Starting phenix.real_space_refine
on Tue Mar  3 23:59:53 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7x58_33011/03_2026/7x58_33011.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7x58_33011/03_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_33011/03_2026/7x58_33011.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7x58_33011/03_2026/7x58_33011.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7x58_33011/03_2026/7x58_33011.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7x58_33011/03_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-dev-5986/lib/python3.9/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: 2.36, per 1000 atoms: 0.24
  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: 0.73
  Conformation dependent library (CDL) restraints added in 151.3 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: 1.59
  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: 1.82

  Time building geometry restraints manager: 0.99 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'  DT I  14 "
       pdb=" O3'  DT I  14 "
    ideal  model  delta    sigma   weight residual
    1.422  1.463 -0.041 3.00e-02 1.11e+03 1.89e+00
  bond pdb=" CG  LEU B  62 "
       pdb=" CD2 LEU B  62 "
    ideal  model  delta    sigma   weight residual
    1.521  1.485  0.036 3.30e-02 9.18e+02 1.18e+00
  bond pdb=" C3'  DC I  51 "
       pdb=" O3'  DC I  51 "
    ideal  model  delta    sigma   weight residual
    1.422  1.453 -0.031 3.00e-02 1.11e+03 1.10e+00
  bond pdb=" C3'  DC I -48 "
       pdb=" O3'  DC I -48 "
    ideal  model  delta    sigma   weight residual
    1.422  1.453 -0.031 3.00e-02 1.11e+03 1.08e+00
  bond pdb=" C   MET C 120 "
       pdb=" N   PRO C 121 "
    ideal  model  delta    sigma   weight residual
    1.334  1.349 -0.015 1.51e-02 4.39e+03 9.46e-01
  ... (remaining 10421 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.37: 14530
        1.37 -     2.73: 521
        2.73 -     4.10: 29
        4.10 -     5.46: 12
        5.46 -     6.83: 5
  Bond angle restraints: 15097
  Sorted by residual:
  angle pdb=" N   VAL E 117 "
        pdb=" CA  VAL E 117 "
        pdb=" C   VAL E 117 "
      ideal   model   delta    sigma   weight residual
     112.43  109.34    3.09 9.20e-01 1.18e+00 1.13e+01
  angle pdb=" CA  ARG A 131 "
        pdb=" CB  ARG A 131 "
        pdb=" CG  ARG A 131 "
      ideal   model   delta    sigma   weight residual
     114.10  120.56   -6.46 2.00e+00 2.50e-01 1.04e+01
  angle pdb=" CB  ARG A 131 "
        pdb=" CG  ARG A 131 "
        pdb=" CD  ARG A 131 "
      ideal   model   delta    sigma   weight residual
     111.30  104.47    6.83 2.30e+00 1.89e-01 8.82e+00
  angle pdb=" C   ALA C 114 "
        pdb=" N   LYS C 115 "
        pdb=" CA  LYS C 115 "
      ideal   model   delta    sigma   weight residual
     122.61  126.28   -3.67 1.56e+00 4.11e-01 5.54e+00
  angle pdb=" C   ARG D  78 "
        pdb=" N   LYS D  79 "
        pdb=" CA  LYS D  79 "
      ideal   model   delta    sigma   weight residual
     121.54  125.74   -4.20 1.91e+00 2.74e-01 4.85e+00
  ... (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: 1612
       0.062 -    0.124: 104
       0.124 -    0.185: 6
       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:             0.400
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     11.350
  Find NCS groups from input model:        0.150
  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:             0.010
  Load rotamer database and sin/cos tables:1.280
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.420
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7816
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      :  0.003   0.041  10426  Z= 0.153
  Angle     :  0.565   6.829  15097  Z= 0.367
  Chirality :  0.032   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
  covalent geometry    : bond        0.00310 (10426)
  covalent geometry    : angle       0.56478 (15097)
  hydrogen bonds       : bond        0.19993 (  660)
  hydrogen bonds       : angle       5.67620 ( 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  : 0.247 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   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: 0.9085 (t)
REVERT: A   90 MET cc_start: 0.8114 (mmm) cc_final: 0.7792 (mmp)
REVERT: B   31 LYS cc_start: 0.9128 (tttt) cc_final: 0.8903 (ttmm)
REVERT: C  113 HIS cc_start: 0.9068 (t70) cc_final: 0.8687 (t-170)
REVERT: C  126 LEU cc_start: 0.8913 (tp) cc_final: 0.8582 (tp)
REVERT: D   53 GLU cc_start: 0.8764 (tp30) cc_final: 0.8490 (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: 0.7739 (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: 0.8930 (Cg_endo)
REVERT: F   79 LYS cc_start: 0.8776 (mttm) cc_final: 0.8375 (tptp)
REVERT: F   87 VAL cc_start: 0.8283 (t) cc_final: 0.8061 (t)
REVERT: F   91 LYS cc_start: 0.8504 (mttt) cc_final: 0.8160 (mtpt)
REVERT: G   81 ASP cc_start: 0.8219 (t0) cc_final: 0.7963 (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: 0.8856 (ttmm)
  outliers start: 0
  outliers final: 0
  residues processed: 288
  average time/residue: 0.1680
  time to fit residues: 59.6979
Evaluate side-chains
  169 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 169
  time to evaluate  : 0.255 
-------------------------------------------------------------------------------
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:    8.9990
   chunk 53 optimal weight:    0.5980
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:   10.0000
   chunk 62 optimal weight:    8.9990
   chunk 51 optimal weight:    7.9990
   chunk 38 optimal weight:    3.9990
   chunk 61 optimal weight:    8.9990
   chunk 45 optimal weight:    0.8980
   chunk 74 optimal weight:    7.9990
   overall best weight:    2.2986

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

Flipped N/Q/H residues before XYZ refinement:
** A  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  64 ASN
F  75 HIS
G  68 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.095964 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.064309 restraints weight = 31467.470|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.065941 restraints weight = 18164.411|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.067005 restraints weight = 13246.102|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.067643 restraints weight = 11085.155|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.067935 restraints weight = 10061.446|
|-----------------------------------------------------------------------------|
r_work (final): 0.3176
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8053
moved from start:          0.3337

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.064  10426  Z= 0.204
  Angle     :  0.638   8.621  15097  Z= 0.371
  Chirality :  0.035   0.147   1724
  Planarity :  0.005   0.073   1074
  Dihedral  : 31.354 175.082   3290
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 11.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.03 %
    Favored  : 98.97 %
  Rotamer:
    Outliers :  4.35 %
    Allowed  : 22.13 %
    Favored  : 73.52 %
  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:  2.60 (0.23), residues: 450
  sheet:  None (None), residues: 0
  loop : -1.28 (0.40), residues: 130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG C 129 
 TYR   0.017   0.001   TYR B  88 
 PHE   0.010   0.002   PHE E  78 
 HIS   0.009   0.002   HIS E 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00462 (10426)
  covalent geometry    : angle       0.63751 (15097)
  hydrogen bonds       : bond        0.05008 (  660)
  hydrogen bonds       : angle       3.17896 ( 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
  216 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 194
  time to evaluate  : 0.308 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   71 VAL cc_start: 0.9280 (t) cc_final: 0.9071 (t)
REVERT: A   87 SER cc_start: 0.9344 (m) cc_final: 0.8928 (t)
REVERT: A  120 MET cc_start: 0.8423 (mmm) cc_final: 0.8157 (mmm)
REVERT: C   90 MET cc_start: 0.7527 (tpp) cc_final: 0.6974 (tpp)
REVERT: C  105 GLU cc_start: 0.8353 (mt-10) cc_final: 0.7975 (mt-10)
REVERT: C  120 MET cc_start: 0.8307 (OUTLIER) cc_final: 0.8065 (mmt)
REVERT: D   52 GLU cc_start: 0.8514 (tm-30) cc_final: 0.8196 (tm-30)
REVERT: D   84 MET cc_start: 0.8288 (tpp) cc_final: 0.7938 (tpp)
REVERT: D   91 LYS cc_start: 0.8277 (tmtt) cc_final: 0.7706 (mtmm)
REVERT: E   73 GLU cc_start: 0.9139 (tm-30) cc_final: 0.8370 (tm-30)
REVERT: E   90 MET cc_start: 0.7894 (ttt) cc_final: 0.7402 (tmm)
REVERT: E   93 GLN cc_start: 0.8781 (tp40) cc_final: 0.8439 (tp40)
REVERT: E  105 GLU cc_start: 0.8394 (mt-10) cc_final: 0.7813 (mt-10)
REVERT: F   32 PRO cc_start: 0.9168 (Cg_exo) cc_final: 0.8928 (Cg_endo)
REVERT: F   74 GLU cc_start: 0.8931 (mm-30) cc_final: 0.8359 (mm-30)
REVERT: F   79 LYS cc_start: 0.9015 (mttm) cc_final: 0.8348 (tptp)
REVERT: F   84 MET cc_start: 0.8077 (mmm) cc_final: 0.7313 (tpp)
REVERT: F   91 LYS cc_start: 0.8621 (mttt) cc_final: 0.8247 (mtpt)
REVERT: G   83 ARG cc_start: 0.8243 (mtp85) cc_final: 0.7912 (mtp85)
REVERT: G  107 THR cc_start: 0.9390 (m) cc_final: 0.8976 (p)
REVERT: G  108 ASN cc_start: 0.9139 (t0) cc_final: 0.8896 (t0)
REVERT: G  120 MET cc_start: 0.8548 (mmm) cc_final: 0.7917 (mmt)
REVERT: H   47 SER cc_start: 0.9529 (t) cc_final: 0.8930 (t)
REVERT: H   52 GLU cc_start: 0.7885 (tm-30) cc_final: 0.7593 (tm-30)
  outliers start: 22
  outliers final: 11
  residues processed: 201
  average time/residue: 0.1332
  time to fit residues: 34.7661
Evaluate side-chains
  171 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 159
  time to evaluate  : 0.256 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 GLN
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain C residue  101 VAL
Chi-restraints excluded: chain C residue  120 MET
Chi-restraints excluded: chain D residue   71 THR
Chi-restraints excluded: chain E residue   74 ILE
Chi-restraints excluded: chain E residue  101 VAL
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain F residue   71 THR
Chi-restraints excluded: chain G residue   76 GLN
Chi-restraints excluded: chain G residue   96 CYS
Chi-restraints excluded: chain H residue   62 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 22 optimal weight:    0.9980
   chunk 0 optimal weight:    6.9990
   chunk 62 optimal weight:   10.0000
   chunk 33 optimal weight:    3.9990
   chunk 5 optimal weight:    1.9990
   chunk 9 optimal weight:    0.9990
   chunk 76 optimal weight:   10.0000
   chunk 4 optimal weight:    1.9990
   chunk 44 optimal weight:    0.9980
   chunk 71 optimal weight:    8.9990
   chunk 61 optimal weight:    8.9990
   overall best weight:    1.3986

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

Flipped N/Q/H residues before XYZ refinement:
** C  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 125 GLN
G  68 GLN

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 = 0.096509 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3128 r_free = 0.3128 target = 0.064808 restraints weight = 32001.165|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.066392 restraints weight = 19100.878|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.067429 restraints weight = 14157.867|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.068043 restraints weight = 11956.461|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.068401 restraints weight = 10915.515|
|-----------------------------------------------------------------------------|
r_work (final): 0.3181
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8055
moved from start:          0.3815

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  10426  Z= 0.171
  Angle     :  0.589   6.996  15097  Z= 0.349
  Chirality :  0.034   0.159   1724
  Planarity :  0.004   0.034   1074
  Dihedral  : 31.325 176.812   3290
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 11.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.38 %
    Favored  : 98.62 %
  Rotamer:
    Outliers :  6.52 %
    Allowed  : 24.31 %
    Favored  : 69.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.02 (0.34), residues: 580
  helix:  2.85 (0.23), residues: 450
  sheet:  None (None), residues: 0
  loop : -1.29 (0.42), residues: 130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG D  92 
 TYR   0.005   0.001   TYR H  51 
 PHE   0.009   0.001   PHE C  78 
 HIS   0.005   0.001   HIS E 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00381 (10426)
  covalent geometry    : angle       0.58890 (15097)
  hydrogen bonds       : bond        0.04203 (  660)
  hydrogen bonds       : angle       2.94926 ( 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
  216 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 183
  time to evaluate  : 0.252 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   87 SER cc_start: 0.9285 (m) cc_final: 0.8914 (t)
REVERT: A  120 MET cc_start: 0.8385 (mmm) cc_final: 0.8093 (mmm)
REVERT: A  125 GLN cc_start: 0.8478 (mt0) cc_final: 0.8231 (mp10)
REVERT: C   90 MET cc_start: 0.7677 (tpp) cc_final: 0.6832 (tpp)
REVERT: C  105 GLU cc_start: 0.8363 (mt-10) cc_final: 0.7991 (mt-10)
REVERT: C  108 ASN cc_start: 0.9207 (t0) cc_final: 0.8943 (t0)
REVERT: C  120 MET cc_start: 0.8281 (OUTLIER) cc_final: 0.8007 (mmt)
REVERT: D   84 MET cc_start: 0.8212 (tpp) cc_final: 0.8000 (tpp)
REVERT: D   91 LYS cc_start: 0.8375 (tmtt) cc_final: 0.7681 (mtmm)
REVERT: E   73 GLU cc_start: 0.8448 (tm-30) cc_final: 0.8091 (tm-30)
REVERT: E   90 MET cc_start: 0.8008 (ttt) cc_final: 0.7304 (tmm)
REVERT: E   97 GLU cc_start: 0.8512 (mm-30) cc_final: 0.8020 (tt0)
REVERT: E  125 GLN cc_start: 0.8100 (mt0) cc_final: 0.7837 (mt0)
REVERT: F   32 PRO cc_start: 0.9164 (Cg_exo) cc_final: 0.8919 (Cg_endo)
REVERT: F   68 ASP cc_start: 0.8079 (m-30) cc_final: 0.7636 (t70)
REVERT: F   72 TYR cc_start: 0.7891 (m-10) cc_final: 0.7045 (m-10)
REVERT: F   79 LYS cc_start: 0.8915 (mttm) cc_final: 0.8273 (tptp)
REVERT: F   84 MET cc_start: 0.8045 (mmm) cc_final: 0.7607 (tpp)
REVERT: F   88 TYR cc_start: 0.7969 (m-10) cc_final: 0.7663 (m-10)
REVERT: F   91 LYS cc_start: 0.8624 (mttt) cc_final: 0.8182 (mtpt)
REVERT: F   92 ARG cc_start: 0.7991 (mpt180) cc_final: 0.7683 (mtt90)
REVERT: G   62 ILE cc_start: 0.9272 (mt) cc_final: 0.9056 (mt)
REVERT: G   83 ARG cc_start: 0.8025 (mtp85) cc_final: 0.7671 (mtp85)
REVERT: G   90 MET cc_start: 0.8816 (mmp) cc_final: 0.8226 (tpt)
REVERT: G  120 MET cc_start: 0.8597 (mmm) cc_final: 0.8061 (mmt)
REVERT: H   47 SER cc_start: 0.9520 (t) cc_final: 0.8896 (t)
REVERT: H   52 GLU cc_start: 0.7695 (tm-30) cc_final: 0.7277 (tm-30)
  outliers start: 33
  outliers final: 18
  residues processed: 195
  average time/residue: 0.1301
  time to fit residues: 33.1154
Evaluate side-chains
  179 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 160
  time to evaluate  : 0.240 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 GLN
Chi-restraints excluded: chain A residue   96 CYS
Chi-restraints excluded: chain A residue  100 LEU
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain C residue  101 VAL
Chi-restraints excluded: chain C residue  120 MET
Chi-restraints excluded: chain D residue   64 ASN
Chi-restraints excluded: chain D residue   86 VAL
Chi-restraints excluded: chain E residue   60 LEU
Chi-restraints excluded: chain E residue   74 ILE
Chi-restraints excluded: chain E residue  101 VAL
Chi-restraints excluded: chain F residue   49 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  101 VAL
Chi-restraints excluded: chain H residue   62 LEU
Chi-restraints excluded: chain H residue   82 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 20 optimal weight:    0.9990
   chunk 68 optimal weight:   20.0000
   chunk 55 optimal weight:    0.8980
   chunk 10 optimal weight:    1.9990
   chunk 28 optimal weight:   10.0000
   chunk 23 optimal weight:    1.9990
   chunk 58 optimal weight:    9.9990
   chunk 11 optimal weight:    2.9990
   chunk 30 optimal weight:    0.6980
   chunk 43 optimal weight:    0.9980
   chunk 35 optimal weight:    0.4980
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
** C  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  75 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.097060 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.066186 restraints weight = 31179.204|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.067829 restraints weight = 17746.971|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.068876 restraints weight = 12868.300|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.069480 restraints weight = 10779.668|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.069792 restraints weight = 9817.711|
|-----------------------------------------------------------------------------|
r_work (final): 0.3227
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7997
moved from start:          0.4136

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  10426  Z= 0.160
  Angle     :  0.586   6.931  15097  Z= 0.345
  Chirality :  0.034   0.151   1724
  Planarity :  0.004   0.035   1074
  Dihedral  : 31.303 177.237   3290
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 12.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.38 %
    Favored  : 98.62 %
  Rotamer:
    Outliers :  4.74 %
    Allowed  : 27.67 %
    Favored  : 67.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.10 (0.34), residues: 580
  helix:  2.95 (0.23), residues: 450
  sheet:  None (None), residues: 0
  loop : -1.41 (0.41), residues: 130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG H  40 
 TYR   0.009   0.001   TYR B  88 
 PHE   0.007   0.001   PHE E  78 
 HIS   0.009   0.002   HIS D  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00350 (10426)
  covalent geometry    : angle       0.58610 (15097)
  hydrogen bonds       : bond        0.03967 (  660)
  hydrogen bonds       : angle       2.81740 ( 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
  215 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 191
  time to evaluate  : 0.244 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   87 SER cc_start: 0.9257 (m) cc_final: 0.8897 (t)
REVERT: C   90 MET cc_start: 0.7691 (tpp) cc_final: 0.6857 (tpp)
REVERT: C  105 GLU cc_start: 0.8312 (mt-10) cc_final: 0.7953 (mt-10)
REVERT: C  108 ASN cc_start: 0.9171 (t0) cc_final: 0.8956 (t0)
REVERT: C  120 MET cc_start: 0.8162 (OUTLIER) cc_final: 0.7903 (mmt)
REVERT: D   91 LYS cc_start: 0.8310 (tmtt) cc_final: 0.7772 (mtmm)
REVERT: E   73 GLU cc_start: 0.8515 (tm-30) cc_final: 0.8165 (tm-30)
REVERT: E   90 MET cc_start: 0.8043 (ttt) cc_final: 0.7582 (tpp)
REVERT: E   97 GLU cc_start: 0.8440 (mm-30) cc_final: 0.8042 (tt0)
REVERT: F   32 PRO cc_start: 0.9180 (Cg_exo) cc_final: 0.8926 (Cg_endo)
REVERT: F   53 GLU cc_start: 0.8579 (mt-10) cc_final: 0.8344 (mt-10)
REVERT: F   68 ASP cc_start: 0.8019 (m-30) cc_final: 0.7600 (t70)
REVERT: F   72 TYR cc_start: 0.7836 (m-10) cc_final: 0.6628 (m-10)
REVERT: F   74 GLU cc_start: 0.8584 (mm-30) cc_final: 0.7973 (tm-30)
REVERT: F   79 LYS cc_start: 0.8821 (mttm) cc_final: 0.8249 (tptp)
REVERT: F   84 MET cc_start: 0.8002 (mmm) cc_final: 0.7516 (tpp)
REVERT: F   88 TYR cc_start: 0.7935 (m-10) cc_final: 0.7581 (m-10)
REVERT: F   91 LYS cc_start: 0.8701 (mttt) cc_final: 0.8207 (mtpt)
REVERT: F   92 ARG cc_start: 0.7987 (mpt180) cc_final: 0.7556 (mtt90)
REVERT: G   83 ARG cc_start: 0.8032 (mtp85) cc_final: 0.7810 (mtp85)
REVERT: G  107 THR cc_start: 0.9365 (m) cc_final: 0.9054 (p)
REVERT: G  120 MET cc_start: 0.8617 (mmm) cc_final: 0.8016 (mmt)
REVERT: H   47 SER cc_start: 0.9462 (t) cc_final: 0.8805 (t)
REVERT: H   52 GLU cc_start: 0.7644 (tm-30) cc_final: 0.7248 (tm-30)
  outliers start: 24
  outliers final: 17
  residues processed: 200
  average time/residue: 0.1143
  time to fit residues: 30.5486
Evaluate side-chains
  183 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 165
  time to evaluate  : 0.198 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 GLN
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain C residue  101 VAL
Chi-restraints excluded: chain C residue  120 MET
Chi-restraints excluded: chain D residue   90 LEU
Chi-restraints excluded: chain E residue  101 VAL
Chi-restraints excluded: chain F residue   29 ILE
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   76 GLN
Chi-restraints excluded: chain G residue  101 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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 7 optimal weight:    9.9990
   chunk 54 optimal weight:    6.9990
   chunk 28 optimal weight:   10.0000
   chunk 60 optimal weight:   10.0000
   chunk 11 optimal weight:    1.9990
   chunk 34 optimal weight:    0.8980
   chunk 46 optimal weight:    4.9990
   chunk 5 optimal weight:    0.9980
   chunk 13 optimal weight:    3.9990
   chunk 29 optimal weight:    0.9990
   chunk 26 optimal weight:   10.0000
   overall best weight:    1.7786

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

Flipped N/Q/H residues before XYZ refinement:
** C  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  75 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.095127 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3119 r_free = 0.3119 target = 0.063995 restraints weight = 31242.164|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3157 r_free = 0.3157 target = 0.065508 restraints weight = 18539.307|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.066479 restraints weight = 13737.521|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.067060 restraints weight = 11630.967|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.067354 restraints weight = 10639.178|
|-----------------------------------------------------------------------------|
r_work (final): 0.3175
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8059
moved from start:          0.4399

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  10426  Z= 0.181
  Angle     :  0.609   7.829  15097  Z= 0.355
  Chirality :  0.034   0.157   1724
  Planarity :  0.004   0.034   1074
  Dihedral  : 31.498 177.023   3290
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 11.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.72 %
    Favored  : 98.28 %
  Rotamer:
    Outliers :  6.52 %
    Allowed  : 29.25 %
    Favored  : 64.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  3.02 (0.34), residues: 580
  helix:  2.96 (0.23), residues: 448
  sheet:  None (None), residues: 0
  loop : -1.66 (0.40), residues: 132

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D  40 
 TYR   0.008   0.001   TYR D  88 
 PHE   0.009   0.001   PHE E 104 
 HIS   0.010   0.002   HIS D  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00410 (10426)
  covalent geometry    : angle       0.60877 (15097)
  hydrogen bonds       : bond        0.04101 (  660)
  hydrogen bonds       : angle       2.90535 ( 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
  206 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 173
  time to evaluate  : 0.220 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   87 SER cc_start: 0.9294 (m) cc_final: 0.8993 (t)
REVERT: A   97 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.8118 (tt0)
REVERT: C   90 MET cc_start: 0.7698 (tpp) cc_final: 0.7130 (tpp)
REVERT: C  105 GLU cc_start: 0.8326 (mt-10) cc_final: 0.8000 (mt-10)
REVERT: D   87 VAL cc_start: 0.8408 (t) cc_final: 0.8026 (p)
REVERT: D   88 TYR cc_start: 0.7035 (t80) cc_final: 0.6554 (t80)
REVERT: D   91 LYS cc_start: 0.8327 (tmtt) cc_final: 0.7691 (mtmm)
REVERT: E   73 GLU cc_start: 0.8539 (tm-30) cc_final: 0.8325 (tm-30)
REVERT: E   90 MET cc_start: 0.8107 (ttt) cc_final: 0.7602 (tpp)
REVERT: E   97 GLU cc_start: 0.8610 (mm-30) cc_final: 0.8121 (tt0)
REVERT: F   32 PRO cc_start: 0.9128 (Cg_exo) cc_final: 0.8865 (Cg_endo)
REVERT: F   53 GLU cc_start: 0.8430 (mt-10) cc_final: 0.8198 (tt0)
REVERT: F   68 ASP cc_start: 0.8101 (m-30) cc_final: 0.7629 (t70)
REVERT: F   72 TYR cc_start: 0.7952 (m-10) cc_final: 0.6589 (m-10)
REVERT: F   79 LYS cc_start: 0.8969 (mttm) cc_final: 0.8316 (tptp)
REVERT: F   84 MET cc_start: 0.8062 (mmm) cc_final: 0.7501 (tpp)
REVERT: F   88 TYR cc_start: 0.8014 (m-10) cc_final: 0.7679 (m-10)
REVERT: F   91 LYS cc_start: 0.8593 (mttt) cc_final: 0.8259 (mtpt)
REVERT: F   92 ARG cc_start: 0.7926 (mpt180) cc_final: 0.7471 (mtt90)
REVERT: G   83 ARG cc_start: 0.7992 (mtp85) cc_final: 0.7723 (mtp85)
REVERT: G   90 MET cc_start: 0.8840 (mmp) cc_final: 0.8246 (tpt)
REVERT: G  120 MET cc_start: 0.8566 (mmm) cc_final: 0.7961 (mmt)
REVERT: H   47 SER cc_start: 0.9546 (t) cc_final: 0.8797 (t)
REVERT: H   52 GLU cc_start: 0.7818 (tm-30) cc_final: 0.7317 (tm-30)
REVERT: H   68 ASP cc_start: 0.8086 (m-30) cc_final: 0.7676 (m-30)
  outliers start: 33
  outliers final: 25
  residues processed: 190
  average time/residue: 0.1161
  time to fit residues: 29.5197
Evaluate side-chains
  186 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 160
  time to evaluate  : 0.270 
-------------------------------------------------------------------------------
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   97 GLU
Chi-restraints excluded: chain A residue  100 LEU
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 B residue   86 VAL
Chi-restraints excluded: chain C residue   87 SER
Chi-restraints excluded: chain C residue  101 VAL
Chi-restraints excluded: chain D residue   30 THR
Chi-restraints excluded: chain D residue   71 THR
Chi-restraints excluded: chain D residue   75 HIS
Chi-restraints excluded: chain D residue   90 LEU
Chi-restraints excluded: chain E residue  101 VAL
Chi-restraints excluded: chain F residue   29 ILE
Chi-restraints excluded: chain F residue   70 VAL
Chi-restraints excluded: chain F residue   81 VAL
Chi-restraints excluded: chain F residue   90 LEU
Chi-restraints excluded: chain G residue   76 GLN
Chi-restraints excluded: chain G residue  101 VAL
Chi-restraints excluded: chain G residue  117 VAL
Chi-restraints excluded: chain H residue   62 LEU
Chi-restraints excluded: chain H residue   81 VAL
Chi-restraints excluded: chain H residue   86 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 73 optimal weight:   10.0000
   chunk 66 optimal weight:   10.0000
   chunk 54 optimal weight:    3.9990
   chunk 42 optimal weight:    7.9990
   chunk 48 optimal weight:    4.9990
   chunk 12 optimal weight:    0.9990
   chunk 60 optimal weight:   10.0000
   chunk 75 optimal weight:    8.9990
   chunk 39 optimal weight:   10.0000
   chunk 51 optimal weight:    0.9990
   chunk 74 optimal weight:    7.9990
   overall best weight:    3.7990

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

Flipped N/Q/H residues before XYZ refinement:
** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  68 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.092446 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3061 r_free = 0.3061 target = 0.060534 restraints weight = 32546.791|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.3104 r_free = 0.3104 target = 0.062123 restraints weight = 19655.215|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3131 r_free = 0.3131 target = 0.063157 restraints weight = 14674.821|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.063768 restraints weight = 12402.931|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3158 r_free = 0.3158 target = 0.064145 restraints weight = 11341.452|
|-----------------------------------------------------------------------------|
r_work (final): 0.3096
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8224
moved from start:          0.5027

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.052  10426  Z= 0.265
  Angle     :  0.686   8.623  15097  Z= 0.395
  Chirality :  0.037   0.151   1724
  Planarity :  0.005   0.052   1074
  Dihedral  : 32.170 175.311   3290
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 13.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  7.71 %
    Allowed  : 29.45 %
    Favored  : 62.85 %
  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:  2.44 (0.33), residues: 580
  helix:  2.51 (0.23), residues: 450
  sheet:  None (None), residues: 0
  loop : -1.81 (0.40), residues: 130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG D  40 
 TYR   0.015   0.002   TYR B  88 
 PHE   0.015   0.002   PHE E 104 
 HIS   0.014   0.003   HIS D  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00613 (10426)
  covalent geometry    : angle       0.68618 (15097)
  hydrogen bonds       : bond        0.05124 (  660)
  hydrogen bonds       : angle       3.35379 ( 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
  204 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 165
  time to evaluate  : 0.202 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   87 SER cc_start: 0.9396 (m) cc_final: 0.9094 (t)
REVERT: A   90 MET cc_start: 0.8417 (tpt) cc_final: 0.8022 (tpp)
REVERT: A  125 GLN cc_start: 0.8633 (mt0) cc_final: 0.8125 (mp10)
REVERT: B   49 LEU cc_start: 0.8879 (mp) cc_final: 0.8643 (mm)
REVERT: B   79 LYS cc_start: 0.8937 (mttm) cc_final: 0.8720 (tttt)
REVERT: C   90 MET cc_start: 0.7634 (tpp) cc_final: 0.7077 (tpp)
REVERT: C  105 GLU cc_start: 0.8346 (mt-10) cc_final: 0.8045 (mt-10)
REVERT: D   29 ILE cc_start: 0.8581 (mm) cc_final: 0.8253 (mm)
REVERT: D   72 TYR cc_start: 0.7459 (m-10) cc_final: 0.7204 (m-10)
REVERT: D   87 VAL cc_start: 0.8413 (t) cc_final: 0.8118 (p)
REVERT: D   88 TYR cc_start: 0.7291 (t80) cc_final: 0.6894 (t80)
REVERT: D   91 LYS cc_start: 0.8405 (tmtt) cc_final: 0.7722 (mtmm)
REVERT: E   90 MET cc_start: 0.8151 (ttt) cc_final: 0.7647 (tpp)
REVERT: F   32 PRO cc_start: 0.9203 (Cg_exo) cc_final: 0.8914 (Cg_endo)
REVERT: F   79 LYS cc_start: 0.9142 (mttm) cc_final: 0.8463 (tptp)
REVERT: F   84 MET cc_start: 0.8085 (mmm) cc_final: 0.7449 (tpp)
REVERT: F   88 TYR cc_start: 0.8026 (m-10) cc_final: 0.7518 (m-10)
REVERT: F   91 LYS cc_start: 0.8717 (mttt) cc_final: 0.8301 (mtmt)
REVERT: F   92 ARG cc_start: 0.7974 (mpt180) cc_final: 0.7577 (mtt90)
REVERT: G   90 MET cc_start: 0.8817 (mmp) cc_final: 0.8368 (tpt)
REVERT: G  107 THR cc_start: 0.9296 (m) cc_final: 0.8924 (p)
REVERT: G  125 GLN cc_start: 0.8502 (mt0) cc_final: 0.8275 (mt0)
REVERT: H   52 GLU cc_start: 0.7983 (tm-30) cc_final: 0.7484 (tm-30)
  outliers start: 39
  outliers final: 29
  residues processed: 185
  average time/residue: 0.1096
  time to fit residues: 27.5617
Evaluate side-chains
  185 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 156
  time to evaluate  : 0.191 
-------------------------------------------------------------------------------
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  118 THR
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue   65 VAL
Chi-restraints excluded: chain B residue   86 VAL
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain C residue   87 SER
Chi-restraints excluded: chain D residue   43 VAL
Chi-restraints excluded: chain D residue   64 ASN
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 D residue   90 LEU
Chi-restraints excluded: chain E residue  101 VAL
Chi-restraints excluded: chain F residue   29 ILE
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain F residue   70 VAL
Chi-restraints excluded: chain F residue   81 VAL
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  101 VAL
Chi-restraints excluded: chain H residue   62 LEU
Chi-restraints excluded: chain H residue   65 VAL
Chi-restraints excluded: chain H residue   81 VAL
Chi-restraints excluded: chain H residue   86 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 78 optimal weight:   10.0000
   chunk 59 optimal weight:   10.0000
   chunk 60 optimal weight:   10.0000
   chunk 49 optimal weight:    6.9990
   chunk 38 optimal weight:    0.6980
   chunk 22 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9990
   chunk 42 optimal weight:    4.9990
   chunk 3 optimal weight:    0.7980
   chunk 45 optimal weight:    0.8980
   chunk 77 optimal weight:   10.0000
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
A 113 HIS
C  93 GLN
G  68 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.093506 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3088 r_free = 0.3088 target = 0.062501 restraints weight = 32014.942|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3129 r_free = 0.3129 target = 0.064114 restraints weight = 18712.079|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.065164 restraints weight = 13721.236|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3170 r_free = 0.3170 target = 0.065757 restraints weight = 11538.093|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 45)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.066140 restraints weight = 10533.712|
|-----------------------------------------------------------------------------|
r_work (final): 0.3140
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8097
moved from start:          0.5011

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  10426  Z= 0.171
  Angle     :  0.633   7.674  15097  Z= 0.367
  Chirality :  0.034   0.173   1724
  Planarity :  0.004   0.042   1074
  Dihedral  : 31.808 175.929   3290
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 12.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  5.93 %
    Allowed  : 31.62 %
    Favored  : 62.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.79 (0.34), residues: 580
  helix:  2.76 (0.23), residues: 450
  sheet:  None (None), residues: 0
  loop : -1.70 (0.40), residues: 130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D  40 
 TYR   0.012   0.001   TYR C  99 
 PHE   0.012   0.001   PHE G  67 
 HIS   0.002   0.001   HIS E 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00382 (10426)
  covalent geometry    : angle       0.63292 (15097)
  hydrogen bonds       : bond        0.03909 (  660)
  hydrogen bonds       : angle       2.86142 ( 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
  215 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 185
  time to evaluate  : 0.247 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   87 SER cc_start: 0.9329 (m) cc_final: 0.9035 (t)
REVERT: A   97 GLU cc_start: 0.8328 (tt0) cc_final: 0.8128 (tt0)
REVERT: C   90 MET cc_start: 0.7644 (tpp) cc_final: 0.7115 (tpp)
REVERT: C   93 GLN cc_start: 0.9060 (OUTLIER) cc_final: 0.7919 (tp40)
REVERT: C  105 GLU cc_start: 0.8297 (mt-10) cc_final: 0.7924 (mt-10)
REVERT: D   72 TYR cc_start: 0.7406 (m-10) cc_final: 0.7076 (m-10)
REVERT: D   74 GLU cc_start: 0.8461 (mm-30) cc_final: 0.8057 (mm-30)
REVERT: D   91 LYS cc_start: 0.8347 (tmtt) cc_final: 0.7783 (mtmt)
REVERT: E   90 MET cc_start: 0.8180 (ttt) cc_final: 0.7609 (tpp)
REVERT: E   97 GLU cc_start: 0.8688 (mm-30) cc_final: 0.8017 (tt0)
REVERT: F   32 PRO cc_start: 0.9145 (Cg_exo) cc_final: 0.8861 (Cg_endo)
REVERT: F   68 ASP cc_start: 0.8156 (m-30) cc_final: 0.7559 (t70)
REVERT: F   74 GLU cc_start: 0.8644 (mm-30) cc_final: 0.8404 (mm-30)
REVERT: F   79 LYS cc_start: 0.8997 (mttm) cc_final: 0.8413 (tptp)
REVERT: F   84 MET cc_start: 0.8255 (mmm) cc_final: 0.7646 (tpp)
REVERT: F   88 TYR cc_start: 0.8004 (m-10) cc_final: 0.7517 (m-10)
REVERT: F   91 LYS cc_start: 0.8675 (mttt) cc_final: 0.8345 (mtmt)
REVERT: G   83 ARG cc_start: 0.8123 (mtp85) cc_final: 0.7906 (mtp85)
REVERT: G   90 MET cc_start: 0.8865 (mmp) cc_final: 0.8275 (tpt)
REVERT: G  107 THR cc_start: 0.9244 (m) cc_final: 0.8954 (p)
REVERT: G  120 MET cc_start: 0.8607 (mmm) cc_final: 0.7995 (mmt)
REVERT: H   52 GLU cc_start: 0.7826 (tm-30) cc_final: 0.7330 (tm-30)
REVERT: H   92 ARG cc_start: 0.8385 (ttp80) cc_final: 0.8174 (ttp80)
  outliers start: 30
  outliers final: 24
  residues processed: 202
  average time/residue: 0.1171
  time to fit residues: 31.4692
Evaluate side-chains
  186 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 161
  time to evaluate  : 0.152 
-------------------------------------------------------------------------------
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  101 VAL
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue   86 VAL
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain C residue   93 GLN
Chi-restraints excluded: chain D residue   71 THR
Chi-restraints excluded: chain D residue   81 VAL
Chi-restraints excluded: chain D residue   90 LEU
Chi-restraints excluded: chain E residue   74 ILE
Chi-restraints excluded: chain E residue  101 VAL
Chi-restraints excluded: chain F residue   29 ILE
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain F residue   81 VAL
Chi-restraints excluded: chain G residue   76 GLN
Chi-restraints excluded: chain G residue  101 VAL
Chi-restraints excluded: chain G residue  124 ILE
Chi-restraints excluded: chain H residue   62 LEU
Chi-restraints excluded: chain H residue   65 VAL
Chi-restraints excluded: chain H residue   81 VAL
Chi-restraints excluded: chain H residue   82 THR
Chi-restraints excluded: chain H residue   86 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 27 optimal weight:    8.9990
   chunk 37 optimal weight:    9.9990
   chunk 69 optimal weight:   10.0000
   chunk 55 optimal weight:    2.9990
   chunk 1 optimal weight:    0.9980
   chunk 24 optimal weight:    0.7980
   chunk 46 optimal weight:    0.7980
   chunk 2 optimal weight:    7.9990
   chunk 58 optimal weight:   10.0000
   chunk 49 optimal weight:    9.9990
   chunk 35 optimal weight:    1.9990
   overall best weight:    1.5184

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

Flipped N/Q/H residues before XYZ refinement:
C  76 GLN
** E  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  93 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.093473 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3078 r_free = 0.3078 target = 0.062036 restraints weight = 32360.914|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.063603 restraints weight = 19486.187|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.064641 restraints weight = 14494.818|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.065258 restraints weight = 12260.023|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.065597 restraints weight = 11171.627|
|-----------------------------------------------------------------------------|
r_work (final): 0.3124
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8123
moved from start:          0.5179

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  10426  Z= 0.179
  Angle     :  0.640   7.082  15097  Z= 0.369
  Chirality :  0.034   0.176   1724
  Planarity :  0.004   0.037   1074
  Dihedral  : 31.791 176.314   3290
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 12.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.24 %
    Favored  : 97.76 %
  Rotamer:
    Outliers :  5.34 %
    Allowed  : 32.41 %
    Favored  : 62.25 %
  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:  2.82 (0.33), residues: 580
  helix:  2.79 (0.23), residues: 446
  sheet:  None (None), residues: 0
  loop : -1.56 (0.38), residues: 134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG F  39 
 TYR   0.021   0.002   TYR D  88 
 PHE   0.010   0.001   PHE G  67 
 HIS   0.003   0.001   HIS D  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00406 (10426)
  covalent geometry    : angle       0.64026 (15097)
  hydrogen bonds       : bond        0.04068 (  660)
  hydrogen bonds       : angle       2.92045 ( 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
  198 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 171
  time to evaluate  : 0.197 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   87 SER cc_start: 0.9339 (m) cc_final: 0.9027 (t)
REVERT: A   97 GLU cc_start: 0.8339 (tt0) cc_final: 0.8124 (tt0)
REVERT: A  120 MET cc_start: 0.8430 (mmm) cc_final: 0.7840 (mmt)
REVERT: C   90 MET cc_start: 0.7582 (tpp) cc_final: 0.7066 (tpp)
REVERT: C  105 GLU cc_start: 0.8358 (mt-10) cc_final: 0.8003 (mt-10)
REVERT: D   77 LYS cc_start: 0.7786 (mmmt) cc_final: 0.7584 (tmmt)
REVERT: D   91 LYS cc_start: 0.8383 (tmtt) cc_final: 0.7763 (mtmt)
REVERT: E   90 MET cc_start: 0.8122 (ttt) cc_final: 0.7526 (tpp)
REVERT: E   97 GLU cc_start: 0.8552 (mm-30) cc_final: 0.8064 (tt0)
REVERT: F   32 PRO cc_start: 0.9133 (Cg_exo) cc_final: 0.8849 (Cg_endo)
REVERT: F   68 ASP cc_start: 0.8096 (m-30) cc_final: 0.7518 (t70)
REVERT: F   72 TYR cc_start: 0.7885 (m-10) cc_final: 0.7081 (m-10)
REVERT: F   79 LYS cc_start: 0.8990 (mttm) cc_final: 0.8418 (tptp)
REVERT: F   84 MET cc_start: 0.8256 (mmm) cc_final: 0.7614 (tpp)
REVERT: F   88 TYR cc_start: 0.7937 (m-10) cc_final: 0.7599 (m-10)
REVERT: F   91 LYS cc_start: 0.8668 (mttt) cc_final: 0.8388 (mtpt)
REVERT: F   92 ARG cc_start: 0.7926 (mpt180) cc_final: 0.7610 (mtt90)
REVERT: G   90 MET cc_start: 0.8871 (mmp) cc_final: 0.8309 (tpt)
REVERT: G  120 MET cc_start: 0.8511 (mmm) cc_final: 0.7924 (mmt)
REVERT: G  125 GLN cc_start: 0.8468 (mt0) cc_final: 0.8063 (mp10)
REVERT: H   52 GLU cc_start: 0.7862 (tm-30) cc_final: 0.7357 (tm-30)
  outliers start: 27
  outliers final: 23
  residues processed: 189
  average time/residue: 0.0987
  time to fit residues: 25.4379
Evaluate side-chains
  184 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 161
  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   96 CYS
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue   65 VAL
Chi-restraints excluded: chain B residue   86 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   74 ILE
Chi-restraints excluded: chain E residue  101 VAL
Chi-restraints excluded: chain F residue   29 ILE
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain F residue   81 VAL
Chi-restraints excluded: chain G residue   65 LEU
Chi-restraints excluded: chain G residue   76 GLN
Chi-restraints excluded: chain G residue  100 LEU
Chi-restraints excluded: chain G residue  101 VAL
Chi-restraints excluded: chain H residue   62 LEU
Chi-restraints excluded: chain H residue   65 VAL
Chi-restraints excluded: chain H residue   81 VAL
Chi-restraints excluded: chain H residue   86 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 56 optimal weight:   20.0000
   chunk 41 optimal weight:    8.9990
   chunk 44 optimal weight:    2.9990
   chunk 39 optimal weight:    6.9990
   chunk 37 optimal weight:    7.9990
   chunk 21 optimal weight:    0.3980
   chunk 16 optimal weight:    7.9990
   chunk 42 optimal weight:    6.9990
   chunk 20 optimal weight:    2.9990
   chunk 55 optimal weight:    1.9990
   chunk 43 optimal weight:    2.9990
   overall best weight:    2.2788

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

Flipped N/Q/H residues before XYZ refinement:
** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  76 GLN
** E  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.092134 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3047 r_free = 0.3047 target = 0.060679 restraints weight = 31972.978|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3090 r_free = 0.3090 target = 0.062293 restraints weight = 18713.041|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3114 r_free = 0.3114 target = 0.063294 restraints weight = 13681.837|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3133 r_free = 0.3133 target = 0.063971 restraints weight = 11507.307|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.064315 restraints weight = 10435.627|
|-----------------------------------------------------------------------------|
r_work (final): 0.3104
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8145
moved from start:          0.5358

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048  10426  Z= 0.203
  Angle     :  0.654   7.144  15097  Z= 0.376
  Chirality :  0.035   0.158   1724
  Planarity :  0.004   0.037   1074
  Dihedral  : 31.921 175.786   3290
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 12.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.24 %
    Favored  : 97.76 %
  Rotamer:
    Outliers :  4.94 %
    Allowed  : 33.40 %
    Favored  : 61.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.75 (0.33), residues: 580
  helix:  2.72 (0.23), residues: 448
  sheet:  None (None), residues: 0
  loop : -1.57 (0.39), residues: 132

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG F  39 
 TYR   0.022   0.002   TYR D  88 
 PHE   0.013   0.002   PHE C  78 
 HIS   0.003   0.001   HIS D  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00474 (10426)
  covalent geometry    : angle       0.65358 (15097)
  hydrogen bonds       : bond        0.04279 (  660)
  hydrogen bonds       : angle       3.00758 ( 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
  191 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 166
  time to evaluate  : 0.253 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   87 SER cc_start: 0.9332 (m) cc_final: 0.9045 (t)
REVERT: A  120 MET cc_start: 0.8383 (mmm) cc_final: 0.7780 (mmt)
REVERT: C   90 MET cc_start: 0.7593 (tpp) cc_final: 0.7033 (tpp)
REVERT: C  105 GLU cc_start: 0.8382 (mt-10) cc_final: 0.8024 (mt-10)
REVERT: D   53 GLU cc_start: 0.8342 (tt0) cc_final: 0.7896 (tt0)
REVERT: D   77 LYS cc_start: 0.7878 (mmmt) cc_final: 0.7574 (tmmt)
REVERT: D   91 LYS cc_start: 0.8289 (tmtt) cc_final: 0.7641 (mtmt)
REVERT: E   90 MET cc_start: 0.8115 (ttt) cc_final: 0.7560 (tpp)
REVERT: E   97 GLU cc_start: 0.8546 (mm-30) cc_final: 0.8007 (tt0)
REVERT: F   32 PRO cc_start: 0.9138 (Cg_exo) cc_final: 0.8865 (Cg_endo)
REVERT: F   68 ASP cc_start: 0.8150 (m-30) cc_final: 0.7639 (t70)
REVERT: F   72 TYR cc_start: 0.7874 (m-10) cc_final: 0.7158 (m-10)
REVERT: F   79 LYS cc_start: 0.8943 (mttm) cc_final: 0.8407 (tptp)
REVERT: F   84 MET cc_start: 0.8232 (mmm) cc_final: 0.7596 (tpp)
REVERT: F   88 TYR cc_start: 0.7924 (m-10) cc_final: 0.7413 (m-10)
REVERT: F   90 LEU cc_start: 0.8768 (mm) cc_final: 0.8144 (tt)
REVERT: F   91 LYS cc_start: 0.8573 (mttt) cc_final: 0.8195 (mtmt)
REVERT: F   92 ARG cc_start: 0.7896 (mpt180) cc_final: 0.7597 (mtt90)
REVERT: G   90 MET cc_start: 0.8868 (mmp) cc_final: 0.8367 (tpt)
REVERT: G  120 MET cc_start: 0.8492 (mmm) cc_final: 0.7879 (mmt)
REVERT: H   52 GLU cc_start: 0.8002 (tm-30) cc_final: 0.7500 (tm-30)
  outliers start: 25
  outliers final: 23
  residues processed: 183
  average time/residue: 0.1051
  time to fit residues: 26.4695
Evaluate side-chains
  184 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 161
  time to evaluate  : 0.239 
-------------------------------------------------------------------------------
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  126 LEU
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue   65 VAL
Chi-restraints excluded: chain B residue   86 VAL
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain D residue   81 VAL
Chi-restraints excluded: chain D residue   86 VAL
Chi-restraints excluded: chain E residue   74 ILE
Chi-restraints excluded: chain F residue   29 ILE
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain F residue   81 VAL
Chi-restraints excluded: chain G residue   65 LEU
Chi-restraints excluded: chain G residue   76 GLN
Chi-restraints excluded: chain G residue  100 LEU
Chi-restraints excluded: chain G residue  101 VAL
Chi-restraints excluded: chain H residue   62 LEU
Chi-restraints excluded: chain H residue   65 VAL
Chi-restraints excluded: chain H residue   81 VAL
Chi-restraints excluded: chain H residue   86 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 61 optimal weight:   10.0000
   chunk 32 optimal weight:    3.9990
   chunk 1 optimal weight:    0.7980
   chunk 24 optimal weight:    0.8980
   chunk 65 optimal weight:   10.0000
   chunk 14 optimal weight:   10.0000
   chunk 15 optimal weight:    5.9990
   chunk 40 optimal weight:    9.9990
   chunk 66 optimal weight:   10.0000
   chunk 52 optimal weight:    1.9990
   chunk 36 optimal weight:    6.9990
   overall best weight:    2.7386

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

Flipped N/Q/H residues before XYZ refinement:
** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  68 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 = 0.3736 r_free = 0.3736 target = 0.091014 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3023 r_free = 0.3023 target = 0.059829 restraints weight = 31719.749|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 21)----------------|
| r_work = 0.3062 r_free = 0.3062 target = 0.061305 restraints weight = 19343.032|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3088 r_free = 0.3088 target = 0.062287 restraints weight = 14479.800|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3104 r_free = 0.3104 target = 0.062876 restraints weight = 12264.594|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3113 r_free = 0.3113 target = 0.063214 restraints weight = 11195.714|
|-----------------------------------------------------------------------------|
r_work (final): 0.3081
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8176
moved from start:          0.5604

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.058  10426  Z= 0.223
  Angle     :  0.676   8.648  15097  Z= 0.387
  Chirality :  0.036   0.175   1724
  Planarity :  0.004   0.032   1074
  Dihedral  : 32.099 175.338   3290
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 12.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.24 %
    Favored  : 97.76 %
  Rotamer:
    Outliers :  5.14 %
    Allowed  : 33.60 %
    Favored  : 61.26 %
  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:  2.54 (0.33), residues: 580
  helix:  2.56 (0.23), residues: 446
  sheet:  None (None), residues: 0
  loop : -1.53 (0.39), residues: 134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG F  39 
 TYR   0.022   0.002   TYR D  88 
 PHE   0.011   0.002   PHE C 104 
 HIS   0.004   0.001   HIS H  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00523 (10426)
  covalent geometry    : angle       0.67551 (15097)
  hydrogen bonds       : bond        0.04486 (  660)
  hydrogen bonds       : angle       3.10237 ( 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
  192 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 166
  time to evaluate  : 0.237 
Fit side-chains
   revert: symmetry clash
REVERT: A   87 SER cc_start: 0.9352 (m) cc_final: 0.9057 (t)
REVERT: A   97 GLU cc_start: 0.8236 (tt0) cc_final: 0.8029 (tt0)
REVERT: A  120 MET cc_start: 0.8384 (mmm) cc_final: 0.7792 (mmt)
REVERT: C   90 MET cc_start: 0.7636 (tpp) cc_final: 0.7075 (tpp)
REVERT: C  105 GLU cc_start: 0.8330 (mt-10) cc_final: 0.8009 (mt-10)
REVERT: D   53 GLU cc_start: 0.8457 (tt0) cc_final: 0.8251 (tm-30)
REVERT: D   67 ARG cc_start: 0.7925 (ttm110) cc_final: 0.7678 (mtm110)
REVERT: D   91 LYS cc_start: 0.8266 (tmtt) cc_final: 0.7709 (mtmt)
REVERT: E   90 MET cc_start: 0.8131 (ttt) cc_final: 0.7593 (tpp)
REVERT: E   97 GLU cc_start: 0.8534 (mm-30) cc_final: 0.8003 (tt0)
REVERT: F   32 PRO cc_start: 0.9170 (Cg_exo) cc_final: 0.8913 (Cg_endo)
REVERT: F   68 ASP cc_start: 0.8232 (m-30) cc_final: 0.7719 (t70)
REVERT: F   72 TYR cc_start: 0.7820 (m-10) cc_final: 0.6869 (m-10)
REVERT: F   79 LYS cc_start: 0.8934 (mttm) cc_final: 0.8413 (tptp)
REVERT: F   84 MET cc_start: 0.8262 (mmm) cc_final: 0.7582 (tpp)
REVERT: F   88 TYR cc_start: 0.7930 (m-10) cc_final: 0.7407 (m-10)
REVERT: F   90 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8153 (tt)
REVERT: F   91 LYS cc_start: 0.8618 (mttt) cc_final: 0.8197 (mtmt)
REVERT: F   92 ARG cc_start: 0.7864 (mpt180) cc_final: 0.7475 (mtt90)
REVERT: G   90 MET cc_start: 0.8833 (mmp) cc_final: 0.8357 (tpt)
REVERT: H   52 GLU cc_start: 0.7993 (tm-30) cc_final: 0.7495 (tm-30)
  outliers start: 26
  outliers final: 23
  residues processed: 182
  average time/residue: 0.1070
  time to fit residues: 26.5341
Evaluate side-chains
  185 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 161
  time to evaluate  : 0.277 
-------------------------------------------------------------------------------
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  126 LEU
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue   65 VAL
Chi-restraints excluded: chain B residue   86 VAL
Chi-restraints excluded: chain D residue   30 THR
Chi-restraints excluded: chain D residue   81 VAL
Chi-restraints excluded: chain D residue   86 VAL
Chi-restraints excluded: chain E residue   74 ILE
Chi-restraints excluded: chain F residue   29 ILE
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  100 LEU
Chi-restraints excluded: chain G residue  101 VAL
Chi-restraints excluded: chain H residue   62 LEU
Chi-restraints excluded: chain H residue   65 VAL
Chi-restraints excluded: chain H residue   81 VAL
Chi-restraints excluded: chain H residue   86 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 52 optimal weight:    0.9990
   chunk 37 optimal weight:    7.9990
   chunk 71 optimal weight:   10.0000
   chunk 6 optimal weight:    0.9990
   chunk 22 optimal weight:    1.9990
   chunk 44 optimal weight:    0.0970
   chunk 26 optimal weight:    5.9990
   chunk 78 optimal weight:   10.0000
   chunk 76 optimal weight:    8.9990
   chunk 11 optimal weight:    1.9990
   chunk 2 optimal weight:    0.7980
   overall best weight:    0.9784

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

Flipped N/Q/H residues before XYZ refinement:
A  93 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.093685 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3090 r_free = 0.3090 target = 0.062401 restraints weight = 32202.532|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3133 r_free = 0.3133 target = 0.064055 restraints weight = 18744.689|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.065143 restraints weight = 13683.072|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.065760 restraints weight = 11431.378|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.066146 restraints weight = 10378.017|
|-----------------------------------------------------------------------------|
r_work (final): 0.3149
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8097
moved from start:          0.5639

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.062  10426  Z= 0.171
  Angle     :  0.647   9.620  15097  Z= 0.371
  Chirality :  0.034   0.154   1724
  Planarity :  0.004   0.030   1074
  Dihedral  : 31.850 176.170   3290
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 12.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  4.35 %
    Allowed  : 35.18 %
    Favored  : 60.47 %
  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:  2.69 (0.33), residues: 580
  helix:  2.63 (0.23), residues: 448
  sheet:  None (None), residues: 0
  loop : -1.40 (0.40), residues: 132

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG F  39 
 TYR   0.025   0.002   TYR D  88 
 PHE   0.013   0.001   PHE C  78 
 HIS   0.002   0.001   HIS D  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00391 (10426)
  covalent geometry    : angle       0.64741 (15097)
  hydrogen bonds       : bond        0.03945 (  660)
  hydrogen bonds       : angle       2.87052 ( 1653)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1573.46 seconds
wall clock time: 27 minutes 46.45 seconds (1666.45 seconds total)