REVERT: A   66 LEU cc_start: 0.7617 (OUTLIER) cc_final: 0.7324 (pp)
REVERT: A  114 LYS cc_start: 0.7738 (mmmt) cc_final: 0.7388 (mmmt)
REVERT: A  242 LYS cc_start: 0.7045 (mmtt) cc_final: 0.6773 (mtpp)
REVERT: A  334 MET cc_start: 0.7972 (OUTLIER) cc_final: 0.7005 (mtt)
REVERT: A  378 LYS cc_start: 0.8109 (tttt) cc_final: 0.7376 (mtmt)
REVERT: A  466 LYS cc_start: 0.8197 (tptp) cc_final: 0.7643 (tptp)
REVERT: A  495 MET cc_start: 0.7344 (tpp) cc_final: 0.6757 (tpp)
REVERT: A  545 MET cc_start: 0.8484 (tpp) cc_final: 0.8146 (tpp)
REVERT: A  546 LYS cc_start: 0.8129 (mttm) cc_final: 0.7889 (mttt)
REVERT: A  551 LYS cc_start: 0.7111 (ttpp) cc_final: 0.6790 (ptmm)
REVERT: A  764 LYS cc_start: 0.7543 (tptt) cc_final: 0.6674 (tptt)
  outliers start: 6
  outliers final: 3
  residues processed: 44
  average time/residue: 0.1164
  time to fit residues: 6.4871
Evaluate side-chains
  43 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 38
  time to evaluate  : 0.155 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 LEU
Chi-restraints excluded: chain A residue   92 VAL
Chi-restraints excluded: chain A residue  334 MET
Chi-restraints excluded: chain A residue  548 VAL
Chi-restraints excluded: chain A residue  787 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 18 optimal weight:    0.3980
   chunk 16 optimal weight:    0.4980
   chunk 70 optimal weight:    0.9990
   chunk 2 optimal weight:    0.8980
   chunk 78 optimal weight:    0.0010
   chunk 23 optimal weight:    0.8980
   chunk 7 optimal weight:    0.5980
   chunk 44 optimal weight:    0.7980
   chunk 69 optimal weight:    0.2980
   chunk 43 optimal weight:    0.9980
   chunk 3 optimal weight:    2.9990
   overall best weight:    0.3586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 165 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4166 r_free = 0.4166 target = 0.201330 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3961 r_free = 0.3961 target = 0.177445 restraints weight = 5999.425|
|-----------------------------------------------------------------------------|
r_work (start): 0.4211 rms_B_bonded: 1.69
r_work: 0.3897 rms_B_bonded: 4.95 restraints_weight: 0.5000
r_work (final): 0.3897
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7406
moved from start:          0.3044

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   6617  Z= 0.110
  Angle     :  0.436   7.177   8948  Z= 0.220
  Chirality :  0.039   0.136    996
  Planarity :  0.003   0.038   1159
  Dihedral  :  3.548  13.882    890
  Min Nonbonded Distance : 2.610

Molprobity Statistics.
  All-atom Clashscore : 4.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  0.86 %
    Allowed  : 10.37 %
    Favored  : 88.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    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:  1.90 (0.30), residues: 817
  helix:  2.03 (0.26), residues: 408
  sheet:  1.35 (0.62), residues: 80
  loop :  0.34 (0.35), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 625 
 TYR   0.009   0.001   TYR A  93 
 PHE   0.007   0.001   PHE A 754 
 TRP   0.008   0.001   TRP A 222 
 HIS   0.002   0.001   HIS A  67 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00251 /  0.11 ( 6617)
  covalent geometry    : angle       0.43572 /  0.22 ( 8948)
  hydrogen bonds       : bond        0.02981 /  1.91 (  314)
  hydrogen bonds       : angle       3.81586 /  2.73 (  924)

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

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

  1634 Ramachandran restraints generated.
    817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1634 Ramachandran restraints generated.
    817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 39
  time to evaluate  : 0.227 
Fit side-chains
   revert: symmetry clash
REVERT: A   66 LEU cc_start: 0.7611 (OUTLIER) cc_final: 0.7317 (pp)
REVERT: A  114 LYS cc_start: 0.7740 (mmmt) cc_final: 0.7353 (mmmt)
REVERT: A  173 ASP cc_start: 0.7515 (OUTLIER) cc_final: 0.6812 (t70)
REVERT: A  242 LYS cc_start: 0.7099 (mmtt) cc_final: 0.6857 (mtpp)
REVERT: A  334 MET cc_start: 0.7960 (OUTLIER) cc_final: 0.6973 (mtt)
REVERT: A  378 LYS cc_start: 0.8132 (tttt) cc_final: 0.7302 (mtmt)
REVERT: A  466 LYS cc_start: 0.8179 (tptp) cc_final: 0.7651 (tptp)
REVERT: A  545 MET cc_start: 0.8566 (tpp) cc_final: 0.8225 (tpp)
REVERT: A  551 LYS cc_start: 0.7212 (ttpp) cc_final: 0.6930 (ptmm)
REVERT: A  764 LYS cc_start: 0.7575 (tptt) cc_final: 0.6797 (tptt)
  outliers start: 6
  outliers final: 3
  residues processed: 43
  average time/residue: 0.1212
  time to fit residues: 6.6161
Evaluate side-chains
  45 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 39
  time to evaluate  : 0.223 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 LEU
Chi-restraints excluded: chain A residue   92 VAL
Chi-restraints excluded: chain A residue  173 ASP
Chi-restraints excluded: chain A residue  334 MET
Chi-restraints excluded: chain A residue  548 VAL
Chi-restraints excluded: chain A residue  787 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 39 optimal weight:    0.7980
   chunk 30 optimal weight:    0.0570
   chunk 63 optimal weight:    0.0970
   chunk 3 optimal weight:    0.9990
   chunk 35 optimal weight:    1.9990
   chunk 38 optimal weight:    0.0980
   chunk 79 optimal weight:    0.2980
   chunk 72 optimal weight:    3.9990
   chunk 24 optimal weight:    0.9990
   chunk 66 optimal weight:    0.9990
   chunk 14 optimal weight:    1.9990
   overall best weight:    0.2696

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 165 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4444 r_free = 0.4444 target = 0.234520 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.4239 r_free = 0.4239 target = 0.209817 restraints weight = 6342.849|
|-----------------------------------------------------------------------------|
r_work (start): 0.4181 rms_B_bonded: 1.77
r_work: 0.3961 rms_B_bonded: 3.96 restraints_weight: 0.5000
r_work (final): 0.3961
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7317
moved from start:          0.3132

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   6617  Z= 0.090
  Angle     :  0.411   6.400   8948  Z= 0.208
  Chirality :  0.039   0.136    996
  Planarity :  0.003   0.037   1159
  Dihedral  :  3.392  13.605    890
  Min Nonbonded Distance : 2.613

Molprobity Statistics.
  All-atom Clashscore : 4.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.35 %
    Favored  : 98.65 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  : 10.09 %
    Favored  : 88.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    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:  2.05 (0.30), residues: 817
  helix:  2.15 (0.26), residues: 414
  sheet:  0.82 (0.57), residues: 96
  loop :  0.55 (0.36), residues: 307

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 625 
 TYR   0.008   0.001   TYR A 600 
 PHE   0.008   0.001   PHE A 754 
 TRP   0.007   0.001   TRP A 222 
 HIS   0.002   0.000   HIS A 826 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00202 /  0.09 ( 6617)
  covalent geometry    : angle       0.41129 /  0.21 ( 8948)
  hydrogen bonds       : bond        0.02699 /  1.73 (  314)
  hydrogen bonds       : angle       3.71596 /  2.65 (  924)

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

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

  1634 Ramachandran restraints generated.
    817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1634 Ramachandran restraints generated.
    817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 38
  time to evaluate  : 0.231 
Fit side-chains
   revert: symmetry clash
REVERT: A   66 LEU cc_start: 0.7576 (OUTLIER) cc_final: 0.7306 (pp)
REVERT: A  114 LYS cc_start: 0.7655 (mmmt) cc_final: 0.7327 (mmmt)
REVERT: A  173 ASP cc_start: 0.7515 (OUTLIER) cc_final: 0.6837 (t70)
REVERT: A  212 LYS cc_start: 0.7504 (OUTLIER) cc_final: 0.7148 (mptt)
REVERT: A  242 LYS cc_start: 0.7109 (mmtt) cc_final: 0.6880 (mtpp)
REVERT: A  334 MET cc_start: 0.7878 (OUTLIER) cc_final: 0.6888 (mtt)
REVERT: A  378 LYS cc_start: 0.8129 (tttt) cc_final: 0.7332 (mtmt)
REVERT: A  466 LYS cc_start: 0.8083 (tptp) cc_final: 0.7562 (tptp)
REVERT: A  495 MET cc_start: 0.7456 (tpp) cc_final: 0.7239 (tpt)
REVERT: A  545 MET cc_start: 0.8468 (tpp) cc_final: 0.8201 (tpp)
REVERT: A  764 LYS cc_start: 0.7480 (tptt) cc_final: 0.6659 (tptt)
  outliers start: 9
  outliers final: 4
  residues processed: 43
  average time/residue: 0.1125
  time to fit residues: 6.2056
Evaluate side-chains
  44 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 36
  time to evaluate  : 0.231 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 LEU
Chi-restraints excluded: chain A residue   92 VAL
Chi-restraints excluded: chain A residue  173 ASP
Chi-restraints excluded: chain A residue  212 LYS
Chi-restraints excluded: chain A residue  299 SER
Chi-restraints excluded: chain A residue  334 MET
Chi-restraints excluded: chain A residue  548 VAL
Chi-restraints excluded: chain A residue  787 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 57 optimal weight:    0.9980
   chunk 53 optimal weight:    0.2980
   chunk 23 optimal weight:    0.7980
   chunk 69 optimal weight:    0.9990
   chunk 22 optimal weight:    0.7980
   chunk 50 optimal weight:    1.9990
   chunk 59 optimal weight:    0.9980
   chunk 55 optimal weight:    2.9990
   chunk 11 optimal weight:    0.0470
   chunk 16 optimal weight:    0.0980
   chunk 66 optimal weight:    0.7980
   overall best weight:    0.4078

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 165 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4164 r_free = 0.4164 target = 0.201212 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3957 r_free = 0.3957 target = 0.177419 restraints weight = 6042.323|
|-----------------------------------------------------------------------------|
r_work (start): 0.4209 rms_B_bonded: 1.68
r_work: 0.3890 rms_B_bonded: 5.00 restraints_weight: 0.5000
r_work (final): 0.3890
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7413
moved from start:          0.3239

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   6617  Z= 0.117
  Angle     :  0.438   6.504   8948  Z= 0.220
  Chirality :  0.039   0.135    996
  Planarity :  0.003   0.038   1159
  Dihedral  :  3.467  13.771    890
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 4.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  : 10.23 %
    Favored  : 88.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    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:  2.03 (0.30), residues: 817
  helix:  2.12 (0.26), residues: 414
  sheet:  0.81 (0.57), residues: 96
  loop :  0.56 (0.37), residues: 307

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 625 
 TYR   0.009   0.001   TYR A  93 
 PHE   0.008   0.001   PHE A 754 
 TRP   0.008   0.001   TRP A 222 
 HIS   0.002   0.001   HIS A 438 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00271 /  0.12 ( 6617)
  covalent geometry    : angle       0.43815 /  0.22 ( 8948)
  hydrogen bonds       : bond        0.02979 /  1.91 (  314)
  hydrogen bonds       : angle       3.74466 /  2.68 (  924)

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

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

  1634 Ramachandran restraints generated.
    817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1634 Ramachandran restraints generated.
    817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  46 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 38
  time to evaluate  : 0.153 
Fit side-chains
   revert: symmetry clash
REVERT: A   66 LEU cc_start: 0.7608 (OUTLIER) cc_final: 0.7324 (pp)
REVERT: A  114 LYS cc_start: 0.7642 (mmmt) cc_final: 0.7288 (mmmt)
REVERT: A  173 ASP cc_start: 0.7592 (OUTLIER) cc_final: 0.6676 (t0)
REVERT: A  212 LYS cc_start: 0.7643 (OUTLIER) cc_final: 0.7297 (mptt)
REVERT: A  242 LYS cc_start: 0.7125 (mmtt) cc_final: 0.6875 (mtpp)
REVERT: A  334 MET cc_start: 0.7921 (OUTLIER) cc_final: 0.6939 (mtt)
REVERT: A  378 LYS cc_start: 0.8193 (tttt) cc_final: 0.7341 (mtmt)
REVERT: A  466 LYS cc_start: 0.8157 (tptp) cc_final: 0.7646 (tptp)
REVERT: A  545 MET cc_start: 0.8573 (tpp) cc_final: 0.8221 (tpp)
REVERT: A  551 LYS cc_start: 0.7249 (ttpp) cc_final: 0.7014 (ptmm)
REVERT: A  764 LYS cc_start: 0.7581 (tptt) cc_final: 0.6772 (tptt)
  outliers start: 8
  outliers final: 4
  residues processed: 43
  average time/residue: 0.1139
  time to fit residues: 6.2006
Evaluate side-chains
  46 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 38
  time to evaluate  : 0.233 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 LEU
Chi-restraints excluded: chain A residue   92 VAL
Chi-restraints excluded: chain A residue  173 ASP
Chi-restraints excluded: chain A residue  212 LYS
Chi-restraints excluded: chain A residue  299 SER
Chi-restraints excluded: chain A residue  334 MET
Chi-restraints excluded: chain A residue  548 VAL
Chi-restraints excluded: chain A residue  787 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 18 optimal weight:    0.0030
   chunk 1 optimal weight:    0.7980
   chunk 46 optimal weight:    1.9990
   chunk 65 optimal weight:    0.9980
   chunk 13 optimal weight:    1.9990
   chunk 71 optimal weight:    0.7980
   chunk 40 optimal weight:    0.6980
   chunk 72 optimal weight:    0.6980
   chunk 37 optimal weight:    0.9990
   chunk 9 optimal weight:    0.1980
   chunk 20 optimal weight:    0.3980
   overall best weight:    0.3990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 165 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4165 r_free = 0.4165 target = 0.201336 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3959 r_free = 0.3959 target = 0.177669 restraints weight = 5912.299|
|-----------------------------------------------------------------------------|
r_work (start): 0.4176 rms_B_bonded: 1.66
r_work: 0.3904 rms_B_bonded: 4.56 restraints_weight: 0.5000
r_work (final): 0.3904
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7407
moved from start:          0.3340

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   6617  Z= 0.114
  Angle     :  0.434   6.477   8948  Z= 0.218
  Chirality :  0.039   0.134    996
  Planarity :  0.003   0.037   1159
  Dihedral  :  3.466  13.933    890
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 3.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  : 10.23 %
    Favored  : 88.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    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:  2.04 (0.30), residues: 817
  helix:  2.14 (0.26), residues: 414
  sheet:  0.81 (0.57), residues: 96
  loop :  0.56 (0.37), residues: 307

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 625 
 TYR   0.009   0.001   TYR A  93 
 PHE   0.007   0.001   PHE A 754 
 TRP   0.008   0.001   TRP A 222 
 HIS   0.003   0.001   HIS A 165 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00262 /  0.11 ( 6617)
  covalent geometry    : angle       0.43350 /  0.22 ( 8948)
  hydrogen bonds       : bond        0.02929 /  1.88 (  314)
  hydrogen bonds       : angle       3.74700 /  2.68 (  924)

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

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

  1634 Ramachandran restraints generated.
    817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1634 Ramachandran restraints generated.
    817 Oldfield, 0 Emsley, 817 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  46 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 38
  time to evaluate  : 0.280 
Fit side-chains
   revert: symmetry clash
REVERT: A   66 LEU cc_start: 0.7645 (OUTLIER) cc_final: 0.7347 (pp)
REVERT: A  114 LYS cc_start: 0.7648 (mmmt) cc_final: 0.7336 (mmmt)
REVERT: A  173 ASP cc_start: 0.7539 (OUTLIER) cc_final: 0.6628 (t0)
REVERT: A  212 LYS cc_start: 0.7632 (mmtm) cc_final: 0.7271 (mptt)
REVERT: A  242 LYS cc_start: 0.7147 (mmtt) cc_final: 0.6903 (mtpp)
REVERT: A  334 MET cc_start: 0.7901 (OUTLIER) cc_final: 0.6921 (mtt)
REVERT: A  378 LYS cc_start: 0.8197 (tttt) cc_final: 0.7806 (tttt)
REVERT: A  466 LYS cc_start: 0.8149 (tptp) cc_final: 0.7655 (tptp)
REVERT: A  545 MET cc_start: 0.8570 (tpp) cc_final: 0.8240 (tpp)
REVERT: A  551 LYS cc_start: 0.7230 (ttpp) cc_final: 0.7025 (ptmm)
REVERT: A  764 LYS cc_start: 0.7546 (tptt) cc_final: 0.6731 (tptt)
  outliers start: 8
  outliers final: 5
  residues processed: 44
  average time/residue: 0.1164
  time to fit residues: 6.5831
Evaluate side-chains
  46 residues out of total 694 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 38
  time to evaluate  : 0.238 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 LEU
Chi-restraints excluded: chain A residue   92 VAL
Chi-restraints excluded: chain A residue  173 ASP
Chi-restraints excluded: chain A residue  299 SER
Chi-restraints excluded: chain A residue  334 MET
Chi-restraints excluded: chain A residue  548 VAL
Chi-restraints excluded: chain A residue  643 THR
Chi-restraints excluded: chain A residue  787 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 40 optimal weight:    0.9990
   chunk 27 optimal weight:    0.7980
   chunk 28 optimal weight:    0.6980
   chunk 33 optimal weight:    0.0070
   chunk 64 optimal weight:    1.9990
   chunk 75 optimal weight:    3.9990
   chunk 50 optimal weight:    1.9990
   chunk 45 optimal weight:    0.5980
   chunk 35 optimal weight:    1.9990
   chunk 23 optimal weight:    0.7980
   chunk 72 optimal weight:    0.6980
   overall best weight:    0.5598

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 165 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4142 r_free = 0.4142 target = 0.198896 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3952 r_free = 0.3952 target = 0.177227 restraints weight = 5974.960|
|-----------------------------------------------------------------------------|
r_work (start): 0.3925 rms_B_bonded: 1.49
r_work: 0.3801 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.3643 rms_B_bonded: 4.66 restraints_weight: 0.2500
r_work (final): 0.3643
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7417
moved from start:          0.3440

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6617  Z= 0.148
  Angle     :  0.469   6.371   8948  Z= 0.236
  Chirality :  0.040   0.136    996
  Planarity :  0.003   0.038   1159
  Dihedral  :  3.610  13.933    890
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 3.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  : 10.23 %
    Favored  : 88.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    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:  1.93 (0.30), residues: 817
  helix:  2.06 (0.26), residues: 408
  sheet:  1.27 (0.62), residues: 80
  loop :  0.39 (0.35), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 625 
 TYR   0.010   0.001   TYR A  93 
 PHE   0.009   0.001   PHE A 726 
 TRP   0.009   0.001   TRP A 222 
 HIS   0.003   0.001   HIS A 438 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00349 /  0.15 ( 6617)
  covalent geometry    : angle       0.46920 /  0.24 ( 8948)
  hydrogen bonds       : bond        0.03249 /  2.09 (  314)
  hydrogen bonds       : angle       3.83048 /  2.74 (  924)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1495.95 seconds
wall clock time: 26 minutes 23.22 seconds (1583.22 seconds total)