Starting phenix.real_space_refine
on Fri Mar 14 00:41:58 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7x58_33011/03_2025/7x58_33011.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7x58_33011/03_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_33011/03_2025/7x58_33011.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7x58_33011/03_2025/7x58_33011.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7x58_33011/03_2025/7x58_33011.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7x58_33011/03_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-5624/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: 5.57, per 1000 atoms: 0.57
  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: 2.68
  Conformation dependent library (CDL) restraints added in 766.1 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: 4.91
  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: 3.61

  Time building geometry restraints manager: 3.08 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:             0.260
  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:          0.380
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     28.330
  Find NCS groups from input model:        0.270
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.760
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.220
-------------------------------------------------------------------------------
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  : 0.790 
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: 0.3401
  time to fit residues: 121.0460
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  : 0.773 
-------------------------------------------------------------------------------
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 = 0.062342 restraints weight = 31559.053|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3113 r_free = 0.3113 target = 0.063860 restraints weight = 18721.086|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3138 r_free = 0.3138 target = 0.064841 restraints weight = 13907.704|
|-----------------------------------------------------------------------------|
r_work (final): 0.3102
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8143
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  : 0.689 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   73 GLU cc_start: 0.8961 (tm-30) cc_final: 0.8754 (tm-30)
REVERT: A   87 SER cc_start: 0.9380 (m) cc_final: 0.8969 (t)
REVERT: A  120 MET cc_start: 0.8461 (mmm) cc_final: 0.8210 (mmm)
REVERT: B   52 GLU cc_start: 0.8102 (tm-30) cc_final: 0.7881 (tm-30)
REVERT: C   90 MET cc_start: 0.7603 (tpp) cc_final: 0.7052 (tpp)
REVERT: C  105 GLU cc_start: 0.8356 (mt-10) cc_final: 0.8010 (mt-10)
REVERT: C  120 MET cc_start: 0.8418 (OUTLIER) cc_final: 0.8124 (mmt)
REVERT: D   52 GLU cc_start: 0.8508 (tm-30) cc_final: 0.8212 (tm-30)
REVERT: D   84 MET cc_start: 0.8291 (tpp) cc_final: 0.7962 (tpp)
REVERT: D   91 LYS cc_start: 0.8422 (tmtt) cc_final: 0.7767 (mtmm)
REVERT: E   73 GLU cc_start: 0.9127 (tm-30) cc_final: 0.8362 (tm-30)
REVERT: E   90 MET cc_start: 0.7842 (ttt) cc_final: 0.7370 (tmm)
REVERT: E  105 GLU cc_start: 0.8380 (mt-10) cc_final: 0.7839 (mt-10)
REVERT: F   32 PRO cc_start: 0.9166 (Cg_exo) cc_final: 0.8945 (Cg_endo)
REVERT: F   53 GLU cc_start: 0.8681 (tp30) cc_final: 0.8476 (tp30)
REVERT: F   74 GLU cc_start: 0.8880 (mm-30) cc_final: 0.8230 (tm-30)
REVERT: F   79 LYS cc_start: 0.9064 (mttm) cc_final: 0.8366 (tptp)
REVERT: F   84 MET cc_start: 0.8080 (mmm) cc_final: 0.7321 (tpp)
REVERT: F   91 LYS cc_start: 0.8644 (mttt) cc_final: 0.8069 (mtpt)
REVERT: G   90 MET cc_start: 0.8778 (mmp) cc_final: 0.8176 (tpt)
REVERT: G  120 MET cc_start: 0.8614 (mmm) cc_final: 0.8346 (mmm)
REVERT: H   52 GLU cc_start: 0.7952 (tm-30) cc_final: 0.7652 (tm-30)
  outliers start: 28
  outliers final: 16
  residues processed: 201
  average time/residue: 0.2767
  time to fit residues: 71.9001
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  : 0.753 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 72 optimal weight:   10.0000
   chunk 46 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9990
   chunk 30 optimal weight:    0.0980
   chunk 10 optimal weight:    1.9990
   chunk 2 optimal weight:    0.0770
   chunk 61 optimal weight:    8.9990
   chunk 32 optimal weight:    1.9990
   chunk 37 optimal weight:    5.9990
   chunk 54 optimal weight:    4.9990
   overall best weight:    1.0344

-------------------------------------------------------------------------------
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 = 0.3831 r_free = 0.3831 target = 0.096480 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.064917 restraints weight = 32041.779|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.066518 restraints weight = 19189.575|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 21)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.067554 restraints weight = 14238.294|
|-----------------------------------------------------------------------------|
r_work (final): 0.3155
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8080
moved from start:          0.3867

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= 0.199
  Angle     :  0.585   6.593  15097  Z= 0.347
  Chirality :  0.034   0.175   1724
  Planarity :  0.004   0.035   1074
  Dihedral  : 31.323 176.681   3290
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 11.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.38 %
    Favored  : 98.62 %
  Rotamer:
    Outliers :  6.32 %
    Allowed  : 24.70 %
    Favored  : 68.97 %
  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:  2.87 (0.23), residues: 450
  sheet:  None (None), residues: 0
  loop : -1.41 (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 C  78 
 TYR   0.009   0.001   TYR H  88 
 ARG   0.007   0.000   ARG D  92 

*********************** 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: 32
    poor density    : 193
  time to evaluate  : 0.799 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   87 SER cc_start: 0.9274 (m) cc_final: 0.8906 (t)
REVERT: A  120 MET cc_start: 0.8362 (mmm) cc_final: 0.7722 (mmm)
REVERT: A  125 GLN cc_start: 0.8548 (mt0) cc_final: 0.8229 (mp10)
REVERT: B   52 GLU cc_start: 0.7942 (tm-30) cc_final: 0.7610 (tm-30)
REVERT: C   90 MET cc_start: 0.7647 (tpp) cc_final: 0.6821 (tpp)
REVERT: C  105 GLU cc_start: 0.8404 (mt-10) cc_final: 0.8018 (mt-10)
REVERT: C  108 ASN cc_start: 0.9198 (t0) cc_final: 0.8938 (t0)
REVERT: C  120 MET cc_start: 0.8242 (OUTLIER) cc_final: 0.7998 (mmt)
REVERT: D   84 MET cc_start: 0.8193 (tpp) cc_final: 0.7978 (tpp)
REVERT: D   88 TYR cc_start: 0.7456 (t80) cc_final: 0.7107 (t80)
REVERT: D   91 LYS cc_start: 0.8320 (tmtt) cc_final: 0.7604 (mtmm)
REVERT: E   73 GLU cc_start: 0.8515 (tm-30) cc_final: 0.8185 (tm-30)
REVERT: E   90 MET cc_start: 0.8008 (ttt) cc_final: 0.7354 (tmm)
REVERT: E   97 GLU cc_start: 0.8584 (mm-30) cc_final: 0.8072 (tt0)
REVERT: F   32 PRO cc_start: 0.9131 (Cg_exo) cc_final: 0.8866 (Cg_endo)
REVERT: F   53 GLU cc_start: 0.8357 (tp30) cc_final: 0.7994 (tp30)
REVERT: F   67 ARG cc_start: 0.8289 (ttm110) cc_final: 0.7745 (ttp-110)
REVERT: F   68 ASP cc_start: 0.8063 (m-30) cc_final: 0.7610 (t0)
REVERT: F   72 TYR cc_start: 0.7915 (m-10) cc_final: 0.6795 (m-10)
REVERT: F   79 LYS cc_start: 0.8962 (mttm) cc_final: 0.8264 (tptp)
REVERT: F   84 MET cc_start: 0.8067 (mmm) cc_final: 0.7592 (tpp)
REVERT: F   88 TYR cc_start: 0.8027 (m-10) cc_final: 0.7676 (m-10)
REVERT: F   91 LYS cc_start: 0.8411 (mttt) cc_final: 0.8020 (mtpt)
REVERT: F   92 ARG cc_start: 0.8005 (mpt180) cc_final: 0.7581 (mtt90)
REVERT: G   83 ARG cc_start: 0.8335 (mtm110) cc_final: 0.7958 (mtp85)
REVERT: G  107 THR cc_start: 0.9403 (m) cc_final: 0.9035 (p)
REVERT: G  120 MET cc_start: 0.8582 (mmm) cc_final: 0.8019 (mmt)
REVERT: H   52 GLU cc_start: 0.7812 (tm-30) cc_final: 0.7382 (tm-30)
  outliers start: 32
  outliers final: 16
  residues processed: 207
  average time/residue: 0.2748
  time to fit residues: 73.9545
Evaluate side-chains
  179 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 162
  time to evaluate  : 0.710 
-------------------------------------------------------------------------------
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 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 E residue   60 LEU
Chi-restraints excluded: chain E residue  101 VAL
Chi-restraints excluded: chain F residue   29 ILE
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:    3.9990
   chunk 6 optimal weight:    3.9990
   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:    0.9990
   chunk 41 optimal weight:    0.9980
   chunk 14 optimal weight:   10.0000
   chunk 71 optimal weight:    9.9990
   chunk 73 optimal weight:   10.0000
   overall best weight:    2.1986

-------------------------------------------------------------------------------
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 = 0.3789 r_free = 0.3789 target = 0.094044 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3078 r_free = 0.3078 target = 0.062392 restraints weight = 31867.256|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.063917 restraints weight = 19199.469|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3143 r_free = 0.3143 target = 0.064917 restraints weight = 14343.055|
|-----------------------------------------------------------------------------|
r_work (final): 0.3099
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8143
moved from start:          0.4260

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= 0.255
  Angle     :  0.611   6.430  15097  Z= 0.357
  Chirality :  0.035   0.142   1724
  Planarity :  0.004   0.034   1074
  Dihedral  : 31.588 176.463   3290
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 11.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.72 %
    Favored  : 98.28 %
  Rotamer:
    Outliers :  6.92 %
    Allowed  : 27.08 %
    Favored  : 66.01 %
  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:  2.93 (0.33), residues: 580
  helix:  2.86 (0.23), residues: 450
  sheet:  None (None), residues: 0
  loop : -1.62 (0.40), residues: 130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.009   0.002   HIS D  75 
 PHE   0.010   0.002   PHE E 104 
 TYR   0.011   0.001   TYR B  88 
 ARG   0.005   0.001   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
  213 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 178
  time to evaluate  : 0.706 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   87 SER cc_start: 0.9325 (m) cc_final: 0.9018 (t)
REVERT: A  120 MET cc_start: 0.8450 (mmm) cc_final: 0.8172 (mmm)
REVERT: B   52 GLU cc_start: 0.7936 (tm-30) cc_final: 0.7601 (tm-30)
REVERT: B   79 LYS cc_start: 0.8898 (mttm) cc_final: 0.8666 (tttt)
REVERT: C   80 THR cc_start: 0.8357 (m) cc_final: 0.8141 (t)
REVERT: C   90 MET cc_start: 0.7612 (tpp) cc_final: 0.6844 (tpp)
REVERT: C  105 GLU cc_start: 0.8376 (mt-10) cc_final: 0.8030 (mt-10)
REVERT: C  131 ARG cc_start: 0.8920 (mmm-85) cc_final: 0.8362 (mtm-85)
REVERT: D   91 LYS cc_start: 0.8293 (tmtt) cc_final: 0.7676 (mtmm)
REVERT: E   73 GLU cc_start: 0.8520 (tm-30) cc_final: 0.8165 (tm-30)
REVERT: E   90 MET cc_start: 0.8115 (ttt) cc_final: 0.7421 (tmm)
REVERT: E   97 GLU cc_start: 0.8596 (mm-30) cc_final: 0.8164 (tt0)
REVERT: E  120 MET cc_start: 0.8619 (mtp) cc_final: 0.8160 (mtp)
REVERT: F   32 PRO cc_start: 0.9149 (Cg_exo) cc_final: 0.8885 (Cg_endo)
REVERT: F   68 ASP cc_start: 0.8131 (m-30) cc_final: 0.7613 (t70)
REVERT: F   72 TYR cc_start: 0.7981 (m-10) cc_final: 0.7022 (m-10)
REVERT: F   74 GLU cc_start: 0.8618 (mm-30) cc_final: 0.8019 (tm-30)
REVERT: F   79 LYS cc_start: 0.9037 (mttm) cc_final: 0.8322 (tptp)
REVERT: F   84 MET cc_start: 0.8056 (mmm) cc_final: 0.7480 (tpp)
REVERT: F   88 TYR cc_start: 0.8045 (m-10) cc_final: 0.7627 (m-10)
REVERT: F   90 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8188 (tt)
REVERT: F   91 LYS cc_start: 0.8541 (mttt) cc_final: 0.8150 (mtpt)
REVERT: F   92 ARG cc_start: 0.7988 (mpt180) cc_final: 0.7604 (mtt90)
REVERT: G   83 ARG cc_start: 0.8324 (mtm110) cc_final: 0.7944 (mtp85)
REVERT: G   90 MET cc_start: 0.8869 (mmp) cc_final: 0.8310 (tpt)
REVERT: G  107 THR cc_start: 0.9296 (m) cc_final: 0.8992 (p)
REVERT: G  120 MET cc_start: 0.8692 (mmm) cc_final: 0.7893 (mmt)
REVERT: H   52 GLU cc_start: 0.7854 (tm-30) cc_final: 0.7374 (tm-30)
REVERT: H   92 ARG cc_start: 0.7950 (tmm160) cc_final: 0.7720 (tmm160)
  outliers start: 35
  outliers final: 25
  residues processed: 193
  average time/residue: 0.2387
  time to fit residues: 61.3166
Evaluate side-chains
  188 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 162
  time to evaluate  : 0.679 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 GLN
Chi-restraints excluded: chain A residue   96 CYS
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue   86 VAL
Chi-restraints excluded: chain C residue   62 ILE
Chi-restraints excluded: chain C residue  101 VAL
Chi-restraints excluded: chain D residue   64 ASN
Chi-restraints excluded: chain D residue   75 HIS
Chi-restraints excluded: chain D residue   81 VAL
Chi-restraints excluded: chain D residue   86 VAL
Chi-restraints excluded: chain D residue   90 LEU
Chi-restraints excluded: chain E residue   74 ILE
Chi-restraints excluded: chain E residue  101 VAL
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain F residue   70 VAL
Chi-restraints excluded: chain F residue   81 VAL
Chi-restraints excluded: chain F residue   86 VAL
Chi-restraints excluded: chain F residue   90 LEU
Chi-restraints excluded: chain G residue   65 LEU
Chi-restraints excluded: chain G residue   76 GLN
Chi-restraints excluded: chain G residue   96 CYS
Chi-restraints excluded: chain G residue  100 LEU
Chi-restraints excluded: chain G residue  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
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 7 optimal weight:    0.5980
   chunk 32 optimal weight:    3.9990
   chunk 9 optimal weight:    0.8980
   chunk 64 optimal weight:   10.0000
   chunk 24 optimal weight:    0.9990
   chunk 19 optimal weight:    6.9990
   chunk 43 optimal weight:    0.9980
   chunk 48 optimal weight:    0.9990
   chunk 58 optimal weight:    9.9990
   chunk 50 optimal weight:    1.9990
   chunk 65 optimal weight:    8.9990
   overall best weight:    0.8984

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.095479 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3119 r_free = 0.3119 target = 0.064049 restraints weight = 30898.962|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.065700 restraints weight = 17633.990|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.066763 restraints weight = 12845.477|
|-----------------------------------------------------------------------------|
r_work (final): 0.3153
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8072
moved from start:          0.4394

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= 0.200
  Angle     :  0.594   6.014  15097  Z= 0.350
  Chirality :  0.034   0.167   1724
  Planarity :  0.004   0.032   1074
  Dihedral  : 31.468 176.846   3290
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 11.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.72 %
    Favored  : 98.28 %
  Rotamer:
    Outliers :  6.13 %
    Allowed  : 30.43 %
    Favored  : 63.44 %
  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:  2.93 (0.24), residues: 450
  sheet:  None (None), residues: 0
  loop : -1.47 (0.41), residues: 130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.018   0.002   HIS D  75 
 PHE   0.007   0.001   PHE A  67 
 TYR   0.008   0.001   TYR H  88 
 ARG   0.005   0.000   ARG F  39 

*********************** 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
  218 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 187
  time to evaluate  : 0.889 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   87 SER cc_start: 0.9232 (m) cc_final: 0.8920 (t)
REVERT: A   90 MET cc_start: 0.8409 (tpt) cc_final: 0.8176 (tpt)
REVERT: B   52 GLU cc_start: 0.7860 (tm-30) cc_final: 0.7526 (tm-30)
REVERT: C   90 MET cc_start: 0.7676 (tpp) cc_final: 0.6930 (tpp)
REVERT: C   92 LEU cc_start: 0.8880 (tt) cc_final: 0.8678 (tt)
REVERT: C   93 GLN cc_start: 0.9116 (OUTLIER) cc_final: 0.8072 (tp40)
REVERT: C  105 GLU cc_start: 0.8344 (mt-10) cc_final: 0.7976 (mt-10)
REVERT: D   87 VAL cc_start: 0.8371 (t) cc_final: 0.7970 (p)
REVERT: D   88 TYR cc_start: 0.7337 (t80) cc_final: 0.7119 (t80)
REVERT: D   91 LYS cc_start: 0.8275 (tmtt) cc_final: 0.7661 (mtmm)
REVERT: E   73 GLU cc_start: 0.8560 (tm-30) cc_final: 0.8238 (tm-30)
REVERT: E   90 MET cc_start: 0.8128 (ttt) cc_final: 0.7583 (tpp)
REVERT: E   97 GLU cc_start: 0.8597 (mm-30) cc_final: 0.8092 (tt0)
REVERT: E  105 GLU cc_start: 0.8386 (mt-10) cc_final: 0.8163 (mt-10)
REVERT: F   32 PRO cc_start: 0.9087 (Cg_exo) cc_final: 0.8811 (Cg_endo)
REVERT: F   53 GLU cc_start: 0.8459 (mt-10) cc_final: 0.8157 (tt0)
REVERT: F   68 ASP cc_start: 0.8079 (m-30) cc_final: 0.7603 (t70)
REVERT: F   72 TYR cc_start: 0.7921 (m-10) cc_final: 0.6623 (m-10)
REVERT: F   74 GLU cc_start: 0.8575 (mm-30) cc_final: 0.8012 (tm-30)
REVERT: F   79 LYS cc_start: 0.8993 (mttm) cc_final: 0.8299 (tptp)
REVERT: F   84 MET cc_start: 0.8095 (mmm) cc_final: 0.7596 (tpp)
REVERT: F   88 TYR cc_start: 0.8062 (m-10) cc_final: 0.7636 (m-10)
REVERT: F   90 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8149 (tt)
REVERT: F   91 LYS cc_start: 0.8569 (mttt) cc_final: 0.8307 (mtpt)
REVERT: F   92 ARG cc_start: 0.7886 (mpt180) cc_final: 0.7481 (mtt90)
REVERT: G   83 ARG cc_start: 0.8302 (mtm110) cc_final: 0.7952 (mtp85)
REVERT: G   90 MET cc_start: 0.8892 (mmp) cc_final: 0.8299 (tpt)
REVERT: G  107 THR cc_start: 0.9249 (m) cc_final: 0.8975 (p)
REVERT: G  120 MET cc_start: 0.8645 (mmm) cc_final: 0.7985 (mmt)
REVERT: H   52 GLU cc_start: 0.7779 (tm-30) cc_final: 0.7324 (tm-30)
  outliers start: 31
  outliers final: 20
  residues processed: 203
  average time/residue: 0.2622
  time to fit residues: 70.2519
Evaluate side-chains
  191 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 169
  time to evaluate  : 0.829 
-------------------------------------------------------------------------------
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 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   93 GLN
Chi-restraints excluded: chain C residue  101 VAL
Chi-restraints excluded: chain D residue   30 THR
Chi-restraints excluded: chain D residue   81 VAL
Chi-restraints excluded: chain D residue   90 LEU
Chi-restraints excluded: chain E residue  101 VAL
Chi-restraints excluded: chain F residue   29 ILE
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  101 VAL
Chi-restraints excluded: chain G residue  124 ILE
Chi-restraints excluded: chain H residue   62 LEU
Chi-restraints excluded: chain H residue   81 VAL
Chi-restraints excluded: chain H residue   82 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 2 optimal weight:    0.1980
   chunk 53 optimal weight:    4.9990
   chunk 14 optimal weight:   10.0000
   chunk 71 optimal weight:   10.0000
   chunk 48 optimal weight:    0.0030
   chunk 9 optimal weight:    0.8980
   chunk 37 optimal weight:    0.9990
   chunk 13 optimal weight:    0.6980
   chunk 32 optimal weight:    1.9990
   chunk 47 optimal weight:    0.9990
   chunk 65 optimal weight:    8.9990
   overall best weight:    0.5592

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.096570 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.065285 restraints weight = 31126.352|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.066956 restraints weight = 17732.231|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.068035 restraints weight = 12853.951|
|-----------------------------------------------------------------------------|
r_work (final): 0.3184
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8045
moved from start:          0.4612

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= 0.190
  Angle     :  0.600   7.962  15097  Z= 0.349
  Chirality :  0.034   0.162   1724
  Planarity :  0.003   0.030   1074
  Dihedral  : 31.406 177.306   3290
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 10.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.72 %
    Favored  : 98.28 %
  Rotamer:
    Outliers :  4.74 %
    Allowed  : 32.41 %
    Favored  : 62.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  2.98 (0.34), residues: 580
  helix:  2.89 (0.23), residues: 450
  sheet:  None (None), residues: 0
  loop : -1.56 (0.41), residues: 130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS A 113 
 PHE   0.008   0.001   PHE E  78 
 TYR   0.011   0.001   TYR B  88 
 ARG   0.004   0.000   ARG D  78 

*********************** 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
  210 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 186
  time to evaluate  : 0.729 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   87 SER cc_start: 0.9226 (m) cc_final: 0.8903 (t)
REVERT: A   90 MET cc_start: 0.8350 (tpt) cc_final: 0.8147 (tpt)
REVERT: A  129 ARG cc_start: 0.8490 (ttm-80) cc_final: 0.8282 (ttm-80)
REVERT: B   52 GLU cc_start: 0.7753 (tm-30) cc_final: 0.7394 (tm-30)
REVERT: C   90 MET cc_start: 0.7615 (tpp) cc_final: 0.7046 (tpp)
REVERT: C   92 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8708 (tt)
REVERT: C  105 GLU cc_start: 0.8239 (mt-10) cc_final: 0.7905 (mt-10)
REVERT: D   53 GLU cc_start: 0.8163 (tt0) cc_final: 0.7916 (tt0)
REVERT: D   77 LYS cc_start: 0.8772 (tptt) cc_final: 0.8556 (tmmt)
REVERT: D   87 VAL cc_start: 0.8365 (t) cc_final: 0.7975 (p)
REVERT: D   91 LYS cc_start: 0.8249 (tmtt) cc_final: 0.7725 (mtmt)
REVERT: E   73 GLU cc_start: 0.8582 (tm-30) cc_final: 0.8250 (tm-30)
REVERT: E   90 MET cc_start: 0.8101 (ttt) cc_final: 0.7604 (tpp)
REVERT: E   97 GLU cc_start: 0.8442 (mm-30) cc_final: 0.8072 (tt0)
REVERT: F   32 PRO cc_start: 0.9112 (Cg_exo) cc_final: 0.8835 (Cg_endo)
REVERT: F   53 GLU cc_start: 0.8346 (mt-10) cc_final: 0.8126 (tt0)
REVERT: F   68 ASP cc_start: 0.8057 (m-30) cc_final: 0.7046 (t70)
REVERT: F   79 LYS cc_start: 0.8928 (mttm) cc_final: 0.8321 (tptp)
REVERT: F   84 MET cc_start: 0.8073 (mmm) cc_final: 0.7716 (tpp)
REVERT: F   88 TYR cc_start: 0.7981 (m-10) cc_final: 0.7469 (m-10)
REVERT: F   90 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.8058 (tt)
REVERT: F   91 LYS cc_start: 0.8576 (mttt) cc_final: 0.8327 (mtpt)
REVERT: G   83 ARG cc_start: 0.8262 (mtm110) cc_final: 0.7994 (mtp85)
REVERT: H   52 GLU cc_start: 0.7777 (tm-30) cc_final: 0.7317 (tm-30)
  outliers start: 24
  outliers final: 19
  residues processed: 196
  average time/residue: 0.2588
  time to fit residues: 66.9332
Evaluate side-chains
  191 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 170
  time to evaluate  : 0.704 
-------------------------------------------------------------------------------
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  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   87 SER
Chi-restraints excluded: chain C residue   92 LEU
Chi-restraints excluded: chain D residue   30 THR
Chi-restraints excluded: chain D residue   81 VAL
Chi-restraints excluded: chain D residue   90 LEU
Chi-restraints excluded: chain F residue   81 VAL
Chi-restraints excluded: chain F residue   90 LEU
Chi-restraints excluded: chain G residue   76 GLN
Chi-restraints excluded: chain G residue  101 VAL
Chi-restraints excluded: chain G residue  117 VAL
Chi-restraints excluded: chain G residue  124 ILE
Chi-restraints excluded: chain H residue   62 LEU
Chi-restraints excluded: chain H residue   81 VAL
Chi-restraints excluded: chain H residue   82 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 48 optimal weight:    0.9980
   chunk 20 optimal weight:    0.7980
   chunk 16 optimal weight:    0.0980
   chunk 64 optimal weight:   10.0000
   chunk 24 optimal weight:    2.9990
   chunk 69 optimal weight:   10.0000
   chunk 35 optimal weight:    1.9990
   chunk 10 optimal weight:    0.7980
   chunk 39 optimal weight:    0.3980
   chunk 53 optimal weight:    0.5980
   chunk 60 optimal weight:   10.0000
   overall best weight:    0.5380

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.097632 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.066302 restraints weight = 32345.882|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.068018 restraints weight = 18633.274|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.069173 restraints weight = 13485.836|
|-----------------------------------------------------------------------------|
r_work (final): 0.3200
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8028
moved from start:          0.4804

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= 0.195
  Angle     :  0.613   6.883  15097  Z= 0.353
  Chirality :  0.034   0.166   1724
  Planarity :  0.004   0.032   1074
  Dihedral  : 31.363 177.638   3290
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 11.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.24 %
    Favored  : 97.76 %
  Rotamer:
    Outliers :  4.35 %
    Allowed  : 33.79 %
    Favored  : 61.86 %
  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:  3.07 (0.34), residues: 580
  helix:  2.95 (0.23), residues: 450
  sheet:  None (None), residues: 0
  loop : -1.55 (0.40), residues: 130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS D  75 
 PHE   0.006   0.001   PHE G  67 
 TYR   0.012   0.001   TYR D  88 
 ARG   0.016   0.000   ARG F  92 

*********************** 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
  197 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 175
  time to evaluate  : 0.786 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   87 SER cc_start: 0.9226 (m) cc_final: 0.8895 (t)
REVERT: A  120 MET cc_start: 0.8598 (mmm) cc_final: 0.8340 (mmm)
REVERT: B   52 GLU cc_start: 0.7712 (tm-30) cc_final: 0.7359 (tm-30)
REVERT: C   62 ILE cc_start: 0.8653 (mt) cc_final: 0.8087 (mt)
REVERT: C   90 MET cc_start: 0.7622 (tpp) cc_final: 0.7305 (tpp)
REVERT: C  105 GLU cc_start: 0.8270 (mt-10) cc_final: 0.7982 (mt-10)
REVERT: D   53 GLU cc_start: 0.8159 (tt0) cc_final: 0.7925 (tt0)
REVERT: D   77 LYS cc_start: 0.8755 (tptt) cc_final: 0.8537 (tmmt)
REVERT: D   88 TYR cc_start: 0.6963 (t80) cc_final: 0.6536 (t80)
REVERT: D   91 LYS cc_start: 0.8237 (tmtt) cc_final: 0.7681 (mtmt)
REVERT: E   73 GLU cc_start: 0.8575 (tm-30) cc_final: 0.8257 (tm-30)
REVERT: E   90 MET cc_start: 0.7999 (ttt) cc_final: 0.7590 (tpp)
REVERT: E   97 GLU cc_start: 0.8486 (mm-30) cc_final: 0.8085 (tt0)
REVERT: F   32 PRO cc_start: 0.9070 (Cg_exo) cc_final: 0.8771 (Cg_endo)
REVERT: F   53 GLU cc_start: 0.8326 (mt-10) cc_final: 0.7904 (mt-10)
REVERT: F   68 ASP cc_start: 0.8328 (m-30) cc_final: 0.7835 (t0)
REVERT: F   74 GLU cc_start: 0.8611 (mm-30) cc_final: 0.8003 (tm-30)
REVERT: F   79 LYS cc_start: 0.8878 (mttm) cc_final: 0.8299 (tptp)
REVERT: F   84 MET cc_start: 0.8124 (mmm) cc_final: 0.7601 (tpp)
REVERT: F   88 TYR cc_start: 0.7860 (m-10) cc_final: 0.7315 (m-10)
REVERT: F   90 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.7947 (tt)
REVERT: F   91 LYS cc_start: 0.8334 (mttt) cc_final: 0.8026 (mtmt)
REVERT: G   78 PHE cc_start: 0.8750 (m-80) cc_final: 0.8411 (m-10)
REVERT: G   83 ARG cc_start: 0.8223 (mtm110) cc_final: 0.7960 (mtp85)
REVERT: G   90 MET cc_start: 0.8805 (mmp) cc_final: 0.8202 (tpt)
REVERT: H   52 GLU cc_start: 0.7744 (tm-30) cc_final: 0.7274 (tm-30)
  outliers start: 22
  outliers final: 18
  residues processed: 185
  average time/residue: 0.2299
  time to fit residues: 57.9596
Evaluate side-chains
  184 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 165
  time to evaluate  : 0.763 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 THR
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 D residue   30 THR
Chi-restraints excluded: chain D residue   81 VAL
Chi-restraints excluded: chain D residue   90 LEU
Chi-restraints excluded: chain E residue  109 LEU
Chi-restraints excluded: chain F residue   70 VAL
Chi-restraints excluded: chain F residue   81 VAL
Chi-restraints excluded: chain F residue   90 LEU
Chi-restraints excluded: chain G residue   76 GLN
Chi-restraints excluded: chain G residue   97 GLU
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 34 optimal weight:    0.2980
   chunk 32 optimal weight:    3.9990
   chunk 21 optimal weight:    3.9990
   chunk 60 optimal weight:   10.0000
   chunk 51 optimal weight:    3.9990
   chunk 49 optimal weight:    0.9980
   chunk 11 optimal weight:    1.9990
   chunk 5 optimal weight:    6.9990
   chunk 55 optimal weight:    5.9990
   chunk 45 optimal weight:    0.3980
   chunk 64 optimal weight:   10.0000
   overall best weight:    1.5384

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

Flipped N/Q/H residues before XYZ refinement:
C  76 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.095585 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3125 r_free = 0.3125 target = 0.064331 restraints weight = 31530.931|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.065991 restraints weight = 18016.830|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.067059 restraints weight = 13025.633|
|-----------------------------------------------------------------------------|
r_work (final): 0.3159
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8069
moved from start:          0.4973

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= 0.227
  Angle     :  0.612   6.903  15097  Z= 0.355
  Chirality :  0.034   0.158   1724
  Planarity :  0.004   0.035   1074
  Dihedral  : 31.528 177.335   3290
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 11.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  5.14 %
    Allowed  : 33.20 %
    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:  3.12 (0.34), residues: 580
  helix:  3.02 (0.24), residues: 448
  sheet:  None (None), residues: 0
  loop : -1.58 (0.39), residues: 132

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS A 113 
 PHE   0.009   0.001   PHE E 104 
 TYR   0.010   0.001   TYR D  88 
 ARG   0.005   0.000   ARG D  40 

*********************** 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
  191 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 165
  time to evaluate  : 0.724 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   87 SER cc_start: 0.9309 (m) cc_final: 0.8984 (t)
REVERT: A  120 MET cc_start: 0.8471 (mmm) cc_final: 0.7953 (mmt)
REVERT: B   52 GLU cc_start: 0.7881 (tm-30) cc_final: 0.7526 (tm-30)
REVERT: C   90 MET cc_start: 0.7630 (tpp) cc_final: 0.7283 (tpp)
REVERT: C  105 GLU cc_start: 0.8396 (mt-10) cc_final: 0.8058 (mt-10)
REVERT: D   77 LYS cc_start: 0.8705 (tptt) cc_final: 0.8497 (tmmt)
REVERT: D   91 LYS cc_start: 0.8313 (tmtt) cc_final: 0.7725 (mtmt)
REVERT: E   73 GLU cc_start: 0.8679 (tm-30) cc_final: 0.8427 (tm-30)
REVERT: E   90 MET cc_start: 0.8108 (ttt) cc_final: 0.7625 (tpp)
REVERT: E   97 GLU cc_start: 0.8484 (mm-30) cc_final: 0.8030 (tt0)
REVERT: F   32 PRO cc_start: 0.9093 (Cg_exo) cc_final: 0.8815 (Cg_endo)
REVERT: F   68 ASP cc_start: 0.8260 (m-30) cc_final: 0.7678 (t70)
REVERT: F   74 GLU cc_start: 0.8728 (mm-30) cc_final: 0.8131 (tm-30)
REVERT: F   79 LYS cc_start: 0.8874 (mttm) cc_final: 0.8356 (tptp)
REVERT: F   84 MET cc_start: 0.8119 (mmm) cc_final: 0.7531 (tpp)
REVERT: F   88 TYR cc_start: 0.7795 (m-10) cc_final: 0.7082 (m-10)
REVERT: F   91 LYS cc_start: 0.8464 (mttt) cc_final: 0.8155 (mtmt)
REVERT: F   92 ARG cc_start: 0.8234 (mtt90) cc_final: 0.7854 (ptm-80)
REVERT: G   83 ARG cc_start: 0.8273 (mtm110) cc_final: 0.7949 (mtp85)
REVERT: G   90 MET cc_start: 0.8828 (mmp) cc_final: 0.8262 (tpt)
REVERT: H   52 GLU cc_start: 0.7848 (tm-30) cc_final: 0.7379 (tm-30)
  outliers start: 26
  outliers final: 22
  residues processed: 179
  average time/residue: 0.2244
  time to fit residues: 54.7387
Evaluate side-chains
  184 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 162
  time to evaluate  : 0.795 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 GLN
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue   96 CYS
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain B residue   86 VAL
Chi-restraints excluded: chain D residue   30 THR
Chi-restraints excluded: chain D residue   81 VAL
Chi-restraints excluded: chain D residue   90 LEU
Chi-restraints excluded: chain E residue  109 LEU
Chi-restraints excluded: chain F residue   29 ILE
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain F residue   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 H residue   47 SER
Chi-restraints excluded: chain H residue   62 LEU
Chi-restraints excluded: chain H residue   81 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 2 optimal weight:    1.9990
   chunk 44 optimal weight:    0.7980
   chunk 18 optimal weight:    0.9980
   chunk 41 optimal weight:    4.9990
   chunk 16 optimal weight:   30.0000
   chunk 47 optimal weight:    0.8980
   chunk 3 optimal weight:    1.9990
   chunk 48 optimal weight:    0.8980
   chunk 1 optimal weight:    1.9990
   chunk 57 optimal weight:   10.0000
   chunk 51 optimal weight:    1.9990
   overall best weight:    1.1182

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.096204 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3138 r_free = 0.3138 target = 0.064930 restraints weight = 31367.167|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.066605 restraints weight = 18013.740|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.067658 restraints weight = 13045.699|
|-----------------------------------------------------------------------------|
r_work (final): 0.3172
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8051
moved from start:          0.5106

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  10426  Z= 0.215
  Angle     :  0.625   8.947  15097  Z= 0.359
  Chirality :  0.034   0.158   1724
  Planarity :  0.004   0.031   1074
  Dihedral  : 31.450 177.369   3290
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 11.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  4.74 %
    Allowed  : 34.78 %
    Favored  : 60.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  2.93 (0.24), residues: 450
  sheet:  None (None), residues: 0
  loop : -1.55 (0.40), residues: 130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS A 113 
 PHE   0.007   0.001   PHE A  67 
 TYR   0.012   0.001   TYR D  88 
 ARG   0.005   0.000   ARG D  40 

*********************** 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
  193 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 169
  time to evaluate  : 0.781 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   87 SER cc_start: 0.9303 (m) cc_final: 0.8985 (t)
REVERT: A  120 MET cc_start: 0.8472 (mmm) cc_final: 0.7997 (mmt)
REVERT: B   52 GLU cc_start: 0.7814 (tm-30) cc_final: 0.7462 (tm-30)
REVERT: C   90 MET cc_start: 0.7599 (tpp) cc_final: 0.7219 (tpp)
REVERT: C   97 GLU cc_start: 0.8709 (mm-30) cc_final: 0.8098 (tt0)
REVERT: C  105 GLU cc_start: 0.8342 (mt-10) cc_final: 0.7839 (mt-10)
REVERT: D   77 LYS cc_start: 0.8735 (tptt) cc_final: 0.8512 (mmmt)
REVERT: D   91 LYS cc_start: 0.8318 (tmtt) cc_final: 0.7693 (mtmt)
REVERT: E   73 GLU cc_start: 0.8706 (tm-30) cc_final: 0.8467 (tm-30)
REVERT: E   90 MET cc_start: 0.8093 (ttt) cc_final: 0.7687 (tpp)
REVERT: E   97 GLU cc_start: 0.8496 (mm-30) cc_final: 0.8038 (tt0)
REVERT: F   27 GLN cc_start: 0.8597 (mm-40) cc_final: 0.8055 (tp-100)
REVERT: F   32 PRO cc_start: 0.9077 (Cg_exo) cc_final: 0.8791 (Cg_endo)
REVERT: F   68 ASP cc_start: 0.8267 (m-30) cc_final: 0.7622 (t0)
REVERT: F   74 GLU cc_start: 0.8638 (mm-30) cc_final: 0.8117 (tm-30)
REVERT: F   79 LYS cc_start: 0.8802 (mttm) cc_final: 0.8314 (tptp)
REVERT: F   84 MET cc_start: 0.8038 (mmm) cc_final: 0.7583 (tpp)
REVERT: F   88 TYR cc_start: 0.7726 (m-10) cc_final: 0.7003 (m-10)
REVERT: F   90 LEU cc_start: 0.8664 (mm) cc_final: 0.7942 (tt)
REVERT: F   91 LYS cc_start: 0.8422 (mttt) cc_final: 0.8076 (mtmt)
REVERT: F   92 ARG cc_start: 0.8177 (mtt90) cc_final: 0.7888 (ptm-80)
REVERT: G   78 PHE cc_start: 0.8772 (m-80) cc_final: 0.8470 (m-10)
REVERT: G   83 ARG cc_start: 0.8281 (mtm110) cc_final: 0.7949 (mtp85)
REVERT: G   90 MET cc_start: 0.8838 (mmp) cc_final: 0.8284 (tpt)
REVERT: H   52 GLU cc_start: 0.7857 (tm-30) cc_final: 0.7377 (tm-30)
  outliers start: 24
  outliers final: 21
  residues processed: 182
  average time/residue: 0.2320
  time to fit residues: 57.5002
Evaluate side-chains
  183 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 162
  time to evaluate  : 0.589 
-------------------------------------------------------------------------------
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   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 D residue   30 THR
Chi-restraints excluded: chain D residue   60 VAL
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   81 VAL
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 G residue  126 LEU
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 35 optimal weight:    8.9990
   chunk 70 optimal weight:   10.0000
   chunk 13 optimal weight:    0.5980
   chunk 26 optimal weight:   40.0000
   chunk 1 optimal weight:    2.9990
   chunk 24 optimal weight:    0.9980
   chunk 8 optimal weight:    0.1980
   chunk 50 optimal weight:    0.9980
   chunk 21 optimal weight:    3.9990
   chunk 11 optimal weight:    0.7980
   chunk 15 optimal weight:    0.8980
   overall best weight:    0.6980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.097728 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.066645 restraints weight = 32010.395|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.068313 restraints weight = 18533.483|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.069414 restraints weight = 13444.993|
|-----------------------------------------------------------------------------|
r_work (final): 0.3200
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8024
moved from start:          0.5289

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  10426  Z= 0.201
  Angle     :  0.620   8.404  15097  Z= 0.356
  Chirality :  0.034   0.175   1724
  Planarity :  0.004   0.029   1074
  Dihedral  : 31.337 177.717   3290
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 11.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  4.35 %
    Allowed  : 35.57 %
    Favored  : 60.08 %
  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:  2.97 (0.33), residues: 580
  helix:  2.86 (0.23), residues: 450
  sheet:  None (None), residues: 0
  loop : -1.51 (0.41), residues: 130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS A 113 
 PHE   0.009   0.001   PHE A  67 
 TYR   0.008   0.001   TYR D  88 
 ARG   0.005   0.000   ARG D  40 

********************** 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
  190 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 168
  time to evaluate  : 0.688 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   87 SER cc_start: 0.9291 (m) cc_final: 0.8971 (t)
REVERT: B   52 GLU cc_start: 0.7763 (tm-30) cc_final: 0.7409 (tm-30)
REVERT: C   90 MET cc_start: 0.7554 (tpp) cc_final: 0.7178 (tpp)
REVERT: C   97 GLU cc_start: 0.8632 (mm-30) cc_final: 0.8041 (tt0)
REVERT: C  105 GLU cc_start: 0.8325 (mt-10) cc_final: 0.7815 (mt-10)
REVERT: D   79 LYS cc_start: 0.7699 (tptp) cc_final: 0.7031 (tmtt)
REVERT: D   91 LYS cc_start: 0.8289 (tmtt) cc_final: 0.7617 (mtmt)
REVERT: E   74 ILE cc_start: 0.9241 (mt) cc_final: 0.8638 (tt)
REVERT: E   90 MET cc_start: 0.8047 (ttt) cc_final: 0.7560 (tpp)
REVERT: E   97 GLU cc_start: 0.8344 (mm-30) cc_final: 0.7952 (tt0)
REVERT: F   27 GLN cc_start: 0.8521 (mm-40) cc_final: 0.8013 (tp-100)
REVERT: F   32 PRO cc_start: 0.9124 (Cg_exo) cc_final: 0.8837 (Cg_endo)
REVERT: F   68 ASP cc_start: 0.8228 (m-30) cc_final: 0.7626 (t0)
REVERT: F   74 GLU cc_start: 0.8617 (mm-30) cc_final: 0.8093 (tm-30)
REVERT: F   79 LYS cc_start: 0.8747 (mttm) cc_final: 0.8310 (tptp)
REVERT: F   84 MET cc_start: 0.7988 (mmm) cc_final: 0.7504 (tpp)
REVERT: F   88 TYR cc_start: 0.7633 (m-10) cc_final: 0.6842 (m-10)
REVERT: F   90 LEU cc_start: 0.8600 (mm) cc_final: 0.7880 (tt)
REVERT: F   91 LYS cc_start: 0.8402 (mttt) cc_final: 0.8060 (mtmt)
REVERT: F   92 ARG cc_start: 0.8186 (mtt90) cc_final: 0.7881 (ptm-80)
REVERT: G   83 ARG cc_start: 0.8231 (mtm110) cc_final: 0.7984 (mtp85)
REVERT: G   90 MET cc_start: 0.8838 (mmp) cc_final: 0.8262 (tpt)
REVERT: H   52 GLU cc_start: 0.7811 (tm-30) cc_final: 0.7340 (tm-30)
  outliers start: 22
  outliers final: 20
  residues processed: 179
  average time/residue: 0.2289
  time to fit residues: 55.9868
Evaluate side-chains
  182 residues out of total 506 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 162
  time to evaluate  : 0.676 
-------------------------------------------------------------------------------
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   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 D residue   30 THR
Chi-restraints excluded: chain D residue   60 VAL
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   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  117 VAL
Chi-restraints excluded: chain G residue  126 LEU
Chi-restraints excluded: chain H residue   47 SER
Chi-restraints excluded: chain H residue   62 LEU
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:    1.9990
   chunk 40 optimal weight:    0.9980
   chunk 15 optimal weight:    5.9990
   chunk 29 optimal weight:    6.9990
   chunk 70 optimal weight:   10.0000
   chunk 12 optimal weight:    0.8980
   chunk 25 optimal weight:   10.0000
   chunk 51 optimal weight:    1.9990
   chunk 62 optimal weight:   10.0000
   chunk 37 optimal weight:   10.0000
   chunk 64 optimal weight:   10.0000
   overall best weight:    2.3786

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.093789 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3088 r_free = 0.3088 target = 0.062637 restraints weight = 31345.898|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3130 r_free = 0.3130 target = 0.064223 restraints weight = 17756.373|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.065272 restraints weight = 12831.122|
|-----------------------------------------------------------------------------|
r_work (final): 0.3120
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8118
moved from start:          0.5356

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.055  10426  Z= 0.284
  Angle     :  0.659  10.140  15097  Z= 0.376
  Chirality :  0.035   0.163   1724
  Planarity :  0.004   0.041   1074
  Dihedral  : 31.698 176.823   3290
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 12.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  4.74 %
    Allowed  : 34.58 %
    Favored  : 60.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  2.91 (0.34), residues: 580
  helix:  2.86 (0.24), residues: 448
  sheet:  None (None), residues: 0
  loop : -1.63 (0.39), residues: 132

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS A 113 
 PHE   0.011   0.002   PHE E 104 
 TYR   0.009   0.001   TYR H  88 
 ARG   0.005   0.001   ARG D  35 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2761.94 seconds
wall clock time: 48 minutes 33.19 seconds (2913.19 seconds total)