Starting phenix.real_space_refine
on Fri Oct 10 10:37:45 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8u1k_41815/10_2025/8u1k_41815.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8u1k_41815/10_2025/8u1k_41815.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8u1k_41815/10_2025/8u1k_41815.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8u1k_41815/10_2025/8u1k_41815.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8u1k_41815/10_2025/8u1k_41815.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8u1k_41815/10_2025/8u1k_41815.map"
  }
  resolution = 3.5
  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=  -0.001 sd=   0.017
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    1970      2.51       5
     N     500      2.21       5
     O     590      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3060
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 306
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 45, 306
          Classifications: {'peptide': 45}
          Link IDs: {'TRANS': 44}
  Restraints were copied for chains:
    B, C, D, E, F, G, H, I, J
  Time building chain proxies: 0.51, per 1000 atoms: 0.17
  Number of scatterers: 3060
  At special positions: 0
  Unit cell: (58.38, 57.546, 118.428, 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     590      8.00
     N     500      7.00
     C    1970      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: 0.28
  Conformation dependent library (CDL) restraints added in 125.8 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  860 Ramachandran restraints generated.
    430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  820

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 0 sheets defined
      77.8% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.10
  Creating SS restraints...
    Processing helix  chain 'A' and resid 3 through 5
      No H-bonds generated for 'chain 'A' and resid 3 through 5'
    Processing helix  chain 'A' and resid 6 through 11
    Processing helix  chain 'A' and resid 17 through 42
      removed outlier: 4.377A  pdb=" N   THR A  23 " --> pdb=" O   THR A  19 " (cutoff:3.500A)
      removed outlier: 4.046A  pdb=" N   THR A  30 " --> pdb=" O   THR A  26 " (cutoff:3.500A)
      removed outlier: 3.886A  pdb=" N   THR A  41 " --> pdb=" O   ALA A  37 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 3 through 5
      No H-bonds generated for 'chain 'B' and resid 3 through 5'
    Processing helix  chain 'B' and resid 6 through 11
    Processing helix  chain 'B' and resid 17 through 42
      removed outlier: 4.377A  pdb=" N   THR B  23 " --> pdb=" O   THR B  19 " (cutoff:3.500A)
      removed outlier: 4.045A  pdb=" N   THR B  30 " --> pdb=" O   THR B  26 " (cutoff:3.500A)
      removed outlier: 3.887A  pdb=" N   THR B  41 " --> pdb=" O   ALA B  37 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 3 through 5
      No H-bonds generated for 'chain 'C' and resid 3 through 5'
    Processing helix  chain 'C' and resid 6 through 11
    Processing helix  chain 'C' and resid 17 through 42
      removed outlier: 4.378A  pdb=" N   THR C  23 " --> pdb=" O   THR C  19 " (cutoff:3.500A)
      removed outlier: 4.046A  pdb=" N   THR C  30 " --> pdb=" O   THR C  26 " (cutoff:3.500A)
      removed outlier: 3.886A  pdb=" N   THR C  41 " --> pdb=" O   ALA C  37 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 3 through 5
      No H-bonds generated for 'chain 'D' and resid 3 through 5'
    Processing helix  chain 'D' and resid 6 through 11
    Processing helix  chain 'D' and resid 17 through 42
      removed outlier: 4.377A  pdb=" N   THR D  23 " --> pdb=" O   THR D  19 " (cutoff:3.500A)
      removed outlier: 4.046A  pdb=" N   THR D  30 " --> pdb=" O   THR D  26 " (cutoff:3.500A)
      removed outlier: 3.887A  pdb=" N   THR D  41 " --> pdb=" O   ALA D  37 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 3 through 5
      No H-bonds generated for 'chain 'E' and resid 3 through 5'
    Processing helix  chain 'E' and resid 6 through 11
    Processing helix  chain 'E' and resid 17 through 42
      removed outlier: 4.378A  pdb=" N   THR E  23 " --> pdb=" O   THR E  19 " (cutoff:3.500A)
      removed outlier: 4.046A  pdb=" N   THR E  30 " --> pdb=" O   THR E  26 " (cutoff:3.500A)
      removed outlier: 3.887A  pdb=" N   THR E  41 " --> pdb=" O   ALA E  37 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 3 through 5
      No H-bonds generated for 'chain 'F' and resid 3 through 5'
    Processing helix  chain 'F' and resid 6 through 11
    Processing helix  chain 'F' and resid 17 through 42
      removed outlier: 4.377A  pdb=" N   THR F  23 " --> pdb=" O   THR F  19 " (cutoff:3.500A)
      removed outlier: 4.046A  pdb=" N   THR F  30 " --> pdb=" O   THR F  26 " (cutoff:3.500A)
      removed outlier: 3.886A  pdb=" N   THR F  41 " --> pdb=" O   ALA F  37 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 3 through 5
      No H-bonds generated for 'chain 'G' and resid 3 through 5'
    Processing helix  chain 'G' and resid 6 through 11
    Processing helix  chain 'G' and resid 17 through 42
      removed outlier: 4.378A  pdb=" N   THR G  23 " --> pdb=" O   THR G  19 " (cutoff:3.500A)
      removed outlier: 4.045A  pdb=" N   THR G  30 " --> pdb=" O   THR G  26 " (cutoff:3.500A)
      removed outlier: 3.886A  pdb=" N   THR G  41 " --> pdb=" O   ALA G  37 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 3 through 5
      No H-bonds generated for 'chain 'H' and resid 3 through 5'
    Processing helix  chain 'H' and resid 6 through 11
    Processing helix  chain 'H' and resid 17 through 42
      removed outlier: 4.377A  pdb=" N   THR H  23 " --> pdb=" O   THR H  19 " (cutoff:3.500A)
      removed outlier: 4.046A  pdb=" N   THR H  30 " --> pdb=" O   THR H  26 " (cutoff:3.500A)
      removed outlier: 3.886A  pdb=" N   THR H  41 " --> pdb=" O   ALA H  37 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 3 through 5
      No H-bonds generated for 'chain 'I' and resid 3 through 5'
    Processing helix  chain 'I' and resid 6 through 11
    Processing helix  chain 'I' and resid 17 through 42
      removed outlier: 4.378A  pdb=" N   THR I  23 " --> pdb=" O   THR I  19 " (cutoff:3.500A)
      removed outlier: 4.045A  pdb=" N   THR I  30 " --> pdb=" O   THR I  26 " (cutoff:3.500A)
      removed outlier: 3.887A  pdb=" N   THR I  41 " --> pdb=" O   ALA I  37 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 3 through 5
      No H-bonds generated for 'chain 'J' and resid 3 through 5'
    Processing helix  chain 'J' and resid 6 through 11
    Processing helix  chain 'J' and resid 17 through 42
      removed outlier: 4.378A  pdb=" N   THR J  23 " --> pdb=" O   THR J  19 " (cutoff:3.500A)
      removed outlier: 4.045A  pdb=" N   THR J  30 " --> pdb=" O   THR J  26 " (cutoff:3.500A)
      removed outlier: 3.886A  pdb=" N   THR J  41 " --> pdb=" O   ALA J  37 " (cutoff:3.500A)

    210 hydrogen bonds defined for protein.
    630 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: 0.42

  Time building geometry restraints manager: 0.37 seconds

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

  Histogram of bond lengths:
        1.23 -     1.29: 480
        1.29 -     1.35: 480
        1.35 -     1.42: 140
        1.42 -     1.48: 550
        1.48 -     1.54: 1420
  Bond restraints: 3070
  Sorted by residual:
  bond pdb=" CA  ALA E  38 "
       pdb=" C   ALA E  38 "
    ideal  model  delta    sigma   weight residual
    1.524  1.516  0.009 1.29e-02 6.01e+03 4.38e-01
  bond pdb=" CA  ALA A  38 "
       pdb=" C   ALA A  38 "
    ideal  model  delta    sigma   weight residual
    1.524  1.516  0.008 1.29e-02 6.01e+03 4.00e-01
  bond pdb=" CA  ALA C  38 "
       pdb=" C   ALA C  38 "
    ideal  model  delta    sigma   weight residual
    1.524  1.516  0.008 1.29e-02 6.01e+03 3.96e-01
  bond pdb=" CA  ALA I  38 "
       pdb=" C   ALA I  38 "
    ideal  model  delta    sigma   weight residual
    1.524  1.516  0.008 1.29e-02 6.01e+03 3.85e-01
  bond pdb=" N   ALA F  38 "
       pdb=" CA  ALA F  38 "
    ideal  model  delta    sigma   weight residual
    1.459  1.451  0.008 1.24e-02 6.50e+03 3.84e-01
  ... (remaining 3065 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.65: 3507
        0.65 -     1.30: 468
        1.30 -     1.95: 195
        1.95 -     2.60: 30
        2.60 -     3.25: 20
  Bond angle restraints: 4220
  Sorted by residual:
  angle pdb=" N   ILE G   4 "
        pdb=" CA  ILE G   4 "
        pdb=" C   ILE G   4 "
      ideal   model   delta    sigma   weight residual
     109.34  112.59   -3.25 2.08e+00 2.31e-01 2.44e+00
  angle pdb=" N   ILE F   4 "
        pdb=" CA  ILE F   4 "
        pdb=" C   ILE F   4 "
      ideal   model   delta    sigma   weight residual
     109.34  112.59   -3.25 2.08e+00 2.31e-01 2.43e+00
  angle pdb=" N   ILE A   4 "
        pdb=" CA  ILE A   4 "
        pdb=" C   ILE A   4 "
      ideal   model   delta    sigma   weight residual
     109.34  112.58   -3.24 2.08e+00 2.31e-01 2.43e+00
  angle pdb=" N   ILE H   4 "
        pdb=" CA  ILE H   4 "
        pdb=" C   ILE H   4 "
      ideal   model   delta    sigma   weight residual
     109.34  112.58   -3.24 2.08e+00 2.31e-01 2.42e+00
  angle pdb=" N   ILE B   4 "
        pdb=" CA  ILE B   4 "
        pdb=" C   ILE B   4 "
      ideal   model   delta    sigma   weight residual
     109.34  112.56   -3.22 2.08e+00 2.31e-01 2.40e+00
  ... (remaining 4215 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -     9.83: 1500
        9.83 -    19.66: 140
       19.66 -    29.49: 70
       29.49 -    39.32: 30
       39.32 -    49.16: 30
  Dihedral angle restraints: 1770
    sinusoidal: 500
      harmonic: 1270
  Sorted by residual:
  dihedral pdb=" N   ILE A   4 "
           pdb=" CA  ILE A   4 "
           pdb=" CB  ILE A   4 "
           pdb=" CG1 ILE A   4 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00  -10.84  -49.16     3      1.50e+01 4.44e-03 8.74e+00
  dihedral pdb=" N   ILE B   4 "
           pdb=" CA  ILE B   4 "
           pdb=" CB  ILE B   4 "
           pdb=" CG1 ILE B   4 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00  -10.85  -49.15     3      1.50e+01 4.44e-03 8.74e+00
  dihedral pdb=" N   ILE I   4 "
           pdb=" CA  ILE I   4 "
           pdb=" CB  ILE I   4 "
           pdb=" CG1 ILE I   4 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00  -10.90  -49.10     3      1.50e+01 4.44e-03 8.73e+00
  ... (remaining 1767 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.021: 282
       0.021 -    0.041: 173
       0.041 -    0.062: 95
       0.062 -    0.083: 50
       0.083 -    0.103: 40
  Chirality restraints: 640
  Sorted by residual:
  chirality pdb=" CA  THR F  30 "
            pdb=" N   THR F  30 "
            pdb=" C   THR F  30 "
            pdb=" CB  THR F  30 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.42    0.10 2.00e-01 2.50e+01 2.67e-01
  chirality pdb=" CA  THR A  30 "
            pdb=" N   THR A  30 "
            pdb=" C   THR A  30 "
            pdb=" CB  THR A  30 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.42    0.10 2.00e-01 2.50e+01 2.59e-01
  chirality pdb=" CA  THR J  30 "
            pdb=" N   THR J  30 "
            pdb=" C   THR J  30 "
            pdb=" CB  THR J  30 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.42    0.10 2.00e-01 2.50e+01 2.57e-01
  ... (remaining 637 not shown)

  Planarity restraints: 490
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY F  25 "    0.008 2.00e-02 2.50e+03   1.52e-02 2.31e+00
        pdb=" C   GLY F  25 "   -0.026 2.00e-02 2.50e+03
        pdb=" O   GLY F  25 "    0.010 2.00e-02 2.50e+03
        pdb=" N   THR F  26 "    0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY J  25 "    0.008 2.00e-02 2.50e+03   1.51e-02 2.28e+00
        pdb=" C   GLY J  25 "   -0.026 2.00e-02 2.50e+03
        pdb=" O   GLY J  25 "    0.010 2.00e-02 2.50e+03
        pdb=" N   THR J  26 "    0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY G  25 "   -0.008 2.00e-02 2.50e+03   1.51e-02 2.28e+00
        pdb=" C   GLY G  25 "    0.026 2.00e-02 2.50e+03
        pdb=" O   GLY G  25 "   -0.010 2.00e-02 2.50e+03
        pdb=" N   THR G  26 "   -0.009 2.00e-02 2.50e+03
  ... (remaining 487 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.74: 509
        2.74 -     3.28: 3380
        3.28 -     3.82: 5155
        3.82 -     4.36: 5996
        4.36 -     4.90: 9519
  Nonbonded interactions: 24559
  Sorted by model distance:
  nonbonded pdb=" O   ARG D  29 "
            pdb=" OG1 THR D  33 "
     model   vdw
     2.206 3.040
  nonbonded pdb=" O   ARG A  29 "
            pdb=" OG1 THR A  33 "
     model   vdw
     2.206 3.040
  nonbonded pdb=" O   ARG J  29 "
            pdb=" OG1 THR J  33 "
     model   vdw
     2.206 3.040
  nonbonded pdb=" O   ARG H  29 "
            pdb=" OG1 THR H  33 "
     model   vdw
     2.207 3.040
  nonbonded pdb=" O   ARG B  29 "
            pdb=" OG1 THR B  33 "
     model   vdw
     2.207 3.040
  ... (remaining 24554 not shown)

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

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
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:             2.100
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.070
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     3.990
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  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:1.020
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    7.270
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7598
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.018   3070  Z= 0.203
  Angle     :  0.609   3.251   4220  Z= 0.377
  Chirality :  0.040   0.103    640
  Planarity :  0.003   0.015    490
  Dihedral  : 13.638  49.155    950
  Min Nonbonded Distance : 2.206

Molprobity Statistics.
  All-atom Clashscore : 12.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 10.00 %
    Favored  : 86.67 %
  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 aren not related in a simple way.
  whole: -5.99 (0.23), residues: 430
  helix: -3.55 (0.17), residues: 340
  sheet:  None (None), residues: 0
  loop : -4.60 (0.29), residues: 90

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG G  29 
 TYR   0.003   0.001   TYR C   6 
 PHE   0.002   0.001   PHE B  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00371 ( 3070)
  covalent geometry    : angle       0.60898 ( 4220)
  hydrogen bonds       : bond        0.05959 (  210)
  hydrogen bonds       : angle       4.99398 (  630)

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

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

  860 Ramachandran restraints generated.
    430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  860 Ramachandran restraints generated.
    430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  225 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 215
  time to evaluate  : 0.105 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   16 VAL cc_start: 0.8181 (m) cc_final: 0.7831 (p)
REVERT: A   23 THR cc_start: 0.7918 (m) cc_final: 0.7493 (p)
REVERT: A   24 LEU cc_start: 0.8794 (tp) cc_final: 0.8574 (tp)
REVERT: A   26 THR cc_start: 0.7855 (t) cc_final: 0.7535 (m)
REVERT: A   29 ARG cc_start: 0.6708 (mtt180) cc_final: 0.6429 (mtt-85)
REVERT: B   18 VAL cc_start: 0.8584 (t) cc_final: 0.8291 (m)
REVERT: B   23 THR cc_start: 0.7839 (m) cc_final: 0.7287 (p)
REVERT: B   24 LEU cc_start: 0.8771 (tp) cc_final: 0.8389 (tp)
REVERT: B   34 LYS cc_start: 0.7539 (mtmm) cc_final: 0.7117 (mtmm)
REVERT: C   18 VAL cc_start: 0.8548 (t) cc_final: 0.8287 (m)
REVERT: C   23 THR cc_start: 0.7859 (m) cc_final: 0.7352 (p)
REVERT: C   34 LYS cc_start: 0.7406 (mtmm) cc_final: 0.7068 (mtmm)
REVERT: D    4 ILE cc_start: 0.8361 (OUTLIER) cc_final: 0.8137 (mp)
REVERT: D   18 VAL cc_start: 0.8513 (t) cc_final: 0.8287 (m)
REVERT: D   23 THR cc_start: 0.7891 (m) cc_final: 0.7252 (p)
REVERT: D   24 LEU cc_start: 0.8740 (tp) cc_final: 0.8517 (tp)
REVERT: D   27 ASN cc_start: 0.7039 (m-40) cc_final: 0.6792 (m110)
REVERT: E   18 VAL cc_start: 0.8614 (t) cc_final: 0.8289 (m)
REVERT: E   27 ASN cc_start: 0.7090 (m-40) cc_final: 0.6839 (m110)
REVERT: F   23 THR cc_start: 0.7904 (m) cc_final: 0.7425 (p)
REVERT: F   26 THR cc_start: 0.8031 (t) cc_final: 0.7751 (m)
REVERT: F   29 ARG cc_start: 0.6889 (mtt180) cc_final: 0.6464 (mtt-85)
REVERT: G   23 THR cc_start: 0.7990 (m) cc_final: 0.7534 (p)
REVERT: G   24 LEU cc_start: 0.8864 (tp) cc_final: 0.8451 (tt)
REVERT: G   26 THR cc_start: 0.8044 (t) cc_final: 0.7399 (m)
REVERT: G   29 ARG cc_start: 0.6552 (mtt180) cc_final: 0.6244 (mtt-85)
REVERT: H   23 THR cc_start: 0.8003 (m) cc_final: 0.7600 (p)
REVERT: H   24 LEU cc_start: 0.8858 (tp) cc_final: 0.8618 (tp)
REVERT: I   23 THR cc_start: 0.7899 (m) cc_final: 0.7374 (p)
REVERT: I   24 LEU cc_start: 0.8800 (tp) cc_final: 0.8525 (tp)
REVERT: J   18 VAL cc_start: 0.8554 (t) cc_final: 0.8305 (m)
REVERT: J   23 THR cc_start: 0.7933 (m) cc_final: 0.7479 (p)
REVERT: J   24 LEU cc_start: 0.8856 (tp) cc_final: 0.8403 (tt)
REVERT: J   34 LYS cc_start: 0.7465 (mtmm) cc_final: 0.7102 (mtmm)
  outliers start: 10
  outliers final: 6
  residues processed: 224
  average time/residue: 0.0541
  time to fit residues: 14.6167
Evaluate side-chains
  222 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 215
  time to evaluate  : 0.106 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue    4 ILE
Chi-restraints excluded: chain D residue    4 ILE
Chi-restraints excluded: chain F residue    4 ILE
Chi-restraints excluded: chain G residue    4 ILE
Chi-restraints excluded: chain H residue    4 ILE
Chi-restraints excluded: chain I residue    4 ILE
Chi-restraints excluded: chain J residue    4 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 24 optimal weight:    0.6980
   chunk 26 optimal weight:    2.9990
   chunk 2 optimal weight:    0.9990
   chunk 16 optimal weight:    0.4980
   chunk 32 optimal weight:    2.9990
   chunk 31 optimal weight:    0.8980
   chunk 25 optimal weight:    2.9990
   chunk 19 optimal weight:    0.9980
   chunk 30 optimal weight:    0.6980
   chunk 22 optimal weight:    8.9990
   chunk 37 optimal weight:    0.7980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
G  27 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.099578 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.089846 restraints weight = 5840.482|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.092040 restraints weight = 2746.287|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.093482 restraints weight = 1599.965|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.094310 restraints weight = 1093.287|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.094882 restraints weight = 849.139|
|-----------------------------------------------------------------------------|
r_work (final): 0.3434
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7515
moved from start:          0.2598

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.016   3070  Z= 0.120
  Angle     :  0.501   4.620   4220  Z= 0.282
  Chirality :  0.038   0.098    640
  Planarity :  0.004   0.034    490
  Dihedral  :  8.666  55.743    474
  Min Nonbonded Distance : 2.609

Molprobity Statistics.
  All-atom Clashscore : 12.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.79 %
    Favored  : 97.21 %
  Rotamer:
    Outliers : 10.00 %
    Allowed  : 32.00 %
    Favored  : 58.00 %
  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 aren not related in a simple way.
  whole: -4.27 (0.33), residues: 430
  helix: -2.39 (0.24), residues: 340
  sheet:  None (None), residues: 0
  loop : -3.73 (0.41), residues: 90

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B  29 
 TYR   0.008   0.002   TYR H   6 
 PHE   0.003   0.001   PHE I  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00229 ( 3070)
  covalent geometry    : angle       0.50060 ( 4220)
  hydrogen bonds       : bond        0.03235 (  210)
  hydrogen bonds       : angle       4.40767 (  630)

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

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

  860 Ramachandran restraints generated.
    430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  860 Ramachandran restraints generated.
    430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  242 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 212
  time to evaluate  : 0.108 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   16 VAL cc_start: 0.8066 (m) cc_final: 0.7816 (p)
REVERT: A   18 VAL cc_start: 0.8772 (t) cc_final: 0.8516 (m)
REVERT: A   23 THR cc_start: 0.7841 (m) cc_final: 0.7378 (p)
REVERT: B   23 THR cc_start: 0.7835 (m) cc_final: 0.7300 (p)
REVERT: B   24 LEU cc_start: 0.8555 (tp) cc_final: 0.8332 (tp)
REVERT: C    4 ILE cc_start: 0.8133 (OUTLIER) cc_final: 0.7869 (mp)
REVERT: C   23 THR cc_start: 0.7732 (m) cc_final: 0.7272 (p)
REVERT: C   28 LEU cc_start: 0.8693 (tp) cc_final: 0.8428 (tt)
REVERT: C   34 LYS cc_start: 0.7414 (mtmm) cc_final: 0.7191 (mtmm)
REVERT: D   18 VAL cc_start: 0.8551 (t) cc_final: 0.8271 (m)
REVERT: D   23 THR cc_start: 0.7865 (m) cc_final: 0.7240 (p)
REVERT: D   27 ASN cc_start: 0.6804 (m-40) cc_final: 0.6521 (m110)
REVERT: E   16 VAL cc_start: 0.8063 (m) cc_final: 0.7848 (m)
REVERT: E   18 VAL cc_start: 0.8668 (t) cc_final: 0.8348 (m)
REVERT: F   23 THR cc_start: 0.7852 (m) cc_final: 0.7362 (p)
REVERT: F   26 THR cc_start: 0.8034 (t) cc_final: 0.7676 (m)
REVERT: G   23 THR cc_start: 0.7945 (m) cc_final: 0.7464 (p)
REVERT: G   24 LEU cc_start: 0.8664 (tp) cc_final: 0.8362 (tt)
REVERT: G   26 THR cc_start: 0.8081 (t) cc_final: 0.7619 (t)
REVERT: H   23 THR cc_start: 0.7912 (m) cc_final: 0.7488 (p)
REVERT: H   24 LEU cc_start: 0.8806 (tp) cc_final: 0.8578 (tp)
REVERT: I   23 THR cc_start: 0.7695 (m) cc_final: 0.7241 (p)
REVERT: I   24 LEU cc_start: 0.8740 (tp) cc_final: 0.8337 (tt)
REVERT: J   18 VAL cc_start: 0.8615 (t) cc_final: 0.8390 (m)
REVERT: J   23 THR cc_start: 0.7712 (m) cc_final: 0.7329 (p)
REVERT: J   24 LEU cc_start: 0.8771 (tp) cc_final: 0.8340 (tt)
  outliers start: 30
  outliers final: 24
  residues processed: 219
  average time/residue: 0.0584
  time to fit residues: 15.4476
Evaluate side-chains
  236 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 211
  time to evaluate  : 0.119 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 VAL
Chi-restraints excluded: chain A residue   30 THR
Chi-restraints excluded: chain B residue   15 VAL
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   41 THR
Chi-restraints excluded: chain C residue    4 ILE
Chi-restraints excluded: chain C residue   15 VAL
Chi-restraints excluded: chain C residue   41 THR
Chi-restraints excluded: chain D residue   15 VAL
Chi-restraints excluded: chain D residue   17 ILE
Chi-restraints excluded: chain E residue   15 VAL
Chi-restraints excluded: chain E residue   23 THR
Chi-restraints excluded: chain E residue   39 VAL
Chi-restraints excluded: chain F residue    4 ILE
Chi-restraints excluded: chain F residue    8 LEU
Chi-restraints excluded: chain F residue   15 VAL
Chi-restraints excluded: chain G residue   15 VAL
Chi-restraints excluded: chain G residue   39 VAL
Chi-restraints excluded: chain H residue    4 ILE
Chi-restraints excluded: chain H residue   15 VAL
Chi-restraints excluded: chain H residue   39 VAL
Chi-restraints excluded: chain I residue    4 ILE
Chi-restraints excluded: chain I residue   17 ILE
Chi-restraints excluded: chain J residue    4 ILE
Chi-restraints excluded: chain J residue   17 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 7 optimal weight:    2.9990
   chunk 22 optimal weight:    0.7980
   chunk 32 optimal weight:    0.8980
   chunk 34 optimal weight:    0.8980
   chunk 4 optimal weight:    0.0980
   chunk 0 optimal weight:    6.9990
   chunk 2 optimal weight:    0.6980
   chunk 38 optimal weight:    1.9990
   chunk 8 optimal weight:    0.0870
   chunk 26 optimal weight:    3.9990
   chunk 24 optimal weight:    4.9990
   overall best weight:    0.5158

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

Flipped N/Q/H residues before XYZ refinement:
J  27 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.101888 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.092191 restraints weight = 5828.431|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.094485 restraints weight = 2707.758|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.095823 restraints weight = 1548.392|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.096746 restraints weight = 1055.710|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.097298 restraints weight = 808.146|
|-----------------------------------------------------------------------------|
r_work (final): 0.3462
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7479
moved from start:          0.3390

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   3070  Z= 0.115
  Angle     :  0.521   6.550   4220  Z= 0.287
  Chirality :  0.038   0.125    640
  Planarity :  0.004   0.047    490
  Dihedral  :  6.667  47.049    470
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 9.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.86 %
    Favored  : 98.14 %
  Rotamer:
    Outliers : 11.33 %
    Allowed  : 34.00 %
    Favored  : 54.67 %
  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 aren not related in a simple way.
  whole: -3.91 (0.33), residues: 430
  helix: -2.12 (0.24), residues: 340
  sheet:  None (None), residues: 0
  loop : -3.63 (0.38), residues: 90

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B  29 
 TYR   0.008   0.001   TYR D   6 
 PHE   0.002   0.000   PHE J  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00228 ( 3070)
  covalent geometry    : angle       0.52056 ( 4220)
  hydrogen bonds       : bond        0.03196 (  210)
  hydrogen bonds       : angle       3.99979 (  630)

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

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

  860 Ramachandran restraints generated.
    430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  860 Ramachandran restraints generated.
    430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  245 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 211
  time to evaluate  : 0.118 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   16 VAL cc_start: 0.7999 (m) cc_final: 0.7747 (p)
REVERT: A   18 VAL cc_start: 0.8741 (t) cc_final: 0.8468 (m)
REVERT: A   23 THR cc_start: 0.7820 (m) cc_final: 0.7398 (p)
REVERT: B   23 THR cc_start: 0.7835 (m) cc_final: 0.7356 (p)
REVERT: B   24 LEU cc_start: 0.8535 (tp) cc_final: 0.7448 (mm)
REVERT: C   23 THR cc_start: 0.7727 (m) cc_final: 0.7233 (p)
REVERT: C   34 LYS cc_start: 0.7333 (mtmm) cc_final: 0.7120 (mtmm)
REVERT: D   18 VAL cc_start: 0.8569 (t) cc_final: 0.8276 (m)
REVERT: D   23 THR cc_start: 0.7827 (m) cc_final: 0.7216 (p)
REVERT: D   24 LEU cc_start: 0.8384 (tp) cc_final: 0.7482 (mm)
REVERT: D   27 ASN cc_start: 0.6479 (m-40) cc_final: 0.6191 (m110)
REVERT: E   18 VAL cc_start: 0.8593 (t) cc_final: 0.8302 (m)
REVERT: F   23 THR cc_start: 0.7710 (m) cc_final: 0.7089 (p)
REVERT: G   23 THR cc_start: 0.7878 (m) cc_final: 0.7318 (p)
REVERT: G   24 LEU cc_start: 0.8425 (tp) cc_final: 0.8166 (tt)
REVERT: H   23 THR cc_start: 0.7906 (m) cc_final: 0.7557 (p)
REVERT: H   24 LEU cc_start: 0.8774 (tp) cc_final: 0.8573 (tp)
REVERT: I   23 THR cc_start: 0.7640 (m) cc_final: 0.7231 (p)
REVERT: I   24 LEU cc_start: 0.8749 (tp) cc_final: 0.8389 (tt)
REVERT: I   39 VAL cc_start: 0.8475 (p) cc_final: 0.8271 (t)
REVERT: J   23 THR cc_start: 0.7726 (m) cc_final: 0.7357 (p)
REVERT: J   24 LEU cc_start: 0.8796 (tp) cc_final: 0.8418 (tt)
REVERT: J   34 LYS cc_start: 0.7398 (mtmt) cc_final: 0.7113 (mtmm)
  outliers start: 34
  outliers final: 26
  residues processed: 217
  average time/residue: 0.0575
  time to fit residues: 14.9820
Evaluate side-chains
  236 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 210
  time to evaluate  : 0.107 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 VAL
Chi-restraints excluded: chain A residue   17 ILE
Chi-restraints excluded: chain A residue   41 THR
Chi-restraints excluded: chain B residue   15 VAL
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain C residue   15 VAL
Chi-restraints excluded: chain C residue   17 ILE
Chi-restraints excluded: chain C residue   41 THR
Chi-restraints excluded: chain D residue   15 VAL
Chi-restraints excluded: chain D residue   17 ILE
Chi-restraints excluded: chain E residue    2 THR
Chi-restraints excluded: chain E residue   15 VAL
Chi-restraints excluded: chain E residue   23 THR
Chi-restraints excluded: chain E residue   39 VAL
Chi-restraints excluded: chain F residue    4 ILE
Chi-restraints excluded: chain F residue   15 VAL
Chi-restraints excluded: chain F residue   24 LEU
Chi-restraints excluded: chain F residue   28 LEU
Chi-restraints excluded: chain F residue   39 VAL
Chi-restraints excluded: chain G residue    8 LEU
Chi-restraints excluded: chain G residue   15 VAL
Chi-restraints excluded: chain G residue   39 VAL
Chi-restraints excluded: chain H residue    4 ILE
Chi-restraints excluded: chain H residue   39 VAL
Chi-restraints excluded: chain I residue    4 ILE
Chi-restraints excluded: chain J residue    4 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 7 optimal weight:    3.9990
   chunk 26 optimal weight:    3.9990
   chunk 13 optimal weight:    0.0020
   chunk 21 optimal weight:    1.9990
   chunk 5 optimal weight:    1.9990
   chunk 6 optimal weight:    0.8980
   chunk 8 optimal weight:    0.0770
   chunk 17 optimal weight:    0.9980
   chunk 15 optimal weight:    0.7980
   chunk 10 optimal weight:    0.7980
   chunk 24 optimal weight:    0.6980
   overall best weight:    0.4746

-------------------------------------------------------------------------------
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 = 0.3584 r_free = 0.3584 target = 0.103352 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.093514 restraints weight = 5965.492|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.095813 restraints weight = 2725.648|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.097225 restraints weight = 1549.950|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.098081 restraints weight = 1045.625|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.098662 restraints weight = 807.344|
|-----------------------------------------------------------------------------|
r_work (final): 0.3491
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7448
moved from start:          0.3896

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   3070  Z= 0.112
  Angle     :  0.517   6.191   4220  Z= 0.283
  Chirality :  0.039   0.135    640
  Planarity :  0.004   0.048    490
  Dihedral  :  5.848  46.639    468
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 11.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.86 %
    Favored  : 98.14 %
  Rotamer:
    Outliers : 14.33 %
    Allowed  : 34.00 %
    Favored  : 51.67 %
  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 aren not related in a simple way.
  whole: -3.53 (0.34), residues: 430
  helix: -1.86 (0.25), residues: 340
  sheet:  None (None), residues: 0
  loop : -3.48 (0.38), residues: 90

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG B  29 
 TYR   0.005   0.001   TYR G   6 
 PHE   0.004   0.001   PHE D  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00231 ( 3070)
  covalent geometry    : angle       0.51719 ( 4220)
  hydrogen bonds       : bond        0.03298 (  210)
  hydrogen bonds       : angle       3.81370 (  630)

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

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

  860 Ramachandran restraints generated.
    430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  860 Ramachandran restraints generated.
    430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  250 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 207
  time to evaluate  : 0.095 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   16 VAL cc_start: 0.7856 (m) cc_final: 0.7625 (p)
REVERT: A   18 VAL cc_start: 0.8780 (t) cc_final: 0.8487 (m)
REVERT: A   23 THR cc_start: 0.7756 (m) cc_final: 0.7348 (p)
REVERT: B   23 THR cc_start: 0.7847 (m) cc_final: 0.7472 (p)
REVERT: B   24 LEU cc_start: 0.8216 (tp) cc_final: 0.7307 (mm)
REVERT: C   18 VAL cc_start: 0.8592 (p) cc_final: 0.8349 (m)
REVERT: C   23 THR cc_start: 0.7664 (m) cc_final: 0.7147 (p)
REVERT: C   24 LEU cc_start: 0.8275 (tp) cc_final: 0.7328 (mm)
REVERT: C   34 LYS cc_start: 0.7296 (mtmm) cc_final: 0.7064 (mtmm)
REVERT: D   18 VAL cc_start: 0.8568 (t) cc_final: 0.8261 (m)
REVERT: D   23 THR cc_start: 0.7772 (m) cc_final: 0.7146 (p)
REVERT: D   24 LEU cc_start: 0.8161 (tp) cc_final: 0.7199 (mm)
REVERT: D   27 ASN cc_start: 0.6414 (m-40) cc_final: 0.6164 (m110)
REVERT: D   34 LYS cc_start: 0.7342 (mtmm) cc_final: 0.7118 (mtmm)
REVERT: E   18 VAL cc_start: 0.8531 (t) cc_final: 0.8273 (m)
REVERT: F   23 THR cc_start: 0.7762 (m) cc_final: 0.7294 (p)
REVERT: F   24 LEU cc_start: 0.8411 (OUTLIER) cc_final: 0.8120 (tt)
REVERT: G   23 THR cc_start: 0.7795 (m) cc_final: 0.7346 (p)
REVERT: H   23 THR cc_start: 0.7918 (m) cc_final: 0.7606 (p)
REVERT: H   24 LEU cc_start: 0.8760 (tp) cc_final: 0.8487 (tt)
REVERT: I   23 THR cc_start: 0.7670 (m) cc_final: 0.7303 (p)
REVERT: I   24 LEU cc_start: 0.8712 (tp) cc_final: 0.8384 (tt)
REVERT: J    2 THR cc_start: 0.7512 (OUTLIER) cc_final: 0.7190 (p)
REVERT: J   23 THR cc_start: 0.7640 (m) cc_final: 0.7356 (p)
REVERT: J   24 LEU cc_start: 0.8797 (tp) cc_final: 0.8439 (tt)
  outliers start: 43
  outliers final: 34
  residues processed: 218
  average time/residue: 0.0555
  time to fit residues: 14.6274
Evaluate side-chains
  242 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 206
  time to evaluate  : 0.105 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 ILE
Chi-restraints excluded: chain A residue   30 THR
Chi-restraints excluded: chain A residue   39 VAL
Chi-restraints excluded: chain A residue   41 THR
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain C residue    9 ILE
Chi-restraints excluded: chain C residue   15 VAL
Chi-restraints excluded: chain C residue   17 ILE
Chi-restraints excluded: chain C residue   30 THR
Chi-restraints excluded: chain C residue   41 THR
Chi-restraints excluded: chain D residue    2 THR
Chi-restraints excluded: chain D residue    9 ILE
Chi-restraints excluded: chain D residue   15 VAL
Chi-restraints excluded: chain D residue   17 ILE
Chi-restraints excluded: chain E residue   17 ILE
Chi-restraints excluded: chain E residue   39 VAL
Chi-restraints excluded: chain F residue   15 VAL
Chi-restraints excluded: chain F residue   17 ILE
Chi-restraints excluded: chain F residue   24 LEU
Chi-restraints excluded: chain F residue   39 VAL
Chi-restraints excluded: chain G residue    2 THR
Chi-restraints excluded: chain G residue    8 LEU
Chi-restraints excluded: chain G residue   15 VAL
Chi-restraints excluded: chain G residue   28 LEU
Chi-restraints excluded: chain G residue   39 VAL
Chi-restraints excluded: chain H residue    2 THR
Chi-restraints excluded: chain H residue    4 ILE
Chi-restraints excluded: chain H residue   17 ILE
Chi-restraints excluded: chain H residue   39 VAL
Chi-restraints excluded: chain I residue    2 THR
Chi-restraints excluded: chain I residue    4 ILE
Chi-restraints excluded: chain J residue    2 THR
Chi-restraints excluded: chain J residue    4 ILE
Chi-restraints excluded: chain J residue   12 LEU
Chi-restraints excluded: chain J residue   15 VAL
Chi-restraints excluded: chain J residue   41 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 10 optimal weight:    1.9990
   chunk 39 optimal weight:    5.9990
   chunk 26 optimal weight:    2.9990
   chunk 23 optimal weight:    2.9990
   chunk 27 optimal weight:    2.9990
   chunk 18 optimal weight:    0.9990
   chunk 13 optimal weight:    8.9990
   chunk 25 optimal weight:    0.9990
   chunk 37 optimal weight:    0.3980
   chunk 32 optimal weight:    2.9990
   chunk 14 optimal weight:    1.9990
   overall best weight:    1.2788

-------------------------------------------------------------------------------
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 = 0.3554 r_free = 0.3554 target = 0.101786 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.091707 restraints weight = 5904.520|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.093915 restraints weight = 2834.052|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.095329 restraints weight = 1676.113|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.096239 restraints weight = 1161.836|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.096691 restraints weight = 897.341|
|-----------------------------------------------------------------------------|
r_work (final): 0.3459
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7528
moved from start:          0.4029

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   3070  Z= 0.174
  Angle     :  0.526   5.137   4220  Z= 0.301
  Chirality :  0.041   0.129    640
  Planarity :  0.004   0.046    490
  Dihedral  :  5.358  42.545    466
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 13.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.79 %
    Favored  : 97.21 %
  Rotamer:
    Outliers : 16.33 %
    Allowed  : 33.00 %
    Favored  : 50.67 %
  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 aren not related in a simple way.
  whole: -3.74 (0.32), residues: 430
  helix: -2.05 (0.24), residues: 340
  sheet:  None (None), residues: 0
  loop : -3.36 (0.38), residues: 90

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG G  29 
 TYR   0.007   0.001   TYR H   6 
 PHE   0.007   0.001   PHE C  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 ( 3070)
  covalent geometry    : angle       0.52641 ( 4220)
  hydrogen bonds       : bond        0.03777 (  210)
  hydrogen bonds       : angle       4.30325 (  630)

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

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

  860 Ramachandran restraints generated.
    430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  860 Ramachandran restraints generated.
    430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  259 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 210
  time to evaluate  : 0.117 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   16 VAL cc_start: 0.7972 (m) cc_final: 0.7719 (p)
REVERT: A   22 THR cc_start: 0.8451 (m) cc_final: 0.8216 (p)
REVERT: A   23 THR cc_start: 0.7766 (m) cc_final: 0.7264 (p)
REVERT: B   23 THR cc_start: 0.7986 (m) cc_final: 0.7571 (p)
REVERT: C   23 THR cc_start: 0.7795 (m) cc_final: 0.7117 (p)
REVERT: C   24 LEU cc_start: 0.8456 (tp) cc_final: 0.7499 (mm)
REVERT: C   27 ASN cc_start: 0.6623 (m-40) cc_final: 0.6246 (m110)
REVERT: C   34 LYS cc_start: 0.7316 (mtmm) cc_final: 0.7062 (mtmm)
REVERT: D   18 VAL cc_start: 0.8528 (t) cc_final: 0.8256 (m)
REVERT: D   23 THR cc_start: 0.7913 (m) cc_final: 0.7309 (p)
REVERT: D   24 LEU cc_start: 0.8377 (tp) cc_final: 0.7439 (mm)
REVERT: D   27 ASN cc_start: 0.6610 (m-40) cc_final: 0.6345 (m110)
REVERT: E   18 VAL cc_start: 0.8508 (t) cc_final: 0.8215 (m)
REVERT: F   23 THR cc_start: 0.7971 (m) cc_final: 0.7456 (p)
REVERT: F   24 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.8178 (tt)
REVERT: F   27 ASN cc_start: 0.6627 (m-40) cc_final: 0.6341 (m-40)
REVERT: F   28 LEU cc_start: 0.8638 (tp) cc_final: 0.8428 (tt)
REVERT: G   23 THR cc_start: 0.7968 (m) cc_final: 0.7481 (p)
REVERT: H   23 THR cc_start: 0.7972 (m) cc_final: 0.7619 (p)
REVERT: H   24 LEU cc_start: 0.8822 (tp) cc_final: 0.8610 (tp)
REVERT: I   23 THR cc_start: 0.7755 (m) cc_final: 0.7337 (p)
REVERT: I   24 LEU cc_start: 0.8755 (tp) cc_final: 0.8366 (tt)
REVERT: J    2 THR cc_start: 0.7644 (OUTLIER) cc_final: 0.7379 (p)
REVERT: J   23 THR cc_start: 0.7717 (m) cc_final: 0.7378 (p)
REVERT: J   24 LEU cc_start: 0.8775 (tp) cc_final: 0.8423 (tt)
REVERT: J   34 LYS cc_start: 0.7374 (mtmt) cc_final: 0.7088 (mtmm)
  outliers start: 49
  outliers final: 41
  residues processed: 219
  average time/residue: 0.0572
  time to fit residues: 15.2034
Evaluate side-chains
  252 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 209
  time to evaluate  : 0.111 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 VAL
Chi-restraints excluded: chain A residue   17 ILE
Chi-restraints excluded: chain A residue   19 THR
Chi-restraints excluded: chain A residue   28 LEU
Chi-restraints excluded: chain A residue   30 THR
Chi-restraints excluded: chain A residue   39 VAL
Chi-restraints excluded: chain A residue   41 THR
Chi-restraints excluded: chain B residue   15 VAL
Chi-restraints excluded: chain B residue   17 ILE
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain C residue    9 ILE
Chi-restraints excluded: chain C residue   15 VAL
Chi-restraints excluded: chain C residue   16 VAL
Chi-restraints excluded: chain C residue   17 ILE
Chi-restraints excluded: chain C residue   30 THR
Chi-restraints excluded: chain C residue   41 THR
Chi-restraints excluded: chain D residue    2 THR
Chi-restraints excluded: chain D residue    9 ILE
Chi-restraints excluded: chain D residue   17 ILE
Chi-restraints excluded: chain D residue   39 VAL
Chi-restraints excluded: chain E residue    2 THR
Chi-restraints excluded: chain E residue   15 VAL
Chi-restraints excluded: chain E residue   17 ILE
Chi-restraints excluded: chain E residue   23 THR
Chi-restraints excluded: chain E residue   39 VAL
Chi-restraints excluded: chain F residue   15 VAL
Chi-restraints excluded: chain F residue   24 LEU
Chi-restraints excluded: chain F residue   39 VAL
Chi-restraints excluded: chain G residue    2 THR
Chi-restraints excluded: chain G residue   15 VAL
Chi-restraints excluded: chain G residue   24 LEU
Chi-restraints excluded: chain G residue   39 VAL
Chi-restraints excluded: chain H residue    2 THR
Chi-restraints excluded: chain H residue   17 ILE
Chi-restraints excluded: chain H residue   39 VAL
Chi-restraints excluded: chain I residue    2 THR
Chi-restraints excluded: chain I residue    4 ILE
Chi-restraints excluded: chain J residue    2 THR
Chi-restraints excluded: chain J residue    4 ILE
Chi-restraints excluded: chain J residue   12 LEU
Chi-restraints excluded: chain J residue   15 VAL
Chi-restraints excluded: chain J residue   17 ILE
Chi-restraints excluded: chain J residue   28 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 17 optimal weight:    8.9990
   chunk 22 optimal weight:    2.9990
   chunk 21 optimal weight:    0.8980
   chunk 15 optimal weight:    4.9990
   chunk 37 optimal weight:    7.9990
   chunk 26 optimal weight:    0.7980
   chunk 18 optimal weight:    0.8980
   chunk 20 optimal weight:    5.9990
   chunk 39 optimal weight:    2.9990
   chunk 1 optimal weight:    7.9990
   chunk 30 optimal weight:    0.9990
   overall best weight:    1.3184

-------------------------------------------------------------------------------
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 = 0.3551 r_free = 0.3551 target = 0.101958 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.091984 restraints weight = 5765.334|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.094211 restraints weight = 2777.507|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.095525 restraints weight = 1644.798|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.096431 restraints weight = 1151.423|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.096973 restraints weight = 893.101|
|-----------------------------------------------------------------------------|
r_work (final): 0.3461
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7525
moved from start:          0.4026

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   3070  Z= 0.181
  Angle     :  0.563   5.782   4220  Z= 0.320
  Chirality :  0.040   0.112    640
  Planarity :  0.004   0.053    490
  Dihedral  :  4.840  35.647    464
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 14.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.79 %
    Favored  : 97.21 %
  Rotamer:
    Outliers : 16.67 %
    Allowed  : 33.67 %
    Favored  : 49.67 %
  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 aren not related in a simple way.
  whole: -3.76 (0.32), residues: 430
  helix: -2.09 (0.24), residues: 340
  sheet:  None (None), residues: 0
  loop : -3.24 (0.40), residues: 90

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG G  29 
 TYR   0.007   0.001   TYR G   6 
 PHE   0.002   0.000   PHE D  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 ( 3070)
  covalent geometry    : angle       0.56266 ( 4220)
  hydrogen bonds       : bond        0.03889 (  210)
  hydrogen bonds       : angle       4.33897 (  630)

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

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

  860 Ramachandran restraints generated.
    430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  860 Ramachandran restraints generated.
    430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  258 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 208
  time to evaluate  : 0.085 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   16 VAL cc_start: 0.8047 (m) cc_final: 0.7786 (p)
REVERT: A   23 THR cc_start: 0.7804 (m) cc_final: 0.7381 (p)
REVERT: B   23 THR cc_start: 0.7943 (m) cc_final: 0.7554 (p)
REVERT: C   23 THR cc_start: 0.7816 (m) cc_final: 0.7002 (p)
REVERT: C   24 LEU cc_start: 0.8484 (tp) cc_final: 0.7533 (mm)
REVERT: C   27 ASN cc_start: 0.6607 (m-40) cc_final: 0.6104 (m110)
REVERT: D   18 VAL cc_start: 0.8501 (t) cc_final: 0.8238 (m)
REVERT: D   23 THR cc_start: 0.7936 (m) cc_final: 0.7290 (p)
REVERT: D   24 LEU cc_start: 0.8375 (tp) cc_final: 0.7440 (mm)
REVERT: D   27 ASN cc_start: 0.6651 (m-40) cc_final: 0.6295 (m110)
REVERT: D   34 LYS cc_start: 0.7370 (mtmm) cc_final: 0.7138 (mtmm)
REVERT: E   18 VAL cc_start: 0.8510 (t) cc_final: 0.8205 (m)
REVERT: F   23 THR cc_start: 0.7980 (m) cc_final: 0.7444 (p)
REVERT: F   24 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8147 (tt)
REVERT: F   27 ASN cc_start: 0.6641 (m-40) cc_final: 0.6309 (m-40)
REVERT: F   28 LEU cc_start: 0.8698 (tp) cc_final: 0.8438 (tt)
REVERT: G   23 THR cc_start: 0.8018 (m) cc_final: 0.7501 (p)
REVERT: H   23 THR cc_start: 0.7935 (m) cc_final: 0.7566 (p)
REVERT: H   24 LEU cc_start: 0.8815 (tp) cc_final: 0.8589 (tp)
REVERT: I   23 THR cc_start: 0.7705 (m) cc_final: 0.7234 (p)
REVERT: I   24 LEU cc_start: 0.8760 (tp) cc_final: 0.8383 (tt)
REVERT: J    2 THR cc_start: 0.7598 (OUTLIER) cc_final: 0.7330 (p)
REVERT: J   23 THR cc_start: 0.7734 (m) cc_final: 0.7421 (p)
REVERT: J   24 LEU cc_start: 0.8791 (tp) cc_final: 0.8357 (tt)
REVERT: J   34 LYS cc_start: 0.7366 (mtmt) cc_final: 0.7046 (mtmm)
  outliers start: 50
  outliers final: 44
  residues processed: 219
  average time/residue: 0.0552
  time to fit residues: 14.6960
Evaluate side-chains
  253 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 207
  time to evaluate  : 0.112 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 VAL
Chi-restraints excluded: chain A residue   17 ILE
Chi-restraints excluded: chain A residue   29 ARG
Chi-restraints excluded: chain A residue   30 THR
Chi-restraints excluded: chain A residue   39 VAL
Chi-restraints excluded: chain A residue   41 THR
Chi-restraints excluded: chain B residue   15 VAL
Chi-restraints excluded: chain B residue   16 VAL
Chi-restraints excluded: chain B residue   17 ILE
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   41 THR
Chi-restraints excluded: chain C residue    9 ILE
Chi-restraints excluded: chain C residue   15 VAL
Chi-restraints excluded: chain C residue   17 ILE
Chi-restraints excluded: chain C residue   30 THR
Chi-restraints excluded: chain C residue   41 THR
Chi-restraints excluded: chain D residue    2 THR
Chi-restraints excluded: chain D residue    9 ILE
Chi-restraints excluded: chain D residue   17 ILE
Chi-restraints excluded: chain D residue   39 VAL
Chi-restraints excluded: chain D residue   41 THR
Chi-restraints excluded: chain E residue    2 THR
Chi-restraints excluded: chain E residue   15 VAL
Chi-restraints excluded: chain E residue   17 ILE
Chi-restraints excluded: chain E residue   23 THR
Chi-restraints excluded: chain E residue   39 VAL
Chi-restraints excluded: chain F residue    2 THR
Chi-restraints excluded: chain F residue   15 VAL
Chi-restraints excluded: chain F residue   24 LEU
Chi-restraints excluded: chain F residue   39 VAL
Chi-restraints excluded: chain G residue    2 THR
Chi-restraints excluded: chain G residue    8 LEU
Chi-restraints excluded: chain G residue   15 VAL
Chi-restraints excluded: chain G residue   24 LEU
Chi-restraints excluded: chain G residue   39 VAL
Chi-restraints excluded: chain H residue    2 THR
Chi-restraints excluded: chain H residue   17 ILE
Chi-restraints excluded: chain H residue   39 VAL
Chi-restraints excluded: chain I residue    2 THR
Chi-restraints excluded: chain J residue    2 THR
Chi-restraints excluded: chain J residue    4 ILE
Chi-restraints excluded: chain J residue   12 LEU
Chi-restraints excluded: chain J residue   15 VAL
Chi-restraints excluded: chain J residue   17 ILE
Chi-restraints excluded: chain J residue   28 LEU
Chi-restraints excluded: chain J residue   41 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 13 optimal weight:    0.7980
   chunk 19 optimal weight:    1.9990
   chunk 1 optimal weight:    2.9990
   chunk 14 optimal weight:    0.7980
   chunk 10 optimal weight:    1.9990
   chunk 29 optimal weight:    3.9990
   chunk 22 optimal weight:    2.9990
   chunk 30 optimal weight:    1.9990
   chunk 25 optimal weight:    7.9990
   chunk 21 optimal weight:    0.8980
   chunk 6 optimal weight:    0.9980
   overall best weight:    1.0982

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

Flipped N/Q/H residues before XYZ refinement:
J  27 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.103067 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.092913 restraints weight = 5868.155|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.095188 restraints weight = 2808.498|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.096605 restraints weight = 1654.970|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.097491 restraints weight = 1144.707|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.098018 restraints weight = 891.463|
|-----------------------------------------------------------------------------|
r_work (final): 0.3475
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7512
moved from start:          0.4310

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   3070  Z= 0.163
  Angle     :  0.572   6.635   4220  Z= 0.321
  Chirality :  0.041   0.170    640
  Planarity :  0.003   0.028    490
  Dihedral  :  4.450  29.327    462
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 14.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.86 %
    Favored  : 98.14 %
  Rotamer:
    Outliers : 17.33 %
    Allowed  : 33.67 %
    Favored  : 49.00 %
  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 aren not related in a simple way.
  whole: -3.57 (0.33), residues: 430
  helix: -1.96 (0.25), residues: 340
  sheet:  None (None), residues: 0
  loop : -3.18 (0.40), residues: 90

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG G  29 
 TYR   0.008   0.001   TYR G   6 
 PHE   0.003   0.000   PHE D  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 ( 3070)
  covalent geometry    : angle       0.57220 ( 4220)
  hydrogen bonds       : bond        0.03965 (  210)
  hydrogen bonds       : angle       4.27669 (  630)

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

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

  860 Ramachandran restraints generated.
    430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  860 Ramachandran restraints generated.
    430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  256 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 204
  time to evaluate  : 0.062 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   16 VAL cc_start: 0.7994 (m) cc_final: 0.7744 (p)
REVERT: A   18 VAL cc_start: 0.8899 (t) cc_final: 0.8619 (m)
REVERT: A   23 THR cc_start: 0.8021 (m) cc_final: 0.7488 (p)
REVERT: B   23 THR cc_start: 0.7913 (m) cc_final: 0.7534 (p)
REVERT: C   23 THR cc_start: 0.7797 (m) cc_final: 0.6976 (p)
REVERT: C   24 LEU cc_start: 0.8419 (tp) cc_final: 0.7405 (mm)
REVERT: C   27 ASN cc_start: 0.6535 (m-40) cc_final: 0.6063 (m110)
REVERT: D   18 VAL cc_start: 0.8506 (t) cc_final: 0.8213 (m)
REVERT: D   23 THR cc_start: 0.7903 (m) cc_final: 0.7224 (p)
REVERT: D   24 LEU cc_start: 0.8214 (tp) cc_final: 0.7394 (mm)
REVERT: D   27 ASN cc_start: 0.6548 (m-40) cc_final: 0.6280 (m110)
REVERT: E   18 VAL cc_start: 0.8472 (t) cc_final: 0.8184 (m)
REVERT: E   24 LEU cc_start: 0.8472 (tp) cc_final: 0.7644 (mm)
REVERT: F   23 THR cc_start: 0.7904 (m) cc_final: 0.7437 (p)
REVERT: F   24 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.8141 (tt)
REVERT: F   27 ASN cc_start: 0.6658 (m-40) cc_final: 0.6395 (m-40)
REVERT: G   23 THR cc_start: 0.8036 (m) cc_final: 0.7518 (p)
REVERT: H   23 THR cc_start: 0.7937 (m) cc_final: 0.7557 (p)
REVERT: I   23 THR cc_start: 0.7694 (m) cc_final: 0.7216 (p)
REVERT: I   24 LEU cc_start: 0.8753 (tp) cc_final: 0.8379 (tt)
REVERT: J    2 THR cc_start: 0.7591 (OUTLIER) cc_final: 0.7359 (p)
REVERT: J   23 THR cc_start: 0.7743 (m) cc_final: 0.7441 (p)
REVERT: J   24 LEU cc_start: 0.8849 (tp) cc_final: 0.8450 (tt)
REVERT: J   34 LYS cc_start: 0.7351 (mtmt) cc_final: 0.7037 (mtmm)
  outliers start: 52
  outliers final: 45
  residues processed: 216
  average time/residue: 0.0541
  time to fit residues: 14.1450
Evaluate side-chains
  250 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 203
  time to evaluate  : 0.109 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 VAL
Chi-restraints excluded: chain A residue   17 ILE
Chi-restraints excluded: chain A residue   19 THR
Chi-restraints excluded: chain A residue   29 ARG
Chi-restraints excluded: chain A residue   30 THR
Chi-restraints excluded: chain A residue   39 VAL
Chi-restraints excluded: chain A residue   41 THR
Chi-restraints excluded: chain B residue   15 VAL
Chi-restraints excluded: chain B residue   16 VAL
Chi-restraints excluded: chain B residue   17 ILE
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   41 THR
Chi-restraints excluded: chain C residue    9 ILE
Chi-restraints excluded: chain C residue   15 VAL
Chi-restraints excluded: chain C residue   16 VAL
Chi-restraints excluded: chain C residue   17 ILE
Chi-restraints excluded: chain C residue   30 THR
Chi-restraints excluded: chain C residue   41 THR
Chi-restraints excluded: chain D residue    2 THR
Chi-restraints excluded: chain D residue    9 ILE
Chi-restraints excluded: chain D residue   17 ILE
Chi-restraints excluded: chain D residue   39 VAL
Chi-restraints excluded: chain D residue   41 THR
Chi-restraints excluded: chain E residue    2 THR
Chi-restraints excluded: chain E residue   15 VAL
Chi-restraints excluded: chain E residue   17 ILE
Chi-restraints excluded: chain E residue   23 THR
Chi-restraints excluded: chain E residue   39 VAL
Chi-restraints excluded: chain F residue    2 THR
Chi-restraints excluded: chain F residue   15 VAL
Chi-restraints excluded: chain F residue   24 LEU
Chi-restraints excluded: chain F residue   39 VAL
Chi-restraints excluded: chain G residue    8 LEU
Chi-restraints excluded: chain G residue   15 VAL
Chi-restraints excluded: chain G residue   24 LEU
Chi-restraints excluded: chain G residue   39 VAL
Chi-restraints excluded: chain H residue    2 THR
Chi-restraints excluded: chain H residue   17 ILE
Chi-restraints excluded: chain H residue   39 VAL
Chi-restraints excluded: chain I residue    2 THR
Chi-restraints excluded: chain I residue    4 ILE
Chi-restraints excluded: chain I residue   17 ILE
Chi-restraints excluded: chain J residue    2 THR
Chi-restraints excluded: chain J residue   12 LEU
Chi-restraints excluded: chain J residue   15 VAL
Chi-restraints excluded: chain J residue   17 ILE
Chi-restraints excluded: chain J residue   41 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 12 optimal weight:    0.9990
   chunk 16 optimal weight:    5.9990
   chunk 15 optimal weight:    0.7980
   chunk 20 optimal weight:    0.5980
   chunk 37 optimal weight:    0.9980
   chunk 18 optimal weight:    1.9990
   chunk 13 optimal weight:    2.9990
   chunk 36 optimal weight:    0.9980
   chunk 6 optimal weight:    3.9990
   chunk 33 optimal weight:   10.0000
   chunk 34 optimal weight:    0.5980
   overall best weight:    0.7980

-------------------------------------------------------------------------------
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 = 0.3585 r_free = 0.3585 target = 0.104021 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.093738 restraints weight = 5902.925|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.096054 restraints weight = 2810.727|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.097522 restraints weight = 1638.205|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.098476 restraints weight = 1116.945|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.099000 restraints weight = 855.757|
|-----------------------------------------------------------------------------|
r_work (final): 0.3489
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7479
moved from start:          0.4509

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3070  Z= 0.144
  Angle     :  0.602   6.357   4220  Z= 0.326
  Chirality :  0.040   0.166    640
  Planarity :  0.003   0.023    490
  Dihedral  :  4.201  14.194    460
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 13.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.79 %
    Favored  : 97.21 %
  Rotamer:
    Outliers : 14.00 %
    Allowed  : 38.67 %
    Favored  : 47.33 %
  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 aren not related in a simple way.
  whole: -3.31 (0.34), residues: 430
  helix: -1.76 (0.25), residues: 340
  sheet:  None (None), residues: 0
  loop : -3.18 (0.40), residues: 90

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG G  29 
 TYR   0.009   0.001   TYR G   6 
 PHE   0.003   0.000   PHE B  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 3070)
  covalent geometry    : angle       0.60188 ( 4220)
  hydrogen bonds       : bond        0.03883 (  210)
  hydrogen bonds       : angle       4.18080 (  630)

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

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

  860 Ramachandran restraints generated.
    430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  860 Ramachandran restraints generated.
    430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  240 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 198
  time to evaluate  : 0.130 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   16 VAL cc_start: 0.7947 (m) cc_final: 0.7709 (p)
REVERT: A   18 VAL cc_start: 0.8899 (t) cc_final: 0.8607 (m)
REVERT: A   23 THR cc_start: 0.7899 (m) cc_final: 0.7428 (p)
REVERT: B   23 THR cc_start: 0.7880 (m) cc_final: 0.7493 (p)
REVERT: C   23 THR cc_start: 0.7756 (m) cc_final: 0.6981 (p)
REVERT: C   24 LEU cc_start: 0.8292 (tp) cc_final: 0.7279 (mm)
REVERT: C   27 ASN cc_start: 0.6489 (m-40) cc_final: 0.6029 (m110)
REVERT: D   18 VAL cc_start: 0.8510 (t) cc_final: 0.8231 (m)
REVERT: D   23 THR cc_start: 0.7918 (m) cc_final: 0.7296 (p)
REVERT: D   24 LEU cc_start: 0.8208 (tp) cc_final: 0.7389 (mm)
REVERT: D   27 ASN cc_start: 0.6661 (m-40) cc_final: 0.6391 (m110)
REVERT: E   18 VAL cc_start: 0.8445 (t) cc_final: 0.8150 (m)
REVERT: E   24 LEU cc_start: 0.8336 (tp) cc_final: 0.7549 (mm)
REVERT: F   23 THR cc_start: 0.7738 (m) cc_final: 0.7304 (p)
REVERT: F   24 LEU cc_start: 0.8279 (OUTLIER) cc_final: 0.8048 (tt)
REVERT: F   27 ASN cc_start: 0.6560 (m-40) cc_final: 0.6303 (m-40)
REVERT: G   23 THR cc_start: 0.7991 (m) cc_final: 0.7500 (p)
REVERT: H   23 THR cc_start: 0.7887 (m) cc_final: 0.7537 (p)
REVERT: I   23 THR cc_start: 0.7692 (m) cc_final: 0.7232 (p)
REVERT: I   24 LEU cc_start: 0.8690 (tp) cc_final: 0.8278 (tt)
REVERT: J    2 THR cc_start: 0.7579 (OUTLIER) cc_final: 0.7339 (p)
REVERT: J   23 THR cc_start: 0.7683 (m) cc_final: 0.7345 (p)
REVERT: J   24 LEU cc_start: 0.8821 (tp) cc_final: 0.8406 (tt)
  outliers start: 42
  outliers final: 38
  residues processed: 207
  average time/residue: 0.0541
  time to fit residues: 13.6426
Evaluate side-chains
  238 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 198
  time to evaluate  : 0.066 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 VAL
Chi-restraints excluded: chain A residue   17 ILE
Chi-restraints excluded: chain A residue   30 THR
Chi-restraints excluded: chain A residue   39 VAL
Chi-restraints excluded: chain A residue   41 THR
Chi-restraints excluded: chain B residue   15 VAL
Chi-restraints excluded: chain B residue   17 ILE
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain C residue    9 ILE
Chi-restraints excluded: chain C residue   15 VAL
Chi-restraints excluded: chain C residue   17 ILE
Chi-restraints excluded: chain C residue   30 THR
Chi-restraints excluded: chain C residue   41 THR
Chi-restraints excluded: chain D residue    2 THR
Chi-restraints excluded: chain D residue    9 ILE
Chi-restraints excluded: chain D residue   17 ILE
Chi-restraints excluded: chain D residue   39 VAL
Chi-restraints excluded: chain E residue    2 THR
Chi-restraints excluded: chain E residue   17 ILE
Chi-restraints excluded: chain E residue   23 THR
Chi-restraints excluded: chain E residue   30 THR
Chi-restraints excluded: chain E residue   39 VAL
Chi-restraints excluded: chain F residue    2 THR
Chi-restraints excluded: chain F residue   15 VAL
Chi-restraints excluded: chain F residue   24 LEU
Chi-restraints excluded: chain F residue   39 VAL
Chi-restraints excluded: chain G residue    8 LEU
Chi-restraints excluded: chain G residue   15 VAL
Chi-restraints excluded: chain G residue   24 LEU
Chi-restraints excluded: chain G residue   39 VAL
Chi-restraints excluded: chain H residue    2 THR
Chi-restraints excluded: chain H residue   17 ILE
Chi-restraints excluded: chain H residue   39 VAL
Chi-restraints excluded: chain I residue    2 THR
Chi-restraints excluded: chain I residue    4 ILE
Chi-restraints excluded: chain J residue    2 THR
Chi-restraints excluded: chain J residue    4 ILE
Chi-restraints excluded: chain J residue   12 LEU
Chi-restraints excluded: chain J residue   17 ILE
Chi-restraints excluded: chain J residue   41 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 33 optimal weight:    8.9990
   chunk 28 optimal weight:    0.0980
   chunk 21 optimal weight:    4.9990
   chunk 9 optimal weight:    0.8980
   chunk 14 optimal weight:    4.9990
   chunk 0 optimal weight:    7.9990
   chunk 38 optimal weight:    0.0770
   chunk 26 optimal weight:    0.9980
   chunk 31 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9990
   chunk 29 optimal weight:    0.8980
   overall best weight:    0.5938

-------------------------------------------------------------------------------
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 = 0.3628 r_free = 0.3628 target = 0.106181 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.096231 restraints weight = 5924.803|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.098535 restraints weight = 2760.375|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.099934 restraints weight = 1573.146|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.100831 restraints weight = 1064.443|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.101437 restraints weight = 813.004|
|-----------------------------------------------------------------------------|
r_work (final): 0.3536
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7442
moved from start:          0.4802

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   3070  Z= 0.129
  Angle     :  0.596   7.966   4220  Z= 0.319
  Chirality :  0.039   0.137    640
  Planarity :  0.003   0.018    490
  Dihedral  :  4.008  14.166    460
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 12.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  Rotamer:
    Outliers : 12.33 %
    Allowed  : 41.67 %
    Favored  : 46.00 %
  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 aren not related in a simple way.
  whole: -3.10 (0.35), residues: 430
  helix: -1.61 (0.26), residues: 340
  sheet:  None (None), residues: 0
  loop : -3.11 (0.40), residues: 90

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG G  29 
 TYR   0.009   0.001   TYR C   6 
 PHE   0.005   0.000   PHE C  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 ( 3070)
  covalent geometry    : angle       0.59570 ( 4220)
  hydrogen bonds       : bond        0.03781 (  210)
  hydrogen bonds       : angle       4.03607 (  630)

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

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

  860 Ramachandran restraints generated.
    430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  860 Ramachandran restraints generated.
    430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  233 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 196
  time to evaluate  : 0.110 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   16 VAL cc_start: 0.7926 (m) cc_final: 0.7674 (p)
REVERT: A   18 VAL cc_start: 0.8912 (t) cc_final: 0.8622 (m)
REVERT: A   23 THR cc_start: 0.7837 (m) cc_final: 0.7401 (p)
REVERT: B   23 THR cc_start: 0.7797 (m) cc_final: 0.7489 (p)
REVERT: C   23 THR cc_start: 0.7675 (m) cc_final: 0.7107 (p)
REVERT: C   24 LEU cc_start: 0.8150 (tp) cc_final: 0.7222 (mm)
REVERT: C   27 ASN cc_start: 0.6435 (m-40) cc_final: 0.6156 (m110)
REVERT: D   18 VAL cc_start: 0.8476 (t) cc_final: 0.8236 (m)
REVERT: D   23 THR cc_start: 0.7812 (m) cc_final: 0.7298 (p)
REVERT: D   24 LEU cc_start: 0.8077 (tp) cc_final: 0.7183 (mm)
REVERT: E   18 VAL cc_start: 0.8424 (t) cc_final: 0.8171 (m)
REVERT: E   24 LEU cc_start: 0.8229 (tp) cc_final: 0.7486 (mm)
REVERT: F   23 THR cc_start: 0.7619 (m) cc_final: 0.6951 (p)
REVERT: F   27 ASN cc_start: 0.6558 (m-40) cc_final: 0.5925 (m-40)
REVERT: G   23 THR cc_start: 0.7901 (m) cc_final: 0.7442 (p)
REVERT: H   23 THR cc_start: 0.7938 (m) cc_final: 0.7607 (p)
REVERT: I   23 THR cc_start: 0.7689 (m) cc_final: 0.7257 (p)
REVERT: I   24 LEU cc_start: 0.8693 (tp) cc_final: 0.8306 (tt)
REVERT: J    2 THR cc_start: 0.7558 (OUTLIER) cc_final: 0.7357 (p)
REVERT: J   23 THR cc_start: 0.7692 (m) cc_final: 0.7436 (p)
REVERT: J   24 LEU cc_start: 0.8839 (tp) cc_final: 0.8467 (tt)
REVERT: J   34 LYS cc_start: 0.7373 (mtmt) cc_final: 0.7082 (mtmm)
  outliers start: 37
  outliers final: 32
  residues processed: 206
  average time/residue: 0.0554
  time to fit residues: 13.7885
Evaluate side-chains
  229 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 196
  time to evaluate  : 0.104 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 VAL
Chi-restraints excluded: chain A residue   17 ILE
Chi-restraints excluded: chain A residue   30 THR
Chi-restraints excluded: chain A residue   39 VAL
Chi-restraints excluded: chain A residue   41 THR
Chi-restraints excluded: chain B residue    2 THR
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain C residue    9 ILE
Chi-restraints excluded: chain C residue   17 ILE
Chi-restraints excluded: chain C residue   30 THR
Chi-restraints excluded: chain C residue   41 THR
Chi-restraints excluded: chain D residue    2 THR
Chi-restraints excluded: chain D residue    9 ILE
Chi-restraints excluded: chain D residue   17 ILE
Chi-restraints excluded: chain E residue    2 THR
Chi-restraints excluded: chain E residue   17 ILE
Chi-restraints excluded: chain E residue   23 THR
Chi-restraints excluded: chain E residue   39 VAL
Chi-restraints excluded: chain F residue    2 THR
Chi-restraints excluded: chain F residue   15 VAL
Chi-restraints excluded: chain F residue   21 VAL
Chi-restraints excluded: chain F residue   39 VAL
Chi-restraints excluded: chain G residue    8 LEU
Chi-restraints excluded: chain G residue   24 LEU
Chi-restraints excluded: chain G residue   39 VAL
Chi-restraints excluded: chain H residue    2 THR
Chi-restraints excluded: chain H residue   39 VAL
Chi-restraints excluded: chain I residue    2 THR
Chi-restraints excluded: chain I residue    4 ILE
Chi-restraints excluded: chain J residue    2 THR
Chi-restraints excluded: chain J residue    4 ILE
Chi-restraints excluded: chain J residue   12 LEU
Chi-restraints excluded: chain J residue   41 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 2 optimal weight:    0.9980
   chunk 1 optimal weight:    1.9990
   chunk 6 optimal weight:    3.9990
   chunk 26 optimal weight:    0.5980
   chunk 9 optimal weight:    3.9990
   chunk 13 optimal weight:    0.9990
   chunk 33 optimal weight:    3.9990
   chunk 21 optimal weight:    0.0970
   chunk 15 optimal weight:    2.9990
   chunk 5 optimal weight:    2.9990
   chunk 37 optimal weight:    5.9990
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
D  27 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.105575 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.095554 restraints weight = 5857.204|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.097821 restraints weight = 2763.261|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.099233 restraints weight = 1606.720|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.100059 restraints weight = 1097.958|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.100644 restraints weight = 862.251|
|-----------------------------------------------------------------------------|
r_work (final): 0.3534
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7456
moved from start:          0.4741

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3070  Z= 0.156
  Angle     :  0.666  12.313   4220  Z= 0.344
  Chirality :  0.042   0.242    640
  Planarity :  0.003   0.034    490
  Dihedral  :  4.124  13.897    460
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 12.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers : 12.67 %
    Allowed  : 43.67 %
    Favored  : 43.67 %
  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 aren not related in a simple way.
  whole: -3.17 (0.35), residues: 430
  helix: -1.67 (0.26), residues: 340
  sheet:  None (None), residues: 0
  loop : -3.04 (0.41), residues: 90

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG G  29 
 TYR   0.008   0.001   TYR G   6 
 PHE   0.002   0.000   PHE A  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 3070)
  covalent geometry    : angle       0.66583 ( 4220)
  hydrogen bonds       : bond        0.04030 (  210)
  hydrogen bonds       : angle       4.31532 (  630)

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

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

  860 Ramachandran restraints generated.
    430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  860 Ramachandran restraints generated.
    430 Oldfield, 0 Emsley, 430 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  230 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 192
  time to evaluate  : 0.067 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   16 VAL cc_start: 0.7949 (m) cc_final: 0.7707 (p)
REVERT: A   18 VAL cc_start: 0.8907 (t) cc_final: 0.8608 (m)
REVERT: A   23 THR cc_start: 0.7887 (m) cc_final: 0.7437 (p)
REVERT: B   23 THR cc_start: 0.7756 (m) cc_final: 0.7344 (p)
REVERT: B   24 LEU cc_start: 0.8138 (tp) cc_final: 0.7145 (mm)
REVERT: C   23 THR cc_start: 0.7740 (m) cc_final: 0.7166 (p)
REVERT: C   24 LEU cc_start: 0.8217 (tp) cc_final: 0.7315 (mm)
REVERT: C   27 ASN cc_start: 0.6495 (m-40) cc_final: 0.6217 (m110)
REVERT: D   18 VAL cc_start: 0.8493 (t) cc_final: 0.8229 (m)
REVERT: D   23 THR cc_start: 0.7814 (m) cc_final: 0.7189 (p)
REVERT: D   24 LEU cc_start: 0.8064 (tp) cc_final: 0.7316 (mm)
REVERT: D   27 ASN cc_start: 0.6811 (m-40) cc_final: 0.6431 (m110)
REVERT: E   18 VAL cc_start: 0.8406 (t) cc_final: 0.8166 (m)
REVERT: E   24 LEU cc_start: 0.8332 (tp) cc_final: 0.7558 (mm)
REVERT: F   23 THR cc_start: 0.7640 (m) cc_final: 0.6976 (p)
REVERT: F   27 ASN cc_start: 0.6568 (m-40) cc_final: 0.5927 (m-40)
REVERT: G   23 THR cc_start: 0.7941 (m) cc_final: 0.7466 (p)
REVERT: H   23 THR cc_start: 0.7978 (m) cc_final: 0.7640 (p)
REVERT: I   23 THR cc_start: 0.7711 (m) cc_final: 0.7280 (p)
REVERT: I   24 LEU cc_start: 0.8716 (tp) cc_final: 0.8334 (tt)
REVERT: J    2 THR cc_start: 0.7563 (OUTLIER) cc_final: 0.7361 (p)
REVERT: J   23 THR cc_start: 0.7671 (m) cc_final: 0.7386 (p)
REVERT: J   24 LEU cc_start: 0.8836 (tp) cc_final: 0.8453 (tt)
REVERT: J   34 LYS cc_start: 0.7380 (mtmt) cc_final: 0.7084 (mtmm)
  outliers start: 38
  outliers final: 36
  residues processed: 203
  average time/residue: 0.0582
  time to fit residues: 14.3424
Evaluate side-chains
  229 residues out of total 300 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 192
  time to evaluate  : 0.109 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 VAL
Chi-restraints excluded: chain A residue   17 ILE
Chi-restraints excluded: chain A residue   30 THR
Chi-restraints excluded: chain A residue   39 VAL
Chi-restraints excluded: chain B residue    2 THR
Chi-restraints excluded: chain B residue   15 VAL
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain C residue    9 ILE
Chi-restraints excluded: chain C residue   16 VAL
Chi-restraints excluded: chain C residue   17 ILE
Chi-restraints excluded: chain C residue   30 THR
Chi-restraints excluded: chain C residue   41 THR
Chi-restraints excluded: chain D residue    2 THR
Chi-restraints excluded: chain D residue    9 ILE
Chi-restraints excluded: chain D residue   17 ILE
Chi-restraints excluded: chain D residue   39 VAL
Chi-restraints excluded: chain E residue    2 THR
Chi-restraints excluded: chain E residue   17 ILE
Chi-restraints excluded: chain E residue   23 THR
Chi-restraints excluded: chain E residue   30 THR
Chi-restraints excluded: chain E residue   39 VAL
Chi-restraints excluded: chain F residue    2 THR
Chi-restraints excluded: chain F residue   15 VAL
Chi-restraints excluded: chain F residue   39 VAL
Chi-restraints excluded: chain G residue    8 LEU
Chi-restraints excluded: chain G residue   24 LEU
Chi-restraints excluded: chain G residue   39 VAL
Chi-restraints excluded: chain H residue    2 THR
Chi-restraints excluded: chain H residue   13 ILE
Chi-restraints excluded: chain H residue   39 VAL
Chi-restraints excluded: chain I residue    2 THR
Chi-restraints excluded: chain I residue    4 ILE
Chi-restraints excluded: chain J residue    2 THR
Chi-restraints excluded: chain J residue    4 ILE
Chi-restraints excluded: chain J residue   12 LEU
Chi-restraints excluded: chain J residue   17 ILE
Chi-restraints excluded: chain J residue   41 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 34 optimal weight:    1.9990
   chunk 38 optimal weight:    0.6980
   chunk 39 optimal weight:    0.9980
   chunk 24 optimal weight:    0.8980
   chunk 19 optimal weight:    4.9990
   chunk 1 optimal weight:    0.9990
   chunk 26 optimal weight:    2.9990
   chunk 27 optimal weight:    3.9990
   chunk 30 optimal weight:    2.9990
   chunk 13 optimal weight:    4.9990
   chunk 23 optimal weight:    1.9990
   overall best weight:    1.1184

-------------------------------------------------------------------------------
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 = 0.3613 r_free = 0.3613 target = 0.105187 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.095190 restraints weight = 5834.594|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.097464 restraints weight = 2758.831|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.098833 restraints weight = 1611.826|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.099715 restraints weight = 1118.227|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.100281 restraints weight = 865.131|
|-----------------------------------------------------------------------------|
r_work (final): 0.3520
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7474
moved from start:          0.4842

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   3070  Z= 0.174
  Angle     :  0.673  11.020   4220  Z= 0.355
  Chirality :  0.043   0.252    640
  Planarity :  0.003   0.023    490
  Dihedral  :  4.252  14.667    460
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 14.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers : 13.67 %
    Allowed  : 42.33 %
    Favored  : 44.00 %
  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 aren not related in a simple way.
  whole: -3.25 (0.35), residues: 430
  helix: -1.77 (0.25), residues: 340
  sheet:  None (None), residues: 0
  loop : -2.90 (0.42), residues: 90

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG E  29 
 TYR   0.009   0.001   TYR G   6 
 PHE   0.003   0.000   PHE E  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 ( 3070)
  covalent geometry    : angle       0.67282 ( 4220)
  hydrogen bonds       : bond        0.04182 (  210)
  hydrogen bonds       : angle       4.42064 (  630)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 723.91 seconds
wall clock time: 13 minutes 10.21 seconds (790.21 seconds total)