Starting phenix.real_space_refine
on Tue Feb  3 12:20:07 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9jhg_61481/02_2026/9jhg_61481.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9jhg_61481/02_2026/9jhg_61481.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.38
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9jhg_61481/02_2026/9jhg_61481.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9jhg_61481/02_2026/9jhg_61481.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9jhg_61481/02_2026/9jhg_61481.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9jhg_61481/02_2026/9jhg_61481.map"
  }
  resolution = 3.38
  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      12      5.16       5
     C     930      2.51       5
     N     222      2.21       5
     O     270      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-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 1434
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 239
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 32, 239
          Classifications: {'peptide': 32}
          Link IDs: {'TRANS': 31}
  Restraints were copied for chains:
    B, C, E, D, F
  Time building chain proxies: 0.29, per 1000 atoms: 0.20
  Number of scatterers: 1434
  At special positions: 0
  Unit cell: (73.87, 75.53, 32.37, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      12     16.00
     O     270      8.00
     N     222      7.00
     C     930      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: 0.11
  Conformation dependent library (CDL) restraints added in 52.7 milliseconds
  

  360 Ramachandran restraints generated.
    180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  360

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 5 sheets defined
      0.0% alpha, 54.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.05
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'C' and resid 2 through 13
      removed outlier: 6.803A  pdb=" N   LEU C  10 " --> pdb=" O   GLY A   9 " (cutoff:3.500A)
      removed outlier: 6.843A  pdb=" N   ASP A  11 " --> pdb=" O   LEU C  10 " (cutoff:3.500A)
      removed outlier: 6.889A  pdb=" N   ILE C  12 " --> pdb=" O   ASP A  11 " (cutoff:3.500A)
      removed outlier: 6.826A  pdb=" N   GLN A  13 " --> pdb=" O   ILE C  12 " (cutoff:3.500A)
      removed outlier: 6.334A  pdb=" N   ILE A   2 " --> pdb=" O   VAL D   3 " (cutoff:3.500A)
      removed outlier: 7.939A  pdb=" N   GLN D   5 " --> pdb=" O   ILE A   2 " (cutoff:3.500A)
      removed outlier: 6.526A  pdb=" N   THR A   4 " --> pdb=" O   GLN D   5 " (cutoff:3.500A)
      removed outlier: 7.856A  pdb=" N   MET D   7 " --> pdb=" O   THR A   4 " (cutoff:3.500A)
      removed outlier: 6.427A  pdb=" N   THR A   6 " --> pdb=" O   MET D   7 " (cutoff:3.500A)
      removed outlier: 8.201A  pdb=" N   GLY D   9 " --> pdb=" O   THR A   6 " (cutoff:3.500A)
      removed outlier: 8.435A  pdb=" N   LYS A   8 " --> pdb=" O   GLY D   9 " (cutoff:3.500A)
      removed outlier: 8.102A  pdb=" N   ASP D  11 " --> pdb=" O   LYS A   8 " (cutoff:3.500A)
      removed outlier: 9.234A  pdb=" N   LEU A  10 " --> pdb=" O   ASP D  11 " (cutoff:3.500A)
      removed outlier: 10.149A  pdb=" N   GLN D  13 " --> pdb=" O   LEU A  10 " (cutoff:3.500A)
      removed outlier: 8.849A  pdb=" N   ILE A  12 " --> pdb=" O   GLN D  13 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 23 through 31
      removed outlier: 8.867A  pdb=" N   MET A  24 " --> pdb=" O   ALA C  25 " (cutoff:3.500A)
      removed outlier: 10.222A  pdb=" N   SER C  27 " --> pdb=" O   MET A  24 " (cutoff:3.500A)
      removed outlier: 5.610A  pdb=" N   ALA A  26 " --> pdb=" O   SER C  27 " (cutoff:3.500A)
      removed outlier: 7.159A  pdb=" N   ILE C  29 " --> pdb=" O   ALA A  26 " (cutoff:3.500A)
      removed outlier: 6.231A  pdb=" N   ASP A  28 " --> pdb=" O   ILE C  29 " (cutoff:3.500A)
      removed outlier: 7.709A  pdb=" N   LEU C  31 " --> pdb=" O   ASP A  28 " (cutoff:3.500A)
      removed outlier: 6.760A  pdb=" N   SER A  30 " --> pdb=" O   LEU C  31 " (cutoff:3.500A)
      removed outlier: 6.867A  pdb=" N   MET D  24 " --> pdb=" O   ALA A  23 " (cutoff:3.500A)
      removed outlier: 6.822A  pdb=" N   ALA A  25 " --> pdb=" O   MET D  24 " (cutoff:3.500A)
      removed outlier: 6.836A  pdb=" N   ALA D  26 " --> pdb=" O   ALA A  25 " (cutoff:3.500A)
      removed outlier: 6.760A  pdb=" N   SER A  27 " --> pdb=" O   ALA D  26 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'E' and resid 2 through 13
      removed outlier: 6.233A  pdb=" N   ILE B   2 " --> pdb=" O   VAL E   3 " (cutoff:3.500A)
      removed outlier: 7.841A  pdb=" N   GLN E   5 " --> pdb=" O   ILE B   2 " (cutoff:3.500A)
      removed outlier: 6.459A  pdb=" N   THR B   4 " --> pdb=" O   GLN E   5 " (cutoff:3.500A)
      removed outlier: 7.789A  pdb=" N   MET E   7 " --> pdb=" O   THR B   4 " (cutoff:3.500A)
      removed outlier: 6.398A  pdb=" N   THR B   6 " --> pdb=" O   MET E   7 " (cutoff:3.500A)
      removed outlier: 8.166A  pdb=" N   GLY E   9 " --> pdb=" O   THR B   6 " (cutoff:3.500A)
      removed outlier: 8.480A  pdb=" N   LYS B   8 " --> pdb=" O   GLY E   9 " (cutoff:3.500A)
      removed outlier: 8.122A  pdb=" N   ASP E  11 " --> pdb=" O   LYS B   8 " (cutoff:3.500A)
      removed outlier: 9.340A  pdb=" N   LEU B  10 " --> pdb=" O   ASP E  11 " (cutoff:3.500A)
      removed outlier: 10.264A  pdb=" N   GLN E  13 " --> pdb=" O   LEU B  10 " (cutoff:3.500A)
      removed outlier: 9.006A  pdb=" N   ILE B  12 " --> pdb=" O   GLN E  13 " (cutoff:3.500A)
      removed outlier: 6.936A  pdb=" N   LEU F  10 " --> pdb=" O   GLY B   9 " (cutoff:3.500A)
      removed outlier: 6.999A  pdb=" N   ASP B  11 " --> pdb=" O   LEU F  10 " (cutoff:3.500A)
      removed outlier: 7.091A  pdb=" N   ILE F  12 " --> pdb=" O   ASP B  11 " (cutoff:3.500A)
      removed outlier: 7.043A  pdb=" N   GLN B  13 " --> pdb=" O   ILE F  12 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'E' and resid 23 through 25
      removed outlier: 6.447A  pdb=" N   ALA B  23 " --> pdb=" O   MET F  24 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'E' and resid 28 through 31
      removed outlier: 6.281A  pdb=" N   ASP B  28 " --> pdb=" O   ILE F  29 " (cutoff:3.500A)
      removed outlier: 7.754A  pdb=" N   LEU F  31 " --> pdb=" O   ASP B  28 " (cutoff:3.500A)
      removed outlier: 6.834A  pdb=" N   SER B  30 " --> pdb=" O   LEU F  31 " (cutoff:3.500A)

    23 hydrogen bonds defined for protein.
    69 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: 0.20

  Time building geometry restraints manager: 0.14 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 417
        1.34 -     1.46: 212
        1.46 -     1.57: 793
        1.57 -     1.69: 0
        1.69 -     1.81: 24
  Bond restraints: 1446
  Sorted by residual:
  bond pdb=" N   VAL C   3 "
       pdb=" CA  VAL C   3 "
    ideal  model  delta    sigma   weight residual
    1.459  1.493 -0.034 1.28e-02 6.10e+03 7.23e+00
  bond pdb=" N   ASP F  28 "
       pdb=" CA  ASP F  28 "
    ideal  model  delta    sigma   weight residual
    1.456  1.489 -0.032 1.21e-02 6.83e+03 7.19e+00
  bond pdb=" N   VAL E   3 "
       pdb=" CA  VAL E   3 "
    ideal  model  delta    sigma   weight residual
    1.459  1.493 -0.034 1.28e-02 6.10e+03 7.18e+00
  bond pdb=" N   ASP A  28 "
       pdb=" CA  ASP A  28 "
    ideal  model  delta    sigma   weight residual
    1.456  1.489 -0.032 1.21e-02 6.83e+03 7.11e+00
  bond pdb=" N   ASP B  28 "
       pdb=" CA  ASP B  28 "
    ideal  model  delta    sigma   weight residual
    1.456  1.488 -0.032 1.21e-02 6.83e+03 7.04e+00
  ... (remaining 1441 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.29: 1544
        1.29 -     2.58: 343
        2.58 -     3.87: 49
        3.87 -     5.17: 14
        5.17 -     6.46: 6
  Bond angle restraints: 1956
  Sorted by residual:
  angle pdb=" C   SER E  30 "
        pdb=" CA  SER E  30 "
        pdb=" CB  SER E  30 "
      ideal   model   delta    sigma   weight residual
     110.16  116.62   -6.46 1.66e+00 3.63e-01 1.51e+01
  angle pdb=" C   SER C  30 "
        pdb=" CA  SER C  30 "
        pdb=" CB  SER C  30 "
      ideal   model   delta    sigma   weight residual
     110.16  116.60   -6.44 1.66e+00 3.63e-01 1.50e+01
  angle pdb=" C   SER F  30 "
        pdb=" CA  SER F  30 "
        pdb=" CB  SER F  30 "
      ideal   model   delta    sigma   weight residual
     110.16  116.58   -6.42 1.66e+00 3.63e-01 1.50e+01
  angle pdb=" C   SER A  30 "
        pdb=" CA  SER A  30 "
        pdb=" CB  SER A  30 "
      ideal   model   delta    sigma   weight residual
     110.16  116.57   -6.41 1.66e+00 3.63e-01 1.49e+01
  angle pdb=" C   SER B  30 "
        pdb=" CA  SER B  30 "
        pdb=" CB  SER B  30 "
      ideal   model   delta    sigma   weight residual
     110.16  116.55   -6.39 1.66e+00 3.63e-01 1.48e+01
  ... (remaining 1951 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -     9.62: 676
        9.62 -    19.24: 98
       19.24 -    28.85: 54
       28.85 -    38.47: 18
       38.47 -    48.09: 18
  Dihedral angle restraints: 864
    sinusoidal: 312
      harmonic: 552
  Sorted by residual:
  dihedral pdb=" CB  MET F   7 "
           pdb=" CG  MET F   7 "
           pdb=" SD  MET F   7 "
           pdb=" CE  MET F   7 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -108.09   48.09     3      1.50e+01 4.44e-03 8.59e+00
  dihedral pdb=" CB  MET D   7 "
           pdb=" CG  MET D   7 "
           pdb=" SD  MET D   7 "
           pdb=" CE  MET D   7 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -108.08   48.08     3      1.50e+01 4.44e-03 8.59e+00
  dihedral pdb=" CB  MET C   7 "
           pdb=" CG  MET C   7 "
           pdb=" SD  MET C   7 "
           pdb=" CE  MET C   7 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -108.06   48.06     3      1.50e+01 4.44e-03 8.59e+00
  ... (remaining 861 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.040: 114
       0.040 -    0.079: 69
       0.079 -    0.119: 38
       0.119 -    0.158: 19
       0.158 -    0.198: 18
  Chirality restraints: 258
  Sorted by residual:
  chirality pdb=" CA  ILE C  29 "
            pdb=" N   ILE C  29 "
            pdb=" C   ILE C  29 "
            pdb=" CB  ILE C  29 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.63   -0.20 2.00e-01 2.50e+01 9.80e-01
  chirality pdb=" CA  ILE E  29 "
            pdb=" N   ILE E  29 "
            pdb=" C   ILE E  29 "
            pdb=" CB  ILE E  29 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.63   -0.20 2.00e-01 2.50e+01 9.67e-01
  chirality pdb=" CA  ILE F  29 "
            pdb=" N   ILE F  29 "
            pdb=" C   ILE F  29 "
            pdb=" CB  ILE F  29 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.63   -0.20 2.00e-01 2.50e+01 9.62e-01
  ... (remaining 255 not shown)

  Planarity restraints: 222
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE B   2 "   -0.005 2.00e-02 2.50e+03   9.20e-03 8.47e-01
        pdb=" C   ILE B   2 "    0.016 2.00e-02 2.50e+03
        pdb=" O   ILE B   2 "   -0.006 2.00e-02 2.50e+03
        pdb=" N   VAL B   3 "   -0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE F   2 "   -0.004 2.00e-02 2.50e+03   9.12e-03 8.32e-01
        pdb=" C   ILE F   2 "    0.016 2.00e-02 2.50e+03
        pdb=" O   ILE F   2 "   -0.006 2.00e-02 2.50e+03
        pdb=" N   VAL F   3 "   -0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE E   2 "   -0.004 2.00e-02 2.50e+03   9.10e-03 8.28e-01
        pdb=" C   ILE E   2 "    0.016 2.00e-02 2.50e+03
        pdb=" O   ILE E   2 "   -0.006 2.00e-02 2.50e+03
        pdb=" N   VAL E   3 "   -0.005 2.00e-02 2.50e+03
  ... (remaining 219 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.75: 127
        2.75 -     3.29: 1314
        3.29 -     3.83: 2020
        3.83 -     4.36: 2669
        4.36 -     4.90: 4640
  Nonbonded interactions: 10770
  Sorted by model distance:
  nonbonded pdb=" CZ2 TRP D  19 "
            pdb=" CD1 LEU D  22 "
     model   vdw
     2.216 3.760
  nonbonded pdb=" CZ2 TRP C  19 "
            pdb=" CD1 LEU C  22 "
     model   vdw
     2.216 3.760
  nonbonded pdb=" CZ2 TRP B  19 "
            pdb=" CD1 LEU B  22 "
     model   vdw
     2.217 3.760
  nonbonded pdb=" CZ2 TRP A  19 "
            pdb=" CD1 LEU A  22 "
     model   vdw
     2.217 3.760
  nonbonded pdb=" CZ2 TRP E  19 "
            pdb=" CD1 LEU E  22 "
     model   vdw
     2.217 3.760
  ... (remaining 10765 not shown)

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

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:             0.800
  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:          0.060
  Check model and map are aligned:         0.000
  Set scattering table:                    0.010
  Process input model:                     3.870
  Find NCS groups from input model:        0.020
  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:1.590
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    6.350
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7096
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      :  0.011   0.035   1446  Z= 0.787
  Angle     :  1.179   6.457   1956  Z= 0.808
  Chirality :  0.080   0.198    258
  Planarity :  0.003   0.009    222
  Dihedral  : 14.457  48.085    504
  Min Nonbonded Distance : 2.216

Molprobity Statistics.
  All-atom Clashscore : 55.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 16.67 %
    Favored  : 83.33 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 23.08 %
    Favored  : 76.92 %
  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: -4.72 (0.52), residues: 180
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.59 (0.39), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.001   0.000   TYR E  20 
 TRP   0.002   0.001   TRP E  19 

Details of bonding type rmsd
  covalent geometry    : bond        0.01134 ( 1446)
  covalent geometry    : angle       1.17891 ( 1956)
  hydrogen bonds       : bond        0.14297 (   23)
  hydrogen bonds       : angle       8.17453 (   69)

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

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

  360 Ramachandran restraints generated.
    180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  360 Ramachandran restraints generated.
    180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  24 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 24
  time to evaluate  : 0.033 
Fit side-chains
REVERT: A   27 SER cc_start: 0.7339 (t) cc_final: 0.7102 (t)
REVERT: D   27 SER cc_start: 0.7766 (t) cc_final: 0.7563 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 24
  average time/residue: 0.0204
  time to fit residues: 0.6340
Evaluate side-chains
  20 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 20
  time to evaluate  : 0.033 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 18
   random chunks:
   chunk 12 optimal weight:    8.9990
   chunk 13 optimal weight:    0.9980
   chunk 1 optimal weight:    0.8980
   chunk 8 optimal weight:    0.8980
   chunk 16 optimal weight:    3.9990
   chunk 15 optimal weight:    0.9980
   chunk 9 optimal weight:    0.7980
   chunk 11 optimal weight:    4.9990
   chunk 6 optimal weight:    1.9990
   chunk 4 optimal weight:    2.9990
   chunk 3 optimal weight:    1.9990
   overall best weight:    0.9180

-------------------------------------------------------------------------------
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 = 0.4573 r_free = 0.4573 target = 0.213866 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4231 r_free = 0.4231 target = 0.163528 restraints weight = 1314.494|
|-----------------------------------------------------------------------------|
r_work (start): 0.4193 rms_B_bonded: 2.55
r_work: 0.4100 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.3983 rms_B_bonded: 4.60 restraints_weight: 0.2500
r_work (final): 0.3983
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7867
moved from start:          0.2538

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.016   1446  Z= 0.102
  Angle     :  0.636   5.839   1956  Z= 0.284
  Chirality :  0.046   0.120    258
  Planarity :  0.002   0.010    222
  Dihedral  :  4.383  13.858    192
  Min Nonbonded Distance : 2.636

Molprobity Statistics.
  All-atom Clashscore : 5.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.78 %
    Favored  : 87.22 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  : 26.92 %
    Favored  : 71.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -4.08 (0.53), residues: 180
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.10 (0.40), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.009   0.002   TYR D  20 
 TRP   0.007   0.002   TRP E  19 

Details of bonding type rmsd
  covalent geometry    : bond        0.00231 ( 1446)
  covalent geometry    : angle       0.63558 ( 1956)
  hydrogen bonds       : bond        0.01490 (   23)
  hydrogen bonds       : angle       5.08318 (   69)

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

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

  360 Ramachandran restraints generated.
    180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  360 Ramachandran restraints generated.
    180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  26 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 24
  time to evaluate  : 0.033 
Fit side-chains
REVERT: F   11 ASP cc_start: 0.6927 (m-30) cc_final: 0.6275 (t70)
  outliers start: 2
  outliers final: 1
  residues processed: 24
  average time/residue: 0.0294
  time to fit residues: 0.8486
Evaluate side-chains
  21 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 20
  time to evaluate  : 0.032 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   24 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 18
   random chunks:
   chunk 3 optimal weight:    4.9990
   chunk 12 optimal weight:    0.7980
   chunk 11 optimal weight:    9.9990
   chunk 15 optimal weight:    0.8980
   chunk 1 optimal weight:    8.9990
   chunk 0 optimal weight:    2.9990
   chunk 8 optimal weight:    8.9990
   chunk 9 optimal weight:    2.9990
   chunk 6 optimal weight:    0.9990
   chunk 16 optimal weight:   10.0000
   chunk 10 optimal weight:   10.0000
   overall best weight:    1.7386

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

Flipped N/Q/H residues before XYZ refinement:
** A  13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D   5 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4487 r_free = 0.4487 target = 0.199361 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4100 r_free = 0.4100 target = 0.147388 restraints weight = 1322.482|
|-----------------------------------------------------------------------------|
r_work (start): 0.4080 rms_B_bonded: 2.56
r_work: 0.3978 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.3858 rms_B_bonded: 4.45 restraints_weight: 0.2500
r_work (final): 0.3858
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7973
moved from start:          0.3056

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   1446  Z= 0.146
  Angle     :  0.584   5.031   1956  Z= 0.279
  Chirality :  0.044   0.128    258
  Planarity :  0.002   0.011    222
  Dihedral  :  4.263  14.486    192
  Min Nonbonded Distance : 2.629

Molprobity Statistics.
  All-atom Clashscore : 6.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.00 %
    Favored  : 90.00 %
  Rotamer:
    Outliers :  5.13 %
    Allowed  : 25.64 %
    Favored  : 69.23 %
  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: -4.03 (0.53), residues: 180
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.06 (0.40), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.010   0.002   TYR D  20 
 TRP   0.005   0.002   TRP A  19 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 ( 1446)
  covalent geometry    : angle       0.58377 ( 1956)
  hydrogen bonds       : bond        0.01400 (   23)
  hydrogen bonds       : angle       4.57173 (   69)

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

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

  360 Ramachandran restraints generated.
    180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  360 Ramachandran restraints generated.
    180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  33 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 25
  time to evaluate  : 0.068 
Fit side-chains
REVERT: C    8 LYS cc_start: 0.7537 (tttm) cc_final: 0.6666 (mttp)
REVERT: C   30 SER cc_start: 0.8575 (m) cc_final: 0.8285 (t)
REVERT: D    8 LYS cc_start: 0.7901 (tttm) cc_final: 0.7103 (mtmm)
  outliers start: 8
  outliers final: 3
  residues processed: 30
  average time/residue: 0.0428
  time to fit residues: 1.5363
Evaluate side-chains
  27 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 24
  time to evaluate  : 0.032 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   30 SER
Chi-restraints excluded: chain E residue   15 VAL
Chi-restraints excluded: chain F residue   30 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 18
   random chunks:
   chunk 9 optimal weight:   10.0000
   chunk 10 optimal weight:    0.9990
   chunk 11 optimal weight:    5.9990
   chunk 12 optimal weight:    0.5980
   chunk 16 optimal weight:    9.9990
   chunk 7 optimal weight:    0.9980
   chunk 6 optimal weight:    9.9990
   chunk 13 optimal weight:    0.9980
   chunk 8 optimal weight:    5.9990
   chunk 5 optimal weight:    9.9990
   chunk 4 optimal weight:    5.9990
   overall best weight:    1.9184

-------------------------------------------------------------------------------
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 = 0.4473 r_free = 0.4473 target = 0.196678 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4087 r_free = 0.4087 target = 0.146387 restraints weight = 1347.204|
|-----------------------------------------------------------------------------|
r_work (start): 0.4072 rms_B_bonded: 2.54
r_work: 0.3968 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.3847 rms_B_bonded: 4.43 restraints_weight: 0.2500
r_work (final): 0.3847
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7989
moved from start:          0.3516

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   1446  Z= 0.151
  Angle     :  0.555   4.448   1956  Z= 0.267
  Chirality :  0.047   0.137    258
  Planarity :  0.002   0.010    222
  Dihedral  :  4.318  15.054    192
  Min Nonbonded Distance : 2.622

Molprobity Statistics.
  All-atom Clashscore : 6.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.00 %
    Favored  : 90.00 %
  Rotamer:
    Outliers :  5.77 %
    Allowed  : 27.56 %
    Favored  : 66.67 %
  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: -3.98 (0.53), residues: 180
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.03 (0.40), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.007   0.001   TYR D  20 
 TRP   0.008   0.002   TRP F  19 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 ( 1446)
  covalent geometry    : angle       0.55467 ( 1956)
  hydrogen bonds       : bond        0.01394 (   23)
  hydrogen bonds       : angle       4.35272 (   69)

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

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

  360 Ramachandran restraints generated.
    180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  360 Ramachandran restraints generated.
    180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  35 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 26
  time to evaluate  : 0.065 
Fit side-chains
REVERT: C    8 LYS cc_start: 0.7561 (tttm) cc_final: 0.6697 (mttp)
REVERT: C   30 SER cc_start: 0.8586 (m) cc_final: 0.8364 (t)
REVERT: D    8 LYS cc_start: 0.7889 (tttm) cc_final: 0.7114 (mtmm)
  outliers start: 9
  outliers final: 4
  residues processed: 30
  average time/residue: 0.0513
  time to fit residues: 1.7871
Evaluate side-chains
  30 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 26
  time to evaluate  : 0.031 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   30 SER
Chi-restraints excluded: chain C residue   31 LEU
Chi-restraints excluded: chain E residue   15 VAL
Chi-restraints excluded: chain F residue   30 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 18
   random chunks:
   chunk 5 optimal weight:    8.9990
   chunk 10 optimal weight:    9.9990
   chunk 12 optimal weight:   10.0000
   chunk 7 optimal weight:    0.4980
   chunk 17 optimal weight:    4.9990
   chunk 6 optimal weight:    8.9990
   chunk 1 optimal weight:    2.9990
   chunk 14 optimal weight:    0.7980
   chunk 11 optimal weight:    0.9980
   chunk 3 optimal weight:    4.9990
   chunk 0 optimal weight:    0.9980
   overall best weight:    1.2582

-------------------------------------------------------------------------------
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 = 0.4511 r_free = 0.4511 target = 0.201031 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4135 r_free = 0.4135 target = 0.151842 restraints weight = 1311.239|
|-----------------------------------------------------------------------------|
r_work (start): 0.4117 rms_B_bonded: 2.54
r_work: 0.4019 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.3899 rms_B_bonded: 4.43 restraints_weight: 0.2500
r_work (final): 0.3899
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7945
moved from start:          0.3763

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.016   1446  Z= 0.108
  Angle     :  0.490   5.144   1956  Z= 0.232
  Chirality :  0.044   0.126    258
  Planarity :  0.002   0.008    222
  Dihedral  :  3.812  13.349    192
  Min Nonbonded Distance : 2.627

Molprobity Statistics.
  All-atom Clashscore : 4.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.89 %
    Favored  : 91.11 %
  Rotamer:
    Outliers :  5.13 %
    Allowed  : 29.49 %
    Favored  : 65.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -3.89 (0.54), residues: 180
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.96 (0.41), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.005   0.001   TYR D  20 
 TRP   0.006   0.001   TRP F  19 

Details of bonding type rmsd
  covalent geometry    : bond        0.00239 ( 1446)
  covalent geometry    : angle       0.48992 ( 1956)
  hydrogen bonds       : bond        0.01258 (   23)
  hydrogen bonds       : angle       4.02009 (   69)

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

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

  360 Ramachandran restraints generated.
    180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  360 Ramachandran restraints generated.
    180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  38 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 30
  time to evaluate  : 0.053 
Fit side-chains
REVERT: C    5 GLN cc_start: 0.8515 (OUTLIER) cc_final: 0.8216 (mt0)
REVERT: C    8 LYS cc_start: 0.7507 (tttm) cc_final: 0.6623 (mttp)
REVERT: D    7 MET cc_start: 0.8197 (OUTLIER) cc_final: 0.7393 (mtm)
  outliers start: 8
  outliers final: 5
  residues processed: 34
  average time/residue: 0.0355
  time to fit residues: 1.4387
Evaluate side-chains
  36 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 29
  time to evaluate  : 0.032 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   24 MET
Chi-restraints excluded: chain B residue   30 SER
Chi-restraints excluded: chain C residue    5 GLN
Chi-restraints excluded: chain C residue   31 LEU
Chi-restraints excluded: chain E residue   15 VAL
Chi-restraints excluded: chain D residue    7 MET
Chi-restraints excluded: chain F residue   30 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 18
   random chunks:
   chunk 8 optimal weight:    7.9990
   chunk 5 optimal weight:   10.0000
   chunk 1 optimal weight:   10.0000
   chunk 11 optimal weight:    0.8980
   chunk 9 optimal weight:    7.9990
   chunk 10 optimal weight:    3.9990
   chunk 7 optimal weight:    1.9990
   chunk 12 optimal weight:    1.9990
   chunk 0 optimal weight:    0.9990
   chunk 3 optimal weight:    1.9990
   chunk 4 optimal weight:    9.9990
   overall best weight:    1.5788

-------------------------------------------------------------------------------
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 = 0.4502 r_free = 0.4502 target = 0.195676 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4101 r_free = 0.4101 target = 0.146117 restraints weight = 1307.316|
|-----------------------------------------------------------------------------|
r_work (start): 0.4075 rms_B_bonded: 2.52
r_work: 0.3976 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.3851 rms_B_bonded: 4.43 restraints_weight: 0.2500
r_work (final): 0.3851
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7974
moved from start:          0.4098

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   1446  Z= 0.125
  Angle     :  0.492   5.302   1956  Z= 0.239
  Chirality :  0.044   0.127    258
  Planarity :  0.002   0.009    222
  Dihedral  :  3.922  14.630    192
  Min Nonbonded Distance : 2.625

Molprobity Statistics.
  All-atom Clashscore : 5.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.00 %
    Favored  : 90.00 %
  Rotamer:
    Outliers :  5.77 %
    Allowed  : 30.77 %
    Favored  : 63.46 %
  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: -3.73 (0.54), residues: 180
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.84 (0.41), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.004   0.001   TYR F  20 
 TRP   0.010   0.002   TRP F  19 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 1446)
  covalent geometry    : angle       0.49197 ( 1956)
  hydrogen bonds       : bond        0.01329 (   23)
  hydrogen bonds       : angle       3.92517 (   69)

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

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

  360 Ramachandran restraints generated.
    180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  360 Ramachandran restraints generated.
    180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  40 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 31
  time to evaluate  : 0.070 
Fit side-chains
REVERT: A   30 SER cc_start: 0.8502 (t) cc_final: 0.8275 (m)
REVERT: C    5 GLN cc_start: 0.8518 (OUTLIER) cc_final: 0.8242 (mt0)
REVERT: C    7 MET cc_start: 0.8315 (OUTLIER) cc_final: 0.7731 (mtm)
REVERT: C    8 LYS cc_start: 0.7511 (tttm) cc_final: 0.6614 (mttp)
REVERT: D    7 MET cc_start: 0.8181 (OUTLIER) cc_final: 0.7338 (mtm)
  outliers start: 9
  outliers final: 4
  residues processed: 34
  average time/residue: 0.0501
  time to fit residues: 1.9914
Evaluate side-chains
  38 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 31
  time to evaluate  : 0.056 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   24 MET
Chi-restraints excluded: chain C residue    5 GLN
Chi-restraints excluded: chain C residue    7 MET
Chi-restraints excluded: chain C residue   31 LEU
Chi-restraints excluded: chain E residue   15 VAL
Chi-restraints excluded: chain D residue    7 MET
Chi-restraints excluded: chain F residue   30 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 18
   random chunks:
   chunk 6 optimal weight:    9.9990
   chunk 2 optimal weight:    7.9990
   chunk 11 optimal weight:   10.0000
   chunk 12 optimal weight:    7.9990
   chunk 4 optimal weight:   10.0000
   chunk 13 optimal weight:    3.9990
   chunk 17 optimal weight:    4.9990
   chunk 15 optimal weight:    7.9990
   chunk 3 optimal weight:    0.9980
   chunk 8 optimal weight:    1.9990
   chunk 0 optimal weight:    0.7980
   overall best weight:    2.5586

-------------------------------------------------------------------------------
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 = 0.4470 r_free = 0.4470 target = 0.191917 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4067 r_free = 0.4067 target = 0.142093 restraints weight = 1337.251|
|-----------------------------------------------------------------------------|
r_work (start): 0.4025 rms_B_bonded: 2.51
r_work: 0.3922 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.3802 rms_B_bonded: 4.29 restraints_weight: 0.2500
r_work (final): 0.3802
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8010
moved from start:          0.4366

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   1446  Z= 0.186
  Angle     :  0.539   5.901   1956  Z= 0.266
  Chirality :  0.043   0.130    258
  Planarity :  0.002   0.009    222
  Dihedral  :  4.338  17.438    192
  Min Nonbonded Distance : 2.619

Molprobity Statistics.
  All-atom Clashscore : 7.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.56 %
    Favored  : 89.44 %
  Rotamer:
    Outliers :  7.69 %
    Allowed  : 27.56 %
    Favored  : 64.74 %
  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: -3.73 (0.53), residues: 180
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.84 (0.41), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.009   0.001   TYR C  20 
 TRP   0.010   0.002   TRP F  19 

Details of bonding type rmsd
  covalent geometry    : bond        0.00420 ( 1446)
  covalent geometry    : angle       0.53860 ( 1956)
  hydrogen bonds       : bond        0.01593 (   23)
  hydrogen bonds       : angle       4.02575 (   69)

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

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

  360 Ramachandran restraints generated.
    180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  360 Ramachandran restraints generated.
    180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 33
  time to evaluate  : 0.038 
Fit side-chains
REVERT: A    7 MET cc_start: 0.8223 (OUTLIER) cc_final: 0.6974 (mtm)
REVERT: C    5 GLN cc_start: 0.8566 (OUTLIER) cc_final: 0.8192 (mt0)
REVERT: C    7 MET cc_start: 0.8312 (OUTLIER) cc_final: 0.7347 (mtm)
REVERT: D    7 MET cc_start: 0.8169 (OUTLIER) cc_final: 0.7236 (mtm)
REVERT: D    8 LYS cc_start: 0.7877 (tttm) cc_final: 0.7064 (mttp)
  outliers start: 12
  outliers final: 5
  residues processed: 37
  average time/residue: 0.0421
  time to fit residues: 1.7894
Evaluate side-chains
  42 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 33
  time to evaluate  : 0.032 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 MET
Chi-restraints excluded: chain A residue   24 MET
Chi-restraints excluded: chain B residue   30 SER
Chi-restraints excluded: chain C residue    5 GLN
Chi-restraints excluded: chain C residue    7 MET
Chi-restraints excluded: chain C residue   27 SER
Chi-restraints excluded: chain C residue   31 LEU
Chi-restraints excluded: chain D residue    7 MET
Chi-restraints excluded: chain F residue   30 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 18
   random chunks:
   chunk 1 optimal weight:    8.9990
   chunk 9 optimal weight:    7.9990
   chunk 6 optimal weight:    7.9990
   chunk 3 optimal weight:    4.9990
   chunk 8 optimal weight:    0.9980
   chunk 14 optimal weight:    5.9990
   chunk 15 optimal weight:    0.6980
   chunk 7 optimal weight:    3.9990
   chunk 17 optimal weight:    0.2980
   chunk 13 optimal weight:    3.9990
   chunk 12 optimal weight:    0.9980
   overall best weight:    1.3982

-------------------------------------------------------------------------------
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 = 0.4535 r_free = 0.4535 target = 0.195975 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4121 r_free = 0.4121 target = 0.147292 restraints weight = 1291.666|
|-----------------------------------------------------------------------------|
r_work (start): 0.4102 rms_B_bonded: 2.52
r_work: 0.4001 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.3876 rms_B_bonded: 4.44 restraints_weight: 0.2500
r_work (final): 0.3876
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7969
moved from start:          0.4491

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.017   1446  Z= 0.113
  Angle     :  0.490   6.270   1956  Z= 0.235
  Chirality :  0.043   0.127    258
  Planarity :  0.002   0.010    222
  Dihedral  :  3.892  13.994    192
  Min Nonbonded Distance : 2.631

Molprobity Statistics.
  All-atom Clashscore : 5.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.33 %
    Favored  : 91.67 %
  Rotamer:
    Outliers :  6.41 %
    Allowed  : 28.21 %
    Favored  : 65.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -3.54 (0.55), residues: 180
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.69 (0.42), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.005   0.001   TYR C  20 
 TRP   0.006   0.001   TRP F  19 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 ( 1446)
  covalent geometry    : angle       0.48953 ( 1956)
  hydrogen bonds       : bond        0.01324 (   23)
  hydrogen bonds       : angle       3.60250 (   69)

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

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

  360 Ramachandran restraints generated.
    180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  360 Ramachandran restraints generated.
    180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 32
  time to evaluate  : 0.068 
Fit side-chains
REVERT: A    7 MET cc_start: 0.8169 (OUTLIER) cc_final: 0.7347 (mtm)
REVERT: C    7 MET cc_start: 0.8279 (OUTLIER) cc_final: 0.7676 (mtm)
REVERT: C    8 LYS cc_start: 0.7593 (tttm) cc_final: 0.6684 (mttp)
REVERT: D    7 MET cc_start: 0.8171 (OUTLIER) cc_final: 0.7225 (mtm)
  outliers start: 10
  outliers final: 4
  residues processed: 35
  average time/residue: 0.0420
  time to fit residues: 1.7490
Evaluate side-chains
  39 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 32
  time to evaluate  : 0.033 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 MET
Chi-restraints excluded: chain A residue   24 MET
Chi-restraints excluded: chain C residue    7 MET
Chi-restraints excluded: chain C residue   27 SER
Chi-restraints excluded: chain C residue   31 LEU
Chi-restraints excluded: chain D residue    7 MET
Chi-restraints excluded: chain F residue   30 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 18
   random chunks:
   chunk 3 optimal weight:    3.9990
   chunk 12 optimal weight:    8.9990
   chunk 6 optimal weight:   10.0000
   chunk 1 optimal weight:    8.9990
   chunk 15 optimal weight:    0.3980
   chunk 10 optimal weight:   10.0000
   chunk 16 optimal weight:    9.9990
   chunk 7 optimal weight:    0.7980
   chunk 17 optimal weight:   10.0000
   chunk 4 optimal weight:    5.9990
   chunk 8 optimal weight:    3.9990
   overall best weight:    3.0386

-------------------------------------------------------------------------------
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 = 0.4425 r_free = 0.4425 target = 0.184916 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3987 r_free = 0.3987 target = 0.135445 restraints weight = 1355.936|
|-----------------------------------------------------------------------------|
r_work (start): 0.3972 rms_B_bonded: 2.68
r_work: 0.3869 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.3736 rms_B_bonded: 4.51 restraints_weight: 0.2500
r_work (final): 0.3736
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7991
moved from start:          0.4591

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.032   1446  Z= 0.214
  Angle     :  0.585   6.236   1956  Z= 0.285
  Chirality :  0.043   0.133    258
  Planarity :  0.002   0.009    222
  Dihedral  :  4.474  18.445    192
  Min Nonbonded Distance : 2.620

Molprobity Statistics.
  All-atom Clashscore : 7.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.11 %
    Favored  : 88.89 %
  Rotamer:
    Outliers :  4.49 %
    Allowed  : 32.69 %
    Favored  : 62.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -3.61 (0.53), residues: 180
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.74 (0.41), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.010   0.002   TYR C  20 
 TRP   0.010   0.002   TRP B  19 

Details of bonding type rmsd
  covalent geometry    : bond        0.00488 ( 1446)
  covalent geometry    : angle       0.58550 ( 1956)
  hydrogen bonds       : bond        0.01688 (   23)
  hydrogen bonds       : angle       3.89308 (   69)

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

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

  360 Ramachandran restraints generated.
    180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  360 Ramachandran restraints generated.
    180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  40 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 33
  time to evaluate  : 0.035 
Fit side-chains
REVERT: A    7 MET cc_start: 0.8290 (OUTLIER) cc_final: 0.6941 (mtm)
REVERT: C    7 MET cc_start: 0.8420 (OUTLIER) cc_final: 0.7395 (mtm)
REVERT: C    8 LYS cc_start: 0.7487 (tttm) cc_final: 0.6585 (mttp)
REVERT: D    7 MET cc_start: 0.8189 (OUTLIER) cc_final: 0.7238 (mtm)
REVERT: D    8 LYS cc_start: 0.7814 (tttm) cc_final: 0.6972 (mttp)
  outliers start: 7
  outliers final: 3
  residues processed: 33
  average time/residue: 0.0442
  time to fit residues: 1.6803
Evaluate side-chains
  39 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 33
  time to evaluate  : 0.032 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 MET
Chi-restraints excluded: chain A residue   24 MET
Chi-restraints excluded: chain C residue    7 MET
Chi-restraints excluded: chain C residue   27 SER
Chi-restraints excluded: chain C residue   31 LEU
Chi-restraints excluded: chain D residue    7 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 18
   random chunks:
   chunk 12 optimal weight:    3.9990
   chunk 3 optimal weight:    0.9980
   chunk 13 optimal weight:    2.9990
   chunk 14 optimal weight:    2.9990
   chunk 2 optimal weight:    6.9990
   chunk 0 optimal weight:    0.7980
   chunk 6 optimal weight:   10.0000
   chunk 9 optimal weight:    0.8980
   chunk 7 optimal weight:    1.9990
   chunk 4 optimal weight:   10.0000
   chunk 5 optimal weight:    6.9990
   overall best weight:    1.5384

-------------------------------------------------------------------------------
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 = 0.4454 r_free = 0.4454 target = 0.199461 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4100 r_free = 0.4100 target = 0.153297 restraints weight = 1269.264|
|-----------------------------------------------------------------------------|
r_work (start): 0.4079 rms_B_bonded: 2.29
r_work: 0.3980 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.3858 rms_B_bonded: 4.11 restraints_weight: 0.2500
r_work (final): 0.3858
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7942
moved from start:          0.4680

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.019   1446  Z= 0.121
  Angle     :  0.516   6.908   1956  Z= 0.242
  Chirality :  0.043   0.129    258
  Planarity :  0.002   0.008    222
  Dihedral  :  4.017  14.878    192
  Min Nonbonded Distance : 2.630

Molprobity Statistics.
  All-atom Clashscore : 5.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.78 %
    Favored  : 92.22 %
  Rotamer:
    Outliers :  3.85 %
    Allowed  : 33.33 %
    Favored  : 62.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -3.53 (0.54), residues: 180
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.68 (0.41), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.005   0.001   TYR C  20 
 TRP   0.005   0.001   TRP B  19 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 ( 1446)
  covalent geometry    : angle       0.51627 ( 1956)
  hydrogen bonds       : bond        0.01356 (   23)
  hydrogen bonds       : angle       3.51696 (   69)

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

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

  360 Ramachandran restraints generated.
    180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  360 Ramachandran restraints generated.
    180 Oldfield, 0 Emsley, 180 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  37 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 31
  time to evaluate  : 0.033 
Fit side-chains
REVERT: A    7 MET cc_start: 0.8204 (OUTLIER) cc_final: 0.7324 (mtm)
REVERT: C    7 MET cc_start: 0.8318 (OUTLIER) cc_final: 0.7657 (mtm)
REVERT: C    8 LYS cc_start: 0.7525 (tttm) cc_final: 0.6635 (mttp)
REVERT: D    7 MET cc_start: 0.8158 (OUTLIER) cc_final: 0.7189 (mtm)
  outliers start: 6
  outliers final: 3
  residues processed: 31
  average time/residue: 0.0399
  time to fit residues: 1.4620
Evaluate side-chains
  36 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 30
  time to evaluate  : 0.050 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 MET
Chi-restraints excluded: chain A residue   24 MET
Chi-restraints excluded: chain C residue    7 MET
Chi-restraints excluded: chain C residue   27 SER
Chi-restraints excluded: chain C residue   31 LEU
Chi-restraints excluded: chain D residue    7 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 18
   random chunks:
   chunk 8 optimal weight:    7.9990
   chunk 4 optimal weight:    9.9990
   chunk 9 optimal weight:    0.4980
   chunk 14 optimal weight:    0.6980
   chunk 15 optimal weight:    8.9990
   chunk 0 optimal weight:   10.0000
   chunk 3 optimal weight:    2.9990
   chunk 5 optimal weight:    6.9990
   chunk 1 optimal weight:    8.9990
   chunk 7 optimal weight:    2.9990
   chunk 13 optimal weight:    1.9990
   overall best weight:    1.8386

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

Flipped N/Q/H residues before XYZ refinement:
A  13 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4468 r_free = 0.4468 target = 0.190871 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4078 r_free = 0.4078 target = 0.142791 restraints weight = 1321.091|
|-----------------------------------------------------------------------------|
r_work (start): 0.4039 rms_B_bonded: 2.58
r_work: 0.3939 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.3814 rms_B_bonded: 4.39 restraints_weight: 0.2500
r_work (final): 0.3814
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7893
moved from start:          0.4744

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   1446  Z= 0.145
  Angle     :  0.561   6.763   1956  Z= 0.274
  Chirality :  0.044   0.165    258
  Planarity :  0.002   0.008    222
  Dihedral  :  4.088  15.570    192
  Min Nonbonded Distance : 2.630

Molprobity Statistics.
  All-atom Clashscore : 7.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.89 %
    Favored  : 91.11 %
  Rotamer:
    Outliers :  4.49 %
    Allowed  : 33.33 %
    Favored  : 62.18 %
  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: -3.56 (0.54), residues: 180
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.70 (0.41), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.007   0.001   TYR C  20 
 TRP   0.006   0.001   TRP B  19 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 ( 1446)
  covalent geometry    : angle       0.56144 ( 1956)
  hydrogen bonds       : bond        0.01387 (   23)
  hydrogen bonds       : angle       3.54630 (   69)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 557.76 seconds
wall clock time: 10 minutes 37.58 seconds (637.58 seconds total)