Starting phenix.real_space_refine
on Fri Aug 22 12:57:26 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7yng_33961/08_2025/7yng_33961.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7yng_33961/08_2025/7yng_33961.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7yng_33961/08_2025/7yng_33961.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7yng_33961/08_2025/7yng_33961.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7yng_33961/08_2025/7yng_33961.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7yng_33961/08_2025/7yng_33961.map"
  }
  resolution = 3.1
  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=   0.002
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: 3
    Type Number    sf(0)   Gaussians
     C    1644      2.51       5
     N     456      2.21       5
     O     528      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 18 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 2628
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 438
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 63, 438
          Classifications: {'peptide': 63}
          Link IDs: {'TRANS': 62}
  Restraints were copied for chains:
    B, C, D, E, F
  Time building chain proxies: 0.58, per 1000 atoms: 0.22
  Number of scatterers: 2628
  At special positions: 0
  Unit cell: (115.54, 102.82, 31.8, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 3
    Type Number    sf(0)
     O     528      8.00
     N     456      7.00
     C    1644      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: 0.14
  Conformation dependent library (CDL) restraints added in 127.6 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  648

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 12 sheets defined
      0.0% alpha, 50.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.13
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'B' and resid 40 through 41
      removed outlier: 6.491A  pdb=" N   VAL A  40 " --> pdb=" O   GLY F  41 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 45 through 58
      removed outlier: 8.372A  pdb=" N   GLU A  46 " --> pdb=" O   GLY B  47 " (cutoff:3.500A)
      removed outlier: 7.818A  pdb=" N   VAL B  49 " --> pdb=" O   GLU A  46 " (cutoff:3.500A)
      removed outlier: 9.203A  pdb=" N   VAL A  48 " --> pdb=" O   VAL B  49 " (cutoff:3.500A)
      removed outlier: 10.416A  pdb=" N   GLY B  51 " --> pdb=" O   VAL A  48 " (cutoff:3.500A)
      removed outlier: 6.161A  pdb=" N   HIS A  50 " --> pdb=" O   GLY B  51 " (cutoff:3.500A)
      removed outlier: 8.608A  pdb=" N   ALA B  53 " --> pdb=" O   HIS A  50 " (cutoff:3.500A)
      removed outlier: 6.530A  pdb=" N   VAL A  52 " --> pdb=" O   ALA B  53 " (cutoff:3.500A)
      removed outlier: 7.905A  pdb=" N   VAL B  55 " --> pdb=" O   VAL A  52 " (cutoff:3.500A)
      removed outlier: 6.531A  pdb=" N   THR A  54 " --> pdb=" O   VAL B  55 " (cutoff:3.500A)
      removed outlier: 8.250A  pdb=" N   GLU B  57 " --> pdb=" O   THR A  54 " (cutoff:3.500A)
      removed outlier: 6.480A  pdb=" N   ALA A  56 " --> pdb=" O   GLU B  57 " (cutoff:3.500A)
      removed outlier: 6.843A  pdb=" N   VAL F  48 " --> pdb=" O   GLY A  47 " (cutoff:3.500A)
      removed outlier: 6.962A  pdb=" N   VAL A  49 " --> pdb=" O   VAL F  48 " (cutoff:3.500A)
      removed outlier: 6.922A  pdb=" N   HIS F  50 " --> pdb=" O   VAL A  49 " (cutoff:3.500A)
      removed outlier: 6.849A  pdb=" N   GLY A  51 " --> pdb=" O   HIS F  50 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 61 through 66
      removed outlier: 6.350A  pdb=" N   GLN A  62 " --> pdb=" O   VAL F  63 " (cutoff:3.500A)
      removed outlier: 7.732A  pdb=" N   ASN F  65 " --> pdb=" O   GLN A  62 " (cutoff:3.500A)
      removed outlier: 6.252A  pdb=" N   THR A  64 " --> pdb=" O   ASN F  65 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 69 through 71
      removed outlier: 6.478A  pdb=" N   VAL A  70 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 74 through 82
      removed outlier: 6.841A  pdb=" N   VAL A  77 " --> pdb=" O   ALA B  76 " (cutoff:3.500A)
      removed outlier: 6.950A  pdb=" N   ALA B  78 " --> pdb=" O   VAL A  77 " (cutoff:3.500A)
      removed outlier: 6.904A  pdb=" N   GLN A  79 " --> pdb=" O   ALA B  78 " (cutoff:3.500A)
      removed outlier: 6.912A  pdb=" N   LYS B  80 " --> pdb=" O   GLN A  79 " (cutoff:3.500A)
      removed outlier: 6.916A  pdb=" N   THR A  81 " --> pdb=" O   LYS B  80 " (cutoff:3.500A)
      removed outlier: 6.867A  pdb=" N   VAL B  82 " --> pdb=" O   THR A  81 " (cutoff:3.500A)
      removed outlier: 6.288A  pdb=" N   VAL A  74 " --> pdb=" O   THR F  75 " (cutoff:3.500A)
      removed outlier: 6.145A  pdb=" N   VAL F  77 " --> pdb=" O   VAL A  74 " (cutoff:3.500A)
      removed outlier: 7.580A  pdb=" N   ALA A  76 " --> pdb=" O   VAL F  77 " (cutoff:3.500A)
      removed outlier: 10.067A  pdb=" N   GLN F  79 " --> pdb=" O   ALA A  76 " (cutoff:3.500A)
      removed outlier: 8.989A  pdb=" N   ALA A  78 " --> pdb=" O   GLN F  79 " (cutoff:3.500A)
      removed outlier: 10.393A  pdb=" N   THR F  81 " --> pdb=" O   ALA A  78 " (cutoff:3.500A)
      removed outlier: 8.701A  pdb=" N   LYS A  80 " --> pdb=" O   THR F  81 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 89 through 92
      removed outlier: 6.707A  pdb=" N   ALA A  89 " --> pdb=" O   ALA F  90 " (cutoff:3.500A)
      removed outlier: 7.942A  pdb=" N   THR F  92 " --> pdb=" O   ALA A  89 " (cutoff:3.500A)
      removed outlier: 6.282A  pdb=" N   ALA A  91 " --> pdb=" O   THR F  92 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 40 through 41
      removed outlier: 6.490A  pdb=" N   VAL C  40 " --> pdb=" O   GLY D  41 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 45 through 58
      removed outlier: 6.840A  pdb=" N   VAL D  48 " --> pdb=" O   GLY C  47 " (cutoff:3.500A)
      removed outlier: 6.959A  pdb=" N   VAL C  49 " --> pdb=" O   VAL D  48 " (cutoff:3.500A)
      removed outlier: 6.917A  pdb=" N   HIS D  50 " --> pdb=" O   VAL C  49 " (cutoff:3.500A)
      removed outlier: 6.844A  pdb=" N   GLY C  51 " --> pdb=" O   HIS D  50 " (cutoff:3.500A)
      removed outlier: 8.378A  pdb=" N   GLU C  46 " --> pdb=" O   GLY E  47 " (cutoff:3.500A)
      removed outlier: 7.827A  pdb=" N   VAL E  49 " --> pdb=" O   GLU C  46 " (cutoff:3.500A)
      removed outlier: 9.214A  pdb=" N   VAL C  48 " --> pdb=" O   VAL E  49 " (cutoff:3.500A)
      removed outlier: 10.429A  pdb=" N   GLY E  51 " --> pdb=" O   VAL C  48 " (cutoff:3.500A)
      removed outlier: 6.175A  pdb=" N   HIS C  50 " --> pdb=" O   GLY E  51 " (cutoff:3.500A)
      removed outlier: 8.625A  pdb=" N   ALA E  53 " --> pdb=" O   HIS C  50 " (cutoff:3.500A)
      removed outlier: 6.547A  pdb=" N   VAL C  52 " --> pdb=" O   ALA E  53 " (cutoff:3.500A)
      removed outlier: 7.920A  pdb=" N   VAL E  55 " --> pdb=" O   VAL C  52 " (cutoff:3.500A)
      removed outlier: 6.549A  pdb=" N   THR C  54 " --> pdb=" O   VAL E  55 " (cutoff:3.500A)
      removed outlier: 8.267A  pdb=" N   GLU E  57 " --> pdb=" O   THR C  54 " (cutoff:3.500A)
      removed outlier: 6.498A  pdb=" N   ALA C  56 " --> pdb=" O   GLU E  57 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'D' and resid 61 through 66
      removed outlier: 6.354A  pdb=" N   GLN C  62 " --> pdb=" O   VAL D  63 " (cutoff:3.500A)
      removed outlier: 7.736A  pdb=" N   ASN D  65 " --> pdb=" O   GLN C  62 " (cutoff:3.500A)
      removed outlier: 6.255A  pdb=" N   THR C  64 " --> pdb=" O   ASN D  65 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'D' and resid 69 through 71
      removed outlier: 6.478A  pdb=" N   VAL C  70 " --> pdb=" O   VAL E  71 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'D' and resid 74 through 82
      removed outlier: 6.283A  pdb=" N   VAL C  74 " --> pdb=" O   THR D  75 " (cutoff:3.500A)
      removed outlier: 6.143A  pdb=" N   VAL D  77 " --> pdb=" O   VAL C  74 " (cutoff:3.500A)
      removed outlier: 7.580A  pdb=" N   ALA C  76 " --> pdb=" O   VAL D  77 " (cutoff:3.500A)
      removed outlier: 10.068A  pdb=" N   GLN D  79 " --> pdb=" O   ALA C  76 " (cutoff:3.500A)
      removed outlier: 8.989A  pdb=" N   ALA C  78 " --> pdb=" O   GLN D  79 " (cutoff:3.500A)
      removed outlier: 10.393A  pdb=" N   THR D  81 " --> pdb=" O   ALA C  78 " (cutoff:3.500A)
      removed outlier: 8.701A  pdb=" N   LYS C  80 " --> pdb=" O   THR D  81 " (cutoff:3.500A)
      removed outlier: 6.850A  pdb=" N   VAL C  77 " --> pdb=" O   ALA E  76 " (cutoff:3.500A)
      removed outlier: 6.956A  pdb=" N   ALA E  78 " --> pdb=" O   VAL C  77 " (cutoff:3.500A)
      removed outlier: 6.908A  pdb=" N   GLN C  79 " --> pdb=" O   ALA E  78 " (cutoff:3.500A)
      removed outlier: 6.912A  pdb=" N   LYS E  80 " --> pdb=" O   GLN C  79 " (cutoff:3.500A)
      removed outlier: 6.915A  pdb=" N   THR C  81 " --> pdb=" O   LYS E  80 " (cutoff:3.500A)
      removed outlier: 6.863A  pdb=" N   VAL E  82 " --> pdb=" O   THR C  81 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'D' and resid 89 through 92
      removed outlier: 6.708A  pdb=" N   ALA C  89 " --> pdb=" O   ALA D  90 " (cutoff:3.500A)
      removed outlier: 7.943A  pdb=" N   THR D  92 " --> pdb=" O   ALA C  89 " (cutoff:3.500A)
      removed outlier: 6.282A  pdb=" N   ALA C  91 " --> pdb=" O   THR D  92 " (cutoff:3.500A)

    44 hydrogen bonds defined for protein.
    132 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: 0.37

  Time building geometry restraints manager: 0.20 seconds

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

  Histogram of bond lengths:
        1.22 -     1.29: 462
        1.29 -     1.35: 408
        1.35 -     1.42: 108
        1.42 -     1.48: 450
        1.48 -     1.55: 1212
  Bond restraints: 2640
  Sorted by residual:
  bond pdb=" CA  SER D  87 "
       pdb=" C   SER D  87 "
    ideal  model  delta    sigma   weight residual
    1.528  1.509  0.019 1.35e-02 5.49e+03 2.00e+00
  bond pdb=" CA  SER A  87 "
       pdb=" C   SER A  87 "
    ideal  model  delta    sigma   weight residual
    1.528  1.509  0.019 1.35e-02 5.49e+03 2.00e+00
  bond pdb=" CA  SER F  87 "
       pdb=" C   SER F  87 "
    ideal  model  delta    sigma   weight residual
    1.528  1.509  0.019 1.35e-02 5.49e+03 1.91e+00
  bond pdb=" CA  SER E  87 "
       pdb=" C   SER E  87 "
    ideal  model  delta    sigma   weight residual
    1.528  1.509  0.019 1.35e-02 5.49e+03 1.89e+00
  bond pdb=" CA  SER B  87 "
       pdb=" C   SER B  87 "
    ideal  model  delta    sigma   weight residual
    1.528  1.510  0.018 1.35e-02 5.49e+03 1.83e+00
  ... (remaining 2635 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.91: 2914
        0.91 -     1.82: 472
        1.82 -     2.73: 130
        2.73 -     3.64: 36
        3.64 -     4.55: 18
  Bond angle restraints: 3570
  Sorted by residual:
  angle pdb=" C   THR A  92 "
        pdb=" N   GLY A  93 "
        pdb=" CA  GLY A  93 "
      ideal   model   delta    sigma   weight residual
     119.99  123.07   -3.08 1.13e+00 7.83e-01 7.42e+00
  angle pdb=" C   THR B  92 "
        pdb=" N   GLY B  93 "
        pdb=" CA  GLY B  93 "
      ideal   model   delta    sigma   weight residual
     119.99  123.05   -3.06 1.13e+00 7.83e-01 7.34e+00
  angle pdb=" C   THR D  92 "
        pdb=" N   GLY D  93 "
        pdb=" CA  GLY D  93 "
      ideal   model   delta    sigma   weight residual
     119.99  123.05   -3.06 1.13e+00 7.83e-01 7.33e+00
  angle pdb=" C   THR C  92 "
        pdb=" N   GLY C  93 "
        pdb=" CA  GLY C  93 "
      ideal   model   delta    sigma   weight residual
     119.99  123.04   -3.05 1.13e+00 7.83e-01 7.31e+00
  angle pdb=" C   THR F  92 "
        pdb=" N   GLY F  93 "
        pdb=" CA  GLY F  93 "
      ideal   model   delta    sigma   weight residual
     119.99  123.04   -3.05 1.13e+00 7.83e-01 7.28e+00
  ... (remaining 3565 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.86: 1368
       14.86 -    29.73: 138
       29.73 -    44.59: 36
       44.59 -    59.46: 0
       59.46 -    74.32: 6
  Dihedral angle restraints: 1548
    sinusoidal: 522
      harmonic: 1026
  Sorted by residual:
  dihedral pdb=" CA  GLY F  93 "
           pdb=" C   GLY F  93 "
           pdb=" N   PHE F  94 "
           pdb=" CA  PHE F  94 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.78   19.22     0      5.00e+00 4.00e-02 1.48e+01
  dihedral pdb=" CA  GLY A  93 "
           pdb=" C   GLY A  93 "
           pdb=" N   PHE A  94 "
           pdb=" CA  PHE A  94 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.79   19.21     0      5.00e+00 4.00e-02 1.48e+01
  dihedral pdb=" CA  GLY D  93 "
           pdb=" C   GLY D  93 "
           pdb=" N   PHE D  94 "
           pdb=" CA  PHE D  94 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.81   19.19     0      5.00e+00 4.00e-02 1.47e+01
  ... (remaining 1545 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.025: 156
       0.025 -    0.050: 144
       0.050 -    0.075: 68
       0.075 -    0.100: 59
       0.100 -    0.125: 41
  Chirality restraints: 468
  Sorted by residual:
  chirality pdb=" CA  VAL C  95 "
            pdb=" N   VAL C  95 "
            pdb=" C   VAL C  95 "
            pdb=" CB  VAL C  95 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 3.92e-01
  chirality pdb=" CA  VAL E  95 "
            pdb=" N   VAL E  95 "
            pdb=" C   VAL E  95 "
            pdb=" CB  VAL E  95 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.12 2.00e-01 2.50e+01 3.86e-01
  chirality pdb=" CA  VAL A  71 "
            pdb=" N   VAL A  71 "
            pdb=" C   VAL A  71 "
            pdb=" CB  VAL A  71 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.12 2.00e-01 2.50e+01 3.83e-01
  ... (remaining 465 not shown)

  Planarity restraints: 444
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU F  83 "    0.005 2.00e-02 2.50e+03   1.01e-02 1.02e+00
        pdb=" C   GLU F  83 "   -0.017 2.00e-02 2.50e+03
        pdb=" O   GLU F  83 "    0.007 2.00e-02 2.50e+03
        pdb=" N   GLY F  84 "    0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU B  83 "    0.005 2.00e-02 2.50e+03   1.00e-02 1.01e+00
        pdb=" C   GLU B  83 "   -0.017 2.00e-02 2.50e+03
        pdb=" O   GLU B  83 "    0.007 2.00e-02 2.50e+03
        pdb=" N   GLY B  84 "    0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU C  83 "   -0.005 2.00e-02 2.50e+03   1.00e-02 1.00e+00
        pdb=" C   GLU C  83 "    0.017 2.00e-02 2.50e+03
        pdb=" O   GLU C  83 "   -0.007 2.00e-02 2.50e+03
        pdb=" N   GLY C  84 "   -0.006 2.00e-02 2.50e+03
  ... (remaining 441 not shown)

  Histogram of nonbonded interaction distances:
        2.19 -     2.73: 156
        2.73 -     3.28: 2535
        3.28 -     3.82: 4208
        3.82 -     4.36: 4429
        4.36 -     4.90: 9232
  Nonbonded interactions: 20560
  Sorted by model distance:
  nonbonded pdb=" NZ  LYS B  60 "
            pdb=" OE1 GLN B  62 "
     model   vdw
     2.192 3.120
  nonbonded pdb=" NZ  LYS E  60 "
            pdb=" OE1 GLN E  62 "
     model   vdw
     2.192 3.120
  nonbonded pdb=" NZ  LYS A  60 "
            pdb=" OE1 GLN A  62 "
     model   vdw
     2.192 3.120
  nonbonded pdb=" NZ  LYS F  60 "
            pdb=" OE1 GLN F  62 "
     model   vdw
     2.192 3.120
  nonbonded pdb=" NZ  LYS C  60 "
            pdb=" OE1 GLN C  62 "
     model   vdw
     2.193 3.120
  ... (remaining 20555 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
}

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:             1.960
  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:          0.030
  Check model and map are aligned:         0.010
  Set scattering table:                    0.000
  Process input model:                     4.280
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.260
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    7.580
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7297
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      :  0.009   0.042   2640  Z= 0.415
  Angle     :  0.851   4.552   3570  Z= 0.495
  Chirality :  0.057   0.125    468
  Planarity :  0.003   0.010    444
  Dihedral  : 13.706  74.320    900
  Min Nonbonded Distance : 2.192

Molprobity Statistics.
  All-atom Clashscore : 9.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.38 %
    Favored  : 89.62 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.44 %
    Favored  : 95.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.25 (0.31), residues: 366
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.23 (0.23), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.003   0.001   TYR D  39 
 PHE   0.011   0.004   PHE D  94 
 HIS   0.007   0.004   HIS D  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00916 ( 2640)
  covalent geometry    : angle       0.85129 ( 3570)
  hydrogen bonds       : bond        0.18834 (   44)
  hydrogen bonds       : angle       7.21686 (  132)

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

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

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  25 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 25
  time to evaluate  : 0.130 
Fit side-chains
REVERT: A   45 LYS cc_start: 0.8481 (mtpp) cc_final: 0.8261 (mttt)
REVERT: F   45 LYS cc_start: 0.8702 (mtpp) cc_final: 0.8415 (mttm)
  outliers start: 0
  outliers final: 0
  residues processed: 25
  average time/residue: 0.1172
  time to fit residues: 3.3018
Evaluate side-chains
  23 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 23
  time to evaluate  : 0.060 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 24 optimal weight:    6.9990
   chunk 26 optimal weight:    4.9990
   chunk 2 optimal weight:    2.9990
   chunk 16 optimal weight:    3.9990
   chunk 32 optimal weight:    0.7980
   chunk 31 optimal weight:    0.8980
   chunk 25 optimal weight:    1.9990
   chunk 19 optimal weight:    0.6980
   chunk 30 optimal weight:    0.3980
   chunk 22 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9990
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
F  79 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4966 r_free = 0.4966 target = 0.229324 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4651 r_free = 0.4651 target = 0.194126 restraints weight = 2645.098|
|-----------------------------------------------------------------------------|
r_work (start): 0.4678 rms_B_bonded: 2.71
r_work: 0.4569 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.4432 rms_B_bonded: 4.97 restraints_weight: 0.2500
r_work (final): 0.4432
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7296
moved from start:          0.1415

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   2640  Z= 0.103
  Angle     :  0.475   4.282   3570  Z= 0.261
  Chirality :  0.051   0.129    468
  Planarity :  0.002   0.009    444
  Dihedral  :  4.624  14.869    378
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 5.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.37 %
    Favored  : 95.63 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  7.41 %
    Favored  : 92.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.09 (0.37), residues: 366
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.35 (0.28), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.004   0.001   TYR B  39 
 PHE   0.006   0.001   PHE F  94 
 HIS   0.002   0.001   HIS D  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00231 ( 2640)
  covalent geometry    : angle       0.47546 ( 3570)
  hydrogen bonds       : bond        0.01597 (   44)
  hydrogen bonds       : angle       4.35979 (  132)

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

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

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  28 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 28
  time to evaluate  : 0.095 
Fit side-chains
REVERT: B   79 GLN cc_start: 0.8833 (tt0) cc_final: 0.8625 (tt0)
REVERT: F   45 LYS cc_start: 0.8652 (mtpp) cc_final: 0.8329 (mttm)
  outliers start: 0
  outliers final: 0
  residues processed: 28
  average time/residue: 0.1054
  time to fit residues: 3.3317
Evaluate side-chains
  26 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 26
  time to evaluate  : 0.103 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 8 optimal weight:    5.9990
   chunk 22 optimal weight:    3.9990
   chunk 6 optimal weight:    2.9990
   chunk 35 optimal weight:   10.0000
   chunk 26 optimal weight:    7.9990
   chunk 4 optimal weight:    0.9990
   chunk 16 optimal weight:    3.9990
   chunk 33 optimal weight:    0.9980
   chunk 31 optimal weight:    0.7980
   chunk 2 optimal weight:    6.9990
   chunk 14 optimal weight:    0.9980
   overall best weight:    1.3584

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4968 r_free = 0.4968 target = 0.228284 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4634 r_free = 0.4634 target = 0.191873 restraints weight = 2626.406|
|-----------------------------------------------------------------------------|
r_work (start): 0.4588 rms_B_bonded: 2.80
r_work: 0.4478 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work (final): 0.4478
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7136
moved from start:          0.1711

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   2640  Z= 0.128
  Angle     :  0.445   3.521   3570  Z= 0.248
  Chirality :  0.051   0.123    468
  Planarity :  0.002   0.009    444
  Dihedral  :  4.365  13.063    378
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 5.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.92 %
    Favored  : 95.08 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  9.26 %
    Favored  : 90.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.65 (0.40), residues: 366
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.01 (0.31), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.008   0.002   TYR C  39 
 PHE   0.007   0.002   PHE F  94 
 HIS   0.004   0.002   HIS A  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 2640)
  covalent geometry    : angle       0.44526 ( 3570)
  hydrogen bonds       : bond        0.01536 (   44)
  hydrogen bonds       : angle       3.87547 (  132)

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

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

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  25 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 25
  time to evaluate  : 0.093 
Fit side-chains
REVERT: F   45 LYS cc_start: 0.8478 (mtpp) cc_final: 0.8205 (mttt)
  outliers start: 0
  outliers final: 0
  residues processed: 25
  average time/residue: 0.0965
  time to fit residues: 2.7771
Evaluate side-chains
  20 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 20
  time to evaluate  : 0.090 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 3 optimal weight:    0.7980
   chunk 15 optimal weight:    0.7980
   chunk 17 optimal weight:   10.0000
   chunk 12 optimal weight:   10.0000
   chunk 21 optimal weight:    0.9980
   chunk 6 optimal weight:    0.5980
   chunk 31 optimal weight:    3.9990
   chunk 23 optimal weight:    0.8980
   chunk 18 optimal weight:    7.9990
   chunk 16 optimal weight:    0.6980
   chunk 22 optimal weight:    0.9990
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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 = 0.4978 r_free = 0.4978 target = 0.229449 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4651 r_free = 0.4651 target = 0.193245 restraints weight = 2548.202|
|-----------------------------------------------------------------------------|
r_work (start): 0.4657 rms_B_bonded: 2.76
r_work: 0.4544 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work (final): 0.4544
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7110
moved from start:          0.2115

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   2640  Z= 0.093
  Angle     :  0.413   3.672   3570  Z= 0.228
  Chirality :  0.051   0.123    468
  Planarity :  0.001   0.008    444
  Dihedral  :  3.992  11.271    378
  Min Nonbonded Distance : 2.612

Molprobity Statistics.
  All-atom Clashscore : 3.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.28 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  9.26 %
    Favored  : 90.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.33 (0.42), residues: 366
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.77 (0.32), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.004   0.001   TYR C  39 
 PHE   0.006   0.001   PHE F  94 
 HIS   0.003   0.001   HIS A  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00211 ( 2640)
  covalent geometry    : angle       0.41311 ( 3570)
  hydrogen bonds       : bond        0.01189 (   44)
  hydrogen bonds       : angle       3.52338 (  132)

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

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

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  26 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 26
  time to evaluate  : 0.096 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 26
  average time/residue: 0.0799
  time to fit residues: 2.4128
Evaluate side-chains
  21 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 21
  time to evaluate  : 0.055 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 25 optimal weight:    6.9990
   chunk 19 optimal weight:    1.9990
   chunk 34 optimal weight:    7.9990
   chunk 11 optimal weight:   10.0000
   chunk 14 optimal weight:    9.9990
   chunk 1 optimal weight:    3.9990
   chunk 30 optimal weight:    8.9990
   chunk 7 optimal weight:    0.7980
   chunk 13 optimal weight:    0.9990
   chunk 28 optimal weight:    0.3980
   chunk 18 optimal weight:    0.0770
   overall best weight:    0.8542

-------------------------------------------------------------------------------
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 = 0.4968 r_free = 0.4968 target = 0.228280 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4644 r_free = 0.4644 target = 0.192042 restraints weight = 2534.279|
|-----------------------------------------------------------------------------|
r_work (start): 0.4645 rms_B_bonded: 2.76
r_work: 0.4530 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work (final): 0.4530
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7106
moved from start:          0.2316

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   2640  Z= 0.094
  Angle     :  0.416   4.943   3570  Z= 0.231
  Chirality :  0.050   0.123    468
  Planarity :  0.002   0.019    444
  Dihedral  :  3.850  10.042    378
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 3.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.28 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 10.37 %
    Favored  : 89.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.18 (0.43), residues: 366
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.65 (0.33), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.005   0.001   TYR C  39 
 PHE   0.006   0.002   PHE D  94 
 HIS   0.003   0.001   HIS A  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00213 ( 2640)
  covalent geometry    : angle       0.41604 ( 3570)
  hydrogen bonds       : bond        0.01134 (   44)
  hydrogen bonds       : angle       3.41218 (  132)

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

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

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  21 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 21
  time to evaluate  : 0.094 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 21
  average time/residue: 0.0956
  time to fit residues: 2.3794
Evaluate side-chains
  17 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 17
  time to evaluate  : 0.102 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 35 optimal weight:    8.9990
   chunk 30 optimal weight:   10.0000
   chunk 2 optimal weight:   10.0000
   chunk 1 optimal weight:    0.9990
   chunk 6 optimal weight:   10.0000
   chunk 14 optimal weight:   10.0000
   chunk 4 optimal weight:    2.9990
   chunk 34 optimal weight:    2.9990
   chunk 15 optimal weight:    0.6980
   chunk 9 optimal weight:    5.9990
   chunk 27 optimal weight:    0.7980
   overall best weight:    1.6986

-------------------------------------------------------------------------------
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 = 0.4920 r_free = 0.4920 target = 0.223585 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4588 r_free = 0.4588 target = 0.187516 restraints weight = 2602.081|
|-----------------------------------------------------------------------------|
r_work (start): 0.4564 rms_B_bonded: 2.72
r_work: 0.4453 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work (final): 0.4453
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7171
moved from start:          0.2199

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   2640  Z= 0.147
  Angle     :  0.457   4.818   3570  Z= 0.252
  Chirality :  0.051   0.126    468
  Planarity :  0.002   0.013    444
  Dihedral  :  4.165  11.168    378
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 4.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.64 %
    Favored  : 95.36 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 11.85 %
    Favored  : 88.15 %
  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 aren not related in a simple way.
  whole: -2.18 (0.43), residues: 366
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.65 (0.33), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.009   0.002   TYR C  39 
 PHE   0.006   0.002   PHE C  94 
 HIS   0.005   0.003   HIS A  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 ( 2640)
  covalent geometry    : angle       0.45652 ( 3570)
  hydrogen bonds       : bond        0.01488 (   44)
  hydrogen bonds       : angle       3.57447 (  132)

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

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

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  18 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 18
  time to evaluate  : 0.091 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 18
  average time/residue: 0.0949
  time to fit residues: 2.0348
Evaluate side-chains
  16 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 16
  time to evaluate  : 0.091 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 2 optimal weight:    9.9990
   chunk 9 optimal weight:    0.0170
   chunk 8 optimal weight:    4.9990
   chunk 12 optimal weight:   10.0000
   chunk 24 optimal weight:    3.9990
   chunk 1 optimal weight:    3.9990
   chunk 29 optimal weight:   10.0000
   chunk 5 optimal weight:   10.0000
   chunk 27 optimal weight:    0.6980
   chunk 7 optimal weight:    0.8980
   chunk 35 optimal weight:    3.9990
   overall best weight:    1.9222

-------------------------------------------------------------------------------
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 = 0.4901 r_free = 0.4901 target = 0.221741 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4571 r_free = 0.4571 target = 0.185896 restraints weight = 2598.068|
|-----------------------------------------------------------------------------|
r_work (start): 0.4555 rms_B_bonded: 2.67
r_work: 0.4442 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.4303 rms_B_bonded: 4.94 restraints_weight: 0.2500
r_work (final): 0.4303
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7298
moved from start:          0.2236

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.022   2640  Z= 0.161
  Angle     :  0.499   7.140   3570  Z= 0.272
  Chirality :  0.051   0.126    468
  Planarity :  0.002   0.009    444
  Dihedral  :  4.294  11.866    378
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 5.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.92 %
    Favored  : 95.08 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 12.22 %
    Favored  : 87.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.21 (0.43), residues: 366
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.68 (0.33), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.009   0.002   TYR C  39 
 PHE   0.007   0.002   PHE D  94 
 HIS   0.005   0.003   HIS A  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00364 ( 2640)
  covalent geometry    : angle       0.49936 ( 3570)
  hydrogen bonds       : bond        0.01541 (   44)
  hydrogen bonds       : angle       3.64866 (  132)

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

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

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  19 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 19
  time to evaluate  : 0.056 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 19
  average time/residue: 0.0933
  time to fit residues: 2.0992
Evaluate side-chains
  19 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 19
  time to evaluate  : 0.106 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 12 optimal weight:   10.0000
   chunk 30 optimal weight:    8.9990
   chunk 22 optimal weight:    0.4980
   chunk 31 optimal weight:    2.9990
   chunk 26 optimal weight:    3.9990
   chunk 11 optimal weight:   10.0000
   chunk 35 optimal weight:    5.9990
   chunk 6 optimal weight:    3.9990
   chunk 34 optimal weight:    3.9990
   chunk 4 optimal weight:    1.9990
   chunk 16 optimal weight:    3.9990
   overall best weight:    2.6988

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

Flipped N/Q/H residues before XYZ refinement:
B  79 GLN
D  79 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4864 r_free = 0.4864 target = 0.218172 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4529 r_free = 0.4529 target = 0.181999 restraints weight = 2698.969|
|-----------------------------------------------------------------------------|
r_work (start): 0.4500 rms_B_bonded: 2.74
r_work: 0.4385 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work: 0.4247 rms_B_bonded: 4.99 restraints_weight: 0.2500
r_work (final): 0.4247
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7343
moved from start:          0.2237

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.025   2640  Z= 0.217
  Angle     :  0.549   6.585   3570  Z= 0.302
  Chirality :  0.052   0.126    468
  Planarity :  0.002   0.007    444
  Dihedral  :  4.721  13.901    378
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 5.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.28 %
    Favored  : 93.72 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 13.33 %
    Favored  : 86.67 %
  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 aren not related in a simple way.
  whole: -2.26 (0.42), residues: 366
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.71 (0.32), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.011   0.003   TYR C  39 
 PHE   0.008   0.002   PHE C  94 
 HIS   0.006   0.003   HIS A  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00492 ( 2640)
  covalent geometry    : angle       0.54898 ( 3570)
  hydrogen bonds       : bond        0.01870 (   44)
  hydrogen bonds       : angle       3.89442 (  132)

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

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

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  20 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 20
  time to evaluate  : 0.101 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 20
  average time/residue: 0.0866
  time to fit residues: 2.0686
Evaluate side-chains
  19 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 19
  time to evaluate  : 0.093 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 12 optimal weight:   10.0000
   chunk 15 optimal weight:    0.8980
   chunk 16 optimal weight:    0.9990
   chunk 5 optimal weight:    6.9990
   chunk 17 optimal weight:    0.0020
   chunk 27 optimal weight:    2.9990
   chunk 10 optimal weight:    4.9990
   chunk 8 optimal weight:    4.9990
   chunk 11 optimal weight:    2.9990
   chunk 20 optimal weight:    2.9990
   chunk 25 optimal weight:    1.9990
   overall best weight:    1.3794

-------------------------------------------------------------------------------
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 = 0.4900 r_free = 0.4900 target = 0.221597 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4572 r_free = 0.4572 target = 0.185422 restraints weight = 2634.895|
|-----------------------------------------------------------------------------|
r_work (start): 0.4568 rms_B_bonded: 2.74
r_work: 0.4454 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work: 0.4320 rms_B_bonded: 4.96 restraints_weight: 0.2500
r_work (final): 0.4320
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7260
moved from start:          0.2509

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.018   2640  Z= 0.123
  Angle     :  0.461   6.419   3570  Z= 0.253
  Chirality :  0.051   0.127    468
  Planarity :  0.002   0.008    444
  Dihedral  :  4.135  12.410    378
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 5.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.55 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 14.44 %
    Favored  : 85.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.23 (0.43), residues: 366
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.69 (0.32), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.007   0.002   TYR C  39 
 PHE   0.006   0.002   PHE C  94 
 HIS   0.003   0.002   HIS C  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 ( 2640)
  covalent geometry    : angle       0.46148 ( 3570)
  hydrogen bonds       : bond        0.01304 (   44)
  hydrogen bonds       : angle       3.59777 (  132)

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

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

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  20 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 20
  time to evaluate  : 0.090 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 20
  average time/residue: 0.1007
  time to fit residues: 2.3694
Evaluate side-chains
  19 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 19
  time to evaluate  : 0.088 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 16 optimal weight:    5.9990
   chunk 13 optimal weight:    0.8980
   chunk 18 optimal weight:    0.0010
   chunk 10 optimal weight:    6.9990
   chunk 7 optimal weight:    4.9990
   chunk 3 optimal weight:    0.9980
   chunk 2 optimal weight:    9.9990
   chunk 21 optimal weight:    0.5980
   chunk 4 optimal weight:    0.7980
   chunk 33 optimal weight:    0.2980
   chunk 15 optimal weight:    0.7980
   overall best weight:    0.4986

-------------------------------------------------------------------------------
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 = 0.4990 r_free = 0.4990 target = 0.229780 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4666 r_free = 0.4666 target = 0.194070 restraints weight = 2575.748|
|-----------------------------------------------------------------------------|
r_work (start): 0.4672 rms_B_bonded: 2.70
r_work: 0.4569 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.4437 rms_B_bonded: 4.84 restraints_weight: 0.2500
r_work (final): 0.4437
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7141
moved from start:          0.2969

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   2640  Z= 0.074
  Angle     :  0.415   6.118   3570  Z= 0.227
  Chirality :  0.050   0.124    468
  Planarity :  0.001   0.008    444
  Dihedral  :  3.528  10.414    378
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 2.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 14.07 %
    Favored  : 85.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.08 (0.43), residues: 366
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.57 (0.33), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.003   0.001   TYR C  39 
 PHE   0.005   0.001   PHE A  94 
 HIS   0.001   0.001   HIS C  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00164 ( 2640)
  covalent geometry    : angle       0.41475 ( 3570)
  hydrogen bonds       : bond        0.00972 (   44)
  hydrogen bonds       : angle       3.38023 (  132)

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

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

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  732 Ramachandran restraints generated.
    366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  23 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 23
  time to evaluate  : 0.057 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 23
  average time/residue: 0.0571
  time to fit residues: 1.5537
Evaluate side-chains
  22 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 22
  time to evaluate  : 0.055 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 32 optimal weight:    6.9990
   chunk 17 optimal weight:   10.0000
   chunk 14 optimal weight:    9.9990
   chunk 13 optimal weight:    8.9990
   chunk 25 optimal weight:    3.9990
   chunk 0 optimal weight:   10.0000
   chunk 35 optimal weight:    9.9990
   chunk 22 optimal weight:    5.9990
   chunk 10 optimal weight:    2.9990
   chunk 33 optimal weight:    7.9990
   chunk 23 optimal weight:    1.9990
   overall best weight:    4.3990

-------------------------------------------------------------------------------
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 = 0.4822 r_free = 0.4822 target = 0.213951 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4476 r_free = 0.4476 target = 0.177387 restraints weight = 2692.684|
|-----------------------------------------------------------------------------|
r_work (start): 0.4458 rms_B_bonded: 2.73
r_work: 0.4344 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.4205 rms_B_bonded: 4.95 restraints_weight: 0.2500
r_work (final): 0.4205
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7389
moved from start:          0.2424

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.036   2640  Z= 0.340
  Angle     :  0.690   7.545   3570  Z= 0.382
  Chirality :  0.056   0.131    468
  Planarity :  0.003   0.009    444
  Dihedral  :  5.157  14.896    378
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 6.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.19 %
    Favored  : 94.81 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 15.56 %
    Favored  : 84.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.38 (0.42), residues: 366
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.80 (0.32), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.016   0.004   TYR C  39 
 PHE   0.010   0.003   PHE C  94 
 HIS   0.008   0.005   HIS A  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00770 ( 2640)
  covalent geometry    : angle       0.69017 ( 3570)
  hydrogen bonds       : bond        0.02413 (   44)
  hydrogen bonds       : angle       4.05107 (  132)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 928.39 seconds
wall clock time: 16 minutes 40.95 seconds (1000.95 seconds total)