Starting phenix.real_space_refine
on Tue Feb  3 14:22:54 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9hx3_52456/02_2026/9hx3_52456.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9hx3_52456/02_2026/9hx3_52456.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9hx3_52456/02_2026/9hx3_52456.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9hx3_52456/02_2026/9hx3_52456.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9hx3_52456/02_2026/9hx3_52456.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9hx3_52456/02_2026/9hx3_52456.cif"
  }
  resolution = 3.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S       5      5.16       5
     C    2345      2.51       5
     N     600      2.21       5
     O     680      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.00s

  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: 3630
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 726
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 93, 726
          Classifications: {'peptide': 93}
          Link IDs: {'PTRANS': 4, 'TRANS': 88}
          Chain breaks: 1
  Restraints were copied for chains:
    C, B, E, D
  Time building chain proxies: 0.63, per 1000 atoms: 0.17
  Number of scatterers: 3630
  At special positions: 0
  Unit cell: (90.88, 71.68, 42.24, 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       5     16.00
     O     680      8.00
     N     600      7.00
     C    2345      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: 0.29
  Conformation dependent library (CDL) restraints added in 136.3 milliseconds
  

  890 Ramachandran restraints generated.
    445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  880

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 11 sheets defined
      0.0% alpha, 35.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.18
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 16
      removed outlier: 6.518A  pdb=" N   MET C  13 " --> pdb=" O   VAL B  14 " (cutoff:3.500A)
      removed outlier: 8.240A  pdb=" N   VAL B  16 " --> pdb=" O   MET C  13 " (cutoff:3.500A)
      removed outlier: 6.363A  pdb=" N   LYS C  15 " --> pdb=" O   VAL B  16 " (cutoff:3.500A)
      removed outlier: 6.504A  pdb=" N   MET E  13 " --> pdb=" O   VAL D  14 " (cutoff:3.500A)
      removed outlier: 8.236A  pdb=" N   VAL D  16 " --> pdb=" O   MET E  13 " (cutoff:3.500A)
      removed outlier: 6.349A  pdb=" N   LYS E  15 " --> pdb=" O   VAL D  16 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 19 through 21
      removed outlier: 6.508A  pdb=" N   VAL A  20 " --> pdb=" O   ARG B  21 " (cutoff:3.500A)
      removed outlier: 6.552A  pdb=" N   VAL C  20 " --> pdb=" O   ARG D  21 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 25 through 27
      removed outlier: 6.391A  pdb=" N   ALA C  25 " --> pdb=" O   ILE B  26 " (cutoff:3.500A)
      removed outlier: 6.334A  pdb=" N   ALA E  25 " --> pdb=" O   ILE D  26 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 30 through 33
      removed outlier: 6.284A  pdb=" N   VAL A  30 " --> pdb=" O   HIS B  31 " (cutoff:3.500A)
      removed outlier: 8.154A  pdb=" N   PHE B  33 " --> pdb=" O   VAL A  30 " (cutoff:3.500A)
      removed outlier: 6.481A  pdb=" N   VAL A  32 " --> pdb=" O   PHE B  33 " (cutoff:3.500A)
      removed outlier: 6.320A  pdb=" N   VAL C  30 " --> pdb=" O   HIS D  31 " (cutoff:3.500A)
      removed outlier: 8.179A  pdb=" N   PHE D  33 " --> pdb=" O   VAL C  30 " (cutoff:3.500A)
      removed outlier: 6.516A  pdb=" N   VAL C  32 " --> pdb=" O   PHE D  33 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 62 through 66
      removed outlier: 6.763A  pdb=" N   GLU B  63 " --> pdb=" O   GLU A  62 " (cutoff:3.500A)
      removed outlier: 6.800A  pdb=" N   GLU C  63 " --> pdb=" O   PHE B  64 " (cutoff:3.500A)
      removed outlier: 8.462A  pdb=" N   GLU B  66 " --> pdb=" O   GLU C  63 " (cutoff:3.500A)
      removed outlier: 6.227A  pdb=" N   VAL C  65 " --> pdb=" O   GLU B  66 " (cutoff:3.500A)
      removed outlier: 6.856A  pdb=" N   GLU D  63 " --> pdb=" O   GLU C  62 " (cutoff:3.500A)
      removed outlier: 6.771A  pdb=" N   GLU E  63 " --> pdb=" O   PHE D  64 " (cutoff:3.500A)
      removed outlier: 8.450A  pdb=" N   GLU D  66 " --> pdb=" O   GLU E  63 " (cutoff:3.500A)
      removed outlier: 6.206A  pdb=" N   VAL E  65 " --> pdb=" O   GLU D  66 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 71 through 73
      removed outlier: 6.294A  pdb=" N   GLU A  72 " --> pdb=" O   ILE B  73 " (cutoff:3.500A)
      removed outlier: 6.333A  pdb=" N   GLU C  72 " --> pdb=" O   ILE D  73 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 76 through 77
      removed outlier: 6.768A  pdb=" N   LYS C  76 " --> pdb=" O   SER B  77 " (cutoff:3.500A)
      removed outlier: 6.728A  pdb=" N   LYS E  76 " --> pdb=" O   SER D  77 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 92 through 98
      removed outlier: 6.526A  pdb=" N   GLU A  92 " --> pdb=" O   VAL B  93 " (cutoff:3.500A)
      removed outlier: 7.864A  pdb=" N   PHE B  95 " --> pdb=" O   GLU A  92 " (cutoff:3.500A)
      removed outlier: 6.166A  pdb=" N   VAL A  94 " --> pdb=" O   PHE B  95 " (cutoff:3.500A)
      removed outlier: 7.878A  pdb=" N   ALA B  97 " --> pdb=" O   VAL A  94 " (cutoff:3.500A)
      removed outlier: 6.949A  pdb=" N   THR A  96 " --> pdb=" O   ALA B  97 " (cutoff:3.500A)
      removed outlier: 6.586A  pdb=" N   GLU C  92 " --> pdb=" O   VAL D  93 " (cutoff:3.500A)
      removed outlier: 7.910A  pdb=" N   PHE D  95 " --> pdb=" O   GLU C  92 " (cutoff:3.500A)
      removed outlier: 6.219A  pdb=" N   VAL C  94 " --> pdb=" O   PHE D  95 " (cutoff:3.500A)
      removed outlier: 7.929A  pdb=" N   ALA D  97 " --> pdb=" O   VAL C  94 " (cutoff:3.500A)
      removed outlier: 7.008A  pdb=" N   THR C  96 " --> pdb=" O   ALA D  97 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 103 through 110
      removed outlier: 6.817A  pdb=" N   ALA B 109 " --> pdb=" O   ALA A 108 " (cutoff:3.500A)
      removed outlier: 6.778A  pdb=" N   LEU A 110 " --> pdb=" O   ALA B 109 " (cutoff:3.500A)
      removed outlier: 6.507A  pdb=" N   ARG C 103 " --> pdb=" O   ARG B 104 " (cutoff:3.500A)
      removed outlier: 7.797A  pdb=" N   THR B 106 " --> pdb=" O   ARG C 103 " (cutoff:3.500A)
      removed outlier: 6.365A  pdb=" N   TYR C 105 " --> pdb=" O   THR B 106 " (cutoff:3.500A)
      removed outlier: 8.010A  pdb=" N   ALA B 108 " --> pdb=" O   TYR C 105 " (cutoff:3.500A)
      removed outlier: 8.883A  pdb=" N   ILE C 107 " --> pdb=" O   ALA B 108 " (cutoff:3.500A)
      removed outlier: 6.442A  pdb=" N   LEU B 110 " --> pdb=" O   ILE C 107 " (cutoff:3.500A)
      removed outlier: 9.053A  pdb=" N   ALA C 109 " --> pdb=" O   LEU B 110 " (cutoff:3.500A)
      removed outlier: 6.914A  pdb=" N   ALA D 109 " --> pdb=" O   ALA C 108 " (cutoff:3.500A)
      removed outlier: 6.875A  pdb=" N   LEU C 110 " --> pdb=" O   ALA D 109 " (cutoff:3.500A)
      removed outlier: 6.476A  pdb=" N   ARG E 103 " --> pdb=" O   ARG D 104 " (cutoff:3.500A)
      removed outlier: 7.769A  pdb=" N   THR D 106 " --> pdb=" O   ARG E 103 " (cutoff:3.500A)
      removed outlier: 6.331A  pdb=" N   TYR E 105 " --> pdb=" O   THR D 106 " (cutoff:3.500A)
      removed outlier: 7.980A  pdb=" N   ALA D 108 " --> pdb=" O   TYR E 105 " (cutoff:3.500A)
      removed outlier: 8.815A  pdb=" N   ILE E 107 " --> pdb=" O   ALA D 108 " (cutoff:3.500A)
      removed outlier: 6.383A  pdb=" N   LEU D 110 " --> pdb=" O   ILE E 107 " (cutoff:3.500A)
      removed outlier: 8.975A  pdb=" N   ALA E 109 " --> pdb=" O   LEU D 110 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 114 through 115
      removed outlier: 6.971A  pdb=" N   TYR A 114 " --> pdb=" O   SER B 115 " (cutoff:3.500A)
      removed outlier: 7.028A  pdb=" N   TYR C 114 " --> pdb=" O   SER D 115 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 121 through 122
      removed outlier: 6.204A  pdb=" N   VAL A 121 " --> pdb=" O   VAL B 122 " (cutoff:3.500A)
      removed outlier: 6.239A  pdb=" N   VAL C 121 " --> pdb=" O   VAL D 122 " (cutoff:3.500A)

    60 hydrogen bonds defined for protein.
    180 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: 0.53

  Time building geometry restraints manager: 0.41 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1140
        1.34 -     1.46: 735
        1.46 -     1.57: 1830
        1.57 -     1.69: 0
        1.69 -     1.80: 10
  Bond restraints: 3715
  Sorted by residual:
  bond pdb=" C   LEU B  82 "
       pdb=" N   GLY B  83 "
    ideal  model  delta    sigma   weight residual
    1.331  1.319  0.012 1.46e-02 4.69e+03 6.22e-01
  bond pdb=" C   LEU E  82 "
       pdb=" N   GLY E  83 "
    ideal  model  delta    sigma   weight residual
    1.331  1.319  0.011 1.46e-02 4.69e+03 5.69e-01
  bond pdb=" CG  PRO E  24 "
       pdb=" CD  PRO E  24 "
    ideal  model  delta    sigma   weight residual
    1.503  1.478  0.025 3.40e-02 8.65e+02 5.53e-01
  bond pdb=" C   LEU C  82 "
       pdb=" N   GLY C  83 "
    ideal  model  delta    sigma   weight residual
    1.331  1.320  0.011 1.46e-02 4.69e+03 5.44e-01
  bond pdb=" C   LEU A  82 "
       pdb=" N   GLY A  83 "
    ideal  model  delta    sigma   weight residual
    1.331  1.320  0.011 1.46e-02 4.69e+03 5.22e-01
  ... (remaining 3710 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.83: 4418
        0.83 -     1.65: 522
        1.65 -     2.48: 96
        2.48 -     3.30: 9
        3.30 -     4.13: 10
  Bond angle restraints: 5055
  Sorted by residual:
  angle pdb=" N   PHE A  64 "
        pdb=" CA  PHE A  64 "
        pdb=" C   PHE A  64 "
      ideal   model   delta    sigma   weight residual
     109.07  111.71   -2.64 1.52e+00 4.33e-01 3.01e+00
  angle pdb=" N   PHE D  64 "
        pdb=" CA  PHE D  64 "
        pdb=" C   PHE D  64 "
      ideal   model   delta    sigma   weight residual
     109.07  111.70   -2.63 1.52e+00 4.33e-01 3.00e+00
  angle pdb=" N   PHE B  64 "
        pdb=" CA  PHE B  64 "
        pdb=" C   PHE B  64 "
      ideal   model   delta    sigma   weight residual
     109.07  111.68   -2.61 1.52e+00 4.33e-01 2.96e+00
  angle pdb=" N   PHE C  64 "
        pdb=" CA  PHE C  64 "
        pdb=" C   PHE C  64 "
      ideal   model   delta    sigma   weight residual
     109.07  111.67   -2.60 1.52e+00 4.33e-01 2.92e+00
  angle pdb=" N   PHE E  64 "
        pdb=" CA  PHE E  64 "
        pdb=" C   PHE E  64 "
      ideal   model   delta    sigma   weight residual
     109.07  111.66   -2.59 1.52e+00 4.33e-01 2.91e+00
  ... (remaining 5050 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    11.16: 1859
       11.16 -    22.32: 236
       22.32 -    33.48: 55
       33.48 -    44.64: 20
       44.64 -    55.80: 20
  Dihedral angle restraints: 2190
    sinusoidal: 830
      harmonic: 1360
  Sorted by residual:
  dihedral pdb=" CA  ILE D  26 "
           pdb=" C   ILE D  26 "
           pdb=" N   ASN D  27 "
           pdb=" CA  ASN D  27 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.91   19.09     0      5.00e+00 4.00e-02 1.46e+01
  dihedral pdb=" CA  ILE E  26 "
           pdb=" C   ILE E  26 "
           pdb=" N   ASN E  27 "
           pdb=" CA  ASN E  27 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.92   19.08     0      5.00e+00 4.00e-02 1.46e+01
  dihedral pdb=" CA  ILE A  26 "
           pdb=" C   ILE A  26 "
           pdb=" N   ASN A  27 "
           pdb=" CA  ASN A  27 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.93   19.07     0      5.00e+00 4.00e-02 1.46e+01
  ... (remaining 2187 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 298
       0.026 -    0.051: 184
       0.051 -    0.076: 29
       0.076 -    0.102: 41
       0.102 -    0.127: 43
  Chirality restraints: 595
  Sorted by residual:
  chirality pdb=" CA  VAL B  65 "
            pdb=" N   VAL B  65 "
            pdb=" C   VAL B  65 "
            pdb=" CB  VAL B  65 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.02e-01
  chirality pdb=" CA  VAL A  65 "
            pdb=" N   VAL A  65 "
            pdb=" C   VAL A  65 "
            pdb=" CB  VAL A  65 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 3.97e-01
  chirality pdb=" CA  VAL D  65 "
            pdb=" N   VAL D  65 "
            pdb=" C   VAL D  65 "
            pdb=" CB  VAL D  65 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.12 2.00e-01 2.50e+01 3.89e-01
  ... (remaining 592 not shown)

  Planarity restraints: 625
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER E  23 "    0.019 5.00e-02 4.00e+02   2.94e-02 1.38e+00
        pdb=" N   PRO E  24 "   -0.051 5.00e-02 4.00e+02
        pdb=" CA  PRO E  24 "    0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO E  24 "    0.016 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER C  23 "    0.019 5.00e-02 4.00e+02   2.94e-02 1.38e+00
        pdb=" N   PRO C  24 "   -0.051 5.00e-02 4.00e+02
        pdb=" CA  PRO C  24 "    0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO C  24 "    0.016 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER B  23 "    0.019 5.00e-02 4.00e+02   2.94e-02 1.38e+00
        pdb=" N   PRO B  24 "   -0.051 5.00e-02 4.00e+02
        pdb=" CA  PRO B  24 "    0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO B  24 "    0.016 5.00e-02 4.00e+02
  ... (remaining 622 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.76: 485
        2.76 -     3.30: 3510
        3.30 -     3.83: 6232
        3.83 -     4.37: 7344
        4.37 -     4.90: 14781
  Nonbonded interactions: 32352
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 105 "
            pdb=" OD2 ASP B  74 "
     model   vdw
     2.229 3.040
  nonbonded pdb=" OH  TYR C 105 "
            pdb=" OD2 ASP D  74 "
     model   vdw
     2.233 3.040
  nonbonded pdb=" OD2 ASP E  74 "
            pdb=" OH  TYR D 105 "
     model   vdw
     2.245 3.040
  nonbonded pdb=" OD2 ASP C  74 "
            pdb=" OH  TYR B 105 "
     model   vdw
     2.254 3.040
  nonbonded pdb=" O   SER A 100 "
            pdb=" OG  SER B 100 "
     model   vdw
     2.372 3.040
  ... (remaining 32347 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 'C'
  selection = chain 'B'
  selection = chain 'E'
  selection = chain 'D'
}

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:             0.560
  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:          0.050
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.420
  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:9.320
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.400
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8103
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      :  0.004   0.025   3715  Z= 0.167
  Angle     :  0.596   4.130   5055  Z= 0.355
  Chirality :  0.047   0.127    595
  Planarity :  0.004   0.029    625
  Dihedral  : 12.586  55.797   1310
  Min Nonbonded Distance : 2.229

Molprobity Statistics.
  All-atom Clashscore : 5.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.49 %
    Favored  : 95.51 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  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: -3.14 (0.28), residues: 445
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.38 (0.22), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 104 
 TYR   0.011   0.001   TYR D 114 
 PHE   0.006   0.001   PHE C  64 
 TRP   0.001   0.000   TRP B  79 
 HIS   0.002   0.001   HIS D  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00372 ( 3715)
  covalent geometry    : angle       0.59630 ( 5055)
  hydrogen bonds       : bond        0.15314 (   60)
  hydrogen bonds       : angle       8.30069 (  180)

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

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

  890 Ramachandran restraints generated.
    445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  890 Ramachandran restraints generated.
    445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 93
  time to evaluate  : 0.138 
Fit side-chains
REVERT: A   15 LYS cc_start: 0.8740 (mtpt) cc_final: 0.8351 (mtpm)
REVERT: A   21 ARG cc_start: 0.8554 (ttt180) cc_final: 0.7313 (pmt170)
REVERT: A   34 ARG cc_start: 0.7907 (mtp85) cc_final: 0.7045 (mmt-90)
REVERT: A  104 ARG cc_start: 0.7774 (mtt180) cc_final: 0.7259 (mmp-170)
REVERT: A  119 THR cc_start: 0.8880 (t) cc_final: 0.8664 (p)
REVERT: C   27 ASN cc_start: 0.8673 (m-40) cc_final: 0.8353 (m110)
REVERT: C   70 LYS cc_start: 0.9043 (tttt) cc_final: 0.8705 (tttt)
REVERT: C   78 TYR cc_start: 0.8970 (m-80) cc_final: 0.8739 (m-80)
REVERT: B   15 LYS cc_start: 0.8079 (mtpt) cc_final: 0.7713 (mtpp)
REVERT: B   23 SER cc_start: 0.9101 (p) cc_final: 0.8900 (m)
REVERT: B   80 LYS cc_start: 0.8562 (tttt) cc_final: 0.8147 (tttt)
REVERT: B   89 GLU cc_start: 0.8985 (mt-10) cc_final: 0.8757 (mt-10)
REVERT: E   89 GLU cc_start: 0.8951 (mt-10) cc_final: 0.8298 (pm20)
REVERT: E  104 ARG cc_start: 0.7910 (mtt180) cc_final: 0.7018 (ptt-90)
REVERT: D   13 MET cc_start: 0.7786 (ttm) cc_final: 0.7575 (tmm)
REVERT: D   15 LYS cc_start: 0.8368 (mtpt) cc_final: 0.8035 (mtpm)
REVERT: D   27 ASN cc_start: 0.8719 (m-40) cc_final: 0.8442 (m-40)
REVERT: D   60 THR cc_start: 0.8909 (m) cc_final: 0.8663 (m)
  outliers start: 0
  outliers final: 1
  residues processed: 93
  average time/residue: 0.6339
  time to fit residues: 60.2430
Evaluate side-chains
  63 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 62
  time to evaluate  : 0.119 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   35 LYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 24 optimal weight:   10.0000
   chunk 26 optimal weight:   10.0000
   chunk 2 optimal weight:    9.9990
   chunk 16 optimal weight:   10.0000
   chunk 32 optimal weight:    6.9990
   chunk 31 optimal weight:    8.9990
   chunk 25 optimal weight:    0.9990
   chunk 19 optimal weight:    8.9990
   chunk 30 optimal weight:    0.0370
   chunk 22 optimal weight:    8.9990
   chunk 37 optimal weight:    0.9980
   overall best weight:    3.6064

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

Flipped N/Q/H residues before XYZ refinement:
** A  31 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 = 0.3719 r_free = 0.3719 target = 0.107638 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.092018 restraints weight = 5573.441|
|-----------------------------------------------------------------------------|
r_work (start): 0.3500 rms_B_bonded: 2.87
r_work: 0.3357 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work: 0.3242 rms_B_bonded: 4.96 restraints_weight: 0.2500
r_work (final): 0.3242
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8096
moved from start:          0.2124

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046   3715  Z= 0.218
  Angle     :  0.611   4.647   5055  Z= 0.338
  Chirality :  0.052   0.136    595
  Planarity :  0.004   0.036    625
  Dihedral  :  6.114  43.105    504
  Min Nonbonded Distance : 2.617

Molprobity Statistics.
  All-atom Clashscore : 6.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 12.91 %
    Favored  : 85.06 %
  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 (0.33), residues: 445
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.69 (0.25), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG D 104 
 TYR   0.018   0.002   TYR B 114 
 PHE   0.017   0.002   PHE D  64 
 TRP   0.004   0.001   TRP D  79 
 HIS   0.004   0.001   HIS A  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00530 ( 3715)
  covalent geometry    : angle       0.61148 ( 5055)
  hydrogen bonds       : bond        0.02816 (   60)
  hydrogen bonds       : angle       5.97118 (  180)

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

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

  890 Ramachandran restraints generated.
    445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  890 Ramachandran restraints generated.
    445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 70
  time to evaluate  : 0.137 
Fit side-chains
REVERT: A   15 LYS cc_start: 0.8951 (mtpt) cc_final: 0.8580 (mtpp)
REVERT: A   21 ARG cc_start: 0.8863 (ttt180) cc_final: 0.6708 (pmt170)
REVERT: A   34 ARG cc_start: 0.8258 (mtp85) cc_final: 0.7100 (tpt170)
REVERT: A   72 GLU cc_start: 0.8970 (mt-10) cc_final: 0.8706 (mt-10)
REVERT: A  104 ARG cc_start: 0.8211 (mtt180) cc_final: 0.7119 (tpm170)
REVERT: C   34 ARG cc_start: 0.8407 (mtp-110) cc_final: 0.8147 (mtp85)
REVERT: C   35 LYS cc_start: 0.7936 (ttpp) cc_final: 0.7730 (ttpp)
REVERT: C   74 ASP cc_start: 0.9053 (t0) cc_final: 0.8793 (t0)
REVERT: C   78 TYR cc_start: 0.9045 (m-80) cc_final: 0.8768 (m-80)
REVERT: B   15 LYS cc_start: 0.8036 (mtpt) cc_final: 0.7596 (mtpp)
REVERT: B   80 LYS cc_start: 0.8471 (tttt) cc_final: 0.8045 (tttt)
REVERT: B   89 GLU cc_start: 0.8974 (mt-10) cc_final: 0.8712 (mt-10)
REVERT: E   76 LYS cc_start: 0.8890 (OUTLIER) cc_final: 0.8500 (mptt)
REVERT: E   89 GLU cc_start: 0.9125 (mt-10) cc_final: 0.8196 (pm20)
REVERT: E  104 ARG cc_start: 0.8536 (mtt180) cc_final: 0.6930 (ptt90)
REVERT: E  107 ILE cc_start: 0.9188 (mt) cc_final: 0.8933 (mt)
REVERT: D   13 MET cc_start: 0.7702 (ttm) cc_final: 0.7272 (tmm)
REVERT: D   15 LYS cc_start: 0.8148 (mtpt) cc_final: 0.7806 (mtpt)
REVERT: D   35 LYS cc_start: 0.8109 (ttpp) cc_final: 0.7852 (mtmt)
REVERT: D   60 THR cc_start: 0.8623 (m) cc_final: 0.8411 (m)
REVERT: D   92 GLU cc_start: 0.8298 (OUTLIER) cc_final: 0.8092 (mt-10)
  outliers start: 8
  outliers final: 2
  residues processed: 72
  average time/residue: 0.6985
  time to fit residues: 51.3144
Evaluate side-chains
  67 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 63
  time to evaluate  : 0.133 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   34 ARG
Chi-restraints excluded: chain E residue   76 LYS
Chi-restraints excluded: chain D residue   76 LYS
Chi-restraints excluded: chain D residue   92 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 43 optimal weight:    6.9990
   chunk 9 optimal weight:   10.0000
   chunk 7 optimal weight:    0.8980
   chunk 32 optimal weight:    6.9990
   chunk 20 optimal weight:   10.0000
   chunk 4 optimal weight:    4.9990
   chunk 23 optimal weight:    8.9990
   chunk 12 optimal weight:    7.9990
   chunk 18 optimal weight:    8.9990
   chunk 33 optimal weight:    9.9990
   chunk 44 optimal weight:    6.9990
   overall best weight:    5.3788

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

Flipped N/Q/H residues before XYZ refinement:
** A  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E  27 ASN
D  27 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.101648 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.086366 restraints weight = 5982.718|
|-----------------------------------------------------------------------------|
r_work (start): 0.3452 rms_B_bonded: 2.82
r_work: 0.3308 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.3194 rms_B_bonded: 4.87 restraints_weight: 0.2500
r_work (final): 0.3194
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8177
moved from start:          0.2936

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.056   3715  Z= 0.301
  Angle     :  0.632   4.782   5055  Z= 0.350
  Chirality :  0.053   0.146    595
  Planarity :  0.003   0.024    625
  Dihedral  :  5.637  19.704    500
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 8.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  3.80 %
    Allowed  : 16.20 %
    Favored  : 80.00 %
  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: -1.82 (0.35), residues: 445
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.38 (0.27), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D 104 
 TYR   0.015   0.002   TYR D 114 
 PHE   0.016   0.003   PHE A  64 
 TRP   0.007   0.002   TRP D  79 
 HIS   0.004   0.001   HIS A  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00717 ( 3715)
  covalent geometry    : angle       0.63201 ( 5055)
  hydrogen bonds       : bond        0.02992 (   60)
  hydrogen bonds       : angle       5.82158 (  180)

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

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

  890 Ramachandran restraints generated.
    445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  890 Ramachandran restraints generated.
    445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 74
  time to evaluate  : 0.087 
Fit side-chains
REVERT: A   15 LYS cc_start: 0.8987 (mtpt) cc_final: 0.8711 (mtmt)
REVERT: A   21 ARG cc_start: 0.8970 (ttt180) cc_final: 0.6606 (pmt170)
REVERT: A   34 ARG cc_start: 0.8313 (mtp85) cc_final: 0.7127 (tpt170)
REVERT: A   72 GLU cc_start: 0.8908 (mt-10) cc_final: 0.8703 (mt-10)
REVERT: A  104 ARG cc_start: 0.8245 (mtt180) cc_final: 0.7137 (tpm170)
REVERT: C   74 ASP cc_start: 0.9232 (t0) cc_final: 0.8649 (t0)
REVERT: C   92 GLU cc_start: 0.8414 (mp0) cc_final: 0.8178 (mp0)
REVERT: B   15 LYS cc_start: 0.8116 (mtpt) cc_final: 0.7735 (mtpp)
REVERT: B   18 ASP cc_start: 0.8455 (t70) cc_final: 0.8228 (t0)
REVERT: B   74 ASP cc_start: 0.9219 (t0) cc_final: 0.8928 (t0)
REVERT: B   80 LYS cc_start: 0.8550 (tttt) cc_final: 0.8098 (tttp)
REVERT: E   33 PHE cc_start: 0.8306 (t80) cc_final: 0.8040 (t80)
REVERT: E   62 GLU cc_start: 0.7936 (tt0) cc_final: 0.7361 (mt-10)
REVERT: E   89 GLU cc_start: 0.9102 (mt-10) cc_final: 0.8230 (pm20)
REVERT: E  104 ARG cc_start: 0.8627 (mtt180) cc_final: 0.8274 (ttm110)
REVERT: D   13 MET cc_start: 0.7827 (ttm) cc_final: 0.7393 (tmm)
REVERT: D   15 LYS cc_start: 0.8139 (mtpt) cc_final: 0.7794 (mtpt)
REVERT: D   92 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.8208 (mt-10)
  outliers start: 15
  outliers final: 5
  residues processed: 78
  average time/residue: 0.5722
  time to fit residues: 45.5597
Evaluate side-chains
  72 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 66
  time to evaluate  : 0.089 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   76 LYS
Chi-restraints excluded: chain B residue   13 MET
Chi-restraints excluded: chain B residue   76 LYS
Chi-restraints excluded: chain E residue   34 ARG
Chi-restraints excluded: chain E residue  117 SER
Chi-restraints excluded: chain D residue   92 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 25 optimal weight:    4.9990
   chunk 22 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9990
   chunk 42 optimal weight:    9.9990
   chunk 16 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 13 optimal weight:    0.8980
   chunk 29 optimal weight:    9.9990
   chunk 23 optimal weight:    8.9990
   chunk 5 optimal weight:    7.9990
   chunk 20 optimal weight:   10.0000
   overall best weight:    2.1788

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

Flipped N/Q/H residues before XYZ refinement:
** A  31 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 = 0.3692 r_free = 0.3692 target = 0.103645 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.088480 restraints weight = 5732.925|
|-----------------------------------------------------------------------------|
r_work (start): 0.3499 rms_B_bonded: 2.75
r_work: 0.3362 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work: 0.3252 rms_B_bonded: 4.76 restraints_weight: 0.2500
r_work (final): 0.3252
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8075
moved from start:          0.3167

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3715  Z= 0.145
  Angle     :  0.553   4.215   5055  Z= 0.305
  Chirality :  0.050   0.137    595
  Planarity :  0.003   0.023    625
  Dihedral  :  5.354  20.076    500
  Min Nonbonded Distance : 2.644

Molprobity Statistics.
  All-atom Clashscore : 7.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 19.49 %
    Favored  : 77.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -1.63 (0.36), residues: 445
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.23 (0.28), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 104 
 TYR   0.016   0.002   TYR C 105 
 PHE   0.014   0.002   PHE A  64 
 TRP   0.002   0.001   TRP D  79 
 HIS   0.003   0.001   HIS A  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00348 ( 3715)
  covalent geometry    : angle       0.55315 ( 5055)
  hydrogen bonds       : bond        0.02125 (   60)
  hydrogen bonds       : angle       5.74741 (  180)

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

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

  890 Ramachandran restraints generated.
    445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  890 Ramachandran restraints generated.
    445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 70
  time to evaluate  : 0.086 
Fit side-chains
REVERT: A   21 ARG cc_start: 0.8884 (ttt180) cc_final: 0.6590 (pmt170)
REVERT: A   34 ARG cc_start: 0.8267 (mtp85) cc_final: 0.7108 (tpt170)
REVERT: A  104 ARG cc_start: 0.8102 (mtt180) cc_final: 0.6976 (tpm170)
REVERT: C   13 MET cc_start: 0.7912 (ttp) cc_final: 0.7257 (tpp)
REVERT: C   74 ASP cc_start: 0.9154 (t0) cc_final: 0.8611 (t0)
REVERT: C  104 ARG cc_start: 0.8344 (ttm-80) cc_final: 0.8130 (ttm-80)
REVERT: B   15 LYS cc_start: 0.8011 (mtpt) cc_final: 0.7694 (mtpp)
REVERT: B   18 ASP cc_start: 0.8389 (t70) cc_final: 0.8139 (t0)
REVERT: B   74 ASP cc_start: 0.9188 (t0) cc_final: 0.8926 (t0)
REVERT: B   80 LYS cc_start: 0.8518 (tttt) cc_final: 0.8078 (tttp)
REVERT: E   33 PHE cc_start: 0.8284 (t80) cc_final: 0.8068 (t80)
REVERT: E   62 GLU cc_start: 0.7896 (tt0) cc_final: 0.7318 (mt-10)
REVERT: E   89 GLU cc_start: 0.8998 (mt-10) cc_final: 0.8222 (pm20)
REVERT: E  104 ARG cc_start: 0.8584 (mtt180) cc_final: 0.8223 (ttm110)
REVERT: E  107 ILE cc_start: 0.9127 (mt) cc_final: 0.8833 (mp)
REVERT: D   13 MET cc_start: 0.7728 (ttm) cc_final: 0.7155 (tmm)
REVERT: D   15 LYS cc_start: 0.8070 (mtpt) cc_final: 0.7725 (mtpt)
REVERT: D   92 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.8053 (mt-10)
  outliers start: 10
  outliers final: 3
  residues processed: 73
  average time/residue: 0.5160
  time to fit residues: 38.4839
Evaluate side-chains
  71 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 67
  time to evaluate  : 0.079 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   21 ARG
Chi-restraints excluded: chain B residue   76 LYS
Chi-restraints excluded: chain E residue   34 ARG
Chi-restraints excluded: chain D residue   92 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 30 optimal weight:    0.5980
   chunk 36 optimal weight:   10.0000
   chunk 31 optimal weight:    9.9990
   chunk 12 optimal weight:   10.0000
   chunk 14 optimal weight:    9.9990
   chunk 23 optimal weight:    3.9990
   chunk 37 optimal weight:    0.6980
   chunk 34 optimal weight:    7.9990
   chunk 27 optimal weight:    1.9990
   chunk 33 optimal weight:   10.0000
   chunk 18 optimal weight:   10.0000
   overall best weight:    3.0586

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

Flipped N/Q/H residues before XYZ refinement:
** A  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A  88 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.102977 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.087799 restraints weight = 5309.439|
|-----------------------------------------------------------------------------|
r_work (start): 0.3496 rms_B_bonded: 2.75
r_work: 0.3364 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.3255 rms_B_bonded: 4.73 restraints_weight: 0.2500
r_work (final): 0.3255
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8131
moved from start:          0.3295

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   3715  Z= 0.183
  Angle     :  0.552   4.146   5055  Z= 0.305
  Chirality :  0.050   0.134    595
  Planarity :  0.003   0.022    625
  Dihedral  :  5.308  19.585    500
  Min Nonbonded Distance : 2.619

Molprobity Statistics.
  All-atom Clashscore : 7.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.80 %
    Favored  : 98.20 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 17.47 %
    Favored  : 78.99 %
  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: -1.54 (0.37), residues: 445
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.16 (0.28), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  34 
 TYR   0.015   0.002   TYR C 114 
 PHE   0.014   0.002   PHE A  64 
 TRP   0.003   0.001   TRP D  79 
 HIS   0.002   0.001   HIS A  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00441 ( 3715)
  covalent geometry    : angle       0.55242 ( 5055)
  hydrogen bonds       : bond        0.02177 (   60)
  hydrogen bonds       : angle       5.65480 (  180)

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

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

  890 Ramachandran restraints generated.
    445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  890 Ramachandran restraints generated.
    445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 69
  time to evaluate  : 0.085 
Fit side-chains
REVERT: A   21 ARG cc_start: 0.8899 (ttt180) cc_final: 0.6609 (pmt170)
REVERT: A   34 ARG cc_start: 0.8340 (mtp85) cc_final: 0.7142 (tpt170)
REVERT: A   70 LYS cc_start: 0.9241 (OUTLIER) cc_final: 0.8987 (ttpp)
REVERT: A  104 ARG cc_start: 0.8161 (mtt180) cc_final: 0.7077 (tpm170)
REVERT: C   13 MET cc_start: 0.7972 (OUTLIER) cc_final: 0.7313 (tpp)
REVERT: C   74 ASP cc_start: 0.9306 (t0) cc_final: 0.8816 (t0)
REVERT: B   15 LYS cc_start: 0.8097 (mtpt) cc_final: 0.7826 (mtpp)
REVERT: B   18 ASP cc_start: 0.8407 (t70) cc_final: 0.8154 (t0)
REVERT: B   74 ASP cc_start: 0.9213 (t0) cc_final: 0.8952 (t0)
REVERT: B   80 LYS cc_start: 0.8533 (tttt) cc_final: 0.8087 (tttp)
REVERT: E   62 GLU cc_start: 0.7951 (tt0) cc_final: 0.7387 (mt-10)
REVERT: E   89 GLU cc_start: 0.9007 (mt-10) cc_final: 0.8225 (pm20)
REVERT: E  104 ARG cc_start: 0.8707 (mtt180) cc_final: 0.8371 (ttm110)
REVERT: E  107 ILE cc_start: 0.9097 (mt) cc_final: 0.8846 (mp)
REVERT: D   13 MET cc_start: 0.7816 (ttm) cc_final: 0.7270 (tmm)
REVERT: D   15 LYS cc_start: 0.8085 (mtpt) cc_final: 0.7730 (mtpt)
REVERT: D   92 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.8080 (mt-10)
  outliers start: 14
  outliers final: 7
  residues processed: 72
  average time/residue: 0.5361
  time to fit residues: 39.4818
Evaluate side-chains
  75 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 65
  time to evaluate  : 0.080 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 LYS
Chi-restraints excluded: chain C residue   13 MET
Chi-restraints excluded: chain C residue   76 LYS
Chi-restraints excluded: chain C residue  117 SER
Chi-restraints excluded: chain B residue   21 ARG
Chi-restraints excluded: chain B residue   76 LYS
Chi-restraints excluded: chain B residue  117 SER
Chi-restraints excluded: chain E residue   34 ARG
Chi-restraints excluded: chain E residue  117 SER
Chi-restraints excluded: chain D residue   92 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 33 optimal weight:   10.0000
   chunk 42 optimal weight:    8.9990
   chunk 30 optimal weight:    8.9990
   chunk 39 optimal weight:    2.9990
   chunk 44 optimal weight:   10.0000
   chunk 21 optimal weight:   10.0000
   chunk 26 optimal weight:    2.9990
   chunk 6 optimal weight:   10.0000
   chunk 1 optimal weight:   10.0000
   chunk 19 optimal weight:    8.9990
   chunk 14 optimal weight:   10.0000
   overall best weight:    6.5990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.098725 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.083552 restraints weight = 5552.131|
|-----------------------------------------------------------------------------|
r_work (start): 0.3424 rms_B_bonded: 2.70
r_work: 0.3294 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.3186 rms_B_bonded: 4.63 restraints_weight: 0.2500
r_work (final): 0.3186
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8153
moved from start:          0.3511

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.062   3715  Z= 0.361
  Angle     :  0.647   5.245   5055  Z= 0.359
  Chirality :  0.054   0.145    595
  Planarity :  0.003   0.021    625
  Dihedral  :  5.594  19.472    500
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 8.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.80 %
    Favored  : 98.20 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 18.73 %
    Favored  : 77.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -1.62 (0.36), residues: 445
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.23 (0.28), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A  21 
 TYR   0.014   0.002   TYR B  78 
 PHE   0.018   0.003   PHE A  64 
 TRP   0.008   0.002   TRP D  79 
 HIS   0.007   0.002   HIS C  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00863 ( 3715)
  covalent geometry    : angle       0.64710 ( 5055)
  hydrogen bonds       : bond        0.02658 (   60)
  hydrogen bonds       : angle       5.63966 (  180)

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

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

  890 Ramachandran restraints generated.
    445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  890 Ramachandran restraints generated.
    445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 76
  time to evaluate  : 0.089 
Fit side-chains
REVERT: A   13 MET cc_start: 0.8481 (OUTLIER) cc_final: 0.7749 (tmm)
REVERT: A   21 ARG cc_start: 0.8926 (ttt180) cc_final: 0.6635 (pmt170)
REVERT: A   34 ARG cc_start: 0.8277 (mtp85) cc_final: 0.7087 (tpt170)
REVERT: A   58 LEU cc_start: 0.8792 (tp) cc_final: 0.8374 (tt)
REVERT: A   70 LYS cc_start: 0.9208 (OUTLIER) cc_final: 0.8937 (ttpp)
REVERT: A  104 ARG cc_start: 0.8096 (mtt180) cc_final: 0.6984 (mmt-90)
REVERT: C   74 ASP cc_start: 0.9386 (t0) cc_final: 0.8816 (t0)
REVERT: B   74 ASP cc_start: 0.9180 (t0) cc_final: 0.8855 (t0)
REVERT: B   80 LYS cc_start: 0.8476 (tttt) cc_final: 0.8014 (tttp)
REVERT: E   62 GLU cc_start: 0.7893 (tt0) cc_final: 0.7300 (mt-10)
REVERT: E   89 GLU cc_start: 0.8971 (mt-10) cc_final: 0.8147 (pm20)
REVERT: E  104 ARG cc_start: 0.8668 (mtt180) cc_final: 0.8327 (mtp85)
REVERT: E  107 ILE cc_start: 0.9161 (mt) cc_final: 0.8861 (mp)
REVERT: D   13 MET cc_start: 0.7756 (ttm) cc_final: 0.7359 (tmm)
REVERT: D   15 LYS cc_start: 0.8208 (mtpt) cc_final: 0.7726 (mtpt)
REVERT: D   18 ASP cc_start: 0.8636 (t70) cc_final: 0.8233 (t0)
REVERT: D   92 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.8069 (mt-10)
  outliers start: 13
  outliers final: 6
  residues processed: 79
  average time/residue: 0.5475
  time to fit residues: 44.1627
Evaluate side-chains
  82 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 73
  time to evaluate  : 0.083 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 MET
Chi-restraints excluded: chain A residue   70 LYS
Chi-restraints excluded: chain C residue   76 LYS
Chi-restraints excluded: chain B residue   21 ARG
Chi-restraints excluded: chain B residue   76 LYS
Chi-restraints excluded: chain B residue  117 SER
Chi-restraints excluded: chain E residue   34 ARG
Chi-restraints excluded: chain E residue  117 SER
Chi-restraints excluded: chain D residue   92 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 18 optimal weight:    6.9990
   chunk 21 optimal weight:    4.9990
   chunk 44 optimal weight:    2.9990
   chunk 13 optimal weight:    1.9990
   chunk 17 optimal weight:    0.7980
   chunk 22 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9990
   chunk 2 optimal weight:    2.9990
   chunk 25 optimal weight:    3.9990
   chunk 32 optimal weight:    0.8980
   chunk 34 optimal weight:    2.9990
   overall best weight:    1.3386

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

Flipped N/Q/H residues before XYZ refinement:
A  31 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.104053 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.089060 restraints weight = 5494.166|
|-----------------------------------------------------------------------------|
r_work (start): 0.3521 rms_B_bonded: 2.76
r_work: 0.3387 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work: 0.3277 rms_B_bonded: 4.80 restraints_weight: 0.2500
r_work (final): 0.3277
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8117
moved from start:          0.3578

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   3715  Z= 0.115
  Angle     :  0.538   5.541   5055  Z= 0.296
  Chirality :  0.049   0.133    595
  Planarity :  0.003   0.022    625
  Dihedral  :  5.259  19.704    500
  Min Nonbonded Distance : 2.605

Molprobity Statistics.
  All-atom Clashscore : 8.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.80 %
    Favored  : 98.20 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 19.49 %
    Favored  : 77.47 %
  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: -1.51 (0.38), residues: 445
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.15 (0.29), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 103 
 TYR   0.013   0.001   TYR C 114 
 PHE   0.014   0.002   PHE B  64 
 TRP   0.002   0.001   TRP C  79 
 HIS   0.006   0.001   HIS C  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 ( 3715)
  covalent geometry    : angle       0.53815 ( 5055)
  hydrogen bonds       : bond        0.02003 (   60)
  hydrogen bonds       : angle       5.59856 (  180)

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

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

  890 Ramachandran restraints generated.
    445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  890 Ramachandran restraints generated.
    445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 72
  time to evaluate  : 0.084 
Fit side-chains
REVERT: A   13 MET cc_start: 0.8489 (OUTLIER) cc_final: 0.7768 (tmm)
REVERT: A   17 LEU cc_start: 0.9321 (mp) cc_final: 0.9117 (mp)
REVERT: A   21 ARG cc_start: 0.8926 (ttt180) cc_final: 0.6645 (pmt170)
REVERT: A   34 ARG cc_start: 0.8284 (mtp85) cc_final: 0.7109 (tpt170)
REVERT: A  104 ARG cc_start: 0.8153 (mtt180) cc_final: 0.7019 (tpm170)
REVERT: C   13 MET cc_start: 0.7554 (ttt) cc_final: 0.7261 (tmm)
REVERT: C   74 ASP cc_start: 0.9310 (t0) cc_final: 0.8726 (t0)
REVERT: B   74 ASP cc_start: 0.9221 (t0) cc_final: 0.8902 (t0)
REVERT: B   80 LYS cc_start: 0.8531 (tttt) cc_final: 0.8098 (tttp)
REVERT: E   62 GLU cc_start: 0.7944 (tt0) cc_final: 0.7385 (mt-10)
REVERT: E   89 GLU cc_start: 0.8998 (mt-10) cc_final: 0.8222 (pm20)
REVERT: E  104 ARG cc_start: 0.8614 (mtt180) cc_final: 0.8330 (ttm110)
REVERT: D   13 MET cc_start: 0.7807 (ttm) cc_final: 0.7388 (tmm)
REVERT: D   15 LYS cc_start: 0.8074 (mtpt) cc_final: 0.7539 (mtpt)
REVERT: D   18 ASP cc_start: 0.8752 (t70) cc_final: 0.8319 (t0)
REVERT: D   92 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.8082 (mt-10)
  outliers start: 12
  outliers final: 7
  residues processed: 74
  average time/residue: 0.5417
  time to fit residues: 41.0463
Evaluate side-chains
  79 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 70
  time to evaluate  : 0.084 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 MET
Chi-restraints excluded: chain C residue   76 LYS
Chi-restraints excluded: chain C residue  117 SER
Chi-restraints excluded: chain B residue   21 ARG
Chi-restraints excluded: chain B residue  117 SER
Chi-restraints excluded: chain E residue   34 ARG
Chi-restraints excluded: chain E residue   76 LYS
Chi-restraints excluded: chain E residue  117 SER
Chi-restraints excluded: chain D residue   92 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 32 optimal weight:    0.3980
   chunk 14 optimal weight:    9.9990
   chunk 43 optimal weight:    5.9990
   chunk 25 optimal weight:    9.9990
   chunk 42 optimal weight:   10.0000
   chunk 37 optimal weight:    7.9990
   chunk 38 optimal weight:   10.0000
   chunk 36 optimal weight:    5.9990
   chunk 10 optimal weight:    5.9990
   chunk 41 optimal weight:    3.9990
   overall best weight:    4.4788

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.101305 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.086200 restraints weight = 5923.510|
|-----------------------------------------------------------------------------|
r_work (start): 0.3464 rms_B_bonded: 2.79
r_work: 0.3324 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.3215 rms_B_bonded: 4.81 restraints_weight: 0.2500
r_work (final): 0.3215
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8160
moved from start:          0.3658

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.045   3715  Z= 0.250
  Angle     :  0.599   6.089   5055  Z= 0.330
  Chirality :  0.051   0.137    595
  Planarity :  0.003   0.021    625
  Dihedral  :  5.346  19.368    500
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 8.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 20.25 %
    Favored  : 76.96 %
  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: -1.52 (0.38), residues: 445
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.15 (0.29), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  34 
 TYR   0.012   0.002   TYR B 114 
 PHE   0.015   0.003   PHE D  64 
 TRP   0.004   0.001   TRP D  79 
 HIS   0.006   0.001   HIS C  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00595 ( 3715)
  covalent geometry    : angle       0.59888 ( 5055)
  hydrogen bonds       : bond        0.02307 (   60)
  hydrogen bonds       : angle       5.55057 (  180)

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

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

  890 Ramachandran restraints generated.
    445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  890 Ramachandran restraints generated.
    445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 71
  time to evaluate  : 0.087 
Fit side-chains
REVERT: A   17 LEU cc_start: 0.9307 (mp) cc_final: 0.9081 (mp)
REVERT: A   21 ARG cc_start: 0.8958 (ttt180) cc_final: 0.6730 (pmt170)
REVERT: A   34 ARG cc_start: 0.8276 (mtp85) cc_final: 0.7099 (tpt170)
REVERT: A  104 ARG cc_start: 0.8208 (mtt180) cc_final: 0.6949 (tpm170)
REVERT: C   15 LYS cc_start: 0.8116 (mtpt) cc_final: 0.7429 (mttt)
REVERT: C   74 ASP cc_start: 0.9364 (t0) cc_final: 0.8810 (t0)
REVERT: B   74 ASP cc_start: 0.9256 (t0) cc_final: 0.8884 (t0)
REVERT: B   80 LYS cc_start: 0.8512 (tttt) cc_final: 0.8075 (tttp)
REVERT: E   62 GLU cc_start: 0.8040 (tt0) cc_final: 0.7438 (mt-10)
REVERT: E   89 GLU cc_start: 0.8965 (mt-10) cc_final: 0.8167 (pm20)
REVERT: E  104 ARG cc_start: 0.8613 (mtt180) cc_final: 0.8279 (mtp85)
REVERT: D   13 MET cc_start: 0.7784 (ttm) cc_final: 0.7388 (tmm)
REVERT: D   15 LYS cc_start: 0.8300 (mtpt) cc_final: 0.7828 (mtpt)
REVERT: D   18 ASP cc_start: 0.8745 (t70) cc_final: 0.8327 (t0)
  outliers start: 11
  outliers final: 7
  residues processed: 75
  average time/residue: 0.6250
  time to fit residues: 47.8117
Evaluate side-chains
  78 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 71
  time to evaluate  : 0.084 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   76 LYS
Chi-restraints excluded: chain B residue   21 ARG
Chi-restraints excluded: chain B residue   76 LYS
Chi-restraints excluded: chain B residue  117 SER
Chi-restraints excluded: chain E residue   34 ARG
Chi-restraints excluded: chain E residue   76 LYS
Chi-restraints excluded: chain E residue  117 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 2 optimal weight:    0.9980
   chunk 36 optimal weight:    5.9990
   chunk 4 optimal weight:    1.9990
   chunk 6 optimal weight:   10.0000
   chunk 38 optimal weight:    4.9990
   chunk 39 optimal weight:    8.9990
   chunk 1 optimal weight:    0.8980
   chunk 3 optimal weight:    2.9990
   chunk 5 optimal weight:    2.9990
   chunk 25 optimal weight:    3.9990
   chunk 17 optimal weight:    0.8980
   overall best weight:    1.5584

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.103556 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.088834 restraints weight = 5339.588|
|-----------------------------------------------------------------------------|
r_work (start): 0.3534 rms_B_bonded: 2.71
r_work: 0.3400 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work: 0.3289 rms_B_bonded: 4.77 restraints_weight: 0.2500
r_work (final): 0.3289
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8066
moved from start:          0.3714

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   3715  Z= 0.116
  Angle     :  0.536   6.451   5055  Z= 0.294
  Chirality :  0.049   0.135    595
  Planarity :  0.003   0.023    625
  Dihedral  :  5.144  19.595    500
  Min Nonbonded Distance : 2.647

Molprobity Statistics.
  All-atom Clashscore : 7.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 21.01 %
    Favored  : 76.96 %
  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: -1.50 (0.38), residues: 445
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.13 (0.29), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 103 
 TYR   0.012   0.001   TYR B 114 
 PHE   0.013   0.001   PHE C  64 
 TRP   0.002   0.001   TRP B  79 
 HIS   0.006   0.001   HIS C  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 ( 3715)
  covalent geometry    : angle       0.53650 ( 5055)
  hydrogen bonds       : bond        0.01934 (   60)
  hydrogen bonds       : angle       5.52297 (  180)

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

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

  890 Ramachandran restraints generated.
    445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  890 Ramachandran restraints generated.
    445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 72
  time to evaluate  : 0.086 
Fit side-chains
REVERT: A   21 ARG cc_start: 0.8937 (ttt180) cc_final: 0.6712 (pmt170)
REVERT: A   34 ARG cc_start: 0.8262 (mtp85) cc_final: 0.6885 (tpt170)
REVERT: A   70 LYS cc_start: 0.9214 (OUTLIER) cc_final: 0.8985 (ttpp)
REVERT: A  104 ARG cc_start: 0.8132 (mtt180) cc_final: 0.7006 (mmt-90)
REVERT: C   15 LYS cc_start: 0.8171 (mtpt) cc_final: 0.7536 (mttt)
REVERT: C   74 ASP cc_start: 0.9286 (t0) cc_final: 0.8766 (t0)
REVERT: B   74 ASP cc_start: 0.9217 (t0) cc_final: 0.8905 (t0)
REVERT: B   80 LYS cc_start: 0.8492 (tttt) cc_final: 0.8055 (tttp)
REVERT: E   62 GLU cc_start: 0.7993 (tt0) cc_final: 0.7360 (mt-10)
REVERT: E   89 GLU cc_start: 0.8974 (mt-10) cc_final: 0.8137 (pm20)
REVERT: E  104 ARG cc_start: 0.8598 (mtt180) cc_final: 0.8260 (mtp85)
REVERT: D   13 MET cc_start: 0.7728 (ttm) cc_final: 0.7314 (tmm)
REVERT: D   15 LYS cc_start: 0.8028 (mtpt) cc_final: 0.7522 (mtpt)
REVERT: D   18 ASP cc_start: 0.8790 (t70) cc_final: 0.8359 (t0)
REVERT: D   92 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.8102 (mt-10)
  outliers start: 8
  outliers final: 3
  residues processed: 74
  average time/residue: 0.6413
  time to fit residues: 48.4255
Evaluate side-chains
  76 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 71
  time to evaluate  : 0.119 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 LYS
Chi-restraints excluded: chain B residue   21 ARG
Chi-restraints excluded: chain E residue   34 ARG
Chi-restraints excluded: chain E residue   76 LYS
Chi-restraints excluded: chain D residue   92 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 3 optimal weight:    3.9990
   chunk 22 optimal weight:   10.0000
   chunk 20 optimal weight:    8.9990
   chunk 35 optimal weight:    0.6980
   chunk 37 optimal weight:    5.9990
   chunk 8 optimal weight:    4.9990
   chunk 2 optimal weight:    0.9990
   chunk 30 optimal weight:    6.9990
   chunk 7 optimal weight:    3.9990
   chunk 27 optimal weight:   10.0000
   chunk 14 optimal weight:    0.1980
   overall best weight:    1.9786

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.103173 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.088432 restraints weight = 5609.083|
|-----------------------------------------------------------------------------|
r_work (start): 0.3533 rms_B_bonded: 2.71
r_work: 0.3394 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.3283 rms_B_bonded: 4.76 restraints_weight: 0.2500
r_work (final): 0.3283
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8114
moved from start:          0.3813

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3715  Z= 0.136
  Angle     :  0.559   8.753   5055  Z= 0.302
  Chirality :  0.050   0.132    595
  Planarity :  0.003   0.023    625
  Dihedral  :  5.097  20.003    500
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 8.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  : 21.77 %
    Favored  : 76.96 %
  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: -1.48 (0.38), residues: 445
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.12 (0.29), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 104 
 TYR   0.012   0.001   TYR C 114 
 PHE   0.012   0.002   PHE C  64 
 TRP   0.002   0.001   TRP A  79 
 HIS   0.006   0.001   HIS C  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 ( 3715)
  covalent geometry    : angle       0.55903 ( 5055)
  hydrogen bonds       : bond        0.01946 (   60)
  hydrogen bonds       : angle       5.43480 (  180)

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

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

  890 Ramachandran restraints generated.
    445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  890 Ramachandran restraints generated.
    445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 67
  time to evaluate  : 0.086 
Fit side-chains
REVERT: A   21 ARG cc_start: 0.8936 (ttt180) cc_final: 0.6735 (pmt170)
REVERT: A   34 ARG cc_start: 0.8250 (mtp85) cc_final: 0.6911 (tpt170)
REVERT: A   70 LYS cc_start: 0.9233 (OUTLIER) cc_final: 0.9004 (ttpp)
REVERT: A  104 ARG cc_start: 0.8207 (mtt180) cc_final: 0.7084 (mmt-90)
REVERT: C   13 MET cc_start: 0.7537 (ttt) cc_final: 0.7185 (tmm)
REVERT: C   74 ASP cc_start: 0.9312 (t0) cc_final: 0.8784 (t0)
REVERT: B   74 ASP cc_start: 0.9232 (t0) cc_final: 0.8911 (t0)
REVERT: B   80 LYS cc_start: 0.8546 (tttt) cc_final: 0.8093 (tttp)
REVERT: E   62 GLU cc_start: 0.8074 (tt0) cc_final: 0.7448 (mt-10)
REVERT: E   89 GLU cc_start: 0.8970 (mt-10) cc_final: 0.8145 (pm20)
REVERT: E  104 ARG cc_start: 0.8583 (mtt180) cc_final: 0.8249 (mtp85)
REVERT: D   13 MET cc_start: 0.7739 (ttm) cc_final: 0.7309 (tmm)
REVERT: D   15 LYS cc_start: 0.8276 (mtpt) cc_final: 0.7807 (mtpt)
REVERT: D   18 ASP cc_start: 0.8804 (t70) cc_final: 0.8381 (t0)
REVERT: D   92 GLU cc_start: 0.8411 (OUTLIER) cc_final: 0.8133 (mt-10)
  outliers start: 5
  outliers final: 3
  residues processed: 68
  average time/residue: 0.6086
  time to fit residues: 42.2187
Evaluate side-chains
  72 residues out of total 395 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 67
  time to evaluate  : 0.083 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 LYS
Chi-restraints excluded: chain B residue   21 ARG
Chi-restraints excluded: chain E residue   34 ARG
Chi-restraints excluded: chain E residue   76 LYS
Chi-restraints excluded: chain D residue   92 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 41 optimal weight:   10.0000
   chunk 14 optimal weight:    0.0070
   chunk 37 optimal weight:   10.0000
   chunk 34 optimal weight:    9.9990
   chunk 22 optimal weight:    8.9990
   chunk 24 optimal weight:    9.9990
   chunk 2 optimal weight:    3.9990
   chunk 12 optimal weight:    6.9990
   chunk 39 optimal weight:    0.9990
   chunk 32 optimal weight:    0.0970
   chunk 13 optimal weight:    8.9990
   overall best weight:    2.4202

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

Flipped N/Q/H residues before XYZ refinement:
D  98 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.103315 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.088570 restraints weight = 5558.924|
|-----------------------------------------------------------------------------|
r_work (start): 0.3524 rms_B_bonded: 2.70
r_work: 0.3386 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work: 0.3272 rms_B_bonded: 4.76 restraints_weight: 0.2500
r_work (final): 0.3272
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8185
moved from start:          0.3853

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   3715  Z= 0.154
  Angle     :  0.565   8.750   5055  Z= 0.305
  Chirality :  0.050   0.133    595
  Planarity :  0.003   0.022    625
  Dihedral  :  5.093  18.792    500
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 8.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 21.01 %
    Favored  : 76.96 %
  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: -1.51 (0.38), residues: 445
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.14 (0.29), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 103 
 TYR   0.011   0.002   TYR C 114 
 PHE   0.012   0.002   PHE C  64 
 TRP   0.002   0.001   TRP A  79 
 HIS   0.006   0.001   HIS C  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00372 ( 3715)
  covalent geometry    : angle       0.56500 ( 5055)
  hydrogen bonds       : bond        0.01942 (   60)
  hydrogen bonds       : angle       5.39738 (  180)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1249.52 seconds
wall clock time: 22 minutes 0.68 seconds (1320.68 seconds total)