Starting phenix.real_space_refine
on Wed Mar  4 06:29:42 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7ohc_12900/03_2026/7ohc_12900.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ohc_12900/03_2026/7ohc_12900.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7ohc_12900/03_2026/7ohc_12900.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ohc_12900/03_2026/7ohc_12900.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ohc_12900/03_2026/7ohc_12900.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ohc_12900/03_2026/7ohc_12900.cif"
  }
  resolution = 2.5
  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=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P     289      5.49       5
     S      12      5.16       5
     C    6648      2.51       5
     N    2262      2.21       5
     O    2808      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 36 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 12019
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 802
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 802
          Classifications: {'peptide': 97}
          Link IDs: {'PTRANS': 3, 'TRANS': 93}
    Chain: "B"
      Number of atoms: 653
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 82, 653
          Classifications: {'peptide': 82}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 80}
    Chain: "C"
      Number of atoms: 843
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 109, 843
          Classifications: {'peptide': 109}
          Link IDs: {'PTRANS': 5, 'TRANS': 103}
    Chain: "D"
      Number of atoms: 767
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 767
          Classifications: {'peptide': 97}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 94}
    Chain: "E"
      Number of atoms: 811
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 98, 811
          Classifications: {'peptide': 98}
          Link IDs: {'PTRANS': 4, 'TRANS': 93}
    Chain: "F"
      Number of atoms: 638
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 80, 638
          Classifications: {'peptide': 80}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 78}
    Chain: "G"
      Number of atoms: 818
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 106, 818
          Classifications: {'peptide': 106}
          Link IDs: {'PTRANS': 5, 'TRANS': 100}
    Chain: "H"
      Number of atoms: 745
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 745
          Classifications: {'peptide': 95}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 92}
    Chain: "I"
      Number of atoms: 2955
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 2955
          Classifications: {'DNA': 145}
          Link IDs: {'rna3p': 144}
    Chain: "J"
      Number of atoms: 2987
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 2987
          Classifications: {'DNA': 145}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 144}
  Time building chain proxies: 2.78, per 1000 atoms: 0.23
  Number of scatterers: 12019
  At special positions: 0
  Unit cell: (74.55, 119.7, 115.5, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      12     16.00
     P     289     15.00
     O    2808      8.00
     N    2262      7.00
     C    6648      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.98
  Conformation dependent library (CDL) restraints added in 348.4 milliseconds
  

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1432

  Finding SS restraints...
    Secondary structure from input PDB file:
      34 helices and 10 sheets defined
      72.3% alpha, 3.1% beta
      144 base pairs and 274 stacking pairs defined.
    Time for finding SS restraints: 2.00
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 57
    Processing helix  chain 'A' and resid 63 through 79
      removed outlier: 4.244A  pdb=" N   ASP A  77 " --> pdb=" O   GLU A  73 " (cutoff:3.500A)
      removed outlier: 4.228A  pdb=" N   PHE A  78 " --> pdb=" O   ILE A  74 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 114
    Processing helix  chain 'A' and resid 120 through 131
    Processing helix  chain 'B' and resid 30 through 41
    Processing helix  chain 'B' and resid 49 through 76
    Processing helix  chain 'B' and resid 82 through 93
    Processing helix  chain 'C' and resid 16 through 22
    Processing helix  chain 'C' and resid 26 through 37
    Processing helix  chain 'C' and resid 45 through 73
      removed outlier: 4.340A  pdb=" N   VAL C  49 " --> pdb=" O   ALA C  45 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 90
    Processing helix  chain 'C' and resid 90 through 97
    Processing helix  chain 'D' and resid 34 through 46
    Processing helix  chain 'D' and resid 52 through 81
    Processing helix  chain 'D' and resid 87 through 99
    Processing helix  chain 'D' and resid 100 through 121
    Processing helix  chain 'E' and resid 44 through 57
    Processing helix  chain 'E' and resid 63 through 76
    Processing helix  chain 'E' and resid 85 through 114
    Processing helix  chain 'E' and resid 120 through 131
    Processing helix  chain 'F' and resid 23 through 29
      removed outlier: 4.030A  pdb=" N   ILE F  26 " --> pdb=" O   ARG F  23 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 30 through 41
    Processing helix  chain 'F' and resid 49 through 76
    Processing helix  chain 'F' and resid 82 through 94
    Processing helix  chain 'G' and resid 16 through 22
    Processing helix  chain 'G' and resid 26 through 37
    Processing helix  chain 'G' and resid 45 through 73
      removed outlier: 4.355A  pdb=" N   VAL G  49 " --> pdb=" O   ALA G  45 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 79 through 90
    Processing helix  chain 'G' and resid 91 through 97
    Processing helix  chain 'G' and resid 112 through 116
    Processing helix  chain 'H' and resid 34 through 46
    Processing helix  chain 'H' and resid 52 through 81
    Processing helix  chain 'H' and resid 87 through 99
    Processing helix  chain 'H' and resid 100 through 122
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 6.917A  pdb=" N   ARG A  83 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119
    Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98
      removed outlier: 6.461A  pdb=" N   THR B  96 " --> pdb=" O   THR G 101 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43
      removed outlier: 7.407A  pdb=" N   ARG C  42 " --> pdb=" O   ILE D  86 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78
    Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102
    Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84
      removed outlier: 6.754A  pdb=" N   ARG E  83 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119
    Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43
      removed outlier: 7.182A  pdb=" N   ARG G  42 " --> pdb=" O   ILE H  86 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78

    419 hydrogen bonds defined for protein.
    1242 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      367 hydrogen bonds
      730 hydrogen bond angles
      0 basepair planarities
      144 basepair parallelities
      274 stacking parallelities
  Total time for adding SS restraints: 2.26

  Time building geometry restraints manager: 1.31 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1813
        1.33 -     1.45: 4503
        1.45 -     1.57: 5904
        1.57 -     1.69: 580
        1.69 -     1.81: 22
  Bond restraints: 12822
  Sorted by residual:
  bond pdb=" CB  GLU H 110 "
       pdb=" CG  GLU H 110 "
    ideal  model  delta    sigma   weight residual
    1.520  1.407  0.113 3.00e-02 1.11e+03 1.41e+01
  bond pdb=" CG  GLU H 110 "
       pdb=" CD  GLU H 110 "
    ideal  model  delta    sigma   weight residual
    1.516  1.428  0.088 2.50e-02 1.60e+03 1.24e+01
  bond pdb=" C3'  DC I  49 "
       pdb=" O3'  DC I  49 "
    ideal  model  delta    sigma   weight residual
    1.422  1.494 -0.072 3.00e-02 1.11e+03 5.75e+00
  bond pdb=" CB  ASN C  73 "
       pdb=" CG  ASN C  73 "
    ideal  model  delta    sigma   weight residual
    1.516  1.569 -0.053 2.50e-02 1.60e+03 4.57e+00
  bond pdb=" CD  GLU H 110 "
       pdb=" OE2 GLU H 110 "
    ideal  model  delta    sigma   weight residual
    1.249  1.209  0.040 1.90e-02 2.77e+03 4.39e+00
  ... (remaining 12817 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.09: 17923
        2.09 -     4.17: 563
        4.17 -     6.26: 40
        6.26 -     8.34: 19
        8.34 -    10.43: 11
  Bond angle restraints: 18556
  Sorted by residual:
  angle pdb=" CA  ASN C  73 "
        pdb=" CB  ASN C  73 "
        pdb=" CG  ASN C  73 "
      ideal   model   delta    sigma   weight residual
     112.60  118.94   -6.34 1.00e+00 1.00e+00 4.03e+01
  angle pdb=" C   ASN C  73 "
        pdb=" CA  ASN C  73 "
        pdb=" CB  ASN C  73 "
      ideal   model   delta    sigma   weight residual
     110.56  119.26   -8.70 1.69e+00 3.50e-01 2.65e+01
  angle pdb=" CA  THR A  58 "
        pdb=" CB  THR A  58 "
        pdb=" CG2 THR A  58 "
      ideal   model   delta    sigma   weight residual
     110.50  118.23   -7.73 1.70e+00 3.46e-01 2.07e+01
  angle pdb=" N   ASN C  73 "
        pdb=" CA  ASN C  73 "
        pdb=" CB  ASN C  73 "
      ideal   model   delta    sigma   weight residual
     110.56  104.19    6.37 1.46e+00 4.69e-01 1.90e+01
  angle pdb=" CA  LYS G  74 "
        pdb=" CB  LYS G  74 "
        pdb=" CG  LYS G  74 "
      ideal   model   delta    sigma   weight residual
     114.10  122.71   -8.61 2.00e+00 2.50e-01 1.85e+01
  ... (remaining 18551 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.47: 4465
       21.47 -    42.93: 1384
       42.93 -    64.40: 1085
       64.40 -    85.87: 47
       85.87 -   107.34: 4
  Dihedral angle restraints: 6985
    sinusoidal: 4767
      harmonic: 2218
  Sorted by residual:
  dihedral pdb=" CA  PRO H 100 "
           pdb=" C   PRO H 100 "
           pdb=" N   GLY H 101 "
           pdb=" CA  GLY H 101 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.60  -18.40     0      5.00e+00 4.00e-02 1.35e+01
  dihedral pdb=" CA  PRO D 100 "
           pdb=" C   PRO D 100 "
           pdb=" N   GLY D 101 "
           pdb=" CA  GLY D 101 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.86  -18.14     0      5.00e+00 4.00e-02 1.32e+01
  dihedral pdb=" CA  PHE E  84 "
           pdb=" C   PHE E  84 "
           pdb=" N   GLN E  85 "
           pdb=" CA  GLN E  85 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.69   17.31     0      5.00e+00 4.00e-02 1.20e+01
  ... (remaining 6982 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.082: 1910
       0.082 -    0.165: 191
       0.165 -    0.247: 9
       0.247 -    0.330: 0
       0.330 -    0.412: 1
  Chirality restraints: 2111
  Sorted by residual:
  chirality pdb=" CB  THR D 116 "
            pdb=" CA  THR D 116 "
            pdb=" OG1 THR D 116 "
            pdb=" CG2 THR D 116 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.14    0.41 2.00e-01 2.50e+01 4.24e+00
  chirality pdb=" CB  THR A  58 "
            pdb=" CA  THR A  58 "
            pdb=" OG1 THR A  58 "
            pdb=" CG2 THR A  58 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.30    0.25 2.00e-01 2.50e+01 1.52e+00
  chirality pdb=" CB  THR H 112 "
            pdb=" CA  THR H 112 "
            pdb=" OG1 THR H 112 "
            pdb=" CG2 THR H 112 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.31    0.24 2.00e-01 2.50e+01 1.46e+00
  ... (remaining 2108 not shown)

  Planarity restraints: 1344
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN C  73 "   -0.018 2.00e-02 2.50e+03   3.58e-02 1.28e+01
        pdb=" C   ASN C  73 "    0.062 2.00e-02 2.50e+03
        pdb=" O   ASN C  73 "   -0.024 2.00e-02 2.50e+03
        pdb=" N   LYS C  74 "   -0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR A  58 "   -0.017 2.00e-02 2.50e+03   3.29e-02 1.08e+01
        pdb=" C   THR A  58 "    0.057 2.00e-02 2.50e+03
        pdb=" O   THR A  58 "   -0.021 2.00e-02 2.50e+03
        pdb=" N   GLU A  59 "   -0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DC I  69 "    0.036 2.00e-02 2.50e+03   2.11e-02 9.97e+00
        pdb=" N1   DC I  69 "   -0.049 2.00e-02 2.50e+03
        pdb=" C2   DC I  69 "    0.010 2.00e-02 2.50e+03
        pdb=" O2   DC I  69 "   -0.008 2.00e-02 2.50e+03
        pdb=" N3   DC I  69 "    0.001 2.00e-02 2.50e+03
        pdb=" C4   DC I  69 "    0.007 2.00e-02 2.50e+03
        pdb=" N4   DC I  69 "    0.008 2.00e-02 2.50e+03
        pdb=" C5   DC I  69 "   -0.002 2.00e-02 2.50e+03
        pdb=" C6   DC I  69 "   -0.003 2.00e-02 2.50e+03
  ... (remaining 1341 not shown)

  Histogram of nonbonded interaction distances:
        2.19 -     2.73: 951
        2.73 -     3.28: 10386
        3.28 -     3.82: 24870
        3.82 -     4.36: 30273
        4.36 -     4.90: 41885
  Nonbonded interactions: 108365
  Sorted by model distance:
  nonbonded pdb=" O   ASN C  73 "
            pdb=" ND2 ASN C  73 "
     model   vdw
     2.193 3.120
  nonbonded pdb=" OG1 THR D  29 "
            pdb=" OP1  DT I  30 "
     model   vdw
     2.238 3.040
  nonbonded pdb=" O2   DC I -23 "
            pdb=" N2   DG J  23 "
     model   vdw
     2.255 2.496
  nonbonded pdb=" OG1 THR H  87 "
            pdb=" OE1 GLU H  90 "
     model   vdw
     2.275 3.040
  nonbonded pdb=" OD2 ASP D  65 "
            pdb=" OH  TYR F  98 "
     model   vdw
     2.299 3.040
  ... (remaining 108360 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = (chain 'E' and resid 38 through 134)
}
ncs_group {
  reference = (chain 'B' and resid 23 through 102)
  selection = chain 'F'
}
ncs_group {
  reference = (chain 'C' and resid 13 through 118)
  selection = chain 'G'
}
ncs_group {
  reference = (chain 'D' and resid 28 through 122)
  selection = chain 'H'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.510
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.170
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     13.490
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:6.770
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.180
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7963
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      :  0.005   0.113  12822  Z= 0.235
  Angle     :  0.856  10.429  18556  Z= 0.503
  Chirality :  0.049   0.412   2111
  Planarity :  0.006   0.052   1344
  Dihedral  : 29.622 107.336   5553
  Min Nonbonded Distance : 2.193

Molprobity Statistics.
  All-atom Clashscore : 4.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  : 15.70 %
    Favored  : 84.14 %
  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:  0.04 (0.27), residues: 748
  helix:  0.44 (0.20), residues: 537
  sheet:  None (None), residues: 0
  loop : -0.81 (0.35), residues: 211

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG E  72 
 TYR   0.051   0.003   TYR H 118 
 PHE   0.029   0.003   PHE G  25 
 HIS   0.006   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00531 (12822)
  covalent geometry    : angle       0.85629 (18556)
  hydrogen bonds       : bond        0.10696 (  786)
  hydrogen bonds       : angle       4.11912 ( 1972)

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

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

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 205
  time to evaluate  : 0.324 
Fit side-chains
REVERT: A   42 ARG cc_start: 0.7818 (mmm160) cc_final: 0.7580 (mmm-85)
REVERT: A   50 GLU cc_start: 0.8333 (mt-10) cc_final: 0.7984 (mt-10)
REVERT: C   90 ASP cc_start: 0.8094 (t70) cc_final: 0.7798 (t0)
REVERT: D   31 LYS cc_start: 0.8728 (mptt) cc_final: 0.8420 (mmtm)
REVERT: D   68 GLU cc_start: 0.7743 (tm-30) cc_final: 0.7362 (tp30)
REVERT: D   90 GLU cc_start: 0.8180 (mp0) cc_final: 0.7932 (mp0)
REVERT: D  105 LYS cc_start: 0.8506 (ttmm) cc_final: 0.8266 (ttpp)
REVERT: E  129 ARG cc_start: 0.8251 (tpt90) cc_final: 0.8010 (tpt90)
REVERT: G   74 LYS cc_start: 0.8830 (ptpp) cc_final: 0.8400 (mtmm)
REVERT: G   99 ARG cc_start: 0.7960 (mmm160) cc_final: 0.7691 (mmm-85)
REVERT: H   65 ASP cc_start: 0.8752 (t70) cc_final: 0.8469 (t0)
REVERT: H   76 ARG cc_start: 0.7811 (mtp180) cc_final: 0.7532 (mtm-85)
  outliers start: 1
  outliers final: 1
  residues processed: 205
  average time/residue: 0.9189
  time to fit residues: 198.4890
Evaluate side-chains
  184 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 183
  time to evaluate  : 0.327 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   73 ASN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 49 optimal weight:    0.6980
   chunk 97 optimal weight:    5.9990
   chunk 53 optimal weight:   10.0000
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    5.9990
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    6.9990
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    0.7980
   chunk 61 optimal weight:    6.9990
   chunk 45 optimal weight:    0.1980
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  24 GLN
C 104 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.106906 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.085654 restraints weight = 20348.602|
|-----------------------------------------------------------------------------|
r_work (start): 0.3357 rms_B_bonded: 1.37
r_work: 0.3174 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.3034 rms_B_bonded: 4.30 restraints_weight: 0.2500
r_work (final): 0.3034
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8338
moved from start:          0.1328

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  12822  Z= 0.163
  Angle     :  0.569   6.192  18556  Z= 0.347
  Chirality :  0.034   0.157   2111
  Planarity :  0.004   0.045   1344
  Dihedral  : 31.367 101.018   4030
  Min Nonbonded Distance : 2.149

Molprobity Statistics.
  All-atom Clashscore : 7.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.47 %
    Favored  : 98.53 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 19.00 %
    Favored  : 79.12 %
  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:  1.77 (0.29), residues: 748
  helix:  1.77 (0.21), residues: 547
  sheet:  None (None), residues: 0
  loop : -0.42 (0.37), residues: 201

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG H  30 
 TYR   0.013   0.001   TYR H  37 
 PHE   0.011   0.001   PHE G  25 
 HIS   0.004   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00351 (12822)
  covalent geometry    : angle       0.56950 (18556)
  hydrogen bonds       : bond        0.04190 (  786)
  hydrogen bonds       : angle       3.06279 ( 1972)

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

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

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 190
  time to evaluate  : 0.290 
Fit side-chains
REVERT: A   42 ARG cc_start: 0.7884 (mmm160) cc_final: 0.7604 (mmm-85)
REVERT: A   50 GLU cc_start: 0.8665 (mt-10) cc_final: 0.8338 (mt-10)
REVERT: A  120 MET cc_start: 0.8787 (mmm) cc_final: 0.8530 (mmt)
REVERT: C   73 ASN cc_start: 0.9072 (OUTLIER) cc_final: 0.8593 (t160)
REVERT: C   90 ASP cc_start: 0.8457 (t70) cc_final: 0.8187 (t70)
REVERT: D   68 GLU cc_start: 0.8567 (tm-30) cc_final: 0.8147 (tp30)
REVERT: E   68 GLN cc_start: 0.9192 (OUTLIER) cc_final: 0.8747 (tt0)
REVERT: E  129 ARG cc_start: 0.8622 (tpt90) cc_final: 0.8194 (tpt90)
REVERT: G  113 SER cc_start: 0.8835 (m) cc_final: 0.8615 (p)
REVERT: H   39 TYR cc_start: 0.8194 (t80) cc_final: 0.7960 (t80)
REVERT: H   65 ASP cc_start: 0.9025 (t70) cc_final: 0.8742 (t0)
REVERT: H   76 ARG cc_start: 0.8207 (mtp180) cc_final: 0.7978 (mtm-85)
  outliers start: 12
  outliers final: 2
  residues processed: 191
  average time/residue: 0.8733
  time to fit residues: 175.8571
Evaluate side-chains
  183 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 179
  time to evaluate  : 0.331 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 GLU
Chi-restraints excluded: chain C residue   73 ASN
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain E residue   68 GLN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 76 optimal weight:    6.9990
   chunk 43 optimal weight:    2.9990
   chunk 18 optimal weight:    2.9990
   chunk 58 optimal weight:    8.9990
   chunk 13 optimal weight:    5.9990
   chunk 98 optimal weight:    6.9990
   chunk 94 optimal weight:    5.9990
   chunk 89 optimal weight:    6.9990
   chunk 95 optimal weight:    4.9990
   chunk 87 optimal weight:   10.0000
   chunk 79 optimal weight:    5.9990
   overall best weight:    4.5990

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

Flipped N/Q/H residues before XYZ refinement:
** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 104 GLN
F  25 ASN
H  46 HIS
H  81 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.100657 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.078702 restraints weight = 20606.725|
|-----------------------------------------------------------------------------|
r_work (start): 0.3224 rms_B_bonded: 1.44
r_work: 0.3034 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.2890 rms_B_bonded: 4.28 restraints_weight: 0.2500
r_work (final): 0.2890
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8459
moved from start:          0.2181

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.058  12822  Z= 0.382
  Angle     :  0.673   5.912  18556  Z= 0.400
  Chirality :  0.043   0.183   2111
  Planarity :  0.005   0.040   1344
  Dihedral  : 31.743 114.568   4030
  Min Nonbonded Distance : 2.258

Molprobity Statistics.
  All-atom Clashscore : 5.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  3.77 %
    Allowed  : 17.27 %
    Favored  : 78.96 %
  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:  1.83 (0.29), residues: 748
  helix:  1.80 (0.22), residues: 547
  sheet:  None (None), residues: 0
  loop : -0.34 (0.38), residues: 201

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B  35 
 TYR   0.016   0.002   TYR E  54 
 PHE   0.028   0.002   PHE G  25 
 HIS   0.007   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00863 (12822)
  covalent geometry    : angle       0.67322 (18556)
  hydrogen bonds       : bond        0.05836 (  786)
  hydrogen bonds       : angle       3.17395 ( 1972)

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

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

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  210 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 186
  time to evaluate  : 0.307 
Fit side-chains
REVERT: A   42 ARG cc_start: 0.8323 (mmm160) cc_final: 0.7564 (mmm160)
REVERT: C   64 GLU cc_start: 0.8588 (tt0) cc_final: 0.8194 (tp30)
REVERT: C   73 ASN cc_start: 0.9069 (OUTLIER) cc_final: 0.8566 (t0)
REVERT: D   90 GLU cc_start: 0.8884 (mp0) cc_final: 0.8507 (mp0)
REVERT: E   68 GLN cc_start: 0.9205 (OUTLIER) cc_final: 0.8688 (tt0)
REVERT: E  120 MET cc_start: 0.8808 (OUTLIER) cc_final: 0.7859 (mpp)
REVERT: F   80 THR cc_start: 0.9359 (t) cc_final: 0.9071 (m)
REVERT: G  113 SER cc_start: 0.8998 (m) cc_final: 0.8774 (p)
REVERT: H   30 ARG cc_start: 0.6741 (mtp-110) cc_final: 0.6338 (mtt180)
REVERT: H   65 ASP cc_start: 0.9065 (t70) cc_final: 0.8817 (t0)
  outliers start: 24
  outliers final: 8
  residues processed: 190
  average time/residue: 0.8678
  time to fit residues: 173.9753
Evaluate side-chains
  188 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 177
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue   76 GLN
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain A residue  105 GLU
Chi-restraints excluded: chain C residue   73 ASN
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain E residue   68 GLN
Chi-restraints excluded: chain E residue  120 MET
Chi-restraints excluded: chain F residue   59 LYS
Chi-restraints excluded: chain H residue   52 SER
Chi-restraints excluded: chain H residue   53 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 15 optimal weight:    0.9990
   chunk 41 optimal weight:    1.9990
   chunk 8 optimal weight:    7.9990
   chunk 37 optimal weight:    2.9990
   chunk 1 optimal weight:    2.9990
   chunk 50 optimal weight:    0.1980
   chunk 10 optimal weight:    0.9980
   chunk 70 optimal weight:    0.9980
   chunk 74 optimal weight:    4.9990
   chunk 64 optimal weight:    2.9990
   chunk 5 optimal weight:    0.8980
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
B  25 ASN
C  31 HIS
** E  76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  46 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.102720 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.081048 restraints weight = 20321.027|
|-----------------------------------------------------------------------------|
r_work (start): 0.3284 rms_B_bonded: 1.36
r_work: 0.3101 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.2962 rms_B_bonded: 4.23 restraints_weight: 0.2500
r_work (final): 0.2962
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8418
moved from start:          0.2164

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  12822  Z= 0.166
  Angle     :  0.608   5.984  18556  Z= 0.370
  Chirality :  0.036   0.150   2111
  Planarity :  0.005   0.047   1344
  Dihedral  : 31.749 117.340   4030
  Min Nonbonded Distance : 2.189

Molprobity Statistics.
  All-atom Clashscore : 6.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 19.62 %
    Favored  : 76.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.11 (0.30), residues: 748
  helix:  2.00 (0.22), residues: 547
  sheet:  None (None), residues: 0
  loop : -0.21 (0.38), residues: 201

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B  95 
 TYR   0.021   0.002   TYR G  57 
 PHE   0.010   0.001   PHE A  67 
 HIS   0.003   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00357 (12822)
  covalent geometry    : angle       0.60789 (18556)
  hydrogen bonds       : bond        0.04856 (  786)
  hydrogen bonds       : angle       3.13595 ( 1972)

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

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

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  210 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 188
  time to evaluate  : 0.323 
Fit side-chains
REVERT: A   42 ARG cc_start: 0.8352 (mmm160) cc_final: 0.8030 (mmm-85)
REVERT: A   50 GLU cc_start: 0.8589 (mt-10) cc_final: 0.8369 (mt-10)
REVERT: A   56 LYS cc_start: 0.9061 (OUTLIER) cc_final: 0.8760 (ptpp)
REVERT: C   64 GLU cc_start: 0.8447 (tt0) cc_final: 0.8082 (tp30)
REVERT: C   73 ASN cc_start: 0.9001 (OUTLIER) cc_final: 0.8485 (t0)
REVERT: C   90 ASP cc_start: 0.8339 (t70) cc_final: 0.8034 (t70)
REVERT: D   54 LYS cc_start: 0.9027 (mmmt) cc_final: 0.8656 (mmtp)
REVERT: D   90 GLU cc_start: 0.8862 (OUTLIER) cc_final: 0.8653 (mp0)
REVERT: E   68 GLN cc_start: 0.9183 (OUTLIER) cc_final: 0.8727 (tt0)
REVERT: F   68 ASP cc_start: 0.9204 (m-30) cc_final: 0.8921 (m-30)
REVERT: F   93 GLN cc_start: 0.8521 (OUTLIER) cc_final: 0.7235 (mp10)
REVERT: G  113 SER cc_start: 0.8981 (m) cc_final: 0.8765 (p)
REVERT: H   30 ARG cc_start: 0.6699 (mtp-110) cc_final: 0.6349 (mtt180)
REVERT: H   65 ASP cc_start: 0.9015 (t70) cc_final: 0.8749 (t0)
REVERT: H   76 ARG cc_start: 0.8223 (mtp180) cc_final: 0.7904 (mtm-85)
  outliers start: 22
  outliers final: 9
  residues processed: 191
  average time/residue: 0.8802
  time to fit residues: 177.1501
Evaluate side-chains
  200 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 186
  time to evaluate  : 0.317 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 LYS
Chi-restraints excluded: chain A residue   76 GLN
Chi-restraints excluded: chain A residue  105 GLU
Chi-restraints excluded: chain A residue  133 GLU
Chi-restraints excluded: chain C residue   73 ASN
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain D residue   90 GLU
Chi-restraints excluded: chain E residue   68 GLN
Chi-restraints excluded: chain F residue   59 LYS
Chi-restraints excluded: chain F residue   77 LYS
Chi-restraints excluded: chain F residue   93 GLN
Chi-restraints excluded: chain G residue   74 LYS
Chi-restraints excluded: chain H residue   52 SER
Chi-restraints excluded: chain H residue   53 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 87 optimal weight:   10.0000
   chunk 77 optimal weight:    5.9990
   chunk 8 optimal weight:    1.9990
   chunk 49 optimal weight:    3.9990
   chunk 16 optimal weight:    4.9990
   chunk 57 optimal weight:    3.9990
   chunk 84 optimal weight:    8.9990
   chunk 70 optimal weight:    3.9990
   chunk 19 optimal weight:    1.9990
   chunk 18 optimal weight:    3.9990
   chunk 82 optimal weight:    6.9990
   overall best weight:    3.1990

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

Flipped N/Q/H residues before XYZ refinement:
A 125 GLN
H  46 HIS
H  81 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.101459 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.080251 restraints weight = 20559.009|
|-----------------------------------------------------------------------------|
r_work (start): 0.3261 rms_B_bonded: 1.33
r_work: 0.3078 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.2941 rms_B_bonded: 4.13 restraints_weight: 0.2500
r_work (final): 0.2941
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8450
moved from start:          0.2242

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.057  12822  Z= 0.292
  Angle     :  0.615   5.592  18556  Z= 0.371
  Chirality :  0.038   0.187   2111
  Planarity :  0.004   0.043   1344
  Dihedral  : 31.395 121.450   4030
  Min Nonbonded Distance : 2.229

Molprobity Statistics.
  All-atom Clashscore : 6.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  3.77 %
    Allowed  : 20.41 %
    Favored  : 75.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.24 (0.30), residues: 748
  helix:  2.09 (0.22), residues: 547
  sheet:  None (None), residues: 0
  loop : -0.16 (0.39), residues: 201

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B  95 
 TYR   0.022   0.002   TYR G  57 
 PHE   0.018   0.002   PHE G  25 
 HIS   0.005   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00657 (12822)
  covalent geometry    : angle       0.61476 (18556)
  hydrogen bonds       : bond        0.05236 (  786)
  hydrogen bonds       : angle       3.07810 ( 1972)

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

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

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 185
  time to evaluate  : 0.375 
Fit side-chains
   revert: symmetry clash
REVERT: C   64 GLU cc_start: 0.8570 (tt0) cc_final: 0.8190 (tp30)
REVERT: C   73 ASN cc_start: 0.8998 (OUTLIER) cc_final: 0.8471 (t0)
REVERT: C   90 ASP cc_start: 0.8461 (t70) cc_final: 0.8138 (t70)
REVERT: D   54 LYS cc_start: 0.8957 (mmmt) cc_final: 0.8631 (mmtp)
REVERT: E   68 GLN cc_start: 0.9193 (OUTLIER) cc_final: 0.8665 (tt0)
REVERT: F   80 THR cc_start: 0.9369 (t) cc_final: 0.9090 (m)
REVERT: F   93 GLN cc_start: 0.8548 (OUTLIER) cc_final: 0.7248 (mp10)
REVERT: G   74 LYS cc_start: 0.8986 (OUTLIER) cc_final: 0.8481 (mtmm)
REVERT: G  113 SER cc_start: 0.8979 (m) cc_final: 0.8772 (p)
REVERT: H   30 ARG cc_start: 0.6773 (mtp-110) cc_final: 0.6469 (mtt180)
REVERT: H   65 ASP cc_start: 0.9027 (t70) cc_final: 0.8782 (t0)
  outliers start: 24
  outliers final: 10
  residues processed: 189
  average time/residue: 0.9487
  time to fit residues: 188.8970
Evaluate side-chains
  194 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 180
  time to evaluate  : 0.295 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue   76 GLN
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain A residue  105 GLU
Chi-restraints excluded: chain A residue  133 GLU
Chi-restraints excluded: chain B residue   79 LYS
Chi-restraints excluded: chain C residue   73 ASN
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain E residue   68 GLN
Chi-restraints excluded: chain F residue   77 LYS
Chi-restraints excluded: chain F residue   93 GLN
Chi-restraints excluded: chain G residue   74 LYS
Chi-restraints excluded: chain H residue   52 SER
Chi-restraints excluded: chain H residue   53 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 68 optimal weight:    4.9990
   chunk 49 optimal weight:    1.9990
   chunk 85 optimal weight:   10.0000
   chunk 14 optimal weight:    0.9990
   chunk 10 optimal weight:    1.9990
   chunk 84 optimal weight:    8.9990
   chunk 8 optimal weight:    7.9990
   chunk 6 optimal weight:    0.7980
   chunk 65 optimal weight:    3.9990
   chunk 5 optimal weight:    0.9990
   chunk 7 optimal weight:    0.7980
   overall best weight:    1.1186

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

Flipped N/Q/H residues before XYZ refinement:
** E  76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  46 HIS
H  81 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.102455 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.080699 restraints weight = 20292.469|
|-----------------------------------------------------------------------------|
r_work (start): 0.3279 rms_B_bonded: 1.35
r_work: 0.3096 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.2959 rms_B_bonded: 4.20 restraints_weight: 0.2500
r_work (final): 0.2959
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8421
moved from start:          0.2239

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.066  12822  Z= 0.185
  Angle     :  0.601   6.037  18556  Z= 0.363
  Chirality :  0.035   0.176   2111
  Planarity :  0.004   0.047   1344
  Dihedral  : 31.431 122.372   4030
  Min Nonbonded Distance : 2.192

Molprobity Statistics.
  All-atom Clashscore : 6.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 20.41 %
    Favored  : 76.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.37 (0.30), residues: 748
  helix:  2.17 (0.22), residues: 547
  sheet:  None (None), residues: 0
  loop : -0.07 (0.39), residues: 201

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B  95 
 TYR   0.030   0.002   TYR G  57 
 PHE   0.009   0.001   PHE G  25 
 HIS   0.004   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00409 (12822)
  covalent geometry    : angle       0.60063 (18556)
  hydrogen bonds       : bond        0.04817 (  786)
  hydrogen bonds       : angle       3.07753 ( 1972)

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

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

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 186
  time to evaluate  : 0.335 
Fit side-chains
REVERT: A   42 ARG cc_start: 0.8358 (mmm160) cc_final: 0.8113 (mmm-85)
REVERT: A   56 LYS cc_start: 0.9084 (OUTLIER) cc_final: 0.8756 (ptpp)
REVERT: C   64 GLU cc_start: 0.8553 (tt0) cc_final: 0.8166 (tp30)
REVERT: C   73 ASN cc_start: 0.8975 (OUTLIER) cc_final: 0.8448 (t0)
REVERT: C   90 ASP cc_start: 0.8427 (t70) cc_final: 0.8091 (t70)
REVERT: D   54 LYS cc_start: 0.8965 (mmmt) cc_final: 0.8644 (mmtp)
REVERT: E   68 GLN cc_start: 0.9131 (OUTLIER) cc_final: 0.8918 (tt0)
REVERT: F   93 GLN cc_start: 0.8515 (OUTLIER) cc_final: 0.7217 (mp10)
REVERT: G   74 LYS cc_start: 0.8985 (OUTLIER) cc_final: 0.8521 (mtmm)
REVERT: G  113 SER cc_start: 0.8956 (m) cc_final: 0.8747 (p)
REVERT: H   30 ARG cc_start: 0.6727 (mtp-110) cc_final: 0.6427 (mtt180)
REVERT: H   65 ASP cc_start: 0.8996 (t70) cc_final: 0.8738 (t0)
  outliers start: 20
  outliers final: 8
  residues processed: 190
  average time/residue: 0.9050
  time to fit residues: 181.3932
Evaluate side-chains
  199 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 186
  time to evaluate  : 0.332 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 LYS
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue   76 GLN
Chi-restraints excluded: chain A residue  105 GLU
Chi-restraints excluded: chain A residue  133 GLU
Chi-restraints excluded: chain C residue   73 ASN
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain E residue   68 GLN
Chi-restraints excluded: chain F residue   77 LYS
Chi-restraints excluded: chain F residue   93 GLN
Chi-restraints excluded: chain G residue   74 LYS
Chi-restraints excluded: chain H residue   52 SER
Chi-restraints excluded: chain H residue   53 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 11 optimal weight:    7.9990
   chunk 79 optimal weight:    5.9990
   chunk 60 optimal weight:    0.5980
   chunk 13 optimal weight:    0.9980
   chunk 94 optimal weight:    4.9990
   chunk 80 optimal weight:    4.9990
   chunk 46 optimal weight:    0.5980
   chunk 92 optimal weight:    2.9990
   chunk 19 optimal weight:    0.9990
   chunk 76 optimal weight:    5.9990
   chunk 99 optimal weight:   10.0000
   overall best weight:    1.2384

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

Flipped N/Q/H residues before XYZ refinement:
A 125 GLN
** E  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  46 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.102738 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.081521 restraints weight = 20393.397|
|-----------------------------------------------------------------------------|
r_work (start): 0.3282 rms_B_bonded: 1.32
r_work: 0.3102 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.2963 rms_B_bonded: 4.14 restraints_weight: 0.2500
r_work (final): 0.2963
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8420
moved from start:          0.2255

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051  12822  Z= 0.191
  Angle     :  0.595   6.341  18556  Z= 0.360
  Chirality :  0.035   0.217   2111
  Planarity :  0.004   0.049   1344
  Dihedral  : 31.370 122.922   4030
  Min Nonbonded Distance : 2.198

Molprobity Statistics.
  All-atom Clashscore : 7.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 20.57 %
    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:  2.48 (0.30), residues: 748
  helix:  2.25 (0.22), residues: 547
  sheet:  None (None), residues: 0
  loop : -0.02 (0.39), residues: 201

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D  83 
 TYR   0.022   0.002   TYR G  57 
 PHE   0.009   0.001   PHE A  67 
 HIS   0.004   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00425 (12822)
  covalent geometry    : angle       0.59549 (18556)
  hydrogen bonds       : bond        0.04470 (  786)
  hydrogen bonds       : angle       3.03330 ( 1972)

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

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

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 185
  time to evaluate  : 0.322 
Fit side-chains
   revert: symmetry clash
REVERT: A   56 LYS cc_start: 0.9116 (OUTLIER) cc_final: 0.8816 (ptpp)
REVERT: A  120 MET cc_start: 0.9008 (OUTLIER) cc_final: 0.8608 (mtt)
REVERT: C   64 GLU cc_start: 0.8554 (tt0) cc_final: 0.8170 (tp30)
REVERT: C   73 ASN cc_start: 0.8970 (OUTLIER) cc_final: 0.8448 (t0)
REVERT: C   90 ASP cc_start: 0.8430 (t70) cc_final: 0.8107 (t70)
REVERT: D   31 LYS cc_start: 0.8971 (mppt) cc_final: 0.8760 (mptt)
REVERT: D   54 LYS cc_start: 0.8958 (mmmt) cc_final: 0.8639 (mmtp)
REVERT: E   68 GLN cc_start: 0.9134 (OUTLIER) cc_final: 0.8626 (tt0)
REVERT: F   93 GLN cc_start: 0.8520 (OUTLIER) cc_final: 0.7215 (mp10)
REVERT: G   74 LYS cc_start: 0.8982 (OUTLIER) cc_final: 0.8482 (mtmm)
REVERT: G  113 SER cc_start: 0.8957 (m) cc_final: 0.8754 (p)
REVERT: H   30 ARG cc_start: 0.6738 (mtp-110) cc_final: 0.6441 (mtt180)
REVERT: H   65 ASP cc_start: 0.8994 (t70) cc_final: 0.8755 (t0)
REVERT: H   76 ARG cc_start: 0.8296 (mtp180) cc_final: 0.7954 (mtm-85)
  outliers start: 22
  outliers final: 10
  residues processed: 189
  average time/residue: 0.8933
  time to fit residues: 177.8552
Evaluate side-chains
  200 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 184
  time to evaluate  : 0.324 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 LYS
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue   76 GLN
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain A residue  105 GLU
Chi-restraints excluded: chain A residue  120 MET
Chi-restraints excluded: chain A residue  133 GLU
Chi-restraints excluded: chain B residue   79 LYS
Chi-restraints excluded: chain C residue   73 ASN
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain E residue   68 GLN
Chi-restraints excluded: chain F residue   77 LYS
Chi-restraints excluded: chain F residue   93 GLN
Chi-restraints excluded: chain G residue   74 LYS
Chi-restraints excluded: chain H residue   52 SER
Chi-restraints excluded: chain H residue   53 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 52 optimal weight:    3.9990
   chunk 77 optimal weight:    5.9990
   chunk 85 optimal weight:   10.0000
   chunk 79 optimal weight:    5.9990
   chunk 56 optimal weight:    4.9990
   chunk 64 optimal weight:    0.0770
   chunk 21 optimal weight:    2.9990
   chunk 81 optimal weight:    5.9990
   chunk 31 optimal weight:    0.7980
   chunk 4 optimal weight:    1.9990
   chunk 71 optimal weight:    0.6980
   overall best weight:    1.3142

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

Flipped N/Q/H residues before XYZ refinement:
** E  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  46 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.103277 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.082080 restraints weight = 20375.429|
|-----------------------------------------------------------------------------|
r_work (start): 0.3289 rms_B_bonded: 1.32
r_work: 0.3109 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.2973 rms_B_bonded: 4.14 restraints_weight: 0.2500
r_work (final): 0.2973
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8414
moved from start:          0.2264

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  12822  Z= 0.182
  Angle     :  0.588   6.582  18556  Z= 0.356
  Chirality :  0.035   0.144   2111
  Planarity :  0.004   0.042   1344
  Dihedral  : 31.310 123.413   4030
  Min Nonbonded Distance : 2.192

Molprobity Statistics.
  All-atom Clashscore : 7.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 20.09 %
    Favored  : 76.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.50 (0.30), residues: 748
  helix:  2.26 (0.22), residues: 547
  sheet:  None (None), residues: 0
  loop :  0.01 (0.39), residues: 201

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG G  71 
 TYR   0.025   0.002   TYR G  57 
 PHE   0.009   0.001   PHE A  67 
 HIS   0.005   0.001   HIS H  46 

Details of bonding type rmsd
  covalent geometry    : bond        0.00400 (12822)
  covalent geometry    : angle       0.58756 (18556)
  hydrogen bonds       : bond        0.04342 (  786)
  hydrogen bonds       : angle       3.01067 ( 1972)

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

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

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  210 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 188
  time to evaluate  : 0.328 
Fit side-chains
   revert: symmetry clash
REVERT: A   56 LYS cc_start: 0.9114 (OUTLIER) cc_final: 0.8817 (ptpp)
REVERT: A  120 MET cc_start: 0.9015 (OUTLIER) cc_final: 0.8602 (mtt)
REVERT: C   64 GLU cc_start: 0.8547 (tt0) cc_final: 0.8160 (tp30)
REVERT: C   73 ASN cc_start: 0.8969 (OUTLIER) cc_final: 0.8439 (t0)
REVERT: C   90 ASP cc_start: 0.8460 (t70) cc_final: 0.8120 (t70)
REVERT: D   31 LYS cc_start: 0.8978 (OUTLIER) cc_final: 0.8767 (mptt)
REVERT: D   54 LYS cc_start: 0.8956 (mmmt) cc_final: 0.8636 (mmtp)
REVERT: E   68 GLN cc_start: 0.9173 (OUTLIER) cc_final: 0.8657 (tt0)
REVERT: F   93 GLN cc_start: 0.8507 (OUTLIER) cc_final: 0.7194 (mp10)
REVERT: G   74 LYS cc_start: 0.8987 (OUTLIER) cc_final: 0.8547 (mtmm)
REVERT: H   30 ARG cc_start: 0.6743 (mtp-110) cc_final: 0.6456 (mtt180)
REVERT: H   65 ASP cc_start: 0.8976 (t70) cc_final: 0.8735 (t0)
  outliers start: 22
  outliers final: 11
  residues processed: 190
  average time/residue: 0.9029
  time to fit residues: 180.8309
Evaluate side-chains
  203 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 185
  time to evaluate  : 0.263 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 ARG
Chi-restraints excluded: chain A residue   56 LYS
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue   76 GLN
Chi-restraints excluded: chain A residue  105 GLU
Chi-restraints excluded: chain A residue  120 MET
Chi-restraints excluded: chain A residue  133 GLU
Chi-restraints excluded: chain B residue   79 LYS
Chi-restraints excluded: chain C residue   73 ASN
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain D residue   31 LYS
Chi-restraints excluded: chain E residue   68 GLN
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain F residue   77 LYS
Chi-restraints excluded: chain F residue   93 GLN
Chi-restraints excluded: chain G residue   74 LYS
Chi-restraints excluded: chain H residue   52 SER
Chi-restraints excluded: chain H residue   53 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 23 optimal weight:    6.9990
   chunk 22 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9990
   chunk 61 optimal weight:    1.9990
   chunk 37 optimal weight:    0.9990
   chunk 10 optimal weight:    0.0870
   chunk 99 optimal weight:    9.9990
   chunk 79 optimal weight:    5.9990
   chunk 55 optimal weight:    7.9990
   chunk 62 optimal weight:    2.9990
   chunk 40 optimal weight:    3.9990
   overall best weight:    1.2166

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

Flipped N/Q/H residues before XYZ refinement:
** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  46 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.103347 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.082207 restraints weight = 20275.170|
|-----------------------------------------------------------------------------|
r_work (start): 0.3297 rms_B_bonded: 1.32
r_work: 0.3118 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.2982 rms_B_bonded: 4.12 restraints_weight: 0.2500
r_work (final): 0.2982
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8407
moved from start:          0.2265

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.075  12822  Z= 0.182
  Angle     :  0.586   6.717  18556  Z= 0.354
  Chirality :  0.034   0.141   2111
  Planarity :  0.004   0.043   1344
  Dihedral  : 31.240 123.872   4030
  Min Nonbonded Distance : 2.194

Molprobity Statistics.
  All-atom Clashscore : 7.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 20.41 %
    Favored  : 76.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.56 (0.30), residues: 748
  helix:  2.29 (0.22), residues: 547
  sheet:  None (None), residues: 0
  loop :  0.06 (0.40), residues: 201

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG D  83 
 TYR   0.028   0.002   TYR G  57 
 PHE   0.009   0.001   PHE A  67 
 HIS   0.004   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00402 (12822)
  covalent geometry    : angle       0.58605 (18556)
  hydrogen bonds       : bond        0.04241 (  786)
  hydrogen bonds       : angle       2.99400 ( 1972)

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

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

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  210 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 188
  time to evaluate  : 0.307 
Fit side-chains
REVERT: A   42 ARG cc_start: 0.8337 (OUTLIER) cc_final: 0.8115 (mtp-110)
REVERT: A   56 LYS cc_start: 0.9113 (OUTLIER) cc_final: 0.8816 (ptpp)
REVERT: A  120 MET cc_start: 0.8995 (OUTLIER) cc_final: 0.8561 (mtt)
REVERT: C   64 GLU cc_start: 0.8541 (tt0) cc_final: 0.8157 (tp30)
REVERT: C   73 ASN cc_start: 0.8962 (OUTLIER) cc_final: 0.8433 (t0)
REVERT: C   90 ASP cc_start: 0.8452 (t70) cc_final: 0.8119 (t70)
REVERT: D   31 LYS cc_start: 0.9010 (OUTLIER) cc_final: 0.8774 (mptt)
REVERT: D   54 LYS cc_start: 0.8949 (mmmt) cc_final: 0.8626 (mmtp)
REVERT: E   68 GLN cc_start: 0.9169 (OUTLIER) cc_final: 0.8642 (tt0)
REVERT: E  120 MET cc_start: 0.8555 (OUTLIER) cc_final: 0.7817 (mtt)
REVERT: F   93 GLN cc_start: 0.8504 (OUTLIER) cc_final: 0.7188 (mp10)
REVERT: G   74 LYS cc_start: 0.8985 (OUTLIER) cc_final: 0.8512 (mtmm)
REVERT: H   30 ARG cc_start: 0.6757 (mtp-110) cc_final: 0.6482 (mtt180)
  outliers start: 22
  outliers final: 11
  residues processed: 191
  average time/residue: 0.8954
  time to fit residues: 180.3600
Evaluate side-chains
  206 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 186
  time to evaluate  : 0.396 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 ARG
Chi-restraints excluded: chain A residue   56 LYS
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue   76 GLN
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain A residue  105 GLU
Chi-restraints excluded: chain A residue  120 MET
Chi-restraints excluded: chain A residue  133 GLU
Chi-restraints excluded: chain B residue   79 LYS
Chi-restraints excluded: chain C residue   73 ASN
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain D residue   31 LYS
Chi-restraints excluded: chain E residue   68 GLN
Chi-restraints excluded: chain E residue  120 MET
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain F residue   77 LYS
Chi-restraints excluded: chain F residue   93 GLN
Chi-restraints excluded: chain G residue   74 LYS
Chi-restraints excluded: chain H residue   52 SER
Chi-restraints excluded: chain H residue   53 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 20 optimal weight:    0.0980
   chunk 78 optimal weight:    4.9990
   chunk 67 optimal weight:    5.9990
   chunk 55 optimal weight:    3.9990
   chunk 97 optimal weight:    5.9990
   chunk 92 optimal weight:    4.9990
   chunk 6 optimal weight:    3.9990
   chunk 15 optimal weight:    0.7980
   chunk 23 optimal weight:    6.9990
   chunk 87 optimal weight:   10.0000
   chunk 29 optimal weight:    0.2980
   overall best weight:    1.8384

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.102943 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.081264 restraints weight = 20323.660|
|-----------------------------------------------------------------------------|
r_work (start): 0.3290 rms_B_bonded: 1.37
r_work: 0.3108 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.2973 rms_B_bonded: 4.21 restraints_weight: 0.2500
r_work (final): 0.2973
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8404
moved from start:          0.2339

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037  12822  Z= 0.205
  Angle     :  0.585   7.086  18556  Z= 0.354
  Chirality :  0.035   0.138   2111
  Planarity :  0.004   0.049   1344
  Dihedral  : 31.023 126.738   4030
  Min Nonbonded Distance : 2.193

Molprobity Statistics.
  All-atom Clashscore : 7.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 20.72 %
    Favored  : 76.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.62 (0.30), residues: 748
  helix:  2.32 (0.22), residues: 547
  sheet:  None (None), residues: 0
  loop :  0.14 (0.40), residues: 201

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG D  83 
 TYR   0.031   0.002   TYR G  57 
 PHE   0.009   0.002   PHE G  25 
 HIS   0.005   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00455 (12822)
  covalent geometry    : angle       0.58482 (18556)
  hydrogen bonds       : bond        0.04406 (  786)
  hydrogen bonds       : angle       2.97877 ( 1972)

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

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

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 185
  time to evaluate  : 0.268 
Fit side-chains
REVERT: A   42 ARG cc_start: 0.8371 (OUTLIER) cc_final: 0.8093 (mtp-110)
REVERT: A   50 GLU cc_start: 0.8639 (mt-10) cc_final: 0.8412 (mt-10)
REVERT: C   73 ASN cc_start: 0.8953 (OUTLIER) cc_final: 0.8366 (t0)
REVERT: C   90 ASP cc_start: 0.8447 (t70) cc_final: 0.8130 (t70)
REVERT: D   31 LYS cc_start: 0.8964 (OUTLIER) cc_final: 0.8707 (mptt)
REVERT: D   54 LYS cc_start: 0.8947 (mmmt) cc_final: 0.8610 (mmtp)
REVERT: E   68 GLN cc_start: 0.9169 (OUTLIER) cc_final: 0.8701 (tt0)
REVERT: E   79 LYS cc_start: 0.9094 (tttp) cc_final: 0.8891 (tttm)
REVERT: E  120 MET cc_start: 0.8587 (OUTLIER) cc_final: 0.8343 (mtp)
REVERT: F   93 GLN cc_start: 0.8520 (OUTLIER) cc_final: 0.7178 (mp10)
REVERT: G   74 LYS cc_start: 0.8982 (OUTLIER) cc_final: 0.8507 (mtmm)
REVERT: H   30 ARG cc_start: 0.6813 (mtp-110) cc_final: 0.6566 (mtt180)
REVERT: H   76 ARG cc_start: 0.8353 (mtp180) cc_final: 0.8072 (mtm-85)
  outliers start: 20
  outliers final: 9
  residues processed: 188
  average time/residue: 0.8366
  time to fit residues: 166.0870
Evaluate side-chains
  196 residues out of total 637 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 180
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 ARG
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue   76 GLN
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain A residue  105 GLU
Chi-restraints excluded: chain B residue   79 LYS
Chi-restraints excluded: chain C residue   73 ASN
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain D residue   31 LYS
Chi-restraints excluded: chain E residue   68 GLN
Chi-restraints excluded: chain E residue  120 MET
Chi-restraints excluded: chain F residue   77 LYS
Chi-restraints excluded: chain F residue   93 GLN
Chi-restraints excluded: chain G residue   74 LYS
Chi-restraints excluded: chain H residue   52 SER
Chi-restraints excluded: chain H residue   53 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 94 optimal weight:    4.9990
   chunk 49 optimal weight:    3.9990
   chunk 53 optimal weight:    7.9990
   chunk 14 optimal weight:    2.9990
   chunk 20 optimal weight:    1.9990
   chunk 30 optimal weight:    0.8980
   chunk 89 optimal weight:    6.9990
   chunk 58 optimal weight:   10.0000
   chunk 41 optimal weight:    0.8980
   chunk 17 optimal weight:    1.9990
   chunk 10 optimal weight:    0.2980
   overall best weight:    1.2184

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

Flipped N/Q/H residues before XYZ refinement:
** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 125 GLN
** E  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.103253 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.081638 restraints weight = 20349.178|
|-----------------------------------------------------------------------------|
r_work (start): 0.3296 rms_B_bonded: 1.36
r_work: 0.3114 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.2977 rms_B_bonded: 4.21 restraints_weight: 0.2500
r_work (final): 0.2977
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8402
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   0.040  12822  Z= 0.185
  Angle     :  0.589   6.883  18556  Z= 0.355
  Chirality :  0.034   0.138   2111
  Planarity :  0.004   0.046   1344
  Dihedral  : 31.027 126.847   4030
  Min Nonbonded Distance : 2.188

Molprobity Statistics.
  All-atom Clashscore : 7.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 22.45 %
    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:  2.65 (0.30), residues: 748
  helix:  2.33 (0.22), residues: 547
  sheet:  None (None), residues: 0
  loop :  0.16 (0.40), residues: 201

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG D  83 
 TYR   0.024   0.002   TYR G  57 
 PHE   0.009   0.001   PHE E  67 
 HIS   0.004   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00410 (12822)
  covalent geometry    : angle       0.58924 (18556)
  hydrogen bonds       : bond        0.04342 (  786)
  hydrogen bonds       : angle       2.96949 ( 1972)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5644.89 seconds
wall clock time: 96 minutes 20.22 seconds (5780.22 seconds total)