Starting phenix.real_space_refine
on Tue Mar  3 23:13:12 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7uxe_26858/03_2026/7uxe_26858.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7uxe_26858/03_2026/7uxe_26858.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7uxe_26858/03_2026/7uxe_26858.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7uxe_26858/03_2026/7uxe_26858.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7uxe_26858/03_2026/7uxe_26858.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7uxe_26858/03_2026/7uxe_26858.map"
  }
  resolution = 3.38
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.004 sd=   0.196
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      30      5.16       5
     C    6080      2.51       5
     N    1670      2.21       5
     O    1700      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 20 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9480
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 948
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 115, 948
          Classifications: {'peptide': 115}
          Link IDs: {'PTRANS': 5, 'TRANS': 109}
  Restraints were copied for chains:
    B, C, D, E, F, G, H, I, J
  Time building chain proxies: 0.97, per 1000 atoms: 0.10
  Number of scatterers: 9480
  At special positions: 0
  Unit cell: (118.75, 116.85, 59.85, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      30     16.00
     O    1700      8.00
     N    1670      7.00
     C    6080      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: 0.90
  Conformation dependent library (CDL) restraints added in 370.4 milliseconds
  

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2240

  Finding SS restraints...
    Secondary structure from input PDB file:
      60 helices and 0 sheets defined
      67.0% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.17
  Creating SS restraints...
    Processing helix  chain 'A' and resid 26 through 39
      removed outlier: 3.598A  pdb=" N   GLY A  39 " --> pdb=" O   LEU A  35 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 43 through 50
    Processing helix  chain 'A' and resid 58 through 67
    Processing helix  chain 'A' and resid 69 through 82
    Processing helix  chain 'A' and resid 90 through 104
    Processing helix  chain 'A' and resid 108 through 123
      removed outlier: 3.904A  pdb=" N   ARG A 112 " --> pdb=" O   LYS A 108 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 26 through 39
      removed outlier: 3.599A  pdb=" N   GLY B  39 " --> pdb=" O   LEU B  35 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 43 through 50
    Processing helix  chain 'B' and resid 58 through 67
    Processing helix  chain 'B' and resid 69 through 82
    Processing helix  chain 'B' and resid 90 through 104
    Processing helix  chain 'B' and resid 108 through 123
      removed outlier: 3.904A  pdb=" N   ARG B 112 " --> pdb=" O   LYS B 108 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 26 through 39
      removed outlier: 3.599A  pdb=" N   GLY C  39 " --> pdb=" O   LEU C  35 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 43 through 50
    Processing helix  chain 'C' and resid 58 through 67
    Processing helix  chain 'C' and resid 69 through 82
    Processing helix  chain 'C' and resid 90 through 104
    Processing helix  chain 'C' and resid 108 through 123
      removed outlier: 3.904A  pdb=" N   ARG C 112 " --> pdb=" O   LYS C 108 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 26 through 39
      removed outlier: 3.597A  pdb=" N   GLY D  39 " --> pdb=" O   LEU D  35 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 43 through 50
    Processing helix  chain 'D' and resid 58 through 67
    Processing helix  chain 'D' and resid 69 through 82
    Processing helix  chain 'D' and resid 90 through 104
    Processing helix  chain 'D' and resid 108 through 123
      removed outlier: 3.903A  pdb=" N   ARG D 112 " --> pdb=" O   LYS D 108 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 26 through 39
      removed outlier: 3.598A  pdb=" N   GLY E  39 " --> pdb=" O   LEU E  35 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 43 through 50
    Processing helix  chain 'E' and resid 58 through 67
    Processing helix  chain 'E' and resid 69 through 82
    Processing helix  chain 'E' and resid 90 through 104
    Processing helix  chain 'E' and resid 108 through 123
      removed outlier: 3.903A  pdb=" N   ARG E 112 " --> pdb=" O   LYS E 108 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 26 through 39
      removed outlier: 3.597A  pdb=" N   GLY F  39 " --> pdb=" O   LEU F  35 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 43 through 50
    Processing helix  chain 'F' and resid 58 through 67
    Processing helix  chain 'F' and resid 69 through 82
    Processing helix  chain 'F' and resid 90 through 104
    Processing helix  chain 'F' and resid 108 through 123
      removed outlier: 3.904A  pdb=" N   ARG F 112 " --> pdb=" O   LYS F 108 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 26 through 39
      removed outlier: 3.597A  pdb=" N   GLY G  39 " --> pdb=" O   LEU G  35 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 43 through 50
    Processing helix  chain 'G' and resid 58 through 67
    Processing helix  chain 'G' and resid 69 through 82
    Processing helix  chain 'G' and resid 90 through 104
    Processing helix  chain 'G' and resid 108 through 123
      removed outlier: 3.904A  pdb=" N   ARG G 112 " --> pdb=" O   LYS G 108 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 26 through 39
      removed outlier: 3.598A  pdb=" N   GLY H  39 " --> pdb=" O   LEU H  35 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 43 through 50
    Processing helix  chain 'H' and resid 58 through 67
    Processing helix  chain 'H' and resid 69 through 82
    Processing helix  chain 'H' and resid 90 through 104
    Processing helix  chain 'H' and resid 108 through 123
      removed outlier: 3.904A  pdb=" N   ARG H 112 " --> pdb=" O   LYS H 108 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 26 through 39
      removed outlier: 3.599A  pdb=" N   GLY I  39 " --> pdb=" O   LEU I  35 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 43 through 50
    Processing helix  chain 'I' and resid 58 through 67
    Processing helix  chain 'I' and resid 69 through 82
    Processing helix  chain 'I' and resid 90 through 104
    Processing helix  chain 'I' and resid 108 through 123
      removed outlier: 3.903A  pdb=" N   ARG I 112 " --> pdb=" O   LYS I 108 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 26 through 39
      removed outlier: 3.597A  pdb=" N   GLY J  39 " --> pdb=" O   LEU J  35 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 43 through 50
    Processing helix  chain 'J' and resid 58 through 67
    Processing helix  chain 'J' and resid 69 through 82
    Processing helix  chain 'J' and resid 90 through 104
    Processing helix  chain 'J' and resid 108 through 123
      removed outlier: 3.904A  pdb=" N   ARG J 112 " --> pdb=" O   LYS J 108 " (cutoff:3.500A)

    510 hydrogen bonds defined for protein.
    1530 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: 0.85

  Time building geometry restraints manager: 1.20 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3078
        1.34 -     1.46: 1455
        1.46 -     1.57: 5127
        1.57 -     1.69: 0
        1.69 -     1.80: 60
  Bond restraints: 9720
  Sorted by residual:
  bond pdb=" CA  THR F 106 "
       pdb=" CB  THR F 106 "
    ideal  model  delta    sigma   weight residual
    1.533  1.559 -0.026 2.15e-02 2.16e+03 1.46e+00
  bond pdb=" CA  THR J 106 "
       pdb=" CB  THR J 106 "
    ideal  model  delta    sigma   weight residual
    1.533  1.559 -0.026 2.15e-02 2.16e+03 1.42e+00
  bond pdb=" CA  THR I 106 "
       pdb=" CB  THR I 106 "
    ideal  model  delta    sigma   weight residual
    1.533  1.559 -0.026 2.15e-02 2.16e+03 1.42e+00
  bond pdb=" CA  THR E 106 "
       pdb=" CB  THR E 106 "
    ideal  model  delta    sigma   weight residual
    1.533  1.559 -0.025 2.15e-02 2.16e+03 1.41e+00
  bond pdb=" CA  THR B 106 "
       pdb=" CB  THR B 106 "
    ideal  model  delta    sigma   weight residual
    1.533  1.559 -0.025 2.15e-02 2.16e+03 1.40e+00
  ... (remaining 9715 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.32: 11927
        1.32 -     2.64: 933
        2.64 -     3.96: 207
        3.96 -     5.28: 59
        5.28 -     6.60: 14
  Bond angle restraints: 13140
  Sorted by residual:
  angle pdb=" N   ILE D 125 "
        pdb=" CA  ILE D 125 "
        pdb=" C   ILE D 125 "
      ideal   model   delta    sigma   weight residual
     111.77  108.23    3.54 1.04e+00 9.25e-01 1.16e+01
  angle pdb=" N   ILE C 125 "
        pdb=" CA  ILE C 125 "
        pdb=" C   ILE C 125 "
      ideal   model   delta    sigma   weight residual
     111.77  108.24    3.53 1.04e+00 9.25e-01 1.15e+01
  angle pdb=" N   ILE G 125 "
        pdb=" CA  ILE G 125 "
        pdb=" C   ILE G 125 "
      ideal   model   delta    sigma   weight residual
     111.77  108.25    3.52 1.04e+00 9.25e-01 1.15e+01
  angle pdb=" N   ILE E 125 "
        pdb=" CA  ILE E 125 "
        pdb=" C   ILE E 125 "
      ideal   model   delta    sigma   weight residual
     111.77  108.26    3.51 1.04e+00 9.25e-01 1.14e+01
  angle pdb=" N   ILE H 125 "
        pdb=" CA  ILE H 125 "
        pdb=" C   ILE H 125 "
      ideal   model   delta    sigma   weight residual
     111.77  108.26    3.51 1.04e+00 9.25e-01 1.14e+01
  ... (remaining 13135 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    11.87: 4239
       11.87 -    23.74: 839
       23.74 -    35.61: 492
       35.61 -    47.48: 187
       47.48 -    59.35: 93
  Dihedral angle restraints: 5850
    sinusoidal: 2430
      harmonic: 3420
  Sorted by residual:
  dihedral pdb=" CA  GLU C 124 "
           pdb=" C   GLU C 124 "
           pdb=" N   ILE C 125 "
           pdb=" CA  ILE C 125 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -163.56  -16.44     0      5.00e+00 4.00e-02 1.08e+01
  dihedral pdb=" CA  GLU H 124 "
           pdb=" C   GLU H 124 "
           pdb=" N   ILE H 125 "
           pdb=" CA  ILE H 125 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.58  -16.42     0      5.00e+00 4.00e-02 1.08e+01
  dihedral pdb=" CA  GLU I 124 "
           pdb=" C   GLU I 124 "
           pdb=" N   ILE I 125 "
           pdb=" CA  ILE I 125 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.58  -16.42     0      5.00e+00 4.00e-02 1.08e+01
  ... (remaining 5847 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.024: 686
       0.024 -    0.048: 387
       0.048 -    0.071: 224
       0.071 -    0.095: 73
       0.095 -    0.119: 20
  Chirality restraints: 1390
  Sorted by residual:
  chirality pdb=" CA  ILE D 125 "
            pdb=" N   ILE D 125 "
            pdb=" C   ILE D 125 "
            pdb=" CB  ILE D 125 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.55e-01
  chirality pdb=" CA  ILE E 125 "
            pdb=" N   ILE E 125 "
            pdb=" C   ILE E 125 "
            pdb=" CB  ILE E 125 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.43e-01
  chirality pdb=" CA  ILE J 125 "
            pdb=" N   ILE J 125 "
            pdb=" C   ILE J 125 "
            pdb=" CB  ILE J 125 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.35e-01
  ... (remaining 1387 not shown)

  Planarity restraints: 1690
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR J 106 "   -0.013 2.00e-02 2.50e+03   2.50e-02 6.24e+00
        pdb=" C   THR J 106 "    0.043 2.00e-02 2.50e+03
        pdb=" O   THR J 106 "   -0.016 2.00e-02 2.50e+03
        pdb=" N   VAL J 107 "   -0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR F 106 "   -0.012 2.00e-02 2.50e+03   2.49e-02 6.21e+00
        pdb=" C   THR F 106 "    0.043 2.00e-02 2.50e+03
        pdb=" O   THR F 106 "   -0.016 2.00e-02 2.50e+03
        pdb=" N   VAL F 107 "   -0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR H 106 "   -0.012 2.00e-02 2.50e+03   2.49e-02 6.18e+00
        pdb=" C   THR H 106 "    0.043 2.00e-02 2.50e+03
        pdb=" O   THR H 106 "   -0.016 2.00e-02 2.50e+03
        pdb=" N   VAL H 107 "   -0.015 2.00e-02 2.50e+03
  ... (remaining 1687 not shown)

  Histogram of nonbonded interaction distances:
        2.03 -     2.60: 90
        2.60 -     3.18: 8187
        3.18 -     3.75: 14095
        3.75 -     4.33: 18161
        4.33 -     4.90: 30697
  Nonbonded interactions: 71230
  Sorted by model distance:
  nonbonded pdb=" O   ALA C  61 "
            pdb=" NH2 ARG D  44 "
     model   vdw
     2.026 3.120
  nonbonded pdb=" O   ALA H  61 "
            pdb=" NH2 ARG I  44 "
     model   vdw
     2.027 3.120
  nonbonded pdb=" O   ALA E  61 "
            pdb=" NH2 ARG F  44 "
     model   vdw
     2.059 3.120
  nonbonded pdb=" NH2 ARG A  44 "
            pdb=" O   ALA J  61 "
     model   vdw
     2.071 3.120
  nonbonded pdb=" O   ALA B  61 "
            pdb=" NH2 ARG C  44 "
     model   vdw
     2.083 3.120
  ... (remaining 71225 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: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
  selection = chain 'G'
  selection = chain 'H'
  selection = chain 'I'
  selection = chain 'J'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.570
  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:          0.150
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     8.030
  Find NCS groups from input model:        0.070
  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:1.190
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.090
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7541
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      :  0.005   0.036   9720  Z= 0.209
  Angle     :  0.863   6.601  13140  Z= 0.519
  Chirality :  0.039   0.119   1390
  Planarity :  0.005   0.025   1690
  Dihedral  : 19.495  59.348   3610
  Min Nonbonded Distance : 2.026

Molprobity Statistics.
  All-atom Clashscore : 14.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.16 %
    Favored  : 85.84 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 34.10 %
    Favored  : 63.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.79 (0.24), residues: 1130
  helix: -0.30 (0.19), residues: 770
  sheet:  None (None), residues: 0
  loop : -5.50 (0.18), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG F  44 
 TYR   0.022   0.003   TYR J  40 
 PHE   0.008   0.001   PHE D  64 
 TRP   0.018   0.002   TRP A  50 
 HIS   0.002   0.001   HIS I  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00458 ( 9720)
  covalent geometry    : angle       0.86291 (13140)
  hydrogen bonds       : bond        0.17284 (  510)
  hydrogen bonds       : angle       5.78954 ( 1530)

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

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

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  231 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 211
  time to evaluate  : 0.340 
Fit side-chains
REVERT: A   54 HIS cc_start: 0.6975 (m-70) cc_final: 0.6501 (m-70)
REVERT: B   38 GLN cc_start: 0.8494 (tp40) cc_final: 0.8232 (tp-100)
REVERT: B   54 HIS cc_start: 0.7007 (m-70) cc_final: 0.6580 (m-70)
REVERT: B   77 LYS cc_start: 0.7821 (mtpt) cc_final: 0.7612 (tttp)
REVERT: D   38 GLN cc_start: 0.8546 (tp40) cc_final: 0.8228 (tp-100)
REVERT: D   54 HIS cc_start: 0.7001 (m-70) cc_final: 0.6531 (m-70)
REVERT: D   77 LYS cc_start: 0.7928 (mtpt) cc_final: 0.7719 (ttmm)
REVERT: F   54 HIS cc_start: 0.7045 (m-70) cc_final: 0.6580 (m-70)
REVERT: G   38 GLN cc_start: 0.8473 (tp40) cc_final: 0.8220 (tp-100)
REVERT: G   54 HIS cc_start: 0.7002 (m-70) cc_final: 0.6580 (m-70)
REVERT: I   38 GLN cc_start: 0.8437 (tp40) cc_final: 0.8198 (tp40)
REVERT: I   54 HIS cc_start: 0.6948 (m-70) cc_final: 0.6474 (m-70)
REVERT: I   77 LYS cc_start: 0.7856 (mtpt) cc_final: 0.7637 (ttmm)
REVERT: I  101 MET cc_start: 0.8789 (ttp) cc_final: 0.8579 (ttp)
REVERT: J   54 HIS cc_start: 0.6827 (m-70) cc_final: 0.6495 (m-70)
  outliers start: 20
  outliers final: 0
  residues processed: 231
  average time/residue: 0.1479
  time to fit residues: 42.5320
Evaluate side-chains
  193 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 193
  time to evaluate  : 0.353 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 108 optimal weight:    3.9990
   chunk 49 optimal weight:    7.9990
   chunk 97 optimal weight:    0.8980
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    7.9990
   chunk 33 optimal weight:   10.0000
   chunk 65 optimal weight:    0.8980
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    2.9990
   chunk 100 optimal weight:    0.9990
   chunk 106 optimal weight:    0.9980
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
E 100 GLN
J 100 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4046 r_free = 0.4046 target = 0.182765 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.138529 restraints weight = 10880.216|
|-----------------------------------------------------------------------------|
r_work (start): 0.3492 rms_B_bonded: 2.95
r_work: 0.3301 rms_B_bonded: 4.37 restraints_weight: 0.5000
r_work (final): 0.3301
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7486
moved from start:          0.1667

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9720  Z= 0.149
  Angle     :  0.661   4.515  13140  Z= 0.362
  Chirality :  0.038   0.125   1390
  Planarity :  0.006   0.063   1690
  Dihedral  :  5.404  17.277   1260
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 11.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.10 %
    Favored  : 86.90 %
  Rotamer:
    Outliers :  4.20 %
    Allowed  : 27.90 %
    Favored  : 67.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.88 (0.24), residues: 1130
  helix:  0.43 (0.18), residues: 780
  sheet:  None (None), residues: 0
  loop : -5.40 (0.20), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG E  44 
 TYR   0.015   0.002   TYR C  40 
 PHE   0.010   0.001   PHE J  64 
 TRP   0.012   0.002   TRP E  50 
 HIS   0.002   0.001   HIS D  96 

Details of bonding type rmsd
  covalent geometry    : bond        0.00336 ( 9720)
  covalent geometry    : angle       0.66147 (13140)
  hydrogen bonds       : bond        0.04953 (  510)
  hydrogen bonds       : angle       4.16951 ( 1530)

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

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

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  259 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 217
  time to evaluate  : 0.359 
Fit side-chains
REVERT: A   54 HIS cc_start: 0.6600 (m-70) cc_final: 0.6358 (m-70)
REVERT: B   63 ILE cc_start: 0.8721 (mt) cc_final: 0.8514 (mp)
REVERT: B   73 ARG cc_start: 0.7213 (OUTLIER) cc_final: 0.6828 (mtm180)
REVERT: B  122 LEU cc_start: 0.8575 (mt) cc_final: 0.8219 (tt)
REVERT: C  122 LEU cc_start: 0.8682 (mt) cc_final: 0.8221 (tt)
REVERT: D   54 HIS cc_start: 0.6652 (m-70) cc_final: 0.6256 (m-70)
REVERT: E   38 GLN cc_start: 0.8323 (tp-100) cc_final: 0.8050 (tp-100)
REVERT: E  122 LEU cc_start: 0.8506 (mt) cc_final: 0.8273 (tt)
REVERT: F   54 HIS cc_start: 0.6800 (m-70) cc_final: 0.6418 (m-70)
REVERT: F  122 LEU cc_start: 0.8538 (mt) cc_final: 0.8314 (tt)
REVERT: G   54 HIS cc_start: 0.6666 (m-70) cc_final: 0.6465 (m-70)
REVERT: G   73 ARG cc_start: 0.7150 (OUTLIER) cc_final: 0.6725 (mtm180)
REVERT: G  122 LEU cc_start: 0.8589 (mt) cc_final: 0.8219 (tt)
REVERT: H  122 LEU cc_start: 0.8676 (mt) cc_final: 0.8238 (tt)
REVERT: I   54 HIS cc_start: 0.6633 (m-70) cc_final: 0.6278 (m-70)
REVERT: J   38 GLN cc_start: 0.8319 (tp-100) cc_final: 0.8056 (tp-100)
REVERT: J  122 LEU cc_start: 0.8559 (mt) cc_final: 0.8299 (tt)
  outliers start: 42
  outliers final: 8
  residues processed: 251
  average time/residue: 0.1261
  time to fit residues: 40.5168
Evaluate side-chains
  211 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 201
  time to evaluate  : 0.247 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 ASP
Chi-restraints excluded: chain B residue   18 ASP
Chi-restraints excluded: chain B residue   73 ARG
Chi-restraints excluded: chain B residue   90 ASN
Chi-restraints excluded: chain E residue   18 ASP
Chi-restraints excluded: chain F residue   18 ASP
Chi-restraints excluded: chain G residue   18 ASP
Chi-restraints excluded: chain G residue   73 ARG
Chi-restraints excluded: chain G residue   90 ASN
Chi-restraints excluded: chain J residue   18 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 76 optimal weight:    0.9990
   chunk 12 optimal weight:    0.4980
   chunk 9 optimal weight:    1.9990
   chunk 26 optimal weight:   20.0000
   chunk 50 optimal weight:    0.8980
   chunk 41 optimal weight:    0.8980
   chunk 35 optimal weight:    5.9990
   chunk 7 optimal weight:    2.9990
   chunk 96 optimal weight:    2.9990
   chunk 77 optimal weight:   10.0000
   chunk 81 optimal weight:    0.8980
   overall best weight:    0.8382

-------------------------------------------------------------------------------
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 = 0.4044 r_free = 0.4044 target = 0.182645 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.138015 restraints weight = 10818.889|
|-----------------------------------------------------------------------------|
r_work (start): 0.3534 rms_B_bonded: 2.96
r_work: 0.3348 rms_B_bonded: 4.25 restraints_weight: 0.5000
r_work (final): 0.3348
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7311
moved from start:          0.2549

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9720  Z= 0.133
  Angle     :  0.620   6.095  13140  Z= 0.334
  Chirality :  0.037   0.118   1390
  Planarity :  0.006   0.071   1690
  Dihedral  :  5.101  16.259   1260
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 7.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.81 %
    Favored  : 86.19 %
  Rotamer:
    Outliers :  5.10 %
    Allowed  : 26.90 %
    Favored  : 68.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.26 (0.25), residues: 1130
  helix:  0.90 (0.18), residues: 790
  sheet:  None (None), residues: 0
  loop : -5.34 (0.21), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG J  44 
 TYR   0.019   0.002   TYR C  40 
 PHE   0.016   0.001   PHE C  64 
 TRP   0.009   0.001   TRP J  50 
 HIS   0.002   0.000   HIS B  96 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 ( 9720)
  covalent geometry    : angle       0.61995 (13140)
  hydrogen bonds       : bond        0.04366 (  510)
  hydrogen bonds       : angle       3.80734 ( 1530)

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

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

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  253 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 202
  time to evaluate  : 0.353 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   54 HIS cc_start: 0.6637 (m-70) cc_final: 0.6292 (m-70)
REVERT: A   73 ARG cc_start: 0.7254 (OUTLIER) cc_final: 0.6702 (mtp180)
REVERT: A   81 ASN cc_start: 0.8930 (m-40) cc_final: 0.8726 (m-40)
REVERT: B  122 LEU cc_start: 0.8575 (mt) cc_final: 0.8232 (tt)
REVERT: C  122 LEU cc_start: 0.8615 (mt) cc_final: 0.8198 (tt)
REVERT: D   54 HIS cc_start: 0.6680 (m-70) cc_final: 0.6331 (m-70)
REVERT: D   62 ARG cc_start: 0.8298 (tpt170) cc_final: 0.8089 (tmt-80)
REVERT: E   38 GLN cc_start: 0.8190 (tp-100) cc_final: 0.7986 (tp-100)
REVERT: E   73 ARG cc_start: 0.7185 (OUTLIER) cc_final: 0.6714 (mtm180)
REVERT: E  122 LEU cc_start: 0.8550 (mt) cc_final: 0.8283 (tt)
REVERT: F   54 HIS cc_start: 0.6723 (m-70) cc_final: 0.6381 (m-70)
REVERT: F   73 ARG cc_start: 0.7257 (OUTLIER) cc_final: 0.6680 (mtm180)
REVERT: F  122 LEU cc_start: 0.8465 (mt) cc_final: 0.8203 (tt)
REVERT: G  122 LEU cc_start: 0.8572 (mt) cc_final: 0.8226 (tt)
REVERT: H  122 LEU cc_start: 0.8633 (mt) cc_final: 0.8218 (tt)
REVERT: I   54 HIS cc_start: 0.6641 (m-70) cc_final: 0.6261 (m-70)
REVERT: I   62 ARG cc_start: 0.8246 (tpt170) cc_final: 0.7983 (tmt-80)
REVERT: I   73 ARG cc_start: 0.7112 (OUTLIER) cc_final: 0.6607 (mtm180)
REVERT: J   73 ARG cc_start: 0.7189 (OUTLIER) cc_final: 0.6709 (mtm180)
REVERT: J  122 LEU cc_start: 0.8594 (mt) cc_final: 0.8287 (tt)
  outliers start: 51
  outliers final: 28
  residues processed: 231
  average time/residue: 0.1401
  time to fit residues: 41.1840
Evaluate side-chains
  224 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 191
  time to evaluate  : 0.364 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 ASP
Chi-restraints excluded: chain A residue   73 ARG
Chi-restraints excluded: chain A residue  127 PHE
Chi-restraints excluded: chain B residue   18 ASP
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain B residue  127 PHE
Chi-restraints excluded: chain C residue   18 ASP
Chi-restraints excluded: chain C residue   37 VAL
Chi-restraints excluded: chain C residue  127 PHE
Chi-restraints excluded: chain D residue   18 ASP
Chi-restraints excluded: chain D residue   37 VAL
Chi-restraints excluded: chain D residue  113 LEU
Chi-restraints excluded: chain D residue  127 PHE
Chi-restraints excluded: chain E residue   37 VAL
Chi-restraints excluded: chain E residue   73 ARG
Chi-restraints excluded: chain E residue  127 PHE
Chi-restraints excluded: chain F residue   18 ASP
Chi-restraints excluded: chain F residue   73 ARG
Chi-restraints excluded: chain F residue  127 PHE
Chi-restraints excluded: chain G residue   18 ASP
Chi-restraints excluded: chain G residue   37 VAL
Chi-restraints excluded: chain G residue  127 PHE
Chi-restraints excluded: chain H residue   18 ASP
Chi-restraints excluded: chain H residue   37 VAL
Chi-restraints excluded: chain H residue  127 PHE
Chi-restraints excluded: chain I residue   18 ASP
Chi-restraints excluded: chain I residue   37 VAL
Chi-restraints excluded: chain I residue   73 ARG
Chi-restraints excluded: chain I residue  113 LEU
Chi-restraints excluded: chain I residue  127 PHE
Chi-restraints excluded: chain J residue   37 VAL
Chi-restraints excluded: chain J residue   73 ARG
Chi-restraints excluded: chain J residue  127 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 18 optimal weight:    4.9990
   chunk 16 optimal weight:    6.9990
   chunk 19 optimal weight:    0.7980
   chunk 64 optimal weight:    0.0870
   chunk 100 optimal weight:    0.3980
   chunk 26 optimal weight:    6.9990
   chunk 49 optimal weight:    3.9990
   chunk 67 optimal weight:    0.9990
   chunk 54 optimal weight:    0.8980
   chunk 38 optimal weight:    8.9990
   chunk 31 optimal weight:    0.0370
   overall best weight:    0.4436

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

Flipped N/Q/H residues before XYZ refinement:
C  38 GLN
C 100 GLN
** E  54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H 100 GLN
** J  54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4074 r_free = 0.4074 target = 0.185096 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.140355 restraints weight = 10856.551|
|-----------------------------------------------------------------------------|
r_work (start): 0.3527 rms_B_bonded: 2.99
r_work: 0.3335 rms_B_bonded: 4.31 restraints_weight: 0.5000
r_work (final): 0.3335
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7270
moved from start:          0.2943

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9720  Z= 0.121
  Angle     :  0.595   5.337  13140  Z= 0.321
  Chirality :  0.036   0.162   1390
  Planarity :  0.006   0.059   1690
  Dihedral  :  4.972  16.373   1260
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 7.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.98 %
    Favored  : 86.02 %
  Rotamer:
    Outliers :  4.30 %
    Allowed  : 28.30 %
    Favored  : 67.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.77 (0.26), residues: 1130
  helix:  1.37 (0.19), residues: 780
  sheet:  None (None), residues: 0
  loop : -5.25 (0.21), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  44 
 TYR   0.016   0.002   TYR E  40 
 PHE   0.012   0.001   PHE E  64 
 TRP   0.007   0.001   TRP E  50 
 HIS   0.002   0.000   HIS D  96 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 ( 9720)
  covalent geometry    : angle       0.59508 (13140)
  hydrogen bonds       : bond        0.03779 (  510)
  hydrogen bonds       : angle       3.63117 ( 1530)

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

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

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  235 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 192
  time to evaluate  : 0.351 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   54 HIS cc_start: 0.6567 (m-70) cc_final: 0.6188 (m-70)
REVERT: A   81 ASN cc_start: 0.8950 (m-40) cc_final: 0.8720 (m-40)
REVERT: A  122 LEU cc_start: 0.8541 (mt) cc_final: 0.8176 (tt)
REVERT: B   73 ARG cc_start: 0.6951 (OUTLIER) cc_final: 0.6586 (mtm180)
REVERT: B  109 ASP cc_start: 0.7451 (OUTLIER) cc_final: 0.7176 (m-30)
REVERT: B  122 LEU cc_start: 0.8512 (mt) cc_final: 0.8218 (tt)
REVERT: C   40 TYR cc_start: 0.8440 (m-80) cc_final: 0.8163 (m-80)
REVERT: C  122 LEU cc_start: 0.8537 (mt) cc_final: 0.8172 (tt)
REVERT: D   54 HIS cc_start: 0.6588 (m-70) cc_final: 0.6152 (m-70)
REVERT: D   62 ARG cc_start: 0.8257 (tpt170) cc_final: 0.8015 (tmt-80)
REVERT: E  122 LEU cc_start: 0.8468 (mt) cc_final: 0.8255 (tt)
REVERT: F   73 ARG cc_start: 0.7188 (OUTLIER) cc_final: 0.6622 (mtm180)
REVERT: F  122 LEU cc_start: 0.8508 (mt) cc_final: 0.8170 (tt)
REVERT: G   73 ARG cc_start: 0.6959 (OUTLIER) cc_final: 0.6593 (mtm180)
REVERT: G  109 ASP cc_start: 0.7450 (OUTLIER) cc_final: 0.7132 (m-30)
REVERT: G  122 LEU cc_start: 0.8505 (mt) cc_final: 0.8194 (tt)
REVERT: H   40 TYR cc_start: 0.8427 (m-80) cc_final: 0.8154 (m-80)
REVERT: H  122 LEU cc_start: 0.8507 (mt) cc_final: 0.8174 (tt)
REVERT: I   54 HIS cc_start: 0.6548 (m-70) cc_final: 0.6191 (m-70)
REVERT: I   62 ARG cc_start: 0.8266 (tpt170) cc_final: 0.7991 (tmt-80)
REVERT: J  122 LEU cc_start: 0.8548 (mt) cc_final: 0.8311 (tt)
  outliers start: 43
  outliers final: 14
  residues processed: 227
  average time/residue: 0.1360
  time to fit residues: 39.3172
Evaluate side-chains
  204 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 185
  time to evaluate  : 0.335 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain B residue   73 ARG
Chi-restraints excluded: chain B residue  109 ASP
Chi-restraints excluded: chain B residue  127 PHE
Chi-restraints excluded: chain C residue   37 VAL
Chi-restraints excluded: chain C residue   99 LEU
Chi-restraints excluded: chain C residue  127 PHE
Chi-restraints excluded: chain D residue  113 LEU
Chi-restraints excluded: chain F residue   73 ARG
Chi-restraints excluded: chain G residue   18 ASP
Chi-restraints excluded: chain G residue   37 VAL
Chi-restraints excluded: chain G residue   73 ARG
Chi-restraints excluded: chain G residue  109 ASP
Chi-restraints excluded: chain G residue  127 PHE
Chi-restraints excluded: chain H residue   37 VAL
Chi-restraints excluded: chain H residue  127 PHE
Chi-restraints excluded: chain I residue   37 VAL
Chi-restraints excluded: chain I residue  113 LEU
Chi-restraints excluded: chain I residue  127 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 85 optimal weight:    3.9990
   chunk 39 optimal weight:    8.9990
   chunk 92 optimal weight:    8.9990
   chunk 64 optimal weight:    3.9990
   chunk 12 optimal weight:    0.4980
   chunk 98 optimal weight:    2.9990
   chunk 23 optimal weight:    0.0980
   chunk 95 optimal weight:    3.9990
   chunk 83 optimal weight:    6.9990
   chunk 76 optimal weight:    0.6980
   chunk 34 optimal weight:    0.1980
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
** B 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 100 GLN
I 100 GLN
** J  54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4036 r_free = 0.4036 target = 0.182316 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.136407 restraints weight = 10924.027|
|-----------------------------------------------------------------------------|
r_work (start): 0.3472 rms_B_bonded: 3.00
r_work: 0.3283 rms_B_bonded: 4.33 restraints_weight: 0.5000
r_work (final): 0.3283
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7404
moved from start:          0.3514

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9720  Z= 0.129
  Angle     :  0.589   5.851  13140  Z= 0.317
  Chirality :  0.037   0.147   1390
  Planarity :  0.003   0.022   1690
  Dihedral  :  4.728  15.330   1260
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 6.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.10 %
    Favored  : 86.90 %
  Rotamer:
    Outliers :  4.30 %
    Allowed  : 27.00 %
    Favored  : 68.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.39 (0.26), residues: 1130
  helix:  1.60 (0.19), residues: 790
  sheet:  None (None), residues: 0
  loop : -5.16 (0.23), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E  62 
 TYR   0.010   0.001   TYR B  40 
 PHE   0.008   0.001   PHE B  64 
 TRP   0.004   0.001   TRP G  43 
 HIS   0.002   0.000   HIS J  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 9720)
  covalent geometry    : angle       0.58898 (13140)
  hydrogen bonds       : bond        0.03865 (  510)
  hydrogen bonds       : angle       3.51556 ( 1530)

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

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

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 186
  time to evaluate  : 0.366 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   81 ASN cc_start: 0.8967 (m-40) cc_final: 0.8740 (m-40)
REVERT: A  122 LEU cc_start: 0.8500 (mt) cc_final: 0.8235 (tt)
REVERT: B  122 LEU cc_start: 0.8547 (mt) cc_final: 0.8295 (tt)
REVERT: C   73 ARG cc_start: 0.6916 (OUTLIER) cc_final: 0.6624 (mtm180)
REVERT: C  122 LEU cc_start: 0.8528 (mt) cc_final: 0.8228 (tt)
REVERT: D   18 ASP cc_start: 0.6458 (m-30) cc_final: 0.6227 (p0)
REVERT: D  113 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.8037 (tp)
REVERT: F  122 LEU cc_start: 0.8502 (mt) cc_final: 0.8241 (tt)
REVERT: G   62 ARG cc_start: 0.8071 (tpt170) cc_final: 0.7865 (tpt170)
REVERT: G  122 LEU cc_start: 0.8550 (mt) cc_final: 0.8289 (tt)
REVERT: H   73 ARG cc_start: 0.6922 (OUTLIER) cc_final: 0.6625 (mtm180)
REVERT: H  122 LEU cc_start: 0.8514 (mt) cc_final: 0.8259 (tt)
REVERT: I   18 ASP cc_start: 0.6476 (m-30) cc_final: 0.6195 (p0)
REVERT: I   54 HIS cc_start: 0.6587 (m-70) cc_final: 0.6155 (m-70)
REVERT: I  113 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.8099 (tp)
  outliers start: 43
  outliers final: 23
  residues processed: 215
  average time/residue: 0.1133
  time to fit residues: 32.6416
Evaluate side-chains
  207 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 180
  time to evaluate  : 0.345 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 ASP
Chi-restraints excluded: chain A residue  107 VAL
Chi-restraints excluded: chain B residue   18 ASP
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain B residue  127 PHE
Chi-restraints excluded: chain C residue   18 ASP
Chi-restraints excluded: chain C residue   37 VAL
Chi-restraints excluded: chain C residue   73 ARG
Chi-restraints excluded: chain C residue  109 ASP
Chi-restraints excluded: chain D residue   37 VAL
Chi-restraints excluded: chain D residue   99 LEU
Chi-restraints excluded: chain D residue  113 LEU
Chi-restraints excluded: chain D residue  127 PHE
Chi-restraints excluded: chain E residue  127 PHE
Chi-restraints excluded: chain F residue   18 ASP
Chi-restraints excluded: chain F residue  107 VAL
Chi-restraints excluded: chain G residue   18 ASP
Chi-restraints excluded: chain G residue   37 VAL
Chi-restraints excluded: chain G residue  127 PHE
Chi-restraints excluded: chain H residue   18 ASP
Chi-restraints excluded: chain H residue   37 VAL
Chi-restraints excluded: chain H residue   73 ARG
Chi-restraints excluded: chain H residue  109 ASP
Chi-restraints excluded: chain I residue   37 VAL
Chi-restraints excluded: chain I residue   99 LEU
Chi-restraints excluded: chain I residue  113 LEU
Chi-restraints excluded: chain J residue  127 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 79 optimal weight:    7.9990
   chunk 73 optimal weight:    1.9990
   chunk 20 optimal weight:    0.6980
   chunk 86 optimal weight:    0.0670
   chunk 12 optimal weight:    0.4980
   chunk 105 optimal weight:    0.9990
   chunk 58 optimal weight:    0.9980
   chunk 74 optimal weight:    0.9990
   chunk 31 optimal weight:    0.8980
   chunk 13 optimal weight:    5.9990
   chunk 100 optimal weight:    0.0020
   overall best weight:    0.4326

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

Flipped N/Q/H residues before XYZ refinement:
A 100 GLN
C  38 GLN
F 100 GLN
H  38 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4046 r_free = 0.4046 target = 0.183798 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.138739 restraints weight = 10890.387|
|-----------------------------------------------------------------------------|
r_work (start): 0.3521 rms_B_bonded: 3.00
r_work: 0.3336 rms_B_bonded: 4.37 restraints_weight: 0.5000
r_work (final): 0.3336
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7542
moved from start:          0.3814

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9720  Z= 0.115
  Angle     :  0.586   6.769  13140  Z= 0.311
  Chirality :  0.036   0.178   1390
  Planarity :  0.003   0.025   1690
  Dihedral  :  4.523  14.728   1260
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 5.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.39 %
    Favored  : 87.61 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  : 27.80 %
    Favored  : 68.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.13 (0.26), residues: 1130
  helix:  1.84 (0.18), residues: 790
  sheet:  None (None), residues: 0
  loop : -5.18 (0.22), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  36 
 TYR   0.022   0.002   TYR B  72 
 PHE   0.007   0.001   PHE E  64 
 TRP   0.004   0.001   TRP G  43 
 HIS   0.002   0.001   HIS H  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 ( 9720)
  covalent geometry    : angle       0.58570 (13140)
  hydrogen bonds       : bond        0.03126 (  510)
  hydrogen bonds       : angle       3.40905 ( 1530)

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

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

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  225 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 189
  time to evaluate  : 0.259 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   81 ASN cc_start: 0.9006 (m-40) cc_final: 0.8804 (m-40)
REVERT: B   55 MET cc_start: 0.7243 (mmm) cc_final: 0.6982 (mmp)
REVERT: B   73 ARG cc_start: 0.7010 (OUTLIER) cc_final: 0.6694 (mtm180)
REVERT: C   55 MET cc_start: 0.7040 (mmm) cc_final: 0.6839 (mmp)
REVERT: C   73 ARG cc_start: 0.7091 (OUTLIER) cc_final: 0.6791 (mtm180)
REVERT: D   55 MET cc_start: 0.7291 (mmm) cc_final: 0.7036 (mmp)
REVERT: D   73 ARG cc_start: 0.7313 (OUTLIER) cc_final: 0.6710 (mtm110)
REVERT: D  113 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.8233 (tp)
REVERT: G   62 ARG cc_start: 0.8297 (tpt170) cc_final: 0.8070 (tpt170)
REVERT: H   73 ARG cc_start: 0.7096 (OUTLIER) cc_final: 0.6791 (mtm180)
REVERT: I   54 HIS cc_start: 0.6671 (m-70) cc_final: 0.6329 (m-70)
REVERT: I   55 MET cc_start: 0.7102 (mmm) cc_final: 0.6885 (mmp)
REVERT: I  113 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8274 (tp)
REVERT: J   50 TRP cc_start: 0.8506 (m100) cc_final: 0.8278 (m100)
  outliers start: 36
  outliers final: 19
  residues processed: 216
  average time/residue: 0.1136
  time to fit residues: 32.1369
Evaluate side-chains
  198 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 173
  time to evaluate  : 0.340 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 VAL
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain B residue   73 ARG
Chi-restraints excluded: chain C residue   37 VAL
Chi-restraints excluded: chain C residue   73 ARG
Chi-restraints excluded: chain C residue   99 LEU
Chi-restraints excluded: chain D residue   37 VAL
Chi-restraints excluded: chain D residue   73 ARG
Chi-restraints excluded: chain D residue   99 LEU
Chi-restraints excluded: chain D residue  107 VAL
Chi-restraints excluded: chain D residue  113 LEU
Chi-restraints excluded: chain E residue  127 PHE
Chi-restraints excluded: chain F residue  107 VAL
Chi-restraints excluded: chain G residue   37 VAL
Chi-restraints excluded: chain H residue   37 VAL
Chi-restraints excluded: chain H residue   73 ARG
Chi-restraints excluded: chain H residue   99 LEU
Chi-restraints excluded: chain H residue  109 ASP
Chi-restraints excluded: chain I residue   37 VAL
Chi-restraints excluded: chain I residue   99 LEU
Chi-restraints excluded: chain I residue  107 VAL
Chi-restraints excluded: chain I residue  113 LEU
Chi-restraints excluded: chain I residue  127 PHE
Chi-restraints excluded: chain J residue   37 VAL
Chi-restraints excluded: chain J residue  127 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 51 optimal weight:    0.7980
   chunk 94 optimal weight:    7.9990
   chunk 4 optimal weight:    0.8980
   chunk 43 optimal weight:    1.9990
   chunk 17 optimal weight:    8.9990
   chunk 81 optimal weight:   20.0000
   chunk 41 optimal weight:    0.6980
   chunk 36 optimal weight:    3.9990
   chunk 89 optimal weight:   10.0000
   chunk 79 optimal weight:    5.9990
   chunk 56 optimal weight:   10.0000
   overall best weight:    1.6784

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

Flipped N/Q/H residues before XYZ refinement:
A  54 HIS
** A 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 100 GLN
** D 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 100 GLN
F 100 GLN
H 100 GLN
J 100 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3963 r_free = 0.3963 target = 0.175499 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.130654 restraints weight = 11020.366|
|-----------------------------------------------------------------------------|
r_work (start): 0.3431 rms_B_bonded: 2.99
r_work: 0.3246 rms_B_bonded: 4.28 restraints_weight: 0.5000
r_work (final): 0.3246
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7658
moved from start:          0.3944

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056   9720  Z= 0.161
  Angle     :  0.661   9.935  13140  Z= 0.348
  Chirality :  0.041   0.189   1390
  Planarity :  0.004   0.027   1690
  Dihedral  :  4.582  14.227   1260
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 7.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.19 %
    Favored  : 86.81 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 28.30 %
    Favored  : 69.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.05 (0.26), residues: 1130
  helix:  1.88 (0.18), residues: 790
  sheet:  None (None), residues: 0
  loop : -5.11 (0.23), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D  44 
 TYR   0.014   0.002   TYR I  72 
 PHE   0.009   0.001   PHE F  64 
 TRP   0.005   0.001   TRP G  50 
 HIS   0.003   0.001   HIS J  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00390 ( 9720)
  covalent geometry    : angle       0.66123 (13140)
  hydrogen bonds       : bond        0.03873 (  510)
  hydrogen bonds       : angle       3.44795 ( 1530)

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

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

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  192 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 170
  time to evaluate  : 0.400 
Fit side-chains
   revert: symmetry clash
REVERT: A   81 ASN cc_start: 0.9080 (m-40) cc_final: 0.8857 (m-40)
REVERT: C   73 ARG cc_start: 0.7175 (OUTLIER) cc_final: 0.6815 (mtm180)
REVERT: D  113 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8439 (tp)
REVERT: F   73 ARG cc_start: 0.7398 (OUTLIER) cc_final: 0.6830 (mtm180)
REVERT: G   55 MET cc_start: 0.7207 (mmm) cc_final: 0.6976 (mmp)
REVERT: H   73 ARG cc_start: 0.7177 (OUTLIER) cc_final: 0.6824 (mtm180)
REVERT: I  113 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8435 (tp)
REVERT: J   50 TRP cc_start: 0.8490 (m100) cc_final: 0.8264 (m100)
  outliers start: 22
  outliers final: 11
  residues processed: 186
  average time/residue: 0.1233
  time to fit residues: 29.8958
Evaluate side-chains
  183 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 167
  time to evaluate  : 0.356 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 VAL
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain C residue   73 ARG
Chi-restraints excluded: chain D residue   37 VAL
Chi-restraints excluded: chain D residue   99 LEU
Chi-restraints excluded: chain D residue  107 VAL
Chi-restraints excluded: chain D residue  113 LEU
Chi-restraints excluded: chain E residue   37 VAL
Chi-restraints excluded: chain F residue   73 ARG
Chi-restraints excluded: chain F residue  107 VAL
Chi-restraints excluded: chain G residue  127 PHE
Chi-restraints excluded: chain H residue   73 ARG
Chi-restraints excluded: chain I residue   99 LEU
Chi-restraints excluded: chain I residue  107 VAL
Chi-restraints excluded: chain I residue  113 LEU
Chi-restraints excluded: chain J residue   37 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 21 optimal weight:    0.9990
   chunk 61 optimal weight:    5.9990
   chunk 43 optimal weight:    0.7980
   chunk 78 optimal weight:    3.9990
   chunk 15 optimal weight:    7.9990
   chunk 53 optimal weight:    5.9990
   chunk 108 optimal weight:    0.9980
   chunk 80 optimal weight:    1.9990
   chunk 85 optimal weight:    2.9990
   chunk 100 optimal weight:    2.9990
   chunk 77 optimal weight:   20.0000
   overall best weight:    1.5586

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

Flipped N/Q/H residues before XYZ refinement:
** A 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3984 r_free = 0.3984 target = 0.176923 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.132454 restraints weight = 11051.539|
|-----------------------------------------------------------------------------|
r_work (start): 0.3422 rms_B_bonded: 3.01
r_work: 0.3233 rms_B_bonded: 4.29 restraints_weight: 0.5000
r_work (final): 0.3233
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7477
moved from start:          0.4120

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057   9720  Z= 0.155
  Angle     :  0.668   8.581  13140  Z= 0.353
  Chirality :  0.042   0.217   1390
  Planarity :  0.004   0.028   1690
  Dihedral  :  4.717  16.331   1260
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 6.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.54 %
    Favored  : 86.46 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 27.80 %
    Favored  : 70.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.02 (0.26), residues: 1130
  helix:  1.88 (0.18), residues: 790
  sheet:  None (None), residues: 0
  loop : -5.00 (0.24), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG F  36 
 TYR   0.011   0.002   TYR B  72 
 PHE   0.009   0.001   PHE C  64 
 TRP   0.011   0.001   TRP C  50 
 HIS   0.003   0.001   HIS H  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00377 ( 9720)
  covalent geometry    : angle       0.66782 (13140)
  hydrogen bonds       : bond        0.03727 (  510)
  hydrogen bonds       : angle       3.50756 ( 1530)

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

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

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 166
  time to evaluate  : 0.363 
Fit side-chains
REVERT: A   73 ARG cc_start: 0.7046 (OUTLIER) cc_final: 0.6616 (mtp180)
REVERT: A   81 ASN cc_start: 0.9034 (m-40) cc_final: 0.8804 (m-40)
REVERT: B   55 MET cc_start: 0.6976 (mmm) cc_final: 0.6762 (mmp)
REVERT: C   55 MET cc_start: 0.7035 (mmm) cc_final: 0.6825 (mmp)
REVERT: C   73 ARG cc_start: 0.7149 (OUTLIER) cc_final: 0.6821 (mtm180)
REVERT: D  113 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.8187 (tp)
REVERT: G   73 ARG cc_start: 0.7009 (OUTLIER) cc_final: 0.6625 (mtm180)
REVERT: H   73 ARG cc_start: 0.7154 (OUTLIER) cc_final: 0.6826 (mtm180)
REVERT: I  113 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8249 (tp)
REVERT: J   50 TRP cc_start: 0.8526 (m100) cc_final: 0.8303 (m100)
  outliers start: 21
  outliers final: 12
  residues processed: 181
  average time/residue: 0.1271
  time to fit residues: 29.8779
Evaluate side-chains
  181 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 163
  time to evaluate  : 0.362 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 ARG
Chi-restraints excluded: chain A residue  107 VAL
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain C residue   73 ARG
Chi-restraints excluded: chain C residue   99 LEU
Chi-restraints excluded: chain D residue   37 VAL
Chi-restraints excluded: chain D residue   99 LEU
Chi-restraints excluded: chain D residue  113 LEU
Chi-restraints excluded: chain E residue   37 VAL
Chi-restraints excluded: chain F residue  107 VAL
Chi-restraints excluded: chain G residue   73 ARG
Chi-restraints excluded: chain H residue   73 ARG
Chi-restraints excluded: chain H residue   99 LEU
Chi-restraints excluded: chain I residue   37 VAL
Chi-restraints excluded: chain I residue   99 LEU
Chi-restraints excluded: chain I residue  107 VAL
Chi-restraints excluded: chain I residue  113 LEU
Chi-restraints excluded: chain J residue   37 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 33 optimal weight:   20.0000
   chunk 47 optimal weight:    0.7980
   chunk 35 optimal weight:    6.9990
   chunk 63 optimal weight:    0.6980
   chunk 11 optimal weight:   20.0000
   chunk 105 optimal weight:    8.9990
   chunk 59 optimal weight:    0.0060
   chunk 96 optimal weight:    0.8980
   chunk 107 optimal weight:    2.9990
   chunk 106 optimal weight:    1.9990
   chunk 29 optimal weight:    0.3980
   overall best weight:    0.5596

-------------------------------------------------------------------------------
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 = 0.4022 r_free = 0.4022 target = 0.180548 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.137087 restraints weight = 11001.777|
|-----------------------------------------------------------------------------|
r_work (start): 0.3481 rms_B_bonded: 3.00
r_work: 0.3291 rms_B_bonded: 4.32 restraints_weight: 0.5000
r_work (final): 0.3291
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7417
moved from start:          0.4335

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.060   9720  Z= 0.130
  Angle     :  0.659   8.123  13140  Z= 0.349
  Chirality :  0.040   0.216   1390
  Planarity :  0.004   0.029   1690
  Dihedral  :  4.514  16.147   1260
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 6.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.86 %
    Favored  : 88.14 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 28.40 %
    Favored  : 69.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.07 (0.26), residues: 1130
  helix:  1.97 (0.18), residues: 790
  sheet:  None (None), residues: 0
  loop : -5.03 (0.22), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  36 
 TYR   0.013   0.001   TYR B  72 
 PHE   0.007   0.001   PHE H  64 
 TRP   0.012   0.001   TRP C  50 
 HIS   0.003   0.001   HIS A  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 ( 9720)
  covalent geometry    : angle       0.65917 (13140)
  hydrogen bonds       : bond        0.03147 (  510)
  hydrogen bonds       : angle       3.47529 ( 1530)

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

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

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 178
  time to evaluate  : 0.277 
Fit side-chains
REVERT: A   73 ARG cc_start: 0.6991 (OUTLIER) cc_final: 0.6586 (mtp180)
REVERT: A   81 ASN cc_start: 0.9006 (m-40) cc_final: 0.8783 (m-40)
REVERT: C   73 ARG cc_start: 0.6947 (OUTLIER) cc_final: 0.6675 (mtm180)
REVERT: D   55 MET cc_start: 0.7091 (mmm) cc_final: 0.6822 (mmp)
REVERT: D  113 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.8117 (tp)
REVERT: G   55 MET cc_start: 0.7264 (mmm) cc_final: 0.7029 (mmp)
REVERT: H   73 ARG cc_start: 0.6982 (OUTLIER) cc_final: 0.6685 (mtm180)
REVERT: I   55 MET cc_start: 0.7052 (mmm) cc_final: 0.6802 (mmp)
REVERT: I  113 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.8163 (tp)
REVERT: J   50 TRP cc_start: 0.8486 (m100) cc_final: 0.8190 (m100)
  outliers start: 18
  outliers final: 12
  residues processed: 192
  average time/residue: 0.1278
  time to fit residues: 31.7982
Evaluate side-chains
  187 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 170
  time to evaluate  : 0.311 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 ARG
Chi-restraints excluded: chain A residue  107 VAL
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain C residue   73 ARG
Chi-restraints excluded: chain C residue   99 LEU
Chi-restraints excluded: chain D residue   37 VAL
Chi-restraints excluded: chain D residue   99 LEU
Chi-restraints excluded: chain D residue  107 VAL
Chi-restraints excluded: chain D residue  113 LEU
Chi-restraints excluded: chain E residue   37 VAL
Chi-restraints excluded: chain F residue  107 VAL
Chi-restraints excluded: chain H residue   73 ARG
Chi-restraints excluded: chain H residue   99 LEU
Chi-restraints excluded: chain I residue   99 LEU
Chi-restraints excluded: chain I residue  107 VAL
Chi-restraints excluded: chain I residue  113 LEU
Chi-restraints excluded: chain J residue   37 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 18 optimal weight:    0.7980
   chunk 11 optimal weight:    9.9990
   chunk 106 optimal weight:    7.9990
   chunk 34 optimal weight:    5.9990
   chunk 64 optimal weight:    3.9990
   chunk 65 optimal weight:    0.6980
   chunk 100 optimal weight:    0.9990
   chunk 27 optimal weight:    4.9990
   chunk 82 optimal weight:    0.8980
   chunk 49 optimal weight:    0.8980
   chunk 2 optimal weight:    0.7980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
** A 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4008 r_free = 0.4008 target = 0.179207 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.135807 restraints weight = 10988.933|
|-----------------------------------------------------------------------------|
r_work (start): 0.3466 rms_B_bonded: 2.99
r_work: 0.3279 rms_B_bonded: 4.28 restraints_weight: 0.5000
r_work (final): 0.3279
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7410
moved from start:          0.4467

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.063   9720  Z= 0.136
  Angle     :  0.671   8.522  13140  Z= 0.355
  Chirality :  0.041   0.219   1390
  Planarity :  0.004   0.028   1690
  Dihedral  :  4.481  16.537   1260
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 6.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.86 %
    Favored  : 88.14 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 28.00 %
    Favored  : 70.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.16 (0.26), residues: 1130
  helix:  2.01 (0.18), residues: 790
  sheet:  None (None), residues: 0
  loop : -4.93 (0.22), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  36 
 TYR   0.017   0.002   TYR C  72 
 PHE   0.007   0.001   PHE H  64 
 TRP   0.014   0.001   TRP C  50 
 HIS   0.002   0.001   HIS A  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 ( 9720)
  covalent geometry    : angle       0.67080 (13140)
  hydrogen bonds       : bond        0.03321 (  510)
  hydrogen bonds       : angle       3.45570 ( 1530)

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

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

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 173
  time to evaluate  : 0.315 
Fit side-chains
REVERT: A   81 ASN cc_start: 0.9016 (m-40) cc_final: 0.8802 (m-40)
REVERT: B   55 MET cc_start: 0.7079 (mmm) cc_final: 0.6828 (mmp)
REVERT: B   63 ILE cc_start: 0.8741 (mt) cc_final: 0.8510 (mp)
REVERT: C   73 ARG cc_start: 0.6914 (OUTLIER) cc_final: 0.6649 (mtm180)
REVERT: D   55 MET cc_start: 0.7204 (mmm) cc_final: 0.6962 (mmp)
REVERT: D  113 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.8157 (tp)
REVERT: H   73 ARG cc_start: 0.6937 (OUTLIER) cc_final: 0.6646 (mtm180)
REVERT: I   55 MET cc_start: 0.7120 (mmm) cc_final: 0.6866 (mmp)
REVERT: I  113 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.8195 (tp)
REVERT: J   50 TRP cc_start: 0.8444 (m100) cc_final: 0.8142 (m100)
  outliers start: 18
  outliers final: 13
  residues processed: 186
  average time/residue: 0.1241
  time to fit residues: 30.0355
Evaluate side-chains
  189 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 172
  time to evaluate  : 0.337 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 VAL
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain C residue   73 ARG
Chi-restraints excluded: chain C residue   99 LEU
Chi-restraints excluded: chain D residue   37 VAL
Chi-restraints excluded: chain D residue   99 LEU
Chi-restraints excluded: chain D residue  107 VAL
Chi-restraints excluded: chain D residue  113 LEU
Chi-restraints excluded: chain E residue   37 VAL
Chi-restraints excluded: chain F residue  107 VAL
Chi-restraints excluded: chain G residue   37 VAL
Chi-restraints excluded: chain H residue   73 ARG
Chi-restraints excluded: chain H residue   99 LEU
Chi-restraints excluded: chain I residue   99 LEU
Chi-restraints excluded: chain I residue  107 VAL
Chi-restraints excluded: chain I residue  113 LEU
Chi-restraints excluded: chain J residue   37 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 71 optimal weight:    0.7980
   chunk 17 optimal weight:    3.9990
   chunk 7 optimal weight:    0.6980
   chunk 49 optimal weight:    0.1980
   chunk 29 optimal weight:    0.9980
   chunk 34 optimal weight:    7.9990
   chunk 10 optimal weight:    1.9990
   chunk 16 optimal weight:    3.9990
   chunk 61 optimal weight:    5.9990
   chunk 106 optimal weight:    0.0670
   chunk 19 optimal weight:    0.9990
   overall best weight:    0.5518

-------------------------------------------------------------------------------
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 = 0.4024 r_free = 0.4024 target = 0.180960 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.137863 restraints weight = 10940.875|
|-----------------------------------------------------------------------------|
r_work (start): 0.3478 rms_B_bonded: 2.99
r_work: 0.3291 rms_B_bonded: 4.28 restraints_weight: 0.5000
r_work (final): 0.3291
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7357
moved from start:          0.4571

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.059   9720  Z= 0.129
  Angle     :  0.659   8.576  13140  Z= 0.352
  Chirality :  0.040   0.215   1390
  Planarity :  0.003   0.029   1690
  Dihedral  :  4.364  16.289   1260
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 6.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.68 %
    Favored  : 88.32 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 27.80 %
    Favored  : 70.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.22 (0.26), residues: 1130
  helix:  2.05 (0.18), residues: 790
  sheet:  None (None), residues: 0
  loop : -4.88 (0.22), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  36 
 TYR   0.012   0.001   TYR B  72 
 PHE   0.005   0.001   PHE H  21 
 TRP   0.012   0.001   TRP C  50 
 HIS   0.002   0.000   HIS C  54 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 9720)
  covalent geometry    : angle       0.65861 (13140)
  hydrogen bonds       : bond        0.03091 (  510)
  hydrogen bonds       : angle       3.44599 ( 1530)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1970.00 seconds
wall clock time: 34 minutes 25.88 seconds (2065.88 seconds total)