Starting phenix.real_space_refine
on Fri Sep 11 12:41:51 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7x58_33011/09_2026/7x58_33011.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7x58_33011/09_2026/7x58_33011.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.93
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7x58_33011/09_2026/7x58_33011.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7x58_33011/09_2026/7x58_33011.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7x58_33011/09_2026/7x58_33011.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7x58_33011/09_2026/7x58_33011.cif"
  }
  resolution = 3.93
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   1.000
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: 5
    Type Number    sf(0)   Gaussians
     P     242      5.49       5
     S      20      5.16       5
     C    5377      2.51       5
     N    1846      2.21       5
     O    2290      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 26 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 9775
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 619
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 76, 619
          Classifications: {'peptide': 76}
          Link IDs: {'PTRANS': 2, 'TRANS': 73}
    Chain: "B"
      Number of atoms: 587
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 73, 587
          Classifications: {'peptide': 73}
          Link IDs: {'PTRANS': 1, 'TRANS': 71}
    Chain: "C"
      Number of atoms: 625
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 77, 625
          Classifications: {'peptide': 77}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 74}
    Chain: "D"
      Number of atoms: 576
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 72, 576
          Classifications: {'peptide': 72}
          Link IDs: {'PTRANS': 1, 'TRANS': 70}
    Chain: "E"
      Number of atoms: 619
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 76, 619
          Classifications: {'peptide': 76}
          Link IDs: {'PTRANS': 2, 'TRANS': 73}
    Chain: "F"
      Number of atoms: 576
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 72, 576
          Classifications: {'peptide': 72}
          Link IDs: {'PTRANS': 1, 'TRANS': 70}
    Chain: "G"
      Number of atoms: 625
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 77, 625
          Classifications: {'peptide': 77}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 74}
    Chain: "H"
      Number of atoms: 587
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 73, 587
          Classifications: {'peptide': 73}
          Link IDs: {'PTRANS': 1, 'TRANS': 71}
    Chain: "I"
      Number of atoms: 2463
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 121, 2463
          Classifications: {'DNA': 121}
          Link IDs: {'rna3p': 120}
    Chain: "J"
      Number of atoms: 2498
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 121, 2498
          Classifications: {'DNA': 121}
          Link IDs: {'rna3p': 120}
  Time building chain proxies: 1.98, per 1000 atoms: 0.20
  Number of scatterers: 9775
  At special positions: 0
  Unit cell: (121.8, 95.55, 110.25, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      20     16.00
     P     242     15.00
     O    2290      8.00
     N    1846      7.00
     C    5377      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: 0.83
  Conformation dependent library (CDL) restraints added in 182.4 milliseconds
  

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1128

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 7 sheets defined
      79.9% alpha, 2.3% beta
      117 base pairs and 201 stacking pairs defined.
    Time for finding SS restraints: 1.44
  Creating SS restraints...
    Processing helix  chain 'A' and resid 63 through 79
      removed outlier: 3.748A  pdb=" N   ASP A  77 " --> pdb=" O   GLU A  73 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   PHE A  78 " --> pdb=" O   ILE A  74 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 114
    Processing helix  chain 'A' and resid 120 through 132
    Processing helix  chain 'B' and resid 24 through 29
      removed outlier: 3.593A  pdb=" N   ILE B  29 " --> pdb=" O   ILE B  26 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 30 through 41
    Processing helix  chain 'B' and resid 49 through 76
    Processing helix  chain 'B' and resid 82 through 95
      removed outlier: 3.674A  pdb=" N   ARG B  95 " --> pdb=" O   LYS B  91 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 63 through 79
      removed outlier: 3.899A  pdb=" N   ASP C  77 " --> pdb=" O   GLU C  73 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   PHE C  78 " --> pdb=" O   ILE C  74 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 85 through 114
    Processing helix  chain 'C' and resid 120 through 132
    Processing helix  chain 'D' and resid 25 through 29
      removed outlier: 3.542A  pdb=" N   ILE D  29 " --> pdb=" O   ILE D  26 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 30 through 41
    Processing helix  chain 'D' and resid 49 through 76
      removed outlier: 3.529A  pdb=" N   GLU D  53 " --> pdb=" O   LEU D  49 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 82 through 95
    Processing helix  chain 'E' and resid 63 through 79
      removed outlier: 3.511A  pdb=" N   ASP E  77 " --> pdb=" O   GLU E  73 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 85 through 114
    Processing helix  chain 'E' and resid 120 through 131
      removed outlier: 3.572A  pdb=" N   ILE E 124 " --> pdb=" O   MET E 120 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 24 through 29
    Processing helix  chain 'F' and resid 30 through 41
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 3.552A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 95
    Processing helix  chain 'G' and resid 63 through 79
      removed outlier: 3.848A  pdb=" N   ASP G  77 " --> pdb=" O   GLU G  73 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   PHE G  78 " --> pdb=" O   ILE G  74 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 85 through 114
    Processing helix  chain 'G' and resid 120 through 132
    Processing helix  chain 'H' and resid 25 through 29
    Processing helix  chain 'H' and resid 30 through 41
    Processing helix  chain 'H' and resid 49 through 76
    Processing helix  chain 'H' and resid 82 through 94
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 6.793A  pdb=" N   ARG A  83 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119
    Processing sheet with id=AA3, first strand: chain 'C' and resid 118 through 119
      removed outlier: 3.637A  pdb=" N   ILE C 119 " --> pdb=" O   ARG D  45 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'E' and resid 83 through 84
      removed outlier: 7.198A  pdb=" N   ARG E  83 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'E' and resid 118 through 119
      removed outlier: 3.666A  pdb=" N   ILE E 119 " --> pdb=" O   ARG F  45 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'G' and resid 83 through 84
      removed outlier: 6.804A  pdb=" N   ARG G  83 " --> pdb=" O   VAL H  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'G' and resid 118 through 119

    357 hydrogen bonds defined for protein.
    1047 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      303 hydrogen bonds
      606 hydrogen bond angles
      0 basepair planarities
      117 basepair parallelities
      201 stacking parallelities
  Total time for adding SS restraints: 1.75

  Time building geometry restraints manager: 1.11 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 1842
        1.33 -     1.45: 3403
        1.45 -     1.57: 4667
        1.57 -     1.69: 482
        1.69 -     1.81: 32
  Bond restraints: 10426
  Sorted by residual:
  bond pdb=" C3'  DC I  -8 "
       pdb=" C2'  DC I  -8 "
    ideal  model  delta    sigma   weight residual
    1.516  1.544 -0.028 8.00e-03 1.56e+04 1.22e+01
  bond pdb=" C3'  DA J  45 "
       pdb=" C2'  DA J  45 "
    ideal  model  delta    sigma   weight residual
    1.516  1.542 -0.026 8.00e-03 1.56e+04 1.09e+01
  bond pdb=" C3'  DG I -53 "
       pdb=" C2'  DG I -53 "
    ideal  model  delta    sigma   weight residual
    1.516  1.542 -0.026 8.00e-03 1.56e+04 1.08e+01
  bond pdb=" C3'  DC I -18 "
       pdb=" C2'  DC I -18 "
    ideal  model  delta    sigma   weight residual
    1.516  1.542 -0.026 8.00e-03 1.56e+04 1.06e+01
  bond pdb=" C3'  DC I  51 "
       pdb=" C2'  DC I  51 "
    ideal  model  delta    sigma   weight residual
    1.516  1.542 -0.026 8.00e-03 1.56e+04 1.05e+01
  ... (remaining 10421 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.37: 13965
        1.37 -     2.73: 1077
        2.73 -     4.10: 38
        4.10 -     5.46: 12
        5.46 -     6.83: 5
  Bond angle restraints: 15097
  Sorted by residual:
  angle pdb=" N3   DT I  33 "
        pdb=" C4   DT I  33 "
        pdb=" O4   DT I  33 "
      ideal   model   delta    sigma   weight residual
     119.90  122.39   -2.49 6.00e-01 2.78e+00 1.72e+01
  angle pdb=" N3   DT I -37 "
        pdb=" C4   DT I -37 "
        pdb=" O4   DT I -37 "
      ideal   model   delta    sigma   weight residual
     119.90  122.39   -2.49 6.00e-01 2.78e+00 1.72e+01
  angle pdb=" N3   DT J  31 "
        pdb=" C4   DT J  31 "
        pdb=" O4   DT J  31 "
      ideal   model   delta    sigma   weight residual
     119.90  122.38   -2.48 6.00e-01 2.78e+00 1.71e+01
  angle pdb=" N3   DT J  11 "
        pdb=" C4   DT J  11 "
        pdb=" O4   DT J  11 "
      ideal   model   delta    sigma   weight residual
     119.90  122.38   -2.48 6.00e-01 2.78e+00 1.71e+01
  angle pdb=" N3   DT J -18 "
        pdb=" C4   DT J -18 "
        pdb=" O4   DT J -18 "
      ideal   model   delta    sigma   weight residual
     119.90  122.38   -2.48 6.00e-01 2.78e+00 1.71e+01
  ... (remaining 15092 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.47: 4570
       35.47 -    70.94: 1069
       70.94 -   106.41: 11
      106.41 -   141.88: 1
      141.88 -   177.36: 3
  Dihedral angle restraints: 5654
    sinusoidal: 3922
      harmonic: 1732
  Sorted by residual:
  dihedral pdb=" C4'  DC I  51 "
           pdb=" C3'  DC I  51 "
           pdb=" O3'  DC I  51 "
           pdb=" P    DA I  52 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -140.00   37.36 -177.36     1      3.50e+01 8.16e-04 1.57e+01
  dihedral pdb=" C4'  DT I  14 "
           pdb=" C3'  DT I  14 "
           pdb=" O3'  DT I  14 "
           pdb=" P    DT I  15 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   53.77  166.23     1      3.50e+01 8.16e-04 1.54e+01
  dihedral pdb=" C4'  DC I -48 "
           pdb=" C3'  DC I -48 "
           pdb=" O3'  DC I -48 "
           pdb=" P    DG I -47 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   74.13  145.87     1      3.50e+01 8.16e-04 1.43e+01
  ... (remaining 5651 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.062: 1409
       0.062 -    0.124: 306
       0.124 -    0.185: 7
       0.185 -    0.247: 1
       0.247 -    0.309: 1
  Chirality restraints: 1724
  Sorted by residual:
  chirality pdb=" CG  LEU H  62 "
            pdb=" CB  LEU H  62 "
            pdb=" CD1 LEU H  62 "
            pdb=" CD2 LEU H  62 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.90    0.31 2.00e-01 2.50e+01 2.39e+00
  chirality pdb=" CA  ARG A 131 "
            pdb=" N   ARG A 131 "
            pdb=" C   ARG A 131 "
            pdb=" CB  ARG A 131 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 9.66e-01
  chirality pdb=" CG  LEU B  62 "
            pdb=" CB  LEU B  62 "
            pdb=" CD1 LEU B  62 "
            pdb=" CD2 LEU B  62 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.76    0.17 2.00e-01 2.50e+01 7.53e-01
  ... (remaining 1721 not shown)

  Planarity restraints: 1074
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS B  31 "   -0.022 5.00e-02 4.00e+02   3.27e-02 1.71e+00
        pdb=" N   PRO B  32 "    0.057 5.00e-02 4.00e+02
        pdb=" CA  PRO B  32 "   -0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO B  32 "   -0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS H  31 "   -0.022 5.00e-02 4.00e+02   3.25e-02 1.69e+00
        pdb=" N   PRO H  32 "    0.056 5.00e-02 4.00e+02
        pdb=" CA  PRO H  32 "   -0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO H  32 "   -0.018 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A  65 "   -0.017 5.00e-02 4.00e+02   2.64e-02 1.11e+00
        pdb=" N   PRO A  66 "    0.046 5.00e-02 4.00e+02
        pdb=" CA  PRO A  66 "   -0.013 5.00e-02 4.00e+02
        pdb=" CD  PRO A  66 "   -0.015 5.00e-02 4.00e+02
  ... (remaining 1071 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 1171
        2.76 -     3.29: 8687
        3.29 -     3.83: 19177
        3.83 -     4.36: 22265
        4.36 -     4.90: 30841
  Nonbonded interactions: 82141
  Sorted by model distance:
  nonbonded pdb=" OG1 THR F  73 "
            pdb=" OD2 ASP F  85 "
     model   vdw
     2.221 3.040
  nonbonded pdb=" NH2 ARG G  63 "
            pdb=" OP1  DA I  18 "
     model   vdw
     2.267 3.120
  nonbonded pdb=" O2   DT I -24 "
            pdb=" N2   DG J  25 "
     model   vdw
     2.280 3.120
  nonbonded pdb=" NH1 ARG B  78 "
            pdb=" OP2  DC I  -2 "
     model   vdw
     2.293 3.120
  nonbonded pdb=" NH2 ARG C  72 "
            pdb=" OP1  DC I -54 "
     model   vdw
     2.345 3.120
  ... (remaining 82136 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = (chain 'C' and resid 59 through 134)
  selection = chain 'E'
  selection = (chain 'G' and resid 59 through 134)
}
ncs_group {
  reference = (chain 'B' and resid 24 through 95)
  selection = chain 'D'
  selection = chain 'F'
  selection = (chain 'H' and resid 24 through 95)
}

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:             0.570
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.020
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     10.540
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:0.970
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.400
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8003
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  10426  Z= 0.493
  Angle     :  0.733   6.829  15097  Z= 0.641
  Chirality :  0.045   0.309   1724
  Planarity :  0.003   0.033   1074
  Dihedral  : 27.062 177.356   4526
  Min Nonbonded Distance : 2.221

Molprobity Statistics.
  All-atom Clashscore : 7.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.86 %
    Favored  : 99.14 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  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:  0.68 (0.29), residues: 580
  helix:  1.04 (0.21), residues: 434
  sheet:  None (None), residues: 0
  loop : -1.21 (0.37), residues: 146

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E 129 
 TYR   0.004   0.001   TYR B  88 
 PHE   0.013   0.001   PHE H  61 
 HIS   0.001   0.000   HIS C 113 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00538 /  0.49 (10426)
  covalent geometry    : angle       0.73294 /  0.64 (15097)
  hydrogen bonds       : bond        0.19993 / 13.55 (  660)
  hydrogen bonds       : angle       5.67620 /  4.19 ( 1653)

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

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

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  288 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 288
  time to evaluate  : 0.195 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   81 ASP cc_start: 0.8253 (t0) cc_final: 0.8051 (t70)
REVERT: A   87 SER cc_start: 0.9347 (m) cc_final: 0.9083 (t)
REVERT: A   90 MET cc_start: 0.8114 (mmm) cc_final: 0.7795 (mmp)
REVERT: B   31 LYS cc_start: 0.9128 (tttt) cc_final: 0.8904 (ttmm)
REVERT: C   65 LEU cc_start: 0.9070 (mt) cc_final: 0.8775 (mt)
REVERT: C  113 HIS cc_start: 0.9068 (t70) cc_final: 0.8690 (t-170)
REVERT: C  126 LEU cc_start: 0.8913 (tp) cc_final: 0.8583 (tp)
REVERT: D   53 GLU cc_start: 0.8764 (tp30) cc_final: 0.8491 (tp30)
REVERT: D   84 MET cc_start: 0.8110 (tpp) cc_final: 0.7858 (tpp)
REVERT: D   91 LYS cc_start: 0.8313 (tmtt) cc_final: 0.7740 (mtpt)
REVERT: E   90 MET cc_start: 0.8014 (ttt) cc_final: 0.7336 (tmm)
REVERT: F   32 PRO cc_start: 0.9229 (Cg_exo) cc_final: 0.8950 (Cg_endo)
REVERT: F   79 LYS cc_start: 0.8776 (mttm) cc_final: 0.8376 (tptp)
REVERT: F   87 VAL cc_start: 0.8283 (t) cc_final: 0.8060 (t)
REVERT: F   91 LYS cc_start: 0.8504 (mttt) cc_final: 0.8162 (mtpt)
REVERT: G   81 ASP cc_start: 0.8219 (t0) cc_final: 0.7976 (t70)
REVERT: G  107 THR cc_start: 0.9274 (m) cc_final: 0.8713 (p)
REVERT: H   31 LYS cc_start: 0.9110 (tttt) cc_final: 0.8853 (ttmm)
  outliers start: 0
  outliers final: 0
  residues processed: 288
  average time/residue: 0.1413
  time to fit residues: 51.1645
Evaluate side-chains
  172 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 172
  time to evaluate  : 0.259 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 49 optimal weight:    0.3980
   chunk 53 optimal weight:    0.6980
   chunk 5 optimal weight:    4.9990
   chunk 33 optimal weight:    8.9990
   chunk 65 optimal weight:   30.0000
   chunk 62 optimal weight:   20.0000
   chunk 51 optimal weight:    0.0170
   chunk 38 optimal weight:    0.7980
   chunk 61 optimal weight:   20.0000
   chunk 45 optimal weight:    0.8980
   chunk 74 optimal weight:   30.0000
   overall best weight:    0.5618

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
F  64 ASN
F  75 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.099117 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3184 r_free = 0.3184 target = 0.067287 restraints weight = 31892.431|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.069053 restraints weight = 18058.088|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.070182 restraints weight = 12995.177|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.070867 restraints weight = 10831.855|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.071087 restraints weight = 9815.938|
|-----------------------------------------------------------------------------|
r_work (final): 0.3246
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8151
moved from start:          0.2792

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058  10426  Z= 0.188
  Angle     :  0.714   8.763  15097  Z= 0.421
  Chirality :  0.044   0.269   1724
  Planarity :  0.007   0.123   1074
  Dihedral  : 31.020 172.767   3290
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 12.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.69 %
    Favored  : 99.31 %
  Rotamer:
    Outliers :  4.94 %
    Allowed  : 21.34 %
    Favored  : 73.72 %
  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:  2.27 (0.32), residues: 580
  helix:  2.27 (0.23), residues: 448
  sheet:  None (None), residues: 0
  loop : -1.30 (0.38), residues: 132

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.025   0.001   ARG G  83 
 TYR   0.019   0.001   TYR B  88 
 PHE   0.011   0.002   PHE E  78 
 HIS   0.007   0.002   HIS E 113 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00328 /  0.19 (10426)
  covalent geometry    : angle       0.71416 /  0.42 (15097)
  hydrogen bonds       : bond        0.07179 /  4.82 (  660)
  hydrogen bonds       : angle       3.37731 /  2.49 ( 1653)

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

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

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  219 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 194
  time to evaluate  : 0.164 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   73 GLU cc_start: 0.8635 (tm-30) cc_final: 0.8397 (tm-30)
REVERT: A   87 SER cc_start: 0.9347 (m) cc_final: 0.8904 (t)
REVERT: C   64 LYS cc_start: 0.9262 (tttp) cc_final: 0.8873 (tmtt)
REVERT: C   90 MET cc_start: 0.7534 (tpp) cc_final: 0.6727 (tpp)
REVERT: C  105 GLU cc_start: 0.8313 (mt-10) cc_final: 0.8023 (mt-10)
REVERT: C  109 LEU cc_start: 0.9167 (OUTLIER) cc_final: 0.8857 (mm)
REVERT: C  113 HIS cc_start: 0.9058 (t70) cc_final: 0.8768 (t-170)
REVERT: D   90 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8635 (tt)
REVERT: D   91 LYS cc_start: 0.8122 (tmtt) cc_final: 0.7677 (mtmt)
REVERT: E   73 GLU cc_start: 0.9070 (tm-30) cc_final: 0.8326 (tm-30)
REVERT: E   90 MET cc_start: 0.7840 (ttt) cc_final: 0.7411 (tpp)
REVERT: E  105 GLU cc_start: 0.8334 (mt-10) cc_final: 0.8133 (mt-10)
REVERT: F   74 GLU cc_start: 0.8864 (OUTLIER) cc_final: 0.8137 (tm-30)
REVERT: F   79 LYS cc_start: 0.8943 (mttm) cc_final: 0.8350 (tptp)
REVERT: F   84 MET cc_start: 0.8020 (mmm) cc_final: 0.7302 (tpp)
REVERT: F   91 LYS cc_start: 0.8418 (mttt) cc_final: 0.8135 (mtpt)
REVERT: G   61 LEU cc_start: 0.9283 (mt) cc_final: 0.9057 (mp)
REVERT: G   73 GLU cc_start: 0.8482 (tm-30) cc_final: 0.8138 (tm-30)
REVERT: G   83 ARG cc_start: 0.8254 (OUTLIER) cc_final: 0.8040 (mtp85)
REVERT: G  107 THR cc_start: 0.9382 (m) cc_final: 0.8942 (p)
REVERT: H   52 GLU cc_start: 0.7700 (tm-30) cc_final: 0.7397 (tm-30)
  outliers start: 25
  outliers final: 10
  residues processed: 204
  average time/residue: 0.1176
  time to fit residues: 31.3031
Evaluate side-chains
  177 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 163
  time to evaluate  : 0.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain C residue   89 VAL
Chi-restraints excluded: chain C residue  109 LEU
Chi-restraints excluded: chain D residue   49 LEU
Chi-restraints excluded: chain D residue   81 VAL
Chi-restraints excluded: chain D residue   86 VAL
Chi-restraints excluded: chain D residue   90 LEU
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain F residue   59 LYS
Chi-restraints excluded: chain F residue   74 GLU
Chi-restraints excluded: chain F residue   86 VAL
Chi-restraints excluded: chain G residue   76 GLN
Chi-restraints excluded: chain G residue   83 ARG
Chi-restraints excluded: chain G residue   96 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 22 optimal weight:    2.9990
   chunk 0 optimal weight:    7.9990
   chunk 62 optimal weight:   30.0000
   chunk 33 optimal weight:    3.9990
   chunk 5 optimal weight:    1.9990
   chunk 9 optimal weight:    3.9990
   chunk 76 optimal weight:   30.0000
   chunk 4 optimal weight:    0.9990
   chunk 44 optimal weight:    2.9990
   chunk 71 optimal weight:   30.0000
   chunk 61 optimal weight:   30.0000
   overall best weight:    2.5990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 125 GLN
F  64 ASN
G  68 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.096683 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3121 r_free = 0.3121 target = 0.064400 restraints weight = 31441.153|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.066100 restraints weight = 18048.886|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.067207 restraints weight = 13056.714|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.067832 restraints weight = 10888.173|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.068227 restraints weight = 9895.945|
|-----------------------------------------------------------------------------|
r_work (final): 0.3185
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8226
moved from start:          0.3295

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053  10426  Z= 0.202
  Angle     :  0.690   6.952  15097  Z= 0.405
  Chirality :  0.043   0.321   1724
  Planarity :  0.005   0.054   1074
  Dihedral  : 31.474 171.939   3290
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 12.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.03 %
    Favored  : 98.97 %
  Rotamer:
    Outliers :  7.91 %
    Allowed  : 21.54 %
    Favored  : 70.55 %
  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:  2.36 (0.32), residues: 580
  helix:  2.34 (0.23), residues: 450
  sheet:  None (None), residues: 0
  loop : -1.34 (0.41), residues: 130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 129 
 TYR   0.011   0.002   TYR D  72 
 PHE   0.010   0.002   PHE B  61 
 HIS   0.006   0.002   HIS B  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00401 /  0.20 (10426)
  covalent geometry    : angle       0.69036 /  0.41 (15097)
  hydrogen bonds       : bond        0.06054 /  4.12 (  660)
  hydrogen bonds       : angle       3.29330 /  2.41 ( 1653)

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

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

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 172
  time to evaluate  : 0.184 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   73 GLU cc_start: 0.8844 (tm-30) cc_final: 0.8572 (tm-30)
REVERT: A   87 SER cc_start: 0.9313 (m) cc_final: 0.8915 (t)
REVERT: A  125 GLN cc_start: 0.8365 (mt0) cc_final: 0.8087 (mp10)
REVERT: C   61 LEU cc_start: 0.9312 (mp) cc_final: 0.8928 (mp)
REVERT: C   90 MET cc_start: 0.7660 (tpp) cc_final: 0.7085 (tpp)
REVERT: C  105 GLU cc_start: 0.8342 (mt-10) cc_final: 0.7886 (mt-10)
REVERT: C  109 LEU cc_start: 0.9163 (OUTLIER) cc_final: 0.8852 (mm)
REVERT: D   52 GLU cc_start: 0.8480 (tm-30) cc_final: 0.8253 (tm-30)
REVERT: D   88 TYR cc_start: 0.7385 (t80) cc_final: 0.6759 (t80)
REVERT: D   91 LYS cc_start: 0.8211 (tmtt) cc_final: 0.7737 (ptmm)
REVERT: E   73 GLU cc_start: 0.8639 (tm-30) cc_final: 0.8321 (tm-30)
REVERT: E   90 MET cc_start: 0.7991 (ttt) cc_final: 0.7503 (tpp)
REVERT: E   97 GLU cc_start: 0.8342 (mm-30) cc_final: 0.7760 (pt0)
REVERT: E  105 GLU cc_start: 0.8399 (mt-10) cc_final: 0.8073 (mt-10)
REVERT: F   67 ARG cc_start: 0.8220 (ttm110) cc_final: 0.7736 (ttm110)
REVERT: F   79 LYS cc_start: 0.8966 (mttm) cc_final: 0.8386 (tptp)
REVERT: F   84 MET cc_start: 0.8053 (mmm) cc_final: 0.7463 (tpp)
REVERT: F   88 TYR cc_start: 0.8016 (m-10) cc_final: 0.7595 (m-10)
REVERT: F   91 LYS cc_start: 0.8574 (mttt) cc_final: 0.8218 (mtpt)
REVERT: G  120 MET cc_start: 0.8413 (mmm) cc_final: 0.7818 (mmt)
REVERT: H   52 GLU cc_start: 0.7794 (tm-30) cc_final: 0.7427 (tm-30)
  outliers start: 40
  outliers final: 27
  residues processed: 190
  average time/residue: 0.1051
  time to fit residues: 26.8910
Evaluate side-chains
  179 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 151
  time to evaluate  : 0.247 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 GLN
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain B residue   57 VAL
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain C residue   89 VAL
Chi-restraints excluded: chain C residue  101 VAL
Chi-restraints excluded: chain C residue  109 LEU
Chi-restraints excluded: chain D residue   49 LEU
Chi-restraints excluded: chain D residue   60 VAL
Chi-restraints excluded: chain D residue   81 VAL
Chi-restraints excluded: chain D residue   86 VAL
Chi-restraints excluded: chain E residue   60 LEU
Chi-restraints excluded: chain E residue   70 LEU
Chi-restraints excluded: chain E residue   74 ILE
Chi-restraints excluded: chain E residue  109 LEU
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain F residue   59 LYS
Chi-restraints excluded: chain F residue   71 THR
Chi-restraints excluded: chain F residue   74 GLU
Chi-restraints excluded: chain F residue   86 VAL
Chi-restraints excluded: chain G residue   76 GLN
Chi-restraints excluded: chain G residue   96 CYS
Chi-restraints excluded: chain G residue   97 GLU
Chi-restraints excluded: chain G residue  134 ARG
Chi-restraints excluded: chain H residue   62 LEU
Chi-restraints excluded: chain H residue   92 ARG
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 20 optimal weight:    0.9980
   chunk 68 optimal weight:   50.0000
   chunk 55 optimal weight:    0.7980
   chunk 10 optimal weight:    1.9990
   chunk 28 optimal weight:    9.9990
   chunk 23 optimal weight:    6.9990
   chunk 58 optimal weight:   30.0000
   chunk 11 optimal weight:    2.9990
   chunk 30 optimal weight:   10.0000
   chunk 43 optimal weight:    2.9990
   chunk 35 optimal weight:    8.9990
   overall best weight:    1.9586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 125 GLN
F  64 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.096300 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3116 r_free = 0.3116 target = 0.064242 restraints weight = 32252.011|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 20)----------------|
| r_work = 0.3158 r_free = 0.3158 target = 0.065848 restraints weight = 19332.840|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.066908 restraints weight = 14351.275|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.067492 restraints weight = 12072.835|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.067492 restraints weight = 11040.465|
|-----------------------------------------------------------------------------|
r_work (final): 0.3157
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8257
moved from start:          0.3513

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  10426  Z= 0.178
  Angle     :  0.657   6.739  15097  Z= 0.389
  Chirality :  0.043   0.340   1724
  Planarity :  0.004   0.034   1074
  Dihedral  : 31.612 171.883   3290
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 11.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.38 %
    Favored  : 98.62 %
  Rotamer:
    Outliers :  5.53 %
    Allowed  : 24.51 %
    Favored  : 69.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.52 (0.33), residues: 580
  helix:  2.49 (0.23), residues: 450
  sheet:  None (None), residues: 0
  loop : -1.44 (0.42), residues: 130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG G  83 
 TYR   0.008   0.001   TYR B  88 
 PHE   0.014   0.002   PHE E  78 
 HIS   0.004   0.001   HIS B  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00336 /  0.18 (10426)
  covalent geometry    : angle       0.65654 /  0.39 (15097)
  hydrogen bonds       : bond        0.05322 /  3.59 (  660)
  hydrogen bonds       : angle       3.11481 /  2.29 ( 1653)

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

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

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 166
  time to evaluate  : 0.156 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   73 GLU cc_start: 0.8843 (tm-30) cc_final: 0.8583 (tm-30)
REVERT: A   87 SER cc_start: 0.9304 (m) cc_final: 0.8926 (t)
REVERT: A   90 MET cc_start: 0.8849 (mmp) cc_final: 0.8236 (tpt)
REVERT: A   97 GLU cc_start: 0.8186 (mt-10) cc_final: 0.7975 (mt-10)
REVERT: A  125 GLN cc_start: 0.8424 (mt0) cc_final: 0.7988 (mp10)
REVERT: B   84 MET cc_start: 0.8262 (tpp) cc_final: 0.8013 (tpt)
REVERT: C   90 MET cc_start: 0.7659 (tpp) cc_final: 0.7072 (tpp)
REVERT: C  105 GLU cc_start: 0.8358 (mt-10) cc_final: 0.7939 (mt-10)
REVERT: D   52 GLU cc_start: 0.8391 (tm-30) cc_final: 0.8186 (tm-30)
REVERT: D   53 GLU cc_start: 0.8655 (tp30) cc_final: 0.8435 (tt0)
REVERT: D   88 TYR cc_start: 0.7385 (t80) cc_final: 0.6761 (t80)
REVERT: D   91 LYS cc_start: 0.8249 (tmtt) cc_final: 0.7691 (ptmm)
REVERT: E   73 GLU cc_start: 0.8606 (tm-30) cc_final: 0.8243 (tm-30)
REVERT: E   90 MET cc_start: 0.7921 (ttt) cc_final: 0.7452 (tpp)
REVERT: E   97 GLU cc_start: 0.8276 (mm-30) cc_final: 0.7783 (pt0)
REVERT: E  105 GLU cc_start: 0.8368 (mt-10) cc_final: 0.8115 (mt-10)
REVERT: F   53 GLU cc_start: 0.8927 (tp30) cc_final: 0.8686 (tp30)
REVERT: F   79 LYS cc_start: 0.8940 (mttm) cc_final: 0.8391 (tptp)
REVERT: F   84 MET cc_start: 0.8013 (mmm) cc_final: 0.7339 (tpp)
REVERT: F   91 LYS cc_start: 0.8579 (mttt) cc_final: 0.8164 (mtpt)
REVERT: G  120 MET cc_start: 0.8482 (mmm) cc_final: 0.7943 (mmt)
REVERT: G  125 GLN cc_start: 0.8585 (mt0) cc_final: 0.8229 (mp10)
REVERT: H   52 GLU cc_start: 0.7782 (tm-30) cc_final: 0.7412 (tm-30)
  outliers start: 28
  outliers final: 20
  residues processed: 177
  average time/residue: 0.1020
  time to fit residues: 24.7672
Evaluate side-chains
  173 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 153
  time to evaluate  : 0.167 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 GLN
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain C residue  101 VAL
Chi-restraints excluded: chain D residue   49 LEU
Chi-restraints excluded: chain D residue   71 THR
Chi-restraints excluded: chain D residue   81 VAL
Chi-restraints excluded: chain D residue   86 VAL
Chi-restraints excluded: chain E residue  109 LEU
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain F residue   74 GLU
Chi-restraints excluded: chain F residue   86 VAL
Chi-restraints excluded: chain G residue   65 LEU
Chi-restraints excluded: chain G residue   76 GLN
Chi-restraints excluded: chain G residue   96 CYS
Chi-restraints excluded: chain G residue  117 VAL
Chi-restraints excluded: chain H residue   62 LEU
Chi-restraints excluded: chain H residue   82 THR
Chi-restraints excluded: chain H residue   92 ARG
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 7 optimal weight:    3.9990
   chunk 54 optimal weight:    6.9990
   chunk 28 optimal weight:   10.0000
   chunk 60 optimal weight:   20.0000
   chunk 11 optimal weight:    1.9990
   chunk 34 optimal weight:    0.7980
   chunk 46 optimal weight:    0.9980
   chunk 5 optimal weight:    7.9990
   chunk 13 optimal weight:    1.9990
   chunk 29 optimal weight:    6.9990
   chunk 26 optimal weight:    9.9990
   overall best weight:    1.9586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 125 GLN
F  64 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.095671 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3101 r_free = 0.3101 target = 0.063585 restraints weight = 31821.267|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.065169 restraints weight = 18995.200|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.066203 restraints weight = 14111.361|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3184 r_free = 0.3184 target = 0.066808 restraints weight = 11928.968|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.067134 restraints weight = 10880.607|
|-----------------------------------------------------------------------------|
r_work (final): 0.3156
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8257
moved from start:          0.3704

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  10426  Z= 0.176
  Angle     :  0.667   8.893  15097  Z= 0.392
  Chirality :  0.042   0.346   1724
  Planarity :  0.004   0.032   1074
  Dihedral  : 31.725 172.155   3290
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 11.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.55 %
    Favored  : 98.45 %
  Rotamer:
    Outliers :  6.32 %
    Allowed  : 25.89 %
    Favored  : 67.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.64 (0.33), residues: 580
  helix:  2.60 (0.23), residues: 452
  sheet:  None (None), residues: 0
  loop : -1.55 (0.42), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG G  83 
 TYR   0.008   0.001   TYR H  51 
 PHE   0.007   0.001   PHE C 104 
 HIS   0.004   0.001   HIS H  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00334 /  0.18 (10426)
  covalent geometry    : angle       0.66687 /  0.39 (15097)
  hydrogen bonds       : bond        0.05063 /  3.41 (  660)
  hydrogen bonds       : angle       3.04757 /  2.24 ( 1653)

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

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

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 166
  time to evaluate  : 0.252 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   73 GLU cc_start: 0.8902 (tm-30) cc_final: 0.8638 (tm-30)
REVERT: A   87 SER cc_start: 0.9296 (m) cc_final: 0.8917 (t)
REVERT: A   90 MET cc_start: 0.8869 (mmp) cc_final: 0.8270 (tpt)
REVERT: C   90 MET cc_start: 0.7657 (tpp) cc_final: 0.7018 (tpp)
REVERT: C  105 GLU cc_start: 0.8380 (mt-10) cc_final: 0.7988 (mt-10)
REVERT: D   87 VAL cc_start: 0.8416 (t) cc_final: 0.8207 (p)
REVERT: D   88 TYR cc_start: 0.7392 (t80) cc_final: 0.6827 (t80)
REVERT: D   91 LYS cc_start: 0.8266 (tmtt) cc_final: 0.7811 (ptmm)
REVERT: E   73 GLU cc_start: 0.8554 (tm-30) cc_final: 0.8156 (tm-30)
REVERT: E   90 MET cc_start: 0.7907 (ttt) cc_final: 0.7312 (tmm)
REVERT: E   93 GLN cc_start: 0.8822 (tp40) cc_final: 0.8622 (tp40)
REVERT: E   97 GLU cc_start: 0.8236 (mm-30) cc_final: 0.7786 (pt0)
REVERT: E  105 GLU cc_start: 0.8350 (mt-10) cc_final: 0.8088 (mt-10)
REVERT: F   53 GLU cc_start: 0.8863 (tp30) cc_final: 0.8553 (tp30)
REVERT: F   72 TYR cc_start: 0.7997 (m-10) cc_final: 0.7037 (m-10)
REVERT: F   79 LYS cc_start: 0.8813 (mttm) cc_final: 0.8316 (tptp)
REVERT: F   84 MET cc_start: 0.7936 (mmm) cc_final: 0.7595 (tpp)
REVERT: F   91 LYS cc_start: 0.8646 (mttt) cc_final: 0.8214 (mtpt)
REVERT: F   92 ARG cc_start: 0.7747 (mpt180) cc_final: 0.7385 (mtt90)
REVERT: G  120 MET cc_start: 0.8497 (mmm) cc_final: 0.7909 (mmt)
REVERT: H   52 GLU cc_start: 0.7805 (tm-30) cc_final: 0.7407 (tm-30)
  outliers start: 32
  outliers final: 21
  residues processed: 178
  average time/residue: 0.1043
  time to fit residues: 25.0617
Evaluate side-chains
  171 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 150
  time to evaluate  : 0.245 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 GLN
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain C residue  101 VAL
Chi-restraints excluded: chain D residue   86 VAL
Chi-restraints excluded: chain D residue   90 LEU
Chi-restraints excluded: chain E residue   60 LEU
Chi-restraints excluded: chain E residue  109 LEU
Chi-restraints excluded: chain F residue   29 ILE
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain F residue   86 VAL
Chi-restraints excluded: chain F residue   90 LEU
Chi-restraints excluded: chain G residue   76 GLN
Chi-restraints excluded: chain G residue   96 CYS
Chi-restraints excluded: chain H residue   62 LEU
Chi-restraints excluded: chain H residue   81 VAL
Chi-restraints excluded: chain H residue   82 THR
Chi-restraints excluded: chain H residue   92 ARG
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 73 optimal weight:   30.0000
   chunk 66 optimal weight:   20.0000
   chunk 54 optimal weight:    0.7980
   chunk 42 optimal weight:    6.9990
   chunk 48 optimal weight:    0.6980
   chunk 12 optimal weight:    1.9990
   chunk 60 optimal weight:   30.0000
   chunk 75 optimal weight:   30.0000
   chunk 39 optimal weight:    1.9990
   chunk 51 optimal weight:    2.9990
   chunk 74 optimal weight:   20.0000
   overall best weight:    1.6986

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
D  75 HIS
F  64 ASN
G  68 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.095683 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3114 r_free = 0.3114 target = 0.064064 restraints weight = 31977.029|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3158 r_free = 0.3158 target = 0.065746 restraints weight = 18530.406|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.066824 restraints weight = 13436.224|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.067461 restraints weight = 11221.637|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.067844 restraints weight = 10194.170|
|-----------------------------------------------------------------------------|
r_work (final): 0.3173
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8245
moved from start:          0.3855

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.060  10426  Z= 0.170
  Angle     :  0.660   7.469  15097  Z= 0.388
  Chirality :  0.042   0.349   1724
  Planarity :  0.004   0.032   1074
  Dihedral  : 31.797 172.411   3290
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 10.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  7.11 %
    Allowed  : 26.48 %
    Favored  : 66.40 %
  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:  2.61 (0.33), residues: 580
  helix:  2.61 (0.23), residues: 452
  sheet:  None (None), residues: 0
  loop : -1.71 (0.42), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 129 
 TYR   0.013   0.001   TYR B  88 
 PHE   0.012   0.002   PHE E  78 
 HIS   0.011   0.002   HIS D  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00323 /  0.17 (10426)
  covalent geometry    : angle       0.65970 /  0.39 (15097)
  hydrogen bonds       : bond        0.04822 /  3.23 (  660)
  hydrogen bonds       : angle       2.98123 /  2.19 ( 1653)

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

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

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 163
  time to evaluate  : 0.311 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   73 GLU cc_start: 0.8921 (tm-30) cc_final: 0.8651 (tm-30)
REVERT: A   90 MET cc_start: 0.8887 (mmp) cc_final: 0.8251 (tpt)
REVERT: C   90 MET cc_start: 0.7632 (tpp) cc_final: 0.6840 (tpp)
REVERT: C  105 GLU cc_start: 0.8420 (mt-10) cc_final: 0.8033 (mt-10)
REVERT: D   53 GLU cc_start: 0.8590 (tt0) cc_final: 0.8383 (tt0)
REVERT: D   72 TYR cc_start: 0.7620 (m-10) cc_final: 0.7193 (m-10)
REVERT: D   87 VAL cc_start: 0.8434 (t) cc_final: 0.8217 (p)
REVERT: D   88 TYR cc_start: 0.7353 (t80) cc_final: 0.6725 (t80)
REVERT: D   91 LYS cc_start: 0.8267 (tmtt) cc_final: 0.7817 (ptmm)
REVERT: E   73 GLU cc_start: 0.8535 (tm-30) cc_final: 0.8119 (tm-30)
REVERT: E   90 MET cc_start: 0.7876 (ttt) cc_final: 0.7455 (tpp)
REVERT: E   93 GLN cc_start: 0.8853 (tp40) cc_final: 0.8648 (tp40)
REVERT: E  105 GLU cc_start: 0.8356 (mt-10) cc_final: 0.8096 (mt-10)
REVERT: F   53 GLU cc_start: 0.8849 (tp30) cc_final: 0.8474 (tp30)
REVERT: F   68 ASP cc_start: 0.8021 (m-30) cc_final: 0.7477 (t0)
REVERT: F   72 TYR cc_start: 0.7933 (m-10) cc_final: 0.7084 (m-10)
REVERT: F   79 LYS cc_start: 0.9075 (mttm) cc_final: 0.8385 (tptp)
REVERT: F   84 MET cc_start: 0.7953 (mmm) cc_final: 0.7665 (tpp)
REVERT: F   91 LYS cc_start: 0.8641 (mttt) cc_final: 0.8203 (mtpt)
REVERT: F   92 ARG cc_start: 0.7733 (mpt180) cc_final: 0.7452 (mtt90)
REVERT: G   90 MET cc_start: 0.8853 (mmp) cc_final: 0.8219 (tpt)
REVERT: G  120 MET cc_start: 0.8517 (mmm) cc_final: 0.7999 (mmt)
REVERT: H   52 GLU cc_start: 0.7829 (tm-30) cc_final: 0.7393 (tm-30)
  outliers start: 36
  outliers final: 31
  residues processed: 181
  average time/residue: 0.1166
  time to fit residues: 28.2951
Evaluate side-chains
  185 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 154
  time to evaluate  : 0.272 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 GLN
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue  100 LEU
Chi-restraints excluded: chain A residue  118 THR
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain C residue  101 VAL
Chi-restraints excluded: chain D residue   64 ASN
Chi-restraints excluded: chain D residue   75 HIS
Chi-restraints excluded: chain D residue   81 VAL
Chi-restraints excluded: chain D residue   86 VAL
Chi-restraints excluded: chain D residue   90 LEU
Chi-restraints excluded: chain E residue   70 LEU
Chi-restraints excluded: chain E residue   74 ILE
Chi-restraints excluded: chain E residue  109 LEU
Chi-restraints excluded: chain F residue   29 ILE
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain F residue   86 VAL
Chi-restraints excluded: chain F residue   90 LEU
Chi-restraints excluded: chain G residue   65 LEU
Chi-restraints excluded: chain G residue   76 GLN
Chi-restraints excluded: chain G residue   96 CYS
Chi-restraints excluded: chain G residue  100 LEU
Chi-restraints excluded: chain G residue  117 VAL
Chi-restraints excluded: chain G residue  124 ILE
Chi-restraints excluded: chain H residue   62 LEU
Chi-restraints excluded: chain H residue   81 VAL
Chi-restraints excluded: chain H residue   82 THR
Chi-restraints excluded: chain H residue   92 ARG
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 78 optimal weight:   50.0000
   chunk 59 optimal weight:   30.0000
   chunk 60 optimal weight:   30.0000
   chunk 49 optimal weight:    3.9990
   chunk 38 optimal weight:    1.9990
   chunk 22 optimal weight:    3.9990
   chunk 18 optimal weight:    0.8980
   chunk 42 optimal weight:    6.9990
   chunk 3 optimal weight:    0.8980
   chunk 45 optimal weight:    0.9980
   chunk 77 optimal weight:   30.0000
   overall best weight:    1.7584

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
E 125 GLN
F  64 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.095409 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3101 r_free = 0.3101 target = 0.063330 restraints weight = 32120.180|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3143 r_free = 0.3143 target = 0.064980 restraints weight = 18848.536|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.066051 restraints weight = 13833.662|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.066716 restraints weight = 11604.022|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.067097 restraints weight = 10527.597|
|-----------------------------------------------------------------------------|
r_work (final): 0.3163
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8259
moved from start:          0.3952

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055  10426  Z= 0.170
  Angle     :  0.662   6.837  15097  Z= 0.388
  Chirality :  0.042   0.349   1724
  Planarity :  0.004   0.026   1074
  Dihedral  : 31.841 172.566   3290
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 10.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  6.52 %
    Allowed  : 26.88 %
    Favored  : 66.60 %
  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:  2.70 (0.33), residues: 580
  helix:  2.69 (0.23), residues: 452
  sheet:  None (None), residues: 0
  loop : -1.76 (0.41), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D  40 
 TYR   0.007   0.001   TYR H  51 
 PHE   0.007   0.001   PHE E 104 
 HIS   0.015   0.002   HIS D  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00323 /  0.17 (10426)
  covalent geometry    : angle       0.66212 /  0.39 (15097)
  hydrogen bonds       : bond        0.04772 /  3.19 (  660)
  hydrogen bonds       : angle       2.96283 /  2.18 ( 1653)

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

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

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 158
  time to evaluate  : 0.259 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   73 GLU cc_start: 0.8908 (tm-30) cc_final: 0.8663 (tm-30)
REVERT: A  120 MET cc_start: 0.8468 (mmm) cc_final: 0.8000 (mmt)
REVERT: C   90 MET cc_start: 0.7668 (tpp) cc_final: 0.6844 (tpp)
REVERT: C  105 GLU cc_start: 0.8425 (mt-10) cc_final: 0.8035 (mt-10)
REVERT: D   53 GLU cc_start: 0.8613 (tt0) cc_final: 0.8370 (tt0)
REVERT: D   79 LYS cc_start: 0.7832 (tptp) cc_final: 0.7565 (tptp)
REVERT: D   84 MET cc_start: 0.8047 (tpp) cc_final: 0.7824 (tpp)
REVERT: D   88 TYR cc_start: 0.7347 (t80) cc_final: 0.6944 (t80)
REVERT: D   91 LYS cc_start: 0.8305 (tmtt) cc_final: 0.7752 (mtmm)
REVERT: E   73 GLU cc_start: 0.8534 (tm-30) cc_final: 0.8129 (tm-30)
REVERT: E   90 MET cc_start: 0.7953 (ttt) cc_final: 0.7246 (tmm)
REVERT: E   93 GLN cc_start: 0.8897 (tp40) cc_final: 0.8653 (tp40)
REVERT: E   97 GLU cc_start: 0.8435 (mm-30) cc_final: 0.7932 (tt0)
REVERT: E  105 GLU cc_start: 0.8336 (mt-10) cc_final: 0.8074 (mt-10)
REVERT: F   68 ASP cc_start: 0.8012 (m-30) cc_final: 0.7473 (t0)
REVERT: F   72 TYR cc_start: 0.7892 (m-10) cc_final: 0.6991 (m-10)
REVERT: F   79 LYS cc_start: 0.9070 (mttm) cc_final: 0.8431 (tptp)
REVERT: F   84 MET cc_start: 0.7934 (mmm) cc_final: 0.7663 (tpp)
REVERT: F   91 LYS cc_start: 0.8643 (mttt) cc_final: 0.8205 (mtpt)
REVERT: F   92 ARG cc_start: 0.7746 (mpt180) cc_final: 0.7449 (mtt90)
REVERT: G  120 MET cc_start: 0.8576 (mmm) cc_final: 0.7980 (mmt)
REVERT: H   52 GLU cc_start: 0.7826 (tm-30) cc_final: 0.7388 (tm-30)
  outliers start: 33
  outliers final: 28
  residues processed: 174
  average time/residue: 0.1092
  time to fit residues: 25.8662
Evaluate side-chains
  179 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 151
  time to evaluate  : 0.257 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 GLN
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue  100 LEU
Chi-restraints excluded: chain A residue  118 THR
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain C residue  101 VAL
Chi-restraints excluded: chain D residue   81 VAL
Chi-restraints excluded: chain D residue   86 VAL
Chi-restraints excluded: chain D residue   90 LEU
Chi-restraints excluded: chain E residue  109 LEU
Chi-restraints excluded: chain F residue   29 ILE
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain F residue   74 GLU
Chi-restraints excluded: chain F residue   86 VAL
Chi-restraints excluded: chain F residue   90 LEU
Chi-restraints excluded: chain G residue   65 LEU
Chi-restraints excluded: chain G residue   76 GLN
Chi-restraints excluded: chain G residue   96 CYS
Chi-restraints excluded: chain G residue  100 LEU
Chi-restraints excluded: chain G residue  117 VAL
Chi-restraints excluded: chain G residue  124 ILE
Chi-restraints excluded: chain H residue   62 LEU
Chi-restraints excluded: chain H residue   81 VAL
Chi-restraints excluded: chain H residue   82 THR
Chi-restraints excluded: chain H residue   92 ARG
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 27 optimal weight:    9.9990
   chunk 37 optimal weight:    9.9990
   chunk 69 optimal weight:   30.0000
   chunk 55 optimal weight:    0.9980
   chunk 1 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9980
   chunk 46 optimal weight:    0.6980
   chunk 2 optimal weight:    0.9990
   chunk 58 optimal weight:   30.0000
   chunk 49 optimal weight:    3.9990
   chunk 35 optimal weight:    8.9990
   overall best weight:    1.1384

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** C  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  75 HIS
F  64 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.095746 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3124 r_free = 0.3124 target = 0.064246 restraints weight = 32063.336|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.065919 restraints weight = 18605.926|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.067023 restraints weight = 13516.783|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.067668 restraints weight = 11264.296|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.068054 restraints weight = 10192.117|
|-----------------------------------------------------------------------------|
r_work (final): 0.3184
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8239
moved from start:          0.4061

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  10426  Z= 0.159
  Angle     :  0.661   6.969  15097  Z= 0.386
  Chirality :  0.042   0.349   1724
  Planarity :  0.004   0.036   1074
  Dihedral  : 31.836 172.787   3290
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 11.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  6.32 %
    Allowed  : 28.26 %
    Favored  : 65.42 %
  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:  2.71 (0.33), residues: 580
  helix:  2.71 (0.23), residues: 452
  sheet:  None (None), residues: 0
  loop : -1.81 (0.41), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D  39 
 TYR   0.011   0.001   TYR B  88 
 PHE   0.012   0.001   PHE E  78 
 HIS   0.006   0.001   HIS D  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00287 /  0.16 (10426)
  covalent geometry    : angle       0.66120 /  0.39 (15097)
  hydrogen bonds       : bond        0.04599 /  3.07 (  660)
  hydrogen bonds       : angle       2.87690 /  2.12 ( 1653)

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

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

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 162
  time to evaluate  : 0.245 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   90 MET cc_start: 0.8815 (mmp) cc_final: 0.8193 (tpt)
REVERT: A   97 GLU cc_start: 0.8227 (mt-10) cc_final: 0.7789 (tt0)
REVERT: A  120 MET cc_start: 0.8444 (mmm) cc_final: 0.7983 (mmt)
REVERT: C   90 MET cc_start: 0.7673 (tpp) cc_final: 0.6862 (tpp)
REVERT: C  105 GLU cc_start: 0.8385 (mt-10) cc_final: 0.8021 (mt-10)
REVERT: D   53 GLU cc_start: 0.8603 (tt0) cc_final: 0.8398 (tt0)
REVERT: D   84 MET cc_start: 0.8090 (tpp) cc_final: 0.7880 (tpp)
REVERT: D   88 TYR cc_start: 0.7401 (t80) cc_final: 0.7027 (t80)
REVERT: D   91 LYS cc_start: 0.8246 (tmtt) cc_final: 0.7727 (mtmm)
REVERT: E   73 GLU cc_start: 0.8511 (tm-30) cc_final: 0.8165 (tm-30)
REVERT: E   90 MET cc_start: 0.7952 (ttt) cc_final: 0.7477 (tpp)
REVERT: E   93 GLN cc_start: 0.8927 (tp40) cc_final: 0.8610 (tp40)
REVERT: E   97 GLU cc_start: 0.8361 (mm-30) cc_final: 0.7919 (tt0)
REVERT: E  105 GLU cc_start: 0.8313 (mt-10) cc_final: 0.8036 (mt-10)
REVERT: F   53 GLU cc_start: 0.8834 (tp30) cc_final: 0.8383 (tp30)
REVERT: F   68 ASP cc_start: 0.7975 (m-30) cc_final: 0.7411 (t0)
REVERT: F   72 TYR cc_start: 0.7823 (m-10) cc_final: 0.6909 (m-10)
REVERT: F   79 LYS cc_start: 0.9048 (mttm) cc_final: 0.8397 (tptp)
REVERT: F   84 MET cc_start: 0.7923 (mmm) cc_final: 0.7690 (tpp)
REVERT: F   91 LYS cc_start: 0.8627 (mttt) cc_final: 0.8184 (mtpt)
REVERT: F   92 ARG cc_start: 0.7809 (mpt180) cc_final: 0.7525 (mtt90)
REVERT: G   90 MET cc_start: 0.8803 (mmp) cc_final: 0.8157 (tpt)
REVERT: G  120 MET cc_start: 0.8557 (mmm) cc_final: 0.7933 (mmt)
REVERT: H   52 GLU cc_start: 0.7800 (tm-30) cc_final: 0.7345 (tm-30)
  outliers start: 32
  outliers final: 27
  residues processed: 179
  average time/residue: 0.1133
  time to fit residues: 27.3143
Evaluate side-chains
  180 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 153
  time to evaluate  : 0.240 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 GLN
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue   96 CYS
Chi-restraints excluded: chain A residue  100 LEU
Chi-restraints excluded: chain A residue  124 ILE
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain C residue  101 VAL
Chi-restraints excluded: chain D residue   49 LEU
Chi-restraints excluded: chain D residue   81 VAL
Chi-restraints excluded: chain D residue   90 LEU
Chi-restraints excluded: chain E residue  109 LEU
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain F residue   81 VAL
Chi-restraints excluded: chain F residue   90 LEU
Chi-restraints excluded: chain G residue   65 LEU
Chi-restraints excluded: chain G residue   76 GLN
Chi-restraints excluded: chain G residue   96 CYS
Chi-restraints excluded: chain G residue  100 LEU
Chi-restraints excluded: chain G residue  117 VAL
Chi-restraints excluded: chain G residue  124 ILE
Chi-restraints excluded: chain H residue   62 LEU
Chi-restraints excluded: chain H residue   81 VAL
Chi-restraints excluded: chain H residue   82 THR
Chi-restraints excluded: chain H residue   92 ARG
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 56 optimal weight:   50.0000
   chunk 41 optimal weight:    0.9990
   chunk 44 optimal weight:    0.8980
   chunk 39 optimal weight:   10.0000
   chunk 37 optimal weight:    2.9990
   chunk 21 optimal weight:    0.1980
   chunk 16 optimal weight:    6.9990
   chunk 42 optimal weight:    6.9990
   chunk 20 optimal weight:    0.8980
   chunk 55 optimal weight:    0.7980
   chunk 43 optimal weight:    0.9990
   overall best weight:    0.7582

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** C  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  75 HIS
F  64 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.096640 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3136 r_free = 0.3136 target = 0.064788 restraints weight = 32171.299|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.066447 restraints weight = 19159.443|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.067516 restraints weight = 14083.973|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.068195 restraints weight = 11826.825|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.068569 restraints weight = 10734.074|
|-----------------------------------------------------------------------------|
r_work (final): 0.3192
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8228
moved from start:          0.4157

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  10426  Z= 0.155
  Angle     :  0.659   8.240  15097  Z= 0.386
  Chirality :  0.042   0.345   1724
  Planarity :  0.004   0.033   1074
  Dihedral  : 31.805 173.132   3290
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 11.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.24 %
    Favored  : 97.76 %
  Rotamer:
    Outliers :  5.34 %
    Allowed  : 30.24 %
    Favored  : 64.43 %
  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:  2.71 (0.33), residues: 580
  helix:  2.69 (0.23), residues: 454
  sheet:  None (None), residues: 0
  loop : -1.79 (0.41), residues: 126

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG H  40 
 TYR   0.007   0.001   TYR H  51 
 PHE   0.008   0.001   PHE A  67 
 HIS   0.012   0.002   HIS D  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00279 /  0.15 (10426)
  covalent geometry    : angle       0.65871 /  0.39 (15097)
  hydrogen bonds       : bond        0.04506 /  3.00 (  660)
  hydrogen bonds       : angle       2.83588 /  2.09 ( 1653)

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

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

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 162
  time to evaluate  : 0.246 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   90 MET cc_start: 0.8823 (mmp) cc_final: 0.8186 (tpt)
REVERT: A   97 GLU cc_start: 0.8203 (mt-10) cc_final: 0.7777 (tt0)
REVERT: A  120 MET cc_start: 0.8475 (mmm) cc_final: 0.7827 (mmt)
REVERT: A  123 ASP cc_start: 0.9195 (m-30) cc_final: 0.8989 (m-30)
REVERT: C   90 MET cc_start: 0.7667 (tpp) cc_final: 0.6831 (tpp)
REVERT: C  105 GLU cc_start: 0.8361 (mt-10) cc_final: 0.8000 (mt-10)
REVERT: D   53 GLU cc_start: 0.8546 (tt0) cc_final: 0.8346 (tt0)
REVERT: D   88 TYR cc_start: 0.7407 (t80) cc_final: 0.6994 (t80)
REVERT: D   91 LYS cc_start: 0.8269 (tmtt) cc_final: 0.7715 (mtmm)
REVERT: E   73 GLU cc_start: 0.8553 (tm-30) cc_final: 0.8228 (tm-30)
REVERT: E   90 MET cc_start: 0.7904 (ttt) cc_final: 0.7451 (tpp)
REVERT: E   93 GLN cc_start: 0.8875 (tp40) cc_final: 0.8514 (tp40)
REVERT: E   97 GLU cc_start: 0.8360 (mm-30) cc_final: 0.7937 (tt0)
REVERT: E  105 GLU cc_start: 0.8301 (mt-10) cc_final: 0.8028 (mt-10)
REVERT: F   68 ASP cc_start: 0.7985 (m-30) cc_final: 0.7472 (t0)
REVERT: F   72 TYR cc_start: 0.7911 (m-10) cc_final: 0.6956 (m-10)
REVERT: F   79 LYS cc_start: 0.9004 (mttm) cc_final: 0.8408 (tptp)
REVERT: F   91 LYS cc_start: 0.8649 (mttt) cc_final: 0.8324 (mtpt)
REVERT: F   92 ARG cc_start: 0.7796 (mpt180) cc_final: 0.7500 (mtt90)
REVERT: G   90 MET cc_start: 0.8824 (mmp) cc_final: 0.8187 (tpt)
REVERT: G  120 MET cc_start: 0.8568 (mmm) cc_final: 0.8016 (mmt)
REVERT: H   52 GLU cc_start: 0.7751 (tm-30) cc_final: 0.7281 (tm-30)
  outliers start: 27
  outliers final: 27
  residues processed: 174
  average time/residue: 0.1088
  time to fit residues: 25.6551
Evaluate side-chains
  182 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 155
  time to evaluate  : 0.288 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 GLN
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue   96 CYS
Chi-restraints excluded: chain A residue  124 ILE
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain C residue  101 VAL
Chi-restraints excluded: chain D residue   49 LEU
Chi-restraints excluded: chain D residue   75 HIS
Chi-restraints excluded: chain D residue   81 VAL
Chi-restraints excluded: chain D residue   90 LEU
Chi-restraints excluded: chain E residue  101 VAL
Chi-restraints excluded: chain E residue  109 LEU
Chi-restraints excluded: chain F residue   29 ILE
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain F residue   90 LEU
Chi-restraints excluded: chain G residue   65 LEU
Chi-restraints excluded: chain G residue   76 GLN
Chi-restraints excluded: chain G residue   96 CYS
Chi-restraints excluded: chain G residue   97 GLU
Chi-restraints excluded: chain G residue  117 VAL
Chi-restraints excluded: chain G residue  124 ILE
Chi-restraints excluded: chain H residue   62 LEU
Chi-restraints excluded: chain H residue   82 THR
Chi-restraints excluded: chain H residue   92 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 61 optimal weight:   30.0000
   chunk 32 optimal weight:    3.9990
   chunk 1 optimal weight:    1.9990
   chunk 24 optimal weight:    0.8980
   chunk 65 optimal weight:   30.0000
   chunk 14 optimal weight:   10.0000
   chunk 15 optimal weight:    6.9990
   chunk 40 optimal weight:    9.9990
   chunk 66 optimal weight:   30.0000
   chunk 52 optimal weight:    4.9990
   chunk 36 optimal weight:    0.9990
   overall best weight:    2.5788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  93 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.095272 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3103 r_free = 0.3103 target = 0.063361 restraints weight = 32064.627|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.064971 restraints weight = 19377.426|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.065991 restraints weight = 14391.718|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.066629 restraints weight = 12142.966|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.066840 restraints weight = 11039.533|
|-----------------------------------------------------------------------------|
r_work (final): 0.3151
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8273
moved from start:          0.4232

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049  10426  Z= 0.190
  Angle     :  0.688   6.991  15097  Z= 0.397
  Chirality :  0.042   0.346   1724
  Planarity :  0.004   0.032   1074
  Dihedral  : 31.885 173.096   3290
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 11.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  5.73 %
    Allowed  : 30.43 %
    Favored  : 63.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.68 (0.33), residues: 580
  helix:  2.68 (0.23), residues: 454
  sheet:  None (None), residues: 0
  loop : -1.86 (0.41), residues: 126

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG H  40 
 TYR   0.012   0.001   TYR D  72 
 PHE   0.010   0.002   PHE E  78 
 HIS   0.021   0.003   HIS D  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00388 /  0.19 (10426)
  covalent geometry    : angle       0.68778 /  0.40 (15097)
  hydrogen bonds       : bond        0.04693 /  3.14 (  660)
  hydrogen bonds       : angle       2.92541 /  2.16 ( 1653)

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

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

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 159
  time to evaluate  : 0.247 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   90 MET cc_start: 0.8837 (mmp) cc_final: 0.8243 (tpt)
REVERT: A   97 GLU cc_start: 0.8214 (mt-10) cc_final: 0.7786 (tt0)
REVERT: A  120 MET cc_start: 0.8366 (mmm) cc_final: 0.7878 (mmt)
REVERT: C   90 MET cc_start: 0.7668 (tpp) cc_final: 0.6886 (tpp)
REVERT: C  105 GLU cc_start: 0.8412 (mt-10) cc_final: 0.8072 (mt-10)
REVERT: D   87 VAL cc_start: 0.8407 (t) cc_final: 0.8040 (p)
REVERT: D   88 TYR cc_start: 0.7367 (t80) cc_final: 0.6991 (t80)
REVERT: D   91 LYS cc_start: 0.8285 (tmtt) cc_final: 0.7753 (mtmm)
REVERT: E   73 GLU cc_start: 0.8566 (tm-30) cc_final: 0.8245 (tm-30)
REVERT: E   90 MET cc_start: 0.7927 (ttt) cc_final: 0.7475 (tpp)
REVERT: E   93 GLN cc_start: 0.8906 (tp40) cc_final: 0.8525 (tp40)
REVERT: E   97 GLU cc_start: 0.8475 (mm-30) cc_final: 0.7988 (tt0)
REVERT: E  105 GLU cc_start: 0.8311 (mt-10) cc_final: 0.8064 (mt-10)
REVERT: F   68 ASP cc_start: 0.8035 (m-30) cc_final: 0.7492 (t0)
REVERT: F   72 TYR cc_start: 0.7932 (m-10) cc_final: 0.6960 (m-10)
REVERT: F   79 LYS cc_start: 0.9031 (mttm) cc_final: 0.8398 (tptp)
REVERT: F   91 LYS cc_start: 0.8661 (mttt) cc_final: 0.8181 (mtpt)
REVERT: F   92 ARG cc_start: 0.7798 (mpt180) cc_final: 0.7452 (mtt90)
REVERT: G   90 MET cc_start: 0.8869 (mmp) cc_final: 0.8246 (tpt)
REVERT: G  120 MET cc_start: 0.8503 (mmm) cc_final: 0.7941 (mmt)
REVERT: H   52 GLU cc_start: 0.7826 (tm-30) cc_final: 0.7337 (tm-30)
  outliers start: 29
  outliers final: 25
  residues processed: 171
  average time/residue: 0.1062
  time to fit residues: 24.7365
Evaluate side-chains
  180 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 155
  time to evaluate  : 0.222 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 GLN
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue   96 CYS
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain C residue  101 VAL
Chi-restraints excluded: chain D residue   49 LEU
Chi-restraints excluded: chain D residue   81 VAL
Chi-restraints excluded: chain D residue   90 LEU
Chi-restraints excluded: chain E residue  101 VAL
Chi-restraints excluded: chain E residue  109 LEU
Chi-restraints excluded: chain F residue   29 ILE
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain F residue   74 GLU
Chi-restraints excluded: chain F residue   81 VAL
Chi-restraints excluded: chain F residue   90 LEU
Chi-restraints excluded: chain G residue   65 LEU
Chi-restraints excluded: chain G residue   76 GLN
Chi-restraints excluded: chain G residue   96 CYS
Chi-restraints excluded: chain G residue   97 GLU
Chi-restraints excluded: chain G residue  117 VAL
Chi-restraints excluded: chain H residue   62 LEU
Chi-restraints excluded: chain H residue   82 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 52 optimal weight:    0.8980
   chunk 37 optimal weight:    4.9990
   chunk 71 optimal weight:   30.0000
   chunk 6 optimal weight:    0.6980
   chunk 22 optimal weight:    6.9990
   chunk 44 optimal weight:    3.9990
   chunk 26 optimal weight:    0.0040
   chunk 78 optimal weight:   50.0000
   chunk 76 optimal weight:   30.0000
   chunk 11 optimal weight:    0.9990
   chunk 2 optimal weight:    0.9980
   overall best weight:    0.7194

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** C  93 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 = 0.3834 r_free = 0.3834 target = 0.096421 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3133 r_free = 0.3133 target = 0.064591 restraints weight = 32308.281|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.066235 restraints weight = 19308.015|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.067319 restraints weight = 14242.288|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.067986 restraints weight = 11928.587|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.068336 restraints weight = 10823.096|
|-----------------------------------------------------------------------------|
r_work (final): 0.3188
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8231
moved from start:          0.4318

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  10426  Z= 0.154
  Angle     :  0.666   7.640  15097  Z= 0.387
  Chirality :  0.042   0.348   1724
  Planarity :  0.004   0.035   1074
  Dihedral  : 31.858 173.320   3290
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 11.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  5.14 %
    Allowed  : 30.83 %
    Favored  : 64.03 %
  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:  2.72 (0.33), residues: 580
  helix:  2.71 (0.23), residues: 454
  sheet:  None (None), residues: 0
  loop : -1.84 (0.40), residues: 126

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG H  40 
 TYR   0.013   0.001   TYR F  88 
 PHE   0.007   0.001   PHE A  67 
 HIS   0.005   0.001   HIS D  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00282 /  0.15 (10426)
  covalent geometry    : angle       0.66629 /  0.39 (15097)
  hydrogen bonds       : bond        0.04394 /  2.91 (  660)
  hydrogen bonds       : angle       2.83216 /  2.09 ( 1653)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1501.32 seconds
wall clock time: 26 minutes 32.45 seconds (1592.45 seconds total)