Starting phenix.real_space_refine
on Wed Mar  5 19:04:25 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ot4_17168/03_2025/8ot4_17168.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ot4_17168/03_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_17168/03_2025/8ot4_17168.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ot4_17168/03_2025/8ot4_17168.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ot4_17168/03_2025/8ot4_17168.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ot4_17168/03_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-5624/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: 1.48, per 1000 atoms: 0.43
  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: 0.74
  Conformation dependent library (CDL) restraints added in 432.1 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: 0.32
  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: 0.10

  Time building geometry restraints manager: 0.91 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: 0.04
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:             0.320
  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:          0.150
  Check model and map are aligned:         0.020
  Set scattering table:                    0.040
  Process input model:                     10.690
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:10.960
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.300
-------------------------------------------------------------------------------
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 

*********************** 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  : 0.419 
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: 1.1559
  time to fit residues: 154.4067
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  : 0.396 
-------------------------------------------------------------------------------
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 = 0.4945 r_free = 0.4945 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: 0.4066 rms_B_bonded: 3.63 restraints_weight: 0.2500
r_work (final): 0.4066
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7562
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 

*********************** 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  : 0.411 
Fit side-chains
   revert: symmetry clash
REVERT: A   13 HIS cc_start: 0.7368 (OUTLIER) cc_final: 0.6988 (m90)
REVERT: B   11 GLU cc_start: 0.7653 (mt-10) cc_final: 0.7237 (tt0)
REVERT: C    3 GLU cc_start: 0.7571 (OUTLIER) cc_final: 0.6926 (tm-30)
REVERT: D   28 LYS cc_start: 0.8652 (ttpp) cc_final: 0.8411 (tmtp)
REVERT: E   13 HIS cc_start: 0.6344 (OUTLIER) cc_final: 0.5669 (m-70)
REVERT: E   28 LYS cc_start: 0.8504 (tmtp) cc_final: 0.8000 (ttmt)
REVERT: F    3 GLU cc_start: 0.7420 (OUTLIER) cc_final: 0.7043 (tm-30)
REVERT: G    3 GLU cc_start: 0.7660 (tt0) cc_final: 0.7025 (tm-30)
REVERT: H   28 LYS cc_start: 0.8570 (tmtp) cc_final: 0.8187 (tttt)
REVERT: I   28 LYS cc_start: 0.8705 (tmtp) cc_final: 0.8202 (ttmt)
REVERT: J    3 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.7007 (tm-30)
REVERT: J   28 LYS cc_start: 0.8698 (tmmm) cc_final: 0.8234 (ttpt)
  outliers start: 10
  outliers final: 0
  residues processed: 94
  average time/residue: 1.2958
  time to fit residues: 125.0405
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  : 0.390 
-------------------------------------------------------------------------------
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:    0.9980
   chunk 0 optimal weight:    0.6980
   chunk 1 optimal weight:    3.9990
   chunk 3 optimal weight:    6.9990
   overall best weight:    3.1386

-------------------------------------------------------------------------------
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 = 0.4323 r_free = 0.4323 target = 0.121815 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4072 r_free = 0.4072 target = 0.102655 restraints weight = 5280.692|
|-----------------------------------------------------------------------------|
r_work (start): 0.4030 rms_B_bonded: 2.95
r_work: 0.3880 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.3880
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7621
moved from start:          0.5002

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.037   3516  Z= 0.374
  Angle     :  0.803   5.953   4704  Z= 0.437
  Chirality :  0.052   0.126    480
  Planarity :  0.003   0.013    624
  Dihedral  :  6.417  22.169    456
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 9.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.71 %
    Favored  : 99.29 %
  Rotamer:
    Outliers :  4.89 %
    Allowed  : 25.00 %
    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: -2.75 (0.33), residues: 420
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.09 (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 J   5 

*********************** 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
  103 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 86
  time to evaluate  : 0.365 
Fit side-chains
   revert: symmetry clash
REVERT: A   11 GLU cc_start: 0.7703 (mt-10) cc_final: 0.6965 (tt0)
REVERT: A   28 LYS cc_start: 0.6075 (OUTLIER) cc_final: 0.4843 (tppt)
REVERT: C    3 GLU cc_start: 0.7985 (OUTLIER) cc_final: 0.7135 (tm-30)
REVERT: C   11 GLU cc_start: 0.8517 (mt-10) cc_final: 0.8058 (mt-10)
REVERT: C   13 HIS cc_start: 0.7463 (m90) cc_final: 0.7200 (m90)
REVERT: C   23 ASP cc_start: 0.8300 (m-30) cc_final: 0.8079 (m-30)
REVERT: C   28 LYS cc_start: 0.8632 (OUTLIER) cc_final: 0.8116 (ttmt)
REVERT: D   11 GLU cc_start: 0.7953 (tt0) cc_final: 0.7288 (tt0)
REVERT: D   28 LYS cc_start: 0.8479 (ttpp) cc_final: 0.7954 (ttmt)
REVERT: E   13 HIS cc_start: 0.7344 (m-70) cc_final: 0.6505 (m90)
REVERT: E   28 LYS cc_start: 0.8328 (tmtp) cc_final: 0.7862 (ttmt)
REVERT: G   11 GLU cc_start: 0.8018 (tt0) cc_final: 0.7528 (tt0)
REVERT: I   13 HIS cc_start: 0.7489 (m-70) cc_final: 0.7262 (m90)
REVERT: J    3 GLU cc_start: 0.7723 (OUTLIER) cc_final: 0.7467 (tt0)
REVERT: J    5 ARG cc_start: 0.8267 (OUTLIER) cc_final: 0.7746 (ttp80)
REVERT: L    5 ARG cc_start: 0.8215 (mtp180) cc_final: 0.6724 (tpt170)
  outliers start: 17
  outliers final: 3
  residues processed: 87
  average time/residue: 1.5852
  time to fit residues: 140.8967
Evaluate side-chains
  90 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 82
  time to evaluate  : 0.413 
-------------------------------------------------------------------------------
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 J residue    3 GLU
Chi-restraints excluded: chain J residue    5 ARG
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:    0.7980
   chunk 3 optimal weight:    4.9990
   chunk 23 optimal weight:    3.9990
   chunk 11 optimal weight:    3.9990
   chunk 22 optimal weight:    2.9990
   chunk 6 optimal weight:    5.9990
   chunk 28 optimal weight:    0.6980
   chunk 18 optimal weight:    0.6980
   chunk 21 optimal weight:    4.9990
   chunk 15 optimal weight:    0.8980
   chunk 12 optimal weight:    2.9990
   overall best weight:    1.2182

-------------------------------------------------------------------------------
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 = 0.4587 r_free = 0.4587 target = 0.229298 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4921 r_free = 0.4921 target = 0.193168 restraints weight = 4790.233|
|-----------------------------------------------------------------------------|
r_work (start): 0.4243 rms_B_bonded: 1.56
r_work: 0.4137 rms_B_bonded: 2.04 restraints_weight: 0.5000
r_work: 0.4007 rms_B_bonded: 3.48 restraints_weight: 0.2500
r_work (final): 0.4007
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7704
moved from start:          0.5108

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025   3516  Z= 0.168
  Angle     :  0.627   4.424   4704  Z= 0.333
  Chirality :  0.050   0.128    480
  Planarity :  0.002   0.010    624
  Dihedral  :  5.732  19.973    456
  Min Nonbonded Distance : 2.641

Molprobity Statistics.
  All-atom Clashscore : 6.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  5.17 %
    Allowed  : 27.01 %
    Favored  : 67.82 %
  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   0.004   0.001   HIS J  13 
 PHE   0.014   0.002   PHE L   4 
 TYR   0.005   0.001   TYR K  10 
 ARG   0.001   0.000   ARG H   5 

*********************** 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
  105 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 87
  time to evaluate  : 0.362 
Fit side-chains
REVERT: A   11 GLU cc_start: 0.7689 (mt-10) cc_final: 0.7003 (tt0)
REVERT: B   13 HIS cc_start: 0.4428 (OUTLIER) cc_final: 0.3898 (m-70)
REVERT: C    3 GLU cc_start: 0.7973 (OUTLIER) cc_final: 0.7144 (tm-30)
REVERT: C    5 ARG cc_start: 0.8339 (mtp180) cc_final: 0.8003 (mtp180)
REVERT: C   11 GLU cc_start: 0.8126 (mt-10) cc_final: 0.7492 (mt-10)
REVERT: C   13 HIS cc_start: 0.7481 (m90) cc_final: 0.6994 (m90)
REVERT: C   28 LYS cc_start: 0.8664 (OUTLIER) cc_final: 0.8344 (ttmt)
REVERT: D   11 GLU cc_start: 0.7803 (tt0) cc_final: 0.6839 (tt0)
REVERT: D   28 LYS cc_start: 0.8623 (ttpp) cc_final: 0.8190 (ttmt)
REVERT: E   13 HIS cc_start: 0.7164 (m-70) cc_final: 0.6407 (m90)
REVERT: E   28 LYS cc_start: 0.8468 (tmtp) cc_final: 0.8053 (ttmt)
REVERT: F    3 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7045 (tm-30)
REVERT: G    3 GLU cc_start: 0.7542 (tt0) cc_final: 0.6897 (tm-30)
REVERT: H   28 LYS cc_start: 0.8505 (tmtp) cc_final: 0.8040 (ttmt)
REVERT: I    3 GLU cc_start: 0.7797 (OUTLIER) cc_final: 0.7575 (tt0)
REVERT: I   13 HIS cc_start: 0.7206 (m-70) cc_final: 0.6977 (m90)
REVERT: J   28 LYS cc_start: 0.8715 (tmmm) cc_final: 0.8326 (ttpt)
REVERT: L    5 ARG cc_start: 0.8216 (mtp180) cc_final: 0.6724 (tpt170)
  outliers start: 18
  outliers final: 3
  residues processed: 89
  average time/residue: 1.5361
  time to fit residues: 139.6916
Evaluate side-chains
  91 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 83
  time to evaluate  : 0.364 
-------------------------------------------------------------------------------
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 L residue   13 HIS
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:    0.7980
   chunk 6 optimal weight:    8.9990
   chunk 13 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9990
   chunk 21 optimal weight:    4.9990
   chunk 5 optimal weight:    3.9990
   chunk 19 optimal weight:    0.9990
   chunk 2 optimal weight:    4.9990
   chunk 27 optimal weight:    1.9990
   overall best weight:    1.3588

-------------------------------------------------------------------------------
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**
** 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 = 0.4334 r_free = 0.4334 target = 0.123287 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4057 r_free = 0.4057 target = 0.101061 restraints weight = 5193.945|
|-----------------------------------------------------------------------------|
r_work (start): 0.4063 rms_B_bonded: 3.13
r_work: 0.3912 rms_B_bonded: 3.60 restraints_weight: 0.5000
r_work (final): 0.3912
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7473
moved from start:          0.5259

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   3516  Z= 0.180
  Angle     :  0.626   4.722   4704  Z= 0.336
  Chirality :  0.051   0.129    480
  Planarity :  0.002   0.009    624
  Dihedral  :  5.679  19.623    456
  Min Nonbonded Distance : 2.651

Molprobity Statistics.
  All-atom Clashscore : 6.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  4.31 %
    Allowed  : 28.16 %
    Favored  : 67.53 %
  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 (0.27), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.001   HIS D  13 
 PHE   0.015   0.003   PHE E   4 
 TYR   0.005   0.001   TYR D  10 
 ARG   0.001   0.000   ARG E   5 

*********************** 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
  100 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 85
  time to evaluate  : 0.439 
Fit side-chains
REVERT: A   11 GLU cc_start: 0.7602 (mt-10) cc_final: 0.6741 (tt0)
REVERT: B   11 GLU cc_start: 0.7211 (tm-30) cc_final: 0.6638 (tm-30)
REVERT: B   13 HIS cc_start: 0.4444 (OUTLIER) cc_final: 0.3275 (m-70)
REVERT: C    3 GLU cc_start: 0.7699 (OUTLIER) cc_final: 0.6615 (tm-30)
REVERT: C    5 ARG cc_start: 0.8253 (mtp180) cc_final: 0.7782 (mtp180)
REVERT: C   11 GLU cc_start: 0.8351 (mt-10) cc_final: 0.7660 (mt-10)
REVERT: C   13 HIS cc_start: 0.7668 (m90) cc_final: 0.6973 (m90)
REVERT: C   28 LYS cc_start: 0.8485 (OUTLIER) cc_final: 0.8129 (ttpt)
REVERT: D   28 LYS cc_start: 0.8438 (ttpp) cc_final: 0.7917 (ttmt)
REVERT: E   13 HIS cc_start: 0.6968 (m-70) cc_final: 0.6241 (m90)
REVERT: E   28 LYS cc_start: 0.8157 (tmtp) cc_final: 0.7732 (ttmt)
REVERT: F    3 GLU cc_start: 0.7679 (OUTLIER) cc_final: 0.6583 (tm-30)
REVERT: F    5 ARG cc_start: 0.8085 (ttp80) cc_final: 0.7850 (tpp80)
REVERT: F   11 GLU cc_start: 0.8035 (mt-10) cc_final: 0.7605 (mt-10)
REVERT: G    3 GLU cc_start: 0.7322 (tt0) cc_final: 0.6557 (tm-30)
REVERT: G   28 LYS cc_start: 0.8144 (OUTLIER) cc_final: 0.7787 (ttmt)
REVERT: H   28 LYS cc_start: 0.8207 (tmtp) cc_final: 0.7715 (ttmt)
REVERT: I    3 GLU cc_start: 0.7589 (OUTLIER) cc_final: 0.7343 (tt0)
REVERT: I   13 HIS cc_start: 0.7000 (m-70) cc_final: 0.6718 (m90)
REVERT: J    3 GLU cc_start: 0.7580 (tt0) cc_final: 0.6753 (tm-30)
REVERT: J   28 LYS cc_start: 0.8600 (OUTLIER) cc_final: 0.8155 (ttpt)
REVERT: L    5 ARG cc_start: 0.8096 (mtp180) cc_final: 0.6443 (tpt170)
  outliers start: 15
  outliers final: 3
  residues processed: 86
  average time/residue: 1.5286
  time to fit residues: 134.4828
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  : 0.390 
-------------------------------------------------------------------------------
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 G residue   28 LYS
Chi-restraints excluded: chain H residue   13 HIS
Chi-restraints excluded: chain I residue    3 GLU
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:    0.7980
   chunk 21 optimal weight:    9.9990
   chunk 5 optimal weight:    0.7980
   chunk 18 optimal weight:    0.9990
   chunk 6 optimal weight:    8.9990
   chunk 23 optimal weight:    6.9990
   chunk 1 optimal weight:    4.9990
   chunk 12 optimal weight:    0.9990
   chunk 34 optimal weight:    0.0770
   chunk 3 optimal weight:    3.9990
   chunk 14 optimal weight:    0.8980
   overall best weight:    0.7140

-------------------------------------------------------------------------------
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 = 0.4625 r_free = 0.4625 target = 0.234741 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4957 r_free = 0.4957 target = 0.198331 restraints weight = 4779.922|
|-----------------------------------------------------------------------------|
r_work (start): 0.4243 rms_B_bonded: 1.62
r_work: 0.4132 rms_B_bonded: 2.07 restraints_weight: 0.5000
r_work: 0.4002 rms_B_bonded: 3.48 restraints_weight: 0.2500
r_work (final): 0.4002
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7626
moved from start:          0.5399

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3516  Z= 0.122
  Angle     :  0.561   4.289   4704  Z= 0.300
  Chirality :  0.050   0.125    480
  Planarity :  0.002   0.008    624
  Dihedral  :  5.267  17.550    456
  Min Nonbonded Distance : 2.644

Molprobity Statistics.
  All-atom Clashscore : 4.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.43 %
    Favored  : 98.57 %
  Rotamer:
    Outliers :  4.31 %
    Allowed  : 27.59 %
    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: -2.44 (0.36), residues: 420
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.85 (0.28), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.009   0.001   HIS G  13 
 PHE   0.009   0.002   PHE E   4 
 TYR   0.013   0.001   TYR K  10 
 ARG   0.001   0.000   ARG G   5 

*********************** 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
  103 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 88
  time to evaluate  : 0.368 
Fit side-chains
   revert: symmetry clash
REVERT: A   11 GLU cc_start: 0.7605 (mt-10) cc_final: 0.6767 (tt0)
REVERT: B   11 GLU cc_start: 0.7419 (tm-30) cc_final: 0.6867 (tm-30)
REVERT: B   13 HIS cc_start: 0.4685 (OUTLIER) cc_final: 0.3462 (m-70)
REVERT: C    3 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.6887 (tm-30)
REVERT: C    5 ARG cc_start: 0.8257 (mtp180) cc_final: 0.7908 (mtp180)
REVERT: C   28 LYS cc_start: 0.8613 (OUTLIER) cc_final: 0.8317 (ttpt)
REVERT: D   28 LYS cc_start: 0.8565 (ttpp) cc_final: 0.8216 (ttmt)
REVERT: E   28 LYS cc_start: 0.8325 (tmtp) cc_final: 0.7979 (ttmt)
REVERT: F    3 GLU cc_start: 0.7872 (tt0) cc_final: 0.6868 (tm-30)
REVERT: G    3 GLU cc_start: 0.7569 (tt0) cc_final: 0.6931 (tm-30)
REVERT: H   28 LYS cc_start: 0.8501 (tmtp) cc_final: 0.8062 (ttmt)
REVERT: I    3 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.7613 (tt0)
REVERT: J    3 GLU cc_start: 0.7767 (tt0) cc_final: 0.7107 (tm-30)
REVERT: J    5 ARG cc_start: 0.8173 (OUTLIER) cc_final: 0.7684 (ttp80)
REVERT: J   28 LYS cc_start: 0.8714 (OUTLIER) cc_final: 0.8271 (ttpt)
REVERT: K    3 GLU cc_start: 0.7708 (tt0) cc_final: 0.7136 (tm-30)
REVERT: L    5 ARG cc_start: 0.8155 (mtp180) cc_final: 0.6753 (tpt170)
  outliers start: 15
  outliers final: 2
  residues processed: 88
  average time/residue: 1.3669
  time to fit residues: 123.2917
Evaluate side-chains
  83 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 75
  time to evaluate  : 0.371 
-------------------------------------------------------------------------------
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 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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 31 optimal weight:    0.9990
   chunk 30 optimal weight:    5.9990
   chunk 12 optimal weight:    9.9990
   chunk 22 optimal weight:    3.9990
   chunk 14 optimal weight:    6.9990
   chunk 2 optimal weight:    4.9990
   chunk 8 optimal weight:    0.5980
   chunk 17 optimal weight:    5.9990
   chunk 32 optimal weight:    0.0670
   chunk 21 optimal weight:    8.9990
   chunk 34 optimal weight:    3.9990
   overall best weight:    1.9324

-------------------------------------------------------------------------------
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**
** G  13 HIS ** 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 = 0.4583 r_free = 0.4583 target = 0.227821 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4907 r_free = 0.4907 target = 0.189165 restraints weight = 4843.751|
|-----------------------------------------------------------------------------|
r_work (start): 0.4158 rms_B_bonded: 1.63
r_work: 0.4042 rms_B_bonded: 2.07 restraints_weight: 0.5000
r_work: 0.3907 rms_B_bonded: 3.46 restraints_weight: 0.2500
r_work (final): 0.3907
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7721
moved from start:          0.5526

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.031   3516  Z= 0.242
  Angle     :  0.661   5.736   4704  Z= 0.360
  Chirality :  0.051   0.131    480
  Planarity :  0.002   0.010    624
  Dihedral  :  5.758  18.733    456
  Min Nonbonded Distance : 2.636

Molprobity Statistics.
  All-atom Clashscore : 6.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  4.02 %
    Allowed  : 29.60 %
    Favored  : 66.38 %
  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: -2.61 (0.36), residues: 420
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.98 (0.27), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.001   HIS J  13 
 PHE   0.018   0.003   PHE E   4 
 TYR   0.004   0.001   TYR F  10 
 ARG   0.002   0.000   ARG G   5 

*********************** 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
  92 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 78
  time to evaluate  : 0.385 
Fit side-chains
REVERT: A   11 GLU cc_start: 0.7710 (mt-10) cc_final: 0.6956 (tt0)
REVERT: A   28 LYS cc_start: 0.5861 (OUTLIER) cc_final: 0.4395 (tppt)
REVERT: C    3 GLU cc_start: 0.7938 (OUTLIER) cc_final: 0.7053 (tm-30)
REVERT: C    5 ARG cc_start: 0.8311 (mtp180) cc_final: 0.7934 (mtp180)
REVERT: C   11 GLU cc_start: 0.8325 (mt-10) cc_final: 0.7692 (mt-10)
REVERT: C   13 HIS cc_start: 0.7563 (m90) cc_final: 0.7108 (m90)
REVERT: C   28 LYS cc_start: 0.8620 (OUTLIER) cc_final: 0.8228 (ttmt)
REVERT: D   28 LYS cc_start: 0.8602 (ttpp) cc_final: 0.8076 (ttmt)
REVERT: E   28 LYS cc_start: 0.8417 (tmtp) cc_final: 0.8096 (ttmt)
REVERT: G    3 GLU cc_start: 0.7591 (tt0) cc_final: 0.6865 (tm-30)
REVERT: H   28 LYS cc_start: 0.8459 (tmtp) cc_final: 0.8004 (ttmt)
REVERT: J    3 GLU cc_start: 0.7710 (tt0) cc_final: 0.7029 (tm-30)
REVERT: J    5 ARG cc_start: 0.8250 (OUTLIER) cc_final: 0.7712 (ttp80)
REVERT: J   28 LYS cc_start: 0.8769 (OUTLIER) cc_final: 0.8337 (ttpt)
REVERT: K    5 ARG cc_start: 0.8138 (mtp180) cc_final: 0.6642 (tpt170)
REVERT: L    3 GLU cc_start: 0.7690 (tt0) cc_final: 0.7470 (tt0)
REVERT: L    5 ARG cc_start: 0.8200 (mtp180) cc_final: 0.6885 (tpt170)
  outliers start: 14
  outliers final: 6
  residues processed: 82
  average time/residue: 1.5349
  time to fit residues: 128.6535
Evaluate side-chains
  88 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 77
  time to evaluate  : 0.349 
-------------------------------------------------------------------------------
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 D residue   12 VAL
Chi-restraints excluded: chain D residue   23 ASP
Chi-restraints excluded: chain E residue   35 MET
Chi-restraints excluded: chain H residue   23 ASP
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 14 optimal weight:    0.1980
   chunk 9 optimal weight:    7.9990
   chunk 3 optimal weight:    0.6980
   chunk 26 optimal weight:    5.9990
   chunk 19 optimal weight:    0.9990
   chunk 33 optimal weight:    0.9980
   chunk 21 optimal weight:    6.9990
   chunk 15 optimal weight:    5.9990
   chunk 5 optimal weight:    3.9990
   chunk 35 optimal weight:    0.0370
   chunk 31 optimal weight:    2.9990
   overall best weight:    0.5860

-------------------------------------------------------------------------------
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**
L  13 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4644 r_free = 0.4644 target = 0.236997 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4969 r_free = 0.4969 target = 0.200061 restraints weight = 4641.011|
|-----------------------------------------------------------------------------|
r_work (start): 0.4521 rms_B_bonded: 1.63
r_work: 0.4928 rms_B_bonded: 1.35 restraints_weight: 0.5000
r_work: 0.4843 rms_B_bonded: 2.38 restraints_weight: 0.2500
r_work (final): 0.4843
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7654
moved from start:          0.5578

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   3516  Z= 0.113
  Angle     :  0.560   4.442   4704  Z= 0.300
  Chirality :  0.051   0.127    480
  Planarity :  0.002   0.010    624
  Dihedral  :  5.193  16.321    456
  Min Nonbonded Distance : 2.633

Molprobity Statistics.
  All-atom Clashscore : 5.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.71 %
    Favored  : 99.29 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 30.75 %
    Favored  : 66.38 %
  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: -2.45 (0.37), residues: 420
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.86 (0.28), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS F  13 
 PHE   0.009   0.001   PHE I   4 
 TYR   0.014   0.001   TYR K  10 
 ARG   0.001   0.000   ARG G   5 

*********************** 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
  92 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 82
  time to evaluate  : 0.402 
Fit side-chains
REVERT: D   10 TYR cc_start: 0.7619 (t80) cc_final: 0.7310 (t80)
REVERT: J   28 LYS cc_start: 0.8419 (OUTLIER) cc_final: 0.8097 (ttpt)
REVERT: K    5 ARG cc_start: 0.7625 (mtp180) cc_final: 0.7247 (mmt-90)
REVERT: L    5 ARG cc_start: 0.7839 (mtp180) cc_final: 0.7435 (tpt170)
  outliers start: 10
  outliers final: 3
  residues processed: 84
  average time/residue: 1.3679
  time to fit residues: 117.7812
Evaluate side-chains
  75 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 71
  time to evaluate  : 0.410 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   12 VAL
Chi-restraints excluded: chain E residue   13 HIS
Chi-restraints excluded: chain J residue   28 LYS
Chi-restraints excluded: chain L 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:    5.9990
   chunk 23 optimal weight:    6.9990
   chunk 32 optimal weight:    3.9990
   chunk 33 optimal weight:    5.9990
   chunk 15 optimal weight:    0.9990
   chunk 12 optimal weight:   10.0000
   chunk 34 optimal weight:    4.9990
   chunk 11 optimal weight:    7.9990
   chunk 3 optimal weight:    3.9990
   chunk 35 optimal weight:    2.9990
   chunk 18 optimal weight:    2.9990
   overall best weight:    2.9990

-------------------------------------------------------------------------------
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**
** C  13 HIS ** 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
** 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: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4349 r_free = 0.4349 target = 0.120956 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4085 r_free = 0.4085 target = 0.100635 restraints weight = 5254.691|
|-----------------------------------------------------------------------------|
r_work (start): 0.4055 rms_B_bonded: 3.03
r_work: 0.3904 rms_B_bonded: 3.28 restraints_weight: 0.5000
r_work (final): 0.3904
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7620
moved from start:          0.5846

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.038   3516  Z= 0.357
  Angle     :  0.817   6.567   4704  Z= 0.449
  Chirality :  0.053   0.134    480
  Planarity :  0.003   0.016    624
  Dihedral  :  6.027  19.982    456
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 11.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.29 %
    Favored  : 95.71 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 34.48 %
    Favored  : 62.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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 (0.35), residues: 420
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.10 (0.27), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.010   0.001   HIS C  13 
 PHE   0.032   0.004   PHE C   4 
 TYR   0.006   0.001   TYR J  10 
 ARG   0.002   0.000   ARG F   5 

*********************** 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
  85 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 76
  time to evaluate  : 0.419 
Fit side-chains
REVERT: A    5 ARG cc_start: 0.8601 (mtp180) cc_final: 0.6885 (ptt-90)
REVERT: B   11 GLU cc_start: 0.7207 (tm-30) cc_final: 0.6747 (tp30)
REVERT: C   11 GLU cc_start: 0.8333 (mt-10) cc_final: 0.7983 (mt-10)
REVERT: D   28 LYS cc_start: 0.8420 (tmtp) cc_final: 0.7907 (ttmt)
REVERT: H    3 GLU cc_start: 0.7131 (tm-30) cc_final: 0.6898 (tm-30)
REVERT: J    5 ARG cc_start: 0.8293 (ttp80) cc_final: 0.8040 (ttp80)
REVERT: J   28 LYS cc_start: 0.8715 (tmmm) cc_final: 0.8250 (ttpt)
REVERT: K    3 GLU cc_start: 0.7578 (OUTLIER) cc_final: 0.7204 (tm-30)
REVERT: K    5 ARG cc_start: 0.8016 (mtp180) cc_final: 0.6305 (tpt170)
REVERT: L    5 ARG cc_start: 0.8212 (mtp180) cc_final: 0.6697 (tpt170)
  outliers start: 9
  outliers final: 6
  residues processed: 79
  average time/residue: 1.5918
  time to fit residues: 128.4774
Evaluate side-chains
  82 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 75
  time to evaluate  : 0.397 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   12 VAL
Chi-restraints excluded: chain E residue   23 ASP
Chi-restraints excluded: chain E residue   35 MET
Chi-restraints excluded: chain H residue   23 ASP
Chi-restraints excluded: chain I residue    3 GLU
Chi-restraints excluded: chain K residue    3 GLU
Chi-restraints excluded: chain L 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:    3.9990
   chunk 7 optimal weight:    0.9990
   chunk 28 optimal weight:    0.6980
   chunk 13 optimal weight:    0.9990
   chunk 23 optimal weight:    0.8980
   chunk 16 optimal weight:    0.7980
   chunk 33 optimal weight:    3.9990
   chunk 21 optimal weight:    4.9990
   chunk 1 optimal weight:    0.9990
   chunk 14 optimal weight:    0.9980
   chunk 12 optimal weight:    3.9990
   overall best weight:    0.8782

-------------------------------------------------------------------------------
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 = 0.4640 r_free = 0.4640 target = 0.231751 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4977 r_free = 0.4977 target = 0.193343 restraints weight = 4731.956|
|-----------------------------------------------------------------------------|
r_work (start): 0.4248 rms_B_bonded: 1.50
r_work: 0.4143 rms_B_bonded: 1.91 restraints_weight: 0.5000
r_work: 0.4019 rms_B_bonded: 3.20 restraints_weight: 0.2500
r_work (final): 0.4019
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7664
moved from start:          0.5906

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   3516  Z= 0.154
  Angle     :  0.694   7.261   4704  Z= 0.373
  Chirality :  0.051   0.130    480
  Planarity :  0.002   0.015    624
  Dihedral  :  5.664  21.929    456
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 7.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 37.36 %
    Favored  : 61.21 %
  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: -2.55 (0.37), 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   0.007   0.001   HIS J  13 
 PHE   0.015   0.002   PHE I  19 
 TYR   0.013   0.001   TYR K  10 
 ARG   0.002   0.000   ARG G   5 

********************** 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
  74 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 69
  time to evaluate  : 0.405 
Fit side-chains
REVERT: B   28 LYS cc_start: 0.5554 (tppt) cc_final: 0.5141 (tppt)
REVERT: C    1 ASP cc_start: 0.7209 (p0) cc_final: 0.6283 (m-30)
REVERT: D   28 LYS cc_start: 0.8550 (tmtp) cc_final: 0.8075 (ttpt)
REVERT: J   28 LYS cc_start: 0.8738 (tmmm) cc_final: 0.8314 (ttpt)
REVERT: K    3 GLU cc_start: 0.7788 (OUTLIER) cc_final: 0.7453 (tm-30)
REVERT: K    5 ARG cc_start: 0.7982 (mtp180) cc_final: 0.6515 (mmt-90)
REVERT: L    5 ARG cc_start: 0.8183 (mtp180) cc_final: 0.6864 (tpt170)
  outliers start: 5
  outliers final: 2
  residues processed: 71
  average time/residue: 1.5588
  time to fit residues: 113.2216
Evaluate side-chains
  70 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 67
  time to evaluate  : 0.409 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   12 VAL
Chi-restraints excluded: chain K residue    3 GLU
Chi-restraints excluded: chain L 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:    6.9990
   chunk 6 optimal weight:    4.9990
   chunk 26 optimal weight:    0.2980
   chunk 25 optimal weight:    3.9990
   chunk 13 optimal weight:    0.6980
   chunk 19 optimal weight:    0.9990
   chunk 35 optimal weight:    4.9990
   chunk 20 optimal weight:    1.9990
   chunk 8 optimal weight:    4.9990
   chunk 4 optimal weight:    0.4980
   chunk 3 optimal weight:    5.9990
   overall best weight:    0.8984

-------------------------------------------------------------------------------
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**
** 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 = 0.4650 r_free = 0.4650 target = 0.235119 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.4981 r_free = 0.4981 target = 0.195300 restraints weight = 4701.894|
|-----------------------------------------------------------------------------|
r_work (start): 0.4252 rms_B_bonded: 1.65
r_work: 0.4138 rms_B_bonded: 2.10 restraints_weight: 0.5000
r_work: 0.4009 rms_B_bonded: 3.48 restraints_weight: 0.2500
r_work (final): 0.4009
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7656
moved from start:          0.5902

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   3516  Z= 0.152
  Angle     :  0.672   6.189   4704  Z= 0.362
  Chirality :  0.051   0.128    480
  Planarity :  0.002   0.017    624
  Dihedral  :  5.513  21.169    456
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 6.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 37.07 %
    Favored  : 61.49 %
  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: -2.44 (0.37), residues: 420
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.85 (0.28), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS J  13 
 PHE   0.016   0.002   PHE F   4 
 TYR   0.004   0.001   TYR J  10 
 ARG   0.002   0.000   ARG G   5 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3253.48 seconds
wall clock time: 56 minutes 47.39 seconds (3407.39 seconds total)