Starting phenix.real_space_refine
on Tue Jul 29 23:28:58 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6t93_10408/07_2025/6t93_10408.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6t93_10408/07_2025/6t93_10408.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.49
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6t93_10408/07_2025/6t93_10408.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6t93_10408/07_2025/6t93_10408.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6t93_10408/07_2025/6t93_10408.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6t93_10408/07_2025/6t93_10408.cif"
  }
  resolution = 3.49
  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=   0.003 sd=   0.051
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     300      5.49       5
     S      14      5.16       5
     C    6730      2.51       5
     N    2287      2.21       5
     O    2868      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 24 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 12199
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 790
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 96, 790
          Classifications: {'peptide': 96}
          Link IDs: {'PTRANS': 3, 'TRANS': 92}
    Chain: "B"
      Number of atoms: 646
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 81, 646
          Classifications: {'peptide': 81}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 79}
    Chain: "C"
      Number of atoms: 835
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 835
          Classifications: {'peptide': 108}
          Link IDs: {'PTRANS': 5, 'TRANS': 102}
    Chain: "D"
      Number of atoms: 736
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 736
          Classifications: {'peptide': 94}
          Link IDs: {'PTRANS': 2, 'TRANS': 91}
    Chain: "E"
      Number of atoms: 790
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 96, 790
          Classifications: {'peptide': 96}
          Link IDs: {'PTRANS': 3, 'TRANS': 92}
    Chain: "F"
      Number of atoms: 646
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 81, 646
          Classifications: {'peptide': 81}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 79}
    Chain: "G"
      Number of atoms: 835
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 835
          Classifications: {'peptide': 108}
          Link IDs: {'PTRANS': 5, 'TRANS': 102}
    Chain: "H"
      Number of atoms: 736
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 736
          Classifications: {'peptide': 94}
          Link IDs: {'PTRANS': 2, 'TRANS': 91}
    Chain: "I"
      Number of atoms: 3072
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 151, 3072
          Classifications: {'DNA': 151}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 150}
    Chain: "J"
      Number of atoms: 3113
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 151, 3113
          Classifications: {'DNA': 151}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 150}
  Time building chain proxies: 7.66, per 1000 atoms: 0.63
  Number of scatterers: 12199
  At special positions: 0
  Unit cell: (73.96, 121.26, 117.82, 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      14     16.00
     P     300     15.00
     O    2868      8.00
     N    2287      7.00
     C    6730      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: 3.94
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1412

  Finding SS restraints...
    Secondary structure from input PDB file:
      35 helices and 10 sheets defined
      70.7% alpha, 2.9% beta
      151 base pairs and 279 stacking pairs defined.
    Time for finding SS restraints: 6.59
  Creating SS restraints...
    Processing helix  chain 'A' and resid 45 through 58
    Processing helix  chain 'A' and resid 64 through 77
    Processing helix  chain 'A' and resid 86 through 115
    Processing helix  chain 'A' and resid 121 through 132
      removed outlier: 3.502A  pdb=" N   ILE A 125 " --> pdb=" O   MET A 121 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 26 through 30
    Processing helix  chain 'B' and resid 31 through 42
    Processing helix  chain 'B' and resid 50 through 77
    Processing helix  chain 'B' and resid 83 through 93
    Processing helix  chain 'C' and resid 17 through 23
      removed outlier: 3.717A  pdb=" N   ARG C  21 " --> pdb=" O   THR C  17 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 28 through 37
    Processing helix  chain 'C' and resid 47 through 74
    Processing helix  chain 'C' and resid 80 through 90
    Processing helix  chain 'C' and resid 91 through 98
    Processing helix  chain 'C' and resid 113 through 117
    Processing helix  chain 'D' and resid 38 through 50
    Processing helix  chain 'D' and resid 56 through 85
    Processing helix  chain 'D' and resid 91 through 103
    Processing helix  chain 'D' and resid 104 through 125
    Processing helix  chain 'E' and resid 45 through 58
      removed outlier: 3.530A  pdb=" N   ARG E  50 " --> pdb=" O   THR E  46 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 64 through 77
      removed outlier: 3.699A  pdb=" N   PHE E  68 " --> pdb=" O   ARG E  64 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 86 through 115
    Processing helix  chain 'E' and resid 121 through 132
    Processing helix  chain 'F' and resid 31 through 42
    Processing helix  chain 'F' and resid 50 through 77
      removed outlier: 3.598A  pdb=" N   GLU F  54 " --> pdb=" O   LEU F  50 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 83 through 93
      removed outlier: 3.519A  pdb=" N   ARG F  93 " --> pdb=" O   TYR F  89 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 17 through 22
      removed outlier: 3.571A  pdb=" N   ARG G  21 " --> pdb=" O   THR G  17 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 28 through 37
    Processing helix  chain 'G' and resid 47 through 73
    Processing helix  chain 'G' and resid 80 through 91
    Processing helix  chain 'G' and resid 93 through 98
    Processing helix  chain 'G' and resid 113 through 117
    Processing helix  chain 'H' and resid 38 through 48
    Processing helix  chain 'H' and resid 56 through 85
    Processing helix  chain 'H' and resid 91 through 103
    Processing helix  chain 'H' and resid 104 through 125
      removed outlier: 3.535A  pdb=" N   HIS H 110 " --> pdb=" O   GLU H 106 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 84 through 85
      removed outlier: 7.007A  pdb=" N   ARG A  84 " --> pdb=" O   VAL B  82 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 119 through 120
    Processing sheet with id=AA3, first strand: chain 'B' and resid 98 through 99
    Processing sheet with id=AA4, first strand: chain 'C' and resid 43 through 44
      removed outlier: 7.190A  pdb=" N   ARG C  43 " --> pdb=" O   ILE D  90 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'C' and resid 78 through 79
    Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 103
    Processing sheet with id=AA7, first strand: chain 'E' and resid 84 through 85
      removed outlier: 6.887A  pdb=" N   ARG E  84 " --> pdb=" O   VAL F  82 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'E' and resid 119 through 120
    Processing sheet with id=AA9, first strand: chain 'G' and resid 43 through 44
      removed outlier: 7.000A  pdb=" N   ARG G  43 " --> pdb=" O   ILE H  90 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'G' and resid 78 through 79

    398 hydrogen bonds defined for protein.
    1176 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      380 hydrogen bonds
      760 hydrogen bond angles
      0 basepair planarities
      151 basepair parallelities
      279 stacking parallelities
  Total time for adding SS restraints: 6.31

  Time building geometry restraints manager: 3.68 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1888
        1.32 -     1.44: 4716
        1.44 -     1.57: 5804
        1.57 -     1.69: 600
        1.69 -     1.81: 24
  Bond restraints: 13032
  Sorted by residual:
  bond pdb=" CD  ARG E 129 "
       pdb=" NE  ARG E 129 "
    ideal  model  delta    sigma   weight residual
    1.458  1.395  0.063 1.40e-02 5.10e+03 2.05e+01
  bond pdb=" CD  ARG D 100 "
       pdb=" NE  ARG D 100 "
    ideal  model  delta    sigma   weight residual
    1.458  1.395  0.063 1.40e-02 5.10e+03 2.03e+01
  bond pdb=" CD  ARG B  93 "
       pdb=" NE  ARG B  93 "
    ideal  model  delta    sigma   weight residual
    1.458  1.395  0.063 1.40e-02 5.10e+03 2.00e+01
  bond pdb=" CD  ARG A 129 "
       pdb=" NE  ARG A 129 "
    ideal  model  delta    sigma   weight residual
    1.458  1.396  0.062 1.40e-02 5.10e+03 1.96e+01
  bond pdb=" CD  ARG F  93 "
       pdb=" NE  ARG F  93 "
    ideal  model  delta    sigma   weight residual
    1.458  1.398  0.060 1.40e-02 5.10e+03 1.86e+01
  ... (remaining 13027 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.88: 17023
        1.88 -     3.76: 1660
        3.76 -     5.64: 173
        5.64 -     7.51: 32
        7.51 -     9.39: 5
  Bond angle restraints: 18893
  Sorted by residual:
  angle pdb=" C   HIS D  50 "
        pdb=" N   PRO D  51 "
        pdb=" CA  PRO D  51 "
      ideal   model   delta    sigma   weight residual
     119.56  127.54   -7.98 1.02e+00 9.61e-01 6.12e+01
  angle pdb=" C   HIS H  50 "
        pdb=" N   PRO H  51 "
        pdb=" CA  PRO H  51 "
      ideal   model   delta    sigma   weight residual
     119.56  127.23   -7.67 1.02e+00 9.61e-01 5.66e+01
  angle pdb=" C   LEU D 103 "
        pdb=" N   PRO D 104 "
        pdb=" CA  PRO D 104 "
      ideal   model   delta    sigma   weight residual
     119.78  126.98   -7.20 1.03e+00 9.43e-01 4.88e+01
  angle pdb=" C   PHE C  26 "
        pdb=" N   PRO C  27 "
        pdb=" CA  PRO C  27 "
      ideal   model   delta    sigma   weight residual
     119.76  126.26   -6.50 1.00e+00 1.00e+00 4.22e+01
  angle pdb=" C   ILE G  80 "
        pdb=" N   PRO G  81 "
        pdb=" CA  PRO G  81 "
      ideal   model   delta    sigma   weight residual
     119.32  126.49   -7.17 1.14e+00 7.69e-01 3.95e+01
  ... (remaining 18888 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.25: 5714
       34.25 -    68.50: 1356
       68.50 -   102.75: 12
      102.75 -   137.00: 0
      137.00 -   171.25: 4
  Dihedral angle restraints: 7086
    sinusoidal: 4894
      harmonic: 2192
  Sorted by residual:
  dihedral pdb=" C4'  DT J  89 "
           pdb=" C3'  DT J  89 "
           pdb=" O3'  DT J  89 "
           pdb=" P    DA J  90 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   48.75  171.25     1      3.50e+01 8.16e-04 1.56e+01
  dihedral pdb=" C4'  DT J  15 "
           pdb=" C3'  DT J  15 "
           pdb=" O3'  DT J  15 "
           pdb=" P    DC J  16 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   56.09  163.91     1      3.50e+01 8.16e-04 1.54e+01
  dihedral pdb=" C4'  DG I   3 "
           pdb=" C3'  DG I   3 "
           pdb=" O3'  DG I   3 "
           pdb=" P    DG I   4 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   63.58  156.42     1      3.50e+01 8.16e-04 1.50e+01
  ... (remaining 7083 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.063: 1519
       0.063 -    0.127: 549
       0.127 -    0.190: 70
       0.190 -    0.253: 6
       0.253 -    0.317: 2
  Chirality restraints: 2146
  Sorted by residual:
  chirality pdb=" CA  LYS F  32 "
            pdb=" N   LYS F  32 "
            pdb=" C   LYS F  32 "
            pdb=" CB  LYS F  32 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.19    0.32 2.00e-01 2.50e+01 2.50e+00
  chirality pdb=" CA  LEU A  66 "
            pdb=" N   LEU A  66 "
            pdb=" C   LEU A  66 "
            pdb=" CB  LEU A  66 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.24    0.27 2.00e-01 2.50e+01 1.89e+00
  chirality pdb=" CA  LYS B  32 "
            pdb=" N   LYS B  32 "
            pdb=" C   LYS B  32 "
            pdb=" CB  LYS B  32 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.26    0.25 2.00e-01 2.50e+01 1.60e+00
  ... (remaining 2143 not shown)

  Planarity restraints: 1346
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS G  37 "   -0.020 2.00e-02 2.50e+03   3.98e-02 1.59e+01
        pdb=" C   LYS G  37 "    0.069 2.00e-02 2.50e+03
        pdb=" O   LYS G  37 "   -0.026 2.00e-02 2.50e+03
        pdb=" N   GLY G  38 "   -0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR F  52 "    0.055 2.00e-02 2.50e+03   2.79e-02 1.55e+01
        pdb=" CG  TYR F  52 "   -0.039 2.00e-02 2.50e+03
        pdb=" CD1 TYR F  52 "   -0.026 2.00e-02 2.50e+03
        pdb=" CD2 TYR F  52 "   -0.017 2.00e-02 2.50e+03
        pdb=" CE1 TYR F  52 "    0.003 2.00e-02 2.50e+03
        pdb=" CE2 TYR F  52 "   -0.007 2.00e-02 2.50e+03
        pdb=" CZ  TYR F  52 "    0.009 2.00e-02 2.50e+03
        pdb=" OH  TYR F  52 "    0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY B 103 "   -0.019 2.00e-02 2.50e+03   3.90e-02 1.52e+01
        pdb=" C   GLY B 103 "    0.067 2.00e-02 2.50e+03
        pdb=" O   GLY B 103 "   -0.024 2.00e-02 2.50e+03
        pdb=" OXT GLY B 103 "   -0.024 2.00e-02 2.50e+03
  ... (remaining 1343 not shown)

  Histogram of nonbonded interaction distances:
        2.43 -     2.93: 4776
        2.93 -     3.42: 10638
        3.42 -     3.91: 24618
        3.91 -     4.41: 29004
        4.41 -     4.90: 36678
  Nonbonded interactions: 105714
  Sorted by model distance:
  nonbonded pdb=" NZ  LYS F  60 "
            pdb=" OE2 GLU F  64 "
     model   vdw
     2.435 3.120
  nonbonded pdb=" O   ARG A  43 "
            pdb=" OG1 THR A  46 "
     model   vdw
     2.481 3.040
  nonbonded pdb=" N   GLY C  38 "
            pdb=" N   ASN C  39 "
     model   vdw
     2.491 2.560
  nonbonded pdb=" N   GLY G  38 "
            pdb=" N   ASN G  39 "
     model   vdw
     2.493 2.560
  nonbonded pdb=" N   ASP D  52 "
            pdb=" OD1 ASP D  52 "
     model   vdw
     2.497 3.120
  ... (remaining 105709 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 'E'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'F'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'G'
}
ncs_group {
  reference = chain 'D'
  selection = chain 'H'
}

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=0.00 max=1.00 mean=0.99
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.040
  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:          0.530
  Check model and map are aligned:         0.100
  Set scattering table:                    0.120
  Process input model:                     35.950
  Find NCS groups from input model:        0.250
  Set up NCS constraints:                  0.090
  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:3.790
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   41.890
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8366
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      :  0.014   0.118  13032  Z= 0.728
  Angle     :  1.153   9.394  18893  Z= 0.772
  Chirality :  0.062   0.317   2146
  Planarity :  0.010   0.069   1346
  Dihedral  : 27.104 171.253   5674
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 0.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.27 %
    Favored  : 99.73 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.16 %
    Favored  : 99.84 %
  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:  0.78 (0.26), residues: 742
  helix:  0.67 (0.19), residues: 528
  sheet:  None (None), residues: 0
  loop :  0.50 (0.36), residues: 214

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.013   0.003   HIS H  50 
 PHE   0.032   0.007   PHE D  71 
 TYR   0.055   0.011   TYR F  52 
 ARG   0.016   0.002   ARG B  37 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.16604 (  778)
  hydrogen bonds       : angle       5.31406 ( 1936)
  covalent geometry    : bond        0.01445 (13032)
  covalent geometry    : angle       1.15255 (18893)

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

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

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  308 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 308
  time to evaluate  : 0.975 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   75 ILE cc_start: 0.9462 (mt) cc_final: 0.9125 (mm)
REVERT: A   77 GLN cc_start: 0.8200 (pt0) cc_final: 0.7993 (pp30)
REVERT: A   82 ASP cc_start: 0.8647 (m-30) cc_final: 0.8388 (m-30)
REVERT: A  114 HIS cc_start: 0.8772 (t70) cc_final: 0.8462 (t-90)
REVERT: B   24 ARG cc_start: 0.8295 (mtm110) cc_final: 0.8031 (ppt170)
REVERT: B   97 THR cc_start: 0.8583 (m) cc_final: 0.8379 (p)
REVERT: C   74 ASN cc_start: 0.8984 (m-40) cc_final: 0.8406 (t0)
REVERT: C  102 THR cc_start: 0.8968 (m) cc_final: 0.8690 (p)
REVERT: D   35 LYS cc_start: 0.8194 (mmtt) cc_final: 0.7583 (mmtm)
REVERT: D   52 ASP cc_start: 0.8489 (p0) cc_final: 0.8131 (p0)
REVERT: D   60 MET cc_start: 0.9081 (tpp) cc_final: 0.8869 (tpp)
REVERT: D   72 GLU cc_start: 0.8212 (mm-30) cc_final: 0.7934 (tp30)
REVERT: D   80 ARG cc_start: 0.8635 (mtm-85) cc_final: 0.8274 (mtm-85)
REVERT: E  104 LEU cc_start: 0.9483 (tp) cc_final: 0.9220 (tp)
REVERT: E  121 MET cc_start: 0.8348 (mmm) cc_final: 0.8148 (mmm)
REVERT: G   37 LYS cc_start: 0.7759 (mttm) cc_final: 0.7536 (mttp)
REVERT: G  105 GLN cc_start: 0.8637 (mp10) cc_final: 0.8409 (mp10)
REVERT: G  119 LYS cc_start: 0.8693 (pttt) cc_final: 0.8380 (tppt)
REVERT: H   80 ARG cc_start: 0.8980 (mtm-85) cc_final: 0.8187 (mtm-85)
  outliers start: 0
  outliers final: 0
  residues processed: 308
  average time/residue: 0.3223
  time to fit residues: 136.5049
Evaluate side-chains
  227 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 227
  time to evaluate  : 1.643 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 86 optimal weight:    8.9990
   chunk 77 optimal weight:    2.9990
   chunk 42 optimal weight:    0.9990
   chunk 26 optimal weight:    5.9990
   chunk 52 optimal weight:    1.9990
   chunk 41 optimal weight:    0.9990
   chunk 79 optimal weight:    5.9990
   chunk 30 optimal weight:    0.9990
   chunk 48 optimal weight:    0.9990
   chunk 59 optimal weight:    0.0770
   chunk 92 optimal weight:    5.9990
   overall best weight:    0.8146

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

Flipped N/Q/H residues before XYZ refinement:
A  40 HIS
** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  85 GLN
D 110 HIS
E  40 HIS
E  77 GLN
G  69 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.074014 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3056 r_free = 0.3056 target = 0.055756 restraints weight = 43991.668|
|-----------------------------------------------------------------------------|
r_work (start): 0.3018 rms_B_bonded: 2.43
r_work: 0.2859 rms_B_bonded: 4.45 restraints_weight: 0.5000
r_work (final): 0.2859
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8486
moved from start:          0.2606

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049  13032  Z= 0.176
  Angle     :  0.640   7.933  18893  Z= 0.379
  Chirality :  0.037   0.178   2146
  Planarity :  0.005   0.037   1346
  Dihedral  : 30.286 179.252   4172
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 8.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.13 %
    Favored  : 99.87 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 15.24 %
    Favored  : 82.22 %
  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:  3.03 (0.29), residues: 742
  helix:  2.58 (0.21), residues: 538
  sheet:  None (None), residues: 0
  loop :  0.49 (0.37), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.008   0.001   HIS B  76 
 PHE   0.012   0.002   PHE A  68 
 TYR   0.016   0.002   TYR H  41 
 ARG   0.004   0.001   ARG G  36 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05814 (  778)
  hydrogen bonds       : angle       3.14049 ( 1936)
  covalent geometry    : bond        0.00386 (13032)
  covalent geometry    : angle       0.64036 (18893)

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

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

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  300 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 284
  time to evaluate  : 0.998 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   77 GLN cc_start: 0.8027 (pt0) cc_final: 0.7739 (pp30)
REVERT: A  114 HIS cc_start: 0.8932 (t70) cc_final: 0.8547 (t-90)
REVERT: B   74 THR cc_start: 0.9257 (m) cc_final: 0.8929 (p)
REVERT: B   97 THR cc_start: 0.8997 (m) cc_final: 0.8623 (p)
REVERT: B   99 TYR cc_start: 0.8988 (m-10) cc_final: 0.8699 (m-80)
REVERT: C   57 GLU cc_start: 0.9052 (tt0) cc_final: 0.8763 (tt0)
REVERT: C   74 ASN cc_start: 0.8810 (m-40) cc_final: 0.8442 (t0)
REVERT: C   93 GLU cc_start: 0.9404 (mp0) cc_final: 0.8951 (mp0)
REVERT: C  102 THR cc_start: 0.9121 (m) cc_final: 0.8765 (p)
REVERT: C  103 ILE cc_start: 0.9334 (mm) cc_final: 0.9053 (mm)
REVERT: D   52 ASP cc_start: 0.8868 (p0) cc_final: 0.8587 (p0)
REVERT: D   69 ASP cc_start: 0.8949 (t0) cc_final: 0.8735 (t0)
REVERT: D   89 THR cc_start: 0.9132 (p) cc_final: 0.8832 (p)
REVERT: D   94 GLU cc_start: 0.8907 (mp0) cc_final: 0.8083 (mp0)
REVERT: D  120 THR cc_start: 0.8938 (p) cc_final: 0.8692 (t)
REVERT: D  121 LYS cc_start: 0.9582 (ttmt) cc_final: 0.9225 (ttpp)
REVERT: G   40 TYR cc_start: 0.8788 (m-80) cc_final: 0.8382 (m-80)
REVERT: G  119 LYS cc_start: 0.8919 (pttt) cc_final: 0.8611 (tppt)
REVERT: H   77 GLU cc_start: 0.8944 (mm-30) cc_final: 0.8689 (mm-30)
REVERT: H   85 ASN cc_start: 0.9338 (m-40) cc_final: 0.9120 (m110)
REVERT: H   96 GLN cc_start: 0.8530 (tt0) cc_final: 0.8295 (tt0)
  outliers start: 16
  outliers final: 10
  residues processed: 293
  average time/residue: 0.3985
  time to fit residues: 159.2223
Evaluate side-chains
  255 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 245
  time to evaluate  : 1.620 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  110 LEU
Chi-restraints excluded: chain A residue  119 THR
Chi-restraints excluded: chain B residue   27 ILE
Chi-restraints excluded: chain B residue   48 SER
Chi-restraints excluded: chain C residue   50 VAL
Chi-restraints excluded: chain F residue   30 ILE
Chi-restraints excluded: chain G residue   34 LEU
Chi-restraints excluded: chain G residue   63 ILE
Chi-restraints excluded: chain G residue   86 LEU
Chi-restraints excluded: chain H residue   91 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 40 optimal weight:    7.9990
   chunk 26 optimal weight:   40.0000
   chunk 63 optimal weight:   10.0000
   chunk 15 optimal weight:    8.9990
   chunk 87 optimal weight:   10.0000
   chunk 96 optimal weight:   10.0000
   chunk 68 optimal weight:    6.9990
   chunk 32 optimal weight:    8.9990
   chunk 61 optimal weight:    2.9990
   chunk 90 optimal weight:   10.0000
   chunk 73 optimal weight:   10.0000
   overall best weight:    7.1990

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

Flipped N/Q/H residues before XYZ refinement:
** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  50 HIS
G  32 HIS
G  95 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.065413 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2848 r_free = 0.2848 target = 0.047266 restraints weight = 46287.176|
|-----------------------------------------------------------------------------|
r_work (start): 0.2812 rms_B_bonded: 2.48
r_work: 0.2640 rms_B_bonded: 4.43 restraints_weight: 0.5000
r_work (final): 0.2640
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8782
moved from start:          0.4108

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.107  13032  Z= 0.390
  Angle     :  0.744   9.503  18893  Z= 0.426
  Chirality :  0.042   0.199   2146
  Planarity :  0.006   0.052   1346
  Dihedral  : 30.862 177.684   4172
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 11.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.94 %
    Favored  : 99.06 %
  Rotamer:
    Outliers :  6.83 %
    Allowed  : 15.87 %
    Favored  : 77.30 %
  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:  2.89 (0.29), residues: 742
  helix:  2.60 (0.21), residues: 540
  sheet:  None (None), residues: 0
  loop : -0.01 (0.37), residues: 202

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.008   0.002   HIS B  76 
 PHE   0.011   0.002   PHE D  71 
 TYR   0.015   0.002   TYR A 100 
 ARG   0.006   0.001   ARG D  34 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06797 (  778)
  hydrogen bonds       : angle       3.74857 ( 1936)
  covalent geometry    : bond        0.00889 (13032)
  covalent geometry    : angle       0.74435 (18893)

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

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

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  289 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 246
  time to evaluate  : 1.287 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   74 GLU cc_start: 0.8751 (tt0) cc_final: 0.8285 (mt-10)
REVERT: A   77 GLN cc_start: 0.8996 (pt0) cc_final: 0.8594 (pp30)
REVERT: B   24 ARG cc_start: 0.8541 (mtm110) cc_final: 0.8283 (mmt180)
REVERT: B   74 THR cc_start: 0.9505 (OUTLIER) cc_final: 0.9200 (p)
REVERT: B   99 TYR cc_start: 0.9140 (m-10) cc_final: 0.8901 (m-80)
REVERT: C   74 ASN cc_start: 0.9003 (m-40) cc_final: 0.8602 (t0)
REVERT: C   93 GLU cc_start: 0.9578 (mp0) cc_final: 0.9241 (mp0)
REVERT: C   96 LYS cc_start: 0.9268 (ttpt) cc_final: 0.9056 (tmmt)
REVERT: C  102 THR cc_start: 0.9228 (m) cc_final: 0.8856 (p)
REVERT: D   52 ASP cc_start: 0.9014 (p0) cc_final: 0.8767 (p0)
REVERT: D   69 ASP cc_start: 0.9103 (t0) cc_final: 0.8809 (t0)
REVERT: D   77 GLU cc_start: 0.9386 (tp30) cc_final: 0.9161 (tp30)
REVERT: D   94 GLU cc_start: 0.9110 (mp0) cc_final: 0.8200 (mp0)
REVERT: E   82 ASP cc_start: 0.9326 (t0) cc_final: 0.9120 (t0)
REVERT: E  126 GLN cc_start: 0.9135 (mt0) cc_final: 0.8895 (mt0)
REVERT: F   54 GLU cc_start: 0.9128 (tp30) cc_final: 0.8799 (tt0)
REVERT: F   85 MET cc_start: 0.9051 (mmm) cc_final: 0.8197 (mmm)
REVERT: F   89 TYR cc_start: 0.9293 (m-10) cc_final: 0.9092 (m-80)
REVERT: G   76 LYS cc_start: 0.8835 (mmtt) cc_final: 0.8453 (mmmm)
REVERT: G   92 GLU cc_start: 0.8654 (pm20) cc_final: 0.8073 (pm20)
REVERT: G   93 GLU cc_start: 0.9038 (mm-30) cc_final: 0.8803 (mp0)
REVERT: G  119 LYS cc_start: 0.9130 (pttt) cc_final: 0.8857 (tppt)
REVERT: H   77 GLU cc_start: 0.8965 (mm-30) cc_final: 0.8662 (mm-30)
REVERT: H  114 GLU cc_start: 0.9220 (mm-30) cc_final: 0.8670 (mm-30)
REVERT: H  117 LYS cc_start: 0.8966 (mtmm) cc_final: 0.8359 (mttp)
  outliers start: 43
  outliers final: 35
  residues processed: 272
  average time/residue: 0.3254
  time to fit residues: 121.9257
Evaluate side-chains
  257 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 221
  time to evaluate  : 1.497 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 VAL
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue  108 THR
Chi-restraints excluded: chain A residue  110 LEU
Chi-restraints excluded: chain A residue  118 VAL
Chi-restraints excluded: chain A residue  119 THR
Chi-restraints excluded: chain B residue   35 ILE
Chi-restraints excluded: chain B residue   48 SER
Chi-restraints excluded: chain B residue   61 VAL
Chi-restraints excluded: chain B residue   74 THR
Chi-restraints excluded: chain C residue   31 VAL
Chi-restraints excluded: chain C residue   44 VAL
Chi-restraints excluded: chain C residue   50 VAL
Chi-restraints excluded: chain C residue   60 THR
Chi-restraints excluded: chain C residue  101 VAL
Chi-restraints excluded: chain D residue   74 ILE
Chi-restraints excluded: chain D residue  101 LEU
Chi-restraints excluded: chain D residue  119 VAL
Chi-restraints excluded: chain E residue   61 LEU
Chi-restraints excluded: chain E residue   81 THR
Chi-restraints excluded: chain E residue  108 THR
Chi-restraints excluded: chain E residue  118 VAL
Chi-restraints excluded: chain F residue   61 VAL
Chi-restraints excluded: chain F residue   87 VAL
Chi-restraints excluded: chain G residue   39 ASN
Chi-restraints excluded: chain G residue   44 VAL
Chi-restraints excluded: chain G residue   63 ILE
Chi-restraints excluded: chain G residue   86 LEU
Chi-restraints excluded: chain G residue  112 ILE
Chi-restraints excluded: chain H residue   70 ILE
Chi-restraints excluded: chain H residue   81 LEU
Chi-restraints excluded: chain H residue   90 ILE
Chi-restraints excluded: chain H residue   91 THR
Chi-restraints excluded: chain H residue   95 ILE
Chi-restraints excluded: chain H residue   99 VAL
Chi-restraints excluded: chain H residue  119 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 51 optimal weight:    1.9990
   chunk 28 optimal weight:    2.9990
   chunk 97 optimal weight:    8.9990
   chunk 86 optimal weight:   10.0000
   chunk 23 optimal weight:    4.9990
   chunk 48 optimal weight:    0.9990
   chunk 22 optimal weight:    0.9990
   chunk 75 optimal weight:   10.0000
   chunk 61 optimal weight:    0.9990
   chunk 59 optimal weight:    4.9990
   chunk 2 optimal weight:    5.9990
   overall best weight:    1.5990

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

Flipped N/Q/H residues before XYZ refinement:
** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  74 ASN
** D  85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 110 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.069474 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2946 r_free = 0.2946 target = 0.050977 restraints weight = 44334.546|
|-----------------------------------------------------------------------------|
r_work (start): 0.2914 rms_B_bonded: 2.30
r_work: 0.2746 rms_B_bonded: 4.31 restraints_weight: 0.5000
r_work (final): 0.2746
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8705
moved from start:          0.4283

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059  13032  Z= 0.170
  Angle     :  0.602   6.384  18893  Z= 0.354
  Chirality :  0.034   0.154   2146
  Planarity :  0.004   0.038   1346
  Dihedral  : 30.322 173.019   4172
  Min Nonbonded Distance : 2.388

Molprobity Statistics.
  All-atom Clashscore : 8.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.54 %
    Favored  : 99.46 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 21.43 %
    Favored  : 75.71 %
  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:  3.37 (0.30), residues: 742
  helix:  3.00 (0.21), residues: 540
  sheet:  None (None), residues: 0
  loop :  0.03 (0.37), residues: 202

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS F  76 
 PHE   0.014   0.001   PHE D  71 
 TYR   0.013   0.001   TYR C  58 
 ARG   0.005   0.000   ARG D 100 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04740 (  778)
  hydrogen bonds       : angle       2.91531 ( 1936)
  covalent geometry    : bond        0.00379 (13032)
  covalent geometry    : angle       0.60243 (18893)

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

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

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  273 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 255
  time to evaluate  : 1.011 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   74 GLU cc_start: 0.8871 (tt0) cc_final: 0.8453 (mt-10)
REVERT: A   77 GLN cc_start: 0.8964 (pt0) cc_final: 0.8467 (pp30)
REVERT: A   80 LYS cc_start: 0.8939 (tppp) cc_final: 0.8430 (ttmm)
REVERT: A  114 HIS cc_start: 0.9113 (t70) cc_final: 0.8733 (t-90)
REVERT: B   74 THR cc_start: 0.9460 (OUTLIER) cc_final: 0.9075 (p)
REVERT: B   99 TYR cc_start: 0.9107 (m-10) cc_final: 0.8793 (m-80)
REVERT: C   74 ASN cc_start: 0.8950 (m110) cc_final: 0.8697 (t0)
REVERT: C   93 GLU cc_start: 0.9476 (mp0) cc_final: 0.9117 (mp0)
REVERT: C  102 THR cc_start: 0.9201 (m) cc_final: 0.8973 (p)
REVERT: C  103 ILE cc_start: 0.9385 (mm) cc_final: 0.9184 (mm)
REVERT: D   52 ASP cc_start: 0.8998 (p0) cc_final: 0.8672 (p0)
REVERT: D   66 PHE cc_start: 0.9306 (t80) cc_final: 0.9081 (t80)
REVERT: D   69 ASP cc_start: 0.9129 (t0) cc_final: 0.8906 (t0)
REVERT: D   72 GLU cc_start: 0.9207 (mm-30) cc_final: 0.8960 (mm-30)
REVERT: D   94 GLU cc_start: 0.8997 (mp0) cc_final: 0.8215 (mp0)
REVERT: D  121 LYS cc_start: 0.9696 (ttmm) cc_final: 0.9390 (ttpp)
REVERT: E   82 ASP cc_start: 0.9293 (t0) cc_final: 0.8969 (t0)
REVERT: E  116 LYS cc_start: 0.9332 (mtpp) cc_final: 0.9128 (ttmm)
REVERT: F   85 MET cc_start: 0.8890 (mmm) cc_final: 0.8177 (mmm)
REVERT: G   65 GLU cc_start: 0.8714 (tm-30) cc_final: 0.8436 (tm-30)
REVERT: G   76 LYS cc_start: 0.8666 (mmtt) cc_final: 0.8312 (mmmm)
REVERT: G   92 GLU cc_start: 0.8708 (pm20) cc_final: 0.8416 (pm20)
REVERT: G  105 GLN cc_start: 0.8831 (mp10) cc_final: 0.8459 (mp10)
REVERT: G  119 LYS cc_start: 0.9167 (pttt) cc_final: 0.8910 (tppt)
REVERT: H  114 GLU cc_start: 0.9147 (mm-30) cc_final: 0.8556 (mm-30)
REVERT: H  117 LYS cc_start: 0.8947 (mtmm) cc_final: 0.8430 (mttp)
  outliers start: 18
  outliers final: 11
  residues processed: 261
  average time/residue: 0.3090
  time to fit residues: 109.6309
Evaluate side-chains
  237 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 225
  time to evaluate  : 1.021 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue  110 LEU
Chi-restraints excluded: chain A residue  119 THR
Chi-restraints excluded: chain B residue   74 THR
Chi-restraints excluded: chain C residue   41 SER
Chi-restraints excluded: chain E residue   81 THR
Chi-restraints excluded: chain F residue   31 THR
Chi-restraints excluded: chain F residue   55 THR
Chi-restraints excluded: chain G residue   39 ASN
Chi-restraints excluded: chain G residue   63 ILE
Chi-restraints excluded: chain G residue  112 ILE
Chi-restraints excluded: chain H residue   91 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 68 optimal weight:    5.9990
   chunk 46 optimal weight:    5.9990
   chunk 26 optimal weight:    0.2980
   chunk 5 optimal weight:    7.9990
   chunk 23 optimal weight:    7.9990
   chunk 76 optimal weight:   10.0000
   chunk 18 optimal weight:    0.8980
   chunk 43 optimal weight:    2.9990
   chunk 59 optimal weight:    2.9990
   chunk 58 optimal weight:    6.9990
   chunk 97 optimal weight:   10.0000
   overall best weight:    2.6386

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

Flipped N/Q/H residues before XYZ refinement:
D  85 ASN
G  69 ASN
G  74 ASN
G  95 ASN
H  85 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.068877 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2943 r_free = 0.2943 target = 0.050569 restraints weight = 44023.036|
|-----------------------------------------------------------------------------|
r_work (start): 0.2902 rms_B_bonded: 2.46
r_work: 0.2731 rms_B_bonded: 4.39 restraints_weight: 0.5000
r_work (final): 0.2731
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8703
moved from start:          0.4619

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.063  13032  Z= 0.200
  Angle     :  0.611  11.286  18893  Z= 0.357
  Chirality :  0.034   0.154   2146
  Planarity :  0.004   0.037   1346
  Dihedral  : 30.160 174.960   4172
  Min Nonbonded Distance : 2.202

Molprobity Statistics.
  All-atom Clashscore : 9.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    Favored  : 98.92 %
  Rotamer:
    Outliers :  4.76 %
    Allowed  : 21.27 %
    Favored  : 73.97 %
  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:  3.20 (0.29), residues: 742
  helix:  2.88 (0.21), residues: 540
  sheet:  None (None), residues: 0
  loop : -0.05 (0.37), residues: 202

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS B  76 
 PHE   0.010   0.001   PHE D  71 
 TYR   0.021   0.002   TYR F  89 
 ARG   0.005   0.000   ARG D 100 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04743 (  778)
  hydrogen bonds       : angle       2.96724 ( 1936)
  covalent geometry    : bond        0.00453 (13032)
  covalent geometry    : angle       0.61121 (18893)

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

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

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  264 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 234
  time to evaluate  : 1.330 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   74 GLU cc_start: 0.9030 (OUTLIER) cc_final: 0.8583 (mt-10)
REVERT: A   77 GLN cc_start: 0.8946 (pt0) cc_final: 0.8414 (pp30)
REVERT: B   74 THR cc_start: 0.9449 (OUTLIER) cc_final: 0.9054 (p)
REVERT: C   93 GLU cc_start: 0.9516 (mp0) cc_final: 0.9126 (mp0)
REVERT: C   96 LYS cc_start: 0.9117 (tmmt) cc_final: 0.8867 (tmmt)
REVERT: C  102 THR cc_start: 0.9227 (m) cc_final: 0.8900 (p)
REVERT: D   52 ASP cc_start: 0.9015 (p0) cc_final: 0.8710 (p0)
REVERT: D   60 MET cc_start: 0.9367 (tpp) cc_final: 0.9151 (tpp)
REVERT: D   66 PHE cc_start: 0.9317 (t80) cc_final: 0.9099 (t80)
REVERT: D   69 ASP cc_start: 0.9190 (t0) cc_final: 0.8850 (t0)
REVERT: D   94 GLU cc_start: 0.9040 (mp0) cc_final: 0.8236 (mp0)
REVERT: D  121 LYS cc_start: 0.9694 (ttmm) cc_final: 0.9377 (ttpp)
REVERT: E   82 ASP cc_start: 0.9313 (t0) cc_final: 0.8997 (t0)
REVERT: E   86 GLN cc_start: 0.8368 (mt0) cc_final: 0.8103 (mt0)
REVERT: F   27 ILE cc_start: 0.9334 (mt) cc_final: 0.9067 (tp)
REVERT: F   28 GLN cc_start: 0.9025 (mp10) cc_final: 0.8737 (mm-40)
REVERT: F   85 MET cc_start: 0.8952 (mmm) cc_final: 0.8305 (mmm)
REVERT: G   65 GLU cc_start: 0.8758 (tm-30) cc_final: 0.8469 (tm-30)
REVERT: G   76 LYS cc_start: 0.8646 (mmtt) cc_final: 0.8163 (mmmm)
REVERT: G   93 GLU cc_start: 0.8335 (pm20) cc_final: 0.8066 (pm20)
REVERT: G  119 LYS cc_start: 0.9228 (pttt) cc_final: 0.9018 (tppt)
  outliers start: 30
  outliers final: 23
  residues processed: 250
  average time/residue: 0.3375
  time to fit residues: 115.7014
Evaluate side-chains
  246 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 221
  time to evaluate  : 1.845 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   52 ILE
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue   74 GLU
Chi-restraints excluded: chain A residue  113 ILE
Chi-restraints excluded: chain A residue  118 VAL
Chi-restraints excluded: chain A residue  119 THR
Chi-restraints excluded: chain B residue   48 SER
Chi-restraints excluded: chain B residue   50 LEU
Chi-restraints excluded: chain B residue   61 VAL
Chi-restraints excluded: chain B residue   71 VAL
Chi-restraints excluded: chain B residue   74 THR
Chi-restraints excluded: chain C residue   41 SER
Chi-restraints excluded: chain E residue   81 THR
Chi-restraints excluded: chain E residue  110 LEU
Chi-restraints excluded: chain E residue  118 VAL
Chi-restraints excluded: chain F residue   31 THR
Chi-restraints excluded: chain G residue   35 LEU
Chi-restraints excluded: chain G residue   39 ASN
Chi-restraints excluded: chain G residue   44 VAL
Chi-restraints excluded: chain G residue   63 ILE
Chi-restraints excluded: chain G residue   86 LEU
Chi-restraints excluded: chain G residue  112 ILE
Chi-restraints excluded: chain H residue   91 THR
Chi-restraints excluded: chain H residue   99 VAL
Chi-restraints excluded: chain H residue  119 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 94 optimal weight:   10.0000
   chunk 41 optimal weight:    0.8980
   chunk 19 optimal weight:    0.7980
   chunk 86 optimal weight:   10.0000
   chunk 51 optimal weight:    0.8980
   chunk 28 optimal weight:    7.9990
   chunk 69 optimal weight:    0.7980
   chunk 7 optimal weight:    8.9990
   chunk 13 optimal weight:    0.8980
   chunk 88 optimal weight:   10.0000
   chunk 84 optimal weight:   10.0000
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
C  74 ASN
G  74 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.071235 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3009 r_free = 0.3009 target = 0.053209 restraints weight = 44629.924|
|-----------------------------------------------------------------------------|
r_work (start): 0.2965 rms_B_bonded: 2.52
r_work: 0.2798 rms_B_bonded: 4.44 restraints_weight: 0.5000
r_work (final): 0.2798
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8629
moved from start:          0.4900

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  13032  Z= 0.156
  Angle     :  0.595   8.658  18893  Z= 0.348
  Chirality :  0.033   0.149   2146
  Planarity :  0.004   0.038   1346
  Dihedral  : 29.923 174.853   4172
  Min Nonbonded Distance : 2.153

Molprobity Statistics.
  All-atom Clashscore : 8.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    Favored  : 98.92 %
  Rotamer:
    Outliers :  3.65 %
    Allowed  : 23.65 %
    Favored  : 72.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  3.25 (0.30), residues: 742
  helix:  2.91 (0.22), residues: 540
  sheet:  None (None), residues: 0
  loop :  0.00 (0.37), residues: 202

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS A 114 
 PHE   0.012   0.001   PHE D  71 
 TYR   0.027   0.002   TYR F  89 
 ARG   0.006   0.000   ARG D 100 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04143 (  778)
  hydrogen bonds       : angle       2.76806 ( 1936)
  covalent geometry    : bond        0.00340 (13032)
  covalent geometry    : angle       0.59472 (18893)

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

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

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  273 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 250
  time to evaluate  : 1.414 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   74 GLU cc_start: 0.9012 (OUTLIER) cc_final: 0.8350 (mt-10)
REVERT: A   77 GLN cc_start: 0.8908 (pt0) cc_final: 0.8312 (pp30)
REVERT: A  114 HIS cc_start: 0.9116 (t70) cc_final: 0.8868 (t-90)
REVERT: B   24 ARG cc_start: 0.7287 (mmt180) cc_final: 0.6948 (mmm160)
REVERT: B   74 THR cc_start: 0.9308 (OUTLIER) cc_final: 0.8858 (p)
REVERT: B   80 LYS cc_start: 0.8928 (mtmm) cc_final: 0.8534 (mtmm)
REVERT: B   97 THR cc_start: 0.9473 (m) cc_final: 0.9263 (p)
REVERT: C   65 GLU cc_start: 0.9213 (tp30) cc_final: 0.8855 (tp30)
REVERT: C   93 GLU cc_start: 0.9492 (mp0) cc_final: 0.8823 (mp0)
REVERT: C   96 LYS cc_start: 0.9105 (tmmt) cc_final: 0.8896 (tmmt)
REVERT: C  102 THR cc_start: 0.9188 (m) cc_final: 0.8939 (p)
REVERT: D   52 ASP cc_start: 0.8990 (p0) cc_final: 0.8690 (p0)
REVERT: D   60 MET cc_start: 0.9352 (tpp) cc_final: 0.9119 (tpp)
REVERT: D   66 PHE cc_start: 0.9283 (t80) cc_final: 0.9037 (t80)
REVERT: D   69 ASP cc_start: 0.9212 (t0) cc_final: 0.8894 (t0)
REVERT: D   72 GLU cc_start: 0.9160 (mm-30) cc_final: 0.8952 (mm-30)
REVERT: D   94 GLU cc_start: 0.8953 (mp0) cc_final: 0.8166 (mp0)
REVERT: D  121 LYS cc_start: 0.9685 (ttmm) cc_final: 0.9340 (ttpp)
REVERT: E   58 SER cc_start: 0.9153 (m) cc_final: 0.8883 (p)
REVERT: E   82 ASP cc_start: 0.9308 (t0) cc_final: 0.8994 (t0)
REVERT: E   86 GLN cc_start: 0.8209 (mt0) cc_final: 0.7922 (mt0)
REVERT: F   27 ILE cc_start: 0.9338 (mt) cc_final: 0.8970 (tp)
REVERT: F   28 GLN cc_start: 0.9036 (mp10) cc_final: 0.8714 (mm-40)
REVERT: G   25 GLN cc_start: 0.9090 (mm-40) cc_final: 0.8778 (mp10)
REVERT: G   65 GLU cc_start: 0.8807 (tm-30) cc_final: 0.8502 (tm-30)
REVERT: G   76 LYS cc_start: 0.8603 (mmtt) cc_final: 0.8074 (mmmm)
REVERT: G   91 ASP cc_start: 0.8946 (t70) cc_final: 0.8612 (t0)
REVERT: G  101 VAL cc_start: 0.9423 (t) cc_final: 0.9120 (p)
REVERT: H   69 ASP cc_start: 0.8529 (t0) cc_final: 0.8304 (t0)
REVERT: H  114 GLU cc_start: 0.9102 (mm-30) cc_final: 0.8758 (mm-30)
  outliers start: 23
  outliers final: 16
  residues processed: 260
  average time/residue: 0.3836
  time to fit residues: 135.9872
Evaluate side-chains
  251 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 233
  time to evaluate  : 1.526 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 SER
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue   74 GLU
Chi-restraints excluded: chain A residue  113 ILE
Chi-restraints excluded: chain A residue  119 THR
Chi-restraints excluded: chain B residue   48 SER
Chi-restraints excluded: chain B residue   50 LEU
Chi-restraints excluded: chain B residue   71 VAL
Chi-restraints excluded: chain B residue   74 THR
Chi-restraints excluded: chain C residue   50 VAL
Chi-restraints excluded: chain E residue  118 VAL
Chi-restraints excluded: chain F residue   31 THR
Chi-restraints excluded: chain F residue   55 THR
Chi-restraints excluded: chain G residue   39 ASN
Chi-restraints excluded: chain G residue   63 ILE
Chi-restraints excluded: chain G residue   86 LEU
Chi-restraints excluded: chain G residue  112 ILE
Chi-restraints excluded: chain H residue   99 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 43 optimal weight:    2.9990
   chunk 2 optimal weight:    3.9990
   chunk 29 optimal weight:   10.0000
   chunk 79 optimal weight:   10.0000
   chunk 7 optimal weight:    8.9990
   chunk 67 optimal weight:    3.9990
   chunk 12 optimal weight:    8.9990
   chunk 41 optimal weight:    0.9990
   chunk 19 optimal weight:    0.5980
   chunk 37 optimal weight:    0.9990
   chunk 73 optimal weight:   10.0000
   overall best weight:    1.9188

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

Flipped N/Q/H residues before XYZ refinement:
** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  74 ASN
** F  26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  74 ASN
H  85 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.070251 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2986 r_free = 0.2986 target = 0.052228 restraints weight = 44576.282|
|-----------------------------------------------------------------------------|
r_work (start): 0.2941 rms_B_bonded: 2.50
r_work: 0.2772 rms_B_bonded: 4.44 restraints_weight: 0.5000
r_work (final): 0.2772
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8653
moved from start:          0.5101

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  13032  Z= 0.177
  Angle     :  0.601   6.759  18893  Z= 0.351
  Chirality :  0.034   0.174   2146
  Planarity :  0.004   0.036   1346
  Dihedral  : 29.941 176.842   4172
  Min Nonbonded Distance : 2.157

Molprobity Statistics.
  All-atom Clashscore : 8.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.48 %
    Favored  : 98.52 %
  Rotamer:
    Outliers :  4.29 %
    Allowed  : 23.33 %
    Favored  : 72.38 %
  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:  3.23 (0.30), residues: 742
  helix:  2.91 (0.22), residues: 540
  sheet:  None (None), residues: 0
  loop : -0.06 (0.38), residues: 202

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS B  76 
 PHE   0.011   0.001   PHE A  79 
 TYR   0.023   0.002   TYR A 100 
 ARG   0.005   0.000   ARG E 130 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04385 (  778)
  hydrogen bonds       : angle       2.84824 ( 1936)
  covalent geometry    : bond        0.00395 (13032)
  covalent geometry    : angle       0.60096 (18893)

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

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

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  269 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 242
  time to evaluate  : 1.144 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   69 GLN cc_start: 0.9445 (tt0) cc_final: 0.8979 (tm-30)
REVERT: A   74 GLU cc_start: 0.8997 (OUTLIER) cc_final: 0.8577 (mt-10)
REVERT: A   77 GLN cc_start: 0.8859 (pt0) cc_final: 0.8215 (pp30)
REVERT: A  114 HIS cc_start: 0.9147 (t70) cc_final: 0.8936 (t-90)
REVERT: B   74 THR cc_start: 0.9236 (OUTLIER) cc_final: 0.8743 (p)
REVERT: B   80 LYS cc_start: 0.8953 (mtmm) cc_final: 0.8574 (mtmm)
REVERT: C   57 GLU cc_start: 0.9186 (mm-30) cc_final: 0.8971 (mm-30)
REVERT: C   65 GLU cc_start: 0.9254 (tt0) cc_final: 0.8876 (tp30)
REVERT: C   93 GLU cc_start: 0.9427 (mp0) cc_final: 0.9127 (mp0)
REVERT: C  102 THR cc_start: 0.9165 (m) cc_final: 0.8910 (p)
REVERT: D   52 ASP cc_start: 0.9000 (p0) cc_final: 0.8704 (p0)
REVERT: D   60 MET cc_start: 0.9383 (tpp) cc_final: 0.9119 (tpp)
REVERT: D   66 PHE cc_start: 0.9298 (t80) cc_final: 0.9093 (t80)
REVERT: D   69 ASP cc_start: 0.9233 (t0) cc_final: 0.8876 (t0)
REVERT: D   72 GLU cc_start: 0.9174 (mm-30) cc_final: 0.8908 (mm-30)
REVERT: D   94 GLU cc_start: 0.9025 (mp0) cc_final: 0.8146 (mp0)
REVERT: D  121 LYS cc_start: 0.9677 (ttmm) cc_final: 0.9370 (ttpp)
REVERT: E   58 SER cc_start: 0.9178 (m) cc_final: 0.8969 (p)
REVERT: E   82 ASP cc_start: 0.9322 (t0) cc_final: 0.9015 (t0)
REVERT: E   86 GLN cc_start: 0.8287 (mt0) cc_final: 0.7952 (mt0)
REVERT: E  130 ARG cc_start: 0.9022 (tpt90) cc_final: 0.8779 (tpt90)
REVERT: F   27 ILE cc_start: 0.9360 (mt) cc_final: 0.9105 (tp)
REVERT: F   28 GLN cc_start: 0.9010 (mp10) cc_final: 0.8678 (mm-40)
REVERT: G   65 GLU cc_start: 0.8826 (tm-30) cc_final: 0.8492 (tm-30)
REVERT: G   91 ASP cc_start: 0.8915 (t70) cc_final: 0.8643 (t0)
REVERT: H   69 ASP cc_start: 0.8640 (t0) cc_final: 0.8369 (t0)
REVERT: H  114 GLU cc_start: 0.9093 (mm-30) cc_final: 0.8872 (mm-30)
  outliers start: 27
  outliers final: 20
  residues processed: 256
  average time/residue: 0.3152
  time to fit residues: 109.6617
Evaluate side-chains
  253 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 231
  time to evaluate  : 0.878 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   52 ILE
Chi-restraints excluded: chain A residue   58 SER
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue   74 GLU
Chi-restraints excluded: chain A residue   83 LEU
Chi-restraints excluded: chain A residue  113 ILE
Chi-restraints excluded: chain A residue  118 VAL
Chi-restraints excluded: chain A residue  119 THR
Chi-restraints excluded: chain B residue   71 VAL
Chi-restraints excluded: chain B residue   74 THR
Chi-restraints excluded: chain C residue   50 VAL
Chi-restraints excluded: chain E residue   81 THR
Chi-restraints excluded: chain E residue  110 LEU
Chi-restraints excluded: chain E residue  118 VAL
Chi-restraints excluded: chain F residue   31 THR
Chi-restraints excluded: chain G residue   39 ASN
Chi-restraints excluded: chain G residue   63 ILE
Chi-restraints excluded: chain G residue   86 LEU
Chi-restraints excluded: chain G residue  112 ILE
Chi-restraints excluded: chain H residue   72 GLU
Chi-restraints excluded: chain H residue   99 VAL
Chi-restraints excluded: chain H residue  119 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 39 optimal weight:    3.9990
   chunk 31 optimal weight:    0.9980
   chunk 17 optimal weight:    6.9990
   chunk 80 optimal weight:   10.0000
   chunk 72 optimal weight:   10.0000
   chunk 99 optimal weight:   10.0000
   chunk 20 optimal weight:    2.9990
   chunk 70 optimal weight:   10.0000
   chunk 42 optimal weight:    6.9990
   chunk 13 optimal weight:    0.8980
   chunk 61 optimal weight:    6.9990
   overall best weight:    3.1786

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

Flipped N/Q/H residues before XYZ refinement:
A  69 GLN
A 109 ASN
** B  76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  74 ASN
C  85 GLN
** D  85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  85 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.069146 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2955 r_free = 0.2955 target = 0.050918 restraints weight = 44571.493|
|-----------------------------------------------------------------------------|
r_work (start): 0.2903 rms_B_bonded: 2.53
r_work: 0.2728 rms_B_bonded: 4.48 restraints_weight: 0.5000
r_work (final): 0.2728
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8698
moved from start:          0.5209

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.061  13032  Z= 0.218
  Angle     :  0.641  12.339  18893  Z= 0.369
  Chirality :  0.035   0.183   2146
  Planarity :  0.004   0.035   1346
  Dihedral  : 30.028 177.555   4172
  Min Nonbonded Distance : 2.175

Molprobity Statistics.
  All-atom Clashscore : 9.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.75 %
    Favored  : 98.25 %
  Rotamer:
    Outliers :  4.60 %
    Allowed  : 24.44 %
    Favored  : 70.95 %
  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 (0.30), residues: 742
  helix:  2.75 (0.22), residues: 542
  sheet:  None (None), residues: 0
  loop : -0.29 (0.37), residues: 200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS H  83 
 PHE   0.016   0.001   PHE A  79 
 TYR   0.023   0.002   TYR B  89 
 ARG   0.006   0.000   ARG H  80 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04723 (  778)
  hydrogen bonds       : angle       3.05474 ( 1936)
  covalent geometry    : bond        0.00494 (13032)
  covalent geometry    : angle       0.64061 (18893)

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

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

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  259 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 230
  time to evaluate  : 0.934 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   77 GLN cc_start: 0.9038 (pt0) cc_final: 0.8455 (pp30)
REVERT: B   74 THR cc_start: 0.9330 (OUTLIER) cc_final: 0.8963 (p)
REVERT: B   80 LYS cc_start: 0.9059 (mtmm) cc_final: 0.8677 (mtmm)
REVERT: B   97 THR cc_start: 0.9410 (m) cc_final: 0.9151 (p)
REVERT: C   57 GLU cc_start: 0.9202 (mm-30) cc_final: 0.8903 (mm-30)
REVERT: C   93 GLU cc_start: 0.9515 (mp0) cc_final: 0.8834 (mp0)
REVERT: C  102 THR cc_start: 0.9204 (m) cc_final: 0.8869 (p)
REVERT: D   52 ASP cc_start: 0.9029 (p0) cc_final: 0.8751 (p0)
REVERT: D   60 MET cc_start: 0.9429 (tpp) cc_final: 0.8960 (tpp)
REVERT: D   66 PHE cc_start: 0.9333 (t80) cc_final: 0.9086 (t80)
REVERT: D   69 ASP cc_start: 0.9244 (t0) cc_final: 0.8885 (t0)
REVERT: D   94 GLU cc_start: 0.9054 (mp0) cc_final: 0.8187 (mp0)
REVERT: E   58 SER cc_start: 0.9213 (m) cc_final: 0.8999 (p)
REVERT: E   82 ASP cc_start: 0.9268 (t0) cc_final: 0.8962 (t0)
REVERT: E   86 GLN cc_start: 0.8403 (mt0) cc_final: 0.8080 (mt0)
REVERT: F   28 GLN cc_start: 0.9059 (mp10) cc_final: 0.8824 (mp10)
REVERT: F   60 LYS cc_start: 0.8682 (ttmt) cc_final: 0.8272 (ttmt)
REVERT: F   64 GLU cc_start: 0.9070 (mt-10) cc_final: 0.8794 (mp0)
REVERT: F   93 ARG cc_start: 0.9282 (ptm-80) cc_final: 0.8810 (ptm160)
REVERT: F   99 TYR cc_start: 0.9374 (m-10) cc_final: 0.9136 (m-10)
REVERT: G   62 GLU cc_start: 0.8717 (mm-30) cc_final: 0.8476 (mm-30)
REVERT: G   65 GLU cc_start: 0.8888 (tm-30) cc_final: 0.8684 (tm-30)
REVERT: H   69 ASP cc_start: 0.8667 (t0) cc_final: 0.8368 (t0)
  outliers start: 29
  outliers final: 25
  residues processed: 247
  average time/residue: 0.2642
  time to fit residues: 89.2457
Evaluate side-chains
  252 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 226
  time to evaluate  : 0.880 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 VAL
Chi-restraints excluded: chain A residue   52 ILE
Chi-restraints excluded: chain A residue   58 SER
Chi-restraints excluded: chain A residue   61 LEU
Chi-restraints excluded: chain A residue   74 GLU
Chi-restraints excluded: chain A residue   83 LEU
Chi-restraints excluded: chain A residue  113 ILE
Chi-restraints excluded: chain A residue  118 VAL
Chi-restraints excluded: chain A residue  119 THR
Chi-restraints excluded: chain B residue   71 VAL
Chi-restraints excluded: chain B residue   74 THR
Chi-restraints excluded: chain C residue   41 SER
Chi-restraints excluded: chain C residue   50 VAL
Chi-restraints excluded: chain C residue   74 ASN
Chi-restraints excluded: chain E residue   81 THR
Chi-restraints excluded: chain E residue  110 LEU
Chi-restraints excluded: chain E residue  118 VAL
Chi-restraints excluded: chain E residue  120 ILE
Chi-restraints excluded: chain F residue   31 THR
Chi-restraints excluded: chain G residue   35 LEU
Chi-restraints excluded: chain G residue   39 ASN
Chi-restraints excluded: chain G residue   63 ILE
Chi-restraints excluded: chain G residue   86 LEU
Chi-restraints excluded: chain H residue   72 GLU
Chi-restraints excluded: chain H residue   99 VAL
Chi-restraints excluded: chain H residue  119 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 11 optimal weight:    0.7980
   chunk 51 optimal weight:    5.9990
   chunk 95 optimal weight:   10.0000
   chunk 49 optimal weight:    0.8980
   chunk 6 optimal weight:    0.8980
   chunk 29 optimal weight:    8.9990
   chunk 16 optimal weight:    4.9990
   chunk 27 optimal weight:   10.0000
   chunk 30 optimal weight:    0.9980
   chunk 35 optimal weight:    0.9990
   chunk 85 optimal weight:   10.0000
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
A  69 GLN
A 109 ASN
C  74 ASN
** D  85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  85 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.071366 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3015 r_free = 0.3015 target = 0.053371 restraints weight = 44174.769|
|-----------------------------------------------------------------------------|
r_work (start): 0.2969 rms_B_bonded: 2.52
r_work: 0.2799 rms_B_bonded: 4.47 restraints_weight: 0.5000
r_work (final): 0.2799
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8635
moved from start:          0.5353

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053  13032  Z= 0.161
  Angle     :  0.646  19.013  18893  Z= 0.366
  Chirality :  0.034   0.169   2146
  Planarity :  0.004   0.038   1346
  Dihedral  : 29.902 178.454   4172
  Min Nonbonded Distance : 2.190

Molprobity Statistics.
  All-atom Clashscore : 8.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    Favored  : 98.92 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 26.35 %
    Favored  : 70.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  2.79 (0.30), residues: 742
  helix:  2.54 (0.22), residues: 546
  sheet:  None (None), residues: 0
  loop : -0.18 (0.38), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS B  76 
 PHE   0.013   0.001   PHE A  79 
 TYR   0.021   0.002   TYR B  89 
 ARG   0.006   0.000   ARG D  80 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04071 (  778)
  hydrogen bonds       : angle       2.92421 ( 1936)
  covalent geometry    : bond        0.00356 (13032)
  covalent geometry    : angle       0.64556 (18893)

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

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

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  260 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 242
  time to evaluate  : 0.898 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   74 GLU cc_start: 0.9098 (OUTLIER) cc_final: 0.8653 (mt-10)
REVERT: A   77 GLN cc_start: 0.8956 (pt0) cc_final: 0.8361 (pp30)
REVERT: B   74 THR cc_start: 0.9339 (m) cc_final: 0.8901 (p)
REVERT: B   80 LYS cc_start: 0.9048 (mtmm) cc_final: 0.8724 (mtmm)
REVERT: C   57 GLU cc_start: 0.9169 (mm-30) cc_final: 0.8909 (mm-30)
REVERT: C   65 GLU cc_start: 0.9192 (tp30) cc_final: 0.8814 (tp30)
REVERT: C   93 GLU cc_start: 0.9394 (mp0) cc_final: 0.9159 (mp0)
REVERT: C  102 THR cc_start: 0.9196 (m) cc_final: 0.8919 (p)
REVERT: D   52 ASP cc_start: 0.8994 (p0) cc_final: 0.8688 (p0)
REVERT: D   60 MET cc_start: 0.9404 (tpp) cc_final: 0.9140 (tpp)
REVERT: D   69 ASP cc_start: 0.9238 (t0) cc_final: 0.8913 (t0)
REVERT: D   72 GLU cc_start: 0.9188 (mm-30) cc_final: 0.8962 (mm-30)
REVERT: D   94 GLU cc_start: 0.8972 (mp0) cc_final: 0.8136 (mp0)
REVERT: D  106 GLU cc_start: 0.7108 (tm-30) cc_final: 0.6902 (tm-30)
REVERT: E   60 GLU cc_start: 0.8475 (pm20) cc_final: 0.8257 (pm20)
REVERT: E   82 ASP cc_start: 0.9218 (t0) cc_final: 0.8960 (t0)
REVERT: E   86 GLN cc_start: 0.8191 (mt0) cc_final: 0.7890 (mt0)
REVERT: E  121 MET cc_start: 0.7997 (mmm) cc_final: 0.7746 (mmm)
REVERT: F   27 ILE cc_start: 0.9426 (OUTLIER) cc_final: 0.9054 (tp)
REVERT: F   28 GLN cc_start: 0.9037 (mp10) cc_final: 0.8702 (mm-40)
REVERT: F   64 GLU cc_start: 0.8987 (mt-10) cc_final: 0.8715 (mp0)
REVERT: F   93 ARG cc_start: 0.9215 (ptm-80) cc_final: 0.8742 (ptm160)
REVERT: G   25 GLN cc_start: 0.9110 (mm-40) cc_final: 0.8743 (mp10)
REVERT: G   65 GLU cc_start: 0.8964 (tm-30) cc_final: 0.8749 (tm-30)
REVERT: H   60 MET cc_start: 0.9079 (tpp) cc_final: 0.8713 (tpp)
REVERT: H   69 ASP cc_start: 0.8570 (t0) cc_final: 0.8269 (t0)
REVERT: H  117 LYS cc_start: 0.8919 (ptpp) cc_final: 0.8711 (ptpp)
  outliers start: 18
  outliers final: 12
  residues processed: 252
  average time/residue: 0.2671
  time to fit residues: 92.5244
Evaluate side-chains
  245 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 231
  time to evaluate  : 0.950 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 SER
Chi-restraints excluded: chain A residue   74 GLU
Chi-restraints excluded: chain A residue   83 LEU
Chi-restraints excluded: chain A residue  109 ASN
Chi-restraints excluded: chain A residue  113 ILE
Chi-restraints excluded: chain A residue  118 VAL
Chi-restraints excluded: chain A residue  119 THR
Chi-restraints excluded: chain C residue   41 SER
Chi-restraints excluded: chain E residue   81 THR
Chi-restraints excluded: chain E residue  110 LEU
Chi-restraints excluded: chain F residue   27 ILE
Chi-restraints excluded: chain F residue   31 THR
Chi-restraints excluded: chain G residue   63 ILE
Chi-restraints excluded: chain G residue   86 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 29 optimal weight:    9.9990
   chunk 77 optimal weight:   10.0000
   chunk 48 optimal weight:    0.1980
   chunk 51 optimal weight:    0.6980
   chunk 84 optimal weight:   10.0000
   chunk 6 optimal weight:    5.9990
   chunk 75 optimal weight:   10.0000
   chunk 64 optimal weight:    4.9990
   chunk 11 optimal weight:    5.9990
   chunk 49 optimal weight:    1.9990
   chunk 38 optimal weight:    4.9990
   overall best weight:    2.5786

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

Flipped N/Q/H residues before XYZ refinement:
A  69 GLN
A 109 ASN
B  65 ASN
** B  76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  90 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.069846 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.2969 r_free = 0.2969 target = 0.051457 restraints weight = 44685.891|
|-----------------------------------------------------------------------------|
r_work (start): 0.2928 rms_B_bonded: 2.51
r_work: 0.2758 rms_B_bonded: 4.48 restraints_weight: 0.5000
r_work (final): 0.2758
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8671
moved from start:          0.5420

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.058  13032  Z= 0.200
  Angle     :  0.658  18.487  18893  Z= 0.375
  Chirality :  0.035   0.184   2146
  Planarity :  0.004   0.036   1346
  Dihedral  : 29.963 178.111   4172
  Min Nonbonded Distance : 2.379

Molprobity Statistics.
  All-atom Clashscore : 9.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 27.46 %
    Favored  : 70.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  2.71 (0.30), residues: 742
  helix:  2.49 (0.22), residues: 546
  sheet:  None (None), residues: 0
  loop : -0.23 (0.39), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS H  83 
 PHE   0.013   0.001   PHE A  79 
 TYR   0.032   0.002   TYR B  89 
 ARG   0.008   0.000   ARG D  80 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04556 (  778)
  hydrogen bonds       : angle       3.06892 ( 1936)
  covalent geometry    : bond        0.00454 (13032)
  covalent geometry    : angle       0.65821 (18893)

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

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

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  250 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 234
  time to evaluate  : 0.895 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   69 GLN cc_start: 0.9438 (tt0) cc_final: 0.9095 (tm-30)
REVERT: A   74 GLU cc_start: 0.9054 (OUTLIER) cc_final: 0.8662 (mt-10)
REVERT: A   77 GLN cc_start: 0.8989 (pt0) cc_final: 0.8397 (pp30)
REVERT: B   80 LYS cc_start: 0.9073 (mtmm) cc_final: 0.8731 (mtmm)
REVERT: C   57 GLU cc_start: 0.9194 (mm-30) cc_final: 0.8904 (mm-30)
REVERT: C   65 GLU cc_start: 0.9231 (tp30) cc_final: 0.8852 (tp30)
REVERT: C   85 GLN cc_start: 0.9072 (tp40) cc_final: 0.8537 (tm-30)
REVERT: C   93 GLU cc_start: 0.9515 (mp0) cc_final: 0.8830 (mp0)
REVERT: C  102 THR cc_start: 0.9192 (m) cc_final: 0.8907 (p)
REVERT: D   52 ASP cc_start: 0.9002 (p0) cc_final: 0.8702 (p0)
REVERT: D   60 MET cc_start: 0.9424 (tpp) cc_final: 0.8950 (tpp)
REVERT: D   69 ASP cc_start: 0.9255 (t0) cc_final: 0.8897 (t0)
REVERT: D   72 GLU cc_start: 0.9216 (mm-30) cc_final: 0.8985 (mm-30)
REVERT: D   94 GLU cc_start: 0.9054 (mp0) cc_final: 0.8110 (mp0)
REVERT: E   82 ASP cc_start: 0.9266 (t0) cc_final: 0.8957 (t0)
REVERT: E   86 GLN cc_start: 0.8301 (mt0) cc_final: 0.7996 (mt0)
REVERT: E  121 MET cc_start: 0.8210 (mmm) cc_final: 0.8004 (mmm)
REVERT: F   28 GLN cc_start: 0.9051 (mp10) cc_final: 0.8532 (mp10)
REVERT: F   64 GLU cc_start: 0.9018 (mt-10) cc_final: 0.8744 (mp0)
REVERT: F   93 ARG cc_start: 0.9273 (ptm-80) cc_final: 0.8836 (ptm160)
REVERT: G   65 GLU cc_start: 0.9114 (tm-30) cc_final: 0.8756 (tm-30)
REVERT: G   91 ASP cc_start: 0.8686 (t70) cc_final: 0.8076 (t70)
REVERT: H   60 MET cc_start: 0.9109 (tpp) cc_final: 0.8766 (tpp)
REVERT: H   69 ASP cc_start: 0.8622 (t0) cc_final: 0.8359 (t0)
REVERT: H  114 GLU cc_start: 0.8954 (mm-30) cc_final: 0.8697 (mm-30)
  outliers start: 16
  outliers final: 14
  residues processed: 241
  average time/residue: 0.2629
  time to fit residues: 86.4412
Evaluate side-chains
  247 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 232
  time to evaluate  : 0.857 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 VAL
Chi-restraints excluded: chain A residue   58 SER
Chi-restraints excluded: chain A residue   74 GLU
Chi-restraints excluded: chain A residue   83 LEU
Chi-restraints excluded: chain A residue  109 ASN
Chi-restraints excluded: chain A residue  118 VAL
Chi-restraints excluded: chain A residue  119 THR
Chi-restraints excluded: chain C residue   41 SER
Chi-restraints excluded: chain C residue   80 ILE
Chi-restraints excluded: chain E residue   81 THR
Chi-restraints excluded: chain E residue  110 LEU
Chi-restraints excluded: chain F residue   27 ILE
Chi-restraints excluded: chain F residue   31 THR
Chi-restraints excluded: chain G residue   86 LEU
Chi-restraints excluded: chain H residue   72 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 10 optimal weight:    0.7980
   chunk 45 optimal weight:    4.9990
   chunk 56 optimal weight:    2.9990
   chunk 55 optimal weight:    0.4980
   chunk 66 optimal weight:    5.9990
   chunk 82 optimal weight:   10.0000
   chunk 70 optimal weight:    3.9990
   chunk 90 optimal weight:   10.0000
   chunk 0 optimal weight:   10.0000
   chunk 44 optimal weight:    0.9990
   chunk 73 optimal weight:   10.0000
   overall best weight:    1.8586

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

Flipped N/Q/H residues before XYZ refinement:
A 109 ASN
** B  76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  85 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.070587 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2990 r_free = 0.2990 target = 0.052344 restraints weight = 44464.578|
|-----------------------------------------------------------------------------|
r_work (start): 0.2940 rms_B_bonded: 2.55
r_work: 0.2772 rms_B_bonded: 4.51 restraints_weight: 0.5000
r_work (final): 0.2772
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8651
moved from start:          0.5478

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057  13032  Z= 0.182
  Angle     :  0.655  17.205  18893  Z= 0.374
  Chirality :  0.034   0.180   2146
  Planarity :  0.004   0.036   1346
  Dihedral  : 29.952 178.001   4172
  Min Nonbonded Distance : 2.399

Molprobity Statistics.
  All-atom Clashscore : 10.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 27.94 %
    Favored  : 69.68 %
  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:  2.69 (0.30), residues: 742
  helix:  2.47 (0.22), residues: 546
  sheet:  None (None), residues: 0
  loop : -0.23 (0.39), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS B  76 
 PHE   0.014   0.001   PHE A  79 
 TYR   0.025   0.002   TYR F  89 
 ARG   0.007   0.000   ARG D  80 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04348 (  778)
  hydrogen bonds       : angle       3.03185 ( 1936)
  covalent geometry    : bond        0.00408 (13032)
  covalent geometry    : angle       0.65492 (18893)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5882.07 seconds
wall clock time: 109 minutes 11.57 seconds (6551.57 seconds total)