Starting phenix.real_space_refine
on Fri May  9 17:56:24 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ot4_17168/05_2025/8ot4_17168.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ot4_17168/05_2025/8ot4_17168.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.97
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ot4_17168/05_2025/8ot4_17168.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ot4_17168/05_2025/8ot4_17168.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ot4_17168/05_2025/8ot4_17168.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ot4_17168/05_2025/8ot4_17168.cif"
  }
  resolution = 2.97
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
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: 4
    Type Number    sf(0)   Gaussians
     S      12      5.16       5
     C    2184      2.51       5
     N     600      2.21       5
     O     648      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 48 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 3444
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 287
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 37, 287
          Classifications: {'peptide': 37}
          Link IDs: {'TRANS': 36}
  Restraints were copied for chains:
    C, B, E, D, G, F, I, H, K, J, L
  Time building chain proxies: 1.42, per 1000 atoms: 0.41
  Number of scatterers: 3444
  At special positions: 0
  Unit cell: (75.92, 80.08, 49.92, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      12     16.00
     O     648      8.00
     N     600      7.00
     C    2184      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: 0.71
  Conformation dependent library (CDL) restraints added in 386.3 milliseconds
  

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  768

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 4 sheets defined
      0.0% alpha, 18.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.34
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 12
      removed outlier: 6.588A  pdb=" N   GLU A  11 " --> pdb=" O   VAL C  12 " (cutoff:3.500A)
      removed outlier: 6.588A  pdb=" N   GLU C  11 " --> pdb=" O   VAL E  12 " (cutoff:3.500A)
      removed outlier: 6.589A  pdb=" N   GLU E  11 " --> pdb=" O   VAL G  12 " (cutoff:3.500A)
      removed outlier: 6.589A  pdb=" N   GLU G  11 " --> pdb=" O   VAL I  12 " (cutoff:3.500A)
      removed outlier: 6.588A  pdb=" N   GLU I  11 " --> pdb=" O   VAL K  12 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 18 through 24
      removed outlier: 6.562A  pdb=" N   VAL A  18 " --> pdb=" O   PHE C  19 " (cutoff:3.500A)
      removed outlier: 7.899A  pdb=" N   ALA C  21 " --> pdb=" O   VAL A  18 " (cutoff:3.500A)
      removed outlier: 6.313A  pdb=" N   PHE A  20 " --> pdb=" O   ALA C  21 " (cutoff:3.500A)
      removed outlier: 7.573A  pdb=" N   ASP C  23 " --> pdb=" O   PHE A  20 " (cutoff:3.500A)
      removed outlier: 8.067A  pdb=" N   GLU A  22 " --> pdb=" O   ASP C  23 " (cutoff:3.500A)
      removed outlier: 6.562A  pdb=" N   VAL C  18 " --> pdb=" O   PHE E  19 " (cutoff:3.500A)
      removed outlier: 7.899A  pdb=" N   ALA E  21 " --> pdb=" O   VAL C  18 " (cutoff:3.500A)
      removed outlier: 6.313A  pdb=" N   PHE C  20 " --> pdb=" O   ALA E  21 " (cutoff:3.500A)
      removed outlier: 7.573A  pdb=" N   ASP E  23 " --> pdb=" O   PHE C  20 " (cutoff:3.500A)
      removed outlier: 8.067A  pdb=" N   GLU C  22 " --> pdb=" O   ASP E  23 " (cutoff:3.500A)
      removed outlier: 6.563A  pdb=" N   VAL E  18 " --> pdb=" O   PHE G  19 " (cutoff:3.500A)
      removed outlier: 7.899A  pdb=" N   ALA G  21 " --> pdb=" O   VAL E  18 " (cutoff:3.500A)
      removed outlier: 6.313A  pdb=" N   PHE E  20 " --> pdb=" O   ALA G  21 " (cutoff:3.500A)
      removed outlier: 7.573A  pdb=" N   ASP G  23 " --> pdb=" O   PHE E  20 " (cutoff:3.500A)
      removed outlier: 8.066A  pdb=" N   GLU E  22 " --> pdb=" O   ASP G  23 " (cutoff:3.500A)
      removed outlier: 6.562A  pdb=" N   VAL G  18 " --> pdb=" O   PHE I  19 " (cutoff:3.500A)
      removed outlier: 7.900A  pdb=" N   ALA I  21 " --> pdb=" O   VAL G  18 " (cutoff:3.500A)
      removed outlier: 6.313A  pdb=" N   PHE G  20 " --> pdb=" O   ALA I  21 " (cutoff:3.500A)
      removed outlier: 7.573A  pdb=" N   ASP I  23 " --> pdb=" O   PHE G  20 " (cutoff:3.500A)
      removed outlier: 8.067A  pdb=" N   GLU G  22 " --> pdb=" O   ASP I  23 " (cutoff:3.500A)
      removed outlier: 6.563A  pdb=" N   VAL I  18 " --> pdb=" O   PHE K  19 " (cutoff:3.500A)
      removed outlier: 7.899A  pdb=" N   ALA K  21 " --> pdb=" O   VAL I  18 " (cutoff:3.500A)
      removed outlier: 6.313A  pdb=" N   PHE I  20 " --> pdb=" O   ALA K  21 " (cutoff:3.500A)
      removed outlier: 7.573A  pdb=" N   ASP K  23 " --> pdb=" O   PHE I  20 " (cutoff:3.500A)
      removed outlier: 8.067A  pdb=" N   GLU I  22 " --> pdb=" O   ASP K  23 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'B' and resid 11 through 12
      removed outlier: 6.589A  pdb=" N   GLU B  11 " --> pdb=" O   VAL D  12 " (cutoff:3.500A)
      removed outlier: 6.589A  pdb=" N   GLU D  11 " --> pdb=" O   VAL F  12 " (cutoff:3.500A)
      removed outlier: 6.588A  pdb=" N   GLU F  11 " --> pdb=" O   VAL H  12 " (cutoff:3.500A)
      removed outlier: 6.589A  pdb=" N   GLU H  11 " --> pdb=" O   VAL J  12 " (cutoff:3.500A)
      removed outlier: 6.588A  pdb=" N   GLU J  11 " --> pdb=" O   VAL L  12 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'B' and resid 18 through 24
      removed outlier: 6.563A  pdb=" N   VAL B  18 " --> pdb=" O   PHE D  19 " (cutoff:3.500A)
      removed outlier: 7.900A  pdb=" N   ALA D  21 " --> pdb=" O   VAL B  18 " (cutoff:3.500A)
      removed outlier: 6.313A  pdb=" N   PHE B  20 " --> pdb=" O   ALA D  21 " (cutoff:3.500A)
      removed outlier: 7.573A  pdb=" N   ASP D  23 " --> pdb=" O   PHE B  20 " (cutoff:3.500A)
      removed outlier: 8.066A  pdb=" N   GLU B  22 " --> pdb=" O   ASP D  23 " (cutoff:3.500A)
      removed outlier: 6.563A  pdb=" N   VAL D  18 " --> pdb=" O   PHE F  19 " (cutoff:3.500A)
      removed outlier: 7.898A  pdb=" N   ALA F  21 " --> pdb=" O   VAL D  18 " (cutoff:3.500A)
      removed outlier: 6.314A  pdb=" N   PHE D  20 " --> pdb=" O   ALA F  21 " (cutoff:3.500A)
      removed outlier: 7.573A  pdb=" N   ASP F  23 " --> pdb=" O   PHE D  20 " (cutoff:3.500A)
      removed outlier: 8.067A  pdb=" N   GLU D  22 " --> pdb=" O   ASP F  23 " (cutoff:3.500A)
      removed outlier: 6.563A  pdb=" N   VAL F  18 " --> pdb=" O   PHE H  19 " (cutoff:3.500A)
      removed outlier: 7.900A  pdb=" N   ALA H  21 " --> pdb=" O   VAL F  18 " (cutoff:3.500A)
      removed outlier: 6.313A  pdb=" N   PHE F  20 " --> pdb=" O   ALA H  21 " (cutoff:3.500A)
      removed outlier: 7.573A  pdb=" N   ASP H  23 " --> pdb=" O   PHE F  20 " (cutoff:3.500A)
      removed outlier: 8.066A  pdb=" N   GLU F  22 " --> pdb=" O   ASP H  23 " (cutoff:3.500A)
      removed outlier: 6.562A  pdb=" N   VAL H  18 " --> pdb=" O   PHE J  19 " (cutoff:3.500A)
      removed outlier: 7.899A  pdb=" N   ALA J  21 " --> pdb=" O   VAL H  18 " (cutoff:3.500A)
      removed outlier: 6.313A  pdb=" N   PHE H  20 " --> pdb=" O   ALA J  21 " (cutoff:3.500A)
      removed outlier: 7.573A  pdb=" N   ASP J  23 " --> pdb=" O   PHE H  20 " (cutoff:3.500A)
      removed outlier: 8.067A  pdb=" N   GLU H  22 " --> pdb=" O   ASP J  23 " (cutoff:3.500A)
      removed outlier: 6.562A  pdb=" N   VAL J  18 " --> pdb=" O   PHE L  19 " (cutoff:3.500A)
      removed outlier: 7.900A  pdb=" N   ALA L  21 " --> pdb=" O   VAL J  18 " (cutoff:3.500A)
      removed outlier: 6.314A  pdb=" N   PHE J  20 " --> pdb=" O   ALA L  21 " (cutoff:3.500A)
      removed outlier: 7.573A  pdb=" N   ASP L  23 " --> pdb=" O   PHE J  20 " (cutoff:3.500A)
      removed outlier: 8.066A  pdb=" N   GLU J  22 " --> pdb=" O   ASP L  23 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4

    No hydrogen bonds 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: 0.09

  Time building geometry restraints manager: 0.85 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 800
        1.33 -     1.45: 808
        1.45 -     1.56: 1884
        1.56 -     1.68: 0
        1.68 -     1.80: 24
  Bond restraints: 3516
  Sorted by residual:
  bond pdb=" N   VAL K  36 "
       pdb=" CA  VAL K  36 "
    ideal  model  delta    sigma   weight residual
    1.459  1.493 -0.035 1.19e-02 7.06e+03 8.42e+00
  bond pdb=" N   VAL G  36 "
       pdb=" CA  VAL G  36 "
    ideal  model  delta    sigma   weight residual
    1.459  1.493 -0.034 1.19e-02 7.06e+03 8.31e+00
  bond pdb=" N   VAL I  36 "
       pdb=" CA  VAL I  36 "
    ideal  model  delta    sigma   weight residual
    1.459  1.493 -0.034 1.19e-02 7.06e+03 8.26e+00
  bond pdb=" N   VAL J  36 "
       pdb=" CA  VAL J  36 "
    ideal  model  delta    sigma   weight residual
    1.459  1.493 -0.034 1.19e-02 7.06e+03 8.21e+00
  bond pdb=" N   VAL D  36 "
       pdb=" CA  VAL D  36 "
    ideal  model  delta    sigma   weight residual
    1.459  1.493 -0.034 1.19e-02 7.06e+03 8.20e+00
  ... (remaining 3511 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.06: 3163
        2.06 -     4.11: 1219
        4.11 -     6.17: 250
        6.17 -     8.23: 48
        8.23 -    10.29: 24
  Bond angle restraints: 4704
  Sorted by residual:
  angle pdb=" N   GLU E  22 "
        pdb=" CA  GLU E  22 "
        pdb=" C   GLU E  22 "
      ideal   model   delta    sigma   weight residual
     112.04  101.75   10.29 1.44e+00 4.82e-01 5.10e+01
  angle pdb=" N   GLU L  22 "
        pdb=" CA  GLU L  22 "
        pdb=" C   GLU L  22 "
      ideal   model   delta    sigma   weight residual
     112.04  101.77   10.27 1.44e+00 4.82e-01 5.09e+01
  angle pdb=" N   GLU J  22 "
        pdb=" CA  GLU J  22 "
        pdb=" C   GLU J  22 "
      ideal   model   delta    sigma   weight residual
     112.04  101.77   10.27 1.44e+00 4.82e-01 5.09e+01
  angle pdb=" N   GLU B  22 "
        pdb=" CA  GLU B  22 "
        pdb=" C   GLU B  22 "
      ideal   model   delta    sigma   weight residual
     112.04  101.78   10.26 1.44e+00 4.82e-01 5.08e+01
  angle pdb=" N   GLU F  22 "
        pdb=" CA  GLU F  22 "
        pdb=" C   GLU F  22 "
      ideal   model   delta    sigma   weight residual
     112.04  101.78   10.26 1.44e+00 4.82e-01 5.08e+01
  ... (remaining 4699 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    10.93: 1560
       10.93 -    21.86: 240
       21.86 -    32.78: 132
       32.78 -    43.71: 12
       43.71 -    54.64: 36
  Dihedral angle restraints: 1980
    sinusoidal: 768
      harmonic: 1212
  Sorted by residual:
  dihedral pdb=" CA  ILE E  31 "
           pdb=" CB  ILE E  31 "
           pdb=" CG1 ILE E  31 "
           pdb=" CD1 ILE E  31 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00  109.27  -49.27     3      1.50e+01 4.44e-03 8.75e+00
  dihedral pdb=" CA  ILE C  31 "
           pdb=" CB  ILE C  31 "
           pdb=" CG1 ILE C  31 "
           pdb=" CD1 ILE C  31 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00  109.27  -49.27     3      1.50e+01 4.44e-03 8.75e+00
  dihedral pdb=" CA  ILE F  31 "
           pdb=" CB  ILE F  31 "
           pdb=" CG1 ILE F  31 "
           pdb=" CD1 ILE F  31 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00  109.26  -49.26     3      1.50e+01 4.44e-03 8.75e+00
  ... (remaining 1977 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.056: 74
       0.056 -    0.112: 186
       0.112 -    0.168: 135
       0.168 -    0.224: 73
       0.224 -    0.280: 12
  Chirality restraints: 480
  Sorted by residual:
  chirality pdb=" CA  ILE G  31 "
            pdb=" N   ILE G  31 "
            pdb=" C   ILE G  31 "
            pdb=" CB  ILE G  31 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.71   -0.28 2.00e-01 2.50e+01 1.96e+00
  chirality pdb=" CA  ILE F  31 "
            pdb=" N   ILE F  31 "
            pdb=" C   ILE F  31 "
            pdb=" CB  ILE F  31 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.71   -0.28 2.00e-01 2.50e+01 1.95e+00
  chirality pdb=" CA  ILE J  31 "
            pdb=" N   ILE J  31 "
            pdb=" C   ILE J  31 "
            pdb=" CB  ILE J  31 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.71   -0.28 2.00e-01 2.50e+01 1.94e+00
  ... (remaining 477 not shown)

  Planarity restraints: 624
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE I  31 "   -0.019 2.00e-02 2.50e+03   3.86e-02 1.49e+01
        pdb=" C   ILE I  31 "    0.067 2.00e-02 2.50e+03
        pdb=" O   ILE I  31 "   -0.024 2.00e-02 2.50e+03
        pdb=" N   ILE I  32 "   -0.024 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE K  31 "   -0.019 2.00e-02 2.50e+03   3.86e-02 1.49e+01
        pdb=" C   ILE K  31 "    0.067 2.00e-02 2.50e+03
        pdb=" O   ILE K  31 "   -0.024 2.00e-02 2.50e+03
        pdb=" N   ILE K  32 "   -0.024 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE E  31 "   -0.019 2.00e-02 2.50e+03   3.85e-02 1.48e+01
        pdb=" C   ILE E  31 "    0.067 2.00e-02 2.50e+03
        pdb=" O   ILE E  31 "   -0.024 2.00e-02 2.50e+03
        pdb=" N   ILE E  32 "   -0.024 2.00e-02 2.50e+03
  ... (remaining 621 not shown)

  Histogram of nonbonded interaction distances:
        2.53 -     3.00: 1668
        3.00 -     3.48: 3051
        3.48 -     3.95: 5775
        3.95 -     4.43: 6610
        4.43 -     4.90: 12473
  Nonbonded interactions: 29577
  Sorted by model distance:
  nonbonded pdb=" N   HIS E  13 "
            pdb=" O   HIS E  13 "
     model   vdw
     2.527 2.496
  nonbonded pdb=" N   HIS I  13 "
            pdb=" O   HIS I  13 "
     model   vdw
     2.528 2.496
  nonbonded pdb=" N   HIS C  13 "
            pdb=" O   HIS C  13 "
     model   vdw
     2.528 2.496
  nonbonded pdb=" N   HIS F  13 "
            pdb=" O   HIS F  13 "
     model   vdw
     2.528 2.496
  nonbonded pdb=" N   HIS H  13 "
            pdb=" O   HIS H  13 "
     model   vdw
     2.528 2.496
  ... (remaining 29572 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: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'E'
  selection = chain 'D'
  selection = chain 'G'
  selection = chain 'F'
  selection = chain 'I'
  selection = chain 'H'
  selection = chain 'K'
  selection = chain 'J'
  selection = chain 'L'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.340
  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:             0.000
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.020
  Set scattering table:                    0.040
  Process input model:                     10.180
  Find NCS groups from input model:        0.080
  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:10.190
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.000
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7247
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      :  0.012   0.036   3516  Z= 0.892
  Angle     :  2.301  10.287   4704  Z= 1.670
  Chirality :  0.127   0.280    480
  Planarity :  0.014   0.039    624
  Dihedral  : 15.194  54.635   1212
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 0.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.90 %
    Favored  : 93.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.85 (0.21), residues: 420
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.93 (0.16), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.002   HIS A   6 
 PHE   0.012   0.003   PHE I   4 
 TYR   0.005   0.002   TYR C  10 
 ARG   0.002   0.001   ARG K   5 

Details of bonding type rmsd
  covalent geometry    : bond        0.01186 ( 3516)
  covalent geometry    : angle       2.30127 ( 4704)

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

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

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 130
  time to evaluate  : 0.364 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   10 TYR cc_start: 0.7942 (t80) cc_final: 0.5769 (p90)
REVERT: L    5 ARG cc_start: 0.7697 (mtp180) cc_final: 0.6683 (tpt170)
  outliers start: 0
  outliers final: 0
  residues processed: 130
  average time/residue: 1.1430
  time to fit residues: 152.5967
Evaluate side-chains
  108 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 108
  time to evaluate  : 0.403 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 30 optimal weight:    4.9990
   chunk 27 optimal weight:    0.9990
   chunk 15 optimal weight:    3.9990
   chunk 9 optimal weight:    2.9990
   chunk 18 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9990
   chunk 28 optimal weight:    0.7980
   chunk 10 optimal weight:    0.9980
   chunk 17 optimal weight:    0.5980
   chunk 21 optimal weight:    0.9990
   chunk 32 optimal weight:    0.7980
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
B   6 HIS
** B  13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D   6 HIS
E   6 HIS
** E  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F   6 HIS
F  15 GLN
G   6 HIS
H   6 HIS
I   6 HIS
J   6 HIS
K   6 HIS
L   6 HIS
L  27 ASN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4628 r_free = 0.4628 target = 0.238323 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4946 r_free = 0.4946 target = 0.203960 restraints weight = 4607.227|
|-----------------------------------------------------------------------------|
r_work (start): 0.4306 rms_B_bonded: 1.64
r_work: 0.4198 rms_B_bonded: 2.11 restraints_weight: 0.5000
r_work: 0.4067 rms_B_bonded: 3.62 restraints_weight: 0.2500
r_work (final): 0.4067
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7560
moved from start:          0.3583

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.017   3516  Z= 0.128
  Angle     :  0.619   4.894   4704  Z= 0.327
  Chirality :  0.049   0.128    480
  Planarity :  0.002   0.012    624
  Dihedral  :  5.548  14.913    456
  Min Nonbonded Distance : 2.624

Molprobity Statistics.
  All-atom Clashscore : 6.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 25.29 %
    Favored  : 71.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.77 (0.32), residues: 420
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.11 (0.24), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.010   0.002   HIS E  13 
 PHE   0.013   0.003   PHE G  20 
 TYR   0.011   0.001   TYR I  10 
 ARG   0.001   0.000   ARG J   5 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 ( 3516)
  covalent geometry    : angle       0.61905 ( 4704)

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

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

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 94
  time to evaluate  : 0.423 
Fit side-chains
   revert: symmetry clash
REVERT: A   13 HIS cc_start: 0.7367 (OUTLIER) cc_final: 0.6988 (m90)
REVERT: B   11 GLU cc_start: 0.7655 (mt-10) cc_final: 0.7237 (tt0)
REVERT: C    3 GLU cc_start: 0.7569 (OUTLIER) cc_final: 0.6924 (tm-30)
REVERT: D   28 LYS cc_start: 0.8651 (ttpp) cc_final: 0.8411 (tmtp)
REVERT: E   13 HIS cc_start: 0.6341 (OUTLIER) cc_final: 0.5666 (m-70)
REVERT: E   28 LYS cc_start: 0.8503 (tmtp) cc_final: 0.7999 (ttmt)
REVERT: F    3 GLU cc_start: 0.7418 (OUTLIER) cc_final: 0.7040 (tm-30)
REVERT: G    3 GLU cc_start: 0.7660 (tt0) cc_final: 0.7023 (tm-30)
REVERT: H   28 LYS cc_start: 0.8567 (tmtp) cc_final: 0.8184 (tttt)
REVERT: I   28 LYS cc_start: 0.8703 (tmtp) cc_final: 0.8200 (ttmt)
REVERT: J    3 GLU cc_start: 0.7788 (OUTLIER) cc_final: 0.7005 (tm-30)
REVERT: J   28 LYS cc_start: 0.8696 (tmmm) cc_final: 0.8232 (ttpt)
  outliers start: 10
  outliers final: 0
  residues processed: 94
  average time/residue: 1.3640
  time to fit residues: 131.4772
Evaluate side-chains
  84 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 79
  time to evaluate  : 0.412 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 HIS
Chi-restraints excluded: chain C residue    3 GLU
Chi-restraints excluded: chain E residue   13 HIS
Chi-restraints excluded: chain F residue    3 GLU
Chi-restraints excluded: chain J residue    3 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 8 optimal weight:    6.9990
   chunk 15 optimal weight:    7.9990
   chunk 16 optimal weight:    4.9990
   chunk 29 optimal weight:    7.9990
   chunk 6 optimal weight:    4.9990
   chunk 20 optimal weight:    7.9990
   chunk 19 optimal weight:    4.9990
   chunk 23 optimal weight:    0.7980
   chunk 0 optimal weight:    0.6980
   chunk 1 optimal weight:    3.9990
   chunk 3 optimal weight:    6.9990
   overall best weight:    3.0986

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

Flipped N/Q/H residues before XYZ refinement:
A   6 HIS
** B  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C   6 HIS
C  15 GLN
** E  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
J  15 GLN
L  13 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4329 r_free = 0.4329 target = 0.122239 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4079 r_free = 0.4079 target = 0.103081 restraints weight = 5270.394|
|-----------------------------------------------------------------------------|
r_work (start): 0.4036 rms_B_bonded: 2.95
r_work: 0.3886 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.3886
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7616
moved from start:          0.4945

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.036   3516  Z= 0.366
  Angle     :  0.799   5.788   4704  Z= 0.435
  Chirality :  0.052   0.126    480
  Planarity :  0.003   0.013    624
  Dihedral  :  6.352  21.767    456
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 8.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.24 %
    Favored  : 99.76 %
  Rotamer:
    Outliers :  4.31 %
    Allowed  : 25.57 %
    Favored  : 70.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.73 (0.33), residues: 420
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.07 (0.25), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.010   0.001   HIS E  13 
 PHE   0.028   0.005   PHE A   4 
 TYR   0.005   0.001   TYR G  10 
 ARG   0.001   0.000   ARG F   5 

Details of bonding type rmsd
  covalent geometry    : bond        0.00803 ( 3516)
  covalent geometry    : angle       0.79866 ( 4704)

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

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

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 85
  time to evaluate  : 0.456 
Fit side-chains
   revert: symmetry clash
REVERT: A   11 GLU cc_start: 0.7681 (mt-10) cc_final: 0.6889 (tt0)
REVERT: A   28 LYS cc_start: 0.6264 (OUTLIER) cc_final: 0.5024 (tppt)
REVERT: C    3 GLU cc_start: 0.7970 (OUTLIER) cc_final: 0.7080 (tm-30)
REVERT: C   13 HIS cc_start: 0.7444 (m90) cc_final: 0.7197 (m90)
REVERT: C   23 ASP cc_start: 0.8300 (m-30) cc_final: 0.8077 (m-30)
REVERT: C   28 LYS cc_start: 0.8634 (OUTLIER) cc_final: 0.8122 (ttmt)
REVERT: D   11 GLU cc_start: 0.7939 (tt0) cc_final: 0.6996 (tt0)
REVERT: D   28 LYS cc_start: 0.8483 (ttpp) cc_final: 0.7953 (ttmt)
REVERT: E   13 HIS cc_start: 0.7320 (m-70) cc_final: 0.6445 (m90)
REVERT: E   28 LYS cc_start: 0.8322 (tmtp) cc_final: 0.7854 (ttmt)
REVERT: G   11 GLU cc_start: 0.7992 (tt0) cc_final: 0.7144 (tt0)
REVERT: I   13 HIS cc_start: 0.7441 (m-70) cc_final: 0.7157 (m90)
REVERT: L    5 ARG cc_start: 0.8218 (mtp180) cc_final: 0.6719 (tpt170)
  outliers start: 15
  outliers final: 3
  residues processed: 86
  average time/residue: 1.6371
  time to fit residues: 143.8187
Evaluate side-chains
  88 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 82
  time to evaluate  : 0.408 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 LYS
Chi-restraints excluded: chain B residue   13 HIS
Chi-restraints excluded: chain C residue    3 GLU
Chi-restraints excluded: chain C residue   28 LYS
Chi-restraints excluded: chain F residue    3 GLU
Chi-restraints excluded: chain K residue   28 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 25 optimal weight:    0.9990
   chunk 3 optimal weight:    5.9990
   chunk 23 optimal weight:    3.9990
   chunk 11 optimal weight:    3.9990
   chunk 22 optimal weight:    3.9990
   chunk 6 optimal weight:    6.9990
   chunk 28 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9980
   chunk 21 optimal weight:    4.9990
   chunk 15 optimal weight:    0.9980
   chunk 12 optimal weight:    1.9990
   overall best weight:    1.3986

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

Flipped N/Q/H residues before XYZ refinement:
** B  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4329 r_free = 0.4329 target = 0.122994 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4054 r_free = 0.4054 target = 0.101126 restraints weight = 5240.968|
|-----------------------------------------------------------------------------|
r_work (start): 0.4051 rms_B_bonded: 3.09
r_work: 0.3900 rms_B_bonded: 3.54 restraints_weight: 0.5000
r_work (final): 0.3900
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7536
moved from start:          0.5106

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.024   3516  Z= 0.185
  Angle     :  0.639   4.447   4704  Z= 0.341
  Chirality :  0.050   0.129    480
  Planarity :  0.002   0.010    624
  Dihedral  :  5.803  20.710    456
  Min Nonbonded Distance : 2.647

Molprobity Statistics.
  All-atom Clashscore : 6.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  5.46 %
    Allowed  : 26.15 %
    Favored  : 68.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.62 (0.35), residues: 420
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.99 (0.27), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS J  13 
 PHE   0.016   0.003   PHE J   4 
 TYR   0.004   0.001   TYR K  10 
 ARG   0.001   0.000   ARG H   5 

Details of bonding type rmsd
  covalent geometry    : bond        0.00411 ( 3516)
  covalent geometry    : angle       0.63936 ( 4704)

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

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

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 85
  time to evaluate  : 0.421 
Fit side-chains
REVERT: A   11 GLU cc_start: 0.7611 (mt-10) cc_final: 0.6824 (tt0)
REVERT: B   13 HIS cc_start: 0.4157 (OUTLIER) cc_final: 0.3675 (m-70)
REVERT: C    3 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.6854 (tm-30)
REVERT: C    5 ARG cc_start: 0.8285 (mtp180) cc_final: 0.7837 (mtp180)
REVERT: C   11 GLU cc_start: 0.8386 (mt-10) cc_final: 0.7627 (mt-10)
REVERT: C   13 HIS cc_start: 0.7417 (m90) cc_final: 0.6900 (m90)
REVERT: C   28 LYS cc_start: 0.8549 (OUTLIER) cc_final: 0.8206 (ttmt)
REVERT: D   11 GLU cc_start: 0.8147 (tt0) cc_final: 0.7493 (tt0)
REVERT: D   28 LYS cc_start: 0.8472 (ttpp) cc_final: 0.8177 (tmtp)
REVERT: E   13 HIS cc_start: 0.7022 (m-70) cc_final: 0.6321 (m90)
REVERT: E   28 LYS cc_start: 0.8257 (tmtp) cc_final: 0.7821 (ttmt)
REVERT: F    3 GLU cc_start: 0.7731 (OUTLIER) cc_final: 0.6652 (tm-30)
REVERT: G    3 GLU cc_start: 0.7536 (tt0) cc_final: 0.6654 (tm-30)
REVERT: G    5 ARG cc_start: 0.8079 (mtp180) cc_final: 0.7845 (ttp80)
REVERT: H   28 LYS cc_start: 0.8335 (tmtp) cc_final: 0.7839 (ttmt)
REVERT: I   13 HIS cc_start: 0.7157 (m-70) cc_final: 0.6858 (m90)
REVERT: J    3 GLU cc_start: 0.7528 (tt0) cc_final: 0.6707 (tm-30)
REVERT: J    5 ARG cc_start: 0.8193 (OUTLIER) cc_final: 0.7523 (ttp80)
REVERT: J   28 LYS cc_start: 0.8636 (tmmm) cc_final: 0.8243 (ttpt)
REVERT: L    5 ARG cc_start: 0.8152 (mtp180) cc_final: 0.6444 (tpt170)
  outliers start: 19
  outliers final: 6
  residues processed: 87
  average time/residue: 1.5525
  time to fit residues: 138.1086
Evaluate side-chains
  92 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 81
  time to evaluate  : 0.398 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 HIS
Chi-restraints excluded: chain B residue   13 HIS
Chi-restraints excluded: chain C residue    3 GLU
Chi-restraints excluded: chain C residue   28 LYS
Chi-restraints excluded: chain D residue   23 ASP
Chi-restraints excluded: chain F residue    3 GLU
Chi-restraints excluded: chain H residue   13 HIS
Chi-restraints excluded: chain I residue    3 GLU
Chi-restraints excluded: chain J residue    5 ARG
Chi-restraints excluded: chain L residue   13 HIS
Chi-restraints excluded: chain L residue   28 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 26 optimal weight:    6.9990
   chunk 35 optimal weight:    4.9990
   chunk 20 optimal weight:    0.6980
   chunk 6 optimal weight:    8.9990
   chunk 13 optimal weight:    0.9980
   chunk 25 optimal weight:    0.8980
   chunk 21 optimal weight:   10.0000
   chunk 5 optimal weight:    4.9990
   chunk 19 optimal weight:    0.9990
   chunk 2 optimal weight:    4.9990
   chunk 27 optimal weight:    3.9990
   overall best weight:    1.5184

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

Flipped N/Q/H residues before XYZ refinement:
** B  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4320 r_free = 0.4320 target = 0.122021 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4042 r_free = 0.4042 target = 0.100071 restraints weight = 5256.676|
|-----------------------------------------------------------------------------|
r_work (start): 0.4048 rms_B_bonded: 3.13
r_work: 0.3895 rms_B_bonded: 3.57 restraints_weight: 0.5000
r_work (final): 0.3895
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7576
moved from start:          0.5197

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.024   3516  Z= 0.196
  Angle     :  0.638   4.815   4704  Z= 0.342
  Chirality :  0.051   0.129    480
  Planarity :  0.002   0.009    624
  Dihedral  :  5.703  19.585    456
  Min Nonbonded Distance : 2.648

Molprobity Statistics.
  All-atom Clashscore : 6.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  4.89 %
    Allowed  : 26.15 %
    Favored  : 68.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.60 (0.35), residues: 420
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.97 (0.27), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.008   0.001   HIS G  13 
 PHE   0.016   0.003   PHE E   4 
 TYR   0.003   0.001   TYR D  10 
 ARG   0.001   0.000   ARG E   5 

Details of bonding type rmsd
  covalent geometry    : bond        0.00436 ( 3516)
  covalent geometry    : angle       0.63843 ( 4704)

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

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

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 84
  time to evaluate  : 0.400 
Fit side-chains
REVERT: A   11 GLU cc_start: 0.7649 (mt-10) cc_final: 0.6834 (tt0)
REVERT: B   11 GLU cc_start: 0.7551 (tm-30) cc_final: 0.7096 (tm-30)
REVERT: B   13 HIS cc_start: 0.4454 (OUTLIER) cc_final: 0.3382 (m-70)
REVERT: C    3 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.6733 (tm-30)
REVERT: C    5 ARG cc_start: 0.8308 (mtp180) cc_final: 0.7861 (mtp180)
REVERT: C   11 GLU cc_start: 0.8379 (mt-10) cc_final: 0.7677 (mt-10)
REVERT: C   13 HIS cc_start: 0.7531 (m90) cc_final: 0.6965 (m90)
REVERT: C   28 LYS cc_start: 0.8541 (OUTLIER) cc_final: 0.8164 (ttpt)
REVERT: D   11 GLU cc_start: 0.8002 (tt0) cc_final: 0.7347 (tt0)
REVERT: D   28 LYS cc_start: 0.8502 (ttpp) cc_final: 0.7975 (ttmt)
REVERT: E   13 HIS cc_start: 0.7214 (m-70) cc_final: 0.6616 (m90)
REVERT: E   28 LYS cc_start: 0.8272 (tmtp) cc_final: 0.7889 (ttmt)
REVERT: F    3 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.6762 (tm-30)
REVERT: F    5 ARG cc_start: 0.8153 (ttp80) cc_final: 0.7942 (tpp80)
REVERT: G    3 GLU cc_start: 0.7535 (tt0) cc_final: 0.6678 (tm-30)
REVERT: G    5 ARG cc_start: 0.8101 (mtp180) cc_final: 0.7831 (ttp80)
REVERT: H   28 LYS cc_start: 0.8358 (tmtp) cc_final: 0.7865 (ttmt)
REVERT: I   13 HIS cc_start: 0.7144 (m-70) cc_final: 0.6929 (m90)
REVERT: J    3 GLU cc_start: 0.7612 (tt0) cc_final: 0.6756 (tm-30)
REVERT: J    5 ARG cc_start: 0.8226 (OUTLIER) cc_final: 0.7599 (ttp80)
REVERT: J   28 LYS cc_start: 0.8682 (OUTLIER) cc_final: 0.8311 (ttpt)
REVERT: L    5 ARG cc_start: 0.8179 (mtp180) cc_final: 0.6567 (tpt170)
  outliers start: 17
  outliers final: 4
  residues processed: 85
  average time/residue: 1.5206
  time to fit residues: 132.1151
Evaluate side-chains
  92 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 82
  time to evaluate  : 0.329 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   13 HIS
Chi-restraints excluded: chain C residue    3 GLU
Chi-restraints excluded: chain C residue   28 LYS
Chi-restraints excluded: chain D residue   23 ASP
Chi-restraints excluded: chain F residue    3 GLU
Chi-restraints excluded: chain H residue   13 HIS
Chi-restraints excluded: chain I residue    3 GLU
Chi-restraints excluded: chain J residue    5 ARG
Chi-restraints excluded: chain J residue   28 LYS
Chi-restraints excluded: chain L residue   28 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 11 optimal weight:    6.9990
   chunk 21 optimal weight:    8.9990
   chunk 5 optimal weight:    0.7980
   chunk 18 optimal weight:    8.9990
   chunk 6 optimal weight:    7.9990
   chunk 23 optimal weight:    5.9990
   chunk 1 optimal weight:    4.9990
   chunk 12 optimal weight:    1.9990
   chunk 34 optimal weight:    0.9980
   chunk 3 optimal weight:    3.9990
   chunk 14 optimal weight:    3.9990
   overall best weight:    2.3586

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

Flipped N/Q/H residues before XYZ refinement:
** B  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4345 r_free = 0.4345 target = 0.122190 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4084 r_free = 0.4084 target = 0.102181 restraints weight = 5380.365|
|-----------------------------------------------------------------------------|
r_work (start): 0.4046 rms_B_bonded: 3.01
r_work: 0.3894 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.3894
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7612
moved from start:          0.5481

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.028   3516  Z= 0.284
  Angle     :  0.700   5.626   4704  Z= 0.380
  Chirality :  0.051   0.131    480
  Planarity :  0.003   0.010    624
  Dihedral  :  6.058  21.236    456
  Min Nonbonded Distance : 2.640

Molprobity Statistics.
  All-atom Clashscore : 7.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  4.60 %
    Allowed  : 26.72 %
    Favored  : 68.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.74 (0.35), residues: 420
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.08 (0.26), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS J  13 
 PHE   0.020   0.003   PHE E   4 
 TYR   0.011   0.001   TYR K  10 
 ARG   0.001   0.000   ARG B   5 

Details of bonding type rmsd
  covalent geometry    : bond        0.00623 ( 3516)
  covalent geometry    : angle       0.70000 ( 4704)

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

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

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 84
  time to evaluate  : 0.435 
Fit side-chains
REVERT: A   11 GLU cc_start: 0.7699 (mt-10) cc_final: 0.6886 (tt0)
REVERT: A   28 LYS cc_start: 0.5766 (OUTLIER) cc_final: 0.4340 (tppt)
REVERT: B   11 GLU cc_start: 0.7334 (tm-30) cc_final: 0.6966 (tm-30)
REVERT: B   13 HIS cc_start: 0.4799 (OUTLIER) cc_final: 0.3433 (m-70)
REVERT: C    3 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.6957 (tm-30)
REVERT: C    5 ARG cc_start: 0.8292 (mtp180) cc_final: 0.7877 (mtp180)
REVERT: C   11 GLU cc_start: 0.8477 (mt-10) cc_final: 0.7964 (mt-10)
REVERT: C   13 HIS cc_start: 0.7591 (m90) cc_final: 0.7155 (m90)
REVERT: C   28 LYS cc_start: 0.8538 (OUTLIER) cc_final: 0.8114 (ttmt)
REVERT: D   11 GLU cc_start: 0.8085 (tt0) cc_final: 0.7529 (tt0)
REVERT: D   28 LYS cc_start: 0.8505 (ttpp) cc_final: 0.7941 (ttmt)
REVERT: E   13 HIS cc_start: 0.7300 (m-70) cc_final: 0.6892 (m90)
REVERT: E   28 LYS cc_start: 0.8341 (tmtp) cc_final: 0.7975 (ttmt)
REVERT: F    3 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.6734 (tm-30)
REVERT: F    5 ARG cc_start: 0.8138 (ttp80) cc_final: 0.7906 (tpp80)
REVERT: G    3 GLU cc_start: 0.7536 (tt0) cc_final: 0.6947 (tm-30)
REVERT: G   13 HIS cc_start: 0.7013 (m170) cc_final: 0.6664 (m-70)
REVERT: H   28 LYS cc_start: 0.8320 (tmtp) cc_final: 0.7830 (ttmt)
REVERT: J    3 GLU cc_start: 0.7629 (tt0) cc_final: 0.6764 (tm-30)
REVERT: J    5 ARG cc_start: 0.8256 (OUTLIER) cc_final: 0.7698 (ttp80)
REVERT: J   28 LYS cc_start: 0.8774 (OUTLIER) cc_final: 0.8406 (ttpt)
REVERT: K    5 ARG cc_start: 0.8098 (mtp180) cc_final: 0.6422 (tpt170)
REVERT: L    3 GLU cc_start: 0.7655 (tt0) cc_final: 0.7445 (tt0)
REVERT: L    5 ARG cc_start: 0.8172 (mtp180) cc_final: 0.6714 (tpt170)
  outliers start: 16
  outliers final: 3
  residues processed: 86
  average time/residue: 1.5606
  time to fit residues: 137.0987
Evaluate side-chains
  92 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 82
  time to evaluate  : 0.407 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 LYS
Chi-restraints excluded: chain B residue   13 HIS
Chi-restraints excluded: chain C residue    3 GLU
Chi-restraints excluded: chain C residue   28 LYS
Chi-restraints excluded: chain F residue    3 GLU
Chi-restraints excluded: chain H residue   23 ASP
Chi-restraints excluded: chain I residue    3 GLU
Chi-restraints excluded: chain J residue    5 ARG
Chi-restraints excluded: chain J residue   28 LYS
Chi-restraints excluded: chain L residue   28 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 31 optimal weight:    0.6980
   chunk 30 optimal weight:    4.9990
   chunk 12 optimal weight:    9.9990
   chunk 22 optimal weight:    0.9980
   chunk 14 optimal weight:    0.8980
   chunk 2 optimal weight:    0.0980
   chunk 8 optimal weight:    0.9980
   chunk 17 optimal weight:    0.3980
   chunk 32 optimal weight:    0.6980
   chunk 21 optimal weight:    6.9990
   chunk 34 optimal weight:    0.9990
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
** B  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4636 r_free = 0.4636 target = 0.237591 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4971 r_free = 0.4971 target = 0.201091 restraints weight = 4730.689|
|-----------------------------------------------------------------------------|
r_work (start): 0.4511 rms_B_bonded: 1.62
r_work: 0.4931 rms_B_bonded: 1.34 restraints_weight: 0.5000
r_work: 0.4840 rms_B_bonded: 2.38 restraints_weight: 0.2500
r_work (final): 0.4840
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7663
moved from start:          0.5392

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   3516  Z= 0.108
  Angle     :  0.542   3.826   4704  Z= 0.291
  Chirality :  0.051   0.128    480
  Planarity :  0.002   0.010    624
  Dihedral  :  5.244  18.047    456
  Min Nonbonded Distance : 2.651

Molprobity Statistics.
  All-atom Clashscore : 4.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.71 %
    Favored  : 99.29 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 28.74 %
    Favored  : 68.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.47 (0.36), residues: 420
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.87 (0.28), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.007   0.001   HIS J  13 
 PHE   0.008   0.001   PHE J   4 
 TYR   0.003   0.000   TYR J  10 
 ARG   0.002   0.000   ARG G   5 

Details of bonding type rmsd
  covalent geometry    : bond        0.00243 ( 3516)
  covalent geometry    : angle       0.54211 ( 4704)

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

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

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 85
  time to evaluate  : 0.384 
Fit side-chains
   revert: symmetry clash
REVERT: J   28 LYS cc_start: 0.8404 (OUTLIER) cc_final: 0.8081 (ttpt)
REVERT: K    5 ARG cc_start: 0.7632 (mtp180) cc_final: 0.7246 (mmt-90)
REVERT: L    5 ARG cc_start: 0.7836 (mtp180) cc_final: 0.7475 (tpt170)
  outliers start: 11
  outliers final: 2
  residues processed: 88
  average time/residue: 1.4958
  time to fit residues: 134.6373
Evaluate side-chains
  74 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 71
  time to evaluate  : 0.387 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue    3 GLU
Chi-restraints excluded: chain J residue   28 LYS
Chi-restraints excluded: chain K residue   28 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 14 optimal weight:    4.9990
   chunk 9 optimal weight:    7.9990
   chunk 3 optimal weight:    1.9990
   chunk 26 optimal weight:    4.9990
   chunk 19 optimal weight:    0.9990
   chunk 33 optimal weight:    3.9990
   chunk 21 optimal weight:    5.9990
   chunk 15 optimal weight:    2.9990
   chunk 5 optimal weight:    3.9990
   chunk 35 optimal weight:    0.0770
   chunk 31 optimal weight:    2.9990
   overall best weight:    1.8146

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

Flipped N/Q/H residues before XYZ refinement:
** B  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
I  13 HIS
** J  13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
L  13 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4599 r_free = 0.4599 target = 0.230662 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4948 r_free = 0.4948 target = 0.190361 restraints weight = 4775.509|
|-----------------------------------------------------------------------------|
r_work (start): 0.4174 rms_B_bonded: 1.60
r_work: 0.4058 rms_B_bonded: 2.06 restraints_weight: 0.5000
r_work: 0.3928 rms_B_bonded: 3.41 restraints_weight: 0.2500
r_work (final): 0.3928
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7699
moved from start:          0.5609

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.033   3516  Z= 0.231
  Angle     :  0.701   5.224   4704  Z= 0.380
  Chirality :  0.051   0.129    480
  Planarity :  0.002   0.010    624
  Dihedral  :  5.718  16.696    456
  Min Nonbonded Distance : 2.622

Molprobity Statistics.
  All-atom Clashscore : 8.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 33.62 %
    Favored  : 63.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.60 (0.36), residues: 420
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.97 (0.27), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.008   0.001   HIS D  13 
 PHE   0.022   0.003   PHE C   4 
 TYR   0.005   0.001   TYR D  10 
 ARG   0.001   0.000   ARG F   5 

Details of bonding type rmsd
  covalent geometry    : bond        0.00518 ( 3516)
  covalent geometry    : angle       0.70105 ( 4704)

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

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

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 71
  time to evaluate  : 0.380 
Fit side-chains
   revert: symmetry clash
REVERT: A   11 GLU cc_start: 0.7823 (tt0) cc_final: 0.7493 (tt0)
REVERT: B   13 HIS cc_start: 0.4904 (m-70) cc_final: 0.4559 (t-90)
REVERT: C   28 LYS cc_start: 0.8382 (ttpt) cc_final: 0.8152 (ttpt)
REVERT: D   28 LYS cc_start: 0.8595 (tmtp) cc_final: 0.8096 (ttpt)
REVERT: J   28 LYS cc_start: 0.8792 (OUTLIER) cc_final: 0.8379 (ttpt)
REVERT: K    5 ARG cc_start: 0.8092 (mtp180) cc_final: 0.6610 (tpt170)
REVERT: L    5 ARG cc_start: 0.8204 (mtp180) cc_final: 0.6903 (tpt170)
  outliers start: 9
  outliers final: 3
  residues processed: 73
  average time/residue: 1.4904
  time to fit residues: 111.4151
Evaluate side-chains
  74 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 70
  time to evaluate  : 0.404 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   23 ASP
Chi-restraints excluded: chain I residue   35 MET
Chi-restraints excluded: chain J residue   28 LYS
Chi-restraints excluded: chain K residue   28 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 7 optimal weight:    0.9990
   chunk 23 optimal weight:    5.9990
   chunk 32 optimal weight:    3.9990
   chunk 33 optimal weight:    3.9990
   chunk 15 optimal weight:    5.9990
   chunk 12 optimal weight:    8.9990
   chunk 34 optimal weight:    0.9980
   chunk 11 optimal weight:    6.9990
   chunk 3 optimal weight:    3.9990
   chunk 35 optimal weight:    0.0010
   chunk 18 optimal weight:    0.9990
   overall best weight:    1.3992

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

Flipped N/Q/H residues before XYZ refinement:
** B  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** I  13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4615 r_free = 0.4615 target = 0.231441 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4955 r_free = 0.4955 target = 0.191786 restraints weight = 4679.812|
|-----------------------------------------------------------------------------|
r_work (start): 0.4194 rms_B_bonded: 1.62
r_work: 0.4082 rms_B_bonded: 2.05 restraints_weight: 0.5000
r_work: 0.3948 rms_B_bonded: 3.43 restraints_weight: 0.2500
r_work (final): 0.3948
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7676
moved from start:          0.5673

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   3516  Z= 0.191
  Angle     :  0.682   6.507   4704  Z= 0.367
  Chirality :  0.051   0.128    480
  Planarity :  0.002   0.015    624
  Dihedral  :  5.690  18.278    456
  Min Nonbonded Distance : 2.630

Molprobity Statistics.
  All-atom Clashscore : 7.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 34.48 %
    Favored  : 64.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.58 (0.36), residues: 420
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.96 (0.28), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.001   HIS J  13 
 PHE   0.019   0.002   PHE C   4 
 TYR   0.004   0.001   TYR K  10 
 ARG   0.002   0.000   ARG G   5 

Details of bonding type rmsd
  covalent geometry    : bond        0.00433 ( 3516)
  covalent geometry    : angle       0.68152 ( 4704)

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

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

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 71
  time to evaluate  : 0.374 
Fit side-chains
REVERT: A   11 GLU cc_start: 0.7864 (tt0) cc_final: 0.7658 (tt0)
REVERT: C   28 LYS cc_start: 0.8356 (ttpt) cc_final: 0.8148 (ttpt)
REVERT: D   28 LYS cc_start: 0.8537 (tmtp) cc_final: 0.8030 (ttpt)
REVERT: G    3 GLU cc_start: 0.7500 (tm-30) cc_final: 0.7292 (tm-30)
REVERT: H    3 GLU cc_start: 0.7290 (tm-30) cc_final: 0.6942 (tm-30)
REVERT: J   28 LYS cc_start: 0.8734 (OUTLIER) cc_final: 0.8319 (ttpt)
REVERT: K    5 ARG cc_start: 0.8090 (mtp180) cc_final: 0.6640 (tpt170)
REVERT: L    5 ARG cc_start: 0.8188 (mtp180) cc_final: 0.6884 (tpt170)
  outliers start: 5
  outliers final: 2
  residues processed: 71
  average time/residue: 1.5569
  time to fit residues: 113.0596
Evaluate side-chains
  71 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 68
  time to evaluate  : 0.383 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue   35 MET
Chi-restraints excluded: chain J residue   28 LYS
Chi-restraints excluded: chain K residue   28 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 20 optimal weight:    5.9990
   chunk 7 optimal weight:    6.9990
   chunk 28 optimal weight:    4.9990
   chunk 13 optimal weight:    1.9990
   chunk 23 optimal weight:    5.9990
   chunk 16 optimal weight:    5.9990
   chunk 33 optimal weight:    6.9990
   chunk 21 optimal weight:    3.9990
   chunk 1 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9990
   chunk 12 optimal weight:    3.9990
   overall best weight:    2.5990

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

Flipped N/Q/H residues before XYZ refinement:
** B  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** I  13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4354 r_free = 0.4354 target = 0.122228 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4081 r_free = 0.4081 target = 0.101275 restraints weight = 5266.111|
|-----------------------------------------------------------------------------|
r_work (start): 0.4049 rms_B_bonded: 3.03
r_work: 0.3902 rms_B_bonded: 3.31 restraints_weight: 0.5000
r_work (final): 0.3902
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7609
moved from start:          0.5828

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.042   3516  Z= 0.318
  Angle     :  0.806   7.476   4704  Z= 0.439
  Chirality :  0.053   0.132    480
  Planarity :  0.003   0.016    624
  Dihedral  :  6.172  18.771    456
  Min Nonbonded Distance : 2.609

Molprobity Statistics.
  All-atom Clashscore : 10.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 34.77 %
    Favored  : 63.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.83 (0.35), residues: 420
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.15 (0.26), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.008   0.001   HIS J  13 
 PHE   0.027   0.004   PHE C   4 
 TYR   0.006   0.001   TYR F  10 
 ARG   0.002   0.000   ARG F   5 

Details of bonding type rmsd
  covalent geometry    : bond        0.00703 ( 3516)
  covalent geometry    : angle       0.80556 ( 4704)

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

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

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 74
  time to evaluate  : 0.414 
Fit side-chains
REVERT: A   11 GLU cc_start: 0.7904 (tt0) cc_final: 0.7464 (tt0)
REVERT: B   11 GLU cc_start: 0.7159 (tm-30) cc_final: 0.6758 (tp30)
REVERT: C   28 LYS cc_start: 0.8238 (ttpt) cc_final: 0.7998 (ttpt)
REVERT: D   28 LYS cc_start: 0.8320 (tmtp) cc_final: 0.7801 (ttmt)
REVERT: H    3 GLU cc_start: 0.7130 (tm-30) cc_final: 0.6920 (tm-30)
REVERT: I    3 GLU cc_start: 0.7594 (tt0) cc_final: 0.6844 (tm-30)
REVERT: J   28 LYS cc_start: 0.8718 (OUTLIER) cc_final: 0.8268 (ttpt)
REVERT: K    5 ARG cc_start: 0.8080 (mtp180) cc_final: 0.6424 (tpt170)
REVERT: L    5 ARG cc_start: 0.8186 (mtp180) cc_final: 0.6680 (tpt170)
  outliers start: 6
  outliers final: 4
  residues processed: 75
  average time/residue: 1.5556
  time to fit residues: 119.3521
Evaluate side-chains
  78 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 73
  time to evaluate  : 0.362 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   23 ASP
Chi-restraints excluded: chain H residue   23 ASP
Chi-restraints excluded: chain I residue   35 MET
Chi-restraints excluded: chain J residue   28 LYS
Chi-restraints excluded: chain K residue   28 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 18 optimal weight:    8.9990
   chunk 6 optimal weight:    4.9990
   chunk 26 optimal weight:    0.8980
   chunk 25 optimal weight:    0.6980
   chunk 13 optimal weight:    0.6980
   chunk 19 optimal weight:    0.9990
   chunk 35 optimal weight:    2.9990
   chunk 20 optimal weight:    0.6980
   chunk 8 optimal weight:    0.7980
   chunk 4 optimal weight:    0.8980
   chunk 3 optimal weight:    4.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** B  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** I  13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4635 r_free = 0.4635 target = 0.234426 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4965 r_free = 0.4965 target = 0.195288 restraints weight = 4701.145|
|-----------------------------------------------------------------------------|
r_work (start): 0.4231 rms_B_bonded: 1.65
r_work: 0.4119 rms_B_bonded: 2.08 restraints_weight: 0.5000
r_work: 0.3991 rms_B_bonded: 3.46 restraints_weight: 0.2500
r_work (final): 0.3991
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7653
moved from start:          0.5827

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   3516  Z= 0.143
  Angle     :  0.679   6.178   4704  Z= 0.363
  Chirality :  0.052   0.127    480
  Planarity :  0.002   0.017    624
  Dihedral  :  5.731  20.861    456
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 7.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.43 %
    Favored  : 98.57 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 35.92 %
    Favored  : 62.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.54 (0.36), residues: 420
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.93 (0.28), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS J  13 
 PHE   0.012   0.002   PHE C   4 
 TYR   0.005   0.001   TYR J  10 
 ARG   0.003   0.000   ARG G   5 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 ( 3516)
  covalent geometry    : angle       0.67922 ( 4704)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3281.91 seconds
wall clock time: 57 minutes 41.11 seconds (3461.11 seconds total)