Starting phenix.real_space_refine
on Sat Apr  4 20:05:11 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9m5k_63644/04_2026/9m5k_63644.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9m5k_63644/04_2026/9m5k_63644.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9m5k_63644/04_2026/9m5k_63644.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9m5k_63644/04_2026/9m5k_63644.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9m5k_63644/04_2026/9m5k_63644.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9m5k_63644/04_2026/9m5k_63644.cif"
  }
  resolution = 3.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.004
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 3
    Type Number    sf(0)   Gaussians
     C    1119      2.51       5
     N     315      2.21       5
     O     363      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 1797
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "C"
      Number of atoms: 599
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 87, 599
          Classifications: {'peptide': 87}
          Link IDs: {'TRANS': 86}
  Restraints were copied for chains:
    A, B
  Time building chain proxies: 0.23, per 1000 atoms: 0.13
  Number of scatterers: 1797
  At special positions: 0
  Unit cell: (74.7, 78.02, 31.54, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 3
    Type Number    sf(0)
     O     363      8.00
     N     315      7.00
     C    1119      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: 0.07
  Conformation dependent library (CDL) restraints added in 44.0 milliseconds
  

  510 Ramachandran restraints generated.
    255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  444

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 8 sheets defined
      0.0% alpha, 34.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.04
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'C' and resid 25 through 30
      removed outlier: 6.786A  pdb=" N   VAL C  26 " --> pdb=" O   GLY A  25 " (cutoff:3.500A)
      removed outlier: 6.853A  pdb=" N   ALA A  27 " --> pdb=" O   VAL C  26 " (cutoff:3.500A)
      removed outlier: 6.904A  pdb=" N   GLU C  28 " --> pdb=" O   ALA A  27 " (cutoff:3.500A)
      removed outlier: 6.924A  pdb=" N   ALA A  29 " --> pdb=" O   GLU C  28 " (cutoff:3.500A)
      removed outlier: 6.808A  pdb=" N   VAL A  26 " --> pdb=" O   GLY B  25 " (cutoff:3.500A)
      removed outlier: 6.873A  pdb=" N   ALA B  27 " --> pdb=" O   VAL A  26 " (cutoff:3.500A)
      removed outlier: 6.924A  pdb=" N   GLU A  28 " --> pdb=" O   ALA B  27 " (cutoff:3.500A)
      removed outlier: 6.941A  pdb=" N   ALA B  29 " --> pdb=" O   GLU A  28 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 36 through 37
      removed outlier: 6.680A  pdb=" N   GLY C  36 " --> pdb=" O   VAL A  37 " (cutoff:3.500A)
      removed outlier: 6.683A  pdb=" N   GLY A  36 " --> pdb=" O   VAL B  37 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'C' and resid 45 through 52
      removed outlier: 6.350A  pdb=" N   LYS C  45 " --> pdb=" O   GLU A  46 " (cutoff:3.500A)
      removed outlier: 5.930A  pdb=" N   VAL A  48 " --> pdb=" O   LYS C  45 " (cutoff:3.500A)
      removed outlier: 7.525A  pdb=" N   GLY C  47 " --> pdb=" O   VAL A  48 " (cutoff:3.500A)
      removed outlier: 10.046A  pdb=" N   HIS A  50 " --> pdb=" O   GLY C  47 " (cutoff:3.500A)
      removed outlier: 7.031A  pdb=" N   VAL C  49 " --> pdb=" O   HIS A  50 " (cutoff:3.500A)
      removed outlier: 8.684A  pdb=" N   VAL A  52 " --> pdb=" O   VAL C  49 " (cutoff:3.500A)
      removed outlier: 6.914A  pdb=" N   GLY C  51 " --> pdb=" O   VAL A  52 " (cutoff:3.500A)
      removed outlier: 6.356A  pdb=" N   LYS A  45 " --> pdb=" O   GLU B  46 " (cutoff:3.500A)
      removed outlier: 5.942A  pdb=" N   VAL B  48 " --> pdb=" O   LYS A  45 " (cutoff:3.500A)
      removed outlier: 7.544A  pdb=" N   GLY A  47 " --> pdb=" O   VAL B  48 " (cutoff:3.500A)
      removed outlier: 10.067A  pdb=" N   HIS B  50 " --> pdb=" O   GLY A  47 " (cutoff:3.500A)
      removed outlier: 7.050A  pdb=" N   VAL A  49 " --> pdb=" O   HIS B  50 " (cutoff:3.500A)
      removed outlier: 8.705A  pdb=" N   VAL B  52 " --> pdb=" O   VAL A  49 " (cutoff:3.500A)
      removed outlier: 6.930A  pdb=" N   GLY A  51 " --> pdb=" O   VAL B  52 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'C' and resid 58 through 59
    Processing sheet with id=AA5, first strand: chain 'C' and resid 62 through 66
      removed outlier: 6.634A  pdb=" N   GLN A  62 " --> pdb=" O   VAL B  63 " (cutoff:3.500A)
      removed outlier: 8.085A  pdb=" N   ASN B  65 " --> pdb=" O   GLN A  62 " (cutoff:3.500A)
      removed outlier: 6.375A  pdb=" N   THR A  64 " --> pdb=" O   ASN B  65 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 69 through 71
      removed outlier: 6.425A  pdb=" N   ALA C  69 " --> pdb=" O   VAL A  70 " (cutoff:3.500A)
      removed outlier: 6.448A  pdb=" N   ALA A  69 " --> pdb=" O   VAL B  70 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'C' and resid 76 through 78
    Processing sheet with id=AA8, first strand: chain 'C' and resid 88 through 96
      removed outlier: 8.073A  pdb=" N   ALA C  89 " --> pdb=" O   ALA A  90 " (cutoff:3.500A)
      removed outlier: 7.582A  pdb=" N   THR A  92 " --> pdb=" O   ALA C  89 " (cutoff:3.500A)
      removed outlier: 9.082A  pdb=" N   ALA C  91 " --> pdb=" O   THR A  92 " (cutoff:3.500A)
      removed outlier: 8.385A  pdb=" N   PHE A  94 " --> pdb=" O   ALA C  91 " (cutoff:3.500A)
      removed outlier: 6.662A  pdb=" N   GLY C  93 " --> pdb=" O   PHE A  94 " (cutoff:3.500A)
      removed outlier: 7.860A  pdb=" N   LYS A  96 " --> pdb=" O   GLY C  93 " (cutoff:3.500A)
      removed outlier: 6.437A  pdb=" N   VAL C  95 " --> pdb=" O   LYS A  96 " (cutoff:3.500A)
      removed outlier: 8.100A  pdb=" N   ALA A  89 " --> pdb=" O   ALA B  90 " (cutoff:3.500A)
      removed outlier: 7.606A  pdb=" N   THR B  92 " --> pdb=" O   ALA A  89 " (cutoff:3.500A)
      removed outlier: 9.111A  pdb=" N   ALA A  91 " --> pdb=" O   THR B  92 " (cutoff:3.500A)
      removed outlier: 8.410A  pdb=" N   PHE B  94 " --> pdb=" O   ALA A  91 " (cutoff:3.500A)
      removed outlier: 6.673A  pdb=" N   GLY A  93 " --> pdb=" O   PHE B  94 " (cutoff:3.500A)
      removed outlier: 7.858A  pdb=" N   LYS B  96 " --> pdb=" O   GLY A  93 " (cutoff:3.500A)
      removed outlier: 6.435A  pdb=" N   VAL A  95 " --> pdb=" O   LYS B  96 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8

    12 hydrogen bonds defined for protein.
    36 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: 0.11

  Time building geometry restraints manager: 0.11 seconds

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

  Histogram of bond lengths:
        1.22 -     1.29: 324
        1.29 -     1.35: 279
        1.35 -     1.42: 54
        1.42 -     1.48: 300
        1.48 -     1.55: 846
  Bond restraints: 1803
  Sorted by residual:
  bond pdb=" CA  ALA B  30 "
       pdb=" C   ALA B  30 "
    ideal  model  delta    sigma   weight residual
    1.526  1.514  0.012 1.08e-02 8.57e+03 1.19e+00
  bond pdb=" CA  ALA C  30 "
       pdb=" C   ALA C  30 "
    ideal  model  delta    sigma   weight residual
    1.526  1.514  0.012 1.08e-02 8.57e+03 1.18e+00
  bond pdb=" CB  GLN A  24 "
       pdb=" CG  GLN A  24 "
    ideal  model  delta    sigma   weight residual
    1.520  1.487  0.033 3.00e-02 1.11e+03 1.18e+00
  bond pdb=" CB  GLN B  24 "
       pdb=" CG  GLN B  24 "
    ideal  model  delta    sigma   weight residual
    1.520  1.487  0.033 3.00e-02 1.11e+03 1.18e+00
  bond pdb=" CB  GLN C  24 "
       pdb=" CG  GLN C  24 "
    ideal  model  delta    sigma   weight residual
    1.520  1.488  0.032 3.00e-02 1.11e+03 1.14e+00
  ... (remaining 1798 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.63: 1761
        0.63 -     1.26: 445
        1.26 -     1.90: 155
        1.90 -     2.53: 54
        2.53 -     3.16: 15
  Bond angle restraints: 2430
  Sorted by residual:
  angle pdb=" CA  LEU A  38 "
        pdb=" C   LEU A  38 "
        pdb=" N   TYR A  39 "
      ideal   model   delta    sigma   weight residual
     114.98  117.40   -2.42 1.34e+00 5.57e-01 3.26e+00
  angle pdb=" CA  LEU B  38 "
        pdb=" C   LEU B  38 "
        pdb=" N   TYR B  39 "
      ideal   model   delta    sigma   weight residual
     114.98  117.39   -2.41 1.34e+00 5.57e-01 3.24e+00
  angle pdb=" CA  LEU C  38 "
        pdb=" C   LEU C  38 "
        pdb=" N   TYR C  39 "
      ideal   model   delta    sigma   weight residual
     114.98  117.37   -2.39 1.34e+00 5.57e-01 3.18e+00
  angle pdb=" N   GLY A  84 "
        pdb=" CA  GLY A  84 "
        pdb=" C   GLY A  84 "
      ideal   model   delta    sigma   weight residual
     111.36  113.20   -1.84 1.17e+00 7.31e-01 2.48e+00
  angle pdb=" N   GLY B  84 "
        pdb=" CA  GLY B  84 "
        pdb=" C   GLY B  84 "
      ideal   model   delta    sigma   weight residual
     111.36  113.17   -1.81 1.17e+00 7.31e-01 2.40e+00
  ... (remaining 2425 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.42: 966
       14.42 -    28.85: 75
       28.85 -    43.27: 18
       43.27 -    57.69: 3
       57.69 -    72.11: 9
  Dihedral angle restraints: 1071
    sinusoidal: 366
      harmonic: 705
  Sorted by residual:
  dihedral pdb=" CA  VAL B  82 "
           pdb=" C   VAL B  82 "
           pdb=" N   GLU B  83 "
           pdb=" CA  GLU B  83 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.66  -18.34     0      5.00e+00 4.00e-02 1.35e+01
  dihedral pdb=" CA  VAL A  82 "
           pdb=" C   VAL A  82 "
           pdb=" N   GLU A  83 "
           pdb=" CA  GLU A  83 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.67  -18.33     0      5.00e+00 4.00e-02 1.34e+01
  dihedral pdb=" CA  VAL C  82 "
           pdb=" C   VAL C  82 "
           pdb=" N   GLU C  83 "
           pdb=" CA  GLU C  83 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.70  -18.30     0      5.00e+00 4.00e-02 1.34e+01
  ... (remaining 1068 not shown)

  Histogram of chiral volume deviations from ideal:
       0.001 -    0.026: 85
       0.026 -    0.051: 108
       0.051 -    0.077: 55
       0.077 -    0.102: 43
       0.102 -    0.128: 21
  Chirality restraints: 312
  Sorted by residual:
  chirality pdb=" CA  ILE A  88 "
            pdb=" N   ILE A  88 "
            pdb=" C   ILE A  88 "
            pdb=" CB  ILE A  88 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.07e-01
  chirality pdb=" CA  ILE B  88 "
            pdb=" N   ILE B  88 "
            pdb=" C   ILE B  88 "
            pdb=" CB  ILE B  88 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.06e-01
  chirality pdb=" CA  ILE C  88 "
            pdb=" N   ILE C  88 "
            pdb=" C   ILE C  88 "
            pdb=" CB  ILE C  88 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.84e-01
  ... (remaining 309 not shown)

  Planarity restraints: 306
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR C  39 "    0.010 2.00e-02 2.50e+03   6.35e-03 8.07e-01
        pdb=" CG  TYR C  39 "   -0.015 2.00e-02 2.50e+03
        pdb=" CD1 TYR C  39 "    0.001 2.00e-02 2.50e+03
        pdb=" CD2 TYR C  39 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE1 TYR C  39 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 TYR C  39 "    0.003 2.00e-02 2.50e+03
        pdb=" CZ  TYR C  39 "    0.000 2.00e-02 2.50e+03
        pdb=" OH  TYR C  39 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B  39 "    0.009 2.00e-02 2.50e+03   6.30e-03 7.94e-01
        pdb=" CG  TYR B  39 "   -0.015 2.00e-02 2.50e+03
        pdb=" CD1 TYR B  39 "    0.001 2.00e-02 2.50e+03
        pdb=" CD2 TYR B  39 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE1 TYR B  39 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 TYR B  39 "    0.003 2.00e-02 2.50e+03
        pdb=" CZ  TYR B  39 "    0.000 2.00e-02 2.50e+03
        pdb=" OH  TYR B  39 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A  39 "    0.009 2.00e-02 2.50e+03   6.17e-03 7.62e-01
        pdb=" CG  TYR A  39 "   -0.014 2.00e-02 2.50e+03
        pdb=" CD1 TYR A  39 "    0.002 2.00e-02 2.50e+03
        pdb=" CD2 TYR A  39 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE1 TYR A  39 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 TYR A  39 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ  TYR A  39 "   -0.000 2.00e-02 2.50e+03
        pdb=" OH  TYR A  39 "    0.002 2.00e-02 2.50e+03
  ... (remaining 303 not shown)

  Histogram of nonbonded interaction distances:
        2.28 -     2.80: 451
        2.80 -     3.33: 1468
        3.33 -     3.85: 2804
        3.85 -     4.38: 3079
        4.38 -     4.90: 6272
  Nonbonded interactions: 14074
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU A  46 "
            pdb=" NZ  LYS B  80 "
     model   vdw
     2.280 3.120
  nonbonded pdb=" OE1 GLU C  46 "
            pdb=" NZ  LYS A  80 "
     model   vdw
     2.287 3.120
  nonbonded pdb=" OH  TYR A  39 "
            pdb=" O   SER B  42 "
     model   vdw
     2.332 3.040
  nonbonded pdb=" OH  TYR C  39 "
            pdb=" O   SER A  42 "
     model   vdw
     2.339 3.040
  nonbonded pdb=" OG1 THR B  33 "
            pdb=" OE2 GLU B  35 "
     model   vdw
     2.474 3.040
  ... (remaining 14069 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: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'C'
  selection = chain 'A'
  selection = chain 'B'
}

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:             1.200
  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:          0.030
  Check model and map are aligned:         0.000
  Set scattering table:                    0.010
  Process input model:                     2.000
  Find NCS groups from input model:        0.010
  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:0.730
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    3.980
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8508
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      :  0.008   0.033   1803  Z= 0.374
  Angle     :  0.716   3.161   2430  Z= 0.427
  Chirality :  0.057   0.128    312
  Planarity :  0.003   0.008    306
  Dihedral  : 14.013  72.111    627
  Min Nonbonded Distance : 2.280

Molprobity Statistics.
  All-atom Clashscore : 9.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.29 %
    Favored  : 84.71 %
  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: -5.40 (0.35), residues: 255
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.11 (0.27), residues: 255

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.015   0.004   TYR B  39 
 PHE   0.011   0.003   PHE C  94 
 HIS   0.003   0.002   HIS C  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00822 ( 1803)
  covalent geometry    : angle       0.71606 ( 2430)
  hydrogen bonds       : bond        0.19058 (   12)
  hydrogen bonds       : angle       9.19710 (   36)

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

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

  510 Ramachandran restraints generated.
    255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  510 Ramachandran restraints generated.
    255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  16 residues out of total 177 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 16
  time to evaluate  : 0.033 
Fit side-chains
REVERT: B   60 LYS cc_start: 0.8974 (mttp) cc_final: 0.8763 (mttt)
  outliers start: 0
  outliers final: 0
  residues processed: 16
  average time/residue: 0.0371
  time to fit residues: 0.7118
Evaluate side-chains
  14 residues out of total 177 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 14
  time to evaluate  : 0.032 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 12 optimal weight:    3.9990
   chunk 13 optimal weight:    4.9990
   chunk 1 optimal weight:    3.9990
   chunk 8 optimal weight:   10.0000
   chunk 16 optimal weight:   10.0000
   chunk 15 optimal weight:    4.9990
   chunk 9 optimal weight:    0.7980
   chunk 11 optimal weight:    0.9980
   chunk 18 optimal weight:    2.9990
   chunk 6 optimal weight:    3.9990
   chunk 4 optimal weight:    1.9990
   overall best weight:    2.1586

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

Flipped N/Q/H residues before XYZ refinement:
C  50 HIS
A  24 GLN
A  50 HIS
B  24 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.117476 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.096508 restraints weight = 1924.439|
|-----------------------------------------------------------------------------|
r_work (start): 0.3436 rms_B_bonded: 2.08
r_work: 0.3312 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.3189 rms_B_bonded: 3.81 restraints_weight: 0.2500
r_work (final): 0.3189
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8626
moved from start:          0.1164

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025   1803  Z= 0.176
  Angle     :  0.503   2.639   2430  Z= 0.289
  Chirality :  0.055   0.134    312
  Planarity :  0.002   0.008    306
  Dihedral  :  5.472  18.159    261
  Min Nonbonded Distance : 2.622

Molprobity Statistics.
  All-atom Clashscore : 4.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.98 %
    Favored  : 89.02 %
  Rotamer:
    Outliers :  0.56 %
    Allowed  :  6.78 %
    Favored  : 92.66 %
  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: -4.76 (0.38), residues: 255
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.62 (0.29), residues: 255

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.011   0.003   TYR A  39 
 PHE   0.007   0.002   PHE A  94 
 HIS   0.001   0.001   HIS B  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00399 ( 1803)
  covalent geometry    : angle       0.50283 ( 2430)
  hydrogen bonds       : bond        0.03005 (   12)
  hydrogen bonds       : angle       5.25461 (   36)

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

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

  510 Ramachandran restraints generated.
    255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  510 Ramachandran restraints generated.
    255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  15 residues out of total 177 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 14
  time to evaluate  : 0.033 
Fit side-chains
REVERT: C   23 LYS cc_start: 0.8304 (ttpt) cc_final: 0.8084 (tttt)
  outliers start: 1
  outliers final: 1
  residues processed: 14
  average time/residue: 0.0430
  time to fit residues: 0.7505
Evaluate side-chains
  14 residues out of total 177 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 13
  time to evaluate  : 0.040 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   72 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 17 optimal weight:    9.9990
   chunk 23 optimal weight:    8.9990
   chunk 22 optimal weight:    6.9990
   chunk 15 optimal weight:    3.9990
   chunk 2 optimal weight:    3.9990
   chunk 1 optimal weight:    5.9990
   chunk 12 optimal weight:    3.9990
   chunk 8 optimal weight:   10.0000
   chunk 0 optimal weight:    4.9990
   chunk 20 optimal weight:    2.9990
   chunk 16 optimal weight:    6.9990
   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  79 GLN ** 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 = 0.3657 r_free = 0.3657 target = 0.111722 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.091090 restraints weight = 1983.270|
|-----------------------------------------------------------------------------|
r_work (start): 0.3372 rms_B_bonded: 2.12
r_work: 0.3250 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.3123 rms_B_bonded: 3.81 restraints_weight: 0.2500
r_work (final): 0.3123
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8660
moved from start:          0.1185

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.042   1803  Z= 0.307
  Angle     :  0.584   3.048   2430  Z= 0.339
  Chirality :  0.058   0.140    312
  Planarity :  0.002   0.009    306
  Dihedral  :  5.759  17.562    261
  Min Nonbonded Distance : 2.626

Molprobity Statistics.
  All-atom Clashscore : 7.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 16.47 %
    Favored  : 83.53 %
  Rotamer:
    Outliers :  1.13 %
    Allowed  :  9.04 %
    Favored  : 89.83 %
  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: -4.51 (0.40), residues: 255
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.43 (0.30), residues: 255

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.015   0.004   TYR C  39 
 PHE   0.010   0.002   PHE B  94 
 HIS   0.002   0.001   HIS B  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00714 ( 1803)
  covalent geometry    : angle       0.58396 ( 2430)
  hydrogen bonds       : bond        0.02826 (   12)
  hydrogen bonds       : angle       4.65044 (   36)

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

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

  510 Ramachandran restraints generated.
    255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  510 Ramachandran restraints generated.
    255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  15 residues out of total 177 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 13
  time to evaluate  : 0.034 
Fit side-chains
  outliers start: 2
  outliers final: 1
  residues processed: 14
  average time/residue: 0.0576
  time to fit residues: 0.9268
Evaluate side-chains
  14 residues out of total 177 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 13
  time to evaluate  : 0.035 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   72 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 2 optimal weight:    0.0470
   chunk 19 optimal weight:    5.9990
   chunk 3 optimal weight:    4.9990
   chunk 15 optimal weight:    6.9990
   chunk 11 optimal weight:    0.7980
   chunk 20 optimal weight:    6.9990
   chunk 7 optimal weight:    5.9990
   chunk 4 optimal weight:    8.9990
   chunk 13 optimal weight:    0.0870
   chunk 0 optimal weight:   10.0000
   chunk 9 optimal weight:    5.9990
   overall best weight:    2.3860

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

Flipped N/Q/H residues before XYZ refinement:
B  50 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 = 0.114486 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.094136 restraints weight = 1907.426|
|-----------------------------------------------------------------------------|
r_work (start): 0.3431 rms_B_bonded: 2.08
r_work: 0.3314 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.3191 rms_B_bonded: 3.75 restraints_weight: 0.2500
r_work (final): 0.3191
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8631
moved from start:          0.1490

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   1803  Z= 0.192
  Angle     :  0.492   2.656   2430  Z= 0.287
  Chirality :  0.054   0.134    312
  Planarity :  0.002   0.008    306
  Dihedral  :  5.406  17.017    261
  Min Nonbonded Distance : 2.629

Molprobity Statistics.
  All-atom Clashscore : 5.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.33 %
    Favored  : 86.67 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  :  9.04 %
    Favored  : 88.70 %
  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: -4.27 (0.41), residues: 255
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.25 (0.32), residues: 255

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.012   0.003   TYR C  39 
 PHE   0.008   0.002   PHE A  94 
 HIS   0.002   0.001   HIS B  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00441 ( 1803)
  covalent geometry    : angle       0.49215 ( 2430)
  hydrogen bonds       : bond        0.01813 (   12)
  hydrogen bonds       : angle       4.35197 (   36)

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

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

  510 Ramachandran restraints generated.
    255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  510 Ramachandran restraints generated.
    255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  17 residues out of total 177 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 13
  time to evaluate  : 0.085 
Fit side-chains
REVERT: C   23 LYS cc_start: 0.8542 (ttmt) cc_final: 0.8336 (tttt)
  outliers start: 4
  outliers final: 2
  residues processed: 15
  average time/residue: 0.0757
  time to fit residues: 1.3517
Evaluate side-chains
  15 residues out of total 177 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 13
  time to evaluate  : 0.065 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   72 THR
Chi-restraints excluded: chain B residue   74 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 16 optimal weight:    9.9990
   chunk 10 optimal weight:    7.9990
   chunk 19 optimal weight:    1.9990
   chunk 7 optimal weight:    0.0670
   chunk 3 optimal weight:    1.9990
   chunk 23 optimal weight:    9.9990
   chunk 17 optimal weight:    7.9990
   chunk 21 optimal weight:    0.1980
   chunk 15 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9990
   chunk 9 optimal weight:    2.9990
   overall best weight:    1.0524

-------------------------------------------------------------------------------
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 = 0.3791 r_free = 0.3791 target = 0.120482 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.100100 restraints weight = 1872.140|
|-----------------------------------------------------------------------------|
r_work (start): 0.3514 rms_B_bonded: 2.07
r_work: 0.3400 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.3279 rms_B_bonded: 3.79 restraints_weight: 0.2500
r_work (final): 0.3279
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8576
moved from start:          0.1807

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.016   1803  Z= 0.095
  Angle     :  0.400   2.091   2430  Z= 0.234
  Chirality :  0.053   0.129    312
  Planarity :  0.001   0.007    306
  Dihedral  :  4.833  14.797    261
  Min Nonbonded Distance : 2.625

Molprobity Statistics.
  All-atom Clashscore : 4.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.55 %
    Favored  : 87.45 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  :  9.04 %
    Favored  : 89.27 %
  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: -3.99 (0.42), residues: 255
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.04 (0.32), residues: 255

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.009   0.002   TYR A  39 
 PHE   0.004   0.001   PHE A  94 
 HIS   0.001   0.001   HIS A  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00210 ( 1803)
  covalent geometry    : angle       0.39976 ( 2430)
  hydrogen bonds       : bond        0.01275 (   12)
  hydrogen bonds       : angle       4.40832 (   36)

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

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

  510 Ramachandran restraints generated.
    255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  510 Ramachandran restraints generated.
    255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  16 residues out of total 177 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 13
  time to evaluate  : 0.068 
Fit side-chains
  outliers start: 3
  outliers final: 2
  residues processed: 15
  average time/residue: 0.0682
  time to fit residues: 1.2389
Evaluate side-chains
  15 residues out of total 177 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 13
  time to evaluate  : 0.063 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   72 THR
Chi-restraints excluded: chain B residue   74 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 15 optimal weight:   10.0000
   chunk 7 optimal weight:    0.3980
   chunk 19 optimal weight:    6.9990
   chunk 18 optimal weight:    0.0870
   chunk 0 optimal weight:   10.0000
   chunk 17 optimal weight:    5.9990
   chunk 20 optimal weight:    3.9990
   chunk 6 optimal weight:    8.9990
   chunk 10 optimal weight:    2.9990
   chunk 22 optimal weight:    3.9990
   chunk 4 optimal weight:    0.8980
   overall best weight:    1.6762

-------------------------------------------------------------------------------
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 = 0.3764 r_free = 0.3764 target = 0.118120 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.097388 restraints weight = 1834.668|
|-----------------------------------------------------------------------------|
r_work (start): 0.3476 rms_B_bonded: 2.07
r_work: 0.3360 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.3233 rms_B_bonded: 3.76 restraints_weight: 0.2500
r_work (final): 0.3233
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8599
moved from start:          0.1773

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   1803  Z= 0.139
  Angle     :  0.428   2.134   2430  Z= 0.251
  Chirality :  0.053   0.130    312
  Planarity :  0.002   0.009    306
  Dihedral  :  4.928  14.831    261
  Min Nonbonded Distance : 2.623

Molprobity Statistics.
  All-atom Clashscore : 5.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.73 %
    Favored  : 86.27 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  :  8.47 %
    Favored  : 88.70 %
  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: -3.80 (0.44), residues: 255
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.89 (0.34), residues: 255

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.011   0.003   TYR A  39 
 PHE   0.006   0.001   PHE B  94 
 HIS   0.002   0.001   HIS A  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 1803)
  covalent geometry    : angle       0.42767 ( 2430)
  hydrogen bonds       : bond        0.01329 (   12)
  hydrogen bonds       : angle       4.27987 (   36)

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

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

  510 Ramachandran restraints generated.
    255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  510 Ramachandran restraints generated.
    255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  17 residues out of total 177 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 12
  time to evaluate  : 0.038 
Fit side-chains
  outliers start: 5
  outliers final: 2
  residues processed: 15
  average time/residue: 0.0556
  time to fit residues: 1.0256
Evaluate side-chains
  14 residues out of total 177 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 12
  time to evaluate  : 0.060 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   72 THR
Chi-restraints excluded: chain B residue   74 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 7 optimal weight:    0.0980
   chunk 15 optimal weight:    0.7980
   chunk 12 optimal weight:    8.9990
   chunk 5 optimal weight:    0.2980
   chunk 3 optimal weight:    3.9990
   chunk 11 optimal weight:    1.9990
   chunk 14 optimal weight:    2.9990
   chunk 22 optimal weight:    2.9990
   chunk 4 optimal weight:    4.9990
   chunk 10 optimal weight:    6.9990
   chunk 1 optimal weight:    6.9990
   overall best weight:    1.2384

-------------------------------------------------------------------------------
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 = 0.3801 r_free = 0.3801 target = 0.120511 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.099641 restraints weight = 1819.577|
|-----------------------------------------------------------------------------|
r_work (start): 0.3514 rms_B_bonded: 2.08
r_work: 0.3399 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.3274 rms_B_bonded: 3.80 restraints_weight: 0.2500
r_work (final): 0.3274
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8580
moved from start:          0.1919

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.015   1803  Z= 0.112
  Angle     :  0.448   3.663   2430  Z= 0.261
  Chirality :  0.054   0.134    312
  Planarity :  0.001   0.010    306
  Dihedral  :  4.766  14.559    261
  Min Nonbonded Distance : 2.612

Molprobity Statistics.
  All-atom Clashscore : 5.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.16 %
    Favored  : 87.84 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  :  8.47 %
    Favored  : 89.83 %
  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: -3.64 (0.45), residues: 255
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.76 (0.34), residues: 255

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.010   0.002   TYR A  39 
 PHE   0.005   0.001   PHE B  94 
 HIS   0.001   0.001   HIS A  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00248 ( 1803)
  covalent geometry    : angle       0.44779 ( 2430)
  hydrogen bonds       : bond        0.01167 (   12)
  hydrogen bonds       : angle       4.30002 (   36)

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

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

  510 Ramachandran restraints generated.
    255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  510 Ramachandran restraints generated.
    255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  15 residues out of total 177 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 12
  time to evaluate  : 0.061 
Fit side-chains
  outliers start: 3
  outliers final: 2
  residues processed: 14
  average time/residue: 0.0698
  time to fit residues: 1.1964
Evaluate side-chains
  14 residues out of total 177 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 12
  time to evaluate  : 0.063 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   72 THR
Chi-restraints excluded: chain B residue   74 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 19 optimal weight:    6.9990
   chunk 18 optimal weight:    5.9990
   chunk 13 optimal weight:    4.9990
   chunk 22 optimal weight:    6.9990
   chunk 0 optimal weight:   10.0000
   chunk 10 optimal weight:    4.9990
   chunk 5 optimal weight:    2.9990
   chunk 12 optimal weight:    7.9990
   chunk 23 optimal weight:    5.9990
   chunk 16 optimal weight:    9.9990
   chunk 9 optimal weight:    3.9990
   overall best weight:    4.5990

-------------------------------------------------------------------------------
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 = 0.3667 r_free = 0.3667 target = 0.111493 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.090164 restraints weight = 1950.796|
|-----------------------------------------------------------------------------|
r_work (start): 0.3364 rms_B_bonded: 2.18
r_work: 0.3239 rms_B_bonded: 2.39 restraints_weight: 0.5000
r_work: 0.3109 rms_B_bonded: 3.87 restraints_weight: 0.2500
r_work (final): 0.3109
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8666
moved from start:          0.1587

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.039   1803  Z= 0.348
  Angle     :  0.624   3.376   2430  Z= 0.365
  Chirality :  0.059   0.142    312
  Planarity :  0.003   0.010    306
  Dihedral  :  5.632  16.984    261
  Min Nonbonded Distance : 2.622

Molprobity Statistics.
  All-atom Clashscore : 6.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 16.86 %
    Favored  : 83.14 %
  Rotamer:
    Outliers :  0.56 %
    Allowed  : 10.17 %
    Favored  : 89.27 %
  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: -3.72 (0.45), residues: 255
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.83 (0.35), residues: 255

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.016   0.004   TYR C  39 
 PHE   0.009   0.002   PHE B  94 
 HIS   0.002   0.001   HIS A  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00803 ( 1803)
  covalent geometry    : angle       0.62422 ( 2430)
  hydrogen bonds       : bond        0.01935 (   12)
  hydrogen bonds       : angle       4.22493 (   36)

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

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

  510 Ramachandran restraints generated.
    255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  510 Ramachandran restraints generated.
    255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  18 residues out of total 177 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 17
  time to evaluate  : 0.066 
Fit side-chains
  outliers start: 1
  outliers final: 1
  residues processed: 17
  average time/residue: 0.0680
  time to fit residues: 1.3768
Evaluate side-chains
  18 residues out of total 177 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 17
  time to evaluate  : 0.065 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   72 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 9 optimal weight:    6.9990
   chunk 21 optimal weight:    3.9990
   chunk 3 optimal weight:    0.3980
   chunk 18 optimal weight:    0.0010
   chunk 23 optimal weight:    0.9980
   chunk 22 optimal weight:    0.9990
   chunk 17 optimal weight:    0.0070
   chunk 1 optimal weight:    0.0870
   chunk 10 optimal weight:    4.9990
   chunk 8 optimal weight:    2.9990
   chunk 4 optimal weight:    5.9990
   overall best weight:    0.2982

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

Flipped N/Q/H residues before XYZ refinement:
A  99 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3890 r_free = 0.3890 target = 0.126241 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.106183 restraints weight = 1829.159|
|-----------------------------------------------------------------------------|
r_work (start): 0.3612 rms_B_bonded: 2.03
r_work: 0.3502 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.3377 rms_B_bonded: 3.80 restraints_weight: 0.2500
r_work (final): 0.3377
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8512
moved from start:          0.2216

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.001   0.015   1803  Z= 0.073
  Angle     :  0.429   3.439   2430  Z= 0.249
  Chirality :  0.053   0.138    312
  Planarity :  0.001   0.011    306
  Dihedral  :  4.635  14.982    261
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 4.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.02 %
    Favored  : 90.98 %
  Rotamer:
    Outliers :  0.56 %
    Allowed  :  8.47 %
    Favored  : 90.96 %
  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: -3.49 (0.46), residues: 255
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.65 (0.35), residues: 255

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.010   0.002   TYR A  39 
 PHE   0.002   0.001   PHE C  94 
 HIS   0.001   0.000   HIS C  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00147 ( 1803)
  covalent geometry    : angle       0.42899 ( 2430)
  hydrogen bonds       : bond        0.01060 (   12)
  hydrogen bonds       : angle       4.73420 (   36)

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

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

  510 Ramachandran restraints generated.
    255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  510 Ramachandran restraints generated.
    255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  14 residues out of total 177 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 13
  time to evaluate  : 0.048 
Fit side-chains
REVERT: B   46 GLU cc_start: 0.7970 (mt-10) cc_final: 0.7646 (tt0)
  outliers start: 1
  outliers final: 0
  residues processed: 14
  average time/residue: 0.0855
  time to fit residues: 1.3945
Evaluate side-chains
  13 residues out of total 177 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 13
  time to evaluate  : 0.061 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 3 optimal weight:    2.9990
   chunk 17 optimal weight:    9.9990
   chunk 20 optimal weight:    4.9990
   chunk 21 optimal weight:    2.9990
   chunk 2 optimal weight:    0.9980
   chunk 9 optimal weight:    5.9990
   chunk 5 optimal weight:    4.9990
   chunk 16 optimal weight:   10.0000
   chunk 12 optimal weight:    2.9990
   chunk 4 optimal weight:    2.9990
   chunk 13 optimal weight:    3.9990
   overall best weight:    2.5988

-------------------------------------------------------------------------------
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 = 0.3730 r_free = 0.3730 target = 0.115567 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.093973 restraints weight = 1896.561|
|-----------------------------------------------------------------------------|
r_work (start): 0.3434 rms_B_bonded: 2.19
r_work: 0.3311 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.3178 rms_B_bonded: 3.88 restraints_weight: 0.2500
r_work (final): 0.3178
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8626
moved from start:          0.1815

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.023   1803  Z= 0.205
  Angle     :  0.513   3.471   2430  Z= 0.299
  Chirality :  0.055   0.137    312
  Planarity :  0.002   0.012    306
  Dihedral  :  5.055  15.534    261
  Min Nonbonded Distance : 2.616

Molprobity Statistics.
  All-atom Clashscore : 5.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.51 %
    Favored  : 85.49 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  9.60 %
    Favored  : 90.40 %
  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: -3.42 (0.47), residues: 255
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.60 (0.36), residues: 255

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.012   0.003   TYR C  39 
 PHE   0.007   0.002   PHE B  94 
 HIS   0.002   0.001   HIS A  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00468 ( 1803)
  covalent geometry    : angle       0.51273 ( 2430)
  hydrogen bonds       : bond        0.01522 (   12)
  hydrogen bonds       : angle       4.24403 (   36)

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

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

  510 Ramachandran restraints generated.
    255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  510 Ramachandran restraints generated.
    255 Oldfield, 0 Emsley, 255 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  15 residues out of total 177 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 15
  time to evaluate  : 0.068 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 15
  average time/residue: 0.0872
  time to fit residues: 1.5206
Evaluate side-chains
  15 residues out of total 177 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 15
  time to evaluate  : 0.038 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 3 optimal weight:    1.9990
   chunk 21 optimal weight:    2.9990
   chunk 18 optimal weight:    0.8980
   chunk 13 optimal weight:    0.9990
   chunk 11 optimal weight:    0.9990
   chunk 14 optimal weight:    0.9990
   chunk 17 optimal weight:    5.9990
   chunk 19 optimal weight:    0.7980
   chunk 10 optimal weight:    4.9990
   chunk 20 optimal weight:    2.9990
   chunk 1 optimal weight:    7.9990
   overall best weight:    0.9386

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

Flipped N/Q/H residues before XYZ refinement:
A  99 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.121728 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.100672 restraints weight = 1876.213|
|-----------------------------------------------------------------------------|
r_work (start): 0.3543 rms_B_bonded: 2.13
r_work: 0.3415 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.3287 rms_B_bonded: 3.95 restraints_weight: 0.2500
r_work (final): 0.3287
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8566
moved from start:          0.2110

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.014   1803  Z= 0.096
  Angle     :  0.444   4.393   2430  Z= 0.258
  Chirality :  0.053   0.131    312
  Planarity :  0.002   0.014    306
  Dihedral  :  4.705  15.082    261
  Min Nonbonded Distance : 2.621

Molprobity Statistics.
  All-atom Clashscore : 5.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.16 %
    Favored  : 87.84 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 10.17 %
    Favored  : 89.83 %
  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: -3.28 (0.47), residues: 255
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.49 (0.36), residues: 255

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.010   0.002   TYR A  39 
 PHE   0.004   0.001   PHE B  94 
 HIS   0.001   0.000   HIS A  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00204 ( 1803)
  covalent geometry    : angle       0.44387 ( 2430)
  hydrogen bonds       : bond        0.01027 (   12)
  hydrogen bonds       : angle       4.37974 (   36)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 701.91 seconds
wall clock time: 13 minutes 16.55 seconds (796.55 seconds total)