Starting phenix.real_space_refine
on Wed Feb  4 05:41:29 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9lab_62924/02_2026/9lab_62924.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9lab_62924/02_2026/9lab_62924.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9lab_62924/02_2026/9lab_62924.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9lab_62924/02_2026/9lab_62924.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9lab_62924/02_2026/9lab_62924.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9lab_62924/02_2026/9lab_62924.cif"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
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: 4
    Type Number    sf(0)   Gaussians
     S      24      5.16       5
     C    5800      2.51       5
     N    1440      2.21       5
     O    1728      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 40 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8992
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "B"
      Number of atoms: 1124
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 155, 1124
          Classifications: {'peptide': 155}
          Link IDs: {'PTRANS': 9, 'TRANS': 145}
          Chain breaks: 2
  Restraints were copied for chains:
    C, D, E, F, G, H, I
  Time building chain proxies: 1.02, per 1000 atoms: 0.11
  Number of scatterers: 8992
  At special positions: 0
  Unit cell: (78.02, 78.85, 190.07, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      24     16.00
     O    1728      8.00
     N    1440      7.00
     C    5800      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: 1.02
  Conformation dependent library (CDL) restraints added in 381.7 milliseconds
  

  2384 Ramachandran restraints generated.
    1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2240

  Finding SS restraints...
    Secondary structure from input PDB file:
      24 helices and 24 sheets defined
      36.1% alpha, 16.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.34
  Creating SS restraints...
    Processing helix  chain 'B' and resid 8 through 23
    Processing helix  chain 'B' and resid 33 through 63
    Processing helix  chain 'B' and resid 91 through 99
      removed outlier: 3.901A  pdb=" N   ALA B  97 " --> pdb=" O   ALA B  93 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 8 through 23
    Processing helix  chain 'C' and resid 33 through 63
    Processing helix  chain 'C' and resid 91 through 99
      removed outlier: 3.901A  pdb=" N   ALA C  97 " --> pdb=" O   ALA C  93 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 8 through 23
    Processing helix  chain 'D' and resid 33 through 63
    Processing helix  chain 'D' and resid 91 through 99
      removed outlier: 3.902A  pdb=" N   ALA D  97 " --> pdb=" O   ALA D  93 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 8 through 23
    Processing helix  chain 'E' and resid 33 through 63
    Processing helix  chain 'E' and resid 91 through 99
      removed outlier: 3.901A  pdb=" N   ALA E  97 " --> pdb=" O   ALA E  93 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 8 through 23
    Processing helix  chain 'F' and resid 33 through 63
    Processing helix  chain 'F' and resid 91 through 99
      removed outlier: 3.902A  pdb=" N   ALA F  97 " --> pdb=" O   ALA F  93 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 8 through 23
    Processing helix  chain 'G' and resid 33 through 63
    Processing helix  chain 'G' and resid 91 through 99
      removed outlier: 3.902A  pdb=" N   ALA G  97 " --> pdb=" O   ALA G  93 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 8 through 23
    Processing helix  chain 'H' and resid 33 through 63
    Processing helix  chain 'H' and resid 91 through 99
      removed outlier: 3.902A  pdb=" N   ALA H  97 " --> pdb=" O   ALA H  93 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 8 through 23
    Processing helix  chain 'I' and resid 33 through 63
    Processing helix  chain 'I' and resid 91 through 99
      removed outlier: 3.901A  pdb=" N   ALA I  97 " --> pdb=" O   ALA I  93 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 73 through 74
    Processing sheet with id=AA2, first strand: chain 'B' and resid 83 through 84
    Processing sheet with id=AA3, first strand: chain 'B' and resid 103 through 105
      removed outlier: 6.389A  pdb=" N   ASP B 104 " --> pdb=" O   ILE B 118 " (cutoff:3.500A)
      removed outlier: 4.794A  pdb=" N   GLN B 132 " --> pdb=" O   CYS B 139 " (cutoff:3.500A)
      removed outlier: 8.391A  pdb=" N   CYS B 139 " --> pdb=" O   GLN B 132 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 73 through 74
    Processing sheet with id=AA5, first strand: chain 'C' and resid 83 through 84
    Processing sheet with id=AA6, first strand: chain 'C' and resid 103 through 105
      removed outlier: 6.389A  pdb=" N   ASP C 104 " --> pdb=" O   ILE C 118 " (cutoff:3.500A)
      removed outlier: 4.795A  pdb=" N   GLN C 132 " --> pdb=" O   CYS C 139 " (cutoff:3.500A)
      removed outlier: 8.391A  pdb=" N   CYS C 139 " --> pdb=" O   GLN C 132 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 73 through 74
    Processing sheet with id=AA8, first strand: chain 'D' and resid 83 through 84
    Processing sheet with id=AA9, first strand: chain 'D' and resid 103 through 105
      removed outlier: 6.389A  pdb=" N   ASP D 104 " --> pdb=" O   ILE D 118 " (cutoff:3.500A)
      removed outlier: 4.794A  pdb=" N   GLN D 132 " --> pdb=" O   CYS D 139 " (cutoff:3.500A)
      removed outlier: 8.392A  pdb=" N   CYS D 139 " --> pdb=" O   GLN D 132 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'E' and resid 73 through 74
    Processing sheet with id=AB2, first strand: chain 'E' and resid 83 through 84
    Processing sheet with id=AB3, first strand: chain 'E' and resid 103 through 105
      removed outlier: 6.389A  pdb=" N   ASP E 104 " --> pdb=" O   ILE E 118 " (cutoff:3.500A)
      removed outlier: 4.795A  pdb=" N   GLN E 132 " --> pdb=" O   CYS E 139 " (cutoff:3.500A)
      removed outlier: 8.391A  pdb=" N   CYS E 139 " --> pdb=" O   GLN E 132 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'F' and resid 73 through 74
    Processing sheet with id=AB5, first strand: chain 'F' and resid 83 through 84
    Processing sheet with id=AB6, first strand: chain 'F' and resid 103 through 105
      removed outlier: 6.390A  pdb=" N   ASP F 104 " --> pdb=" O   ILE F 118 " (cutoff:3.500A)
      removed outlier: 4.794A  pdb=" N   GLN F 132 " --> pdb=" O   CYS F 139 " (cutoff:3.500A)
      removed outlier: 8.391A  pdb=" N   CYS F 139 " --> pdb=" O   GLN F 132 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'G' and resid 73 through 74
    Processing sheet with id=AB8, first strand: chain 'G' and resid 83 through 84
    Processing sheet with id=AB9, first strand: chain 'G' and resid 103 through 105
      removed outlier: 6.389A  pdb=" N   ASP G 104 " --> pdb=" O   ILE G 118 " (cutoff:3.500A)
      removed outlier: 4.795A  pdb=" N   GLN G 132 " --> pdb=" O   CYS G 139 " (cutoff:3.500A)
      removed outlier: 8.392A  pdb=" N   CYS G 139 " --> pdb=" O   GLN G 132 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'H' and resid 73 through 74
    Processing sheet with id=AC2, first strand: chain 'H' and resid 83 through 84
    Processing sheet with id=AC3, first strand: chain 'H' and resid 103 through 105
      removed outlier: 6.389A  pdb=" N   ASP H 104 " --> pdb=" O   ILE H 118 " (cutoff:3.500A)
      removed outlier: 4.794A  pdb=" N   GLN H 132 " --> pdb=" O   CYS H 139 " (cutoff:3.500A)
      removed outlier: 8.392A  pdb=" N   CYS H 139 " --> pdb=" O   GLN H 132 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'I' and resid 73 through 74
    Processing sheet with id=AC5, first strand: chain 'I' and resid 83 through 84
    Processing sheet with id=AC6, first strand: chain 'I' and resid 103 through 105
      removed outlier: 6.389A  pdb=" N   ASP I 104 " --> pdb=" O   ILE I 118 " (cutoff:3.500A)
      removed outlier: 4.795A  pdb=" N   GLN I 132 " --> pdb=" O   CYS I 139 " (cutoff:3.500A)
      removed outlier: 8.392A  pdb=" N   CYS I 139 " --> pdb=" O   GLN I 132 " (cutoff:3.500A)

    504 hydrogen bonds defined for protein.
    1416 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.35

  Time building geometry restraints manager: 1.29 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2848
        1.34 -     1.46: 1660
        1.46 -     1.57: 4596
        1.57 -     1.69: 0
        1.69 -     1.80: 40
  Bond restraints: 9144
  Sorted by residual:
  bond pdb=" CB  TRP D 116 "
       pdb=" CG  TRP D 116 "
    ideal  model  delta    sigma   weight residual
    1.498  1.469  0.029 3.10e-02 1.04e+03 8.50e-01
  bond pdb=" CB  TRP E 116 "
       pdb=" CG  TRP E 116 "
    ideal  model  delta    sigma   weight residual
    1.498  1.469  0.029 3.10e-02 1.04e+03 8.46e-01
  bond pdb=" CB  TRP H 116 "
       pdb=" CG  TRP H 116 "
    ideal  model  delta    sigma   weight residual
    1.498  1.470  0.028 3.10e-02 1.04e+03 8.41e-01
  bond pdb=" CB  TRP G 116 "
       pdb=" CG  TRP G 116 "
    ideal  model  delta    sigma   weight residual
    1.498  1.470  0.028 3.10e-02 1.04e+03 8.31e-01
  bond pdb=" CB  TRP C 116 "
       pdb=" CG  TRP C 116 "
    ideal  model  delta    sigma   weight residual
    1.498  1.470  0.028 3.10e-02 1.04e+03 8.28e-01
  ... (remaining 9139 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.22: 11919
        1.22 -     2.45: 397
        2.45 -     3.67: 98
        3.67 -     4.89: 10
        4.89 -     6.11: 8
  Bond angle restraints: 12432
  Sorted by residual:
  angle pdb=" N   PRO F 125 "
        pdb=" CA  PRO F 125 "
        pdb=" C   PRO F 125 "
      ideal   model   delta    sigma   weight residual
     112.47  108.68    3.79 2.06e+00 2.36e-01 3.39e+00
  angle pdb=" N   PRO D 125 "
        pdb=" CA  PRO D 125 "
        pdb=" C   PRO D 125 "
      ideal   model   delta    sigma   weight residual
     112.47  108.68    3.79 2.06e+00 2.36e-01 3.39e+00
  angle pdb=" N   PRO B 125 "
        pdb=" CA  PRO B 125 "
        pdb=" C   PRO B 125 "
      ideal   model   delta    sigma   weight residual
     112.47  108.68    3.79 2.06e+00 2.36e-01 3.38e+00
  angle pdb=" N   PRO G 125 "
        pdb=" CA  PRO G 125 "
        pdb=" C   PRO G 125 "
      ideal   model   delta    sigma   weight residual
     112.47  108.69    3.78 2.06e+00 2.36e-01 3.36e+00
  angle pdb=" N   PRO E 125 "
        pdb=" CA  PRO E 125 "
        pdb=" C   PRO E 125 "
      ideal   model   delta    sigma   weight residual
     112.47  108.69    3.78 2.06e+00 2.36e-01 3.36e+00
  ... (remaining 12427 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    11.44: 4616
       11.44 -    22.88: 584
       22.88 -    34.33: 152
       34.33 -    45.77: 56
       45.77 -    57.21: 40
  Dihedral angle restraints: 5448
    sinusoidal: 1960
      harmonic: 3488
  Sorted by residual:
  dihedral pdb=" CA  THR I 124 "
           pdb=" C   THR I 124 "
           pdb=" N   PRO I 125 "
           pdb=" CA  PRO I 125 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.37   20.63     0      5.00e+00 4.00e-02 1.70e+01
  dihedral pdb=" CA  THR D 124 "
           pdb=" C   THR D 124 "
           pdb=" N   PRO D 125 "
           pdb=" CA  PRO D 125 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.40   20.60     0      5.00e+00 4.00e-02 1.70e+01
  dihedral pdb=" CA  THR C 124 "
           pdb=" C   THR C 124 "
           pdb=" N   PRO C 125 "
           pdb=" CA  PRO C 125 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.41   20.59     0      5.00e+00 4.00e-02 1.70e+01
  ... (remaining 5445 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.025: 800
       0.025 -    0.050: 488
       0.050 -    0.075: 151
       0.075 -    0.100: 50
       0.100 -    0.125: 39
  Chirality restraints: 1528
  Sorted by residual:
  chirality pdb=" CA  ILE F  83 "
            pdb=" N   ILE F  83 "
            pdb=" C   ILE F  83 "
            pdb=" CB  ILE F  83 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.89e-01
  chirality pdb=" CA  ILE B  83 "
            pdb=" N   ILE B  83 "
            pdb=" C   ILE B  83 "
            pdb=" CB  ILE B  83 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.81e-01
  chirality pdb=" CA  ILE I  83 "
            pdb=" N   ILE I  83 "
            pdb=" C   ILE I  83 "
            pdb=" CB  ILE I  83 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.72e-01
  ... (remaining 1525 not shown)

  Planarity restraints: 1560
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL E 112 "    0.007 2.00e-02 2.50e+03   1.38e-02 1.91e+00
        pdb=" C   VAL E 112 "   -0.024 2.00e-02 2.50e+03
        pdb=" O   VAL E 112 "    0.009 2.00e-02 2.50e+03
        pdb=" N   THR E 113 "    0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL H 112 "    0.007 2.00e-02 2.50e+03   1.38e-02 1.90e+00
        pdb=" C   VAL H 112 "   -0.024 2.00e-02 2.50e+03
        pdb=" O   VAL H 112 "    0.009 2.00e-02 2.50e+03
        pdb=" N   THR H 113 "    0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL C 112 "   -0.007 2.00e-02 2.50e+03   1.38e-02 1.89e+00
        pdb=" C   VAL C 112 "    0.024 2.00e-02 2.50e+03
        pdb=" O   VAL C 112 "   -0.009 2.00e-02 2.50e+03
        pdb=" N   THR C 113 "   -0.008 2.00e-02 2.50e+03
  ... (remaining 1557 not shown)

  Histogram of nonbonded interaction distances:
        2.12 -     2.68: 272
        2.68 -     3.23: 8654
        3.23 -     3.79: 13829
        3.79 -     4.34: 16973
        4.34 -     4.90: 28308
  Nonbonded interactions: 68036
  Sorted by model distance:
  nonbonded pdb=" O   THR G 157 "
            pdb=" OG1 THR G 157 "
     model   vdw
     2.120 3.040
  nonbonded pdb=" O   THR F 157 "
            pdb=" OG1 THR F 157 "
     model   vdw
     2.120 3.040
  nonbonded pdb=" O   THR C 157 "
            pdb=" OG1 THR C 157 "
     model   vdw
     2.120 3.040
  nonbonded pdb=" O   THR H 157 "
            pdb=" OG1 THR H 157 "
     model   vdw
     2.120 3.040
  nonbonded pdb=" O   THR B 157 "
            pdb=" OG1 THR B 157 "
     model   vdw
     2.120 3.040
  ... (remaining 68031 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: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
  selection = chain 'G'
  selection = chain 'H'
  selection = chain 'I'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.970
  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:             0.020
  Extract box with map and model:          0.220
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     9.020
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.320
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.690
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8780
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      :  0.006   0.029   9144  Z= 0.271
  Angle     :  0.587   6.115  12432  Z= 0.309
  Chirality :  0.038   0.125   1528
  Planarity :  0.003   0.022   1560
  Dihedral  : 12.703  57.209   3208
  Min Nonbonded Distance : 2.120

Molprobity Statistics.
  All-atom Clashscore : 7.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.71 %
    Favored  : 93.29 %
  Rotamer:
    Outliers :  4.35 %
    Allowed  :  5.33 %
    Favored  : 90.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.98 (0.21), residues: 1192
  helix:  1.02 (0.23), residues: 448
  sheet: -0.59 (0.32), residues: 208
  loop : -3.91 (0.17), residues: 536

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.000   0.000   ARG F  38 
 TYR   0.009   0.001   TYR E 131 
 PHE   0.007   0.001   PHE C 140 
 TRP   0.001   0.001   TRP I 116 
 HIS   0.002   0.001   HIS H 133 

Details of bonding type rmsd
  covalent geometry    : bond        0.00614 ( 9144)
  covalent geometry    : angle       0.58653 (12432)
  hydrogen bonds       : bond        0.16281 (  504)
  hydrogen bonds       : angle       6.22603 ( 1416)

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

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

  2384 Ramachandran restraints generated.
    1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2384 Ramachandran restraints generated.
    1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  274 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 234
  time to evaluate  : 0.346 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  124 THR cc_start: 0.8478 (OUTLIER) cc_final: 0.8271 (m)
REVERT: B  131 TYR cc_start: 0.9038 (p90) cc_final: 0.8676 (p90)
REVERT: C   29 LYS cc_start: 0.8442 (tttt) cc_final: 0.7438 (mptt)
REVERT: C   84 LEU cc_start: 0.9153 (tp) cc_final: 0.8939 (tt)
REVERT: C   85 ASP cc_start: 0.8727 (t0) cc_final: 0.8515 (t0)
REVERT: D   29 LYS cc_start: 0.8629 (tttt) cc_final: 0.7620 (mptt)
REVERT: E   29 LYS cc_start: 0.8574 (tttt) cc_final: 0.7629 (mptt)
REVERT: E   85 ASP cc_start: 0.8817 (t0) cc_final: 0.8363 (t0)
REVERT: E  132 GLN cc_start: 0.8520 (tt0) cc_final: 0.8308 (tt0)
REVERT: F   50 GLN cc_start: 0.8928 (tt0) cc_final: 0.8719 (tt0)
REVERT: F   85 ASP cc_start: 0.8485 (t0) cc_final: 0.8155 (t0)
REVERT: G   85 ASP cc_start: 0.8768 (t0) cc_final: 0.8394 (t0)
REVERT: G   96 GLU cc_start: 0.8322 (mt-10) cc_final: 0.8041 (mm-30)
REVERT: G  124 THR cc_start: 0.8736 (OUTLIER) cc_final: 0.8492 (m)
REVERT: G  132 GLN cc_start: 0.8776 (tt0) cc_final: 0.8551 (tt0)
REVERT: H   43 GLN cc_start: 0.9055 (mt0) cc_final: 0.8761 (tt0)
REVERT: H   85 ASP cc_start: 0.8687 (t0) cc_final: 0.8444 (t0)
REVERT: H  115 ASP cc_start: 0.8498 (m-30) cc_final: 0.8134 (t0)
REVERT: H  124 THR cc_start: 0.8646 (OUTLIER) cc_final: 0.8425 (m)
REVERT: I   25 THR cc_start: 0.8829 (OUTLIER) cc_final: 0.8146 (p)
REVERT: I   43 GLN cc_start: 0.8963 (mt0) cc_final: 0.8745 (mt0)
REVERT: I   85 ASP cc_start: 0.8679 (t0) cc_final: 0.8365 (t0)
REVERT: I  110 GLN cc_start: 0.8029 (pp30) cc_final: 0.7811 (pp30)
REVERT: I  124 THR cc_start: 0.8600 (OUTLIER) cc_final: 0.8293 (m)
  outliers start: 40
  outliers final: 8
  residues processed: 267
  average time/residue: 0.1122
  time to fit residues: 39.8751
Evaluate side-chains
  179 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 166
  time to evaluate  : 0.406 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   80 THR
Chi-restraints excluded: chain B residue  124 THR
Chi-restraints excluded: chain C residue   80 THR
Chi-restraints excluded: chain D residue   80 THR
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain G residue  124 THR
Chi-restraints excluded: chain G residue  157 THR
Chi-restraints excluded: chain H residue   80 THR
Chi-restraints excluded: chain H residue  124 THR
Chi-restraints excluded: chain H residue  157 THR
Chi-restraints excluded: chain I residue   25 THR
Chi-restraints excluded: chain I residue   80 THR
Chi-restraints excluded: chain I residue  124 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 108 optimal weight:    1.9990
   chunk 49 optimal weight:    4.9990
   chunk 97 optimal weight:    8.9990
   chunk 113 optimal weight:    5.9990
   chunk 53 optimal weight:    9.9990
   chunk 5 optimal weight:    0.1980
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    9.9990
   chunk 51 optimal weight:   10.0000
   chunk 117 optimal weight:    4.9990
   overall best weight:    3.0388

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

Flipped N/Q/H residues before XYZ refinement:
** E  70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  50 GLN
** G 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3021 r_free = 0.3021 target = 0.064374 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2647 r_free = 0.2647 target = 0.048386 restraints weight = 27382.855|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2694 r_free = 0.2694 target = 0.050205 restraints weight = 14670.966|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2725 r_free = 0.2725 target = 0.051477 restraints weight = 9991.561|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.2746 r_free = 0.2746 target = 0.052355 restraints weight = 7803.242|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.2758 r_free = 0.2758 target = 0.052849 restraints weight = 6615.584|
|-----------------------------------------------------------------------------|
r_work (final): 0.2752
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8739
moved from start:          0.1897

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   9144  Z= 0.175
  Angle     :  0.570   5.666  12432  Z= 0.299
  Chirality :  0.039   0.160   1528
  Planarity :  0.004   0.033   1560
  Dihedral  :  5.456  57.794   1269
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 5.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.20 %
    Favored  : 94.80 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  : 12.83 %
    Favored  : 85.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.60 (0.23), residues: 1192
  helix:  2.34 (0.25), residues: 456
  sheet:  0.29 (0.31), residues: 208
  loop : -3.45 (0.19), residues: 528

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG D  38 
 TYR   0.024   0.001   TYR C 131 
 PHE   0.011   0.001   PHE E   7 
 TRP   0.004   0.001   TRP F 116 
 HIS   0.001   0.000   HIS C 133 

Details of bonding type rmsd
  covalent geometry    : bond        0.00413 ( 9144)
  covalent geometry    : angle       0.57047 (12432)
  hydrogen bonds       : bond        0.04409 (  504)
  hydrogen bonds       : angle       4.12355 ( 1416)

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

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

  2384 Ramachandran restraints generated.
    1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2384 Ramachandran restraints generated.
    1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  214 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 201
  time to evaluate  : 0.330 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  131 TYR cc_start: 0.8981 (p90) cc_final: 0.8566 (p90)
REVERT: B  132 GLN cc_start: 0.8560 (tt0) cc_final: 0.8263 (tt0)
REVERT: C   29 LYS cc_start: 0.8433 (tttt) cc_final: 0.7428 (mptt)
REVERT: C   84 LEU cc_start: 0.9121 (tp) cc_final: 0.8913 (tt)
REVERT: C   85 ASP cc_start: 0.8730 (t0) cc_final: 0.8310 (t0)
REVERT: D   29 LYS cc_start: 0.8504 (tttt) cc_final: 0.7547 (mptt)
REVERT: D   70 GLN cc_start: 0.8866 (mt0) cc_final: 0.8261 (mp10)
REVERT: D   85 ASP cc_start: 0.8687 (t0) cc_final: 0.8334 (t0)
REVERT: E   29 LYS cc_start: 0.8563 (tttt) cc_final: 0.7678 (mptt)
REVERT: E   70 GLN cc_start: 0.8859 (mt0) cc_final: 0.8198 (mp10)
REVERT: E   85 ASP cc_start: 0.8765 (t0) cc_final: 0.8236 (t0)
REVERT: E   96 GLU cc_start: 0.8562 (mt-10) cc_final: 0.8294 (mt-10)
REVERT: E  131 TYR cc_start: 0.9011 (p90) cc_final: 0.8690 (p90)
REVERT: F   50 GLN cc_start: 0.8947 (tt0) cc_final: 0.8675 (tt0)
REVERT: F   85 ASP cc_start: 0.8458 (t0) cc_final: 0.8056 (t0)
REVERT: G   50 GLN cc_start: 0.8763 (tt0) cc_final: 0.8478 (tt0)
REVERT: G   65 LYS cc_start: 0.9185 (mmtp) cc_final: 0.8916 (mmtp)
REVERT: G   85 ASP cc_start: 0.8695 (t0) cc_final: 0.8240 (t0)
REVERT: G   96 GLU cc_start: 0.8483 (mt-10) cc_final: 0.8199 (mm-30)
REVERT: G  132 GLN cc_start: 0.8785 (tt0) cc_final: 0.8535 (tt0)
REVERT: H   43 GLN cc_start: 0.9079 (mt0) cc_final: 0.8868 (tt0)
REVERT: H   85 ASP cc_start: 0.8648 (t0) cc_final: 0.8279 (t0)
REVERT: H  115 ASP cc_start: 0.8629 (m-30) cc_final: 0.8075 (t0)
REVERT: H  124 THR cc_start: 0.8546 (OUTLIER) cc_final: 0.8320 (m)
REVERT: H  157 THR cc_start: 0.8181 (OUTLIER) cc_final: 0.7980 (t)
REVERT: I   50 GLN cc_start: 0.8768 (tt0) cc_final: 0.8528 (tt0)
REVERT: I   85 ASP cc_start: 0.8563 (t0) cc_final: 0.8114 (t0)
REVERT: I  147 LYS cc_start: 0.8787 (ttmm) cc_final: 0.8342 (ttmm)
REVERT: I  160 GLU cc_start: 0.7457 (mp0) cc_final: 0.7084 (mp0)
  outliers start: 13
  outliers final: 4
  residues processed: 209
  average time/residue: 0.0984
  time to fit residues: 28.4976
Evaluate side-chains
  171 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 165
  time to evaluate  : 0.301 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   25 THR
Chi-restraints excluded: chain F residue   49 ILE
Chi-restraints excluded: chain F residue   80 THR
Chi-restraints excluded: chain G residue   49 ILE
Chi-restraints excluded: chain H residue  124 THR
Chi-restraints excluded: chain H residue  157 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 3 optimal weight:    0.9980
   chunk 56 optimal weight:    3.9990
   chunk 113 optimal weight:    6.9990
   chunk 109 optimal weight:    3.9990
   chunk 15 optimal weight:    2.9990
   chunk 114 optimal weight:    8.9990
   chunk 55 optimal weight:    6.9990
   chunk 85 optimal weight:   10.0000
   chunk 89 optimal weight:    8.9990
   chunk 108 optimal weight:    0.9980
   chunk 82 optimal weight:    6.9990
   overall best weight:    2.5986

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

Flipped N/Q/H residues before XYZ refinement:
** E  70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 110 GLN
** G 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3033 r_free = 0.3033 target = 0.064850 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2662 r_free = 0.2662 target = 0.048793 restraints weight = 27215.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.2708 r_free = 0.2708 target = 0.050613 restraints weight = 14696.504|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.2739 r_free = 0.2739 target = 0.051894 restraints weight = 10025.875|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2760 r_free = 0.2760 target = 0.052765 restraints weight = 7813.554|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.2772 r_free = 0.2772 target = 0.053317 restraints weight = 6641.297|
|-----------------------------------------------------------------------------|
r_work (final): 0.2765
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8730
moved from start:          0.2355

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   9144  Z= 0.154
  Angle     :  0.549   6.740  12432  Z= 0.284
  Chirality :  0.039   0.181   1528
  Planarity :  0.004   0.034   1560
  Dihedral  :  4.406  36.224   1258
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 6.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.87 %
    Favored  : 95.13 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 15.98 %
    Favored  : 82.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.05 (0.25), residues: 1192
  helix:  2.84 (0.25), residues: 456
  sheet:  0.17 (0.31), residues: 264
  loop : -3.33 (0.21), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D  38 
 TYR   0.012   0.001   TYR I 131 
 PHE   0.008   0.001   PHE C 103 
 TRP   0.002   0.000   TRP I 116 
 HIS   0.001   0.001   HIS C 133 

Details of bonding type rmsd
  covalent geometry    : bond        0.00368 ( 9144)
  covalent geometry    : angle       0.54903 (12432)
  hydrogen bonds       : bond        0.03833 (  504)
  hydrogen bonds       : angle       3.89830 ( 1416)

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

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

  2384 Ramachandran restraints generated.
    1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2384 Ramachandran restraints generated.
    1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 183
  time to evaluate  : 0.383 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   85 ASP cc_start: 0.8775 (t0) cc_final: 0.8226 (t0)
REVERT: B  132 GLN cc_start: 0.8574 (tt0) cc_final: 0.8216 (tt0)
REVERT: C   29 LYS cc_start: 0.8437 (tttt) cc_final: 0.7410 (mptt)
REVERT: C   84 LEU cc_start: 0.9128 (tp) cc_final: 0.8900 (tt)
REVERT: C   85 ASP cc_start: 0.8729 (t0) cc_final: 0.8297 (t0)
REVERT: D   29 LYS cc_start: 0.8485 (tttt) cc_final: 0.7533 (mptt)
REVERT: D   70 GLN cc_start: 0.8816 (mt0) cc_final: 0.8202 (mp10)
REVERT: D   85 ASP cc_start: 0.8735 (t0) cc_final: 0.8371 (t0)
REVERT: D  138 ASN cc_start: 0.8157 (m-40) cc_final: 0.7724 (p0)
REVERT: E   29 LYS cc_start: 0.8572 (tttt) cc_final: 0.7706 (mptt)
REVERT: E  131 TYR cc_start: 0.9006 (p90) cc_final: 0.8716 (p90)
REVERT: F   50 GLN cc_start: 0.8928 (tt0) cc_final: 0.8568 (tt0)
REVERT: F   85 ASP cc_start: 0.8490 (t0) cc_final: 0.8116 (t0)
REVERT: G   50 GLN cc_start: 0.8682 (tt0) cc_final: 0.8405 (tt0)
REVERT: G   65 LYS cc_start: 0.9156 (mmtp) cc_final: 0.8902 (mmtp)
REVERT: G   70 GLN cc_start: 0.8595 (mt0) cc_final: 0.8145 (mp10)
REVERT: G   85 ASP cc_start: 0.8723 (t0) cc_final: 0.8225 (t0)
REVERT: G   96 GLU cc_start: 0.8521 (mt-10) cc_final: 0.8183 (mm-30)
REVERT: H   66 GLU cc_start: 0.8085 (pm20) cc_final: 0.7836 (pp20)
REVERT: H   85 ASP cc_start: 0.8650 (t0) cc_final: 0.8201 (t0)
REVERT: H  115 ASP cc_start: 0.8594 (m-30) cc_final: 0.8076 (t0)
REVERT: H  124 THR cc_start: 0.8552 (OUTLIER) cc_final: 0.8315 (m)
REVERT: I   85 ASP cc_start: 0.8502 (t0) cc_final: 0.8117 (t0)
REVERT: I   96 GLU cc_start: 0.8660 (mt-10) cc_final: 0.8251 (mt-10)
REVERT: I  147 LYS cc_start: 0.8844 (ttmm) cc_final: 0.8266 (ttmm)
REVERT: I  160 GLU cc_start: 0.7492 (mp0) cc_final: 0.7023 (mp0)
  outliers start: 16
  outliers final: 6
  residues processed: 189
  average time/residue: 0.0861
  time to fit residues: 22.8915
Evaluate side-chains
  170 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 163
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   69 SER
Chi-restraints excluded: chain E residue   69 SER
Chi-restraints excluded: chain F residue   58 SER
Chi-restraints excluded: chain F residue   74 SER
Chi-restraints excluded: chain H residue  124 THR
Chi-restraints excluded: chain I residue   69 SER
Chi-restraints excluded: chain I residue  139 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 89 optimal weight:    8.9990
   chunk 0 optimal weight:   10.0000
   chunk 49 optimal weight:    0.7980
   chunk 69 optimal weight:    6.9990
   chunk 55 optimal weight:    7.9990
   chunk 98 optimal weight:    6.9990
   chunk 102 optimal weight:    5.9990
   chunk 30 optimal weight:    2.9990
   chunk 57 optimal weight:    4.9990
   chunk 107 optimal weight:    4.9990
   chunk 67 optimal weight:    6.9990
   overall best weight:    3.9588

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

Flipped N/Q/H residues before XYZ refinement:
** E  70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 110 GLN
H  50 GLN
** I 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3007 r_free = 0.3007 target = 0.063827 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2633 r_free = 0.2633 target = 0.047704 restraints weight = 27751.457|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2679 r_free = 0.2679 target = 0.049487 restraints weight = 14918.679|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.2710 r_free = 0.2710 target = 0.050742 restraints weight = 10222.365|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.2730 r_free = 0.2730 target = 0.051596 restraints weight = 7991.115|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.2742 r_free = 0.2742 target = 0.052071 restraints weight = 6793.758|
|-----------------------------------------------------------------------------|
r_work (final): 0.2735
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8762
moved from start:          0.2493

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051   9144  Z= 0.217
  Angle     :  0.605   8.747  12432  Z= 0.305
  Chirality :  0.039   0.171   1528
  Planarity :  0.004   0.035   1560
  Dihedral  :  4.473  36.146   1257
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 6.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.71 %
    Favored  : 93.29 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 20.98 %
    Favored  : 76.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.11 (0.25), residues: 1192
  helix:  2.86 (0.25), residues: 456
  sheet: -0.18 (0.41), residues: 160
  loop : -2.37 (0.22), residues: 576

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG H  38 
 TYR   0.013   0.001   TYR C 131 
 PHE   0.010   0.001   PHE C 103 
 TRP   0.002   0.001   TRP F 116 
 HIS   0.002   0.000   HIS C 133 

Details of bonding type rmsd
  covalent geometry    : bond        0.00517 ( 9144)
  covalent geometry    : angle       0.60499 (12432)
  hydrogen bonds       : bond        0.04210 (  504)
  hydrogen bonds       : angle       3.95969 ( 1416)

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

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

  2384 Ramachandran restraints generated.
    1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2384 Ramachandran restraints generated.
    1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 167
  time to evaluate  : 0.415 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   85 ASP cc_start: 0.8894 (t0) cc_final: 0.8401 (t0)
REVERT: B  131 TYR cc_start: 0.8973 (p90) cc_final: 0.8547 (p90)
REVERT: B  132 GLN cc_start: 0.8587 (tt0) cc_final: 0.8262 (tt0)
REVERT: C   29 LYS cc_start: 0.8473 (tttt) cc_final: 0.7452 (mptt)
REVERT: C   84 LEU cc_start: 0.9141 (tp) cc_final: 0.8925 (tt)
REVERT: C   85 ASP cc_start: 0.8780 (t0) cc_final: 0.8324 (t0)
REVERT: C  106 LYS cc_start: 0.8969 (tptm) cc_final: 0.8630 (tppt)
REVERT: D   29 LYS cc_start: 0.8442 (tttt) cc_final: 0.7485 (mptt)
REVERT: D   70 GLN cc_start: 0.8862 (mt0) cc_final: 0.8449 (mm110)
REVERT: D   85 ASP cc_start: 0.8794 (t0) cc_final: 0.8436 (t0)
REVERT: E   29 LYS cc_start: 0.8567 (tttt) cc_final: 0.7695 (mptt)
REVERT: E   70 GLN cc_start: 0.8858 (mt0) cc_final: 0.8487 (mm110)
REVERT: E   96 GLU cc_start: 0.8510 (mt-10) cc_final: 0.8245 (mt-10)
REVERT: E  131 TYR cc_start: 0.9005 (p90) cc_final: 0.8729 (p90)
REVERT: F   50 GLN cc_start: 0.8955 (tt0) cc_final: 0.8574 (tt0)
REVERT: F   85 ASP cc_start: 0.8481 (t0) cc_final: 0.8105 (t0)
REVERT: G   50 GLN cc_start: 0.8667 (tt0) cc_final: 0.8443 (tt0)
REVERT: G   85 ASP cc_start: 0.8711 (t0) cc_final: 0.8253 (t0)
REVERT: G   96 GLU cc_start: 0.8545 (mt-10) cc_final: 0.8267 (mm-30)
REVERT: H   29 LYS cc_start: 0.9011 (ttpt) cc_final: 0.8799 (ttpp)
REVERT: H   69 SER cc_start: 0.8987 (m) cc_final: 0.8606 (p)
REVERT: H   85 ASP cc_start: 0.8614 (t0) cc_final: 0.8253 (t0)
REVERT: H  115 ASP cc_start: 0.8617 (m-30) cc_final: 0.8159 (t0)
REVERT: H  124 THR cc_start: 0.8523 (OUTLIER) cc_final: 0.8287 (m)
REVERT: I   66 GLU cc_start: 0.8003 (pm20) cc_final: 0.7707 (pp20)
REVERT: I   85 ASP cc_start: 0.8528 (t0) cc_final: 0.8051 (t0)
REVERT: I  147 LYS cc_start: 0.8874 (ttmm) cc_final: 0.8253 (ttmm)
REVERT: I  160 GLU cc_start: 0.7534 (mp0) cc_final: 0.6980 (mp0)
  outliers start: 19
  outliers final: 15
  residues processed: 175
  average time/residue: 0.0899
  time to fit residues: 22.3314
Evaluate side-chains
  175 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 159
  time to evaluate  : 0.338 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  101 ILE
Chi-restraints excluded: chain B residue  124 THR
Chi-restraints excluded: chain C residue   69 SER
Chi-restraints excluded: chain D residue   69 SER
Chi-restraints excluded: chain E residue   25 THR
Chi-restraints excluded: chain E residue   69 SER
Chi-restraints excluded: chain E residue  132 GLN
Chi-restraints excluded: chain F residue   58 SER
Chi-restraints excluded: chain F residue   74 SER
Chi-restraints excluded: chain G residue   81 ILE
Chi-restraints excluded: chain G residue  124 THR
Chi-restraints excluded: chain H residue  124 THR
Chi-restraints excluded: chain H residue  139 CYS
Chi-restraints excluded: chain I residue   69 SER
Chi-restraints excluded: chain I residue  124 THR
Chi-restraints excluded: chain I residue  139 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 71 optimal weight:   20.0000
   chunk 84 optimal weight:    1.9990
   chunk 97 optimal weight:    9.9990
   chunk 106 optimal weight:    2.9990
   chunk 62 optimal weight:    8.9990
   chunk 56 optimal weight:   10.0000
   chunk 98 optimal weight:    7.9990
   chunk 108 optimal weight:    2.9990
   chunk 1 optimal weight:    5.9990
   chunk 38 optimal weight:    0.9980
   chunk 76 optimal weight:    2.9990
   overall best weight:    2.3988

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

Flipped N/Q/H residues before XYZ refinement:
F 110 GLN
H  50 GLN
H 110 GLN
I 110 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3038 r_free = 0.3038 target = 0.065183 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2673 r_free = 0.2673 target = 0.049169 restraints weight = 27328.614|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.2720 r_free = 0.2720 target = 0.050990 restraints weight = 14611.999|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2750 r_free = 0.2750 target = 0.052268 restraints weight = 9980.662|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.2771 r_free = 0.2771 target = 0.053151 restraints weight = 7768.546|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.2784 r_free = 0.2784 target = 0.053693 restraints weight = 6590.913|
|-----------------------------------------------------------------------------|
r_work (final): 0.2777
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8720
moved from start:          0.2751

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   9144  Z= 0.150
  Angle     :  0.555   7.333  12432  Z= 0.283
  Chirality :  0.039   0.165   1528
  Planarity :  0.004   0.036   1560
  Dihedral  :  4.311  36.913   1257
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 5.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.45 %
    Favored  : 94.55 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 21.52 %
    Favored  : 75.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.37 (0.25), residues: 1192
  helix:  3.10 (0.25), residues: 456
  sheet: -0.15 (0.41), residues: 160
  loop : -2.20 (0.23), residues: 576

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D  38 
 TYR   0.016   0.001   TYR H 131 
 PHE   0.007   0.001   PHE C 103 
 TRP   0.002   0.000   TRP C 116 
 HIS   0.001   0.000   HIS C 133 

Details of bonding type rmsd
  covalent geometry    : bond        0.00364 ( 9144)
  covalent geometry    : angle       0.55526 (12432)
  hydrogen bonds       : bond        0.03542 (  504)
  hydrogen bonds       : angle       3.73008 ( 1416)

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

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

  2384 Ramachandran restraints generated.
    1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2384 Ramachandran restraints generated.
    1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 168
  time to evaluate  : 0.343 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   85 ASP cc_start: 0.8847 (t0) cc_final: 0.8352 (t0)
REVERT: B  131 TYR cc_start: 0.8984 (p90) cc_final: 0.8749 (p90)
REVERT: B  132 GLN cc_start: 0.8548 (tt0) cc_final: 0.8206 (tt0)
REVERT: C   29 LYS cc_start: 0.8451 (tttt) cc_final: 0.7443 (mptt)
REVERT: C   85 ASP cc_start: 0.8699 (t0) cc_final: 0.8291 (t0)
REVERT: C  106 LYS cc_start: 0.8932 (tptm) cc_final: 0.8584 (tppt)
REVERT: D   29 LYS cc_start: 0.8404 (tttt) cc_final: 0.7304 (mmtm)
REVERT: D   70 GLN cc_start: 0.8818 (mt0) cc_final: 0.8528 (mm110)
REVERT: D   85 ASP cc_start: 0.8766 (t0) cc_final: 0.8409 (t0)
REVERT: D  138 ASN cc_start: 0.8215 (m-40) cc_final: 0.7815 (p0)
REVERT: E   29 LYS cc_start: 0.8499 (tttt) cc_final: 0.7696 (mptt)
REVERT: E   96 GLU cc_start: 0.8507 (mt-10) cc_final: 0.8249 (mt-10)
REVERT: E  131 TYR cc_start: 0.8992 (p90) cc_final: 0.8724 (p90)
REVERT: F   50 GLN cc_start: 0.8939 (tt0) cc_final: 0.8551 (tt0)
REVERT: F   85 ASP cc_start: 0.8467 (t0) cc_final: 0.8092 (t0)
REVERT: G   50 GLN cc_start: 0.8641 (tt0) cc_final: 0.8413 (tt0)
REVERT: G   65 LYS cc_start: 0.9239 (mmtp) cc_final: 0.9039 (mmtp)
REVERT: G   85 ASP cc_start: 0.8675 (t0) cc_final: 0.8207 (t0)
REVERT: G   96 GLU cc_start: 0.8528 (mt-10) cc_final: 0.8238 (mm-30)
REVERT: H   29 LYS cc_start: 0.9032 (ttpt) cc_final: 0.8818 (ttpp)
REVERT: H   65 LYS cc_start: 0.9359 (mtpt) cc_final: 0.9001 (mtpp)
REVERT: H   66 GLU cc_start: 0.8158 (pm20) cc_final: 0.7756 (pp20)
REVERT: H   69 SER cc_start: 0.9001 (m) cc_final: 0.8589 (p)
REVERT: H   85 ASP cc_start: 0.8624 (t0) cc_final: 0.8227 (t0)
REVERT: H  115 ASP cc_start: 0.8625 (m-30) cc_final: 0.8145 (t0)
REVERT: H  124 THR cc_start: 0.8523 (OUTLIER) cc_final: 0.8298 (m)
REVERT: I   85 ASP cc_start: 0.8477 (t0) cc_final: 0.8031 (t0)
REVERT: I  147 LYS cc_start: 0.8849 (ttmm) cc_final: 0.8235 (ttmm)
REVERT: I  160 GLU cc_start: 0.7538 (mp0) cc_final: 0.6976 (mp0)
  outliers start: 23
  outliers final: 16
  residues processed: 182
  average time/residue: 0.0853
  time to fit residues: 22.0340
Evaluate side-chains
  173 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 156
  time to evaluate  : 0.261 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  124 THR
Chi-restraints excluded: chain C residue   69 SER
Chi-restraints excluded: chain C residue  101 ILE
Chi-restraints excluded: chain D residue   69 SER
Chi-restraints excluded: chain E residue   25 THR
Chi-restraints excluded: chain E residue   69 SER
Chi-restraints excluded: chain E residue  132 GLN
Chi-restraints excluded: chain F residue   58 SER
Chi-restraints excluded: chain G residue   49 ILE
Chi-restraints excluded: chain G residue   81 ILE
Chi-restraints excluded: chain G residue  124 THR
Chi-restraints excluded: chain G residue  132 GLN
Chi-restraints excluded: chain H residue  124 THR
Chi-restraints excluded: chain H residue  139 CYS
Chi-restraints excluded: chain I residue   69 SER
Chi-restraints excluded: chain I residue  124 THR
Chi-restraints excluded: chain I residue  139 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 116 optimal weight:    0.2980
   chunk 77 optimal weight:   10.0000
   chunk 60 optimal weight:    2.9990
   chunk 51 optimal weight:    9.9990
   chunk 3 optimal weight:    1.9990
   chunk 71 optimal weight:   20.0000
   chunk 26 optimal weight:    7.9990
   chunk 13 optimal weight:    1.9990
   chunk 54 optimal weight:    7.9990
   chunk 63 optimal weight:    0.9990
   chunk 28 optimal weight:    9.9990
   overall best weight:    1.6588

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3059 r_free = 0.3059 target = 0.066108 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2700 r_free = 0.2700 target = 0.050169 restraints weight = 27057.550|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2746 r_free = 0.2746 target = 0.052020 restraints weight = 14309.676|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2776 r_free = 0.2776 target = 0.053303 restraints weight = 9719.734|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.2797 r_free = 0.2797 target = 0.054202 restraints weight = 7547.021|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.2810 r_free = 0.2810 target = 0.054755 restraints weight = 6376.100|
|-----------------------------------------------------------------------------|
r_work (final): 0.2802
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8693
moved from start:          0.2969

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9144  Z= 0.124
  Angle     :  0.548   7.253  12432  Z= 0.282
  Chirality :  0.038   0.159   1528
  Planarity :  0.004   0.046   1560
  Dihedral  :  4.213  37.214   1257
  Min Nonbonded Distance : 2.385

Molprobity Statistics.
  All-atom Clashscore : 6.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.79 %
    Favored  : 94.21 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 21.74 %
    Favored  : 75.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.54 (0.26), residues: 1192
  helix:  3.20 (0.25), residues: 456
  sheet:  0.42 (0.32), residues: 264
  loop : -2.82 (0.23), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D  38 
 TYR   0.013   0.001   TYR H 131 
 PHE   0.006   0.001   PHE D 103 
 TRP   0.002   0.000   TRP C 116 
 HIS   0.001   0.000   HIS C 133 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 ( 9144)
  covalent geometry    : angle       0.54829 (12432)
  hydrogen bonds       : bond        0.03187 (  504)
  hydrogen bonds       : angle       3.59920 ( 1416)

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

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

  2384 Ramachandran restraints generated.
    1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2384 Ramachandran restraints generated.
    1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 176
  time to evaluate  : 0.277 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   85 ASP cc_start: 0.8852 (t0) cc_final: 0.8414 (t0)
REVERT: B  132 GLN cc_start: 0.8536 (tt0) cc_final: 0.8200 (tt0)
REVERT: C   29 LYS cc_start: 0.8439 (tttt) cc_final: 0.7458 (mptt)
REVERT: C   85 ASP cc_start: 0.8718 (t0) cc_final: 0.8280 (t0)
REVERT: C  106 LYS cc_start: 0.8909 (tptm) cc_final: 0.8566 (tppt)
REVERT: D   29 LYS cc_start: 0.8349 (tttt) cc_final: 0.7267 (mmtm)
REVERT: D   70 GLN cc_start: 0.8772 (mt0) cc_final: 0.8413 (mm110)
REVERT: D   85 ASP cc_start: 0.8774 (t0) cc_final: 0.8398 (t0)
REVERT: D  138 ASN cc_start: 0.8175 (m-40) cc_final: 0.7851 (p0)
REVERT: E   29 LYS cc_start: 0.8409 (tttt) cc_final: 0.7642 (mptt)
REVERT: E   96 GLU cc_start: 0.8503 (mt-10) cc_final: 0.8227 (mt-10)
REVERT: F   50 GLN cc_start: 0.8925 (tt0) cc_final: 0.8546 (tt0)
REVERT: F   85 ASP cc_start: 0.8477 (t0) cc_final: 0.8073 (t0)
REVERT: G   50 GLN cc_start: 0.8609 (tt0) cc_final: 0.8369 (tt0)
REVERT: G   85 ASP cc_start: 0.8633 (t0) cc_final: 0.8177 (t0)
REVERT: G   96 GLU cc_start: 0.8510 (mt-10) cc_final: 0.8280 (mm-30)
REVERT: H   65 LYS cc_start: 0.9363 (mtpt) cc_final: 0.9009 (mtpp)
REVERT: H   66 GLU cc_start: 0.8146 (pm20) cc_final: 0.7763 (pp20)
REVERT: H   69 SER cc_start: 0.8997 (m) cc_final: 0.8596 (p)
REVERT: H   85 ASP cc_start: 0.8577 (t0) cc_final: 0.8182 (t0)
REVERT: H  115 ASP cc_start: 0.8542 (m-30) cc_final: 0.8008 (t0)
REVERT: I   66 GLU cc_start: 0.7960 (pm20) cc_final: 0.7655 (pp20)
REVERT: I   85 ASP cc_start: 0.8464 (t0) cc_final: 0.8065 (t0)
REVERT: I  147 LYS cc_start: 0.8850 (ttmm) cc_final: 0.8274 (ttmm)
REVERT: I  160 GLU cc_start: 0.7481 (mp0) cc_final: 0.6986 (mp0)
  outliers start: 22
  outliers final: 15
  residues processed: 188
  average time/residue: 0.0819
  time to fit residues: 22.2534
Evaluate side-chains
  172 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 157
  time to evaluate  : 0.410 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  119 ASP
Chi-restraints excluded: chain B residue  124 THR
Chi-restraints excluded: chain E residue   25 THR
Chi-restraints excluded: chain E residue   69 SER
Chi-restraints excluded: chain E residue  132 GLN
Chi-restraints excluded: chain F residue   58 SER
Chi-restraints excluded: chain F residue   88 MET
Chi-restraints excluded: chain G residue   81 ILE
Chi-restraints excluded: chain G residue  124 THR
Chi-restraints excluded: chain G residue  132 GLN
Chi-restraints excluded: chain G residue  166 ILE
Chi-restraints excluded: chain H residue  139 CYS
Chi-restraints excluded: chain I residue   69 SER
Chi-restraints excluded: chain I residue  124 THR
Chi-restraints excluded: chain I residue  139 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 45 optimal weight:    4.9990
   chunk 79 optimal weight:    5.9990
   chunk 18 optimal weight:    0.9980
   chunk 85 optimal weight:    8.9990
   chunk 101 optimal weight:    1.9990
   chunk 99 optimal weight:    5.9990
   chunk 33 optimal weight:    6.9990
   chunk 65 optimal weight:    9.9990
   chunk 60 optimal weight:    0.8980
   chunk 19 optimal weight:    0.9980
   chunk 69 optimal weight:    9.9990
   overall best weight:    1.9784

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

Flipped N/Q/H residues before XYZ refinement:
** F 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3059 r_free = 0.3059 target = 0.066040 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2700 r_free = 0.2700 target = 0.050131 restraints weight = 27364.627|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2746 r_free = 0.2746 target = 0.051961 restraints weight = 14466.176|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2777 r_free = 0.2777 target = 0.053255 restraints weight = 9839.048|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.2797 r_free = 0.2797 target = 0.054128 restraints weight = 7634.213|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2810 r_free = 0.2810 target = 0.054714 restraints weight = 6463.161|
|-----------------------------------------------------------------------------|
r_work (final): 0.2803
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8697
moved from start:          0.3103

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9144  Z= 0.137
  Angle     :  0.563   6.672  12432  Z= 0.291
  Chirality :  0.039   0.170   1528
  Planarity :  0.004   0.045   1560
  Dihedral  :  4.103  24.492   1256
  Min Nonbonded Distance : 2.397

Molprobity Statistics.
  All-atom Clashscore : 6.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.54 %
    Favored  : 94.46 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 23.04 %
    Favored  : 74.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.60 (0.26), residues: 1192
  helix:  3.15 (0.25), residues: 456
  sheet:  0.43 (0.32), residues: 264
  loop : -2.64 (0.24), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D  38 
 TYR   0.012   0.001   TYR H 131 
 PHE   0.007   0.001   PHE D 140 
 TRP   0.003   0.000   TRP C 116 
 HIS   0.002   0.001   HIS E 133 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 ( 9144)
  covalent geometry    : angle       0.56283 (12432)
  hydrogen bonds       : bond        0.03258 (  504)
  hydrogen bonds       : angle       3.59364 ( 1416)

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

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

  2384 Ramachandran restraints generated.
    1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2384 Ramachandran restraints generated.
    1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 160
  time to evaluate  : 0.349 
Fit side-chains
   revert: symmetry clash
REVERT: B   85 ASP cc_start: 0.8836 (t0) cc_final: 0.8457 (t0)
REVERT: B  132 GLN cc_start: 0.8562 (tt0) cc_final: 0.8197 (tt0)
REVERT: C   29 LYS cc_start: 0.8412 (tttt) cc_final: 0.7452 (mptt)
REVERT: C  106 LYS cc_start: 0.8899 (tptm) cc_final: 0.8573 (tppt)
REVERT: D   29 LYS cc_start: 0.8347 (tttt) cc_final: 0.7272 (mmtm)
REVERT: D   70 GLN cc_start: 0.8778 (mt0) cc_final: 0.8388 (mm110)
REVERT: D   85 ASP cc_start: 0.8786 (t0) cc_final: 0.8403 (t0)
REVERT: D  138 ASN cc_start: 0.8161 (m-40) cc_final: 0.7854 (p0)
REVERT: E   29 LYS cc_start: 0.8416 (tttt) cc_final: 0.7651 (mptt)
REVERT: E   70 GLN cc_start: 0.8836 (mt0) cc_final: 0.8484 (mm110)
REVERT: E   96 GLU cc_start: 0.8503 (mt-10) cc_final: 0.8232 (mt-10)
REVERT: F   50 GLN cc_start: 0.8939 (tt0) cc_final: 0.8538 (tt0)
REVERT: F   66 GLU cc_start: 0.8185 (pm20) cc_final: 0.7847 (pp20)
REVERT: F   85 ASP cc_start: 0.8491 (t0) cc_final: 0.8073 (t0)
REVERT: G   50 GLN cc_start: 0.8644 (tt0) cc_final: 0.8398 (tt0)
REVERT: G   85 ASP cc_start: 0.8597 (t0) cc_final: 0.8143 (t0)
REVERT: G   96 GLU cc_start: 0.8517 (mt-10) cc_final: 0.8300 (mm-30)
REVERT: H   65 LYS cc_start: 0.9342 (mtpt) cc_final: 0.8984 (mtpp)
REVERT: H   66 GLU cc_start: 0.8161 (pm20) cc_final: 0.7797 (pp20)
REVERT: H   69 SER cc_start: 0.9004 (m) cc_final: 0.8619 (p)
REVERT: H   85 ASP cc_start: 0.8601 (t0) cc_final: 0.8196 (t0)
REVERT: H  115 ASP cc_start: 0.8534 (m-30) cc_final: 0.8048 (t0)
REVERT: I   85 ASP cc_start: 0.8475 (t0) cc_final: 0.8077 (t0)
REVERT: I  147 LYS cc_start: 0.8837 (ttmm) cc_final: 0.8261 (ttmm)
REVERT: I  160 GLU cc_start: 0.7470 (mp0) cc_final: 0.6957 (mp0)
  outliers start: 22
  outliers final: 20
  residues processed: 172
  average time/residue: 0.0870
  time to fit residues: 21.6289
Evaluate side-chains
  170 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 150
  time to evaluate  : 0.343 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   81 ILE
Chi-restraints excluded: chain B residue  119 ASP
Chi-restraints excluded: chain B residue  124 THR
Chi-restraints excluded: chain C residue   69 SER
Chi-restraints excluded: chain D residue   69 SER
Chi-restraints excluded: chain E residue   25 THR
Chi-restraints excluded: chain E residue   69 SER
Chi-restraints excluded: chain E residue  132 GLN
Chi-restraints excluded: chain F residue   58 SER
Chi-restraints excluded: chain F residue   88 MET
Chi-restraints excluded: chain G residue   49 ILE
Chi-restraints excluded: chain G residue   81 ILE
Chi-restraints excluded: chain G residue  124 THR
Chi-restraints excluded: chain G residue  132 GLN
Chi-restraints excluded: chain G residue  166 ILE
Chi-restraints excluded: chain H residue  139 CYS
Chi-restraints excluded: chain I residue   69 SER
Chi-restraints excluded: chain I residue  121 THR
Chi-restraints excluded: chain I residue  124 THR
Chi-restraints excluded: chain I residue  139 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 76 optimal weight:    0.0770
   chunk 92 optimal weight:    0.4980
   chunk 90 optimal weight:    0.9990
   chunk 112 optimal weight:    0.9980
   chunk 16 optimal weight:    6.9990
   chunk 24 optimal weight:    0.5980
   chunk 1 optimal weight:    7.9990
   chunk 81 optimal weight:    7.9990
   chunk 5 optimal weight:    0.5980
   chunk 74 optimal weight:    8.9990
   chunk 69 optimal weight:   10.0000
   overall best weight:    0.5538

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

Flipped N/Q/H residues before XYZ refinement:
** B  70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 132 GLN
F  70 GLN
** F 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
I 132 GLN
** I 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3130 r_free = 0.3130 target = 0.069033 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2781 r_free = 0.2781 target = 0.053248 restraints weight = 27065.409|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2827 r_free = 0.2827 target = 0.055128 restraints weight = 14289.091|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2858 r_free = 0.2858 target = 0.056457 restraints weight = 9662.845|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.2876 r_free = 0.2876 target = 0.057311 restraints weight = 7461.528|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2890 r_free = 0.2890 target = 0.057951 restraints weight = 6331.649|
|-----------------------------------------------------------------------------|
r_work (final): 0.2886
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8615
moved from start:          0.3515

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9144  Z= 0.102
  Angle     :  0.537   6.468  12432  Z= 0.280
  Chirality :  0.038   0.161   1528
  Planarity :  0.004   0.049   1560
  Dihedral  :  3.909  21.607   1256
  Min Nonbonded Distance : 2.420

Molprobity Statistics.
  All-atom Clashscore : 5.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.53 %
    Favored  : 95.47 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 24.67 %
    Favored  : 73.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.81 (0.26), residues: 1192
  helix:  3.32 (0.25), residues: 456
  sheet: -0.21 (0.40), residues: 160
  loop : -1.70 (0.24), residues: 576

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D  38 
 TYR   0.012   0.001   TYR H 131 
 PHE   0.006   0.001   PHE I 140 
 TRP   0.004   0.000   TRP E 116 
 HIS   0.002   0.001   HIS C 133 

Details of bonding type rmsd
  covalent geometry    : bond        0.00251 ( 9144)
  covalent geometry    : angle       0.53654 (12432)
  hydrogen bonds       : bond        0.02571 (  504)
  hydrogen bonds       : angle       3.50888 ( 1416)

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

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

  2384 Ramachandran restraints generated.
    1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2384 Ramachandran restraints generated.
    1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  213 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 197
  time to evaluate  : 0.326 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  132 GLN cc_start: 0.8479 (tt0) cc_final: 0.8122 (tt0)
REVERT: B  138 ASN cc_start: 0.8477 (m-40) cc_final: 0.7602 (p0)
REVERT: C   29 LYS cc_start: 0.8369 (tttt) cc_final: 0.7426 (mptt)
REVERT: C  106 LYS cc_start: 0.8843 (tptm) cc_final: 0.8512 (tppt)
REVERT: C  138 ASN cc_start: 0.8392 (m-40) cc_final: 0.7684 (p0)
REVERT: D   29 LYS cc_start: 0.8273 (tttt) cc_final: 0.7250 (mmtm)
REVERT: D   85 ASP cc_start: 0.8748 (t0) cc_final: 0.8392 (t0)
REVERT: D  106 LYS cc_start: 0.8701 (tttm) cc_final: 0.8372 (ttmm)
REVERT: E   29 LYS cc_start: 0.8399 (tttt) cc_final: 0.7695 (mptt)
REVERT: E   50 GLN cc_start: 0.8289 (tt0) cc_final: 0.7966 (tt0)
REVERT: E   96 GLU cc_start: 0.8528 (mt-10) cc_final: 0.8294 (mt-10)
REVERT: F   50 GLN cc_start: 0.8873 (tt0) cc_final: 0.8542 (tt0)
REVERT: F   66 GLU cc_start: 0.8096 (pm20) cc_final: 0.7764 (pp20)
REVERT: F   85 ASP cc_start: 0.8474 (t0) cc_final: 0.8003 (t0)
REVERT: F  138 ASN cc_start: 0.8931 (m-40) cc_final: 0.8139 (p0)
REVERT: G   70 GLN cc_start: 0.8469 (mt0) cc_final: 0.8181 (mp10)
REVERT: G   85 ASP cc_start: 0.8505 (t0) cc_final: 0.7964 (t0)
REVERT: G   96 GLU cc_start: 0.8467 (mt-10) cc_final: 0.8256 (mm-30)
REVERT: H   29 LYS cc_start: 0.8960 (ttpt) cc_final: 0.8744 (ttpp)
REVERT: H   69 SER cc_start: 0.9012 (m) cc_final: 0.8605 (p)
REVERT: H   85 ASP cc_start: 0.8510 (t0) cc_final: 0.8113 (t0)
REVERT: H  115 ASP cc_start: 0.8417 (m-30) cc_final: 0.7839 (t0)
REVERT: H  138 ASN cc_start: 0.8651 (m-40) cc_final: 0.7551 (p0)
REVERT: I   85 ASP cc_start: 0.8434 (t0) cc_final: 0.8088 (t0)
REVERT: I  147 LYS cc_start: 0.8810 (ttmm) cc_final: 0.8251 (ttmm)
REVERT: I  160 GLU cc_start: 0.7413 (mp0) cc_final: 0.6932 (mp0)
  outliers start: 16
  outliers final: 11
  residues processed: 203
  average time/residue: 0.0916
  time to fit residues: 26.2592
Evaluate side-chains
  176 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 165
  time to evaluate  : 0.361 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  124 THR
Chi-restraints excluded: chain E residue  132 GLN
Chi-restraints excluded: chain F residue   58 SER
Chi-restraints excluded: chain G residue  124 THR
Chi-restraints excluded: chain G residue  132 GLN
Chi-restraints excluded: chain G residue  166 ILE
Chi-restraints excluded: chain H residue  124 THR
Chi-restraints excluded: chain I residue  121 THR
Chi-restraints excluded: chain I residue  124 THR
Chi-restraints excluded: chain I residue  132 GLN
Chi-restraints excluded: chain I residue  139 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 30 optimal weight:    1.9990
   chunk 44 optimal weight:    7.9990
   chunk 66 optimal weight:    0.2980
   chunk 118 optimal weight:   10.0000
   chunk 3 optimal weight:    0.9990
   chunk 7 optimal weight:    0.8980
   chunk 12 optimal weight:    0.9990
   chunk 46 optimal weight:    9.9990
   chunk 69 optimal weight:    5.9990
   chunk 78 optimal weight:    0.9990
   chunk 15 optimal weight:    5.9990
   overall best weight:    0.8386

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

Flipped N/Q/H residues before XYZ refinement:
** B  70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3124 r_free = 0.3124 target = 0.068768 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2776 r_free = 0.2776 target = 0.053101 restraints weight = 27242.546|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.2821 r_free = 0.2821 target = 0.054943 restraints weight = 14671.224|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2851 r_free = 0.2851 target = 0.056227 restraints weight = 9948.682|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.2871 r_free = 0.2871 target = 0.057102 restraints weight = 7731.242|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.2882 r_free = 0.2882 target = 0.057570 restraints weight = 6542.601|
|-----------------------------------------------------------------------------|
r_work (final): 0.2874
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8636
moved from start:          0.3703

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   9144  Z= 0.110
  Angle     :  0.558   8.583  12432  Z= 0.287
  Chirality :  0.039   0.178   1528
  Planarity :  0.004   0.047   1560
  Dihedral  :  3.910  21.188   1256
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 6.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.20 %
    Favored  : 94.80 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 25.22 %
    Favored  : 72.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.88 (0.26), residues: 1192
  helix:  3.32 (0.25), residues: 456
  sheet: -0.22 (0.40), residues: 160
  loop : -1.59 (0.24), residues: 576

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D  38 
 TYR   0.013   0.001   TYR E 131 
 PHE   0.007   0.001   PHE G  73 
 TRP   0.004   0.001   TRP C 116 
 HIS   0.003   0.001   HIS I 133 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 ( 9144)
  covalent geometry    : angle       0.55762 (12432)
  hydrogen bonds       : bond        0.02745 (  504)
  hydrogen bonds       : angle       3.46219 ( 1416)

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

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

  2384 Ramachandran restraints generated.
    1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2384 Ramachandran restraints generated.
    1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 169
  time to evaluate  : 0.260 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  119 ASP cc_start: 0.8040 (OUTLIER) cc_final: 0.7834 (t0)
REVERT: B  132 GLN cc_start: 0.8459 (tt0) cc_final: 0.8111 (tt0)
REVERT: B  138 ASN cc_start: 0.8433 (m-40) cc_final: 0.7531 (p0)
REVERT: C   29 LYS cc_start: 0.8380 (tttt) cc_final: 0.7448 (mptt)
REVERT: C  106 LYS cc_start: 0.8808 (tptm) cc_final: 0.8491 (tppt)
REVERT: C  138 ASN cc_start: 0.8544 (m-40) cc_final: 0.7676 (p0)
REVERT: D   29 LYS cc_start: 0.8256 (tttt) cc_final: 0.7252 (mmtm)
REVERT: D   85 ASP cc_start: 0.8818 (t0) cc_final: 0.8488 (t0)
REVERT: D  106 LYS cc_start: 0.8692 (tttm) cc_final: 0.8408 (ttmm)
REVERT: E   29 LYS cc_start: 0.8385 (tttt) cc_final: 0.7688 (mptt)
REVERT: E   50 GLN cc_start: 0.8202 (tt0) cc_final: 0.7830 (tt0)
REVERT: E   96 GLU cc_start: 0.8478 (mt-10) cc_final: 0.8271 (mt-10)
REVERT: F   50 GLN cc_start: 0.8867 (tt0) cc_final: 0.8539 (tt0)
REVERT: F   66 GLU cc_start: 0.8068 (pm20) cc_final: 0.7822 (pp20)
REVERT: F   85 ASP cc_start: 0.8462 (t0) cc_final: 0.8034 (t0)
REVERT: F  138 ASN cc_start: 0.8923 (m-40) cc_final: 0.8166 (p0)
REVERT: G   69 SER cc_start: 0.9100 (t) cc_final: 0.8783 (p)
REVERT: G   85 ASP cc_start: 0.8402 (t0) cc_final: 0.7787 (t0)
REVERT: H   29 LYS cc_start: 0.8914 (ttpt) cc_final: 0.8697 (ttpp)
REVERT: H   65 LYS cc_start: 0.9326 (mtpp) cc_final: 0.8999 (mtpp)
REVERT: H   66 GLU cc_start: 0.8149 (pm20) cc_final: 0.7923 (pp20)
REVERT: H   69 SER cc_start: 0.8999 (m) cc_final: 0.8582 (p)
REVERT: H   85 ASP cc_start: 0.8512 (t0) cc_final: 0.8130 (t0)
REVERT: H  115 ASP cc_start: 0.8362 (m-30) cc_final: 0.7844 (t0)
REVERT: H  138 ASN cc_start: 0.8625 (m-40) cc_final: 0.7547 (p0)
REVERT: I   66 GLU cc_start: 0.7949 (pm20) cc_final: 0.7737 (pp20)
REVERT: I   85 ASP cc_start: 0.8415 (t0) cc_final: 0.8097 (t0)
REVERT: I  147 LYS cc_start: 0.8767 (ttmm) cc_final: 0.8197 (ttmm)
REVERT: I  160 GLU cc_start: 0.7352 (mp0) cc_final: 0.6906 (mp0)
  outliers start: 18
  outliers final: 9
  residues processed: 176
  average time/residue: 0.0850
  time to fit residues: 21.6321
Evaluate side-chains
  164 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 154
  time to evaluate  : 0.402 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  119 ASP
Chi-restraints excluded: chain B residue  124 THR
Chi-restraints excluded: chain C residue   69 SER
Chi-restraints excluded: chain F residue   58 SER
Chi-restraints excluded: chain G residue  124 THR
Chi-restraints excluded: chain G residue  166 ILE
Chi-restraints excluded: chain H residue  124 THR
Chi-restraints excluded: chain I residue  121 THR
Chi-restraints excluded: chain I residue  124 THR
Chi-restraints excluded: chain I residue  139 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 91 optimal weight:    3.9990
   chunk 50 optimal weight:    0.9990
   chunk 105 optimal weight:    0.7980
   chunk 36 optimal weight:    9.9990
   chunk 107 optimal weight:    0.4980
   chunk 70 optimal weight:    4.9990
   chunk 112 optimal weight:    7.9990
   chunk 56 optimal weight:    7.9990
   chunk 96 optimal weight:    5.9990
   chunk 12 optimal weight:    0.9980
   chunk 13 optimal weight:    1.9990
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
** F 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3122 r_free = 0.3122 target = 0.068694 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2769 r_free = 0.2769 target = 0.052853 restraints weight = 27182.004|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2815 r_free = 0.2815 target = 0.054695 restraints weight = 14565.190|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2845 r_free = 0.2845 target = 0.055990 restraints weight = 9871.062|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.2864 r_free = 0.2864 target = 0.056832 restraints weight = 7670.288|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2876 r_free = 0.2876 target = 0.057368 restraints weight = 6538.090|
|-----------------------------------------------------------------------------|
r_work (final): 0.2870
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8635
moved from start:          0.3775

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   9144  Z= 0.117
  Angle     :  0.578   8.644  12432  Z= 0.298
  Chirality :  0.039   0.173   1528
  Planarity :  0.004   0.052   1560
  Dihedral  :  3.930  20.854   1256
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 6.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.37 %
    Favored  : 94.63 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  : 25.87 %
    Favored  : 72.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.96 (0.25), residues: 1192
  helix:  3.31 (0.25), residues: 456
  sheet:  0.76 (0.34), residues: 224
  loop : -2.12 (0.25), residues: 512

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D  38 
 TYR   0.010   0.001   TYR E 131 
 PHE   0.006   0.001   PHE C 103 
 TRP   0.004   0.001   TRP E 116 
 HIS   0.002   0.001   HIS D 133 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 ( 9144)
  covalent geometry    : angle       0.57810 (12432)
  hydrogen bonds       : bond        0.02790 (  504)
  hydrogen bonds       : angle       3.50406 ( 1416)

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

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

  2384 Ramachandran restraints generated.
    1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2384 Ramachandran restraints generated.
    1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 166
  time to evaluate  : 0.418 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   99 MET cc_start: 0.7275 (mtt) cc_final: 0.6177 (mtt)
REVERT: B  132 GLN cc_start: 0.8473 (tt0) cc_final: 0.8138 (tt0)
REVERT: B  138 ASN cc_start: 0.8403 (m-40) cc_final: 0.7465 (p0)
REVERT: B  160 GLU cc_start: 0.6939 (pm20) cc_final: 0.6159 (pm20)
REVERT: C   29 LYS cc_start: 0.8380 (tttt) cc_final: 0.7436 (mptt)
REVERT: C  106 LYS cc_start: 0.8861 (tptm) cc_final: 0.8535 (tppt)
REVERT: C  138 ASN cc_start: 0.8598 (m-40) cc_final: 0.7681 (p0)
REVERT: D   29 LYS cc_start: 0.8250 (tttt) cc_final: 0.7245 (mmtm)
REVERT: D   85 ASP cc_start: 0.8878 (t0) cc_final: 0.8549 (t0)
REVERT: D  106 LYS cc_start: 0.8743 (tttm) cc_final: 0.8425 (ttmm)
REVERT: E   29 LYS cc_start: 0.8345 (tttt) cc_final: 0.7668 (mptt)
REVERT: E   50 GLN cc_start: 0.8264 (tt0) cc_final: 0.7948 (tt0)
REVERT: F   50 GLN cc_start: 0.8884 (tt0) cc_final: 0.8561 (tt0)
REVERT: F   66 GLU cc_start: 0.8085 (pm20) cc_final: 0.7878 (pp20)
REVERT: F   85 ASP cc_start: 0.8466 (t0) cc_final: 0.8060 (t0)
REVERT: F  138 ASN cc_start: 0.8925 (m-40) cc_final: 0.8112 (p0)
REVERT: G   11 GLU cc_start: 0.8210 (tt0) cc_final: 0.7997 (tm-30)
REVERT: G   29 LYS cc_start: 0.8910 (ttpt) cc_final: 0.8183 (ttmm)
REVERT: G   69 SER cc_start: 0.9045 (t) cc_final: 0.8755 (p)
REVERT: G   85 ASP cc_start: 0.8438 (t0) cc_final: 0.7807 (t0)
REVERT: H   29 LYS cc_start: 0.8945 (ttpt) cc_final: 0.8742 (ttpp)
REVERT: H   65 LYS cc_start: 0.9311 (mtpp) cc_final: 0.9022 (mtpp)
REVERT: H   66 GLU cc_start: 0.8195 (pm20) cc_final: 0.7935 (pp20)
REVERT: H   69 SER cc_start: 0.9014 (m) cc_final: 0.8604 (p)
REVERT: H   85 ASP cc_start: 0.8553 (t0) cc_final: 0.8142 (t0)
REVERT: H  115 ASP cc_start: 0.8414 (m-30) cc_final: 0.7843 (t0)
REVERT: H  138 ASN cc_start: 0.8632 (m-40) cc_final: 0.7535 (p0)
REVERT: I   85 ASP cc_start: 0.8433 (t0) cc_final: 0.8154 (t0)
REVERT: I  147 LYS cc_start: 0.8809 (ttmm) cc_final: 0.8236 (ttmm)
REVERT: I  160 GLU cc_start: 0.7353 (mp0) cc_final: 0.6918 (mp0)
  outliers start: 13
  outliers final: 12
  residues processed: 171
  average time/residue: 0.0805
  time to fit residues: 20.0529
Evaluate side-chains
  170 residues out of total 920 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 158
  time to evaluate  : 0.349 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  124 THR
Chi-restraints excluded: chain C residue   69 SER
Chi-restraints excluded: chain E residue  132 GLN
Chi-restraints excluded: chain F residue   58 SER
Chi-restraints excluded: chain F residue  166 ILE
Chi-restraints excluded: chain G residue   81 ILE
Chi-restraints excluded: chain G residue  124 THR
Chi-restraints excluded: chain G residue  166 ILE
Chi-restraints excluded: chain H residue  124 THR
Chi-restraints excluded: chain I residue  121 THR
Chi-restraints excluded: chain I residue  124 THR
Chi-restraints excluded: chain I residue  139 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 87 optimal weight:    3.9990
   chunk 32 optimal weight:   10.0000
   chunk 52 optimal weight:    9.9990
   chunk 82 optimal weight:   10.0000
   chunk 108 optimal weight:    0.8980
   chunk 55 optimal weight:    9.9990
   chunk 43 optimal weight:    0.6980
   chunk 36 optimal weight:   10.0000
   chunk 103 optimal weight:    2.9990
   chunk 80 optimal weight:    6.9990
   chunk 71 optimal weight:    8.9990
   overall best weight:    3.1186

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

Flipped N/Q/H residues before XYZ refinement:
** F 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3049 r_free = 0.3049 target = 0.065477 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2681 r_free = 0.2681 target = 0.049406 restraints weight = 27295.356|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2725 r_free = 0.2725 target = 0.051167 restraints weight = 14732.300|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2752 r_free = 0.2752 target = 0.052332 restraints weight = 10141.153|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.2773 r_free = 0.2773 target = 0.053198 restraints weight = 8017.247|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.2785 r_free = 0.2785 target = 0.053727 restraints weight = 6825.363|
|-----------------------------------------------------------------------------|
r_work (final): 0.2778
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8721
moved from start:          0.3477

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046   9144  Z= 0.189
  Angle     :  0.626   8.413  12432  Z= 0.320
  Chirality :  0.040   0.170   1528
  Planarity :  0.004   0.049   1560
  Dihedral  :  4.130  21.605   1256
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 7.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.71 %
    Favored  : 93.29 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 25.87 %
    Favored  : 71.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.78 (0.25), residues: 1192
  helix:  3.08 (0.25), residues: 456
  sheet:  0.72 (0.34), residues: 224
  loop : -2.16 (0.24), residues: 512

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG H  38 
 TYR   0.010   0.001   TYR I 164 
 PHE   0.010   0.001   PHE C 103 
 TRP   0.004   0.001   TRP F 116 
 HIS   0.001   0.000   HIS D 133 

Details of bonding type rmsd
  covalent geometry    : bond        0.00456 ( 9144)
  covalent geometry    : angle       0.62615 (12432)
  hydrogen bonds       : bond        0.03717 (  504)
  hydrogen bonds       : angle       3.62351 ( 1416)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1557.27 seconds
wall clock time: 27 minutes 48.17 seconds (1668.17 seconds total)