Starting phenix.real_space_refine
on Tue Feb  3 13:16:57 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9rax_53882/02_2026/9rax_53882.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9rax_53882/02_2026/9rax_53882.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.76
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9rax_53882/02_2026/9rax_53882.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9rax_53882/02_2026/9rax_53882.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9rax_53882/02_2026/9rax_53882.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9rax_53882/02_2026/9rax_53882.cif"
  }
  resolution = 2.76
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.010
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      10      5.16       5
     C    1940      2.51       5
     N     530      2.21       5
     O     580      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3060
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 306
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 40, 306
          Classifications: {'peptide': 40}
          Modifications used: {'COO': 1}
          Link IDs: {'TRANS': 39}
  Restraints were copied for chains:
    B, C, D, E, F, G, H, I, J
  Time building chain proxies: 0.48, per 1000 atoms: 0.16
  Number of scatterers: 3060
  At special positions: 0
  Unit cell: (93.45, 130.2, 38.85, 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      10     16.00
     O     580      8.00
     N     530      7.00
     C    1940      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: 0.24
  Conformation dependent library (CDL) restraints added in 113.9 milliseconds
  

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  680

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 6 sheets defined
      0.0% alpha, 35.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.11
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'A' and resid 10 through 13
    Processing sheet with id=AA2, first strand: chain 'A' and resid 16 through 22
      removed outlier: 6.414A  pdb=" N   LYS A  16 " --> pdb=" O   LEU C  17 " (cutoff:3.500A)
      removed outlier: 7.819A  pdb=" N   PHE C  19 " --> pdb=" O   LYS A  16 " (cutoff:3.500A)
      removed outlier: 6.130A  pdb=" N   VAL A  18 " --> pdb=" O   PHE C  19 " (cutoff:3.500A)
      removed outlier: 7.904A  pdb=" N   ALA C  21 " --> pdb=" O   VAL A  18 " (cutoff:3.500A)
      removed outlier: 6.270A  pdb=" N   PHE A  20 " --> pdb=" O   ALA C  21 " (cutoff:3.500A)
      removed outlier: 6.414A  pdb=" N   LYS C  16 " --> pdb=" O   LEU E  17 " (cutoff:3.500A)
      removed outlier: 7.819A  pdb=" N   PHE E  19 " --> pdb=" O   LYS C  16 " (cutoff:3.500A)
      removed outlier: 6.131A  pdb=" N   VAL C  18 " --> pdb=" O   PHE E  19 " (cutoff:3.500A)
      removed outlier: 7.905A  pdb=" N   ALA E  21 " --> pdb=" O   VAL C  18 " (cutoff:3.500A)
      removed outlier: 6.270A  pdb=" N   PHE C  20 " --> pdb=" O   ALA E  21 " (cutoff:3.500A)
      removed outlier: 6.413A  pdb=" N   LYS E  16 " --> pdb=" O   LEU G  17 " (cutoff:3.500A)
      removed outlier: 7.817A  pdb=" N   PHE G  19 " --> pdb=" O   LYS E  16 " (cutoff:3.500A)
      removed outlier: 6.128A  pdb=" N   VAL E  18 " --> pdb=" O   PHE G  19 " (cutoff:3.500A)
      removed outlier: 7.903A  pdb=" N   ALA G  21 " --> pdb=" O   VAL E  18 " (cutoff:3.500A)
      removed outlier: 6.267A  pdb=" N   PHE E  20 " --> pdb=" O   ALA G  21 " (cutoff:3.500A)
      removed outlier: 6.418A  pdb=" N   LYS G  16 " --> pdb=" O   LEU I  17 " (cutoff:3.500A)
      removed outlier: 7.823A  pdb=" N   PHE I  19 " --> pdb=" O   LYS G  16 " (cutoff:3.500A)
      removed outlier: 6.133A  pdb=" N   VAL G  18 " --> pdb=" O   PHE I  19 " (cutoff:3.500A)
      removed outlier: 7.907A  pdb=" N   ALA I  21 " --> pdb=" O   VAL G  18 " (cutoff:3.500A)
      removed outlier: 6.273A  pdb=" N   PHE G  20 " --> pdb=" O   ALA I  21 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 31 through 36
      removed outlier: 6.622A  pdb=" N   LEU A  34 " --> pdb=" O   GLY C  33 " (cutoff:3.500A)
      removed outlier: 6.754A  pdb=" N   MET C  35 " --> pdb=" O   LEU A  34 " (cutoff:3.500A)
      removed outlier: 6.773A  pdb=" N   VAL A  36 " --> pdb=" O   MET C  35 " (cutoff:3.500A)
      removed outlier: 6.622A  pdb=" N   LEU C  34 " --> pdb=" O   GLY E  33 " (cutoff:3.500A)
      removed outlier: 6.755A  pdb=" N   MET E  35 " --> pdb=" O   LEU C  34 " (cutoff:3.500A)
      removed outlier: 6.774A  pdb=" N   VAL C  36 " --> pdb=" O   MET E  35 " (cutoff:3.500A)
      removed outlier: 6.625A  pdb=" N   LEU E  34 " --> pdb=" O   GLY G  33 " (cutoff:3.500A)
      removed outlier: 6.755A  pdb=" N   MET G  35 " --> pdb=" O   LEU E  34 " (cutoff:3.500A)
      removed outlier: 6.774A  pdb=" N   VAL E  36 " --> pdb=" O   MET G  35 " (cutoff:3.500A)
      removed outlier: 6.619A  pdb=" N   LEU G  34 " --> pdb=" O   GLY I  33 " (cutoff:3.500A)
      removed outlier: 6.753A  pdb=" N   MET I  35 " --> pdb=" O   LEU G  34 " (cutoff:3.500A)
      removed outlier: 6.772A  pdb=" N   VAL G  36 " --> pdb=" O   MET I  35 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 10 through 13
      removed outlier: 6.344A  pdb=" N   GLU B  11 " --> pdb=" O   VAL D  12 " (cutoff:3.500A)
      removed outlier: 6.330A  pdb=" N   GLU D  11 " --> pdb=" O   VAL F  12 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 16 through 22
      removed outlier: 6.412A  pdb=" N   LYS B  16 " --> pdb=" O   LEU D  17 " (cutoff:3.500A)
      removed outlier: 7.819A  pdb=" N   PHE D  19 " --> pdb=" O   LYS B  16 " (cutoff:3.500A)
      removed outlier: 6.131A  pdb=" N   VAL B  18 " --> pdb=" O   PHE D  19 " (cutoff:3.500A)
      removed outlier: 7.906A  pdb=" N   ALA D  21 " --> pdb=" O   VAL B  18 " (cutoff:3.500A)
      removed outlier: 6.272A  pdb=" N   PHE B  20 " --> pdb=" O   ALA D  21 " (cutoff:3.500A)
      removed outlier: 6.204A  pdb=" N   LYS D  16 " --> pdb=" O   LEU F  17 " (cutoff:3.500A)
      removed outlier: 7.602A  pdb=" N   PHE F  19 " --> pdb=" O   LYS D  16 " (cutoff:3.500A)
      removed outlier: 5.920A  pdb=" N   VAL D  18 " --> pdb=" O   PHE F  19 " (cutoff:3.500A)
      removed outlier: 7.684A  pdb=" N   ALA F  21 " --> pdb=" O   VAL D  18 " (cutoff:3.500A)
      removed outlier: 6.057A  pdb=" N   PHE D  20 " --> pdb=" O   ALA F  21 " (cutoff:3.500A)
      removed outlier: 6.422A  pdb=" N   LYS H  16 " --> pdb=" O   LEU J  17 " (cutoff:3.500A)
      removed outlier: 7.826A  pdb=" N   PHE J  19 " --> pdb=" O   LYS H  16 " (cutoff:3.500A)
      removed outlier: 6.134A  pdb=" N   VAL H  18 " --> pdb=" O   PHE J  19 " (cutoff:3.500A)
      removed outlier: 7.908A  pdb=" N   ALA J  21 " --> pdb=" O   VAL H  18 " (cutoff:3.500A)
      removed outlier: 6.271A  pdb=" N   PHE H  20 " --> pdb=" O   ALA J  21 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 31 through 36
      removed outlier: 6.656A  pdb=" N   LEU B  34 " --> pdb=" O   GLY D  33 " (cutoff:3.500A)
      removed outlier: 6.789A  pdb=" N   MET D  35 " --> pdb=" O   LEU B  34 " (cutoff:3.500A)
      removed outlier: 6.806A  pdb=" N   VAL B  36 " --> pdb=" O   MET D  35 " (cutoff:3.500A)
      removed outlier: 6.779A  pdb=" N   GLY D  37 " --> pdb=" O   VAL B  36 " (cutoff:3.500A)
      removed outlier: 8.820A  pdb=" N   ILE D  31 " --> pdb=" O   ILE F  32 " (cutoff:3.500A)
      removed outlier: 9.411A  pdb=" N   LEU F  34 " --> pdb=" O   ILE D  31 " (cutoff:3.500A)
      removed outlier: 6.280A  pdb=" N   GLY D  33 " --> pdb=" O   LEU F  34 " (cutoff:3.500A)
      removed outlier: 8.124A  pdb=" N   VAL F  36 " --> pdb=" O   GLY D  33 " (cutoff:3.500A)
      removed outlier: 5.981A  pdb=" N   MET D  35 " --> pdb=" O   VAL F  36 " (cutoff:3.500A)
      removed outlier: 6.578A  pdb=" N   LEU F  34 " --> pdb=" O   GLY H  33 " (cutoff:3.500A)
      removed outlier: 6.795A  pdb=" N   MET H  35 " --> pdb=" O   LEU F  34 " (cutoff:3.500A)
      removed outlier: 6.729A  pdb=" N   VAL F  36 " --> pdb=" O   MET H  35 " (cutoff:3.500A)
      removed outlier: 6.594A  pdb=" N   LEU H  34 " --> pdb=" O   GLY J  33 " (cutoff:3.500A)
      removed outlier: 6.725A  pdb=" N   MET J  35 " --> pdb=" O   LEU H  34 " (cutoff:3.500A)
      removed outlier: 6.747A  pdb=" N   VAL H  36 " --> pdb=" O   MET J  35 " (cutoff:3.500A)

    38 hydrogen bonds defined for protein.
    114 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.44

  Time building geometry restraints manager: 0.33 seconds

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

  Histogram of bond lengths:
        1.19 -     1.31: 550
        1.31 -     1.43: 850
        1.43 -     1.56: 1700
        1.56 -     1.68: 0
        1.68 -     1.80: 20
  Bond restraints: 3120
  Sorted by residual:
  bond pdb=" C   ILE E  31 "
       pdb=" O   ILE E  31 "
    ideal  model  delta    sigma   weight residual
    1.237  1.194  0.043 1.07e-02 8.73e+03 1.59e+01
  bond pdb=" C   ILE H  31 "
       pdb=" O   ILE H  31 "
    ideal  model  delta    sigma   weight residual
    1.237  1.194  0.043 1.07e-02 8.73e+03 1.58e+01
  bond pdb=" C   ILE D  31 "
       pdb=" O   ILE D  31 "
    ideal  model  delta    sigma   weight residual
    1.237  1.194  0.043 1.07e-02 8.73e+03 1.58e+01
  bond pdb=" C   ILE B  31 "
       pdb=" O   ILE B  31 "
    ideal  model  delta    sigma   weight residual
    1.237  1.195  0.042 1.07e-02 8.73e+03 1.53e+01
  bond pdb=" C   ILE F  31 "
       pdb=" O   ILE F  31 "
    ideal  model  delta    sigma   weight residual
    1.237  1.195  0.042 1.07e-02 8.73e+03 1.53e+01
  ... (remaining 3115 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.90: 3020
        1.90 -     3.80: 870
        3.80 -     5.70: 190
        5.70 -     7.60: 70
        7.60 -     9.50: 40
  Bond angle restraints: 4190
  Sorted by residual:
  angle pdb=" N   ALA E  30 "
        pdb=" CA  ALA E  30 "
        pdb=" C   ALA E  30 "
      ideal   model   delta    sigma   weight residual
     110.28  119.29   -9.01 1.48e+00 4.57e-01 3.71e+01
  angle pdb=" N   ALA H  30 "
        pdb=" CA  ALA H  30 "
        pdb=" C   ALA H  30 "
      ideal   model   delta    sigma   weight residual
     110.28  119.27   -8.99 1.48e+00 4.57e-01 3.69e+01
  angle pdb=" N   ALA B  30 "
        pdb=" CA  ALA B  30 "
        pdb=" C   ALA B  30 "
      ideal   model   delta    sigma   weight residual
     110.28  119.27   -8.99 1.48e+00 4.57e-01 3.69e+01
  angle pdb=" N   ALA A  30 "
        pdb=" CA  ALA A  30 "
        pdb=" C   ALA A  30 "
      ideal   model   delta    sigma   weight residual
     110.28  119.27   -8.99 1.48e+00 4.57e-01 3.69e+01
  angle pdb=" N   ALA I  30 "
        pdb=" CA  ALA I  30 "
        pdb=" C   ALA I  30 "
      ideal   model   delta    sigma   weight residual
     110.28  119.26   -8.98 1.48e+00 4.57e-01 3.68e+01
  ... (remaining 4185 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -     9.53: 1400
        9.53 -    19.05: 150
       19.05 -    28.57: 110
       28.57 -    38.10: 60
       38.10 -    47.62: 30
  Dihedral angle restraints: 1750
    sinusoidal: 670
      harmonic: 1080
  Sorted by residual:
  dihedral pdb=" C   GLN C  15 "
           pdb=" N   GLN C  15 "
           pdb=" CA  GLN C  15 "
           pdb=" CB  GLN C  15 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -116.05   -6.55     0      2.50e+00 1.60e-01 6.87e+00
  dihedral pdb=" C   GLN E  15 "
           pdb=" N   GLN E  15 "
           pdb=" CA  GLN E  15 "
           pdb=" CB  GLN E  15 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -116.09   -6.51     0      2.50e+00 1.60e-01 6.79e+00
  dihedral pdb=" C   GLN J  15 "
           pdb=" N   GLN J  15 "
           pdb=" CA  GLN J  15 "
           pdb=" CB  GLN J  15 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -116.09   -6.51     0      2.50e+00 1.60e-01 6.77e+00
  ... (remaining 1747 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.046: 112
       0.046 -    0.092: 175
       0.092 -    0.138: 73
       0.138 -    0.184: 43
       0.184 -    0.230: 37
  Chirality restraints: 440
  Sorted by residual:
  chirality pdb=" CG  LEU E  34 "
            pdb=" CB  LEU E  34 "
            pdb=" CD1 LEU E  34 "
            pdb=" CD2 LEU E  34 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.82    0.23 2.00e-01 2.50e+01 1.33e+00
  chirality pdb=" CG  LEU H  34 "
            pdb=" CB  LEU H  34 "
            pdb=" CD1 LEU H  34 "
            pdb=" CD2 LEU H  34 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.82    0.23 2.00e-01 2.50e+01 1.30e+00
  chirality pdb=" CA  HIS J  14 "
            pdb=" N   HIS J  14 "
            pdb=" C   HIS J  14 "
            pdb=" CB  HIS J  14 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.28e+00
  ... (remaining 437 not shown)

  Planarity restraints: 560
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER G  26 "    0.013 2.00e-02 2.50e+03   2.66e-02 7.07e+00
        pdb=" C   SER G  26 "   -0.046 2.00e-02 2.50e+03
        pdb=" O   SER G  26 "    0.017 2.00e-02 2.50e+03
        pdb=" N   ASN G  27 "    0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER I  26 "    0.013 2.00e-02 2.50e+03   2.66e-02 7.05e+00
        pdb=" C   SER I  26 "   -0.046 2.00e-02 2.50e+03
        pdb=" O   SER I  26 "    0.017 2.00e-02 2.50e+03
        pdb=" N   ASN I  27 "    0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER H  26 "   -0.013 2.00e-02 2.50e+03   2.65e-02 7.05e+00
        pdb=" C   SER H  26 "    0.046 2.00e-02 2.50e+03
        pdb=" O   SER H  26 "   -0.017 2.00e-02 2.50e+03
        pdb=" N   ASN H  27 "   -0.016 2.00e-02 2.50e+03
  ... (remaining 557 not shown)

  Histogram of nonbonded interaction distances:
        2.61 -     3.07: 2154
        3.07 -     3.53: 3198
        3.53 -     3.99: 5013
        3.99 -     4.44: 6029
        4.44 -     4.90: 10753
  Nonbonded interactions: 27147
  Sorted by model distance:
  nonbonded pdb=" O   HIS D   6 "
            pdb=" N   ASP F   7 "
     model   vdw
     2.614 3.120
  nonbonded pdb=" N   MET H  35 "
            pdb=" O   MET H  35 "
     model   vdw
     2.624 2.496
  nonbonded pdb=" N   MET D  35 "
            pdb=" O   MET D  35 "
     model   vdw
     2.624 2.496
  nonbonded pdb=" N   MET I  35 "
            pdb=" O   MET I  35 "
     model   vdw
     2.624 2.496
  nonbonded pdb=" N   MET E  35 "
            pdb=" O   MET E  35 "
     model   vdw
     2.624 2.496
  ... (remaining 27142 not shown)

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

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.360
  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:          0.080
  Check model and map are aligned:         0.010
  Set scattering table:                    0.000
  Process input model:                     4.870
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:8.790
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.140
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7983
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      :  0.014   0.046   3120  Z= 1.052
  Angle     :  2.086   9.497   4190  Z= 1.447
  Chirality :  0.101   0.230    440
  Planarity :  0.007   0.027    560
  Dihedral  : 14.886  47.624   1070
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 6.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.26 %
    Favored  : 94.74 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.45 %
    Favored  : 93.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.07 (0.39), residues: 380
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop :  0.83 (0.30), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG C   5 
 TYR   0.002   0.001   TYR D  10 
 PHE   0.018   0.004   PHE F  19 
 HIS   0.002   0.001   HIS J  14 

Details of bonding type rmsd
  covalent geometry    : bond        0.01413 ( 3120)
  covalent geometry    : angle       2.08605 ( 4190)
  hydrogen bonds       : bond        0.04912 (   38)
  hydrogen bonds       : angle       5.11506 (  114)

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

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

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 119
  time to evaluate  : 0.124 
Fit side-chains
REVERT: A    5 ARG cc_start: 0.7544 (mtp180) cc_final: 0.7116 (ppt170)
REVERT: B    5 ARG cc_start: 0.7439 (mtp180) cc_final: 0.6970 (ppt90)
REVERT: B   20 PHE cc_start: 0.7791 (t80) cc_final: 0.7573 (t80)
REVERT: E   35 MET cc_start: 0.8745 (mtp) cc_final: 0.8463 (mtp)
REVERT: F    5 ARG cc_start: 0.7297 (mtp180) cc_final: 0.6710 (ttt180)
REVERT: H   20 PHE cc_start: 0.7676 (t80) cc_final: 0.7454 (t80)
REVERT: I    5 ARG cc_start: 0.7220 (mtp180) cc_final: 0.6682 (tpm170)
REVERT: J    5 ARG cc_start: 0.7176 (mtp180) cc_final: 0.6690 (tpm170)
REVERT: J   20 PHE cc_start: 0.7939 (t80) cc_final: 0.7680 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 119
  average time/residue: 0.5316
  time to fit residues: 64.7520
Evaluate side-chains
  88 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 88
  time to evaluate  : 0.073 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 24 optimal weight:    4.9990
   chunk 26 optimal weight:    2.9990
   chunk 2 optimal weight:    1.9990
   chunk 16 optimal weight:   10.0000
   chunk 32 optimal weight:   10.0000
   chunk 31 optimal weight:    0.7980
   chunk 25 optimal weight:    1.9990
   chunk 19 optimal weight:    0.5980
   chunk 30 optimal weight:    2.9990
   chunk 22 optimal weight:    0.9980
   chunk 37 optimal weight:    0.9980
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
A  15 GLN
D  15 GLN
G  15 GLN
H  15 GLN
I  15 GLN
J  15 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4479 r_free = 0.4479 target = 0.154790 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4053 r_free = 0.4053 target = 0.125384 restraints weight = 3555.967|
|-----------------------------------------------------------------------------|
r_work (start): 0.4051 rms_B_bonded: 2.23
r_work: 0.3916 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.3787 rms_B_bonded: 4.05 restraints_weight: 0.2500
r_work (final): 0.3787
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8245
moved from start:          0.3131

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.017   3120  Z= 0.122
  Angle     :  0.466   3.918   4190  Z= 0.274
  Chirality :  0.051   0.129    440
  Planarity :  0.003   0.034    560
  Dihedral  :  6.235  23.431    420
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 6.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  5.81 %
    Allowed  : 18.39 %
    Favored  : 75.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.48 (0.37), residues: 380
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -0.36 (0.28), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG G   5 
 TYR   0.004   0.001   TYR E  10 
 PHE   0.012   0.001   PHE F  20 
 HIS   0.002   0.001   HIS A   6 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 ( 3120)
  covalent geometry    : angle       0.46631 ( 4190)
  hydrogen bonds       : bond        0.01985 (   38)
  hydrogen bonds       : angle       4.80452 (  114)

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

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

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 87
  time to evaluate  : 0.077 
Fit side-chains
   revert: symmetry clash
REVERT: A    5 ARG cc_start: 0.7742 (mtp180) cc_final: 0.6838 (ppt170)
REVERT: A   20 PHE cc_start: 0.8320 (t80) cc_final: 0.7917 (t80)
REVERT: B    5 ARG cc_start: 0.7756 (mtp180) cc_final: 0.6639 (ppt90)
REVERT: B   20 PHE cc_start: 0.8325 (t80) cc_final: 0.8061 (t80)
REVERT: C    5 ARG cc_start: 0.7460 (mtp85) cc_final: 0.6270 (ttt90)
REVERT: D    5 ARG cc_start: 0.7539 (mtp-110) cc_final: 0.7101 (ttp-110)
REVERT: D   20 PHE cc_start: 0.8299 (t80) cc_final: 0.8061 (t80)
REVERT: F    5 ARG cc_start: 0.6976 (mtp180) cc_final: 0.6473 (ttt-90)
REVERT: F   28 LYS cc_start: 0.8353 (mttt) cc_final: 0.8062 (mttp)
REVERT: G    5 ARG cc_start: 0.7344 (mtp85) cc_final: 0.6412 (ttt90)
REVERT: G   28 LYS cc_start: 0.8679 (mttt) cc_final: 0.8461 (mttm)
REVERT: H    5 ARG cc_start: 0.7692 (mtp85) cc_final: 0.6675 (ttt90)
REVERT: I    5 ARG cc_start: 0.7405 (mtp180) cc_final: 0.6938 (tpm170)
REVERT: J    5 ARG cc_start: 0.7222 (mtp180) cc_final: 0.6601 (tpm170)
REVERT: J    7 ASP cc_start: 0.8501 (m-30) cc_final: 0.8032 (m-30)
  outliers start: 18
  outliers final: 6
  residues processed: 96
  average time/residue: 0.4156
  time to fit residues: 40.7805
Evaluate side-chains
  90 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 84
  time to evaluate  : 0.071 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   34 LEU
Chi-restraints excluded: chain C residue   22 GLU
Chi-restraints excluded: chain C residue   34 LEU
Chi-restraints excluded: chain C residue   36 VAL
Chi-restraints excluded: chain F residue   22 GLU
Chi-restraints excluded: chain G residue   22 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 7 optimal weight:    9.9990
   chunk 22 optimal weight:    9.9990
   chunk 32 optimal weight:    9.9990
   chunk 34 optimal weight:    9.9990
   chunk 4 optimal weight:   20.0000
   chunk 0 optimal weight:   20.0000
   chunk 2 optimal weight:    8.9990
   chunk 38 optimal weight:    0.0980
   chunk 8 optimal weight:    9.9990
   chunk 26 optimal weight:    3.9990
   chunk 24 optimal weight:   10.0000
   overall best weight:    6.6188

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

Flipped N/Q/H residues before XYZ refinement:
A  15 GLN
B  15 GLN
D  15 GLN
I  15 GLN
J  15 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4115 r_free = 0.4115 target = 0.128698 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.099990 restraints weight = 3869.183|
|-----------------------------------------------------------------------------|
r_work (start): 0.3683 rms_B_bonded: 2.17
r_work: 0.3519 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.3388 rms_B_bonded: 3.72 restraints_weight: 0.2500
r_work (final): 0.3388
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8601
moved from start:          0.4235

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.047   3120  Z= 0.425
  Angle     :  0.612   6.359   4190  Z= 0.337
  Chirality :  0.055   0.155    440
  Planarity :  0.003   0.021    560
  Dihedral  :  6.367  26.268    420
  Min Nonbonded Distance : 2.611

Molprobity Statistics.
  All-atom Clashscore : 6.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  4.52 %
    Allowed  : 20.97 %
    Favored  : 74.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.53 (0.34), residues: 380
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.16 (0.26), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG G   5 
 TYR   0.005   0.001   TYR A  10 
 PHE   0.015   0.002   PHE G  20 
 HIS   0.005   0.002   HIS D  13 

Details of bonding type rmsd
  covalent geometry    : bond        0.00945 ( 3120)
  covalent geometry    : angle       0.61165 ( 4190)
  hydrogen bonds       : bond        0.04043 (   38)
  hydrogen bonds       : angle       4.70544 (  114)

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

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

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 86
  time to evaluate  : 0.123 
Fit side-chains
REVERT: A   22 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.8264 (tt0)
REVERT: A   28 LYS cc_start: 0.8946 (mttt) cc_final: 0.8713 (mttp)
REVERT: B    5 ARG cc_start: 0.7747 (mtp180) cc_final: 0.6533 (ppt90)
REVERT: C    5 ARG cc_start: 0.7669 (mtp85) cc_final: 0.6812 (ttt90)
REVERT: D   28 LYS cc_start: 0.8846 (mttt) cc_final: 0.8585 (mttp)
REVERT: E    5 ARG cc_start: 0.7531 (mtp180) cc_final: 0.6297 (ttt-90)
REVERT: E   16 LYS cc_start: 0.8744 (ttpt) cc_final: 0.8507 (ttpt)
REVERT: F    5 ARG cc_start: 0.7249 (mtp180) cc_final: 0.6800 (ttt-90)
REVERT: F   16 LYS cc_start: 0.8709 (ttpt) cc_final: 0.8456 (ttpt)
REVERT: G    5 ARG cc_start: 0.7701 (mtp85) cc_final: 0.6803 (ttt90)
REVERT: H    5 ARG cc_start: 0.7707 (mtp85) cc_final: 0.6630 (ttt90)
REVERT: H   20 PHE cc_start: 0.8560 (t80) cc_final: 0.8343 (t80)
REVERT: H   28 LYS cc_start: 0.9011 (mttt) cc_final: 0.8743 (mttm)
REVERT: I    5 ARG cc_start: 0.7567 (mtp180) cc_final: 0.6954 (tpm170)
REVERT: J    5 ARG cc_start: 0.7357 (mtp180) cc_final: 0.6775 (tpm170)
  outliers start: 14
  outliers final: 2
  residues processed: 94
  average time/residue: 0.6416
  time to fit residues: 61.4099
Evaluate side-chains
  85 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 82
  time to evaluate  : 0.071 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 GLU
Chi-restraints excluded: chain D residue    8 SER
Chi-restraints excluded: chain J residue   15 GLN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 7 optimal weight:    4.9990
   chunk 26 optimal weight:    1.9990
   chunk 13 optimal weight:    2.9990
   chunk 21 optimal weight:    2.9990
   chunk 5 optimal weight:    2.9990
   chunk 6 optimal weight:    1.9990
   chunk 8 optimal weight:   10.0000
   chunk 17 optimal weight:    0.9990
   chunk 15 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9990
   chunk 24 optimal weight:    0.0980
   overall best weight:    1.2188

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

Flipped N/Q/H residues before XYZ refinement:
A  15 GLN
I  15 GLN
J  15 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4242 r_free = 0.4242 target = 0.137300 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.108901 restraints weight = 3753.284|
|-----------------------------------------------------------------------------|
r_work (start): 0.3836 rms_B_bonded: 2.18
r_work: 0.3689 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.3557 rms_B_bonded: 3.88 restraints_weight: 0.2500
r_work (final): 0.3557
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8490
moved from start:          0.4401

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.016   3120  Z= 0.113
  Angle     :  0.408   3.680   4190  Z= 0.226
  Chirality :  0.049   0.129    440
  Planarity :  0.002   0.019    560
  Dihedral  :  5.226  23.951    420
  Min Nonbonded Distance : 2.670

Molprobity Statistics.
  All-atom Clashscore : 6.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 25.81 %
    Favored  : 72.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.77 (0.34), residues: 380
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.34 (0.26), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG D   5 
 TYR   0.010   0.001   TYR H  10 
 PHE   0.007   0.001   PHE F  20 
 HIS   0.002   0.000   HIS A  13 

Details of bonding type rmsd
  covalent geometry    : bond        0.00243 ( 3120)
  covalent geometry    : angle       0.40793 ( 4190)
  hydrogen bonds       : bond        0.02091 (   38)
  hydrogen bonds       : angle       4.54392 (  114)

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

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

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 85
  time to evaluate  : 0.121 
Fit side-chains
REVERT: A   22 GLU cc_start: 0.8541 (OUTLIER) cc_final: 0.8198 (tt0)
REVERT: B    5 ARG cc_start: 0.7869 (mtp180) cc_final: 0.6559 (pmt170)
REVERT: C    5 ARG cc_start: 0.7656 (mtp85) cc_final: 0.7040 (ttt90)
REVERT: D    5 ARG cc_start: 0.7677 (mtp85) cc_final: 0.6555 (ttt90)
REVERT: D   28 LYS cc_start: 0.8797 (mttt) cc_final: 0.8549 (mttp)
REVERT: E    5 ARG cc_start: 0.7535 (mtp180) cc_final: 0.6539 (ttt-90)
REVERT: E   16 LYS cc_start: 0.8739 (ttpt) cc_final: 0.8431 (ttpt)
REVERT: E   28 LYS cc_start: 0.9070 (mttp) cc_final: 0.8781 (mttp)
REVERT: F    5 ARG cc_start: 0.7163 (mtp180) cc_final: 0.6406 (ttt-90)
REVERT: F   16 LYS cc_start: 0.8564 (ttpt) cc_final: 0.8318 (ttpt)
REVERT: G    5 ARG cc_start: 0.7757 (mtp85) cc_final: 0.6892 (ttt90)
REVERT: G    7 ASP cc_start: 0.8451 (m-30) cc_final: 0.7890 (m-30)
REVERT: H    5 ARG cc_start: 0.7663 (mtp85) cc_final: 0.6819 (ttt90)
REVERT: H   20 PHE cc_start: 0.8440 (t80) cc_final: 0.8202 (t80)
REVERT: H   28 LYS cc_start: 0.8966 (mttt) cc_final: 0.8678 (mttm)
REVERT: I    5 ARG cc_start: 0.7501 (mtp180) cc_final: 0.6906 (tpm170)
REVERT: I   28 LYS cc_start: 0.8976 (mttt) cc_final: 0.8680 (mttp)
REVERT: J    5 ARG cc_start: 0.7396 (mtp180) cc_final: 0.6913 (tpm170)
REVERT: J    7 ASP cc_start: 0.8367 (m-30) cc_final: 0.7849 (m-30)
  outliers start: 6
  outliers final: 1
  residues processed: 90
  average time/residue: 0.5619
  time to fit residues: 51.6326
Evaluate side-chains
  83 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 81
  time to evaluate  : 0.077 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 GLU
Chi-restraints excluded: chain B residue   34 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 10 optimal weight:   10.0000
   chunk 39 optimal weight:    1.9990
   chunk 26 optimal weight:    6.9990
   chunk 23 optimal weight:    0.7980
   chunk 27 optimal weight:    0.9980
   chunk 18 optimal weight:    0.9980
   chunk 13 optimal weight:    0.9990
   chunk 25 optimal weight:    6.9990
   chunk 37 optimal weight:    3.9990
   chunk 32 optimal weight:    8.9990
   chunk 14 optimal weight:    9.9990
   overall best weight:    1.1584

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

Flipped N/Q/H residues before XYZ refinement:
A  15 GLN
I  15 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4312 r_free = 0.4312 target = 0.140655 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.110855 restraints weight = 3442.524|
|-----------------------------------------------------------------------------|
r_work (start): 0.3862 rms_B_bonded: 2.18
r_work: 0.3712 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.3575 rms_B_bonded: 3.84 restraints_weight: 0.2500
r_work (final): 0.3575
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8404
moved from start:          0.4613

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.015   3120  Z= 0.104
  Angle     :  0.377   3.418   4190  Z= 0.210
  Chirality :  0.049   0.126    440
  Planarity :  0.002   0.021    560
  Dihedral  :  4.837  25.384    420
  Min Nonbonded Distance : 2.675

Molprobity Statistics.
  All-atom Clashscore : 4.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 26.77 %
    Favored  : 71.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.94 (0.35), residues: 380
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.47 (0.27), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG D   5 
 TYR   0.007   0.001   TYR H  10 
 PHE   0.006   0.001   PHE F  20 
 HIS   0.002   0.000   HIS A  13 

Details of bonding type rmsd
  covalent geometry    : bond        0.00223 ( 3120)
  covalent geometry    : angle       0.37738 ( 4190)
  hydrogen bonds       : bond        0.01905 (   38)
  hydrogen bonds       : angle       4.45925 (  114)

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

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

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 77
  time to evaluate  : 0.075 
Fit side-chains
REVERT: B    5 ARG cc_start: 0.7774 (mtp180) cc_final: 0.6468 (pmt170)
REVERT: C    5 ARG cc_start: 0.7592 (mtp85) cc_final: 0.7059 (ttt90)
REVERT: D    5 ARG cc_start: 0.7625 (mtp85) cc_final: 0.6624 (ttt90)
REVERT: E    5 ARG cc_start: 0.7513 (mtp180) cc_final: 0.6587 (ttt-90)
REVERT: E   16 LYS cc_start: 0.8735 (ttpt) cc_final: 0.8435 (ttpt)
REVERT: E   28 LYS cc_start: 0.9145 (mttp) cc_final: 0.8828 (mttp)
REVERT: F    5 ARG cc_start: 0.6991 (mtp180) cc_final: 0.6479 (ttt-90)
REVERT: F   16 LYS cc_start: 0.8555 (ttpt) cc_final: 0.8325 (ttpt)
REVERT: G    5 ARG cc_start: 0.7737 (mtp85) cc_final: 0.6984 (ttt90)
REVERT: G    7 ASP cc_start: 0.8463 (m-30) cc_final: 0.7719 (m-30)
REVERT: H    5 ARG cc_start: 0.7633 (mtp85) cc_final: 0.6887 (ttt90)
REVERT: H   16 LYS cc_start: 0.8375 (ttmt) cc_final: 0.7920 (tttt)
REVERT: H   20 PHE cc_start: 0.8348 (t80) cc_final: 0.8096 (t80)
REVERT: H   28 LYS cc_start: 0.8851 (mttt) cc_final: 0.8505 (mttm)
REVERT: I    5 ARG cc_start: 0.7365 (mtp180) cc_final: 0.6811 (tpm170)
REVERT: I    7 ASP cc_start: 0.8366 (m-30) cc_final: 0.7863 (m-30)
REVERT: I   28 LYS cc_start: 0.9036 (mttt) cc_final: 0.8718 (mttp)
REVERT: J    5 ARG cc_start: 0.7433 (mtp180) cc_final: 0.6982 (tpm170)
REVERT: J    7 ASP cc_start: 0.8376 (m-30) cc_final: 0.8058 (m-30)
  outliers start: 4
  outliers final: 1
  residues processed: 80
  average time/residue: 0.5002
  time to fit residues: 40.9474
Evaluate side-chains
  77 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 76
  time to evaluate  : 0.113 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   34 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 17 optimal weight:   10.0000
   chunk 22 optimal weight:    7.9990
   chunk 21 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9980
   chunk 37 optimal weight:    0.9990
   chunk 26 optimal weight:   10.0000
   chunk 18 optimal weight:    2.9990
   chunk 20 optimal weight:   20.0000
   chunk 39 optimal weight:    2.9990
   chunk 1 optimal weight:    8.9990
   chunk 30 optimal weight:    1.9990
   overall best weight:    1.7988

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

Flipped N/Q/H residues before XYZ refinement:
A  15 GLN
I  15 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4262 r_free = 0.4262 target = 0.137043 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.106975 restraints weight = 3459.161|
|-----------------------------------------------------------------------------|
r_work (start): 0.3805 rms_B_bonded: 2.17
r_work: 0.3645 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.3504 rms_B_bonded: 3.81 restraints_weight: 0.2500
r_work (final): 0.3504
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8451
moved from start:          0.4652

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   3120  Z= 0.140
  Angle     :  0.397   4.122   4190  Z= 0.215
  Chirality :  0.049   0.129    440
  Planarity :  0.002   0.018    560
  Dihedral  :  4.820  25.848    420
  Min Nonbonded Distance : 2.671

Molprobity Statistics.
  All-atom Clashscore : 5.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 26.77 %
    Favored  : 71.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.05 (0.35), residues: 380
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.55 (0.27), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D   5 
 TYR   0.004   0.001   TYR E  10 
 PHE   0.006   0.001   PHE F  20 
 HIS   0.003   0.001   HIS A  13 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 ( 3120)
  covalent geometry    : angle       0.39748 ( 4190)
  hydrogen bonds       : bond        0.02332 (   38)
  hydrogen bonds       : angle       4.38641 (  114)

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

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

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 86
  time to evaluate  : 0.120 
Fit side-chains
REVERT: A   22 GLU cc_start: 0.8506 (OUTLIER) cc_final: 0.8185 (tt0)
REVERT: A   28 LYS cc_start: 0.8961 (mttt) cc_final: 0.8743 (mttp)
REVERT: B    5 ARG cc_start: 0.7772 (mtp180) cc_final: 0.6494 (pmt170)
REVERT: C    5 ARG cc_start: 0.7599 (mtp85) cc_final: 0.7086 (ttt90)
REVERT: D    5 ARG cc_start: 0.7692 (mtp85) cc_final: 0.6779 (ttt90)
REVERT: D   28 LYS cc_start: 0.8883 (mttt) cc_final: 0.8631 (mttp)
REVERT: E    5 ARG cc_start: 0.7553 (mtp180) cc_final: 0.6469 (ttt-90)
REVERT: E   16 LYS cc_start: 0.8659 (ttpt) cc_final: 0.8356 (ttpt)
REVERT: F    5 ARG cc_start: 0.6999 (mtp180) cc_final: 0.6407 (ttt-90)
REVERT: F   16 LYS cc_start: 0.8557 (ttpt) cc_final: 0.8329 (ttpt)
REVERT: G    5 ARG cc_start: 0.7750 (mtp85) cc_final: 0.7173 (ttt90)
REVERT: H    5 ARG cc_start: 0.7635 (mtp85) cc_final: 0.6906 (ttt90)
REVERT: H   16 LYS cc_start: 0.8321 (ttmt) cc_final: 0.7875 (tttt)
REVERT: H   20 PHE cc_start: 0.8374 (t80) cc_final: 0.8117 (t80)
REVERT: H   28 LYS cc_start: 0.9059 (mttt) cc_final: 0.8722 (mttm)
REVERT: I    5 ARG cc_start: 0.7349 (mtp180) cc_final: 0.6709 (tpm170)
REVERT: I   28 LYS cc_start: 0.9109 (mttt) cc_final: 0.8840 (mttp)
REVERT: J    5 ARG cc_start: 0.7370 (mtp180) cc_final: 0.6947 (tpm170)
REVERT: J    7 ASP cc_start: 0.8383 (m-30) cc_final: 0.8049 (m-30)
  outliers start: 6
  outliers final: 2
  residues processed: 91
  average time/residue: 0.5929
  time to fit residues: 55.0057
Evaluate side-chains
  85 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 82
  time to evaluate  : 0.072 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 GLU
Chi-restraints excluded: chain A residue   34 LEU
Chi-restraints excluded: chain B residue   34 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 13 optimal weight:    8.9990
   chunk 19 optimal weight:    6.9990
   chunk 1 optimal weight:   10.0000
   chunk 14 optimal weight:    6.9990
   chunk 10 optimal weight:   10.0000
   chunk 29 optimal weight:    8.9990
   chunk 22 optimal weight:    0.9980
   chunk 30 optimal weight:    7.9990
   chunk 25 optimal weight:   10.0000
   chunk 21 optimal weight:    4.9990
   chunk 6 optimal weight:    2.9990
   overall best weight:    4.5988

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

Flipped N/Q/H residues before XYZ refinement:
A  15 GLN
G  15 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4094 r_free = 0.4094 target = 0.127050 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.098299 restraints weight = 3792.319|
|-----------------------------------------------------------------------------|
r_work (start): 0.3653 rms_B_bonded: 2.12
r_work: 0.3495 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.3364 rms_B_bonded: 3.67 restraints_weight: 0.2500
r_work (final): 0.3364
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8618
moved from start:          0.4779

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.037   3120  Z= 0.309
  Angle     :  0.492   5.267   4190  Z= 0.260
  Chirality :  0.051   0.133    440
  Planarity :  0.002   0.015    560
  Dihedral  :  5.329  27.200    420
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 6.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.53 %
    Favored  : 99.47 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 26.13 %
    Favored  : 71.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.17 (0.35), residues: 380
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.64 (0.27), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D   5 
 TYR   0.005   0.001   TYR E  10 
 PHE   0.009   0.002   PHE F  19 
 HIS   0.004   0.001   HIS A  13 

Details of bonding type rmsd
  covalent geometry    : bond        0.00679 ( 3120)
  covalent geometry    : angle       0.49155 ( 4190)
  hydrogen bonds       : bond        0.03353 (   38)
  hydrogen bonds       : angle       4.48132 (  114)

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

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

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 85
  time to evaluate  : 0.075 
Fit side-chains
REVERT: A   22 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.8246 (tt0)
REVERT: B    5 ARG cc_start: 0.7691 (mtp180) cc_final: 0.6636 (ppt90)
REVERT: C    5 ARG cc_start: 0.7610 (mtp85) cc_final: 0.7168 (ttt90)
REVERT: D    5 ARG cc_start: 0.7673 (mtp85) cc_final: 0.6792 (ttt90)
REVERT: D   28 LYS cc_start: 0.9080 (mttt) cc_final: 0.8868 (mttp)
REVERT: E    5 ARG cc_start: 0.7607 (mtp180) cc_final: 0.6719 (ttt-90)
REVERT: E   16 LYS cc_start: 0.8739 (ttpt) cc_final: 0.8438 (ttpt)
REVERT: E   28 LYS cc_start: 0.9230 (mttp) cc_final: 0.8987 (mttp)
REVERT: F    5 ARG cc_start: 0.7211 (mtp180) cc_final: 0.6584 (ttt-90)
REVERT: F   16 LYS cc_start: 0.8610 (ttpt) cc_final: 0.8388 (ttpt)
REVERT: G    5 ARG cc_start: 0.7762 (mtp85) cc_final: 0.7126 (ttt90)
REVERT: G    7 ASP cc_start: 0.8457 (m-30) cc_final: 0.7543 (m-30)
REVERT: H    5 ARG cc_start: 0.7759 (mtp85) cc_final: 0.7057 (ttt90)
REVERT: H   16 LYS cc_start: 0.8453 (ttmt) cc_final: 0.8077 (tttt)
REVERT: H   20 PHE cc_start: 0.8471 (t80) cc_final: 0.8225 (t80)
REVERT: H   28 LYS cc_start: 0.9213 (mttt) cc_final: 0.8917 (mttm)
REVERT: I    5 ARG cc_start: 0.7458 (mtp180) cc_final: 0.6815 (tpm170)
REVERT: I   16 LYS cc_start: 0.8741 (ttpt) cc_final: 0.8472 (ttpt)
REVERT: J    5 ARG cc_start: 0.7399 (mtp180) cc_final: 0.6996 (tpm170)
  outliers start: 8
  outliers final: 1
  residues processed: 88
  average time/residue: 0.7845
  time to fit residues: 70.2760
Evaluate side-chains
  82 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 80
  time to evaluate  : 0.125 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 GLU
Chi-restraints excluded: chain F residue   22 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 12 optimal weight:    8.9990
   chunk 16 optimal weight:   20.0000
   chunk 15 optimal weight:    3.9990
   chunk 20 optimal weight:    4.9990
   chunk 37 optimal weight:    2.9990
   chunk 18 optimal weight:    9.9990
   chunk 13 optimal weight:    5.9990
   chunk 36 optimal weight:    9.9990
   chunk 6 optimal weight:    6.9990
   chunk 33 optimal weight:    2.9990
   chunk 34 optimal weight:    4.9990
   overall best weight:    3.9990

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

Flipped N/Q/H residues before XYZ refinement:
A  15 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4107 r_free = 0.4107 target = 0.127884 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.099366 restraints weight = 3764.654|
|-----------------------------------------------------------------------------|
r_work (start): 0.3666 rms_B_bonded: 2.08
r_work: 0.3512 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.3379 rms_B_bonded: 3.65 restraints_weight: 0.2500
r_work (final): 0.3379
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8618
moved from start:          0.4909

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.034   3120  Z= 0.273
  Angle     :  0.474   5.246   4190  Z= 0.251
  Chirality :  0.050   0.129    440
  Planarity :  0.002   0.011    560
  Dihedral  :  5.218  26.130    420
  Min Nonbonded Distance : 2.650

Molprobity Statistics.
  All-atom Clashscore : 6.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.32 %
    Favored  : 98.68 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 26.77 %
    Favored  : 71.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.23 (0.35), residues: 380
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.69 (0.27), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG D   5 
 TYR   0.007   0.001   TYR A  10 
 PHE   0.008   0.001   PHE D  19 
 HIS   0.004   0.001   HIS A  13 

Details of bonding type rmsd
  covalent geometry    : bond        0.00601 ( 3120)
  covalent geometry    : angle       0.47376 ( 4190)
  hydrogen bonds       : bond        0.03153 (   38)
  hydrogen bonds       : angle       4.47831 (  114)

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

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

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 83
  time to evaluate  : 0.146 
Fit side-chains
REVERT: B    5 ARG cc_start: 0.7690 (mtp180) cc_final: 0.6600 (ppt90)
REVERT: C    5 ARG cc_start: 0.7623 (mtp85) cc_final: 0.7202 (ttt90)
REVERT: D    5 ARG cc_start: 0.7697 (mtp85) cc_final: 0.6929 (ttt90)
REVERT: D   28 LYS cc_start: 0.9098 (mttt) cc_final: 0.8847 (mttp)
REVERT: E    5 ARG cc_start: 0.7584 (mtp180) cc_final: 0.6732 (ttt-90)
REVERT: E   16 LYS cc_start: 0.8714 (ttpt) cc_final: 0.8408 (ttpt)
REVERT: E   28 LYS cc_start: 0.9287 (mttp) cc_final: 0.9050 (mttp)
REVERT: F    5 ARG cc_start: 0.7180 (mtp180) cc_final: 0.6589 (ttt-90)
REVERT: F   16 LYS cc_start: 0.8624 (ttpt) cc_final: 0.8402 (ttpt)
REVERT: G    5 ARG cc_start: 0.7713 (mtp85) cc_final: 0.7122 (ttt90)
REVERT: G    7 ASP cc_start: 0.8428 (OUTLIER) cc_final: 0.7480 (m-30)
REVERT: H    5 ARG cc_start: 0.7868 (mtp85) cc_final: 0.7183 (ttt90)
REVERT: H   16 LYS cc_start: 0.8407 (ttmt) cc_final: 0.8014 (tttt)
REVERT: H   20 PHE cc_start: 0.8440 (t80) cc_final: 0.8205 (t80)
REVERT: H   28 LYS cc_start: 0.9247 (mttt) cc_final: 0.8956 (mttm)
REVERT: I    5 ARG cc_start: 0.7472 (mtp180) cc_final: 0.6890 (tpm170)
REVERT: I   16 LYS cc_start: 0.8731 (ttpt) cc_final: 0.8380 (ttpt)
REVERT: I   28 LYS cc_start: 0.9201 (mttt) cc_final: 0.8999 (mttp)
REVERT: J    5 ARG cc_start: 0.7396 (mtp180) cc_final: 0.7064 (tpm170)
  outliers start: 6
  outliers final: 2
  residues processed: 86
  average time/residue: 0.7679
  time to fit residues: 67.2951
Evaluate side-chains
  82 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 79
  time to evaluate  : 0.143 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   34 LEU
Chi-restraints excluded: chain F residue    8 SER
Chi-restraints excluded: chain G residue    7 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 33 optimal weight:    1.9990
   chunk 28 optimal weight:   20.0000
   chunk 21 optimal weight:    1.9990
   chunk 9 optimal weight:    8.9990
   chunk 14 optimal weight:   10.0000
   chunk 0 optimal weight:   10.0000
   chunk 38 optimal weight:    6.9990
   chunk 26 optimal weight:    9.9990
   chunk 31 optimal weight:    7.9990
   chunk 10 optimal weight:    6.9990
   chunk 29 optimal weight:    2.9990
   overall best weight:    4.1990

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

Flipped N/Q/H residues before XYZ refinement:
A  15 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4078 r_free = 0.4078 target = 0.125149 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.097293 restraints weight = 3910.615|
|-----------------------------------------------------------------------------|
r_work (start): 0.3645 rms_B_bonded: 2.10
r_work: 0.3485 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.3354 rms_B_bonded: 3.72 restraints_weight: 0.2500
r_work (final): 0.3354
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8636
moved from start:          0.5067

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.034   3120  Z= 0.286
  Angle     :  0.487   5.417   4190  Z= 0.257
  Chirality :  0.050   0.129    440
  Planarity :  0.002   0.010    560
  Dihedral  :  5.261  26.688    420
  Min Nonbonded Distance : 2.641

Molprobity Statistics.
  All-atom Clashscore : 6.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 27.42 %
    Favored  : 70.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.25 (0.35), residues: 380
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.71 (0.27), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG D   5 
 TYR   0.009   0.001   TYR A  10 
 PHE   0.009   0.001   PHE F  20 
 HIS   0.004   0.001   HIS A  13 

Details of bonding type rmsd
  covalent geometry    : bond        0.00629 ( 3120)
  covalent geometry    : angle       0.48671 ( 4190)
  hydrogen bonds       : bond        0.03244 (   38)
  hydrogen bonds       : angle       4.53862 (  114)

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

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

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 83
  time to evaluate  : 0.076 
Fit side-chains
REVERT: B    5 ARG cc_start: 0.7680 (mtp180) cc_final: 0.6623 (pmt170)
REVERT: C    5 ARG cc_start: 0.7595 (mtp85) cc_final: 0.7160 (ttt90)
REVERT: D    5 ARG cc_start: 0.7708 (mtp85) cc_final: 0.6917 (ttt90)
REVERT: E    5 ARG cc_start: 0.7625 (mtp180) cc_final: 0.6805 (ttt-90)
REVERT: E   16 LYS cc_start: 0.8739 (ttpt) cc_final: 0.8438 (ttpt)
REVERT: E   28 LYS cc_start: 0.9316 (mttp) cc_final: 0.9066 (mttp)
REVERT: F    5 ARG cc_start: 0.7175 (mtp180) cc_final: 0.6539 (ttt-90)
REVERT: F   16 LYS cc_start: 0.8652 (ttpt) cc_final: 0.8436 (ttpt)
REVERT: G    5 ARG cc_start: 0.7700 (mtp85) cc_final: 0.7148 (ttt90)
REVERT: G    7 ASP cc_start: 0.8442 (OUTLIER) cc_final: 0.7528 (m-30)
REVERT: H    5 ARG cc_start: 0.7829 (mtp85) cc_final: 0.7307 (ttt90)
REVERT: H   16 LYS cc_start: 0.8490 (ttmt) cc_final: 0.8125 (tttt)
REVERT: H   20 PHE cc_start: 0.8451 (t80) cc_final: 0.8239 (t80)
REVERT: H   28 LYS cc_start: 0.9244 (mttt) cc_final: 0.8958 (mttm)
REVERT: I    5 ARG cc_start: 0.7432 (mtp180) cc_final: 0.6888 (tpm170)
REVERT: I   16 LYS cc_start: 0.8756 (ttpt) cc_final: 0.8410 (ttpt)
REVERT: I   28 LYS cc_start: 0.9219 (mttt) cc_final: 0.8989 (mttp)
REVERT: J    5 ARG cc_start: 0.7391 (mtp180) cc_final: 0.6912 (tpm170)
  outliers start: 6
  outliers final: 2
  residues processed: 85
  average time/residue: 0.6899
  time to fit residues: 59.7241
Evaluate side-chains
  84 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 81
  time to evaluate  : 0.126 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   34 LEU
Chi-restraints excluded: chain F residue    8 SER
Chi-restraints excluded: chain G residue    7 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 2 optimal weight:    5.9990
   chunk 1 optimal weight:    4.9990
   chunk 6 optimal weight:    7.9990
   chunk 26 optimal weight:   10.0000
   chunk 9 optimal weight:    1.9990
   chunk 13 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   chunk 21 optimal weight:    1.9990
   chunk 15 optimal weight:    0.5980
   chunk 5 optimal weight:    2.9990
   chunk 37 optimal weight:    2.9990
   overall best weight:    1.9188

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

Flipped N/Q/H residues before XYZ refinement:
A  15 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4148 r_free = 0.4148 target = 0.130027 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.102570 restraints weight = 3796.245|
|-----------------------------------------------------------------------------|
r_work (start): 0.3736 rms_B_bonded: 2.13
r_work: 0.3573 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.3442 rms_B_bonded: 3.82 restraints_weight: 0.2500
r_work (final): 0.3442
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8556
moved from start:          0.5152

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   3120  Z= 0.149
  Angle     :  0.416   4.563   4190  Z= 0.223
  Chirality :  0.049   0.126    440
  Planarity :  0.001   0.013    560
  Dihedral  :  4.760  24.264    420
  Min Nonbonded Distance : 2.655

Molprobity Statistics.
  All-atom Clashscore : 5.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.53 %
    Favored  : 99.47 %
  Rotamer:
    Outliers :  0.97 %
    Allowed  : 28.39 %
    Favored  : 70.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.29 (0.35), residues: 380
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.73 (0.27), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG D   5 
 TYR   0.005   0.001   TYR A  10 
 PHE   0.010   0.001   PHE F  20 
 HIS   0.003   0.001   HIS A  13 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 ( 3120)
  covalent geometry    : angle       0.41554 ( 4190)
  hydrogen bonds       : bond        0.02362 (   38)
  hydrogen bonds       : angle       4.39129 (  114)

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

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

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  760 Ramachandran restraints generated.
    380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 87
  time to evaluate  : 0.128 
Fit side-chains
REVERT: B    5 ARG cc_start: 0.7790 (mtp180) cc_final: 0.6622 (ppt90)
REVERT: C    5 ARG cc_start: 0.7611 (mtp85) cc_final: 0.7244 (ttt90)
REVERT: D    5 ARG cc_start: 0.7746 (mtp85) cc_final: 0.6925 (ttt90)
REVERT: E    5 ARG cc_start: 0.7532 (mtp180) cc_final: 0.6764 (ttt-90)
REVERT: E   16 LYS cc_start: 0.8697 (ttpt) cc_final: 0.8378 (ttpt)
REVERT: E   28 LYS cc_start: 0.9301 (mttp) cc_final: 0.9072 (mttp)
REVERT: F    5 ARG cc_start: 0.7183 (mtp180) cc_final: 0.6341 (ttt90)
REVERT: G    5 ARG cc_start: 0.7624 (mtp85) cc_final: 0.7193 (ttt90)
REVERT: G    7 ASP cc_start: 0.8466 (m-30) cc_final: 0.7828 (m-30)
REVERT: H    5 ARG cc_start: 0.7776 (mtp85) cc_final: 0.7315 (ttt90)
REVERT: H   16 LYS cc_start: 0.8390 (ttmt) cc_final: 0.7993 (tttt)
REVERT: H   20 PHE cc_start: 0.8453 (t80) cc_final: 0.8245 (t80)
REVERT: H   28 LYS cc_start: 0.9297 (mttt) cc_final: 0.9025 (mttm)
REVERT: I    5 ARG cc_start: 0.7418 (mtp180) cc_final: 0.6842 (tpm170)
REVERT: I   28 LYS cc_start: 0.9214 (mttt) cc_final: 0.8999 (mttp)
REVERT: J    5 ARG cc_start: 0.7243 (mtp180) cc_final: 0.6894 (tpm170)
REVERT: J    7 ASP cc_start: 0.8264 (m-30) cc_final: 0.7935 (m-30)
  outliers start: 3
  outliers final: 2
  residues processed: 88
  average time/residue: 0.5516
  time to fit residues: 49.5417
Evaluate side-chains
  87 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 85
  time to evaluate  : 0.073 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   34 LEU
Chi-restraints excluded: chain F residue    8 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 34 optimal weight:    7.9990
   chunk 38 optimal weight:    7.9990
   chunk 39 optimal weight:    2.9990
   chunk 24 optimal weight:   20.0000
   chunk 19 optimal weight:    5.9990
   chunk 1 optimal weight:    0.0670
   chunk 26 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9990
   chunk 30 optimal weight:    3.9990
   chunk 13 optimal weight:    0.0980
   chunk 23 optimal weight:    4.9990
   overall best weight:    1.2324

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

Flipped N/Q/H residues before XYZ refinement:
A  15 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4174 r_free = 0.4174 target = 0.131662 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.103406 restraints weight = 3787.331|
|-----------------------------------------------------------------------------|
r_work (start): 0.3766 rms_B_bonded: 2.17
r_work: 0.3597 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.3467 rms_B_bonded: 3.89 restraints_weight: 0.2500
r_work (final): 0.3467
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8521
moved from start:          0.5151

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.015   3120  Z= 0.109
  Angle     :  0.400   4.135   4190  Z= 0.217
  Chirality :  0.049   0.125    440
  Planarity :  0.001   0.014    560
  Dihedral  :  4.527  24.622    420
  Min Nonbonded Distance : 2.653

Molprobity Statistics.
  All-atom Clashscore : 5.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.32 %
    Favored  : 98.68 %
  Rotamer:
    Outliers :  0.97 %
    Allowed  : 30.32 %
    Favored  : 68.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.31 (0.36), residues: 380
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.75 (0.27), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG D   5 
 TYR   0.004   0.001   TYR F  10 
 PHE   0.005   0.001   PHE C  20 
 HIS   0.002   0.000   HIS A  13 

Details of bonding type rmsd
  covalent geometry    : bond        0.00235 ( 3120)
  covalent geometry    : angle       0.39951 ( 4190)
  hydrogen bonds       : bond        0.01963 (   38)
  hydrogen bonds       : angle       4.32139 (  114)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1548.79 seconds
wall clock time: 27 minutes 3.36 seconds (1623.36 seconds total)