Starting phenix.real_space_refine
on Sat Aug 23 11:32:38 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8guk_34275/08_2025/8guk_34275.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8guk_34275/08_2025/8guk_34275.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.51
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8guk_34275/08_2025/8guk_34275.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8guk_34275/08_2025/8guk_34275.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8guk_34275/08_2025/8guk_34275.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8guk_34275/08_2025/8guk_34275.cif"
  }
  resolution = 2.51
  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=  -0.005 sd=   0.055
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     294      5.49       5
     S      14      5.16       5
     C    6686      2.51       5
     N    2277      2.21       5
     O    2827      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 31 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 12098
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 810
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 98, 810
          Classifications: {'peptide': 98}
          Link IDs: {'PTRANS': 4, 'TRANS': 93}
    Chain: "B"
      Number of atoms: 641
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 80, 641
          Classifications: {'peptide': 80}
          Link IDs: {'PTRANS': 1, 'TRANS': 78}
    Chain: "C"
      Number of atoms: 846
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 110, 846
          Classifications: {'peptide': 110}
          Link IDs: {'PTRANS': 5, 'TRANS': 104}
    Chain: "D"
      Number of atoms: 736
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 736
          Classifications: {'peptide': 94}
          Link IDs: {'PTRANS': 2, 'TRANS': 91}
    Chain: "E"
      Number of atoms: 810
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 98, 810
          Classifications: {'peptide': 98}
          Link IDs: {'PTRANS': 4, 'TRANS': 93}
    Chain: "F"
      Number of atoms: 641
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 80, 641
          Classifications: {'peptide': 80}
          Link IDs: {'PTRANS': 1, 'TRANS': 78}
    Chain: "G"
      Number of atoms: 851
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 111, 851
          Classifications: {'peptide': 111}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 105}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "H"
      Number of atoms: 736
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 736
          Classifications: {'peptide': 94}
          Link IDs: {'PTRANS': 2, 'TRANS': 91}
    Chain: "I"
      Number of atoms: 2996
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 147, 2996
          Classifications: {'DNA': 147}
          Link IDs: {'rna3p': 146}
    Chain: "J"
      Number of atoms: 3031
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 147, 3031
          Classifications: {'DNA': 147}
          Link IDs: {'rna3p': 146}
  Time building chain proxies: 3.19, per 1000 atoms: 0.26
  Number of scatterers: 12098
  At special positions: 0
  Unit cell: (72.45, 113.4, 119.7, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      14     16.00
     P     294     15.00
     O    2827      8.00
     N    2277      7.00
     C    6686      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: 1.04
  Conformation dependent library (CDL) restraints added in 358.7 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  1498 Ramachandran restraints generated.
    749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1430

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 10 sheets defined
      73.7% alpha, 2.9% beta
      146 base pairs and 260 stacking pairs defined.
    Time for finding SS restraints: 2.06
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 57
    Processing helix  chain 'A' and resid 63 through 79
    Processing helix  chain 'A' and resid 85 through 114
    Processing helix  chain 'A' and resid 120 through 132
    Processing helix  chain 'B' and resid 24 through 29
    Processing helix  chain 'B' and resid 30 through 41
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 3.552A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 93
    Processing helix  chain 'C' and resid 16 through 21
    Processing helix  chain 'C' and resid 26 through 37
    Processing helix  chain 'C' and resid 45 through 73
      removed outlier: 4.373A  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 'C' and resid 112 through 116
    Processing helix  chain 'D' and resid 37 through 49
    Processing helix  chain 'D' and resid 55 through 84
    Processing helix  chain 'D' and resid 90 through 102
    Processing helix  chain 'D' and resid 103 through 123
      removed outlier: 3.593A  pdb=" N   ALA D 107 " --> pdb=" O   PRO D 103 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 44 through 57
    Processing helix  chain 'E' and resid 63 through 79
      removed outlier: 4.096A  pdb=" N   ASP E  77 " --> pdb=" O   GLU E  73 " (cutoff:3.500A)
      removed outlier: 4.304A  pdb=" N   PHE E  78 " --> pdb=" O   ILE E  74 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 85 through 114
    Processing helix  chain 'E' and resid 120 through 132
    Processing helix  chain 'F' and resid 24 through 29
    Processing helix  chain 'F' and resid 30 through 41
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 3.576A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 93
    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: 4.228A  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 90 through 97
    Processing helix  chain 'G' and resid 112 through 116
    Processing helix  chain 'H' and resid 37 through 49
    Processing helix  chain 'H' and resid 55 through 84
    Processing helix  chain 'H' and resid 90 through 102
    Processing helix  chain 'H' and resid 103 through 124
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 6.643A  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 97 through 98
    Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43
      removed outlier: 7.120A  pdb=" N   ARG C  42 " --> pdb=" O   ILE D  89 " (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: 6.724A  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: 7.137A  pdb=" N   ARG G  42 " --> pdb=" O   ILE H  89 " (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

    424 hydrogen bonds defined for protein.
    1242 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      375 hydrogen bonds
      750 hydrogen bond angles
      0 basepair planarities
      146 basepair parallelities
      260 stacking parallelities
  Total time for adding SS restraints: 2.22

  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: 2168
        1.33 -     1.45: 4244
        1.45 -     1.57: 5889
        1.57 -     1.69: 586
        1.69 -     1.80: 24
  Bond restraints: 12911
  Sorted by residual:
  bond pdb=" C3'  DA I 131 "
       pdb=" O3'  DA I 131 "
    ideal  model  delta    sigma   weight residual
    1.422  1.465 -0.043 3.00e-02 1.11e+03 2.02e+00
  bond pdb=" C3'  DA I  41 "
       pdb=" O3'  DA I  41 "
    ideal  model  delta    sigma   weight residual
    1.422  1.462 -0.040 3.00e-02 1.11e+03 1.80e+00
  bond pdb=" C3'  DT I  77 "
       pdb=" O3'  DT I  77 "
    ideal  model  delta    sigma   weight residual
    1.422  1.462 -0.040 3.00e-02 1.11e+03 1.76e+00
  bond pdb=" C3'  DT I  32 "
       pdb=" O3'  DT I  32 "
    ideal  model  delta    sigma   weight residual
    1.422  1.461 -0.039 3.00e-02 1.11e+03 1.73e+00
  bond pdb=" C3'  DG I  33 "
       pdb=" O3'  DG I  33 "
    ideal  model  delta    sigma   weight residual
    1.422  1.461 -0.039 3.00e-02 1.11e+03 1.73e+00
  ... (remaining 12906 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.80: 18219
        1.80 -     3.60: 441
        3.60 -     5.40: 24
        5.40 -     7.20: 5
        7.20 -     9.00: 1
  Bond angle restraints: 18690
  Sorted by residual:
  angle pdb=" CA  ASN G  73 "
        pdb=" CB  ASN G  73 "
        pdb=" CG  ASN G  73 "
      ideal   model   delta    sigma   weight residual
     112.60  115.67   -3.07 1.00e+00 1.00e+00 9.40e+00
  angle pdb=" C   GLY C  37 "
        pdb=" N   ASN C  38 "
        pdb=" CA  ASN C  38 "
      ideal   model   delta    sigma   weight residual
     121.54  127.28   -5.74 1.91e+00 2.74e-01 9.04e+00
  angle pdb=" N   ASN G  73 "
        pdb=" CA  ASN G  73 "
        pdb=" C   ASN G  73 "
      ideal   model   delta    sigma   weight residual
     113.16  109.60    3.56 1.24e+00 6.50e-01 8.26e+00
  angle pdb=" CB  ARG B  23 "
        pdb=" CG  ARG B  23 "
        pdb=" CD  ARG B  23 "
      ideal   model   delta    sigma   weight residual
     111.30  117.75   -6.45 2.30e+00 1.89e-01 7.87e+00
  angle pdb=" C   THR A  80 "
        pdb=" N   ASP A  81 "
        pdb=" CA  ASP A  81 "
      ideal   model   delta    sigma   weight residual
     122.82  126.62   -3.80 1.42e+00 4.96e-01 7.17e+00
  ... (remaining 18685 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.01: 5451
       35.01 -    70.02: 1530
       70.02 -   105.03: 28
      105.03 -   140.04: 1
      140.04 -   175.04: 7
  Dihedral angle restraints: 7017
    sinusoidal: 4800
      harmonic: 2217
  Sorted by residual:
  dihedral pdb=" C4'  DT I  32 "
           pdb=" C3'  DT I  32 "
           pdb=" O3'  DT I  32 "
           pdb=" P    DG I  33 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   44.96  175.04     1      3.50e+01 8.16e-04 1.56e+01
  dihedral pdb=" C4'  DG J   4 "
           pdb=" C3'  DG J   4 "
           pdb=" O3'  DG J   4 "
           pdb=" P    DG J   5 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -140.00   33.09 -173.09     1      3.50e+01 8.16e-04 1.56e+01
  dihedral pdb=" C4'  DT I  77 "
           pdb=" C3'  DT I  77 "
           pdb=" O3'  DT I  77 "
           pdb=" P    DC I  78 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -140.00   29.87 -169.87     1      3.50e+01 8.16e-04 1.56e+01
  ... (remaining 7014 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.033: 1505
       0.033 -    0.065: 485
       0.065 -    0.098: 87
       0.098 -    0.131: 42
       0.131 -    0.163: 6
  Chirality restraints: 2125
  Sorted by residual:
  chirality pdb=" CB  THR H 119 "
            pdb=" CA  THR H 119 "
            pdb=" OG1 THR H 119 "
            pdb=" CG2 THR H 119 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.39    0.16 2.00e-01 2.50e+01 6.66e-01
  chirality pdb=" CA  ASP A  81 "
            pdb=" N   ASP A  81 "
            pdb=" C   ASP A  81 "
            pdb=" CB  ASP A  81 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.22e-01
  chirality pdb=" CA  ASP B  24 "
            pdb=" N   ASP B  24 "
            pdb=" C   ASP B  24 "
            pdb=" CB  ASP B  24 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.81e-01
  ... (remaining 2122 not shown)

  Planarity restraints: 1345
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN G  73 "    0.010 2.00e-02 2.50e+03   1.93e-02 3.71e+00
        pdb=" C   ASN G  73 "   -0.033 2.00e-02 2.50e+03
        pdb=" O   ASN G  73 "    0.013 2.00e-02 2.50e+03
        pdb=" N   LYS G  74 "    0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS E  37 "   -0.030 5.00e-02 4.00e+02   4.67e-02 3.48e+00
        pdb=" N   PRO E  38 "    0.081 5.00e-02 4.00e+02
        pdb=" CA  PRO E  38 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO E  38 "   -0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLU H  71 "    0.009 2.00e-02 2.50e+03   1.75e-02 3.05e+00
        pdb=" CD  GLU H  71 "   -0.030 2.00e-02 2.50e+03
        pdb=" OE1 GLU H  71 "    0.011 2.00e-02 2.50e+03
        pdb=" OE2 GLU H  71 "    0.011 2.00e-02 2.50e+03
  ... (remaining 1342 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 1260
        2.74 -     3.28: 10901
        3.28 -     3.82: 25697
        3.82 -     4.36: 29975
        4.36 -     4.90: 42058
  Nonbonded interactions: 109891
  Sorted by model distance:
  nonbonded pdb=" N   GLN C 104 "
            pdb=" OE2 GLU E  94 "
     model   vdw
     2.202 3.120
  nonbonded pdb=" O   HIS F  75 "
            pdb=" NH2 ARG H  92 "
     model   vdw
     2.237 3.120
  nonbonded pdb=" OE1 GLU D  76 "
            pdb=" NH2 ARG D  79 "
     model   vdw
     2.238 3.120
  nonbonded pdb=" OE1 GLU E  73 "
            pdb=" ND2 ASN F  25 "
     model   vdw
     2.245 3.120
  nonbonded pdb=" O   HIS B  75 "
            pdb=" NH1 ARG D  92 "
     model   vdw
     2.247 3.120
  ... (remaining 109886 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'E'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'F'
}
ncs_group {
  reference = chain 'C'
  selection = (chain 'G' and resid 10 through 119)
}
ncs_group {
  reference = chain 'D'
  selection = chain 'H'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 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:             2.630
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.190
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     13.820
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.130
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.990
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8248
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      :  0.004   0.045  12911  Z= 0.182
  Angle     :  0.602   9.002  18690  Z= 0.359
  Chirality :  0.035   0.163   2125
  Planarity :  0.005   0.060   1345
  Dihedral  : 29.885 175.045   5587
  Min Nonbonded Distance : 2.202

Molprobity Statistics.
  All-atom Clashscore : 10.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 31.23 %
    Favored  : 65.62 %
  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 aren not related in a simple way.
  whole:  2.28 (0.30), residues: 749
  helix:  2.15 (0.22), residues: 549
  sheet:  None (None), residues: 0
  loop : -0.28 (0.40), residues: 200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.001   ARG H  99 
 TYR   0.019   0.001   TYR H  83 
 PHE   0.009   0.001   PHE E  67 
 HIS   0.004   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00407 (12911)
  covalent geometry    : angle       0.60212 (18690)
  hydrogen bonds       : bond        0.09278 (  799)
  hydrogen bonds       : angle       3.78834 ( 1992)

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

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

  1498 Ramachandran restraints generated.
    749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1498 Ramachandran restraints generated.
    749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 181
  time to evaluate  : 0.333 
Fit side-chains
REVERT: D   92 ARG cc_start: 0.8694 (OUTLIER) cc_final: 0.7898 (ttm-80)
REVERT: H   63 ASN cc_start: 0.8792 (t0) cc_final: 0.8397 (m-40)
  outliers start: 20
  outliers final: 13
  residues processed: 196
  average time/residue: 0.8084
  time to fit residues: 167.7510
Evaluate side-chains
  191 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 177
  time to evaluate  : 0.384 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   47 SER
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue   95 ARG
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain C residue   49 VAL
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain D residue   92 ARG
Chi-restraints excluded: chain D residue   95 GLN
Chi-restraints excluded: chain D residue  112 SER
Chi-restraints excluded: chain E residue   46 VAL
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue   18 SER
Chi-restraints excluded: chain H residue  106 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 49 optimal weight:    0.5980
   chunk 97 optimal weight:    2.9990
   chunk 53 optimal weight:    0.6980
   chunk 5 optimal weight:    0.5980
   chunk 33 optimal weight:    0.7980
   chunk 65 optimal weight:    0.8980
   chunk 62 optimal weight:    0.5980
   chunk 51 optimal weight:    0.9980
   chunk 100 optimal weight:    2.9990
   chunk 38 optimal weight:    0.9990
   chunk 61 optimal weight:    0.7980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** A  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 108 ASN
B  25 ASN
** B  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 108 ASN
F  27 GLN
F  93 GLN
G  73 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.104373 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.083253 restraints weight = 19419.774|
|-----------------------------------------------------------------------------|
r_work (start): 0.3250 rms_B_bonded: 1.25
r_work: 0.3094 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.2971 rms_B_bonded: 4.12 restraints_weight: 0.2500
r_work (final): 0.2971
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8413
moved from start:          0.0819

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  12911  Z= 0.184
  Angle     :  0.584   8.279  18690  Z= 0.349
  Chirality :  0.035   0.156   2125
  Planarity :  0.004   0.039   1345
  Dihedral  : 31.886 174.831   4087
  Min Nonbonded Distance : 2.343

Molprobity Statistics.
  All-atom Clashscore : 8.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  4.89 %
    Allowed  : 25.87 %
    Favored  : 69.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.43 (0.30), residues: 749
  helix:  2.23 (0.22), residues: 555
  sheet:  None (None), residues: 0
  loop : -0.20 (0.40), residues: 194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG H  99 
 TYR   0.015   0.001   TYR H  83 
 PHE   0.011   0.001   PHE E  67 
 HIS   0.005   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00409 (12911)
  covalent geometry    : angle       0.58423 (18690)
  hydrogen bonds       : bond        0.03693 (  799)
  hydrogen bonds       : angle       3.13445 ( 1992)

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

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

  1498 Ramachandran restraints generated.
    749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1498 Ramachandran restraints generated.
    749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  228 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 197
  time to evaluate  : 0.347 
Fit side-chains
REVERT: A   94 GLU cc_start: 0.8527 (mm-30) cc_final: 0.8261 (mm-30)
REVERT: A  120 MET cc_start: 0.8758 (OUTLIER) cc_final: 0.8222 (mtt)
REVERT: C   77 ARG cc_start: 0.8558 (OUTLIER) cc_final: 0.7702 (ttp-170)
REVERT: D   34 LYS cc_start: 0.8716 (mmmm) cc_final: 0.8440 (mppt)
REVERT: D   40 TYR cc_start: 0.9034 (m-80) cc_final: 0.8821 (m-80)
REVERT: D   93 GLU cc_start: 0.8245 (mp0) cc_final: 0.7978 (mp0)
REVERT: F   22 LEU cc_start: 0.6511 (OUTLIER) cc_final: 0.6255 (tp)
REVERT: G  104 GLN cc_start: 0.8421 (mm-40) cc_final: 0.8050 (mm110)
REVERT: H   63 ASN cc_start: 0.8754 (t0) cc_final: 0.8458 (m-40)
  outliers start: 31
  outliers final: 18
  residues processed: 210
  average time/residue: 0.8206
  time to fit residues: 182.8301
Evaluate side-chains
  206 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 185
  time to evaluate  : 0.329 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  120 MET
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain C residue   41 GLU
Chi-restraints excluded: chain C residue   49 VAL
Chi-restraints excluded: chain C residue   77 ARG
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain C residue  108 LEU
Chi-restraints excluded: chain D residue   33 ARG
Chi-restraints excluded: chain D residue   48 VAL
Chi-restraints excluded: chain D residue   55 SER
Chi-restraints excluded: chain E residue   46 VAL
Chi-restraints excluded: chain E residue   86 SER
Chi-restraints excluded: chain F residue   22 LEU
Chi-restraints excluded: chain F residue   92 ARG
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue   75 LYS
Chi-restraints excluded: chain G residue   92 GLU
Chi-restraints excluded: chain G residue   99 LYS
Chi-restraints excluded: chain G residue  101 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 23 optimal weight:    3.9990
   chunk 46 optimal weight:    1.9990
   chunk 48 optimal weight:    1.9990
   chunk 77 optimal weight:    2.9990
   chunk 74 optimal weight:    5.9990
   chunk 91 optimal weight:    2.9990
   chunk 15 optimal weight:    1.9990
   chunk 100 optimal weight:    2.9990
   chunk 94 optimal weight:    1.9990
   chunk 71 optimal weight:    0.7980
   chunk 97 optimal weight:    2.9990
   overall best weight:    1.7588

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

Flipped N/Q/H residues before XYZ refinement:
** A  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  84 GLN
D  67 ASN
D  95 GLN
F  27 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.100552 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.079032 restraints weight = 19083.112|
|-----------------------------------------------------------------------------|
r_work (start): 0.3154 rms_B_bonded: 1.26
r_work: 0.2990 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.2862 rms_B_bonded: 4.05 restraints_weight: 0.2500
r_work (final): 0.2862
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8481
moved from start:          0.1248

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.052  12911  Z= 0.317
  Angle     :  0.646  10.513  18690  Z= 0.381
  Chirality :  0.041   0.171   2125
  Planarity :  0.005   0.039   1345
  Dihedral  : 32.363 172.871   4071
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 7.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  Rotamer:
    Outliers :  5.05 %
    Allowed  : 26.97 %
    Favored  : 67.98 %
  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 aren not related in a simple way.
  whole:  2.13 (0.30), residues: 749
  helix:  2.01 (0.22), residues: 555
  sheet:  None (None), residues: 0
  loop : -0.31 (0.39), residues: 194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG H  99 
 TYR   0.015   0.002   TYR H  83 
 PHE   0.011   0.002   PHE A  67 
 HIS   0.005   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00720 (12911)
  covalent geometry    : angle       0.64574 (18690)
  hydrogen bonds       : bond        0.04925 (  799)
  hydrogen bonds       : angle       3.25884 ( 1992)

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

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

  1498 Ramachandran restraints generated.
    749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1498 Ramachandran restraints generated.
    749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  215 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 183
  time to evaluate  : 0.284 
Fit side-chains
REVERT: A   53 ARG cc_start: 0.8782 (OUTLIER) cc_final: 0.7903 (ttp-110)
REVERT: A   59 GLU cc_start: 0.8998 (pm20) cc_final: 0.8778 (pm20)
REVERT: B   79 LYS cc_start: 0.9208 (OUTLIER) cc_final: 0.8624 (mtmm)
REVERT: C   77 ARG cc_start: 0.8601 (OUTLIER) cc_final: 0.7529 (ttp-170)
REVERT: D   40 TYR cc_start: 0.9142 (m-80) cc_final: 0.8889 (m-80)
REVERT: D   93 GLU cc_start: 0.8423 (mp0) cc_final: 0.8164 (mp0)
REVERT: E   59 GLU cc_start: 0.8996 (pm20) cc_final: 0.8728 (pm20)
REVERT: F   95 ARG cc_start: 0.8815 (OUTLIER) cc_final: 0.8341 (mtp85)
REVERT: G   90 ASP cc_start: 0.8865 (t0) cc_final: 0.8663 (t0)
REVERT: H   63 ASN cc_start: 0.8863 (t0) cc_final: 0.8423 (m-40)
  outliers start: 32
  outliers final: 20
  residues processed: 200
  average time/residue: 0.8893
  time to fit residues: 187.9686
Evaluate side-chains
  197 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 173
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 ARG
Chi-restraints excluded: chain A residue   76 GLN
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue   79 LYS
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain C residue   41 GLU
Chi-restraints excluded: chain C residue   49 VAL
Chi-restraints excluded: chain C residue   77 ARG
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain C residue  108 LEU
Chi-restraints excluded: chain D residue   48 VAL
Chi-restraints excluded: chain E residue   46 VAL
Chi-restraints excluded: chain E residue   64 LYS
Chi-restraints excluded: chain E residue   86 SER
Chi-restraints excluded: chain F residue   80 THR
Chi-restraints excluded: chain F residue   92 ARG
Chi-restraints excluded: chain F residue   95 ARG
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue   92 GLU
Chi-restraints excluded: chain G residue   99 LYS
Chi-restraints excluded: chain G residue  101 THR
Chi-restraints excluded: chain H residue   47 GLN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 34 optimal weight:    0.8980
   chunk 37 optimal weight:    2.9990
   chunk 75 optimal weight:    3.9990
   chunk 63 optimal weight:    1.9990
   chunk 64 optimal weight:    2.9990
   chunk 31 optimal weight:    0.7980
   chunk 99 optimal weight:    1.9990
   chunk 19 optimal weight:    1.9990
   chunk 94 optimal weight:    1.9990
   chunk 76 optimal weight:    2.9990
   chunk 39 optimal weight:    0.9980
   overall best weight:    1.3384

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
** B  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D  63 ASN
D  95 GLN
F  27 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.100903 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.079411 restraints weight = 18978.817|
|-----------------------------------------------------------------------------|
r_work (start): 0.3169 rms_B_bonded: 1.24
r_work: 0.3007 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.2880 rms_B_bonded: 4.05 restraints_weight: 0.2500
r_work (final): 0.2880
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8454
moved from start:          0.1317

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.047  12911  Z= 0.264
  Angle     :  0.618   8.782  18690  Z= 0.368
  Chirality :  0.038   0.163   2125
  Planarity :  0.005   0.040   1345
  Dihedral  : 32.253 173.901   4071
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 7.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  4.73 %
    Allowed  : 27.60 %
    Favored  : 67.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.18 (0.30), residues: 749
  helix:  2.04 (0.22), residues: 556
  sheet:  None (None), residues: 0
  loop : -0.29 (0.39), residues: 193

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG H  99 
 TYR   0.015   0.002   TYR H  83 
 PHE   0.011   0.002   PHE A  67 
 HIS   0.004   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00597 (12911)
  covalent geometry    : angle       0.61816 (18690)
  hydrogen bonds       : bond        0.04436 (  799)
  hydrogen bonds       : angle       3.18861 ( 1992)

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

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

  1498 Ramachandran restraints generated.
    749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1498 Ramachandran restraints generated.
    749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  211 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 181
  time to evaluate  : 0.319 
Fit side-chains
REVERT: A   53 ARG cc_start: 0.8758 (OUTLIER) cc_final: 0.7873 (ttp-110)
REVERT: A   59 GLU cc_start: 0.9009 (pm20) cc_final: 0.8764 (pm20)
REVERT: C   56 GLU cc_start: 0.9046 (tt0) cc_final: 0.8832 (tt0)
REVERT: C   77 ARG cc_start: 0.8550 (OUTLIER) cc_final: 0.7430 (ttp-170)
REVERT: D   33 ARG cc_start: 0.7660 (OUTLIER) cc_final: 0.7037 (mmt-90)
REVERT: D   40 TYR cc_start: 0.9131 (m-80) cc_final: 0.8846 (m-80)
REVERT: D   93 GLU cc_start: 0.8384 (mp0) cc_final: 0.8151 (mp0)
REVERT: E   59 GLU cc_start: 0.8987 (pm20) cc_final: 0.8714 (pm20)
REVERT: F   95 ARG cc_start: 0.8805 (OUTLIER) cc_final: 0.8383 (mtp85)
REVERT: G   73 ASN cc_start: 0.8563 (t160) cc_final: 0.8035 (t0)
REVERT: H   63 ASN cc_start: 0.8874 (t0) cc_final: 0.8396 (m-40)
  outliers start: 30
  outliers final: 19
  residues processed: 197
  average time/residue: 0.9059
  time to fit residues: 188.6556
Evaluate side-chains
  200 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 177
  time to evaluate  : 0.237 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 ARG
Chi-restraints excluded: chain A residue   64 LYS
Chi-restraints excluded: chain A residue   76 GLN
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain C residue   41 GLU
Chi-restraints excluded: chain C residue   49 VAL
Chi-restraints excluded: chain C residue   59 THR
Chi-restraints excluded: chain C residue   77 ARG
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain C residue  108 LEU
Chi-restraints excluded: chain D residue   33 ARG
Chi-restraints excluded: chain D residue   48 VAL
Chi-restraints excluded: chain E residue   46 VAL
Chi-restraints excluded: chain E residue   64 LYS
Chi-restraints excluded: chain E residue   86 SER
Chi-restraints excluded: chain F residue   80 THR
Chi-restraints excluded: chain F residue   92 ARG
Chi-restraints excluded: chain F residue   95 ARG
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue   92 GLU
Chi-restraints excluded: chain G residue   99 LYS
Chi-restraints excluded: chain G residue  101 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 92 optimal weight:    2.9990
   chunk 72 optimal weight:    0.8980
   chunk 11 optimal weight:    0.8980
   chunk 47 optimal weight:    0.5980
   chunk 6 optimal weight:    0.5980
   chunk 39 optimal weight:    4.9990
   chunk 23 optimal weight:    4.9990
   chunk 0 optimal weight:    3.9990
   chunk 56 optimal weight:    0.5980
   chunk 97 optimal weight:    1.9990
   chunk 8 optimal weight:    0.6980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
B  25 ASN
** B  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D  63 ASN
D  95 GLN
F  27 GLN
G  24 GLN
G 104 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.101777 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.080176 restraints weight = 19221.825|
|-----------------------------------------------------------------------------|
r_work (start): 0.3187 rms_B_bonded: 1.23
r_work: 0.3024 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.2898 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.2898
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8437
moved from start:          0.1321

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  12911  Z= 0.196
  Angle     :  0.607   8.530  18690  Z= 0.363
  Chirality :  0.037   0.166   2125
  Planarity :  0.005   0.042   1345
  Dihedral  : 32.269 174.673   4069
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 8.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  4.57 %
    Allowed  : 28.08 %
    Favored  : 67.35 %
  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 aren not related in a simple way.
  whole:  2.23 (0.30), residues: 749
  helix:  2.08 (0.22), residues: 556
  sheet:  None (None), residues: 0
  loop : -0.27 (0.39), residues: 193

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.020   0.001   ARG H  99 
 TYR   0.017   0.002   TYR H  83 
 PHE   0.012   0.002   PHE E  67 
 HIS   0.004   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00435 (12911)
  covalent geometry    : angle       0.60737 (18690)
  hydrogen bonds       : bond        0.04193 (  799)
  hydrogen bonds       : angle       3.18834 ( 1992)

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

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

  1498 Ramachandran restraints generated.
    749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1498 Ramachandran restraints generated.
    749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  211 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 182
  time to evaluate  : 0.326 
Fit side-chains
REVERT: A   53 ARG cc_start: 0.8756 (OUTLIER) cc_final: 0.7872 (ttp-110)
REVERT: A   59 GLU cc_start: 0.9024 (pm20) cc_final: 0.8744 (pm20)
REVERT: C   56 GLU cc_start: 0.9059 (tt0) cc_final: 0.8841 (tt0)
REVERT: C   77 ARG cc_start: 0.8541 (OUTLIER) cc_final: 0.7371 (ttp-170)
REVERT: C  104 GLN cc_start: 0.8771 (mm-40) cc_final: 0.8570 (mm110)
REVERT: D   93 GLU cc_start: 0.8369 (mp0) cc_final: 0.8113 (mp0)
REVERT: E   49 ARG cc_start: 0.9003 (OUTLIER) cc_final: 0.8204 (ptp90)
REVERT: E   59 GLU cc_start: 0.8954 (pm20) cc_final: 0.8677 (pm20)
REVERT: G   73 ASN cc_start: 0.8543 (t160) cc_final: 0.7999 (t0)
REVERT: H   63 ASN cc_start: 0.8900 (t0) cc_final: 0.8425 (m-40)
  outliers start: 29
  outliers final: 19
  residues processed: 196
  average time/residue: 0.8729
  time to fit residues: 181.1845
Evaluate side-chains
  200 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 178
  time to evaluate  : 0.411 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 ARG
Chi-restraints excluded: chain A residue   76 GLN
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain C residue   41 GLU
Chi-restraints excluded: chain C residue   49 VAL
Chi-restraints excluded: chain C residue   59 THR
Chi-restraints excluded: chain C residue   77 ARG
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain C residue  108 LEU
Chi-restraints excluded: chain D residue   48 VAL
Chi-restraints excluded: chain E residue   46 VAL
Chi-restraints excluded: chain E residue   49 ARG
Chi-restraints excluded: chain E residue   64 LYS
Chi-restraints excluded: chain E residue   86 SER
Chi-restraints excluded: chain F residue   80 THR
Chi-restraints excluded: chain F residue   92 ARG
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue   74 LYS
Chi-restraints excluded: chain G residue   92 GLU
Chi-restraints excluded: chain G residue   99 LYS
Chi-restraints excluded: chain G residue  101 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 17 optimal weight:    7.9990
   chunk 38 optimal weight:    0.5980
   chunk 8 optimal weight:    0.8980
   chunk 83 optimal weight:    2.9990
   chunk 94 optimal weight:    1.9990
   chunk 50 optimal weight:    0.6980
   chunk 98 optimal weight:    2.9990
   chunk 57 optimal weight:    1.9990
   chunk 69 optimal weight:    0.9990
   chunk 91 optimal weight:    1.9990
   chunk 6 optimal weight:    1.9990
   overall best weight:    1.0384

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
B  25 ASN
** B  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D  95 GLN
F  27 GLN
G 104 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.101683 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.080270 restraints weight = 19111.212|
|-----------------------------------------------------------------------------|
r_work (start): 0.3190 rms_B_bonded: 1.24
r_work: 0.3029 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.2903 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.2903
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8427
moved from start:          0.1342

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040  12911  Z= 0.227
  Angle     :  0.607   8.487  18690  Z= 0.362
  Chirality :  0.037   0.159   2125
  Planarity :  0.004   0.039   1345
  Dihedral  : 32.171 174.733   4069
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 7.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  4.57 %
    Allowed  : 28.23 %
    Favored  : 67.19 %
  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 aren not related in a simple way.
  whole:  2.29 (0.30), residues: 749
  helix:  2.13 (0.22), residues: 556
  sheet:  None (None), residues: 0
  loop : -0.26 (0.39), residues: 193

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG H  99 
 TYR   0.017   0.002   TYR H  83 
 PHE   0.012   0.002   PHE E  67 
 HIS   0.003   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00512 (12911)
  covalent geometry    : angle       0.60737 (18690)
  hydrogen bonds       : bond        0.04110 (  799)
  hydrogen bonds       : angle       3.13786 ( 1992)

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

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

  1498 Ramachandran restraints generated.
    749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1498 Ramachandran restraints generated.
    749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  214 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 185
  time to evaluate  : 0.339 
Fit side-chains
REVERT: A   53 ARG cc_start: 0.8739 (OUTLIER) cc_final: 0.7877 (ttp-110)
REVERT: A   59 GLU cc_start: 0.8996 (pm20) cc_final: 0.8675 (pm20)
REVERT: A  120 MET cc_start: 0.8795 (mtt) cc_final: 0.8120 (mtt)
REVERT: C   56 GLU cc_start: 0.9098 (tt0) cc_final: 0.8828 (tt0)
REVERT: C   77 ARG cc_start: 0.8536 (OUTLIER) cc_final: 0.7411 (ttp-170)
REVERT: D   33 ARG cc_start: 0.7674 (OUTLIER) cc_final: 0.7078 (mmt-90)
REVERT: D   34 LYS cc_start: 0.8733 (mmmm) cc_final: 0.8399 (mppt)
REVERT: D   40 TYR cc_start: 0.9036 (m-80) cc_final: 0.8835 (m-80)
REVERT: D   76 GLU cc_start: 0.8857 (tp30) cc_final: 0.8417 (tp30)
REVERT: D   79 ARG cc_start: 0.8682 (mtm-85) cc_final: 0.8164 (mtm-85)
REVERT: D   93 GLU cc_start: 0.8309 (mp0) cc_final: 0.7987 (mp0)
REVERT: E   49 ARG cc_start: 0.8973 (OUTLIER) cc_final: 0.8141 (ptp90)
REVERT: E   59 GLU cc_start: 0.8953 (pm20) cc_final: 0.8284 (pm20)
REVERT: G   73 ASN cc_start: 0.8557 (t160) cc_final: 0.8043 (t0)
REVERT: H   63 ASN cc_start: 0.8867 (t0) cc_final: 0.8372 (m-40)
REVERT: H  116 LYS cc_start: 0.8898 (OUTLIER) cc_final: 0.8542 (ptpp)
  outliers start: 29
  outliers final: 19
  residues processed: 198
  average time/residue: 0.9112
  time to fit residues: 190.5234
Evaluate side-chains
  203 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 179
  time to evaluate  : 0.329 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 ARG
Chi-restraints excluded: chain A residue   64 LYS
Chi-restraints excluded: chain A residue   76 GLN
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain C residue   41 GLU
Chi-restraints excluded: chain C residue   49 VAL
Chi-restraints excluded: chain C residue   59 THR
Chi-restraints excluded: chain C residue   77 ARG
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain C residue  108 LEU
Chi-restraints excluded: chain D residue   33 ARG
Chi-restraints excluded: chain D residue   48 VAL
Chi-restraints excluded: chain E residue   46 VAL
Chi-restraints excluded: chain E residue   49 ARG
Chi-restraints excluded: chain E residue   64 LYS
Chi-restraints excluded: chain E residue   86 SER
Chi-restraints excluded: chain F residue   80 THR
Chi-restraints excluded: chain F residue   92 ARG
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue   92 GLU
Chi-restraints excluded: chain G residue   99 LYS
Chi-restraints excluded: chain G residue  101 THR
Chi-restraints excluded: chain H residue  116 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 20 optimal weight:    0.6980
   chunk 82 optimal weight:    1.9990
   chunk 63 optimal weight:    4.9990
   chunk 25 optimal weight:    1.9990
   chunk 55 optimal weight:    0.8980
   chunk 64 optimal weight:    1.9990
   chunk 14 optimal weight:    1.9990
   chunk 59 optimal weight:    0.7980
   chunk 16 optimal weight:    0.8980
   chunk 0 optimal weight:    2.9990
   chunk 2 optimal weight:    0.9990
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
B  25 ASN
** B  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D  95 GLN
F  27 GLN
** G  73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 104 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.102338 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.081023 restraints weight = 18975.555|
|-----------------------------------------------------------------------------|
r_work (start): 0.3196 rms_B_bonded: 1.23
r_work: 0.3037 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.2911 rms_B_bonded: 4.04 restraints_weight: 0.2500
r_work (final): 0.2911
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8420
moved from start:          0.1356

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040  12911  Z= 0.209
  Angle     :  0.607   8.431  18690  Z= 0.362
  Chirality :  0.037   0.168   2125
  Planarity :  0.004   0.055   1345
  Dihedral  : 32.170 174.968   4069
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 8.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  4.26 %
    Allowed  : 28.86 %
    Favored  : 66.88 %
  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 aren not related in a simple way.
  whole:  2.28 (0.30), residues: 749
  helix:  2.12 (0.22), residues: 556
  sheet:  None (None), residues: 0
  loop : -0.26 (0.39), residues: 193

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG H  99 
 TYR   0.020   0.002   TYR H  83 
 PHE   0.012   0.002   PHE E  67 
 HIS   0.003   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00468 (12911)
  covalent geometry    : angle       0.60664 (18690)
  hydrogen bonds       : bond        0.04002 (  799)
  hydrogen bonds       : angle       3.14186 ( 1992)

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

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

  1498 Ramachandran restraints generated.
    749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1498 Ramachandran restraints generated.
    749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 182
  time to evaluate  : 0.370 
Fit side-chains
REVERT: A   53 ARG cc_start: 0.8739 (OUTLIER) cc_final: 0.7852 (ttp-110)
REVERT: A   59 GLU cc_start: 0.9007 (pm20) cc_final: 0.8714 (pm20)
REVERT: A  120 MET cc_start: 0.8808 (mtt) cc_final: 0.8139 (mtt)
REVERT: C   77 ARG cc_start: 0.8534 (OUTLIER) cc_final: 0.7416 (ttp-170)
REVERT: D   33 ARG cc_start: 0.7688 (OUTLIER) cc_final: 0.7110 (mmt-90)
REVERT: D   34 LYS cc_start: 0.8720 (mmmm) cc_final: 0.8406 (mppt)
REVERT: D   76 GLU cc_start: 0.8896 (tp30) cc_final: 0.8402 (tp30)
REVERT: D   79 ARG cc_start: 0.8679 (mtm-85) cc_final: 0.8146 (mtm-85)
REVERT: D   93 GLU cc_start: 0.8294 (mp0) cc_final: 0.7954 (mp0)
REVERT: E   49 ARG cc_start: 0.8974 (OUTLIER) cc_final: 0.8161 (ptp90)
REVERT: E   59 GLU cc_start: 0.8954 (pm20) cc_final: 0.8274 (pm20)
REVERT: G   73 ASN cc_start: 0.8558 (t160) cc_final: 0.8045 (t0)
REVERT: H   63 ASN cc_start: 0.8874 (t0) cc_final: 0.8395 (m-40)
REVERT: H  116 LYS cc_start: 0.8926 (OUTLIER) cc_final: 0.8547 (ptpp)
  outliers start: 27
  outliers final: 20
  residues processed: 194
  average time/residue: 0.9150
  time to fit residues: 187.6021
Evaluate side-chains
  204 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 179
  time to evaluate  : 0.345 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 ARG
Chi-restraints excluded: chain A residue   64 LYS
Chi-restraints excluded: chain A residue   76 GLN
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain C residue   41 GLU
Chi-restraints excluded: chain C residue   49 VAL
Chi-restraints excluded: chain C residue   59 THR
Chi-restraints excluded: chain C residue   77 ARG
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain C residue  108 LEU
Chi-restraints excluded: chain D residue   33 ARG
Chi-restraints excluded: chain D residue   48 VAL
Chi-restraints excluded: chain E residue   46 VAL
Chi-restraints excluded: chain E residue   49 ARG
Chi-restraints excluded: chain E residue   64 LYS
Chi-restraints excluded: chain E residue   86 SER
Chi-restraints excluded: chain F residue   80 THR
Chi-restraints excluded: chain F residue   92 ARG
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue   74 LYS
Chi-restraints excluded: chain G residue   92 GLU
Chi-restraints excluded: chain G residue   99 LYS
Chi-restraints excluded: chain G residue  101 THR
Chi-restraints excluded: chain H residue  116 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 87 optimal weight:    3.9990
   chunk 35 optimal weight:    0.0870
   chunk 67 optimal weight:    0.6980
   chunk 56 optimal weight:    0.5980
   chunk 55 optimal weight:    0.6980
   chunk 94 optimal weight:    1.9990
   chunk 79 optimal weight:    2.9990
   chunk 36 optimal weight:    0.7980
   chunk 76 optimal weight:    2.9990
   chunk 37 optimal weight:    3.9990
   chunk 62 optimal weight:    0.6980
   overall best weight:    0.5558

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
B  25 ASN
** B  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D  95 GLN
F  27 GLN
** G  73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 104 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.102731 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.081380 restraints weight = 18897.516|
|-----------------------------------------------------------------------------|
r_work (start): 0.3203 rms_B_bonded: 1.23
r_work: 0.3044 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.2917 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.2917
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8446
moved from start:          0.1388

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  12911  Z= 0.187
  Angle     :  0.607   8.307  18690  Z= 0.362
  Chirality :  0.036   0.178   2125
  Planarity :  0.005   0.055   1345
  Dihedral  : 32.174 175.214   4069
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 8.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  4.26 %
    Allowed  : 29.18 %
    Favored  : 66.56 %
  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 aren not related in a simple way.
  whole:  2.33 (0.30), residues: 749
  helix:  2.16 (0.22), residues: 556
  sheet:  None (None), residues: 0
  loop : -0.25 (0.40), residues: 193

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.000   ARG H  99 
 TYR   0.020   0.001   TYR H  83 
 PHE   0.013   0.002   PHE E  67 
 HIS   0.003   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00417 (12911)
  covalent geometry    : angle       0.60704 (18690)
  hydrogen bonds       : bond        0.03917 (  799)
  hydrogen bonds       : angle       3.13563 ( 1992)

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

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

  1498 Ramachandran restraints generated.
    749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1498 Ramachandran restraints generated.
    749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 182
  time to evaluate  : 0.338 
Fit side-chains
REVERT: A   53 ARG cc_start: 0.8762 (OUTLIER) cc_final: 0.7884 (ttp-110)
REVERT: A   59 GLU cc_start: 0.9023 (pm20) cc_final: 0.8747 (pm20)
REVERT: A  120 MET cc_start: 0.8812 (mtt) cc_final: 0.8150 (mtt)
REVERT: C   77 ARG cc_start: 0.8571 (OUTLIER) cc_final: 0.7454 (ttp-170)
REVERT: D   33 ARG cc_start: 0.7699 (OUTLIER) cc_final: 0.7128 (mmt-90)
REVERT: D   34 LYS cc_start: 0.8751 (mmmm) cc_final: 0.8467 (mppt)
REVERT: D   76 GLU cc_start: 0.8908 (tp30) cc_final: 0.8413 (tp30)
REVERT: D   79 ARG cc_start: 0.8723 (mtm-85) cc_final: 0.8168 (mtm-85)
REVERT: D   93 GLU cc_start: 0.8313 (mp0) cc_final: 0.7992 (mp0)
REVERT: E   49 ARG cc_start: 0.9003 (OUTLIER) cc_final: 0.8183 (ptp90)
REVERT: E   59 GLU cc_start: 0.8950 (pm20) cc_final: 0.8287 (pm20)
REVERT: G   73 ASN cc_start: 0.8556 (t160) cc_final: 0.8057 (t0)
REVERT: H   63 ASN cc_start: 0.8881 (t0) cc_final: 0.8432 (m-40)
REVERT: H  116 LYS cc_start: 0.8941 (OUTLIER) cc_final: 0.8564 (ptpp)
  outliers start: 27
  outliers final: 19
  residues processed: 194
  average time/residue: 0.9173
  time to fit residues: 187.9446
Evaluate side-chains
  204 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 180
  time to evaluate  : 0.358 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 ARG
Chi-restraints excluded: chain A residue   64 LYS
Chi-restraints excluded: chain A residue   76 GLN
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain C residue   41 GLU
Chi-restraints excluded: chain C residue   49 VAL
Chi-restraints excluded: chain C residue   77 ARG
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain C residue  108 LEU
Chi-restraints excluded: chain D residue   33 ARG
Chi-restraints excluded: chain D residue   48 VAL
Chi-restraints excluded: chain E residue   46 VAL
Chi-restraints excluded: chain E residue   49 ARG
Chi-restraints excluded: chain E residue   64 LYS
Chi-restraints excluded: chain E residue   86 SER
Chi-restraints excluded: chain F residue   80 THR
Chi-restraints excluded: chain F residue   92 ARG
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue   74 LYS
Chi-restraints excluded: chain G residue   92 GLU
Chi-restraints excluded: chain G residue   99 LYS
Chi-restraints excluded: chain G residue  101 THR
Chi-restraints excluded: chain H residue  116 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 51 optimal weight:    1.9990
   chunk 86 optimal weight:    2.9990
   chunk 91 optimal weight:    2.9990
   chunk 36 optimal weight:    0.9990
   chunk 55 optimal weight:    0.7980
   chunk 72 optimal weight:    0.8980
   chunk 56 optimal weight:    0.9990
   chunk 89 optimal weight:    3.9990
   chunk 31 optimal weight:    0.7980
   chunk 20 optimal weight:    0.9990
   chunk 61 optimal weight:    0.6980
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
B  25 ASN
** B  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D  95 GLN
F  27 GLN
** G  73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 104 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.102832 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.081495 restraints weight = 18911.520|
|-----------------------------------------------------------------------------|
r_work (start): 0.3208 rms_B_bonded: 1.23
r_work: 0.3050 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.2924 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.2924
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8412
moved from start:          0.1354

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040  12911  Z= 0.206
  Angle     :  0.604   7.641  18690  Z= 0.360
  Chirality :  0.036   0.175   2125
  Planarity :  0.005   0.053   1345
  Dihedral  : 32.071 175.429   4069
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 8.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  4.26 %
    Allowed  : 29.65 %
    Favored  : 66.09 %
  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 aren not related in a simple way.
  whole:  2.38 (0.30), residues: 749
  helix:  2.18 (0.22), residues: 556
  sheet:  None (None), residues: 0
  loop : -0.17 (0.40), residues: 193

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG H  99 
 TYR   0.021   0.002   TYR H  83 
 PHE   0.013   0.002   PHE E  67 
 HIS   0.003   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00463 (12911)
  covalent geometry    : angle       0.60364 (18690)
  hydrogen bonds       : bond        0.03852 (  799)
  hydrogen bonds       : angle       3.11648 ( 1992)

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

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

  1498 Ramachandran restraints generated.
    749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1498 Ramachandran restraints generated.
    749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 180
  time to evaluate  : 0.426 
Fit side-chains
REVERT: A   53 ARG cc_start: 0.8733 (OUTLIER) cc_final: 0.7872 (ttp-110)
REVERT: A   59 GLU cc_start: 0.9000 (pm20) cc_final: 0.8710 (pm20)
REVERT: C   77 ARG cc_start: 0.8533 (OUTLIER) cc_final: 0.7416 (ttp-170)
REVERT: D   33 ARG cc_start: 0.7678 (OUTLIER) cc_final: 0.7085 (mmt-90)
REVERT: D   34 LYS cc_start: 0.8753 (mmmm) cc_final: 0.8477 (mppt)
REVERT: D   86 ARG cc_start: 0.8770 (mpt-90) cc_final: 0.8569 (mpt-90)
REVERT: D   93 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.7940 (mp0)
REVERT: E   49 ARG cc_start: 0.8959 (OUTLIER) cc_final: 0.8144 (ptp90)
REVERT: E   59 GLU cc_start: 0.8944 (pm20) cc_final: 0.8250 (pm20)
REVERT: G   73 ASN cc_start: 0.8559 (t160) cc_final: 0.8060 (t0)
REVERT: H   63 ASN cc_start: 0.8840 (t0) cc_final: 0.8398 (m-40)
REVERT: H  116 LYS cc_start: 0.8906 (OUTLIER) cc_final: 0.8517 (ptpp)
  outliers start: 27
  outliers final: 19
  residues processed: 192
  average time/residue: 0.9090
  time to fit residues: 184.4810
Evaluate side-chains
  202 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 177
  time to evaluate  : 0.406 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 ARG
Chi-restraints excluded: chain A residue   64 LYS
Chi-restraints excluded: chain A residue   76 GLN
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain C residue   41 GLU
Chi-restraints excluded: chain C residue   49 VAL
Chi-restraints excluded: chain C residue   77 ARG
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain C residue  108 LEU
Chi-restraints excluded: chain D residue   33 ARG
Chi-restraints excluded: chain D residue   48 VAL
Chi-restraints excluded: chain D residue   93 GLU
Chi-restraints excluded: chain E residue   46 VAL
Chi-restraints excluded: chain E residue   49 ARG
Chi-restraints excluded: chain E residue   64 LYS
Chi-restraints excluded: chain E residue   86 SER
Chi-restraints excluded: chain F residue   80 THR
Chi-restraints excluded: chain F residue   92 ARG
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue   74 LYS
Chi-restraints excluded: chain G residue   92 GLU
Chi-restraints excluded: chain G residue   99 LYS
Chi-restraints excluded: chain G residue  101 THR
Chi-restraints excluded: chain H residue  116 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 30 optimal weight:    1.9990
   chunk 51 optimal weight:    1.9990
   chunk 83 optimal weight:    2.9990
   chunk 15 optimal weight:    0.6980
   chunk 91 optimal weight:    2.9990
   chunk 97 optimal weight:    2.9990
   chunk 82 optimal weight:    1.9990
   chunk 27 optimal weight:    0.0980
   chunk 3 optimal weight:    0.6980
   chunk 76 optimal weight:    2.9990
   chunk 39 optimal weight:    1.9990
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
B  25 ASN
** B  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D  95 GLN
F  27 GLN
** G  73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 104 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.101802 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.080121 restraints weight = 19251.707|
|-----------------------------------------------------------------------------|
r_work (start): 0.3192 rms_B_bonded: 1.25
r_work: 0.3030 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.2903 rms_B_bonded: 4.08 restraints_weight: 0.2500
r_work (final): 0.2903
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8427
moved from start:          0.1410

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041  12911  Z= 0.236
  Angle     :  0.621   8.275  18690  Z= 0.368
  Chirality :  0.037   0.185   2125
  Planarity :  0.005   0.055   1345
  Dihedral  : 32.091 174.746   4069
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 8.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  4.42 %
    Allowed  : 30.13 %
    Favored  : 65.46 %
  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 aren not related in a simple way.
  whole:  2.32 (0.30), residues: 749
  helix:  2.13 (0.22), residues: 556
  sheet:  None (None), residues: 0
  loop : -0.18 (0.40), residues: 193

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG H  99 
 TYR   0.026   0.002   TYR H  83 
 PHE   0.013   0.002   PHE E  67 
 HIS   0.004   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00531 (12911)
  covalent geometry    : angle       0.62082 (18690)
  hydrogen bonds       : bond        0.04237 (  799)
  hydrogen bonds       : angle       3.15535 ( 1992)

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

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

  1498 Ramachandran restraints generated.
    749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1498 Ramachandran restraints generated.
    749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 178
  time to evaluate  : 0.316 
Fit side-chains
REVERT: A   53 ARG cc_start: 0.8744 (OUTLIER) cc_final: 0.7885 (ttp-110)
REVERT: A   59 GLU cc_start: 0.9005 (pm20) cc_final: 0.8698 (pm20)
REVERT: C   77 ARG cc_start: 0.8537 (OUTLIER) cc_final: 0.7420 (ttp-170)
REVERT: D   33 ARG cc_start: 0.7726 (OUTLIER) cc_final: 0.7105 (mmt-90)
REVERT: D   34 LYS cc_start: 0.8739 (mmmm) cc_final: 0.8467 (mppt)
REVERT: D   76 GLU cc_start: 0.8802 (tp30) cc_final: 0.8500 (tp30)
REVERT: D   93 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.7958 (mp0)
REVERT: E   49 ARG cc_start: 0.8975 (OUTLIER) cc_final: 0.8166 (ptp90)
REVERT: E   59 GLU cc_start: 0.8946 (pm20) cc_final: 0.8262 (pm20)
REVERT: G   73 ASN cc_start: 0.8558 (t160) cc_final: 0.8052 (t0)
REVERT: H   63 ASN cc_start: 0.8881 (t0) cc_final: 0.8433 (m-40)
REVERT: H  116 LYS cc_start: 0.8910 (OUTLIER) cc_final: 0.8536 (ptpp)
  outliers start: 28
  outliers final: 19
  residues processed: 191
  average time/residue: 0.9066
  time to fit residues: 183.0950
Evaluate side-chains
  199 residues out of total 635 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 174
  time to evaluate  : 0.389 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 ARG
Chi-restraints excluded: chain A residue   64 LYS
Chi-restraints excluded: chain A residue   76 GLN
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain C residue   41 GLU
Chi-restraints excluded: chain C residue   49 VAL
Chi-restraints excluded: chain C residue   77 ARG
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain C residue  108 LEU
Chi-restraints excluded: chain D residue   33 ARG
Chi-restraints excluded: chain D residue   48 VAL
Chi-restraints excluded: chain D residue   93 GLU
Chi-restraints excluded: chain E residue   46 VAL
Chi-restraints excluded: chain E residue   49 ARG
Chi-restraints excluded: chain E residue   64 LYS
Chi-restraints excluded: chain E residue   86 SER
Chi-restraints excluded: chain F residue   80 THR
Chi-restraints excluded: chain F residue   92 ARG
Chi-restraints excluded: chain F residue   96 THR
Chi-restraints excluded: chain G residue   74 LYS
Chi-restraints excluded: chain G residue   92 GLU
Chi-restraints excluded: chain G residue   99 LYS
Chi-restraints excluded: chain G residue  101 THR
Chi-restraints excluded: chain H residue  116 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 51 optimal weight:    0.7980
   chunk 77 optimal weight:    2.9990
   chunk 3 optimal weight:    0.5980
   chunk 66 optimal weight:    4.9990
   chunk 43 optimal weight:    0.5980
   chunk 38 optimal weight:    0.9980
   chunk 10 optimal weight:    0.5980
   chunk 55 optimal weight:    0.0980
   chunk 95 optimal weight:    1.9990
   chunk 56 optimal weight:    0.6980
   chunk 73 optimal weight:    0.5980
   overall best weight:    0.4980

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
B  25 ASN
** B  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D  95 GLN
F  27 GLN
** G  73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 104 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.102899 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.081508 restraints weight = 18932.245|
|-----------------------------------------------------------------------------|
r_work (start): 0.3200 rms_B_bonded: 1.24
r_work: 0.3038 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.2911 rms_B_bonded: 4.06 restraints_weight: 0.2500
r_work (final): 0.2911
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8426
moved from start:          0.1385

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  12911  Z= 0.187
  Angle     :  0.618   8.340  18690  Z= 0.366
  Chirality :  0.036   0.213   2125
  Planarity :  0.005   0.060   1345
  Dihedral  : 32.117 175.185   4069
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 8.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  4.10 %
    Allowed  : 30.28 %
    Favored  : 65.62 %
  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 aren not related in a simple way.
  whole:  2.39 (0.30), residues: 749
  helix:  2.18 (0.22), residues: 556
  sheet:  None (None), residues: 0
  loop : -0.16 (0.40), residues: 193

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG H  99 
 TYR   0.023   0.002   TYR H  83 
 PHE   0.015   0.002   PHE E  67 
 HIS   0.004   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00418 (12911)
  covalent geometry    : angle       0.61767 (18690)
  hydrogen bonds       : bond        0.04118 (  799)
  hydrogen bonds       : angle       3.14043 ( 1992)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5098.88 seconds
wall clock time: 87 minutes 32.17 seconds (5252.17 seconds total)