Starting phenix.real_space_refine
on Thu Feb 13 21:13:50 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7x58_33011/02_2025/7x58_33011.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7x58_33011/02_2025/7x58_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_33011/02_2025/7x58_33011.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7x58_33011/02_2025/7x58_33011.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7x58_33011/02_2025/7x58_33011.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7x58_33011/02_2025/7x58_33011.cif"
  }
  resolution = 3.93
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 5.32, per 1000 atoms: 0.54
  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: 2.39
  Conformation dependent library (CDL) restraints added in 583.3 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: 4.54
  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: 3.27

  Time building geometry restraints manager: 2.79 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:             0.370
  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:          0.350
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     25.510
  Find NCS groups from input model:        0.250
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.670
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.350
-------------------------------------------------------------------------------
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= 0.176
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  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
 HIS   0.001   0.000   HIS C 113 
 PHE   0.013   0.001   PHE H  61 
 TYR   0.004   0.001   TYR B  88 
 ARG   0.003   0.000   ARG E 129 

*********************** 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  : 0.840 
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: 0.8113 (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: 0.9228 (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: 0.8857 (ttmm)
  outliers start: 0
  outliers final: 0
  residues processed: 288
  average time/residue: 0.3570
  time to fit residues: 126.0815
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  : 0.785 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 67 optimal weight:   10.0000
   chunk 60 optimal weight:   10.0000
   chunk 33 optimal weight:    3.9990
   chunk 20 optimal weight:    8.9990
   chunk 40 optimal weight:   20.0000
   chunk 32 optimal weight:    0.8980
   chunk 62 optimal weight:    8.9990
   chunk 24 optimal weight:    3.9990
   chunk 38 optimal weight:    2.9990
   chunk 46 optimal weight:    3.9990
   chunk 72 optimal weight:   10.0000
   overall best weight:    3.1788

-------------------------------------------------------------------------------
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 = 0.3792 r_free = 0.3792 target = 0.094383 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3073 r_free = 0.3073 target = 0.062340 restraints weight = 31559.086|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3113 r_free = 0.3113 target = 0.063858 restraints weight = 18723.093|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3138 r_free = 0.3138 target = 0.064841 restraints weight = 13912.904|
|-----------------------------------------------------------------------------|
r_work (final): 0.3103
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8145
moved from start:          0.3534

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.071  10426  Z= 0.324
  Angle     :  0.663   8.747  15097  Z= 0.385
  Chirality :  0.036   0.151   1724
  Planarity :  0.005   0.073   1074
  Dihedral  : 31.546 174.350   3290
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 12.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.03 %
    Favored  : 98.97 %
  Rotamer:
    Outliers :  5.53 %
    Allowed  : 21.74 %
    Favored  : 72.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.62 (0.33), residues: 580
  helix:  2.55 (0.23), residues: 450
  sheet:  None (None), residues: 0
  loop : -1.36 (0.41), residues: 130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.009   0.003   HIS E 113 
 PHE   0.011   0.002   PHE E  67 
 TYR   0.016   0.002   TYR B  88 
 ARG   0.007   0.001   ARG D  92 

*********************** 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
  220 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 192
  time to evaluate  : 0.717 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   73 GLU cc_start: 0.8956 (tm-30) cc_final: 0.8749 (tm-30)
REVERT: A   87 SER cc_start: 0.9384 (m) cc_final: 0.8974 (t)
REVERT: A  120 MET cc_start: 0.8461 (mmm) cc_final: 0.8211 (mmm)
REVERT: B   52 GLU cc_start: 0.8097 (tm-30) cc_final: 0.7878 (tm-30)
REVERT: C   90 MET cc_start: 0.7605 (tpp) cc_final: 0.7054 (tpp)
REVERT: C  105 GLU cc_start: 0.8349 (mt-10) cc_final: 0.8005 (mt-10)
REVERT: C  120 MET cc_start: 0.8420 (OUTLIER) cc_final: 0.8125 (mmt)
REVERT: D   52 GLU cc_start: 0.8503 (tm-30) cc_final: 0.8209 (tm-30)
REVERT: D   84 MET cc_start: 0.8290 (tpp) cc_final: 0.7962 (tpp)
REVERT: D   91 LYS cc_start: 0.8422 (tmtt) cc_final: 0.7769 (mtmm)
REVERT: E   73 GLU cc_start: 0.9122 (tm-30) cc_final: 0.8359 (tm-30)
REVERT: E   90 MET cc_start: 0.7844 (ttt) cc_final: 0.7372 (tmm)
REVERT: E  105 GLU cc_start: 0.8374 (mt-10) cc_final: 0.7837 (mt-10)
REVERT: F   32 PRO cc_start: 0.9167 (Cg_exo) cc_final: 0.8947 (Cg_endo)
REVERT: F   53 GLU cc_start: 0.8675 (tp30) cc_final: 0.8469 (tp30)
REVERT: F   74 GLU cc_start: 0.8879 (mm-30) cc_final: 0.8228 (tm-30)
REVERT: F   79 LYS cc_start: 0.9060 (mttm) cc_final: 0.8367 (tptp)
REVERT: F   84 MET cc_start: 0.8080 (mmm) cc_final: 0.7323 (tpp)
REVERT: F   91 LYS cc_start: 0.8645 (mttt) cc_final: 0.8071 (mtpt)
REVERT: G   90 MET cc_start: 0.8774 (mmp) cc_final: 0.8176 (tpt)
REVERT: G  120 MET cc_start: 0.8616 (mmm) cc_final: 0.8349 (mmm)
REVERT: H   52 GLU cc_start: 0.7946 (tm-30) cc_final: 0.7648 (tm-30)
  outliers start: 28
  outliers final: 16
  residues processed: 201
  average time/residue: 0.2927
  time to fit residues: 76.1350
Evaluate side-chains
  175 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 158
  time to evaluate  : 0.705 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 GLN
Chi-restraints excluded: chain A residue  100 LEU
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain C residue   89 VAL
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 D residue   86 VAL
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 F residue   86 VAL
Chi-restraints excluded: chain G residue   65 LEU
Chi-restraints excluded: chain G residue   76 GLN
Chi-restraints excluded: chain G residue   96 CYS
Chi-restraints excluded: chain H residue   62 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 1 optimal weight:    0.9990
   chunk 72 optimal weight:   10.0000
   chunk 46 optimal weight:    0.8980
   chunk 15 optimal weight:    2.9990
   chunk 30 optimal weight:    0.8980
   chunk 10 optimal weight:    2.9990
   chunk 2 optimal weight:    0.0070
   chunk 61 optimal weight:    8.9990
   chunk 32 optimal weight:    0.8980
   chunk 37 optimal weight:    6.9990
   chunk 54 optimal weight:    4.9990
   overall best weight:    0.7400

-------------------------------------------------------------------------------
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
E 125 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 = 0.3842 r_free = 0.3842 target = 0.097085 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3149 r_free = 0.3149 target = 0.065585 restraints weight = 31917.999|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.067199 restraints weight = 19042.041|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.068186 restraints weight = 14101.810|
|-----------------------------------------------------------------------------|
r_work (final): 0.3173
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8066
moved from start:          0.3840

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  10426  Z= 0.194
  Angle     :  0.582   6.251  15097  Z= 0.346
  Chirality :  0.034   0.170   1724
  Planarity :  0.004   0.036   1074
  Dihedral  : 31.276 176.805   3290
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 11.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.38 %
    Favored  : 98.62 %
  Rotamer:
    Outliers :  5.14 %
    Allowed  : 25.69 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.02 (0.34), residues: 580
  helix:  2.87 (0.23), residues: 450
  sheet:  None (None), residues: 0
  loop : -1.36 (0.41), residues: 130

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

*********************** 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
  225 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 199
  time to evaluate  : 0.722 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   87 SER cc_start: 0.9266 (m) cc_final: 0.8897 (t)
REVERT: A  120 MET cc_start: 0.8336 (mmm) cc_final: 0.7733 (mmm)
REVERT: A  125 GLN cc_start: 0.8527 (mt0) cc_final: 0.8213 (mp10)
REVERT: B   52 GLU cc_start: 0.7903 (tm-30) cc_final: 0.7580 (tm-30)
REVERT: C   90 MET cc_start: 0.7647 (tpp) cc_final: 0.6811 (tpp)
REVERT: C  105 GLU cc_start: 0.8374 (mt-10) cc_final: 0.8032 (mt-10)
REVERT: C  108 ASN cc_start: 0.9194 (t0) cc_final: 0.8940 (t0)
REVERT: C  120 MET cc_start: 0.8260 (OUTLIER) cc_final: 0.8018 (mmt)
REVERT: C  131 ARG cc_start: 0.8999 (mmm-85) cc_final: 0.8232 (mtm-85)
REVERT: D   84 MET cc_start: 0.8184 (tpp) cc_final: 0.7964 (tpp)
REVERT: D   88 TYR cc_start: 0.7451 (t80) cc_final: 0.7095 (t80)
REVERT: D   91 LYS cc_start: 0.8314 (tmtt) cc_final: 0.7589 (mtmm)
REVERT: E   73 GLU cc_start: 0.8511 (tm-30) cc_final: 0.8178 (tm-30)
REVERT: E   90 MET cc_start: 0.7967 (ttt) cc_final: 0.7284 (tmm)
REVERT: E   97 GLU cc_start: 0.8572 (mm-30) cc_final: 0.8069 (tt0)
REVERT: F   32 PRO cc_start: 0.9130 (Cg_exo) cc_final: 0.8866 (Cg_endo)
REVERT: F   53 GLU cc_start: 0.8283 (tp30) cc_final: 0.7988 (tp30)
REVERT: F   67 ARG cc_start: 0.8297 (ttm110) cc_final: 0.7759 (ttp-110)
REVERT: F   68 ASP cc_start: 0.8054 (m-30) cc_final: 0.7607 (t0)
REVERT: F   72 TYR cc_start: 0.7900 (m-10) cc_final: 0.7048 (m-10)
REVERT: F   79 LYS cc_start: 0.8919 (mttm) cc_final: 0.8246 (tptp)
REVERT: F   84 MET cc_start: 0.8052 (mmm) cc_final: 0.7598 (tpp)
REVERT: F   88 TYR cc_start: 0.8006 (m-10) cc_final: 0.7664 (m-10)
REVERT: F   91 LYS cc_start: 0.8404 (mttt) cc_final: 0.8024 (mtpt)
REVERT: F   92 ARG cc_start: 0.7945 (mpt180) cc_final: 0.7625 (mtt90)
REVERT: G   83 ARG cc_start: 0.8313 (mtm110) cc_final: 0.7955 (mtp85)
REVERT: G  107 THR cc_start: 0.9383 (m) cc_final: 0.9026 (p)
REVERT: G  120 MET cc_start: 0.8500 (mmm) cc_final: 0.7967 (mmt)
REVERT: H   52 GLU cc_start: 0.7779 (tm-30) cc_final: 0.7371 (tm-30)
  outliers start: 26
  outliers final: 11
  residues processed: 209
  average time/residue: 0.2756
  time to fit residues: 74.7473
Evaluate side-chains
  176 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 164
  time to evaluate  : 0.699 
-------------------------------------------------------------------------------
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 E residue   60 LEU
Chi-restraints excluded: chain E residue  101 VAL
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   47 SER
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 17 optimal weight:    1.9990
   chunk 6 optimal weight:    0.9980
   chunk 65 optimal weight:   10.0000
   chunk 40 optimal weight:   30.0000
   chunk 63 optimal weight:   10.0000
   chunk 52 optimal weight:    0.9980
   chunk 8 optimal weight:    0.8980
   chunk 41 optimal weight:    0.9990
   chunk 14 optimal weight:    9.9990
   chunk 71 optimal weight:   10.0000
   chunk 73 optimal weight:   10.0000
   overall best weight:    1.1784

-------------------------------------------------------------------------------
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
E 125 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.096438 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3128 r_free = 0.3128 target = 0.064677 restraints weight = 31682.873|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.066300 restraints weight = 18524.308|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.067347 restraints weight = 13657.825|
|-----------------------------------------------------------------------------|
r_work (final): 0.3155
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8081
moved from start:          0.4157

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  10426  Z= 0.205
  Angle     :  0.589   7.359  15097  Z= 0.346
  Chirality :  0.034   0.149   1724
  Planarity :  0.004   0.035   1074
  Dihedral  : 31.377 177.080   3290
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 11.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.55 %
    Favored  : 98.45 %
  Rotamer:
    Outliers :  5.93 %
    Allowed  : 28.66 %
    Favored  : 65.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.11 (0.34), residues: 580
  helix:  2.97 (0.23), residues: 450
  sheet:  None (None), residues: 0
  loop : -1.47 (0.41), residues: 130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.009   0.002   HIS D  75 
 PHE   0.008   0.001   PHE E  78 
 TYR   0.010   0.001   TYR B  88 
 ARG   0.006   0.000   ARG F  40 

*********************** 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
  208 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 178
  time to evaluate  : 0.716 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   87 SER cc_start: 0.9258 (m) cc_final: 0.8929 (t)
REVERT: A  120 MET cc_start: 0.8378 (mmm) cc_final: 0.8167 (mmm)
REVERT: B   52 GLU cc_start: 0.7829 (tm-30) cc_final: 0.7539 (tm-30)
REVERT: C   90 MET cc_start: 0.7619 (tpp) cc_final: 0.6807 (tpp)
REVERT: C  105 GLU cc_start: 0.8363 (mt-10) cc_final: 0.8001 (mt-10)
REVERT: C  108 ASN cc_start: 0.9198 (t0) cc_final: 0.8980 (t0)
REVERT: C  120 MET cc_start: 0.8235 (OUTLIER) cc_final: 0.7937 (mmt)
REVERT: C  131 ARG cc_start: 0.9014 (mmm-85) cc_final: 0.8228 (mtm-85)
REVERT: D   72 TYR cc_start: 0.7553 (m-10) cc_final: 0.7250 (m-10)
REVERT: D   74 GLU cc_start: 0.8543 (mm-30) cc_final: 0.8293 (mm-30)
REVERT: D   91 LYS cc_start: 0.8263 (tmtt) cc_final: 0.7684 (mtmm)
REVERT: E   73 GLU cc_start: 0.8525 (tm-30) cc_final: 0.8195 (tm-30)
REVERT: E   82 LEU cc_start: 0.8009 (OUTLIER) cc_final: 0.7757 (mm)
REVERT: E   90 MET cc_start: 0.8043 (ttt) cc_final: 0.7388 (tmm)
REVERT: E   97 GLU cc_start: 0.8514 (mm-30) cc_final: 0.8066 (tt0)
REVERT: E  120 MET cc_start: 0.8545 (mtp) cc_final: 0.8074 (mtp)
REVERT: F   32 PRO cc_start: 0.9127 (Cg_exo) cc_final: 0.8843 (Cg_endo)
REVERT: F   53 GLU cc_start: 0.8105 (tp30) cc_final: 0.7759 (tp30)
REVERT: F   68 ASP cc_start: 0.8052 (m-30) cc_final: 0.7591 (t70)
REVERT: F   72 TYR cc_start: 0.7926 (m-10) cc_final: 0.6983 (m-10)
REVERT: F   79 LYS cc_start: 0.8985 (mttm) cc_final: 0.8307 (tptp)
REVERT: F   84 MET cc_start: 0.8019 (mmm) cc_final: 0.7528 (tpp)
REVERT: F   88 TYR cc_start: 0.8069 (m-10) cc_final: 0.7740 (m-10)
REVERT: F   90 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8093 (tt)
REVERT: F   91 LYS cc_start: 0.8454 (mttt) cc_final: 0.8053 (mtpt)
REVERT: F   92 ARG cc_start: 0.7960 (mpt180) cc_final: 0.7619 (mtt90)
REVERT: G   83 ARG cc_start: 0.8334 (mtm110) cc_final: 0.7948 (mtp85)
REVERT: G   90 MET cc_start: 0.8842 (mmp) cc_final: 0.8243 (tpt)
REVERT: G  117 VAL cc_start: 0.9459 (OUTLIER) cc_final: 0.9243 (m)
REVERT: G  120 MET cc_start: 0.8588 (mmm) cc_final: 0.7817 (mmt)
REVERT: H   52 GLU cc_start: 0.7724 (tm-30) cc_final: 0.7287 (tm-30)
REVERT: H   79 LYS cc_start: 0.8598 (mttt) cc_final: 0.8370 (mtpp)
  outliers start: 30
  outliers final: 20
  residues processed: 192
  average time/residue: 0.2477
  time to fit residues: 63.3202
Evaluate side-chains
  186 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 162
  time to evaluate  : 0.800 
-------------------------------------------------------------------------------
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 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 C residue  120 MET
Chi-restraints excluded: chain D residue   64 ASN
Chi-restraints excluded: chain D residue   81 VAL
Chi-restraints excluded: chain D residue   90 LEU
Chi-restraints excluded: chain E residue   82 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   90 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 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   82 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 7 optimal weight:    4.9990
   chunk 32 optimal weight:    3.9990
   chunk 9 optimal weight:    0.8980
   chunk 64 optimal weight:   10.0000
   chunk 24 optimal weight:    0.7980
   chunk 19 optimal weight:    5.9990
   chunk 43 optimal weight:    0.9990
   chunk 48 optimal weight:    0.9980
   chunk 58 optimal weight:   10.0000
   chunk 50 optimal weight:    1.9990
   chunk 65 optimal weight:    7.9990
   overall best weight:    1.1384

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

Flipped N/Q/H residues before XYZ refinement:
C  93 GLN
D  75 HIS
E 125 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.096413 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.064831 restraints weight = 31586.887|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.066466 restraints weight = 18450.089|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.067531 restraints weight = 13575.921|
|-----------------------------------------------------------------------------|
r_work (final): 0.3160
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8072
moved from start:          0.4375

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= 0.206
  Angle     :  0.593   5.622  15097  Z= 0.348
  Chirality :  0.034   0.161   1724
  Planarity :  0.003   0.034   1074
  Dihedral  : 31.388 177.217   3290
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 11.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  6.72 %
    Allowed  : 30.04 %
    Favored  : 63.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.15 (0.34), residues: 580
  helix:  3.01 (0.24), residues: 450
  sheet:  None (None), residues: 0
  loop : -1.49 (0.41), residues: 130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.010   0.002   HIS D  75 
 PHE   0.008   0.001   PHE E  78 
 TYR   0.011   0.001   TYR E  99 
 ARG   0.004   0.000   ARG H  40 

*********************** 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
  216 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 182
  time to evaluate  : 0.694 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   87 SER cc_start: 0.9257 (m) cc_final: 0.8924 (t)
REVERT: A   97 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.7996 (tt0)
REVERT: B   52 GLU cc_start: 0.7774 (tm-30) cc_final: 0.7461 (tm-30)
REVERT: B   79 LYS cc_start: 0.8837 (mttm) cc_final: 0.8631 (tttt)
REVERT: C   90 MET cc_start: 0.7632 (tpp) cc_final: 0.7101 (tpp)
REVERT: C   93 GLN cc_start: 0.9104 (OUTLIER) cc_final: 0.8039 (tp40)
REVERT: C  105 GLU cc_start: 0.8357 (mt-10) cc_final: 0.7992 (mt-10)
REVERT: C  120 MET cc_start: 0.8177 (OUTLIER) cc_final: 0.7731 (mmt)
REVERT: D   53 GLU cc_start: 0.8102 (tt0) cc_final: 0.7883 (tt0)
REVERT: D   87 VAL cc_start: 0.8357 (t) cc_final: 0.8012 (p)
REVERT: D   88 TYR cc_start: 0.7107 (t80) cc_final: 0.6666 (t80)
REVERT: D   91 LYS cc_start: 0.8304 (tmtt) cc_final: 0.7742 (mtmt)
REVERT: E   73 GLU cc_start: 0.8546 (tm-30) cc_final: 0.8337 (tm-30)
REVERT: E   90 MET cc_start: 0.8110 (ttt) cc_final: 0.7596 (tpp)
REVERT: E   97 GLU cc_start: 0.8580 (mm-30) cc_final: 0.8112 (tt0)
REVERT: E  105 GLU cc_start: 0.8368 (mt-10) cc_final: 0.8144 (mt-10)
REVERT: F   32 PRO cc_start: 0.9113 (Cg_exo) cc_final: 0.8836 (Cg_endo)
REVERT: F   68 ASP cc_start: 0.8092 (m-30) cc_final: 0.7591 (t70)
REVERT: F   72 TYR cc_start: 0.7861 (m-10) cc_final: 0.6579 (m-10)
REVERT: F   84 MET cc_start: 0.8061 (mmm) cc_final: 0.7556 (tpp)
REVERT: F   88 TYR cc_start: 0.8050 (m-10) cc_final: 0.7608 (m-10)
REVERT: F   90 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8126 (tt)
REVERT: F   91 LYS cc_start: 0.8498 (mttt) cc_final: 0.8262 (mtpt)
REVERT: F   92 ARG cc_start: 0.7936 (mpt180) cc_final: 0.7509 (mtt90)
REVERT: G   83 ARG cc_start: 0.8328 (mtm110) cc_final: 0.7973 (mtp85)
REVERT: G  120 MET cc_start: 0.8605 (mmm) cc_final: 0.8363 (mmm)
REVERT: G  125 GLN cc_start: 0.8441 (mt0) cc_final: 0.8059 (mp10)
REVERT: H   52 GLU cc_start: 0.7745 (tm-30) cc_final: 0.7303 (tm-30)
  outliers start: 34
  outliers final: 25
  residues processed: 198
  average time/residue: 0.2592
  time to fit residues: 67.8244
Evaluate side-chains
  192 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 163
  time to evaluate  : 0.697 
-------------------------------------------------------------------------------
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  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   62 ILE
Chi-restraints excluded: chain C residue   87 SER
Chi-restraints excluded: chain C residue   93 GLN
Chi-restraints excluded: chain C residue  101 VAL
Chi-restraints excluded: chain C residue  120 MET
Chi-restraints excluded: chain D residue   30 THR
Chi-restraints excluded: chain D residue   49 LEU
Chi-restraints excluded: chain D residue   71 THR
Chi-restraints excluded: chain D residue   81 VAL
Chi-restraints excluded: chain D residue   90 LEU
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  100 LEU
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   82 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 2 optimal weight:    0.0570
   chunk 53 optimal weight:    3.9990
   chunk 14 optimal weight:   10.0000
   chunk 71 optimal weight:   10.0000
   chunk 48 optimal weight:    0.8980
   chunk 9 optimal weight:    2.9990
   chunk 37 optimal weight:    6.9990
   chunk 13 optimal weight:    0.9990
   chunk 32 optimal weight:    2.9990
   chunk 47 optimal weight:    0.9990
   chunk 65 optimal weight:    8.9990
   overall best weight:    1.1904

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

Flipped N/Q/H residues before XYZ refinement:
C  93 GLN
D  75 HIS
E 125 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.096083 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3136 r_free = 0.3136 target = 0.064868 restraints weight = 31126.553|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.066542 restraints weight = 17633.697|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.067566 restraints weight = 12760.377|
|-----------------------------------------------------------------------------|
r_work (final): 0.3168
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8059
moved from start:          0.4605

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= 0.210
  Angle     :  0.604   7.088  15097  Z= 0.350
  Chirality :  0.034   0.161   1724
  Planarity :  0.004   0.035   1074
  Dihedral  : 31.439 177.298   3290
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 11.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  7.31 %
    Allowed  : 30.43 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.06 (0.34), residues: 580
  helix:  2.96 (0.23), residues: 450
  sheet:  None (None), residues: 0
  loop : -1.61 (0.41), residues: 130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.011   0.002   HIS D  75 
 PHE   0.007   0.001   PHE A  67 
 TYR   0.013   0.001   TYR E  99 
 ARG   0.003   0.000   ARG D  92 

*********************** 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
  214 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 177
  time to evaluate  : 0.766 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   87 SER cc_start: 0.9247 (m) cc_final: 0.8911 (t)
REVERT: A  129 ARG cc_start: 0.8572 (ttm-80) cc_final: 0.8368 (ttm-80)
REVERT: B   52 GLU cc_start: 0.7764 (tm-30) cc_final: 0.7422 (tm-30)
REVERT: B   79 LYS cc_start: 0.8879 (mttm) cc_final: 0.8649 (tttt)
REVERT: C   90 MET cc_start: 0.7622 (tpp) cc_final: 0.7110 (tpp)
REVERT: C   93 GLN cc_start: 0.9093 (OUTLIER) cc_final: 0.8073 (tp40)
REVERT: C  105 GLU cc_start: 0.8362 (mt-10) cc_final: 0.7999 (mt-10)
REVERT: C  120 MET cc_start: 0.8298 (OUTLIER) cc_final: 0.7871 (mmt)
REVERT: D   53 GLU cc_start: 0.8214 (tt0) cc_final: 0.7984 (tt0)
REVERT: D   87 VAL cc_start: 0.8303 (t) cc_final: 0.7917 (p)
REVERT: D   88 TYR cc_start: 0.7271 (t80) cc_final: 0.6725 (t80)
REVERT: D   91 LYS cc_start: 0.8275 (tmtt) cc_final: 0.7653 (mtmm)
REVERT: E   90 MET cc_start: 0.8093 (ttt) cc_final: 0.7584 (tpp)
REVERT: E   97 GLU cc_start: 0.8480 (mm-30) cc_final: 0.8075 (tt0)
REVERT: E  105 GLU cc_start: 0.8371 (mt-10) cc_final: 0.8153 (mt-10)
REVERT: E  120 MET cc_start: 0.8368 (mtp) cc_final: 0.7890 (mtp)
REVERT: F   32 PRO cc_start: 0.9114 (Cg_exo) cc_final: 0.8843 (Cg_endo)
REVERT: F   68 ASP cc_start: 0.8101 (m-30) cc_final: 0.7625 (t70)
REVERT: F   72 TYR cc_start: 0.7867 (m-10) cc_final: 0.6494 (m-10)
REVERT: F   84 MET cc_start: 0.8072 (mmm) cc_final: 0.7522 (tpp)
REVERT: F   88 TYR cc_start: 0.8003 (m-10) cc_final: 0.7567 (m-10)
REVERT: F   90 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.8098 (tt)
REVERT: F   91 LYS cc_start: 0.8600 (mttt) cc_final: 0.8286 (mtpt)
REVERT: F   92 ARG cc_start: 0.7889 (mpt180) cc_final: 0.7383 (mtt90)
REVERT: G   83 ARG cc_start: 0.8343 (mtm110) cc_final: 0.7979 (mtp85)
REVERT: G   90 MET cc_start: 0.8825 (mmp) cc_final: 0.8214 (tpt)
REVERT: G  120 MET cc_start: 0.8585 (mmm) cc_final: 0.8349 (mmm)
REVERT: H   52 GLU cc_start: 0.7802 (tm-30) cc_final: 0.7338 (tm-30)
  outliers start: 37
  outliers final: 25
  residues processed: 195
  average time/residue: 0.2427
  time to fit residues: 62.7576
Evaluate side-chains
  194 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 166
  time to evaluate  : 0.712 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 GLN
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue   96 CYS
Chi-restraints excluded: chain A residue  124 ILE
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain B residue   86 VAL
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain C residue   87 SER
Chi-restraints excluded: chain C residue   93 GLN
Chi-restraints excluded: chain C residue  101 VAL
Chi-restraints excluded: chain C residue  120 MET
Chi-restraints excluded: chain D residue   30 THR
Chi-restraints excluded: chain D residue   49 LEU
Chi-restraints excluded: chain D residue   81 VAL
Chi-restraints excluded: chain D residue   90 LEU
Chi-restraints excluded: chain 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  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   82 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 48 optimal weight:    0.0040
   chunk 20 optimal weight:    0.8980
   chunk 16 optimal weight:    8.9990
   chunk 64 optimal weight:   10.0000
   chunk 24 optimal weight:    0.9990
   chunk 69 optimal weight:   10.0000
   chunk 35 optimal weight:    1.9990
   chunk 10 optimal weight:    0.7980
   chunk 39 optimal weight:    7.9990
   chunk 53 optimal weight:    3.9990
   chunk 60 optimal weight:   10.0000
   overall best weight:    0.9396

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

Flipped N/Q/H residues before XYZ refinement:
D  75 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.096603 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3143 r_free = 0.3143 target = 0.065312 restraints weight = 31768.524|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.066969 restraints weight = 18016.473|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.068051 restraints weight = 13031.981|
|-----------------------------------------------------------------------------|
r_work (final): 0.3182
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8046
moved from start:          0.4756

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= 0.205
  Angle     :  0.610   6.635  15097  Z= 0.353
  Chirality :  0.034   0.161   1724
  Planarity :  0.004   0.035   1074
  Dihedral  : 31.413 177.414   3290
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 11.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  6.32 %
    Allowed  : 32.41 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.99 (0.34), residues: 580
  helix:  2.89 (0.23), residues: 452
  sheet:  None (None), residues: 0
  loop : -1.64 (0.39), residues: 128

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.011   0.002   HIS D  75 
 PHE   0.006   0.001   PHE A  67 
 TYR   0.018   0.001   TYR E  99 
 ARG   0.006   0.000   ARG D  40 

*********************** 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
  198 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 166
  time to evaluate  : 0.721 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   87 SER cc_start: 0.9242 (m) cc_final: 0.8908 (t)
REVERT: A  120 MET cc_start: 0.8576 (mmm) cc_final: 0.8061 (mmt)
REVERT: B   52 GLU cc_start: 0.7718 (tm-30) cc_final: 0.7380 (tm-30)
REVERT: B   79 LYS cc_start: 0.8868 (mttm) cc_final: 0.8639 (tttt)
REVERT: C   90 MET cc_start: 0.7580 (tpp) cc_final: 0.7245 (tpp)
REVERT: C  105 GLU cc_start: 0.8319 (mt-10) cc_final: 0.7979 (mt-10)
REVERT: C  120 MET cc_start: 0.8241 (OUTLIER) cc_final: 0.7792 (mmt)
REVERT: D   91 LYS cc_start: 0.8247 (tmtt) cc_final: 0.7720 (mtmt)
REVERT: E   81 ASP cc_start: 0.7974 (t70) cc_final: 0.7448 (m-30)
REVERT: E   90 MET cc_start: 0.8028 (ttt) cc_final: 0.7611 (tpp)
REVERT: E   97 GLU cc_start: 0.8528 (mm-30) cc_final: 0.8146 (tt0)
REVERT: F   32 PRO cc_start: 0.9111 (Cg_exo) cc_final: 0.8848 (Cg_endo)
REVERT: F   68 ASP cc_start: 0.8059 (m-30) cc_final: 0.7076 (t70)
REVERT: F   84 MET cc_start: 0.8065 (mmm) cc_final: 0.7625 (tpp)
REVERT: F   88 TYR cc_start: 0.7958 (m-10) cc_final: 0.7372 (m-10)
REVERT: F   90 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.8091 (tt)
REVERT: F   91 LYS cc_start: 0.8586 (mttt) cc_final: 0.8288 (mtmt)
REVERT: G   83 ARG cc_start: 0.8319 (mtm110) cc_final: 0.7980 (mtp85)
REVERT: G   90 MET cc_start: 0.8859 (mmp) cc_final: 0.8272 (tpt)
REVERT: G  120 MET cc_start: 0.8595 (mmm) cc_final: 0.8039 (mmt)
REVERT: H   52 GLU cc_start: 0.7785 (tm-30) cc_final: 0.7327 (tm-30)
  outliers start: 32
  outliers final: 26
  residues processed: 182
  average time/residue: 0.2388
  time to fit residues: 58.5649
Evaluate side-chains
  185 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 157
  time to evaluate  : 0.739 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 GLN
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue   96 CYS
Chi-restraints excluded: chain A residue  124 ILE
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain C residue  101 VAL
Chi-restraints excluded: chain C residue  120 MET
Chi-restraints excluded: chain D residue   30 THR
Chi-restraints excluded: chain D residue   49 LEU
Chi-restraints excluded: chain D residue   81 VAL
Chi-restraints excluded: chain D residue   90 LEU
Chi-restraints excluded: chain 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   97 GLU
Chi-restraints excluded: chain G residue  100 LEU
Chi-restraints excluded: chain G residue  101 VAL
Chi-restraints excluded: chain G residue  117 VAL
Chi-restraints excluded: chain G residue  124 ILE
Chi-restraints excluded: chain H residue   62 LEU
Chi-restraints excluded: chain H residue   65 VAL
Chi-restraints excluded: chain H residue   81 VAL
Chi-restraints excluded: chain H residue   82 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 34 optimal weight:    0.6980
   chunk 32 optimal weight:    2.9990
   chunk 21 optimal weight:    0.6980
   chunk 60 optimal weight:   10.0000
   chunk 51 optimal weight:    1.9990
   chunk 49 optimal weight:    6.9990
   chunk 11 optimal weight:    1.9990
   chunk 5 optimal weight:    3.9990
   chunk 55 optimal weight:    1.9990
   chunk 45 optimal weight:    0.7980
   chunk 64 optimal weight:   10.0000
   overall best weight:    1.2384

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

Flipped N/Q/H residues before XYZ refinement:
** A 113 HIS ** 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 = 0.3828 r_free = 0.3828 target = 0.096197 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.064986 restraints weight = 31620.243|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.066654 restraints weight = 18007.024|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.067722 restraints weight = 13013.934|
|-----------------------------------------------------------------------------|
r_work (final): 0.3176
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8053
moved from start:          0.4871

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050  10426  Z= 0.215
  Angle     :  0.619   8.222  15097  Z= 0.356
  Chirality :  0.034   0.175   1724
  Planarity :  0.004   0.034   1074
  Dihedral  : 31.451 177.386   3290
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 11.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  6.52 %
    Allowed  : 31.82 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.04 (0.34), residues: 580
  helix:  2.97 (0.24), residues: 450
  sheet:  None (None), residues: 0
  loop : -1.69 (0.39), residues: 130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.012   0.002   HIS D  75 
 PHE   0.008   0.001   PHE A  67 
 TYR   0.017   0.002   TYR E  99 
 ARG   0.017   0.000   ARG F  92 

*********************** 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
  196 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 163
  time to evaluate  : 0.769 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   87 SER cc_start: 0.9280 (m) cc_final: 0.8953 (t)
REVERT: A  120 MET cc_start: 0.8562 (mmm) cc_final: 0.8203 (mmt)
REVERT: B   52 GLU cc_start: 0.7742 (tm-30) cc_final: 0.7386 (tm-30)
REVERT: B   79 LYS cc_start: 0.8876 (mttm) cc_final: 0.8650 (tttt)
REVERT: C   62 ILE cc_start: 0.8624 (OUTLIER) cc_final: 0.8256 (mt)
REVERT: C   90 MET cc_start: 0.7638 (tpp) cc_final: 0.7038 (tpp)
REVERT: C  105 GLU cc_start: 0.8329 (mt-10) cc_final: 0.7999 (mt-10)
REVERT: D   88 TYR cc_start: 0.6914 (t80) cc_final: 0.6633 (t80)
REVERT: D   91 LYS cc_start: 0.8273 (tmtt) cc_final: 0.7711 (mtmt)
REVERT: E   81 ASP cc_start: 0.7991 (t70) cc_final: 0.7368 (m-30)
REVERT: E   90 MET cc_start: 0.8015 (ttt) cc_final: 0.7613 (tpp)
REVERT: E   97 GLU cc_start: 0.8511 (mm-30) cc_final: 0.8089 (tt0)
REVERT: F   32 PRO cc_start: 0.9096 (Cg_exo) cc_final: 0.8805 (Cg_endo)
REVERT: F   68 ASP cc_start: 0.8351 (m-30) cc_final: 0.7919 (t70)
REVERT: F   84 MET cc_start: 0.8103 (mmm) cc_final: 0.7554 (tpp)
REVERT: F   88 TYR cc_start: 0.7836 (m-10) cc_final: 0.7310 (m-10)
REVERT: F   91 LYS cc_start: 0.8508 (mttt) cc_final: 0.8203 (mtmt)
REVERT: G   83 ARG cc_start: 0.8322 (mtm110) cc_final: 0.7998 (mtp85)
REVERT: G   90 MET cc_start: 0.8845 (mmp) cc_final: 0.8273 (tpt)
REVERT: G  120 MET cc_start: 0.8569 (mmm) cc_final: 0.8357 (mmm)
REVERT: H   52 GLU cc_start: 0.7805 (tm-30) cc_final: 0.7331 (tm-30)
  outliers start: 33
  outliers final: 27
  residues processed: 181
  average time/residue: 0.2370
  time to fit residues: 57.9849
Evaluate side-chains
  186 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 158
  time to evaluate  : 0.779 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue   96 CYS
Chi-restraints excluded: chain A residue  124 ILE
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue   65 VAL
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain B residue   86 VAL
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain D residue   30 THR
Chi-restraints excluded: chain D residue   49 LEU
Chi-restraints excluded: chain D residue   75 HIS
Chi-restraints excluded: chain D residue   81 VAL
Chi-restraints excluded: chain D residue   86 VAL
Chi-restraints excluded: chain D residue   90 LEU
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   97 GLU
Chi-restraints excluded: chain G residue  100 LEU
Chi-restraints excluded: chain G residue  101 VAL
Chi-restraints excluded: chain G residue  117 VAL
Chi-restraints excluded: chain G residue  126 LEU
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
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 2 optimal weight:    0.8980
   chunk 44 optimal weight:    0.9990
   chunk 18 optimal weight:    2.9990
   chunk 41 optimal weight:    0.9980
   chunk 16 optimal weight:    7.9990
   chunk 47 optimal weight:    5.9990
   chunk 3 optimal weight:    0.9990
   chunk 48 optimal weight:    2.9990
   chunk 1 optimal weight:    0.8980
   chunk 57 optimal weight:   10.0000
   chunk 51 optimal weight:    0.9990
   overall best weight:    0.9584

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

Flipped N/Q/H residues before XYZ refinement:
D  75 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.096760 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.066138 restraints weight = 31387.074|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.067746 restraints weight = 18073.668|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.068803 restraints weight = 13152.126|
|-----------------------------------------------------------------------------|
r_work (final): 0.3197
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8028
moved from start:          0.5013

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.063  10426  Z= 0.212
  Angle     :  0.622   8.010  15097  Z= 0.359
  Chirality :  0.034   0.154   1724
  Planarity :  0.004   0.035   1074
  Dihedral  : 31.428 177.477   3290
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 11.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.24 %
    Favored  : 97.76 %
  Rotamer:
    Outliers :  6.13 %
    Allowed  : 32.61 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.00 (0.34), residues: 580
  helix:  2.96 (0.24), residues: 450
  sheet:  None (None), residues: 0
  loop : -1.81 (0.39), residues: 130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.010   0.002   HIS D  75 
 PHE   0.006   0.001   PHE A  67 
 TYR   0.018   0.002   TYR E  99 
 ARG   0.007   0.000   ARG F  39 

*********************** 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
  199 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 168
  time to evaluate  : 0.776 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   87 SER cc_start: 0.9285 (m) cc_final: 0.8957 (t)
REVERT: A  120 MET cc_start: 0.8569 (mmm) cc_final: 0.8198 (mmt)
REVERT: B   52 GLU cc_start: 0.7702 (tm-30) cc_final: 0.7347 (tm-30)
REVERT: B   79 LYS cc_start: 0.8865 (mttm) cc_final: 0.8650 (tttt)
REVERT: C   90 MET cc_start: 0.7694 (tpp) cc_final: 0.7096 (tpp)
REVERT: C   97 GLU cc_start: 0.8268 (mm-30) cc_final: 0.8047 (tt0)
REVERT: C  105 GLU cc_start: 0.8333 (mt-10) cc_final: 0.7999 (mt-10)
REVERT: C  108 ASN cc_start: 0.9253 (t0) cc_final: 0.9037 (t0)
REVERT: C  120 MET cc_start: 0.8260 (OUTLIER) cc_final: 0.7682 (mmt)
REVERT: D   65 VAL cc_start: 0.8511 (p) cc_final: 0.8203 (p)
REVERT: D   88 TYR cc_start: 0.6847 (t80) cc_final: 0.6577 (t80)
REVERT: D   90 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8308 (mm)
REVERT: D   91 LYS cc_start: 0.8149 (tmtt) cc_final: 0.7609 (mtmt)
REVERT: E   81 ASP cc_start: 0.7862 (t70) cc_final: 0.7351 (m-30)
REVERT: E   90 MET cc_start: 0.7960 (ttt) cc_final: 0.7519 (tpp)
REVERT: E   97 GLU cc_start: 0.8479 (mm-30) cc_final: 0.8053 (tt0)
REVERT: F   32 PRO cc_start: 0.9089 (Cg_exo) cc_final: 0.8797 (Cg_endo)
REVERT: F   68 ASP cc_start: 0.8194 (m-30) cc_final: 0.7538 (t0)
REVERT: F   84 MET cc_start: 0.8103 (mmm) cc_final: 0.7563 (tpp)
REVERT: F   88 TYR cc_start: 0.7755 (m-10) cc_final: 0.7059 (m-10)
REVERT: F   91 LYS cc_start: 0.8360 (mttt) cc_final: 0.8056 (mtmt)
REVERT: F   92 ARG cc_start: 0.8054 (mtt90) cc_final: 0.7776 (ptm-80)
REVERT: G   83 ARG cc_start: 0.8312 (mtm110) cc_final: 0.8006 (mtp85)
REVERT: G   90 MET cc_start: 0.8862 (mmp) cc_final: 0.8294 (tpt)
REVERT: G  120 MET cc_start: 0.8508 (mmm) cc_final: 0.7989 (mmt)
REVERT: H   52 GLU cc_start: 0.7817 (tm-30) cc_final: 0.7347 (tm-30)
  outliers start: 31
  outliers final: 28
  residues processed: 185
  average time/residue: 0.2292
  time to fit residues: 57.5153
Evaluate side-chains
  195 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 165
  time to evaluate  : 0.781 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 GLN
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue   96 CYS
Chi-restraints excluded: chain A residue  124 ILE
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain B residue   47 SER
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue   65 VAL
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain B residue   86 VAL
Chi-restraints excluded: chain C residue  120 MET
Chi-restraints excluded: chain D residue   30 THR
Chi-restraints excluded: chain D residue   49 LEU
Chi-restraints excluded: chain D residue   60 VAL
Chi-restraints excluded: chain D residue   64 ASN
Chi-restraints excluded: chain D residue   75 HIS
Chi-restraints excluded: chain D residue   81 VAL
Chi-restraints excluded: chain D residue   90 LEU
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   97 GLU
Chi-restraints excluded: chain G residue  100 LEU
Chi-restraints excluded: chain G residue  101 VAL
Chi-restraints excluded: chain G residue  126 LEU
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
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 35 optimal weight:    7.9990
   chunk 70 optimal weight:   10.0000
   chunk 13 optimal weight:    0.9980
   chunk 26 optimal weight:    5.9990
   chunk 1 optimal weight:    5.9990
   chunk 24 optimal weight:    0.6980
   chunk 8 optimal weight:    0.7980
   chunk 50 optimal weight:    0.5980
   chunk 21 optimal weight:    0.4980
   chunk 11 optimal weight:    0.9990
   chunk 15 optimal weight:    4.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
D  75 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.097672 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.067003 restraints weight = 31253.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.068623 restraints weight = 18144.483|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.069633 restraints weight = 13197.693|
|-----------------------------------------------------------------------------|
r_work (final): 0.3216
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8009
moved from start:          0.5132

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.064  10426  Z= 0.201
  Angle     :  0.622  12.780  15097  Z= 0.356
  Chirality :  0.034   0.271   1724
  Planarity :  0.004   0.033   1074
  Dihedral  : 31.355 177.695   3290
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 11.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  5.34 %
    Allowed  : 33.40 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.00 (0.34), residues: 580
  helix:  2.95 (0.24), residues: 450
  sheet:  None (None), residues: 0
  loop : -1.77 (0.39), residues: 130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.007   0.002   HIS D  75 
 PHE   0.010   0.001   PHE G  78 
 TYR   0.023   0.002   TYR E  99 
 ARG   0.007   0.000   ARG F  39 

********************** 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: 27
    poor density    : 165
  time to evaluate  : 0.661 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   87 SER cc_start: 0.9281 (m) cc_final: 0.8944 (t)
REVERT: A  120 MET cc_start: 0.8403 (mmm) cc_final: 0.8040 (mmt)
REVERT: B   52 GLU cc_start: 0.7683 (tm-30) cc_final: 0.7333 (tm-30)
REVERT: B   79 LYS cc_start: 0.8835 (mttm) cc_final: 0.8604 (tttt)
REVERT: C   90 MET cc_start: 0.7632 (tpp) cc_final: 0.7267 (tpp)
REVERT: C   97 GLU cc_start: 0.8336 (mm-30) cc_final: 0.8075 (tt0)
REVERT: C  105 GLU cc_start: 0.8276 (mt-10) cc_final: 0.7958 (mt-10)
REVERT: C  108 ASN cc_start: 0.9205 (t0) cc_final: 0.8953 (t0)
REVERT: C  120 MET cc_start: 0.8283 (OUTLIER) cc_final: 0.7977 (mmt)
REVERT: D   88 TYR cc_start: 0.6737 (t80) cc_final: 0.6521 (t80)
REVERT: D   90 LEU cc_start: 0.8585 (OUTLIER) cc_final: 0.8362 (mm)
REVERT: D   91 LYS cc_start: 0.8152 (tmtt) cc_final: 0.7633 (mtmt)
REVERT: E   80 THR cc_start: 0.8401 (m) cc_final: 0.7996 (t)
REVERT: E   81 ASP cc_start: 0.7804 (t70) cc_final: 0.7299 (m-30)
REVERT: E   90 MET cc_start: 0.7961 (ttt) cc_final: 0.7581 (tpp)
REVERT: E   97 GLU cc_start: 0.8403 (mm-30) cc_final: 0.8003 (tt0)
REVERT: F   32 PRO cc_start: 0.9102 (Cg_exo) cc_final: 0.8811 (Cg_endo)
REVERT: F   68 ASP cc_start: 0.8210 (m-30) cc_final: 0.7576 (t0)
REVERT: F   74 GLU cc_start: 0.8728 (mm-30) cc_final: 0.8127 (tm-30)
REVERT: F   84 MET cc_start: 0.8025 (mmm) cc_final: 0.7596 (tpp)
REVERT: F   88 TYR cc_start: 0.7615 (m-10) cc_final: 0.6925 (m-10)
REVERT: F   90 LEU cc_start: 0.8545 (mm) cc_final: 0.7863 (tt)
REVERT: F   91 LYS cc_start: 0.8386 (mttt) cc_final: 0.8057 (mtmt)
REVERT: F   92 ARG cc_start: 0.8128 (mtt90) cc_final: 0.7795 (ptm-80)
REVERT: G   78 PHE cc_start: 0.8583 (m-10) cc_final: 0.8361 (m-10)
REVERT: G   83 ARG cc_start: 0.8287 (mtm110) cc_final: 0.7928 (mtp85)
REVERT: G   90 MET cc_start: 0.8841 (mmp) cc_final: 0.8267 (tpt)
REVERT: G  120 MET cc_start: 0.8456 (mmm) cc_final: 0.8023 (mmt)
REVERT: H   52 GLU cc_start: 0.7798 (tm-30) cc_final: 0.7323 (tm-30)
  outliers start: 27
  outliers final: 22
  residues processed: 178
  average time/residue: 0.2396
  time to fit residues: 57.4316
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  : 0.696 
-------------------------------------------------------------------------------
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   47 SER
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain C residue  120 MET
Chi-restraints excluded: chain D residue   30 THR
Chi-restraints excluded: chain D residue   64 ASN
Chi-restraints excluded: chain D residue   75 HIS
Chi-restraints excluded: chain D residue   81 VAL
Chi-restraints excluded: chain D residue   90 LEU
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   97 GLU
Chi-restraints excluded: chain G residue  101 VAL
Chi-restraints excluded: chain G residue  126 LEU
Chi-restraints excluded: chain H residue   49 LEU
Chi-restraints excluded: chain H residue   62 LEU
Chi-restraints excluded: chain H residue   65 VAL
Chi-restraints excluded: chain H residue   81 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 39 optimal weight:    9.9990
   chunk 40 optimal weight:    7.9990
   chunk 15 optimal weight:    4.9990
   chunk 29 optimal weight:    5.9990
   chunk 70 optimal weight:   10.0000
   chunk 12 optimal weight:    1.9990
   chunk 25 optimal weight:    3.9990
   chunk 51 optimal weight:    1.9990
   chunk 62 optimal weight:   10.0000
   chunk 37 optimal weight:    0.9980
   chunk 64 optimal weight:   10.0000
   overall best weight:    2.7988

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

Flipped N/Q/H residues before XYZ refinement:
D  75 HIS
G  68 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.093046 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3062 r_free = 0.3062 target = 0.061542 restraints weight = 31453.882|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3103 r_free = 0.3103 target = 0.063124 restraints weight = 18280.090|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3130 r_free = 0.3130 target = 0.064129 restraints weight = 13353.757|
|-----------------------------------------------------------------------------|
r_work (final): 0.3095
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8156
moved from start:          0.5278

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.086  10426  Z= 0.318
  Angle     :  0.683   8.999  15097  Z= 0.388
  Chirality :  0.037   0.312   1724
  Planarity :  0.004   0.042   1074
  Dihedral  : 31.790 176.557   3290
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 12.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  5.53 %
    Allowed  : 33.60 %
    Favored  : 60.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.73 (0.34), residues: 580
  helix:  2.76 (0.23), residues: 448
  sheet:  None (None), residues: 0
  loop : -1.80 (0.39), residues: 132

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.008   0.002   HIS A 113 
 PHE   0.014   0.002   PHE G  78 
 TYR   0.018   0.002   TYR E  99 
 ARG   0.006   0.001   ARG F  39 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2718.62 seconds
wall clock time: 49 minutes 20.64 seconds (2960.64 seconds total)